Psyllid ID: psy17880

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEcccccccccccccccccccccccEEEcccccccHHHHHHHHHcccccccccccccEEEEcccccccccccccccccccccccEEEEccEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHEEEcccccccccEEEHHccccccccccEccccccccHHHHHHHccccHcccccccHHHHHHHHccccccccEEEHHccccccccccEccccccccHccccccc
Coil and Loop (DISEMBL)
MIKAYCTSckkkcsgevlrvqDKYFHitcfqcsvcknslaqggyfnkdgayyctsdyqkkfgtkcaqcgeyveGEVVTALGktyhqkcftcarcrfskKREIYNWlggrayenrlggray
Flexible Loop (DISEMBL)
mikayctsckkkcsgevLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQkcftcarcrfskkreiynwlggrayenrlggray
Low Complexity Region (SEG)
MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY
Disordered region (IsUnstruct)
***AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYE********
Disordered Region (DISOPRED)
MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY
Disordered Region (DISEMBL)
MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY
Disordered Region (DISPRO)
*IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	120	2.2.26 [Sep-21-2011]
Q8K4G5	861	Actin-binding LIM protein	yes	N/A	0.725	0.101	0.626	1e-31
O14639	778	Actin-binding LIM protein	yes	N/A	0.725	0.111	0.626	1e-30
Q6H8Q1	611	Actin-binding LIM protein	no	N/A	0.741	0.145	0.586	8e-28
Q8BL65	612	Actin-binding LIM protein	no	N/A	0.741	0.145	0.565	1e-26
Q6KC51	612	Actin-binding LIM protein	yes	N/A	0.741	0.145	0.554	2e-25
O94929	683	Actin-binding LIM protein	no	N/A	0.716	0.125	0.522	1e-23
Q69ZX8	682	Actin-binding LIM protein	no	N/A	0.716	0.126	0.522	1e-23
Q9Z1Z9	457	PDZ and LIM domain protei	no	N/A	0.766	0.201	0.372	1e-16
Q3TJD7	457	PDZ and LIM domain protei	no	N/A	0.766	0.201	0.372	2e-16
Q3SX40	424	PDZ and LIM domain protei	no	N/A	0.766	0.216	0.382	3e-16

>sp|Q8K4G5|ABLM1_MOUSE Actin-binding LIM protein 1 OS=Mus musculus GN=Ablim1 PE=1 SV=1

 Score =  135 bits (339), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query: 5   YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
           +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct: 98  HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGDYLCTLDYQRMYGTR 157

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct: 158 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 188

May act as scaffold protein (By similarity). May play a role in the development of the retina. Has been suggested to play a role in axon guidance.
Mus musculus (taxid: 10090)

>sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3

 Score =  131 bits (329), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query: 5   YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
           +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct: 98  HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTR 157

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct: 158 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 188

May act as scaffold protein (By similarity). May play a role in the development of the retina. Has been suggested to play a role in axon guidance.

Homo sapiens (taxid: 9606)

>sp|Q6H8Q1|ABLM2_HUMAN Actin-binding LIM protein 2 OS=Homo sapiens GN=ABLIM2 PE=1 SV=2

 Score =  122 bits (305), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 65/92 (70%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C +C   C GEVLRVQDKYFHI CF C  C   LA+GG+F + G Y CT DYQ+ +GT+C
Sbjct: 24  CNTCGNVCKGEVLRVQDKYFHIKCFVCKACGCDLAEGGFFVRQGEYICTLDYQRLYGTRC 83

Query: 66  AQCGEYVEGEVVTALGKTYHQKCFTCARCRFS 97
             C +++EGEVV+ALGKTYH  CF CA CR  
Sbjct: 84  FSCDQFIEGEVVSALGKTYHPDCFVCAVCRLP 115

May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Homo sapiens (taxid: 9606)

>sp|Q8BL65|ABLM2_MOUSE Actin-binding LIM protein 2 OS=Mus musculus GN=Ablim2 PE=1 SV=1

 Score =  118 bits (295), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 52/92 (56%), Positives = 64/92 (69%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C +C   C GEVLRVQ+KYFHI CF C  C   LA+GG+F + G + CT DYQ+ +GT+C
Sbjct: 24  CNTCGNVCKGEVLRVQNKYFHIRCFVCKACGCDLAEGGFFVRQGEHICTRDYQRLYGTRC 83

Query: 66  AQCGEYVEGEVVTALGKTYHQKCFTCARCRFS 97
             C  ++EGEVV+ALGKTYH  CF CA CR  
Sbjct: 84  FSCDRFIEGEVVSALGKTYHPDCFVCAVCRLP 115

May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Mus musculus (taxid: 10090)

>sp|Q6KC51|ABLM2_RAT Actin-binding LIM protein 2 OS=Rattus norvegicus GN=Ablim2 PE=2 SV=1

 Score =  114 bits (285), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/92 (55%), Positives = 64/92 (69%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C +C   C GEVLRVQ+K+FHI CF C  C   LA+GG+F + G + CT DYQ+ +GT+C
Sbjct: 24  CNTCGNVCKGEVLRVQNKHFHIRCFVCKACGCDLAEGGFFVRQGEHICTRDYQRLYGTRC 83

Query: 66  AQCGEYVEGEVVTALGKTYHQKCFTCARCRFS 97
             C  ++EGEVV+ALGKTYH  CF CA CR  
Sbjct: 84  FSCDCFIEGEVVSALGKTYHPDCFVCAVCRLP 115

May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Rattus norvegicus (taxid: 10116)

>sp|O94929|ABLM3_HUMAN Actin-binding LIM protein 3 OS=Homo sapiens GN=ABLIM3 PE=1 SV=3

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 47/90 (52%), Positives = 62/90 (68%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C  C   C GEV+RV + +FHI CF C VC   LAQ G+F K+  Y CT DYQ+ +GT+C
Sbjct: 23  CYRCGDTCKGEVVRVHNNHFHIRCFTCQVCGCGLAQSGFFFKNQEYICTQDYQQLYGTRC 82

Query: 66  AQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C +++ GEV++ALG+TYH KCF C+ CR
Sbjct: 83  DSCRDFITGEVISALGRTYHPKCFVCSLCR 112

May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Homo sapiens (taxid: 9606)

>sp|Q69ZX8|ABLM3_MOUSE Actin-binding LIM protein 3 OS=Mus musculus GN=Ablim3 PE=1 SV=2

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 47/90 (52%), Positives = 62/90 (68%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C  C   C GEV+RV + +FHI CF C VC   LAQ G+F K+  Y CT DYQ+ +GT+C
Sbjct: 23  CYRCGDTCKGEVVRVHNNHFHIRCFTCQVCGCGLAQSGFFFKNQEYICTQDYQQLYGTRC 82

Query: 66  AQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C +++ GEV++ALG+TYH KCF C+ CR
Sbjct: 83  DSCRDFITGEVISALGRTYHPKCFVCSLCR 112

May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.

Mus musculus (taxid: 10090)

>sp|Q9Z1Z9|PDLI7_RAT PDZ and LIM domain protein 7 OS=Rattus norvegicus GN=Pdlim7 PE=1 SV=1

 Score = 84.7 bits (208), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 35/94 (37%), Positives = 54/94 (57%), Gaps = 2/94 (2%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C  CKKK +GE++      +H+ CF C+ CK  +    ++ ++GA YC  DY+K FGTKC
Sbjct: 341 CAKCKKKITGEIMHALKMTWHVPCFTCAACKTPIRNRAFYMEEGAPYCERDYEKMFGTKC 400

Query: 66  AQCGEYVEG--EVVTALGKTYHQKCFTCARCRFS 97
             C   ++     + ALG ++H  CF CA C+ +
Sbjct: 401 RGCDFKIDAGDRFLEALGFSWHDTCFVCAICQIN 434

May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation e.g (embryonic flat bones mandible and cranium), and endochondral bone formation e.g (embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway.

Rattus norvegicus (taxid: 10116)

>sp|Q3TJD7|PDLI7_MOUSE PDZ and LIM domain protein 7 OS=Mus musculus GN=Pdlim7 PE=2 SV=1

 Score = 84.7 bits (208), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 35/94 (37%), Positives = 54/94 (57%), Gaps = 2/94 (2%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C  CKKK +GE++      +H+ CF C+ CK  +    ++ ++GA YC  DY+K FGTKC
Sbjct: 341 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDYEKMFGTKC 400

Query: 66  AQCGEYVEG--EVVTALGKTYHQKCFTCARCRFS 97
             C   ++     + ALG ++H  CF CA C+ +
Sbjct: 401 RGCDFKIDAGDRFLEALGFSWHDTCFVCAICQIN 434

May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation e.g (embryonic flat bones mandible and cranium), and endochondral bone formation e.g (embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway.

Mus musculus (taxid: 10090)

>sp|Q3SX40|PDLI7_BOVIN PDZ and LIM domain protein 7 OS=Bos taurus GN=PDLIM7 PE=2 SV=1

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 36/94 (38%), Positives = 54/94 (57%), Gaps = 2/94 (2%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C  CKKK +GEV+      +H+ CF C+ CK  +    ++ ++GA YC  DY+K FGTKC
Sbjct: 308 CAKCKKKITGEVMHALKTTWHVHCFTCAACKAPIRNRAFYMEEGAPYCEPDYEKMFGTKC 367

Query: 66  AQCGEYVEG--EVVTALGKTYHQKCFTCARCRFS 97
             C   ++     + ALG ++H  CF CA C+ +
Sbjct: 368 RGCDFKIDAGDRFLEALGFSWHDTCFVCAICQIN 401

May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation e.g (embryonic flat bones mandible and cranium), and endochondral bone formation e.g (embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
321477965	995	hypothetical protein DAPPUDRAFT_95700 [D	0.75	0.090	0.784	2e-42
270013886	806	hypothetical protein TcasGA2_TC012552 [T	0.7	0.104	0.811	5e-40
242017898	785	ablim, putative [Pediculus humanus corpo	0.733	0.112	0.806	1e-39
427782711	735	Putative actin-binding lim zn-finger pro	0.741	0.121	0.736	6e-38
312375194	585	hypothetical protein AND_14456 [Anophele	0.775	0.158	0.698	3e-37
260817802	2313	hypothetical protein BRAFLDRAFT_86604 [B	0.408	0.021	0.709	4e-36
427782719	711	Putative actin-binding lim zn-finger pro	0.75	0.126	0.736	4e-36
357625276	805	hypothetical protein KGM_20056 [Danaus p	0.741	0.110	0.688	1e-34
158294174	830	AGAP005425-PA [Anopheles gambiae str. PE	0.725	0.104	0.698	1e-33
157118566	725	ablim [Aedes aegypti] gi|108875655|gb|EA	0.716	0.118	0.698	1e-33

>gi|321477965|gb|EFX88923.1| hypothetical protein DAPPUDRAFT_95700 [Daphnia pulex]

 Score =  176 bits (446), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 73/93 (78%), Positives = 79/93 (84%)

Query: 3   KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           K  C SCKKKCSGEVLRVQDKYFHI CF+C VC+ SLAQGG+F KDG YYCT DYQ +FG
Sbjct: 161 KTQCQSCKKKCSGEVLRVQDKYFHIACFKCRVCQTSLAQGGFFCKDGEYYCTRDYQDRFG 220

Query: 63  TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           TKC+ CG +VEGEVVTALGKTYH  CFTCARCR
Sbjct: 221 TKCSHCGRFVEGEVVTALGKTYHSSCFTCARCR 253

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270013886|gb|EFA10334.1| hypothetical protein TcasGA2_TC012552 [Tribolium castaneum]

 Score =  168 bits (425), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 73/90 (81%), Positives = 81/90 (90%)

Query: 6   CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
           C +CKKKCSGEVLRVQDKYFH  CF+C VC NSLAQGG+F+KDGAYYCT+DYQ+ FGTKC
Sbjct: 50  CQACKKKCSGEVLRVQDKYFHTQCFKCKVCGNSLAQGGFFSKDGAYYCTADYQRNFGTKC 109

Query: 66  AQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           A C +YVEGEVVTALGKTYH+KCFTC RCR
Sbjct: 110 ATCHDYVEGEVVTALGKTYHKKCFTCDRCR 139

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242017898|ref|XP_002429421.1| ablim, putative [Pediculus humanus corporis] gi|212514347|gb|EEB16683.1| ablim, putative [Pediculus humanus corporis]

 Score =  166 bits (421), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/93 (80%), Positives = 83/93 (89%)

Query: 3   KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           K YC  CKKKCSGEVL+VQDKYFHI+CF+C  CKNSLAQGG+F KDG YYCT+DYQ++FG
Sbjct: 53  KTYCQMCKKKCSGEVLKVQDKYFHISCFKCKACKNSLAQGGFFCKDGDYYCTTDYQRQFG 112

Query: 63  TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           TKC+ CGEYVEGEVVTALG TYHQKCFTC RCR
Sbjct: 113 TKCSHCGEYVEGEVVTALGNTYHQKCFTCGRCR 145

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427782711|gb|JAA56807.1| Putative actin-binding lim zn-finger protein limatin involved in axon guidance [Rhipicephalus pulchellus]

 Score =  161 bits (407), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 70/95 (73%), Positives = 79/95 (83%)

Query: 1  MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
          M K  C  CKKKCSG  LRVQD+YFH+ CF+C+VC +SLAQGG+F +DG YYCT DYQK 
Sbjct: 1  MGKVVCELCKKKCSGNALRVQDRYFHVECFKCAVCTSSLAQGGFFFRDGKYYCTGDYQKM 60

Query: 61 FGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          FGTKCA CG++VEGEVVTALG TYHQKCF CARCR
Sbjct: 61 FGTKCAGCGQFVEGEVVTALGNTYHQKCFVCARCR 95

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312375194|gb|EFR22612.1| hypothetical protein AND_14456 [Anopheles darlingi]

 Score =  159 bits (401), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 65/93 (69%), Positives = 77/93 (82%)

Query: 3   KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           K  C+ C+KKCSGEVLRV D+YFH TCFQC+ C  SLA GG+F+KDG YYCT DYQK FG
Sbjct: 353 KIQCSKCQKKCSGEVLRVSDRYFHKTCFQCTKCNKSLATGGFFSKDGLYYCTLDYQKNFG 412

Query: 63  TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           TKCA C +YVEGEVV+ +G TYHQKCFTC++C+
Sbjct: 413 TKCAACNQYVEGEVVSTMGNTYHQKCFTCSKCK 445

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260817802|ref|XP_002603774.1| hypothetical protein BRAFLDRAFT_86604 [Branchiostoma floridae] gi|229289097|gb|EEN59785.1| hypothetical protein BRAFLDRAFT_86604 [Branchiostoma floridae]

 Score =  155 bits (391), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 66/93 (70%), Positives = 76/93 (81%)

Query: 3   KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           K  C +C++ C+GEVLRVQDK+FHITCF C VC+  LA  G+F KDG YYCT DYQ+ FG
Sbjct: 278 KITCYTCRQPCAGEVLRVQDKHFHITCFVCRVCRRQLATDGFFVKDGMYYCTRDYQEMFG 337

Query: 63  TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           TKC  CG+YVEGEVVTALGKTYHQKCF C+RCR
Sbjct: 338 TKCHGCGDYVEGEVVTALGKTYHQKCFVCSRCR 370

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|427782719|gb|JAA56811.1| Putative actin-binding lim zn-finger protein limatin involved in axon guidance [Rhipicephalus pulchellus]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 70/95 (73%), Positives = 79/95 (83%)

Query: 1  MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
          M K  C  CKKKCSG  LRVQD+YFH+ CF+C+VC +SLAQGG+F +DG YYCT DYQK 
Sbjct: 1  MGKVVCELCKKKCSGNALRVQDRYFHVECFKCAVCTSSLAQGGFFFRDGKYYCTGDYQKM 60

Query: 61 FGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          FGTKCA CG++VEGEVVTALG TYHQKCF CARCR
Sbjct: 61 FGTKCAGCGQFVEGEVVTALGNTYHQKCFVCARCR 95

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357625276|gb|EHJ75777.1| hypothetical protein KGM_20056 [Danaus plexippus]

 Score =  150 bits (378), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/93 (68%), Positives = 73/93 (78%)

Query: 3   KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           K  C +C  KCSGEVLRV DKYFH+ CF C  C  SLA+GG+F KDG YYC  DYQ+ FG
Sbjct: 70  KVVCGACGGKCSGEVLRVTDKYFHMACFTCRTCSASLARGGFFCKDGHYYCPQDYQRAFG 129

Query: 63  TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           T+CA C +YVEGEVV+ALG TYHQKCFTCARC+
Sbjct: 130 TRCAACNQYVEGEVVSALGNTYHQKCFTCARCK 162

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158294174|ref|XP_315432.4| AGAP005425-PA [Anopheles gambiae str. PEST] gi|157015442|gb|EAA11937.4| AGAP005425-PA [Anopheles gambiae str. PEST]

 Score =  147 bits (370), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 78/93 (83%)

Query: 3   KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           K  C+ C+KKCSGEVLRV D+YFH TCFQC+ C  SLA GG+F+KDGAYYCT DYQK +G
Sbjct: 24  KIQCSKCQKKCSGEVLRVSDRYFHKTCFQCTKCNKSLATGGFFSKDGAYYCTLDYQKLYG 83

Query: 63  TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           TKCA C +YVEGEVV+ +G TYHQKCFTC++C+
Sbjct: 84  TKCAACSQYVEGEVVSTMGNTYHQKCFTCSKCK 116

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157118566|ref|XP_001653201.1| ablim [Aedes aegypti] gi|108875655|gb|EAT39880.1| AAEL008358-PA, partial [Aedes aegypti]

 Score =  146 bits (369), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 78/93 (83%)

Query: 3  KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
          K  C+ C+KKCSGEVLRV D+YFH TCFQC+ C  SLA GG+F+KDGAYYCT DYQK +G
Sbjct: 4  KIQCSKCQKKCSGEVLRVSDRYFHKTCFQCTKCNKSLATGGFFSKDGAYYCTLDYQKLYG 63

Query: 63 TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          TKCA C +YVEGEVV+ +G TYHQKCFTC++C+
Sbjct: 64 TKCAACNQYVEGEVVSTMGNTYHQKCFTCSKCK 96

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	120
FB|FBgn0260463	806	Unc-115b [Drosophila melanogas	0.775	0.115	0.677	7.8e-35
FB|FBgn0051352	844	Unc-115a [Drosophila melanogas	0.775	0.110	0.677	8.8e-35
UNIPROTKB|D4A6Z5	261	D4A6Z5 "Uncharacterized protei	0.758	0.348	0.626	1.4e-30
UNIPROTKB|Q5T6N2	702	ABLIM1 "Actin-binding LIM prot	0.758	0.129	0.626	8.2e-30
UNIPROTKB|F1LWK7	655	F1LWK7 "Uncharacterized protei	0.758	0.138	0.626	8.5e-30
UNIPROTKB|F8W8M4	718	ABLIM1 "Actin-binding LIM prot	0.758	0.126	0.626	8.7e-30
UNIPROTKB|F1LX72	701	F1LX72 "Uncharacterized protei	0.758	0.129	0.626	1e-29
UNIPROTKB|O14639	778	ABLIM1 "Actin-binding LIM prot	0.758	0.116	0.626	1.1e-29
UNIPROTKB|F1NC68	609	Gga.10869 "Uncharacterized pro	0.75	0.147	0.622	1.1e-29
UNIPROTKB|F1MI97	790	F1MI97 "Uncharacterized protei	0.758	0.115	0.626	1.1e-29

FB|FBgn0260463 Unc-115b [Drosophila melanogaster (taxid:7227)]

 Score = 386 (140.9 bits), Expect = 7.8e-35, P = 7.8e-35
 Identities = 63/93 (67%), Positives = 73/93 (78%)

Query:     3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
             K YC  C KKCSGEVLRV D +FH  CFQC  CK SLA GG+F KD AYYC  DYQ+ +G
Sbjct:     5 KIYCAKCTKKCSGEVLRVADNHFHKACFQCCQCKKSLATGGFFTKDNAYYCIPDYQRLYG 64

Query:    63 TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             TKCA C +YVEGEVV+ +GKTYHQKCFTC++C+
Sbjct:    65 TKCANCQQYVEGEVVSTMGKTYHQKCFTCSKCK 97

GO:0003779 "actin binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

FB|FBgn0051352 Unc-115a [Drosophila melanogaster (taxid:7227)]

 Score = 386 (140.9 bits), Expect = 8.8e-35, P = 8.8e-35
 Identities = 63/93 (67%), Positives = 73/93 (78%)

Query:     3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
             K YC  C KKCSGEVLRV D +FH  CFQC  CK SLA GG+F KD AYYC  DYQ+ +G
Sbjct:    43 KIYCAKCTKKCSGEVLRVADNHFHKACFQCCQCKKSLATGGFFTKDNAYYCIPDYQRLYG 102

Query:    63 TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             TKCA C +YVEGEVV+ +GKTYHQKCFTC++C+
Sbjct:   103 TKCANCQQYVEGEVVSTMGKTYHQKCFTCSKCK 135

GO:0008270 "zinc ion binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0072499 "photoreceptor cell axon guidance" evidence=IMP

GO:0003779 "actin binding" evidence=ISS

GO:0007411 "axon guidance" evidence=IMP

UNIPROTKB|D4A6Z5 D4A6Z5 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    22 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGDYLCTLDYQRMYGTR 81

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:    82 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 112

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q5T6N2 ABLIM1 "Actin-binding LIM protein 1" [Homo sapiens (taxid:9606)]

 Score = 338 (124.0 bits), Expect = 8.2e-30, P = 8.2e-30
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    22 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTR 81

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:    82 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 112

GO:0003779 "actin binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1LWK7 F1LWK7 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 337 (123.7 bits), Expect = 8.5e-30, P = 8.5e-30
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    21 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGDYLCTLDYQRMYGTR 80

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:    81 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 111

GO:0003779 "actin binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F8W8M4 ABLIM1 "Actin-binding LIM protein 1" [Homo sapiens (taxid:9606)]

 Score = 338 (124.0 bits), Expect = 8.7e-30, P = 8.7e-30
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    38 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTR 97

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:    98 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 128

GO:0003779 "actin binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1LX72 F1LX72 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 337 (123.7 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    21 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGDYLCTLDYQRMYGTR 80

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:    81 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 111

GO:0003779 "actin binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|O14639 ABLIM1 "Actin-binding LIM protein 1" [Homo sapiens (taxid:9606)]

 Score = 338 (124.0 bits), Expect = 1.1e-29, P = 1.1e-29
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    98 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTR 157

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:   158 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 188

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003779 "actin binding" evidence=IEA

GO:0015629 "actin cytoskeleton" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=TAS

GO:0007601 "visual perception" evidence=TAS

GO:0007411 "axon guidance" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1NC68 Gga.10869 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 335 (123.0 bits), Expect = 1.1e-29, P = 1.1e-29
 Identities = 56/90 (62%), Positives = 66/90 (73%)

Query:     6 CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
             C +C K C GEVLRVQ+KYFHI CF C  C   LAQGG+F + G Y CT DYQ+ +GT+C
Sbjct:    20 CNTCGKPCKGEVLRVQNKYFHIKCFVCKACGCDLAQGGFFVRQGDYICTLDYQRLYGTRC 79

Query:    66 AQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
               C E++EGEVV+ALGKTYH  CF CA CR
Sbjct:    80 FSCDEFIEGEVVSALGKTYHPDCFVCAVCR 109

GO:0003779 "actin binding" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030016 "myofibril" evidence=IEA

GO:0045111 "intermediate filament cytoskeleton" evidence=IEA

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

UNIPROTKB|F1MI97 F1MI97 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 338 (124.0 bits), Expect = 1.1e-29, P = 1.1e-29
 Identities = 57/91 (62%), Positives = 67/91 (73%)

Query:     5 YCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
             +C  C + C GEVLRVQ K+FHI CF C VC   LAQGG+F K+G Y CT DYQ+ +GT+
Sbjct:    22 HCHKCGEPCKGEVLRVQTKHFHIKCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTR 81

Query:    65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
             C  CGE+VEGEVVTALGKTYH  CF C  C+
Sbjct:    82 CHGCGEFVEGEVVTALGKTYHPNCFACTICK 112

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

GO:0015629 "actin cytoskeleton" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0003779 "actin binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0007010 "cytoskeleton organization" 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)
O14639	ABLM1_HUMAN	No assigned EC number	0.6263	0.725	0.1118	yes	N/A
Q8K4G5	ABLM1_MOUSE	No assigned EC number	0.6263	0.725	0.1010	yes	N/A
Q6KC51	ABLM2_RAT	No assigned EC number	0.5543	0.7416	0.1454	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	120
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	2e-21
cd09328	56	cd09328, LIM2_abLIM, The second LIM domain on acti	6e-14
pfam00412	58	pfam00412, LIM, LIM domain	7e-09
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	7e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-08
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	7e-07
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	9e-07
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	2e-06
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	3e-06
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-06
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	6e-06
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	7e-06
cd09450	53	cd09450, LIM_ALP, This family represents the LIM d	1e-05
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	1e-05
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	2e-05
cd09372	53	cd09372, LIM2_FBLP-1, The second LIM domain of the	2e-05
cd09451	53	cd09451, LIM_RIL, The LIM domain of RIL	4e-05
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	6e-05
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	6e-05
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	8e-05
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	9e-05
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	1e-04
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	1e-04
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	1e-04
cd09340	58	cd09340, LIM1_Testin_like, The first LIM domain of	2e-04
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	2e-04
cd09452	52	cd09452, LIM1_Enigma, The first LIM domain of Enig	2e-04
cd09354	60	cd09354, LIM2_LPP, The second LIM domain of lipoma	2e-04
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	3e-04
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	3e-04
cd09343	59	cd09343, LIM1_FHL, The first LIM domain of Four an	3e-04
cd09422	62	cd09422, LIM1_FHL2, The first LIM domain of Four a	3e-04
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	4e-04
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	5e-04
cd09393	56	cd09393, LIM3_Lrg1p_like, The third LIM domain of	5e-04
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	6e-04
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	6e-04
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	7e-04
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	7e-04
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	8e-04
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	9e-04
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	0.001
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	0.001
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	0.001
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.001
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	0.001
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	0.001
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	0.002
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	0.002
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.002
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	0.002
cd09330	56	cd09330, LIM4_abLIM, The fourth LIM domain of acti	0.002
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	0.002
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	0.002
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	0.002
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	0.003
cd09355	53	cd09355, LIM2_Ajuba_like, The second LIM domain of	0.003
cd09453	52	cd09453, LIM1_ENH, The first LIM domain of the Eni	0.003
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	0.004

>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins

 Score = 79.6 bits (197), Expect = 2e-21
 Identities = 37/52 (71%), Positives = 39/52 (75%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C KKC GEVLRVQDKYFHI CF C VC   LAQGG+F K+G YYCT DY
Sbjct: 1  CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52

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

>gnl|CDD|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM (abLIM) proteins

 Score = 60.8 bits (148), Expect = 6e-14
 Identities = 24/34 (70%), Positives = 28/34 (82%)

Query: 62 GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          GTKC  C ++VEGEVV+ALGKTYH KCF C+ CR
Sbjct: 1  GTKCDSCQDFVEGEVVSALGKTYHPKCFVCSVCR 34

The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 48.1 bits (115), Expect = 7e-09
 Identities = 24/58 (41%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 6  CTSCKKKCSG--EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61
          C  C K       V R   K +H  CF+C+VC   L  G +F KDG  YC  DY K F
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 47.7 bits (114), Expect = 7e-09
 Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 6  CTSCKKKCSG-EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C K   G E+LR   K +H  CF+CSVC   L    ++ KDG  YC   Y
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

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

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

 Score = 47.4 bits (113), Expect = 1e-08
 Identities = 20/53 (37%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 6  CTSCKKKCSG--EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSD 56
          C  C K   G   VLR   K +H  CF+C+ C   L+   +F KDG  YC   
Sbjct: 2  CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 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|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated LIM protein) family

 Score = 42.7 bits (101), Expect = 7e-07
 Identities = 17/48 (35%), Positives = 23/48 (47%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYC 53
          C  C     G V++ +DK  H  CF C+ C  +L   GYF  +   YC
Sbjct: 1  CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYC 48

This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 42.7 bits (100), Expect = 9e-07
 Identities = 19/52 (36%), Positives = 30/52 (57%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  CKKK +GE++      +H+ CF C+ CK  +    ++ ++GA YC  DY
Sbjct: 1  CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 41.7 bits (98), Expect = 2e-06
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C KK  GEV+    + +H++CF C+ CK  +    +  +DG  YC  DY
Sbjct: 1  CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

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

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

 Score = 41.2 bits (97), Expect = 3e-06
 Identities = 20/53 (37%), Positives = 27/53 (50%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58
          C +CKK   G+V+    K +H   F C+ CK  L    +F +DG  YC  DY 
Sbjct: 1  CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53

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

>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 40.8 bits (95), Expect = 4e-06
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C++K  GEV+    + +H++CF C  C N +    +  +DG  YC +DY
Sbjct: 1  CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin

 Score = 40.4 bits (94), Expect = 6e-06
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58
          C +CKK  +G+V+    K +H   F C+ C+  +    +F +DG  YC  DY 
Sbjct: 2  CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly 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|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family

 Score = 40.3 bits (95), Expect = 7e-06
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 17 VLRVQDKYFHITCFQCSVCKNSLAQGGYFN-KDGAYYCTSDY 57
          V+R +D  FH+ CF C+ C   L +G +F  +DG  YC   Y
Sbjct: 18 VMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59

The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. 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 = 59

>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP, actinin-associated LIM protein

 Score = 39.5 bits (92), Expect = 1e-05
 Identities = 21/48 (43%), Positives = 26/48 (54%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYC 53
          C  C     G V++ +DKY H  CF CS C  +L Q GYF  +G  YC
Sbjct: 1  CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYC 48

This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. 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|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 39.6 bits (93), Expect = 1e-05
 Identities = 16/30 (53%), Positives = 20/30 (66%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARC 94
          CA+CG+ + G+ V ALG  YH  CFTC  C
Sbjct: 1  CAKCGKPITGQFVRALGDVYHLDCFTCHDC 30

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

>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 17 VLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDY 57
          V R +DK FH+ CF C VC+  L+ G   Y   +  + C  DY
Sbjct: 14 VRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1)

 Score = 38.9 bits (91), Expect = 2e-05
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          CA+C   +   ++ ALGK YH  CFTC  C 
Sbjct: 1  CAKCQGVITEHIIRALGKGYHPPCFTCVTCG 31

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 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. Length = 53

>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL

 Score = 38.4 bits (89), Expect = 4e-05
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTS 55
          CT C     G +++ +DK +H  CF C  C  +L Q GYF  D   YC +
Sbjct: 1  CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYCET 50

The LIM domain of RIL: RIL contains an N-terminal PDZ domain, a LIM domain, and a short consensus C-terminal region. It is the smallest molecule in the ALP LIM domain containing protein family. RIL was identified in rat fibroblasts and in human lymphocytes. The LIM domain interacts with the AMPA glutamate receptor in dendritic spines. The consensus C-terminus interacts with PTP-BL, a submembranous protein tyrosine phosphatase and the PDZ domain is responsible to interact with alpha-actinin molecules. 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|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 37.7 bits (88), Expect = 6e-05
 Identities = 17/31 (54%), Positives = 23/31 (74%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          CA C + + G+VVTALGKT+H + F CA C+
Sbjct: 1  CAACKKPIVGQVVTALGKTWHPEHFVCAECK 31

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

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

 Score = 37.9 bits (88), Expect = 6e-05
 Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 6  CTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C+ K    + ++  ++ +H  CF+CSVC +SL+   YF KDG  YC  DY
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSN-WYFEKDGKLYCRKDY 52

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

>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 37.6 bits (87), Expect = 8e-05
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAY--YCTSDYQKKFGT 63
          C  C +K +  +L+   K +H  CF C VCK  L +G  F  D A   +C +DY +++  
Sbjct: 1  CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPL-EGESFIVDQANQPHCVNDYHRRYAP 59

Query: 64 K 64
          +
Sbjct: 60 R 60

The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. 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 o r scaffolds to support the assembly of multimeric protein. Length = 60

>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 37.5 bits (87), Expect = 9e-05
 Identities = 18/47 (38%), Positives = 27/47 (57%)

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           CA C + + G+VVTALG+T+H + F C +C        +    G+AY
Sbjct: 3   CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAY 49

The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 16/32 (50%), Positives = 23/32 (71%), Gaps = 1/32 (3%)

Query: 65 CAQCGEYVEG-EVVTALGKTYHQKCFTCARCR 95
          CA CG+ +EG E++ ALGK +H +CF C+ C 
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCG 32

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|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 36.8 bits (85), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C SC+K  +G+V+    + +H   F C  C   L    +F ++G  YC  DY
Sbjct: 3  CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 6  CTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          CT C  +       RV  + +H +CFQCSVC++ L    Y+ KDG  YC   Y
Sbjct: 1  CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTN-WYYEKDGKLYCHKHY 52

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

>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like family

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 14/36 (38%), Positives = 15/36 (41%)

Query: 22 DKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          D  +H  CF C  C   L    YF  DG  YC   Y
Sbjct: 23 DACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

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

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

 Score = 36.1 bits (84), Expect = 2e-04
 Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 6  CTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C ++  +G+ L   DK +H+ CF+C  C   L  G Y  KDG  YC  DY
Sbjct: 1  CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL-TGEYMGKDGKPYCERDY 52

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

>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 18/52 (34%), Positives = 25/52 (48%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C K   G  L    + +H   F CS CK  L +GG+F + G+ +C   Y
Sbjct: 1  CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred partner (LPP)

 Score = 36.4 bits (84), Expect = 2e-04
 Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGA--YYCTSDYQKKFGT 63
          C+ C K     +LR   K +H  CF C VC  SL  G  F  D     +C  D+ KKF  
Sbjct: 1  CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSL-DGIPFTVDATNQIHCIEDFHKKFAP 59

Query: 64 K 64
          +
Sbjct: 60 R 60

The second 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 = 60

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

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          CA+C + + GEV+ AL +T+H  CF CA C+
Sbjct: 1  CARCHKKILGEVMHALKQTWHVSCFVCAACK 31

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

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

 Score = 35.7 bits (83), Expect = 3e-04
 Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 6  CTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYC 53
          C  C K     E L    K FH +CF+CS C  +L  G Y + +G  YC
Sbjct: 1  CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49

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

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 5  YCTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
           C  CKKK  C  + L  +D+++H  CF+C  C+ SL    +  KD    CT  Y
Sbjct: 4  TCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 36.0 bits (83), Expect = 3e-04
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 6  CTSCKK--KCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61
          C  CKK   C  + L  +D+++H +CF C  CKNSL    +  K+    CT  Y  ++
Sbjct: 5  CEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSNEY 62

The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 62

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

 Score = 35.8 bits (83), Expect = 4e-04
 Identities = 16/30 (53%), Positives = 20/30 (66%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARC 94
          C  C   +EG VVTALGK +H + F CA+C
Sbjct: 3  CGACRRPIEGRVVTALGKHWHVEHFVCAKC 32

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

>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 35.4 bits (81), Expect = 5e-04
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENR 114
           CA+C + + GE++ AL  T+H  CFTCA C+   +   +    G  Y  R
Sbjct: 1   CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCER 50

The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 35.4 bits (82), Expect = 5e-04
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGG----YFNKDGAYYCT 54
          C SC K    E ++ +DK +H+ CF CS C   ++       + NKD    C+
Sbjct: 1  CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCS 53

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

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

 Score = 35.1 bits (81), Expect = 6e-04
 Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 6  CTSCKKKCSGEV--LRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C +K  GE       D+ +HI+CF C  C+ +L    ++  DG  YC  DY
Sbjct: 1  CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

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|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 13/41 (31%), Positives = 20/41 (48%)

Query: 17 VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
           +R     FH+TCF C  C+  L    +++ +G  YC   Y
Sbjct: 47 AVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. 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 = 87

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

 Score = 35.0 bits (81), Expect = 7e-04
 Identities = 14/52 (26%), Positives = 20/52 (38%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C K      +   +  +H  CF C  C      G +F  +G  YC + Y
Sbjct: 1  CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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

>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX protein family

 Score = 35.1 bits (81), Expect = 7e-04
 Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 17 VLRVQDKYFHITCFQCSVCKNSLAQGGYFN-KDGAYYCTSDY 57
          V+R + K +HI CF+CS C   L  G  F  +D   +C +D+
Sbjct: 14 VMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55

The second LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group 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. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 34.8 bits (80), Expect = 8e-04
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 6  CTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFN-KDGAYYCTSD 56
          C++C +    S  V+R Q   +H+ CF CS C N L  G  F+  +G+ +C  D
Sbjct: 1  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54

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

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

 Score = 34.8 bits (80), Expect = 9e-04
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 6  CTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          CT C+K+    E L    + FH +CF+C  C + L+ G Y +  G  YC   +
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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 64  KCAQCGEYVEG--EVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           KCA CG+ + G   V+ ALGK +H +CF CA C      + +    G+ Y
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLY 50

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|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 34.2 bits (78), Expect = 0.001
 Identities = 15/47 (31%), Positives = 24/47 (51%)

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           C +C   + GEV+ AL +T+H  CF C  C    +  +++   G  Y
Sbjct: 1   CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPY 47

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 34.3 bits (79), Expect = 0.001
 Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 2/49 (4%)

Query: 65  CAQCGEYVEGEV--VTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           C +CGE V GE    TA+ + YH  CFTC +C+ + + + +  L G+ Y
Sbjct: 1   CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPY 49

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

 Score = 34.6 bits (80), Expect = 0.001
 Identities = 17/52 (32%), Positives = 24/52 (46%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDY 57
          C  C +   G  L    + +H   F CS C  SLA+ G+  + G+ YC   Y
Sbjct: 1  CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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

>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family

 Score = 34.2 bits (79), Expect = 0.001
 Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 17 VLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDY 57
          V R QD  +H+ CF C +CK  L  G   Y  +D    C  DY
Sbjct: 14 VRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56

The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

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

 Score = 34.2 bits (79), Expect = 0.001
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          C +CGE+V G V+ A+   +H  CF C  C 
Sbjct: 1  CGKCGEFVIGRVIKAMNNNWHPDCFRCEICN 31

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

>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          CA C + +   ++ A GK+YH +CFTC  C+
Sbjct: 1  CAVCDQKITDRMLKATGKSYHPQCFTCVVCK 31

The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. 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 o r scaffolds to support the assembly of multimeric protein. Length = 60

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

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 65 CAQCGEYVEGE--VVTALGKTYHQKCFTCARCR 95
          C+ CG+ +     V+ A G  YH KCFTC+ C 
Sbjct: 1  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCH 33

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

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

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKK 99
          CA C + + G  + ALG+++H + FTC+ C  S  
Sbjct: 1  CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLA 35

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

>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b

 Score = 33.9 bits (77), Expect = 0.002
 Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 17 VLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDY 57
          V R QD  +H+ CF C VCK  LA G   Y  +D    C +DY
Sbjct: 15 VRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57

The second LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM (abLIM) proteins

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARC--RFSKKREIY 103
           C  C +++ G+V+ A GK YH  C  C+RC   F +  E+Y
Sbjct: 1   CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMFGEGEEMY 41

The fourth LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and Lmx1b

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 6  CTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQGGYFN-KDGAYYCTSDY 57
          C+ C +K +    V+R  +  +H+ CF C VC+  L +G  F  K+G   C SDY
Sbjct: 1  CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55

The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4

 Score = 33.8 bits (77), Expect = 0.002
 Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)

Query: 6  CTSCKKKC--SGEVLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDY 57
          CT+C++    +  V + QD  +H+ CF C +C   LA G   Y  +DG   C  DY
Sbjct: 1  CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56

The second LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

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

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 19/41 (46%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 18 LRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58
          LRV ++ +H  C QCSVC+  L    YF +D   YC  DYQ
Sbjct: 14 LRVNERSWHEECLQCSVCQQPLTTSCYF-RDRKLYCKQDYQ 53

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

>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated LIM protein) family

 Score = 33.1 bits (76), Expect = 0.003
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 65  CAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           C +CG  + G VV A  K  H +CF CA C  + K + Y ++    Y
Sbjct: 1   CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELY 47

This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like proteins

 Score = 33.1 bits (76), Expect = 0.003
 Identities = 14/30 (46%), Positives = 18/30 (60%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARC 94
          CA CG  +   ++ ALGK+YH  CF C  C
Sbjct: 1  CAVCGHLIMEMILQALGKSYHPGCFRCCVC 30

The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. 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|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog (ENH) family

 Score = 33.1 bits (75), Expect = 0.003
 Identities = 17/48 (35%), Positives = 25/48 (52%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYC 53
          C +C +   G  L    K +H   F C+ CK+S+A  G+  + GA YC
Sbjct: 1  CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYC 48

The first LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 33.0 bits (76), Expect = 0.004
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 6  CTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGY-FNKD-GAYYCTSDY 57
          C  CKK+    E L  +  +FH +CF+CS C  +L  G Y F++D G +YC   +
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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
KOG1701|consensus	468		99.93
KOG1701|consensus	468		99.92
KOG2272|consensus	332		99.91
KOG4577|consensus	383		99.89
KOG2272|consensus	332		99.87
KOG1703|consensus	479		99.86
KOG1703|consensus	479		99.86
KOG1044|consensus	670		99.83
KOG1044|consensus	670		99.7
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.66
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.64
KOG1700|consensus	200		99.5
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	99.02
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.88
KOG4577|consensus	383		98.36
KOG0490|consensus	235		97.98
KOG1700|consensus	200		97.77
KOG1702|consensus	264		97.54
KOG1702|consensus	264		97.44
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	93.27
KOG0490|consensus	235		92.03
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	91.84
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	90.94
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	90.62
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	87.93
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	87.24
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	87.12
PF02069	52	Metallothio_Pro: Prokaryotic metallothionein; Inte	86.45
PF11781	36	RRN7: RNA polymerase I-specific transcription init	86.14
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	85.81
PF01258	36	zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc f	85.39
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	84.86
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	84.76
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	83.56
PF13248	26	zf-ribbon_3: zinc-ribbon domain	81.47
COG2191	206	Formylmethanofuran dehydrogenase subunit E [Energy	80.18
COG4847	103	Uncharacterized protein conserved in archaea [Func	80.03

>KOG1701|consensus

Probab=99.93  E-value=2.9e-28  Score=175.69  Aligned_cols=117  Identities=32%  Similarity=0.709  Sum_probs=109.1

Q ss_pred             Cccccccccccccc--eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEe
Q psy17880          3 KAYCTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTAL   80 (120)
Q Consensus         3 ~~~C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~   80 (120)
                      ..+|.+|++.|.++  .+.++++.||..||+|..|++.|.++.||..|+++||+.||.... .+|..|+++|++++|.|.
T Consensus       274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLrA~  352 (468)
T KOG1701|consen  274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILRAL  352 (468)
T ss_pred             hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHHhc
Confidence            34899999999765  678999999999999999999999999999999999999999887 899999999999999999


Q ss_pred             CccccccccccccCCCcCCCCceeee-CCeeeeccCCCcCC
Q psy17880         81 GKTYHQKCFTCARCRFSKKREIYNWL-GGRAYENRLGGRAY  120 (120)
Q Consensus        81 ~~~~H~~Cf~C~~C~~~l~~~~~~~~-~g~~yC~~~~~~~~  120 (120)
                      |+.||+.||+|..|++.|++..|.+. ++++||-.|+-+.|
T Consensus       353 GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf  393 (468)
T KOG1701|consen  353 GKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKF  393 (468)
T ss_pred             ccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhc
Confidence            99999999999999999999998876 79999999987765

>KOG1701|consensus

Probab=99.92  E-value=2e-26  Score=166.26  Aligned_cols=116  Identities=27%  Similarity=0.624  Sum_probs=104.2

Q ss_pred             ccccccccccccceEEECCcccccccccccccccccCCCCee-ecCCeeccHhHHHhHhCCCCCCCCCccc---C--c--
Q psy17880          4 AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYF-NKDGAYYCTSDYQKKFGTKCAQCGEYVE---G--E--   75 (120)
Q Consensus         4 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~~~~~C~~C~~~i~---~--~--   75 (120)
                      .+|..|+++|.+.+|.+.|+.||+.||+|..|.+.|++-.|. ..++++||..||.++|+++|+.|+++|.   |  +  
T Consensus       335 ekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etv  414 (468)
T KOG1701|consen  335 EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETV  414 (468)
T ss_pred             HHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceE
Confidence            468999999999999999999999999999999999987776 4678999999999999999999999994   2  2  


Q ss_pred             EEEEeCccccccccccccCCCcCCC----CceeeeCCeeeeccCCCcC
Q psy17880         76 VVTALGKTYHQKCFTCARCRFSKKR----EIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        76 ~~~~~~~~~H~~Cf~C~~C~~~l~~----~~~~~~~g~~yC~~~~~~~  119 (120)
                      .|+++++.||.+|++|..|+.+|+.    ..-|-+||.++|+.+..++
T Consensus       415 Rvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~R  462 (468)
T KOG1701|consen  415 RVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKR  462 (468)
T ss_pred             EEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhh
Confidence            6789999999999999999999982    3588899999999987553

>KOG2272|consensus

Probab=99.91  E-value=1.8e-26  Score=157.15  Aligned_cols=118  Identities=25%  Similarity=0.592  Sum_probs=111.2

Q ss_pred             CCCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEe
Q psy17880          1 MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTAL   80 (120)
Q Consensus         1 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~   80 (120)
                      |.-++|..|.+||+++++.++|+.||.++|+|+.|.+|+-+...|++.|.+||+.+|.++++..|..|+.+|.|+++.+.
T Consensus       193 mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al  272 (332)
T KOG2272|consen  193 MGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSAL  272 (332)
T ss_pred             cCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHh
Confidence            34578999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             CccccccccccccCCCcCC-CCceeeeCCeeeeccCCCc
Q psy17880         81 GKTYHQKCFTCARCRFSKK-REIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        81 ~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~~~~~  118 (120)
                      +++|.++||.|+.|++.|. ...|++.|-+|.|++++.|
T Consensus       273 ~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r  311 (332)
T KOG2272|consen  273 NKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR  311 (332)
T ss_pred             hhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence            9999999999999999996 5579999999999998864

>KOG4577|consensus

Probab=99.89  E-value=1.8e-25  Score=154.77  Aligned_cols=115  Identities=30%  Similarity=0.668  Sum_probs=102.3

Q ss_pred             Cccccccccccccc-eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC-cEE-EE
Q psy17880          3 KAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG-EVV-TA   79 (120)
Q Consensus         3 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~-~~~-~~   79 (120)
                      -++|+.|.+.|.++ ++.++++.||..|++|+.|..+|.+ .+|.+++.+||+++|.++|+.+|..|.+.|+. .+| .|
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            47899999999877 6788999999999999999999986 69999999999999999999999999999975 444 68


Q ss_pred             eCccccccccccccCCCcCCCC-cee-eeCCeeeeccCCCc
Q psy17880         80 LGKTYHQKCFTCARCRFSKKRE-IYN-WLGGRAYENRLGGR  118 (120)
Q Consensus        80 ~~~~~H~~Cf~C~~C~~~l~~~-~~~-~~~g~~yC~~~~~~  118 (120)
                      .+..||.+||.|..|+++|..+ +|| +.|+++.|+.++..
T Consensus       112 qd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~  152 (383)
T KOG4577|consen  112 QDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET  152 (383)
T ss_pred             hcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence            8999999999999999999655 566 45899999998854

>KOG2272|consensus

Probab=99.87  E-value=1.9e-24  Score=147.41  Aligned_cols=114  Identities=24%  Similarity=0.417  Sum_probs=105.9

Q ss_pred             ccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCcc
Q psy17880          4 AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKT   83 (120)
Q Consensus         4 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~   83 (120)
                      -+|.+|+..|+++.+...+..||+.+|.|..|++.|.+ ...+..+.+||.+|+.+.-.|+|..|.+||++++|.++|+.
T Consensus       138 YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~s-daRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKh  216 (332)
T KOG2272|consen  138 YVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTS-DAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKH  216 (332)
T ss_pred             eehhhhhhhcccccccccCCCCCccceecccccccccc-hhhhhccceeccccccccCCcccccccCchHHHHHHHhccc
Confidence            46899999999899999999999999999999999976 45667789999999999888999999999999999999999


Q ss_pred             ccccccccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         84 YHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        84 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      ||.++|+|+.|.+|+-+...++.+|.+||+.++.+
T Consensus       217 WHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~q  251 (332)
T KOG2272|consen  217 WHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQ  251 (332)
T ss_pred             cchhheeehhcCCcccchhhhhhcCchhHHHHHHH
Confidence            99999999999999999999999999999998755

>KOG1703|consensus

Probab=99.86  E-value=9.9e-23  Score=153.33  Aligned_cols=117  Identities=28%  Similarity=0.554  Sum_probs=111.2

Q ss_pred             Ccccccccccccc-ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeC
Q psy17880          3 KAYCTSCKKKCSG-EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALG   81 (120)
Q Consensus         3 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~   81 (120)
                      .+.|..|++.|.+ +++.++++.||+.+|.|..|...+....+...+|.+||..|+...+.+.|.+|+++|.++.|.+.+
T Consensus       303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~  382 (479)
T KOG1703|consen  303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALG  382 (479)
T ss_pred             cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhcc
Confidence            4789999999998 899999999999999999999999888888999999999999999999999999999999999999


Q ss_pred             ccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         82 KTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        82 ~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      +.||++||.|..|+++|.+..|++.||.+||+.++...
T Consensus       383 ~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~  420 (479)
T KOG1703|consen  383 RLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKL  420 (479)
T ss_pred             CeechhceeeecccCCCCCCcccccCCccchhhhHhhh
Confidence            99999999999999999999999999999999988543

>KOG1703|consensus

Probab=99.86  E-value=6e-23  Score=154.51  Aligned_cols=115  Identities=27%  Similarity=0.590  Sum_probs=109.7

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc--CcEEEE
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE--GEVVTA   79 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~--~~~~~~   79 (120)
                      ..+.|.+|+++|.++.|.+.+..||++||.|..|++++....|+..++.+||+.||.++++.+|..|.++++  +..+.+
T Consensus       362 ~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~  441 (479)
T KOG1703|consen  362 FRPNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEA  441 (479)
T ss_pred             hCccccccCCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhc
Confidence            357899999999999999999999999999999999999999999999999999999999999999999986  678999


Q ss_pred             eCccccccccccccCCCcCCCCceeeeCCeeeeccCC
Q psy17880         80 LGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLG  116 (120)
Q Consensus        80 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~  116 (120)
                      .+..||..||+|+.|.+.|.++.|+...++++|+.++
T Consensus       442 ~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  442 DGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             cCccccccceehhhhhccccCCceeecCCccccccCC
Confidence            9999999999999999999999999999999999986

>KOG1044|consensus

Probab=99.83  E-value=1e-21  Score=146.38  Aligned_cols=108  Identities=34%  Similarity=0.807  Sum_probs=97.6

Q ss_pred             Ccccccccccc-ccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeC
Q psy17880          3 KAYCTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALG   81 (120)
Q Consensus         3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~   81 (120)
                      ...|++|++.| .|+.+.++++.||..||+|..|+..|.+ .+..+|+.+||+.+|.+.|+.+|..|.+.|.|.++.+.|
T Consensus       133 ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~  211 (670)
T KOG1044|consen  133 PSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGD  211 (670)
T ss_pred             Cccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccC
Confidence            35799999988 7889999999999999999999999976 699999999999999999999999999999999999999


Q ss_pred             ccccccccccccCCCcCCCCc-eeeeCCeee
Q psy17880         82 KTYHQKCFTCARCRFSKKREI-YNWLGGRAY  111 (120)
Q Consensus        82 ~~~H~~Cf~C~~C~~~l~~~~-~~~~~g~~y  111 (120)
                      ++||+.|-+|++|+..+..++ .|+-+..+|
T Consensus       212 kh~HPtCARCsRCgqmF~eGEEMYlQGs~iW  242 (670)
T KOG1044|consen  212 KHFHPTCARCSRCGQMFGEGEEMYLQGSEIW  242 (670)
T ss_pred             cccCcchhhhhhhccccccchheeecccccc
Confidence            999999999999999998665 554454444

>KOG1044|consensus

Probab=99.70  E-value=5.7e-18  Score=126.55  Aligned_cols=113  Identities=28%  Similarity=0.563  Sum_probs=94.6

Q ss_pred             cccccccccceEEECCcccccccccccccccccCCC-CeeecCCeeccHhHHHhHh--------CCCCCCCCCcc-cCcE
Q psy17880          7 TSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQG-GYFNKDGAYYCTSDYQKKF--------GTKCAQCGEYV-EGEV   76 (120)
Q Consensus         7 ~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~~--------~~~C~~C~~~i-~~~~   76 (120)
                      ..|..-|.++++.++|++||++||.|+.|..+...+ ....-+....|+.|....-        ...|++|++.| .|..
T Consensus        69 ~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~  148 (670)
T KOG1044|consen   69 DDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA  148 (670)
T ss_pred             cchhhhccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce
Confidence            456677889999999999999999999999998766 4445555678888875321        24799999999 6789


Q ss_pred             EEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         77 VTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        77 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +.|.++.||..||+|..|...|. ++|+..||.|||++++...|
T Consensus       149 llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~f  191 (670)
T KOG1044|consen  149 LLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKF  191 (670)
T ss_pred             eeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhc
Confidence            99999999999999999999884 55788999999999998765

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

Probab=99.66  E-value=3.4e-17  Score=90.29  Aligned_cols=56  Identities=29%  Similarity=0.698  Sum_probs=50.6

Q ss_pred             CCCCCCcccCc--EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         65 CAQCGEYVEGE--VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        65 C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |..|+++|.+.  ++.+.|+.||++||+|+.|+++|.++.++..||++||+.++.++|
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            78999999753  346999999999999999999999999999999999999998776

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=99.64  E-value=3.4e-16  Score=86.30  Aligned_cols=56  Identities=39%  Similarity=1.002  Sum_probs=50.6

Q ss_pred             ccccccccccc-e-EEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880          6 CTSCKKKCSGE-V-LRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF   61 (120)
Q Consensus         6 C~~C~~~i~~~-~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~   61 (120)
                      |.+|+++|.+. . +.+.|+.||++||+|+.|+++|.++.++..++++||+.||.++|
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            78999999755 3 36999999999999999999999888999999999999999875

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

>KOG1700|consensus

Probab=99.50  E-value=2.4e-15  Score=101.85  Aligned_cols=117  Identities=32%  Similarity=0.625  Sum_probs=99.8

Q ss_pred             Cccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCC------------------
Q psy17880          3 KAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT------------------   63 (120)
Q Consensus         3 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~------------------   63 (120)
                      ...|.+|++.+. .+.+...|..||..||.|..|.+.|....+..+++.+||+.+|...+++                  
T Consensus         7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD   86 (200)
T ss_pred             cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence            347999999883 3344477889999999999999999988899999999999977666544                  


Q ss_pred             -----------------------CCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         64 -----------------------KCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        64 -----------------------~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                                             .|..|.+.+- .+-+...+..||..||+|+.|+..|+...+...+|.+||..++.+.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~  166 (200)
T KOG1700|consen   87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQL  166 (200)
T ss_pred             cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhee
Confidence                                   6999998884 4667888999999999999999999999999999999999887553

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

Probab=99.02  E-value=2.7e-10  Score=57.30  Aligned_cols=36  Identities=44%  Similarity=1.019  Sum_probs=32.5

Q ss_pred             CCCCCCCcccC--cEEEEeCccccccccccccCCCcCC
Q psy17880         64 KCAQCGEYVEG--EVVTALGKTYHQKCFTCARCRFSKK   99 (120)
Q Consensus        64 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~   99 (120)
                      +|..|+++|.+  ..+.+.++.||++||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            58899999976  6778999999999999999999985

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=98.88  E-value=1.3e-09  Score=54.76  Aligned_cols=36  Identities=42%  Similarity=0.867  Sum_probs=32.1

Q ss_pred             ccccccccccc--ceEEECCcccccccccccccccccC
Q psy17880          5 YCTSCKKKCSG--EVLRVQDKYFHITCFQCSVCKNSLA   40 (120)
Q Consensus         5 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~   40 (120)
                      +|.+|+++|.+  ..+.+.++.||++||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            48899999976  5778889999999999999999985

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

>KOG4577|consensus

Probab=98.36  E-value=4.8e-09  Score=73.64  Aligned_cols=58  Identities=17%  Similarity=0.430  Sum_probs=49.4

Q ss_pred             CCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++|+.|.+.|.++ ++.+.+++||..|++|+.|..+|...=| ..+|.+||+.++-.+|
T Consensus        33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCF-sR~~s~yCkedFfKrf   91 (383)
T KOG4577|consen   33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCF-SREGSVYCKEDFFKRF   91 (383)
T ss_pred             cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHh-hcCCceeehHHHHHHh
Confidence            48999999999887 4579999999999999999999966544 4789999999875544

>KOG0490|consensus

Probab=97.98  E-value=4.6e-07  Score=62.41  Aligned_cols=108  Identities=31%  Similarity=0.695  Sum_probs=82.4

Q ss_pred             cccccccc-eEEECCcccccccccccccccccC-CCCeeecCCeeccHhHHHh--HhCCCCCCCCCccc--CcEEEEeCc
Q psy17880          9 CKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLA-QGGYFNKDGAYYCTSDYQK--KFGTKCAQCGEYVE--GEVVTALGK   82 (120)
Q Consensus         9 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~~~~~C~~c~~~--~~~~~C~~C~~~i~--~~~~~~~~~   82 (120)
                      |+..|.+. .+.+.+..||..|..|..|...+. ....+..++..||..+|..  .+..+|.+|...+.  +++..+..+
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~   81 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEK   81 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcC
Confidence            56667655 355568899999999999999997 2245555999999999998  77789999999984  345566677


Q ss_pred             cccccccccccCCCcCCC-CceeeeCC-eeeeccCCC
Q psy17880         83 TYHQKCFTCARCRFSKKR-EIYNWLGG-RAYENRLGG  117 (120)
Q Consensus        83 ~~H~~Cf~C~~C~~~l~~-~~~~~~~g-~~yC~~~~~  117 (120)
                      . |..||.|..|...+.+ ..+.+.+. +.++.++..
T Consensus        82 ~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~  117 (235)
T KOG0490|consen   82 V-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK  117 (235)
T ss_pred             C-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence            7 9999999999886644 44555544 777777654

>KOG1700|consensus

Probab=97.77  E-value=4.1e-06  Score=56.98  Aligned_cols=55  Identities=29%  Similarity=0.565  Sum_probs=47.8

Q ss_pred             CCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeecc-CCC
Q psy17880         63 TKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENR-LGG  117 (120)
Q Consensus        63 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~-~~~  117 (120)
                      ..|..|++.+. .+.+...|..||..||+|..|.+.|+...+...++.+||+. ++.
T Consensus         8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~   64 (200)
T KOG1700|consen    8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVA   64 (200)
T ss_pred             chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHh
Confidence            58999999883 45556889999999999999999999999999999999999 443

>KOG1702|consensus

Probab=97.54  E-value=6.1e-06  Score=55.73  Aligned_cols=55  Identities=27%  Similarity=0.528  Sum_probs=46.2

Q ss_pred             CCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         64 KCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        64 ~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      .|..|++.+- -+.|.-.++.||..||+|..|+.+|.-..+.-.|.++||+.++..
T Consensus         6 n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpk   61 (264)
T KOG1702|consen    6 NREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPK   61 (264)
T ss_pred             hhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccc
Confidence            4556777663 356777899999999999999999999998889999999999864

>KOG1702|consensus

Probab=97.44  E-value=8e-06  Score=55.18  Aligned_cols=60  Identities=32%  Similarity=0.616  Sum_probs=50.5

Q ss_pred             CCcccccccccc-ccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880          2 IKAYCTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF   61 (120)
Q Consensus         2 ~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~   61 (120)
                      ++..|..|++.+ +-+.+..+++.||..||.|..|+.+|.-.++-..+.++||..+|.+..
T Consensus         3 ~k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen    3 KKCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             ccchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence            456678888876 445677889999999999999999998878888899999999997654

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=93.27  E-value=0.079  Score=28.45  Aligned_cols=37  Identities=32%  Similarity=0.886  Sum_probs=25.8

Q ss_pred             CCCCCCCCCccc--CcEEE--EeCcccccccc----cccc--CCCcC
Q psy17880         62 GTKCAQCGEYVE--GEVVT--ALGKTYHQKCF----TCAR--CRFSK   98 (120)
Q Consensus        62 ~~~C~~C~~~i~--~~~~~--~~~~~~H~~Cf----~C~~--C~~~l   98 (120)
                      +.+|..|+++|.  +++|+  .-+..||.+|.    .|..  |+.++
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence            478999999994  44553  45778999998    4655  55544

>KOG0490|consensus

Probab=92.03  E-value=0.03  Score=38.38  Aligned_cols=50  Identities=24%  Similarity=0.547  Sum_probs=39.9

Q ss_pred             CCCcccCc-EEEEeCccccccccccccCCCcCC--CCceeeeCCeeeeccCCCc
Q psy17880         68 CGEYVEGE-VVTALGKTYHQKCFTCARCRFSKK--REIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        68 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~~~~~  118 (120)
                      |+.+|.+. .+.+.+..||..|..|..|...+.  ...|.. +|..||..++.+
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~   54 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQR   54 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchh
Confidence            56667654 345568999999999999999997  555666 999999998865

>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=91.84  E-value=0.13  Score=25.43  Aligned_cols=31  Identities=39%  Similarity=0.749  Sum_probs=22.3

Q ss_pred             CCCCCCcccCc--EEEEeCccccccccccccCCCcC
Q psy17880         65 CAQCGEYVEGE--VVTALGKTYHQKCFTCARCRFSK   98 (120)
Q Consensus        65 C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l   98 (120)
                      |..|+++|.++  ++...++.|+   |.|..|.+.|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f   33 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF   33 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence            67899999775  5678888888   5556665544

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

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

Probab=90.94  E-value=0.16  Score=28.30  Aligned_cols=45  Identities=20%  Similarity=0.438  Sum_probs=23.1

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG   74 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~   74 (120)
                      ++|+.|...|...-....=+.++|..|-.+.++..|..|..|-..
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~   52 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWI   52 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHH
Confidence            578888888765433455568899999988888889999988743

>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454

Probab=90.62  E-value=0.28  Score=32.06  Aligned_cols=50  Identities=24%  Similarity=0.523  Sum_probs=37.5

Q ss_pred             CeeccHhHHHhHhCCCCCCCCCcccCcE----EEEeCccccccccccccCCCcCCC
Q psy17880         49 GAYYCTSDYQKKFGTKCAQCGEYVEGEV----VTALGKTYHQKCFTCARCRFSKKR  100 (120)
Q Consensus        49 ~~~~C~~c~~~~~~~~C~~C~~~i~~~~----~~~~~~~~H~~Cf~C~~C~~~l~~  100 (120)
                      ..-||..|-.+.. ..|..|+.+|.|.+    +...+..|+.-- -|..|+++++.
T Consensus        27 ~~~fC~kCG~~tI-~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpyPW   80 (158)
T PF10083_consen   27 REKFCSKCGAKTI-TSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPYPW   80 (158)
T ss_pred             HHHHHHHhhHHHH-HHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCCch
Confidence            4558999988877 89999999998852    334466676543 48999998864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

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

Probab=87.93  E-value=0.19  Score=30.52  Aligned_cols=28  Identities=36%  Similarity=0.717  Sum_probs=20.6

Q ss_pred             CCCCCCCcc-cCcEEEEe-Ccccccccccc
Q psy17880         64 KCAQCGEYV-EGEVVTAL-GKTYHQKCFTC   91 (120)
Q Consensus        64 ~C~~C~~~i-~~~~~~~~-~~~~H~~Cf~C   91 (120)
                      +|..|+++| .|+..++. +..-|.+||.=
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~   33 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE   33 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence            588899998 57776654 45779888863

>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=87.24  E-value=0.47  Score=28.46  Aligned_cols=27  Identities=33%  Similarity=0.698  Sum_probs=15.9

Q ss_pred             CCCCCCCCcccCc-EEEEe-Ccccccccc
Q psy17880         63 TKCAQCGEYVEGE-VVTAL-GKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i~~~-~~~~~-~~~~H~~Cf   89 (120)
                      ..|..|+++|... ++.+. |..+|..|+
T Consensus        79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~  107 (109)
T PF10367_consen   79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI  107 (109)
T ss_pred             CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence            4688888877543 33333 445676664

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

>smart00504 Ubox Modified RING finger domain

Probab=87.12  E-value=1.5  Score=23.61  Aligned_cols=43  Identities=14%  Similarity=0.217  Sum_probs=31.7

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCccc
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVE   73 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~   73 (120)
                      |.|..|+..+.. ......|..||..+..+.+  ...|..|++++.
T Consensus         2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence            567888888765 4666778999998887654  356888877774

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

>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel

Probab=86.45  E-value=0.43  Score=25.40  Aligned_cols=25  Identities=20%  Similarity=0.333  Sum_probs=15.3

Q ss_pred             ccccCCCcCCCCceeeeCCeeeecc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENR  114 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~  114 (120)
                      .|..|...++...-+..||+.||..
T Consensus         9 aC~~C~C~V~~~~Ai~~dGk~YCS~   33 (52)
T PF02069_consen    9 ACPSCSCVVSEEEAIQKDGKYYCSE   33 (52)
T ss_dssp             SSTT----B-TTTSEESSS-EESSH
T ss_pred             cCCCCEeEECchHhHHhCCEeeecH
Confidence            3678888888788888999999964

They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.

>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=86.14  E-value=0.62  Score=22.81  Aligned_cols=25  Identities=24%  Similarity=0.404  Sum_probs=17.9

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      .|..|+..    .|...||..||..++-+
T Consensus        10 ~C~~C~~~----~~~~~dG~~yC~~cG~~   34 (36)
T PF11781_consen   10 PCPVCGSR----WFYSDDGFYYCDRCGHQ   34 (36)
T ss_pred             cCCCCCCe----EeEccCCEEEhhhCceE
Confidence            47777554    57778999999877643

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=85.81  E-value=0.26  Score=27.92  Aligned_cols=48  Identities=25%  Similarity=0.522  Sum_probs=20.5

Q ss_pred             CeeccHhHHHhHh-CCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCc
Q psy17880         49 GAYYCTSDYQKKF-GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREI  102 (120)
Q Consensus        49 ~~~~C~~c~~~~~-~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~  102 (120)
                      +..+|..|..... ...|..|++++.  ++.+-|..    =|.|..|+..++..+
T Consensus        16 ~~~~C~~C~~~~~~~a~CPdC~~~Le--~LkACGAv----dYFC~~c~gLiSKkr   64 (70)
T PF07191_consen   16 GHYHCEACQKDYKKEAFCPDCGQPLE--VLKACGAV----DYFCNHCHGLISKKR   64 (70)
T ss_dssp             TEEEETTT--EEEEEEE-TTT-SB-E--EEEETTEE----EEE-TTTT-EE-TTT
T ss_pred             CEEECccccccceecccCCCcccHHH--HHHHhccc----ceeeccCCceeecce
Confidence            4444554443211 156777777763  45555431    145677777776654

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

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

Probab=85.39  E-value=0.18  Score=24.56  Aligned_cols=28  Identities=18%  Similarity=0.468  Sum_probs=18.4

Q ss_pred             ccccccccCCCCeeecCCeeccHhHHHh
Q psy17880         32 CSVCKNSLAQGGYFNKDGAYYCTSDYQK   59 (120)
Q Consensus        32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~   59 (120)
                      |..|+.++.........+..+|..|..+
T Consensus         6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~   33 (36)
T PF01258_consen    6 CEDCGEPIPEERLVAVPGATLCVECQER   33 (36)
T ss_dssp             -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred             ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence            6777777766666666777778777654

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=84.86  E-value=2.4  Score=21.88  Aligned_cols=42  Identities=19%  Similarity=0.515  Sum_probs=28.3

Q ss_pred             cccccccccCCCCeeecCCee-ccHhHHHhHh--CCCCCCCCCccc
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAY-YCTSDYQKKF--GTKCAQCGEYVE   73 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~-~C~~c~~~~~--~~~C~~C~~~i~   73 (120)
                      .|..|...... ..+..=|.. +|..|..+..  ...|..|.++|.
T Consensus         4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            45666665433 344556777 9999998874  478999998885

...

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=84.76  E-value=0.77  Score=29.22  Aligned_cols=23  Identities=17%  Similarity=0.459  Sum_probs=15.4

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGG  117 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~  117 (120)
                      .|..|+.||    |. ++|.+||..|+.
T Consensus        30 hCp~Cg~PL----F~-KdG~v~CPvC~~   52 (131)
T COG1645          30 HCPKCGTPL----FR-KDGEVFCPVCGY   52 (131)
T ss_pred             hCcccCCcc----ee-eCCeEECCCCCc
Confidence            367777776    33 777777777764

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=83.56  E-value=0.95  Score=24.71  Aligned_cols=50  Identities=22%  Similarity=0.487  Sum_probs=28.3

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCG   69 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~   69 (120)
                      +.++|.+|+.+|.+.-        +.--|.|..|+..+..          -|..|-.....-+|..|+
T Consensus         6 ~~~~CtSCg~~i~~~~--------~~~~F~CPnCG~~~I~----------RC~~CRk~~~~Y~CP~CG   55 (59)
T PRK14890          6 EPPKCTSCGIEIAPRE--------KAVKFLCPNCGEVIIY----------RCEKCRKQSNPYTCPKCG   55 (59)
T ss_pred             cCccccCCCCcccCCC--------ccCEeeCCCCCCeeEe----------echhHHhcCCceECCCCC
Confidence            4567888888875321        1112677788776322          166665554444566665

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=81.47  E-value=0.97  Score=20.27  Aligned_cols=12  Identities=17%  Similarity=0.797  Sum_probs=6.5

Q ss_pred             Cccccccccccc
Q psy17880          3 KAYCTSCKKKCS   14 (120)
Q Consensus         3 ~~~C~~C~~~i~   14 (120)
                      ...|..|+..|.
T Consensus         2 ~~~Cp~Cg~~~~   13 (26)
T PF13248_consen    2 EMFCPNCGAEID   13 (26)
T ss_pred             cCCCcccCCcCC
Confidence            345666666543

>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]

Probab=80.18  E-value=0.99  Score=30.85  Aligned_cols=31  Identities=13%  Similarity=0.172  Sum_probs=27.5

Q ss_pred             cccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         89 FTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        89 f~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      -+|+.|+..+....-...||++.|..|+...
T Consensus       173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~  203 (206)
T COG2191         173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK  203 (206)
T ss_pred             eeccccCcccccchhhhcCCceecccccccc
Confidence            6899999999888888999999999998754

>COG4847 Uncharacterized protein conserved in archaea [Function unknown]

Probab=80.03  E-value=0.77  Score=27.49  Aligned_cols=30  Identities=30%  Similarity=0.637  Sum_probs=20.9

Q ss_pred             CCCCCCCcc-cCcEEEEe-Ccccccccccccc
Q psy17880         64 KCAQCGEYV-EGEVVTAL-GKTYHQKCFTCAR   93 (120)
Q Consensus        64 ~C~~C~~~i-~~~~~~~~-~~~~H~~Cf~C~~   93 (120)
                      +|+.|+++| +|+..++. ...-|-+||.=+.
T Consensus         8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~   39 (103)
T COG4847           8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESK   39 (103)
T ss_pred             eEeeeCCEeeeccEEEEeeCCcchHHHHHHHH
Confidence            688898888 67766543 4467888885443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
1v6g_A	81	Solution Structure Of The Lim Domain Of The Human A		6e-11
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		7e-10
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		7e-10
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		3e-09
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		4e-08
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		6e-08
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		1e-07
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		1e-05
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		4e-05
1x64_A	89	Solution Structure Of The Lim Domain Of Alpha-Actin		7e-05
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		5e-04
2cup_A	101	Solution Structure Of The Skeletal Muscle Lim-Prote		5e-04
2dar_A	90	Solution Structure Of First Lim Domain Of Enigma-Li		6e-04

>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin Binding Lim Protein 2 Length = 81

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 25/42 (59%), Positives = 32/42 (76%)
Query: 56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFS 97
          DYQ+ +GT+C  C +++EGEVV+ALGKTYH  CF CA CR  
Sbjct: 9  DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLP 50

>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid Domain Length = 188

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 48/97 (49%), Gaps = 7/97 (7%)
Query: 6   CTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGY--FNKDGAYYCTSDYQKKFG 62
           C  C  K +   +L   D Y+H  C +CS C+  L   G   + K G   C +DY + FG
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67
Query: 63  TK--CAQCGEYVEGE--VVTALGKTYHQKCFTCARCR 95
               C+ CG+ +     V+ A G  YH KCFTC+ CR
Sbjct: 68  NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCR 104

>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim Domains 1 And 2 With The Lim Interacting Domain Of Ldb1 Length = 195

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 48/97 (49%), Gaps = 7/97 (7%)
Query: 6   CTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGY--FNKDGAYYCTSDYQKKFG 62
           C  C  K +   +L   D Y+H  C +CS C+  L   G   + K G   C +DY + FG
Sbjct: 6   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 65
Query: 63  TK--CAQCGEYVEGE--VVTALGKTYHQKCFTCARCR 95
               C+ CG+ +     V+ A G  YH KCFTC+ CR
Sbjct: 66  NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCR 102

>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of Transcription Factors, The Lim-Homeodomain Proteins, In Neural Cell Type Specification Length = 169

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 51/97 (52%), Gaps = 5/97 (5%)
Query: 17  VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEV 76
           +L+V D+++H +C +C+ C+  LA    F++ G+ YC  D+ K+FGTKC  C + +    
Sbjct: 21  ILKVLDRHWHSSCLKCADCQMQLADRC-FSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQ 79
Query: 77  VT--ALGKTYHQKCFTCARC--RFSKKREIYNWLGGR 109
           V   A    YH  CF C  C  + +   E Y    GR
Sbjct: 80  VVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGR 116

>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The Binding Domain Of Isl1 Length = 169

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 17  VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEV 76
           +L+  D+++H  C +CS C   LA+   F++  + YC  D+ K+FGTKCA C   +    
Sbjct: 21  ILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQ 79
Query: 77  VT--ALGKTYHQKCFTCARCR 95
           V   A    YH  CF C  C+
Sbjct: 80  VVRRAQDFVYHLHCFACVVCK 100

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 17  VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEV 76
           +L+  D+++H  C +CS C   LA+   F++  + YC  D+ K+FGTKCA C   +    
Sbjct: 75  ILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQ 133
Query: 77  VT--ALGKTYHQKCFTCARCR 95
           V   A    YH  CF C  C+
Sbjct: 134 VVRRAQDFVYHLHCFACVVCK 154

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 3  KAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61
           ++C  CK++   G+ L   DK +H++CF+C  C   L  G Y +KDG  YC SDY  +F
Sbjct: 15 PSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 73
Query: 62 GT 63
          G+
Sbjct: 74 GS 75

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 6  CTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
          C  C+K     E L    + FHI+CF+CS C N L+ G Y +  G  YC   + + F +K
Sbjct: 18 CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77
Query: 65 CAQCGEYVEG 74
              G Y EG
Sbjct: 78 ----GNYDEG 83

>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21 Crystal Form Length = 131

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 18  LRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFGTK--CAQCGEYVE 73
           L+  D+Y+H  C  C +C   L + G   + K G   C  DY + FG    CA C + + 
Sbjct: 18  LKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIR 77
Query: 74  GEVVT--ALGKTYHQKCFTCARCR 95
              +T     K YH +CF CA C+
Sbjct: 78  AYEMTMRVKDKVYHLECFKCAACQ 101

>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2 Associated Lim Protein Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 4  AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
            C  C     G V++ +DKY H  CF C+ C  +L Q GYF  +G  YC +  + +
Sbjct: 26 PLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARAR 82

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 25/63 (39%)
Query: 1  MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
          M    C  C +      L   D  +H  CF C  C  S + G +F  DG  +C   Y  +
Sbjct: 13 MFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHR 72
Query: 61 FGT 63
           G+
Sbjct: 73 RGS 75

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 6  CTSCKKKCSGEVLRV--QDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
          C  C+K    +   V  +++++H TCF+C+ C + LA   +  KD    C     ++   
Sbjct: 8  CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSP 67
Query: 64 KCAQCGEYVEG--EVVTALGKTYHQKCFT 90
          KC  C + +    + V   G  +H+ CF+
Sbjct: 68 KCKGCFKAIVAGDQNVEYKGTVWHKDCFS 96

>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like Pdz And Lim Domains Protein Length = 90

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 4  AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
            C  C +   G  L    K +H   F C+ CKN++A  G+  + GA YC   Y+K F +
Sbjct: 26 PMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFAS 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	4e-26
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	4e-06
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	4e-23
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	6e-08
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	6e-23
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	1e-07
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-07
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-22
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	3e-19
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	3e-21
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	3e-10
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-20
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-07
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-04
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	4e-20
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	2e-18
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	2e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-17
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	1e-11
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	4e-15
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-13
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	1e-14
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	4e-08
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	1e-14
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	8e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-14
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	6e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	4e-14
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	1e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-14
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-11
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	9e-14
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-05
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-13
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	3e-06
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	2e-13
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	2e-08
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	2e-13
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	3e-10
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	2e-13
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	6e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	3e-13
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	3e-07
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	4e-13
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	9e-05
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	6e-13
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	7e-06
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-12
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-04
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-12
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-04
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	6e-12
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	3e-07
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	8e-12
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	3e-05
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-11
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-11
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-05
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	3e-11
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-11
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	1e-09
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	5e-11
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-05
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	1e-10
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	8e-10
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	8e-05
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	1e-09
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-05
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-09
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	3e-07
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-09
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	7e-08
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	6e-09
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	2e-06
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	2e-08
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	7e-05
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	3e-07
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	2e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	5e-07
2cor_A	79	Pinch protein; LIM domain, particularly interestin	9e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	6e-07
2co8_A	82	NEDD9 interacting protein with calponin homology a	5e-04
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	9e-04

>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 = 92.9 bits (231), Expect = 4e-26
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 4/93 (4%)

Query: 6   CTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
           C  C+K    +   +  +++++H TCF+C+ C + LA   +  KD    C     ++   
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSP 67

Query: 64  KCAQCGEYVEG--EVVTALGKTYHQKCFTCARC 94
           KC  C + +    + V   G  +H+ CF+    
Sbjct: 68  KCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 = 41.6 bits (98), Expect = 4e-06
 Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 60  KFGTKCAQCGEYVEGE--VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
              + C +C + +  +   V    + +H  CF CA+C      E +     +  
Sbjct: 3   SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKIL 56

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

 Score = 86.3 bits (214), Expect = 4e-23
 Identities = 29/97 (29%), Positives = 43/97 (44%), Gaps = 7/97 (7%)

Query: 6   CTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFG 62
           C  C++       L+  D+Y+H  C  C +C   L + G   + K G   C  DY + FG
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64

Query: 63  TK--CAQCGEYVEGE--VVTALGKTYHQKCFTCARCR 95
               CA C + +      +    K YH +CF CA C+
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQ 101

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

 Score = 46.7 bits (111), Expect = 6e-08
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 3/66 (4%)

Query: 2   IKAYCTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQG-GYFNKDGAYYCTSDYQ 58
               C SC K+       +RV+DK +H+ CF+C+ C+     G  Y   +    C  D  
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIY 124

Query: 59  KKFGTK 64
           +     
Sbjct: 125 EWTKIN 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 = 86.9 bits (215), Expect = 6e-23
 Identities = 34/111 (30%), Positives = 49/111 (44%), Gaps = 6/111 (5%)

Query: 6   CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
           C  C +      +L+  D+++H  C +CS C   LA    F++  + YC  D+ K+FGTK
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA-ERCFSRGESVYCKDDFFKRFGTK 121

Query: 65  CAQCGEYVE--GEVVTALGKTYHQKCFTCARC--RFSKKREIYNWLGGRAY 111
           CA C   +     V  A    YH  CF C  C  + +   E Y     R  
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLV 172

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

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 6   CTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNSLAQG--GYFNKDGAYYCTSDYQKK 60
           C +C+     +  V R QD  +H+ CF C VCK  LA G   Y  +D    C +DY+  
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA 180

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

 Score = 46.4 bits (110), Expect = 2e-07
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 8/84 (9%)

Query: 28  TCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGE-VVTALGKTYHQ 86
                       A  G  ++ G+              CA C +++    ++ AL + +H 
Sbjct: 26  RLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHS 85

Query: 87  KCFTCARCR-------FSKKREIY 103
           KC  C+ C        FS+   +Y
Sbjct: 86  KCLKCSDCHVPLAERCFSRGESVY 109

>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 = 85.3 bits (211), Expect = 2e-22
 Identities = 34/111 (30%), Positives = 48/111 (43%), Gaps = 6/111 (5%)

Query: 6   CTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
           C  C +      +L+  D+++H  C +CS C   LA    F++  + YC  D+ K+FGTK
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA-ERCFSRGESVYCKDDFFKRFGTK 67

Query: 65  CAQCGE--YVEGEVVTALGKTYHQKCFTCARCR--FSKKREIYNWLGGRAY 111
           CA C         V  A    YH  CF C  C+   +   E Y     R  
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLV 118

>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 = 77.2 bits (190), Expect = 3e-19
 Identities = 25/99 (25%), Positives = 35/99 (35%), Gaps = 4/99 (4%)

Query: 6   CTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNSLAQG--GYFNKDGAYYCTSDYQKKF 61
           C +C+     +  V R QD  +H+ CF C VCK  LA G   Y  +D    C +DY+   
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

Query: 62  GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKR 100
                  G    G  + A     H              +
Sbjct: 128 QGGSGGSGGSGGGTPMVAASPERHDGGLQANPVEVQSYQ 166

>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 = 82.8 bits (204), Expect = 3e-21
 Identities = 35/97 (36%), Positives = 48/97 (49%), Gaps = 7/97 (7%)

Query: 6   CTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFG 62
           C  C  K +   +L   D Y+H  C +CS C+  L   G   + K G   C +DY + FG
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67

Query: 63  --TKCAQCGEYVEGE--VVTALGKTYHQKCFTCARCR 95
               C+ CG+ +     V+ A G  YH KCFTC+ CR
Sbjct: 68  NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCR 104

>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 = 53.9 bits (129), Expect = 3e-10
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 2   IKAYCTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQG-GYFNKDGAYYCTSDYQ 58
               C++C +       V+R Q   +H+ CF CS C+N L  G  +   +G+ +C  D  
Sbjct: 68  NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRP 127

Query: 59  KKFGTKCAQCGE 70
                     G 
Sbjct: 128 TALINGHLNSGG 139

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

 Score = 79.4 bits (196), Expect = 2e-20
 Identities = 25/111 (22%), Positives = 44/111 (39%), Gaps = 5/111 (4%)

Query: 6   CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
           C  C +   S E  + +++ +H+  F C  C + LA   Y   +    C   Y K     
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVV 65

Query: 65  CAQCGEYVEGE--VVTALGKTYH--QKCFTCARCRFSKKREIYNWLGGRAY 111
           C  C   ++ E   VT    ++H   +CF C+ C      + +  + G  +
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVF 116

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

 Score = 45.9 bits (109), Expect = 1e-07
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 5   YCTSCKKKCSGEVLRV--QDKYFHIT--CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
            C  C      EV RV   +  +H +  CF CS C   L    +   +G  +C+ + +K+
Sbjct: 65  VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR 124

Query: 61  F 61
            
Sbjct: 125 M 125

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 64  KCAQCGEYV-EGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           +CA C E +   E   A  + +H K F C  C      EIY  +  +  
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPV 53

>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 = 77.1 bits (190), Expect = 4e-20
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C     G V++ +DKY H  CF C+ C  +L Q GYF  +G  YC +  + +     
Sbjct: 28 CDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPS 87

Query: 66 A 66
          +
Sbjct: 88 S 88

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

 Score = 49.4 bits (118), Expect = 3e-09
 Identities = 18/48 (37%), Positives = 26/48 (54%)

Query: 64  KCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
            C +CG  + G VV A  K  H +CF CA C  + K++ Y ++ G  Y
Sbjct: 27  LCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELY 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 = 72.5 bits (178), Expect = 2e-18
 Identities = 14/61 (22%), Positives = 29/61 (47%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C     G  ++++D++ H  C+ C+ C  +L Q G+F  +   YC    +++     
Sbjct: 18 CDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS 77

Query: 66 A 66
          +
Sbjct: 78 S 78

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

 Score = 47.1 bits (112), Expect = 2e-08
 Identities = 12/57 (21%), Positives = 25/57 (43%)

Query: 55  SDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           S    +    C +CG  + G  V    +  H +C+ C  C  + K++ + ++  + Y
Sbjct: 8   SIGNAQKLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIY 64

>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 = 69.8 bits (171), Expect = 3e-17
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C +   G  L    K +H   F C+ CKN++A  G+  + GA YC   Y+K F +  
Sbjct: 28 CAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGP 87

Query: 66 A 66
          +
Sbjct: 88 S 88

>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 = 55.5 bits (134), Expect = 1e-11
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 40 AQGGYFNKDGAYYCTSDY-QKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          + G   ++D            K    CA C + + G  + ALGK++H + F CA C+
Sbjct: 2  SSGSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCK 58

>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 = 63.9 bits (156), Expect = 4e-15
 Identities = 17/61 (27%), Positives = 25/61 (40%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C +      L   D  +H  CF C  C  S + G +F  DG  +C   Y  + G+  
Sbjct: 18 CGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGP 77

Query: 66 A 66
          +
Sbjct: 78 S 78

>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 = 60.0 bits (146), Expect = 2e-13
 Identities = 16/63 (25%), Positives = 25/63 (39%)

Query: 49  GAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGG 108
            +     D+   F  KC  C   V    ++A+   +H +CF C  C  S     +  L G
Sbjct: 2   SSGSSGKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDG 61

Query: 109 RAY 111
           R +
Sbjct: 62  RPF 64

>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 = 62.7 bits (153), Expect = 1e-14
 Identities = 13/61 (21%), Positives = 29/61 (47%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  CKK  +   +  +++ +H  CF C+ C+  L+   +  +D   YC + +   + +  
Sbjct: 8  CVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGP 67

Query: 66 A 66
          +
Sbjct: 68 S 68

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

 Score = 45.8 bits (109), Expect = 4e-08
 Identities = 11/37 (29%), Positives = 18/37 (48%)

Query: 59 KKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
              + C QC + +    VT   + +H++CF C  CR
Sbjct: 2  SSGSSGCVQCKKPITTGGVTYREQPWHKECFVCTACR 38

>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 = 62.4 bits (152), Expect = 1e-14
 Identities = 16/61 (26%), Positives = 24/61 (39%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C K  +   +  QD+ +H  CF C  C   LA   +   +  YYC   Y+       
Sbjct: 8  CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPS 67

Query: 66 A 66
          +
Sbjct: 68 S 68

>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 = 45.1 bits (107), Expect = 8e-08
 Identities = 9/53 (16%), Positives = 20/53 (37%)

Query: 59  KKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
               + C +C + +    +T   + +H  CF C  C      + +  +  + Y
Sbjct: 2   SSGSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYY 54

>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 = 62.1 bits (151), Expect = 2e-14
 Identities = 14/61 (22%), Positives = 29/61 (47%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C +   G V++  +  +H  CF+C +C+  LA  G+    G + C   + ++  +  
Sbjct: 8  CHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGP 67

Query: 66 A 66
          +
Sbjct: 68 S 68

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

 Score = 45.5 bits (108), Expect = 6e-08
 Identities = 13/32 (40%), Positives = 21/32 (65%)

Query: 64 KCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           C QCGE++ G V+ A+  ++H +CF C  C+
Sbjct: 7  GCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQ 38

>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 = 61.6 bits (150), Expect = 4e-14
 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGG-YFNKDGAYYCTSDYQKKFGTK 64
          C +C +     +LR   K +H  CF C VC   L       +     +C  D+ +KF + 
Sbjct: 18 CATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASG 77

Query: 65 CA 66
           +
Sbjct: 78 PS 79

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

 Score = 47.7 bits (114), Expect = 1e-08
 Identities = 14/44 (31%), Positives = 19/44 (43%)

Query: 52 YCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
                      KCA C + +   ++ A+GK YH  CFTC  C 
Sbjct: 5  SSGEGCYVATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCH 48

>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 = 61.6 bits (150), Expect = 4e-14
 Identities = 14/61 (22%), Positives = 29/61 (47%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C K  +   +  +D+ +H  C  C+ C+  LA   + ++D   YC + + + F +  
Sbjct: 18 CARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGP 77

Query: 66 A 66
          +
Sbjct: 78 S 78

>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 = 55.0 bits (133), Expect = 1e-11
 Identities = 12/47 (25%), Positives = 23/47 (48%)

Query: 49 GAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
           +      Y+ KF  +CA+C + +    VT   + +H++C  C  C+
Sbjct: 2  SSGSSGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQ 48

>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 = 60.5 bits (147), Expect = 9e-14
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 6  CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
          C  CK++   G+ L   DK +H++CF+C  C   L  G Y +KDG  YC SDY  +FG+ 
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQFGSG 76

Query: 65 CA 66
           +
Sbjct: 77 PS 78

>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 = 39.7 bits (93), Expect = 1e-05
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 54 TSDYQKKFGTKCAQCGEYV-EGEVVTALGKTYHQKCFTCARCR 95
              + +  + CA C E +  G+ + AL K +H  CF C  C 
Sbjct: 7  GKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCS 49

>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 = 60.5 bits (147), Expect = 1e-13
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 6  CTSCKK--KCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
          C++C +        L    + +H  CF CS C+  L    +    GA+YC   Y+ KF +
Sbjct: 8  CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS 67

Query: 64 KCA 66
            +
Sbjct: 68 GPS 70

>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 = 40.8 bits (96), Expect = 3e-06
 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 60 KFGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCR 95
             + C+ CGE V      +   G+T+H+ CF C+ C 
Sbjct: 3  SGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCE 40

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

 Score = 59.8 bits (145), Expect = 2e-13
 Identities = 25/40 (62%), Positives = 32/40 (80%)

Query: 56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          DYQ+ +GT+C  C +++EGEVV+ALGKTYH  CF CA CR
Sbjct: 9  DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCR 48

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

 Score = 46.7 bits (111), Expect = 2e-08
 Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 1/58 (1%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYF-NKDGAYYCTSDYQKKFG 62
          C SC +   GEV+    K +H  CF C+VC+     G           C         
Sbjct: 18 CFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV 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 = 59.8 bits (145), Expect = 2e-13
 Identities = 16/65 (24%), Positives = 21/65 (32%), Gaps = 2/65 (3%)

Query: 49  GAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR--FSKKREIYNWL 106
            +     DY  KFG  C  C   + G  + A    YH +CF C  C+             
Sbjct: 2   SSGSSGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQ 61

Query: 107 GGRAY 111
               Y
Sbjct: 62  HATLY 66

>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 = 51.7 bits (124), Expect = 3e-10
 Identities = 12/63 (19%), Positives = 21/63 (33%), Gaps = 2/63 (3%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFGT 63
          C  C    +G  +   +  +H  CF C  CK  +  G      +    YC   + +    
Sbjct: 18 CHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSG 77

Query: 64 KCA 66
            +
Sbjct: 78 PSS 80

>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 = 59.2 bits (144), Expect = 2e-13
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
          C +C++   G V+    K +H+  F C+ C+       ++ + G  YC + Y + FG 
Sbjct: 8  CGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD 65

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

 Score = 48.1 bits (115), Expect = 6e-09
 Identities = 14/36 (38%), Positives = 19/36 (52%)

Query: 60 KFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
               C  C   +EG VV A+GK +H + F CA+C 
Sbjct: 3  MGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCE 38

>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 = 59.0 bits (143), Expect = 3e-13
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 5  YCTSCKKKCSGEV--LRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
           C  C++    +   L  +D++FH  CF+C  C+ SLA   +  +D    C   Y   F 
Sbjct: 17 TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 63 TKCA 66
          +  +
Sbjct: 77 SGPS 80

>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 = 44.0 bits (104), Expect = 3e-07
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 52  YCTSDYQKKFGTKCAQCGEYVEGEV--VTALGKTYHQKCFTCARCRFSKKREIYNWLGGR 109
                Y   F   CA+C + +  +   +    + +H+ CF C RC+ S   E +      
Sbjct: 5   SSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSE 64

Query: 110 AY 111
             
Sbjct: 65  LL 66

>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 = 59.0 bits (143), Expect = 4e-13
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 6  CTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
          C +C +     E ++   + FH  CF C VC+ +L        D   YC S Y KK+G K
Sbjct: 10 CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPK 69

Query: 65 CAQCGE 70
              G+
Sbjct: 70 GYGYGQ 75

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

 Score = 37.4 bits (87), Expect = 9e-05
 Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 62  GTKCAQCGEYV-EGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           G KC  CG  V   E V   G+++H+ CF C  CR +             Y
Sbjct: 7   GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVY 57

>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 = 58.2 bits (141), Expect = 6e-13
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 6  CTSCKK--KCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
          C  CKK        +  +   +H TCF C  C+  +    +  KD   +C   Y+K+  +
Sbjct: 8  CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHAS 67

Query: 64 KCA 66
            +
Sbjct: 68 GPS 70

>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 = 40.1 bits (94), Expect = 7e-06
 Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 60 KFGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCR 95
             + C +C + +      +   G ++H+ CF C RC+
Sbjct: 3  SGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQ 40

>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 = 57.6 bits (139), Expect = 2e-12
 Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 6  CTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
          C  C+K     E L    + FHI+CF+CS C N L+ G Y +  G  YC   + + F +K
Sbjct: 18 CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77

Query: 65 CAQCG 69
               
Sbjct: 78 GNYDE 82

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

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)

Query: 64 KCAQCGEYV-EGEVVTALGKTYHQKCFTCARCR 95
           C +C + V   E + A  + +H  CF C+ C 
Sbjct: 17 TCVECQKTVYPMERLLANQQVFHISCFRCSYCN 49

>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 = 58.2 bits (140), Expect = 2e-12
 Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 6   CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFG 62
           C  C  K     +L   D Y+H  C +CS C+  L   G   + K G   C +DY + FG
Sbjct: 64  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 123

>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 = 37.8 bits (87), Expect = 1e-04
 Identities = 9/45 (20%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 52 YCTSDYQKKFGTKCAQCGEYV-EGEVVTALGKTYHQKCFTCARCR 95
                      +CA CG  + +  ++ A+   +H +C  C+ C+
Sbjct: 51 GGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQ 95

>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 = 55.5 bits (134), Expect = 8e-12
 Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 3/66 (4%)

Query: 6  CTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
          C  C +   G+   +   D+ FH+ CF CS C+  L    ++  +   YC   Y      
Sbjct: 8  CGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL-E 66

Query: 64 KCAQCG 69
               G
Sbjct: 67 SGPSSG 72

>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 = 38.2 bits (89), Expect = 3e-05
 Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 64 KCAQCGEYVEGE--VVTALGKTYHQKCFTCARCR 95
           C  CGE V G+   V AL + +H  CF C+ CR
Sbjct: 7  GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCR 40

>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 = 57.3 bits (138), Expect = 2e-11
 Identities = 34/140 (24%), Positives = 46/140 (32%), Gaps = 50/140 (35%)

Query: 6   CTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK 64
           C  C+K     E ++ +   FH +CF C VCK +L            YC S Y KK+G K
Sbjct: 10  CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK 69

Query: 65  CAQ------------------------------------------------CGEYV-EGE 75
                                                              CG+ V   E
Sbjct: 70  GKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAE 129

Query: 76  VVTALGKTYHQKCFTCARCR 95
            V   GK++H+ CF CA+C 
Sbjct: 130 KVIGAGKSWHKSCFRCAKCG 149

>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 = 56.2 bits (135), Expect = 4e-11
 Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 5   YCTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
            C  C +   + E +    K +H +CF+C+ C  SL      +KDG  YC   Y K FG 
Sbjct: 117 GCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGP 176

Query: 64  KCAQCGE 70
           K    G+
Sbjct: 177 KGFGFGQ 183

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

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 62  GTKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAY 111
           G KC  C + V   E V   G ++H+ CF C  C+ +         G   Y
Sbjct: 7   GKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIY 57

>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 = 55.1 bits (132), Expect = 3e-11
 Identities = 17/97 (17%), Positives = 29/97 (29%), Gaps = 7/97 (7%)

Query: 6   CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFG 62
           C  C++       L+  D+Y+H  C  C +C   L + G   + K G   C  DY +  G
Sbjct: 6   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG 65

Query: 63  TKCAQCGEYVEGE----VVTALGKTYHQKCFTCARCR 95
           +                 +         +        
Sbjct: 66  SGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLEN 102

>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 = 54.3 bits (131), Expect = 3e-11
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 6  CTSCKK--KCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT 63
          C  C K      + +  +   +H  CF CS CK  +  G +F K   +YC + ++ KF +
Sbjct: 18 CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAS 77

Query: 64 KCA 66
            +
Sbjct: 78 GPS 80

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

 Score = 50.1 bits (120), Expect = 1e-09
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 49 GAYYCTSDYQKKFGTKCAQCGEYVEG--EVVTALGKTYHQKCFTCARCR 95
           +        ++   KC  C + +    + V   G  +H+ CFTC+ C+
Sbjct: 2  SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCK 50

>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 = 53.3 bits (128), Expect = 5e-11
 Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 4/66 (6%)

Query: 5  YCTSCKKKCSG----EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
           C  C    SG    + +  +++ +H  CF C  C  SL   G+  +     C    +  
Sbjct: 7  GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 61 FGTKCA 66
           G    
Sbjct: 67 SGPSSG 72

>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 = 38.3 bits (89), Expect = 3e-05
 Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 4/40 (10%)

Query: 60 KFGTKCAQCGEYVEG----EVVTALGKTYHQKCFTCARCR 95
             + CA C   + G    + ++   + +H  CF C +C 
Sbjct: 3  SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCS 42

>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 = 53.4 bits (128), Expect = 1e-10
 Identities = 25/85 (29%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 6  CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGG--YFNKDGAYYCTSDYQKKFG 62
          C  C  K     +L   D Y+H  C +CS C+  L   G   + K G   C +DY + FG
Sbjct: 8  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67

Query: 63 TKCA--QCGEYVEGEVVTALGKTYH 85
             A    G    G  V  +G+   
Sbjct: 68 NSGAGGSGGHMGSGGDVMVVGEPTL 92

>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 = 50.4 bits (121), Expect = 8e-10
 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 6  CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSD-YQKKFGT 63
          C  C K+    E +    K +H  C +C  C  +L  GG+   +G  YC    Y   FG 
Sbjct: 3  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62

Query: 64 KCAQCGE 70
          K    G 
Sbjct: 63 KGFGRGG 69

>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 = 37.3 bits (87), Expect = 8e-05
 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 64 KCAQCGEYV-EGEVVTALGKTYHQKCFTCARCR 95
          KC +C + V   E VT+LGK +H+ C  C +C 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCG 34

>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 = 50.2 bits (120), Expect = 1e-09
 Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 4/69 (5%)

Query: 5  YCTSCKKKCSG----EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
           C +C K  SG    + +  QD  +H  CF C  C  SL   G+  ++   +C       
Sbjct: 7  GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 61 FGTKCAQCG 69
                   
Sbjct: 67 DTDISGPSS 75

>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 = 39.5 bits (92), Expect = 2e-05
 Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 4/40 (10%)

Query: 60 KFGTKCAQCGEYVEG----EVVTALGKTYHQKCFTCARCR 95
             + C  C + + G    + +      +H +CF C +C 
Sbjct: 3  SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCS 42

>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 = 49.7 bits (119), Expect = 2e-09
 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 3/68 (4%)

Query: 1  MIKAYCTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58
          +  A C  CK     + +++    + +H  CF C+ C     +G ++  +G  YC  D+Q
Sbjct: 9  LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQ 68

Query: 59 KKFGTKCA 66
            F   C 
Sbjct: 69 MLFA-PCW 75

>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 = 43.5 bits (103), Expect = 3e-07
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 53 CTSDYQKKFGTKCAQCGE--YVEGEVVTALGKTYHQKCFTCARCR 95
                      C +C        ++V + G+ YH++CF CA+C 
Sbjct: 2  SEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCF 46

>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 = 48.9 bits (117), Expect = 3e-09
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 6  CTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG 62
          C  CK     + +++    + +H  CF C+ C     +G ++  +G  YC  D+Q  F 
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72

>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 = 45.5 bits (108), Expect = 7e-08
 Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 56 DYQKKFGTKCAQCGE--YVEGEVVTALGKTYHQKCFTCARCR 95
           +Q      C +C        ++V + G+ YH++CF CA+C 
Sbjct: 5  YFQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCF 46

>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 = 48.2 bits (115), Expect = 6e-09
 Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 5/49 (10%)

Query: 52 YCTSDYQKKFGTKCAQCGEYVEG-----EVVTALGKTYHQKCFTCARCR 95
               Y+     KCA C   + G      VV   G+++H  CF C +C 
Sbjct: 5  SSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCS 53

>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 = 41.7 bits (98), Expect = 2e-06
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 5/60 (8%)

Query: 5  YCTSCKKKCSG-----EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQK 59
           C  CK   +G      V+  + + +H  CF C  C  +LA   +       YC    +K
Sbjct: 17 KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

>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 = 47.0 bits (112), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 6  CTSCKKK-CSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSD-YQKKFGT 63
          C  C K     E +    K +H  C +C  C  +L  GG+   DG  +C    Y   FG+
Sbjct: 12 CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGS 71

Query: 64 KC 65
            
Sbjct: 72 GP 73

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

 Score = 37.4 bits (87), Expect = 7e-05
 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 64 KCAQCGEYV-EGEVVTALGKTYHQKCFTCARCR 95
          KC +C + V   E V++LGK +H+ C  C RC 
Sbjct: 11 KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCS 43

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

 Score = 43.9 bits (103), Expect = 3e-07
 Identities = 13/37 (35%), Positives = 17/37 (45%)

Query: 59 KKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
              + C  C +Y+ G V+ A  K YH  C  C RC 
Sbjct: 2  SSGSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCG 38

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

 Score = 38.9 bits (90), Expect = 2e-05
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQG-GYFNKDGAYYCTSDYQKK 60
          C SC+K  +G VL   +K++H +C  C  C    A+G   + +  + +  +  Q  
Sbjct: 8  CDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAA 63

>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 = 43.2 bits (102), Expect = 5e-07
 Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 1/61 (1%)

Query: 6  CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC 65
          C  C      + L  ++  +H   F C+ C   L         G  YC   + K   +  
Sbjct: 18 CQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKEL-TADARELKGELYCLPCHDKMGVSGP 76

Query: 66 A 66
          +
Sbjct: 77 S 77

>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 = 40.2 bits (94), Expect = 9e-06
 Identities = 8/31 (25%), Positives = 13/31 (41%)

Query: 65 CAQCGEYVEGEVVTALGKTYHQKCFTCARCR 95
          C +C   ++ + +      YH   F CA C 
Sbjct: 18 CQKCHAIIDEQPLIFKNDPYHPDHFNCANCG 48

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

 Score = 43.4 bits (102), Expect = 6e-07
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 6  CTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGY--FNKDGAYYCTSDYQK 59
          C  C +     E L V   +FH +CF+C  C+ +L  GGY     DG +YC     +
Sbjct: 18 CALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ 74

>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 = 35.3 bits (81), Expect = 5e-04
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)

Query: 62 GTKCAQCGEYV-EGEVVTALGKTYHQKCFTCARCR 95
          G  CA CGE++   E +   G  +H+ CF C  C 
Sbjct: 15 GDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCE 49

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens} Length = 65

 Score = 34.4 bits (79), Expect = 9e-04
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 5  YCTSCKKKCSGEVLRV--QDKYFHIT--CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60
           C  C      EV RV   +  +H +  CF CS C   L    +   +G  +C+ + +K+
Sbjct: 4  VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR 63

Query: 61 F 61
           
Sbjct: 64 M 64

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	100.0
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	100.0
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	100.0
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.98
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.97
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.97
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.96
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.93
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.89
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.87
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.86
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.85
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.85
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.84
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.83
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.81
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.81
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.8
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.79
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.78
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.77
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.77
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.77
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.77
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.76
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.76
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.76
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.76
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.75
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.74
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.74
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.74
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.73
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.73
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.73
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.73
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.72
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.72
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.72
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.71
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.71
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.71
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.71
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.71
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.71
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.7
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.7
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.7
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.7
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.69
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.68
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.68
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.68
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.67
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.67
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.66
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.66
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	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
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.66
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.65
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.65
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.65
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.65
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.65
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.64
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.64
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.63
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.63
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.62
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.62
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.61
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.6
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.59
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.59
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.58
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.58
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.54
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.51
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.5
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.48
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.45
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.39
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.11
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.03
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	94.22
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	90.21
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	88.71
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	88.6
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	87.77
1jjd_A	55	Metallothionein, SMTA; zinc finger, zinc cluster,	85.48
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	85.46
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	83.78
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	83.45
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	81.76
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	81.58
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	81.48
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	81.4
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	81.32
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	81.09
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	80.72
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	80.63
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	80.45
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	80.39

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

Probab=100.00  E-value=9.8e-36  Score=187.63  Aligned_cols=119  Identities=20%  Similarity=0.396  Sum_probs=111.2

Q ss_pred             CCccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc--CcEEE
Q psy17880          2 IKAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE--GEVVT   78 (120)
Q Consensus         2 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~--~~~~~   78 (120)
                      ..++|.+|+++|. ++++.++|+.||++||+|+.|+++|.+..|+.+++++||+.||.++++++|..|+++|.  +.+|+
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~   81 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVT   81 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSCEEE
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCceEEE
Confidence            4689999999997 56899999999999999999999999888999999999999999999999999999997  46899


Q ss_pred             EeCcccc--ccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         79 ALGKTYH--QKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        79 ~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +.++.||  ++||+|..|+++|.++.|+..||++||+.++.+.|
T Consensus        82 a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           82 YNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             ETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             CCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence            9999999  99999999999999889999999999998776665

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

Probab=100.00  E-value=6.4e-35  Score=184.96  Aligned_cols=118  Identities=25%  Similarity=0.545  Sum_probs=108.1

Q ss_pred             CCccccccccccccc-eEEECCcccccccccccccccccCC--CCeeecCCeeccHhHHHhHhCC--CCCCCCCcccC--
Q psy17880          2 IKAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQ--GGYFNKDGAYYCTSDYQKKFGT--KCAQCGEYVEG--   74 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~~~~--~C~~C~~~i~~--   74 (120)
                      ++++|.+|+++|.+. ++.++++.||++||+|+.|+++|..  ..|+.+++++||+.||.+++++  +|..|+++|.+  
T Consensus         1 s~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e   80 (131)
T 2xjy_A            1 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYE   80 (131)
T ss_dssp             CCCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTS
T ss_pred             CcccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccc
Confidence            468999999999877 6899999999999999999999963  5799999999999999999999  99999999975  


Q ss_pred             cEEEEeCccccccccccccCCCcCC-CCceeeeCCeeeeccCCCcC
Q psy17880         75 EVVTALGKTYHQKCFTCARCRFSKK-REIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        75 ~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~~~~~~  119 (120)
                      .+|.+.++.||++||+|..|+++|+ +..|+..||++||+.++.+.
T Consensus        81 ~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~  126 (131)
T 2xjy_A           81 MTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEW  126 (131)
T ss_dssp             EEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHH
T ss_pred             eeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHH
Confidence            5889999999999999999999995 66799999999999998654

>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=100.00  E-value=8.8e-33  Score=184.78  Aligned_cols=119  Identities=30%  Similarity=0.715  Sum_probs=108.7

Q ss_pred             CCccccccccccccc-eEEECCcccccccccccccccccCC--CCeeecCCeeccHhHHHhHhCC--CCCCCCCcccC--
Q psy17880          2 IKAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQ--GGYFNKDGAYYCTSDYQKKFGT--KCAQCGEYVEG--   74 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~~~~--~C~~C~~~i~~--   74 (120)
                      ..++|.+|+++|.+. ++.++++.||++||+|..|+++|..  ..|+.+++++||+.||.+++++  +|..|+++|.+  
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e   83 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASE   83 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTS
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCc
Confidence            468999999999877 6889999999999999999999985  5799999999999999999998  79999999974  


Q ss_pred             cEEEEeCccccccccccccCCCcCC-CCceeeeCCeeeeccCCCcCC
Q psy17880         75 EVVTALGKTYHQKCFTCARCRFSKK-REIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        75 ~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .+|.+.++.||++||+|..|+++|. +..|+..+|++||+.++.+.|
T Consensus        84 ~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~  130 (188)
T 1rut_X           84 LVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTAL  130 (188)
T ss_dssp             EEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTT
T ss_pred             EEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHh
Confidence            4789999999999999999999996 567999999999999997764

>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=99.98  E-value=1.2e-32  Score=184.68  Aligned_cols=118  Identities=32%  Similarity=0.663  Sum_probs=108.6

Q ss_pred             Cccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCC-----------------
Q psy17880          3 KAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK-----------------   64 (120)
Q Consensus         3 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~-----------------   64 (120)
                      .++|.+|+++|. ++.+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++                 
T Consensus         7 ~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~~~~~~   86 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTDKGE   86 (192)
T ss_dssp             CEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCCCCCC
T ss_pred             CCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccEecCCCc
Confidence            468999999995 77888999999999999999999999888999999999999999999876                 


Q ss_pred             -------------------------------CCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeee
Q psy17880         65 -------------------------------CAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYE  112 (120)
Q Consensus        65 -------------------------------C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC  112 (120)
                                                     |..|+++|. ++.|.+.++.||++||+|+.|+++|.++.|+..||++||
T Consensus        87 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC  166 (192)
T 1b8t_A           87 SLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYC  166 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEE
T ss_pred             ccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeC
Confidence                                           778999996 578889999999999999999999998899999999999


Q ss_pred             ccCCCcCC
Q psy17880        113 NRLGGRAY  120 (120)
Q Consensus       113 ~~~~~~~~  120 (120)
                      +.++.+.|
T Consensus       167 ~~cy~~~f  174 (192)
T 1b8t_A          167 KGCYAKNF  174 (192)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhc
Confidence            99986654

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

Probab=99.97  E-value=8.6e-32  Score=177.27  Aligned_cols=116  Identities=28%  Similarity=0.586  Sum_probs=101.9

Q ss_pred             CCccccccccccccc-eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC-c-EEE
Q psy17880          2 IKAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG-E-VVT   78 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~-~-~~~   78 (120)
                      ..++|.+|+++|.+. ++.++|+.||++||+|..|+++|.+.. +.++|++||+.||.++++++|..|+++|.+ + ++.
T Consensus         5 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~v~~   83 (169)
T 2rgt_A            5 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRR   83 (169)
T ss_dssp             --CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCTTSEEEE
T ss_pred             CCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeecccccccccccccccccccCCCcEEEE
Confidence            357899999999766 688999999999999999999998865 689999999999999999999999999975 3 668


Q ss_pred             EeCccccccccccccCCCcCCC-Ccee-eeCCeeeeccCCCc
Q psy17880         79 ALGKTYHQKCFTCARCRFSKKR-EIYN-WLGGRAYENRLGGR  118 (120)
Q Consensus        79 ~~~~~~H~~Cf~C~~C~~~l~~-~~~~-~~~g~~yC~~~~~~  118 (120)
                      +.++.||++||+|..|+++|.. +.|+ ..||++||+.++.+
T Consensus        84 a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~  125 (169)
T 2rgt_A           84 AQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET  125 (169)
T ss_dssp             ETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHH
T ss_pred             cCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHH
Confidence            9999999999999999999974 4565 45899999988754

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

Probab=99.97  E-value=3.3e-31  Score=176.31  Aligned_cols=115  Identities=28%  Similarity=0.589  Sum_probs=102.3

Q ss_pred             Cccccccccccccc-eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC--cEEEE
Q psy17880          3 KAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG--EVVTA   79 (120)
Q Consensus         3 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~--~~~~~   79 (120)
                      .++|.+|+++|.+. ++.++++.||++||+|..|+++|.+.. +.+++++||+.||.++++++|..|+++|.+  .++.+
T Consensus        60 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~~v~~a  138 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRA  138 (182)
T ss_dssp             CCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCC-EEETTEEECHHHHHHTTSCCCTTTCCCCCSSCCCCEE
T ss_pred             CCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCc-eeECCEeeecCccccccccccccCCCccCCCceEEec
Confidence            57899999999876 678999999999999999999998865 579999999999999999999999999975  36789


Q ss_pred             eCccccccccccccCCCcCCC-Ccee-eeCCeeeeccCCCc
Q psy17880         80 LGKTYHQKCFTCARCRFSKKR-EIYN-WLGGRAYENRLGGR  118 (120)
Q Consensus        80 ~~~~~H~~Cf~C~~C~~~l~~-~~~~-~~~g~~yC~~~~~~  118 (120)
                      .++.||++||+|..|+++|.. ..|+ ..||++||+.++.+
T Consensus       139 ~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~  179 (182)
T 2jtn_A          139 QDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET  179 (182)
T ss_dssp             TTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHH
T ss_pred             CCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHH
Confidence            999999999999999999975 4565 45899999988753

>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=99.96  E-value=1.2e-29  Score=154.07  Aligned_cols=94  Identities=23%  Similarity=0.574  Sum_probs=87.9

Q ss_pred             CCccccccccccc--cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc--CcEE
Q psy17880          2 IKAYCTSCKKKCS--GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE--GEVV   77 (120)
Q Consensus         2 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~--~~~~   77 (120)
                      ..++|.+|+++|.  ++++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|..|+++|.  +.+|
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~   83 (101)
T 2cup_A            4 GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNV   83 (101)
T ss_dssp             CCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSSCEE
T ss_pred             CCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCCeEE
Confidence            3578999999995  67899999999999999999999998878999999999999999999999999999997  4689


Q ss_pred             EEeCccccccccccccCC
Q psy17880         78 TALGKTYHQKCFTCARCR   95 (120)
Q Consensus        78 ~~~~~~~H~~Cf~C~~C~   95 (120)
                      ++.++.||++||+|..|+
T Consensus        84 ~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           84 EYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             ESSSCEEETTTCCCTTCC
T ss_pred             EeCCcchHHhCCCCCCCC
Confidence            999999999999999985

>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=99.93  E-value=9.9e-27  Score=145.75  Aligned_cols=106  Identities=23%  Similarity=0.417  Sum_probs=93.5

Q ss_pred             CCccccccccccccc-eEEECCcccccccccccccccccCC--CCeeecCCeeccHhHHHhHhCC--CCCCCCCcccCcE
Q psy17880          2 IKAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQ--GGYFNKDGAYYCTSDYQKKFGT--KCAQCGEYVEGEV   76 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~~~~--~C~~C~~~i~~~~   76 (120)
                      ..++|.+|+++|.+. ++.++++.||++||+|+.|+++|.+  ..|+.+++++||..||.+++++  +|+.|+++|.+..
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~   83 (122)
T 1m3v_A            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGD   83 (122)
T ss_dssp             CCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEE
T ss_pred             CCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchh
Confidence            467999999999876 5899999999999999999999973  5799999999999999999999  9999999998766


Q ss_pred             EEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         77 VTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        77 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |++.++             .+|.++.|+..||+|||..++.+.+
T Consensus        84 ~~~~g~-------------~~l~g~~f~~~~~~~yC~~~~~~~~  114 (122)
T 1m3v_A           84 VMVVGE-------------PTLMGGEFGDEDERLITRLENTQFD  114 (122)
T ss_dssp             SSSSSS-------------SSCCSCTTCCTTCCCCEECTTTTTT
T ss_pred             eEEcCC-------------cCCCCCccEecCCEeEccCcchhch
Confidence            655553             3678889999999999999997753

>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=99.89  E-value=8.7e-24  Score=130.89  Aligned_cols=100  Identities=19%  Similarity=0.351  Sum_probs=85.2

Q ss_pred             CCccccccccccccc-eEEECCcccccccccccccccccCC--CCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEE
Q psy17880          2 IKAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQ--GGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVT   78 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~   78 (120)
                      +.++|.+|+++|.+. ++.++++.||++||+|+.|+++|.+  ..|+.+++++||+.||.++|+++|..|..   +.+|+
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~---~~~~~   78 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSG---GDVMV   78 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBS---CSCCC
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCC---CceeE
Confidence            467899999999877 7899999999999999999999975  57999999999999999999999988862   33332


Q ss_pred             EeCccccccccccccCCCc-CCCCceeeeCCeeeeccCCCcC
Q psy17880         79 ALGKTYHQKCFTCARCRFS-KKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        79 ~~~~~~H~~Cf~C~~C~~~-l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                                     |..+ |.++.|+..|+++||..++.++
T Consensus        79 ---------------~~~~~~~g~~f~~~~~~~~C~~~~~~~  105 (114)
T 1j2o_A           79 ---------------VGEPTLMGGEFGDEDERLITRLENTQF  105 (114)
T ss_dssp             ---------------SSCSSTTSSBCCCSSSCCCEEEECTTC
T ss_pred             ---------------cCCccCCCCeeEEcCCEeecchhhhcc
Confidence                           3344 5677899999999999998765

>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=99.87  E-value=3.6e-23  Score=121.06  Aligned_cols=73  Identities=21%  Similarity=0.438  Sum_probs=68.6

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCccc--CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +|++||+.||.++++++|+.|+++|.  +.+|.+.++.||++||+|+.|+++|.++.|+..+|++||+.++.+.|
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~   75 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF   75 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCG
T ss_pred             CCceechhHhCcccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhc
Confidence            57899999999999999999999997  67889999999999999999999999889999999999999998765

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

Probab=99.86  E-value=2.8e-23  Score=120.97  Aligned_cols=73  Identities=19%  Similarity=0.424  Sum_probs=68.4

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +|++||++||.++++++|..|+++|.++.|.+.++.||++||+|+.|+++|.++.|+..||++||+.++.+.|
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f   73 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELF   73 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHT
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecCcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHc
Confidence            5789999999999999999999999888999999999999999999999999889999999999999886654

>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=99.85  E-value=3.6e-23  Score=120.51  Aligned_cols=72  Identities=22%  Similarity=0.422  Sum_probs=67.6

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      ++++||++||.++++++|+.|+++|.++.|.+.++.||++||+|+.|+++|.++.|+..||++||+.++.+.
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~   72 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHR   72 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHH
T ss_pred             CCCccchhHHhhhcCCccccCCCeecceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHH
Confidence            478999999999999999999999999999999999999999999999999988999999999999987654

>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=99.85  E-value=1e-22  Score=117.73  Aligned_cols=71  Identities=21%  Similarity=0.489  Sum_probs=66.2

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCcccC-----cEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVEG-----EVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~~-----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      ++++||++||.++++++|++|+++|.+     ++|.+.++.||++||+|+.|+++|.++.|+..+|++||+.++.+
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            468999999999999999999999986     78999999999999999999999999899999999999988643

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

Probab=99.84  E-value=1.5e-22  Score=118.35  Aligned_cols=73  Identities=18%  Similarity=0.306  Sum_probs=67.5

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCccc--CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++.+||++||.++++++|..|+++|.  +.+|.+.++.||++||+|..|+++|..+.|+..+|++||+.++.+.|
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f   75 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF   75 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHT
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHh
Confidence            46899999999999999999999997  56899999999999999999999999999999999999999886654

>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=99.83  E-value=2.7e-22  Score=117.11  Aligned_cols=72  Identities=22%  Similarity=0.350  Sum_probs=66.1

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeee-CCeeeeccCCCcCC
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWL-GGRAYENRLGGRAY  120 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~g~~yC~~~~~~~~  120 (120)
                      ++++||++||. +++++|+.|+++|.+++|.+.++.||++||+|+.|+++|.+..|... ||++||+.++.+.|
T Consensus         2 ~g~~yC~~~y~-~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f   74 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKF   74 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBCTTTCCBCCSCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHT
T ss_pred             cCCEECHHHhh-cCCCccccCCCeecceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHh
Confidence            57999999999 78899999999999999999999999999999999999998888876 79999999887654

>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=99.81  E-value=5.8e-22  Score=115.65  Aligned_cols=72  Identities=24%  Similarity=0.480  Sum_probs=65.0

Q ss_pred             CCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCC-Ccee-eeCCeeeeccCCCcC
Q psy17880         48 DGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKR-EIYN-WLGGRAYENRLGGRA  119 (120)
Q Consensus        48 ~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~-~~~g~~yC~~~~~~~  119 (120)
                      ++.+||+.||.++++++|..|+++|.+++|.+.++.||++||+|..|+++|.. ..|. ..+|++||+.++.+.
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~   74 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   74 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcCceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHH
Confidence            36799999999999999999999999989999999999999999999999975 5677 489999999987654

>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=99.81  E-value=4.1e-20  Score=106.52  Aligned_cols=70  Identities=29%  Similarity=0.602  Sum_probs=65.5

Q ss_pred             ccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccH-hHHHhHhCCCCCCCCCccc
Q psy17880          4 AYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCT-SDYQKKFGTKCAQCGEYVE   73 (120)
Q Consensus         4 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~-~c~~~~~~~~C~~C~~~i~   73 (120)
                      ++|.+|+++|. ++.+.++++.||++||+|..|+++|.++.|+.+++++||. .||.++++++|..|++++.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~~~~   72 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCcee
Confidence            58999999996 8889999999999999999999999988899999999999 6999999999999998764

>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=99.80  E-value=1.2e-20  Score=110.07  Aligned_cols=71  Identities=37%  Similarity=0.690  Sum_probs=63.3

Q ss_pred             CeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCC-eeeeccCCCcC
Q psy17880         49 GAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGG-RAYENRLGGRA  119 (120)
Q Consensus        49 ~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g-~~yC~~~~~~~  119 (120)
                      +.+||+.||.++++++|+.|+++|.+++|.+.++.||++||+|..|+++|..+.++..++ .+||+.++.+.
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~   73 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPV   73 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCC
T ss_pred             CCCcchHHHHhHhCCcCccccCEeccceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhccc
Confidence            578999999999999999999999999999999999999999999999998776555555 57999988654

>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=99.79  E-value=2.2e-19  Score=101.60  Aligned_cols=66  Identities=24%  Similarity=0.553  Sum_probs=61.8

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.++.+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|++
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A            4 GSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             CCCCCSSSCCCCCTTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCCC
T ss_pred             CcCCCcccCCEeCcceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCCC
Confidence            457899999999988999999999999999999999998888999999999999999999999974

>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=99.78  E-value=3.1e-19  Score=101.25  Aligned_cols=66  Identities=20%  Similarity=0.513  Sum_probs=61.7

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.++.+.++++.||++||+|..|+++|.+..|+.+++++||..||.++++++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            4 GSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CCCBCSSSCCBCCSSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCCCcccCCeeccceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            357899999999988999999999999999999999998888999999999999999999999863

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

Probab=99.77  E-value=6e-19  Score=104.76  Aligned_cols=66  Identities=30%  Similarity=0.620  Sum_probs=61.8

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.++++.++++.||++||+|..|+++|.+..|+.+++++||..||.++++++|+.
T Consensus        24 ~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           24 RTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             CCCBBSSSCCBCCSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCCccCCCEecceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            356899999999999999999999999999999999999888999999999999999999999963

>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=99.77  E-value=1.9e-19  Score=103.76  Aligned_cols=68  Identities=24%  Similarity=0.502  Sum_probs=63.5

Q ss_pred             CCcccccccccccc----ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCC
Q psy17880          2 IKAYCTSCKKKCSG----EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCG   69 (120)
Q Consensus         2 ~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~   69 (120)
                      ..++|.+|+++|.+    +++.++++.||++||+|+.|+++|.+..|+.+++++||..||.++++++|+.++
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             cCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            35789999999987    799999999999999999999999988899999999999999999999998775

>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=99.77  E-value=6.1e-19  Score=101.61  Aligned_cols=62  Identities=16%  Similarity=0.433  Sum_probs=57.7

Q ss_pred             hHhCCCCCCCCCcccC----cEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         59 KKFGTKCAQCGEYVEG----EVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        59 ~~~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++++++|..|+++|.+    ++|.+.++.||++||+|+.|+++|.+..|+..||++||+.++.+.|
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f   67 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMD   67 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCC
T ss_pred             CccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhh
Confidence            3567999999999986    8999999999999999999999999889999999999999998876

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

Probab=99.77  E-value=2.7e-19  Score=104.29  Aligned_cols=70  Identities=30%  Similarity=0.620  Sum_probs=56.2

Q ss_pred             Ccccccccccc-ccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcc
Q psy17880          3 KAYCTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYV   72 (120)
Q Consensus         3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i   72 (120)
                      .++|.+|+++| .++.+.+.++.||++||+|+.|+++|....|+.+++++||+.||.++++++|..|++..
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----------
T ss_pred             CCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            57899999999 57789999999999999999999999988899999999999999999999999998653

>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=99.76  E-value=1e-18  Score=101.48  Aligned_cols=66  Identities=26%  Similarity=0.654  Sum_probs=61.8

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|++|+++|.++.|.++++.||++||+|+.|+++|.++.|+.+++++||+.||.++++++|+.
T Consensus        14 ~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           14 FSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CSCBCTTTCCBCCSSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             cCCccccCCCeecceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            357899999999999999999999999999999999998888999999999999999999999974

>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=99.76  E-value=9.6e-19  Score=99.67  Aligned_cols=66  Identities=26%  Similarity=0.597  Sum_probs=61.1

Q ss_pred             CCccccccccccc--cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCS--GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.  ++++.+.++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            4578999999997  57899999999999999999999999888999999999999999999999963

>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=99.76  E-value=7.3e-19  Score=98.63  Aligned_cols=63  Identities=24%  Similarity=0.654  Sum_probs=58.9

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK   64 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~   64 (120)
                      ..++|.+|+++|.++++.+.++.||++||+|+.|+++|.++.|+.+++++||+.||.++++++
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            4 GVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCCEETTTTEECCSCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCCCcccCCEecceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            467899999999988999999999999999999999999888999999999999999998764

>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=99.76  E-value=1.5e-18  Score=98.87  Aligned_cols=66  Identities=23%  Similarity=0.558  Sum_probs=60.8

Q ss_pred             CCccccccccccc--cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCS--GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.  +.++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            3578999999997  45899999999999999999999999888999999999999999999999973

>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=1.5e-18  Score=99.96  Aligned_cols=66  Identities=27%  Similarity=0.635  Sum_probs=61.0

Q ss_pred             CCccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccH-hHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCT-SDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~-~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|. ++.+.++++.||++||+|..|+++|.+..|+.+++++||. .||.++++++|.+
T Consensus         8 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            8 MASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             CCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            4578999999997 7889999999999999999999999988899999999999 7999999999863

>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=99.74  E-value=2.3e-18  Score=100.28  Aligned_cols=66  Identities=24%  Similarity=0.568  Sum_probs=60.2

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeec-CCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNK-DGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.++++.++++.||++||+|+.|+++|.+..|+.. ++++||+.||.++++++|++
T Consensus        14 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           14 TLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             SCCBCTTTCCBCCSCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CCCccccCCCeecceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            3578999999999999999999999999999999999987777765 78999999999999999974

>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=99.74  E-value=2.4e-18  Score=99.90  Aligned_cols=65  Identities=22%  Similarity=0.536  Sum_probs=61.1

Q ss_pred             CccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      .++|.+|+++|.++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++|+.
T Consensus        15 ~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           15 APRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             SCCCTTTCCCCCSCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CCcCCCCCCEecCcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            57899999999888999999999999999999999998878999999999999999999999863

>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=2.3e-18  Score=100.15  Aligned_cols=64  Identities=38%  Similarity=0.867  Sum_probs=59.2

Q ss_pred             Cccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          3 KAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         3 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      .++|.+|+++|. ++.+.++++.||++||+|..|+++|.+ .|+.+++++||+.||.++|+++|+.
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            568999999995 778999999999999999999999986 6999999999999999999999974

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

Probab=99.73  E-value=6.5e-18  Score=95.74  Aligned_cols=63  Identities=22%  Similarity=0.576  Sum_probs=59.0

Q ss_pred             CccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCC
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC   65 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C   65 (120)
                      .++|.+|+++|.++++.++++.||++||+|..|+++|.+..|+.+++++||..||.+++++..
T Consensus         5 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   67 (70)
T 2d8x_A            5 SSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGP   67 (70)
T ss_dssp             SSBCSSSCCBCCSCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCS
T ss_pred             CCcCccCCCEecceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCC
Confidence            568999999999999999999999999999999999998888899999999999999998764

>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=99.73  E-value=2.5e-19  Score=100.57  Aligned_cols=61  Identities=28%  Similarity=0.424  Sum_probs=56.3

Q ss_pred             HhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         60 KFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        60 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +++++|+.|+++|.+++|.+.++.||++||+|+.|+++|.++.|+..||++||+.++.+.|
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f   63 (66)
T 1nyp_A            3 MGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF   63 (66)
T ss_dssp             CCCCEETTTTEECCSCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHC
T ss_pred             cCCCCCcccCCEecceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHh
Confidence            3568999999999988999999999999999999999999999999999999999987654

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

Probab=99.73  E-value=3.1e-18  Score=98.74  Aligned_cols=65  Identities=25%  Similarity=0.655  Sum_probs=58.4

Q ss_pred             CCccccccccccc--cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCC
Q psy17880          2 IKAYCTSCKKKCS--GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCA   66 (120)
Q Consensus         2 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~   66 (120)
                      ..++|.+|+++|.  +.++.+.++.||++||+|..|+++|.++.|+.+++++||+.||.++++++|+
T Consensus        10 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A           10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            4578999999995  5678899999999999999999999988899999999999999999999986

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

Probab=99.73  E-value=2.8e-18  Score=97.80  Aligned_cols=63  Identities=22%  Similarity=0.579  Sum_probs=58.3

Q ss_pred             Ccccccccccccc----ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCC
Q psy17880          3 KAYCTSCKKKCSG----EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKC   65 (120)
Q Consensus         3 ~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C   65 (120)
                      .++|.+|+++|.+    +++.++++.||++||+|..|+++|.+..|+.+++++||..||.++++|++
T Consensus         5 ~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            5 SSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             SCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            5789999999986    68899999999999999999999998889999999999999999998865

>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=99.72  E-value=6.9e-18  Score=99.93  Aligned_cols=64  Identities=31%  Similarity=0.719  Sum_probs=60.1

Q ss_pred             CccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCC
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCA   66 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~   66 (120)
                      .++|.+|+++|.++++.++++.||++||+|..|+++|.+..|+.+++++||+.||.+++++++.
T Consensus        25 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           25 MPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CCCcccCCCEecccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4689999999999999999999999999999999999888899999999999999999998875

>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=99.72  E-value=1.1e-18  Score=99.79  Aligned_cols=60  Identities=27%  Similarity=0.479  Sum_probs=54.8

Q ss_pred             HhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCC-CCceeeeCCeeeeccCCCcC
Q psy17880         60 KFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKK-REIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        60 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~~~~~~  119 (120)
                      +++++|+.|+++|.+++|.+.++.||++||+|+.|+++|. +..|+..+|++||+.++...
T Consensus         3 ~~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~   63 (73)
T 1wig_A            3 SGSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAA   63 (73)
T ss_dssp             CSCCSCSSSCCCCSSCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHT
T ss_pred             cCcCCcccCCCEecCeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHh
Confidence            4678999999999999999999999999999999999998 67899999999999987554

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

Probab=99.72  E-value=3.5e-18  Score=99.11  Aligned_cols=64  Identities=22%  Similarity=0.565  Sum_probs=59.7

Q ss_pred             CccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCC
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCA   66 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~   66 (120)
                      .++|.+|+++|.++++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++++++..
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCccccCCCCccCcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4689999999998999999999999999999999999877899999999999999999998764

>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=99.71  E-value=2.4e-18  Score=97.98  Aligned_cols=61  Identities=15%  Similarity=0.353  Sum_probs=55.5

Q ss_pred             HhCCCCCCCCCccc--CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         60 KFGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        60 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +++++|..|+++|.  +.+|.+.++.||++||+|..|+++|.++.|+..||++||+.++.+.|
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f   65 (72)
T 1x4k_A            3 SGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH   65 (72)
T ss_dssp             SCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHT
T ss_pred             ccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHh
Confidence            46789999999997  46899999999999999999999999999999999999999886654

>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=99.71  E-value=2.7e-18  Score=100.16  Aligned_cols=65  Identities=26%  Similarity=0.586  Sum_probs=60.2

Q ss_pred             Cccccccccccc--cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          3 KAYCTSCKKKCS--GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         3 ~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      .++|.+|+++|.  +.++.++++.||++||+|+.|+++|.++.|+.+++++||+.||.++++++|++
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           15 ANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             SCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             CCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            568999999997  66888899999999999999999999888999999999999999999999863

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

Probab=99.71  E-value=1.3e-18  Score=98.65  Aligned_cols=60  Identities=23%  Similarity=0.388  Sum_probs=55.5

Q ss_pred             hCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         61 FGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++++|..|+++|.++.|.+.++.||++||+|..|+++|.++.|+..||++||+.++.+.|
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f   63 (70)
T 2d8z_A            4 GSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY   63 (70)
T ss_dssp             CCCBCSSSCCBCCSSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHT
T ss_pred             CCCCCcccCCeeccceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHh
Confidence            568999999999988899999999999999999999999889999999999999886654

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

Probab=99.71  E-value=1.7e-18  Score=102.74  Aligned_cols=64  Identities=25%  Similarity=0.439  Sum_probs=58.5

Q ss_pred             HHhHhCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         57 YQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        57 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +...+.++|..|+++|.+++|.+.++.||++||+|..|+++|.+..|+..+|++||+.++.+.|
T Consensus        20 ~~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f   83 (90)
T 2dar_A           20 PAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF   83 (90)
T ss_dssp             CTTTCCCBBSSSCCBCCSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHT
T ss_pred             CCCCCCCCCccCCCEecceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHc
Confidence            4556679999999999999999999999999999999999999889999999999999987654

>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=99.71  E-value=9.8e-18  Score=97.25  Aligned_cols=64  Identities=20%  Similarity=0.343  Sum_probs=58.2

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCA   66 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~   66 (120)
                      ..++|.+|+++|.+++|.++++.||++||+|..|+++|.+. ++.+++++||..||.++++|.+.
T Consensus        14 ~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           14 GKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTAD-ARELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCBCTTTCCBCCSCCCCCSSSCCCTTTSBCSSSCCBCCTT-CEEETTEEECHHHHHTTSCCSSC
T ss_pred             CCCCCccCCCEecceEEEECcceeCCCCCEeCCCCCccCCC-CEeECCEEeCHHHHHHhCCCCCC
Confidence            45789999999999999999999999999999999999876 46999999999999999988654

>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=99.71  E-value=2e-17  Score=96.36  Aligned_cols=64  Identities=27%  Similarity=0.664  Sum_probs=59.5

Q ss_pred             Cccccccccccc--cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCC
Q psy17880          3 KAYCTSCKKKCS--GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCA   66 (120)
Q Consensus         3 ~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~   66 (120)
                      .++|.+|+++|.  +.++.++++.||++||+|..|+++|.+..|+.+++++||+.||.+++++++.
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             CCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            578999999997  6689999999999999999999999988899999999999999999998875

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

Probab=99.70  E-value=1.6e-18  Score=98.03  Aligned_cols=59  Identities=15%  Similarity=0.356  Sum_probs=54.6

Q ss_pred             hCCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         61 FGTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        61 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      ++++|..|+++|.++.|.+.++.||++||+|+.|+++|.+..|+..||++||+.++.+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~   62 (69)
T 2cur_A            4 GSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNF   62 (69)
T ss_dssp             CCCCCSSSCCCCCTTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHH
T ss_pred             CcCCCcccCCEeCcceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHH
Confidence            46899999999998899999999999999999999999988999999999999987654

>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=99.70  E-value=2.8e-18  Score=97.80  Aligned_cols=60  Identities=18%  Similarity=0.387  Sum_probs=55.3

Q ss_pred             hCCCCCCCCCcccC----cEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         61 FGTKCAQCGEYVEG----EVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++++|..|+++|.+    ++|.+.++.||++||+|+.|+++|.+..|+..||++||+.++.+.|
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~   67 (72)
T 1x4l_A            4 GSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDIS   67 (72)
T ss_dssp             CSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCC
T ss_pred             CCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCccc
Confidence            46899999999986    7899999999999999999999999889999999999999987765

>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=2e-18  Score=98.33  Aligned_cols=61  Identities=23%  Similarity=0.431  Sum_probs=55.6

Q ss_pred             HhCCCCCCCCCccc--CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         60 KFGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        60 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +++++|..|+++|.  +++|.+.++.||++||+|+.|+++|.++.|+..+|++||+.++.+.|
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f   65 (72)
T 1wyh_A            3 SGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF   65 (72)
T ss_dssp             CCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHT
T ss_pred             ccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHc
Confidence            46789999999997  57899999999999999999999999999999999999999887654

>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=2.5e-18  Score=97.47  Aligned_cols=58  Identities=28%  Similarity=0.606  Sum_probs=54.3

Q ss_pred             CCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         62 GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        62 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      .++|..|+++|.+++|.+.++.||++||+|..|+++|..+.|+..||++||+.++.+.
T Consensus         5 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~   62 (70)
T 2d8x_A            5 SSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNRE   62 (70)
T ss_dssp             SSBCSSSCCBCCSCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHH
T ss_pred             CCcCccCCCEecceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhh
Confidence            4789999999999999999999999999999999999999999999999999988654

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

Probab=99.69  E-value=4.2e-17  Score=96.91  Aligned_cols=66  Identities=33%  Similarity=0.737  Sum_probs=60.6

Q ss_pred             Ccccccccccccc-ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCC
Q psy17880          3 KAYCTSCKKKCSG-EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQC   68 (120)
Q Consensus         3 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C   68 (120)
                      .++|.+|+++|.+ +.+.++++.||++||+|..|+++|....|+.+++++||+.||.++++++|..+
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~   81 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD   81 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCC
T ss_pred             CCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCcc
Confidence            4689999999964 78899999999999999999999998889999999999999999999999744

>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=99.68  E-value=2.2e-17  Score=94.39  Aligned_cols=62  Identities=23%  Similarity=0.413  Sum_probs=56.7

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccC-CCCeeecCCeeccHhHHHhHhCC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLA-QGGYFNKDGAYYCTSDYQKKFGT   63 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~~~~~C~~c~~~~~~~   63 (120)
                      ..++|.+|+++|.+++|.++++.||++||+|..|+++|. +..|+.+++++||..||.++++.
T Consensus         4 ~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            4 GSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             SCCSCSSSCCCCSSCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSS
T ss_pred             CcCCcccCCCEecCeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcc
Confidence            457899999999999999999999999999999999998 66899999999999999987754

>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=99.68  E-value=4.9e-17  Score=92.52  Aligned_cols=65  Identities=23%  Similarity=0.576  Sum_probs=57.6

Q ss_pred             CCcccccccccccc--ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCC
Q psy17880          2 IKAYCTSCKKKCSG--EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQ   67 (120)
Q Consensus         2 ~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~   67 (120)
                      ..++|.+|+++|.+  .++.++++.||++||+|..|+++|.+..|+.+++++||+.||.+++ .+|..
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~-~~~~~   70 (72)
T 1x61_A            4 GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL-ESGPS   70 (72)
T ss_dssp             CCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHH-HTCSS
T ss_pred             CCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHH-ccCCC
Confidence            46789999999964  5889999999999999999999998778999999999999999988 44543

>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=99.68  E-value=1.7e-17  Score=95.44  Aligned_cols=60  Identities=25%  Similarity=0.531  Sum_probs=54.4

Q ss_pred             hCCCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeec-cCCCcCC
Q psy17880         61 FGTKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYEN-RLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~-~~~~~~~  120 (120)
                      ++++|..|+++|. ++.|.+.++.||++||+|..|+++|.++.|+..||++||+ .++.+.|
T Consensus         8 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f   69 (76)
T 2cu8_A            8 MASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF   69 (76)
T ss_dssp             CCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHS
T ss_pred             CCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhc
Confidence            4589999999997 7899999999999999999999999988999999999999 6876544

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

Probab=99.67  E-value=1.9e-17  Score=92.62  Aligned_cols=57  Identities=18%  Similarity=0.359  Sum_probs=51.1

Q ss_pred             hCCCCCCCCCccc--CcEEEEeCcccc--ccccccccCCCcCCCCceeeeCCeeee-ccCCC
Q psy17880         61 FGTKCAQCGEYVE--GEVVTALGKTYH--QKCFTCARCRFSKKREIYNWLGGRAYE-NRLGG  117 (120)
Q Consensus        61 ~~~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~g~~yC-~~~~~  117 (120)
                      |+++|..|+++|.  ++.|++.++.||  ++||+|+.|+++|.++.|+..||+||| +.++.
T Consensus         1 fa~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~   62 (65)
T 2iyb_E            1 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK   62 (65)
T ss_dssp             -CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHH
T ss_pred             CcCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhh
Confidence            4678999999997  689999999999  999999999999999999999999999 55543

>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=99.67  E-value=7.9e-17  Score=107.63  Aligned_cols=69  Identities=32%  Similarity=0.623  Sum_probs=64.5

Q ss_pred             ccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcc
Q psy17880          4 AYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYV   72 (120)
Q Consensus         4 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i   72 (120)
                      ++|.+|+++|. ++.|.++++.||++||+|..|+++|.++.|+.+++++||+.||.++++++|..|++++
T Consensus       116 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~  185 (192)
T 1b8t_A          116 DGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA  185 (192)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             CcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCcc
Confidence            46999999996 5678899999999999999999999888899999999999999999999999999985

>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=99.66  E-value=1.1e-17  Score=97.01  Aligned_cols=58  Identities=19%  Similarity=0.344  Sum_probs=53.3

Q ss_pred             CCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++|..|+++|.+++|.+.++.||++||+|..|+++|.++.| ..||++||+.++.+.|
T Consensus        15 ~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f-~~~g~~yC~~cy~~~f   72 (79)
T 2cor_A           15 KYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMG   72 (79)
T ss_dssp             CCBCTTTCCBCCSCCCCCSSSCCCTTTSBCSSSCCBCCTTCE-EETTEEECHHHHHTTS
T ss_pred             CCCCccCCCEecceEEEECcceeCCCCCEeCCCCCccCCCCE-eECCEEeCHHHHHHhC
Confidence            589999999999989999999999999999999999998765 8899999999987765

>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=99.66  E-value=7.8e-18  Score=95.66  Aligned_cols=61  Identities=25%  Similarity=0.527  Sum_probs=54.7

Q ss_pred             HhCCCCCCCCCcccC-c-EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         60 KFGTKCAQCGEYVEG-E-VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        60 ~~~~~C~~C~~~i~~-~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++++|..|+++|.+ + +|.+.++.||++||+|+.|+++|..+.|+..||++||+.++.+.|
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf   71 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF   71 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHT
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhh
Confidence            456899999999974 3 678999999999999999999999889999999999999987765

>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=99.66  E-value=3.5e-17  Score=94.12  Aligned_cols=58  Identities=29%  Similarity=0.557  Sum_probs=52.8

Q ss_pred             CCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeec-cCCCcCC
Q psy17880         63 TKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYEN-RLGGRAY  120 (120)
Q Consensus        63 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~-~~~~~~~  120 (120)
                      |+|..|+++|. ++.|.+.++.||++||+|..|+++|.++.|+..||++||+ .++.+.|
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f   60 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMF   60 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHh
Confidence            57999999997 7899999999999999999999999998999999999999 5876543

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

Probab=99.66  E-value=1.2e-17  Score=95.04  Aligned_cols=59  Identities=31%  Similarity=0.558  Sum_probs=53.5

Q ss_pred             hCCCCCCCCCcccC--cEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         61 FGTKCAQCGEYVEG--EVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        61 ~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      ++++|..|+++|.+  .+|.+.++.||++||+|..|+++|.+..|+..||++||+.++.+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~   64 (72)
T 1x61_A            4 GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVAT   64 (72)
T ss_dssp             CCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHH
Confidence            46899999999974  589999999999999999999999888899999999999988654

>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-17  Score=97.97  Aligned_cols=59  Identities=31%  Similarity=0.589  Sum_probs=54.8

Q ss_pred             CCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++|..|+++|.+++|.+.++.||++||+|..|+++|..+.|+..||++||+.|+.+.|
T Consensus        25 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f   83 (89)
T 1x64_A           25 MPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARART   83 (89)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHS
T ss_pred             CCCcccCCCEecccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHh
Confidence            47899999999999999999999999999999999999889999999999999987654

>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=99.66  E-value=3.5e-17  Score=95.12  Aligned_cols=57  Identities=28%  Similarity=0.558  Sum_probs=52.2

Q ss_pred             CCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         63 TKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        63 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++|..|+++|. +++|.+.++.||++||+|..|+++|.+ .|+..||++||+.|+.+.|
T Consensus        16 ~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~f   73 (80)
T 2dj7_A           16 SHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQF   73 (80)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHT
T ss_pred             CCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHc
Confidence            78999999996 788999999999999999999999985 6899999999999987655

>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=99.65  E-value=1.2e-16  Score=90.70  Aligned_cols=61  Identities=28%  Similarity=0.731  Sum_probs=55.0

Q ss_pred             CCcccccccccccc-c-eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880          2 IKAYCTSCKKKCSG-E-VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus         2 ~~~~C~~C~~~i~~-~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      ..++|.+|+++|.+ + ++.+.++.||++||+|+.|+++|.++.++.+++++||+.||.++|+
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            46789999999963 3 6789999999999999999999988789999999999999998874

>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=99.65  E-value=1.6e-16  Score=92.38  Aligned_cols=64  Identities=19%  Similarity=0.507  Sum_probs=57.7

Q ss_pred             CccccccccccccceEEECCcccccccccccccccccCC-CCee-ecCCeeccHhHHHhHhCCCCC
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQ-GGYF-NKDGAYYCTSDYQKKFGTKCA   66 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~-~~~~~~~C~~c~~~~~~~~C~   66 (120)
                      .++|.+|+++|.++++.++++.||++||+|..|+++|.. ..|. .+++++||+.||.+++++.++
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           15 GEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             SCBCTTTCCBCCSCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             CCcCccCCCCcCceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            468999999999889999999999999999999999975 4666 589999999999999988775

>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=99.65  E-value=8e-17  Score=93.99  Aligned_cols=59  Identities=27%  Similarity=0.429  Sum_probs=53.1

Q ss_pred             CCCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCcee--eeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYN--WLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~--~~~g~~yC~~~~~~~~  120 (120)
                      .++|..|+++|. ++.|.+.++.||++||+|+.|+++|..+.|.  ..||++||+.|+.+.|
T Consensus        15 ~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~   76 (82)
T 2co8_A           15 GDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTD   76 (82)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCC
T ss_pred             CCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhh
Confidence            378999999994 6788899999999999999999999999888  4699999999998865

>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=99.65  E-value=5.4e-18  Score=98.30  Aligned_cols=58  Identities=19%  Similarity=0.447  Sum_probs=53.8

Q ss_pred             CCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         62 GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        62 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      .++|..|+++|.+++|.+.++.||++||+|..|+++|....|+..||++||+.|+.+.
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~   72 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARER   72 (79)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHH
T ss_pred             CCccccCCCCccCcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHH
Confidence            4799999999999999999999999999999999999888899999999999988654

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

Probab=99.65  E-value=2.6e-17  Score=94.78  Aligned_cols=60  Identities=23%  Similarity=0.526  Sum_probs=54.2

Q ss_pred             hCCCCCCCCCccc--CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         61 FGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++++|..|+++|.  +.+|.+.++.||++||+|..|+++|.++.|+..||++||+.++.+.|
T Consensus        10 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f   71 (77)
T 1g47_A           10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF   71 (77)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHC
T ss_pred             CCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHh
Confidence            3589999999995  56789999999999999999999999889999999999999987654

>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=99.64  E-value=4.4e-17  Score=94.79  Aligned_cols=59  Identities=31%  Similarity=0.633  Sum_probs=53.6

Q ss_pred             CCCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++|..|+++|. ++.|.+.++.||++||+|+.|+++|..+.|+..||++||+.++.+.|
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f   66 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKY   66 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHC
T ss_pred             CCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHh
Confidence            589999999994 78999999999999999999999999989999999999999886654

>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=99.64  E-value=2.2e-16  Score=90.91  Aligned_cols=57  Identities=26%  Similarity=0.621  Sum_probs=53.2

Q ss_pred             Ccccccccccccc-----ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHh
Q psy17880          3 KAYCTSCKKKCSG-----EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQK   59 (120)
Q Consensus         3 ~~~C~~C~~~i~~-----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~   59 (120)
                      .++|++|+++|.+     +++.++++.||++||+|+.|+++|.+..|+.+++++||+.||.+
T Consensus        15 ~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           15 AKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             CccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            5789999999986     78999999999999999999999998889999999999999975

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

Probab=99.63  E-value=2e-16  Score=88.40  Aligned_cols=58  Identities=19%  Similarity=0.547  Sum_probs=53.2

Q ss_pred             Cccccccccccc--cceEEECCcccc--cccccccccccccCCCCeeecCCeecc-HhHHHhH
Q psy17880          3 KAYCTSCKKKCS--GEVLRVQDKYFH--ITCFQCSVCKNSLAQGGYFNKDGAYYC-TSDYQKK   60 (120)
Q Consensus         3 ~~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~C-~~c~~~~   60 (120)
                      .++|.+|+++|.  ++.+.++++.||  ++||+|+.|+++|.+..|+.+++++|| .+||.++
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            468999999997  679999999999  999999999999998889999999999 8898753

>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=99.63  E-value=1.6e-16  Score=95.91  Aligned_cols=60  Identities=20%  Similarity=0.428  Sum_probs=55.2

Q ss_pred             hCCCCCCCCCccc--CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         61 FGTKCAQCGEYVE--GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++++|..|+++|.  +++|.+.++.||++||+|..|+++|.++.|+..||++||+.++.+.|
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~   65 (101)
T 2cup_A            4 GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTRED   65 (101)
T ss_dssp             CCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCC
T ss_pred             CCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhc
Confidence            4689999999995  67999999999999999999999999888999999999999987765

>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=4.7e-16  Score=97.17  Aligned_cols=60  Identities=32%  Similarity=0.756  Sum_probs=54.5

Q ss_pred             Cccccccccccccc-eEEECCcccccccccccccccccC--CCCeeecCCeeccHhHHHhHhC
Q psy17880          3 KAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLA--QGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus         3 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      .++|.+|+++|.+. ++.++++.||++||+|..|+++|.  +..|+.+++++||+.||.++|+
T Consensus        61 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           61 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            46899999999877 689999999999999999999997  3579999999999999999874

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

Probab=99.61  E-value=2e-16  Score=99.06  Aligned_cols=60  Identities=23%  Similarity=0.355  Sum_probs=54.7

Q ss_pred             hCCCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         61 FGTKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++++|..|+++|. +++|.+.|+.||++||+|+.|+++|.+..|+..||++||+.++.+.|
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   62 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNH   62 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHS
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCc
Confidence            4689999999997 57899999999999999999999999989999999999999886543

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

Probab=99.60  E-value=1.2e-16  Score=99.87  Aligned_cols=60  Identities=18%  Similarity=0.368  Sum_probs=54.1

Q ss_pred             hCCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCC--CCceeeeCCeeeeccCCCcCC
Q psy17880         61 FGTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKK--REIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        61 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +.++|..|+++|.+. +|.+.++.||++||+|..|+++|.  +..|+..||++||+.|+.+.|
T Consensus        60 ~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~F  122 (123)
T 2l4z_A           60 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF  122 (123)
T ss_dssp             SCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHC
T ss_pred             cCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhc
Confidence            357999999999876 699999999999999999999997  467999999999999998766

>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=99.59  E-value=1.8e-16  Score=94.12  Aligned_cols=59  Identities=25%  Similarity=0.484  Sum_probs=53.7

Q ss_pred             CCCCCCCCCcccC-cEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVEG-EVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++|..|+++|.+ +.|.+.++.||++||+|..|+++|..+.|+..||++||+.|+.+.|
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f   74 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLF   74 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHS
T ss_pred             CCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHh
Confidence            4799999999964 7889999999999999999999999988999999999999886654

>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=99.59  E-value=2.8e-16  Score=91.65  Aligned_cols=63  Identities=30%  Similarity=0.686  Sum_probs=55.2

Q ss_pred             Ccccccccccc-ccceEEECCcccccccccccccccccCCCCee--ecCCeeccHhHHHhHhCCCC
Q psy17880          3 KAYCTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYF--NKDGAYYCTSDYQKKFGTKC   65 (120)
Q Consensus         3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~--~~~~~~~C~~c~~~~~~~~C   65 (120)
                      .++|.+|+++| .++.+.++++.||++||+|..|+++|....|+  .+++++||+.||.++++...
T Consensus        15 ~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~   80 (82)
T 2co8_A           15 GDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPS   80 (82)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCC
T ss_pred             CCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCC
Confidence            56899999999 46778899999999999999999999988877  47999999999998876543

>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=99.58  E-value=2.3e-16  Score=97.35  Aligned_cols=59  Identities=19%  Similarity=0.358  Sum_probs=52.6

Q ss_pred             CCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCC--CceeeeCCeeeeccCCCcCC
Q psy17880         62 GTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKR--EIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        62 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .++|+.|+++|.+. +|.+.++.||++||+|+.|+++|..  ..|+..||+|||+.|+.+.|
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f   64 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLG   64 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHH
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHh
Confidence            37899999999876 8999999999999999999999975  57999999999999886543

>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=99.54  E-value=3.7e-16  Score=97.50  Aligned_cols=59  Identities=19%  Similarity=0.345  Sum_probs=52.5

Q ss_pred             hCCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCC--CCceeeeCCeeeeccCCCcC
Q psy17880         61 FGTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKK--REIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        61 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~~~~~~  119 (120)
                      +.++|+.|+++|.+. +|.+.++.||++||+|+.|+++|.  +..|+..||++||+.|+.+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~   65 (122)
T 1m3v_A            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL   65 (122)
T ss_dssp             CCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHH
T ss_pred             CCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHH
Confidence            458999999999876 689999999999999999999997  35799999999999988654

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

Probab=99.51  E-value=3.4e-15  Score=93.92  Aligned_cols=57  Identities=19%  Similarity=0.419  Sum_probs=51.2

Q ss_pred             CCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCC--CceeeeCCeeeeccCCCcC
Q psy17880         63 TKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKR--EIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        63 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~g~~yC~~~~~~~  119 (120)
                      ++|..|+++|.+. +|.+.++.||++||+|+.|+++|+.  ..|+..||++||+.|+.+.
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~   62 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   62 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHH
T ss_pred             ccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhh
Confidence            6899999999876 7899999999999999999999963  5799999999999987653

>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=99.50  E-value=9.4e-15  Score=84.82  Aligned_cols=59  Identities=27%  Similarity=0.559  Sum_probs=51.3

Q ss_pred             CccccccccccccceEEECCcccccccccccccccccCCCCeeecCC-eeccHhHHHhHh
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDG-AYYCTSDYQKKF   61 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~-~~~C~~c~~~~~   61 (120)
                      .++|.+|+++|.++++.++++.||++||+|..|+++|..+.++..++ .+||..||.+.+
T Consensus        15 ~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~   74 (81)
T 1v6g_A           15 GTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVS   74 (81)
T ss_dssp             CCBCTTTCCBCCSCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCS
T ss_pred             CCcCccccCEeccceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccC
Confidence            46899999999999999999999999999999999998766665555 579999997655

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

Probab=99.48  E-value=5e-15  Score=98.09  Aligned_cols=72  Identities=18%  Similarity=0.355  Sum_probs=59.5

Q ss_pred             CCeeccHhHHH---hHhCCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         48 DGAYYCTSDYQ---KKFGTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        48 ~~~~~C~~c~~---~~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      ++..+|...+.   ....++|..|+++|.+. ++.+.++.||++||+|+.|+++|.+..| ..||++||+.|+.+.|
T Consensus        43 ~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f  118 (182)
T 2jtn_A           43 DDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF  118 (182)
T ss_dssp             SSSCSSSSSCCCCCCCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTT
T ss_pred             ccccccccccccCCCCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCcccccc
Confidence            45567776654   33348999999999875 6789999999999999999999988776 6899999999987654

>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=99.45  E-value=9.4e-15  Score=97.27  Aligned_cols=59  Identities=19%  Similarity=0.349  Sum_probs=52.8

Q ss_pred             hCCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCC--CceeeeCCeeeeccCCCcC
Q psy17880         61 FGTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKR--EIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        61 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~g~~yC~~~~~~~  119 (120)
                      ..++|..|+++|.+. +|.+.++.||++||+|+.|+++|..  ..|+..||++||+.|+.+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~   65 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL   65 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHH
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccc
Confidence            458999999999876 6899999999999999999999975  6899999999999987653

>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=99.39  E-value=4.1e-14  Score=92.67  Aligned_cols=57  Identities=21%  Similarity=0.471  Sum_probs=50.1

Q ss_pred             CCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         62 GTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        62 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      .++|..|+++|.+. +|.+.|+.||++||+|+.|+++|.+..| ..||++||+.|+.+.
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~   63 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKR   63 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCE-ESSSCEECHHHHHHH
T ss_pred             CCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCc-ccCCeeeeccccccc
Confidence            47999999999875 6889999999999999999999988775 789999999887553

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

Probab=98.11  E-value=7.4e-07  Score=42.05  Aligned_cols=29  Identities=31%  Similarity=0.769  Sum_probs=25.4

Q ss_pred             CCcccccccccc-ccceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      |...|..|++++ ..+.+.+.|+.||..||
T Consensus         2 m~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            2 MNPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCCcCCccCCEEecceeEEECCeEecccCC
Confidence            678999999998 46777889999999997

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

Probab=98.03  E-value=8.6e-07  Score=41.81  Aligned_cols=28  Identities=43%  Similarity=0.930  Sum_probs=24.6

Q ss_pred             CCCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         62 GTKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        62 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      +++|..|++.+ ..+.|.+.|+.||..||
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            47899999999 45788899999999998

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=94.22  E-value=0.012  Score=35.83  Aligned_cols=90  Identities=21%  Similarity=0.438  Sum_probs=51.1

Q ss_pred             ccccccccccccc-------eEEECCcccccccc--------cccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCC
Q psy17880          4 AYCTSCKKKCSGE-------VLRVQDKYFHITCF--------QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQC   68 (120)
Q Consensus         4 ~~C~~C~~~i~~~-------~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C   68 (120)
                      ..|..|...+.+.       ++..=|..||..|+        .|..|++.+.........         .......|..|
T Consensus         8 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~---------i~~~~~~C~iC   78 (133)
T 4ap4_A            8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY---------IGSGTVSCPIC   78 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECB---------CSSSSCBCTTT
T ss_pred             CCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccccccc---------cCCCCCCCCCC
Confidence            3577777665332       33333667777766        677788877654332110         00112567777


Q ss_pred             CCcccCc-------EEEEeCcccccccc--------ccccCCCcCCCCc
Q psy17880         69 GEYVEGE-------VVTALGKTYHQKCF--------TCARCRFSKKREI  102 (120)
Q Consensus        69 ~~~i~~~-------~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~  102 (120)
                      ...+...       ++..-|..||..|.        .|-.|..++..+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           79 MDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             CCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            6665321       33344667777766        4778887776554

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=90.21  E-value=0.26  Score=27.91  Aligned_cols=65  Identities=15%  Similarity=0.426  Sum_probs=34.6

Q ss_pred             CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeC
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALG   81 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~   81 (120)
                      |...|..|+.+|..     .++.     +.|..|++.+...                    ..|..|++++.  ++.+-|
T Consensus         1 M~~~CP~C~~~l~~-----~~~~-----~~C~~C~~~~~~~--------------------afCPeCgq~Le--~lkACG   48 (81)
T 2jrp_A            1 MEITCPVCHHALER-----NGDT-----AHCETCAKDFSLQ--------------------ALCPDCRQPLQ--VLKACG   48 (81)
T ss_dssp             CCCCCSSSCSCCEE-----CSSE-----EECTTTCCEEEEE--------------------EECSSSCSCCC--EEEETT
T ss_pred             CCCCCCCCCCcccc-----CCCc-----eECccccccCCCc--------------------ccCcchhhHHH--HHHhcC
Confidence            34678888877752     1222     3466666654331                    24555666553  233333


Q ss_pred             ccccccccccccCCCcCCCCc
Q psy17880         82 KTYHQKCFTCARCRFSKKREI  102 (120)
Q Consensus        82 ~~~H~~Cf~C~~C~~~l~~~~  102 (120)
                      ..    =+.|-.|+..++..+
T Consensus        49 A~----~yFC~~C~~LiSkkr   65 (81)
T 2jrp_A           49 AV----DYFCQNGHGLISKKR   65 (81)
T ss_dssp             EE----EECCTTTTCCCCTTS
T ss_pred             Cc----CeeeccCCCEeecce
Confidence            22    255677777776554

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=88.71  E-value=0.81  Score=24.89  Aligned_cols=46  Identities=20%  Similarity=0.340  Sum_probs=34.8

Q ss_pred             ccccccccccccCCCCeeecCCeeccHhHHHhHhC---CCCCCCCCcccC
Q psy17880         28 TCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG---TKCAQCGEYVEG   74 (120)
Q Consensus        28 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~---~~C~~C~~~i~~   74 (120)
                      +-|.|..|...+.+ .....-|..||..|..+.+.   ..|..|++++..
T Consensus         7 ~~~~C~IC~~~~~~-Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            7 EYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             ccCCCCCccccccC-CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            45788899888765 45567899999999887653   468888888753

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.60  E-value=0.66  Score=24.44  Aligned_cols=46  Identities=22%  Similarity=0.474  Sum_probs=33.3

Q ss_pred             ccccccccccccCCCCeeecCCeeccHhHHHhHh---CCCCCCCCCcccC
Q psy17880         28 TCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF---GTKCAQCGEYVEG   74 (120)
Q Consensus        28 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~---~~~C~~C~~~i~~   74 (120)
                      +=+.|..|...+... ....=|..||..|..+.+   ...|..|..+|..
T Consensus        14 ~~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           14 DKYKCEKCHLVLCSP-KQTECGHRFCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             CCEECTTTCCEESSC-CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             cCCCCCCCChHhcCe-eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            346788888877653 445678889999998776   2578888887743

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=87.77  E-value=0.94  Score=24.31  Aligned_cols=46  Identities=24%  Similarity=0.526  Sum_probs=31.9

Q ss_pred             ccccccccccccCCCCee-ecCCeeccHhHHHhHh--CCCCCCCCCcccC
Q psy17880         28 TCFQCSVCKNSLAQGGYF-NKDGAYYCTSDYQKKF--GTKCAQCGEYVEG   74 (120)
Q Consensus        28 ~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~~--~~~C~~C~~~i~~   74 (120)
                      +-+.|..|...+.. ... ..=+..||..|..+.+  ...|..|.++|..
T Consensus        14 ~~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (72)
T 2djb_A           14 PYILCSICKGYLID-ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ   62 (72)
T ss_dssp             GGGSCTTTSSCCSS-CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCS
T ss_pred             CCCCCCCCChHHHC-cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCc
Confidence            34678888777765 333 3667888998887654  4678888887743

>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1

Probab=85.48  E-value=0.43  Score=24.97  Aligned_cols=24  Identities=17%  Similarity=0.176  Sum_probs=20.4

Q ss_pred             ccccCCCcCCCCceeeeCCeeeec
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYEN  113 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~  113 (120)
                      .|..|+..++..+-+..||+.||.
T Consensus         9 aC~~C~c~Vs~~eai~~dGK~YCS   32 (55)
T 1jjd_A            9 ACEPCLCNVDPSKAIDRNGLYYCS   32 (55)
T ss_dssp             SSTTCCCCBCTTTSEESSSCEESS
T ss_pred             cCCCCeeEechHHhhhcCCeEEeh
Confidence            378888888888888899999993

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=85.46  E-value=0.29  Score=25.48  Aligned_cols=45  Identities=13%  Similarity=0.486  Sum_probs=26.0

Q ss_pred             ccccccccccCCC-----C-eeecCCeeccHhHHHhHh--CCCCCCCCCcccC
Q psy17880         30 FQCSVCKNSLAQG-----G-YFNKDGAYYCTSDYQKKF--GTKCAQCGEYVEG   74 (120)
Q Consensus        30 f~C~~C~~~l~~~-----~-~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~~   74 (120)
                      +.|..|...+...     . ....=|..+|..|..+.+  ...|..|..++..
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   56 (64)
T 2xeu_A            4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   56 (64)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTT
T ss_pred             CCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCc
Confidence            4566666655321     1 334556777777776543  3567777766643

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.78  E-value=1.3  Score=23.62  Aligned_cols=44  Identities=20%  Similarity=0.362  Sum_probs=31.8

Q ss_pred             cccccccccccCCCCeeecCCeeccHhHHHhHhC-----CCCCCCCCccc
Q psy17880         29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG-----TKCAQCGEYVE   73 (120)
Q Consensus        29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~-----~~C~~C~~~i~   73 (120)
                      -+.|..|...+.. .....=|..||..|..+.+.     ..|..|..+|.
T Consensus        20 ~~~C~IC~~~~~~-~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   68 (73)
T 2ysl_A           20 EVICPICLDILQK-PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVR   68 (73)
T ss_dssp             CCBCTTTCSBCSS-EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCC
T ss_pred             CCEeccCCcccCC-eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCC
Confidence            4678888877764 34456788899999987663     36888877774

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=83.45  E-value=0.2  Score=26.79  Aligned_cols=44  Identities=14%  Similarity=0.508  Sum_probs=24.2

Q ss_pred             ccccccccccCCC-----C-eeecCCeeccHhHHHhHh--CCCCCCCCCccc
Q psy17880         30 FQCSVCKNSLAQG-----G-YFNKDGAYYCTSDYQKKF--GTKCAQCGEYVE   73 (120)
Q Consensus        30 f~C~~C~~~l~~~-----~-~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~   73 (120)
                      +.|..|...+...     . ....=|..||..|..+.+  ...|..|..++.
T Consensus        11 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   62 (71)
T 3ng2_A           11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN   62 (71)
T ss_dssp             CBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccC
Confidence            5666666655321     1 334456677777775532  246666666653

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=81.76  E-value=0.97  Score=26.83  Aligned_cols=45  Identities=22%  Similarity=0.382  Sum_probs=33.4

Q ss_pred             ccccccccccccCCCCeee-cCCeeccHhHHHhHhCCCCCCCCCccc
Q psy17880         28 TCFQCSVCKNSLAQGGYFN-KDGAYYCTSDYQKKFGTKCAQCGEYVE   73 (120)
Q Consensus        28 ~Cf~C~~C~~~l~~~~~~~-~~~~~~C~~c~~~~~~~~C~~C~~~i~   73 (120)
                      +-+.|..|...+.. .... .=|..||..|..+.....|..|..++.
T Consensus        21 ~~~~C~IC~~~~~~-pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~   66 (117)
T 1jm7_B           21 KLLRCSRCTNILRE-PVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAW   66 (117)
T ss_dssp             HTTSCSSSCSCCSS-CBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCS
T ss_pred             hCCCCCCCChHhhC-ccEeCCCCCHHHHHHHHHHhcCCCcCCCCcCc
Confidence            34678888777754 3444 678888998888777678989988874

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=81.58  E-value=1.6  Score=25.66  Aligned_cols=42  Identities=17%  Similarity=0.312  Sum_probs=27.2

Q ss_pred             ccccccccCCCCeeecCCeeccHhHHHhH---hCCCCCCCCCccc
Q psy17880         32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKK---FGTKCAQCGEYVE   73 (120)
Q Consensus        32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~---~~~~C~~C~~~i~   73 (120)
                      |..|+.|+..-.-..-=..++|.+|+...   -...|..|..+|.
T Consensus         4 C~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            4 CDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             CTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             cCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            55666666432122333567899998753   3478999999995

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=81.48  E-value=1.8  Score=22.55  Aligned_cols=45  Identities=24%  Similarity=0.489  Sum_probs=28.8

Q ss_pred             cccccccc-ccCCCC---eeecCCeeccHhHHHhHh---CCCCCCCCCcccC
Q psy17880         30 FQCSVCKN-SLAQGG---YFNKDGAYYCTSDYQKKF---GTKCAQCGEYVEG   74 (120)
Q Consensus        30 f~C~~C~~-~l~~~~---~~~~~~~~~C~~c~~~~~---~~~C~~C~~~i~~   74 (120)
                      +.|..|.. .+....   ....=|..+|..|..+.+   ...|..|.+++..
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   55 (65)
T 1g25_A            4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCcccc
Confidence            45667766 443321   234567888988887763   2568888888753

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=81.40  E-value=1.8  Score=21.57  Aligned_cols=43  Identities=16%  Similarity=0.447  Sum_probs=20.9

Q ss_pred             cccccccccCCC---CeeecCCeeccHhHHHhHh--CCCCCCCCCccc
Q psy17880         31 QCSVCKNSLAQG---GYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVE   73 (120)
Q Consensus        31 ~C~~C~~~l~~~---~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~   73 (120)
                      .|..|...+...   .....=+..+|..|..+.+  ...|..|..+|.
T Consensus         7 ~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            7 GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             cCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            455555544321   1222335556666665432  255666666554

>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=81.32  E-value=0.6  Score=27.94  Aligned_cols=75  Identities=21%  Similarity=0.470  Sum_probs=43.8

Q ss_pred             cccccccccc--------ccceEEEC--CcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc
Q psy17880          4 AYCTSCKKKC--------SGEVLRVQ--DKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE   73 (120)
Q Consensus         4 ~~C~~C~~~i--------~~~~~~~~--~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~   73 (120)
                      .+|..|...-        .++.|.-.  ++.||+.|+.=..-   +   .-....+..+|..|      ..|..|++.-.
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~~~---~---~~~~~~~~W~C~~C------~~C~~C~~~~~   69 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLN---M---TEAVKTYKWQCIEC------KSCILCGTSEN   69 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCCHH---H---HHHHHHTTCCCGGG------CCCTTTTCCTT
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCChhh---h---hhccCCCccCcccc------CccCcccccCC
Confidence            5677776543        23455544  67888888642210   0   00123445678777      57999988764


Q ss_pred             C-cEEE--EeCccccccccc
Q psy17880         74 G-EVVT--ALGKTYHQKCFT   90 (120)
Q Consensus        74 ~-~~~~--~~~~~~H~~Cf~   90 (120)
                      + .+|.  .-++.||..|..
T Consensus        70 ~~~ll~Cd~C~~~yH~~Cl~   89 (114)
T 2kwj_A           70 DDQLLFCDDCDRGYHMYCLN   89 (114)
T ss_dssp             TTTEEECSSSCCEEETTTSS
T ss_pred             CCceEEcCCCCccccccccC
Confidence            3 3443  335689988764

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.09  E-value=1.8  Score=23.70  Aligned_cols=44  Identities=23%  Similarity=0.596  Sum_probs=30.5

Q ss_pred             cccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCccc
Q psy17880         29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVE   73 (120)
Q Consensus        29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~   73 (120)
                      -+.|..|...+.. .....=+..||..|..+.+  ...|..|..++.
T Consensus        15 ~~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           15 PFRCFICRQAFQN-PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CSBCSSSCSBCCS-EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCcCCCchhcC-eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3677888777754 3445667888888887654  357888887775

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=80.72  E-value=2.3  Score=25.96  Aligned_cols=44  Identities=14%  Similarity=0.425  Sum_probs=30.1

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCcccC
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVEG   74 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~~   74 (120)
                      +.|..|...+.. .....=|..||..|..+.+  ...|..|..+|..
T Consensus        54 ~~C~iC~~~~~~-~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           54 LQCIICSEYFIE-AVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             SBCTTTCSBCSS-EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             CCCcccCcccCC-ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            567888777654 3455667888888876543  2568888877754

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=80.63  E-value=1.7  Score=24.77  Aligned_cols=44  Identities=20%  Similarity=0.474  Sum_probs=29.8

Q ss_pred             cccccccccccCCCCeee-cCCeeccHhHHHhHhC--CCCCCCCCccc
Q psy17880         29 CFQCSVCKNSLAQGGYFN-KDGAYYCTSDYQKKFG--TKCAQCGEYVE   73 (120)
Q Consensus        29 Cf~C~~C~~~l~~~~~~~-~~~~~~C~~c~~~~~~--~~C~~C~~~i~   73 (120)
                      -+.|..|...+.. .... .=|..||..|..+.+.  ..|..|..++.
T Consensus        22 ~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   68 (99)
T 2y43_A           22 LLRCGICFEYFNI-AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT   68 (99)
T ss_dssp             HTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             CCCcccCChhhCC-cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCC
Confidence            4678888777754 3333 5678888888876553  46777777764

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=80.45  E-value=2.5  Score=24.54  Aligned_cols=48  Identities=6%  Similarity=-0.055  Sum_probs=36.3

Q ss_pred             ccccccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCcccC
Q psy17880         26 HITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVEG   74 (120)
Q Consensus        26 H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~~   74 (120)
                      -++-|.|..|...+.+ ......|..||..|-.+.+  ...|..|++++..
T Consensus        26 ~p~~~~CpI~~~~m~d-PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           26 APDEFRDPLMDTLMTD-PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             CSTTTBCTTTCSBCSS-EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             CcHhhCCcCccCcccC-CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            3567999999888865 5667789999999877654  2577788777743

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=80.39  E-value=2.2  Score=22.34  Aligned_cols=43  Identities=16%  Similarity=0.309  Sum_probs=24.6

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCccc
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVE   73 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~   73 (120)
                      .|..|...+........=+..+|..|..+.+  ...|..|..++.
T Consensus         7 ~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            4556655554322334456667777765432  356777777664

---

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	120
d1v6ga1	41	g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abL	1e-11
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	3e-11
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	1e-05
d1u5sb1	31	g.39.1.3 (B:72-102) Pinch (particularly interestin	7e-04
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	8e-04
d1b8ta4	49	g.39.1.3 (A:144-192) Cysteine-rich (intestinal) pr	0.001

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]} Length = 41

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]

 Score = 53.3 bits (128), Expect = 1e-11
 Identities = 20/33 (60%), Positives = 27/33 (81%)

Query: 56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKC 88
          DYQ+ +GT+C  C +++EGEVV+ALGKTYH  C
Sbjct: 9  DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDC 41

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (125), Expect = 3e-11
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCF 89
          D+   F  KC  C   V    ++A+   +H +CF
Sbjct: 2  DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF 35

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (88), Expect = 1e-05
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 64 KCAQCGEYVEGEVVTALGKTYHQKCF 89
           CA C + + G  + ALGK++H + F
Sbjct: 20 MCAHCNQVIRGPFLVALGKSWHPEEF 45

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 31

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (75), Expect = 7e-04
 Identities = 10/27 (37%), Positives = 13/27 (48%)

Query: 59 KKFGTKCAQCGEYVEGEVVTALGKTYH 85
                C  C   +EG VV A+GK +H
Sbjct: 2  SMGVPICGACRRPIEGRVVNAMGKQWH 28

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (75), Expect = 8e-04
 Identities = 10/32 (31%), Positives = 16/32 (50%)

Query: 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61
          F C+ C     +G ++  +G  YC  D+Q  F
Sbjct: 1  FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 32

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 49

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 = 32.4 bits (74), Expect = 0.001
 Identities = 15/40 (37%), Positives = 18/40 (45%)

Query: 32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEY 71
          C+ C  SL      +KDG  YC   Y K FG K    G+ 
Sbjct: 2  CAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQG 41

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	120
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.06
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	99.05
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	99.01
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.99
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.99
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.91
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.9
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.84
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.82
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.81
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.73
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.72
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.71
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.65
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.6
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.55
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.55
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.54
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.5
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.49
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.48
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.47
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	98.44
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.44
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.42
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.36
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.35
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.35
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.35
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.34
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.3
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.29
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.29
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.25
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.24
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.24
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.2
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.19
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.19
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.17
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.17
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.16
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.15
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.11
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.1
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.1
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	98.1
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.1
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.08
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.06
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.05
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.04
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	98.04
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.03
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.02
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.01
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.99
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.97
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.93
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.93
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.92
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.9
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.89
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.88
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.87
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.87
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.86
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.85
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.85
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.79
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.76
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.76
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.74
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.73
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.72
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.68
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.66
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.65
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.62
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.59
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.56
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.54
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.52
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.46
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.42
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.4
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.39
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.37
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.32
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.3
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.3
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.3
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.23
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.1
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.05
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.95
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.88
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.86
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.85
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.82
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.78
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.75
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	96.74
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.72
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.66
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.61
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.59
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.47
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.45
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.33
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.27
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.21
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.21
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.42
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	95.36
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.33
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.14
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	94.53
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	94.33
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.25
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	93.8
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	93.42
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	92.86
d2co8a1	33	Nedd9 interacting protein with calponin homology,	92.78
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	92.48
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	91.55
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	90.35
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	90.33
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	87.01
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	86.15
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	83.81
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	82.21
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	81.21

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=2e-15  Score=72.51  Aligned_cols=34  Identities=29%  Similarity=0.737  Sum_probs=32.4

Q ss_pred             HHHhHhCCCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        56 c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      +|.++|+++|+.|+++|.|++|+|+|+.||++||
T Consensus         2 DY~~~fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           2 DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             cHHHHhChhhhhcCCcccchheeecCCccCcccC
Confidence            5788899999999999999999999999999998

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.06  E-value=3.6e-11  Score=57.35  Aligned_cols=29  Identities=24%  Similarity=0.614  Sum_probs=27.5

Q ss_pred             CCccccccccccccceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      ..++|++|+++|.|++|.++|+.||++||
T Consensus         7 fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           7 FSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             hChhhhhcCCcccchheeecCCccCcccC
Confidence            46899999999999999999999999998

>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=99.05  E-value=3.8e-11  Score=59.42  Aligned_cols=28  Identities=36%  Similarity=0.827  Sum_probs=26.9

Q ss_pred             CCCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         62 GTKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        62 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      .|+|+.|+++|.|.+|+|+|+.||++||
T Consensus        18 ~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CeeccccCCcccCceeeecCCccCcCCC
Confidence            4899999999999999999999999998

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=7.3e-11  Score=56.16  Aligned_cols=34  Identities=29%  Similarity=0.803  Sum_probs=32.3

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHhHhCC
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT   63 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~   63 (120)
                      |+|+.|+++|.+..|++++|++||+.||.++++|
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            7899999999998999999999999999999976

>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=98.99  E-value=1.5e-11  Score=57.36  Aligned_cols=34  Identities=29%  Similarity=0.719  Sum_probs=32.1

Q ss_pred             HHHhHhCCCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        56 c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      ||+++|+++|..|+++|+.--|++.++.||.+||
T Consensus         2 CyE~kfa~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           2 CYENKFAPRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             chHHHHHHHHhhcCCccccCceeecCCcchhhhC
Confidence            7888999999999999988889999999999998

>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=98.99  E-value=1.6e-11  Score=57.49  Aligned_cols=33  Identities=36%  Similarity=0.852  Sum_probs=28.7

Q ss_pred             HHHhHhCCCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        56 c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      ||.... .+|..|+++|.++++.|.|+.||+.||
T Consensus         3 Cy~~tl-EkC~~C~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           3 CYVATL-EKCATCSQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCSSC-CBCTTTCCBCCSCCEEETTEEECTTTC
T ss_pred             hHHHHH-HHHHHhchHHHHHHHHHhCCCCCCCCC
Confidence            444333 799999999999999999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=1.2e-10  Score=56.59  Aligned_cols=34  Identities=59%  Similarity=1.252  Sum_probs=32.2

Q ss_pred             hHHHhHhCCCCCCCCCcccCcEEEEeCccccccc
Q psy17880         55 SDYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKC   88 (120)
Q Consensus        55 ~c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~C   88 (120)
                      .+|.++|+.+|..|++.|+|++|+|.+++||++|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeeeeeEecCcccCCCC
Confidence            4689999999999999999999999999999987

>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=98.90  E-value=2.9e-10  Score=56.17  Aligned_cols=28  Identities=25%  Similarity=0.500  Sum_probs=26.5

Q ss_pred             CccccccccccccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      .++|+.|+++|.|..++++|+.||+++|
T Consensus        18 ~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CeeccccCCcccCceeeecCCccCcCCC
Confidence            3789999999999999999999999998

>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=98.84  E-value=1.1e-10  Score=52.92  Aligned_cols=28  Identities=36%  Similarity=0.638  Sum_probs=25.8

Q ss_pred             hCCCCCCCCCcccCcEEEEeCccccccc
Q psy17880         61 FGTKCAQCGEYVEGEVVTALGKTYHQKC   88 (120)
Q Consensus        61 ~~~~C~~C~~~i~~~~~~~~~~~~H~~C   88 (120)
                      ..|+|+.|.+||.+++|+++|+.||+++
T Consensus         4 g~p~C~~C~~PI~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           4 GVPICGACRRPIEGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCEETTTTEECCSCEECCTTSBEETTT
T ss_pred             CCcchhhcCCchhhhHhhhhccccCCCC
Confidence            4589999999999999999999999985

>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=98.82  E-value=1.8e-10  Score=54.80  Aligned_cols=32  Identities=22%  Similarity=0.382  Sum_probs=29.0

Q ss_pred             cccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         89 FTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        89 f~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |+|+.|+++|.++.|++.||+|||+.|+.+.|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lF   32 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF   32 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhc
Confidence            78999999999999999999999999876544

>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=98.81  E-value=5.6e-10  Score=50.56  Aligned_cols=29  Identities=24%  Similarity=0.565  Sum_probs=26.7

Q ss_pred             CCCccccccccccccceEEECCccccccc
Q psy17880          1 MIKAYCTSCKKKCSGEVLRVQDKYFHITC   29 (120)
Q Consensus         1 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~C   29 (120)
                      |..++|+.|++||.+++++++|+.||+++
T Consensus         3 mg~p~C~~C~~PI~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEECCSCEECCTTSBEETTT
T ss_pred             cCCcchhhcCCchhhhHhhhhccccCCCC
Confidence            56789999999999999999999999974

>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=98.73  E-value=5.1e-10  Score=53.51  Aligned_cols=34  Identities=26%  Similarity=0.559  Sum_probs=30.5

Q ss_pred             HHHhHhCCCCCCCCCccc-C-cEEEEeCcccccccc
Q psy17880         56 DYQKKFGTKCAQCGEYVE-G-EVVTALGKTYHQKCF   89 (120)
Q Consensus        56 c~~~~~~~~C~~C~~~i~-~-~~~~~~~~~~H~~Cf   89 (120)
                      ||.+.++++|..|+++|. | +.|.+.|+.||.+||
T Consensus         2 Cy~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           2 CTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            677888999999999995 4 589999999999998

>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=98.72  E-value=9.1e-09  Score=51.93  Aligned_cols=40  Identities=38%  Similarity=0.740  Sum_probs=36.3

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGE   70 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~   70 (120)
                      +|..|++.|++.....+|+++||+.||.++|+|+...-+.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~   40 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQ   40 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCccc
Confidence            5899999999888999999999999999999999877653

>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=98.65  E-value=4.9e-09  Score=48.86  Aligned_cols=28  Identities=29%  Similarity=0.680  Sum_probs=26.3

Q ss_pred             CccccccccccccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      -..|..|+++|.+.++.+.|+.|||.||
T Consensus         8 lEkC~~C~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCSCCEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHHHHHHHhCCCCCCCCC
Confidence            3579999999999999999999999998

>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=98.60  E-value=1.7e-08  Score=46.09  Aligned_cols=32  Identities=19%  Similarity=0.593  Sum_probs=29.4

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      .|..|.++|++++|..+|++|||..||.++|+
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            47889999999999999999999999998874

>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=98.55  E-value=3.3e-08  Score=45.33  Aligned_cols=32  Identities=31%  Similarity=0.807  Sum_probs=29.2

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      +|..|.+|+.++.|++.+|+|||+.+|.++.+
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            58899999999999999999999999998753

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=3.6e-08  Score=44.41  Aligned_cols=32  Identities=25%  Similarity=0.629  Sum_probs=29.3

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      .|..|+++|+++.|.++|+++||.+||-++|+
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            47889999999999999999999999998763

>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=98.50  E-value=1.1e-08  Score=46.91  Aligned_cols=27  Identities=22%  Similarity=0.277  Sum_probs=25.2

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLG  116 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~  116 (120)
                      .|..|.+|+.+++|++.||+|||+.|+
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~Hy   27 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHY   27 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhh
Confidence            488999999999999999999999886

>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=98.49  E-value=1.7e-08  Score=44.52  Aligned_cols=25  Identities=28%  Similarity=0.830  Sum_probs=22.8

Q ss_pred             CCCCCCcccC----cEEEEeCcccccccc
Q psy17880         65 CAQCGEYVEG----EVVTALGKTYHQKCF   89 (120)
Q Consensus        65 C~~C~~~i~~----~~~~~~~~~~H~~Cf   89 (120)
                      |+.|.+||++    .+|.+.++.||.+||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            7899999975    699999999999998

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.48  E-value=4e-08  Score=43.38  Aligned_cols=30  Identities=37%  Similarity=0.807  Sum_probs=27.8

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHh
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQK   59 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~   59 (120)
                      |+|+.|++.|.+.....+||.+||+.||.+
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            789999999988888899999999999975

>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=98.47  E-value=3.6e-08  Score=43.37  Aligned_cols=25  Identities=24%  Similarity=0.820  Sum_probs=22.7

Q ss_pred             CCCCCCcccC----cEEEEeCcccccccc
Q psy17880         65 CAQCGEYVEG----EVVTALGKTYHQKCF   89 (120)
Q Consensus        65 C~~C~~~i~~----~~~~~~~~~~H~~Cf   89 (120)
                      |..|.+||+|    .+|.+.++.||.+||
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            7889999975    699999999999998

>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=98.44  E-value=4.7e-09  Score=48.11  Aligned_cols=33  Identities=36%  Similarity=0.712  Sum_probs=30.4

Q ss_pred             HHHhHhCCCCCCCCCcccCcEEEEeCccccccc
Q psy17880         56 DYQKKFGTKCAQCGEYVEGEVVTALGKTYHQKC   88 (120)
Q Consensus        56 c~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~C   88 (120)
                      +|..+|+..|..|++.|+|.+|++.+..||++|
T Consensus         2 dYw~kfge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           2 DYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             cHHHHHHHHhhhhHhhcccceeeecccccCCCC
Confidence            466788999999999999999999999999997

>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=98.44  E-value=6.6e-08  Score=43.62  Aligned_cols=28  Identities=29%  Similarity=0.674  Sum_probs=24.9

Q ss_pred             Cccccccccccccc-eEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCSGE-VLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf   30 (120)
                      ...|++|+++|.++ ++.++++.||.+|+
T Consensus         2 ~~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           2 WKRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             ccccCCCCCccchhhhhccchhhhhhhhC
Confidence            56899999999888 67899999999985

>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=98.36  E-value=1.4e-07  Score=42.33  Aligned_cols=31  Identities=45%  Similarity=1.016  Sum_probs=27.7

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      +|..|++.|.+ .|..+||.|||+.+|...|+
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            58899999976 69999999999999998874

>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=98.35  E-value=5e-08  Score=43.86  Aligned_cols=30  Identities=17%  Similarity=0.227  Sum_probs=25.1

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +|..|++.|+ ++|+-.||.|||+++++..|
T Consensus         1 kC~~C~~vL~-gEYm~kdG~PyCe~DY~~~F   30 (31)
T d2dj7a1           1 KCQTCSVILT-GEYISKDGVPYCESDYHAQF   30 (31)
T ss_dssp             BCSSSCCBCS-SCCEEETTEEECTTHHHHHT
T ss_pred             CccccCcccc-ceeecCCCCcccHHHHHHhc
Confidence            5889999885 45788999999999987665

>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=98.35  E-value=1.6e-07  Score=46.72  Aligned_cols=34  Identities=35%  Similarity=0.826  Sum_probs=31.4

Q ss_pred             cccccccccCCCCeeecCCeecc-HhHHHhHhCCC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYC-TSDYQKKFGTK   64 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C-~~c~~~~~~~~   64 (120)
                      +|..|++.|++....++++++|| +.||.++|+|+
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPk   35 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPK   35 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCC
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCC
Confidence            58899999999999999999999 77999999985

>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=98.35  E-value=5.6e-08  Score=43.08  Aligned_cols=29  Identities=31%  Similarity=0.769  Sum_probs=25.8

Q ss_pred             CCcccccccccc-ccceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      |++.|++|++.+ +.+.+..+++.||..||
T Consensus         1 Mn~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           1 MNPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCCcccccCCccccHHHhhhhHHHHhhccC
Confidence            678999999988 56788899999999997

>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=98.30  E-value=2e-07  Score=41.81  Aligned_cols=29  Identities=24%  Similarity=0.529  Sum_probs=25.9

Q ss_pred             CCcccccccccc-ccceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      |++.|.+|++++ ..+.+..+|+.||..|+
T Consensus         1 M~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           1 MASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCCcCCCCCCceeeHHhhccCCcccccccC
Confidence            678999999999 67888999999999885

>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=98.29  E-value=3.5e-07  Score=41.67  Aligned_cols=34  Identities=26%  Similarity=0.789  Sum_probs=31.6

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHhHhCC
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT   63 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~   63 (120)
                      |+|+.|.+|+-+...+.+.|..||+.+|.++|+.
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            7899999999888999999999999999999864

>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=98.29  E-value=2e-07  Score=41.83  Aligned_cols=28  Identities=25%  Similarity=0.670  Sum_probs=24.3

Q ss_pred             CCccccccccccccc-eEEECCccccccc
Q psy17880          2 IKAYCTSCKKKCSGE-VLRVQDKYFHITC   29 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~C   29 (120)
                      +...|++|+++|.++ ++.++++.||.+|
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            346799999999888 6789999999887

>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=98.25  E-value=4.6e-07  Score=48.07  Aligned_cols=34  Identities=38%  Similarity=0.697  Sum_probs=31.6

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhCCC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK   64 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~   64 (120)
                      .|..|++.|++.....+++++||+.||.++|+|+
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPk   34 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK   34 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCC
Confidence            3889999999989999999999999999999986

>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=98.24  E-value=3.4e-07  Score=41.20  Aligned_cols=27  Identities=26%  Similarity=0.817  Sum_probs=24.0

Q ss_pred             CCCCCCCCcccCc-EEEEeCcccccccc
Q psy17880         63 TKCAQCGEYVEGE-VVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf   89 (120)
                      ..|++|+++|.++ ++.+.++.||..|.
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            5799999999987 56899999999884

>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=98.20  E-value=5.3e-08  Score=47.52  Aligned_cols=31  Identities=23%  Similarity=0.372  Sum_probs=28.2

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +|+.|++.|+.++|...+|.+||+.|+.|-|
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF   31 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLF   31 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHS
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHH
Confidence            6899999999999999999999999987644

>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=98.19  E-value=5.7e-07  Score=43.75  Aligned_cols=34  Identities=35%  Similarity=0.836  Sum_probs=31.0

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhCCC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTK   64 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~   64 (120)
                      +|+.|++.|..+.|...+|.+||+.||.++|.++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhh
Confidence            5889999999999999999999999999998653

>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=98.19  E-value=3.2e-07  Score=42.39  Aligned_cols=28  Identities=21%  Similarity=0.542  Sum_probs=25.5

Q ss_pred             CccccccccccccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      .+.|.+|+++|...-|+..++.||.+||
T Consensus         8 a~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           8 APRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             SCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             HHHHhhcCCccccCceeecCCcchhhhC
Confidence            5689999999988888999999999998

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.17  E-value=4.5e-07  Score=41.80  Aligned_cols=28  Identities=36%  Similarity=0.870  Sum_probs=25.1

Q ss_pred             Ccccccccccc-ccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      ...|+.|++.| .|+.+.++++.||..||
T Consensus         8 ~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           8 PSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             CccccccchhhhCCceeeeeecceeeeeC
Confidence            45799999999 67899999999999998

>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=98.17  E-value=9e-07  Score=39.94  Aligned_cols=32  Identities=22%  Similarity=0.671  Sum_probs=29.1

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      .|..|.++|+..+|..+++..||..||++.|+
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            37889999999999999999999999999874

>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=98.15  E-value=1.9e-07  Score=42.58  Aligned_cols=32  Identities=22%  Similarity=0.264  Sum_probs=28.8

Q ss_pred             cccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         89 FTCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        89 f~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |.|+.|.+|+-+...++.+|.+||+.++.+-|
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLf   32 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLF   32 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHC
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHh
Confidence            78999999999999999999999999886643

>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=98.11  E-value=1.4e-06  Score=39.27  Aligned_cols=32  Identities=34%  Similarity=0.795  Sum_probs=29.1

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      .|..|.+||+..+|..+++..||..||+++|+
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            37789999999999999999999999999874

>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=98.10  E-value=5.4e-07  Score=41.52  Aligned_cols=27  Identities=41%  Similarity=0.919  Sum_probs=24.6

Q ss_pred             CCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      ..|+.|++.| .|..+.+.++.||.+||
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            5799999999 46899999999999998

>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=98.10  E-value=1.6e-06  Score=39.04  Aligned_cols=31  Identities=42%  Similarity=0.903  Sum_probs=28.3

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF   61 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~   61 (120)
                      .|+.|+.+|.+-.|+...|++||+.||++.+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHT
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhc
Confidence            3788999999889999999999999999865

>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=98.10  E-value=5.5e-07  Score=41.09  Aligned_cols=27  Identities=26%  Similarity=0.689  Sum_probs=26.1

Q ss_pred             CCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      |.|..|+..|.|.+|.+.++.+|++||
T Consensus         9 p~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             ccccccCCCcEeEEEEeccccCCCCCC
Confidence            789999999999999999999999997

>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=98.10  E-value=3.4e-07  Score=46.05  Aligned_cols=31  Identities=19%  Similarity=0.322  Sum_probs=28.0

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +|..|++.|+.......||+|||+.++.+.|
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~f   31 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNF   31 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHT
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhcc
Confidence            6899999999989999999999999987765

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.08  E-value=8.5e-07  Score=40.13  Aligned_cols=27  Identities=41%  Similarity=0.922  Sum_probs=23.5

Q ss_pred             CCCCCCCCccc--CcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYVE--GEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i~--~~~~~~~~~~~H~~Cf   89 (120)
                      ..|++|++.|.  +.++.+.+..||.+||
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            36999999995  3588999999999998

>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=98.06  E-value=9.1e-07  Score=39.63  Aligned_cols=26  Identities=19%  Similarity=0.694  Sum_probs=23.1

Q ss_pred             CCCCCCCCcccCc-EEEEeCccccccc
Q psy17880         63 TKCAQCGEYVEGE-VVTALGKTYHQKC   88 (120)
Q Consensus        63 ~~C~~C~~~i~~~-~~~~~~~~~H~~C   88 (120)
                      ..|++|+++|.++ ++.+.++.||.+|
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            5799999999987 5689999999887

>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=98.05  E-value=2.5e-07  Score=42.12  Aligned_cols=30  Identities=17%  Similarity=0.135  Sum_probs=26.4

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGRA  119 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~  119 (120)
                      .|..|+++|.++.|...|++|||-.++..-
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~l   30 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDL   30 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHH
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhh
Confidence            378999999999999999999998887543

>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=98.04  E-value=8.3e-07  Score=38.99  Aligned_cols=25  Identities=28%  Similarity=0.873  Sum_probs=22.1

Q ss_pred             cccccccccc----ceEEECCcccccccc
Q psy17880          6 CTSCKKKCSG----EVLRVQDKYFHITCF   30 (120)
Q Consensus         6 C~~C~~~i~~----~~~~~~~~~~H~~Cf   30 (120)
                      |++|.+||.|    +++...++.||.+||
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    589999999999997

>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=98.04  E-value=1.9e-06  Score=38.20  Aligned_cols=29  Identities=28%  Similarity=0.723  Sum_probs=26.8

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHh
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQK   59 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~   59 (120)
                      .|..|+++|++.+|...++++||-+||..
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

>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=98.03  E-value=1.3e-06  Score=41.38  Aligned_cols=29  Identities=21%  Similarity=0.492  Sum_probs=25.1

Q ss_pred             CCccccccccccc--cceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKCS--GEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf   30 (120)
                      ..+.|..|+++|.  ++.|.+.|+.||..||
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            3578999999994  4589999999999998

>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=98.02  E-value=2.1e-06  Score=38.78  Aligned_cols=25  Identities=16%  Similarity=0.329  Sum_probs=23.6

Q ss_pred             ccccCCCcCCCCceeeeCCeeeecc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENR  114 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~  114 (120)
                      +|..|++.|+.++..+.||+|||.+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~   25 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHK   25 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTT
T ss_pred             CchhcccccCCCCccccCCCcCcCc
Confidence            5899999999999999999999986

>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=98.01  E-value=1.4e-06  Score=38.18  Aligned_cols=25  Identities=40%  Similarity=0.913  Sum_probs=22.0

Q ss_pred             cccccccccc----ceEEECCcccccccc
Q psy17880          6 CTSCKKKCSG----EVLRVQDKYFHITCF   30 (120)
Q Consensus         6 C~~C~~~i~~----~~~~~~~~~~H~~Cf   30 (120)
                      |.+|.+||.|    +++...++.||.+||
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            7899999963    489999999999997

>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=97.99  E-value=1.3e-06  Score=39.83  Aligned_cols=28  Identities=21%  Similarity=0.612  Sum_probs=26.2

Q ss_pred             CccccccccccccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      -+.|.+|+..|-|.++.+.++.+||+||
T Consensus         8 lp~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             CccccccCCCcEeEEEEeccccCCCCCC
Confidence            3689999999999999999999999997

>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=97.97  E-value=1.1e-06  Score=42.65  Aligned_cols=27  Identities=41%  Similarity=0.802  Sum_probs=26.1

Q ss_pred             CCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      |.|..|+..|.|.+|.+.++.+|++||
T Consensus        19 P~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          19 PLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             ccccccCCCcEEEEEEeccccCCCCCC
Confidence            789999999999999999999999998

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.93  E-value=2.9e-06  Score=37.89  Aligned_cols=28  Identities=39%  Similarity=0.867  Sum_probs=24.8

Q ss_pred             CCCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         62 GTKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        62 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      .++|++|++++ ..+.+...|+.||..|+
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            47899999999 57889999999999884

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=97.93  E-value=1.5e-06  Score=43.21  Aligned_cols=31  Identities=13%  Similarity=0.210  Sum_probs=26.3

Q ss_pred             ccccCCCcCCCCceeeeCCeeee-ccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYE-NRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC-~~~~~~~~  120 (120)
                      +|..|++.|+.+...+.||+||| +.++...|
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~F   32 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMF   32 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhcc
Confidence            68999999999999999999999 55765443

>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=97.92  E-value=2.5e-06  Score=39.89  Aligned_cols=28  Identities=29%  Similarity=0.611  Sum_probs=25.1

Q ss_pred             CCCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         62 GTKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        62 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      ..+|..|++.+ .-+.+.+.|+.||.+||
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            36899999999 45899999999999998

>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=97.90  E-value=6.2e-06  Score=36.62  Aligned_cols=30  Identities=23%  Similarity=0.620  Sum_probs=27.2

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhH
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKK   60 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~   60 (120)
                      .|..|+..|.++.||..+.+.||+.||...
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            478899999999999999999999999764

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.89  E-value=1.3e-06  Score=38.40  Aligned_cols=29  Identities=24%  Similarity=0.347  Sum_probs=26.4

Q ss_pred             cccccCCCcCCCCceeeeCCeeeeccCCC
Q psy17880         89 FTCARCRFSKKREIYNWLGGRAYENRLGG  117 (120)
Q Consensus        89 f~C~~C~~~l~~~~~~~~~g~~yC~~~~~  117 (120)
                      |+|+.|++.|........||.+||+.++.
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cya   29 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYA   29 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeee
Confidence            78999999999988999999999998764

>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=97.88  E-value=2.9e-06  Score=40.78  Aligned_cols=26  Identities=35%  Similarity=0.701  Sum_probs=24.5

Q ss_pred             ccccccccccccceEEECCccccccc
Q psy17880          4 AYCTSCKKKCSGEVLRVQDKYFHITC   29 (120)
Q Consensus         4 ~~C~~C~~~i~~~~~~~~~~~~H~~C   29 (120)
                      ..|..|.+-|+|++|.+.++.|||+|
T Consensus        16 ~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          16 TRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             cccccccCEeeeeeeEecCcccCCCC
Confidence            47999999999999999999999987

>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=97.87  E-value=3.2e-06  Score=36.24  Aligned_cols=25  Identities=28%  Similarity=0.865  Sum_probs=21.9

Q ss_pred             CCCCCCccc-C-cEEEEeCcccccccc
Q psy17880         65 CAQCGEYVE-G-EVVTALGKTYHQKCF   89 (120)
Q Consensus        65 C~~C~~~i~-~-~~~~~~~~~~H~~Cf   89 (120)
                      |..|.+.|. | +.|++.|..||..||
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            778999995 4 589999999999998

>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=97.87  E-value=1.2e-06  Score=38.87  Aligned_cols=26  Identities=38%  Similarity=0.921  Sum_probs=24.3

Q ss_pred             CCCCCCCCcccCcEEEEeCccccccc
Q psy17880         63 TKCAQCGEYVEGEVVTALGKTYHQKC   88 (120)
Q Consensus        63 ~~C~~C~~~i~~~~~~~~~~~~H~~C   88 (120)
                      .-|..|.+.|+|+++++.+++||+.|
T Consensus         6 sgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhhhhhccccccCCCC
Confidence            56999999999999999999999987

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.86  E-value=1.8e-06  Score=42.36  Aligned_cols=27  Identities=41%  Similarity=0.977  Sum_probs=24.3

Q ss_pred             CCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      ++|..|++.+ .-+.+.+.|+.||..||
T Consensus        16 ~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          16 DGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            6899999999 45788999999999998

>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=97.85  E-value=2.9e-06  Score=41.15  Aligned_cols=28  Identities=36%  Similarity=0.812  Sum_probs=26.2

Q ss_pred             CccccccccccccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      -+.|.+|+..|-|.++.+.++.+|++||
T Consensus        18 LP~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             CccccccCCCcEEEEEEeccccCCCCCC
Confidence            3689999999999999999999999997

>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=97.85  E-value=6.1e-06  Score=37.19  Aligned_cols=32  Identities=34%  Similarity=0.835  Sum_probs=28.2

Q ss_pred             cccccccccCCCCeeecCCeeccH-hHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCT-SDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~-~c~~~~~~   62 (120)
                      +|..|++.|..+...+++|++||. .||..+|+
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            588999999999999999999996 59988774

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.79  E-value=1.5e-06  Score=39.15  Aligned_cols=29  Identities=17%  Similarity=0.188  Sum_probs=26.1

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      .|+.|+++|....|++.+|.+||+.++.+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~   29 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEK   29 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHH
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHH
Confidence            38899999999999999999999988754

>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=97.76  E-value=3.4e-06  Score=37.41  Aligned_cols=28  Identities=25%  Similarity=0.546  Sum_probs=25.4

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGG  117 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~  117 (120)
                      .|+.|+..|....+++.++++||++|.+
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr   28 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHAR   28 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhh
Confidence            4899999999999999999999999875

>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=97.76  E-value=3.2e-06  Score=39.66  Aligned_cols=28  Identities=39%  Similarity=0.809  Sum_probs=24.7

Q ss_pred             CCCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         62 GTKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        62 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      +.+|..|++.+ +-+.+.+.|+.||.+||
T Consensus         8 ~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeEEEecCcEeccccC
Confidence            37899999999 45788999999999998

>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=97.74  E-value=8.7e-06  Score=36.21  Aligned_cols=31  Identities=39%  Similarity=0.784  Sum_probs=27.6

Q ss_pred             ccccccccCCCCeeecCCeeccHhHHHhHhC
Q psy17880         32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      |-.|++.|++.....+++++||+.||-++++
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            6789999998888999999999999988764

>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=97.73  E-value=7.1e-06  Score=36.99  Aligned_cols=28  Identities=29%  Similarity=0.788  Sum_probs=23.9

Q ss_pred             Cccccccccccc--cceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKCS--GEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf   30 (120)
                      ...|++|++.|+  +-++.+.+..||.+||
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            467999999995  3478899999999998

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=2.9e-06  Score=38.04  Aligned_cols=29  Identities=14%  Similarity=0.235  Sum_probs=25.9

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      .|+.|+++|.++.|...|+.|||-.++..
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~   29 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGE   29 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHH
T ss_pred             CccccCccccCCccccCCCCccHHHHhHh
Confidence            48899999999999999999999887653

>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=97.68  E-value=5.4e-06  Score=35.46  Aligned_cols=25  Identities=44%  Similarity=1.006  Sum_probs=21.6

Q ss_pred             CCCCCCccc-C-cEEEEeCcccccccc
Q psy17880         65 CAQCGEYVE-G-EVVTALGKTYHQKCF   89 (120)
Q Consensus        65 C~~C~~~i~-~-~~~~~~~~~~H~~Cf   89 (120)
                      |..|.+.|+ | +.+.+.|.+||..||
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            678999994 4 578999999999998

>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=97.66  E-value=1.3e-05  Score=37.43  Aligned_cols=29  Identities=34%  Similarity=0.775  Sum_probs=25.3

Q ss_pred             CCcccccccccc-ccceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      ....|..|++.+ .-+.+.++|+.||..||
T Consensus         6 ~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           6 ARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            356899999998 56788999999999998

>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=97.65  E-value=1.4e-05  Score=34.07  Aligned_cols=25  Identities=24%  Similarity=0.709  Sum_probs=21.2

Q ss_pred             CCCCCCccc--CcEEEEeCcccccccc
Q psy17880         65 CAQCGEYVE--GEVVTALGKTYHQKCF   89 (120)
Q Consensus        65 C~~C~~~i~--~~~~~~~~~~~H~~Cf   89 (120)
                      |..|.+||-  ..-+...++.||..||
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            678999994  3578899999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.62  E-value=5.1e-06  Score=36.62  Aligned_cols=28  Identities=43%  Similarity=0.930  Sum_probs=24.1

Q ss_pred             CCCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         62 GTKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        62 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      ++.|++|++.+ +.+-|.-.++.||..||
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            47899999998 45678888999999998

>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=97.59  E-value=3.5e-05  Score=34.27  Aligned_cols=28  Identities=18%  Similarity=0.479  Sum_probs=23.1

Q ss_pred             ccccCCCcC-CCCceeeeCCeeeeccCCC
Q psy17880         90 TCARCRFSK-KREIYNWLGGRAYENRLGG  117 (120)
Q Consensus        90 ~C~~C~~~l-~~~~~~~~~g~~yC~~~~~  117 (120)
                      .|+.|...| .++.|...+|.+||+.+.-
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~p   29 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDRP   29 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGCC
T ss_pred             CcccccccccCCceeEEecCEEEEecCCc
Confidence            488898888 5567999999999998753

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.56  E-value=1.6e-05  Score=38.92  Aligned_cols=28  Identities=25%  Similarity=0.560  Sum_probs=24.2

Q ss_pred             Ccccccccccc-ccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      ...|..|++.+ ..+.+.+.|+.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            35799999998 56778899999999998

>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=97.54  E-value=4.8e-05  Score=33.28  Aligned_cols=31  Identities=35%  Similarity=0.882  Sum_probs=28.2

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF   61 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~   61 (120)
                      +|+.|.+.++.+.|+.++...||..|.+.+|
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            4889999999889999999999999998776

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.52  E-value=6.6e-06  Score=43.50  Aligned_cols=31  Identities=19%  Similarity=0.365  Sum_probs=27.6

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      .|..|++.|+.......++++||+.++++.|
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~f   31 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKY   31 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHH
T ss_pred             CchhcCCccCCCccccCCCcccchhhhcccc
Confidence            3889999999999999999999999987654

>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=97.46  E-value=5.9e-05  Score=34.24  Aligned_cols=32  Identities=25%  Similarity=0.588  Sum_probs=26.9

Q ss_pred             cccccccccCCCCeee-cCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLAQGGYFN-KDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~-~~~~~~C~~c~~~~~~   62 (120)
                      +|..|++.|++-.|.. .++++||..+|.++|+
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            4788999999887774 5789999999999873

>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=97.42  E-value=4e-05  Score=32.57  Aligned_cols=25  Identities=28%  Similarity=0.894  Sum_probs=20.9

Q ss_pred             ccccccccc--cceEEECCcccccccc
Q psy17880          6 CTSCKKKCS--GEVLRVQDKYFHITCF   30 (120)
Q Consensus         6 C~~C~~~i~--~~~~~~~~~~~H~~Cf   30 (120)
                      |..|.+||.  .+-+...++.||..||
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            678999994  4567888999999997

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.40  E-value=1.9e-05  Score=35.46  Aligned_cols=30  Identities=10%  Similarity=0.136  Sum_probs=26.6

Q ss_pred             cccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         91 CARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        91 C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |..|++||+..+|...|+..||-.++...|
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcccccccccCCCCceEeecchhhc
Confidence            789999999999999999999998876544

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.39  E-value=2e-05  Score=35.33  Aligned_cols=30  Identities=13%  Similarity=0.167  Sum_probs=26.6

Q ss_pred             cccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         91 CARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        91 C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |..|.+||+..+|...++..||-.++..+|
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcccccccccCCCcEEEEecccccc
Confidence            789999999999999999999998876544

>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=97.37  E-value=3.2e-05  Score=36.14  Aligned_cols=28  Identities=32%  Similarity=0.688  Sum_probs=24.1

Q ss_pred             Ccccccccccc-ccceEEECCcccccccc
Q psy17880          3 KAYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      ..+|..|++.+ .-+.+.++|+.||..||
T Consensus         8 ~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeEEEecCcEeccccC
Confidence            46799999988 55677899999999998

>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=97.32  E-value=4e-06  Score=37.21  Aligned_cols=28  Identities=14%  Similarity=0.316  Sum_probs=24.9

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGG  117 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~  117 (120)
                      .|+.|+..|....+.+.++++||++|.+
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr   28 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHAR   28 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhh
Confidence            3889999998888999999999999875

>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=97.30  E-value=6.5e-05  Score=32.06  Aligned_cols=25  Identities=36%  Similarity=0.854  Sum_probs=21.3

Q ss_pred             cccccccc-cc-ceEEECCcccccccc
Q psy17880          6 CTSCKKKC-SG-EVLRVQDKYFHITCF   30 (120)
Q Consensus         6 C~~C~~~i-~~-~~~~~~~~~~H~~Cf   30 (120)
                      |..|.+.| +| +.+...|.+||..||
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            67899998 44 588999999999997

>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=97.30  E-value=1.9e-05  Score=35.12  Aligned_cols=30  Identities=20%  Similarity=0.365  Sum_probs=27.3

Q ss_pred             cccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         91 CARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        91 C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      |..|++.|+.......++.+||+.++++.|
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkky   31 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKY   31 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccC
Confidence            778999999999999999999999988765

>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=97.30  E-value=2.9e-05  Score=34.30  Aligned_cols=26  Identities=38%  Similarity=0.821  Sum_probs=24.0

Q ss_pred             ccccccccccccceEEECCccccccc
Q psy17880          4 AYCTSCKKKCSGEVLRVQDKYFHITC   29 (120)
Q Consensus         4 ~~C~~C~~~i~~~~~~~~~~~~H~~C   29 (120)
                      .-|..|.+-|.|+++.+.++.|||.|
T Consensus         6 sgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhhhhhccccccCCCC
Confidence            45899999999999999999999987

>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=97.23  E-value=5.4e-05  Score=32.23  Aligned_cols=25  Identities=28%  Similarity=0.781  Sum_probs=20.9

Q ss_pred             cccccccc-cc-ceEEECCcccccccc
Q psy17880          6 CTSCKKKC-SG-EVLRVQDKYFHITCF   30 (120)
Q Consensus         6 C~~C~~~i-~~-~~~~~~~~~~H~~Cf   30 (120)
                      |..|.+.| +| +.+...|.+||..||
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            67899988 44 478889999999997

>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=97.10  E-value=0.0001  Score=32.34  Aligned_cols=29  Identities=21%  Similarity=0.356  Sum_probs=25.9

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      +|..|-.||.++.|...|++++|.++..|
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~sr   29 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTTR   29 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHTT
T ss_pred             CchhhccccccCcccccCCeEeecccccc
Confidence            58889999999999999999999987654

>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=97.05  E-value=0.00032  Score=30.86  Aligned_cols=29  Identities=34%  Similarity=0.799  Sum_probs=25.4

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHh
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQK   59 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~   59 (120)
                      .|++|+..|....+|..++++||+.+-..
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            48999999998889999999999988654

>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=96.95  E-value=0.00015  Score=32.03  Aligned_cols=27  Identities=22%  Similarity=0.396  Sum_probs=24.7

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLG  116 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~  116 (120)
                      .|..|+..|.++-|+-++.+.||+.++
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CY   27 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCY   27 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHH
T ss_pred             CeeEeCceecCCcceEeecccccccee
Confidence            478999999999999999999999876

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.88  E-value=0.00019  Score=31.59  Aligned_cols=27  Identities=11%  Similarity=0.181  Sum_probs=23.3

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLG  116 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~  116 (120)
                      .|+.|+++|.+.+|...+++.||-.++
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCY   27 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCY   27 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeee
Confidence            478899999999999999999997654

>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=96.86  E-value=0.00011  Score=31.64  Aligned_cols=26  Identities=42%  Similarity=0.997  Sum_probs=21.0

Q ss_pred             CCCCCCCCcc-cCcEEEEeCccccccc
Q psy17880         63 TKCAQCGEYV-EGEVVTALGKTYHQKC   88 (120)
Q Consensus        63 ~~C~~C~~~i-~~~~~~~~~~~~H~~C   88 (120)
                      .+|.+|++.+ ..+.|.-.|+.||..|
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            4689999999 4566777899999876

>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=96.85  E-value=0.0004  Score=30.39  Aligned_cols=28  Identities=25%  Similarity=0.568  Sum_probs=24.9

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHH
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQ   58 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~   58 (120)
                      +|+.|-.+|..+.|..+|++++|..|..
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5888999999999999999999998853

>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=96.82  E-value=0.00021  Score=30.73  Aligned_cols=26  Identities=23%  Similarity=0.524  Sum_probs=21.3

Q ss_pred             cccccccccc-ccceEEECCccccccc
Q psy17880          4 AYCTSCKKKC-SGEVLRVQDKYFHITC   29 (120)
Q Consensus         4 ~~C~~C~~~i-~~~~~~~~~~~~H~~C   29 (120)
                      ..|.+|++.+ ..+.+...|++||..|
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            4799999988 4567778899999876

>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=96.78  E-value=0.00043  Score=29.45  Aligned_cols=27  Identities=26%  Similarity=0.716  Sum_probs=23.1

Q ss_pred             cccccccccc-ccceEEECCcccccccc
Q psy17880          4 AYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         4 ~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      ..|+.|.+.+ ..+-+...|++||..||
T Consensus         1 nkcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           1 NKCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             CBCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             CccccccceEeeeeeeeecCceeccccC
Confidence            3689999988 56788899999999987

>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=96.75  E-value=0.00021  Score=31.21  Aligned_cols=31  Identities=16%  Similarity=0.231  Sum_probs=26.2

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~  120 (120)
                      +|+.|++.|..++|..++...||-.+..+.|
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            4899999999999999999999987655443

>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=96.74  E-value=0.00028  Score=32.08  Aligned_cols=29  Identities=21%  Similarity=0.375  Sum_probs=25.6

Q ss_pred             CCccccccccccccceEEECCcccccccc
Q psy17880          2 IKAYCTSCKKKCSGEVLRVQDKYFHITCF   30 (120)
Q Consensus         2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   30 (120)
                      .+-+|.+|+..|+++-+...+..||+..|
T Consensus         7 Gk~vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           7 GKYICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCBCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             hhHHHHHHHhhhhcCcceecCCCCCCCCC
Confidence            46789999999998888899999999876

>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=96.72  E-value=0.00023  Score=32.15  Aligned_cols=26  Identities=19%  Similarity=0.616  Sum_probs=23.6

Q ss_pred             ccccccccccccceEEECCccccccc
Q psy17880          4 AYCTSCKKKCSGEVLRVQDKYFHITC   29 (120)
Q Consensus         4 ~~C~~C~~~i~~~~~~~~~~~~H~~C   29 (120)
                      ..|..|.+.|+|.++.+.+..|||+|
T Consensus         9 e~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           9 EFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             HHhhhhHhhcccceeeecccccCCCC
Confidence            57999999999999989899999997

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.66  E-value=0.00029  Score=31.61  Aligned_cols=27  Identities=37%  Similarity=0.808  Sum_probs=23.3

Q ss_pred             CCCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      .+|..|.+.+ ..+-|.-.|+.||..||
T Consensus         8 ~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           8 KKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             EECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             ceeccccceEeeeeeeeecCcccccccC
Confidence            5899999988 45667899999999997

>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=96.61  E-value=0.00063  Score=28.91  Aligned_cols=26  Identities=42%  Similarity=0.981  Sum_probs=22.4

Q ss_pred             CCCCCCCcc-cCcEEEEeCcccccccc
Q psy17880         64 KCAQCGEYV-EGEVVTALGKTYHQKCF   89 (120)
Q Consensus        64 ~C~~C~~~i-~~~~~~~~~~~~H~~Cf   89 (120)
                      +|..|.+.+ ..+-|.-.|+.||..||
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            688899988 46778999999999997

>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=96.59  E-value=0.00032  Score=31.63  Aligned_cols=32  Identities=34%  Similarity=0.828  Sum_probs=26.2

Q ss_pred             cccccccccC--CCCeeecCCeeccHhHHHhHhC
Q psy17880         31 QCSVCKNSLA--QGGYFNKDGAYYCTSDYQKKFG   62 (120)
Q Consensus        31 ~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~~~~   62 (120)
                      +|+-|+..|.  ++..|.+.+.++|+.+|.++|+
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            4677777774  3478999999999999999885

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.47  E-value=0.0006  Score=30.52  Aligned_cols=27  Identities=30%  Similarity=0.695  Sum_probs=23.1

Q ss_pred             cccccccccc-ccceEEECCcccccccc
Q psy17880          4 AYCTSCKKKC-SGEVLRVQDKYFHITCF   30 (120)
Q Consensus         4 ~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   30 (120)
                      ..|+.|.+.+ ..+.+...|++||..||
T Consensus         8 ~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           8 KKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             EECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             ceeccccceEeeeeeeeecCcccccccC
Confidence            4699999988 56778899999999997

>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=96.45  E-value=0.0004  Score=30.60  Aligned_cols=30  Identities=27%  Similarity=0.634  Sum_probs=25.3

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhH
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKK   60 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~   60 (120)
                      .|++|+..|....+|..++++||+.+-..+
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            488999999887889899999999886543

>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=96.33  E-value=0.0014  Score=29.66  Aligned_cols=28  Identities=21%  Similarity=0.599  Sum_probs=22.7

Q ss_pred             CCccccccccccc--cceEEECCccccccc
Q psy17880          2 IKAYCTSCKKKCS--GEVLRVQDKYFHITC   29 (120)
Q Consensus         2 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~C   29 (120)
                      ++..|.+|+....  +++|...|..||+.|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            4567999998873  558899999999887

>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=96.27  E-value=0.001  Score=27.68  Aligned_cols=25  Identities=32%  Similarity=0.844  Sum_probs=20.5

Q ss_pred             ccccccccc--cceEEECCcccccccc
Q psy17880          6 CTSCKKKCS--GEVLRVQDKYFHITCF   30 (120)
Q Consensus         6 C~~C~~~i~--~~~~~~~~~~~H~~Cf   30 (120)
                      |..|++.+.  +.-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            778999874  4567889999999987

>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=96.21  E-value=0.00044  Score=31.27  Aligned_cols=31  Identities=13%  Similarity=0.042  Sum_probs=25.8

Q ss_pred             ccccCCCcCCCCceeee-CCeeeeccCCCcCC
Q psy17880         90 TCARCRFSKKREIYNWL-GGRAYENRLGGRAY  120 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~-~g~~yC~~~~~~~~  120 (120)
                      +|..|++.|.+-.|... ++++||-.++-|.|
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkf   32 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKF   32 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhc
Confidence            48889999999988876 79999998876654

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.21  E-value=0.001  Score=27.68  Aligned_cols=25  Identities=48%  Similarity=0.990  Sum_probs=21.0

Q ss_pred             CCCCCCcccC--cEEEEeCcccccccc
Q psy17880         65 CAQCGEYVEG--EVVTALGKTYHQKCF   89 (120)
Q Consensus        65 C~~C~~~i~~--~~~~~~~~~~H~~Cf   89 (120)
                      |..|++-+.+  .-+.+.++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            6789988865  478899999999987

>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=95.42  E-value=0.0086  Score=26.76  Aligned_cols=31  Identities=26%  Similarity=0.611  Sum_probs=24.4

Q ss_pred             ccccccccccCCC-Cee-ecCCeeccHhHHHhH
Q psy17880         30 FQCSVCKNSLAQG-GYF-NKDGAYYCTSDYQKK   60 (120)
Q Consensus        30 f~C~~C~~~l~~~-~~~-~~~~~~~C~~c~~~~   60 (120)
                      |.|..|+..++++ .|. ....++||-.||.+.
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            6789999999877 444 456799999999764

>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=95.36  E-value=0.016  Score=25.43  Aligned_cols=28  Identities=14%  Similarity=0.312  Sum_probs=25.0

Q ss_pred             cccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         91 CARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        91 C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      |..|+.+|-++.|...+..++|.+++..
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cgsg   29 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCGSG   29 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTTCC
T ss_pred             CccceEEEEeeeeeeccCcEEehhcCCC
Confidence            6788889999999999999999999864

>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=95.33  E-value=0.0074  Score=26.20  Aligned_cols=29  Identities=24%  Similarity=0.497  Sum_probs=23.3

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhH
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKK   60 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~   60 (120)
                      .|+.|++.|.. .-....|.+||..|..+.
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            37889999976 467788999999998763

>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=95.14  E-value=0.0061  Score=26.77  Aligned_cols=26  Identities=35%  Similarity=0.940  Sum_probs=21.1

Q ss_pred             cccccccccCCC-CeeecCCeeccHhH
Q psy17880         31 QCSVCKNSLAQG-GYFNKDGAYYCTSD   56 (120)
Q Consensus        31 ~C~~C~~~l~~~-~~~~~~~~~~C~~c   56 (120)
                      .|+.|...|..+ .|...+|.+||+.+
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D   27 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHD   27 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGG
T ss_pred             CcccccccccCCceeEEecCEEEEecC
Confidence            478898888655 78889999999876

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.53  E-value=0.0044  Score=27.97  Aligned_cols=27  Identities=19%  Similarity=0.503  Sum_probs=22.8

Q ss_pred             CCCCCCCCcccCcEEEEeCcccccccc
Q psy17880         63 TKCAQCGEYVEGEVVTALGKTYHQKCF   89 (120)
Q Consensus        63 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf   89 (120)
                      -.|..|...|.+.-+.+.+..||+.+|
T Consensus         9 ~vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           9 YICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CBCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             HHHHHHHhhhhcCcceecCCCCCCCCC
Confidence            468888888888778889999999876

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.33  E-value=0.0062  Score=26.72  Aligned_cols=29  Identities=17%  Similarity=0.150  Sum_probs=25.1

Q ss_pred             ccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880         90 TCARCRFSKKREIYNWLGGRAYENRLGGR  118 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~  118 (120)
                      +|..|...|.+..|+..-|+.+|..+..|
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            58899999999999999999999877543

>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=94.25  E-value=0.005  Score=28.75  Aligned_cols=28  Identities=25%  Similarity=0.599  Sum_probs=18.2

Q ss_pred             ccccccccc-ccceEEE-CCcccccccccc
Q psy17880          5 YCTSCKKKC-SGEVLRV-QDKYFHITCFQC   32 (120)
Q Consensus         5 ~C~~C~~~i-~~~~~~~-~~~~~H~~Cf~C   32 (120)
                      .|.+|++.+ .|+-+-+ .+..|||.|-.-
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~~~   30 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACRQA   30 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHHHH
T ss_pred             CcchhhccccccceeeecCCceeCCccccc
Confidence            488888887 4553333 356799887543

>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=93.80  E-value=0.039  Score=24.05  Aligned_cols=30  Identities=23%  Similarity=0.654  Sum_probs=26.0

Q ss_pred             cccccccccCCCCeeecCCeeccHhHHHhH
Q psy17880         31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKK   60 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~   60 (120)
                      +|..|...|.+..|.-..|..+|..|..+.
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            578899999988899999999999998653

>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=93.42  E-value=0.023  Score=24.88  Aligned_cols=25  Identities=24%  Similarity=0.712  Sum_probs=20.5

Q ss_pred             ccccccccCCCCeeecCCeeccHhH
Q psy17880         32 CSVCKNSLAQGGYFNKDGAYYCTSD   56 (120)
Q Consensus        32 C~~C~~~l~~~~~~~~~~~~~C~~c   56 (120)
                      |..|+.+|.++.|......++|.+|
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            6678888888888888888888766

>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=92.86  E-value=0.045  Score=23.15  Aligned_cols=27  Identities=22%  Similarity=0.536  Sum_probs=22.3

Q ss_pred             ccccccccCCCCeeecCCeeccHhHHH
Q psy17880         32 CSVCKNSLAQGGYFNKDGAYYCTSDYQ   58 (120)
Q Consensus        32 C~~C~~~l~~~~~~~~~~~~~C~~c~~   58 (120)
                      |..|+.+|.+..|....+.++|.+|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            677888998888888888899998854

>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=92.78  E-value=0.065  Score=23.48  Aligned_cols=29  Identities=17%  Similarity=0.153  Sum_probs=22.3

Q ss_pred             ccccCCCcCCCCceee--eCCeeeeccCCCc
Q psy17880         90 TCARCRFSKKREIYNW--LGGRAYENRLGGR  118 (120)
Q Consensus        90 ~C~~C~~~l~~~~~~~--~~g~~yC~~~~~~  118 (120)
                      +|..|...|..+.|..  .||..||..+.-|
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlpq   31 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ   31 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccCC
Confidence            4788888998776554  5899999887643

>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=92.48  E-value=0.039  Score=30.73  Aligned_cols=45  Identities=22%  Similarity=0.407  Sum_probs=30.7

Q ss_pred             cccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc
Q psy17880         29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE   73 (120)
Q Consensus        29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~   73 (120)
                      -+.|..|...+........-|..||..|..+.+...|..|..++.
T Consensus        22 ~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~   66 (97)
T d1jm7b_          22 LLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAW   66 (97)
T ss_dssp             TTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCS
T ss_pred             cCCCccCCchhhcCceeCCCCCchhHHHHHHHHhccccccCCcCc
Confidence            367888877775532223457888888877766667888877664

>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=91.55  E-value=0.09  Score=26.15  Aligned_cols=43  Identities=9%  Similarity=0.061  Sum_probs=29.9

Q ss_pred             cccccccccCCCCeee-cCCeeccHhHHHhHhC--CCCCCCCCcccC
Q psy17880         31 QCSVCKNSLAQGGYFN-KDGAYYCTSDYQKKFG--TKCAQCGEYVEG   74 (120)
Q Consensus        31 ~C~~C~~~l~~~~~~~-~~~~~~C~~c~~~~~~--~~C~~C~~~i~~   74 (120)
                      .|..|...+.+ .... ..|..||.+|-.+-+.  ..|..|++++..
T Consensus         2 ~C~Ic~~~~~~-Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~   47 (56)
T d2baya1           2 LCAISGKVPRR-PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSI   47 (56)
T ss_dssp             CCTTTCSCCSS-EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCG
T ss_pred             CCccCCchHHh-cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCH
Confidence            57778777754 3444 5789999888655332  678888888853

>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=90.35  E-value=0.17  Score=21.99  Aligned_cols=29  Identities=28%  Similarity=0.668  Sum_probs=22.0

Q ss_pred             cccccccccCC--CCeeecCCeeccHhHHHh
Q psy17880         31 QCSVCKNSLAQ--GGYFNKDGAYYCTSDYQK   59 (120)
Q Consensus        31 ~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~   59 (120)
                      .|.-|+-.|++  +..|.+.+.++|+.+|.+
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhc
Confidence            45666666653  468889999999999976

>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=90.33  E-value=0.12  Score=23.57  Aligned_cols=10  Identities=30%  Similarity=0.946  Sum_probs=4.5

Q ss_pred             cccccccccC
Q psy17880         31 QCSVCKNSLA   40 (120)
Q Consensus        31 ~C~~C~~~l~   40 (120)
                      .|+.|+++++
T Consensus         2 vC~vCr~pFP   11 (40)
T d1v6ga2           2 VCAVCRLPFP   11 (40)
T ss_dssp             SCSSSCCCCC
T ss_pred             cccccCCCCC
Confidence            4444444443

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.01  E-value=0.32  Score=25.72  Aligned_cols=47  Identities=9%  Similarity=0.078  Sum_probs=36.5

Q ss_pred             cccccccccccccCCCCeeecCCeeccHhHHHhHh---CCCCCCCCCcccC
Q psy17880         27 ITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF---GTKCAQCGEYVEG   74 (120)
Q Consensus        27 ~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~---~~~C~~C~~~i~~   74 (120)
                      ++-|.|..|...+.+ ......|..||..|-.+.+   +..|..|+.+|..
T Consensus         5 P~~l~CpIc~~l~~d-Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMRE-PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCSS-EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhhh-hcccCCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            567899999988866 4667789999999876643   3578899888853

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.15  E-value=0.67  Score=24.17  Aligned_cols=48  Identities=19%  Similarity=0.297  Sum_probs=36.6

Q ss_pred             cccccccccccccCCCCeeecCCeeccHhHHHhHh---CCCCCCCCCcccCc
Q psy17880         27 ITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF---GTKCAQCGEYVEGE   75 (120)
Q Consensus        27 ~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~---~~~C~~C~~~i~~~   75 (120)
                      ++-|.|..|...+.+ ......|..||..|..+.+   ...|..|+.++...
T Consensus         6 P~~l~CpIc~~~m~d-PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           6 PEYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CccCCCcCcCchhhC-ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            355899999988865 4667899999999987644   24688888888543

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.81  E-value=0.19  Score=24.99  Aligned_cols=41  Identities=15%  Similarity=0.309  Sum_probs=21.1

Q ss_pred             ccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcc
Q psy17880         30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYV   72 (120)
Q Consensus        30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i   72 (120)
                      +.|..|...+.+ .....=|..||..|..+ ....|..|..+|
T Consensus         7 l~C~IC~~~~~~-p~~lpCgH~fC~~Ci~~-~~~~CP~Cr~~~   47 (56)
T d1bora_           7 LRCQQCQAEAKC-PKLLPCLHTLCSGCLEA-SGMQCPICQAPW   47 (56)
T ss_dssp             SSCSSSCSSCBC-CSCSTTSCCSBTTTCSS-SSSSCSSCCSSS
T ss_pred             CCCcccCcccCC-CEEecCCCHHhHHHHHc-CCCcCcCCCCcc
Confidence            466666665543 22233455666666433 234555555555

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.21  E-value=0.27  Score=26.72  Aligned_cols=46  Identities=17%  Similarity=0.383  Sum_probs=35.2

Q ss_pred             ccccccccccccCCCCeeecCCeeccHhHHHhHh---CCCCCCCCCcccC
Q psy17880         28 TCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF---GTKCAQCGEYVEG   74 (120)
Q Consensus        28 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~---~~~C~~C~~~i~~   74 (120)
                      +-+.|..|...+.. .....=|..||..|-.+.+   +..|..|..++..
T Consensus        22 ~~l~C~IC~~~~~~-pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          22 KSISCQICEHILAD-PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HHTBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCcCCccCCcchhc-ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            45789999887754 4667789999999987643   3679999888753

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=81.21  E-value=0.9  Score=23.06  Aligned_cols=42  Identities=17%  Similarity=0.276  Sum_probs=21.4

Q ss_pred             ccccccccCCCCeeecCCeeccHhHHHhH--hCCCCCCCCCccc
Q psy17880         32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKK--FGTKCAQCGEYVE   73 (120)
Q Consensus        32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~--~~~~C~~C~~~i~   73 (120)
                      |..|...+........=+..+|..|..+-  ....|..|..+|.
T Consensus         8 C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           8 CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CccCCcCccCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            44554444332222344556666666432  2356777766664