Citrus Sinensis ID: 029735

---

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-------19
Protein Sequence
MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVEAVTENATA
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEcEEEEEcccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccEEEEEEEEEEcccccccccEEEHHccccccccccccccccEEccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEcccccccccEEEcccccEccccccccccccEEccHHHHHHccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
masfagttqkckaceKTVYLVDQLTAdnkvyhkacfrchhckgtlklsnycsfegvlyckphfdQLFKMTgsldksfegtpktvrversadqvtnsrvssmfagtqdkcvackktvypiekvavdgtsyhkacfrcthggcvispsnyvahehRLYCRHHHnqlfkqkgnfsqldnheQVEAVTENATA
Flexible Loop (DISEMBL)
masfagttqkckaceKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDksfegtpktvrversadqvtnsrvssmfagtqdkcvaCKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVEavtenata
Low Complexity Region (SEG)
MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVEAVTENATA
Disordered region (IsUnstruct)
********QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS****************************MFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ**********************
Disordered Region (DISOPRED)
******TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK***********************
Disordered Region (DISEMBL)
**********CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQV*********
Disordered Region (DISPRO)
********QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLD********************************DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVEAVTENATA
Positional Conservation
no confident homologs detected

---

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	189	2.2.26 [Sep-21-2011]
P29675	219	Pollen-specific protein S	N/A	no	0.989	0.853	0.684	2e-72
Q4U4S6	3784	Xin actin-binding repeat-	yes	no	0.402	0.020	0.5	4e-18
P50462	194	Cysteine and glycine-rich	no	no	0.899	0.876	0.305	1e-16
Q9UHB6	759	LIM domain and actin-bind	no	no	0.603	0.150	0.365	2e-16
B0KYV5	756	LIM domain and actin-bind	yes	no	0.333	0.083	0.454	4e-16
P50461	194	Cysteine and glycine-rich	no	no	0.910	0.886	0.31	5e-16
Q4U0T9	194	Cysteine and glycine-rich	no	no	0.888	0.865	0.312	6e-16
Q0VFX8	208	Cysteine-rich protein 2 O	no	no	0.846	0.769	0.304	7e-16
Q9ERG0	753	LIM domain and actin-bind	no	no	0.380	0.095	0.465	1e-15
P50463	194	Cysteine and glycine-rich	no	no	0.899	0.876	0.295	4e-15

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

 Score =  271 bits (694), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 130/190 (68%), Positives = 153/190 (80%), Gaps = 3/190 (1%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           M SF GTTQKC  CEKTVYLVD+L A+ +VYHKACFRCHHC  TLKLSN+ SF+GV+YC+
Sbjct: 1   MKSFTGTTQKCTVCEKTVYLVDKLVANQRVYHKACFRCHHCNSTLKLSNFNSFDGVVYCR 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNS--RVSSMFAGTQDKCVACKKTVYP 118
            HFDQLFK TGSL+KSF+GTPK  + ER+  Q T S  R+SS F GT+DKC AC K VYP
Sbjct: 61  HHFDQLFKRTGSLEKSFDGTPK-FKPERTFSQETQSANRLSSFFEGTRDKCNACAKIVYP 119

Query: 119 IEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHE 178
           IE+V VDGT+YH+ACF+C HGGC ISPSNY+AHE RLYC+HHH QLFK+KGN+SQL+  E
Sbjct: 120 IERVKVDGTAYHRACFKCCHGGCTISPSNYIAHEGRLYCKHHHIQLFKKKGNYSQLEVEE 179

Query: 179 QVEAVTENAT 188
            V A  E+ T
Sbjct: 180 TVAAPAESET 189

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

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

 Score = 90.9 bits (224), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 38/76 (50%), Positives = 50/76 (65%)

Query: 2    ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKP 61
            ++F    + C  C+KTVY ++ L AD + +HK+CFRCHHC   L L NY S  G +YCKP
Sbjct: 3248 SAFLSDKEICIICQKTVYPMECLIADKQNFHKSCFRCHHCSSKLSLGNYASLHGRIYCKP 3307

Query: 62   HFDQLFKMTGSLDKSF 77
            HF QLFK  G+ D+ F
Sbjct: 3308 HFKQLFKSKGNYDEGF 3323

Protects actin filaments from depolymerization.

Mus musculus (taxid: 10090)

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

 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 59/193 (30%), Positives = 89/193 (46%), Gaps = 23/193 (11%)

Query: 6   GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
           G   KC ACEKTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK  + +
Sbjct: 5   GGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGR 64

Query: 66  LFKMTGS----------------LDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKC 109
            +   G                 L   F+ +PK  R   +++    S+ S+ F G  +KC
Sbjct: 65  RYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTSNP---SKFSAKF-GESEKC 120

Query: 110 VACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKG 169
             C K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + + F   G
Sbjct: 121 PRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

Query: 170 -NFSQLDNHEQVE 181
             F  L   +QVE
Sbjct: 181 IGFGGLT--QQVE 191

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|Q9UHB6|LIMA1_HUMAN LIM domain and actin-binding protein 1 OS=Homo sapiens GN=LIMA1 PE=1 SV=1

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/134 (36%), Positives = 68/134 (50%), Gaps = 20/134 (14%)

Query: 5   AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFD 64
           A   + C  C+KTVY +++L A+ +V+H +CFRC +C   L L  Y S  G +YCKPHF+
Sbjct: 384 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFN 443

Query: 65  QLFKMTGSLDKSFEGTP----------KTVRVERSADQVTNSRVSSMFAGTQDKCVACKK 114
           QLFK  G+ D+ F   P              +ER A Q+ N+R +    G +D       
Sbjct: 444 QLFKSKGNYDEGFGHRPHKDLWASKNENEEILERPA-QLANARETPHSPGVEDA------ 496

Query: 115 TVYPIEKVAVDGTS 128
              PI KV V   S
Sbjct: 497 ---PIAKVGVLAAS 507

Binds to actin monomers and filaments. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments.

Homo sapiens (taxid: 9606)

>sp|B0KYV5|LIMA1_PIG LIM domain and actin-binding protein 1 OS=Sus scrofa GN=LIMA1 PE=2 SV=1

 Score = 84.3 bits (207), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 35/77 (45%), Positives = 49/77 (63%)

Query: 5   AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFD 64
           A   + C  C+KTVY +++L A+ +V+H +CFRC +C   L L  Y S  G +YCKPHF+
Sbjct: 380 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFN 439

Query: 65  QLFKMTGSLDKSFEGTP 81
           QLFK  G+ D+ F   P
Sbjct: 440 QLFKSKGNYDEGFGHRP 456

Binds to actin monomers and filaments. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments.

Sus scrofa (taxid: 9823)

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

 Score = 84.3 bits (207), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 62/200 (31%), Positives = 89/200 (44%), Gaps = 28/200 (14%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           M ++ G   KC ACEKTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK
Sbjct: 1   MPNWGGGA-KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 59

Query: 61  PHFDQLFKMTGS----------------LDKSFEGTPKTVRVERSADQVTNSRVSSMFA- 103
             + + +   G                 L   F+ +PK  R       VT S  S   A 
Sbjct: 60  VCYGRRYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKPAR------SVTTSNPSKFTAK 113

Query: 104 -GTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHN 162
            G  +KC  C K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + 
Sbjct: 114 FGESEKCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYA 173

Query: 163 QLFKQKG-NFSQLDNHEQVE 181
           + F   G  F  L   +QVE
Sbjct: 174 KNFGPTGIGFGGLT--QQVE 191

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

 Score = 84.0 bits (206), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 61/195 (31%), Positives = 86/195 (44%), Gaps = 27/195 (13%)

Query: 6   GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
           G   KC ACEKTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK  + +
Sbjct: 5   GGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGR 64

Query: 66  LFKMTG----------------SLDKSFEGTPKTVRVERSADQVTNSRVSSMFA--GTQD 107
            +   G                 L   F+ +PK  R        T S   S FA  G  +
Sbjct: 65  RYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKQAR------SATTSSNPSKFAKFGESE 118

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ 167
           KC  C K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + + F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 168 KG-NFSQLDNHEQVE 181
            G  F  L +  QVE
Sbjct: 179 TGIGFGGLTH--QVE 191

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

 Score = 83.6 bits (205), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 85/184 (46%), Gaps = 24/184 (13%)

Query: 10  KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC-KPHFDQLFK 68
           KC  C+KTVY  +++++  K +H+ C RC HC  TL    +   +G  +C KP +  LF 
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHRFCLRCEHCSKTLTPGGHAEHDGKPFCHKPCYATLFG 63

Query: 69  MTG--------------SLDKSFEGTPKTVRVERSADQVTN------SRVSSM--FAGTQ 106
             G              S +K     P  V V R+ ++  +      S+ SS+  F G  
Sbjct: 64  PKGVNIGGAGSYIYEKPSAEKPQVTGPIEVPVARTEERKASGPPKGPSKASSVTTFTGEP 123

Query: 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC-RHHHNQLF 165
           + C  C K VY  EKV   G  +H+ C RC   G  ++P  +  H+ + YC +  +  LF
Sbjct: 124 NMCPRCNKRVYFAEKVTSLGKDWHRPCLRCERCGKTLTPGGHAEHDGQPYCHKPCYGILF 183

Query: 166 KQKG 169
             KG
Sbjct: 184 GPKG 187

Bos taurus (taxid: 9913)

>sp|Q9ERG0|LIMA1_MOUSE LIM domain and actin-binding protein 1 OS=Mus musculus GN=Lima1 PE=1 SV=3

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 34/73 (46%), Positives = 48/73 (65%)

Query: 5   AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFD 64
           A   + C  C+KTVY +++L A+ +V+H +CFRC +C   L L  Y S  G +YCKPHF+
Sbjct: 382 APAKESCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFN 441

Query: 65  QLFKMTGSLDKSF 77
           QLFK  G+ D+ F
Sbjct: 442 QLFKSKGNYDEGF 454

Binds to actin monomers and filaments. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments.

Mus musculus (taxid: 10090)

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

 Score = 80.9 bits (198), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 88/193 (45%), Gaps = 23/193 (11%)

Query: 6   GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
           G   KC AC+KTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK  + +
Sbjct: 5   GGGAKCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGR 64

Query: 66  LFKMTG----------------SLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKC 109
            +   G                 L   F+ +PK  R   +++    S+ S+ F G  +KC
Sbjct: 65  KYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTSNP---SKFSAKF-GESEKC 120

Query: 110 VACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKG 169
             C K+VY  EKV   G  +HK CF C   G  +  +N    +  LYC+  + + F   G
Sbjct: 121 PRCGKSVYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

Query: 170 -NFSQLDNHEQVE 181
             F  L +  QVE
Sbjct: 181 IGFGGLTH--QVE 191

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)

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	189
255540771	190	Pollen-specific protein SF3, putative [R	0.989	0.984	0.936	1e-98
351727601	192	uncharacterized protein LOC100500444 [Gl	0.984	0.968	0.887	1e-94
224119250	191	predicted protein [Populus trichocarpa]	1.0	0.989	0.878	4e-94
351724581	192	uncharacterized protein LOC100500501 [Gl	0.984	0.968	0.882	8e-94
224133452	191	predicted protein [Populus trichocarpa]	1.0	0.989	0.868	5e-93
356513577	215	PREDICTED: pollen-specific protein SF3-l	0.978	0.860	0.854	1e-92
356565033	209	PREDICTED: pollen-specific protein SF3-l	0.994	0.899	0.852	5e-92
62183959	179	putative pollen specific LIM domain-cont	0.941	0.994	0.877	4e-90
225457122	182	PREDICTED: pollen-specific protein SF3 [	0.947	0.983	0.885	4e-90
113205158	184	Pollen-specific protein SF3, putative [S	0.941	0.967	0.853	2e-88

>gi|255540771|ref|XP_002511450.1| Pollen-specific protein SF3, putative [Ricinus communis] gi|223550565|gb|EEF52052.1| Pollen-specific protein SF3, putative [Ricinus communis]

 Score =  364 bits (934), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 176/188 (93%), Positives = 180/188 (95%), Gaps = 1/188 (0%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MA+FAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNY SFEGVLYCK
Sbjct: 1   MATFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYSSFEGVLYCK 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQV-TNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQLFKMTGSLDKSFEGTPKTVRV+RSADQ  +NSRVSSMFAGTQDKCVACKKTVYPI
Sbjct: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVDRSADQFNSNSRVSSMFAGTQDKCVACKKTVYPI 120

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHE RLYCRHHHNQLFKQKGNFSQLD HE 
Sbjct: 121 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEQRLYCRHHHNQLFKQKGNFSQLDKHEH 180

Query: 180 VEAVTENA 187
           V+ VTE A
Sbjct: 181 VKPVTETA 188

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727601|ref|NP_001238190.1| uncharacterized protein LOC100500444 [Glycine max] gi|255630349|gb|ACU15531.1| unknown [Glycine max]

 Score =  351 bits (900), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 166/187 (88%), Positives = 176/187 (94%), Gaps = 1/187 (0%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MASFAGTTQKCKACEKTVYLVDQLTADNK+YHK+CFRC+HCKGTLKLSNYCSFEGVLYCK
Sbjct: 2   MASFAGTTQKCKACEKTVYLVDQLTADNKIYHKSCFRCYHCKGTLKLSNYCSFEGVLYCK 61

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQV-TNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQLFK TGSLDKSFEG P+T R+ERSADQV TN++VS++FAGTQ+KCVACKKTVYPI
Sbjct: 62  PHFDQLFKKTGSLDKSFEGIPRTARLERSADQVQTNTKVSNLFAGTQEKCVACKKTVYPI 121

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH QLFKQKGNFSQLD  E 
Sbjct: 122 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHTQLFKQKGNFSQLDKQEN 181

Query: 180 VEAVTEN 186
            E V EN
Sbjct: 182 DEGVAEN 188

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119250|ref|XP_002318024.1| predicted protein [Populus trichocarpa] gi|222858697|gb|EEE96244.1| predicted protein [Populus trichocarpa]

 Score =  348 bits (894), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 167/190 (87%), Positives = 176/190 (92%), Gaps = 1/190 (0%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MA FAGTTQKCK+CEKTVY VDQLTAD+KVYHKACFRCHHCKGTLKLSNY SFEGVLYCK
Sbjct: 1   MAPFAGTTQKCKSCEKTVYFVDQLTADDKVYHKACFRCHHCKGTLKLSNYSSFEGVLYCK 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQV-TNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQL KMTGSLDKSF+GT KTVRV+RSADQV +NS+VSSMFAGTQ+KCVACKKTVYPI
Sbjct: 61  PHFDQLLKMTGSLDKSFKGTSKTVRVDRSADQVQSNSKVSSMFAGTQEKCVACKKTVYPI 120

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           E+VAVDGTSYHKACFRC HGGCVISPSN+VAHEHRLYCRHHHNQLFKQKGNFSQLD HE 
Sbjct: 121 ERVAVDGTSYHKACFRCAHGGCVISPSNFVAHEHRLYCRHHHNQLFKQKGNFSQLDKHEH 180

Query: 180 VEAVTENATA 189
           V  V E A A
Sbjct: 181 VTPVKETAAA 190

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724581|ref|NP_001235271.1| uncharacterized protein LOC100500501 [Glycine max] gi|255630484|gb|ACU15600.1| unknown [Glycine max]

 Score =  348 bits (892), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 165/187 (88%), Positives = 175/187 (93%), Gaps = 1/187 (0%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MASFAGTTQKCKACEKTVYLVDQLTADNK+YHK+CFRC+HCKGTLKLSNYCSFEGVLYCK
Sbjct: 2   MASFAGTTQKCKACEKTVYLVDQLTADNKIYHKSCFRCYHCKGTLKLSNYCSFEGVLYCK 61

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQV-TNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQLFK TGSLDKSFEG P+T R+ERS DQV TN++VS++FAGTQ+KCVACKKTVYPI
Sbjct: 62  PHFDQLFKKTGSLDKSFEGIPRTARLERSTDQVQTNNKVSNLFAGTQEKCVACKKTVYPI 121

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           EKVAVDGT YHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH QLFKQKGNFSQLD  E 
Sbjct: 122 EKVAVDGTFYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHTQLFKQKGNFSQLDKQEN 181

Query: 180 VEAVTEN 186
            E VTEN
Sbjct: 182 DEGVTEN 188

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133452|ref|XP_002321571.1| predicted protein [Populus trichocarpa] gi|222868567|gb|EEF05698.1| predicted protein [Populus trichocarpa]

 Score =  345 bits (885), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 165/190 (86%), Positives = 175/190 (92%), Gaps = 1/190 (0%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MA+FAGTTQKCKAC+KTVYLVDQLT DNK YHKACFRCHHCKGTLKLSNY SFEGVLYC+
Sbjct: 1   MATFAGTTQKCKACDKTVYLVDQLTVDNKFYHKACFRCHHCKGTLKLSNYSSFEGVLYCQ 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQV-TNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQLFKMTGSLDKSFEGTPKTVR +RSADQV +NS+VSSMFAGTQ+KCVAC KTVYP+
Sbjct: 61  PHFDQLFKMTGSLDKSFEGTPKTVRGDRSADQVLSNSKVSSMFAGTQEKCVACNKTVYPL 120

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           EKVAVDGTSYHKACFRC HGGCVISPSNYVAHEHRLYCRHHHNQLFK+KGNFSQ   HE 
Sbjct: 121 EKVAVDGTSYHKACFRCAHGGCVISPSNYVAHEHRLYCRHHHNQLFKEKGNFSQFGKHEH 180

Query: 180 VEAVTENATA 189
           +  V E ATA
Sbjct: 181 LTPVDETATA 190

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513577|ref|XP_003525489.1| PREDICTED: pollen-specific protein SF3-like [Glycine max]

 Score =  343 bits (881), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 158/185 (85%), Positives = 171/185 (92%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MASFAGTTQKC ACEK VY V+QLTADNKVYHK+CFRCHHCKGTLKLSNYCSFEGVLYCK
Sbjct: 1   MASFAGTTQKCTACEKKVYWVEQLTADNKVYHKSCFRCHHCKGTLKLSNYCSFEGVLYCK 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE 120
           PHF QLFKMTGSLDKSFEG P++VRVERSADQV  ++VS +F+GTQ+KCV CKKTVYPIE
Sbjct: 61  PHFHQLFKMTGSLDKSFEGVPRSVRVERSADQVQTNKVSRLFSGTQEKCVGCKKTVYPIE 120

Query: 121 KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQV 180
           KVAVDG SYHK+CFRCTHGGCVISPSNY+AHEHRLYCRHHH QLFKQKGNFSQLD HE V
Sbjct: 121 KVAVDGKSYHKSCFRCTHGGCVISPSNYIAHEHRLYCRHHHTQLFKQKGNFSQLDKHENV 180

Query: 181 EAVTE 185
           + +TE
Sbjct: 181 QVITE 185

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565033|ref|XP_003550749.1| PREDICTED: pollen-specific protein SF3-like [Glycine max]

 Score =  342 bits (877), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 162/190 (85%), Positives = 175/190 (92%), Gaps = 2/190 (1%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MASFAGTTQKC ACEK VY V+QLTADNKVYHK+CFRCHHCKGTLKLSNYCSFEGVLYCK
Sbjct: 1   MASFAGTTQKCTACEKKVYWVEQLTADNKVYHKSCFRCHHCKGTLKLSNYCSFEGVLYCK 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQV-TNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQLFKMTGSLDKSFEG P++ RVERSADQV +N++VS +F+GTQ+KCV CKKTVYPI
Sbjct: 61  PHFDQLFKMTGSLDKSFEGIPRSARVERSADQVQSNNKVSRLFSGTQEKCVGCKKTVYPI 120

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           EKVAVDG SYHK+CFRCTHGGCVISPSNYVAHEHRLYCRHHH QLFKQKGNFSQLD H+ 
Sbjct: 121 EKVAVDGKSYHKSCFRCTHGGCVISPSNYVAHEHRLYCRHHHTQLFKQKGNFSQLDKHDS 180

Query: 180 VEAV-TENAT 188
           V+ V TEN T
Sbjct: 181 VQVVITENTT 190

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62183959|gb|AAX73300.1| putative pollen specific LIM domain-containing protein [Solanum lycopersicum]

 Score =  335 bits (860), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 157/179 (87%), Positives = 171/179 (95%), Gaps = 1/179 (0%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MASF GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNY SFEGVLYC+
Sbjct: 1   MASFGGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYNSFEGVLYCR 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE 120
           PHFDQLFKMTGSLDKSFEG PKTVR ERSADQ +NS+VSS+F GTQDKCVACKKTVYP+E
Sbjct: 61  PHFDQLFKMTGSLDKSFEGAPKTVR-ERSADQGSNSKVSSLFGGTQDKCVACKKTVYPLE 119

Query: 121 KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           KVAVDGTSYH+ CF+C+HGGCVISPSNYVAHEHRLYCRHHH QLFK++GNFSQ+++HE+
Sbjct: 120 KVAVDGTSYHRPCFKCSHGGCVISPSNYVAHEHRLYCRHHHTQLFKERGNFSQMEDHEK 178

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457122|ref|XP_002283525.1| PREDICTED: pollen-specific protein SF3 [Vitis vinifera] gi|297733831|emb|CBI15078.3| unnamed protein product [Vitis vinifera]

 Score =  335 bits (860), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 162/183 (88%), Positives = 170/183 (92%), Gaps = 4/183 (2%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MA+FAGTTQKCKACEKTVYLVD+LTADNKVYHKACFRCHHCKGTLKLSNY SFEGVLYCK
Sbjct: 1   MATFAGTTQKCKACEKTVYLVDELTADNKVYHKACFRCHHCKGTLKLSNYSSFEGVLYCK 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQ-VTNSRVSSMFAGTQDKCVACKKTVYPI 119
           PHFDQLFKMTGSLDKSFEG PKTV   RS DQ  TNS+VSSMFAGTQ+KCVACKKTVYPI
Sbjct: 61  PHFDQLFKMTGSLDKSFEGAPKTV---RSVDQGQTNSKVSSMFAGTQEKCVACKKTVYPI 117

Query: 120 EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQ 179
           EKV VDGTSYHKACFRCTHGGC ISPSNY+AHEHRLYCRHHH+QLFK+KGNFSQLD  EQ
Sbjct: 118 EKVGVDGTSYHKACFRCTHGGCTISPSNYIAHEHRLYCRHHHSQLFKEKGNFSQLDKQEQ 177

Query: 180 VEA 182
           V+ 
Sbjct: 178 VKG 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|113205158|gb|AAX95760.2| Pollen-specific protein SF3, putative [Solanum lycopersicum]

 Score =  330 bits (846), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 157/184 (85%), Positives = 171/184 (92%), Gaps = 6/184 (3%)

Query: 1   MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
           MASF GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNY SFEGVLYC+
Sbjct: 1   MASFGGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYNSFEGVLYCR 60

Query: 61  PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE 120
           PHFDQLFKMTGSLDKSFEG PKTVR ERSADQ +NS+VSS+F GTQDKCVACKKTVYP+E
Sbjct: 61  PHFDQLFKMTGSLDKSFEGAPKTVR-ERSADQGSNSKVSSLFGGTQDKCVACKKTVYPLE 119

Query: 121 K-----VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLD 175
           K     VAVDGTSYH+ CF+C+HGGCVISPSNYVAHEHRLYCRHHH QLFK++GNFSQ++
Sbjct: 120 KTRAEQVAVDGTSYHRPCFKCSHGGCVISPSNYVAHEHRLYCRHHHTQLFKERGNFSQME 179

Query: 176 NHEQ 179
           +HE+
Sbjct: 180 DHEK 183

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

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	189
TAIR|locus:2012798	190	WLIM1 "AT1G10200" [Arabidopsis	0.915	0.910	0.731	3.6e-73
TAIR|locus:2061171	200	WLIM2a "WLIM2a" [Arabidopsis t	0.989	0.935	0.569	5.1e-58
TAIR|locus:2198210	205	PLIM2b "PLIM2b" [Arabidopsis t	0.915	0.843	0.544	2.1e-54
TAIR|locus:2050735	226	PLIM2a "PLIM2a" [Arabidopsis t	0.888	0.743	0.568	4.3e-54
TAIR|locus:2098871	213	PLIM2c "PLIM2c" [Arabidopsis t	0.910	0.807	0.551	8.9e-54
DICTYBASE|DDB_G0290575	472	DDB_G0290575 "LIM-type zinc fi	0.825	0.330	0.359	1.2e-20
UNIPROTKB|F1NSM0	688	F1NSM0 "Uncharacterized protei	0.354	0.097	0.522	2.5e-19
MGI|MGI:1330824	194	Csrp3 "cysteine and glycine-ri	0.899	0.876	0.331	3.1e-19
UNIPROTKB|E2R9P5	194	CSRP3 "Uncharacterized protein	0.899	0.876	0.331	8.3e-19
UNIPROTKB|Q4U0T9	194	CSRP3 "Cysteine and glycine-ri	0.920	0.896	0.317	1.7e-18

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

 Score = 739 (265.2 bits), Expect = 3.6e-73, P = 3.6e-73
 Identities = 128/175 (73%), Positives = 152/175 (86%)

Query:     3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
             +FAGTTQKC AC+KTVYLVD+LTADN+VYHKACFRCHHCKGTLKLSNY SFEGVLYC+PH
Sbjct:     2 AFAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNYNSFEGVLYCRPH 61

Query:    63 FDQLFKMTGSLDKSFEGTPKTVRVER--SADQVTNSRVSSMFAGTQDKCVACKKTVYPIE 120
             FDQ FK TGSL+KSFEGTPK  + +R    ++   ++VS+MF GT++KCV C KTVYPIE
Sbjct:    62 FDQNFKRTGSLEKSFEGTPKIGKPDRPLEGERPAGTKVSNMFGGTREKCVGCDKTVYPIE 121

Query:   121 KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLD 175
             KV+V+GT YHK+CF+CTHGGC ISPSNY+AHE +LYC+HHH QL K+KGN SQL+
Sbjct:   122 KVSVNGTLYHKSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLIKEKGNLSQLE 176

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 596 (214.9 bits), Expect = 5.1e-58, P = 5.1e-58
 Identities = 107/188 (56%), Positives = 136/188 (72%)

Query:     3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
             SF GT QKC+ACEKTVY V+ L+AD   YHKACF+C HCK  L+LSNY S EGV+YC+PH
Sbjct:     2 SFTGTQQKCRACEKTVYPVELLSADGISYHKACFKCSHCKSRLQLSNYSSMEGVVYCRPH 61

Query:    63 FDQLFKMTGSLDKSFEGTPKTVRVERSAD-QVTNSRVSSMFAGTQDKCVACKKTVYPIEK 121
             F+QLFK +GS  K+F+   K +  + + +   T SR++ MF+GTQDKC  C KTVYPIEK
Sbjct:    62 FEQLFKESGSFSKNFQSPAKPLTDKPTPELNRTPSRLAGMFSGTQDKCATCTKTVYPIEK 121

Query:   122 VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVE 181
             V V+   YHK+CF+C+HGGC ISPSNY A E  LYC+HH  QLFK+KG+++ L     ++
Sbjct:   122 VTVESQCYHKSCFKCSHGGCPISPSNYAALEGILYCKHHFAQLFKEKGSYNHLIKSASIK 181

Query:   182 AVTENATA 189
               T  ATA
Sbjct:   182 RATAAATA 189

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0000271 "polysaccharide biosynthetic process" evidence=RCA

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0009825 "multidimensional cell growth" evidence=RCA

GO:0009932 "cell tip growth" evidence=RCA

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

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

GO:0048767 "root hair elongation" evidence=RCA

GO:0071555 "cell wall organization" evidence=RCA

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

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 98/180 (54%), Positives = 131/180 (72%)

Query:     3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
             SF GT  KC  C+KTVY+VD L+ +   YHK+CFRC HCKGTL++SNY S +GVLYCK H
Sbjct:     2 SFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKTH 61

Query:    63 FDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV 122
             F+QLFK +G+  K+F+   KT + E +    T S++SS+F GTQDKC AC+KTVYP+EK+
Sbjct:    62 FEQLFKESGNFSKNFQ-PGKTEKPELTR---TPSKISSIFCGTQDKCAACEKTVYPLEKI 117

Query:   123 AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFS---QLDNHEQ 179
              ++G  +HK CFRC HGGC ++ S+Y + +  LYCRHH NQLF +KGN++   Q  NH +
Sbjct:   118 QMEGECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFMEKGNYAHVLQAANHRR 177

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 99/174 (56%), Positives = 129/174 (74%)

Query:     3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
             SF GT  KCKAC+KTVY++D LT +   YHK+CFRC HCKGTL +SNY S +GVLYCKPH
Sbjct:     2 SFTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCTHCKGTLVISNYSSMDGVLYCKPH 61

Query:    63 FDQLFKMTGSLDKSFEGTPKTVRVERSADQVTN--SRVSSMFAGTQDKCVACKKTVYPIE 120
             F+QLFK +G+  K+F+   KT   E+  D +T   S++SS F+GTQDKC  CKKTVYP+E
Sbjct:    62 FEQLFKESGNYSKNFQAG-KT---EKPNDHLTRTPSKLSSFFSGTQDKCATCKKTVYPLE 117

Query:   121 KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL 174
             KV ++G SYHK CFRCTH GC ++ S+Y +    LYC+ H NQLF +KG+++ +
Sbjct:   118 KVTMEGESYHKTCFRCTHSGCPLTHSSYASLNGVLYCKVHFNQLFLEKGSYNHV 171

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 556 (200.8 bits), Expect = 8.9e-54, P = 8.9e-54
 Identities = 96/174 (55%), Positives = 128/174 (73%)

Query:     1 MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
             MA+F GTT KCKAC+KTVY++D +T +   YHK+CFRC HC GTL + NY S +GVLYCK
Sbjct:     1 MAAFTGTTDKCKACDKTVYVMDLMTLEGMPYHKSCFRCSHCNGTLVICNYSSMDGVLYCK 60

Query:    61 PHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE 120
              HF+QLFK +G+  K+F+   KT +    A +  N R+SS F+GTQDKC ACKKTVYP+E
Sbjct:    61 THFEQLFKESGNFSKNFQTAGKTEK-SNDATKAPN-RLSSFFSGTQDKCAACKKTVYPLE 118

Query:   121 KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL 174
             K+ ++G SYHK CFRC H GC ++ S+Y A +  LYC+ H +QLF +KGN++ +
Sbjct:   119 KMTMEGESYHKTCFRCAHSGCPLTHSSYAALDGVLYCKVHFSQLFLEKGNYNHV 172

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 249 (92.7 bits), Expect = 1.2e-20, P = 1.2e-20
 Identities = 60/167 (35%), Positives = 77/167 (46%)

Query:     1 MASFAGTTQKCKACEKTVYLVDQLTA----DNKVYHKACFRCHHCKGTLKLSNYCSFEGV 56
             M +  GT +KC AC KTVYL +++      D K +HK C +C HCK TL L NY S  GV
Sbjct:     1 MVNIGGTQEKCTACAKTVYLTEKIVVEDKEDKKTFHKLCLKCTHCKLTLSLGNYASLNGV 60

Query:    57 LYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTV 116
              YCKPHF QLF   G+ D   EG  K+   E+   Q T +  SS     + K    K+T 
Sbjct:    61 FYCKPHFKQLFATKGNYD---EGFGKSKHSEKWTPQATPTGTSSFIPVEESKSSEKKETP 117

Query:   117 YPIEKVAVDGTSYHKACFRCTH--GGCVISPSN--YVAHEHRLYCRH 159
               I       T     C +  +     V+       V H+  L C H
Sbjct:   118 TTISSKFSGSTEKCNLCNKTVYLTEKIVVEDKEDKKVLHKQCLKCTH 164

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|F1NSM0 F1NSM0 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 220 (82.5 bits), Expect = 2.5e-19, Sum P(2) = 2.5e-19
 Identities = 35/67 (52%), Positives = 46/67 (68%)

Query:    11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMT 70
             C  C++ VY +++L AD + +HK+CFRCHHC   L L NY S  G +YCKPHF QLFK  
Sbjct:   217 CTLCQQRVYPMERLVADKQSFHKSCFRCHHCGSQLSLGNYASLHGQIYCKPHFKQLFKSK 276

Query:    71 GSLDKSF 77
             G+ D+ F
Sbjct:   277 GNYDEGF 283

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 64/193 (33%), Positives = 91/193 (47%)

Query:     6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK----- 60
             G   KC ACEKTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK     
Sbjct:     5 GGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGR 64

Query:    61 ---PH---FDQ----LFKMTGS-LDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKC 109
                P    F Q    L   TG  L   F+ +PK  R   +++    S+ S+ F G  +KC
Sbjct:    65 RYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTSNP---SKFSAKF-GESEKC 120

Query:   110 VACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKG 169
               C K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + + F   G
Sbjct:   121 PRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

Query:   170 -NFSQLDNHEQVE 181
               F  L   +QVE
Sbjct:   181 IGFGGLT--QQVE 191

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

GO:0003300 "cardiac muscle hypertrophy" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005856 "cytoskeleton" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0030154 "cell differentiation" evidence=IEA

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

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

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

GO:0042805 "actinin binding" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

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

GO:0055003 "cardiac myofibril assembly" evidence=IMP

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

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

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 64/193 (33%), Positives = 90/193 (46%)

Query:     6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK----- 60
             G   KC ACEKTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK     
Sbjct:     5 GGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGR 64

Query:    61 ---PH---FDQ----LFKMTGS-LDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKC 109
                P    + Q    L   TG  L   F+ +PK  R   SA     S+ ++ F G  +KC
Sbjct:    65 RYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKPAR---SATTSNPSKFTAKF-GESEKC 120

Query:   110 VACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKG 169
               C K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + + F   G
Sbjct:   121 PRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

Query:   170 -NFSQLDNHEQVE 181
               F  L   +QVE
Sbjct:   181 IGFGGLT--QQVE 191

GO:0060048 "cardiac muscle contraction" evidence=IEA

GO:0055003 "cardiac myofibril assembly" evidence=IEA

GO:0042805 "actinin binding" evidence=IEA

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

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

GO:0031433 "telethonin binding" evidence=IEA

GO:0030018 "Z disc" evidence=IEA

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

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

GO:0003300 "cardiac muscle hypertrophy" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q4U0T9 CSRP3 "Cysteine and glycine-rich protein 3" [Bos taurus (taxid:9913)]

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 60/189 (31%), Positives = 88/189 (46%)

Query:     6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
             G   KC ACEKTVY  +++  + + +HK CF C  C+  L  +   + E  +YCK  + +
Sbjct:     5 GGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGR 64

Query:    66 LFKMTGSLDKSFEGTPKT-------VRVERSADQVTNSRVSS---MFA--GTQDKCVACK 113
              +   G       G   T       ++ ++S  Q  ++  SS    FA  G  +KC  C 
Sbjct:    65 RYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKQARSATTSSNPSKFAKFGESEKCPRCG 124

Query:   114 KTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKG-NFS 172
             K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + + F   G  F 
Sbjct:   125 KSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTGIGFG 184

Query:   173 QLDNHEQVE 181
              L  H QVE
Sbjct:   185 GL-TH-QVE 191

GO:0030018 "Z disc" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0060048 "cardiac muscle contraction" evidence=IEA

GO:0055003 "cardiac myofibril assembly" evidence=IEA

GO:0042805 "actinin binding" evidence=IEA

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

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

GO:0031433 "telethonin binding" evidence=IEA

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

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

GO:0003300 "cardiac muscle hypertrophy" evidence=IEA

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

GO:0007517 "muscle organ development" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P29675	SF3_HELAN	No assigned EC number	0.6842	0.9894	0.8538	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pm.C_LG_XII000273 hypothetical protein (191 aa) (Populus trichocarpa)

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	189
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	8e-37
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	2e-36
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	4e-23
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-19
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	4e-18
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	6e-17
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	9e-17
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	2e-14
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	3e-14
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	5e-13
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	1e-12
pfam00412	58	pfam00412, LIM, LIM domain	4e-12
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	2e-11
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	9e-11
pfam00412	58	pfam00412, LIM, LIM domain	5e-10
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	7e-10
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	1e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-09
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	7e-09
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-08
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	3e-08
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	4e-08
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	5e-08
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	2e-07
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-07
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	2e-07
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	2e-07
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	5e-07
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	6e-07
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	1e-06
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	1e-06
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	2e-06
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	3e-06
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	3e-06
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	5e-06
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	8e-06
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	2e-05
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	2e-05
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	4e-05
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	5e-05
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	5e-05
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	7e-05
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	7e-05
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	9e-05
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	9e-05
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	1e-04
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	1e-04
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	1e-04
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	1e-04
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	1e-04
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	2e-04
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	2e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	2e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	2e-04
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	2e-04
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	4e-04
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	5e-04
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	8e-04
cd09345	54	cd09345, LIM2_FHL, The second LIM domain of Four a	0.001
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	0.002
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	0.002
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	0.002
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	0.002
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	0.003

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

 Score =  121 bits (306), Expect = 8e-37
 Identities = 53/62 (85%), Positives = 57/62 (91%)

Query: 7  TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66
          TTQKCKAC+KTVYLVDQL+AD  VYHK+CFRC HCKGTLKLSNY S EGVLYCKPHF+QL
Sbjct: 1  TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 67 FK 68
          FK
Sbjct: 61 FK 62

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 =  120 bits (303), Expect = 2e-36
 Identities = 49/61 (80%), Positives = 56/61 (91%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQK 168
           CVAC KTVYPIEKV V+GTSYHK+CF+C+HGGC ISPSNY AHE RLYC+HHH+QLFK+K
Sbjct: 1   CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 169 G 169
           G
Sbjct: 61  G 61

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

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

 Score = 86.6 bits (215), Expect = 4e-23
 Identities = 33/53 (62%), Positives = 40/53 (75%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C  C KTVY +++L AD K++HK+CFRC HC  TL+L NY 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|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein SF3

 Score = 77.5 bits (191), Expect = 2e-19
 Identities = 31/63 (49%), Positives = 42/63 (66%)

Query: 105 TQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL 164
           T  KC AC KTVY +++++ DG  YHK+CFRC+H    +  SNY + E  LYC+ H  QL
Sbjct: 1   TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 165 FKQ 167
           FK+
Sbjct: 61  FKE 63

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

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

 Score = 73.5 bits (181), Expect = 4e-18
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           C  C KTVYP+E++  DG  +HK+CFRC+H    +   NY + E +LYC+ H 
Sbjct: 1   CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53

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

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

 Score = 71.0 bits (174), Expect = 6e-17
 Identities = 28/53 (52%), Positives = 36/53 (67%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C  C+K VY +++L AD + +HK+CFRC HC   L L NY S  G +YCKPHF
Sbjct: 1  CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

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

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

 Score = 70.6 bits (173), Expect = 9e-17
 Identities = 31/61 (50%), Positives = 40/61 (65%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMT 70
          C AC KTVY ++++T +   YHK+CF+C H   T+  SNY + EG LYCK H  QLFK  
Sbjct: 1  CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 71 G 71
          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|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

 Score = 64.5 bits (157), Expect = 2e-14
 Identities = 26/53 (49%), Positives = 37/53 (69%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C +C+KTVY +++L A+ ++YH +CFRC +C   L L  Y S  G +YCKPHF
Sbjct: 1  CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

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

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

 Score = 63.6 bits (155), Expect = 3e-14
 Identities = 27/53 (50%), Positives = 36/53 (67%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C++C K VY ++++ A+  +YHK CFRC  C   LK+ NY 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 = 60.4 bits (146), Expect = 5e-13
 Identities = 26/53 (49%), Positives = 35/53 (66%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C +C+KTVY +++L AD  V+H +CF C HC   L L +Y +  G  YCKPHF
Sbjct: 1  CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53

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

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

 Score = 59.6 bits (145), Expect = 1e-12
 Identities = 23/55 (41%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYC--SFEGVLYCKPHF 63
          C  C+K VY++++L+A+   +H++CF+C +C  TL+L  Y     +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|215907 pfam00412, LIM, LIM domain

 Score = 58.1 bits (141), Expect = 4e-12
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 109 CVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
           C  C K +Y  E V    G  +H  CFRC   G  + P ++   + +LYC+H + +LF
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 56.2 bits (136), Expect = 2e-11
 Identities = 21/53 (39%), Positives = 30/53 (56%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C  C KTVY  ++L   +K++HK CF+C  C  TL + NY  +    YC  H+
Sbjct: 1  CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

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

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

 Score = 54.4 bits (131), Expect = 9e-11
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHH 160
           C  C+K VYP+E++  D  ++HK+CFRC H    +S  NY +   R+YC+ H
Sbjct: 1   CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPH 52

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

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

 Score = 52.7 bits (127), Expect = 5e-10
 Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 11 CKACEKTVYLVDQLT-ADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          C  C K +Y  + +  A  KV+H  CFRC  C   L   ++   +G 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 = 52.4 bits (126), Expect = 7e-10
 Identities = 23/54 (42%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNY--VAHEHRLYCRHH 160
           C  C KT YP E V  DGT YHK CF+C   G  +S   +  V  +  +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|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 = 51.3 bits (123), Expect = 1e-09
 Identities = 21/52 (40%), Positives = 29/52 (55%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHH 160
           C +C K VY +E++  +   YHK CFRC      +   NY +HE  LYC+ H
Sbjct: 1   CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVH 52

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

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

 Score = 51.6 bits (124), Expect = 1e-09
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 108 KCVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHH 160
           KC  C K +Y  E+V    G  +H  CF+C   G  +S   +   + +LYC+  
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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

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

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
          KC  C K +Y  ++ L A  KV+H  CF+C  C   L    +   +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|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

 Score = 49.5 bits (118), Expect = 7e-09
 Identities = 20/52 (38%), Positives = 33/52 (63%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHH 160
           CV+C+KTVYP+E++  +   YH +CFRC++    +S   Y +    +YC+ H
Sbjct: 1   CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPH 52

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

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

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 15/53 (28%), Positives = 24/53 (45%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C  C K +   + L A  K +H  CF+C  C   L   ++   +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|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting with CasL)

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAH--EHRLYCRHH 160
           C  CKK VY +E+++ +G  +H++CF+C++ G  +    Y     + + YC+ H
Sbjct: 1   CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPH 54

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

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

 Score = 47.2 bits (113), Expect = 4e-08
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          C  C K+VY  +++ A  K +HK+CF C  C   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|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 = 19/54 (35%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYC--SFEGVLYCKPH 62
          C  C KT Y  + +  D   YHK CF+C  C   L L  +     +G +YC  H
Sbjct: 1  CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           C  C KTVYP EK+      +HK CF+C   G  ++  NY  +  + YC  H+
Sbjct: 1   CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 12/53 (22%), Positives = 23/53 (43%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           C  C K +   E +   G  +H  CF+C+  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|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 19/53 (35%), Positives = 32/53 (60%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           C  C   VYP EK+     ++HKACF C     +++ +N+V+H+ + YC+ H+
Sbjct: 1   CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAHN 53

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 19/51 (37%), Positives = 25/51 (49%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKP 61
          C  C K VY  ++ T+  + +HK C RC  CK TL    +   EG  YC  
Sbjct: 1  CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

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

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

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 21/52 (40%), Positives = 27/52 (51%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKP 61
          KC  C K+VY  ++  A    +HK CF+C  C   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|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 44.2 bits (104), Expect = 6e-07
 Identities = 20/52 (38%), Positives = 30/52 (57%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHH 160
           C +C+KTVYP+E++  D   +H +CF C H    +S  +Y A     YC+ H
Sbjct: 1   CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPH 52

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

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

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 21/53 (39%), Positives = 31/53 (58%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C  C K VY  +++   +K +HKACF C  CK TL ++NY  ++   YC  H+
Sbjct: 1  CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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

>gnl|CDD|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 = 43.9 bits (104), Expect = 1e-06
 Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNY--CSFEGVLYCKPHF 63
          C AC + V+LV +   D K+YH+ CFRC  C  TL   +Y      G   C  H 
Sbjct: 1  CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 42.7 bits (101), Expect = 2e-06
 Identities = 18/51 (35%), Positives = 23/51 (45%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRH 159
           C  C K VY  EK    G  +HK C RC      ++P  +  HE + 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|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 42.3 bits (99), Expect = 3e-06
 Identities = 20/53 (37%), Positives = 29/53 (54%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           C  C K VYP EKV     ++HKACF C      ++ +NY  ++ + YC  H+
Sbjct: 1   CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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

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

 Score = 42.3 bits (99), Expect = 3e-06
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          C  C K+VY  +++    K +HK CFRC  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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 41.8 bits (99), Expect = 5e-06
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           C  C K+VY  E+V   G S+HK+CF C      +  +    H+  +YC+
Sbjct: 1   CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

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

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

 Score = 41.4 bits (97), Expect = 8e-06
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          C  C K+VY  +++    K +HK CFRC  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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 20/51 (39%), Positives = 30/51 (58%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          KC ACEKTVY  +++  + + +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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 21/51 (41%), Positives = 30/51 (58%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           KC AC+KTVY  E++  +G S+HK CF C      +  +   AHE  +YC+
Sbjct: 1   KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCK 51

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

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

 Score = 39.5 bits (92), Expect = 4e-05
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
          C  C   VY  +++   ++ +HKACF C  CK  L ++N+ S +   YC+ H
Sbjct: 1  CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

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

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

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 19/50 (38%), Positives = 25/50 (50%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           C  C K+VY  EKV   G  +HK CFRC   G  +  +     +  LYC+
Sbjct: 1   CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50

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

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

 Score = 39.1 bits (91), Expect = 5e-05
 Identities = 17/50 (34%), Positives = 25/50 (50%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           C  C K+VY  EK+   G  +HK CFRC   G  +  +     +  +YC+
Sbjct: 1   CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

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

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

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC 59
           C +C   V+L ++L  + KVYH+ CF+C  C   L   ++   E   YC
Sbjct: 4  PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

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

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

 Score = 38.8 bits (90), Expect = 7e-05
 Identities = 20/51 (39%), Positives = 28/51 (54%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           KC AC +TVY  E+V  DG S+HK CF C      +  +    H+  +YC+
Sbjct: 1   KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCK 51

The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 38.6 bits (90), Expect = 9e-05
 Identities = 15/51 (29%), Positives = 29/51 (56%)

Query: 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC 157
           + C +C   V+  E++ ++G  YH+ CF+C   G  ++P ++   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|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein (CRP)

 Score = 38.4 bits (89), Expect = 9e-05
 Identities = 21/50 (42%), Positives = 30/50 (60%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           C AC+KTVY  E+V  +G S+HK+CF C      +  +   AHE  +YC+
Sbjct: 1   CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCK 50

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

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

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 20/54 (37%), Positives = 28/54 (51%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           KC  C K+VY  E+    G  +HK CF+C     ++  +N   HE  LYC+  H
Sbjct: 1   KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQCH 54

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

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

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          C ACEKTVY  +++  + + +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|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          C  C  +VY  +++    K +HK CFRC  C  +L+ +     EG +YCK
Sbjct: 1  CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

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

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

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 16/49 (32%), Positives = 25/49 (51%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC 59
          C  C K VY  +++ +  + +H+ C RC  CK TL    +   +G  YC
Sbjct: 1  CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49

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

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

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 9  QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          +KC  C+KTVY  +++  + + +HK+CF C  CK  L  +        +YCK
Sbjct: 1  KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCK 52

The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           KC  C+KTVY  E+V  +G S+HK+CF C      +  +    H   +YC+
Sbjct: 2   KCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCK 52

The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC 157
           C  C KTVY  EKV+  G ++H+ C +C     ++SP  +  H+ + 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|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal Protein (CRIP)

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 16/49 (32%), Positives = 27/49 (55%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC 59
          C  C+K VY  +++T+  K +H+ C +C  C  TL   ++   +G  YC
Sbjct: 1  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49

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

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

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRH 159
           C  C K VY  E+V   G  +H+ C +C   G  ++P ++  H+ + YC H
Sbjct: 1   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNH 51

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

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

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C  C   +     + A N+ +H  CFRC  C  +L  + Y   +G LYC+  +
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLS-NWYFEKDGKLYCRKDY 52

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

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

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          KC AC +TVY  +++  D + +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|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 = 36.2 bits (84), Expect = 5e-04
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEH--RLYCRHHH 161
           C AC + V+ +++  VDG  YH+ CFRC      + P +Y A        C HHH
Sbjct: 1   CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 35.9 bits (82), Expect = 8e-04
 Identities = 17/50 (34%), Positives = 24/50 (48%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           C  C  +VY  EK+   G  +HK CFRC   G  +  +     E  +YC+
Sbjct: 1   CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

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

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 109 CVACKKTVYP-IEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC 157
           C AC K + P  +K+   G  +H+ CF C+     I   +++  + ++YC
Sbjct: 1   CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYC 50

The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 16/49 (32%), Positives = 23/49 (46%)

Query: 109 CVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC 157
           C  C K VY  EKV   G ++H+ C RC      ++   +  H+   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|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein (TLP)

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 15/49 (30%), Positives = 26/49 (53%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC 59
          C  C+KTVY  +++++  K +H+ C +C  C   L    +   +G  YC
Sbjct: 1  CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

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

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          C +C +++Y    L A N  +H  CFRC  C  +L    Y   +G L+CK  +
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLS-HWYYEKDGRLFCKKDY 73

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

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 25 TADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          TA ++VYH +CF CH C+  L+   + + +G  YC+
Sbjct: 16 TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCE 51

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

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

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 11 CKACEKTVYLVDQL-TADNKVYHKACFRCHHCKGTLKL-SNYCSFEGVLYCKPHF 63
          C  C + +   D +  A + VYH ACF C  CK  L     +   E  + CK H+
Sbjct: 1  CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	189
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.94
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.88
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.86
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.85
KOG1700	200	consensus Regulatory protein MLP and related LIM p	99.84
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.82
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.81
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.8
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.77
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.74
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.62
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.57
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.33
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.86
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.69
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.36
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	98.27
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	98.06
KOG0490	235	consensus Transcription factor, contains HOX domai	97.76
KOG0490	235	consensus Transcription factor, contains HOX domai	94.04
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.78
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	85.99
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	85.44
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	84.61
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	84.37
PF14471	51	DUF4428: Domain of unknown function (DUF4428)	83.56
PF11781	36	RRN7: RNA polymerase I-specific transcription init	82.28
PF14471	51	DUF4428: Domain of unknown function (DUF4428)	81.14
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	80.86
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	80.6

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

Probab=99.94  E-value=1e-28  Score=201.76  Aligned_cols=126  Identities=21%  Similarity=0.559  Sum_probs=114.4

Q ss_pred             CCcccCCccccccc-eEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcccccc
Q 029735            9 QKCKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVE   87 (189)
Q Consensus         9 ~~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~   87 (189)
                      .+|.+|+|.|+... .+.||++.||..||+|..|++.|.++.||.+|+++||+.||....                    
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            48999999997554 589999999999999999999999999999999999999998765                    


Q ss_pred             CccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeee-cCCccccHhHHHhhhc
Q 029735           88 RSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVA-HEHRLYCRHHHNQLFK  166 (189)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~-~dg~~yC~~c~~~~~~  166 (189)
                                         .+|..|+++|.+. .+.+.|+.||+.||+|..|++.|++..|.. .++++||..||+++|+
T Consensus       335 -------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA  394 (468)
T KOG1701|consen  335 -------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA  394 (468)
T ss_pred             -------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC
Confidence                               7899999999864 379999999999999999999999987865 5799999999999999


Q ss_pred             CCCCCCCC
Q 029735          167 QKGNFSQL  174 (189)
Q Consensus       167 ~k~~~~~~  174 (189)
                      +||+.+..
T Consensus       395 PrCs~C~~  402 (468)
T KOG1701|consen  395 PRCSVCGN  402 (468)
T ss_pred             cchhhccC
Confidence            99986543

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

Probab=99.88  E-value=2.8e-24  Score=175.89  Aligned_cols=124  Identities=25%  Similarity=0.622  Sum_probs=110.3

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeee-cCCeeeecccHHHHhhccCCCCCCCCCCCccc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCS-FEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTV   84 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   84 (189)
                      ....+|..|++.|+ +.+|.|+|+.||+.||+|-.|.+.|++..|.+ .++++||.+||++.|+                
T Consensus       332 ~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA----------------  394 (468)
T KOG1701|consen  332 DTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA----------------  394 (468)
T ss_pred             HHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC----------------
Confidence            34568999999995 78899999999999999999999999989975 5999999999999998                


Q ss_pred             cccCccCcCCcccccccCCCCCCCCccCCcccccCc------eeeccCccccccCceeCCCCCcCCC----CCeeecCCc
Q 029735           85 RVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE------KVAVDGTSYHKACFRCTHGGCVISP----SNYVAHEHR  154 (189)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~g~~~H~~Cf~C~~C~~~l~~----~~~~~~dg~  154 (189)
                                            ++|+.|+++|.+.+      +|.++++.||.+|++|.+|+.+|+.    ...|..||.
T Consensus       395 ----------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~H  452 (468)
T KOG1701|consen  395 ----------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGH  452 (468)
T ss_pred             ----------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCc
Confidence                                  89999999998754      4789999999999999999999984    347889999


Q ss_pred             cccHhHHHhhhcCC
Q 029735          155 LYCRHHHNQLFKQK  168 (189)
Q Consensus       155 ~yC~~c~~~~~~~k  168 (189)
                      ++|+.|..++....
T Consensus       453 llCk~Ch~~Rl~~~  466 (468)
T KOG1701|consen  453 LLCKTCHLKRLQAG  466 (468)
T ss_pred             eeechhhhhhhccc
Confidence            99999998876543

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

Probab=99.86  E-value=2.5e-23  Score=160.04  Aligned_cols=173  Identities=17%  Similarity=0.253  Sum_probs=128.4

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhcc-----CCCCCCCCCCC
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMT-----GSLDKSFEGTP   81 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~-----~~~~~~~~~~~   81 (189)
                      .+|.|++|++.| .+.++.+++.+||+.||+|..|++.|.+..|+-.+|+.+|..|.++..+..     |..+...+...
T Consensus        72 faPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~  150 (332)
T KOG2272|consen   72 FAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ  150 (332)
T ss_pred             hchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence            368899999999 599999999999999999999999999999999999999999998754321     12222222222


Q ss_pred             ccccccCccCcCC-------------ccccc-ccC------CCCCCCCccCCcccccCceeeccCccccccCceeCCCCC
Q 029735           82 KTVRVERSADQVT-------------NSRVS-SMF------AGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGC  141 (189)
Q Consensus        82 ~~~~~~~~~~~~~-------------~~~~~-~~~------~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~  141 (189)
                      -+...+.|+++.-             ...+. +++      .-+.+.|..|.++|... .|.++|+.||.+.|+|+.|.+
T Consensus       151 ~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~Cek  229 (332)
T KOG2272|consen  151 PLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEK  229 (332)
T ss_pred             cccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHH-HHHHhccccchhheeehhcCC
Confidence            3333334443110             00000 110      01238999999999743 378999999999999999999


Q ss_pred             cCCCCCeeecCCccccHhHHHhhhcCCCCCCCCCChhHHH
Q 029735          142 VISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVE  181 (189)
Q Consensus       142 ~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~~~~~~~  181 (189)
                      |+-+-..+++.|.+||+.||.++||.-|-.+...-.-.|.
T Consensus       230 PFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv  269 (332)
T KOG2272|consen  230 PFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVV  269 (332)
T ss_pred             cccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHH
Confidence            9988889999999999999999999998765544444443

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

Probab=99.85  E-value=2.4e-23  Score=162.79  Aligned_cols=142  Identities=24%  Similarity=0.511  Sum_probs=117.0

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV   86 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   86 (189)
                      ..++|++|.+.|.+.-++.++++.||..|++|+.|..+|.. ..+.+++.+||+.+|.++|+                  
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            56899999999987778999999999999999999999975 46689999999999999998                  


Q ss_pred             cCccCcCCcccccccCCCCCCCCccCCcccccCcee-eccCccccccCceeCCCCCcCCCC-Cee-ecCCccccHhHHHh
Q 029735           87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISPS-NYV-AHEHRLYCRHHHNQ  163 (189)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~-~~~-~~dg~~yC~~c~~~  163 (189)
                                          .+|..|.+.|.+...| .+.+.+||..||.|..|+++|..+ .|| +.|+++.|+.+|+.
T Consensus        93 --------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~  152 (383)
T KOG4577|consen   93 --------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET  152 (383)
T ss_pred             --------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence                                8999999999987755 688999999999999999999874 465 56899999999998


Q ss_pred             hhcCCCCCCCCCChhHHHHHhhccCC
Q 029735          164 LFKQKGNFSQLDNHEQVEAVTENATA  189 (189)
Q Consensus       164 ~~~~k~~~~~~~~~~~~~~~~~~~~~  189 (189)
                      .-..-+.  +..+.....|.+..|||
T Consensus       153 Ak~k~~~--~l~gd~~nKRPRTTItA  176 (383)
T KOG4577|consen  153 AKQKHCN--ELEGDASNKRPRTTITA  176 (383)
T ss_pred             HHhcccc--ccccccccCCCcceeeH
Confidence            8665554  22222333444444443

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

Probab=99.84  E-value=1.6e-21  Score=149.86  Aligned_cols=183  Identities=44%  Similarity=0.824  Sum_probs=145.4

Q ss_pred             CcCCCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC-CCCCCCCC
Q 029735            2 ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS-LDKSFEGT   80 (189)
Q Consensus         2 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~-~~~~~~~~   80 (189)
                      |++......|..|++.|+..+.+...|..||+.||+|..|.+.|....+...++.+||..+|...+++... ....++..
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            45677788999999999999998899999999999999999999999999999999999998888877653 33433322


Q ss_pred             CccccccCccC--cCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccH
Q 029735           81 PKTVRVERSAD--QVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR  158 (189)
Q Consensus        81 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~  158 (189)
                      ..+.....+..  .+........+.++...|.+|.+.+++.+.+...+..||..||+|+.|+..|....+...+|.+||.
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            22222222222  1222234455667779999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhcCCCCCCCCCChhHHHHHh
Q 029735          159 HHHNQLFKQKGNFSQLDNHEQVEAVT  184 (189)
Q Consensus       159 ~c~~~~~~~k~~~~~~~~~~~~~~~~  184 (189)
                      .++..++-.+..+..+..+....+.+
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (200)
T KOG1700|consen  161 HHFAQLFKGKGNYNEGFGARENKEAA  186 (200)
T ss_pred             hhhheeecCCCcccccchhhhhhhhh
Confidence            99998887777777666655544443

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

Probab=99.82  E-value=8.1e-22  Score=151.73  Aligned_cols=117  Identities=20%  Similarity=0.506  Sum_probs=108.0

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV   86 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   86 (189)
                      +.++|+.|.++| .+.++.++|+.||.+.|+|+.|-+|+-+...|++.|..||+.+|.++++                  
T Consensus       194 gipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG------------------  254 (332)
T KOG2272|consen  194 GIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFG------------------  254 (332)
T ss_pred             CCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhh------------------
Confidence            468999999999 4678899999999999999999999988899999999999999999998                  


Q ss_pred             cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCC-CCeeecCCccccHhHHHh
Q 029735           87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHHHNQ  163 (189)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~dg~~yC~~c~~~  163 (189)
                                          ..|-.|+.+|.+ +.+.++++.|.++||+|+.|.+.|.. ..|++.|-.|.|+.||.+
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 --------------------NLCFICNRVIGG-DVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR  311 (332)
T ss_pred             --------------------hhheecCCccCc-cHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence                                899999999974 55899999999999999999999987 468999999999999974

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

Probab=99.81  E-value=1e-20  Score=159.92  Aligned_cols=165  Identities=18%  Similarity=0.354  Sum_probs=114.9

Q ss_pred             CCcccCCccccccceEeeCCccccccccccccccccccCCCeeecC-CeeeecccHHHHh------------hccCCC--
Q 029735            9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE-GVLYCKPHFDQLF------------KMTGSL--   73 (189)
Q Consensus         9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~-g~~yC~~cy~~~~------------~~~~~~--   73 (189)
                      -.|.+|.+... +++|.+.+++||..||.|..|+..|..+.|+.++ .++|+........            .++|..  
T Consensus        17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs   95 (670)
T KOG1044|consen   17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS   95 (670)
T ss_pred             eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence            46999999994 9999999999999999999999999999988774 4677763322211            111110  


Q ss_pred             --CCCCCCCCccccccCccC-c--CCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCe
Q 029735           74 --DKSFEGTPKTVRVERSAD-Q--VTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNY  148 (189)
Q Consensus        74 --~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~  148 (189)
                        ..+|....+++..++... +  +.+.........++..|++|++.|..+..+.++++.||..||+|..|...|.+ .|
T Consensus        96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey  174 (670)
T KOG1044|consen   96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EY  174 (670)
T ss_pred             ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-ee
Confidence              111111111111111110 0  00000111111234789999999998888899999999999999999999986 58


Q ss_pred             eecCCccccHhHHHhhhcCCCCCCCCC
Q 029735          149 VAHEHRLYCRHHHNQLFKQKGNFSQLD  175 (189)
Q Consensus       149 ~~~dg~~yC~~c~~~~~~~k~~~~~~~  175 (189)
                      +..||.|||+.+|++.||-||..++.+
T Consensus       175 ~skdg~pyce~dy~~~fgvkc~~c~~f  201 (670)
T KOG1044|consen  175 MSKDGVPYCEKDYQAKFGVKCEECEKF  201 (670)
T ss_pred             eccCCCcchhhhhhhhcCeehHHhhhh
Confidence            999999999999999999999755443

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

Probab=99.80  E-value=2.8e-20  Score=160.44  Aligned_cols=127  Identities=24%  Similarity=0.536  Sum_probs=116.9

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV   86 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   86 (189)
                      ..+.|..|.+.|.....+.++++.||+.+|.|..|...|....|...+|.+||..|+.+.++                  
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            45899999999953388999999999999999999999998899999999999999999987                  


Q ss_pred             cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735           87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                                          +.|.+|+++|.+. .|.+.++.||++||.|..|+++|....|+..||.+||+.||+++++
T Consensus       364 --------------------p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~  422 (479)
T KOG1703|consen  364 --------------------PNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT  422 (479)
T ss_pred             --------------------ccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc
Confidence                                8999999999864 4888899999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 029735          167 QKGNFS  172 (189)
Q Consensus       167 ~k~~~~  172 (189)
                      +++.++
T Consensus       423 ~~~~~~  428 (479)
T KOG1703|consen  423 TKCDYC  428 (479)
T ss_pred             ccchhc
Confidence            888655

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

Probab=99.77  E-value=6.8e-20  Score=158.05  Aligned_cols=116  Identities=28%  Similarity=0.671  Sum_probs=106.7

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV   86 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   86 (189)
                      ..++|.+|+++|. ++.|.+.++.||++||.|..|+++|.+..|+..++.+||+.||.+++.                  
T Consensus       362 ~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~------------------  422 (479)
T KOG1703|consen  362 FRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT------------------  422 (479)
T ss_pred             hCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc------------------
Confidence            4689999999994 888999999999999999999999999999999999999999999986                  


Q ss_pred             cCccCcCCcccccccCCCCCCCCccCCcccccCce-eeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHH
Q 029735           87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH  161 (189)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~  161 (189)
                                          ++|..|.++|..... +.+++..||..||+|..|.+.|..+.|+...++|+|..|+
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                                689999998874433 7999999999999999999999999999999999999875

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

Probab=99.74  E-value=4.5e-19  Score=150.06  Aligned_cols=115  Identities=23%  Similarity=0.560  Sum_probs=104.6

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRV   86 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   86 (189)
                      +...|++|++.|..+..|.|+++.||..||+|..|+..| .+.|..++|.+||+.||++.|+                  
T Consensus       132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fg------------------  192 (670)
T KOG1044|consen  132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFG------------------  192 (670)
T ss_pred             CCccccchhhhhhccceeeeeccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcC------------------
Confidence            467899999999999999999999999999999999999 5789999999999999999998                  


Q ss_pred             cCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCC-CCeeecCCccccHhHH
Q 029735           87 ERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHHH  161 (189)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~dg~~yC~~c~  161 (189)
                                          .+|..|.+.|.+. .+.+.|++||+.|-+|+.|+.+++. +.+|..+..+|-..|-
T Consensus       193 --------------------vkc~~c~~fisgk-vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~  247 (670)
T KOG1044|consen  193 --------------------VKCEECEKFISGK-VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCK  247 (670)
T ss_pred             --------------------eehHHhhhhhhhh-hhhccCcccCcchhhhhhhccccccchheeeccccccCCccc
Confidence                                8999999999864 3789999999999999999999987 4578888888887775

>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=99.62  E-value=4.2e-16  Score=96.78  Aligned_cols=57  Identities=30%  Similarity=0.771  Sum_probs=52.7

Q ss_pred             cccCCccccccceE-eeCCccccccccccccccccccCCCeeecCCeeeecccHHHHh
Q 029735           11 CKACEKTVYLVDQL-TADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF   67 (189)
Q Consensus        11 C~~C~~~I~~~~~~-~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   67 (189)
                      |.+|+++|.+++.+ .++|+.||++||+|..|+++|.+..|+..+|++||..||.++|
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            78999999877765 7999999999999999999999888999999999999998875

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

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

Probab=99.57  E-value=2.6e-15  Score=93.18  Aligned_cols=57  Identities=26%  Similarity=0.708  Sum_probs=52.9

Q ss_pred             CccCCcccccCcee-eccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhh
Q 029735          109 CVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF  165 (189)
Q Consensus       109 C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~  165 (189)
                      |.+|+++|.+.+.+ .+.|+.||++||+|..|+++|..+.++..+|++||+.||.++|
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            78999999988765 6999999999999999999999988999999999999999886

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=99.33  E-value=1.4e-13  Score=108.32  Aligned_cols=80  Identities=16%  Similarity=0.337  Sum_probs=73.3

Q ss_pred             CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC-CCCCCChhHHHHHh
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN-FSQLDNHEQVEAVT  184 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~-~~~~~~~~~~~~~~  184 (189)
                      .++|++|.+.|.+...+.++++.||..|++|+.|+.+|.. ..+.++|.+||+++|.++||+||+ ...|+.+.+|.|.+
T Consensus        33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkA  111 (383)
T KOG4577|consen   33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKA  111 (383)
T ss_pred             cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence            3899999999998776789999999999999999999986 578899999999999999999999 68899999999987


Q ss_pred             hc
Q 029735          185 EN  186 (189)
Q Consensus       185 ~~  186 (189)
                      ++
T Consensus       112 qd  113 (383)
T KOG4577|consen  112 QD  113 (383)
T ss_pred             hc
Confidence            75

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

Probab=98.86  E-value=1.5e-09  Score=61.25  Aligned_cols=37  Identities=38%  Similarity=0.730  Sum_probs=33.5

Q ss_pred             CcccCCcccccc-ceEeeCCcccccccccccccccccc
Q 029735           10 KCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGTLK   46 (189)
Q Consensus        10 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~   46 (189)
                      +|.+|+++|.++ ..+.++++.||+.||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999876 6788999999999999999999985

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

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

Probab=98.69  E-value=1.2e-08  Score=57.48  Aligned_cols=37  Identities=27%  Similarity=0.633  Sum_probs=32.9

Q ss_pred             CCccCCcccccC-ceeeccCccccccCceeCCCCCcCC
Q 029735          108 KCVACKKTVYPI-EKVAVDGTSYHKACFRCTHGGCVIS  144 (189)
Q Consensus       108 ~C~~C~~~I~~~-~~v~~~g~~~H~~Cf~C~~C~~~l~  144 (189)
                      +|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            488999999986 4578899999999999999999885

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=98.36  E-value=1.6e-07  Score=72.45  Aligned_cols=69  Identities=43%  Similarity=0.809  Sum_probs=62.0

Q ss_pred             CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC-CCCC
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN-FSQL  174 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~-~~~~  174 (189)
                      ...|..|++.|+..+++...|..||+.||+|..|.+.|..+.+...++.+||..++...++++.. +..+
T Consensus         7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~   76 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKG   76 (200)
T ss_pred             cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccc
Confidence            36899999999998888899999999999999999999998888999999999988888888876 5554

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=98.27  E-value=9.6e-08  Score=72.32  Aligned_cols=75  Identities=28%  Similarity=0.585  Sum_probs=62.0

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCCCChhHHHHHhhc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHEQVEAVTEN  186 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~~~~~~~~~~~~  186 (189)
                      ..|..|++.+++.|.|.-+++.||..||+|..|+.+|...++...|.++||..+|.+..     +.-...-+...|+.+|
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~-----at~~adTPEm~Rik~n   79 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV-----ATVMADTPEMRRIKEN   79 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce-----eeeecCCHHHHHHHhh
Confidence            57889999999999999999999999999999999999888888999999999997654     3333444555555554

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=98.06  E-value=4e-07  Score=69.01  Aligned_cols=61  Identities=36%  Similarity=0.811  Sum_probs=55.5

Q ss_pred             CCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      ...|..|++.+++.|.|.-+++.||..||+|..|+-+|.-..|-..+.++||..+|.+..+
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence            4678999999999999999999999999999999999988888888999999999976654

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

Probab=97.76  E-value=4.9e-06  Score=65.31  Aligned_cols=112  Identities=18%  Similarity=0.502  Sum_probs=86.2

Q ss_pred             cCCccccccceEeeCCcccccccccccccccccc--CCCeeecCCeeeecccHHH--HhhccCCCCCCCCCCCccccccC
Q 029735           13 ACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK--LSNYCSFEGVLYCKPHFDQ--LFKMTGSLDKSFEGTPKTVRVER   88 (189)
Q Consensus        13 ~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~--~~~~~~~~~~~~~~~~~~~~~~~   88 (189)
                      .|+..|.+...+.+.+..||..|..|..|...|.  ...|.. +|..||..+|.+  .+.                    
T Consensus         1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~--------------------   59 (235)
T KOG0490|consen    1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS--------------------   59 (235)
T ss_pred             CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc--------------------
Confidence            3677886666678889999999999999999997  445555 999999999987  332                    


Q ss_pred             ccCcCCcccccccCCCCCCCCccCCcccccCcee-eccCccccccCceeCCCCCcCCC-CCeeec-CCccccHhHHHhh
Q 029735           89 SADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGTSYHKACFRCTHGGCVISP-SNYVAH-EHRLYCRHHHNQL  164 (189)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~-dg~~yC~~c~~~~  164 (189)
                                        .+|.+|...+...+.+ .+..+. |..||.|..|...+.. ..+.+. +.+.+|.+++.+.
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                              6899999988665544 455555 9999999999886655 345444 4589998887654

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

Probab=94.04  E-value=0.024  Score=44.31  Aligned_cols=74  Identities=14%  Similarity=0.362  Sum_probs=53.6

Q ss_pred             CCcccccCceeeccCccccccCceeCCCCCcCC--CCCeeecCCccccHhHHHh--hhcCCCCC-CCCC-ChhHHHHHhh
Q 029735          112 CKKTVYPIEKVAVDGTSYHKACFRCTHGGCVIS--PSNYVAHEHRLYCRHHHNQ--LFKQKGNF-SQLD-NHEQVEAVTE  185 (189)
Q Consensus       112 C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~--~~~~~~~dg~~yC~~c~~~--~~~~k~~~-~~~~-~~~~~~~~~~  185 (189)
                      |+..|.+...+.+.+..||..|..|..|...|.  ...|.. +|..||..++.+  .+..++.- .-.. +-..++++++
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~   80 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFE   80 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhc
Confidence            566676655566679999999999999999997  444555 999999999998  77777763 3332 3334666554


Q ss_pred             c
Q 029735          186 N  186 (189)
Q Consensus       186 ~  186 (189)
                      +
T Consensus        81 ~   81 (235)
T KOG0490|consen   81 K   81 (235)
T ss_pred             C
Confidence            3

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.78  E-value=0.18  Score=30.31  Aligned_cols=37  Identities=27%  Similarity=0.626  Sum_probs=25.7

Q ss_pred             CCCccCCcccccCceee---ccCccccccCc----eeCC--CCCcC
Q 029735          107 DKCVACKKTVYPIEKVA---VDGTSYHKACF----RCTH--GGCVI  143 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~---~~g~~~H~~Cf----~C~~--C~~~l  143 (189)
                      .+|..|+++|.+.+.+.   .-+..||++|+    .|..  |+..+
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            78999999997544332   45788999887    4554  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=85.99  E-value=0.55  Score=26.00  Aligned_cols=32  Identities=25%  Similarity=0.476  Sum_probs=22.3

Q ss_pred             cccCCccccccc-eEeeCCccccccccccccccccc
Q 029735           11 CKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTL   45 (189)
Q Consensus        11 C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L   45 (189)
                      |.-|+++|.+.. .+...++.||.   -|..|...|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~f---CC~tC~~~f   33 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYF---CCPTCLSQF   33 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEE---ECHHHHHHH
Confidence            678999996443 47889999994   445555554

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

>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=85.44  E-value=0.7  Score=31.37  Aligned_cols=29  Identities=24%  Similarity=0.417  Sum_probs=15.7

Q ss_pred             CCCcccCCccccccce-EeeCCcccccccc
Q 029735            8 TQKCKACEKTVYLVDQ-LTADNKVYHKACF   36 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~-~~~~~~~~H~~CF   36 (189)
                      ...|..|+++|..... +...|..+|..|+
T Consensus        78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~  107 (109)
T PF10367_consen   78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI  107 (109)
T ss_pred             CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence            4457777777754333 2334455666654

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 [].

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=84.61  E-value=0.52  Score=23.16  Aligned_cols=9  Identities=22%  Similarity=0.785  Sum_probs=6.1

Q ss_pred             cccCCcccc
Q 029735           11 CKACEKTVY   19 (189)
Q Consensus        11 C~~C~~~I~   19 (189)
                      |+.|+..|.
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            667777774

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

Probab=84.37  E-value=0.4  Score=32.74  Aligned_cols=31  Identities=32%  Similarity=0.568  Sum_probs=19.6

Q ss_pred             CcccCCccccccceEeeC-Ccccccccccccc
Q 029735           10 KCKACEKTVYLVDQLTAD-NKVYHKACFRCHH   40 (189)
Q Consensus        10 ~C~~C~~~I~~~~~~~~~-~~~~H~~CF~C~~   40 (189)
                      +|..|+++|+.|+.+.+. +..-|-.||+=..
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~   35 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA   35 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence            577777777777765443 3456777776543

>PF14471 DUF4428: Domain of unknown function (DUF4428)

Probab=83.56  E-value=0.61  Score=27.76  Aligned_cols=29  Identities=24%  Similarity=0.584  Sum_probs=22.4

Q ss_pred             ccccccccccCCC-eeecCCeeeecccHHHH
Q 029735           37 RCHHCKGTLKLSN-YCSFEGVLYCKPHFDQL   66 (189)
Q Consensus        37 ~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~   66 (189)
                      .|+.|+..++--. +-..|| +.|..|+.++
T Consensus         1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl   30 (51)
T PF14471_consen    1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL   30 (51)
T ss_pred             CCCccccccccccceeccCc-cchHHHHHHh
Confidence            4888999885433 557787 7999999887

>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=82.28  E-value=0.85  Score=25.05  Aligned_cols=24  Identities=25%  Similarity=0.483  Sum_probs=17.7

Q ss_pred             cccccccccccCCCeeecCCeeeecccH
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHF   63 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy   63 (189)
                      +.|..|+..    .|...+|..||..|-
T Consensus         9 ~~C~~C~~~----~~~~~dG~~yC~~cG   32 (36)
T PF11781_consen    9 EPCPVCGSR----WFYSDDGFYYCDRCG   32 (36)
T ss_pred             CcCCCCCCe----EeEccCCEEEhhhCc
Confidence            347777665    467889999998775

>PF14471 DUF4428: Domain of unknown function (DUF4428)

Probab=81.14  E-value=1.3  Score=26.30  Aligned_cols=29  Identities=17%  Similarity=0.423  Sum_probs=22.4

Q ss_pred             eeCCCCCcCCC-CCeeecCCccccHhHHHhh
Q 029735          135 RCTHGGCVISP-SNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       135 ~C~~C~~~l~~-~~~~~~dg~~yC~~c~~~~  164 (189)
                      .|..|+..++. ..+-..|| ..|..|+.++
T Consensus         1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl   30 (51)
T PF14471_consen    1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL   30 (51)
T ss_pred             CCCccccccccccceeccCc-cchHHHHHHh
Confidence            37888888876 33567788 6899999887

>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=80.86  E-value=1.3  Score=29.93  Aligned_cols=29  Identities=28%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             CCCccCCcccccCce-eeccCccccccCce
Q 029735          107 DKCVACKKTVYPIEK-VAVDGTSYHKACFR  135 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~  135 (189)
                      ..|..|+++|..... +...|..+|..|++
T Consensus        79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            679999999876443 34567778887753

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 [].

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production

Probab=80.60  E-value=0.78  Score=30.69  Aligned_cols=30  Identities=23%  Similarity=0.518  Sum_probs=19.3

Q ss_pred             ccccccccccccccccCCCeeecCCeeeecccHHHH
Q 029735           31 YHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL   66 (189)
Q Consensus        31 ~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   66 (189)
                      |-..=-.|..|...+..      .|..||..|..+.
T Consensus        40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk   69 (90)
T PF10235_consen   40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK   69 (90)
T ss_pred             ccccCcccccccccccc------CCCccChhhhccc
Confidence            44433467888777743      2567999996544

This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	189
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		2e-16
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		3e-12
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		1e-12
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		5e-07
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		9e-07
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		2e-06
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		4e-06
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		7e-06
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		2e-05
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		1e-05
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		8e-05
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		2e-05
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		2e-04
2o10_A	60	Solution Structure Of The N-Terminal Lim Domain Of		3e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		3e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		2e-04
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		4e-05
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		7e-04
1a7i_A	81	Amino-Terminal Lim Domain From Quail Cysteine And G		7e-05

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 50/79 (63%)
Query: 5  AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFD 64
          A   + C  C+KTVY +++L A+ +V+H +CFRC +C   L L  Y S  G +YCKPHF+
Sbjct: 12 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFN 71
Query: 65 QLFKMTGSLDKSFEGTPKT 83
          QLFK  G+ D+ F   P +
Sbjct: 72 QLFKSKGNYDEGFGSGPSS 90

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 46/71 (64%)
Query: 103 AGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHN 162
           A  ++ CV C+KTVYP+E++  +   +H +CFRC++    +S   Y +   R+YC+ H N
Sbjct: 12  APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFN 71
Query: 163 QLFKQKGNFSQ 173
           QLFK KGN+ +
Sbjct: 72  QLFKSKGNYDE 82

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 75/173 (43%), Gaps = 10/173 (5%)
Query: 6   GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
           G  +KC  C+K VY  +++  +   +HK+CF C  CK  L  +        +YCK  + +
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGK 64
Query: 66  LFKMTGSLDKSFEGTPKTVRVER--------SADQVTNSRVSSMF--AGTQDKCVACKKT 115
            +   G       GT  T + E          + + TN   S M    G  D C  C + 
Sbjct: 65  KYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQA 124
Query: 116 VYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQK 168
           VY  EKV   G S+HK+CFRC   G  +  +     +  +YC+  + + 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 = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 35/66 (53%)
Query: 6  GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
          G  +KC AC  +VY  +++    K +HK CFRC  C  +L+ +     EG +YCK  + +
Sbjct: 34 GGAEKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAK 93
Query: 66 LFKMTG 71
           F   G
Sbjct: 94 NFGPKG 99

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 88  RSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSN 147
           R       S+ +  F G  +KC AC  +VY  EKV   G  +HK CFRC   G  +  + 
Sbjct: 19  RPTTNPNTSKFAQKFGGA-EKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTT 77
Query: 148 YVAHEHRLYCRHHHNQLFKQKG 169
               E  +YC+  + + F  KG
Sbjct: 78  LTEKEGEIYCKGCYAKNFGPKG 99

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 34/66 (51%)
Query: 6  GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
          G  +KC  C  +VY  +++    K +HK CFRC  C  +L+ +     EG +YCK  + +
Sbjct: 34 GGAEKCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAK 93
Query: 66 LFKMTG 71
           F   G
Sbjct: 94 NFGPKG 99

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 88  RSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSN 147
           R       S+ +  F G  +KC  C  +VY  EKV   G  +HK CFRC   G  +  + 
Sbjct: 19  RPTTNPNTSKFAQKFGGA-EKCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTT 77
Query: 148 YVAHEHRLYCRHHHNQLFKQKG 169
               E  +YC+  + + F  KG
Sbjct: 78  LTEKEGEIYCKGCYAKNFGPKG 99

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 35/67 (52%)
Query: 1  MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          MA   G +  C  C + VY  +++    K +HK+CFRC  C  +L+ +     +G +YCK
Sbjct: 1  MAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCK 60
Query: 61 PHFDQLF 67
            + + F
Sbjct: 61 GCYAKNF 67

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 32/65 (49%)
Query: 104 GTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQ 163
           G  D C  C + VY  EKV   G S+HK+CFRC   G  +  +     +  +YC+  + +
Sbjct: 6   GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAK 65
Query: 164 LFKQK 168
            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 = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          KC  C K+VY  +++    K +HK CFRC  C  +L+ +N    +G LYCK  + + F
Sbjct: 1  KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 30/58 (51%)
Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
           KC  C K+VY  EKV   G  +HK CFRC   G  +  +N    +  LYC+  + + F
Sbjct: 1   KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 5  AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNY--CSFEGVLYCKPH 62
          AG    C  C + +Y++++L  +   +H++CFRCH C+ TL    Y     +G  YC  H
Sbjct: 12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQH 71
Query: 63 FDQ 65
            Q
Sbjct: 72 LPQ 74

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 103 AGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAH--EHRLYCRHH 160
           AG  D C  C + +Y +E++ V+G  +H++CFRC      + P  Y  H  +   YC  H
Sbjct: 12  AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQH 71
Query: 161 HNQ 163
             Q
Sbjct: 72  LPQ 74

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 30/51 (58%)
Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR 158
           KC AC+KTVY  E++  +G S+HK CF C      +  +   AHE  +YC+
Sbjct: 3   KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 53

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK-PHFDQLFK 68
          KC  C+K VY  +++T+  K +H+ C +C  C  TL    +   EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 69 MTG 71
            G
Sbjct: 62 PKG 64

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHH-HNQLFK 166
           KC  C K VY  E+V   G  +H+ C +C   G  ++   +  HE + YC H  ++ +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 167 QKG 169
            KG
Sbjct: 62  PKG 64

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 9  QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC-KPHFDQLF 67
           KC  C+KTVY  +++++  K +HK C +C  C  TL    +   +G  +C KP +  LF
Sbjct: 10 SKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 27/50 (54%)
Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC 157
           KC  C KTVY  EKV+  G  +HK C +C      ++P  +  H+ + +C
Sbjct: 11  KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFC 60

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 35/66 (53%)
Query: 104 GTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQ 163
           G  +KC AC +TVY  E+V  DG S+H+ CF C      +  +    H+  +YC+  + +
Sbjct: 5   GGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGK 64
Query: 164 LFKQKG 169
            +  KG
Sbjct: 65  KYGPKG 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	189
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-45
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	6e-29
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	3e-25
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	4e-24
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	6e-24
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	9e-23
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	1e-21
2co8_A	82	NEDD9 interacting protein with calponin homology a	2e-21
2co8_A	82	NEDD9 interacting protein with calponin homology a	7e-19
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-20
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-19
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	5e-17
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-13
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-15
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	6e-08
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	4e-15
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	6e-12
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-13
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-07
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	9e-13
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	4e-12
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	1e-09
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	5e-12
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-09
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-11
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-09
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	7e-11
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	6e-07
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-10
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	6e-10
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	9e-07
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	1e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-08
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-09
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-06
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	2e-09
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	2e-06
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	3e-09
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-06
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	5e-08
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	5e-09
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	8e-07
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	5e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-07
2cuq_A	80	Four and A half LIM domains 3; structural genomics	6e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-06
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	7e-09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	6e-06
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	9e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	5e-07
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	2e-08
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	9e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	4e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-06
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-05
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	6e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	2e-05
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	9e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	3e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-05
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	4e-07
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	4e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	4e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	3e-04
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	4e-06
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	2e-04
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	4e-05
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	5e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	6e-05
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	4e-04
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	8e-04
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	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 =  147 bits (371), Expect = 3e-45
 Identities = 46/178 (25%), Positives = 72/178 (40%), Gaps = 10/178 (5%)

Query: 3   SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
              G  +KC  C+K VY  +++  +   +HK+CF C  CK  L  +        +YCK  
Sbjct: 2   PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSC 61

Query: 63  FDQLFKMTGSLDKSFEGTP----------KTVRVERSADQVTNSRVSSMFAGTQDKCVAC 112
           + + +   G       GT           K    +       N+   +   G  D C  C
Sbjct: 62  YGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRC 121

Query: 113 KKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN 170
            + VY  EKV   G S+HK+CFRC   G  +  +     +  +YC+  + + F  KG 
Sbjct: 122 GQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF 179

>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 =  102 bits (255), Expect = 6e-29
 Identities = 36/83 (43%), Positives = 51/83 (61%)

Query: 1  MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          M   A   + C  C+KTVY +++L A+ +V+H +CFRC +C   L L  Y S  G +YCK
Sbjct: 8  MKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCK 67

Query: 61 PHFDQLFKMTGSLDKSFEGTPKT 83
          PHF+QLFK  G+ D+ F   P +
Sbjct: 68 PHFNQLFKSKGNYDEGFGSGPSS 90

>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 = 92.6 bits (230), Expect = 3e-25
 Identities = 30/80 (37%), Positives = 48/80 (60%)

Query: 94  TNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEH 153
           + S      A  ++ CV C+KTVYP+E++  +   +H +CFRC++    +S   Y +   
Sbjct: 3   SGSSGMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHG 62

Query: 154 RLYCRHHHNQLFKQKGNFSQ 173
           R+YC+ H NQLFK KGN+ +
Sbjct: 63  RIYCKPHFNQLFKSKGNYDE 82

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 89.4 bits (222), Expect = 4e-24
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 2  ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYC-K 60
          +  +G   KC  C+KTVY  +++++  K +HK C +C  C  TL    +   +G  +C K
Sbjct: 3  SGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHK 62

Query: 61 PHFDQLFKMTGS 72
          P +  LF    S
Sbjct: 63 PCYATLFGSGPS 74

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 89.0 bits (221), Expect = 6e-24
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 99  SSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYC- 157
           SS  +G   KC  C KTVY  EKV+  G  +HK C +C      ++P  +  H+ + +C 
Sbjct: 2   SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCH 61

Query: 158 RHHHNQLFKQKGN 170
           +  +  LF    +
Sbjct: 62  KPCYATLFGSGPS 74

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

 Score = 85.9 bits (213), Expect = 9e-23
 Identities = 19/70 (27%), Positives = 33/70 (47%)

Query: 3  SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPH 62
             G   KC AC +TVY  +++  D + +H+ CF C  C+  L  +     +  +YCK  
Sbjct: 2  PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61

Query: 63 FDQLFKMTGS 72
          + + +   G 
Sbjct: 62 YGKKYGPKGY 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 = 83.2 bits (206), Expect = 1e-21
 Identities = 22/69 (31%), Positives = 35/69 (50%)

Query: 102 FAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
             G  +KC AC +TVY  E+V  DG S+H+ CF C      +  +    H+  +YC+  +
Sbjct: 3   NWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCY 62

Query: 162 NQLFKQKGN 170
            + +  KG 
Sbjct: 63  GKKYGPKGY 71

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

 Score = 83.1 bits (205), Expect = 2e-21
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 4  FAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSF--EGVLYCKP 61
           AG    C  C + +Y++++L  +   +H++CFRCH C+ TL    Y     +G  YC  
Sbjct: 11 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQ 70

Query: 62 HFDQLFKMTGS 72
          H  Q      S
Sbjct: 71 HLPQTDSGPSS 81

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

 Score = 76.1 bits (187), Expect = 7e-19
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 95  NSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEH- 153
            S      AG  D C  C + +Y +E++ V+G  +H++CFRC      + P  Y  H   
Sbjct: 4   GSSGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGD 63

Query: 154 -RLYCRHHHNQLFK 166
              YC  H  Q   
Sbjct: 64  GHFYCLQHLPQTDS 77

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

 Score = 79.7 bits (197), Expect = 2e-20
 Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRH-HHNQLFK 166
           KC  C K VY  E+V   G  +H+ C +C   G  ++   +  HE + YC H  ++ +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 167 QKGN 170
            KG 
Sbjct: 62  PKGF 65

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

 Score = 77.8 bits (192), Expect = 1e-19
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK-PHFDQLFK 68
          KC  C+K VY  +++T+  K +H+ C +C  C  TL    +   EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 69 MTG 71
            G
Sbjct: 62 PKG 64

>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 = 70.9 bits (174), Expect = 5e-17
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C+ C+      ++ + ++ ++YH+ CF C  C        +  FEG  YC+  F  LF
Sbjct: 13 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 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 = 60.9 bits (148), Expect = 3e-13
 Identities = 20/61 (32%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 106 QDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL 164
              C  CK    P EK V  +G  YH+ CF C           +   E R YC H    L
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 165 F 165
           F
Sbjct: 71  F 71

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

 Score = 68.2 bits (167), Expect = 2e-15
 Identities = 28/167 (16%), Positives = 46/167 (27%), Gaps = 40/167 (23%)

Query: 7   TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE--GVLYCKPHFD 64
           +   C  C++ +     L A ++ +H+ C  C  C   L       +   G   C+  + 
Sbjct: 1   SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 60

Query: 65  QLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-A 123
           +LF                                    G    C +C K +   E    
Sbjct: 61  RLF------------------------------------GQDGLCASCDKRIRAYEMTMR 84

Query: 124 VDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHHHNQLFKQKG 169
           V    YH  CF+C            Y+     + C     +  K  G
Sbjct: 85  VKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 131

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

 Score = 48.2 bits (115), Expect = 6e-08
 Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 6   GTTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKL-SNYCSFEGVLYCKPHF 63
           G    C +C+K +   +  +   +KVYH  CF+C  C+    +   Y      + C+   
Sbjct: 64  GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI 123

Query: 64  DQLFKMTG 71
            +  K+ G
Sbjct: 124 YEWTKING 131

>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 = 66.3 bits (162), Expect = 4e-15
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 7  TTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
           +  C+ C+      ++ + ++ ++YH+ CF C  C        +  FEG  YC+  F  
Sbjct: 10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 66 LF 67
          LF
Sbjct: 70 LF 71

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 77

 Score = 57.8 bits (140), Expect = 6e-12
 Identities = 20/62 (32%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 105 TQDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQ 163
               C  CK    P EK V  +G  YH+ CF C           +   E R YC H    
Sbjct: 10  ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 164 LF 165
           LF
Sbjct: 70  LF 71

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

 Score = 63.2 bits (154), Expect = 2e-13
 Identities = 23/159 (14%), Positives = 46/159 (28%), Gaps = 41/159 (25%)

Query: 10  KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKM 69
           +C  C++ ++  +   A+N+ +H   F C  C   L    Y        CKP + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNH-- 62

Query: 70  TGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAV-DGTS 128
                                                  C  C   + P  +    +  S
Sbjct: 63  ------------------------------------AVVCQGCHNAIDPEVQRVTYNNFS 86

Query: 129 YHKA--CFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
           +H +  CF C+     +    ++  E  ++C     +  
Sbjct: 87  WHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

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

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 9/61 (14%), Positives = 23/61 (37%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ 167
           +C  C + ++  E    +  ++H   F C     +++   YV    +  C+  + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAV 64

Query: 168 K 168
            
Sbjct: 65  V 65

>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 = 62.2 bits (151), Expect = 9e-13
 Identities = 30/162 (18%), Positives = 50/162 (30%), Gaps = 42/162 (25%)

Query: 10  KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKM 69
            C  C++ +     L A ++ +H  C +C  C   L    + S    +YCK  F + F  
Sbjct: 8   MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF-- 64

Query: 70  TGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGTS 128
                                                 KC AC+  + P + V       
Sbjct: 65  ------------------------------------GTKCAACQLGIPPTQVVRRAQDFV 88

Query: 129 YHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQLFKQK 168
           YH  CF C      ++     Y+  + RL C+  +    +  
Sbjct: 89  YHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG 130

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

 Score = 58.5 bits (142), Expect = 4e-12
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          KCK C K +   DQ +     V+HK CF C +CK  +   ++       YC    +  F
Sbjct: 17 KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

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

 Score = 51.6 bits (124), Expect = 1e-09
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 108 KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK 166
           KC  C K +   ++ V   GT +HK CF C++   VI   ++       YC   H   F 
Sbjct: 17  KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA 76

Query: 167 QK 168
             
Sbjct: 77  SG 78

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

 Score = 57.8 bits (140), Expect = 5e-12
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C AC +TV    + L    + +H+ CF C  C+  L   ++   +G  YC P ++  F
Sbjct: 7  GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 65

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

 Score = 50.8 bits (122), Expect = 2e-09
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 108 KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
            C AC +TV P  + +   G ++H+ CF C+     +   ++V  +   YC   +   F
Sbjct: 7   GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 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 = 55.9 bits (135), Expect = 3e-11
 Identities = 12/59 (20%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C+ C+KT+    + +      +H+ CF CH C+  +   ++   +   +C P +++  
Sbjct: 7  GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

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

 Score = 50.1 bits (120), Expect = 4e-09
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 108 KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
            C  CKKT+ P  + +   G+S+H+ CF C      I   +++  +++ +C   + +  
Sbjct: 7   GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score = 57.7 bits (139), Expect = 7e-11
 Identities = 30/166 (18%), Positives = 51/166 (30%), Gaps = 40/166 (24%)

Query: 7   TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE--GVLYCKPHFD 64
           + ++C  C   +     L A +  +H  C +C  C+  L      S+   G++ C+  + 
Sbjct: 4   SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 65  QLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-A 123
           +LF                                    G    C AC +++   E V  
Sbjct: 64  RLF------------------------------------GNSGACSACGQSIPASELVMR 87

Query: 124 VDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHHHNQLFKQK 168
             G  YH  CF C+     + P   +      L+C H         
Sbjct: 88  AQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALING 133

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score = 46.5 bits (110), Expect = 6e-07
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 6   GTTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKL-SNYCSFEGVLYCKPHF 63
           G +  C AC +++   +  + A   VYH  CF C  C+  L     +    G L+C+   
Sbjct: 67  GNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDR 126

Query: 64  DQLF 67
               
Sbjct: 127 PTAL 130

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

 Score = 56.5 bits (136), Expect = 2e-10
 Identities = 30/157 (19%), Positives = 49/157 (31%), Gaps = 42/157 (26%)

Query: 10  KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKM 69
            C  C++ +     L A ++ +H  C +C  C   L    + S    +YCK  F + F  
Sbjct: 62  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF-- 118

Query: 70  TGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGTS 128
                                                 KC AC+  + P + V       
Sbjct: 119 ------------------------------------GTKCAACQLGIPPTQVVRRAQDFV 142

Query: 129 YHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQ 163
           YH  CF C      ++     Y+  + RL C+  +  
Sbjct: 143 YHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 179

>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 = 53.2 bits (128), Expect = 6e-10
 Identities = 22/131 (16%), Positives = 36/131 (27%), Gaps = 40/131 (30%)

Query: 10  KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68
            C  C K +    + +   N+ +H  CFRC  C   L    + + +  + C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 69  MTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV-AVDGT 127
                                                  KC  C K +   ++     GT
Sbjct: 67  --------------------------------------PKCKGCFKAIVAGDQNVEYKGT 88

Query: 128 SYHKACFRCTH 138
            +HK CF    
Sbjct: 89  VWHKDCFSGPS 99

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

 Score = 44.7 bits (106), Expect = 9e-07
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 108 KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK 166
            CV C+K +    K V      +H  CFRC      ++   +VA ++++ C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 167 QK 168
            K
Sbjct: 67  PK 68

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

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C AC + +     + A  K +H   F C  C+       +   +G+ YC+ H++QLF
Sbjct: 7  ICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

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

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 4/66 (6%)

Query: 100 SMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRH 159
           SM       C AC++ +     V   G  +H   F C           +   +   YC  
Sbjct: 2   SMGV---PICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCET 57

Query: 160 HHNQLF 165
           H+NQLF
Sbjct: 58  HYNQLF 63

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

 Score = 51.3 bits (123), Expect = 2e-09
 Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 5  AGTTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHF 63
          +  +  C  C + V      + A ++V+H  CF C  C+  L+  ++ + E   YC+  +
Sbjct: 2  SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61

Query: 64 DQLF 67
              
Sbjct: 62 VATL 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 = 43.6 bits (103), Expect = 1e-06
 Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 1/64 (1%)

Query: 103 AGTQDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH 161
           +     C  C + V      V      +H  CF C+     +   ++ A E R YC   +
Sbjct: 2   SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61

Query: 162 NQLF 165
               
Sbjct: 62  VATL 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 = 51.3 bits (123), Expect = 2e-09
 Identities = 21/67 (31%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 2  ASFAGTTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK 60
          A  A     C  C   +  V   + A +K  H  CF C  C   LK   Y   EG LYC+
Sbjct: 19 AGSAQRMPLCDKCGSGI--VGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCE 76

Query: 61 PHFDQLF 67
           H     
Sbjct: 77 THARART 83

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

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 16/76 (21%), Positives = 19/76 (25%), Gaps = 1/76 (1%)

Query: 93  VTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHE 152
           VT     +  A     C  C   +     V       H  CF C      +    Y   E
Sbjct: 12  VTKVHGGAGSAQRMPLCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVE 70

Query: 153 HRLYCRHHHNQLFKQK 168
             LYC  H        
Sbjct: 71  GELYCETHARARTSGP 86

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

 Score = 50.9 bits (122), Expect = 3e-09
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C  C++ +     L A +K +H +CF+C  C   L    Y S +GV YC+  +   F
Sbjct: 17 HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 73

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

 Score = 42.8 bits (101), Expect = 2e-06
 Identities = 11/58 (18%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
            C  CK+ +   + +      +H +CF+C     +++   Y++ +   YC   ++  F
Sbjct: 17  HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 73

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

 Score = 50.0 bits (120), Expect = 5e-09
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C  C+K +     +T   + +HK CF C  C+  L    + + +   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 = 47.3 bits (113), Expect = 5e-08
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ 167
            CV CKK +     V      +HK CF CT     +S   + A +   YC +    L+  
Sbjct: 7   GCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS 65

Query: 168 K 168
            
Sbjct: 66  G 66

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 50.0 bits (120), Expect = 5e-09
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          KC  C + V L + L+A + V+H  CF C  C  +    ++   +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 = 13/61 (21%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ 167
           KC  C + V     ++   T +H  CF C       S  ++   + R +C  H++     
Sbjct: 17  KCGGCNRPVLE-NYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGS 75

Query: 168 K 168
            
Sbjct: 76  G 76

>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 = 50.0 bits (120), Expect = 6e-09
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          +C  C KT+     +T  ++ +H+ C  C  C+  L    + S +   YC   F +LF
Sbjct: 17 RCARCSKTL-TQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELF 73

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

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ 167
           +C  C KT+     V      +H+ C  CT     ++   + + +   YC     +LF  
Sbjct: 17  RCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75

Query: 168 K 168
            
Sbjct: 76  G 76

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

 Score = 49.8 bits (119), Expect = 7e-09
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 3/60 (5%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK 68
           C  C   +  V   +   ++  H  C+ C  C   LK   +   E  +YC+ H  +   
Sbjct: 17 MCDKCGTGI--VGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVS 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 = 41.7 bits (98), Expect = 6e-06
 Identities = 14/63 (22%), Positives = 20/63 (31%), Gaps = 5/63 (7%)

Query: 108 KCVACKKTVYPIEKVAVD--GTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
            C  C      I  V V       H  C+ CT  G  +    +   E ++YC  H  +  
Sbjct: 17  MCDKCGT---GIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERV 73

Query: 166 KQK 168
              
Sbjct: 74  SGP 76

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

 Score = 49.4 bits (118), Expect = 9e-09
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C  C++ +    + L  +++ +H+ CFRC  C+ +L    +   +  L C   +   F
Sbjct: 17 TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

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

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 108 KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
            C  C++ +    + +  +   +H+ CFRC      ++   +   +  L C   +   F
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

>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 = 48.5 bits (116), Expect = 2e-08
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C  C K +     +T  ++ +H  CF C  C   L    + + E   YC   +    
Sbjct: 7  GCVKCNKAI-TSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFV 63

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

 Score = 46.6 bits (111), Expect = 9e-08
 Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 1/62 (1%)

Query: 107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK 166
             CV C K +     +      +H  CF C      ++   + A E + YC   +     
Sbjct: 6   SGCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64

Query: 167 QK 168
             
Sbjct: 65  GP 66

>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 = 4e-08
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 10 KCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
           C  C + +      L A  K +H   F C HCK T+    +   +G LYC+  +++ F
Sbjct: 27 MCAHCNQVI--RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

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

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLF 165
            C  C + +     +   G S+H   F C H    ++   +V  +  LYC   + + F
Sbjct: 27  MCAHCNQVIRG-PFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 47.5 bits (113), Expect = 4e-08
 Identities = 9/61 (14%), Positives = 21/61 (34%), Gaps = 3/61 (4%)

Query: 10 KCKACEKTVYLVDQ---LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66
           C  C   +  +     ++ + + +H  CF C  C  +L    + +    + C      +
Sbjct: 7  GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 67 F 67
           
Sbjct: 67 S 67

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 7/61 (11%), Positives = 18/61 (29%), Gaps = 3/61 (4%)

Query: 108 KCVACKKTVYPIEK---VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL 164
            C  C   +  +     ++ +   +H  CF C      +    ++     + C      +
Sbjct: 7   GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 165 F 165
            
Sbjct: 67  S 67

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

 Score = 47.4 bits (113), Expect = 6e-08
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 4  FAGTTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYC-SFEGVLYCKP 61
          +  T +KC  C + +  +D+ L A  K YH  CF C  C   L    +       ++C  
Sbjct: 11 YVATLEKCATCSQPI--LDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIE 68

Query: 62 HFDQLF 67
           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 = 40.4 bits (95), Expect = 2e-05
 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 102 FAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSN-YVAHEHRLYCRHH 160
           +  T +KC  C + +     +   G +YH  CF C      +      V    +++C   
Sbjct: 11  YVATLEKCATCSQPILD-RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 161 HNQLF 165
            ++ F
Sbjct: 70  FHRKF 74

>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 = 46.3 bits (110), Expect = 9e-08
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 8  TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          +  C  C + + +   + A N  +H  CFRC  C+  L    +    G   C+P  ++  
Sbjct: 5  SSGCHQCGEFI-IGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 63

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

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ 167
            C  C + +     +     S+H  CFRC     V++   +V +  R  CR  HN+    
Sbjct: 7   GCHQCGEFIIG-RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKAS 65

Query: 168 K 168
            
Sbjct: 66  G 66

>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 = 47.8 bits (113), Expect = 1e-07
 Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 5   AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE--GVLYCKPH 62
             + ++C  C   +     L A +  +H  C +C  C+  L      S+   G++ C+  
Sbjct: 58  GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 117

Query: 63  FDQLF 67
           + +LF
Sbjct: 118 YIRLF 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 = 42.0 bits (98), Expect = 1e-05
 Identities = 9/65 (13%), Positives = 24/65 (36%), Gaps = 2/65 (3%)

Query: 103 AGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEH--RLYCRHH 160
             +  +C  C   +     +    + +H  C +C+     +      ++     + CR+ 
Sbjct: 58  GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 117

Query: 161 HNQLF 165
           + +LF
Sbjct: 118 YIRLF 122

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

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 4/61 (6%)

Query: 10 KCKACEKTVYLVDQ----LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ 65
          KC  C+  +    +    +  + + +H  CF C  C   L    +   +  +YC     +
Sbjct: 17 KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 66 L 66
          L
Sbjct: 77 L 77

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

 Score = 42.1 bits (99), Expect = 4e-06
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 108 KCVACKKTVYPIEK----VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQ 163
           KC  CK  +    K    VA +G S+H  CF C      ++   +V H+ ++YC     +
Sbjct: 17  KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 164 L 164
           L
Sbjct: 77  L 77

>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 = 42.2 bits (99), Expect = 4e-06
 Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 10 KCKACEKTVYLVDQ---LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL 66
           C AC K +  +     +   +  +H  CF C  C  +L    + +    ++C+     +
Sbjct: 7  GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 67 F 67
           
Sbjct: 67 D 67

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

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 108 KCVACKKTVYPI---EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL 164
            CVAC K +  +   + +    + +H  CF C      +    ++     ++C+   + +
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 165 F 165
            
Sbjct: 67  D 67

>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 = 31/68 (45%), Gaps = 2/68 (2%)

Query: 7  TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE--GVLYCKPHFD 64
          + ++C  C   +     L A +  +H  C +C  C+  L      S+   G++ C+  + 
Sbjct: 4  SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 65 QLFKMTGS 72
          +LF  +G+
Sbjct: 64 RLFGNSGA 71

>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 = 38.8 bits (90), Expect = 2e-04
 Identities = 10/64 (15%), Positives = 22/64 (34%), Gaps = 2/64 (3%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSN--YVAHEHRLYCRHHHNQLF 165
           +C  C   +     +    + +H  C +C+     +             + CR+ + +LF
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 166 KQKG 169
              G
Sbjct: 67  GNSG 70

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

 Score = 39.4 bits (92), Expect = 4e-05
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 3/60 (5%)

Query: 10 KCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKL--SNYCSFEGVLYCKPHFDQLF 67
           C  C   +     + A    YH  CF C  CK  ++   +        LYC    +++ 
Sbjct: 17 FCHGCSLLM-TGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

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

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 3/63 (4%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQLF 165
            C  C   +     VA +   YH  CF C     +I    +  +     LYC   HN++ 
Sbjct: 17  FCHGCSLLMTGPFMVAGE-FKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

Query: 166 KQK 168
              
Sbjct: 76  SGP 78

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

 Score = 39.0 bits (91), Expect = 6e-05
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 11 CKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF 67
          C+ C   +     L   N  YH   F C +C   L  ++    +G LYC P  D++ 
Sbjct: 18 CQKC-HAIIDEQPLIFKNDPYHPDHFNCANCGKELT-ADARELKGELYCLPCHDKMG 72

>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 = 4e-04
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACF 134
            C  C K VYP EKV      +HKACF
Sbjct: 5   NCARCGKIVYPTEKVNCLDKFWHKACF 31

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

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

Query: 9  QKCKACEKTVYLVDQLTADNKVYHKACF 36
            C  C K VY  +++   +K +HKACF
Sbjct: 4  PNCARCGKIVYPTEKVNCLDKFWHKACF 31

>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 = 37.3 bits (86), Expect = 4e-04
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 6  GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFE--GVLYCKPHF 63
          G+   C  C++ +     L A ++ +H+ C  C  C   L       +   G   C+  +
Sbjct: 1  GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 64 DQLFKMTG 71
           +L    G
Sbjct: 61 LRLGGSGG 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	189
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	100.0
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.98
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.97
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.97
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.96
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.96
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.93
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.91
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.86
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.84
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	99.83
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.83
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.81
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.79
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.78
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.77
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.77
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.76
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.76
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.75
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.74
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.73
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.72
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.72
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.71
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.71
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.71
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.71
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.71
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.71
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.7
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.7
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.7
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.7
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.7
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.7
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle 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	99.69
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.69
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.69
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.69
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.68
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.67
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.67
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.67
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.67
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.67
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	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
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.66
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.66
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.66
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.66
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.65
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.65
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.65
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.64
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.64
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.63
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.63
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.63
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.62
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.62
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.61
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	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	99.6
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.6
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.59
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.59
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.59
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.58
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.57
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.57
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.57
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.55
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.53
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.53
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.5
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.44
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.43
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.53
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.53
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	91.41
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	89.71
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	89.35
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	84.84
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	81.08

>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=4.8e-34  Score=218.05  Aligned_cols=166  Identities=28%  Similarity=0.592  Sum_probs=133.4

Q ss_pred             cCCCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCc
Q 029735            3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPK   82 (189)
Q Consensus         3 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~   82 (189)
                      ...++.++|.+|+++|+.++.|.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++++++|.......+.  
T Consensus         2 ~~~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~--   79 (192)
T 1b8t_A            2 PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGT--   79 (192)
T ss_dssp             CCCCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCC--
T ss_pred             CCCCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCcccccccccccc--
Confidence            335567899999999987889999999999999999999999998899999999999999999999988643221111  


Q ss_pred             cccccCccC--------------cCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCe
Q 029735           83 TVRVERSAD--------------QVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNY  148 (189)
Q Consensus        83 ~~~~~~~~~--------------~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~  148 (189)
                       ...+++|+              ....+.+...+ ++.++|..|+++|.+.+.|.++++.||++||+|..|+++|..+.|
T Consensus        80 -~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~-~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~  157 (192)
T 1b8t_A           80 -LSTDKGESLGIKYEEGQSHRPTNPNASRMAQKV-GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTL  157 (192)
T ss_dssp             -CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSE
T ss_pred             -EecCCCcccccccccccccCCCCcCcccccccc-CCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcc
Confidence             11122222              11111122222 234689999999998888899999999999999999999988889


Q ss_pred             eecCCccccHhHHHhhhcCCCCCC
Q 029735          149 VAHEHRLYCRHHHNQLFKQKGNFS  172 (189)
Q Consensus       149 ~~~dg~~yC~~c~~~~~~~k~~~~  172 (189)
                      +.+||++||+.||.++|+++|...
T Consensus       158 ~~~~g~~yC~~cy~~~f~~kc~~C  181 (192)
T 1b8t_A          158 ADKDGEIYCKGCYAKNFGPKGFGF  181 (192)
T ss_dssp             EEETTEEEEHHHHHHHTCCCCCCC
T ss_pred             cccCCEEeCHHHHHHhcCCcCCCC
Confidence            999999999999999999999843

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

Probab=99.98  E-value=9e-33  Score=198.76  Aligned_cols=124  Identities=22%  Similarity=0.472  Sum_probs=112.3

Q ss_pred             CCCcccCCccccccceEeeCCccccccccccccccccccC--CCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcccc
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKL--SNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVR   85 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~   85 (189)
                      .++|.+|+++|.+.+.|.++|+.||++||+|..|+.+|..  ..|+.++|++||+.||.++++                 
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            4789999999986667999999999999999999999963  579999999999999999997                 


Q ss_pred             ccCccCcCCcccccccCCCCCC--CCccCCcccccCce-eeccCccccccCceeCCCCCcCC-CCCeeecCCccccHhHH
Q 029735           86 VERSADQVTNSRVSSMFAGTQD--KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVIS-PSNYVAHEHRLYCRHHH  161 (189)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~-~~~~~~~dg~~yC~~c~  161 (189)
                                           +  +|..|+++|.+.+. +.++++.||++||+|..|+++|. +..|+..+|++||..||
T Consensus        65 ---------------------~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~  123 (131)
T 2xjy_A           65 ---------------------QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI  123 (131)
T ss_dssp             ---------------------CCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGH
T ss_pred             ---------------------CccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHH
Confidence                                 5  89999999997654 68999999999999999999995 45689999999999999


Q ss_pred             HhhhcCCC
Q 029735          162 NQLFKQKG  169 (189)
Q Consensus       162 ~~~~~~k~  169 (189)
                      .++|++++
T Consensus       124 ~~~~~~~~  131 (131)
T 2xjy_A          124 YEWTKING  131 (131)
T ss_dssp             HHHHHHHC
T ss_pred             HHHhhccC
Confidence            99998654

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

Probab=99.97  E-value=5e-32  Score=193.66  Aligned_cols=120  Identities=20%  Similarity=0.508  Sum_probs=111.8

Q ss_pred             CCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcccccc
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVE   87 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~   87 (189)
                      .++|.+|+++|..++.+.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++++                   
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~-------------------   63 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHA-------------------   63 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSC-------------------
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcC-------------------
Confidence            5789999999987889999999999999999999999998899999999999999999987                   


Q ss_pred             CccCcCCcccccccCCCCCCCCccCCcccccCc-eeeccCcccc--ccCceeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735           88 RSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE-KVAVDGTSYH--KACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~g~~~H--~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                                         ++|.+|+++|.+.+ .|.++++.||  ++||+|..|+++|.+..|+..||++||..++.++
T Consensus        64 -------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~  124 (126)
T 2xqn_T           64 -------------------VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR  124 (126)
T ss_dssp             -------------------CBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHS
T ss_pred             -------------------ccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhh
Confidence                               89999999999754 4789999999  9999999999999988899999999999888876


Q ss_pred             h
Q 029735          165 F  165 (189)
Q Consensus       165 ~  165 (189)
                      |
T Consensus       125 f  125 (126)
T 2xqn_T          125 M  125 (126)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=2.6e-31  Score=202.23  Aligned_cols=127  Identities=21%  Similarity=0.520  Sum_probs=111.8

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccC--CCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKL--SNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTV   84 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   84 (189)
                      ..++|.+|+++|.+.+.|.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++++                
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            46899999999986667999999999999999999999986  589999999999999999997                


Q ss_pred             cccCccCcCCcccccccCCCCCC--CCccCCcccccCce-eeccCccccccCceeCCCCCcCCC-CCeeecCCccccHhH
Q 029735           85 RVERSADQVTNSRVSSMFAGTQD--KCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISP-SNYVAHEHRLYCRHH  160 (189)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~~~dg~~yC~~c  160 (189)
                                            +  +|..|+++|.+.+. +.++++.||++||+|..|+++|.. ..|+..++++||..|
T Consensus        68 ----------------------~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c  125 (188)
T 1rut_X           68 ----------------------NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHD  125 (188)
T ss_dssp             ----------------------CCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGG
T ss_pred             ----------------------cCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHH
Confidence                                  5  79999999997664 689999999999999999999964 568899999999999


Q ss_pred             HHhhhcCCCCC
Q 029735          161 HNQLFKQKGNF  171 (189)
Q Consensus       161 ~~~~~~~k~~~  171 (189)
                      |.++|++++..
T Consensus       126 ~~~~~~~~~~~  136 (188)
T 1rut_X          126 RPTALINGHLN  136 (188)
T ss_dssp             CCTTTC-----
T ss_pred             HHHHhcccccc
Confidence            99999999864

>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=9.9e-30  Score=190.44  Aligned_cols=124  Identities=23%  Similarity=0.483  Sum_probs=108.8

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcccc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVR   85 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~   85 (189)
                      .+.++|.+|+++|.+.++|.++|+.||++||+|..|+++|.+.. +.++|++||+.||.++++                 
T Consensus         4 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~-----------------   65 (169)
T 2rgt_A            4 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFG-----------------   65 (169)
T ss_dssp             ---CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHS-----------------
T ss_pred             CCCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeeccccccccc-----------------
Confidence            34689999999998766899999999999999999999998776 489999999999999998                 


Q ss_pred             ccCccCcCCcccccccCCCCCCCCccCCcccccCce-eeccCccccccCceeCCCCCcCCC-CCee-ecCCccccHhHHH
Q 029735           86 VERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISP-SNYV-AHEHRLYCRHHHN  162 (189)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~-~~dg~~yC~~c~~  162 (189)
                                           ++|..|+++|.+.+. +.++++.||++||+|..|+++|.. ..|+ ..||++||..||.
T Consensus        66 ---------------------~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~  124 (169)
T 2rgt_A           66 ---------------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE  124 (169)
T ss_dssp             ---------------------CBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHH
T ss_pred             ---------------------ccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHH
Confidence                                 899999999998775 479999999999999999999985 3454 4689999999999


Q ss_pred             hhhcCC
Q 029735          163 QLFKQK  168 (189)
Q Consensus       163 ~~~~~k  168 (189)
                      ++++..
T Consensus       125 ~~~~~~  130 (169)
T 2rgt_A          125 TAKQGG  130 (169)
T ss_dssp             HHHHCC
T ss_pred             HHhhcc
Confidence            998653

>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=2.8e-29  Score=190.06  Aligned_cols=122  Identities=23%  Similarity=0.510  Sum_probs=107.8

Q ss_pred             CCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccc
Q 029735            5 AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTV   84 (189)
Q Consensus         5 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   84 (189)
                      ....++|.+|+++|...+.+.++|+.||+.||+|..|+++|.+..| .++|++||..||.++|+                
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            3456899999999987677899999999999999999999987765 79999999999999997                


Q ss_pred             cccCccCcCCcccccccCCCCCCCCccCCcccccCce-eeccCccccccCceeCCCCCcCCC-CCee-ecCCccccHhHH
Q 029735           85 RVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISP-SNYV-AHEHRLYCRHHH  161 (189)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~-~~~~-~~dg~~yC~~c~  161 (189)
                                            ++|..|+++|.+.+. +.+.++.||++||+|..|+++|.. ..|+ ..+|++||..||
T Consensus       120 ----------------------~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy  177 (182)
T 2jtn_A          120 ----------------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY  177 (182)
T ss_dssp             ----------------------CCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHH
T ss_pred             ----------------------cccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHH
Confidence                                  899999999997664 478999999999999999999985 3455 568999999999


Q ss_pred             Hhhh
Q 029735          162 NQLF  165 (189)
Q Consensus       162 ~~~~  165 (189)
                      .++.
T Consensus       178 ~~~~  181 (182)
T 2jtn_A          178 ETAK  181 (182)
T ss_dssp             HHHT
T ss_pred             HHhh
Confidence            8763

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

Probab=99.93  E-value=6.6e-27  Score=160.78  Aligned_cols=97  Identities=25%  Similarity=0.579  Sum_probs=89.1

Q ss_pred             CCCCCcccCCccccc-cceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccc
Q 029735            6 GTTQKCKACEKTVYL-VDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTV   84 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~-~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   84 (189)
                      ...++|.+|+++|.. ++.|.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++++                
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            457899999999975 678999999999999999999999988889999999999999999887                


Q ss_pred             cccCccCcCCcccccccCCCCCCCCccCCcccccCc-eeeccCccccccCceeCCCC
Q 029735           85 RVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIE-KVAVDGTSYHKACFRCTHGG  140 (189)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~g~~~H~~Cf~C~~C~  140 (189)
                                            ++|..|+++|.+++ .|.++++.||++||+|..|+
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                                  89999999999654 58999999999999999985

>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=2.5e-25  Score=158.04  Aligned_cols=114  Identities=18%  Similarity=0.311  Sum_probs=99.6

Q ss_pred             CCCCCcccCCccccccceEeeCCcccccccccccccccccc--CCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK--LSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKT   83 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~   83 (189)
                      ...++|.+|+++|.+.+.|.++++.||++||+|..|+++|.  +..|+.++|++||..||.++|+               
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~---------------   67 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG---------------   67 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHC---------------
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcC---------------
Confidence            35789999999998777799999999999999999999997  3579999999999999999997               


Q ss_pred             ccccCccCcCCcccccccCCCCCC--CCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHH
Q 029735           84 VRVERSADQVTNSRVSSMFAGTQD--KCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH  161 (189)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~  161 (189)
                                             +  +|..|+++|.+.+ +++.++             .+|.++.|+.+|++|||..||
T Consensus        68 -----------------------~~~~C~~C~~~I~~~~-~~~~g~-------------~~l~g~~f~~~~~~~yC~~~~  110 (122)
T 1m3v_A           68 -----------------------NSGAGGSGGHMGSGGD-VMVVGE-------------PTLMGGEFGDEDERLITRLEN  110 (122)
T ss_dssp             -----------------------CCCSSSCSSCCSCCEE-SSSSSS-------------SSCCSCTTCCTTCCCCEECTT
T ss_pred             -----------------------CCCccccCCCCcCchh-eEEcCC-------------cCCCCCccEecCCEeEccCcc
Confidence                                   5  8999999998755 566553             357778899999999999999


Q ss_pred             HhhhcCCCCC
Q 029735          162 NQLFKQKGNF  171 (189)
Q Consensus       162 ~~~~~~k~~~  171 (189)
                      .+++.++++-
T Consensus       111 ~~~~~~~g~~  120 (122)
T 1m3v_A          111 TQFDAANGID  120 (122)
T ss_dssp             TTTTCCSCCC
T ss_pred             hhchhhcCCC
Confidence            9999887763

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

Probab=99.86  E-value=2.3e-22  Score=140.99  Aligned_cols=109  Identities=17%  Similarity=0.233  Sum_probs=89.2

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccC--CCeeecCCeeeecccHHHHhhccCCCCCCCCCCCccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKL--SNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKTV   84 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   84 (189)
                      +.++|.+|+++|.+.+.|.++++.||++||+|+.|+++|.+  ..|+.++|++||+.||.++|+                
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~----------------   65 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG----------------   65 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHT----------------
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhC----------------
Confidence            56899999999987668999999999999999999999975  579999999999999999998                


Q ss_pred             cccCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCc-CCCCCeeecCCccccHhHHHh
Q 029735           85 RVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCV-ISPSNYVAHEHRLYCRHHHNQ  163 (189)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~-l~~~~~~~~dg~~yC~~c~~~  163 (189)
                                            ++|..|..    ++.+.               |..+ |.++.|+.+|++|||..|+.+
T Consensus        66 ----------------------~~c~~c~~----~~~~~---------------~~~~~~~g~~f~~~~~~~~C~~~~~~  104 (114)
T 1j2o_A           66 ----------------------SGGHMGSG----GDVMV---------------VGEPTLMGGEFGDEDERLITRLENTQ  104 (114)
T ss_dssp             ----------------------SCCSSCBS----CSCCC---------------SSCSSTTSSBCCCSSSCCCEEEECTT
T ss_pred             ----------------------cccCcCCC----CceeE---------------cCCccCCCCeeEEcCCEeecchhhhc
Confidence                                  56665541    11111               2344 556679999999999999999


Q ss_pred             hhcCCCCCC
Q 029735          164 LFKQKGNFS  172 (189)
Q Consensus       164 ~~~~k~~~~  172 (189)
                      +.++.++.+
T Consensus       105 ~~~~~g~~~  113 (114)
T 1j2o_A          105 FDAANGIDD  113 (114)
T ss_dssp             CCCTTSSCC
T ss_pred             cccccCCCC
Confidence            888777643

>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=1.5e-21  Score=128.39  Aligned_cols=79  Identities=19%  Similarity=0.354  Sum_probs=73.1

Q ss_pred             CCeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccC
Q 029735           54 EGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus        54 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      +|++||++||.++++                                      ++|..|+++|.+ +.|.++++.||++|
T Consensus         1 gg~~yC~~~y~~~~~--------------------------------------~~C~~C~~~I~~-~~v~a~~~~~H~~C   41 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFS--------------------------------------PKCGGCNRPVLE-NYLSAMDTVWHPEC   41 (80)
T ss_dssp             CCCCCCCCCCCCCCS--------------------------------------CBCTTTCCBCCS-SCEEETTEEECTTT
T ss_pred             CCCccchhHHhhhcC--------------------------------------CccccCCCeecc-eeEEECCCeEecCc
Confidence            478999999988876                                      899999999997 55899999999999


Q ss_pred             ceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          134 FRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       134 f~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      |+|..|+++|..+.|+.++|++||+.||.++|+++|..
T Consensus        42 F~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           42 FVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             CChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            99999999999888999999999999999999999974

>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=1.7e-21  Score=128.12  Aligned_cols=79  Identities=19%  Similarity=0.438  Sum_probs=73.2

Q ss_pred             CCeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccC
Q 029735           54 EGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus        54 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      +|++||++||.++++                                      ++|..|+++|.+. .|.++++.||++|
T Consensus         1 gg~~yC~~cy~~~~~--------------------------------------~~C~~C~~~I~~~-~v~a~~~~~H~~C   41 (80)
T 2cuq_A            1 GSSGSSGPCYENKFA--------------------------------------PRCARCSKTLTQG-GVTYRDQPWHREC   41 (80)
T ss_dssp             CCCCSCCCCCCCCSS--------------------------------------CCCTTTCCCCCSC-CEESSSSEECTTT
T ss_pred             CCcEEcHHHHccccC--------------------------------------CcCCCCCCEecCc-EEEECCchhhhhh
Confidence            578999999998876                                      8999999999864 6899999999999


Q ss_pred             ceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          134 FRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       134 f~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      |+|..|+++|.+..|+.++|++||+.||.++|+++|+.
T Consensus        42 F~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           42 LVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             CBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            99999999998888999999999999999999999975

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

Probab=99.83  E-value=2.1e-21  Score=128.26  Aligned_cols=80  Identities=23%  Similarity=0.412  Sum_probs=73.5

Q ss_pred             CCeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCcccccCce-eeccCcccccc
Q 029735           54 EGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEK-VAVDGTSYHKA  132 (189)
Q Consensus        54 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~  132 (189)
                      ++.+||++||.++++                                      ++|.+|+++|.+.+. |.++++.||++
T Consensus         1 ~~~~yC~~cy~~~~~--------------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~   42 (82)
T 1x63_A            1 GSSGSSGKCTTREDS--------------------------------------PKCKGCFKAIVAGDQNVEYKGTVWHKD   42 (82)
T ss_dssp             CCSCCCCCCCSCCCS--------------------------------------CBCSSSCCBCCSSSCEEECSSCEEETT
T ss_pred             CCCcCchhHHccccC--------------------------------------CcCccCCcccccCceEEEECccccccc
Confidence            367999999988876                                      899999999997664 78999999999


Q ss_pred             CceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          133 CFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       133 Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ||+|..|+++|..+.|+.++|++||+.||.++|++++..
T Consensus        43 CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~   81 (82)
T 1x63_A           43 CFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS   81 (82)
T ss_dssp             TCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSC
T ss_pred             cCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCCC
Confidence            999999999999888999999999999999999999875

>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=99.83  E-value=9.1e-22  Score=130.03  Aligned_cols=80  Identities=16%  Similarity=0.440  Sum_probs=73.1

Q ss_pred             CCeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCccccc-CceeeccCcccccc
Q 029735           54 EGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYP-IEKVAVDGTSYHKA  132 (189)
Q Consensus        54 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~-~~~v~~~g~~~H~~  132 (189)
                      +|++||+.||.++++                                      ++|..|+++|.+ ...+.++++.||++
T Consensus         1 ~g~~yC~~~y~~~~~--------------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~   42 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFA--------------------------------------NTCAECQQLIGHDSRELFYEDRHFHEG   42 (82)
T ss_dssp             CCCCCCCCCCCCCCS--------------------------------------CBCTTTCCBCCSSCCBCCCSSCCCBTT
T ss_pred             CCceechhHhCcccC--------------------------------------CcCccCCCccccCcEEEEeCCcccccc
Confidence            588999999998887                                      899999999994 34468899999999


Q ss_pred             CceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          133 CFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       133 Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ||+|..|+++|.+..|+.++|+|||+.||.++|+++|..
T Consensus        43 CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           43 CFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             TSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             CCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            999999999999888999999999999999999999974

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

Probab=99.81  E-value=1.3e-20  Score=124.18  Aligned_cols=64  Identities=17%  Similarity=0.468  Sum_probs=58.5

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeec-CCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAH-EHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~-dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|.+ ..|.++++.||++||+|..|+++|.+..|+.. +|+|||+.||.++|+++|..
T Consensus        16 ~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           16 EKCATCSQPILD-RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CBCTTTCCBCCS-CCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CccccCCCeecc-eeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            899999999995 46899999999999999999999998778765 79999999999999999974

>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=4.7e-20  Score=121.50  Aligned_cols=67  Identities=27%  Similarity=0.699  Sum_probs=58.0

Q ss_pred             CcCCCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735            2 ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         2 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      |+|.+..++|.+|+++|..++.+.++++.||++||+|..|+++|....|+.+++++||..||.++++
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            6778889999999999988889999999999999999999999998889999999999999999998

>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=1.3e-19  Score=119.29  Aligned_cols=77  Identities=19%  Similarity=0.397  Sum_probs=69.0

Q ss_pred             CeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCc
Q 029735           55 GVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus        55 g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +.+||+.||.++++                                      ++|..|+++|. .+.|.++++.||++||
T Consensus         2 ~~~yC~~~y~~~~~--------------------------------------~~C~~C~~~I~-~~~~~a~~~~~H~~CF   42 (81)
T 1x6a_A            2 SSGSSGKDYWGKFG--------------------------------------EFCHGCSLLMT-GPFMVAGEFKYHPECF   42 (81)
T ss_dssp             CCCCCCCCSSCCSS--------------------------------------CBCTTTCCBCC-SCCBCCTTCCBCTTSC
T ss_pred             CCccchhHHhhhcC--------------------------------------CcCccCCCCcC-ceEEEECCceeccccC
Confidence            67999999998887                                      89999999999 4558999999999999


Q ss_pred             eeCCCCCcCCC-CCee-ecCCccccHhHHHhhhcCCCC
Q 029735          135 RCTHGGCVISP-SNYV-AHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       135 ~C~~C~~~l~~-~~~~-~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      +|..|+++|.. ..|+ ..+|+|||+.||.++|+++++
T Consensus        43 ~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           43 ACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             BCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             CccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            99999999975 5576 589999999999999998875

>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=99.77  E-value=9.4e-20  Score=118.82  Aligned_cols=73  Identities=23%  Similarity=0.554  Sum_probs=66.1

Q ss_pred             CCeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCccccc----CceeeccCccc
Q 029735           54 EGVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYP----IEKVAVDGTSY  129 (189)
Q Consensus        54 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~----~~~v~~~g~~~  129 (189)
                      ++++||++||.++++                                      ++|++|+++|.+    .+.+.++++.|
T Consensus         1 g~~~yC~~cy~~~~~--------------------------------------~~C~~C~~~I~~~g~~~~~~~a~~~~~   42 (77)
T 2egq_A            1 GSSGSSGDCYKNFVA--------------------------------------KKCAGCKNPITGFGKGSSVVAYEGQSW   42 (77)
T ss_dssp             CCSSCCTTCCCSCCC--------------------------------------CCCSSSCCCCCCCSSCCCEEEETTEEE
T ss_pred             CCCeEchhHhchhhC--------------------------------------ccCcccCCcccCCCCCceeEEECccee
Confidence            478999999998876                                      899999999995    35689999999


Q ss_pred             cccCceeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          130 HKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       130 H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      |++||+|..|+++|.+..|+.++|+|||+.||.++
T Consensus        43 H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           43 HDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             ETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             CcccCEehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            99999999999999988899999999999999763

>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=99.77  E-value=5.7e-19  Score=114.85  Aligned_cols=70  Identities=30%  Similarity=0.723  Sum_probs=65.0

Q ss_pred             CcCCCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeec-ccHHHHhhccC
Q 029735            2 ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK-PHFDQLFKMTG   71 (189)
Q Consensus         2 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~-~cy~~~~~~~~   71 (189)
                      ++|+...++|.+|+++|..++.|.++++.||++||+|..|+++|.+..|+.+++++||. .||.++|+++|
T Consensus         3 ~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc   73 (76)
T 2cu8_A            3 SGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGP   73 (76)
T ss_dssp             CSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSC
T ss_pred             cccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhccccc
Confidence            56788899999999999888999999999999999999999999988899999999999 79999998655

>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=1e-18  Score=117.50  Aligned_cols=72  Identities=39%  Similarity=0.834  Sum_probs=68.0

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCCCChh
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDNHE  178 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~~~~  178 (189)
                      ++|..|+++|.+.+.|.++++.||++||+|..|+++|..+.|+.+||++||+.||.++|+++|+++.++++.
T Consensus        16 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~~   87 (91)
T 2d8y_A           16 ETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSG   87 (91)
T ss_dssp             CBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCCC
T ss_pred             CcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCCC
Confidence            799999999998888999999999999999999999998889999999999999999999999999988764

>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=99.76  E-value=7.2e-19  Score=114.37  Aligned_cols=60  Identities=33%  Similarity=0.843  Sum_probs=57.1

Q ss_pred             CCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeec-ccHHHHhh
Q 029735            9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCK-PHFDQLFK   68 (189)
Q Consensus         9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~-~cy~~~~~   68 (189)
                      |+|.+|+++|..++.|.++|+.||++||+|..|+++|.+..|+.++|++||. .||.++++
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            5799999999878999999999999999999999999988999999999999 69999998

>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=1.3e-18  Score=113.14  Aligned_cols=70  Identities=30%  Similarity=0.600  Sum_probs=63.9

Q ss_pred             CCCCCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccH-hHHHhhhcCCCCC
Q 029735          102 FAGTQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR-HHHNQLFKQKGNF  171 (189)
Q Consensus       102 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~-~c~~~~~~~k~~~  171 (189)
                      |.+..++|..|+++|.+.+.|.++++.||++||+|..|+++|....|+.+|+++||+ .||.++|+++|..
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            344458999999999988889999999999999999999999988899999999999 7999999999964

>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=99.74  E-value=2.7e-18  Score=112.83  Aligned_cols=66  Identities=29%  Similarity=0.619  Sum_probs=60.4

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      .+.++|.+|+++|+.++.|.++++.||++||+|..|+++|.+ .|+.+++++||+.||.++|+++|+
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~   78 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPS   78 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCST
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCC
Confidence            457899999999988899999999999999999999999985 799999999999999999996664

>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=99.73  E-value=8.5e-18  Score=112.78  Aligned_cols=64  Identities=20%  Similarity=0.425  Sum_probs=59.9

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|. .+.|.++++.||++||+|..|+++|....|+.++|++||+.||.++|+++|..
T Consensus        26 ~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           26 PMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             CBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            89999999997 45689999999999999999999999888999999999999999999999974

>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=99.72  E-value=4.7e-18  Score=114.27  Aligned_cols=73  Identities=45%  Similarity=1.023  Sum_probs=66.7

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCC
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEG   79 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~   79 (189)
                      ..++|.+|+++|.+.+.|.++++.||++||+|..|+++|....|+.+++++||..||.++++++|+.+..|..
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~   86 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGS   86 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCC
Confidence            4679999999998778999999999999999999999999888999999999999999999998887666643

>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=99.72  E-value=6.3e-18  Score=111.02  Aligned_cols=64  Identities=17%  Similarity=0.514  Sum_probs=60.2

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|...+.|.++++.||++||+|..|+++|.+ .|+.+||+|||+.||.++|+++|..
T Consensus        16 ~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           16 SHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            789999999998888999999999999999999999985 6899999999999999999999974

>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=7.5e-18  Score=107.48  Aligned_cols=65  Identities=20%  Similarity=0.540  Sum_probs=59.6

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ...++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+++++++||..||.++++++|
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C   67 (69)
T 2cur_A            3 SGSSGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPS   67 (69)
T ss_dssp             CCCCCCSSSCCCCC-TTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSC
T ss_pred             CCcCCCcccCCEeC-cceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCC
Confidence            45789999999996 678999999999999999999999998899999999999999999998544

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

Probab=99.71  E-value=4.1e-18  Score=112.08  Aligned_cols=65  Identities=32%  Similarity=0.703  Sum_probs=57.7

Q ss_pred             CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      .++|..|+++|.+.+.+.+.++.||++||+|..|+++|....|+.+++++||+.||.++|+++|.
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   71 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGY   71 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----
T ss_pred             CCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCccc
Confidence            48999999999888889999999999999999999999988899999999999999999999998

>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=99.71  E-value=5e-18  Score=110.37  Aligned_cols=68  Identities=16%  Similarity=0.463  Sum_probs=63.0

Q ss_pred             CCCccCCccccc---CceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCC
Q 029735          107 DKCVACKKTVYP---IEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~---~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~  174 (189)
                      ++|..|+++|.+   .+.|.++++.||++||+|..|+++|....|+.+||+|||+.||.++|+++|..++|
T Consensus         6 ~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~sg   76 (76)
T 1x68_A            6 SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSSG   76 (76)
T ss_dssp             CCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSCC
T ss_pred             CCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCCC
Confidence            799999999995   35689999999999999999999999888999999999999999999999997765

>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=1.1e-17  Score=107.45  Aligned_cols=66  Identities=27%  Similarity=0.619  Sum_probs=60.4

Q ss_pred             CCCCcccCCcccccc-ceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            7 TTQKCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      ..++|.+|+++|.++ +.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|+
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   70 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPS   70 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCC
Confidence            467999999999874 789999999999999999999999988999999999999999999996653

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

Probab=99.71  E-value=7e-18  Score=109.82  Aligned_cols=69  Identities=25%  Similarity=0.584  Sum_probs=61.0

Q ss_pred             cCCCCCCCcccCCccccccc-eEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            3 SFAGTTQKCKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         3 ~~~~~~~~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      +.....++|.+|+++|.+++ .+.++|+.||++||+|..|+++|.++.|+.++|++||+.||.++++++|
T Consensus         6 ~~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C   75 (77)
T 1g47_A            6 ANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCW   75 (77)
T ss_dssp             CSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC-
T ss_pred             ccCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhccc
Confidence            44556789999999998544 5789999999999999999999998899999999999999999998655

>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=1e-17  Score=107.11  Aligned_cols=66  Identities=24%  Similarity=0.568  Sum_probs=60.0

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      ...++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+++++++||..||.++++++|+
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   68 (70)
T 2d8z_A            3 SGSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPS   68 (70)
T ss_dssp             CCCCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCT
T ss_pred             CCCCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccC
Confidence            35689999999996 6779999999999999999999999888999999999999999999986553

>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=99.70  E-value=1.8e-17  Score=106.54  Aligned_cols=65  Identities=25%  Similarity=0.523  Sum_probs=60.9

Q ss_pred             CCCccCCcccccC-ceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPI-EKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~-~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|.+. +.+.++++.||++||+|..|+++|..+.|+.++|++||+.||.++|+++|+.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             CCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            7999999999975 5678999999999999999999999888999999999999999999999975

>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=1.5e-17  Score=106.89  Aligned_cols=66  Identities=20%  Similarity=0.585  Sum_probs=60.3

Q ss_pred             CCCCcccCCcccccc-ceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            7 TTQKCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      ..++|.+|+++|.++ ..|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|+
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   70 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPS   70 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCC
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCC
Confidence            467999999999875 489999999999999999999999988999999999999999999996653

>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=99.70  E-value=1.3e-17  Score=111.83  Aligned_cols=66  Identities=29%  Similarity=0.600  Sum_probs=60.7

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      ...++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||..||.++|+++|+
T Consensus        23 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~   88 (90)
T 2dar_A           23 KRTPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPS   88 (90)
T ss_dssp             TCCCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCC
T ss_pred             CCCCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCC
Confidence            35688999999995 8899999999999999999999999988999999999999999999997664

>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=99.70  E-value=1.7e-17  Score=106.14  Aligned_cols=65  Identities=22%  Similarity=0.507  Sum_probs=59.7

Q ss_pred             CCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhcc
Q 029735            5 AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMT   70 (189)
Q Consensus         5 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~   70 (189)
                      +++.++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||..||.+++++.
T Consensus         2 s~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   66 (70)
T 2d8x_A            2 SSGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASG   66 (70)
T ss_dssp             CCCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCC
T ss_pred             CCCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCC
Confidence            356789999999996 68899999999999999999999999889999999999999999999743

>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=2e-17  Score=106.32  Aligned_cols=65  Identities=23%  Similarity=0.543  Sum_probs=60.9

Q ss_pred             CCCccCCcccccCc-eeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIE-KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~-~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|.+.+ .+.++++.||++||+|..|+++|..+.|+.+||++||+.||.++|+++|..
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            79999999999864 578999999999999999999999888999999999999999999999975

>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=99.70  E-value=8.6e-18  Score=110.55  Aligned_cols=77  Identities=18%  Similarity=0.398  Sum_probs=66.6

Q ss_pred             CeeeecccHHHHhhccCCCCCCCCCCCccccccCccCcCCcccccccCCCCCCCCccCCcccccCceeeccCccccccCc
Q 029735           55 GVLYCKPHFDQLFKMTGSLDKSFEGTPKTVRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus        55 g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ..+||+.||.++++                                      ++|..|+++|.+ +.|.++++.||++||
T Consensus         2 ~~~yC~~dy~~~~~--------------------------------------~~C~~C~~~I~~-~~v~a~~~~wH~~CF   42 (81)
T 1v6g_A            2 SSGSSGLDYQRLYG--------------------------------------TRCFSCDQFIEG-EVVSALGKTYHPDCF   42 (81)
T ss_dssp             CCCCCCSCGGGSCC--------------------------------------CBCTTTCCBCCS-CCEEETTEEECTTTS
T ss_pred             CCCcchHHHHhHhC--------------------------------------CcCccccCEecc-ceEEECCceeCccCC
Confidence            46899999999987                                      899999999994 568999999999999


Q ss_pred             eeCCCCCcCCCCCeeecCC-ccccHhHHHhhhcCCCC
Q 029735          135 RCTHGGCVISPSNYVAHEH-RLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg-~~yC~~c~~~~~~~k~~  170 (189)
                      +|..|+++|..+.++..++ .+||..||.++++..++
T Consensus        43 ~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~~~~s   79 (81)
T 1v6g_A           43 VCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVSGPS   79 (81)
T ss_dssp             SCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSSCCCC
T ss_pred             ccccCCCCCCCCCEEEeCCCCEEChhhhcccCCCCCC
Confidence            9999999998766666555 57999999988877654

>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=99.70  E-value=2.8e-17  Score=105.03  Aligned_cols=64  Identities=27%  Similarity=0.524  Sum_probs=59.9

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|.+ +.|.++++.||++||+|..|+++|....|+.+|+++||+.||.++|+++|..
T Consensus         6 ~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            6 SGCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CBCSSSCCBCCS-SEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCcccCCeecc-ceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            789999999986 4589999999999999999999999888999999999999999999999974

>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=1.7e-17  Score=107.79  Aligned_cols=68  Identities=29%  Similarity=0.595  Sum_probs=62.7

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccH-hHHHhhhcCCCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCR-HHHNQLFKQKGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~-~c~~~~~~~k~~~~~~  174 (189)
                      ++|..|+++|..++.|.++++.||++||+|..|+++|..+.|+.+||.+||+ .||.++|+++|..+.+
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~   69 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGG   69 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCC
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCC
Confidence            4799999999977889999999999999999999999988899999999999 6999999999986543

>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=1.1e-17  Score=105.82  Aligned_cols=62  Identities=26%  Similarity=0.539  Sum_probs=58.0

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKM   69 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   69 (189)
                      ..++|.+|+++|. ++.|.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++|++
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            4678999999997 8899999999999999999999999988999999999999999999874

>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=99.69  E-value=1.5e-17  Score=108.11  Aligned_cols=65  Identities=17%  Similarity=0.411  Sum_probs=58.6

Q ss_pred             CCCCcccCCccccc---cceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            7 TTQKCKACEKTVYL---VDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         7 ~~~~C~~C~~~I~~---~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ..++|.+|+++|.+   .+.|.++++.||++||+|..|+++|.+..|+.+++++||..||.++++++|
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C   71 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDIS   71 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSS
T ss_pred             cCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcC
Confidence            46799999999973   378999999999999999999999998889999999999999999988433

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

Probab=99.69  E-value=3.2e-17  Score=104.52  Aligned_cols=63  Identities=19%  Similarity=0.509  Sum_probs=59.2

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      ++|..|+++|.+ +.|.++++.||++||+|..|+++|.+..|+.++|++||+.||.++|+++|.
T Consensus         6 ~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   68 (69)
T 2cur_A            6 SGCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS   68 (69)
T ss_dssp             CCCSSSCCCCCT-TCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCC
T ss_pred             CCCcccCCEeCc-ceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCC
Confidence            799999999985 468999999999999999999999988899999999999999999999985

>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=1.4e-17  Score=105.33  Aligned_cols=61  Identities=25%  Similarity=0.404  Sum_probs=57.6

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQK  168 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k  168 (189)
                      ++|.+|+++|. ++.+.++++.||++||+|..|+++|.+..|+.+||.+||+.||.++|++|
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            78999999999 56689999999999999999999999888999999999999999999986

>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=1.3e-17  Score=107.15  Aligned_cols=64  Identities=14%  Similarity=0.409  Sum_probs=58.5

Q ss_pred             CCCCCcccCCccccc---cceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhc
Q 029735            6 GTTQKCKACEKTVYL---VDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKM   69 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~---~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   69 (189)
                      ...++|.+|+++|.+   .++|.++++.||++||+|..|+++|.+..|+.+++++||..||.++++|
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            457899999999974   3689999999999999999999999988999999999999999998874

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

Probab=99.67  E-value=2.5e-17  Score=107.87  Aligned_cols=65  Identities=18%  Similarity=0.406  Sum_probs=59.4

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ...++|.+|+++|. +++|.++++.||++||+|..|+++|.+..|+.+++++||..||.+++++++
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            34679999999997 578999999999999999999999988889999999999999999998654

>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=4e-17  Score=106.21  Aligned_cols=64  Identities=31%  Similarity=0.566  Sum_probs=58.0

Q ss_pred             CCCccCCcccccCce-eeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC
Q 029735          107 DKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      ++|.+|+++|.+.+. +.++|+.||++||+|..|+++|..+.|+.+||++||+.||.++|+++|.
T Consensus        12 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A           12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            899999999986554 5799999999999999999999988899999999999999999999986

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.67  E-value=5.7e-17  Score=104.17  Aligned_cols=63  Identities=11%  Similarity=0.459  Sum_probs=58.1

Q ss_pred             CCCccCCccccc---CceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCC
Q 029735          107 DKCVACKKTVYP---IEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKG  169 (189)
Q Consensus       107 ~~C~~C~~~I~~---~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~  169 (189)
                      ++|..|+++|.+   .+.|.++++.||++||+|..|+++|.+..|+.++|++||..||.++|+|++
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            799999999996   355789999999999999999999998889999999999999999999875

>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=99.67  E-value=7.1e-17  Score=106.31  Aligned_cols=66  Identities=27%  Similarity=0.594  Sum_probs=60.1

Q ss_pred             CCCCcccCCccccccc-eEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            7 TTQKCKACEKTVYLVD-QLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~-~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      ..++|.+|+++|.+++ .|.++++.||++||+|..|+++|....|+.+++++||+.||.++++++++
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            3679999999998655 58999999999999999999999988999999999999999999987664

>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=8.8e-17  Score=112.45  Aligned_cols=67  Identities=18%  Similarity=0.353  Sum_probs=61.3

Q ss_pred             CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCC--CCeeecCCccccHhHHHhhhcCCCCCC
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQLFKQKGNFS  172 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~--~~~~~~dg~~yC~~c~~~~~~~k~~~~  172 (189)
                      .++|.+|+++|.+.+.+.++++.||++||+|..|+++|..  ..|+.+||+|||+.||.++|+++|...
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c   71 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMG   71 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSC
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcC
Confidence            3799999999998777899999999999999999999985  479999999999999999999998744

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

Probab=99.66  E-value=1.1e-16  Score=102.21  Aligned_cols=64  Identities=23%  Similarity=0.454  Sum_probs=59.0

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|.+ +.|.++++.||++||+|..|+++|....|+.++|++||+.||.++|+++...
T Consensus         6 ~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~s   69 (70)
T 2d8x_A            6 SGCHQCGEFIIG-RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPSS   69 (70)
T ss_dssp             SBCSSSCCBCCS-CCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSCC
T ss_pred             CcCccCCCEecc-eEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCCC
Confidence            789999999985 5589999999999999999999999988899999999999999999988653

>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=1.9e-16  Score=105.92  Aligned_cols=64  Identities=20%  Similarity=0.389  Sum_probs=59.4

Q ss_pred             CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      .++|..|+++|.+ +.+.++++.||++||+|..|+++|....|+.+||++||+.||.++|++|+.
T Consensus        25 ~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           25 MPLCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CCBCTTTCCBCCS-CCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CCCcccCCCEecc-cEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            3789999999997 558999999999999999999999988899999999999999999999974

>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=8.7e-17  Score=103.29  Aligned_cols=63  Identities=22%  Similarity=0.569  Sum_probs=57.7

Q ss_pred             CCCCCcccCCcccccc-ceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735            6 GTTQKCKACEKTVYLV-DQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      ...++|.+|+++|.++ ..+.++++.||++||+|..|+++|.+..|+.+++++||..||.++++
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            3568999999999864 48999999999999999999999988889999999999999999985

>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=6.5e-17  Score=108.23  Aligned_cols=64  Identities=28%  Similarity=0.533  Sum_probs=58.8

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ..++|.+|+++|. +++|.++++.||++||+|..|+++|....|+.+++++||+.||.++|++++
T Consensus        24 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~   87 (89)
T 1x64_A           24 RMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPS   87 (89)
T ss_dssp             SCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCC
T ss_pred             cCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            4578999999997 588999999999999999999999988889999999999999999998654

>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=5.9e-17  Score=106.06  Aligned_cols=64  Identities=19%  Similarity=0.408  Sum_probs=59.2

Q ss_pred             CCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      .++|..|+++|.+ +.|.++++.||++||+|..|+++|....|+.+|+++||+.||.++|++++.
T Consensus        15 ~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           15 LPMCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCSSSCCCCCS-SCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCccccCCCCccC-cEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            3799999999996 468999999999999999999999877799999999999999999999975

>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=99.66  E-value=1e-16  Score=105.07  Aligned_cols=65  Identities=26%  Similarity=0.568  Sum_probs=59.6

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|+
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   78 (80)
T 2cuq_A           14 FAPRCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPS   78 (80)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTT
T ss_pred             cCCcCCCCCCEec-CcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCC
Confidence            4689999999996 5789999999999999999999999888999999999999999999996664

>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=99.66  E-value=1.1e-16  Score=104.94  Aligned_cols=64  Identities=23%  Similarity=0.611  Sum_probs=59.1

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|.++.|+.+++++||+.||.++++++|
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C   77 (80)
T 1x3h_A           14 FSPKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGP   77 (80)
T ss_dssp             CSCBCTTTCCBCC-SSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSC
T ss_pred             cCCccccCCCeec-ceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCC
Confidence            3679999999997 588999999999999999999999998889999999999999999999555

>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=99.65  E-value=8.3e-17  Score=106.02  Aligned_cols=65  Identities=20%  Similarity=0.550  Sum_probs=59.1

Q ss_pred             CCCCcccCCccccc-cceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            7 TTQKCKACEKTVYL-VDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         7 ~~~~C~~C~~~I~~-~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ..++|.+|+++|.+ +..+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C   79 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGP   79 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSS
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCC
Confidence            46799999999973 567889999999999999999999998899999999999999999998655

>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=99.65  E-value=1.3e-16  Score=104.78  Aligned_cols=65  Identities=26%  Similarity=0.516  Sum_probs=58.6

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeec-CCeeeecccHHHHhhccC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSF-EGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~-~g~~yC~~cy~~~~~~~~   71 (189)
                      ...++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+.. ++++||..||.++|+++|
T Consensus        13 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C   78 (81)
T 2dlo_A           13 ATLEKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGP   78 (81)
T ss_dssp             SSCCBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSS
T ss_pred             cCCCccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcC
Confidence            45789999999997 678999999999999999999999988788876 799999999999999655

>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=99.65  E-value=9.4e-17  Score=105.12  Aligned_cols=64  Identities=25%  Similarity=0.479  Sum_probs=57.4

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccC
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTG   71 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   71 (189)
                      ...++|.+|+++|. ++.|.++|+.||++||+|..|+++|.+.. +.+++++||..||.++|+|.+
T Consensus        13 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~g~~yC~~cy~~~f~p~~   76 (79)
T 2cor_A           13 LGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVSGP   76 (79)
T ss_dssp             CCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCCSS
T ss_pred             cCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCCCC
Confidence            34689999999997 78899999999999999999999998765 599999999999999998644

>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=99.64  E-value=5.4e-17  Score=107.01  Aligned_cols=64  Identities=33%  Similarity=0.800  Sum_probs=58.1

Q ss_pred             CCCCCCcccCCccccccceEeeCCccccccccccccccccccCCCee--ecCCeeeecccHHHHhh
Q 029735            5 AGTTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYC--SFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         5 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~--~~~g~~yC~~cy~~~~~   68 (189)
                      .++.++|.+|+++|+.++.|.++++.||++||+|..|+++|....|+  ++++++||+.||.++++
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            44578999999999888899999999999999999999999988887  47999999999988875

>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=99.64  E-value=2.6e-16  Score=103.01  Aligned_cols=63  Identities=17%  Similarity=0.372  Sum_probs=57.4

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNF  171 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~  171 (189)
                      ++|..|+++|. ++.|.++++.||++||+|..|+++|.... +.+||++||+.||.++|+|+++.
T Consensus        16 ~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~g~~yC~~cy~~~f~p~~ss   78 (79)
T 2cor_A           16 YICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVSGPSS   78 (79)
T ss_dssp             CBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCCSSCC
T ss_pred             CCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCCCCCC
Confidence            79999999999 45589999999999999999999999874 58999999999999999998764

>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=99.63  E-value=2.1e-16  Score=101.23  Aligned_cols=62  Identities=26%  Similarity=0.726  Sum_probs=56.8

Q ss_pred             CCCCcccCCccccccce-EeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735            7 TTQKCKACEKTVYLVDQ-LTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~-~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      ..++|.+|+++|..++. +.++|+.||++||+|..|+++|.++.|+.++|++||+.||.++|+
T Consensus        10 ~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             TTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             CCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            46799999999987774 689999999999999999999988889999999999999999874

>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=99.63  E-value=1.9e-16  Score=102.10  Aligned_cols=61  Identities=20%  Similarity=0.343  Sum_probs=56.0

Q ss_pred             CCCCcccCCccccccceEeeCCcccccccccccccccccc-CCCeeecCCeeeecccHHHHhh
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK-LSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|. +..|+.+++++||..||.++++
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            4689999999996 58899999999999999999999998 6689999999999999998875

>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=99.63  E-value=2.5e-16  Score=103.80  Aligned_cols=65  Identities=28%  Similarity=0.681  Sum_probs=58.3

Q ss_pred             CCCCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCee--ecCCccccHhHHHhhhcCCC
Q 029735          105 TQDKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYV--AHEHRLYCRHHHNQLFKQKG  169 (189)
Q Consensus       105 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~--~~dg~~yC~~c~~~~~~~k~  169 (189)
                      +.++|.+|+++|+..+.|.++++.||++||+|..|+++|....|+  .+||++||+.||.++|+...
T Consensus        14 ~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~   80 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPS   80 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCC
T ss_pred             CCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCC
Confidence            348999999999988888999999999999999999999998887  47999999999999887643

>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=99.62  E-value=2.3e-16  Score=111.73  Aligned_cols=62  Identities=21%  Similarity=0.537  Sum_probs=56.1

Q ss_pred             CCCCcccCCccccccceEeeCCcccccccccccccccccc--CCCeeecCCeeeecccHHHHhh
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK--LSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      ..++|.+|+++|...+.|.++++.||+.||+|..|+++|.  +..|+.++|++||+.||.++|+
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            3578999999998666799999999999999999999997  3579999999999999999874

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

Probab=99.62  E-value=4.5e-16  Score=118.31  Aligned_cols=61  Identities=30%  Similarity=0.788  Sum_probs=57.8

Q ss_pred             CCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      .++|.+|+++|.+++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++
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            4679999999987889999999999999999999999988899999999999999999998

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

Probab=99.61  E-value=7.6e-16  Score=99.24  Aligned_cols=63  Identities=13%  Similarity=0.325  Sum_probs=56.9

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCC-CCCeeecCCccccHhHHHhhhcCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVIS-PSNYVAHEHRLYCRHHHNQLFKQKGN  170 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~-~~~~~~~dg~~yC~~c~~~~~~~k~~  170 (189)
                      ++|..|+++|.+ +.|.++++.||++||+|..|+++|. +..|+..++++||..||.++++.+-.
T Consensus         6 ~~C~~C~~~I~~-~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~~~   69 (73)
T 1wig_A            6 SGCDSCEKYITG-RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTEDSG   69 (73)
T ss_dssp             CSCSSSCCCCSS-CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSSCC
T ss_pred             CCcccCCCEecC-eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccccc
Confidence            899999999997 5589999999999999999999998 56788999999999999998876544

>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=99.61  E-value=5.6e-16  Score=105.88  Aligned_cols=69  Identities=20%  Similarity=0.439  Sum_probs=62.8

Q ss_pred             CCCccCCccccc-CceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCCC
Q 029735          107 DKCVACKKTVYP-IEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLD  175 (189)
Q Consensus       107 ~~C~~C~~~I~~-~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~  175 (189)
                      ++|.+|+++|.. .+.+.++++.||++||+|..|+++|.+..|+.+||++||+.||.++|+++|..+...
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~   75 (101)
T 2cup_A            6 SGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKA   75 (101)
T ss_dssp             CBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCB
T ss_pred             CcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCc
Confidence            799999999985 566899999999999999999999988889999999999999999999999865443

>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=1.2e-15  Score=97.92  Aligned_cols=61  Identities=21%  Similarity=0.423  Sum_probs=56.1

Q ss_pred             CCCccCCcccccCc-eeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcC
Q 029735          107 DKCVACKKTVYPIE-KVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ  167 (189)
Q Consensus       107 ~~C~~C~~~I~~~~-~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~  167 (189)
                      ++|.+|+++|.+.+ .+.++++.||++||+|..|+++|.+..|+.++|++||+.||.++|+.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~~   67 (72)
T 1x61_A            6 SGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES   67 (72)
T ss_dssp             CCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHHT
T ss_pred             CCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHcc
Confidence            79999999999754 58899999999999999999999877899999999999999999954

>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=99.60  E-value=5.8e-16  Score=99.17  Aligned_cols=60  Identities=33%  Similarity=0.657  Sum_probs=55.9

Q ss_pred             CCCccCCcccccCce-eeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          107 DKCVACKKTVYPIEK-VAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      ++|.+|+++|.+.+. +.+.++.||++||+|..|+++|..+.|+.+||++||+.||.++||
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 579999999999999999999988889999999999999999985

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

Probab=99.60  E-value=7.3e-16  Score=109.46  Aligned_cols=68  Identities=13%  Similarity=0.306  Sum_probs=63.2

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~  174 (189)
                      ++|.+|+++|.+++.+.++|+.||++||+|..|+++|.+..|+.+||++||+.||.++|+++|..+..
T Consensus         4 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~   71 (126)
T 2xqn_T            4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHN   71 (126)
T ss_dssp             CBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCS
T ss_pred             CCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCC
Confidence            78999999999877789999999999999999999999888999999999999999999999986544

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

Probab=99.59  E-value=4.2e-16  Score=98.17  Aligned_cols=59  Identities=24%  Similarity=0.620  Sum_probs=54.0

Q ss_pred             CCCcccCCccccc-cceEeeCCcccc--ccccccccccccccCCCeeecCCeeee-cccHHHH
Q 029735            8 TQKCKACEKTVYL-VDQLTADNKVYH--KACFRCHHCKGTLKLSNYCSFEGVLYC-KPHFDQL   66 (189)
Q Consensus         8 ~~~C~~C~~~I~~-~~~~~~~~~~~H--~~CF~C~~C~~~L~~~~f~~~~g~~yC-~~cy~~~   66 (189)
                      +++|.+|+++|.+ ++.|.++|+.||  ++||+|+.|+++|.+..|+.++|++|| .+||.++
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            4689999999987 478999999999  999999999999998899999999999 8998754

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

Probab=99.59  E-value=6.4e-16  Score=109.30  Aligned_cols=68  Identities=15%  Similarity=0.377  Sum_probs=61.5

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCC--CCeeecCCccccHhHHHhhhcC--CCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQLFKQ--KGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~--~~~~~~dg~~yC~~c~~~~~~~--k~~~~~~  174 (189)
                      ++|..|+++|.+.+.+.++++.||++||+|..|+++|..  ..|+.+||++||+.||.++|++  +|..+..
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~   77 (122)
T 1m3v_A            6 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGH   77 (122)
T ss_dssp             CCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSC
T ss_pred             CCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCC
Confidence            799999999998777899999999999999999999973  5689999999999999999999  8875543

>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=99.59  E-value=8.2e-16  Score=99.97  Aligned_cols=60  Identities=20%  Similarity=0.572  Sum_probs=54.6

Q ss_pred             CCCCcccCCccccc----cceEeeCCccccccccccccccccccCCCeeecCCeeeecccHHHH
Q 029735            7 TTQKCKACEKTVYL----VDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQL   66 (189)
Q Consensus         7 ~~~~C~~C~~~I~~----~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   66 (189)
                      ..++|++|+++|.+    .+.+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            46899999999973    3789999999999999999999999988899999999999999753

>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=99.58  E-value=1.5e-15  Score=99.62  Aligned_cols=63  Identities=22%  Similarity=0.481  Sum_probs=56.2

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccC-CCee-ecCCeeeecccHHHHhhcc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKL-SNYC-SFEGVLYCKPHFDQLFKMT   70 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~-~~f~-~~~g~~yC~~cy~~~~~~~   70 (189)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|.. ..|. .+++++||+.||.+++++.
T Consensus        14 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~   78 (81)
T 1x6a_A           14 FGEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGP   78 (81)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTT
T ss_pred             cCCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCC
Confidence            4678999999997 888999999999999999999999975 5677 5899999999999999843

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

Probab=99.57  E-value=1.7e-15  Score=107.20  Aligned_cols=60  Identities=15%  Similarity=0.411  Sum_probs=55.6

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCC--CCCeeecCCccccHhHHHhhhc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVIS--PSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~--~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      ++|.+|+++|.+.+.+.++++.||++||+|..|+++|.  +..|+.++|++||+.||.++||
T Consensus        62 ~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           62 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             SBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            79999999999877789999999999999999999997  3579999999999999999986

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

Probab=99.57  E-value=1.6e-15  Score=114.41  Aligned_cols=67  Identities=16%  Similarity=0.440  Sum_probs=60.9

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~  174 (189)
                      ++|..|+++|.+.+.+.++++.||++||+|..|+++|....| .+||++||+.||.++|+++|..+..
T Consensus        61 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~~C~~  127 (182)
T 2jtn_A           61 PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQL  127 (182)
T ss_dssp             CBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCTTTCC
T ss_pred             CcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccccCCC
Confidence            799999999998766789999999999999999999998664 7899999999999999999986544

>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=8.4e-15  Score=104.58  Aligned_cols=68  Identities=19%  Similarity=0.344  Sum_probs=61.1

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCC--CCeeecCCccccHhHHHhhhcC--CCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQLFKQ--KGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~--~~~~~~dg~~yC~~c~~~~~~~--k~~~~~~  174 (189)
                      +.|..|+++|.+.+.+.++++.||++||+|..|+++|..  ..|+.+||+|||+.||.++|++  +|..+..
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            789999999998766899999999999999999999963  5699999999999999999999  8875443

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

Probab=99.53  E-value=4.2e-15  Score=93.54  Aligned_cols=58  Identities=19%  Similarity=0.549  Sum_probs=53.3

Q ss_pred             CCCccCCcccccC-ceeeccCcccc--ccCceeCCCCCcCCCCCeeecCCcccc-HhHHHhh
Q 029735          107 DKCVACKKTVYPI-EKVAVDGTSYH--KACFRCTHGGCVISPSNYVAHEHRLYC-RHHHNQL  164 (189)
Q Consensus       107 ~~C~~C~~~I~~~-~~v~~~g~~~H--~~Cf~C~~C~~~l~~~~~~~~dg~~yC-~~c~~~~  164 (189)
                      ++|.+|+++|.+. +.|.++++.||  ++||+|..|+++|.+..|+.+||+||| ..||.++
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 56899999999  999999999999998889999999999 8998765

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

Probab=99.50  E-value=2.1e-14  Score=106.93  Aligned_cols=67  Identities=16%  Similarity=0.415  Sum_probs=60.8

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~  174 (189)
                      +.|..|+++|.+.+.+.++|+.||++||+|..|+++|.... +.+||++||+.||.++|+++|..+..
T Consensus         7 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~   73 (169)
T 2rgt_A            7 PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQL   73 (169)
T ss_dssp             CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCC
T ss_pred             CccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeeccccccccccccccccc
Confidence            78999999999876678999999999999999999999865 47899999999999999999986544

>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=99.44  E-value=3.2e-14  Score=93.31  Aligned_cols=61  Identities=21%  Similarity=0.481  Sum_probs=52.5

Q ss_pred             CCCCcccCCccccccceEeeCCccccccccccccccccccCCCeeecCC-eeeecccHHHHhh
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLKLSNYCSFEG-VLYCKPHFDQLFK   68 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~cy~~~~~   68 (189)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|..+.++..++ .+||..||.+++.
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           14 YGTRCFSCDQFIE-GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCCBCTTTCCBCC-SCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             hCCcCccccCEec-cceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            3579999999997 78999999999999999999999998776665555 5799999977654

>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=99.43  E-value=4.2e-14  Score=107.07  Aligned_cols=68  Identities=13%  Similarity=0.340  Sum_probs=61.1

Q ss_pred             CCCccCCcccccCceeeccCccccccCceeCCCCCcCCC--CCeeecCCccccHhHHHhhhcC--CCCCCCC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACFRCTHGGCVISP--SNYVAHEHRLYCRHHHNQLFKQ--KGNFSQL  174 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~--~~~~~~dg~~yC~~c~~~~~~~--k~~~~~~  174 (189)
                      +.|..|+++|.+.+.+.++++.||++||+|..|+++|..  ..|+.+||++||+.||.++|++  +|..+..
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            789999999997766899999999999999999999985  5799999999999999999999  6875443

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

Probab=98.53  E-value=3e-08  Score=52.60  Aligned_cols=29  Identities=38%  Similarity=0.879  Sum_probs=27.4

Q ss_pred             CCCcccCCccccccceEeeCCcccccccc
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      +++|++|++.|+..|.+.++|+.||..||
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            56899999999999999999999999998

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

Probab=98.53  E-value=3.5e-08  Score=52.31  Aligned_cols=28  Identities=50%  Similarity=0.949  Sum_probs=26.9

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ++|+.|++.|++.|++.+.|+.||+.||
T Consensus         4 ~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            4 PNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcCCccCCEEecceeEEECCeEecccCC
Confidence            7899999999999999999999999998

>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=91.41  E-value=0.55  Score=31.50  Aligned_cols=96  Identities=18%  Similarity=0.363  Sum_probs=55.8

Q ss_pred             CCCCCcccCCccccccceEe--eCCccccccccccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCCCCCCcc
Q 029735            6 GTTQKCKACEKTVYLVDQLT--ADNKVYHKACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSFEGTPKT   83 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~--~~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~   83 (189)
                      .....|..|+..=...+.|.  .=++.||..|+.=.     +.    ....+..+|..|                     
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~-----~~----~~~~~~W~C~~C---------------------   54 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIA-----VT----PLKRAGWQCPEC---------------------   54 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCC-----CC----TTTSTTCCCTTT---------------------
T ss_pred             CCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCc-----cc----cccccCccCCcC---------------------
Confidence            34567999987632122232  23578888876422     11    123567788877                     


Q ss_pred             ccccCccCcCCcccccccCCCCCCCCccCCcccccCcee--eccCccccccCceeCCCCCcCCCCCeeecCCccccHhHH
Q 029735           84 VRVERSADQVTNSRVSSMFAGTQDKCVACKKTVYPIEKV--AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHH  161 (189)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v--~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~  161 (189)
                                             ..|..|++.-.+...+  ..-++.||..|..-     +|..    ...+.-+|..|.
T Consensus        55 -----------------------~~C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~p-----pl~~----~P~g~W~C~~C~  102 (111)
T 2ysm_A           55 -----------------------KVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQP-----VMKS----VPTNGWKCKNCR  102 (111)
T ss_dssp             -----------------------CCCTTTCCCSCCTTEEECSSSCCEEEGGGSSS-----CCSS----CCSSCCCCHHHH
T ss_pred             -----------------------CcccccCccCCCCCeeECCCCCcHHhHHhcCC-----cccc----CCCCCcCCcCCc
Confidence                                   3577888765443333  34467899888632     2321    224677898885


Q ss_pred             Hh
Q 029735          162 NQ  163 (189)
Q Consensus       162 ~~  163 (189)
                      ..
T Consensus       103 ~c  104 (111)
T 2ysm_A          103 IC  104 (111)
T ss_dssp             CC
T ss_pred             Cc
Confidence            44

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.71  E-value=0.2  Score=31.37  Aligned_cols=36  Identities=11%  Similarity=0.313  Sum_probs=26.1

Q ss_pred             CcCCCCCCCcccCCccccccceEeeCCccccccccc
Q 029735            2 ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACFR   37 (189)
Q Consensus         2 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~   37 (189)
                      ..|......|..|...|..+.....-+..||..|+.
T Consensus         9 ~~y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~   44 (74)
T 2ct0_A            9 ETYPDAVKICNICHSLLIQGQSCETCGIRMHLPCVA   44 (74)
T ss_dssp             CCCSSSSCBCSSSCCBCSSSEECSSSCCEECHHHHH
T ss_pred             hhccCCCCcCcchhhHcccCCccCCCCchhhHHHHH
Confidence            456777889999999997665544455667877763

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=89.35  E-value=0.41  Score=32.44  Aligned_cols=49  Identities=16%  Similarity=0.316  Sum_probs=29.9

Q ss_pred             CCCccCCcccccCcee--eccCccccccCceeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          107 DKCVACKKTVYPIEKV--AVDGTSYHKACFRCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v--~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      ..|..|++...+.+.|  ..-.+.||..|..     .+|..    ...|.-+|..|-...
T Consensus        59 ~~C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~-----ppl~~----~P~g~W~C~~C~~~~  109 (114)
T 2kwj_A           59 KSCILCGTSENDDQLLFCDDCDRGYHMYCLN-----PPVAE----PPEGSWSCHLCWELL  109 (114)
T ss_dssp             CCCTTTTCCTTTTTEEECSSSCCEEETTTSS-----SCCSS----CCSSCCCCHHHHHHH
T ss_pred             CccCcccccCCCCceEEcCCCCccccccccC-----CCccC----CCCCCeECccccchh
Confidence            4688888765544444  2445789988853     23322    235678899886543

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=84.84  E-value=0.7  Score=31.33  Aligned_cols=15  Identities=13%  Similarity=0.383  Sum_probs=8.1

Q ss_pred             cCCeeeecccHHHHh
Q 029735           53 FEGVLYCKPHFDQLF   67 (189)
Q Consensus        53 ~~g~~yC~~cy~~~~   67 (189)
                      .=|..||..|..+..
T Consensus        31 ~CgH~fc~~Ci~~~~   45 (133)
T 4ap4_A           31 ECGHVFCSQCLRDSL   45 (133)
T ss_dssp             TTCCEEEHHHHHHHH
T ss_pred             CCCChhhHHHHHHHH
Confidence            345556666665543

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=81.08  E-value=2.6  Score=26.73  Aligned_cols=27  Identities=15%  Similarity=0.548  Sum_probs=16.2

Q ss_pred             CCcccCCccccccceEeeCCcccccccccccccccccc
Q 029735            9 QKCKACEKTVYLVDQLTADNKVYHKACFRCHHCKGTLK   46 (189)
Q Consensus         9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~   46 (189)
                      ..|+.|+.+|..      .++.     +.|..|++.+.
T Consensus         3 ~~CP~C~~~l~~------~~~~-----~~C~~C~~~~~   29 (81)
T 2jrp_A            3 ITCPVCHHALER------NGDT-----AHCETCAKDFS   29 (81)
T ss_dssp             CCCSSSCSCCEE------CSSE-----EECTTTCCEEE
T ss_pred             CCCCCCCCcccc------CCCc-----eECccccccCC
Confidence            468888888742      2332     34677777653

---

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	189
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	1e-15
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	1e-13
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	2e-10
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	6e-10
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	3e-10
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	1e-09
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	5e-10
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	1e-09
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	8e-05
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	0.001
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	2e-04
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	8e-04
d1zfoa_	30	g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 982	8e-04
d1zfoa_	30	g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 982	0.003
d1a7ia1	28	g.39.1.3 (A:8-35) Cysteine-rich (intestinal) prote	0.002
d1ibia1	28	g.39.1.3 (A:117-144) Cysteine-rich (intestinal) pr	0.003

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 42

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (160), Expect = 1e-15
 Identities = 21/41 (51%), Positives = 26/41 (63%)

Query: 37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSF 77
          RC +C   L L  Y S  G +YCKPHF+QLFK  G+ D+ F
Sbjct: 1  RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF 41

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 42

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (147), Expect = 1e-13
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQ 173
           RC++    +S   Y +   R+YC+ H NQLFK KGN+ +
Sbjct: 1   RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDE 39

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (123), Expect = 2e-10
 Identities = 12/32 (37%), Positives = 21/32 (65%)

Query: 103 AGTQDKCVACKKTVYPIEKVAVDGTSYHKACF 134
           AG  D C  C + +Y +E++ V+G  +H++CF
Sbjct: 5   AGAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.2 bits (120), Expect = 6e-10
 Identities = 9/32 (28%), Positives = 19/32 (59%)

Query: 5  AGTTQKCKACEKTVYLVDQLTADNKVYHKACF 36
          AG    C  C + +Y++++L  +   +H++CF
Sbjct: 5  AGAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>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 = 51.4 bits (123), Expect = 3e-10
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 1  MASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACF 36
          MA   G +  C  C + VY  +++    K +HK+CF
Sbjct: 8  MAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 43

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 49.5 bits (118), Expect = 1e-09
 Identities = 19/43 (44%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 94  TNSRVSSM--FAGTQDKCVACKKTVYPIEKVAVDGTSYHKACF 134
           TN   S M    G  D C  C + VY  EKV   G S+HK+CF
Sbjct: 1   TNPNASRMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (121), Expect = 5e-10
 Identities = 13/32 (40%), Positives = 22/32 (68%)

Query: 103 AGTQDKCVACKKTVYPIEKVAVDGTSYHKACF 134
           A  ++ CV C+KTVYP+E++  +   +H +CF
Sbjct: 4   APARETCVECQKTVYPMERLLANQQVFHISCF 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 = 49.4 bits (118), Expect = 1e-09
 Identities = 13/32 (40%), Positives = 22/32 (68%)

Query: 5  AGTTQKCKACEKTVYLVDQLTADNKVYHKACF 36
          A   + C  C+KTVY +++L A+ +V+H +CF
Sbjct: 4  APARETCVECQKTVYPMERLLANQQVFHISCF 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 = 36.4 bits (84), Expect = 8e-05
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 104 GTQDKCVACKKTVYPIEKVAVDGTSYHKACF 134
           G   KC  C+K VY  E+V  +G+S+HK+CF
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 35

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 33.0 bits (75), Expect = 0.001
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 6  GTTQKCKACEKTVYLVDQLTADNKVYHKACF 36
          G  +KC  C+K VY  +++  +   +HK+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 = 16/26 (61%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKAC 133
           KC  C KTVY  EKV+  G  +HK C
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFC 29

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.6 bits (77), Expect = 8e-04
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 8  TQKCKACEKTVYLVDQLTADNKVYHKAC 35
            KC  C+KTVY  +++++  K +HK C
Sbjct: 2  ASKCPKCDKTVYFAEKVSSLGKDWHKFC 29

>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 = 33.7 bits (77), Expect = 8e-04
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 108 KCVACKKTVYPIEKVAVDGTSYHKACF 134
            C  C K VYP EKV      +HKACF
Sbjct: 4   NCARCGKIVYPTEKVNCLDKFWHKACF 30

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

 Score = 31.8 bits (72), Expect = 0.003
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 9  QKCKACEKTVYLVDQLTADNKVYHKACF 36
            C  C K VY  +++   +K +HKACF
Sbjct: 3  PNCARCGKIVYPTEKVNCLDKFWHKACF 30

>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 = 32.3 bits (73), Expect = 0.002
 Identities = 15/28 (53%), Positives = 20/28 (71%)

Query: 107 DKCVACKKTVYPIEKVAVDGTSYHKACF 134
           +KC AC +TVY  E+V  DG S+H+ CF
Sbjct: 1   NKCGACGRTVYHAEEVQCDGRSFHRCCF 28

>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 = 31.8 bits (72), Expect = 0.003
 Identities = 12/27 (44%), Positives = 15/27 (55%)

Query: 107 DKCVACKKTVYPIEKVAVDGTSYHKAC 133
           +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	189
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	99.11
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.99
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.99
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.91
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.85
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.79
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.75
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.71
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.7
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.66
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.66
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.65
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.64
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.63
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.63
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.61
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.58
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.57
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.57
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.56
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.54
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.54
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.53
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.52
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.5
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.49
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.48
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.47
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.46
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.44
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.44
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.44
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.43
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.4
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.36
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.35
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.34
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.34
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.34
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.32
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.29
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.24
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.24
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.24
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.23
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.17
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.17
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.15
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.1
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.09
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.09
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.08
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.08
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.06
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.06
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.06
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.05
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.98
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.97
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.96
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.95
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.94
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.91
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.89
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.88
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.87
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.85
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.83
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.81
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.78
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.78
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.76
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.74
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.74
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.72
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.71
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.71
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.69
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.65
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.64
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.63
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.62
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.57
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.54
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.51
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.49
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.43
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.4
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.38
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.37
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.29
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.26
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.19
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.17
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.17
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.17
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.15
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.07
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.06
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.01
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.94
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.76
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.67
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.65
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.62
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.6
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.27
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.24
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.17
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	96.1
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.08
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	95.76
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.34
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.21
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.2
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.93
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	94.71
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	94.62
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.61
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.39
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.03
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	93.47
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	92.85
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	92.36
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	91.15
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	89.92
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	88.83
d2co8a1	33	Nedd9 interacting protein with calponin homology,	88.82
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	87.81
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	87.28
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	85.86
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	83.86
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	83.66
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	81.33

>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=99.11  E-value=3.7e-11  Score=65.95  Aligned_cols=42  Identities=38%  Similarity=0.696  Sum_probs=39.7

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCCCCCCCC
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGNFSQLDN  176 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~~~~~~~  176 (189)
                      +|..|++.|..++|...+|.+||+.||.++|++|++++++++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny~~gfg   42 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFG   42 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCCCCCCC
Confidence            699999999999999999999999999999999999998864

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=6.3e-11  Score=63.04  Aligned_cols=34  Identities=26%  Similarity=0.494  Sum_probs=32.6

Q ss_pred             ceeCCCCCcCCCCCeeecCCccccHhHHHhhhcC
Q 029735          134 FRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ  167 (189)
Q Consensus       134 f~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~  167 (189)
                      |+|+.|+++|+.+.|+++||+|||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7899999999999999999999999999999987

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=5.8e-11  Score=63.19  Aligned_cols=34  Identities=32%  Similarity=0.715  Sum_probs=32.4

Q ss_pred             cccccccccccCCCeeecCCeeeecccHHHHhhc
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKM   69 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   69 (189)
                      |+|+.|+++|.+..|++++|++||+.||.++|+|
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            7999999999999999999999999999999974

>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=98.91  E-value=6.4e-10  Score=62.98  Aligned_cols=41  Identities=24%  Similarity=0.502  Sum_probs=37.1

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC-CCCCC
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN-FSQLD  175 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~-~~~~~  175 (189)
                      +|..|++.|++....++||+|||+.||.++||||+. +..+.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~ga   42 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA   42 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccCc
Confidence            689999999998889999999999999999999998 66554

>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=98.85  E-value=1.9e-10  Score=61.24  Aligned_cols=27  Identities=30%  Similarity=0.711  Sum_probs=24.9

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ++|..|+++|.+ +.|+|+|+.||++||
T Consensus         9 pkC~~C~~~I~g-~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           9 PKCGGCNRPVLE-NYLSAMDTVWHPECF   35 (35)
T ss_dssp             CBCTTTCCBCCS-SCEEETTEEECTTTC
T ss_pred             hhhhhcCCcccc-hheeecCCccCcccC
Confidence            899999999985 459999999999998

>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=98.79  E-value=1.4e-09  Score=57.78  Aligned_cols=30  Identities=37%  Similarity=0.772  Sum_probs=27.4

Q ss_pred             CCCCCcccCCccccccceEeeCCcccccccc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      -.+++|.+|+++| .+++|.|+|+.||++||
T Consensus         6 ~fapkC~~C~~~I-~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           6 MFSPKCGGCNRPV-LENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCSCBCTTTCCBC-CSSCEEETTEEECTTTC
T ss_pred             HhChhhhhcCCcc-cchheeecCCccCcccC
Confidence            3478999999999 48999999999999998

>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=98.75  E-value=1.6e-09  Score=59.33  Aligned_cols=41  Identities=51%  Similarity=1.117  Sum_probs=38.1

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhhccCCCCCCC
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGSLDKSF   77 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~   77 (189)
                      +|+.|++.|..+.|...+|.+||++||.++|.++++.+++|
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            69999999999999999999999999999999999887765

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.71  E-value=3e-09  Score=59.02  Aligned_cols=40  Identities=43%  Similarity=0.829  Sum_probs=33.0

Q ss_pred             CcccccccCCCCCCCCccCCcccccCceeeccCccccccCc
Q 029735           94 TNSRVSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus        94 ~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +++++...+.+ .++|..|++.|++.|++.+.|+.||+.||
T Consensus         4 ~~sk~~~~~g~-~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3           4 NASRMAQKVGG-SDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCCCCCC-CEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CccccccccCC-CCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            34455544543 48999999999999999999999999998

>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=98.70  E-value=4.6e-09  Score=58.65  Aligned_cols=36  Identities=25%  Similarity=0.553  Sum_probs=34.0

Q ss_pred             eeCCCCCcCCCCCeeecCCcccc-HhHHHhhhcCCCC
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYC-RHHHNQLFKQKGN  170 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC-~~c~~~~~~~k~~  170 (189)
                      +|..|++.|+++...++||+||| +.||.++||||+.
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~   37 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF   37 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCcc
Confidence            68999999999999999999999 6799999999997

>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=98.66  E-value=4.7e-09  Score=58.19  Aligned_cols=34  Identities=29%  Similarity=0.766  Sum_probs=30.9

Q ss_pred             cCCCCCCCcccCCccccccceEeeCCcccccccc
Q 029735            3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         3 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ...++...|..|++.|+..|.+.++|+.||..||
T Consensus        10 ~~~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          10 QKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             cccCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            4456678999999999999999999999999998

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.66  E-value=6.4e-09  Score=57.28  Aligned_cols=31  Identities=26%  Similarity=0.400  Sum_probs=28.2

Q ss_pred             CCCCCCcccCCccccccceEeeCCcccccccc
Q 029735            5 AGTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         5 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ....+.|..|+++| .+..|.|+|+.||++||
T Consensus        15 ~~r~P~C~~C~~pI-~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          15 GKRTPMCAHCNQVI-RGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TTCCCBBSSSCCBC-CSCEEEETTEEECTTTC
T ss_pred             CCCCeeccccCCcc-cCceeeecCCccCcCCC
Confidence            45679999999999 59999999999999998

>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=98.65  E-value=2.2e-09  Score=55.61  Aligned_cols=27  Identities=26%  Similarity=0.668  Sum_probs=25.3

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ..|..|+++|..+. |++.++.||++||
T Consensus         9 ~~C~~Ckk~It~GG-vtY~dqpWHkeCF   35 (35)
T d2cuqa2           9 PRCARCSKTLTQGG-VTYRDQPWHRECL   35 (35)
T ss_dssp             CCCTTTCCCCCSCC-EESSSSEECTTTC
T ss_pred             HHHhhcCCccccCc-eeecCCcchhhhC
Confidence            89999999999776 9999999999998

>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=98.64  E-value=7.2e-09  Score=58.55  Aligned_cols=36  Identities=28%  Similarity=0.649  Sum_probs=33.2

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      +|..|++.|++....++|+++||+.||.++|+|++.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~   36 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF   36 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCcc
Confidence            689999999999999999999999999999997663

>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=1.1e-08  Score=52.10  Aligned_cols=32  Identities=22%  Similarity=0.410  Sum_probs=29.9

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      .|..|.++|.+..|..+|++|||..||..+|+
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            48899999999999999999999999999985

>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=98.63  E-value=5.4e-09  Score=51.64  Aligned_cols=29  Identities=38%  Similarity=0.879  Sum_probs=27.5

Q ss_pred             CCCcccCCccccccceEeeCCcccccccc
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ++.|++|++.+++.|.|+-+++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHHhhhhHHHHhhccC
Confidence            47899999999999999999999999998

>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=98.61  E-value=8.7e-09  Score=51.63  Aligned_cols=29  Identities=38%  Similarity=0.890  Sum_probs=27.1

Q ss_pred             CCCcccCCccccccceEeeCCcccccccc
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ++.|++|+++|+..|.+..+|+.||..|+
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            47899999999999999999999999985

>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=98.58  E-value=2.9e-08  Score=59.16  Aligned_cols=42  Identities=14%  Similarity=0.291  Sum_probs=37.0

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhcCCCC-CCCCCC
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQKGN-FSQLDN  176 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~k~~-~~~~~~  176 (189)
                      .|..|++.|++....+++++|||+.||.++||||+. +..+.+
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~G~gag   43 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAG   43 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccccccccc
Confidence            388999999999999999999999999999999997 555443

>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=98.57  E-value=4.6e-09  Score=56.00  Aligned_cols=28  Identities=39%  Similarity=0.823  Sum_probs=25.9

Q ss_pred             CCCccCCcccccCce-eeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEK-VAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf  134 (189)
                      ++|.+|+++|.++.+ |.+.|+.||..||
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            899999999997765 8999999999998

>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=98.57  E-value=1e-08  Score=52.18  Aligned_cols=32  Identities=22%  Similarity=0.566  Sum_probs=29.7

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      .|..|.++|.++.|.++|++|||-.||..+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            48899999999999999999999999999874

>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=98.56  E-value=2.1e-08  Score=52.94  Aligned_cols=32  Identities=38%  Similarity=0.985  Sum_probs=29.3

Q ss_pred             CCCCCCCccCCcccccCceeeccCccccccCc
Q 029735          103 AGTQDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       103 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +++..+|..|++.|++.|++.+.|+.||+.||
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            34558999999999999999999999999998

>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=98.54  E-value=1.9e-08  Score=50.41  Aligned_cols=28  Identities=50%  Similarity=0.896  Sum_probs=26.6

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ++|++|+++|+..|.+..+|+.||+.|+
T Consensus         3 ~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           3 SKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CcCCCCCCceeeHHhhccCCcccccccC
Confidence            7899999999999999999999999885

>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=98.54  E-value=3.1e-08  Score=50.66  Aligned_cols=32  Identities=16%  Similarity=0.278  Sum_probs=29.3

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      +|..|.+++.++.|++.||+|||+.||+++-|
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            58999999999999999999999999998753

>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=98.53  E-value=2.2e-08  Score=51.96  Aligned_cols=33  Identities=33%  Similarity=0.747  Sum_probs=29.5

Q ss_pred             cCCCCCCCcccCCccccccceEeeCCcccccccc
Q 029735            3 SFAGTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         3 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      -|..+..+|..|+++|. +..|.|+|+.||+.||
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            36677889999999994 7889999999999998

>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=98.52  E-value=2e-08  Score=53.04  Aligned_cols=33  Identities=27%  Similarity=0.834  Sum_probs=30.6

Q ss_pred             CCCCCCCcccCCccccccceEeeCCcccccccc
Q 029735            4 FAGTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         4 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      .+++..+|..|++.|++.|.+.++|+.||..||
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             cCCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            356788999999999999999999999999998

>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=98.50  E-value=3.2e-08  Score=49.58  Aligned_cols=31  Identities=16%  Similarity=0.555  Sum_probs=28.1

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      +|..|++.|.+ .|..+||.|||+.+|+..||
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            58999999986 58999999999999999986

>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=98.49  E-value=3.4e-08  Score=51.93  Aligned_cols=32  Identities=41%  Similarity=0.915  Sum_probs=29.4

Q ss_pred             CCCCCCcccCCccccccceEeeCCcccccccc
Q 029735            5 AGTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         5 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      +....+|..|++.|+..|.+.++|+.||..||
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            34578999999999999999999999999998

>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=98.48  E-value=3.9e-08  Score=54.83  Aligned_cols=35  Identities=31%  Similarity=0.752  Sum_probs=32.7

Q ss_pred             ccccccccccCCCeeecCCeeee-cccHHHHhhccC
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYC-KPHFDQLFKMTG   71 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC-~~cy~~~~~~~~   71 (189)
                      +|..|++.|+++...++|++||| ++||.++|+|++
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

>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=98.48  E-value=4.5e-08  Score=51.46  Aligned_cols=29  Identities=41%  Similarity=1.091  Sum_probs=27.7

Q ss_pred             CCCCccCCcccccCceeeccCccccccCc
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      .++|..|++.|++.|++.+.|+.||+.||
T Consensus         7 ~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeEecCCeehhhccC
Confidence            37999999999999999999999999998

>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=98.47  E-value=2.8e-08  Score=48.84  Aligned_cols=30  Identities=33%  Similarity=0.803  Sum_probs=28.2

Q ss_pred             cccccccccccCCCeeecCCeeeecccHHH
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQ   65 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   65 (189)
                      |+|+.|++.|.+.....+||++||+.||.+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            899999999999999999999999999975

>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=98.46  E-value=6.5e-08  Score=48.51  Aligned_cols=32  Identities=19%  Similarity=0.455  Sum_probs=29.9

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      .|..|+++|.+..|..+|..|||.+||..+|+
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            48999999999999999999999999999885

>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=98.44  E-value=4e-08  Score=48.46  Aligned_cols=28  Identities=50%  Similarity=0.949  Sum_probs=26.8

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +.|++|++.|++.|.+.-+++.||+.||
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

>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=98.44  E-value=6.4e-08  Score=49.17  Aligned_cols=34  Identities=26%  Similarity=0.412  Sum_probs=31.7

Q ss_pred             ceeCCCCCcCCCCCeeecCCccccHhHHHhhhcC
Q 029735          134 FRCTHGGCVISPSNYVAHEHRLYCRHHHNQLFKQ  167 (189)
Q Consensus       134 f~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~~  167 (189)
                      |+|+.|.+|+-+...+++.|..||+.||.++||.
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            7899999999888899999999999999999975

>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=98.44  E-value=4.8e-08  Score=49.00  Aligned_cols=32  Identities=28%  Similarity=0.586  Sum_probs=29.8

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      .|+.|+++|+++.|..+|.+|||..||..+|+
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

>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=98.43  E-value=6.4e-08  Score=48.46  Aligned_cols=31  Identities=32%  Similarity=0.792  Sum_probs=27.8

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      +|..|++.| .+.|..+||.|||+.||+..|+
T Consensus         1 kC~~C~~vL-~gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVIL-TGEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBC-SSCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCccc-cceeecCCCCcccHHHHHHhcC
Confidence            589999999 4789999999999999998874

>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=98.40  E-value=6.4e-08  Score=49.82  Aligned_cols=30  Identities=27%  Similarity=0.613  Sum_probs=28.1

Q ss_pred             CCCCcccCCccccccceEeeCCcccccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      +...|++|++.|..+..|.++++.||.+||
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            567899999999999999999999999998

>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=98.36  E-value=9.3e-08  Score=48.85  Aligned_cols=31  Identities=16%  Similarity=0.576  Sum_probs=28.9

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF   67 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   67 (189)
                      +|..|.+++.+..|++.+|+|||+.+|.++.
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            5899999999999999999999999999875

>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=1.3e-07  Score=48.96  Aligned_cols=29  Identities=31%  Similarity=0.786  Sum_probs=25.3

Q ss_pred             CCCCCccCCcccccCceeeccCccccccCc
Q 029735          105 TQDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       105 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +..+|..|+++|.+. .+.+.|+.||+.||
T Consensus         7 tlEkC~~C~~~I~dr-iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           7 TLEKCATCSQPILDR-ILRAMGKAYHPGCF   35 (35)
T ss_dssp             SCCBCTTTCCBCCSC-CEEETTEEECTTTC
T ss_pred             HHHHHHHhchHHHHH-HHHHhCCCCCCCCC
Confidence            348999999999864 37999999999998

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.34  E-value=1.1e-07  Score=52.30  Aligned_cols=28  Identities=21%  Similarity=0.438  Sum_probs=25.1

Q ss_pred             CCCCccCCcccccCceeeccCccccccCc
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      .+.|..|+++|.+. .|+++|+.||++||
T Consensus        18 ~P~C~~C~~pI~g~-~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGP-FLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSC-EEEETTEEECTTTC
T ss_pred             CeeccccCCcccCc-eeeecCCccCcCCC
Confidence            48999999999854 58999999999998

>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=98.34  E-value=1.3e-07  Score=50.20  Aligned_cols=30  Identities=37%  Similarity=0.771  Sum_probs=27.2

Q ss_pred             CCCCcccCCccccccc-eEeeCCcccccccc
Q 029735            7 TTQKCKACEKTVYLVD-QLTADNKVYHKACF   36 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~-~~~~~~~~~H~~CF   36 (189)
                      .+++|.+|+++|.++. .|.+.|+.||..||
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            4789999999998776 59999999999998

>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=98.32  E-value=1.7e-07  Score=47.32  Aligned_cols=32  Identities=19%  Similarity=0.548  Sum_probs=29.3

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHh-HHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRH-HHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~-c~~~~~~  166 (189)
                      +|..|++.|..+...++||+|||.. ||..+||
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            5899999999999999999999975 9999986

>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=98.29  E-value=1.7e-07  Score=45.97  Aligned_cols=30  Identities=23%  Similarity=0.610  Sum_probs=27.8

Q ss_pred             ceeCCCCCcCCCCCeeecCCccccHhHHHh
Q 029735          134 FRCTHGGCVISPSNYVAHEHRLYCRHHHNQ  163 (189)
Q Consensus       134 f~C~~C~~~l~~~~~~~~dg~~yC~~c~~~  163 (189)
                      |+|+.|++.|.+.....+||++||+.||.+
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            799999999998888899999999999975

>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=98.24  E-value=3.2e-07  Score=45.88  Aligned_cols=29  Identities=21%  Similarity=0.464  Sum_probs=25.4

Q ss_pred             CCCCcccCCccccccceEeeCCccccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKAC   35 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   35 (189)
                      ....|++|+++|.+...|.++++.||..|
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            34679999999987778999999999987

>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=98.24  E-value=2.8e-07  Score=54.82  Aligned_cols=36  Identities=22%  Similarity=0.534  Sum_probs=33.5

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhhccCC
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFKMTGS   72 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   72 (189)
                      .|..|++.|++....++++++||+.||.++|+|++.
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~   36 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGK   36 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCcc
Confidence            488999999999999999999999999999999874

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=1.7e-07  Score=47.01  Aligned_cols=28  Identities=21%  Similarity=0.362  Sum_probs=25.0

Q ss_pred             CCCCcccCCccccccceEeeCCccccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKAC   35 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   35 (189)
                      +.++|+.|.+||. +..+.++|+.||++.
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            4689999999994 799999999999874

>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=2.7e-07  Score=46.30  Aligned_cols=28  Identities=21%  Similarity=0.478  Sum_probs=25.3

Q ss_pred             CCcccCCccccccceEeeCCcccccccc
Q 029735            9 QKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         9 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ..|++|+++|.+...|.++++.||..|+
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            5799999999877789999999999985

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.17  E-value=4.2e-07  Score=45.88  Aligned_cols=35  Identities=31%  Similarity=0.816  Sum_probs=31.6

Q ss_pred             CcCCCCCCCcccCCccccccceEeeCCcccccccc
Q 029735            2 ASFAGTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         2 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      |...++..+|+.|.+.++..|.+...|++||..||
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            45567788999999999999999999999999998

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.17  E-value=4.2e-07  Score=45.67  Aligned_cols=32  Identities=31%  Similarity=0.871  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      .|+.|+.+|.+..|.+.+|.+||+.||.+.++
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            48999999999999999999999999998753

>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=98.10  E-value=8.5e-07  Score=44.59  Aligned_cols=32  Identities=16%  Similarity=0.597  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      .|..|..+|+..+|..+++..||.+||++.|+
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            37889999999999999999999999998874

>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=98.09  E-value=8.8e-07  Score=44.60  Aligned_cols=32  Identities=28%  Similarity=0.757  Sum_probs=28.7

Q ss_pred             ccccccccccCCCeeecCCeeeec-ccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCK-PHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~-~cy~~~~~   68 (189)
                      +|..|++.|..+...+++|+|||. +||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            589999999999999999999996 59988874

>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=98.09  E-value=7.4e-07  Score=45.18  Aligned_cols=33  Identities=30%  Similarity=0.735  Sum_probs=31.3

Q ss_pred             cccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      |+|+.|.+++-+...+++.|..||+.+|.++|+
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            789999999988899999999999999999986

>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=98.08  E-value=8.9e-07  Score=45.45  Aligned_cols=28  Identities=21%  Similarity=0.611  Sum_probs=26.6

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ..|++|++.|..+..+.++++.||..||
T Consensus         9 ~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccccccchhhhCCceeeeeecceeeeeC
Confidence            7899999999998889999999999998

>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=98.06  E-value=1.6e-06  Score=43.53  Aligned_cols=32  Identities=22%  Similarity=0.522  Sum_probs=29.1

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      .|+.|+++|....|++..|.+||+.||.+.|+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            38899999999889999999999999999874

>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=98.06  E-value=1.1e-06  Score=44.06  Aligned_cols=32  Identities=25%  Similarity=0.676  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      .|..|..+|+..+|..+++..||.+||++.|+
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

>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=98.06  E-value=1.6e-06  Score=43.58  Aligned_cols=31  Identities=10%  Similarity=0.344  Sum_probs=29.2

Q ss_pred             eCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          136 CTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       136 C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      |..|..+|+..+|..+++..||-.||++.|+
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            7899999999999999999999999999885

>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=98.05  E-value=1.5e-06  Score=43.55  Aligned_cols=31  Identities=16%  Similarity=0.369  Sum_probs=29.2

Q ss_pred             eCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          136 CTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       136 C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      |..|..+|+..+|..+++..||..||+++|+
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            7899999999999999999999999999885

>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=97.98  E-value=1.4e-06  Score=41.61  Aligned_cols=26  Identities=27%  Similarity=0.783  Sum_probs=23.8

Q ss_pred             cccCCccccccc-eEeeCCcccccccc
Q 029735           11 CKACEKTVYLVD-QLTADNKVYHKACF   36 (189)
Q Consensus        11 C~~C~~~I~~~~-~~~~~~~~~H~~CF   36 (189)
                      |..|.+.|+++. .+...|..||..||
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            789999999986 58999999999998

>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=97.97  E-value=1.1e-06  Score=42.40  Aligned_cols=27  Identities=33%  Similarity=0.871  Sum_probs=25.0

Q ss_pred             CCcccCCccccccceEeeCCccccccc
Q 029735            9 QKCKACEKTVYLVDQLTADNKVYHKAC   35 (189)
Q Consensus         9 ~~C~~C~~~I~~~~~~~~~~~~~H~~C   35 (189)
                      .+|++|++.++..|.+.-.|+.||..|
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            479999999999999999999999987

>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=97.96  E-value=1.5e-06  Score=41.44  Aligned_cols=26  Identities=35%  Similarity=0.778  Sum_probs=23.8

Q ss_pred             cccCCccccccc-eEeeCCcccccccc
Q 029735           11 CKACEKTVYLVD-QLTADNKVYHKACF   36 (189)
Q Consensus        11 C~~C~~~I~~~~-~~~~~~~~~H~~CF   36 (189)
                      |..|.+.|+++. .+...|..||..||
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            789999999986 58999999999998

>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=97.95  E-value=2.4e-06  Score=42.58  Aligned_cols=27  Identities=15%  Similarity=0.349  Sum_probs=24.7

Q ss_pred             CCCccCCcccccCceeeccCccccccC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      ..|++|+++|.+...+.+.++.||..|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            679999999998877899999999887

>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=97.94  E-value=1.3e-06  Score=46.95  Aligned_cols=32  Identities=25%  Similarity=0.677  Sum_probs=26.1

Q ss_pred             ccccCCCCCCCCccCCcccccCceeeccCccccccC
Q 029735           98 VSSMFAGTQDKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus        98 ~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      |..+|.   .+|..|++.|. ++.|.+.++.||+.|
T Consensus        10 Yq~~fG---~~C~~C~~~It-G~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          10 YQRLYG---TRCFSCDQFIE-GEVVSALGKTYHPDC   41 (41)
T ss_dssp             GGGSCC---CBCTTTCCBCC-SCCEEETTEEECTTT
T ss_pred             HHHHhC---cccccccCEee-eeeeEecCcccCCCC
Confidence            444444   89999999997 566899999999987

>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=97.91  E-value=1.7e-06  Score=41.77  Aligned_cols=27  Identities=44%  Similarity=0.941  Sum_probs=25.1

Q ss_pred             CCCccCCcccccCceeeccCccccccC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      .+|++|++.++..|.|.-.|+.||+.|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            579999999999999999999999987

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.89  E-value=2.3e-06  Score=42.44  Aligned_cols=31  Identities=13%  Similarity=0.399  Sum_probs=28.5

Q ss_pred             eCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          136 CTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       136 C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      |..|.+.|++.....+++++||+.||.++||
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            7789999999888999999999999999875

>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=97.85  E-value=4.2e-06  Score=41.29  Aligned_cols=29  Identities=21%  Similarity=0.545  Sum_probs=26.9

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQ   65 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   65 (189)
                      .|..|.++|++.+|...++++||.+||..
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

>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=3.9e-06  Score=43.11  Aligned_cols=29  Identities=24%  Similarity=0.647  Sum_probs=25.3

Q ss_pred             CCCCcccCCccccccceEeeCCcccccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      .+++|..|+++|. .-.|...++.||.+||
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            3689999999995 5668889999999998

>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=97.81  E-value=3.8e-06  Score=42.01  Aligned_cols=28  Identities=14%  Similarity=0.430  Sum_probs=25.4

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ..|++|+++|.+...+.+.++.||..|+
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            5799999999988778999999999884

>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=97.78  E-value=6.4e-06  Score=39.29  Aligned_cols=27  Identities=41%  Similarity=1.080  Sum_probs=25.9

Q ss_pred             CcccCCccccccceEeeCCcccccccc
Q 029735           10 KCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus        10 ~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      +|+.|.+.++..+.+..+|++||..||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            699999999999999999999999998

>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=97.78  E-value=4.9e-06  Score=40.59  Aligned_cols=26  Identities=19%  Similarity=0.710  Sum_probs=22.5

Q ss_pred             cccCCccccc---cceEeeCCcccccccc
Q 029735           11 CKACEKTVYL---VDQLTADNKVYHKACF   36 (189)
Q Consensus        11 C~~C~~~I~~---~~~~~~~~~~~H~~CF   36 (189)
                      |..|.+||..   +.++...++.||..||
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            7899999953   3579999999999998

>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=97.76  E-value=5.8e-06  Score=40.98  Aligned_cols=31  Identities=19%  Similarity=0.613  Sum_probs=28.0

Q ss_pred             cccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           38 CHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        38 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      |-.|++.|++..-..+++++||+.||.+.++
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7789999999999999999999999988763

>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=97.74  E-value=5.9e-06  Score=41.57  Aligned_cols=29  Identities=31%  Similarity=0.770  Sum_probs=25.5

Q ss_pred             CCCcccCCccccccce-EeeCCcccccccc
Q 029735            8 TQKCKACEKTVYLVDQ-LTADNKVYHKACF   36 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~-~~~~~~~~H~~CF   36 (189)
                      +..|.+|++.|.+.|. +.+.+..||..||
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            3569999999988885 6999999999998

>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=97.72  E-value=4.3e-06  Score=41.81  Aligned_cols=26  Identities=23%  Similarity=0.469  Sum_probs=22.9

Q ss_pred             CCCccCCcccccCceeeccCccccccC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      ++|+.|++||.+ ..|.++|+.||++.
T Consensus         6 p~C~~C~~PI~~-~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           6 PICGACRRPIEG-RVVNAMGKQWHVEH   31 (31)
T ss_dssp             CEETTTTEECCS-CEECCTTSBEETTT
T ss_pred             cchhhcCCchhh-hHhhhhccccCCCC
Confidence            899999999986 45899999999863

>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=97.71  E-value=7.1e-06  Score=39.01  Aligned_cols=26  Identities=38%  Similarity=0.949  Sum_probs=23.2

Q ss_pred             CccCCcccccCce-eeccCccccccCc
Q 029735          109 CVACKKTVYPIEK-VAVDGTSYHKACF  134 (189)
Q Consensus       109 C~~C~~~I~~~~~-v~~~g~~~H~~Cf  134 (189)
                      |..|.+.|.++.+ +.+.|..||..||
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            7789999998865 7999999999998

>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=97.71  E-value=9.3e-06  Score=40.12  Aligned_cols=30  Identities=20%  Similarity=0.566  Sum_probs=27.2

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQL   66 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   66 (189)
                      .|..|+..|.++.|+..+++.||++||...
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

>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=97.69  E-value=6.5e-06  Score=39.24  Aligned_cols=26  Identities=42%  Similarity=1.034  Sum_probs=23.1

Q ss_pred             CccCCcccccCce-eeccCccccccCc
Q 029735          109 CVACKKTVYPIEK-VAVDGTSYHKACF  134 (189)
Q Consensus       109 C~~C~~~I~~~~~-v~~~g~~~H~~Cf  134 (189)
                      |..|.+.|.++.+ +.+.|..||..||
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            6789999998865 7999999999998

>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=97.65  E-value=1.2e-05  Score=39.11  Aligned_cols=26  Identities=27%  Similarity=0.672  Sum_probs=22.4

Q ss_pred             cccCCccccc---cceEeeCCcccccccc
Q 029735           11 CKACEKTVYL---VDQLTADNKVYHKACF   36 (189)
Q Consensus        11 C~~C~~~I~~---~~~~~~~~~~~H~~CF   36 (189)
                      |..|.+||..   ..++...++.||.+||
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            7899999953   3579999999999998

>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=97.64  E-value=1e-05  Score=40.69  Aligned_cols=28  Identities=36%  Similarity=0.782  Sum_probs=25.4

Q ss_pred             CCCccCCcccccCcee-eccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKV-AVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf  134 (189)
                      -.|.+|++.|.+.|.| .+.+..||..||
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            4699999999999986 799999999998

>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=97.63  E-value=1.4e-05  Score=39.40  Aligned_cols=29  Identities=34%  Similarity=0.694  Sum_probs=26.1

Q ss_pred             CCCCCcccCCccccccceEeeCCccccccc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKAC   35 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   35 (189)
                      +++.-|..|.+.| .+.+|.+.++.||+.|
T Consensus         3 sgssgC~~C~~~I-tGkVLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYI-TGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCC-SSCCBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhh-hhhhhhccccccCCCC
Confidence            4667899999999 5999999999999987

>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=97.62  E-value=1.4e-05  Score=40.56  Aligned_cols=32  Identities=19%  Similarity=0.398  Sum_probs=27.9

Q ss_pred             ccccccccccCCCeee-cCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKLSNYCS-FEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~-~~g~~yC~~cy~~~~~   68 (189)
                      +|..|++.|.+..|.. .++++||.+||++.|+
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            5889999999889976 4899999999999874

>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=97.57  E-value=1.3e-05  Score=39.03  Aligned_cols=26  Identities=19%  Similarity=0.787  Sum_probs=21.9

Q ss_pred             CccCCcccccC---ceeeccCccccccCc
Q 029735          109 CVACKKTVYPI---EKVAVDGTSYHKACF  134 (189)
Q Consensus       109 C~~C~~~I~~~---~~v~~~g~~~H~~Cf  134 (189)
                      |..|.+||.+.   ..|.+.++.||.+||
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            77899999854   248999999999998

>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=97.54  E-value=2.1e-05  Score=42.09  Aligned_cols=27  Identities=26%  Similarity=0.646  Sum_probs=25.1

Q ss_pred             CCCcccCCccccccceEeeCCccccccc
Q 029735            8 TQKCKACEKTVYLVDQLTADNKVYHKAC   35 (189)
Q Consensus         8 ~~~C~~C~~~I~~~~~~~~~~~~~H~~C   35 (189)
                      ..+|..|++.| .+++|.|.++.||+.|
T Consensus        15 G~~C~~C~~~I-tG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          15 GTRCFSCDQFI-EGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CCBCTTTCCBC-CSCCEEETTEEECTTT
T ss_pred             CcccccccCEe-eeeeeEecCcccCCCC
Confidence            56899999999 6999999999999987

>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=97.51  E-value=4.3e-05  Score=37.56  Aligned_cols=30  Identities=17%  Similarity=0.386  Sum_probs=27.1

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      .|..|+++|.+..|...+++.||-+||...
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~~   30 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKNF   30 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeeccc
Confidence            488999999999999999999999999753

>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=97.49  E-value=1.9e-05  Score=39.63  Aligned_cols=30  Identities=47%  Similarity=0.979  Sum_probs=27.2

Q ss_pred             CCCCCccCCcccccCceeeccCccccccCc
Q 029735          105 TQDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       105 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +..+|..|.+.++-.|-|.-.|+.||+.||
T Consensus         6 gg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           6 GGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCceeccccceEeeeeeeeecCcccccccC
Confidence            347999999999988889999999999998

>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=97.43  E-value=6e-05  Score=38.17  Aligned_cols=32  Identities=9%  Similarity=0.237  Sum_probs=27.6

Q ss_pred             eeCCCCCcCCCCCeee-cCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVA-HEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~-~dg~~yC~~c~~~~~~  166 (189)
                      .|..|++.|++-.|.. .++++||-.+|+++|+
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            4889999999877765 5799999999999985

>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=97.40  E-value=3.7e-05  Score=36.35  Aligned_cols=26  Identities=27%  Similarity=0.747  Sum_probs=21.7

Q ss_pred             cccCCccccccc-eEeeCCcccccccc
Q 029735           11 CKACEKTVYLVD-QLTADNKVYHKACF   36 (189)
Q Consensus        11 C~~C~~~I~~~~-~~~~~~~~~H~~CF   36 (189)
                      |..|.+||-.+. .|...+++||..||
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            788999995443 58889999999998

>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=97.38  E-value=3e-05  Score=37.68  Aligned_cols=26  Identities=31%  Similarity=0.866  Sum_probs=21.8

Q ss_pred             CccCCcccccC---ceeeccCccccccCc
Q 029735          109 CVACKKTVYPI---EKVAVDGTSYHKACF  134 (189)
Q Consensus       109 C~~C~~~I~~~---~~v~~~g~~~H~~Cf  134 (189)
                      |..|.+||.+.   ..|.+.++.||.+||
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            77899999854   248899999999998

>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=97.37  E-value=7.1e-05  Score=37.80  Aligned_cols=30  Identities=13%  Similarity=0.381  Sum_probs=27.1

Q ss_pred             CCCCCcccCCccccccceEeeCCcccccccc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ...+.|.+|+--|. +.++.+.++.+|++||
T Consensus         6 qklp~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           6 QKLPMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             ccCccccccCCCcE-eEEEEeccccCCCCCC
Confidence            45789999999995 8999999999999998

>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=97.29  E-value=8.6e-05  Score=40.00  Aligned_cols=29  Identities=24%  Similarity=0.524  Sum_probs=26.5

Q ss_pred             CCCCcccCCccccccceEeeCCcccccccc
Q 029735            7 TTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         7 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      ..+.|.+|+.-|. +.++.+.++.+|++||
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            4689999999995 8999999999999998

>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=97.26  E-value=7.6e-05  Score=35.45  Aligned_cols=27  Identities=56%  Similarity=1.144  Sum_probs=25.1

Q ss_pred             CCccCCcccccCceeeccCccccccCc
Q 029735          108 KCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       108 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +|..|.+.++-.|-|.-.|+.||+.||
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            699999999988889999999999997

>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=97.19  E-value=0.00013  Score=36.82  Aligned_cols=27  Identities=19%  Similarity=0.496  Sum_probs=24.5

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      +.|.+|+..|.+. .|.+.++.+|++||
T Consensus         9 p~CdkCg~GIVG~-~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVGV-FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCSS-CEECSSCEECTTTT
T ss_pred             ccccccCCCcEeE-EEEeccccCCCCCC
Confidence            8999999999865 48999999999997

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.17  E-value=0.00016  Score=35.44  Aligned_cols=30  Identities=23%  Similarity=0.458  Sum_probs=26.2

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      .|+.|+..|....++..++++||+.|...+
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~R   30 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARAR   30 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhcc
Confidence            489999999998899999999999997643

>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=97.17  E-value=0.00018  Score=34.97  Aligned_cols=32  Identities=22%  Similarity=0.544  Sum_probs=29.0

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      .|+.|+..|+.++|+......||-.|++.+|+
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            48899999999999999999999999998874

>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=97.17  E-value=0.00013  Score=35.53  Aligned_cols=31  Identities=19%  Similarity=0.544  Sum_probs=28.2

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHHh
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQLF   67 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   67 (189)
                      +|+.|...+..+.|+.+....||..|.+..|
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            4899999999999999999999999998765

>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=97.15  E-value=0.00013  Score=39.28  Aligned_cols=28  Identities=21%  Similarity=0.416  Sum_probs=25.0

Q ss_pred             CCCCccCCcccccCceeeccCccccccCc
Q 029735          106 QDKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       106 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      .+.|.+|+..|.+. .|.++++.+|++||
T Consensus        18 LP~CdkCg~GIVG~-~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGA-VVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSC-CEESSSCEECTTTC
T ss_pred             CccccccCCCcEEE-EEEeccccCCCCCC
Confidence            38999999999865 48999999999998

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.07  E-value=0.00015  Score=35.53  Aligned_cols=29  Identities=38%  Similarity=0.736  Sum_probs=25.8

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQ   65 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   65 (189)
                      .|+.|+..|....++..++++||+.+...
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            48999999999999999999999987654

>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=97.06  E-value=0.00013  Score=34.45  Aligned_cols=26  Identities=31%  Similarity=0.750  Sum_probs=21.3

Q ss_pred             CccCCcccccCc-eeeccCccccccCc
Q 029735          109 CVACKKTVYPIE-KVAVDGTSYHKACF  134 (189)
Q Consensus       109 C~~C~~~I~~~~-~v~~~g~~~H~~Cf  134 (189)
                      |..|.+||.... -+...++.||..||
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            678999996443 27899999999998

>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=97.01  E-value=0.00026  Score=34.80  Aligned_cols=29  Identities=21%  Similarity=0.387  Sum_probs=26.4

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHh
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQ  163 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~  163 (189)
                      .|..|+..|.++.|+..+.+.||+.||-.
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeee
Confidence            48899999999999999999999999965

>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=96.94  E-value=0.00036  Score=35.27  Aligned_cols=34  Identities=18%  Similarity=0.508  Sum_probs=28.2

Q ss_pred             CcCCCCCCCcccCCccccccc-eEeeCCccccccc
Q 029735            2 ASFAGTTQKCKACEKTVYLVD-QLTADNKVYHKAC   35 (189)
Q Consensus         2 ~~~~~~~~~C~~C~~~I~~~~-~~~~~~~~~H~~C   35 (189)
                      |+.+-.+..|.+|+.-..+.| .|..+|..||..|
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            455667788999999987776 5889999999987

>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=96.76  E-value=0.00016  Score=36.41  Aligned_cols=26  Identities=19%  Similarity=0.457  Sum_probs=21.8

Q ss_pred             CCCccCCcccccCceeeccCccccccC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      ..|..|.+.|.+ -.+.+....||++|
T Consensus         9 e~C~~C~~~itG-pvMvAG~~K~HPEC   34 (34)
T d1x6aa1           9 EFCHGCSLLMTG-PFMVAGEFKYHPEC   34 (34)
T ss_dssp             CBCTTTCCBCCS-CCBCCTTCCBCTTS
T ss_pred             HHhhhhHhhccc-ceeeecccccCCCC
Confidence            899999998874 34678889999998

>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=96.67  E-value=0.00019  Score=35.26  Aligned_cols=29  Identities=28%  Similarity=0.573  Sum_probs=25.7

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQ   65 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   65 (189)
                      .|+.|+..|....++..++++||+.+...
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            48999999998899999999999988654

>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=96.65  E-value=0.00047  Score=31.94  Aligned_cols=26  Identities=31%  Similarity=0.685  Sum_probs=21.8

Q ss_pred             cccCCcccccc-ceEeeCCcccccccc
Q 029735           11 CKACEKTVYLV-DQLTADNKVYHKACF   36 (189)
Q Consensus        11 C~~C~~~I~~~-~~~~~~~~~~H~~CF   36 (189)
                      |++|++.+..+ .-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            78999988643 468999999999998

>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=96.62  E-value=0.0006  Score=34.28  Aligned_cols=30  Identities=20%  Similarity=0.390  Sum_probs=25.7

Q ss_pred             CCCCCCcccCCccccccceEeeCCccccccc
Q 029735            5 AGTTQKCKACEKTVYLVDQLTADNKVYHKAC   35 (189)
Q Consensus         5 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   35 (189)
                      +.....|..|.+.| ++.++.+.+..||++|
T Consensus         5 ~kfge~C~~C~~~i-tGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           5 GKFGEFCHGCSLLM-TGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCBCTTTCCBC-CSCCBCCTTCCBCTTS
T ss_pred             HHHHHHhhhhHhhc-ccceeeecccccCCCC
Confidence            34567899999987 5889999999999998

>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=96.60  E-value=0.0002  Score=35.19  Aligned_cols=30  Identities=23%  Similarity=0.498  Sum_probs=25.8

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      .|+.|+..|....++..++++||+.|...+
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            488999999887788999999999997654

>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=96.27  E-value=0.00089  Score=32.58  Aligned_cols=27  Identities=19%  Similarity=0.503  Sum_probs=24.8

Q ss_pred             ccccccccccCCCeeecCCeeeecccH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHF   63 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy   63 (189)
                      +|+.|-.+|....|..+|++++|..|-
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~   27 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCT   27 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHH
T ss_pred             CchhhccccccCcccccCCeEeecccc
Confidence            588899999999999999999999885

>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=96.24  E-value=0.0019  Score=31.54  Aligned_cols=26  Identities=23%  Similarity=0.584  Sum_probs=22.8

Q ss_pred             CCCccCCcccccCceeeccCccccccC
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKAC  133 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~C  133 (189)
                      .-|..|.+.|.+. .+.+.++.||+.|
T Consensus         6 sgC~~C~~~ItGk-VLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGR-VLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSC-CBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhh-hhhccccccCCCC
Confidence            6799999999864 4799999999987

>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=96.17  E-value=0.0015  Score=30.23  Aligned_cols=26  Identities=27%  Similarity=0.552  Sum_probs=21.2

Q ss_pred             CccCCcccccC-ceeeccCccccccCc
Q 029735          109 CVACKKTVYPI-EKVAVDGTSYHKACF  134 (189)
Q Consensus       109 C~~C~~~I~~~-~~v~~~g~~~H~~Cf  134 (189)
                      |.+|++.+.+. ..+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            67899887654 348999999999997

>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=96.10  E-value=0.0021  Score=31.50  Aligned_cols=30  Identities=23%  Similarity=0.569  Sum_probs=27.4

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQL   66 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   66 (189)
                      +|..|...|.+..|....|+.+|.+|..+.
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            589999999999999999999999998764

>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=96.08  E-value=0.0015  Score=32.73  Aligned_cols=32  Identities=22%  Similarity=0.646  Sum_probs=26.6

Q ss_pred             ccccccccccC--CCeeecCCeeeecccHHHHhh
Q 029735           37 RCHHCKGTLKL--SNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        37 ~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      +|+.|+..|.+  .+.+.+.|.++|+.+|.++|+
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            57788888863  467899999999999999884

>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=0.0034  Score=30.81  Aligned_cols=27  Identities=22%  Similarity=0.657  Sum_probs=22.7

Q ss_pred             ccccccccccCC-CeeecCCeeeecccH
Q 029735           37 RCHHCKGTLKLS-NYCSFEGVLYCKPHF   63 (189)
Q Consensus        37 ~C~~C~~~L~~~-~f~~~~g~~yC~~cy   63 (189)
                      +|+.|...|.++ .|...+|.+||+.+-
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            488999888766 688999999999874

>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=95.76  E-value=0.0035  Score=30.40  Aligned_cols=28  Identities=18%  Similarity=0.522  Sum_probs=25.2

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHH
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHN  162 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~  162 (189)
                      +|..|-.+|..+.|...|++++|..|-.
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            5889999999999999999999998854

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.34  E-value=0.0022  Score=32.09  Aligned_cols=32  Identities=16%  Similarity=0.404  Sum_probs=26.7

Q ss_pred             eeCCCCCcCCC--CCeeecCCccccHhHHHhhhc
Q 029735          135 RCTHGGCVISP--SNYVAHEHRLYCRHHHNQLFK  166 (189)
Q Consensus       135 ~C~~C~~~l~~--~~~~~~dg~~yC~~c~~~~~~  166 (189)
                      +|+-|+..|..  ...+.+.|.+.|+.+|.++||
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            47778888864  457889999999999999986

>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=95.21  E-value=0.0069  Score=30.21  Aligned_cols=31  Identities=26%  Similarity=0.650  Sum_probs=24.9

Q ss_pred             cccccccccccCC-Ceeec-CCeeeecccHHHH
Q 029735           36 FRCHHCKGTLKLS-NYCSF-EGVLYCKPHFDQL   66 (189)
Q Consensus        36 F~C~~C~~~L~~~-~f~~~-~g~~yC~~cy~~~   66 (189)
                      |.|..|+.-+.++ .|... -.++||..||.+.
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            7899999999877 56654 5689999999764

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.20  E-value=0.0044  Score=30.03  Aligned_cols=29  Identities=31%  Similarity=0.765  Sum_probs=23.2

Q ss_pred             ccccccccccCCCeeecCCeeeecccHHHH
Q 029735           37 RCHHCKGTLKLSNYCSFEGVLYCKPHFDQL   66 (189)
Q Consensus        37 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   66 (189)
                      .|+.|++.|.. .-.+..|++||-+|..+.
T Consensus         1 nC~~Cgkelta-dArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTA-DARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCT-TCEEETTEEECHHHHHTT
T ss_pred             Cccccccccch-hHHHhcCCEEEEeccccc
Confidence            37899999953 456889999999998753

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.93  E-value=0.0058  Score=31.86  Aligned_cols=28  Identities=18%  Similarity=0.502  Sum_probs=20.7

Q ss_pred             CcccCCccccccceE-eeCCccccccccc
Q 029735           10 KCKACEKTVYLVDQL-TADNKVYHKACFR   37 (189)
Q Consensus        10 ~C~~C~~~I~~~~~~-~~~~~~~H~~CF~   37 (189)
                      .|.+|++....++-+ .-.+..||+.|-.
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            489999998777654 4456789998743

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.71  E-value=0.0082  Score=30.19  Aligned_cols=30  Identities=23%  Similarity=0.389  Sum_probs=25.2

Q ss_pred             CCCCCcccCCccccccceEeeCCcccccccc
Q 029735            6 GTTQKCKACEKTVYLVDQLTADNKVYHKACF   36 (189)
Q Consensus         6 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF   36 (189)
                      .+.-+|.+|...| +++-|...+..||+..|
T Consensus         6 lGk~vC~KCh~iI-dd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           6 LGKYICQKCHAII-DEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCBCTTTCCBC-CSCCCCCSSSCCCTTTS
T ss_pred             hhhHHHHHHHhhh-hcCcceecCCCCCCCCC
Confidence            3567899999999 46778899999999876

>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=94.62  E-value=0.0079  Score=30.20  Aligned_cols=27  Identities=41%  Similarity=0.837  Sum_probs=23.6

Q ss_pred             CCCccCCcccccCce-eeccCccccccC
Q 029735          107 DKCVACKKTVYPIEK-VAVDGTSYHKAC  133 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~-v~~~g~~~H~~C  133 (189)
                      ..|.+|+....+.|+ |...|..||..|
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            579999999998886 578999999877

>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=94.61  E-value=0.019  Score=28.57  Aligned_cols=31  Identities=29%  Similarity=0.656  Sum_probs=24.6

Q ss_pred             ceeCCCCCcCCCC-CeeecC-CccccHhHHHhh
Q 029735          134 FRCTHGGCVISPS-NYVAHE-HRLYCRHHHNQL  164 (189)
Q Consensus       134 f~C~~C~~~l~~~-~~~~~d-g~~yC~~c~~~~  164 (189)
                      |.|..|+.-|+.+ .|...+ .++||-.||.+.
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            6789999888774 566654 799999999874

>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=94.39  E-value=0.017  Score=27.85  Aligned_cols=29  Identities=21%  Similarity=0.505  Sum_probs=23.0

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      .|+.|++.|... -.+..|.+||..|..+.
T Consensus         1 nC~~Cgkeltad-ArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTAD-ARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCTT-CEEETTEEECHHHHHTT
T ss_pred             Cccccccccchh-HHHhcCCEEEEeccccc
Confidence            378899999874 45678999999998763

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.03  E-value=0.0092  Score=31.07  Aligned_cols=27  Identities=26%  Similarity=0.501  Sum_probs=19.9

Q ss_pred             CCccCCcccccCcee-eccCccccccCc
Q 029735          108 KCVACKKTVYPIEKV-AVDGTSYHKACF  134 (189)
Q Consensus       108 ~C~~C~~~I~~~~~v-~~~g~~~H~~Cf  134 (189)
                      .|.+|++....+|-+ ...+..||+.|-
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            488999988777644 455678999874

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.47  E-value=0.043  Score=26.68  Aligned_cols=30  Identities=30%  Similarity=0.517  Sum_probs=26.2

Q ss_pred             eeCCCCCcCCCCCeeecCCccccHhHHHhh
Q 029735          135 RCTHGGCVISPSNYVAHEHRLYCRHHHNQL  164 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~~~dg~~yC~~c~~~~  164 (189)
                      +|..|...|....|+...|+.+|+.|..+.
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            588999999988898889999999998764

>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=92.85  E-value=0.046  Score=26.61  Aligned_cols=26  Identities=15%  Similarity=0.425  Sum_probs=23.1

Q ss_pred             cccccccccCCCeeecCCeeeecccH
Q 029735           38 CHHCKGTLKLSNYCSFEGVLYCKPHF   63 (189)
Q Consensus        38 C~~C~~~L~~~~f~~~~g~~yC~~cy   63 (189)
                      |..|+.+|.+..|......++|.+|-
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            67888999999999999999999984

>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=92.36  E-value=0.038  Score=26.91  Aligned_cols=27  Identities=19%  Similarity=0.518  Sum_probs=21.2

Q ss_pred             eeCCCCCcCCC-CCeeecCCccccHhHH
Q 029735          135 RCTHGGCVISP-SNYVAHEHRLYCRHHH  161 (189)
Q Consensus       135 ~C~~C~~~l~~-~~~~~~dg~~yC~~c~  161 (189)
                      .|+.|...|-. ..|...+|.+||+.+-
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            47888888765 4588899999998763

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.15  E-value=0.075  Score=26.54  Aligned_cols=27  Identities=19%  Similarity=0.422  Sum_probs=22.6

Q ss_pred             CCCccCCcccccCceeeccCccccccCc
Q 029735          107 DKCVACKKTVYPIEKVAVDGTSYHKACF  134 (189)
Q Consensus       107 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf  134 (189)
                      ..|..|...|.+. -+.+.+..||+..|
T Consensus         9 ~vC~KCh~iIdd~-pL~Fr~d~YHp~HF   35 (35)
T d2cora2           9 YICQKCHAIIDEQ-PLIFKNDPYHPDHF   35 (35)
T ss_dssp             CBCTTTCCBCCSC-CCCCSSSCCCTTTS
T ss_pred             HHHHHHHhhhhcC-cceecCCCCCCCCC
Confidence            6899999888653 48899999999876

>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=89.92  E-value=0.079  Score=25.75  Aligned_cols=25  Identities=8%  Similarity=0.533  Sum_probs=21.3

Q ss_pred             eCCCCCcCCCCCeeecCCccccHhH
Q 029735          136 CTHGGCVISPSNYVAHEHRLYCRHH  160 (189)
Q Consensus       136 C~~C~~~l~~~~~~~~dg~~yC~~c  160 (189)
                      |..|+.+|-+..|...+..++|++|
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            6788888888888888888999887

>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=88.83  E-value=0.13  Score=32.16  Aligned_cols=33  Identities=15%  Similarity=0.372  Sum_probs=23.2

Q ss_pred             cccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      +.|..|...+........=|..||..|..+.+.
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            678888888865433335688999999766543

>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=88.82  E-value=0.084  Score=25.79  Aligned_cols=28  Identities=25%  Similarity=0.612  Sum_probs=21.9

Q ss_pred             eeCCCCCcCCCCCee--ecCCccccHhHHH
Q 029735          135 RCTHGGCVISPSNYV--AHEHRLYCRHHHN  162 (189)
Q Consensus       135 ~C~~C~~~l~~~~~~--~~dg~~yC~~c~~  162 (189)
                      +|..|...|..+.|.  ..||..||..|+.
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlp   30 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLP   30 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccC
Confidence            578889888887765  4589999987754

>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=87.81  E-value=0.12  Score=24.25  Aligned_cols=27  Identities=15%  Similarity=0.314  Sum_probs=22.4

Q ss_pred             cccccccccCCCeeecCCeeeecccHH
Q 029735           38 CHHCKGTLKLSNYCSFEGVLYCKPHFD   64 (189)
Q Consensus        38 C~~C~~~L~~~~f~~~~g~~yC~~cy~   64 (189)
                      |..|+.+|.+..|...-..++|.+|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            678888998889988777899998853

>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=87.28  E-value=0.14  Score=24.83  Aligned_cols=30  Identities=20%  Similarity=0.362  Sum_probs=22.6

Q ss_pred             ccccccccccC--CCeeecCCeeeecccHHHH
Q 029735           37 RCHHCKGTLKL--SNYCSFEGVLYCKPHFDQL   66 (189)
Q Consensus        37 ~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~   66 (189)
                      +|.-|+..|..  ...+.+.+.++|+.+|.++
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            56667777753  3567899999999999764

>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=85.86  E-value=0.34  Score=26.90  Aligned_cols=33  Identities=12%  Similarity=0.163  Sum_probs=23.0

Q ss_pred             cccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      +.|..|...+.+.......|..||..|..+-..
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~   33 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVK   33 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHH
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHh
Confidence            358888888854333346799999999766543

>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=83.86  E-value=0.31  Score=24.77  Aligned_cols=28  Identities=14%  Similarity=0.247  Sum_probs=12.1

Q ss_pred             cccccccccccCCC-eeecCCeeeecccH
Q 029735           36 FRCHHCKGTLKLSN-YCSFEGVLYCKPHF   63 (189)
Q Consensus        36 F~C~~C~~~L~~~~-f~~~~g~~yC~~cy   63 (189)
                      |.|+.|+.++..+. -.....+-.|+.|.
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs   29 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCS   29 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHH
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcC
Confidence            44555555554332 22233344454443

>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=83.66  E-value=0.21  Score=23.71  Aligned_cols=28  Identities=25%  Similarity=0.532  Sum_probs=18.2

Q ss_pred             cccccccccccCCCeeecCCeeeecccH
Q 029735           36 FRCHHCKGTLKLSNYCSFEGVLYCKPHF   63 (189)
Q Consensus        36 F~C~~C~~~L~~~~f~~~~g~~yC~~cy   63 (189)
                      .+|..|+.---...-...+|++.|+++|
T Consensus         4 vrcdvcgeytyeadakllngkpvckpdy   31 (33)
T d2gvia2           4 VRCDVCGEYTYEADAKLLNGKPVCKPDY   31 (33)
T ss_dssp             EECTTTCCEEEGGGCEEETTEEECHHHH
T ss_pred             eEEeeccceeeccchhhhCCCcccCccc
Confidence            3567776644333334568899999887

>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=81.33  E-value=1  Score=26.63  Aligned_cols=35  Identities=6%  Similarity=0.111  Sum_probs=27.3

Q ss_pred             ccccccccccccccCCCeeecCCeeeecccHHHHhh
Q 029735           33 KACFRCHHCKGTLKLSNYCSFEGVLYCKPHFDQLFK   68 (189)
Q Consensus        33 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   68 (189)
                      ++-|.|..|...+.+. ....-|..||..|..+.+.
T Consensus         5 P~~l~CpIc~~l~~dP-v~~~cGhtfc~~ci~~~l~   39 (80)
T d2c2la2           5 PDYLCGKISFELMREP-CITPSGITYDRKDIEEHLQ   39 (80)
T ss_dssp             CSTTBCTTTCSBCSSE-EECSSCCEEETTHHHHHHH
T ss_pred             CccccCcCcCchhhhh-cccCCcCeecHHHHHHHHh
Confidence            4568999999988654 4567899999999877553