Citrus Sinensis ID: 041875

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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
MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAASADQNPEAEATEAKEH
Secondary Structure (PSIPRED)
cccccccccccccccEEEEcEEEEEccccccccccccccccccccccccEEccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccEEEEEEEEEEcccccccccEEEEcccccccccccccccccEcccccHHHHcccccccccccccccccccccccHHHHHHccccccHccccccEEEEcEEEEEcccccccccEEEHHccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mafcgtqekckacdktvHIIDMVTADGISYHKICfkcshcngklvmgnfssmegvlyckphfEQLFKEtgsftnklkpaqkngltrtpskfstmfcgtqdkctsckktvyplekvtvegesfhktcfrcshggcllttssyaALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAASadqnpeaeateakeh
Flexible Loop (DISEMBL)
mafcgtqekckacdktVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSftnklkpaqkngltrtpskfstmfcgtqdkctsckktVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAASADQNPeaeateakeh
Low Complexity Region (SEG)
MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAASADQNPEAEATEAKEH
Disordered region (IsUnstruct)
***CGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFT****************KFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKT*************************
Disordered Region (DISOPRED)
**FCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKG*********************************
Disordered Region (DISEMBL)
********KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTAS***********************
Disordered Region (DISPRO)
*******EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET*S**************************TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTK**************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAASADQNPEAEATEAKEH
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	195	2.2.26 [Sep-21-2011]
P29675	219	Pollen-specific protein S	N/A	no	0.964	0.858	0.450	6e-46
P50462	194	Cysteine and glycine-rich	yes	no	0.887	0.891	0.336	6e-19
P50461	194	Cysteine and glycine-rich	yes	no	0.887	0.891	0.331	2e-18
P50463	194	Cysteine and glycine-rich	yes	no	0.820	0.824	0.346	3e-18
Q0VFX8	208	Cysteine-rich protein 2 O	yes	no	0.887	0.831	0.308	3e-17
Q4U0T9	194	Cysteine and glycine-rich	no	no	0.820	0.824	0.324	5e-17
P36201	208	Cysteine-rich protein 2 O	no	no	0.789	0.740	0.331	1e-16
P52943	208	Cysteine-rich protein 2 O	no	no	0.789	0.740	0.331	2e-16
Q9DCT8	208	Cysteine-rich protein 2 O	no	no	0.789	0.740	0.320	8e-16
Q4U4S6	3784	Xin actin-binding repeat-	no	no	0.364	0.018	0.478	2e-15

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

 Score =  183 bits (465), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 91/202 (45%), Positives = 133/202 (65%), Gaps = 14/202 (6%)

Query: 2   AFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPH 61
           +F GT +KC  C+KTV+++D + A+   YHK CF+C HCN  L + NF+S +GV+YC+ H
Sbjct: 3   SFTGTTQKCTVCEKTVYLVDKLVANQRVYHKACFRCHHCNSTLKLSNFNSFDGVVYCRHH 62

Query: 62  FEQLFKETGSF------TNKLKPAQK-NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEK 114
           F+QLFK TGS       T K KP +  +  T++ ++ S+ F GT+DKC +C K VYP+E+
Sbjct: 63  FDQLFKRTGSLEKSFDGTPKFKPERTFSQETQSANRLSSFFEGTRDKCNACAKIVYPIER 122

Query: 115 VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQK 174
           V V+G ++H+ CF+C HGGC ++ S+Y A +G LYCK H  QLFK+KG Y+ L      +
Sbjct: 123 VKVDGTAYHRACFKCCHGGCTISPSNYIAHEGRLYCKHHHIQLFKKKGNYSQL----EVE 178

Query: 175 KIVAASAD---QNPEAEATEAK 193
           + VAA A+   QN E +  E +
Sbjct: 179 ETVAAPAESETQNTETQNAETQ 200

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 = 94.0 bits (232), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 66/196 (33%), Positives = 93/196 (47%), Gaps = 23/196 (11%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M   G   KC AC+KTV+  + +  +G S+HK CF C  C   L     ++ E  +YCK 
Sbjct: 1   MPNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKETG--------------------SFTNKLKPAQKNGLTRTPSKFSTMFCGTQD 100
            + + +   G                     F    KPA +   T  PSKFS  F G  +
Sbjct: 61  CYGRRYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPA-RAATTSNPSKFSAKF-GESE 118

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
           KC  C K+VY  EKV   G+ +HKTCFRC+  G  L +++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 161 KGC-YNHLTKTASQKK 175
            G  +  LT+   +K+
Sbjct: 179 TGIGFGGLTQQVEKKE 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 = 65/196 (33%), Positives = 94/196 (47%), Gaps = 23/196 (11%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M   G   KC AC+KTV+  + +  +G S+HK CF C  C   L     ++ E  +YCK 
Sbjct: 1   MPNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKETG--------------------SFTNKLKPAQKNGLTRTPSKFSTMFCGTQD 100
            + + +   G                     F    KPA ++  T  PSKF+  F G  +
Sbjct: 61  CYGRRYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKPA-RSVTTSNPSKFTAKF-GESE 118

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
           KC  C K+VY  EKV   G+ +HKTCFRC+  G  L +++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 161 KGC-YNHLTKTASQKK 175
            G  +  LT+   +K+
Sbjct: 179 TGIGFGGLTQQVEKKE 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 = 91.3 bits (225), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 63/182 (34%), Positives = 85/182 (46%), Gaps = 22/182 (12%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M   G   KC ACDKTV+  + +  +G S+HK CF C  C   L     ++ E  +YCK 
Sbjct: 1   MPNWGGGAKCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKETG--------------------SFTNKLKPAQKNGLTRTPSKFSTMFCGTQD 100
            + + +   G                     F    KPA +   T  PSKFS  F G  +
Sbjct: 61  CYGRKYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPA-RAATTSNPSKFSAKF-GESE 118

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
           KC  C K+VY  EKV   G+ +HKTCF C+  G  L +++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 161 KG 162
            G
Sbjct: 179 TG 180

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

Rattus norvegicus (taxid: 10116)

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

 Score = 88.2 bits (217), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 94/211 (44%), Gaps = 38/211 (18%)

Query: 9   KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC-KPHFEQLFK 67
           KC  CDKTV+  + V++ G  +H+ C +C HC+  L  G  +  +G  +C KP +  LF 
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHRFCLRCEHCSKTLTPGGHAEHDGKPFCHKPCYATLFG 63

Query: 68  E-------TGSFTNKLKPAQK-------------------NGLTRTPSKFS--TMFCGTQ 99
                    GS+  +   A+K                   +G  + PSK S  T F G  
Sbjct: 64  PKGVNIGGAGSYIYEKPSAEKPQVTGPIEVPVARTEERKASGPPKGPSKASSVTTFTGEP 123

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC-KSHFAQLF 158
           + C  C K VY  EKVT  G+ +H+ C RC   G  LT   +A  DG  YC K  +  LF
Sbjct: 124 NMCPRCNKRVYFAEKVTSLGKDWHRPCLRCERCGKTLTPGGHAEHDGQPYCHKPCYGILF 183

Query: 159 KEKGCYNHLTKTASQKKIVAASADQNPEAEA 189
             KG         +   + +   D++PE +A
Sbjct: 184 GPKG--------VNTGAVGSYIYDKDPEGKA 206

Bos taurus (taxid: 9913)

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

 Score = 87.4 bits (215), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 59/182 (32%), Positives = 84/182 (46%), Gaps = 22/182 (12%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M   G   KC AC+KTV+  + +  +G S+HK CF C  C   L     ++ E  +YCK 
Sbjct: 1   MPNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKETG--------------------SFTNKLKPAQKNGLTRTPSKFSTMFCGTQD 100
            + + +   G                     F    K A+    +  PSKF+    G  +
Sbjct: 61  CYGRRYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKQARSATTSSNPSKFAKF--GESE 118

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
           KC  C K+VY  EKV   G+ +HKTCFRC+  G  L +++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 161 KG 162
            G
Sbjct: 179 TG 180

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

Bos taurus (taxid: 9913)

>sp|P36201|CRIP2_RAT Cysteine-rich protein 2 OS=Rattus norvegicus GN=Crip2 PE=2 SV=1

 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 81/184 (44%), Gaps = 30/184 (16%)

Query: 9   KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC-KPHFEQLFK 67
           KC  CDKTV+  + V++ G  +HK C KC  CN  L  G  +  +G  +C KP +  LF 
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCNKTLTPGGHAEHDGKPFCHKPCYATLFG 63

Query: 68  E-------TGSFTNKLKPAQK-------------------NGLTRTPSKFS--TMFCGTQ 99
                    GS+  +  P +                    +G  + PSK S  T F G  
Sbjct: 64  PKGVNIGGAGSYIYEKPPTEAPQVTGPIEVPVVRTEERKTSGPPKGPSKASSVTTFTGEP 123

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC-KSHFAQLF 158
           + C  C K VY  EKVT  G+ +H+ C RC      LT   +A  DG  YC K  +  LF
Sbjct: 124 NMCPRCNKRVYFAEKVTSLGKDWHRPCLRCERCSKTLTPGGHAEHDGQPYCHKPCYGILF 183

Query: 159 KEKG 162
             KG
Sbjct: 184 GPKG 187

Rattus norvegicus (taxid: 10116)

>sp|P52943|CRIP2_HUMAN Cysteine-rich protein 2 OS=Homo sapiens GN=CRIP2 PE=1 SV=1

 Score = 85.1 bits (209), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 83/184 (45%), Gaps = 30/184 (16%)

Query: 9   KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC-KPHFEQLFK 67
           KC  CDKTV+  + V++ G  +HK C KC  C+  L  G  +  +G  +C KP +  LF 
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG 63

Query: 68  ETG-------------------SFTNKLK-PAQK------NGLTRTPSKFS--TMFCGTQ 99
             G                     T  ++ PA +      +G  + PS+ S  T F G  
Sbjct: 64  PKGVNIGGAGSYIYEKPLAEGPQVTGPIEVPAARAEERKASGPPKGPSRASSVTTFTGEP 123

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC-KSHFAQLF 158
           + C  C K VY  EKVT  G+ +H+ C RC   G  LT   +A  DG  YC K  +  LF
Sbjct: 124 NTCPRCSKKVYFAEKVTSLGKDWHRPCLRCERCGKTLTPGGHAEHDGQPYCHKPCYGILF 183

Query: 159 KEKG 162
             KG
Sbjct: 184 GPKG 187

Homo sapiens (taxid: 9606)

>sp|Q9DCT8|CRIP2_MOUSE Cysteine-rich protein 2 OS=Mus musculus GN=Crip2 PE=1 SV=1

 Score = 83.6 bits (205), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 59/184 (32%), Positives = 79/184 (42%), Gaps = 30/184 (16%)

Query: 9   KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC-KPHFEQLFK 67
           KC  CDKTV+  + V++ G  +HK C KC  CN  L  G  +  +G  +C KP +  LF 
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCNKTLTPGGHAEHDGKPFCHKPCYATLFG 63

Query: 68  ETGSFTN--------------------------KLKPAQKNGLTRTPSKFS--TMFCGTQ 99
             G                              + +  + +G  + PSK S  T F G  
Sbjct: 64  PKGVNIGGAGSYIYEKPQTEAPQVTGPIEVPVVRTEERKTSGPPKGPSKASSVTTFTGEP 123

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC-KSHFAQLF 158
           + C  C K VY  EKVT  G+ +H+ C RC      LT   +A  DG  YC K  +  LF
Sbjct: 124 NMCPRCNKRVYFAEKVTSLGKDWHRPCLRCERCSKTLTPGGHAEHDGQPYCHKPCYGILF 183

Query: 159 KEKG 162
             KG
Sbjct: 184 GPKG 187

Mus musculus (taxid: 10090)

>sp|Q4U4S6|XIRP2_MOUSE Xin actin-binding repeat-containing protein 2 OS=Mus musculus GN=Xirp2 PE=1 SV=1

 Score = 82.4 bits (202), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 34/71 (47%), Positives = 51/71 (71%)

Query: 2    AFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPH 61
            AF   +E C  C KTV+ ++ + AD  ++HK CF+C HC+ KL +GN++S+ G +YCKPH
Sbjct: 3249 AFLSDKEICIICQKTVYPMECLIADKQNFHKSCFRCHHCSSKLSLGNYASLHGRIYCKPH 3308

Query: 62   FEQLFKETGSF 72
            F+QLFK  G++
Sbjct: 3309 FKQLFKSKGNY 3319

Protects actin filaments from depolymerization.

Mus musculus (taxid: 10090)

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	195
225426860	215	PREDICTED: pollen-specific protein SF3 [	0.994	0.902	0.673	7e-76
224074903	212	predicted protein [Populus trichocarpa]	0.964	0.886	0.694	3e-74
255537403	215	Pollen-specific protein SF3, putative [R	0.928	0.841	0.715	1e-72
169908354	216	LIM domain protein 2b [Nicotiana tabacum	0.994	0.898	0.651	2e-71
115447541	206	Os02g0641000 [Oryza sativa Japonica Grou	0.994	0.941	0.661	3e-71
223944239	204	unknown [Zea mays] gi|323388671|gb|ADX60	0.964	0.921	0.670	3e-71
224053939	214	predicted protein [Populus trichocarpa]	0.958	0.873	0.679	2e-70
326522158	203	predicted protein [Hordeum vulgare subsp	0.994	0.955	0.616	8e-69
225454117	220	PREDICTED: pollen-specific protein SF3 [	0.897	0.795	0.683	1e-68
242076584	203	hypothetical protein SORBIDRAFT_06g02360	0.979	0.940	0.632	3e-68

>gi|225426860|ref|XP_002283482.1| PREDICTED: pollen-specific protein SF3 [Vitis vinifera] gi|297742561|emb|CBI34710.3| unnamed protein product [Vitis vinifera]

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 138/205 (67%), Positives = 161/205 (78%), Gaps = 11/205 (5%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M+F GT +KCKACDKTVHIID ++ADGI+YHK CF+CSHCNG LVM N+SSM+GVLYCKP
Sbjct: 1   MSFSGTTQKCKACDKTVHIIDTISADGIAYHKTCFRCSHCNGPLVMSNYSSMDGVLYCKP 60

Query: 61  HFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGE 120
           HFEQLF+E+GS + K + + K  L+RTPSK S+MF GTQDKC+ CKKTVYPLEKVTVEGE
Sbjct: 61  HFEQLFRESGSLSKKFQSSGKADLSRTPSKLSSMFSGTQDKCSLCKKTVYPLEKVTVEGE 120

Query: 121 SFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAAS 180
            +HK+CFRCSHGGC LT SSYAALDGILYCK HF QLF+E+G Y+ L KTAS KK  AA+
Sbjct: 121 FYHKSCFRCSHGGCFLTPSSYAALDGILYCKPHFTQLFRERGSYSTLNKTASMKKSTAAA 180

Query: 181 --ADQN---------PEAEATEAKE 194
              DQN         PE + T   E
Sbjct: 181 PLPDQNSGQEQLATTPEEDPTPGSE 205

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074903|ref|XP_002304483.1| predicted protein [Populus trichocarpa] gi|222841915|gb|EEE79462.1| predicted protein [Populus trichocarpa]

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 132/190 (69%), Positives = 162/190 (85%), Gaps = 2/190 (1%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M F GT EKCKACDKTV+ I++V+ADG+ YHK CFKCSHCNG LVM ++SS++GVLYC+P
Sbjct: 1   MGFTGTLEKCKACDKTVYFIELVSADGVPYHKKCFKCSHCNGLLVMSSYSSIDGVLYCRP 60

Query: 61  HFEQLFKETGSFTNKLKPA--QKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVE 118
           H++QLFKETG+F+ KL+ +  +KNGLT+ PSK S+MF GTQDKC SCKKTVYPLEKVTVE
Sbjct: 61  HYDQLFKETGNFSKKLQSSGEKKNGLTKAPSKLSSMFSGTQDKCASCKKTVYPLEKVTVE 120

Query: 119 GESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVA 178
           GE FHK+CFRCSHGGC +T SSYAALDGILYCK+HF+QLFK+KG Y++LTKT++ KK   
Sbjct: 121 GEFFHKSCFRCSHGGCFITPSSYAALDGILYCKAHFSQLFKQKGSYSYLTKTSTMKKNAV 180

Query: 179 ASADQNPEAE 188
            S ++  EAE
Sbjct: 181 NSPEEKSEAE 190

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537403|ref|XP_002509768.1| Pollen-specific protein SF3, putative [Ricinus communis] gi|223549667|gb|EEF51155.1| Pollen-specific protein SF3, putative [Ricinus communis]

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 131/183 (71%), Positives = 154/183 (84%), Gaps = 2/183 (1%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M F GT EKCKACDKTVH I+M+TADGISYHK CFKCSHC+G+LVM ++SSMEGVLYCKP
Sbjct: 1   MGFSGTTEKCKACDKTVHFIEMITADGISYHKTCFKCSHCDGRLVMSSYSSMEGVLYCKP 60

Query: 61  HFEQLFKETGSFTNKLKPA--QKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVE 118
           HFEQLF+ETGSF  K   +  +KNGL +TPSK S++F GTQDKC  CKKT YPLEK++VE
Sbjct: 61  HFEQLFRETGSFGKKFPSSVEKKNGLVKTPSKLSSLFSGTQDKCAKCKKTAYPLEKLSVE 120

Query: 119 GESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVA 178
           GE +HK+CFRCSHGGC LT S+YAALDG +YCK HFAQLFKEKG Y++LTK+AS KK + 
Sbjct: 121 GEFYHKSCFRCSHGGCYLTPSTYAALDGFIYCKPHFAQLFKEKGSYSYLTKSASVKKNIQ 180

Query: 179 ASA 181
            +A
Sbjct: 181 NTA 183

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 129/198 (65%), Positives = 156/198 (78%), Gaps = 4/198 (2%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           MAF GT +KCKACDKTV+ +D++TADGI+YHK CFKCSHC G LVM N+SSM+GVLYCKP
Sbjct: 1   MAFTGTLDKCKACDKTVYFVDLLTADGITYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60

Query: 61  HFEQLFKETGSFTNKL----KPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVT 116
           HFEQLFKE G+F+       KP +++ LTRTPSK S MF GTQDKC +C KTVYPLEKVT
Sbjct: 61  HFEQLFKECGNFSKNFQTSAKPEREHALTRTPSKLSAMFSGTQDKCAACNKTVYPLEKVT 120

Query: 117 VEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKI 176
           +EGESFHK+CF+C+HGGC LT ++YA+LDG+LYCK HFAQLF EKG Y H+ + A+ KKI
Sbjct: 121 MEGESFHKSCFKCAHGGCPLTHATYASLDGVLYCKHHFAQLFMEKGTYQHVLEAANNKKI 180

Query: 177 VAASADQNPEAEATEAKE 194
            A +   N   +   AKE
Sbjct: 181 NAETPTNNEPEDDEAAKE 198

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115447541|ref|NP_001047550.1| Os02g0641000 [Oryza sativa Japonica Group] gi|49388090|dbj|BAD25223.1| putative LIM domain protein PLIM-2 [Oryza sativa Japonica Group] gi|49388251|dbj|BAD25371.1| putative LIM domain protein PLIM-2 [Oryza sativa Japonica Group] gi|113537081|dbj|BAF09464.1| Os02g0641000 [Oryza sativa Japonica Group] gi|125540456|gb|EAY86851.1| hypothetical protein OsI_08235 [Oryza sativa Indica Group] gi|125583028|gb|EAZ23959.1| hypothetical protein OsJ_07685 [Oryza sativa Japonica Group] gi|338815137|gb|AEJ08684.1| PLIM [Oryza sativa]

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 131/198 (66%), Positives = 159/198 (80%), Gaps = 4/198 (2%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M+F GTQ+KCKACDKTVH ID++TADG+SYHK CFKCSHC G L M N+SSM+GVLYCK 
Sbjct: 1   MSFTGTQDKCKACDKTVHFIDLLTADGVSYHKTCFKCSHCKGTLSMCNYSSMDGVLYCKT 60

Query: 61  HFEQLFKETGSFTNKL----KPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVT 116
           HFEQLFKETGSF+ K     K ++K+   R PSK S+ F GTQDKC +C+KTVYPLEK+T
Sbjct: 61  HFEQLFKETGSFSKKFSQGGKSSEKSDQGRAPSKLSSAFSGTQDKCAACQKTVYPLEKLT 120

Query: 117 VEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKI 176
           +EGES+HK+CF+CSHGGC+LTTSSYAAL+GILYCK HF+QLFKEKG YNHL +TA  K+ 
Sbjct: 121 LEGESYHKSCFKCSHGGCILTTSSYAALNGILYCKIHFSQLFKEKGSYNHLIQTAQSKQK 180

Query: 177 VAASADQNPEAEATEAKE 194
            +  A      EA+E ++
Sbjct: 181 ESEEAAPVAATEASEKEQ 198

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|223944239|gb|ACN26203.1| unknown [Zea mays] gi|323388671|gb|ADX60140.1| LIM transcription factor [Zea mays] gi|413937970|gb|AFW72521.1| putative LIM-type zinc finger domain family protein [Zea mays]

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 128/191 (67%), Positives = 156/191 (81%), Gaps = 3/191 (1%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M+F GTQ+KCKACDKTVHIID++TADG+SYHK CFKCSHC G L + ++SSM+GVLYCK 
Sbjct: 1   MSFTGTQDKCKACDKTVHIIDLLTADGVSYHKTCFKCSHCKGVLSISSYSSMDGVLYCKT 60

Query: 61  HFEQLFKETGSFTNKLK---PAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTV 117
           HFEQLFKETG+F+   +    + KN   + PSK S+ F GTQDKC +C+KTVYPLEK+T+
Sbjct: 61  HFEQLFKETGTFSKNFQGGASSNKNDQAKAPSKLSSAFSGTQDKCAACQKTVYPLEKMTL 120

Query: 118 EGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIV 177
           EGES+HK+CF+CSHGGC+LTTSSYAAL+G+LYCK HF+QLFKEKG YNHL +TA  KK  
Sbjct: 121 EGESYHKSCFKCSHGGCILTTSSYAALNGVLYCKIHFSQLFKEKGSYNHLIETAQTKKNE 180

Query: 178 AASADQNPEAE 188
           AA A   P A+
Sbjct: 181 AAEAGPEPPAD 191

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053939|ref|XP_002298048.1| predicted protein [Populus trichocarpa] gi|222845306|gb|EEE82853.1| predicted protein [Populus trichocarpa]

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 127/187 (67%), Positives = 153/187 (81%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M F GT EKCKACDKTV+ I++V+ADG+ YHK CFKCSHCNG LVM ++SS++GVLYCKP
Sbjct: 1   MGFTGTLEKCKACDKTVYFIELVSADGVPYHKKCFKCSHCNGLLVMSSYSSIDGVLYCKP 60

Query: 61  HFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGE 120
           H++QLFKETG+FT K +P +    T+ PSK S+MF GTQDKC  CKKT YPLEKVTVEGE
Sbjct: 61  HYDQLFKETGNFTKKFQPCEIRFSTKAPSKLSSMFSGTQDKCAFCKKTAYPLEKVTVEGE 120

Query: 121 SFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAAS 180
            +HK+CFRCSHGGC +T SSYAALDGILYCK+HFAQLFK+KG Y++LTKTA+ KK     
Sbjct: 121 FYHKSCFRCSHGGCCITPSSYAALDGILYCKAHFAQLFKQKGSYSYLTKTATMKKNAVNL 180

Query: 181 ADQNPEA 187
            ++  EA
Sbjct: 181 PEEKSEA 187

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326522158|dbj|BAK04207.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  265 bits (677), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 124/201 (61%), Positives = 158/201 (78%), Gaps = 7/201 (3%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M+F GTQ+KC AC+KTVH ID++TADG+ YHK CFKCSHC G L M ++SSM+GVLYCK 
Sbjct: 1   MSFTGTQDKCSACEKTVHFIDLLTADGVIYHKTCFKCSHCKGILSMCSYSSMDGVLYCKT 60

Query: 61  HFEQLFKETGSFTNKLKPAQKNG----LTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVT 116
           HFEQLFKETGSF+ K  P  K+G    LTR PSK S  F GTQDKC +C KTVYPLEK+T
Sbjct: 61  HFEQLFKETGSFSKKFTPGNKSGDKSELTRAPSKLSAAFSGTQDKCAACTKTVYPLEKMT 120

Query: 117 VEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKI 176
           +EG+++HK+CF+CSHGGC+LTTSSYAAL+G+LYCK HF QLF E+G Y+H+ K +  +++
Sbjct: 121 LEGDAYHKSCFKCSHGGCILTTSSYAALNGVLYCKIHFGQLFMERGSYSHMKKKSPSQEV 180

Query: 177 ---VAASADQNPEAEATEAKE 194
              + A+A+  PEAEA   ++
Sbjct: 181 LPDLVAAAEGQPEAEAAPPQD 201

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 123/180 (68%), Positives = 152/180 (84%), Gaps = 5/180 (2%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           MAF GT +KCKACDKTV+++D+++ADG SYHK CFKCSHC G LVM N+SSM+GVLYCKP
Sbjct: 1   MAFTGTLDKCKACDKTVYVVDLLSADGASYHKTCFKCSHCKGTLVMSNYSSMDGVLYCKP 60

Query: 61  HFEQLFKETGSFTNKL----KPAQK-NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV 115
           HFEQLFKE+G+F+       KPA K N L+R PSK S+MF GTQDKC++C+KTVYPLEKV
Sbjct: 61  HFEQLFKESGNFSKNFQTSAKPADKLNELSRAPSKLSSMFSGTQDKCSACRKTVYPLEKV 120

Query: 116 TVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKK 175
           T+EGES+HK+CF+C+HGGC LT SSYAAL+G+LYCK HF+QLF EKG Y+H+ + A+ KK
Sbjct: 121 TLEGESYHKSCFKCAHGGCPLTHSSYAALNGVLYCKHHFSQLFMEKGNYSHVLEAATHKK 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242076584|ref|XP_002448228.1| hypothetical protein SORBIDRAFT_06g023600 [Sorghum bicolor] gi|241939411|gb|EES12556.1| hypothetical protein SORBIDRAFT_06g023600 [Sorghum bicolor]

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 124/196 (63%), Positives = 156/196 (79%), Gaps = 5/196 (2%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M+F GTQ+KC ACDKTVH ID++TADG+ YHK CFKCSHC G L M ++SSM+GVLYCK 
Sbjct: 1   MSFTGTQDKCTACDKTVHFIDLLTADGVIYHKTCFKCSHCKGILSMCSYSSMDGVLYCKT 60

Query: 61  HFEQLFKETGSFTNKLKP---AQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTV 117
           HFEQLFKETGSF+ K  P   + K  L R PSK S+ F GTQDKC +C+KTVYPLEK+T+
Sbjct: 61  HFEQLFKETGSFSKKFTPGCKSDKGELARAPSKLSSAFSGTQDKCAACQKTVYPLEKLTL 120

Query: 118 EGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIV 177
           EGE++HK+CF+CSHGGC+LTTSSYAAL+G+LYCK HF QLF EKG YNH+ K ++ ++++
Sbjct: 121 EGEAYHKSCFKCSHGGCILTTSSYAALNGVLYCKIHFGQLFMEKGSYNHMKKKSTSQEVL 180

Query: 178 A--ASADQNPEAEATE 191
              A+ +Q P+  A E
Sbjct: 181 PDLAAEEQPPQPAAPE 196

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	195
TAIR|locus:2050735	226	PLIM2a "PLIM2a" [Arabidopsis t	0.964	0.831	0.609	2.5e-65
TAIR|locus:2098871	213	PLIM2c "PLIM2c" [Arabidopsis t	0.989	0.906	0.603	2.5e-65
TAIR|locus:2198210	205	PLIM2b "PLIM2b" [Arabidopsis t	0.994	0.946	0.585	3.2e-65
TAIR|locus:2061171	200	WLIM2a "WLIM2a" [Arabidopsis t	0.923	0.9	0.625	3.2e-65
TAIR|locus:2012798	190	WLIM1 "AT1G10200" [Arabidopsis	0.917	0.942	0.505	5.8e-50
UNIPROTKB|F1NWZ2	193	CSRP3 "Uncharacterized protein	0.492	0.497	0.393	2.9e-22
ZFIN|ZDB-GENE-040426-1863	193	csrp2 "cysteine and glycine-ri	0.394	0.398	0.417	2e-21
ZFIN|ZDB-GENE-030909-4	192	csrp1a "cysteine and glycine-r	0.446	0.453	0.4	4.1e-21
MGI|MGI:1202907	193	Csrp2 "cysteine and glycine-ri	0.441	0.445	0.373	1.7e-20
UNIPROTKB|G3V9V9	193	Csrp2 "Cysteine and glycine-ri	0.441	0.445	0.373	1.7e-20

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

 Score = 665 (239.2 bits), Expect = 2.5e-65, P = 2.5e-65
 Identities = 117/192 (60%), Positives = 152/192 (79%)

Query:     1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
             M+F GT +KCKACDKTV+++D++T +G +YHK CF+C+HC G LV+ N+SSM+GVLYCKP
Sbjct:     1 MSFTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCTHCKGTLVISNYSSMDGVLYCKP 60

Query:    61 HFEQLFKETGSFTNKL---KPAQKNG-LTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVT 116
             HFEQLFKE+G+++      K  + N  LTRTPSK S+ F GTQDKC +CKKTVYPLEKVT
Sbjct:    61 HFEQLFKESGNYSKNFQAGKTEKPNDHLTRTPSKLSSFFSGTQDKCATCKKTVYPLEKVT 120

Query:   117 VEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKI 176
             +EGES+HKTCFRC+H GC LT SSYA+L+G+LYCK HF QLF EKG YNH+ + A+  + 
Sbjct:   121 MEGESYHKTCFRCTHSGCPLTHSSYASLNGVLYCKVHFNQLFLEKGSYNHVHQAAANHRR 180

Query:   177 VAASADQNPEAE 188
              A+S   +P ++
Sbjct:   181 SASSGGASPPSD 192

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 = 665 (239.2 bits), Expect = 2.5e-65, P = 2.5e-65
 Identities = 120/199 (60%), Positives = 153/199 (76%)

Query:     2 AFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPH 61
             AF GT +KCKACDKTV+++D++T +G+ YHK CF+CSHCNG LV+ N+SSM+GVLYCK H
Sbjct:     3 AFTGTTDKCKACDKTVYVMDLMTLEGMPYHKSCFRCSHCNGTLVICNYSSMDGVLYCKTH 62

Query:    62 FEQLFKETGSFTNKLKPAQK----NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTV 117
             FEQLFKE+G+F+   + A K    N  T+ P++ S+ F GTQDKC +CKKTVYPLEK+T+
Sbjct:    63 FEQLFKESGNFSKNFQTAGKTEKSNDATKAPNRLSSFFSGTQDKCAACKKTVYPLEKMTM 122

Query:   118 EGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIV 177
             EGES+HKTCFRC+H GC LT SSYAALDG+LYCK HF+QLF EKG YNH+ + A+  +  
Sbjct:   123 EGESYHKTCFRCAHSGCPLTHSSYAALDGVLYCKVHFSQLFLEKGNYNHVLQAAANHRRS 182

Query:   178 AASADQN-P-EAEATEAKE 194
              A  D+  P E EA   +E
Sbjct:   183 TAEEDKTEPKEDEANPTEE 201

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

 Score = 664 (238.8 bits), Expect = 3.2e-65, P = 3.2e-65
 Identities = 116/198 (58%), Positives = 151/198 (76%)

Query:     1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
             M+F GT +KC  CDKTV+++DM++ +G+ YHK CF+C+HC G L M N+SSM+GVLYCK 
Sbjct:     1 MSFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKT 60

Query:    61 HFEQLFKETGSFTNKLKPA--QKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVE 118
             HFEQLFKE+G+F+   +P   +K  LTRTPSK S++FCGTQDKC +C+KTVYPLEK+ +E
Sbjct:    61 HFEQLFKESGNFSKNFQPGKTEKPELTRTPSKISSIFCGTQDKCAACEKTVYPLEKIQME 120

Query:   119 GESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVA 178
             GE FHKTCFRC+HGGC LT SSYA+LD +LYC+ HF QLF EKG Y H+ + A+ ++  +
Sbjct:   121 GECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFMEKGNYAHVLQAANHRRTAS 180

Query:   179 ASA-DQNP-EAEATEAKE 194
              +     P E  A EAKE
Sbjct:   181 GNTLPPEPTEDVAVEAKE 198

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 664 (238.8 bits), Expect = 3.2e-65, P = 3.2e-65
 Identities = 117/187 (62%), Positives = 151/187 (80%)

Query:     1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
             M+F GTQ+KC+AC+KTV+ +++++ADGISYHK CFKCSHC  +L + N+SSMEGV+YC+P
Sbjct:     1 MSFTGTQQKCRACEKTVYPVELLSADGISYHKACFKCSHCKSRLQLSNYSSMEGVVYCRP 60

Query:    61 HFEQLFKETGSFTNKLK-PAQK------NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLE 113
             HFEQLFKE+GSF+   + PA+         L RTPS+ + MF GTQDKC +C KTVYP+E
Sbjct:    61 HFEQLFKESGSFSKNFQSPAKPLTDKPTPELNRTPSRLAGMFSGTQDKCATCTKTVYPIE 120

Query:   114 KVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQ 173
             KVTVE + +HK+CF+CSHGGC ++ S+YAAL+GILYCK HFAQLFKEKG YNHL K+AS 
Sbjct:   121 KVTVESQCYHKSCFKCSHGGCPISPSNYAALEGILYCKHHFAQLFKEKGSYNHLIKSASI 180

Query:   174 KKIVAAS 180
             K+  AA+
Sbjct:   181 KRATAAA 187

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0000271 "polysaccharide biosynthetic process" evidence=RCA

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0009825 "multidimensional cell growth" evidence=RCA

GO:0009932 "cell tip growth" evidence=RCA

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

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

GO:0048767 "root hair elongation" evidence=RCA

GO:0071555 "cell wall organization" evidence=RCA

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

 Score = 520 (188.1 bits), Expect = 5.8e-50, P = 5.8e-50
 Identities = 96/190 (50%), Positives = 126/190 (66%)

Query:     1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
             MAF GT +KC ACDKTV+++D +TAD   YHK CF+C HC G L + N++S EGVLYC+P
Sbjct:     1 MAFAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNYNSFEGVLYCRP 60

Query:    61 HFEQLFKETGSFTNKLKPAQKNGLTRTP--------SKFSTMFCGTQDKCTSCKKTVYPL 112
             HF+Q FK TGS     +   K G    P        +K S MF GT++KC  C KTVYP+
Sbjct:    61 HFDQNFKRTGSLEKSFEGTPKIGKPDRPLEGERPAGTKVSNMFGGTREKCVGCDKTVYPI 120

Query:   113 EKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLT---K 169
             EKV+V G  +HK+CF+C+HGGC ++ S+Y A +G LYCK H  QL KEKG  + L    +
Sbjct:   121 EKVSVNGTLYHKSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLIKEKGNLSQLEGGGE 180

Query:   170 TASQKKIVAA 179
              A++ K+VAA
Sbjct:   181 NAAKDKVVAA 190

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

UNIPROTKB|F1NWZ2 CSRP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 166 (63.5 bits), Expect = 2.9e-22, Sum P(2) = 2.9e-22
 Identities = 39/99 (39%), Positives = 56/99 (56%)

Query:    77 KPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLL 136
             KPA+ +  T  PSKF+       DKC  C K+VY  EK+   G+ +HKTCFRC+  G  L
Sbjct:    97 KPARPSTPTN-PSKFAKKMVDV-DKCPRCGKSVYAAEKIMGGGKPWHKTCFRCAICGKSL 154

Query:   137 TTSSYAALDGILYCKSHFAQLFKEKGC-YNHLTKTASQK 174
              +++    DG LYCK  +A+ F  KG  +  LT+   ++
Sbjct:   155 ESTNVTDKDGELYCKVCYAKNFGPKGIGFGGLTQVEKKE 193

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003300 "cardiac muscle hypertrophy" evidence=IEA

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

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

GO:0030018 "Z disc" evidence=IEA

GO:0031433 "telethonin binding" evidence=IEA

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

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

GO:0042805 "actinin binding" evidence=IEA

GO:0055003 "cardiac myofibril assembly" evidence=IEA

GO:0060048 "cardiac muscle contraction" evidence=IEA

ZFIN|ZDB-GENE-040426-1863 csrp2 "cysteine and glycine-rich protein 2" [Danio rerio (taxid:7955)]

 Score = 162 (62.1 bits), Expect = 2.0e-21, Sum P(2) = 2.0e-21
 Identities = 33/79 (41%), Positives = 47/79 (59%)

Query:    85 TRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAAL 144
             T T SKF+  F G++ KC  C   VY  EK+   G+ +HK CFRC+  G  L +++    
Sbjct:   104 TNT-SKFAQKFGGSE-KCARCGDAVYAAEKIMSAGKPWHKNCFRCAKCGKSLESTTQTEK 161

Query:   145 DGILYCKSHFAQLFKEKGC 163
             DG +YCK+ +A+ F  KGC
Sbjct:   162 DGEIYCKACYAKNFGPKGC 180

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 155 (59.6 bits), Expect = 4.1e-21, Sum P(2) = 4.1e-21
 Identities = 36/90 (40%), Positives = 50/90 (55%)

Query:    75 KLKPAQKNGLTRTP--SKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHG 132
             K+   Q +  T  P  SKF+  F G+ D C  C K VY  EKV   G ++H+ CFRC+  
Sbjct:    90 KVVEPQNHQPTNNPNTSKFAQKFGGS-DVCPRCSKAVYAAEKVIGAGNAWHRGCFRCAMC 148

Query:   133 GCLLTTSSYAALDGILYCKSHFAQLFKEKG 162
             G  L +++ A  DG +YCK  +A+ F  KG
Sbjct:   149 GKGLESTTLADKDGEIYCKGCYAKNFGPKG 178

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

MGI|MGI:1202907 Csrp2 "cysteine and glycine-rich protein 2" [Mus musculus (taxid:10090)]

 Score = 151 (58.2 bits), Expect = 1.7e-20, Sum P(2) = 1.7e-20
 Identities = 34/91 (37%), Positives = 52/91 (57%)

Query:    76 LKP--AQKNGLTRTP--SKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSH 131
             +KP  AQ +  T  P  SKF+  + G + KC+ C  +VY  EK+   G+ +HK CFRC+ 
Sbjct:    90 IKPESAQPHRPTTNPNTSKFAQKYGGAE-KCSRCGDSVYAAEKIIGAGKPWHKNCFRCAK 148

Query:   132 GGCLLTTSSYAALDGILYCKSHFAQLFKEKG 162
              G  L +++    +G +YCK  +A+ F  KG
Sbjct:   149 CGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 179

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|G3V9V9 Csrp2 "Cysteine and glycine-rich protein 2, isoform CRA_b" [Rattus norvegicus (taxid:10116)]

 Score = 151 (58.2 bits), Expect = 1.7e-20, Sum P(2) = 1.7e-20
 Identities = 34/91 (37%), Positives = 52/91 (57%)

Query:    76 LKP--AQKNGLTRTP--SKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSH 131
             +KP  AQ +  T  P  SKF+  + G + KC+ C  +VY  EK+   G+ +HK CFRC+ 
Sbjct:    90 IKPESAQPHRPTTNPNTSKFAQKYGGAE-KCSRCGDSVYAAEKIIGAGKPWHKNCFRCAK 148

Query:   132 GGCLLTTSSYAALDGILYCKSHFAQLFKEKG 162
              G  L +++    +G +YCK  +A+ F  KG
Sbjct:   149 CGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 179

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P50461	CSRP3_HUMAN	No assigned EC number	0.3316	0.8871	0.8917	yes	no
P50462	CSRP3_MOUSE	No assigned EC number	0.3367	0.8871	0.8917	yes	no
Q0VFX8	CRIP2_BOVIN	No assigned EC number	0.3080	0.8871	0.8317	yes	no
P50463	CSRP3_RAT	No assigned EC number	0.3461	0.8205	0.8247	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: 4330114 OsPLIM2a - LIM domain protein, putative actin-binding protein and transcription factor, expressed (206 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	195
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-34
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	2e-30
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-22
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	7e-19
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	5e-18
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	5e-17
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	2e-14
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	1e-13
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	1e-12
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	1e-12
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	2e-11
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	3e-11
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	4e-11
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	6e-11
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	9e-11
pfam00412	58	pfam00412, LIM, LIM domain	3e-10
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	2e-09
pfam00412	58	pfam00412, LIM, LIM domain	5e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	6e-09
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	8e-09
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	2e-08
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	3e-08
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-08
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	5e-08
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	1e-07
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	5e-07
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	7e-07
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	2e-06
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	3e-06
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	3e-06
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	4e-06
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	6e-06
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	1e-05
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	1e-05
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	2e-05
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	3e-05
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	4e-05
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	7e-05
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	7e-05
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	8e-05
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	1e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	1e-04
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	1e-04
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	2e-04
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	2e-04
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	2e-04
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	2e-04
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	2e-04
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	3e-04
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	3e-04
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	3e-04
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	3e-04
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	6e-04
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	0.001
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	0.001
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	0.001
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	0.001
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.002
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	0.002
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	0.003
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	0.003
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	0.003
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	0.003

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

 Score =  116 bits (291), Expect = 2e-34
 Identities = 45/63 (71%), Positives = 55/63 (87%)

Query: 6  TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65
          T +KCKACDKTV+++D ++ADG+ YHK CF+CSHC G L + N+SSMEGVLYCKPHFEQL
Sbjct: 1  TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 66 FKE 68
          FKE
Sbjct: 61 FKE 63

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

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

 Score =  105 bits (264), Expect = 2e-30
 Identities = 42/61 (68%), Positives = 52/61 (85%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEK 161
           C +C KTVYP+EKVTVEG S+HK+CF+CSHGGC ++ S+YAA +G LYCK H +QLFKEK
Sbjct: 1   CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 162 G 162
           G
Sbjct: 61  G 61

The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 61

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

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

Query: 98  TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQL 157
           T  KC +C KTVY +++++ +G  +HK+CFRCSH    L  S+Y++++G+LYCK HF QL
Sbjct: 1   TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 158 FKE 160
           FKE
Sbjct: 61  FKE 63

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

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

 Score = 75.8 bits (187), Expect = 7e-19
 Identities = 29/53 (54%), Positives = 38/53 (71%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C  C KTVYP+E++  +G+ FHK+CFRCSH    L   +YA+L+G LYCK HF
Sbjct: 1   CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53

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

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

 Score = 73.5 bits (181), Expect = 5e-18
 Identities = 30/53 (56%), Positives = 40/53 (75%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C  C KTV+ ++ + ADG  +HK CF+CSHCN  L +GN++S+EG LYCKPHF
Sbjct: 1  CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53

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

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

 Score = 71.3 bits (175), Expect = 5e-17
 Identities = 34/61 (55%), Positives = 41/61 (67%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET 69
          C AC KTV+ I+ VT +G SYHK CFKCSH    +   N+++ EG LYCK H  QLFKE 
Sbjct: 1  CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 70 G 70
          G
Sbjct: 61 G 61

The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 61

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

 Score = 64.4 bits (157), Expect = 2e-14
 Identities = 26/53 (49%), Positives = 38/53 (71%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C  C K V+ ++ + AD  ++HK CF+C HCN KL +GN++S+ G +YCKPHF
Sbjct: 1  CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 62.1 bits (151), Expect = 1e-13
 Identities = 26/53 (49%), Positives = 38/53 (71%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           CT C+K VYP+E++  + ++FHK+CFRC H    L+  +YA+L G +YCK HF
Sbjct: 1   CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 59.5 bits (144), Expect = 1e-12
 Identities = 25/53 (47%), Positives = 38/53 (71%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C +C KTV+ ++ + A+   YH  CF+CS+CN KL +G ++S+ G +YCKPHF
Sbjct: 1  CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

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

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

 Score = 59.5 bits (144), Expect = 1e-12
 Identities = 26/53 (49%), Positives = 37/53 (69%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C SC+KTVYPLE++    + +H +CFRCS+    L+  +YA+L G +YCK HF
Sbjct: 1   CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

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

>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 56.5 bits (136), Expect = 2e-11
 Identities = 24/53 (45%), Positives = 37/53 (69%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C +C KTV+ ++ + AD + +H  CF C HCN KL +G+++++ G  YCKPHF
Sbjct: 1  CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53

This model represents a LIM domain subfamily of Eplin-like family. This family shows highest homology to the LIM domains on Eplin and XIRP2 protein families. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Xirp2 is expressed in muscles and is an important effector of the Ang II signaling pathway in the heart. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 23/53 (43%), Positives = 30/53 (56%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C SC K VY +E++  E   +HK CFRC      L   +Y + +G LYCK HF
Sbjct: 1   CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53

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

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

 Score = 55.5 bits (134), Expect = 4e-11
 Identities = 24/53 (45%), Positives = 35/53 (66%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C++C K V+ ++ + A+   YHK CF+C  CN +L + N+ S EG LYCK HF
Sbjct: 1  CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53

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

>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 55.0 bits (132), Expect = 6e-11
 Identities = 27/53 (50%), Positives = 35/53 (66%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C+SC+KTVYP+E++  +   FH +CF C H    L+  SYAAL G  YCK HF
Sbjct: 1   CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53

This model represents a LIM domain subfamily of Eplin-like family. This family shows highest homology to the LIM domains on Eplin and XIRP2 protein families. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Xirp2 is expressed in muscles and is an important effector of the Ang II signaling pathway in the heart. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 54.6 bits (132), Expect = 9e-11
 Identities = 26/55 (47%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYA--ALDGILYCKSHF 154
           C  CKK VY +E+++ EG  FH++CF+CS+ G  L   +YA    DG  YCK HF
Sbjct: 1   CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55

The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 53.5 bits (129), Expect = 3e-10
 Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 102 CTSCKKTVYPLEKVT-VEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
           C  C K +Y  E V    G+ +H  CFRC+  G  L    +   DG LYCK  + +LF
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 51.3 bits (123), Expect = 2e-09
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYA--ALDGILYCKSH 153
           C  C KT YP E V  +G  +HK CF+C   G  L+  ++     DG +YC  H
Sbjct: 1   CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54

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

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

 Score = 50.0 bits (120), Expect = 5e-09
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 10 CKACDKTVHIIDMVT-ADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
          C  C K ++  ++V  A G  +H  CF+C+ C   L  G+F   +G LYCK  + +LF
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 49.7 bits (119), Expect = 6e-09
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 101 KCTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSH 153
           KC  C K +Y  E+V    G+ +H  CF+C+  G  L+  ++   DG LYCK  
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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

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

 Score = 49.6 bits (119), Expect = 8e-09
 Identities = 23/55 (41%), Positives = 36/55 (65%), Gaps = 2/55 (3%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGN--FSSMEGVLYCKPHF 62
          C  C K V++++ ++A+G+ +H+ CFKCS+C   L +G   F   +G  YCKPHF
Sbjct: 1  CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55

The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C  C KTVYP EK+    + +HK CF+C   G  L   +Y   +   YC +H+
Sbjct: 1   CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

The LIM domain of LIM and SH3 Protein (LASP): LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 47.8 bits (114), Expect = 3e-08
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 9  KCKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPH 61
          KC  C K ++  + V  A G  +H  CFKC+ C   L    F   +G LYCK  
Sbjct: 1  KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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

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

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 17/53 (32%), Positives = 25/53 (47%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C  C K +   E +   G+ +H  CF+CS  G  L   S+   DG  YC+  +
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

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

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

 Score = 47.4 bits (113), Expect = 5e-08
 Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMG--NFSSMEGVLYCKPH 61
          C  C KT +  + V  DG  YHK CFKC  C  +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|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 23/54 (42%), Positives = 33/54 (61%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFA 155
           C  C K+VY  EK+   G+ +HK CFRC+  G  L +++ A  DG +YCK  +A
Sbjct: 1   CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCYA 54

The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 44.6 bits (106), Expect = 5e-07
 Identities = 17/53 (32%), Positives = 26/53 (49%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C  C K +   +++ A G  +H  CFKCS 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|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 44.2 bits (104), Expect = 7e-07
 Identities = 25/54 (46%), Positives = 33/54 (61%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFA 155
           C  C K+VY  EKV   G+ +HKTCFRC+  G  L +++    DG LYCK  +A
Sbjct: 1   CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCYA 54

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 42.7 bits (101), Expect = 2e-06
 Identities = 18/53 (33%), Positives = 24/53 (45%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C  C KTV+  + +      +HK CFKC  C   L M 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|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 23/52 (44%), Positives = 29/52 (55%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
          KC  C K+V+  +   A G  +HK+CFKC  CN  L   N +  EG LYCK 
Sbjct: 1  KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQ 52

The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 42.6 bits (101), Expect = 3e-06
 Identities = 20/50 (40%), Positives = 29/50 (58%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          C  C K+V+  + V A G S+HK CF C+ CN +L     +  +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|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 42.3 bits (100), Expect = 4e-06
 Identities = 18/51 (35%), Positives = 23/51 (45%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
          C  C K V+  +  T+ G  +HK C +C  C   L  G  S  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|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 41.6 bits (98), Expect = 6e-06
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSME--GVLYCKPHF 62
          C AC + VH++     DG  YH+ CF+C  C+  L+ G++ +    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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 41.0 bits (97), Expect = 1e-05
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152
           C  C K+VY  E+V   G+S+HK+CF C+     L +++ A  DG +YCKS
Sbjct: 1   CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKS 51

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

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 20/54 (37%), Positives = 32/54 (59%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFA 155
           C+ C  +VY  EK+   G+ +HK CFRC+  G  L +++    +G +YCK  +A
Sbjct: 1   CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54

The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 24/51 (47%), Positives = 33/51 (64%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152
           C +C+KTVY  E+V  EG SFHK+CF C      L +++ AA +  +YCKS
Sbjct: 1   CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCKS 51

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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 40.1 bits (93), Expect = 3e-05
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152
           KC +C+KTVY  E++   G SFHKTCF C      L +++ AA +  +YCK+
Sbjct: 1   KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKT 52

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

 Score = 39.6 bits (93), Expect = 4e-05
 Identities = 19/50 (38%), Positives = 23/50 (46%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK 151
           C  C K VY  EK T  G  +HK C RC      LT   ++  +G  YC 
Sbjct: 1   CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCN 50

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

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 21/52 (40%), Positives = 29/52 (55%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152
           KC  C K+VY  E+    G  +HK CF+C     LL +++ A  +G LYCK 
Sbjct: 1   KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQ 52

The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC 150
           + C SC   V+  E++ +EG+ +H+TCF+C+  G  LT  S+   +   YC
Sbjct: 3   EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

LIM domain in proteins of unknown function: LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation, and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. The LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 61

>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1 (CRP1)

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 24/52 (46%), Positives = 31/52 (59%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152
           KC  C+KTVY  E+V  EG SFHK+CF C      L +++ A     +YCKS
Sbjct: 2   KCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKS 53

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 8  EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC 58
          E C +C   V + + +  +G  YH+ CFKC+ C  +L  G+F   E   YC
Sbjct: 3  EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

LIM domain in proteins of unknown function: LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation, and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. The LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 61

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 21/49 (42%), Positives = 27/49 (55%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC 150
           C  C K VY  E+VT  G+ +H+ C +C   G  LT  S+A  DG  YC
Sbjct: 1   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49

The LIM domain of Cysteine-Rich Intestinal Protein (CRIP): CRIP is a short protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 20/49 (40%), Positives = 24/49 (48%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC 150
           C  C K VY  EKV   G ++H+ C RC      LT   +A  DG  YC
Sbjct: 1   CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49

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

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

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 18/50 (36%), Positives = 26/50 (52%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          C  C K+V+  + V   G  +HK CF+C+ C   L     +  +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|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 17/52 (32%), Positives = 28/52 (53%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSH 153
           C  C   VYP EK+    +++HK CF C     +LT +++ +     YC++H
Sbjct: 1   CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 23/52 (44%), Positives = 31/52 (59%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152
           KC +C +TVY  E+V  +G SFHK CF C      L +++ A  D  +YCKS
Sbjct: 1   KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKS 52

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

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C  C+  +   + V    + +H  CFRCS     L ++ Y   DG LYC+  +
Sbjct: 1   CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL-SNWYFEKDGKLYCRKDY 52

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

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

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC 58
          C  CDKTV+  + V++ G ++H+ C KC  C+  L  G  +  +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|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          C  C K+V+  + +   G  +HK CF+C+ C   L     +  +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|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 = 37.0 bits (86), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALD--GILYCKSHF 154
           C +C + V+ +++  V+G+ +H+ CFRC      L   SY A    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 = 36.9 bits (85), Expect = 3e-04
 Identities = 19/49 (38%), Positives = 28/49 (57%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC 150
           C  C KTVY  EKV+  G+++H+ C +C     +L+   +A  DG  YC
Sbjct: 1   CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

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

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

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 19/53 (35%), Positives = 26/53 (49%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C  C K VYP EKV    +++HK CF C      L  ++Y       YC +H+
Sbjct: 1   CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 36.1 bits (83), Expect = 6e-04
 Identities = 15/49 (30%), Positives = 24/49 (48%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC 58
          C  C K V+  + V + G ++H+ C +C  C   L  G  +  +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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 20/51 (39%), Positives = 29/51 (56%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          KC AC+KTV+  + +  +G S+HK CF C  C   L     ++ E  +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|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal Protein (CRIP)

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 18/49 (36%), Positives = 26/49 (53%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC 58
          C  CDK V+  + VT+ G  +H+ C KC  C   L  G+ +  +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|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 17/45 (37%), Positives = 24/45 (53%)

Query: 22 MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
          +V ++G  YH+ CF C+ C      G F   EG  YC+  F+ LF
Sbjct: 14 IVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLF 58

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

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

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           CT C   +       V  E++H +CF+CS    LLT   Y   DG LYC  H+
Sbjct: 1   CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYEK-DGKLYCHKHY 52

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

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

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C  C++ +     + A G S+H   F CSHC+  L    F   +G LYC+  +
Sbjct: 1  CAHCNQVI-RGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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

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

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
          C  C+K + + + ++A    +H  CF C  C+   + G+F   EG+ YC+ H+
Sbjct: 1  CGGCNKPI-LENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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

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

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 20/50 (40%), Positives = 28/50 (56%)

Query: 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          C AC+KTV+  + V  +G S+HK CF C  C   L     ++ E  +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|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 20/51 (39%), Positives = 27/51 (52%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          KC AC +TV+  + V  DG S+HK CF C  C   L     +  +  +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|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 102 CTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
           C SC +++Y  + +      +H  CFRC   G  L+   Y   DG L+CK  +
Sbjct: 22  CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEK-DGRLFCKKDY 73

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

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

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 10 CKACDKTVHIIDMVT-ADGISYHKICFKCSHCNGKLVMGN-FSSMEGVLYC 58
          C AC +++   ++V  A G  YH  CF CS C+ +LV G+ F  + G L+C
Sbjct: 1  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	195
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.95
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.9
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.89
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.85
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.83
KOG1700	200	consensus Regulatory protein MLP and related LIM p	99.83
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.82
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.81
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.75
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.69
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.61
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.58
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.22
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.81
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.67
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.54
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	98.39
KOG0490	235	consensus Transcription factor, contains HOX domai	97.87
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	97.79
KOG0490	235	consensus Transcription factor, contains HOX domai	92.26
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	89.27
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	87.91
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	86.75
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	86.23
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	84.98
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	84.94
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	83.62
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	80.74
PF11781	36	RRN7: RNA polymerase I-specific transcription init	80.54
PF01258	36	zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc f	80.19

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

Probab=99.95  E-value=1.1e-29  Score=211.36  Aligned_cols=134  Identities=23%  Similarity=0.512  Sum_probs=123.0

Q ss_pred             CcccccccccccCc-eEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCC
Q 041875            8 EKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTR   86 (195)
Q Consensus         8 ~~C~~C~~~I~~~~-~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~   86 (195)
                      .+|.+|+|.|.... .+.||++.||..||+|..|++.|.++.||..|+++||+.||+...                    
T Consensus       275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl--------------------  334 (468)
T KOG1701|consen  275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL--------------------  334 (468)
T ss_pred             hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--------------------
Confidence            48999999998543 589999999999999999999999999999999999999999876                    


Q ss_pred             CCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeecc-CCccccHHHHHhhhcCCCc-c
Q 041875           87 TPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAAL-DGILYCKSHFAQLFKEKGC-Y  164 (195)
Q Consensus        87 ~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~-dg~~yC~~c~~~~f~~k~~-~  164 (195)
                                   .+|..|+++|+ +.++.+.|+.||..||+|..|.+.|++..|++. ++++||-.||+++|++||+ +
T Consensus       335 -------------ekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C  400 (468)
T KOG1701|consen  335 -------------EKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVC  400 (468)
T ss_pred             -------------HHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhc
Confidence                         79999999998 556799999999999999999999999999887 7999999999999999999 7


Q ss_pred             CCCCCcchhhh
Q 041875          165 NHLTKTASQKK  175 (195)
Q Consensus       165 ~~~~~~~~~~~  175 (195)
                      +..|+|...++
T Consensus       401 ~~PI~P~~G~~  411 (468)
T KOG1701|consen  401 GNPILPRDGKD  411 (468)
T ss_pred             cCCccCCCCCc
Confidence            78888877665

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

Probab=99.90  E-value=1.8e-25  Score=174.99  Aligned_cols=160  Identities=21%  Similarity=0.431  Sum_probs=125.5

Q ss_pred             CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC-Ccc-------ccCCCc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET-GSF-------TNKLKP   78 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~-~~~-------~~~~~~   78 (195)
                      +|.|+.|++.|. |.+|.+++.+||+.||+|..|++.|.+..|+-..|..+|..|.++..+.. |.|       .++-++
T Consensus        73 aPcC~kC~EFii-GrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~  151 (332)
T KOG2272|consen   73 APCCGKCGEFII-GRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQP  151 (332)
T ss_pred             chhhcccccchh-hHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccccc
Confidence            489999999998 99999999999999999999999999999999999999999998744322 111       122222


Q ss_pred             cCCCCCCCCCCCC--------------------ccccC---CCCCcCccCCceeecCceEEECCceecccccccccCCcc
Q 041875           79 AQKNGLTRTPSKF--------------------STMFC---GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCL  135 (195)
Q Consensus        79 ~~~~~~~~~p~~~--------------------~~~~~---~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~  135 (195)
                      .+..+.+.+|-.+                    +..+.   -+.++|..|.++|. +..|.++|+.||.+.|+|+.|.++
T Consensus       152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekP  230 (332)
T KOG2272|consen  152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKP  230 (332)
T ss_pred             ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCc
Confidence            2222222222211                    11111   25689999999997 556789999999999999999999


Q ss_pred             cccCCeeccCCccccHHHHHhhhcCCCc-cCCCC
Q 041875          136 LTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLT  168 (195)
Q Consensus       136 L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~  168 (195)
                      +-+...+++.|.+||+.+|.++||--|. ++.++
T Consensus       231 FlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i  264 (332)
T KOG2272|consen  231 FLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVI  264 (332)
T ss_pred             ccchhhhhhcCchhHHHHHHHHhhhhheecCCcc
Confidence            9999999999999999999999999987 44433

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

Probab=99.89  E-value=1.1e-24  Score=181.63  Aligned_cols=126  Identities=29%  Similarity=0.669  Sum_probs=112.9

Q ss_pred             cCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceee-cCCeecchhhHHHhhccCCccccCCCccCC
Q 041875            3 FCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSS-MEGVLYCKPHFEQLFKETGSFTNKLKPAQK   81 (195)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~   81 (195)
                      |..+.++|..|+++|. +.+|.|+|+.||+.||+|-.|.+.|++..|.+ .++++||..||.+.|+              
T Consensus       330 yq~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA--------------  394 (468)
T KOG1701|consen  330 YQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA--------------  394 (468)
T ss_pred             HHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC--------------
Confidence            5566789999999998 78899999999999999999999999999974 5789999999999998              


Q ss_pred             CCCCCCCCCCccccCCCCCcCccCCceeecCc------eEEECCceecccccccccCCccccc----CCeeccCCccccH
Q 041875           82 NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLE------KVTVEGESFHKTCFRCSHGGCLLTT----SSYAALDGILYCK  151 (195)
Q Consensus        82 ~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~~~~~H~~CF~C~~C~~~L~~----~~~~~~dg~~yC~  151 (195)
                                        ++|+.|+++|++.+      +|+++++.||.+|++|+.|+.+|+.    ...+-.||.++|+
T Consensus       395 ------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk  456 (468)
T KOG1701|consen  395 ------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCK  456 (468)
T ss_pred             ------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeec
Confidence                              99999999999843      4689999999999999999999983    3588999999999


Q ss_pred             HHHHhhhcCC
Q 041875          152 SHFAQLFKEK  161 (195)
Q Consensus       152 ~c~~~~f~~k  161 (195)
                      .|..++....
T Consensus       457 ~Ch~~Rl~~~  466 (468)
T KOG1701|consen  457 TCHLKRLQAG  466 (468)
T ss_pred             hhhhhhhccc
Confidence            9998876554

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

Probab=99.85  E-value=2.3e-23  Score=165.91  Aligned_cols=125  Identities=26%  Similarity=0.543  Sum_probs=111.8

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT   85 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   85 (195)
                      .+++|+.|.+.|.+..++.+++++||..|++|+.|..+|.. ..|.+++.+||+.+|.++|+                  
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG------------------   92 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG------------------   92 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC------------------
Confidence            67899999999997678899999999999999999999986 55669999999999999999                  


Q ss_pred             CCCCCCccccCCCCCcCccCCceeecCceE-EECCceecccccccccCCcccccC-Ceecc-CCccccHHHHHhhhcCCC
Q 041875           86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLTTS-SYAAL-DGILYCKSHFAQLFKEKG  162 (195)
Q Consensus        86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~-dg~~yC~~c~~~~f~~k~  162 (195)
                                    .+|..|...|.+.+.| .+.+..||..||.|..|+++|..+ .|+.+ |++++|+.+|.+.-+..+
T Consensus        93 --------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~  158 (383)
T KOG4577|consen   93 --------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC  158 (383)
T ss_pred             --------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence                          8999999999998887 689999999999999999999955 46654 899999999998766655


Q ss_pred             c
Q 041875          163 C  163 (195)
Q Consensus       163 ~  163 (195)
                      .
T Consensus       159 ~  159 (383)
T KOG4577|consen  159 N  159 (383)
T ss_pred             c
Confidence            3

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

Probab=99.83  E-value=3.2e-22  Score=156.85  Aligned_cols=117  Identities=24%  Similarity=0.534  Sum_probs=110.3

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT   85 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   85 (195)
                      +.++|..|.+||. +.+|.++|++||.+.|+|+.|-+++-+...+++.|..||+.+|.++|+                  
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            5689999999997 788999999999999999999999988899999999999999999999                  


Q ss_pred             CCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCccccc-CCeeccCCccccHHHHHh
Q 041875           86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTT-SSYAALDGILYCKSHFAQ  156 (195)
Q Consensus        86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~-~~~~~~dg~~yC~~c~~~  156 (195)
                                    ..|..|+..|. ++.+.++++.|-.+||+|+.|.+.|.. ..|++.|-.|.|+.||.+
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                          89999999998 888999999999999999999999984 469999999999999985

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

Probab=99.83  E-value=2.2e-21  Score=151.71  Aligned_cols=176  Identities=46%  Similarity=0.860  Sum_probs=144.4

Q ss_pred             CCcCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCC-ccccCCCcc
Q 041875            1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETG-SFTNKLKPA   79 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~-~~~~~~~~~   79 (195)
                      |++.+....|..|++.|+..+.+...|..||+.||+|..|.+.|....+..+++.+||+.||...+++++ .....|+..
T Consensus         1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~   80 (200)
T KOG1700|consen    1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKA   80 (200)
T ss_pred             CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccccccc
Confidence            7888888999999999998888889999999999999999999999999999999999998888888765 233333321


Q ss_pred             CC--------CCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccH
Q 041875           80 QK--------NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK  151 (195)
Q Consensus        80 ~~--------~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~  151 (195)
                      ..        +.....+......+.++...|.+|.+.+++.+.++..+..||+.||+|+.|++.|+.+.+....|.+||.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~  160 (200)
T KOG1700|consen   81 GGLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCK  160 (200)
T ss_pred             CCCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccc
Confidence            11        1111111123344567889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCCCccCCCCCcchhhhh
Q 041875          152 SHFAQLFKEKGCYNHLTKTASQKKI  176 (195)
Q Consensus       152 ~c~~~~f~~k~~~~~~~~~~~~~~~  176 (195)
                      .++.++|-.++.++........++.
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~  185 (200)
T KOG1700|consen  161 HHFAQLFKGKGNYNEGFGARENKEA  185 (200)
T ss_pred             hhhheeecCCCcccccchhhhhhhh
Confidence            9888888888778877766666654

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

Probab=99.82  E-value=1.2e-20  Score=165.50  Aligned_cols=130  Identities=28%  Similarity=0.611  Sum_probs=120.4

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT   85 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   85 (195)
                      ..++|..|.+.|....++.++++.||+.+|.|..|...+..+.+...+|++||..|+...+.                  
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             CCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875           86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN  165 (195)
Q Consensus        86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~  165 (195)
                                    ++|.+|+++|. ++.|.+.+..||++||.|..|++.|....|+..||.+||+.||+++|++++.++
T Consensus       364 --------------p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~  428 (479)
T KOG1703|consen  364 --------------PNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYC  428 (479)
T ss_pred             --------------ccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhc
Confidence                          99999999998 778888899999999999999999999999999999999999999999998766


Q ss_pred             CCC
Q 041875          166 HLT  168 (195)
Q Consensus       166 ~~~  168 (195)
                      ...
T Consensus       429 ~~p  431 (479)
T KOG1703|consen  429 KKP  431 (479)
T ss_pred             cch
Confidence            543

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

Probab=99.81  E-value=1.9e-20  Score=161.24  Aligned_cols=161  Identities=20%  Similarity=0.439  Sum_probs=119.2

Q ss_pred             CcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCC-eecchhhHHHhhccCC---ccccCCCc-----
Q 041875            8 EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEG-VLYCKPHFEQLFKETG---SFTNKLKP-----   78 (195)
Q Consensus         8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g-~~yC~~c~~~~~~~~~---~~~~~~~~-----   78 (195)
                      -.|..|.+.-. ++++.+.+++||..||+|..|++.|..+.|+.+++ .+|+...... |..+.   +....|++     
T Consensus        17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~-~~~gevvsa~gktyh~~cf~c   94 (670)
T KOG1044|consen   17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRA-FVEGEVVSTLGKTYHPKCFSC   94 (670)
T ss_pred             eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhh-hccceeEecccceecccccee
Confidence            36999999998 99999999999999999999999999998887654 5777633221 11111   11111211     


Q ss_pred             ----------cCCC--------CCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCC
Q 041875           79 ----------AQKN--------GLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSS  140 (195)
Q Consensus        79 ----------~~~~--------~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~  140 (195)
                                ++..        .....+...+.....+...|++|++.|..++.+.++++.||..||+|..|+..|.++ 
T Consensus        95 s~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge-  173 (670)
T KOG1044|consen   95 STCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE-  173 (670)
T ss_pred             cccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce-
Confidence                      1100        011122222222223567999999999999999999999999999999999999884 


Q ss_pred             eeccCCccccHHHHHhhhcCCCccCCCCCcc
Q 041875          141 YAALDGILYCKSHFAQLFKEKGCYNHLTKTA  171 (195)
Q Consensus       141 ~~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~  171 (195)
                      |+.+||.|||+.+|.+.||.||..++.++.+
T Consensus       174 y~skdg~pyce~dy~~~fgvkc~~c~~fisg  204 (670)
T KOG1044|consen  174 YMSKDGVPYCEKDYQAKFGVKCEECEKFISG  204 (670)
T ss_pred             eeccCCCcchhhhhhhhcCeehHHhhhhhhh
Confidence            9999999999999999999999976655443

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

Probab=99.75  E-value=1.4e-19  Score=158.88  Aligned_cols=117  Identities=32%  Similarity=0.638  Sum_probs=108.0

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGL   84 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   84 (195)
                      ...+.|.+|+++|. ++.|.+.++.||++||.|..|+++|.+..|+..++.+||+.||..++.                 
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            45689999999998 888999999999999999999999999999999999999999999987                 


Q ss_pred             CCCCCCCccccCCCCCcCccCCceeecCc-eEEECCceecccccccccCCcccccCCeeccCCccccHHHH
Q 041875           85 TRTPSKFSTMFCGTQDKCTSCKKTVYPLE-KVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF  154 (195)
Q Consensus        85 ~~~p~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~  154 (195)
                                     .+|..|.++|.... .+.+.+..||..||+|..|.+.|.++.|+...++|+|..|+
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                           79999999877544 47899999999999999999999999999999999998875

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

Probab=99.69  E-value=4.5e-18  Score=146.68  Aligned_cols=115  Identities=25%  Similarity=0.547  Sum_probs=104.0

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT   85 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   85 (195)
                      +...|++|++.|..+..+.|+++.||..||+|..|+..|. +.|..++|.+||+.||+..|+                  
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 588899999999999999998                  


Q ss_pred             CCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccC-CeeccCCccccHHHH
Q 041875           86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTS-SYAALDGILYCKSHF  154 (195)
Q Consensus        86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~dg~~yC~~c~  154 (195)
                                    .+|..|.+.|. +..+.+.|++||+.|-+|+.|+..+..+ ..++....++-..|-
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                          89999999998 7778999999999999999999999854 577777788766664

>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=99.61  E-value=1.1e-15  Score=96.48  Aligned_cols=57  Identities=37%  Similarity=0.786  Sum_probs=52.7

Q ss_pred             ccccccccccCceE-eeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhh
Q 041875           10 CKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF   66 (195)
Q Consensus        10 C~~C~~~I~~~~~i-~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~   66 (195)
                      |.+|+++|.+++.+ .++|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
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 7999999999999999999999989999999999999998875

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=99.58  E-value=2.4e-15  Score=94.91  Aligned_cols=57  Identities=35%  Similarity=0.769  Sum_probs=53.4

Q ss_pred             CccCCceeecCceE-EECCceecccccccccCCcccccCCeeccCCccccHHHHHhhh
Q 041875          102 CTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF  158 (195)
Q Consensus       102 C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f  158 (195)
                      |.+|+++|.+.+.+ .+.|+.||++||+|..|+++|.++.++..||++||+.||.++|
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            78999999987776 6999999999999999999999888999999999999999987

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=99.22  E-value=6.5e-13  Score=106.48  Aligned_cols=82  Identities=18%  Similarity=0.348  Sum_probs=72.6

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCCCCcchhhhh
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLTKTASQKKI  176 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~~~~~~~  176 (195)
                      ..++|++|.+.|...-.+.++++.||..|++|+.|+.+|.. ..+.++|.+||+.+|.++||+||+ +..+|.|....|+
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk  110 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK  110 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence            45899999999984434589999999999999999999987 588999999999999999999998 8889999998888


Q ss_pred             hhhc
Q 041875          177 VAAS  180 (195)
Q Consensus       177 ~~~~  180 (195)
                      .+..
T Consensus       111 Aqd~  114 (383)
T KOG4577|consen  111 AQDF  114 (383)
T ss_pred             hhcc
Confidence            7653

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

Probab=98.81  E-value=3e-09  Score=61.04  Aligned_cols=37  Identities=38%  Similarity=0.714  Sum_probs=33.6

Q ss_pred             cccccccccccC-ceEeeCCcccccCccccccccccCC
Q 041875            9 KCKACDKTVHII-DMVTADGISYHKICFKCSHCNGKLV   45 (195)
Q Consensus         9 ~C~~C~~~I~~~-~~i~~~g~~~H~~CF~C~~C~~~L~   45 (195)
                      +|.+|+++|.++ ..+.++++.||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999866 6788999999999999999999986

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=98.67  E-value=1.6e-08  Score=58.00  Aligned_cols=37  Identities=32%  Similarity=0.655  Sum_probs=33.0

Q ss_pred             cCccCCceeecC-ceEEECCceecccccccccCCcccc
Q 041875          101 KCTSCKKTVYPL-EKVTVEGESFHKTCFRCSHGGCLLT  137 (195)
Q Consensus       101 ~C~~C~~~I~~~-~~v~~~~~~~H~~CF~C~~C~~~L~  137 (195)
                      +|.+|+++|.+. ..+.+.++.||..||+|..|+++|.
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 5668899999999999999999985

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=98.54  E-value=2.4e-08  Score=78.37  Aligned_cols=68  Identities=43%  Similarity=0.810  Sum_probs=63.5

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCC
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHL  167 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~  167 (195)
                      .+|.+|++.++..+.+...|..||+.||+|..|.+.|..+.+..+++.+||+.+|...|++++. ++..
T Consensus         8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~   76 (200)
T KOG1700|consen    8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKG   76 (200)
T ss_pred             chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccc
Confidence            6999999999998889999999999999999999999999999999999999999999999986 6664

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=98.39  E-value=2.8e-08  Score=76.62  Aligned_cols=81  Identities=28%  Similarity=0.596  Sum_probs=70.0

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCCCcchhhhhhhh
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAA  179 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~~~~~~~~~  179 (195)
                      ..|..|++.+++.+.|..+++.||+.||+|..|+-+|.-..+.-.|.++||..+|.+     -.+.-+..+++.+|+.++
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpk-----q~at~~adTPEm~Rik~n   79 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPK-----QVATVMADTPEMRRIKEN   79 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccc-----ceeeeecCCHHHHHHHhh
Confidence            578899999999999999999999999999999999998888888999999999954     346667888998887777


Q ss_pred             ccCCCC
Q 041875          180 SADQNP  185 (195)
Q Consensus       180 ~~~~~~  185 (195)
                      ...++.
T Consensus        80 ~enqS~   85 (264)
T KOG1702|consen   80 TENQSN   85 (264)
T ss_pred             hccchh
Confidence            666543

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

Probab=97.87  E-value=1.6e-06  Score=69.14  Aligned_cols=111  Identities=23%  Similarity=0.470  Sum_probs=87.4

Q ss_pred             cccccccCceEeeCCcccccCccccccccccCC--CCceeecCCeecchhhHHH--hhccCCccccCCCccCCCCCCCCC
Q 041875           13 CDKTVHIIDMVTADGISYHKICFKCSHCNGKLV--MGNFSSMEGVLYCKPHFEQ--LFKETGSFTNKLKPAQKNGLTRTP   88 (195)
Q Consensus        13 C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~p   88 (195)
                      |+..|.+...+.+.+..||..|+.|..|...|.  ...|.. +|..||..+|.+  .+.                     
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~---------------------   59 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS---------------------   59 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence            677787555677789999999999999999997  445555 999999999987  333                     


Q ss_pred             CCCccccCCCCCcCccCCceeecCceE-EECCceecccccccccCCcccc-cCCeeccCC-ccccHHHHHhh
Q 041875           89 SKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLT-TSSYAALDG-ILYCKSHFAQL  157 (195)
Q Consensus        89 ~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~-~~~~~~~dg-~~yC~~c~~~~  157 (195)
                                 .+|.+|...+...+.+ .+..+. |..||.|..|...+. ...+.+.+. +.+|..++.+.
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                       7999999998766665 455555 999999999999766 445666554 99999888653

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=97.79  E-value=1.8e-06  Score=66.80  Aligned_cols=59  Identities=32%  Similarity=0.656  Sum_probs=53.3

Q ss_pred             CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHh
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL   65 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~   65 (195)
                      ...|..|++.+++.+.|..+++.||..||+|..|+-+|.-.+|-..+.++||..+|...
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq   62 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ   62 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence            35678899999999999999999999999999999999888888889999999999653

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

Probab=92.26  E-value=0.047  Score=43.27  Aligned_cols=58  Identities=21%  Similarity=0.588  Sum_probs=45.7

Q ss_pred             CCceeecCceEEECCceecccccccccCCcccc--cCCeeccCCccccHHHHHh--hhcCCCc
Q 041875          105 CKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHFAQ--LFKEKGC  163 (195)
Q Consensus       105 C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~--~f~~k~~  163 (195)
                      |+..|.+...+.+.+..||..|..|..|...|.  ...+.. +|..||...|..  .+..++.
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~   63 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA   63 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc
Confidence            556666444456669999999999999999997  444555 999999999998  6666665

>smart00504 Ubox Modified RING finger domain

Probab=89.27  E-value=0.59  Score=28.97  Aligned_cols=32  Identities=16%  Similarity=0.161  Sum_probs=26.2

Q ss_pred             cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |.|..|+..+.+ ......|..||+.|..+.+.
T Consensus         2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~   33 (63)
T smart00504        2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL   33 (63)
T ss_pred             cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence            678999998876 45567799999999988775

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

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=87.91  E-value=0.38  Score=29.52  Aligned_cols=37  Identities=27%  Similarity=0.599  Sum_probs=26.1

Q ss_pred             CcCccCCceeecCce-EE--ECCceeccccc----cccc--CCccc
Q 041875          100 DKCTSCKKTVYPLEK-VT--VEGESFHKTCF----RCSH--GGCLL  136 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~-v~--~~~~~~H~~CF----~C~~--C~~~L  136 (195)
                      .+|..|+++|.+.+- |.  .=+..||++|.    .|..  |+..+
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence            799999999975444 43  45788999987    4655  55443

>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=86.75  E-value=0.37  Score=27.20  Aligned_cols=28  Identities=21%  Similarity=0.408  Sum_probs=18.0

Q ss_pred             ccccccccccC-ceEeeCCcccccCcccc
Q 041875           10 CKACDKTVHII-DMVTADGISYHKICFKC   37 (195)
Q Consensus        10 C~~C~~~I~~~-~~i~~~g~~~H~~CF~C   37 (195)
                      |.-|+.+|... .++...++.||.-|-+|
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            56788888732 25677778887655444

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

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

Probab=86.23  E-value=0.31  Score=33.87  Aligned_cols=31  Identities=32%  Similarity=0.557  Sum_probs=23.6

Q ss_pred             CcCccCCceeecCceEEE-CCceecccccccc
Q 041875          100 DKCTSCKKTVYPLEKVTV-EGESFHKTCFRCS  130 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~-~~~~~H~~CF~C~  130 (195)
                      -+|..|+++|..++.+++ .+..-|..||+=.
T Consensus         3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~   34 (101)
T PF09943_consen    3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK   34 (101)
T ss_pred             eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence            478899999988888754 4567888888743

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

Probab=84.98  E-value=0.29  Score=34.01  Aligned_cols=31  Identities=26%  Similarity=0.397  Sum_probs=19.7

Q ss_pred             cccccccccccCceEeeC-CcccccCcccccc
Q 041875            9 KCKACDKTVHIIDMVTAD-GISYHKICFKCSH   39 (195)
Q Consensus         9 ~C~~C~~~I~~~~~i~~~-g~~~H~~CF~C~~   39 (195)
                      +|..|+++|+.|+.+... +..-|-.||+=..
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~   35 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA   35 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence            577777777777765543 3466777776543

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

Probab=84.94  E-value=0.84  Score=29.06  Aligned_cols=33  Identities=15%  Similarity=0.270  Sum_probs=16.8

Q ss_pred             cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ++|+.|...|...-....=...||..|..+.++
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            688999888875433344467899999987776

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=83.62  E-value=0.88  Score=34.89  Aligned_cols=53  Identities=23%  Similarity=0.543  Sum_probs=40.7

Q ss_pred             ccCccccccccccCCCCc-eeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCcee
Q 041875           31 HKICFKCSHCNGKLVMGN-FSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTV  109 (195)
Q Consensus        31 H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I  109 (195)
                      -..++.|-.|-....... +...=|.+||+.|..+.....                              .+|+.|++.|
T Consensus       128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~------------------------------~~CP~C~kkI  177 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT------------------------------NKCPTCRKKI  177 (187)
T ss_pred             cccccCCCceecchhhccccccccchhHHHHHHHHHHHhC------------------------------CCCCCccccc
Confidence            357899999977776553 556779999999999877522                              7999999988


Q ss_pred             ecCc
Q 041875          110 YPLE  113 (195)
Q Consensus       110 ~~~~  113 (195)
                      ...+
T Consensus       178 t~k~  181 (187)
T KOG0320|consen  178 THKQ  181 (187)
T ss_pred             chhh
Confidence            7443

>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=80.74  E-value=1.4  Score=30.33  Aligned_cols=30  Identities=27%  Similarity=0.490  Sum_probs=21.9

Q ss_pred             CCcCccCCceeecCceEE-ECCceecccccc
Q 041875           99 QDKCTSCKKTVYPLEKVT-VEGESFHKTCFR  128 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~-~~~~~~H~~CF~  128 (195)
                      ...|..|+++|.....+. ..|..+|..|++
T Consensus        78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            378999999998544333 457779988864

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 [].

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=80.54  E-value=1.1  Score=25.09  Aligned_cols=24  Identities=29%  Similarity=0.596  Sum_probs=17.8

Q ss_pred             cccccccccCCCCceeecCCeecchhhH
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHF   62 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~   62 (195)
                      +.|..|+..    .|...+|..||..|-
T Consensus         9 ~~C~~C~~~----~~~~~dG~~yC~~cG   32 (36)
T PF11781_consen    9 EPCPVCGSR----WFYSDDGFYYCDRCG   32 (36)
T ss_pred             CcCCCCCCe----EeEccCCEEEhhhCc
Confidence            347777664    567789999998774

>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=80.19  E-value=0.56  Score=26.10  Aligned_cols=28  Identities=18%  Similarity=0.357  Sum_probs=17.1

Q ss_pred             cccCCcccccCCeeccCCccccHHHHHh
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      |..|+..+.........+..+|..|..+
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            6666666666566666677777777654

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	195
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		5e-14
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		5e-14
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		6e-14
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		5e-09
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		7e-09
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		9e-09
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		3e-07
1a7i_A	81	Amino-Terminal Lim Domain From Quail Cysteine And G		5e-06
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		7e-06
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		2e-04
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		1e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		9e-05
2o10_A	60	Solution Structure Of The N-Terminal Lim Domain Of		2e-05
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		1e-04

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)
Query: 6  TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65
           +E C  C KTV+ ++ + A+   +H  CF+CS+CN KL +G ++S+ G +YCKPHF QL
Sbjct: 14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQL 73
Query: 66 FKETGSFTNKLKPAQKNG 83
          FK  G++         +G
Sbjct: 74 FKSKGNYDEGFGSGPSSG 91

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 46/68 (67%)
Query: 98  TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQL 157
            ++ C  C+KTVYP+E++    + FH +CFRCS+    L+  +YA+L G +YCK HF QL
Sbjct: 14  ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQL 73
Query: 158 FKEKGCYN 165
           FK KG Y+
Sbjct: 74  FKSKGNYD 81

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 77/173 (44%), Gaps = 16/173 (9%)
Query: 5   GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ 64
           G  +KC  C K V+  + V  +G S+HK CF C  C   L     +     +YCK  + +
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGK 64
Query: 65  ---------------LFKETG-SFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKT 108
                          L  + G S   K +  Q +  T   +       G  D C  C + 
Sbjct: 65  KYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQA 124
Query: 109 VYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEK 161
           VY  EKV   G+S+HK+CFRC+  G  L +++ A  DG +YCK  +A+ F  K
Sbjct: 125 VYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 89  SKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGIL 148
           SKF+  F G  +KC++C  +VY  EKV   G+ +HK CFRC+  G  L +++    +G +
Sbjct: 27  SKFAQKF-GGAEKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEI 85
Query: 149 YCKSHFAQLFKEKG 162
           YCK  +A+ F  KG
Sbjct: 86  YCKGCYAKNFGPKG 99

>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 = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 89  SKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGIL 148
           SKF+  F G  +KC+ C  +VY  EKV   G+ +HK CFRC+  G  L +++    +G +
Sbjct: 27  SKFAQKF-GGAEKCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEI 85
Query: 149 YCKSHFAQLFKEKG 162
           YCK  +A+ F  KG
Sbjct: 86  YCKGCYAKNFGPKG 99

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 39/65 (60%)
Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQ 156
           G  D C  C + VY  EKV   G+S+HK+CFRC+  G  L +++ A  DG +YCK  +A+
Sbjct: 6   GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAK 65
Query: 157 LFKEK 161
            F  K
Sbjct: 66  NFGPK 70

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 36/58 (62%)
Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
           KC  C K+VY  EKV   G+ +HKTCFRC+  G  L +++    DG LYCK  +A+ F
Sbjct: 1   KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

>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 = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 38/66 (57%)
Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQ 156
           G  +KC +C +TVY  E+V  +G SFH+ CF C      L +++ A  D  +YCKS + +
Sbjct: 5   GGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGK 64
Query: 157 LFKEKG 162
            +  KG
Sbjct: 65  KYGPKG 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 = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC-KPHFEQLF 66
          KC  CDKTV+  + V++ G  +HK C KC  C+  L  G  +  +G  +C KP +  LF
Sbjct: 11 KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC-KSHFAQLF 158
           KC  C KTVY  EKV+  G+ +HK C +C      LT   +A  DG  +C K  +A LF
Sbjct: 11  KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK-PHFEQLFK 67
          KC  CDK V+  + VT+ G  +H+ C KC  C   L  G  +  EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 68 ETG 70
            G
Sbjct: 62 PKG 64

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSH-FAQLFK 159
           KC  C K VY  E+VT  G+ +H+ C +C   G  LT+  +A  +G  YC    ++ +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 160 EKG 162
            KG
Sbjct: 62  PKG 64

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK 151
           KC +C+KTVY  E++   G SFHKTCF C      L +++ AA +  +YCK
Sbjct: 3   KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 53

>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 = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYA--ALDGILYCKSHF 154
           G  D C  C + +Y LE++ V G  FH++CFRC      L    Y     DG  YC  H 
Sbjct: 13  GAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHL 72
Query: 155 AQ 156
            Q
Sbjct: 73  PQ 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	195
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-43
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-14
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-25
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-23
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	6e-22
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	6e-21
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	1e-21
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	9e-21
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-20
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-17
2co8_A	82	NEDD9 interacting protein with calponin homology a	2e-18
2co8_A	82	NEDD9 interacting protein with calponin homology a	3e-18
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-15
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-08
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	6e-15
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	3e-08
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-07
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	1e-14
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-14
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	4e-13
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	4e-13
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-12
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	3e-08
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-11
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	7e-07
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	5e-05
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	7e-11
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	4e-09
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	8e-11
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-07
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-10
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-09
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-10
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-09
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	2e-10
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-08
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	5e-10
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	1e-08
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	5e-09
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	1e-08
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	6e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	6e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	8e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-07
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	1e-08
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	1e-08
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-08
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	4e-07
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-08
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	8e-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	8e-06
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	3e-08
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	7e-07
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-08
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-07
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	3e-08
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	6e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-06
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	5e-08
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	6e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	8e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-06
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	1e-07
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	3e-06
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	3e-07
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	2e-07
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	7e-06
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	5e-07
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	4e-06
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	7e-05
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	7e-05
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	3e-04
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	9e-05
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	3e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	4e-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 =  143 bits (361), Expect = 1e-43
 Identities = 53/179 (29%), Positives = 77/179 (43%), Gaps = 16/179 (8%)

Query: 1   MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
           M   G  +KC  C K V+  + V  +G S+HK CF C  C   L     +     +YCK 
Sbjct: 1   MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKS 60

Query: 61  HFEQLFKETGS----------------FTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTS 104
            + + +   G                    K +  Q +  T   +       G  D C  
Sbjct: 61  CYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPR 120

Query: 105 CKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC 163
           C + VY  EKV   G+S+HK+CFRC+  G  L +++ A  DG +YCK  +A+ F  KG 
Sbjct: 121 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF 179

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

 Score = 66.6 bits (162), Expect = 4e-14
 Identities = 26/72 (36%), Positives = 36/72 (50%)

Query: 95  FCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
             G   KC  C+K VY  E+V  EG SFHK+CF C      L +++ A     +YCKS +
Sbjct: 3   NWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCY 62

Query: 155 AQLFKEKGCYNH 166
            + +  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 = 93.4 bits (232), Expect = 2e-25
 Identities = 33/79 (41%), Positives = 48/79 (60%)

Query: 87  TPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDG 146
           + S         ++ C  C+KTVYP+E++    + FH +CFRCS+    L+  +YA+L G
Sbjct: 3   SGSSGMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHG 62

Query: 147 ILYCKSHFAQLFKEKGCYN 165
            +YCK HF QLFK KG Y+
Sbjct: 63  RIYCKPHFNQLFKSKGNYD 81

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

 Score = 88.0 bits (218), Expect = 2e-23
 Identities = 31/81 (38%), Positives = 48/81 (59%)

Query: 3  FCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62
              +E C  C KTV+ ++ + A+   +H  CF+CS+CN KL +G ++S+ G +YCKPHF
Sbjct: 11 QAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHF 70

Query: 63 EQLFKETGSFTNKLKPAQKNG 83
           QLFK  G++         +G
Sbjct: 71 NQLFKSKGNYDEGFGSGPSSG 91

>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 = 84.0 bits (208), Expect = 6e-22
 Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 92  STMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYC- 150
           S+   G   KC  C KTVY  EKV+  G+ +HK C +C      LT   +A  DG  +C 
Sbjct: 2   SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCH 61

Query: 151 KSHFAQLFKEKG 162
           K  +A LF    
Sbjct: 62  KPCYATLFGSGP 73

>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 = 81.3 bits (201), Expect = 6e-21
 Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 2  AFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYC-KP 60
             G   KC  CDKTV+  + V++ G  +HK C KC  C+  L  G  +  +G  +C KP
Sbjct: 4  GSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKP 63

Query: 61 HFEQLFKETGS 71
           +  LF    S
Sbjct: 64 CYATLFGSGPS 74

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

 Score = 83.2 bits (206), Expect = 1e-21
 Identities = 25/69 (36%), Positives = 38/69 (55%)

Query: 95  FCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154
             G  +KC +C +TVY  E+V  +G SFH+ CF C      L +++ A  D  +YCKS +
Sbjct: 3   NWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCY 62

Query: 155 AQLFKEKGC 163
            + +  KG 
Sbjct: 63  GKKYGPKGY 71

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

 Score = 80.9 bits (200), Expect = 9e-21
 Identities = 22/71 (30%), Positives = 33/71 (46%)

Query: 1  MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKP 60
          M   G   KC AC +TV+  + V  DG S+H+ CF C  C   L     +  +  +YCK 
Sbjct: 1  MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKS 60

Query: 61 HFEQLFKETGS 71
           + + +   G 
Sbjct: 61 CYGKKYGPKGY 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 = 80.1 bits (198), Expect = 2e-20
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK-SHFAQLFK 159
           KC  C K VY  E+VT  G+ +H+ C +C   G  LT+  +A  +G  YC    ++ +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 160 EKGCYNHLTKTASQK 174
            KG      ++ + K
Sbjct: 62  PKGFGRGGAESHTFK 76

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

 Score = 72.4 bits (178), Expect = 2e-17
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK-PHFEQLFK 67
          KC  CDK V+  + VT+ G  +H+ C KC  C   L  G  +  EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 68 ETG 70
            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 = 75.4 bits (185), Expect = 2e-18
 Identities = 24/77 (31%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 88  PSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAAL--D 145
            S       G  D C  C + +Y LE++ V G  FH++CFRC      L    Y     D
Sbjct: 4   GSSGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGD 63

Query: 146 GILYCKSHFAQLFKEKG 162
           G  YC  H  Q      
Sbjct: 64  GHFYCLQHLPQTDSGPS 80

>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 = 74.6 bits (183), Expect = 3e-18
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 2  AFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSM--EGVLYCK 59
             G  + C  C + +++++ +  +G  +H+ CF+C  C   L  G +     +G  YC 
Sbjct: 10 QEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCL 69

Query: 60 PHFEQLFKETGS 71
           H  Q      S
Sbjct: 70 QHLPQTDSGPSS 81

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

 Score = 68.6 bits (168), Expect = 2e-15
 Identities = 27/161 (16%), Positives = 48/161 (29%), Gaps = 34/161 (21%)

Query: 6   TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFS--SMEGVLYCKPHFE 63
           +   C  C + +     + A    +H+ C  C  C  +L           G   C+  + 
Sbjct: 1   SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 60

Query: 64  QLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESF 122
           +LF                              G    C SC K +   E    V+ + +
Sbjct: 61  RLF------------------------------GQDGLCASCDKRIRAYEMTMRVKDKVY 90

Query: 123 HKTCFRCSH-GGCLLTTSSYAALDGILYCKSHFAQLFKEKG 162
           H  CF+C+           Y  ++  + C+    +  K  G
Sbjct: 91  HLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 131

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

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 5   GTQEKCKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMGN-FSSMEGVLYCKPHF 62
           G    C +CDK +   +M        YH  CFKC+ C     +G+ +  +   + C+   
Sbjct: 64  GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI 123

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

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

 Score = 67.0 bits (164), Expect = 6e-15
 Identities = 26/153 (16%), Positives = 49/153 (32%), Gaps = 35/153 (22%)

Query: 9   KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE 68
           +C  CD+ +   +   A+  ++H   F C  C+  L    +  +     CKP + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAV 64

Query: 69  TGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEK-VTVEGESFHKT-- 125
                                            C  C   + P  + VT    S+H +  
Sbjct: 65  --------------------------------VCQGCHNAIDPEVQRVTYNNFSWHASTE 92

Query: 126 CFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
           CF CS     L    +  ++G+++C     +  
Sbjct: 93  CFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

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

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 11/61 (18%), Positives = 23/61 (37%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
           +C  C + ++  E    E +++H   F C     +L    Y  ++    CK  + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAV 64

Query: 161 K 161
            
Sbjct: 65  V 65

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

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 8   EKCKACDKTVHIIDM-VTADGISYH--KICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ 64
             C+ C   +      VT +  S+H    CF CS C+  L+   F  +EG+++C    ++
Sbjct: 64  VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK 123

Query: 65  LF 66
             
Sbjct: 124 RM 125

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

 Score = 65.1 bits (159), Expect = 1e-14
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 7  QEKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65
             C+ C       + +V ++G  YH+ CF C+ C  +   G F   EG  YC+  F+ L
Sbjct: 11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 66 F 66
          F
Sbjct: 71 F 71

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

 Score = 64.3 bits (157), Expect = 2e-14
 Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 99  QDKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQL 157
              C  CK    P EK V   GE +H+ CF C+          +   +G  YC+  F  L
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 158 F 158
           F
Sbjct: 71  F 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 = 60.9 bits (148), Expect = 4e-13
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 1  MAFCGTQEKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59
          MA       C+ C       + +V ++G  YH+ CF C+ C  +   G F   EG  YC+
Sbjct: 5  MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCE 64

Query: 60 PHFEQLF 66
            F+ LF
Sbjct: 65 HDFQMLF 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 = 60.9 bits (148), Expect = 4e-13
 Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 98  TQDKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQ 156
               C  CK    P EK V   GE +H+ CF C+          +   +G  YC+  F  
Sbjct: 10  ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 157 LF 158
           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 = 61.4 bits (149), Expect = 2e-12
 Identities = 33/156 (21%), Positives = 50/156 (32%), Gaps = 36/156 (23%)

Query: 9   KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE 68
            C  CD+ +    ++ A    +H  C KCS C+  L      S    +YCK  F + F  
Sbjct: 8   MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA-ERCFSRGESVYCKDDFFKRF-- 64

Query: 69  TGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTCF 127
                                           KC +C+  + P + V   +   +H  CF
Sbjct: 65  ------------------------------GTKCAACQLGIPPTQVVRRAQDFVYHLHCF 94

Query: 128 RCSHGGCLLTT--SSYAALDGILYCKSHFAQLFKEK 161
            C      L T    Y   D  L CK+ +    +  
Sbjct: 95  ACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG 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 = 50.2 bits (120), Expect = 3e-08
 Identities = 20/125 (16%), Positives = 31/125 (24%), Gaps = 36/125 (28%)

Query: 9   KCKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMGN--FSSMEGVLYCKPHFEQL 65
           KC AC   +    +V  A    YH  CF C  C  +L  G+  +   +  L CK  +E  
Sbjct: 67  KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA 126

Query: 66  FKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKT 125
                                            Q        +      +       H  
Sbjct: 127 K--------------------------------QGGSGGSGGSG-GGTPMVAASPERHDG 153

Query: 126 CFRCS 130
             + +
Sbjct: 154 GLQAN 158

>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 = 58.4 bits (141), Expect = 3e-11
 Identities = 35/152 (23%), Positives = 51/152 (33%), Gaps = 40/152 (26%)

Query: 8   EKCKACDKTVHIID--MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65
             C  CD+  HI+D  ++ A    +H  C KCS C    +     S    +YCK  F + 
Sbjct: 61  PMCAGCDQ--HILDRFILKALDRHWHSKCLKCSDC-HVPLAERCFSRGESVYCKDDFFKR 117

Query: 66  FKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHK 124
           F                                  KC +C+  + P + V   +   +H 
Sbjct: 118 F--------------------------------GTKCAACQLGIPPTQVVRRAQDFVYHL 145

Query: 125 TCFRCSHGGCLLTT--SSYAALDGILYCKSHF 154
            CF C      L T    Y   D  L CK+ +
Sbjct: 146 HCFACVVCKRQLATGDEFYLMEDSRLVCKADY 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 = 46.4 bits (110), Expect = 7e-07
 Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 3/59 (5%)

Query: 9   KCKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMGN--FSSMEGVLYCKPHFEQ 64
           KC AC   +    +V  A    YH  CF C  C  +L  G+  +   +  L CK  +E 
Sbjct: 121 KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 179

>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 = 41.1 bits (96), Expect = 5e-05
 Identities = 16/101 (15%), Positives = 30/101 (29%), Gaps = 7/101 (6%)

Query: 67  KETGSFTNKLKPAQKNGLTRTPSKFSTMFCGT------QDKCTSCKKTVYPLEKVTVEGE 120
            E      +L+  Q +       +  +              C  C + +     +     
Sbjct: 22  DEDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDR 81

Query: 121 SFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEK 161
            +H  C +CS     L    ++     +YCK  F + F  K
Sbjct: 82  HWHSKCLKCSDCHVPLAERCFSR-GESVYCKDDFFKRFGTK 121

>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 = 7e-11
 Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
          KCK C K +   D  V   G  +HK CF CS+C   +  G+F       YC    E  F
Sbjct: 17 KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

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

 Score = 50.4 bits (121), Expect = 4e-09
 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 101 KCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFK 159
           KC  C K +   ++ V  +G  +HK CF CS+   ++ T S+       YC +     F 
Sbjct: 17  KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA 76

Query: 160 EK 161
             
Sbjct: 77  SG 78

>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 = 57.3 bits (138), Expect = 8e-11
 Identities = 28/160 (17%), Positives = 56/160 (35%), Gaps = 34/160 (21%)

Query: 8   EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKL--VMGNFSSMEGVLYCKPHFEQL 65
           ++C  C   +    ++ A    +H  C KCS C  +L  +  +  +  G++ C+  + +L
Sbjct: 6   KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65

Query: 66  FKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHK 124
                                          G    C++C +++   E V   +G  +H 
Sbjct: 66  ------------------------------FGNSGACSACGQSIPASELVMRAQGNVYHL 95

Query: 125 TCFRCSH-GGCLLTTSSYAALDGILYCKSHFAQLFKEKGC 163
            CF CS     L+    +  ++G L+C+            
Sbjct: 96  KCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHL 135

>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 = 48.1 bits (114), Expect = 2e-07
 Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 2/110 (1%)

Query: 3   FCGTQEKCKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMG-NFSSMEGVLYCKP 60
             G    C AC +++   ++V  A G  YH  CF CS C  +LV G  F  + G L+C+ 
Sbjct: 65  LFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEH 124

Query: 61  HFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVY 110
                       +     +  +G         T+  G          T  
Sbjct: 125 DRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRL 174

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 53.9 bits (130), Expect = 2e-10
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           C+ C KT+      +   G S+H+ CF C  C   +   +F   +   +C P +E+  
Sbjct: 7  GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 49.3 bits (118), Expect = 9e-09
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 101 KCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
            C  CKKT+ P  + +  +G S+H+TCF C      + T S+   D   +C   + +  
Sbjct: 7   GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 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 = 53.5 bits (129), Expect = 2e-10
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

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

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

 Score = 50.8 bits (122), Expect = 2e-09
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 101 KCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
            C++C +TV P  + +   G+++H+ CF CS     L + S+    G  YC   +   F
Sbjct: 7   GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 65

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

 Score = 54.3 bits (131), Expect = 2e-10
 Identities = 21/125 (16%), Positives = 34/125 (27%), Gaps = 34/125 (27%)

Query: 9   KCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67
            C  C K +      V      +H  CF+C+ C   L    F + +  + C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 68  ETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTC 126
                                            KC  C K +   ++    +G  +HK C
Sbjct: 67  P--------------------------------KCKGCFKAIVAGDQNVEYKGTVWHKDC 94

Query: 127 FRCSH 131
           F    
Sbjct: 95  FSGPS 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 = 49.7 bits (119), Expect = 1e-08
 Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 101 KCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFK 159
            C  C+K +    K V  +   +H TCFRC+     L   ++ A D  + C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 160 EK 161
            K
Sbjct: 67  PK 68

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

 Score = 50.0 bits (120), Expect = 5e-09
 Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           C  C K +     VT     +HK CF C+ C  +L    F++ +   YC   F  L+
Sbjct: 7  GCVQCKKPI-TTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY 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 = 48.9 bits (117), Expect = 1e-08
 Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
            C  CKK +     VT   + +HK CF C+     L+   + A D   YC + F  L+  
Sbjct: 7   GCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS 65

Query: 161 K 161
            
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 = 49.6 bits (119), Expect = 6e-09
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 9  KCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           C AC +   I   +V A G  +H   F C+ C    +       +G+ YC+ H+ QLF
Sbjct: 7  ICGACRRP--IEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 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 = 46.9 bits (112), Expect = 6e-08
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
            C +C++ +     V   G+ +H   F C+          +    G+ YC++H+ QLF
Sbjct: 7   ICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

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

 Score = 49.6 bits (119), Expect = 8e-09
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 8  EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           +C  C KT+     VT     +H+ C  C+ C   L    F+S +   YC   F +LF
Sbjct: 16 PRCARCSKTL-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 = 45.8 bits (109), Expect = 2e-07
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
           +C  C KT+     VT   + +H+ C  C+     L    + + D   YC + F +LF  
Sbjct: 17  RCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75

Query: 161 K 161
            
Sbjct: 76  G 76

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

 Score = 48.9 bits (117), Expect = 1e-08
 Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 1/62 (1%)

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFK 159
             C  C K +     +T + + +H  CF C      L    + A++   YC   +     
Sbjct: 6   SGCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64

Query: 160 EK 161
             
Sbjct: 65  GP 66

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

 Score = 48.9 bits (117), Expect = 1e-08
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 8  EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
            C  C+K +     +T     +H  CF C  C+ KL    F+++E   YC   ++   
Sbjct: 6  SGCVKCNKAI-TSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFV 63

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

 Score = 49.0 bits (117), Expect = 1e-08
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 3/60 (5%)

Query: 9  KCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67
           C  C     I+   V       H  C+ C+ C   L       +E  +YC+ H  +   
Sbjct: 17 MCDKCGT--GIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVS 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 = 45.1 bits (107), Expect = 4e-07
 Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 1/61 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
            C  C   +     V +     H  C+ C+  G  L    +  ++  +YC+ H  +    
Sbjct: 17  MCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSG 75

Query: 161 K 161
            
Sbjct: 76  P 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 = 48.9 bits (117), Expect = 2e-08
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
          KC  C++ V + + ++A    +H  CF C  C      G+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 = 44.3 bits (105), Expect = 8e-07
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
           KC  C + V     ++     +H  CF C       +T S+  LDG  +C+ H+    
Sbjct: 17  KCGGCNRPVLE-NYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR 73

>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 = 48.3 bits (115), Expect = 2e-08
 Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 8  EKCKACDKTVHIID---MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ 64
            C  C   +  +     ++ +   +H  CF C  C+  LV   F +    + C    + 
Sbjct: 6  SGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKD 65

Query: 65 LF 66
          + 
Sbjct: 66 IS 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 = 41.3 bits (97), Expect = 8e-06
 Identities = 10/61 (16%), Positives = 17/61 (27%), Gaps = 3/61 (4%)

Query: 101 KCTSCKKTVYPLEK---VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQL 157
            C  C   +  L     ++ E   +H  CF C      L    +      + C      +
Sbjct: 7   GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 158 F 158
            
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 = 47.8 bits (114), Expect = 3e-08
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 6  TQEKCKACDKTVHIIDM-VTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ 64
              C  C + V      V A    +H  CF CS C  +L   +F ++E   YC+  +  
Sbjct: 4  GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVA 63

Query: 65 LF 66
            
Sbjct: 64 TL 65

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 44.0 bits (104), Expect = 7e-07
 Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 1/62 (1%)

Query: 98  TQDKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQ 156
               C  C + V      V      FH  CF CS     L    + A++   YC+  +  
Sbjct: 4   GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVA 63

Query: 157 LF 158
             
Sbjct: 64  TL 65

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 48.3 bits (115), Expect = 3e-08
 Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 3/62 (4%)

Query: 6  TQEKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ 64
              C  C     I+  +V A     H  CF C+ CN  L    +  +EG LYC+ H   
Sbjct: 24 RMPLCDKCGSG--IVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARA 81

Query: 65 LF 66
            
Sbjct: 82 RT 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 = 46.7 bits (111), Expect = 1e-07
 Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 1/61 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
            C  C   +     V    +  H  CF C+     L    Y  ++G LYC++H       
Sbjct: 27  LCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSG 85

Query: 161 K 161
            
Sbjct: 86  P 86

>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 = 48.3 bits (115), Expect = 3e-08
 Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 101 KCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFK 159
            C  C++ +    + +  E   FH+ CFRC      L    +   D  L C   +   F 
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 160 EK 161
             
Sbjct: 77  SG 78

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

 Score = 47.5 bits (113), Expect = 6e-08
 Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 8  EKCKACDKTV-HIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
            C  C + + H    +  +   +H+ CF+C  C   L    F+  +  L C   +   F
Sbjct: 16 NTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

>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 = 48.2 bits (115), Expect = 3e-08
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 9  KCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           C  C++   I    + A G S+H   F C+HC   +    F   +G LYC+  +E+ F
Sbjct: 27 MCAHCNQV--IRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 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 = 43.6 bits (103), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158
            C  C + +     +   G+S+H   F C+H    +    +    G LYC+  + + F
Sbjct: 27  MCAHCNQVIRG-PFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

>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 = 47.4 bits (113), Expect = 5e-08
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           C  C + +     + A    +H  CFKC  C   ++ G + S +GV YC+  +   F
Sbjct: 17 HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTC-SVILTGEYISKDGVPYCESDYHAQF 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 = 47.0 bits (112), Expect = 6e-08
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
            C  CK+ +   + +    + +H +CF+C     +L T  Y + DG+ YC+S +   F  
Sbjct: 17  HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVIL-TGEYISKDGVPYCESDYHAQFGS 75

Query: 161 K 161
            
Sbjct: 76  G 76

>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 = 46.7 bits (111), Expect = 8e-08
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
           C  C + + I  ++ A   S+H  CF+C  C   L    F    G   C+P   +  
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 = 42.8 bits (101), Expect = 2e-06
 Identities = 11/61 (18%), Positives = 19/61 (31%), Gaps = 1/61 (1%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE 160
            C  C + +     +     S+H  CFRC     +L    +    G   C+    +    
Sbjct: 7   GCHQCGEFIIG-RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKAS 65

Query: 161 K 161
            
Sbjct: 66  G 66

>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 = 46.7 bits (111), Expect = 1e-07
 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 8  EKCKACDKTV----HIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFE 63
          +KC  C   +        +V  +G S+H  CF C  C+  L    F   +  +YC    +
Sbjct: 16 KKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAK 75

Query: 64 QL 65
          +L
Sbjct: 76 KL 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 = 42.9 bits (101), Expect = 3e-06
 Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 4/61 (6%)

Query: 101 KCTSCKKTVYPLEK----VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQ 156
           KC  CK  +    K    V  EG+S+H  CF C      L    +      +YC     +
Sbjct: 17  KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 157 L 157
           L
Sbjct: 77  L 77

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

 Score = 47.0 bits (111), Expect = 2e-07
 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 5   GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSME--GVLYCKPHF 62
            + ++C  C   +    ++ A    +H  C KCS C  +L     SS    G++ C+  +
Sbjct: 59  LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 118

Query: 63  EQLF 66
            +LF
Sbjct: 119 IRLF 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 = 46.7 bits (110), Expect = 3e-07
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHF 154
            +  +C  C   +     +      +H  C +CS     L    +S     G++ C++ +
Sbjct: 59  LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 118

Query: 155 AQLF 158
            +LF
Sbjct: 119 IRLF 122

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 3  FCGTQEKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFS-SMEGVLYCKP 60
          +  T EKC  C +   I+D ++ A G +YH  CF C  C+  L    F+      ++C  
Sbjct: 11 YVATLEKCATCSQ--PILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIE 68

Query: 61 HFEQLF 66
           F + F
Sbjct: 69 DFHRKF 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 = 41.6 bits (98), Expect = 7e-06
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 95  FCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYA-ALDGILYCKSH 153
           +  T +KC +C + +     +   G+++H  CF C      L    +       ++C   
Sbjct: 11  YVATLEKCATCSQPILD-RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 154 FAQLF 158
           F + 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 = 45.7 bits (108), Expect = 5e-07
 Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 2/82 (2%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHFAQLF 158
           +C  C   +     +      +H  C +CS     L    +S     G++ C++ + +LF
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 159 KEKGCYNHLTKTASQKKIVAAS 180
              G         S   ++   
Sbjct: 67  GNSGAGGSGGHMGSGGDVMVVG 88

>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 = 43.4 bits (102), Expect = 4e-06
 Identities = 15/68 (22%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 6  TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKL--VMGNFSSMEGVLYCKPHFE 63
          + ++C  C   +    ++ A    +H  C KCS C  +L  +  +  +  G++ C+  + 
Sbjct: 4  SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 64 QLFKETGS 71
          +LF  +G+
Sbjct: 64 RLFGNSGA 71

>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 = 13/65 (20%), Positives = 24/65 (36%), Gaps = 3/65 (4%)

Query: 8  EKCKACDKTVHIID---MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ 64
            C AC K +  +     +      +H  CF C  C+  LV   F +    ++C+     
Sbjct: 6  SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSG 65

Query: 65 LFKET 69
          +  + 
Sbjct: 66 MDTDI 70

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

 Score = 38.7 bits (90), Expect = 7e-05
 Identities = 10/63 (15%), Positives = 24/63 (38%), Gaps = 3/63 (4%)

Query: 101 KCTSCKKTVYPL---EKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQL 157
            C +C K +  L   + +  +   +H  CF C      L    +   +  ++C+   + +
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 158 FKE 160
             +
Sbjct: 67  DTD 69

>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 = 39.7 bits (92), Expect = 7e-05
 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 2/69 (2%)

Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTT--SSYAALDGILYCKSHF 154
           G+   C  C++ +     +    + +H+ C  C   GC L           G   C+  +
Sbjct: 1   GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 155 AQLFKEKGC 163
            +L    G 
Sbjct: 61  LRLGGSGGH 69

>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 = 38.1 bits (88), Expect = 3e-04
 Identities = 16/90 (17%), Positives = 28/90 (31%), Gaps = 2/90 (2%)

Query: 5  GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKL--VMGNFSSMEGVLYCKPHF 62
          G+   C  C + +     + A    +H+ C  C  C  +L  V        G   C+  +
Sbjct: 1  GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 63 EQLFKETGSFTNKLKPAQKNGLTRTPSKFS 92
           +L    G   +          T    +F 
Sbjct: 61 LRLGGSGGHMGSGGDVMVVGEPTLMGGEFG 90

>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 = 9e-05
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 3/60 (5%)

Query: 9  KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSME--GVLYCKPHFEQLF 66
           C  C   +     + A    YH  CF C  C   +  G+  ++     LYC     ++ 
Sbjct: 17 FCHGCSLLM-TGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

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

 Score = 35.8 bits (82), Expect = 3e-04
 Identities = 13/27 (48%), Positives = 15/27 (55%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCF 127
            C  C K VYP EKV    + +HK CF
Sbjct: 5   NCARCGKIVYPTEKVNCLDKFWHKACF 31

>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 = 37.1 bits (86), Expect = 4e-04
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 10 CKACDKTVHIID--MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66
          C+ C     IID   +      YH   F C++C  +L   +   ++G LYC P  +++ 
Sbjct: 18 CQKCHA---IIDEQPLIFKNDPYHPDHFNCANCGKELT-ADARELKGELYCLPCHDKMG 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	195
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,	99.97
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.97
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.96
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.96
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.93
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.91
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.87
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.84
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.84
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.84
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.82
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.82
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.79
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.78
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.78
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.76
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.76
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.75
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.75
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.73
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.73
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.72
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.71
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.71
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.71
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.71
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.71
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.7
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.7
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.7
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.7
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.69
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.69
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.69
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.69
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.69
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.69
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.68
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.68
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.68
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.68
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.68
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.68
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.67
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.67
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.67
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.67
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.67
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.66
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.66
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.66
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.65
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.64
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.64
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.63
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.63
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.63
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.62
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.62
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.62
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.62
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.62
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.61
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.61
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.61
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.61
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.61
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.61
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.6
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.6
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.58
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.58
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.57
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.57
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.56
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.55
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.53
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;	99.52
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.52
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.46
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.43
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.37
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.33
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	90.62
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	88.88
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	88.41
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	86.93
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	85.71
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	85.66
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	83.12
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	82.33
1jjd_A	55	Metallothionein, SMTA; zinc finger, zinc cluster,	82.02
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	81.62
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	81.58
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	80.74

>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=7.4e-34  Score=220.72  Aligned_cols=166  Identities=33%  Similarity=0.640  Sum_probs=133.8

Q ss_pred             CCcCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccc-------
Q 041875            1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFT-------   73 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~-------   73 (195)
                      |...++.++|..|+++|..++.|.++|+.||++||+|..|+++|.+..|+.+++++||+.||.++|++++...       
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~   80 (192)
T 1b8t_A            1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTL   80 (192)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCC
T ss_pred             CCCCCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccE
Confidence            6777888999999999988888999999999999999999999999999999999999999999999875311       


Q ss_pred             ---cCCCccCC--CCCCCCC-----CCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeec
Q 041875           74 ---NKLKPAQK--NGLTRTP-----SKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAA  143 (195)
Q Consensus        74 ---~~~~~~~~--~~~~~~p-----~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~  143 (195)
                         ..++....  ......|     ..+ ....++.++|.+|+++|.+.+.|.+.++.||.+||+|..|+++|.++.|+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~-~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~  159 (192)
T 1b8t_A           81 STDKGESLGIKYEEGQSHRPTNPNASRM-AQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLAD  159 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEE
T ss_pred             ecCCCcccccccccccccCCCCcCcccc-ccccCCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccc
Confidence               11100000  0000111     011 111235678999999999888899999999999999999999999888999


Q ss_pred             cCCccccHHHHHhhhcCCCc-cCCC
Q 041875          144 LDGILYCKSHFAQLFKEKGC-YNHL  167 (195)
Q Consensus       144 ~dg~~yC~~c~~~~f~~k~~-~~~~  167 (195)
                      +||++||+.||.++|+++|. ++.+
T Consensus       160 ~~g~~yC~~cy~~~f~~kc~~C~~~  184 (192)
T 1b8t_A          160 KDGEIYCKGCYAKNFGPKGFGFGQG  184 (192)
T ss_dssp             ETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             cCCEEeCHHHHHHhcCCcCCCCCCc
Confidence            99999999999999999998 5544

>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=4.7e-33  Score=203.57  Aligned_cols=124  Identities=21%  Similarity=0.484  Sum_probs=113.7

Q ss_pred             CCcccccccccccCceEeeCCcccccCccccccccccCCC--CceeecCCeecchhhHHHhhccCCccccCCCccCCCCC
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVM--GNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGL   84 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   84 (195)
                      .++|..|+++|.+.++|.++|+.||++||+|..|+++|..  ..|+.++|++||+.||.++++                 
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            5799999999996668999999999999999999999964  589999999999999999998                 


Q ss_pred             CCCCCCCccccCCCCC--cCccCCceeecCc-eEEECCceecccccccccCCcccc-cCCeeccCCccccHHHHHhhhcC
Q 041875           85 TRTPSKFSTMFCGTQD--KCTSCKKTVYPLE-KVTVEGESFHKTCFRCSHGGCLLT-TSSYAALDGILYCKSHFAQLFKE  160 (195)
Q Consensus        85 ~~~p~~~~~~~~~~~~--~C~~C~~~I~~~~-~v~~~~~~~H~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~c~~~~f~~  160 (195)
                                     +  +|.+|+++|.+.+ .|.+.++.||+.||+|..|+++|. +..|+..||++||..||.++|++
T Consensus        65 ---------------~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~  129 (131)
T 2xjy_A           65 ---------------QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKI  129 (131)
T ss_dssp             ---------------CCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHH
T ss_pred             ---------------CccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhc
Confidence                           5  9999999999755 468999999999999999999995 56699999999999999999998


Q ss_pred             CC
Q 041875          161 KG  162 (195)
Q Consensus       161 k~  162 (195)
                      +|
T Consensus       130 ~~  131 (131)
T 2xjy_A          130 NG  131 (131)
T ss_dssp             HC
T ss_pred             cC
Confidence            75

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

Probab=99.97  E-value=5.3e-32  Score=196.77  Aligned_cols=121  Identities=21%  Similarity=0.519  Sum_probs=113.2

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT   85 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   85 (195)
                      ..++|.+|+++|..++++.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++++                  
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            35899999999997889999999999999999999999998899999999999999999998                  


Q ss_pred             CCCCCCccccCCCCCcCccCCceeecCc-eEEECCceec--ccccccccCCcccccCCeeccCCccccHHHHHhhh
Q 041875           86 RTPSKFSTMFCGTQDKCTSCKKTVYPLE-KVTVEGESFH--KTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF  158 (195)
Q Consensus        86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~~~~~H--~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f  158 (195)
                                    ++|.+|+++|.+++ .|.+.++.||  +.||+|..|+++|.+..|+..||++||..+|.++|
T Consensus        64 --------------~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           64 --------------VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             --------------CBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             --------------ccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence                          89999999999754 5799999999  99999999999999888999999999998888876

>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=2.8e-31  Score=205.51  Aligned_cols=126  Identities=21%  Similarity=0.533  Sum_probs=112.5

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCC--CceeecCCeecchhhHHHhhccCCccccCCCccCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVM--GNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNG   83 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~   83 (195)
                      ..++|..|+++|.+.++|.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|+                
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~----------------   67 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG----------------   67 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS----------------
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccc----------------
Confidence            46899999999996668999999999999999999999985  689999999999999999997                


Q ss_pred             CCCCCCCCccccCCCCC--cCccCCceeecCce-EEECCceecccccccccCCcccc-cCCeeccCCccccHHHHHhhhc
Q 041875           84 LTRTPSKFSTMFCGTQD--KCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLT-TSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus        84 ~~~~p~~~~~~~~~~~~--~C~~C~~~I~~~~~-v~~~~~~~H~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                                      +  +|.+|+++|.+.+. |.+.++.||+.||+|..|+++|. +..|+..+|++||+.||.++|+
T Consensus        68 ----------------~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~  131 (188)
T 1rut_X           68 ----------------NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALI  131 (188)
T ss_dssp             ----------------CCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC
T ss_pred             ----------------cCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhc
Confidence                            5  79999999997664 58999999999999999999996 4569999999999999999999


Q ss_pred             CCCc
Q 041875          160 EKGC  163 (195)
Q Consensus       160 ~k~~  163 (195)
                      +++.
T Consensus       132 ~~~~  135 (188)
T 1rut_X          132 NGHL  135 (188)
T ss_dssp             ----
T ss_pred             cccc
Confidence            9996

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

Probab=99.96  E-value=8.8e-30  Score=193.98  Aligned_cols=124  Identities=27%  Similarity=0.508  Sum_probs=109.7

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGL   84 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   84 (195)
                      ++.++|.+|+++|.+.++|.++|+.||++||+|..|+++|.+..| .++|++||+.||.++|+                 
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            456899999999997678999999999999999999999998775 79999999999999998                 


Q ss_pred             CCCCCCCccccCCCCCcCccCCceeecCceE-EECCceecccccccccCCccccc-CCee-ccCCccccHHHHHhhhcCC
Q 041875           85 TRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLTT-SSYA-ALDGILYCKSHFAQLFKEK  161 (195)
Q Consensus        85 ~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~~-~~~~-~~dg~~yC~~c~~~~f~~k  161 (195)
                                     ++|.+|+++|.+.+.+ .+.++.||..||+|..|+++|.. ..|+ ..||++||+.||.++++..
T Consensus        66 ---------------~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~  130 (169)
T 2rgt_A           66 ---------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG  130 (169)
T ss_dssp             ---------------CBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC
T ss_pred             ---------------ccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhcc
Confidence                           8999999999977765 79999999999999999999984 4554 4689999999999998764

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

Probab=99.96  E-value=2.5e-29  Score=193.57  Aligned_cols=122  Identities=26%  Similarity=0.501  Sum_probs=108.7

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCC
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNG   83 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~   83 (195)
                      ....++|..|+++|...+++.++|+.||++||+|..|+++|.+..| .++|++||+.||.++|+                
T Consensus        57 ~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~----------------  119 (182)
T 2jtn_A           57 TPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFG----------------  119 (182)
T ss_dssp             CCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTS----------------
T ss_pred             CCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccc----------------
Confidence            4556899999999997678899999999999999999999998775 79999999999999998                


Q ss_pred             CCCCCCCCccccCCCCCcCccCCceeecCce-EEECCceecccccccccCCccccc-CCee-ccCCccccHHHHHhhh
Q 041875           84 LTRTPSKFSTMFCGTQDKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTT-SSYA-ALDGILYCKSHFAQLF  158 (195)
Q Consensus        84 ~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~~~~~H~~CF~C~~C~~~L~~-~~~~-~~dg~~yC~~c~~~~f  158 (195)
                                      ++|.+|+++|.+.+. +.+.++.||+.||+|..|+++|.. ..|+ ..||++||+.||.++.
T Consensus       120 ----------------~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~~  181 (182)
T 2jtn_A          120 ----------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  181 (182)
T ss_dssp             ----------------CCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHHT
T ss_pred             ----------------cccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHhh
Confidence                            899999999997665 479999999999999999999984 4554 5689999999998753

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

Probab=99.93  E-value=1.3e-26  Score=162.00  Aligned_cols=97  Identities=24%  Similarity=0.533  Sum_probs=89.9

Q ss_pred             CCCCccccccccccc-CceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCC
Q 041875            5 GTQEKCKACDKTVHI-IDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNG   83 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~-~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~   83 (195)
                      ...++|.+|+++|.. +++|.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++++                
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~----------------   66 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS----------------   66 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCC----------------
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcC----------------
Confidence            456899999999985 788999999999999999999999998899999999999999999987                


Q ss_pred             CCCCCCCCccccCCCCCcCccCCceeecCc-eEEECCceecccccccccCC
Q 041875           84 LTRTPSKFSTMFCGTQDKCTSCKKTVYPLE-KVTVEGESFHKTCFRCSHGG  133 (195)
Q Consensus        84 ~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~~~~~H~~CF~C~~C~  133 (195)
                                      ++|.+|+++|.+++ .|.++++.||++||+|..|+
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                            89999999999765 57899999999999999986

>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=2.7e-25  Score=160.58  Aligned_cols=116  Identities=21%  Similarity=0.299  Sum_probs=99.5

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCC--CceeecCCeecchhhHHHhhccCCccccCCCccCCC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVM--GNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKN   82 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~   82 (195)
                      ...++|.+|+++|...++|.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|+++             
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~-------------   69 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNS-------------   69 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCC-------------
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCC-------------
Confidence            456899999999997767999999999999999999999973  57999999999999999999821             


Q ss_pred             CCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCC
Q 041875           83 GLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKG  162 (195)
Q Consensus        83 ~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~  162 (195)
                                       .+|.+|+++|.+. .|++.++             .+|.++.|+.+|++|||..||.+++.++|
T Consensus        70 -----------------~~C~~C~~~I~~~-~~~~~g~-------------~~l~g~~f~~~~~~~yC~~~~~~~~~~~g  118 (122)
T 1m3v_A           70 -----------------GAGGSGGHMGSGG-DVMVVGE-------------PTLMGGEFGDEDERLITRLENTQFDAANG  118 (122)
T ss_dssp             -----------------CSSSCSSCCSCCE-ESSSSSS-------------SSCCSCTTCCTTCCCCEECTTTTTTCCSC
T ss_pred             -----------------CccccCCCCcCch-heEEcCC-------------cCCCCCccEecCCEeEccCcchhchhhcC
Confidence                             2999999999853 3444442             36778899999999999999999999988


Q ss_pred             cc
Q 041875          163 CY  164 (195)
Q Consensus       163 ~~  164 (195)
                      +-
T Consensus       119 ~~  120 (122)
T 1m3v_A          119 ID  120 (122)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.87  E-value=8.2e-23  Score=145.80  Aligned_cols=110  Identities=16%  Similarity=0.227  Sum_probs=91.8

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCC--CceeecCCeecchhhHHHhhccCCccccCCCccCCC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVM--GNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKN   82 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~   82 (195)
                      ++.++|.+|+++|...++|.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|+               
T Consensus         1 g~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~---------------   65 (114)
T 1j2o_A            1 GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG---------------   65 (114)
T ss_dssp             CCCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHT---------------
T ss_pred             CcCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhC---------------
Confidence            467899999999996668999999999999999999999985  589999999999999999998               


Q ss_pred             CCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcc-cccCCeeccCCccccHHHHHhhhcCC
Q 041875           83 GLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCL-LTTSSYAALDGILYCKSHFAQLFKEK  161 (195)
Q Consensus        83 ~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~-L~~~~~~~~dg~~yC~~c~~~~f~~k  161 (195)
                                       ++|..|..    ++.|            .   |+.+ |.++.|+.+|++|||..||.++.+++
T Consensus        66 -----------------~~c~~c~~----~~~~------------~---~~~~~~~g~~f~~~~~~~~C~~~~~~~~~~~  109 (114)
T 1j2o_A           66 -----------------SGGHMGSG----GDVM------------V---VGEPTLMGGEFGDEDERLITRLENTQFDAAN  109 (114)
T ss_dssp             -----------------SCCSSCBS----CSCC------------C---SSCSSTTSSBCCCSSSCCCEEEECTTCCCTT
T ss_pred             -----------------cccCcCCC----Ccee------------E---cCCccCCCCeeEEcCCEeecchhhhcccccc
Confidence                             77776652    1111            1   3344 56778999999999999999999888


Q ss_pred             CccC
Q 041875          162 GCYN  165 (195)
Q Consensus       162 ~~~~  165 (195)
                      |+-+
T Consensus       110 g~~~  113 (114)
T 1j2o_A          110 GIDD  113 (114)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8643

>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=99.84  E-value=6.6e-22  Score=132.26  Aligned_cols=80  Identities=24%  Similarity=0.483  Sum_probs=74.3

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccC
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHG  132 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C  132 (195)
                      +|++||+.||.++++                                ++|.+|+++|. .+.|.+.++.||..||+|..|
T Consensus         1 gg~~yC~~cy~~~~~--------------------------------~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C   47 (80)
T 2cuq_A            1 GSSGSSGPCYENKFA--------------------------------PRCARCSKTLT-QGGVTYRDQPWHRECLVCTGC   47 (80)
T ss_dssp             CCCCSCCCCCCCCSS--------------------------------CCCTTTCCCCC-SCCEESSSSEECTTTCBCSSS
T ss_pred             CCcEEcHHHHccccC--------------------------------CcCCCCCCEec-CcEEEECCchhhhhhCCcccC
Confidence            589999999998887                                89999999998 468899999999999999999


Q ss_pred             CcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875          133 GCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN  165 (195)
Q Consensus       133 ~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~  165 (195)
                      +++|.+..|+.+||++||+.||.++|+++++.+
T Consensus        48 ~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s~   80 (80)
T 2cuq_A           48 QTPLAGQQFTSRDEDPYCVACFGELFASGPSSG   80 (80)
T ss_dssp             CCBCTTCCEEECSSSEEEHHHHHHHTTCSTTCC
T ss_pred             CCcCCCCeeEeECCEEECHHHHHHHcCCCCCCC
Confidence            999998889999999999999999999999743

>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=99.84  E-value=9.5e-22  Score=132.09  Aligned_cols=81  Identities=21%  Similarity=0.350  Sum_probs=74.7

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCce-EEECCceeccccccccc
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSH  131 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~~~~~H~~CF~C~~  131 (195)
                      ++.+||+.||.++++                                ++|.+|+++|.+++. |.+.++.||+.||+|..
T Consensus         1 ~~~~yC~~cy~~~~~--------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~   48 (82)
T 1x63_A            1 GSSGSSGKCTTREDS--------------------------------PKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSN   48 (82)
T ss_dssp             CCSCCCCCCCSCCCS--------------------------------CBCSSSCCBCCSSSCEEECSSCEEETTTCCCSS
T ss_pred             CCCcCchhHHccccC--------------------------------CcCccCCcccccCceEEEECccccccccCchhh
Confidence            468999999998887                                899999999997665 78999999999999999


Q ss_pred             CCcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875          132 GGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN  165 (195)
Q Consensus       132 C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~  165 (195)
                      |+++|..+.|+.++|++||+.||.++|++++..+
T Consensus        49 C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~g   82 (82)
T 1x63_A           49 CKQVIGTGSFFPKGEDFYCVTCHETKFASGPSSG   82 (82)
T ss_dssp             SCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSCC
T ss_pred             CCCccCCCccEeeCCEEECHHHHHHHhCCCCCCC
Confidence            9999998899999999999999999999999754

>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=99.84  E-value=1.3e-21  Score=130.83  Aligned_cols=79  Identities=22%  Similarity=0.421  Sum_probs=73.9

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccC
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHG  132 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C  132 (195)
                      +|++||+.||.++++                                ++|++|+++|. ++.|.+.++.||+.||+|..|
T Consensus         1 gg~~yC~~~y~~~~~--------------------------------~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C   47 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFS--------------------------------PKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDC   47 (80)
T ss_dssp             CCCCCCCCCCCCCCS--------------------------------CBCTTTCCBCC-SSCEEETTEEECTTTCBCSSS
T ss_pred             CCCccchhHHhhhcC--------------------------------CccccCCCeec-ceeEEECCCeEecCcCChhhC
Confidence            578999999998887                                89999999999 478899999999999999999


Q ss_pred             CcccccCCeeccCCccccHHHHHhhhcCCCcc
Q 041875          133 GCLLTTSSYAALDGILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus       133 ~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~  164 (195)
                      +++|.++.|+.+||++||+.||.++||++|.-
T Consensus        48 ~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           48 FTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             CCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            99999888999999999999999999999864

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

Probab=99.82  E-value=9.3e-22  Score=132.17  Aligned_cols=80  Identities=20%  Similarity=0.482  Sum_probs=73.6

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeec-CceEEECCceeccccccccc
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYP-LEKVTVEGESFHKTCFRCSH  131 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~-~~~v~~~~~~~H~~CF~C~~  131 (195)
                      +|++||+.||.++++                                ++|.+|+++|.+ +..|.++++.||+.||+|..
T Consensus         1 ~g~~yC~~~y~~~~~--------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~   48 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFA--------------------------------NTCAECQQLIGHDSRELFYEDRHFHEGCFRCCR   48 (82)
T ss_dssp             CCCCCCCCCCCCCCS--------------------------------CBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTT
T ss_pred             CCceechhHhCcccC--------------------------------CcCccCCCccccCcEEEEeCCccccccCCeecC
Confidence            589999999999987                                899999999995 44567899999999999999


Q ss_pred             CCcccccCCeeccCCccccHHHHHhhhcCCCcc
Q 041875          132 GGCLLTTSSYAALDGILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus       132 C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~  164 (195)
                      |+++|.++.|+.++|++||+.||.++|+++|.-
T Consensus        49 C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           49 CQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             TCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             CCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            999999889999999999999999999999863

>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=99.82  E-value=1.1e-20  Score=126.64  Aligned_cols=78  Identities=15%  Similarity=0.311  Sum_probs=70.8

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccC
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHG  132 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C  132 (195)
                      +|++||+.||. ++.                                ++|++|+++|. ++.|.+.++.||+.||+|..|
T Consensus         2 ~g~~yC~~~y~-~~~--------------------------------~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C   47 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATL--------------------------------EKCATCSQPIL-DRILRAMGKAYHPGCFTCVVC   47 (81)
T ss_dssp             CCCCCCCCCCC-SSC--------------------------------CBCTTTCCBCC-SCCEEETTEEECTTTCBCSSS
T ss_pred             cCCEECHHHhh-cCC--------------------------------CccccCCCeec-ceeEEECCccccHHhcCcccC
Confidence            68999999998 554                                89999999999 568899999999999999999


Q ss_pred             CcccccCCeecc-CCccccHHHHHhhhcCCCcc
Q 041875          133 GCLLTTSSYAAL-DGILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus       133 ~~~L~~~~~~~~-dg~~yC~~c~~~~f~~k~~~  164 (195)
                      +++|.+..|+.. ||++||+.||.++|+++|.-
T Consensus        48 ~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           48 HRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            999998888876 79999999999999999863

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

Probab=99.79  E-value=3.1e-20  Score=124.44  Aligned_cols=67  Identities=31%  Similarity=0.652  Sum_probs=58.2

Q ss_pred             CCcCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |.|.++.++|..|+++|..++.|.++++.||++||+|..|+++|....|+.+++++||+.||.++|+
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~   67 (81)
T 1a7i_A            1 MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   67 (81)
T ss_dssp             -------CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             CCCCCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhC
Confidence            8899999999999999987889999999999999999999999998899999999999999999998

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

Probab=99.78  E-value=9.7e-20  Score=120.77  Aligned_cols=73  Identities=22%  Similarity=0.478  Sum_probs=67.0

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeec----CceEEECCceecccccc
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYP----LEKVTVEGESFHKTCFR  128 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~----~~~v~~~~~~~H~~CF~  128 (195)
                      ++++||+.||.++++                                ++|++|+++|.+    .+.|.+.++.||+.||+
T Consensus         1 g~~~yC~~cy~~~~~--------------------------------~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~   48 (77)
T 2egq_A            1 GSSGSSGDCYKNFVA--------------------------------KKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFH   48 (77)
T ss_dssp             CCSSCCTTCCCSCCC--------------------------------CCCSSSCCCCCCCSSCCCEEEETTEEEETTTCB
T ss_pred             CCCeEchhHhchhhC--------------------------------ccCcccCCcccCCCCCceeEEECcceeCcccCE
Confidence            478999999999887                                899999999994    36789999999999999


Q ss_pred             cccCCcccccCCeeccCCccccHHHHHhh
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSHFAQL  157 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~~  157 (195)
                      |..|+++|.+..|+.++|+|||+.||.++
T Consensus        49 C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           49 CKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             CSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             ehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            99999999988899999999999999763

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

Probab=99.78  E-value=7.6e-20  Score=122.49  Aligned_cols=78  Identities=15%  Similarity=0.327  Sum_probs=70.5

Q ss_pred             CCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccC
Q 041875           53 EGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHG  132 (195)
Q Consensus        53 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C  132 (195)
                      ++.+||+.||.++++                                ++|.+|+++|. ++.|.+.++.||++||+|..|
T Consensus         1 g~~~yC~~~y~~~~~--------------------------------~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C   47 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFG--------------------------------EFCHGCSLLMT-GPFMVAGEFKYHPECFACMSC   47 (81)
T ss_dssp             CCCCCCCCCSSCCSS--------------------------------CBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTT
T ss_pred             CCCccchhHHhhhcC--------------------------------CcCccCCCCcC-ceEEEECCceeccccCCccCC
Confidence            468999999999987                                89999999999 777899999999999999999


Q ss_pred             Cccccc-CCee-ccCCccccHHHHHhhhcCCCc
Q 041875          133 GCLLTT-SSYA-ALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus       133 ~~~L~~-~~~~-~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      +++|.. ..|+ ..+|++||+.||.++|+++++
T Consensus        48 ~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           48 KVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             CCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             CCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            999974 5677 589999999999999998864

>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=99.76  E-value=9.3e-19  Score=115.77  Aligned_cols=68  Identities=34%  Similarity=0.759  Sum_probs=64.4

Q ss_pred             CCcCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecch-hhHHHhhcc
Q 041875            1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK-PHFEQLFKE   68 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~-~c~~~~~~~   68 (195)
                      |.|++..++|.+|+++|..++.|.++++.||++||+|..|+++|.+..|+.+++++||+ .||.++|++
T Consensus         3 ~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~   71 (76)
T 2cu8_A            3 SGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGS   71 (76)
T ss_dssp             CSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCS
T ss_pred             cccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhccc
Confidence            67889999999999999988899999999999999999999999988999999999999 799999983

>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=99.76  E-value=1.5e-18  Score=118.70  Aligned_cols=75  Identities=43%  Similarity=0.891  Sum_probs=69.4

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCCCcch
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTAS  172 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~~  172 (195)
                      +..+|.+|+++|.+.+.|.+.++.||..||+|..|+++|..+.|+.+||++||+.||.++|+++|.+...+....
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~~~   88 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSGP   88 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCCCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCCCC
Confidence            348999999999987889999999999999999999999988899999999999999999999999888877654

>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=99.75  E-value=1.4e-18  Score=114.97  Aligned_cols=70  Identities=36%  Similarity=0.638  Sum_probs=64.6

Q ss_pred             cCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccH-HHHHhhhcCCCcc
Q 041875           95 FCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK-SHFAQLFKEKGCY  164 (195)
Q Consensus        95 ~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~-~c~~~~f~~k~~~  164 (195)
                      +.+..++|.+|+++|.+++.|.+.++.||+.||+|..|+++|.++.|+.+||++||+ .||.++|+++|.-
T Consensus         5 ~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            5 SSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             cCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            445568999999999988899999999999999999999999988899999999999 7999999999863

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

Probab=99.75  E-value=1.7e-18  Score=114.51  Aligned_cols=60  Identities=37%  Similarity=0.827  Sum_probs=57.3

Q ss_pred             CcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecch-hhHHHhhc
Q 041875            8 EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK-PHFEQLFK   67 (195)
Q Consensus         8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~-~c~~~~~~   67 (195)
                      ++|.+|+++|..++.|.++|+.||++||+|..|+++|.++.|+.+++++||+ .||.++|+
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            5799999999988899999999999999999999999998999999999999 69999998

>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=99.73  E-value=5.8e-18  Score=113.15  Aligned_cols=66  Identities=24%  Similarity=0.600  Sum_probs=61.4

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCcc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~  164 (195)
                      +.++|.+|+++|..++.|.++++.||+.||+|..|+++|.+ .|+.+||+|||+.||.++|+++|+-
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           14 GPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             SCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            34899999999998889999999999999999999999985 6999999999999999999999964

>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=99.73  E-value=2.2e-18  Score=115.32  Aligned_cols=71  Identities=37%  Similarity=0.725  Sum_probs=58.2

Q ss_pred             CCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCC
Q 041875           97 GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHL  167 (195)
Q Consensus        97 ~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~  167 (195)
                      ++.++|.+|+++|.+.+.|.+.++.||+.||+|..|+++|..+.|+.+||++||+.||.++|+++|. ++.+
T Consensus         5 ~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g   76 (81)
T 1a7i_A            5 GGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQG   76 (81)
T ss_dssp             ---CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC---------
T ss_pred             CCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCc
Confidence            3458999999999888889999999999999999999999988899999999999999999999997 5433

>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=99.72  E-value=3.7e-18  Score=114.21  Aligned_cols=78  Identities=17%  Similarity=0.348  Sum_probs=68.8

Q ss_pred             CeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCC
Q 041875           54 GVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGG  133 (195)
Q Consensus        54 g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~  133 (195)
                      +.+||+.||.++|+                                ++|++|+++|. ++.|.+.++.||+.||+|..|+
T Consensus         2 ~~~yC~~dy~~~~~--------------------------------~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~   48 (81)
T 1v6g_A            2 SSGSSGLDYQRLYG--------------------------------TRCFSCDQFIE-GEVVSALGKTYHPDCFVCAVCR   48 (81)
T ss_dssp             CCCCCCSCGGGSCC--------------------------------CBCTTTCCBCC-SCCEEETTEEECTTTSSCSSSC
T ss_pred             CCCcchHHHHhHhC--------------------------------CcCccccCEec-cceEEECCceeCccCCccccCC
Confidence            56899999999998                                89999999999 6789999999999999999999


Q ss_pred             cccccCCeeccCC-ccccHHHHHhhhcCCCcc
Q 041875          134 CLLTTSSYAALDG-ILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus       134 ~~L~~~~~~~~dg-~~yC~~c~~~~f~~k~~~  164 (195)
                      ++|..+.++..++ .+||..||.++++..++-
T Consensus        49 ~~L~~~~~~~~~~~~~~C~~C~~~~~~~~~s~   80 (81)
T 1v6g_A           49 LPFPPGDRVTFNGKECMCQKCSLPVSVSGPSS   80 (81)
T ss_dssp             CCCCSSSCEEEETTEEEEHHHHSCCSSCCCCC
T ss_pred             CCCCCCCEEEeCCCCEEChhhhcccCCCCCCC
Confidence            9998766666655 579999999988887653

>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=99.71  E-value=1.3e-17  Score=108.48  Aligned_cols=65  Identities=28%  Similarity=0.576  Sum_probs=60.8

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCcc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~  164 (195)
                      .++|.+|+++|. .+.|.+.++.||+.||+|..|+++|.+..|+.+||++||+.||.++|+++|+-
T Consensus         5 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            5 SSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            389999999998 56789999999999999999999999888999999999999999999999964

>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=99.71  E-value=1.3e-17  Score=108.23  Aligned_cols=64  Identities=19%  Similarity=0.522  Sum_probs=60.3

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      .++|.+|+++|. ++.|.+.++.||+.||+|..|+++|.+..|+.+||++||+.||.++|+++|.
T Consensus         5 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   68 (69)
T 2cur_A            5 SSGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS   68 (69)
T ss_dssp             CCCCSSSCCCCC-TTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCC
T ss_pred             cCCCcccCCEeC-cceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCC
Confidence            489999999998 5788999999999999999999999988899999999999999999999984

>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=99.71  E-value=2.1e-17  Score=112.74  Aligned_cols=67  Identities=19%  Similarity=0.461  Sum_probs=62.2

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN  165 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~  165 (195)
                      ..++|.+|+++|. ++.|.+.++.||+.||+|..|+++|.+..|+.++|++||+.||.++|+++|+.+
T Consensus        24 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s~   90 (90)
T 2dar_A           24 RTPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSSG   90 (90)
T ss_dssp             CCCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCCC
T ss_pred             CCCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCCC
Confidence            4589999999997 778899999999999999999999998889999999999999999999999753

>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=99.71  E-value=9.7e-18  Score=109.57  Aligned_cols=66  Identities=27%  Similarity=0.577  Sum_probs=61.4

Q ss_pred             CcCccCCceeecC-ceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875          100 DKCTSCKKTVYPL-EKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN  165 (195)
Q Consensus       100 ~~C~~C~~~I~~~-~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~  165 (195)
                      ++|.+|+++|.+. +.|.+.++.||..||+|..|+++|.++.|+.++|++||+.||.++|+++|+.|
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~~   72 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSSG   72 (72)
T ss_dssp             CBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCCC
T ss_pred             CCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCCC
Confidence            8999999999975 56789999999999999999999998889999999999999999999999743

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

Probab=99.71  E-value=1.4e-17  Score=111.29  Aligned_cols=64  Identities=25%  Similarity=0.570  Sum_probs=58.8

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET   69 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~   69 (195)
                      .+.++|..|+++|..++.|.++++.||++||+|..|+++|.+ .|+.+++++||+.||.++|+++
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~   76 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSG   76 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCC
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCC
Confidence            356799999999998889999999999999999999999985 7999999999999999999843

>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=99.70  E-value=1.8e-17  Score=108.25  Aligned_cols=66  Identities=27%  Similarity=0.550  Sum_probs=61.5

Q ss_pred             CcCccCCceeecCc-eEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875          100 DKCTSCKKTVYPLE-KVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN  165 (195)
Q Consensus       100 ~~C~~C~~~I~~~~-~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~  165 (195)
                      ++|.+|+++|.+.+ .|.+.++.||..||+|..|+++|.++.|+.+||++||+.||.++|+++|+.+
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~~   72 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSSG   72 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCCC
T ss_pred             CCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCCC
Confidence            89999999999764 6789999999999999999999999899999999999999999999999743

>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=99.70  E-value=1.7e-17  Score=107.60  Aligned_cols=62  Identities=24%  Similarity=0.600  Sum_probs=58.3

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ...++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
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

>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=99.70  E-value=1.5e-17  Score=109.87  Aligned_cols=66  Identities=35%  Similarity=0.729  Sum_probs=61.8

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccH-HHHHhhhcCCCccC
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK-SHFAQLFKEKGCYN  165 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~-~c~~~~f~~k~~~~  165 (195)
                      ++|.+|+++|.+++.|.+.++.||..||+|..|+++|.++.|+.+||.+||+ .||.++|+++|.-+
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C   67 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGR   67 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSC
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCc
Confidence            4799999999988889999999999999999999999988999999999999 79999999999833

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

Probab=99.70  E-value=1e-17  Score=107.67  Aligned_cols=61  Identities=23%  Similarity=0.519  Sum_probs=58.5

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCC
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEK  161 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k  161 (195)
                      ++|++|+++|. ++.|.+.++.||+.||+|..|+++|.++.|+.+||++||+.||.++||+|
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 77889999999999999999999999889999999999999999999986

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

Probab=99.69  E-value=2.6e-17  Score=106.95  Aligned_cols=63  Identities=27%  Similarity=0.595  Sum_probs=58.5

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhcc
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE   68 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~   68 (195)
                      ...++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   65 (70)
T 2d8z_A            3 SGSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS   65 (70)
T ss_dssp             CCCCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCC
T ss_pred             CCCCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhcc
Confidence            35689999999998 6789999999999999999999999988999999999999999999983

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

Probab=99.69  E-value=1.9e-17  Score=109.53  Aligned_cols=67  Identities=31%  Similarity=0.667  Sum_probs=61.5

Q ss_pred             CCcCCCCCccccccccccc-CceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            1 MAFCGTQEKCKACDKTVHI-IDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~-~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |+.....++|.+|+++|.. +.++.++|+.||++||+|..|+++|.++.|+.++|++||+.||.++|+
T Consensus         5 ~~~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~   72 (77)
T 1g47_A            5 MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (77)
T ss_dssp             CCSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCC
T ss_pred             hccCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhh
Confidence            5667778999999999985 456789999999999999999999998899999999999999999998

>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=99.69  E-value=1.7e-17  Score=106.61  Aligned_cols=62  Identities=27%  Similarity=0.621  Sum_probs=58.3

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhcc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE   68 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~   68 (195)
                      ..++|.+|+++|. +++|.++|+.||++||+|..|+++|.+..|+.+++++||+.||.++|++
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            3579999999999 8899999999999999999999999988999999999999999999873

>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=99.69  E-value=5.1e-17  Score=105.62  Aligned_cols=65  Identities=17%  Similarity=0.367  Sum_probs=60.5

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      +.++|..|+++|. ++.|.+.++.||++||+|..|+++|....|+.+||++||+.||.++|+++..
T Consensus         4 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            4 GSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             CSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            4589999999998 6788999999999999999999999988899999999999999999998864

>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=99.69  E-value=7.3e-17  Score=109.81  Aligned_cols=66  Identities=21%  Similarity=0.409  Sum_probs=61.1

Q ss_pred             CCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc
Q 041875           97 GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus        97 ~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      ....+|.+|+++|. .+.|.+.++.||.+||+|..|+++|..+.|+.+||++||+.||.++|++||.
T Consensus        23 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           23 QRMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CSCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CcCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            35589999999999 4778999999999999999999999988899999999999999999999984

>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=4.2e-17  Score=111.47  Aligned_cols=71  Identities=42%  Similarity=0.954  Sum_probs=63.6

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKL   76 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~   76 (195)
                      +.++|..|+++|.+.+.|.++++.||++||+|..|+++|....|+.+++++||+.||.++|++++++...|
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~   84 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF   84 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCc
Confidence            46799999999997789999999999999999999999998889999999999999999999666544433

>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=99.68  E-value=3e-17  Score=109.33  Aligned_cols=65  Identities=17%  Similarity=0.375  Sum_probs=60.5

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      ..++|.+|+++|. ++.|.+.++.||..||+|..|+++|....|+.+||++||+.||.++|+++|.
T Consensus        14 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           14 KLPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4589999999999 4688999999999999999999999987899999999999999999999974

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

Probab=99.68  E-value=1.4e-17  Score=110.13  Aligned_cols=67  Identities=13%  Similarity=0.397  Sum_probs=62.0

Q ss_pred             CcCccCCceeec---CceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCC
Q 041875          100 DKCTSCKKTVYP---LEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNH  166 (195)
Q Consensus       100 ~~C~~C~~~I~~---~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~  166 (195)
                      ++|..|+++|.+   .+.|.+.++.||++||+|..|+++|.+..|+.+||+|||+.||.++|+++|.-++
T Consensus         6 ~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            6 SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             CCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             CCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            899999999994   3678999999999999999999999988899999999999999999999997544

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

Probab=99.68  E-value=4.9e-17  Score=105.70  Aligned_cols=64  Identities=22%  Similarity=0.459  Sum_probs=59.5

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET   69 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~   69 (195)
                      ++.++|..|+++|. +++|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   66 (70)
T 2d8x_A            3 SGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASG   66 (70)
T ss_dssp             CCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCC
T ss_pred             CCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCC
Confidence            56789999999998 78899999999999999999999999989999999999999999999843

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

Probab=99.68  E-value=1.8e-17  Score=109.51  Aligned_cols=61  Identities=21%  Similarity=0.507  Sum_probs=57.3

Q ss_pred             CCccccccccccc---CceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            7 QEKCKACDKTVHI---IDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         7 ~~~C~~C~~~I~~---~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .++|.+|+++|.+   .++|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
T Consensus         5 ~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~   68 (76)
T 1x68_A            5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDT   68 (76)
T ss_dssp             CCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCC
T ss_pred             CCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhC
Confidence            5799999999983   378999999999999999999999998899999999999999999988

>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=99.68  E-value=3.3e-17  Score=107.13  Aligned_cols=64  Identities=14%  Similarity=0.388  Sum_probs=59.2

Q ss_pred             CCcCccCCceeec---CceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCC
Q 041875           99 QDKCTSCKKTVYP---LEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKG  162 (195)
Q Consensus        99 ~~~C~~C~~~I~~---~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~  162 (195)
                      .++|.+|+++|..   .+.|.+.++.||++||+|..|+++|.+..|+.+||++||+.||.++|||++
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            4899999999995   367889999999999999999999998889999999999999999999975

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

Probab=99.68  E-value=5.3e-17  Score=106.03  Aligned_cols=63  Identities=32%  Similarity=0.645  Sum_probs=58.6

Q ss_pred             CCCcccccccccccC-ceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhcc
Q 041875            6 TQEKCKACDKTVHII-DMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE   68 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~-~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~   68 (195)
                      ..++|..|+++|.++ ++|.++++.||++||+|..|+++|....|+.+++++||+.||.++|++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   67 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS   67 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccC
Confidence            357999999999974 789999999999999999999999998999999999999999999983

>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=99.67  E-value=5.7e-17  Score=110.59  Aligned_cols=64  Identities=27%  Similarity=0.635  Sum_probs=59.3

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET   69 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~   69 (195)
                      ...++|..|+++|. +++|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+++
T Consensus        23 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~   86 (90)
T 2dar_A           23 KRTPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASG   86 (90)
T ss_dssp             TCCCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCC
T ss_pred             CCCCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCC
Confidence            35679999999996 88999999999999999999999999889999999999999999999844

>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=99.67  E-value=6.7e-17  Score=115.01  Aligned_cols=66  Identities=18%  Similarity=0.381  Sum_probs=60.8

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCccccc--CCeeccCCccccHHHHHhhhcCCCc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTT--SSYAALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~--~~~~~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      +.++|++|+++|...+.|.+.++.||+.||+|..|+++|..  ..|+.+||+|||+.||.++|+++|.
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~   69 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGH   69 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCS
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccC
Confidence            35899999999996667899999999999999999999984  5799999999999999999999986

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

Probab=99.67  E-value=5.6e-17  Score=107.28  Aligned_cols=65  Identities=29%  Similarity=0.599  Sum_probs=58.8

Q ss_pred             CCcCccCCceeecCce-EEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc
Q 041875           99 QDKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC  163 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~-v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~  163 (195)
                      .++|.+|+++|.+.+. +.+.|+.||..||+|..|+++|.++.|+.+||.+||+.||.++|+++|.
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            4899999999986554 6899999999999999999999988899999999999999999999985

>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=99.67  E-value=6.9e-17  Score=105.49  Aligned_cols=63  Identities=24%  Similarity=0.579  Sum_probs=58.4

Q ss_pred             CCCcccccccccccC-ceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhcc
Q 041875            6 TQEKCKACDKTVHII-DMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE   68 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~-~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~   68 (195)
                      ..++|..|+++|.+. .+|.++|+.||++||+|..|+++|.+..|+.+++++||+.||.++|++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   67 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHAS   67 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSS
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCC
Confidence            357999999999975 589999999999999999999999999999999999999999999983

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

Probab=99.67  E-value=4.5e-17  Score=106.45  Aligned_cols=64  Identities=17%  Similarity=0.427  Sum_probs=58.6

Q ss_pred             CCCCccccccccccc---CceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhcc
Q 041875            5 GTQEKCKACDKTVHI---IDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE   68 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~---~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~   68 (195)
                      ...++|.+|+++|.+   .++|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p   69 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGP   69 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCS
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCC
Confidence            456899999999984   3789999999999999999999999988999999999999999998873

>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=99.66  E-value=2.8e-17  Score=109.47  Aligned_cols=65  Identities=18%  Similarity=0.403  Sum_probs=59.4

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETG   70 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~   70 (195)
                      ...++|..|+++|. +++|.++++.||++||+|..|++.|.+..|+.+++++||+.||.++|++++
T Consensus        13 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g   77 (79)
T 1x62_A           13 QKLPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS   77 (79)
T ss_dssp             CCCCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCC
T ss_pred             CCCCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            45679999999998 578999999999999999999999988789999999999999999998553

>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=99.66  E-value=9.3e-17  Score=109.30  Aligned_cols=64  Identities=27%  Similarity=0.485  Sum_probs=58.9

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET   69 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~   69 (195)
                      ....+|..|+++|. +++|.++++.||++||+|..|++.|....|+.+++++||+.||.++|+++
T Consensus        23 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~   86 (89)
T 1x64_A           23 QRMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGP   86 (89)
T ss_dssp             CSCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSC
T ss_pred             CcCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCC
Confidence            34578999999998 58899999999999999999999999889999999999999999999854

>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=99.66  E-value=1.4e-16  Score=104.02  Aligned_cols=63  Identities=25%  Similarity=0.463  Sum_probs=58.1

Q ss_pred             CCCCcccccccccccC-ceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            5 GTQEKCKACDKTVHII-DMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~-~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ...++|.+|+++|... .+|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
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 58999999999999999999999988889999999999999999986

>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=99.65  E-value=6.4e-17  Score=112.47  Aligned_cols=72  Identities=21%  Similarity=0.384  Sum_probs=64.6

Q ss_pred             CCcCccCCceeec-CceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCCCCc
Q 041875           99 QDKCTSCKKTVYP-LEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLTKT  170 (195)
Q Consensus        99 ~~~C~~C~~~I~~-~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~  170 (195)
                      .++|.+|+++|.+ ++.|.+.++.||..||+|..|+++|.+..|+.+||++||+.||.++|+++|. ++..+.+
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            4899999999985 6778999999999999999999999988899999999999999999999999 4444443

>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=99.64  E-value=2.5e-16  Score=104.88  Aligned_cols=61  Identities=25%  Similarity=0.630  Sum_probs=57.5

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|.++.|+.+++++||+.||.++|+
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~   74 (80)
T 1x3h_A           14 FSPKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRG   74 (80)
T ss_dssp             CSCBCTTTCCBCC-SSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHS
T ss_pred             cCCccccCCCeec-ceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcC
Confidence            3579999999998 588999999999999999999999998899999999999999999998

>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=99.64  E-value=2.6e-16  Score=105.14  Aligned_cols=63  Identities=29%  Similarity=0.556  Sum_probs=57.7

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeec-CCeecchhhHHHhhc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSM-EGVLYCKPHFEQLFK   67 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~-~g~~yC~~c~~~~~~   67 (195)
                      ....++|.+|+++|. +++|.++++.||++||+|..|+++|.+..|+.. ++++||+.||.++|+
T Consensus        12 ~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~   75 (81)
T 2dlo_A           12 VATLEKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   75 (81)
T ss_dssp             CSSCCBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             hcCCCccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhc
Confidence            346789999999998 679999999999999999999999998888876 789999999999998

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

Probab=99.63  E-value=1.2e-16  Score=115.47  Aligned_cols=71  Identities=15%  Similarity=0.341  Sum_probs=64.9

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccC-CCCCc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN-HLTKT  170 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~-~~~~~  170 (195)
                      ++|.+|+++|..++.+.++|+.||+.||+|..|+++|.+..|+.+||++||+.||.++|+++|.-+ ..+.+
T Consensus         4 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~   75 (126)
T 2xqn_T            4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDP   75 (126)
T ss_dssp             CBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCT
T ss_pred             CCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCc
Confidence            899999999997778899999999999999999999998889999999999999999999999844 44443

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

Probab=99.63  E-value=1.5e-16  Score=105.93  Aligned_cols=64  Identities=20%  Similarity=0.432  Sum_probs=58.7

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCcc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCY  164 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~  164 (195)
                      .++|..|+++|. ++.|.+.++.||+.||+|..|+++|.+.. +.+||++||+.||.++|+|+.+.
T Consensus        15 ~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~g~~yC~~cy~~~f~p~~ss   78 (79)
T 2cor_A           15 KYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVSGPSS   78 (79)
T ss_dssp             CCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCCSSCC
T ss_pred             CCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCCCCCC
Confidence            489999999999 77789999999999999999999999875 48899999999999999998764

>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=99.63  E-value=3.5e-16  Score=104.65  Aligned_cols=64  Identities=33%  Similarity=0.601  Sum_probs=59.0

Q ss_pred             CCcccccccccccCc-eEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCC
Q 041875            7 QEKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETG   70 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~-~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~   70 (195)
                      .++|.+|+++|..++ +|.++++.||++||+|..|+++|..+.|+.+++++||+.||.++|++++
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~   79 (82)
T 1x63_A           15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGP   79 (82)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCC
T ss_pred             CCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCC
Confidence            579999999998754 6899999999999999999999999999999999999999999998654

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

Probab=99.62  E-value=1e-16  Score=107.53  Aligned_cols=64  Identities=25%  Similarity=0.717  Sum_probs=58.2

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCcee--ecCCeecchhhHHHhhc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFS--SMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~--~~~g~~yC~~c~~~~~~   67 (195)
                      .++.++|.+|+++|+.++.|.++++.||++||+|..|++.|....|+  .+++++||+.||.++++
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            45678999999999888899999999999999999999999999888  47999999999988775

>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=99.62  E-value=5.2e-16  Score=103.34  Aligned_cols=63  Identities=29%  Similarity=0.585  Sum_probs=58.2

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET   69 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~   69 (195)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+++
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~   76 (80)
T 2cuq_A           14 FAPRCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASG   76 (80)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCS
T ss_pred             cCCcCCCCCCEec-CcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCC
Confidence            4589999999998 57899999999999999999999999889999999999999999999843

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

Probab=99.62  E-value=1.8e-16  Score=106.27  Aligned_cols=64  Identities=36%  Similarity=0.749  Sum_probs=58.3

Q ss_pred             CCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCee--ccCCccccHHHHHhhhcC
Q 041875           97 GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYA--ALDGILYCKSHFAQLFKE  160 (195)
Q Consensus        97 ~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~--~~dg~~yC~~c~~~~f~~  160 (195)
                      ++.++|.+|+++|...+.|.+.++.||..||+|..|+++|....|.  .+||++||+.||.++|+.
T Consensus        13 ~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A           13 GAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCC
T ss_pred             CCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcC
Confidence            4558999999999988889999999999999999999999988887  479999999999998875

>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=99.62  E-value=3.3e-16  Score=102.70  Aligned_cols=61  Identities=15%  Similarity=0.321  Sum_probs=56.3

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCC-CCceeecCCeecchhhHHHhhc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLV-MGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ..++|.+|+++|. +++|.++++.||++||+|..|+++|. +..|+.+++++||..||.+++.
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            4589999999998 68899999999999999999999998 6689999999999999998875

>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=99.62  E-value=2.5e-16  Score=105.44  Aligned_cols=62  Identities=19%  Similarity=0.530  Sum_probs=57.5

Q ss_pred             CCCccccccccccc-CceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            6 TQEKCKACDKTVHI-IDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         6 ~~~~C~~C~~~I~~-~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ..++|.+|+++|.. +.+|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~   76 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS   76 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGG
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcC
Confidence            35799999999984 567899999999999999999999998899999999999999999998

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

Probab=99.61  E-value=4.6e-16  Score=101.30  Aligned_cols=60  Identities=32%  Similarity=0.695  Sum_probs=56.3

Q ss_pred             CcCccCCceeecCce-EEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          100 DKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~-v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      ++|.+|+++|.+.+. +.+.++.||+.||+|..|+++|..+.|+.+||++||+.||.++||
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            799999999998776 479999999999999999999998889999999999999999986

>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=4.8e-16  Score=103.50  Aligned_cols=63  Identities=21%  Similarity=0.475  Sum_probs=57.0

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhcc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKE   68 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~   68 (195)
                      ....++|..|+++|. ++.|.++|+.||++||+|..|+++|.+.. +.+++++||+.||.++|++
T Consensus        12 ~~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~g~~yC~~cy~~~f~p   74 (79)
T 2cor_A           12 GLGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVS   74 (79)
T ss_dssp             CCCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCC
T ss_pred             ccCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCC
Confidence            345689999999999 78899999999999999999999999775 5899999999999999874

>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=99.61  E-value=3.6e-16  Score=112.48  Aligned_cols=73  Identities=19%  Similarity=0.449  Sum_probs=63.9

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccc--cCCeeccCCccccHHHHHhhhcC--CCc-cCCCCCcc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHFAQLFKE--KGC-YNHLTKTA  171 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~~f~~--k~~-~~~~~~~~  171 (195)
                      .++|++|+++|...+.|.+.++.||+.||+|..|+++|.  +..|+.+||++||+.||.++|++  +|. ++..|.+.
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            389999999999776789999999999999999999997  45799999999999999999999  888 44445443

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.61  E-value=7.1e-16  Score=100.63  Aligned_cols=62  Identities=23%  Similarity=0.476  Sum_probs=57.1

Q ss_pred             CCcCccCCceeecC-ceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcC
Q 041875           99 QDKCTSCKKTVYPL-EKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE  160 (195)
Q Consensus        99 ~~~C~~C~~~I~~~-~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~  160 (195)
                      .++|.+|+++|.+. ..|.+.++.||..||+|..|+++|.+..|+.+||++||+.||.++|++
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~~   67 (72)
T 1x61_A            5 SSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES   67 (72)
T ss_dssp             CCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHHT
T ss_pred             CCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHcc
Confidence            38999999999974 468999999999999999999999888899999999999999999964

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

Probab=99.61  E-value=4.6e-16  Score=101.30  Aligned_cols=63  Identities=30%  Similarity=0.734  Sum_probs=57.1

Q ss_pred             CCCCcccccccccccCc-eEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            5 GTQEKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~-~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ...++|.+|+++|..++ ++.++|+.||++||+|..|+++|..+.|+.++|++||+.||.++|+
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            35679999999999766 4689999999999999999999998899999999999999998874

>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=99.61  E-value=4.9e-16  Score=120.13  Aligned_cols=61  Identities=30%  Similarity=0.737  Sum_probs=58.0

Q ss_pred             CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .++|.+|+++|.+++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
T Consensus       115 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~  175 (192)
T 1b8t_A          115 SDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFG  175 (192)
T ss_dssp             CEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTC
T ss_pred             CCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcC
Confidence            5679999999997888999999999999999999999998899999999999999999998

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

Probab=99.60  E-value=3.7e-16  Score=119.85  Aligned_cols=70  Identities=20%  Similarity=0.431  Sum_probs=61.9

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCCC
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTK  169 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~~  169 (195)
                      .++|.+|+++|...+.+.+.++.||+.||+|..|+++|.+..| .+||++||+.||.++|+++|..+...+
T Consensus        60 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~~C~~~I  129 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGI  129 (182)
T ss_dssp             CCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCTTTCCCC
T ss_pred             CCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccccCCCcc
Confidence            4899999999996666789999999999999999999998765 789999999999999999999444433

>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=99.60  E-value=5.5e-16  Score=111.68  Aligned_cols=61  Identities=23%  Similarity=0.530  Sum_probs=55.9

Q ss_pred             CCcccccccccccCceEeeCCcccccCccccccccccCC--CCceeecCCeecchhhHHHhhc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLV--MGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .++|.+|+++|...++|.++++.||++||+|..|+++|.  +..|+.++|++||+.||.++|+
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            479999999999666899999999999999999999997  3589999999999999999874

>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=99.58  E-value=1.3e-15  Score=109.68  Aligned_cols=62  Identities=19%  Similarity=0.490  Sum_probs=56.6

Q ss_pred             CCCcCccCCceeecCceEEECCceecccccccccCCcccc--cCCeeccCCccccHHHHHhhhc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      ..++|.+|+++|.....|.+.++.||..||+|..|+++|.  +..|+.+||++||+.||.++||
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            3589999999999666789999999999999999999997  3579999999999999999997

>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=99.58  E-value=7.7e-16  Score=100.95  Aligned_cols=63  Identities=14%  Similarity=0.297  Sum_probs=57.1

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccc-cCCeeccCCccccHHHHHhhhcCCC
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT-TSSYAALDGILYCKSHFAQLFKEKG  162 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~c~~~~f~~k~  162 (195)
                      .++|++|+++|. ++.|.+.++.||++||+|..|+++|. +..|+.++|++||..||.++++++-
T Consensus         5 ~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~~   68 (73)
T 1wig_A            5 SSGCDSCEKYIT-GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTEDS   68 (73)
T ss_dssp             CCSCSSSCCCCS-SCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSSC
T ss_pred             cCCcccCCCEec-CeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcccc
Confidence            389999999998 47789999999999999999999998 6789999999999999999887653

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

Probab=99.57  E-value=1.3e-15  Score=97.58  Aligned_cols=59  Identities=27%  Similarity=0.680  Sum_probs=54.3

Q ss_pred             CCccccccccccc-CceEeeCCcccc--cCccccccccccCCCCceeecCCeecc-hhhHHHh
Q 041875            7 QEKCKACDKTVHI-IDMVTADGISYH--KICFKCSHCNGKLVMGNFSSMEGVLYC-KPHFEQL   65 (195)
Q Consensus         7 ~~~C~~C~~~I~~-~~~i~~~g~~~H--~~CF~C~~C~~~L~~~~~~~~~g~~yC-~~c~~~~   65 (195)
                      .++|.+|+++|.. ++.|.++|+.||  ++||+|..|+++|.+..|+.++|++|| .+||.++
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            4689999999997 478999999999  999999999999998899999999999 8998754

>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=99.57  E-value=2.4e-15  Score=99.37  Aligned_cols=59  Identities=25%  Similarity=0.628  Sum_probs=54.3

Q ss_pred             CCCccccccccccc----CceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHH
Q 041875            6 TQEKCKACDKTVHI----IDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ   64 (195)
Q Consensus         6 ~~~~C~~C~~~I~~----~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~   64 (195)
                      ..++|.+|+++|.+    .++|.++++.||++||+|..|+++|.+..|+.+++++||+.||.+
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            35899999999993    378999999999999999999999998899999999999999975

>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=4.1e-15  Score=95.23  Aligned_cols=58  Identities=24%  Similarity=0.599  Sum_probs=53.9

Q ss_pred             CcCccCCceeecC-ceEEECCceec--ccccccccCCcccccCCeeccCCcccc-HHHHHhh
Q 041875          100 DKCTSCKKTVYPL-EKVTVEGESFH--KTCFRCSHGGCLLTTSSYAALDGILYC-KSHFAQL  157 (195)
Q Consensus       100 ~~C~~C~~~I~~~-~~v~~~~~~~H--~~CF~C~~C~~~L~~~~~~~~dg~~yC-~~c~~~~  157 (195)
                      ++|++|+++|.++ +.|.+.++.||  ++||+|..|+++|.+..|+.+||+||| ..||.++
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            7899999999974 67899999999  999999999999999899999999999 8999764

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

Probab=99.53  E-value=7.5e-15  Score=106.57  Aligned_cols=68  Identities=18%  Similarity=0.368  Sum_probs=60.9

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCcccc--cCCeeccCCccccHHHHHhhhcC--CCccCCC
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHFAQLFKE--KGCYNHL  167 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~~f~~--k~~~~~~  167 (195)
                      ++|.+|+++|...+.|.++++.||+.||+|..|+++|.  +..|+.+||+|||+.||.++|++  +|..+..
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~   74 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDK   74 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCC
T ss_pred             ccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCC
Confidence            79999999999665789999999999999999999997  35799999999999999999999  8874443

>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=9.2e-15  Score=97.50  Aligned_cols=61  Identities=21%  Similarity=0.511  Sum_probs=55.4

Q ss_pred             CCCcccccccccccCceEeeCCcccccCccccccccccCCC-Ccee-ecCCeecchhhHHHhhc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVM-GNFS-SMEGVLYCKPHFEQLFK   67 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~-~~~~-~~~g~~yC~~c~~~~~~   67 (195)
                      ..++|.+|+++|. +++|.++++.||++||+|..|+++|.. ..|. ++++++||+.||.++|+
T Consensus        14 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~   76 (81)
T 1x6a_A           14 FGEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS   76 (81)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHC
T ss_pred             cCCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhc
Confidence            4579999999999 888999999999999999999999975 5676 58999999999999997

>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=99.52  E-value=1.2e-14  Score=110.12  Aligned_cols=70  Identities=20%  Similarity=0.431  Sum_probs=61.4

Q ss_pred             CCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCCC
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTK  169 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~~  169 (195)
                      .++|.+|+++|...+.|.++|+.||..||+|..|+++|.+..| .+||++||+.||.++|+++|..+...+
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~~C~~C~~~I   75 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGI   75 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCE-ESSSCEECHHHHHHHHSCBCTTTCCBC
T ss_pred             CCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCc-ccCCeeeeccccccccccccccccccc
Confidence            3799999999997667889999999999999999999998764 789999999999999999998444433

>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=99.46  E-value=2.9e-14  Score=109.80  Aligned_cols=68  Identities=18%  Similarity=0.417  Sum_probs=61.1

Q ss_pred             CcCccCCceeecCceEEECCceecccccccccCCccccc--CCeeccCCccccHHHHHhhhcC--CCccCCC
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTT--SSYAALDGILYCKSHFAQLFKE--KGCYNHL  167 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~--~~~~~~dg~~yC~~c~~~~f~~--k~~~~~~  167 (195)
                      ++|..|+++|...+.|.++++.||+.||+|..|+++|..  ..|+.+||++||+.||.++|++  +|..+..
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~   77 (188)
T 1rut_X            6 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQ   77 (188)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCC
T ss_pred             CcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCC
Confidence            799999999996656899999999999999999999985  5799999999999999999999  6874443

>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=99.43  E-value=5e-14  Score=93.94  Aligned_cols=60  Identities=25%  Similarity=0.526  Sum_probs=52.4

Q ss_pred             CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCC-eecchhhHHHhhc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEG-VLYCKPHFEQLFK   67 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g-~~yC~~c~~~~~~   67 (195)
                      .++|..|+++|. +++|.++++.||++||+|..|+++|..+.++..++ .+||..||.+++.
T Consensus        15 ~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           15 GTRCFSCDQFIE-GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCBCTTTCCBCC-SCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             CCcCccccCEec-cceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            469999999998 78999999999999999999999998776665555 5799999987765

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

Probab=98.37  E-value=9.4e-08  Score=51.59  Aligned_cols=29  Identities=31%  Similarity=0.594  Sum_probs=27.3

Q ss_pred             CCcccccccccccCceEeeCCcccccCcc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .+.|..|++.|+..|.+.++|+.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEEECCeEecccCC
Confidence            46899999999999999999999999998

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

Probab=98.33  E-value=1e-07  Score=51.44  Aligned_cols=28  Identities=46%  Similarity=0.961  Sum_probs=27.0

Q ss_pred             CcCccCCceeecCceEEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ++|++|++.|++.|.+.+.|+.||+.||
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            7999999999999999999999999998

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=90.62  E-value=0.39  Score=33.22  Aligned_cols=44  Identities=20%  Similarity=0.441  Sum_probs=28.2

Q ss_pred             CCCCcccccccccccC----c--eEeeCCcccccCcc--------ccccccccCCCCc
Q 041875            5 GTQEKCKACDKTVHII----D--MVTADGISYHKICF--------KCSHCNGKLVMGN   48 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~----~--~i~~~g~~~H~~CF--------~C~~C~~~L~~~~   48 (195)
                      .....|..|...+...    +  ++..=|..||..|+        +|-.|++.+....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            3455788887776422    1  44455677777776        6778888776543

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=88.88  E-value=0.73  Score=28.88  Aligned_cols=50  Identities=12%  Similarity=0.256  Sum_probs=37.9

Q ss_pred             CccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecC
Q 041875           33 ICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPL  112 (195)
Q Consensus        33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~  112 (195)
                      +=|.|..|...+.. .....-|..||..|..+.+..+                             ...|+.|++++...
T Consensus         7 ~~~~C~IC~~~~~~-Pv~~~CgH~fc~~Ci~~~~~~~-----------------------------~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            7 EYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLDAG-----------------------------HKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHTTT-----------------------------CCBCTTTCCBCSSC
T ss_pred             ccCCCCCccccccC-CEEcCCCCeecHHHHHHHHHHC-----------------------------cCCCCCCcCCCChh
Confidence            45889999888864 4555789999999998877521                             26899999988743

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=88.41  E-value=0.42  Score=33.02  Aligned_cols=93  Identities=14%  Similarity=0.290  Sum_probs=61.5

Q ss_pred             ccccccccccCCCC------ceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCc
Q 041875           34 CFKCSHCNGKLVMG------NFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKK  107 (195)
Q Consensus        34 CF~C~~C~~~L~~~------~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~  107 (195)
                      =+.|..|...+...      .....=|..||..|..+.+..+                              ..|+.|.+
T Consensus         7 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~------------------------------~~CP~Cr~   56 (133)
T 4ap4_A            7 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA------------------------------NTCPTCRK   56 (133)
T ss_dssp             SCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTC------------------------------SBCTTTCC
T ss_pred             CCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhC------------------------------CCCCCCCC
Confidence            37888898776432      1444558899999998876522                              68999999


Q ss_pred             eeecCceEEECCceecccccccccCCcccccC----C--eeccCCccccHHHHHhhhc
Q 041875          108 TVYPLEKVTVEGESFHKTCFRCSHGGCLLTTS----S--YAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       108 ~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~----~--~~~~dg~~yC~~c~~~~f~  159 (195)
                      .+...+....   ..-..=+.|..|...+...    .  ....=|..||..|..+.+.
T Consensus        57 ~~~~~~l~~l---~i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~  111 (133)
T 4ap4_A           57 KINHKRYHPI---YIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK  111 (133)
T ss_dssp             BCTTTCEEEC---BCSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHH
T ss_pred             cCcccccccc---ccCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHH
Confidence            9975444321   1123446788888877531    1  2233589999999876554

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=86.93  E-value=0.55  Score=29.09  Aligned_cols=51  Identities=22%  Similarity=0.429  Sum_probs=36.3

Q ss_pred             ccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCc
Q 041875           34 CFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLE  113 (195)
Q Consensus        34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~  113 (195)
                      =+.|..|...+........=|..||..|..+.+...                              ..|+.|.+.|...+
T Consensus        15 ~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~------------------------------~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           15 YILCSICKGYLIDATTITECLHTFCKSCIVRHFYYS------------------------------NRCPKCNIVVHQTQ   64 (72)
T ss_dssp             GGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHC------------------------------SSCTTTCCCCCSSC
T ss_pred             CCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcC------------------------------CcCCCcCcccCccc
Confidence            478888888877532223568899999998776421                              68999999887543


Q ss_pred             e
Q 041875          114 K  114 (195)
Q Consensus       114 ~  114 (195)
                      .
T Consensus        65 ~   65 (72)
T 2djb_A           65 P   65 (72)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=85.71  E-value=1.7  Score=29.43  Aligned_cols=95  Identities=17%  Similarity=0.377  Sum_probs=55.1

Q ss_pred             CCCcccccccccccCceEe--eCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCC
Q 041875            6 TQEKCKACDKTVHIIDMVT--ADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNG   83 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~--~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~   83 (195)
                      ....|..|+..-...+.|.  .=++.||..|+.=..     ..    +..+..+|..|                      
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~-----~~----~~~~~W~C~~C----------------------   54 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV-----TP----LKRAGWQCPEC----------------------   54 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCC-----CT----TTSTTCCCTTT----------------------
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCcc-----cc----ccccCccCCcC----------------------
Confidence            4467899977632122233  335788988875321     10    13456667665                      


Q ss_pred             CCCCCCCCccccCCCCCcCccCCceeecCceEE--ECCceecccccccccCCcccccCCeeccCCccccHHHHHh
Q 041875           84 LTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVT--VEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus        84 ~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~--~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                                      ..|..|++.-....++.  .=++.||..|+.-     +|..    .-.|.-||..|...
T Consensus        55 ----------------~~C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~p-----pl~~----~P~g~W~C~~C~~c  104 (111)
T 2ysm_A           55 ----------------KVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQP-----VMKS----VPTNGWKCKNCRIC  104 (111)
T ss_dssp             ----------------CCCTTTCCCSCCTTEEECSSSCCEEEGGGSSS-----CCSS----CCSSCCCCHHHHCC
T ss_pred             ----------------CcccccCccCCCCCeeECCCCCcHHhHHhcCC-----cccc----CCCCCcCCcCCcCc
Confidence                            35788887655334443  3467899988753     2321    12367789888654

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.66  E-value=0.35  Score=30.76  Aligned_cols=33  Identities=18%  Similarity=0.361  Sum_probs=24.2

Q ss_pred             cCCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            3 FCGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      |......|..|...|..+.....=+..||..|+
T Consensus        11 y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci   43 (74)
T 2ct0_A           11 YPDAVKICNICHSLLIQGQSCETCGIRMHLPCV   43 (74)
T ss_dssp             CSSSSCBCSSSCCBCSSSEECSSSCCEECHHHH
T ss_pred             ccCCCCcCcchhhHcccCCccCCCCchhhHHHH
Confidence            566778999999999866544444556777776

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=83.12  E-value=1.9  Score=28.75  Aligned_cols=51  Identities=6%  Similarity=-0.065  Sum_probs=39.6

Q ss_pred             cCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeec
Q 041875           32 KICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYP  111 (195)
Q Consensus        32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~  111 (195)
                      ++-|.|..|...+.+ ......|..||..|..+.+..                              ...|+.|++++..
T Consensus        27 p~~~~CpI~~~~m~d-PV~~~cGhtf~r~~I~~~l~~------------------------------~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD-PVRLPSGTIMDRSIILRHLLN------------------------------SPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCSS-EEEETTTEEEEHHHHHHHTTS------------------------------CSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCcccC-CeECCCCCEEchHHHHHHHHc------------------------------CCCCCCCCCCCCh
Confidence            667999999988875 555668999999999877641                              1689999998874


Q ss_pred             Cc
Q 041875          112 LE  113 (195)
Q Consensus       112 ~~  113 (195)
                      .+
T Consensus        76 ~~   77 (100)
T 2kre_A           76 SM   77 (100)
T ss_dssp             TS
T ss_pred             hh
Confidence            43

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=82.33  E-value=1.3  Score=29.07  Aligned_cols=33  Identities=12%  Similarity=0.331  Sum_probs=24.7

Q ss_pred             ccccccccccCCCCceee-cCCeecchhhHHHhhc
Q 041875           34 CFKCSHCNGKLVMGNFSS-MEGVLYCKPHFEQLFK   67 (195)
Q Consensus        34 CF~C~~C~~~L~~~~~~~-~~g~~yC~~c~~~~~~   67 (195)
                      =+.|..|...+.. .... .=|..||..|..+.+.
T Consensus        22 ~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~   55 (99)
T 2y43_A           22 LLRCGICFEYFNI-AMIIPQCSHNYCSLCIRKFLS   55 (99)
T ss_dssp             HTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHHT
T ss_pred             CCCcccCChhhCC-cCEECCCCCHhhHHHHHHHHH
Confidence            4788899888765 3333 5688999999988765

>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1

Probab=82.02  E-value=0.86  Score=27.22  Aligned_cols=29  Identities=21%  Similarity=0.450  Sum_probs=23.1

Q ss_pred             ccccCCcccccCCeeccCCcccc-HHHHHh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYC-KSHFAQ  156 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC-~~c~~~  156 (195)
                      .|..|+..++...-+.+||+.|| +.|...
T Consensus         9 aC~~C~c~Vs~~eai~~dGK~YCSe~Ca~g   38 (55)
T 1jjd_A            9 ACEPCLCNVDPSKAIDRNGLYYCSEACADG   38 (55)
T ss_dssp             SSTTCCCCBCTTTSEESSSCEESSHHHHHT
T ss_pred             cCCCCeeEechHHhhhcCCeEEehHHHHcc
Confidence            46778888887778888999998 777654

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=81.62  E-value=1.6  Score=28.08  Aligned_cols=35  Identities=6%  Similarity=-0.056  Sum_probs=28.0

Q ss_pred             cCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           32 KICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ++=|.|..|...+.+ ......|..||..|..+.+.
T Consensus        12 p~~~~CpI~~~~m~d-PV~~~cGhtf~r~~I~~~l~   46 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD-PVRLPSGTVMDRSIILRHLL   46 (85)
T ss_dssp             CTTTBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHH
T ss_pred             chheECcccCchhcC-CeECCCCCEECHHHHHHHHh
Confidence            456999999988875 55556899999999887764

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.58  E-value=1.3  Score=26.68  Aligned_cols=49  Identities=22%  Similarity=0.533  Sum_probs=34.9

Q ss_pred             ccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecC
Q 041875           34 CFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPL  112 (195)
Q Consensus        34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~  112 (195)
                      =+.|..|...+... ....=|..||..|..+.+..                             ....|+.|.+.|...
T Consensus        15 ~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~-----------------------------~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           15 KYKCEKCHLVLCSP-KQTECGHRFCESCMAALLSS-----------------------------SSPKCTACQESIVKD   63 (66)
T ss_dssp             CEECTTTCCEESSC-CCCSSSCCCCHHHHHHHHTT-----------------------------SSCCCTTTCCCCCTT
T ss_pred             CCCCCCCChHhcCe-eECCCCCHHHHHHHHHHHHh-----------------------------CcCCCCCCCcCCChh
Confidence            37788888877643 23456888999999887631                             116899999988743

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=80.74  E-value=2.2  Score=28.29  Aligned_cols=35  Identities=6%  Similarity=-0.166  Sum_probs=27.9

Q ss_pred             cCccccccccccCCCCceeecCC-eecchhhHHHhhc
Q 041875           32 KICFKCSHCNGKLVMGNFSSMEG-VLYCKPHFEQLFK   67 (195)
Q Consensus        32 ~~CF~C~~C~~~L~~~~~~~~~g-~~yC~~c~~~~~~   67 (195)
                      ++=|.|..|...+.+ ......| ..||..|..+.+.
T Consensus        20 p~~~~CpI~~~~m~d-PV~~~cG~htf~r~cI~~~l~   55 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD-PVVLPSSRVTVDRSTIARHLL   55 (98)
T ss_dssp             CTTTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHTT
T ss_pred             cHhcCCcCccccccC-CeECCCCCeEECHHHHHHHHH
Confidence            567999999988875 5555677 9999999988764

---

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	195
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	4e-14
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	2e-12
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	6e-11
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	5e-07
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	4e-10
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	6e-08
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	2e-09
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	2e-07
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	5e-05
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	2e-04
d1a7ia1	28	g.39.1.3 (A:8-35) Cysteine-rich (intestinal) prote	0.001
d1zfoa_	30	g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 982	0.001
d1ibia1	28	g.39.1.3 (A:117-144) Cysteine-rich (intestinal) pr	0.001

>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 = 61.2 bits (149), Expect = 4e-14
 Identities = 20/39 (51%), Positives = 29/39 (74%)

Query: 36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTN 74
          +CS+CN KL +G ++S+ G +YCKPHF QLFK  G++  
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 = 57.0 bits (138), Expect = 2e-12
 Identities = 20/38 (52%), Positives = 26/38 (68%)

Query: 128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN 165
           RCS+    L+  +YA+L G +YCK HF QLFK KG Y+
Sbjct: 1   RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 38

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 43

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

 Score = 53.3 bits (128), Expect = 6e-11
 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 87  TPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCF 127
             S+ +    G  D C  C + VY  EKV   G+S+HK+CF
Sbjct: 4   NASRMAQKV-GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 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 = 42.5 bits (100), Expect = 5e-07
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 5  GTQEKCKACDKTVHIIDMVTADGISYHKICF 35
          G  + C  C + V+  + V   G S+HK CF
Sbjct: 13 GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (122), Expect = 4e-10
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCF 127
           G  D C  C + +Y LE++ V G  FH++CF
Sbjct: 6   GAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (107), Expect = 6e-08
 Identities = 7/31 (22%), Positives = 18/31 (58%)

Query: 5  GTQEKCKACDKTVHIIDMVTADGISYHKICF 35
          G  + C  C + +++++ +  +G  +H+ CF
Sbjct: 6  GAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (118), Expect = 2e-09
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCF 127
             ++ C  C+KTVYP+E++    + FH +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 = 44.0 bits (104), Expect = 2e-07
 Identities = 10/31 (32%), Positives = 17/31 (54%)

Query: 5  GTQEKCKACDKTVHIIDMVTADGISYHKICF 35
            +E C  C KTV+ ++ + A+   +H  CF
Sbjct: 5  PARETCVECQKTVYPMERLLANQQVFHISCF 35

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 35

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

 Score = 36.8 bits (85), Expect = 5e-05
 Identities = 17/31 (54%), Positives = 20/31 (64%)

Query: 97  GTQDKCTSCKKTVYPLEKVTVEGESFHKTCF 127
           G   KC  C+K VY  E+V  EG SFHK+CF
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 35

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]} Length = 30

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

 Score = 35.2 bits (81), Expect = 2e-04
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTC 126
           KC  C KTVY  EKV+  G+ +HK C
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFC 29

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]} Length = 28

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

 Score = 33.4 bits (76), Expect = 0.001
 Identities = 14/28 (50%), Positives = 20/28 (71%)

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTCF 127
           +KC +C +TVY  E+V  +G SFH+ 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 = 33.3 bits (76), Expect = 0.001
 Identities = 13/27 (48%), Positives = 15/27 (55%)

Query: 101 KCTSCKKTVYPLEKVTVEGESFHKTCF 127
            C  C K VYP EKV    + +HK CF
Sbjct: 4   NCARCGKIVYPTEKVNCLDKFWHKACF 30

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]} Length = 28

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

 Score = 33.4 bits (76), Expect = 0.001
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 100 DKCTSCKKTVYPLEKVTVEGESFHKTC 126
           +KC+ C  +VY  EKV   G+ +HK C
Sbjct: 2   EKCSRCGDSVYAAEKVIGAGKPWHKNC 28

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	195
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	99.15
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	99.08
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	99.01
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.97
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.89
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.88
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.86
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.82
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.74
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.73
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.73
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.73
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.64
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.63
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.61
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.61
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.57
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.56
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.52
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.52
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.51
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.51
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.49
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.49
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.49
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.46
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.46
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.46
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.45
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.44
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.44
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.42
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.38
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.38
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.38
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.35
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.34
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.33
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.32
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.31
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.28
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.23
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.22
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.21
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.21
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.21
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.19
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.19
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.17
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.08
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.04
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.03
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.03
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.03
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.01
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.0
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.99
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.99
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.98
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.96
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.95
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.9
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.89
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.88
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.86
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.86
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.85
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.85
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.84
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.84
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.83
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.82
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.82
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.77
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.76
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.74
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.73
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.72
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.72
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.71
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.71
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.68
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.66
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.59
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.55
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.54
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.51
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.44
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.44
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.42
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.42
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.35
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.34
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.21
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.13
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.05
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.99
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.92
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.88
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.83
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.82
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.78
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.74
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.47
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.46
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.46
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.41
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.19
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.18
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.06
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	95.84
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.77
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.66
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.47
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.4
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.2
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	94.65
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	94.63
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	94.47
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.37
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.32
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.1
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	93.65
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	92.58
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	92.56
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	92.25
d2co8a1	33	Nedd9 interacting protein with calponin homology,	91.19
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	90.8
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	90.57
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	90.12
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	89.6
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	89.26
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	88.28
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	87.77
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	85.91
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	85.79
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	85.26
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	84.75
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	84.73
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	83.12
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	81.12
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	80.89

>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=99.15  E-value=1.5e-11  Score=68.93  Aligned_cols=41  Identities=49%  Similarity=0.845  Sum_probs=39.0

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCC
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLT  168 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~  168 (195)
                      +|..|++.|+.++|...+|.+||+.||.++|++||.|++.+
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            69999999999999999999999999999999999998875

>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=99.08  E-value=5e-11  Score=68.94  Aligned_cols=42  Identities=33%  Similarity=0.645  Sum_probs=37.8

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCCCC
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLTK  169 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~~  169 (195)
                      +|..|++.|++....++||+|||+.||.++|||||. |+-...
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            689999999999999999999999999999999998 775443

>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=99.01  E-value=5.8e-11  Score=64.41  Aligned_cols=34  Identities=24%  Similarity=0.532  Sum_probs=32.8

Q ss_pred             cccccCCcccccCCeeccCCccccHHHHHhhhcC
Q 041875          127 FRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE  160 (195)
Q Consensus       127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~  160 (195)
                      |+|..|+++|.++.|+++||+|||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7899999999999999999999999999999997

>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=98.97  E-value=1.5e-10  Score=66.15  Aligned_cols=39  Identities=28%  Similarity=0.572  Sum_probs=36.0

Q ss_pred             ccccCCcccccCCeeccCCcccc-HHHHHhhhcCCCc-cCC
Q 041875          128 RCSHGGCLLTTSSYAALDGILYC-KSHFAQLFKEKGC-YNH  166 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC-~~c~~~~f~~k~~-~~~  166 (195)
                      +|..|++.|+++...++||+||| +.||..+|||||. ++.
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~g~Gg   41 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGG   41 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCC
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCccccCC
Confidence            68999999999999999999999 7899999999997 654

>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=98.89  E-value=1.4e-10  Score=63.00  Aligned_cols=27  Identities=26%  Similarity=0.687  Sum_probs=25.9

Q ss_pred             CcCccCCceeecCceEEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ++|..|+++|. ++.|+++|+.||++||
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            99999999998 7899999999999998

>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=98.88  E-value=5.7e-10  Score=68.05  Aligned_cols=43  Identities=23%  Similarity=0.302  Sum_probs=38.4

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCCCCc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLTKT  170 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~  170 (195)
                      .|..|++.|++....+++++|||+.||.++|||||. |+.....
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~G~gag~   44 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGT   44 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccccccccce
Confidence            388999999999999999999999999999999998 7765444

>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=98.86  E-value=3.6e-10  Score=61.23  Aligned_cols=33  Identities=36%  Similarity=0.817  Sum_probs=31.9

Q ss_pred             cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |+|..|+++|.+..|++++|++||+.||.++|+
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFA   33 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   33 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcC
Confidence            799999999999999999999999999999997

>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=98.82  E-value=9.8e-10  Score=59.54  Aligned_cols=30  Identities=27%  Similarity=0.577  Sum_probs=27.7

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCcc
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      -..++|..|+++|. +++|.|+|+.||++||
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            34689999999998 8999999999999998

>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=98.74  E-value=3e-09  Score=56.45  Aligned_cols=33  Identities=33%  Similarity=0.732  Sum_probs=30.8

Q ss_pred             CcCCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            2 AFCGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         2 ~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .|..+.++|..|+++|. ..+|.|.|+.||+.||
T Consensus         3 Cy~~tlEkC~~C~~~I~-driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           3 CYVATLEKCATCSQPIL-DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCSSCCBCTTTCCBCC-SCCEEETTEEECTTTC
T ss_pred             hHHHHHHHHHHhchHHH-HHHHHHhCCCCCCCCC
Confidence            47888999999999998 7899999999999998

>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=98.73  E-value=2.9e-09  Score=59.44  Aligned_cols=41  Identities=49%  Similarity=1.142  Sum_probs=37.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhccCCccccCC
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKL   76 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~   76 (195)
                      +|..|++.|..++|...+|.+||+.||.++|.++|.++..|
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

>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=98.73  E-value=3.5e-09  Score=61.04  Aligned_cols=35  Identities=26%  Similarity=0.711  Sum_probs=32.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhccCC
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETG   70 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~   70 (195)
                      +|..|++.|++....++|+++||+.||.++|+|++
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            68999999999999999999999999999999664

>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=98.73  E-value=5.4e-09  Score=59.07  Aligned_cols=40  Identities=40%  Similarity=0.831  Sum_probs=32.9

Q ss_pred             CCCCCccccCCCCCcCccCCceeecCceEEECCceeccccc
Q 041875           87 TPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        87 ~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      .|.++...+ ++.++|.+|++.+++.|.+.+.|+.||+.||
T Consensus         4 ~~sk~~~~~-g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3           4 NASRMAQKV-GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCCCC-CCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             Ccccccccc-CCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            344444333 4569999999999999999999999999998

>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=98.64  E-value=7.3e-09  Score=58.17  Aligned_cols=30  Identities=23%  Similarity=0.446  Sum_probs=27.5

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCcc
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      ...++|..|+++|. +.+|.|+|+.||++||
T Consensus        16 ~r~P~C~~C~~pI~-g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          16 KRTPMCAHCNQVIR-GPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TCCCBBSSSCCBCC-SCEEEETTEEECTTTC
T ss_pred             CCCeeccccCCccc-CceeeecCCccCcCCC
Confidence            34589999999997 9999999999999998

>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=98.63  E-value=9.2e-09  Score=53.45  Aligned_cols=32  Identities=25%  Similarity=0.538  Sum_probs=30.1

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      .|..|.++|.+.+|+.+|++|||-.||..+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            47889999999999999999999999999986

>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=98.61  E-value=3.2e-09  Score=56.08  Aligned_cols=27  Identities=30%  Similarity=0.749  Sum_probs=25.4

Q ss_pred             CcCccCCceeecCceEEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ++|..|+++|. ...|++.++.||++||
T Consensus         9 ~~C~~Ckk~It-~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           9 PRCARCSKTLT-QGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCTTTCCCCC-SCCEESSSSEECTTTC
T ss_pred             HHHhhcCCccc-cCceeecCCcchhhhC
Confidence            89999999998 5689999999999998

>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=98.61  E-value=8.3e-09  Score=52.81  Aligned_cols=31  Identities=32%  Similarity=0.758  Sum_probs=28.5

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      +|..|++.|.+ .|..+||.|||+.+|+.+||
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            58899999988 49999999999999999997

>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=98.57  E-value=1.6e-08  Score=52.46  Aligned_cols=34  Identities=26%  Similarity=0.586  Sum_probs=32.3

Q ss_pred             cccccCCcccccCCeeccCCccccHHHHHhhhcC
Q 041875          127 FRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKE  160 (195)
Q Consensus       127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~  160 (195)
                      |+|+.|.+++-+...+++.|..||+.+|.++||.
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            7899999999999999999999999999999984

>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=98.56  E-value=2.1e-08  Score=57.00  Aligned_cols=35  Identities=34%  Similarity=0.841  Sum_probs=32.9

Q ss_pred             ccccccccCCCCceeecCCeecc-hhhHHHhhccCC
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYC-KPHFEQLFKETG   70 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC-~~c~~~~~~~~~   70 (195)
                      +|..|++.|+++...++++++|| +.||..+|+|+|
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG   36 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKG   36 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCC
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCc
Confidence            68999999999999999999999 789999999876

>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=98.52  E-value=2e-08  Score=50.39  Aligned_cols=30  Identities=33%  Similarity=0.794  Sum_probs=28.4

Q ss_pred             cccccCCcccccCCeeccCCccccHHHHHh
Q 041875          127 FRCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      |+|..|++.|.+.....+||.+||+.||.+
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            799999999999999999999999999975

>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=98.51  E-value=2e-08  Score=54.10  Aligned_cols=32  Identities=22%  Similarity=0.749  Sum_probs=30.5

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      +++..+|..|++.|++.|.+.++|+.||+.||
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            57789999999999999999999999999998

>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=98.51  E-value=2.9e-08  Score=53.24  Aligned_cols=32  Identities=31%  Similarity=0.642  Sum_probs=30.2

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      ++.+.+|..|++.|+..|.+.++|+.||..||
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            56778999999999999999999999999998

>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=98.49  E-value=3.7e-08  Score=51.38  Aligned_cols=32  Identities=25%  Similarity=0.451  Sum_probs=29.4

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      +|..|.+++.++.|++.||+|||+.||+++-|
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            48899999999999999999999999998754

>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=98.49  E-value=3.8e-08  Score=50.39  Aligned_cols=32  Identities=25%  Similarity=0.494  Sum_probs=30.2

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      .|..|+++|.+..|+.+|..|||-.||..+|+
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            48899999999999999999999999999985

>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=98.49  E-value=2.7e-08  Score=51.30  Aligned_cols=32  Identities=31%  Similarity=0.580  Sum_probs=29.6

Q ss_pred             ccccCCcccccCCeeccCCccccH-HHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCK-SHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~-~c~~~~f~  159 (195)
                      +|..|++.|..+...++||+|||. +||..+||
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            689999999999999999999995 59999986

>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=98.46  E-value=3.1e-08  Score=55.85  Aligned_cols=32  Identities=34%  Similarity=0.749  Sum_probs=29.6

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .++.+.|..|++.|+..|.+.++|+.||+.||
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            35668999999999999999999999999998

>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=98.46  E-value=1.6e-08  Score=54.95  Aligned_cols=28  Identities=36%  Similarity=0.819  Sum_probs=25.8

Q ss_pred             CcCccCCceeecCce-EEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEK-VTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~-v~~~~~~~H~~CF  127 (195)
                      ++|..|+++|.++.. |.+.|+.||..||
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            899999999998665 7999999999998

>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=98.46  E-value=5.1e-08  Score=49.77  Aligned_cols=28  Identities=50%  Similarity=0.947  Sum_probs=26.8

Q ss_pred             CcCccCCceeecCceEEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ++|++|++++++.|.+..+|+.||+.|+
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            7999999999999999999999999985

>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=98.45  E-value=5e-08  Score=50.59  Aligned_cols=32  Identities=25%  Similarity=0.622  Sum_probs=29.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .|..|.++|.++.|..+|++|||-.||..+|+
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            48899999999999999999999999998874

>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=98.44  E-value=3.4e-08  Score=53.14  Aligned_cols=32  Identities=41%  Similarity=0.980  Sum_probs=29.7

Q ss_pred             CCCCCcCccCCceeecCceEEECCceeccccc
Q 041875           96 CGTQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        96 ~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      .|+..+|..|++.+++.|.+.+.|+.||+.||
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            35668999999999999999999999999998

>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=98.44  E-value=4.9e-08  Score=49.82  Aligned_cols=29  Identities=41%  Similarity=0.840  Sum_probs=27.1

Q ss_pred             CCcccccccccccCceEeeCCcccccCcc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .+.|.+|+++|+..|.+..+|+.||+.|+
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            36899999999999999999999999996

>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=98.42  E-value=4.4e-08  Score=49.09  Aligned_cols=30  Identities=30%  Similarity=0.816  Sum_probs=28.4

Q ss_pred             cccccccccCCCCceeecCCeecchhhHHH
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQ   64 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~   64 (195)
                      |+|..|++.|.+.....+||++||+.||.+
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            899999999999999999999999999974

>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=98.38  E-value=1.1e-07  Score=57.76  Aligned_cols=35  Identities=20%  Similarity=0.493  Sum_probs=33.2

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhccCC
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETG   70 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~   70 (195)
                      .|..|++.|+++....+++++||+.||.++|+|+|
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG   35 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKG   35 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCc
Confidence            48899999999999999999999999999999886

>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=98.38  E-value=1.1e-07  Score=50.96  Aligned_cols=29  Identities=41%  Similarity=1.087  Sum_probs=27.8

Q ss_pred             CCcCccCCceeecCceEEECCceeccccc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ..+|..|++.+++.|.+.+.|+.||+.||
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

>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=98.38  E-value=5.1e-08  Score=49.99  Aligned_cols=28  Identities=25%  Similarity=0.409  Sum_probs=25.5

Q ss_pred             CCCcccccccccccCceEeeCCcccccCc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKIC   34 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~C   34 (195)
                      +.++|+.|.+||. +.+|.++|+.||++.
T Consensus         4 g~p~C~~C~~PI~-~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           4 GVPICGACRRPIE-GRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCEETTTTEECC-SCEECCTTSBEETTT
T ss_pred             CCcchhhcCCchh-hhHhhhhccccCCCC
Confidence            5689999999998 899999999999974

>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=98.35  E-value=1.6e-07  Score=48.06  Aligned_cols=32  Identities=31%  Similarity=0.641  Sum_probs=29.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .|..|+++|.++.|..+|.++||..||.++|+
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            48999999999999999999999999998874

>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=98.34  E-value=1.7e-07  Score=49.58  Aligned_cols=29  Identities=28%  Similarity=0.776  Sum_probs=25.9

Q ss_pred             CCCcCccCCceeecCceEEECCceeccccc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      +..+|.+|+++|. +..+.+.|+.||+.||
T Consensus         7 tlEkC~~C~~~I~-driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           7 TLEKCATCSQPIL-DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             SCCBCTTTCCBCC-SCCEEETTEEECTTTC
T ss_pred             HHHHHHHhchHHH-HHHHHHhCCCCCCCCC
Confidence            4589999999998 5677999999999998

>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=98.33  E-value=1.6e-07  Score=49.33  Aligned_cols=31  Identities=19%  Similarity=0.452  Sum_probs=28.6

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCcc
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .+...|++|++.|..+..+.++++.||..||
T Consensus         6 ~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           6 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cCCccccccchhhhCCceeeeeecceeeeeC
Confidence            4567899999999999999999999999998

>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=98.32  E-value=6.9e-08  Score=48.59  Aligned_cols=28  Identities=32%  Similarity=0.606  Sum_probs=26.8

Q ss_pred             CcccccccccccCceEeeCCcccccCcc
Q 041875            8 EKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      +.|++|++.|++.|.|...++.||+.||
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            6799999999999999999999999998

>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=98.31  E-value=5.7e-08  Score=48.89  Aligned_cols=28  Identities=46%  Similarity=0.961  Sum_probs=27.0

Q ss_pred             CcCccCCceeecCceEEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      +.|++|++.+++.|.+.-+++.||+.||
T Consensus         3 ~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcccccCCccccHHHhhhhHHHHhhccC
Confidence            6899999999999999999999999998

>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=98.28  E-value=2.6e-07  Score=51.72  Aligned_cols=28  Identities=21%  Similarity=0.462  Sum_probs=26.1

Q ss_pred             CCcCccCCceeecCceEEECCceeccccc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      .++|..|+++|. +..|+++|+.||+++|
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            489999999998 8889999999999998

>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=98.23  E-value=3.1e-07  Score=47.03  Aligned_cols=29  Identities=17%  Similarity=0.401  Sum_probs=26.1

Q ss_pred             CCcccccccccccCceEeeCCcccccCcc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      ...|++|+++|.+..++.++++.||..|+
T Consensus         2 ~~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           2 WKRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             ccccCCCCCccchhhhhccchhhhhhhhC
Confidence            46899999999977789999999999995

>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=98.22  E-value=4.2e-07  Score=46.76  Aligned_cols=32  Identities=31%  Similarity=0.825  Sum_probs=29.0

Q ss_pred             ccccccccCCCCceeecCCeecch-hhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCK-PHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~-~c~~~~~~   67 (195)
                      +|..|++.|..+...+++|++||. .||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            689999999999999999999995 69998874

>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=98.21  E-value=5.2e-07  Score=47.28  Aligned_cols=30  Identities=20%  Similarity=0.585  Sum_probs=27.9

Q ss_pred             CCCcCccCCceeecCceEEECCceeccccc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ++..|++|++.|..++.+.++++.||.+||
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            447899999999999999999999999998

>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=98.21  E-value=2.6e-07  Score=46.90  Aligned_cols=31  Identities=26%  Similarity=0.464  Sum_probs=29.0

Q ss_pred             cccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      |-.|.+.|++.....+++.+||+.||.++||
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            7789999999999999999999999999886

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.21  E-value=4.3e-07  Score=47.23  Aligned_cols=31  Identities=23%  Similarity=0.655  Sum_probs=28.5

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhh
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF   66 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~   66 (195)
                      +|..|.+++.++.|++.+|+|||+.+|.++-
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            5899999999999999999999999998763

>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=98.19  E-value=3.1e-07  Score=49.70  Aligned_cols=30  Identities=40%  Similarity=0.687  Sum_probs=26.9

Q ss_pred             CCCcccccccccccCc-eEeeCCcccccCcc
Q 041875            6 TQEKCKACDKTVHIID-MVTADGISYHKICF   35 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~-~i~~~g~~~H~~CF   35 (195)
                      .+++|..|+++|.++. .|.+.|+.||..||
T Consensus         7 ~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           7 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             cCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            3589999999999765 69999999999998

>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=98.19  E-value=5e-07  Score=46.06  Aligned_cols=29  Identities=17%  Similarity=0.376  Sum_probs=26.0

Q ss_pred             CCCcccccccccccCceEeeCCcccccCc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKIC   34 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~C   34 (195)
                      ....|++|+++|.+...+.++++.||..|
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            45789999999997778999999999987

>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=98.17  E-value=5.8e-07  Score=45.80  Aligned_cols=31  Identities=35%  Similarity=0.844  Sum_probs=27.7

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      +|..|++.|. +.|..+||.|||+.||+..|+
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            5899999998 488899999999999998874

>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=98.08  E-value=7.2e-07  Score=43.99  Aligned_cols=27  Identities=44%  Similarity=0.995  Sum_probs=25.5

Q ss_pred             CcCccCCceeecCceEEECCceecccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTC  126 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~C  126 (195)
                      .+|++|++.++..|.|.-.|+.||+.|
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            689999999999999999999999987

>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=98.04  E-value=1.5e-06  Score=44.53  Aligned_cols=31  Identities=16%  Similarity=0.344  Sum_probs=29.4

Q ss_pred             cccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      |..|+.+|...+|..+++..||-.||.++|+
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCCceEeecchhhcC
Confidence            7889999999999999999999999999986

>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=98.03  E-value=1.6e-06  Score=44.41  Aligned_cols=31  Identities=32%  Similarity=0.892  Sum_probs=28.7

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhh
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF   66 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~   66 (195)
                      .|+.|+.+|.+..|++.+|++||+.||++.|
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHT
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhc
Confidence            3889999999999999999999999999765

>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=98.03  E-value=1.1e-06  Score=48.27  Aligned_cols=26  Identities=31%  Similarity=0.729  Sum_probs=24.6

Q ss_pred             CcCccCCceeecCceEEECCceecccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTC  126 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~C  126 (195)
                      .+|..|.+.|. ++.|.+.++.||+.|
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            89999999997 889999999999987

>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=98.01  E-value=1.8e-06  Score=44.20  Aligned_cols=31  Identities=26%  Similarity=0.475  Sum_probs=29.4

Q ss_pred             cccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      |..|+.+|...+|..+++..||-+||.++|+
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCcEEEEeccccccC
Confidence            7889999999999999999999999999986

>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=98.00  E-value=2e-06  Score=44.01  Aligned_cols=31  Identities=23%  Similarity=0.619  Sum_probs=28.9

Q ss_pred             cccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      |+.|.++|....|++..|++||+.||.+.|+
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            7889999999899999999999999999875

>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=97.99  E-value=1.3e-06  Score=44.28  Aligned_cols=31  Identities=19%  Similarity=0.530  Sum_probs=28.5

Q ss_pred             cccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           37 CSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |..|++.|++....++++++||+.||.+.++
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7889999999999999999999999998763

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

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

Probab=97.99  E-value=2.3e-06  Score=44.22  Aligned_cols=33  Identities=30%  Similarity=0.793  Sum_probs=31.3

Q ss_pred             cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |+|..|.+++-+...+++.|..||+.+|.++|+
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

>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=97.98  E-value=1.8e-06  Score=44.41  Aligned_cols=35  Identities=40%  Similarity=0.788  Sum_probs=30.8

Q ss_pred             CCcCCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      |---++...|..|.+.|+..+.|..+|++||+.||
T Consensus         1 mpn~ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCccCCCceeccccceEeeeeeeeecCcccccccC
Confidence            33346678999999999999999999999999998

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.95  E-value=1.2e-06  Score=44.74  Aligned_cols=27  Identities=19%  Similarity=0.438  Sum_probs=24.0

Q ss_pred             CCcCccCCceeecCceEEECCceecccc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTC  126 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~C  126 (195)
                      +++|+.|.+||. +..|.++|+.||++.
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 678899999999863

>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=97.90  E-value=2.3e-06  Score=42.65  Aligned_cols=26  Identities=19%  Similarity=0.637  Sum_probs=23.1

Q ss_pred             cccccccccc---CceEeeCCcccccCcc
Q 041875           10 CKACDKTVHI---IDMVTADGISYHKICF   35 (195)
Q Consensus        10 C~~C~~~I~~---~~~i~~~g~~~H~~CF   35 (195)
                      |..|.+||..   +.+|+..++.||.+||
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            7899999975   3589999999999998

>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=97.88  E-value=3.6e-06  Score=41.04  Aligned_cols=28  Identities=46%  Similarity=0.937  Sum_probs=26.3

Q ss_pred             CcccccccccccCceEeeCCcccccCcc
Q 041875            8 EKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      +.|+.|.+.++..+.|..+|++||+.||
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

>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=97.86  E-value=5.2e-06  Score=41.81  Aligned_cols=29  Identities=28%  Similarity=0.677  Sum_probs=27.1

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHH
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQ   64 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~   64 (195)
                      .|..|.+.|.+..|...++++||-+||..
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

>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=97.86  E-value=4.8e-06  Score=42.74  Aligned_cols=28  Identities=29%  Similarity=0.786  Sum_probs=26.1

Q ss_pred             CcCccCCceeecCceE-EECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKV-TVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v-~~~~~~~H~~CF  127 (195)
                      ..|++|++.|.+.|.| .+.+..||..||
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            5799999999999997 799999999998

>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=97.85  E-value=3.4e-06  Score=41.06  Aligned_cols=26  Identities=35%  Similarity=0.769  Sum_probs=23.7

Q ss_pred             ccccccccccCc-eEeeCCcccccCcc
Q 041875           10 CKACDKTVHIID-MVTADGISYHKICF   35 (195)
Q Consensus        10 C~~C~~~I~~~~-~i~~~g~~~H~~CF   35 (195)
                      |..|.+.|.++. .+...|.+||..||
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            788999999975 69999999999998

>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=97.84  E-value=2.7e-06  Score=41.35  Aligned_cols=26  Identities=35%  Similarity=0.728  Sum_probs=23.7

Q ss_pred             ccccccccccCc-eEeeCCcccccCcc
Q 041875           10 CKACDKTVHIID-MVTADGISYHKICF   35 (195)
Q Consensus        10 C~~C~~~I~~~~-~i~~~g~~~H~~CF   35 (195)
                      |..|.+.|.++. .+...|.+||..||
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            788999999875 68999999999998

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

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

Probab=97.84  E-value=6.7e-06  Score=42.09  Aligned_cols=32  Identities=19%  Similarity=0.534  Sum_probs=29.3

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .|..|..+|+..+|..+++..||..||++.|+
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            37899999999999999999999999998874

>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=97.83  E-value=4.3e-06  Score=43.82  Aligned_cols=29  Identities=28%  Similarity=0.573  Sum_probs=25.5

Q ss_pred             CCCcccccccccccCceEeeCCcccccCcc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .+..|..|+++|. .--|...++.||.+||
T Consensus         7 fa~~C~~Ckk~It-~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           7 FAPRCARCSKTLT-QGGVTYRDQPWHRECL   35 (35)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTC
T ss_pred             HHHHHhhcCCccc-cCceeecCCcchhhhC
Confidence            3579999999998 5568899999999998

>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=97.82  E-value=7e-06  Score=42.56  Aligned_cols=32  Identities=16%  Similarity=0.240  Sum_probs=29.1

Q ss_pred             ccccCCcccccCCeecc-CCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAAL-DGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~-dg~~yC~~c~~~~f~  159 (195)
                      .|..|++.|.+-.|... ++++||-.+|+++|+
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            48899999999999987 699999999999986

>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=97.82  E-value=3.1e-06  Score=41.65  Aligned_cols=27  Identities=37%  Similarity=0.768  Sum_probs=24.9

Q ss_pred             CcccccccccccCceEeeCCcccccCc
Q 041875            8 EKCKACDKTVHIIDMVTADGISYHKIC   34 (195)
Q Consensus         8 ~~C~~C~~~I~~~~~i~~~g~~~H~~C   34 (195)
                      .+|.+|++.++..|.|.-.|+.||+.|
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            579999999999998888999999987

>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=97.77  E-value=5.2e-06  Score=41.26  Aligned_cols=26  Identities=27%  Similarity=0.678  Sum_probs=22.9

Q ss_pred             cccccccccc---CceEeeCCcccccCcc
Q 041875           10 CKACDKTVHI---IDMVTADGISYHKICF   35 (195)
Q Consensus        10 C~~C~~~I~~---~~~i~~~g~~~H~~CF   35 (195)
                      |..|.+||..   ..+|...++.||.+||
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            7899999975   3589999999999998

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.76  E-value=1.1e-05  Score=41.15  Aligned_cols=32  Identities=34%  Similarity=0.702  Sum_probs=29.3

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      .|..|..+|+..+|..+++..||..||+..|+
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            37889999999999999999999999998874

>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=97.73  E-value=1.3e-05  Score=40.45  Aligned_cols=30  Identities=27%  Similarity=0.564  Sum_probs=27.4

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHh
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQL   65 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~   65 (195)
                      .|..|+..|.++.|+..+.+.||+.||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            488999999999999999999999999753

>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=97.72  E-value=6.3e-06  Score=42.30  Aligned_cols=29  Identities=31%  Similarity=0.783  Sum_probs=25.8

Q ss_pred             CCcccccccccccCce-EeeCCcccccCcc
Q 041875            7 QEKCKACDKTVHIIDM-VTADGISYHKICF   35 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~-i~~~g~~~H~~CF   35 (195)
                      +..|++|++.|...+. +.+.+..||..||
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            4679999999998775 6899999999998

>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=97.72  E-value=9.1e-06  Score=39.52  Aligned_cols=26  Identities=46%  Similarity=1.066  Sum_probs=23.2

Q ss_pred             CccCCceeecCce-EEECCceeccccc
Q 041875          102 CTSCKKTVYPLEK-VTVEGESFHKTCF  127 (195)
Q Consensus       102 C~~C~~~I~~~~~-v~~~~~~~H~~CF  127 (195)
                      |..|.+.|+|+-+ +.+.|..||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            7789999999765 7999999999998

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.71  E-value=1.3e-05  Score=40.83  Aligned_cols=28  Identities=14%  Similarity=0.436  Sum_probs=24.6

Q ss_pred             CcCccCCceeecCceEEECCceeccccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ..|++|+++|.+.-.+.+.++.||..|+
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            6899999999965567999999999985

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.71  E-value=1.3e-05  Score=40.68  Aligned_cols=28  Identities=14%  Similarity=0.382  Sum_probs=24.0

Q ss_pred             CCcCccCCceeecCceEEECCceecccc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTC  126 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~C  126 (195)
                      ...|++|+++|...-.+.+.++.||..|
T Consensus         3 ~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           3 LLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            3689999999986556789999999887

>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=97.68  E-value=1.4e-05  Score=40.98  Aligned_cols=31  Identities=55%  Similarity=1.048  Sum_probs=28.5

Q ss_pred             CCCCcCccCCceeecCceEEECCceeccccc
Q 041875           97 GTQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        97 ~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      |+..+|..|.+.++.++-|.-.|+.||+.||
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            4558999999999999999999999999998

>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=97.66  E-value=1.7e-05  Score=41.00  Aligned_cols=33  Identities=15%  Similarity=0.284  Sum_probs=29.1

Q ss_pred             CcCCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            2 AFCGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         2 ~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      .-....+.|.+|+.-|. +.++.+.++.+|++||
T Consensus         3 g~~qklp~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           3 GNAQKLPMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             CccccCccccccCCCcE-eEEEEeccccCCCCCC
Confidence            34456789999999998 8999999999999998

>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=97.59  E-value=1.7e-05  Score=39.44  Aligned_cols=26  Identities=23%  Similarity=0.761  Sum_probs=22.5

Q ss_pred             CccCCceeec---CceEEECCceeccccc
Q 041875          102 CTSCKKTVYP---LEKVTVEGESFHKTCF  127 (195)
Q Consensus       102 C~~C~~~I~~---~~~v~~~~~~~H~~CF  127 (195)
                      |+.|.+||..   ...|++.++.||..||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            7899999985   3468999999999998

>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=97.55  E-value=1.3e-05  Score=38.87  Aligned_cols=26  Identities=35%  Similarity=0.975  Sum_probs=23.1

Q ss_pred             CccCCceeecCce-EEECCceeccccc
Q 041875          102 CTSCKKTVYPLEK-VTVEGESFHKTCF  127 (195)
Q Consensus       102 C~~C~~~I~~~~~-v~~~~~~~H~~CF  127 (195)
                      |..|.+.|+|+-+ +...|..||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            7789999999765 6899999999998

>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=97.54  E-value=2.8e-05  Score=42.80  Aligned_cols=31  Identities=23%  Similarity=0.398  Sum_probs=28.0

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      ....+.|.+|+.-|. +.++.+.++.+|++||
T Consensus        15 ~QkLP~CdkCg~GIV-G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          15 AQRMPLCDKCGSGIV-GAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCSCCBCTTTCCBCC-SCCEESSSCEECTTTC
T ss_pred             cccCccccccCCCcE-EEEEEeccccCCCCCC
Confidence            345689999999998 8999999999999998

>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=97.51  E-value=2.2e-05  Score=42.90  Aligned_cols=27  Identities=33%  Similarity=0.739  Sum_probs=25.0

Q ss_pred             CCcccccccccccCceEeeCCcccccCc
Q 041875            7 QEKCKACDKTVHIIDMVTADGISYHKIC   34 (195)
Q Consensus         7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~C   34 (195)
                      ...|..|++.|. +++|.|.++.||+.|
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

>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=97.44  E-value=3e-05  Score=38.93  Aligned_cols=29  Identities=24%  Similarity=0.584  Sum_probs=26.5

Q ss_pred             CCCCcccccccccccCceEeeCCcccccCc
Q 041875            5 GTQEKCKACDKTVHIIDMVTADGISYHKIC   34 (195)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~C   34 (195)
                      +++.-|..|.+.|. +.++.+.+++||+.|
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            46678999999998 999999999999988

>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=97.44  E-value=4.1e-05  Score=37.94  Aligned_cols=26  Identities=23%  Similarity=0.728  Sum_probs=22.3

Q ss_pred             CccCCceeec---CceEEECCceeccccc
Q 041875          102 CTSCKKTVYP---LEKVTVEGESFHKTCF  127 (195)
Q Consensus       102 C~~C~~~I~~---~~~v~~~~~~~H~~CF  127 (195)
                      |..|.+||..   ...|.+.++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            7889999985   3468999999999998

>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=97.42  E-value=5.2e-05  Score=39.19  Aligned_cols=32  Identities=22%  Similarity=0.421  Sum_probs=27.8

Q ss_pred             ccccccccCCCCceee-cCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLVMGNFSS-MEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~-~~g~~yC~~c~~~~~~   67 (195)
                      +|..|++.|++..|.+ .++++||..||.+.|+
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            5889999999999975 5799999999999874

>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=97.42  E-value=4.8e-05  Score=38.18  Aligned_cols=29  Identities=17%  Similarity=0.440  Sum_probs=26.8

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      .|..|.+.|.+.+|...++++||-.||..
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            48899999999999999999999999964

>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=97.35  E-value=7.2e-05  Score=36.28  Aligned_cols=27  Identities=52%  Similarity=1.147  Sum_probs=25.7

Q ss_pred             cCccCCceeecCceEEECCceeccccc
Q 041875          101 KCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus       101 ~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      +|..|.+.++.++-|.-.|+.||+.||
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            799999999999999999999999998

>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=97.34  E-value=9.6e-05  Score=36.71  Aligned_cols=31  Identities=29%  Similarity=0.608  Sum_probs=28.7

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHhh
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF   66 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~   66 (195)
                      +|+.|...+..+.|+.++..+||..|++..|
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHT
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeecccc
Confidence            5899999999999999999999999998776

>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=97.21  E-value=8.1e-05  Score=35.89  Aligned_cols=26  Identities=27%  Similarity=0.577  Sum_probs=22.1

Q ss_pred             ccccccccccC-ceEeeCCcccccCcc
Q 041875           10 CKACDKTVHII-DMVTADGISYHKICF   35 (195)
Q Consensus        10 C~~C~~~I~~~-~~i~~~g~~~H~~CF   35 (195)
                      |..|.+||..+ ..+...+++||..||
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            78899999743 358889999999998

>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=97.13  E-value=0.00013  Score=36.58  Aligned_cols=29  Identities=21%  Similarity=0.458  Sum_probs=26.5

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      .|..|+..|.+..|+..+.+.||+.||..
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeee
Confidence            47889999999999999999999999964

>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=97.05  E-value=0.00023  Score=35.30  Aligned_cols=32  Identities=22%  Similarity=0.402  Sum_probs=29.5

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      .|+.|+..|.++.|+.+....||-.|...+|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            48899999999999999999999999999885

>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=96.99  E-value=0.0003  Score=35.17  Aligned_cols=29  Identities=34%  Similarity=0.707  Sum_probs=25.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHH
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQ   64 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~   64 (195)
                      .|+.|+..|....++..++++||+.+...
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            48999999998899999999999988754

>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=96.92  E-value=0.00034  Score=35.95  Aligned_cols=28  Identities=18%  Similarity=0.411  Sum_probs=25.6

Q ss_pred             CCcCccCCceeecCceEEECCceeccccc
Q 041875           99 QDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        99 ~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      .+.|.+|+..|. +-.|.++++.+|++||
T Consensus         8 lp~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             CccccccCCCcE-eEEEEeccccCCCCCC
Confidence            489999999998 7788999999999997

>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=96.88  E-value=0.00036  Score=34.90  Aligned_cols=29  Identities=28%  Similarity=0.575  Sum_probs=25.8

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      .|+.|+..|....+++.++++||+.|...
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            48999999998889999999999998754

>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=96.83  E-value=0.00037  Score=38.20  Aligned_cols=29  Identities=21%  Similarity=0.425  Sum_probs=26.2

Q ss_pred             CCCcCccCCceeecCceEEECCceeccccc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      ..+.|.+|+..|. +-.|.++++.+|++||
T Consensus        17 kLP~CdkCg~GIV-G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          17 RMPLCDKCGSGIV-GAVVKARDKYRHPECF   45 (45)
T ss_dssp             SCCBCTTTCCBCC-SCCEESSSCEECTTTC
T ss_pred             cCccccccCCCcE-EEEEEeccccCCCCCC
Confidence            4589999999998 7788999999999998

>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=96.82  E-value=0.0004  Score=33.40  Aligned_cols=26  Identities=31%  Similarity=0.747  Sum_probs=21.3

Q ss_pred             CccCCceeecCc-eEEECCceeccccc
Q 041875          102 CTSCKKTVYPLE-KVTVEGESFHKTCF  127 (195)
Q Consensus       102 C~~C~~~I~~~~-~v~~~~~~~H~~CF  127 (195)
                      |..|.+||.... -+...++.||..||
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            778999998432 36899999999998

>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=96.78  E-value=0.00032  Score=35.96  Aligned_cols=32  Identities=25%  Similarity=0.580  Sum_probs=28.0

Q ss_pred             ccccCCcccc--cCCeeccCCccccHHHHHhhhc
Q 041875          128 RCSHGGCLLT--TSSYAALDGILYCKSHFAQLFK  159 (195)
Q Consensus       128 ~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~~f~  159 (195)
                      +|+-|+..|.  +.+.+.+.|.++|+.+|.++||
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            4777888887  5678999999999999999997

>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=96.74  E-value=0.00065  Score=35.01  Aligned_cols=34  Identities=26%  Similarity=0.561  Sum_probs=28.7

Q ss_pred             CCcCCCCCcccccccccccCc-eEeeCCcccccCc
Q 041875            1 MAFCGTQEKCKACDKTVHIID-MVTADGISYHKIC   34 (195)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~-~i~~~g~~~H~~C   34 (195)
                      |+-+...-.|.+|+.-..+.+ +|..+|..||..|
T Consensus         1 m~~sL~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           1 MANALASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             CchHHHHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            666777789999999887765 6899999999987

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.47  E-value=0.00019  Score=36.92  Aligned_cols=26  Identities=15%  Similarity=0.372  Sum_probs=22.6

Q ss_pred             CcCccCCceeecCceEEECCceecccc
Q 041875          100 DKCTSCKKTVYPLEKVTVEGESFHKTC  126 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~v~~~~~~~H~~C  126 (195)
                      ..|..|...|. +-.+.+.+..||++|
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            89999999776 666788999999987

>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=96.46  E-value=0.00038  Score=34.85  Aligned_cols=30  Identities=20%  Similarity=0.434  Sum_probs=26.0

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHhh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQL  157 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~  157 (195)
                      .|+.|+..|....+++.++++||+.|...+
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            488999999987899999999999997654

>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=96.46  E-value=0.00089  Score=33.26  Aligned_cols=28  Identities=18%  Similarity=0.501  Sum_probs=25.6

Q ss_pred             ccccccccCCCCceeecCCeecchhhHH
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFE   63 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~   63 (195)
                      +|..|-.+|....|...|++++|..|..
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            6899999999999999999999998864

>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=96.41  E-value=0.00027  Score=35.41  Aligned_cols=30  Identities=23%  Similarity=0.537  Sum_probs=25.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHh
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQL   65 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~   65 (195)
                      .|+.|+-.|....|+..++++||+.+...+
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            489999999888888899999999887643

>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=96.19  E-value=0.0013  Score=31.07  Aligned_cols=26  Identities=31%  Similarity=0.439  Sum_probs=21.8

Q ss_pred             cccccccccc-CceEeeCCcccccCcc
Q 041875           10 CKACDKTVHI-IDMVTADGISYHKICF   35 (195)
Q Consensus        10 C~~C~~~I~~-~~~i~~~g~~~H~~CF   35 (195)
                      |..|++.+.. +.-+.+.++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            7889998764 4468899999999998

>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=96.18  E-value=0.00055  Score=35.07  Aligned_cols=32  Identities=28%  Similarity=0.646  Sum_probs=26.8

Q ss_pred             ccccccccCC--CCceeecCCeecchhhHHHhhc
Q 041875           36 KCSHCNGKLV--MGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        36 ~C~~C~~~L~--~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      +|+-|+..|.  +...+.+.|.++|+.+|.++|+
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            5788888885  3478889999999999999884

>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=96.06  E-value=0.0012  Score=32.88  Aligned_cols=28  Identities=21%  Similarity=0.553  Sum_probs=24.3

Q ss_pred             CCCcCccCCceeecCceEEECCceecccc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTC  126 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~C  126 (195)
                      ++.-|..|.+.|. +..+.+.+++||+.|
T Consensus         4 gssgC~~C~~~It-GkVLEAG~khYHP~C   31 (32)
T d1wiga1           4 GSSGCDSCEKYIT-GRVLEAGEKHYHPSC   31 (32)
T ss_dssp             SCCSCSSSCCCCS-SCCBCCSSCCBCTTT
T ss_pred             ccchhhhhhhhhh-hhhhhccccccCCCC
Confidence            3478999999998 777799999999987

>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=95.84  E-value=0.0043  Score=30.99  Aligned_cols=30  Identities=23%  Similarity=0.513  Sum_probs=27.5

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHHh
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQL   65 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~   65 (195)
                      +|..|+..|.+..|+...|..+|..|..+.
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            689999999999999999999999998764

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.77  E-value=0.0037  Score=31.31  Aligned_cols=27  Identities=37%  Similarity=0.889  Sum_probs=22.7

Q ss_pred             ccccccccCCCC-ceeecCCeecchhhH
Q 041875           36 KCSHCNGKLVMG-NFSSMEGVLYCKPHF   62 (195)
Q Consensus        36 ~C~~C~~~L~~~-~~~~~~g~~yC~~c~   62 (195)
                      +|+.|...|..+ .|...+|.+||+.+.
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            588999988766 788899999999764

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.66  E-value=0.0032  Score=31.19  Aligned_cols=28  Identities=21%  Similarity=0.424  Sum_probs=25.1

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHH
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFA  155 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~  155 (195)
                      +|..|-.+|..+.|..+|+++.|..|-.
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            5888999999999999999999998853

>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=95.47  E-value=0.0019  Score=34.44  Aligned_cols=27  Identities=15%  Similarity=0.308  Sum_probs=20.5

Q ss_pred             cccccccccccCceEee-CCcccccCcc
Q 041875            9 KCKACDKTVHIIDMVTA-DGISYHKICF   35 (195)
Q Consensus         9 ~C~~C~~~I~~~~~i~~-~g~~~H~~CF   35 (195)
                      .|++|++....++-+.. .+..||+.|-
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~   28 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACR   28 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHH
T ss_pred             CcchhhccccccceeeecCCceeCCccc
Confidence            48999999888775544 5568999884

>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=95.40  E-value=0.0045  Score=31.61  Aligned_cols=28  Identities=25%  Similarity=0.506  Sum_probs=24.7

Q ss_pred             CCCcccccccccccCceEeeCCcccccCc
Q 041875            6 TQEKCKACDKTVHIIDMVTADGISYHKIC   34 (195)
Q Consensus         6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~C   34 (195)
                      ....|..|.+.|. +-++.+.+..||++|
T Consensus         7 fge~C~~C~~~it-GpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMT-GPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhcc-cceeeecccccCCCC
Confidence            4578999999887 888999999999998

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.20  E-value=0.0099  Score=30.23  Aligned_cols=31  Identities=23%  Similarity=0.605  Sum_probs=25.1

Q ss_pred             cccccccccCCCC-ceee-cCCeecchhhHHHh
Q 041875           35 FKCSHCNGKLVMG-NFSS-MEGVLYCKPHFEQL   65 (195)
Q Consensus        35 F~C~~C~~~L~~~-~~~~-~~g~~yC~~c~~~~   65 (195)
                      |.|..|+.-+.++ .|.. ...++||-.||.+.
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            7899999999777 6764 45789999999764

>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=94.65  E-value=0.011  Score=27.70  Aligned_cols=26  Identities=31%  Similarity=0.597  Sum_probs=20.9

Q ss_pred             CccCCceeec-CceEEECCceeccccc
Q 041875          102 CTSCKKTVYP-LEKVTVEGESFHKTCF  127 (195)
Q Consensus       102 C~~C~~~I~~-~~~v~~~~~~~H~~CF  127 (195)
                      |..|++.+.. +..+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            6788887763 3458999999999997

>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=94.63  E-value=0.0074  Score=30.93  Aligned_cols=27  Identities=41%  Similarity=0.868  Sum_probs=23.6

Q ss_pred             CcCccCCceeecCce-EEECCceecccc
Q 041875          100 DKCTSCKKTVYPLEK-VTVEGESFHKTC  126 (195)
Q Consensus       100 ~~C~~C~~~I~~~~~-v~~~~~~~H~~C  126 (195)
                      ..|.+|+..+.|.|. |...|..||..|
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            589999999998776 578999999987

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.47  E-value=0.019  Score=28.59  Aligned_cols=29  Identities=17%  Similarity=0.369  Sum_probs=26.4

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      +|..|...|....|+...|+.+|.+|..+
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            58999999998889999999999999875

>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=94.37  E-value=0.019  Score=29.18  Aligned_cols=31  Identities=23%  Similarity=0.596  Sum_probs=24.8

Q ss_pred             cccccCCcccccC-Ceecc-CCccccHHHHHhh
Q 041875          127 FRCSHGGCLLTTS-SYAAL-DGILYCKSHFAQL  157 (195)
Q Consensus       127 F~C~~C~~~L~~~-~~~~~-dg~~yC~~c~~~~  157 (195)
                      |.|..|+.-|..+ +|... ..++||-.||.+.
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            6789999999854 56666 4799999999764

>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=94.32  E-value=0.014  Score=28.78  Aligned_cols=28  Identities=32%  Similarity=0.568  Sum_probs=23.1

Q ss_pred             ccccCCcccccCCeeccCCccccHHHHHh
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHFAQ  156 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~~~  156 (195)
                      .|..|++-|... -.+..|.+||.+|..+
T Consensus         1 nC~~Cgkeltad-ArEl~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELTAD-ARELKGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCCTT-CEEETTEEECHHHHHT
T ss_pred             Cccccccccchh-HHHhcCCEEEEecccc
Confidence            378899999874 5778899999999865

>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=94.10  E-value=0.018  Score=28.36  Aligned_cols=28  Identities=29%  Similarity=0.834  Sum_probs=22.8

Q ss_pred             ccccccccCCCCceeecCCeecchhhHHH
Q 041875           36 KCSHCNGKLVMGNFSSMEGVLYCKPHFEQ   64 (195)
Q Consensus        36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~~   64 (195)
                      .|+.|++.|.. .-.+..|.+||.+|..+
T Consensus         1 nC~~Cgkelta-dArEl~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELTA-DARELKGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCCT-TCEEETTEEECHHHHHT
T ss_pred             Cccccccccch-hHHHhcCCEEEEecccc
Confidence            38899999975 44567899999999864

>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=93.65  E-value=0.028  Score=32.36  Aligned_cols=52  Identities=17%  Similarity=0.144  Sum_probs=38.7

Q ss_pred             cccccccccCCCCceee-cCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCc
Q 041875           35 FKCSHCNGKLVMGNFSS-MEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLE  113 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~  113 (195)
                      +.|..|...+.+ .... ..|..||..|..+-+...                              ..|+.|++++...+
T Consensus         1 l~C~Ic~~~~~~-Pv~~~~cGh~fc~~cI~~~l~~~------------------------------~~CP~c~~~l~~~d   49 (56)
T d2baya1           1 MLCAISGKVPRR-PVLSPKSRTIFEKSLLEQYVKDT------------------------------GNDPITNEPLSIEE   49 (56)
T ss_dssp             CCCTTTCSCCSS-EEEETTTTEEEEHHHHHHHHHHH------------------------------SBCTTTCCBCCGGG
T ss_pred             CCCccCCchHHh-cCccCCCCCcccHHHHHHHHhhc------------------------------cCCCccCCcCCHHh
Confidence            468889888865 4443 579999999988766522                              58999999998766


Q ss_pred             eEEE
Q 041875          114 KVTV  117 (195)
Q Consensus       114 ~v~~  117 (195)
                      .+..
T Consensus        50 Lipi   53 (56)
T d2baya1          50 IVEI   53 (56)
T ss_dssp             CEEC
T ss_pred             ceeC
Confidence            6543

>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=92.58  E-value=0.023  Score=30.13  Aligned_cols=28  Identities=18%  Similarity=0.412  Sum_probs=21.1

Q ss_pred             cCccCCceeecCceE-EECCceecccccc
Q 041875          101 KCTSCKKTVYPLEKV-TVEGESFHKTCFR  128 (195)
Q Consensus       101 ~C~~C~~~I~~~~~v-~~~~~~~H~~CF~  128 (195)
                      .|.+|++.+..++-+ .-.+..||+.|-.
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            388999988876554 5667889998743

>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=92.56  E-value=0.036  Score=28.33  Aligned_cols=31  Identities=16%  Similarity=0.254  Sum_probs=25.6

Q ss_pred             CCCCCcccccccccccCceEeeCCcccccCcc
Q 041875            4 CGTQEKCKACDKTVHIIDMVTADGISYHKICF   35 (195)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF   35 (195)
                      ..+.-+|.+|...|. .+-+...|..||+..|
T Consensus         5 glGk~vC~KCh~iId-d~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           5 GLGKYICQKCHAIID-EQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCBCTTTCCBCC-SCCCCCSSSCCCTTTS
T ss_pred             chhhHHHHHHHhhhh-cCcceecCCCCCCCCC
Confidence            456679999999996 5678888999999876

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.25  E-value=0.054  Score=26.90  Aligned_cols=31  Identities=19%  Similarity=0.415  Sum_probs=24.0

Q ss_pred             cccccccccCCCC--ceeecCCeecchhhHHHh
Q 041875           35 FKCSHCNGKLVMG--NFSSMEGVLYCKPHFEQL   65 (195)
Q Consensus        35 F~C~~C~~~L~~~--~~~~~~g~~yC~~c~~~~   65 (195)
                      ++|.-|+..|.+.  ..+.+.+.++|+.+|.++
T Consensus         1 LkC~cC~cRLGEVG~tlytk~nliLCkrDYlRl   33 (33)
T d1j2oa2           1 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   33 (33)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHH
T ss_pred             CccccccccccchhhHHHhhcceeeehhhhhcC
Confidence            4677788888644  567789999999999753

>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=91.19  E-value=0.029  Score=28.06  Aligned_cols=27  Identities=33%  Similarity=0.688  Sum_probs=21.8

Q ss_pred             ccccCCcccccCCeecc--CCccccHHHH
Q 041875          128 RCSHGGCLLTTSSYAAL--DGILYCKSHF  154 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~--dg~~yC~~c~  154 (195)
                      +|..|...|..+.|...  ||..||..|+
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hl   29 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHL   29 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeecc
Confidence            57889999998877654  8999998765

>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=90.80  E-value=0.084  Score=33.66  Aligned_cols=33  Identities=15%  Similarity=0.310  Sum_probs=24.3

Q ss_pred             cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |+|..|...+........=|..||..|..+.+.
T Consensus        23 l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~   55 (97)
T d1jm7b_          23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG   55 (97)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT
T ss_pred             CCCccCCchhhcCceeCCCCCchhHHHHHHHHh
Confidence            688999888865433334589999999877664

>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=90.57  E-value=0.058  Score=26.78  Aligned_cols=26  Identities=23%  Similarity=0.556  Sum_probs=19.8

Q ss_pred             ccccCCcccc-cCCeeccCCccccHHH
Q 041875          128 RCSHGGCLLT-TSSYAALDGILYCKSH  153 (195)
Q Consensus       128 ~C~~C~~~L~-~~~~~~~dg~~yC~~c  153 (195)
                      .|+.|...|- +..|...+|.+||+.+
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            4777777776 5568888999999865

>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=90.12  E-value=0.11  Score=25.81  Aligned_cols=26  Identities=23%  Similarity=0.539  Sum_probs=23.1

Q ss_pred             cccccccCCCCceeecCCeecchhhH
Q 041875           37 CSHCNGKLVMGNFSSMEGVLYCKPHF   62 (195)
Q Consensus        37 C~~C~~~L~~~~~~~~~g~~yC~~c~   62 (195)
                      |..|+..|.+..|......++|..|-
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            77889999999999999999999884

>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=89.60  E-value=0.2  Score=30.51  Aligned_cols=35  Identities=9%  Similarity=0.024  Sum_probs=28.5

Q ss_pred             cCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           32 KICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      ++-|.|..|...+.+ .....-|..||..|..+.+.
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            567999999998875 45667899999999888664

>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=89.26  E-value=0.31  Score=29.43  Aligned_cols=34  Identities=12%  Similarity=0.207  Sum_probs=27.6

Q ss_pred             CccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           33 ICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      +=|.|..|...+.+ ......|..||..|..+.+.
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            34899999998875 45667899999999988764

>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=88.28  E-value=0.093  Score=26.72  Aligned_cols=29  Identities=14%  Similarity=0.449  Sum_probs=24.0

Q ss_pred             CCCcCccCCceeecCceEEECCceeccccc
Q 041875           98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCF  127 (195)
Q Consensus        98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF  127 (195)
                      +.-.|..|...|. .+-+.+.+..||+..|
T Consensus         7 Gk~vC~KCh~iId-d~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           7 GKYICQKCHAIID-EQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCBCTTTCCBCC-SCCCCCSSSCCCTTTS
T ss_pred             hhHHHHHHHhhhh-cCcceecCCCCCCCCC
Confidence            3468999998886 5678899999999776

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.77  E-value=0.28  Score=24.21  Aligned_cols=30  Identities=23%  Similarity=0.452  Sum_probs=23.6

Q ss_pred             ccccCCcccc--cCCeeccCCccccHHHHHhh
Q 041875          128 RCSHGGCLLT--TSSYAALDGILYCKSHFAQL  157 (195)
Q Consensus       128 ~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~~  157 (195)
                      +|.-|+..|.  +...+.+.+.+.|+.+|-++
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            5677777776  55788889999999998753

>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=85.91  E-value=0.31  Score=25.29  Aligned_cols=29  Identities=17%  Similarity=0.277  Sum_probs=19.1

Q ss_pred             cccccccccCCCC-ceeecCCeecchhhHH
Q 041875           35 FKCSHCNGKLVMG-NFSSMEGVLYCKPHFE   63 (195)
Q Consensus        35 F~C~~C~~~L~~~-~~~~~~g~~yC~~c~~   63 (195)
                      |.|+.|+.++..+ .....+.+.+|..|..
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            6777888777655 3334556677777764

>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=85.79  E-value=0.17  Score=24.62  Aligned_cols=27  Identities=26%  Similarity=0.479  Sum_probs=16.2

Q ss_pred             ccccCCcccccCCeeccCCccccHHHH
Q 041875          128 RCSHGGCLLTTSSYAALDGILYCKSHF  154 (195)
Q Consensus       128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~  154 (195)
                      +|.+|+.---...-...+|+|.|+++|
T Consensus         5 rcdvcgeytyeadakllngkpvckpdy   31 (33)
T d2gvia2           5 RCDVCGEYTYEADAKLLNGKPVCKPDY   31 (33)
T ss_dssp             ECTTTCCEEEGGGCEEETTEEECHHHH
T ss_pred             EEeeccceeeccchhhhCCCcccCccc
Confidence            455555533222344567888888876

>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=85.26  E-value=0.27  Score=23.49  Aligned_cols=27  Identities=22%  Similarity=0.412  Sum_probs=22.9

Q ss_pred             cccccccCCCCceeecCCeecchhhHH
Q 041875           37 CSHCNGKLVMGNFSSMEGVLYCKPHFE   63 (195)
Q Consensus        37 C~~C~~~L~~~~~~~~~g~~yC~~c~~   63 (195)
                      |..|.-.|.+..|...-+.++|.+|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            778889999889988788899998864

>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=84.75  E-value=0.46  Score=29.54  Aligned_cols=51  Identities=20%  Similarity=0.457  Sum_probs=38.3

Q ss_pred             CccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecC
Q 041875           33 ICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPL  112 (195)
Q Consensus        33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~  112 (195)
                      +-|.|..|...+.. .....=|..||..|..+.+..+                             ...|+.|..++.+.
T Consensus        22 ~~l~C~IC~~~~~~-pv~~~CgH~FC~~Ci~~~~~~~-----------------------------~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          22 KSISCQICEHILAD-PVETSCKHLFCRICILRCLKVM-----------------------------GSYCPSCRYPCFPT   71 (86)
T ss_dssp             HHTBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHHHT-----------------------------CSBCTTTCCBCCGG
T ss_pred             cCcCCccCCcchhc-ceecCCCChhhHHHHHHHHhhC-----------------------------CCcCcccCCCCChh
Confidence            45889999888764 4555679999999998876422                             15899999988754


Q ss_pred             c
Q 041875          113 E  113 (195)
Q Consensus       113 ~  113 (195)
                      +
T Consensus        72 ~   72 (86)
T d1rmda2          72 D   72 (86)
T ss_dssp             G
T ss_pred             h
Confidence            3

>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=84.73  E-value=0.19  Score=24.88  Aligned_cols=25  Identities=12%  Similarity=0.444  Sum_probs=20.9

Q ss_pred             cccCCcccccCCeeccCCccccHHH
Q 041875          129 CSHGGCLLTTSSYAALDGILYCKSH  153 (195)
Q Consensus       129 C~~C~~~L~~~~~~~~dg~~yC~~c  153 (195)
                      |..|+.+|-+..|...+..++|..|
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            6678888888888888889999776

>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=83.12  E-value=0.4  Score=24.85  Aligned_cols=20  Identities=30%  Similarity=0.730  Sum_probs=11.6

Q ss_pred             CccCCceeecCceEEECCce
Q 041875          102 CTSCKKTVYPLEKVTVEGES  121 (195)
Q Consensus       102 C~~C~~~I~~~~~v~~~~~~  121 (195)
                      |++|.++..++++|+++|+.
T Consensus         3 C~vCr~pFP~GDRVTFnGKe   22 (40)
T d1v6ga2           3 CAVCRLPFPPGDRVTFNGKE   22 (40)
T ss_dssp             CSSSCCCCCSSSCEEEETTE
T ss_pred             ccccCCCCCCCCeEEEcCce
Confidence            55566666555666555553

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=81.12  E-value=0.81  Score=26.72  Aligned_cols=31  Identities=10%  Similarity=0.149  Sum_probs=16.4

Q ss_pred             cccccccCCCCceeecCCeecchhhHHHhhc
Q 041875           37 CSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK   67 (195)
Q Consensus        37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~   67 (195)
                      |..|...+........=|..||..|..+-+.
T Consensus         8 C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~   38 (68)
T d1chca_           8 CPICLEDPSNYSMALPCLHAFCYVCITRWIR   38 (68)
T ss_dssp             CSSCCSCCCSCEEETTTTEEESTTHHHHHHH
T ss_pred             CccCCcCccCCcEEeCCCCcCcHHHHHHHHH
Confidence            4444444433222223356678888876654

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.89  E-value=0.84  Score=28.85  Aligned_cols=35  Identities=6%  Similarity=-0.179  Sum_probs=26.3

Q ss_pred             cCccccccccccCCCCceeecC-CeecchhhHHHhhc
Q 041875           32 KICFKCSHCNGKLVMGNFSSME-GVLYCKPHFEQLFK   67 (195)
Q Consensus        32 ~~CF~C~~C~~~L~~~~~~~~~-g~~yC~~c~~~~~~   67 (195)
                      ++=|.|..|+..+.+ ...... +..||+.|..+.+.
T Consensus        20 P~~f~CPI~~~lm~d-PV~~~~~~~ty~r~~I~~~l~   55 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD-PVVLPSSRVTVDRSTIARHLL   55 (98)
T ss_dssp             CTTTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHTT
T ss_pred             cHHhCCcCchhHHHH-HHhcccccchhhHHHHHHHHH
Confidence            345999999998875 444444 46899999988765