Psyllid ID: psy10221

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-------
Protein Sequence
MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEEEccccHHHcccccccccccccccccEEEEccEEcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHcccccHHcccccccHHHEEEEHHcHHHHHHHHHHHHcccccccccEEEEEcccEEEcccccc
Coil and Loop (DISEMBL)
MFKTIITELRYCVACgesitdkyllqvsdkswhaqclrccicqlvldrhpscfikdeavyckqdyak
Flexible Loop (DISEMBL)
MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLdrhpscfikdeavyckqdyAK
Low Complexity Region (SEG)
MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK
Disordered region (IsUnstruct)
**KTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQ****
Disordered Region (DISOPRED)
***********CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK
Disordered Region (DISEMBL)
MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK
Disordered Region (DISPRO)
MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK
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	67	2.2.26 [Sep-21-2011]
Q8IRC7	275	LIM/homeobox protein Awh	yes	N/A	0.940	0.229	0.587	1e-16
A2PZF9	379	LIM/homeobox protein Lhx9	N/A	N/A	0.835	0.147	0.482	3e-13
Q80W90	388	LIM/homeobox protein Lhx9	yes	N/A	0.820	0.141	0.482	3e-13
A2I8Z7	377	LIM/homeobox protein Lhx9	N/A	N/A	0.835	0.148	0.482	3e-13
Q90881	397	LIM/homeobox protein Lhx9	yes	N/A	0.835	0.141	0.482	4e-13
Q9WUH2	397	LIM/homeobox protein Lhx9	yes	N/A	0.820	0.138	0.482	5e-13
Q9NQ69	397	LIM/homeobox protein Lhx9	yes	N/A	0.820	0.138	0.482	5e-13
Q9Z0S2	406	LIM/homeobox protein Lhx2	no	N/A	0.820	0.135	0.482	8e-13
A0JNI8	397	LIM/homeobox protein Lhx9	yes	N/A	0.820	0.138	0.482	9e-13
Q1LWV4	396	LIM/homeobox protein Lhx9	yes	N/A	0.820	0.138	0.482	1e-12

>sp|Q8IRC7|AWH_DROME LIM/homeobox protein Awh OS=Drosophila melanogaster GN=Awh PE=1 SV=1

 Score = 84.7 bits (208), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 46/63 (73%)

Query: 5  IITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
          + TELR C ACGE I+D++ L+V   SWHA CLRCC+C   LDR  SCFI++  VYCK D
Sbjct: 1  MKTELRSCAACGEPISDRFFLEVGGCSWHAHCLRCCMCMCPLDRQQSCFIRERQVYCKAD 60

Query: 65 YAK 67
          Y+K
Sbjct: 61 YSK 63

Probable transcription factor. Required for the establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings.
Drosophila melanogaster (taxid: 7227)

>sp|A2PZF9|LHX9_GLARU LIM/homeobox protein Lhx9 OS=Glandirana rugosa GN=lhx9 PE=2 SV=1

 Score = 73.9 bits (180), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 53  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 108

May be involved in gonadal development.

Glandirana rugosa (taxid: 8410)

>sp|Q80W90|LHX9_RAT LIM/homeobox protein Lhx9 OS=Rattus norvegicus GN=Lhx9 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 62  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 117

Involved in gonadal development.

Rattus norvegicus (taxid: 10116)

>sp|A2I8Z7|LHX9_ASTFA LIM/homeobox protein Lhx9 OS=Astyanax fasciatus GN=lhx9 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 52  CAGCGSKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 107

May be involved in gonadal development.

Astyanax fasciatus (taxid: 223369)

>sp|Q90881|LHX9_CHICK LIM/homeobox protein Lhx9 OS=Gallus gallus GN=LHX9 PE=2 SV=2

 Score = 73.2 bits (178), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 71  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

May be involved in gonadal development.

Gallus gallus (taxid: 9031)

>sp|Q9WUH2|LHX9_MOUSE LIM/homeobox protein Lhx9 OS=Mus musculus GN=Lhx9 PE=1 SV=3

 Score = 73.2 bits (178), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 71  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

Involved in gonadal development.

Mus musculus (taxid: 10090)

>sp|Q9NQ69|LHX9_HUMAN LIM/homeobox protein Lhx9 OS=Homo sapiens GN=LHX9 PE=1 SV=3

 Score = 73.2 bits (178), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 71  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

Involved in gonadal development.

Homo sapiens (taxid: 9606)

>sp|Q9Z0S2|LHX2_MOUSE LIM/homeobox protein Lhx2 OS=Mus musculus GN=Lhx2 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 53  CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDYYR 108

Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.

Mus musculus (taxid: 10090)

>sp|A0JNI8|LHX9_BOVIN LIM/homeobox protein Lhx9 OS=Bos taurus GN=LHX9 PE=2 SV=2

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 37/56 (66%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 71  CAGCGGKIADRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

Involved in gonadal development.

Bos taurus (taxid: 9913)

>sp|Q1LWV4|LHX9_DANRE LIM/homeobox protein Lhx9 OS=Danio rerio GN=lhx9 PE=2 SV=1

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 12  CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY +
Sbjct: 71  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

May be involved in gonadal development.

Danio rerio (taxid: 7955)

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	67
91078266	343	PREDICTED: similar to GA10520-PA [Tribol	0.910	0.177	0.721	2e-20
270004863	349	arrowhead [Tribolium castaneum]	0.910	0.174	0.721	2e-20
357605400	406	hypothetical protein KGM_21596 [Danaus p	0.985	0.162	0.621	2e-18
379698940	274	arrowhead PA [Bombyx mori] gi|346223348|	0.940	0.229	0.619	2e-17
346223350	105	arrowhead PB [Bombyx mori]	0.910	0.580	0.622	1e-16
328708271	346	PREDICTED: LIM/homeobox protein Awh-like	0.940	0.182	0.587	3e-16
312371800	295	hypothetical protein AND_21634 [Anophele	0.895	0.203	0.616	7e-16
157134682	306	arrowhead [Aedes aegypti] gi|108870378|g	0.895	0.196	0.633	8e-16
170034020	304	arrowhead [Culex quinquefasciatus] gi|16	0.880	0.194	0.627	1e-15
170034030	169	arrowhead [Culex quinquefasciatus] gi|16	1.0	0.396	0.582	2e-15

>gi|91078266|ref|XP_971202.1| PREDICTED: similar to GA10520-PA [Tribolium castaneum]

 Score =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/61 (72%), Positives = 52/61 (85%)

Query: 7   TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
           TE R C ACGE I+DK+LL+VS +SWHA+CLRCC+CQL LDR PSCFI+D A+YCK DYA
Sbjct: 78  TEYRLCSACGEPISDKFLLEVSGRSWHARCLRCCVCQLQLDRQPSCFIRDRAIYCKADYA 137

Query: 67  K 67
           K
Sbjct: 138 K 138

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270004863|gb|EFA01311.1| arrowhead [Tribolium castaneum]

 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/61 (72%), Positives = 52/61 (85%)

Query: 7   TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
           TE R C ACGE I+DK+LL+VS +SWHA+CLRCC+CQL LDR PSCFI+D A+YCK DYA
Sbjct: 64  TEYRLCSACGEPISDKFLLEVSGRSWHARCLRCCVCQLQLDRQPSCFIRDRAIYCKADYA 123

Query: 67  K 67
           K
Sbjct: 124 K 124

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357605400|gb|EHJ64588.1| hypothetical protein KGM_21596 [Danaus plexippus]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 49/66 (74%)

Query: 2   FKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYC 61
           F T  TE R C ACGE I D++LL+V   +WH  CLRCC+C + LDRHPSCF++D  VYC
Sbjct: 128 FSTSGTEHRTCCACGEPIADRFLLEVGGGAWHTGCLRCCVCAVQLDRHPSCFLRDRQVYC 187

Query: 62  KQDYAK 67
           KQDYAK
Sbjct: 188 KQDYAK 193

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|379698940|ref|NP_001243941.1| arrowhead PA [Bombyx mori] gi|346223348|dbj|BAK78925.1| arrowhead PA [Bombyx mori]

 Score = 92.8 bits (229), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 5  IITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
          + TE R C ACGE I D++LL+V   +WH  CLRCC+C + LDRHPSCF++D  VYCKQD
Sbjct: 1  MKTEHRTCCACGEPIADRFLLEVGGAAWHTGCLRCCVCAVQLDRHPSCFLRDRQVYCKQD 60

Query: 65 YAK 67
          YAK
Sbjct: 61 YAK 63

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346223350|dbj|BAK78926.1| arrowhead PB [Bombyx mori]

 Score = 90.5 bits (223), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 38/61 (62%), Positives = 46/61 (75%)

Query: 7  TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
          TE R C ACGE I D++LL+V   +WH  CLRCC+C + LDRHPSCF++D  VYCKQDYA
Sbjct: 3  TEHRTCCACGEPIADRFLLEVGGAAWHTGCLRCCVCAVQLDRHPSCFLRDRQVYCKQDYA 62

Query: 67 K 67
           
Sbjct: 63 N 63

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328708271|ref|XP_001949712.2| PREDICTED: LIM/homeobox protein Awh-like [Acyrthosiphon pisum]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 49/63 (77%)

Query: 5   IITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
           + TE   C  C + ITD++LL+VSDK WH  CLRCC+C LVL+  PSCFIKD+++YC+QD
Sbjct: 54  VKTESLQCRGCSDPITDRFLLKVSDKIWHVSCLRCCVCNLVLEDEPSCFIKDDSIYCRQD 113

Query: 65  YAK 67
           YA+
Sbjct: 114 YAR 116

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312371800|gb|EFR19896.1| hypothetical protein AND_21634 [Anopheles darlingi]

 Score = 87.8 bits (216), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 37/60 (61%), Positives = 45/60 (75%)

Query: 8   ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           ELR C ACGE I+DK+LL V   SWH+ CLRCCIC   LD+ PSC+++D  +YCK DYAK
Sbjct: 236 ELRSCTACGEPISDKFLLDVGGCSWHSACLRCCICHTPLDQQPSCYVRDRQIYCKTDYAK 295

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157134682|ref|XP_001663345.1| arrowhead [Aedes aegypti] gi|108870378|gb|EAT34603.1| AAEL013168-PA, partial [Aedes aegypti]

 Score = 87.8 bits (216), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 38/60 (63%), Positives = 43/60 (71%)

Query: 8  ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          ELR C ACGE I+DKYLL V   SWH+ CLRCCIC   LD  PSCF++D  +YCK DY K
Sbjct: 4  ELRSCTACGEPISDKYLLDVGGCSWHSACLRCCICHNPLDHQPSCFLRDRQIYCKNDYTK 63

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170034020|ref|XP_001844873.1| arrowhead [Culex quinquefasciatus] gi|167875281|gb|EDS38664.1| arrowhead [Culex quinquefasciatus]

 Score = 86.7 bits (213), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/59 (62%), Positives = 44/59 (74%)

Query: 8  ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
          ELR C ACGE I+D+YLL V   SWH+ CLRCCIC   LD+ PSCF++D  +YCK DYA
Sbjct: 6  ELRSCTACGEPISDQYLLDVGGCSWHSACLRCCICHTPLDQQPSCFLRDRQIYCKADYA 64

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170034030|ref|XP_001844878.1| arrowhead [Culex quinquefasciatus] gi|167875286|gb|EDS38669.1| arrowhead [Culex quinquefasciatus]

 Score = 86.7 bits (213), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/67 (58%), Positives = 46/67 (68%)

Query: 1   MFKTIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVY 60
           M + I TELR CVACGE I DKYL  V   SWH  CLRC +C  +L+R PSC+ +D  VY
Sbjct: 103 MMRKIKTELRTCVACGEPIADKYLFDVDGCSWHGSCLRCSVCLTLLERQPSCYFRDRQVY 162

Query: 61  CKQDYAK 67
           C+ DYAK
Sbjct: 163 CRTDYAK 169

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	67
FB|FBgn0013751	275	Awh "Arrowhead" [Drosophila me	0.910	0.221	0.606	1.4e-18
ZFIN|ZDB-GENE-031008-2	332	lhx8a "LIM homeobox 8a" [Danio	0.895	0.180	0.516	2.5e-15
UNIPROTKB|J9PBA6	295	LHX8 "Uncharacterized protein"	0.805	0.183	0.537	1.4e-14
UNIPROTKB|H0YL58	68	LHX8 "LIM/homeobox protein Lhx	0.805	0.794	0.537	2.3e-14
UNIPROTKB|C8YLT4	295	Lhx8 "LIM homeobox 8" [Sus scr	0.805	0.183	0.537	3.2e-14
UNIPROTKB|E2REU0	379	LHX8 "Uncharacterized protein"	0.805	0.142	0.537	4.2e-14
UNIPROTKB|F1P4G9	347	LHX8 "Uncharacterized protein"	0.805	0.155	0.537	5.3e-14
MGI|MGI:1096343	367	Lhx8 "LIM homeobox protein 8"	0.805	0.147	0.537	6.4e-14
UNIPROTKB|G3V6V6	367	Lhx8 "RCG29002" [Rattus norveg	0.805	0.147	0.537	6.4e-14
UNIPROTKB|E1BBB7	371	LHX8 "Uncharacterized protein"	0.805	0.145	0.537	6.6e-14

FB|FBgn0013751 Awh "Arrowhead" [Drosophila melanogaster (taxid:7227)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 37/61 (60%), Positives = 45/61 (73%)

Query:     7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
             TELR C ACGE I+D++ L+V   SWHA CLRCC+C   LDR  SCFI++  VYCK DY+
Sbjct:     3 TELRSCAACGEPISDRFFLEVGGCSWHAHCLRCCMCMCPLDRQQSCFIRERQVYCKADYS 62

Query:    67 K 67
             K
Sbjct:    63 K 63

GO:0007444 "imaginal disc development" evidence=IMP

GO:0005634 "nucleus" evidence=ISS

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

ZFIN|ZDB-GENE-031008-2 lhx8a "LIM homeobox 8a" [Danio rerio (taxid:7955)]

 Score = 196 (74.1 bits), Expect = 2.5e-15, P = 2.5e-15
 Identities = 31/60 (51%), Positives = 42/60 (70%)

Query:     6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             +TE   C +CG  I DKYLL+V+D  WH +CL C +CQ  L RH SC+IK++ ++CK DY
Sbjct:    45 MTEKAICTSCGTEIVDKYLLKVNDMCWHVRCLSCSVCQTSLGRHISCYIKEKEIFCKLDY 104

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|J9PBA6 LHX8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 187 (70.9 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    14 CNSCGREIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 67

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|H0YL58 LHX8 "LIM/homeobox protein Lhx8" [Homo sapiens (taxid:9606)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    14 CNSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 67

GO:0008270 "zinc ion binding" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

UNIPROTKB|C8YLT4 Lhx8 "LIM homeobox 8" [Sus scrofa (taxid:9823)]

 Score = 184 (69.8 bits), Expect = 3.2e-14, P = 3.2e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    14 CNSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 67

GO:0005634 "nucleus" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|E2REU0 LHX8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 187 (70.9 bits), Expect = 4.2e-14, P = 4.2e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    98 CNSCGREIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 151

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1P4G9 LHX8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 185 (70.2 bits), Expect = 5.3e-14, P = 5.3e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    66 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 119

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

MGI|MGI:1096343 Lhx8 "LIM homeobox protein 8" [Mus musculus (taxid:10090)]

 Score = 185 (70.2 bits), Expect = 6.4e-14, P = 6.4e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    96 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 149

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007611 "learning or memory" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008585 "female gonad development" evidence=IMP

GO:0021879 "forebrain neuron differentiation" evidence=IMP

GO:0021884 "forebrain neuron development" evidence=IGI

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|G3V6V6 Lhx8 "RCG29002" [Rattus norvegicus (taxid:10116)]

 Score = 185 (70.2 bits), Expect = 6.4e-14, P = 6.4e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    96 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 149

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

GO:0005634 "nucleus" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|E1BBB7 LHX8 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 185 (70.2 bits), Expect = 6.6e-14, P = 6.6e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query:    12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
             C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct:    96 CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 149

GO:0005634 "nucleus" evidence=IEA

GO:0042475 "odontogenesis of dentin-containing tooth" evidence=IEA

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0007611 "learning or memory" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" 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)
Q8IRC7	AWH_DROME	No assigned EC number	0.5873	0.9402	0.2290	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	67
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	8e-23
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	3e-16
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	4e-14
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	4e-13
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	5e-13
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	3e-12
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	4e-12
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	5e-12
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-10
cd09370	52	cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a	2e-10
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	4e-10
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	7e-10
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	2e-09
pfam00412	58	pfam00412, LIM, LIM domain	3e-09
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	6e-09
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	1e-08
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	1e-08
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	1e-07
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	3e-07
cd09355	53	cd09355, LIM2_Ajuba_like, The second LIM domain of	4e-06
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	9e-06
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	1e-05
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	2e-04
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	3e-04
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	0.001
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	0.001

>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH)

 Score = 81.3 bits (201), Expect = 8e-23
 Identities = 33/54 (61%), Positives = 41/54 (75%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CGE ITD++LL+VS +SWH  CLRCC+CQ  L+R PSCF +D  +YCK DY
Sbjct: 1  CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54

The first LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 64.7 bits (158), Expect = 3e-16
 Identities = 28/54 (51%), Positives = 36/54 (66%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CGE I D++ L   D+ WHA CL+CC C+L LD   SCF +D  +YCK+DY
Sbjct: 1  CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54

The first 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 = 54

>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8

 Score = 59.6 bits (144), Expect = 4e-14
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C +CG  I DKYLL+V+D  WH +CL C +C+  L RH SC+IKD+ ++CK DY
Sbjct: 2  CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55

The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 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. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. 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|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 56.9 bits (137), Expect = 4e-13
 Identities = 27/54 (50%), Positives = 37/54 (68%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64

The first LIM domain of Lhx2: Lhx2 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 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. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to 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 = 64

>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 56.6 bits (137), Expect = 5e-13
 Identities = 27/55 (49%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 12 CVACGESITDKYLLQVS-DKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          CV CG  I D+Y+L+V+ D  WHA CL+C  C   LD   +CF++D   YCK+DY
Sbjct: 1  CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55

The first 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 Is l2 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|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9

 Score = 54.7 bits (131), Expect = 3e-12
 Identities = 27/54 (50%), Positives = 37/54 (68%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CG  I+D+Y L   DK WH +CL+CC C+L L+   +CF KD ++YCK+DY
Sbjct: 1  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54

The first LIM domain of Lhx9: Lhx9 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. Lhx9 is highly homologous to Lhx2. It 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 have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. 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 = 54

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

 Score = 54.3 bits (131), Expect = 4e-12
 Identities = 26/54 (48%), Positives = 38/54 (70%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C   I+D+YLL+V+++SWH +CL+C +CQ  L    SC+ +D  +YCKQDY
Sbjct: 1  CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPL--TTSCYFRDRKLYCKQDY 52

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|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 54.3 bits (130), Expect = 5e-12
 Identities = 25/54 (46%), Positives = 39/54 (72%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C +CG  I D+YLL+V++  WH +CL C +C+  L +H SC+IK++ ++CK DY
Sbjct: 1  CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54

The first LIM domain of Lhx6. Lhx6 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. Lhx6 functions in the brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. 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 = 54

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

 Score = 50.0 bits (120), Expect = 2e-10
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CG+ I  + LL+   K WH +C +C +C   L    S + KD   YC++ Y
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 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|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a

 Score = 50.2 bits (120), Expect = 2e-10
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C   I D++LL+V+D  WH +CL+C  C+  L    +CF +D+ +YCK+DY
Sbjct: 1  CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPL--ETTCFYRDKKLYCKEDY 52

The first LIM domain of Lmx1a: Lmx1a 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. 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. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. 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, Bmp 6, 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. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. 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 = 52

>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4 family

 Score = 49.3 bits (118), Expect = 4e-10
 Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C E I D+++L+V D++WHA+CL+C  C   L     CF ++  VYCK D+
Sbjct: 1  CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTD--KCFARNGHVYCKDDF 52

The first 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 = 52

>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a

 Score = 48.6 bits (116), Expect = 7e-10
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C   I D+++L+V DK WH++CL+C  CQ  L     CF +   VYCK+D+
Sbjct: 4  CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTD--KCFSRGGQVYCKEDF 55

The first LIM domain of Lhx3a: Lhx3a 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. Lhx3a 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 = 56

>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only protein 4)

 Score = 47.4 bits (113), Expect = 2e-09
 Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDY 65
          C  CG  I D++LL   D+ WH  CL+C  CQ  L +   SC+ K   + CK DY
Sbjct: 1  CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55

The first 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|215907 pfam00412, LIM, LIM domain

 Score = 47.3 bits (113), Expect = 3e-09
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 12 CVACGESITDKYLLQVS-DKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  CG+ I D+ L++ +  K WH +C RC +C   L      F KD  +YCK DY K
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPG-DFFEKDGKLYCKHDYFK 56

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

>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 46.1 bits (109), Expect = 6e-09
 Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C + I DK++L+V D+ WH+ CL+C  CQ+ L     CF +   VYCK+D+
Sbjct: 1  CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAER--CFSRAGNVYCKEDF 52

The first 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 = 52

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

 Score = 45.5 bits (108), Expect = 1e-08
 Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C   I DK+LL V D++WHA+C++CC C+  L     CF ++  +YC+ D+
Sbjct: 1  CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTE--KCFSREGKLYCRNDF 52

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

>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 45.7 bits (108), Expect = 1e-08
 Identities = 22/54 (40%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C + I D+++L+V D+ WH++CL+C  CQ  L     CF + ++VYCK D+
Sbjct: 4  CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAE--KCFSRGDSVYCKDDF 55

The first 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 = 55

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

 Score = 43.3 bits (102), Expect = 1e-07
 Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 7  TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
            L  C +CG+SI D   LQ  +  WHA C RCC C   L      + KD  ++CK+DY
Sbjct: 17 NVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHW--YYEKDGRLFCKKDY 73

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

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

 Score = 41.6 bits (98), Expect = 3e-07
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 12 CVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64
          C  CG+ I   + +L+   K WH +C +C  C   L    + F KD  +YCK  
Sbjct: 2  CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL-SGDTFFEKDGKLYCKDC 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|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like proteins

 Score = 39.2 bits (92), Expect = 4e-06
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CG  I +  +LQ   KS+H  C RCC+C   LD  P     +  +YC +DY
Sbjct: 1  CAVCGHLIMEM-ILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53

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

 Score = 38.2 bits (89), Expect = 9e-06
 Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C   I D   +Q  ++ WH  C RC +C   L      F KD  +YC++DY
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL--SNWYFEKDGKLYCRKDY 52

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

>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 37.9 bits (88), Expect = 1e-05
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSC-FIKDEAVYCKQDY 65
          C  C   I D+YLL+  D+ WH  CL+C  C   L    S  + K   + C++DY
Sbjct: 1  CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55

The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. 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|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain Kinase 2)

 Score = 34.8 bits (80), Expect = 2e-04
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CG  I D +  +V  ++WH  C +C +CQ +L      + KD  +YC + Y
Sbjct: 1  CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNW--YYEKDGKLYCHKHY 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|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only protein 2)

 Score = 34.4 bits (79), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL---DRHPSCFIKDEAVYCKQDY 65
          C  C ++I D+Y L+  D+ WH  CL C +C   L    R    + K     C++DY
Sbjct: 1  CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRR--LYYKLGRKLCRRDY 55

The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. 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|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 33.1 bits (76), Expect = 0.001
 Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  CG+ I +   L   DK WH  C +C  C  VL        KD   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|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 33.0 bits (75), Expect = 0.001
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEA--VYCKQDYAK 67
          C  C + ITD+ +L+ + KS+H QC  C +C+  L+     FI D+A   +C  DY +
Sbjct: 1  CAVCDQKITDR-MLKATGKSYHPQCFTCVVCKCPLEGES--FIVDQANQPHCVNDYHR 55

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	67
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.78
KOG1701|consensus	468		99.53
KOG4577|consensus	383		99.35
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	99.27
KOG1701|consensus	468		99.27
KOG1044|consensus	670		99.27
KOG1703|consensus	479		99.25
KOG2272|consensus	332		99.07
KOG4577|consensus	383		98.94
KOG2272|consensus	332		98.81
KOG1700|consensus	200		98.6
KOG1700|consensus	200		98.49
KOG1702|consensus	264		98.44
KOG1703|consensus	479		98.2
KOG1044|consensus	670		98.11
KOG0490|consensus	235		97.02
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	95.0
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	94.68
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	94.55
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	94.1
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	92.87
PF14471	51	DUF4428: Domain of unknown function (DUF4428)	92.16
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	90.74
PF12674	81	Zn_ribbon_2: Putative zinc ribbon domain	88.94
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	88.9
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	88.42
COG2191	206	Formylmethanofuran dehydrogenase subunit E [Energy	87.84
PF04570	58	DUF581: Protein of unknown function (DUF581); Inte	87.8
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	87.52
PF10886	54	DUF2685: Protein of unknown function (DUF2685); In	87.37
PF06689	41	zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IP	87.32
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	85.41
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	84.85
PF00645	82	zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligas	84.57
PF11781	36	RRN7: RNA polymerase I-specific transcription init	84.55
KOG2893|consensus	341		84.51
PF02069	52	Metallothio_Pro: Prokaryotic metallothionein; Inte	84.42
PF13834	99	DUF4193: Domain of unknown function (DUF4193)	84.11
PRK00420	112	hypothetical protein; Validated	81.69
COG4847	103	Uncharacterized protein conserved in archaea [Func	81.08
PF07503	35	zf-HYPF: HypF finger; InterPro: IPR011125 Zinc fin	80.61
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	80.51

>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=99.78  E-value=3.5e-19  Score=79.10  Aligned_cols=55  Identities=33%  Similarity=0.796  Sum_probs=49.1

Q ss_pred             ccccCccccCceee-eecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         12 CVACGESITDKYLL-QVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        12 C~~C~~~i~~~~~~-~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      |.+|+++|.+.+.+ .+.++.||++||+|..|+++|.+.. ++..++++||+.||.+
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~   56 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQK   56 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHH
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhh
Confidence            78999999977665 6999999999999999999998876 6889999999999863

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 ....

>KOG1701|consensus

Probab=99.53  E-value=2.2e-16  Score=90.99  Aligned_cols=63  Identities=33%  Similarity=0.734  Sum_probs=57.0

Q ss_pred             ccccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          4 TIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         4 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      .|+....+|..|++.|.++ ++++.++.||+.||+|..|.+.|++..+....++++||..||+|
T Consensus       329 cyq~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~  391 (468)
T KOG1701|consen  329 CYQDTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHK  391 (468)
T ss_pred             HHHHHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhh
Confidence            3566678999999999997 78999999999999999999999998877778999999999975

>KOG4577|consensus

Probab=99.35  E-value=9.5e-15  Score=81.30  Aligned_cols=58  Identities=40%  Similarity=1.041  Sum_probs=53.8

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      +.+.|++|.+.|.++.++.++++.||..|++|+.|..+|.+.  +|.+++.+||+.+|+|
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr--CFsR~~s~yCkedFfK   89 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR--CFSREGSVYCKEDFFK   89 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH--HhhcCCceeehHHHHH
Confidence            678999999999999999999999999999999999999875  6789999999999875

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

Probab=99.27  E-value=4.6e-12  Score=51.69  Aligned_cols=37  Identities=32%  Similarity=0.889  Sum_probs=32.8

Q ss_pred             cccccCccccCc-eeeeecCceeccccccccccccccC
Q psy10221         11 YCVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLD   47 (67)
Q Consensus        11 ~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~~~l~   47 (67)
                      +|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            488999999975 5678889999999999999999885

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.

>KOG1701|consensus

Probab=99.27  E-value=3.6e-13  Score=77.99  Aligned_cols=58  Identities=22%  Similarity=0.583  Sum_probs=50.4

Q ss_pred             CCccccccCccccCce-eeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+.+|.+|+|.|.... .+.++++.||..||+|..|++.|.+.. +|..|+++||+.||.
T Consensus       273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~-FY~v~~k~~CE~cyq  331 (468)
T KOG1701|consen  273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQS-FYQVDGKPYCEGCYQ  331 (468)
T ss_pred             hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhcccc-ccccCCcccchHHHH
Confidence            3458999999999543 478999999999999999999998765 578999999999985

>KOG1044|consensus

Probab=99.27  E-value=2.2e-12  Score=77.12  Aligned_cols=58  Identities=34%  Similarity=0.796  Sum_probs=52.8

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+...|++|++.|...+.+.++++.||..||+|..|+..|.+.  +..++|.+||+.||+
T Consensus       131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge--y~skdg~pyce~dy~  188 (670)
T KOG1044|consen  131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE--YMSKDGVPYCEKDYQ  188 (670)
T ss_pred             cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce--eeccCCCcchhhhhh
Confidence            4567899999999998889999999999999999999999875  578999999999986

>KOG1703|consensus

Probab=99.25  E-value=1.6e-12  Score=77.17  Aligned_cols=59  Identities=24%  Similarity=0.529  Sum_probs=51.8

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ....+.|.+|+.+|.+. .+.+.+..||+.||.|..|++++.+.. ++.+++.+||+.||.
T Consensus       360 ~~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~-~~~~~~~pyce~~~~  418 (479)
T KOG1703|consen  360 APFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSS-FFESDGEPYCEDHYK  418 (479)
T ss_pred             HhhCccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCc-ccccCCccchhhhHh
Confidence            34568999999999986 677889999999999999999998865 578999999999985

>KOG2272|consensus

Probab=99.07  E-value=1e-11  Score=68.40  Aligned_cols=58  Identities=24%  Similarity=0.619  Sum_probs=50.4

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      -+.++|..|.++|.+. ++.++++.||.+.|+|+.|.+|.-+-. -|++.|..||+.+|.
T Consensus       193 mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGHr-HYEkkGlaYCe~h~~  250 (332)
T KOG2272|consen  193 MGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGHR-HYEKKGLAYCETHYH  250 (332)
T ss_pred             cCCcccccccCchHHH-HHHHhccccchhheeehhcCCcccchh-hhhhcCchhHHHHHH
Confidence            3568999999999975 678999999999999999999986644 378999999999985

>KOG4577|consensus

Probab=98.94  E-value=1.4e-10  Score=64.96  Aligned_cols=61  Identities=28%  Similarity=0.593  Sum_probs=50.2

Q ss_pred             ccCCccccccCccccCceee-eecCceeccccccccccccccCCCCce-eeeCCeecchhhhc
Q psy10221          6 ITELRYCVACGESITDKYLL-QVSDKSWHAQCLRCCICQLVLDRHPSC-FIKDEAVYCKQDYA   66 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~-~~~~~~~h~~cf~C~~C~~~l~~~~~~-~~~~~~~~C~~~y~   66 (67)
                      +.-...|..|.+.|.+..++ .+.+..||..||.|..|++.|..++.+ ++.|+++.|+.+|.
T Consensus        89 KrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE  151 (383)
T KOG4577|consen   89 KRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYE  151 (383)
T ss_pred             HHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHH
Confidence            33456899999999987665 477889999999999999999765544 55889999999984

>KOG2272|consensus

Probab=98.81  E-value=8.5e-10  Score=60.98  Aligned_cols=58  Identities=22%  Similarity=0.596  Sum_probs=52.5

Q ss_pred             CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      ...|-.|+.+|... +++++++.|-++||+|+.|.+-|...+.+++-|-+|.|+.||.|
T Consensus       254 G~~CF~C~~~i~G~-vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r  311 (332)
T KOG2272|consen  254 GNLCFICNRVIGGD-VVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR  311 (332)
T ss_pred             hhhheecCCccCcc-HHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence            35788999999875 78999999999999999999999998888999999999999974

>KOG1700|consensus

Probab=98.60  E-value=5.4e-09  Score=56.41  Aligned_cols=59  Identities=20%  Similarity=0.492  Sum_probs=49.6

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhh
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY   65 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y   65 (67)
                      ......|..|.+.+++.+.+...+..||..||+|+.|+..|.... +...++.++|...+
T Consensus       105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~-~~~~~g~l~~~~~~  163 (200)
T KOG1700|consen  105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKN-YAALEGVLYCKHHF  163 (200)
T ss_pred             hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcc-hhhcCCccccchhh
Confidence            344578999999999988899999999999999999999998865 45678888886543

>KOG1700|consensus

Probab=98.49  E-value=2.7e-08  Score=53.74  Aligned_cols=57  Identities=23%  Similarity=0.458  Sum_probs=48.7

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhh
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY   65 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y   65 (67)
                      ....|..|++.++-.+.+...+..||..||.|..|.+.|.... +..+++.+||+.+|
T Consensus         6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~-~~~~e~~~yc~~~~   62 (200)
T KOG1700|consen    6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSG-YSEHEGVPYCKNCH   62 (200)
T ss_pred             ccchhhhccCcchHHHHHhccCcchhhhHHhcccccccccccc-ccccccccccccch
Confidence            3458999999999777777889999999999999999998755 46699999999854

>KOG1702|consensus

Probab=98.44  E-value=1.4e-08  Score=54.78  Aligned_cols=57  Identities=28%  Similarity=0.626  Sum_probs=47.8

Q ss_pred             ccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      ..|..|++.+++.+.+.-+++.||..||.|..|+.+|.-.. +-.-+.++||..+|.|
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKn-yKgy~kkpycn~hYpk   61 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKN-YKGYDKKPYCNPHYPK   61 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhh-ccccccCCCcCccccc
Confidence            45788999999888888999999999999999999997643 3346788999999864

>KOG1703|consensus

Probab=98.20  E-value=1.1e-06  Score=52.72  Aligned_cols=57  Identities=19%  Similarity=0.535  Sum_probs=49.9

Q ss_pred             CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+.|..|...|.....+.++++.||+.+|.|..|...+..... ...+|.+||..||.
T Consensus       303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~-~~~~g~~~c~~~~~  359 (479)
T KOG1703|consen  303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGP-RELDGKILCHECFH  359 (479)
T ss_pred             cccccccccCcccceeEeeccccccccceeeccccccccCCCc-cccCCCccHHHHHH
Confidence            4889999999998557889999999999999999999987654 67889999998874

>KOG1044|consensus

Probab=98.11  E-value=2.5e-06  Score=52.01  Aligned_cols=53  Identities=21%  Similarity=0.442  Sum_probs=43.9

Q ss_pred             CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecch
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK   62 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~   62 (67)
                      ...|..|.+.-... ++++.++.||..||.|..|+..|..+.++.-.+.++|+.
T Consensus        16 ~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt   68 (670)
T KOG1044|consen   16 GIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGT   68 (670)
T ss_pred             ceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccccceecccceeecc
Confidence            35799999888874 889999999999999999999999887654455667764

>KOG0490|consensus

Probab=97.02  E-value=9.8e-05  Score=40.28  Aligned_cols=53  Identities=49%  Similarity=1.113  Sum_probs=42.3

Q ss_pred             ccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221         14 ACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        14 ~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +|+..|.+...+...+..||..|..|..|...+......+.++|..+|..+|.
T Consensus         1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~   53 (235)
T KOG0490|consen    1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQ   53 (235)
T ss_pred             CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccch
Confidence            36677777777777799999999999999999973333455699999998875

>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=95.00  E-value=0.029  Score=22.62  Aligned_cols=31  Identities=26%  Similarity=0.628  Sum_probs=20.8

Q ss_pred             ccccCccccCcee-eeecCceeccccccccccccc
Q psy10221         12 CVACGESITDKYL-LQVSDKSWHAQCLRCCICQLV   45 (67)
Q Consensus        12 C~~C~~~i~~~~~-~~~~~~~~h~~cf~C~~C~~~   45 (67)
                      |..|+.+|.+..+ +...++.|+   |.|..|...
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~   32 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQ   32 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEE---EECHHHHHH
Confidence            6779999985544 567788887   444555443

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

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

Probab=94.68  E-value=0.04  Score=26.62  Aligned_cols=11  Identities=27%  Similarity=0.900  Sum_probs=5.5

Q ss_pred             ccccccCcccc
Q psy10221         10 RYCVACGESIT   20 (67)
Q Consensus        10 ~~C~~C~~~i~   20 (67)
                      ..|..|++++.
T Consensus        79 ~~C~vC~k~l~   89 (109)
T PF10367_consen   79 TKCSVCGKPLG   89 (109)
T ss_pred             CCccCcCCcCC
Confidence            34555555554

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 [].

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

Probab=94.55  E-value=0.024  Score=29.06  Aligned_cols=21  Identities=38%  Similarity=0.709  Sum_probs=16.4

Q ss_pred             cccccccccCCCCceeeeCCeecchhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      .|..|+.||      |.++|.+||..|
T Consensus        30 hCp~Cg~PL------F~KdG~v~CPvC   50 (131)
T COG1645          30 HCPKCGTPL------FRKDGEVFCPVC   50 (131)
T ss_pred             hCcccCCcc------eeeCCeEECCCC
Confidence            467788777      458999999887

>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=94.10  E-value=0.048  Score=26.35  Aligned_cols=32  Identities=13%  Similarity=0.164  Sum_probs=24.2

Q ss_pred             cccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         36 CLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        36 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      --.|..|+++|....+....+|.++...|..|
T Consensus        78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r  109 (109)
T PF10367_consen   78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR  109 (109)
T ss_pred             CCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence            35799999999886655557788887777654

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 [].

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

Probab=92.87  E-value=0.046  Score=26.84  Aligned_cols=34  Identities=24%  Similarity=0.497  Sum_probs=25.5

Q ss_pred             cccccCccccCceeeeecC-ceecccccccccccc
Q psy10221         11 YCVACGESITDKYLLQVSD-KSWHAQCLRCCICQL   44 (67)
Q Consensus        11 ~C~~C~~~i~~~~~~~~~~-~~~h~~cf~C~~C~~   44 (67)
                      .|..|+++|..++.+++.. ..-|..||.-..-.+
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~k   38 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKASKK   38 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHHHhhh
Confidence            5899999999888877544 557999987554433

>PF14471 DUF4428: Domain of unknown function (DUF4428)

Probab=92.16  E-value=0.08  Score=22.79  Aligned_cols=9  Identities=44%  Similarity=1.224  Sum_probs=4.2

Q ss_pred             ccccCcccc
Q psy10221         12 CVACGESIT   20 (67)
Q Consensus        12 C~~C~~~i~   20 (67)
                      |+.|++.+.
T Consensus         2 C~iCg~kig   10 (51)
T PF14471_consen    2 CAICGKKIG   10 (51)
T ss_pred             CCccccccc
Confidence            444544443

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=90.74  E-value=0.16  Score=18.17  Aligned_cols=10  Identities=50%  Similarity=1.208  Sum_probs=5.3

Q ss_pred             ccccCccccC
Q psy10221         12 CVACGESITD   21 (67)
Q Consensus        12 C~~C~~~i~~   21 (67)
                      |..|+..|.+
T Consensus         2 Cp~CG~~~~~   11 (23)
T PF13240_consen    2 CPNCGAEIED   11 (23)
T ss_pred             CcccCCCCCC
Confidence            4555555543

>PF12674 Zn_ribbon_2: Putative zinc ribbon domain

Probab=88.94  E-value=0.24  Score=23.34  Aligned_cols=28  Identities=25%  Similarity=0.515  Sum_probs=15.2

Q ss_pred             ccccccccCCCCc-eeeeC---Ceecchhhhc
Q psy10221         39 CCICQLVLDRHPS-CFIKD---EAVYCKQDYA   66 (67)
Q Consensus        39 C~~C~~~l~~~~~-~~~~~---~~~~C~~~y~   66 (67)
                      |..|+.||..... .-..|   +.-||.-||.
T Consensus         3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~   34 (81)
T PF12674_consen    3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ   34 (81)
T ss_pred             CCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence            6777777765331 11122   3457777774

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=88.90  E-value=0.34  Score=21.17  Aligned_cols=31  Identities=19%  Similarity=0.471  Sum_probs=20.9

Q ss_pred             cCCccccccCcccc-Cceeee--ecCceeccccc
Q psy10221          7 TELRYCVACGESIT-DKYLLQ--VSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~-~~~~~~--~~~~~~h~~cf   37 (67)
                      .....|..|++.|. ...++.  .=+..+|.+|.
T Consensus         3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             ccCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            34578999999995 222333  23677888886

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=88.42  E-value=0.36  Score=19.86  Aligned_cols=23  Identities=35%  Similarity=0.524  Sum_probs=14.3

Q ss_pred             ccccccccccCCCCceeeeCCeecchhh
Q psy10221         37 LRCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      -.|..|+.||-.     .++|+.+|..|
T Consensus        18 ~~Cp~C~~PL~~-----~k~g~~~Cv~C   40 (41)
T PF06677_consen   18 EHCPDCGTPLMR-----DKDGKIYCVSC   40 (41)
T ss_pred             CccCCCCCeeEE-----ecCCCEECCCC
Confidence            345567766631     36778888765

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

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

Probab=87.84  E-value=0.26  Score=27.19  Aligned_cols=30  Identities=20%  Similarity=0.389  Sum_probs=22.6

Q ss_pred             ccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         37 LRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      -+|+.|+-...... ....+|++.|..||.+
T Consensus       173 v~C~kCGE~~~e~~-~~~~ng~~vC~~C~~~  202 (206)
T COG2191         173 VRCSKCGELFMEPR-AVVLNGKPVCKPCAEK  202 (206)
T ss_pred             eeccccCcccccch-hhhcCCceeccccccc
Confidence            58888988776543 2457899999999863

>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins

Probab=87.80  E-value=0.41  Score=21.24  Aligned_cols=25  Identities=20%  Similarity=0.640  Sum_probs=18.0

Q ss_pred             cccccccccCC-CCceeeeCCeecch
Q psy10221         38 RCCICQLVLDR-HPSCFIKDEAVYCK   62 (67)
Q Consensus        38 ~C~~C~~~l~~-~~~~~~~~~~~~C~   62 (67)
                      .|..|++.|.. .++|.-++...+|.
T Consensus        18 ~C~~C~k~L~~~~DiymYrGd~aFCS   43 (58)
T PF04570_consen   18 FCYLCKKKLDPGKDIYMYRGDKAFCS   43 (58)
T ss_pred             HHHccCCCCCCCCCeeeecccccccc
Confidence            56788999984 45544577888885

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

Probab=87.52  E-value=0.29  Score=21.76  Aligned_cols=17  Identities=29%  Similarity=0.585  Sum_probs=13.2

Q ss_pred             cCCccccccCccccCce
Q psy10221          7 TELRYCVACGESITDKY   23 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~   23 (67)
                      ...+.|..|+..|.+.+
T Consensus         5 ~~~~~CtSCg~~i~~~~   21 (59)
T PRK14890          5 MEPPKCTSCGIEIAPRE   21 (59)
T ss_pred             ccCccccCCCCcccCCC
Confidence            45568999999998654

>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins

Probab=87.37  E-value=0.63  Score=20.32  Aligned_cols=26  Identities=23%  Similarity=0.558  Sum_probs=19.2

Q ss_pred             ccccccCccccCceeeeecCceeccc
Q psy10221         10 RYCVACGESITDKYLLQVSDKSWHAQ   35 (67)
Q Consensus        10 ~~C~~C~~~i~~~~~~~~~~~~~h~~   35 (67)
                      .+|..|+++|.++..+...+..-|+.
T Consensus         2 ~~CvVCKqpi~~a~~v~T~~G~VH~g   27 (54)
T PF10886_consen    2 EICVVCKQPIDDALVVETESGPVHPG   27 (54)
T ss_pred             CeeeeeCCccCcceEEEcCCCccCcH
Confidence            47899999999876666666666653

Their function in unknown.

>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=87.32  E-value=1.1  Score=18.27  Aligned_cols=27  Identities=19%  Similarity=0.301  Sum_probs=11.8

Q ss_pred             cccccccccCCCCceeeeC-Ceecchhh
Q psy10221         38 RCCICQLVLDRHPSCFIKD-EAVYCKQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~-~~~~C~~~   64 (67)
                      +|+.|+++.......+... +...|..|
T Consensus         3 ~CSFCgr~~~~v~~li~g~~~~~IC~~C   30 (41)
T PF06689_consen    3 RCSFCGRPESEVGRLISGPNGAYICDEC   30 (41)
T ss_dssp             B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred             CccCCCCCHHHHhceecCCCCcEECHHH
Confidence            4566666665544333322 44456554

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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.

>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=85.41  E-value=1  Score=18.20  Aligned_cols=31  Identities=19%  Similarity=0.490  Sum_probs=14.0

Q ss_pred             CccccccCccccCceeeeecCceecccccccccccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQL   44 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~   44 (67)
                      ..+|..|+.-|-+--.+...++.|     +|..|+.
T Consensus         2 p~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~   32 (40)
T PF04810_consen    2 PVRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT   32 (40)
T ss_dssp             S-B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred             ccccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence            457788877776543344445555     6666664

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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....

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

Probab=84.85  E-value=0.43  Score=21.27  Aligned_cols=15  Identities=27%  Similarity=0.603  Sum_probs=12.0

Q ss_pred             CccccccCccccCce
Q psy10221          9 LRYCVACGESITDKY   23 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~   23 (67)
                      .+.|..|+..|...+
T Consensus         9 ~~~CtSCg~~i~p~e   23 (61)
T COG2888           9 PPVCTSCGREIAPGE   23 (61)
T ss_pred             CceeccCCCEeccCC
Confidence            678999999996554

>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.57  E-value=0.58  Score=21.73  Aligned_cols=32  Identities=22%  Similarity=0.436  Sum_probs=19.6

Q ss_pred             cCCccccccCccccCcee-ee----e-cC-----ceecccccc
Q psy10221          7 TELRYCVACGESITDKYL-LQ----V-SD-----KSWHAQCLR   38 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~-~~----~-~~-----~~~h~~cf~   38 (67)
                      .+-..|..|++.|...++ +.    . .+     ..+|..||.
T Consensus         5 s~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~   47 (82)
T PF00645_consen    5 SGRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF   47 (82)
T ss_dssp             SSTEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred             CCCccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence            455689999999985433 21    1 12     346888876

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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....

>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=84.55  E-value=0.81  Score=18.20  Aligned_cols=22  Identities=23%  Similarity=0.535  Sum_probs=14.3

Q ss_pred             cccccccccCCCCceeeeCCeecchhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      .|..|+..     .+...+|..||..|
T Consensus        10 ~C~~C~~~-----~~~~~dG~~yC~~c   31 (36)
T PF11781_consen   10 PCPVCGSR-----WFYSDDGFYYCDRC   31 (36)
T ss_pred             cCCCCCCe-----EeEccCCEEEhhhC
Confidence            46666654     23567888888665

>KOG2893|consensus

Probab=84.51  E-value=0.43  Score=27.22  Aligned_cols=40  Identities=25%  Similarity=0.537  Sum_probs=28.6

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCC
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRH   49 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~   49 (67)
                      +..+-|..|+..+.+..++..-.+.=|   |+|.+|.+-|-++
T Consensus         8 ~~kpwcwycnrefddekiliqhqkakh---fkchichkkl~sg   47 (341)
T KOG2893|consen    8 VDKPWCWYCNREFDDEKILIQHQKAKH---FKCHICHKKLFSG   47 (341)
T ss_pred             cCCceeeecccccchhhhhhhhhhhcc---ceeeeehhhhccC
Confidence            345679999999988766655444434   8889999888554

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

Probab=84.42  E-value=0.91  Score=19.69  Aligned_cols=24  Identities=29%  Similarity=0.650  Sum_probs=11.7

Q ss_pred             cccccccccCCCCceeeeCCeecch
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCK   62 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~   62 (67)
                      .|..|...++... .+.++|+.||.
T Consensus         9 aC~~C~C~V~~~~-Ai~~dGk~YCS   32 (52)
T PF02069_consen    9 ACPSCSCVVSEEE-AIQKDGKYYCS   32 (52)
T ss_dssp             SSTT----B-TTT-SEESSS-EESS
T ss_pred             cCCCCEeEECchH-hHHhCCEeeec
Confidence            4566666666433 46788888884

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.

>PF13834 DUF4193: Domain of unknown function (DUF4193)

Probab=84.11  E-value=0.34  Score=23.75  Aligned_cols=29  Identities=28%  Similarity=0.421  Sum_probs=18.4

Q ss_pred             cccccccccccCCCCceeeeCCeecchhh
Q psy10221         36 CLRCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        36 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      =|+|+.|-.--.........+|.++|..|
T Consensus        70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC   98 (99)
T PF13834_consen   70 EFTCSSCFLVHHRSQLAREKDGQPICRDC   98 (99)
T ss_pred             ceeeeeeeeEechhhhccccCCCEecccc
Confidence            37888776543322233457899999877

>PRK00420 hypothetical protein; Validated

Probab=81.69  E-value=0.95  Score=22.74  Aligned_cols=10  Identities=40%  Similarity=0.640  Sum_probs=5.2

Q ss_pred             eCCeecchhh
Q psy10221         55 KDEAVYCKQD   64 (67)
Q Consensus        55 ~~~~~~C~~~   64 (67)
                      ++|+.+|..|
T Consensus        37 k~g~~~Cp~C   46 (112)
T PRK00420         37 KDGEVVCPVH   46 (112)
T ss_pred             CCCceECCCC
Confidence            4555555544

>COG4847 Uncharacterized protein conserved in archaea [Function unknown]

Probab=81.08  E-value=0.53  Score=22.94  Aligned_cols=36  Identities=22%  Similarity=0.348  Sum_probs=25.9

Q ss_pred             cccccCccccCceeeeecC-ceecccccccccccccc
Q psy10221         11 YCVACGESITDKYLLQVSD-KSWHAQCLRCCICQLVL   46 (67)
Q Consensus        11 ~C~~C~~~i~~~~~~~~~~-~~~h~~cf~C~~C~~~l   46 (67)
                      .|..|+.+|..++..+... .+-|-+|+.-+.-+++-
T Consensus         8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~~   44 (103)
T COG4847           8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKPG   44 (103)
T ss_pred             eEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCcC
Confidence            6899999999777766543 45788888766655543

>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=80.61  E-value=0.43  Score=18.92  Aligned_cols=31  Identities=26%  Similarity=0.544  Sum_probs=17.1

Q ss_pred             ccccCccccCceeeeecCceeccccccccccccccC
Q psy10221         12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD   47 (67)
Q Consensus        12 C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~   47 (67)
                      |..|.+.+.+     ..++.||-.-..|..|+..+.
T Consensus         2 C~~C~~Ey~~-----p~~RR~~~~~isC~~CGPr~~   32 (35)
T PF07503_consen    2 CDDCLKEYFD-----PSNRRFHYQFISCTNCGPRYS   32 (35)
T ss_dssp             -HHHHHHHCS-----TTSTTTT-TT--BTTCC-SCC
T ss_pred             CHHHHHHHcC-----CCCCcccCcCccCCCCCCCEE
Confidence            4455544433     346788988899999997764

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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=80.51  E-value=1.4  Score=16.02  Aligned_cols=10  Identities=30%  Similarity=0.886  Sum_probs=4.4

Q ss_pred             cccCccccCc
Q psy10221         13 VACGESITDK   22 (67)
Q Consensus        13 ~~C~~~i~~~   22 (67)
                      ..|+..|.+.
T Consensus         2 ~sC~~~i~~r   11 (24)
T PF07754_consen    2 TSCGRPIAPR   11 (24)
T ss_pred             ccCCCcccCc
Confidence            3444444433

It is likely to bind zinc via its four well-conserved cysteine residues.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	67
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		8e-09
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		2e-08
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		3e-08
1m3v_A	122	Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And		4e-07
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		5e-07
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		5e-07
2l4z_A	123	Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-L		7e-07

>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 = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 41/63 (65%), Gaps = 4/63 (6%)
Query: 6  ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQD 64
          + ++  C  C + I DK++L+V D+ WH+ CL+C  CQ+ L DR   CF +  +VYCK+D
Sbjct: 3  MQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADR---CFSRAGSVYCKED 59
Query: 65 YAK 67
          + K
Sbjct: 60 FFK 62

>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 = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 7  TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
           E+  C  C + I D+++L+  D+ WH++CL+C  C + L     CF + E+VYCK D+ 
Sbjct: 4  PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFF 61
Query: 67 K 67
          K
Sbjct: 62 K 62

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 8   ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           E+  C  C + I D+++L+  D+ WH++CL+C  C + L     CF + E+VYCK D+ K
Sbjct: 59  EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFFK 116

>pdb|1M3V|A Chain A, Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And The N- Terminal Lim Domain Of Lmo4 Length = 122

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
          + C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY +
Sbjct: 6  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

>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 = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
          + C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY +
Sbjct: 4  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 62

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
          + C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY +
Sbjct: 6  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1 (18-82) Length = 123

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 10  RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
           + C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY +
Sbjct: 62  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 120

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	67
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-18
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	2e-15
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-15
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	6e-15
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	1e-04
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	6e-15
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	3e-04
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	8e-15
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-06
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	3e-13
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	1e-05
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	6e-13
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	9e-13
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	8e-11
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-10
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-10
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-04
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-10
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-09
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	4e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	2e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-08
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	4e-08
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-08
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	8e-08
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	8e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	1e-07
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	1e-07
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	3e-07
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	7e-07
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	5e-06
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	9e-07
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	2e-06
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-06
2cuq_A	80	Four and A half LIM domains 3; structural genomics	3e-06
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-06
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	3e-06
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	4e-06
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	5e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	7e-06
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	7e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	8e-06
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-05
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-05
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	1e-04
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	3e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	3e-04

>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 = 72.1 bits (176), Expect = 1e-18
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 7   TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDY 65
              + C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY
Sbjct: 59  LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 118

Query: 66  AK 67
            +
Sbjct: 119 IR 120

>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 = 64.2 bits (156), Expect = 2e-15
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 7  TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDY 65
             + C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY
Sbjct: 3  LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 62

Query: 66 AK 67
           +
Sbjct: 63 IR 64

>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 = 62.8 bits (153), Expect = 2e-15
 Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 6  ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          I    +C  C E I     L   DK WH  C +C  C ++L        KD   YC+ DY
Sbjct: 12 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG--EYISKDGVPYCESDY 69

Query: 66 AK 67
            
Sbjct: 70 HA 71

>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 = 64.2 bits (156), Expect = 6e-15
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 2/61 (3%)

Query: 7   TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
            E+  C  C + I D+++L+  D+ WH++CL+C  C + L     CF + E+VYCK D+ 
Sbjct: 58  PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE--RCFSRGESVYCKDDFF 115

Query: 67  K 67
           K
Sbjct: 116 K 116

>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 = 36.4 bits (84), Expect = 1e-04
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 12  CVACGESITDKYL-LQVSDKSWHAQCLRCCICQLVLDRHPSCFI-KDEAVYCKQDY 65
           C AC   I    +  +  D  +H  C  C +C+  L      ++ +D  + CK DY
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177

>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 = 63.7 bits (155), Expect = 6e-15
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 2/61 (3%)

Query: 7  TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
           E+  C  C + I D+++L+  D+ WH++CL+C  C + L     CF + E+VYCK D+ 
Sbjct: 4  PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE--RCFSRGESVYCKDDFF 61

Query: 67 K 67
          K
Sbjct: 62 K 62

>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 = 35.6 bits (82), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 12  CVACGESITDKYL-LQVSDKSWHAQCLRCCICQLVLDRHPSCFI-KDEAVYCKQDY 65
           C AC   I    +  +  D  +H  C  C +C+  L      ++ +D  + CK DY
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 123

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

 Score = 62.5 bits (152), Expect = 8e-15
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 9  LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
          L  C  C ++I D+Y L+  D+ WH  CL C +C   L +     + K     C++DY +
Sbjct: 2  LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61

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

 Score = 41.7 bits (98), Expect = 1e-06
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 12  CVACGESITDKYL-LQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C +C + I    + ++V DK +H +C +C  CQ          + +  + C+QD  +
Sbjct: 69  CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYE 125

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

 Score = 59.6 bits (144), Expect = 3e-13
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
          C  CG  I D++LL   D  WH++CL+C  CQ  L D   S + K   + C+ DY +
Sbjct: 8  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

>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 = 39.2 bits (91), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 11  YCVACGESITDKYL-LQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
            C ACG+SI    L ++     +H +C  C  C+  L         + +++C+ D 
Sbjct: 71  ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDR 126

>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 = 57.4 bits (138), Expect = 6e-13
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 9  LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDY 65
          L  C  C ++I D+Y L+  D+ WH  CL C +C   L +     + K     C++DY
Sbjct: 3  LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

>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 = 56.2 bits (136), Expect = 9e-13
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C + I D+ L +   K++H  C  C +C   LD  P        ++C +D+ +
Sbjct: 18 CATCSQPILDRIL-RAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHR 72

>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 = 51.6 bits (124), Expect = 8e-11
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          CV C + I  D   +   ++ WH  C RC  C   L  + +   KD  + C +   +
Sbjct: 8  CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCTTR 63

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

 Score = 50.9 bits (122), Expect = 1e-10
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  CG  I   ++ ++ D+  H +C  C  C   L +    F  ++ +YC++   +
Sbjct: 18 CDKCGTGIVGVFV-KLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARE 71

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

 Score = 51.3 bits (123), Expect = 2e-10
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 7  TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
          +E   C  C E I      Q  +++WH +   C  C  +L       + ++   CK  Y 
Sbjct: 1  SEKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEI-YVMVNDKPVCKPCYV 59

Query: 67 K 67
          K
Sbjct: 60 K 60

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

 Score = 34.3 bits (79), Expect = 5e-04
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 11  YCVACGESITDKYL-LQVSDKSWHA--QCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
            C  C  +I  +   +  ++ SWHA  +C  C  C   L         +  V+C  +  K
Sbjct: 65  VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQK-FMPVEGMVFCSVECKK 123

>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 = 50.2 bits (120), Expect = 3e-10
 Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  CG  I    + +  DK  H +C  C  C L L +    F  +  +YC+     
Sbjct: 28 CDKCGSGIVGAVV-KARDKYRHPECFVCADCNLNL-KQKGYFFVEGELYCETHARA 81

>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 = 47.0 bits (112), Expect = 4e-09
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C ACG ++     +Q   +S+H  C  C +C+  LD   +  I D  VYCK  Y K
Sbjct: 10 CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLD-STTVAIHDAEVYCKSCYGK 64

>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 = 44.6 bits (106), Expect = 2e-08
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C AC   I  + +     K WH +   C  C+     H   + +    YC+  Y +
Sbjct: 8  CGACRRPIEGRVV-NAMGKQWHVEHFVCAKCEKPFLGHR-HYERKGLAYCETHYNQ 61

>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 = 45.1 bits (107), Expect = 2e-08
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C + I   +L     KSWH +   C  C+  +        +  A+YC+  Y K
Sbjct: 28 CAHCNQVIRGPFL-VALGKSWHPEEFNCAHCKNTMAYIGF-VEEKGALYCELCYEK 81

>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 = 44.4 bits (105), Expect = 4e-08
 Identities = 18/58 (31%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 11 YCVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
           C  C + I  D   L   D+ +H  C RCC CQ  L   P    +D  + C   Y  
Sbjct: 17 TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEP-FTCQDSELLCNDCYCS 73

>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 = 43.9 bits (104), Expect = 4e-08
 Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C ++I      ++    SWH  C  C  CQ  +    S   KD   +C   Y K
Sbjct: 8  CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG-TKSFIPKDNQNFCVPCYEK 63

>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 = 43.5 bits (103), Expect = 8e-08
 Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C   + + YL    D  WH +C  C  C        S F  D   +C+  Y
Sbjct: 18 CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFSTG-SFFELDGRPFCELHY 69

>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 = 43.5 bits (103), Expect = 8e-08
 Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C ACGE++      L+   ++WH  C  C  C+  L    S      A YC   Y  
Sbjct: 8  CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSR-SFVPDKGAHYCVPCYEN 63

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

 Score = 42.8 bits (101), Expect = 1e-07
 Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  CGE I  + + +  + SWH +C RC +CQ VL              C+  + +
Sbjct: 8  CHQCGEFIIGRVI-KAMNNSWHPECFRCDLCQEVLA-DIGFVKNAGRHLCRPCHNR 61

>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 = 42.9 bits (101), Expect = 1e-07
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          CV C +++     L  + + +H  C RC  C   L    +       +YCK  + +
Sbjct: 18 CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLS-LGTYASLHGRIYCKPHFNQ 72

>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 = 41.6 bits (98), Expect = 3e-07
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          CV C + IT   +    ++ WH +C  C  C+  L        +D+  YC   +  
Sbjct: 8  CVQCKKPITTGGV-TYREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCFCD 61

>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 = 42.7 bits (100), Expect = 7e-07
 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 11  YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
            C  CG+++     +  + KSWH  C RC  C   L+   +   KD  +YCK  YAK
Sbjct: 117 GCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLEST-TLADKDGEIYCKGCYAK 172

>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 = 40.8 bits (95), Expect = 5e-06
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C +++     +Q    S+H  C  C +C+  LD   +  +  + +YCK  Y K
Sbjct: 10 CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGK 64

>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 = 40.4 bits (95), Expect = 9e-07
 Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          CV C ++IT   +    D+ WHA C  C  C   L         ++  YC   Y  
Sbjct: 8  CVKCNKAITSGGI-TYQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYKN 61

>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 = 40.4 bits (95), Expect = 2e-06
 Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C ++I      ++     WH  C  C  C+ V+    S F K E  YC   +  
Sbjct: 18 CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTG-SFFPKGEDFYCVTCHET 73

>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 = 40.1 bits (94), Expect = 2e-06
 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 12 CVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  CGE +      +   D+ +H  C  C  C+  L R    +  +   YC+  Y  
Sbjct: 8  CGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQL-RGQHFYAVERRAYCEGCYVA 63

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

 Score = 39.6 bits (93), Expect = 3e-06
 Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C +++T   +    D+ WH +CL C  CQ  L        +DE  YC   + +
Sbjct: 18 CARCSKTLTQGGV-TYRDQPWHRECLVCTGCQTPLAGQQ-FTSRDEDPYCVACFGE 71

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

 Score = 39.0 bits (91), Expect = 3e-06
 Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 4/61 (6%)

Query: 10 RYCVACGESITDKYLLQV---SDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
            C  C   I+     +     ++ WH  C  C  C L L        + + + C     
Sbjct: 6  SGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRG-FLTERDDILCPDCGK 64

Query: 67 K 67
           
Sbjct: 65 D 65

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

 Score = 39.3 bits (92), Expect = 3e-06
 Identities = 12/54 (22%), Positives = 17/54 (31%), Gaps = 1/54 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C + +     +    K WH  CL+C  C   L         +   YC    
Sbjct: 3  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLT-SGGHAEHEGKPYCNHPC 55

>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 = 39.0 bits (91), Expect = 4e-06
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C +C + I  + +     K++H  C  C +C+L            +   C++  
Sbjct: 18 CFSCDQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCS 70

>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 = 38.5 bits (90), Expect = 5e-06
 Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 2/57 (3%)

Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C       + ++  + + +H QC  C  C          +  +   YC+ D+  
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQF-PEGLFYEFEGRKYCEHDFQM 69

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

 Score = 38.7 bits (90), Expect = 7e-06
 Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 10 RYCVACGESIT---DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
            CVAC + I+       +   D  WH++C  C  C + L        +++ ++C++  +
Sbjct: 6  SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNKEIFCQKCGS 64

Query: 67 K 67
           
Sbjct: 65 G 65

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

 Score = 38.6 bits (90), Expect = 7e-06
 Identities = 10/57 (17%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL-DRHPSCFIKDEAVYCKQDYAK 67
          C  C   +T  ++    +  +H +C  C  C++++ D      ++   +YC + + +
Sbjct: 18 CHGCSLLMTGPFM-VAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNE 73

>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 = 38.4 bits (89), Expect = 8e-06
 Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 1/57 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHP-SCFIKDEAVYCKQDYAK 67
          C  CGE +     L V+   +H  C RC  C+  L          D   YC Q   +
Sbjct: 18 CALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ 74

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

 Score = 37.8 bits (88), Expect = 1e-05
 Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 1/54 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65
          C  C +++     +    K WH  CL+C  C   L         D   +C +  
Sbjct: 12 CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPG-GHAEHDGKPFCHKPC 64

>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 = 37.4 bits (87), Expect = 2e-05
 Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 2/57 (3%)

Query: 12 CVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C       + ++  + + +H QC  C  C          +  +   YC+ D+  
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQF-PEGLFYEFEGRKYCEHDFQM 69

>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 = 35.2 bits (81), Expect = 1e-04
 Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 11 YCVACGESIT----DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66
           C  C   IT       ++    +SWH  C  C  C + L          E VYC     
Sbjct: 17 KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKR-FVFHQEQVYCPDCAK 75

Query: 67 K 67
          K
Sbjct: 76 K 76

>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 = 34.3 bits (78), Expect = 3e-04
 Identities = 10/52 (19%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQ 63
          C +C + IT + L +  +K +H  C  C  C  +       +++  +++   
Sbjct: 8  CDSCEKYITGRVL-EAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPA 58

>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 = 34.4 bits (79), Expect = 3e-04
 Identities = 11/56 (19%), Positives = 17/56 (30%), Gaps = 3/56 (5%)

Query: 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67
          C  C   I ++ L    +  +H     C  C   L            +YC   + K
Sbjct: 18 CQKCHAIIDEQPL-IFKNDPYHPDHFNCANCGKELT--ADARELKGELYCLPCHDK 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	67
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.82
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.82
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.81
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.81
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.81
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.8
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.8
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.8
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.8
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.79
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.79
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.78
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.78
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.78
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.78
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.78
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.78
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.78
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.77
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.77
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.77
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.77
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.77
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.77
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.77
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.76
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.76
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.76
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.75
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.75
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.75
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.75
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.75
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.75
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.74
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.74
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.74
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.72
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.72
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.72
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.71
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.69
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.67
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.64
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.6
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.58
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.54
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.52
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.87
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.85
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	97.58
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	96.06
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	89.28
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	89.2
1jjd_A	55	Metallothionein, SMTA; zinc finger, zinc cluster,	88.64
3nw0_A	238	Non-structural maintenance of chromosomes element	87.91
2das_A	62	Zinc finger MYM-type protein 5; trash domain, stru	85.9
2gvi_A	204	Conserved hypothetical protein; structural genomic	84.78
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	84.09
2ds5_A	51	CLPX, ATP-dependent CLP protease ATP-binding subun	82.21
1ovx_A	67	ATP-dependent CLP protease ATP-binding subunit CL;	82.19
2dmj_A	106	Poly (ADP-ribose) polymerase family, member 1; zin	81.76
1v9x_A	114	Poly (ADP-ribose) polymerase; PARP, DNA repair, in	80.38

>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=99.82  E-value=1.4e-20  Score=86.90  Aligned_cols=62  Identities=23%  Similarity=0.419  Sum_probs=54.9

Q ss_pred             ccccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecch-hhhc
Q psy10221          4 TIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK-QDYA   66 (67)
Q Consensus         4 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~-~~y~   66 (67)
                      ++....+.|.+|+++|.+.+.+.+.++.||++||+|..|+++|.+.. ++.+++.+||+ .||.
T Consensus         4 ~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~cy~   66 (76)
T 2cu8_A            4 GSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGG-HAEHDGKPFCHKPCYA   66 (76)
T ss_dssp             SCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTS-CEEETTEEECTTTHHH
T ss_pred             ccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCc-eEeECCEEecchHHHH
Confidence            45667789999999999777889999999999999999999998754 57899999999 7985

>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=99.82  E-value=9.4e-21  Score=88.67  Aligned_cols=62  Identities=26%  Similarity=0.421  Sum_probs=53.5

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCcee-eeCCeecchhhhcC
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCF-IKDEAVYCKQDYAK   67 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~k   67 (67)
                      ..+...|.+|+++|.+.+.+.++++.||++||+|..|+++|....++. ++++++||+.||.+
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~   74 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ   74 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCC
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHh
Confidence            445689999999999777888999999999999999999998876432 47999999999964

>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=99.81  E-value=2.8e-20  Score=86.73  Aligned_cols=58  Identities=33%  Similarity=0.744  Sum_probs=52.3

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+.+.|..|+++|.+.+.+.++++.||++||+|..|+++|.+ . ++.+++++||+.||.
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~-~~~~~g~~yC~~~y~   70 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-E-YISKDGVPYCESDYH   70 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-C-CEEETTEEECTTHHH
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-C-eEEECCEEECHHHHH
Confidence            456789999999997778999999999999999999999985 3 688999999999985

>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=99.81  E-value=1.4e-20  Score=87.86  Aligned_cols=61  Identities=31%  Similarity=0.604  Sum_probs=51.4

Q ss_pred             cccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          5 IITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         5 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +..+.+.|..|+++|.+.+.+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.
T Consensus         3 ~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~~~~yC~~cy~   63 (81)
T 1a7i_A            3 NWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTT-VAIHDAEVYCKSCYG   63 (81)
T ss_dssp             -----CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSC-CEEETTEEECSHHHH
T ss_pred             CCCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCC-eEeeCCEEECHHHHH
Confidence            4667899999999998777889999999999999999999998765 578999999999985

>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=99.81  E-value=2.4e-20  Score=85.62  Aligned_cols=58  Identities=17%  Similarity=0.484  Sum_probs=51.5

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.|.+|+++|.+. .+.++++.||++||+|..|+++|..+..++.+++++||+.||.
T Consensus         4 ~~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~   61 (73)
T 1wig_A            4 GSSGCDSCEKYITGR-VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQ   61 (73)
T ss_dssp             SCCSCSSSCCCCSSC-CBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             CcCCcccCCCEecCe-eEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHCh
Confidence            467999999999984 6889999999999999999999985455688999999999985

>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=99.80  E-value=5.7e-20  Score=83.66  Aligned_cols=58  Identities=28%  Similarity=0.617  Sum_probs=52.0

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+...|..|+++|.+. .+.+.++.||++||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~c~~   60 (70)
T 2d8x_A            3 SGSSGCHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVLADIG-FVKNAGRHLCRPCHN   60 (70)
T ss_dssp             CCSSBCSSSCCBCCSC-CEEETTEEECTTTSBCSSSCCBCSSSC-CEEETTEEECHHHHH
T ss_pred             CCCCcCccCCCEecce-EEEECcccccccCCEeCCCCCcCCCCc-cEeECCeEECHHHhh
Confidence            4678999999999964 689999999999999999999999864 577999999999985

>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=99.80  E-value=7.4e-20  Score=83.68  Aligned_cols=60  Identities=18%  Similarity=0.542  Sum_probs=52.3

Q ss_pred             cCCccccccCccccC---ceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          7 TELRYCVACGESITD---KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~---~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      ...+.|.+|+++|.+   .+.+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~c~~~   65 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRG-FLTERDDILCPDCGKD   65 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSC-CEECSSSEECHHHHHT
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCc-cEeECCEEEChhHcCc
Confidence            457899999999995   45788999999999999999999998654 5779999999999864

>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=99.80  E-value=1.8e-19  Score=83.14  Aligned_cols=59  Identities=22%  Similarity=0.629  Sum_probs=52.0

Q ss_pred             CCccccccCccccC---ceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          8 ELRYCVACGESITD---KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         8 ~~~~C~~C~~~i~~---~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      -.+.|..|+++|.+   .+.+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.+
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~   65 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKG-FLTQNKEIFCQKCGSG   65 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSC-EEEETTEEEETTTTCC
T ss_pred             cCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCc-eEeECCEEECHHHhhh
Confidence            45789999999995   45789999999999999999999998644 6789999999999964

>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=99.80  E-value=4.8e-20  Score=90.72  Aligned_cols=59  Identities=32%  Similarity=0.749  Sum_probs=52.9

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCC-CCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR-HPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~   66 (67)
                      +.+.|.+|+++|.+.+.+.+.++.||++||+|+.|+++|.+ +..++.+++++||+.||.
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~   61 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL   61 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHH
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHH
Confidence            46889999999998888999999999999999999999985 334688999999999985

>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=99.79  E-value=5.4e-20  Score=91.64  Aligned_cols=59  Identities=36%  Similarity=0.908  Sum_probs=52.2

Q ss_pred             CccccccCccccCceeeeecCceeccccccccccccccCC-CCceeeeCCeecchhhhcC
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR-HPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~k   67 (67)
                      .+.|.+|+++|.+.+++.+.++.||+.||+|..|+++|.+ +..++.++|.+||+.||.+
T Consensus        61 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~  120 (123)
T 2l4z_A           61 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR  120 (123)
T ss_dssp             CSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHH
T ss_pred             CCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhh
Confidence            5789999999998877899999999999999999999973 3446889999999999863

>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=99.79  E-value=6e-20  Score=82.76  Aligned_cols=57  Identities=23%  Similarity=0.602  Sum_probs=50.8

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.|++|+++|.+ +.+.+.++.||++||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus         4 ~~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~y~   60 (66)
T 1nyp_A            4 GVPICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHR-HYERKGLAYCETHYN   60 (66)
T ss_dssp             CCCEETTTTEECCS-CEECCTTSBEETTTCBCTTTCCBCSSSC-CEEETTEEECHHHHH
T ss_pred             CCCCCcccCCEecc-eEEEECccccccCcCEECCCCCCCCCCc-eEeECCcEECHHHHH
Confidence            46789999999994 5788999999999999999999998754 578999999999985

>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=99.78  E-value=1.6e-19  Score=82.53  Aligned_cols=59  Identities=22%  Similarity=0.571  Sum_probs=51.6

Q ss_pred             cCCccccccCccccCc-eeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.+. .++.+++.+||+.||.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~   62 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQ-HFYAVERRAYCEGCYV   62 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTS-CEEESSSCEEEHHHHH
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcC-cCEeeCCeEECHHHHH
Confidence            4568999999999963 478899999999999999999999754 4688999999999985

>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=99.78  E-value=1.9e-19  Score=81.69  Aligned_cols=58  Identities=28%  Similarity=0.643  Sum_probs=51.4

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|..|+++|.+. .+.+.++.||++||+|..|+++|.+. .++.+++++||+.||.
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~   60 (69)
T 2cur_A            3 SGSSGCVKCNKAITSG-GITYQDQPWHADCFVCVTCSKKLAGQ-RFTAVEDQYYCVDCYK   60 (69)
T ss_dssp             CCCCCCSSSCCCCCTT-CEEETTEEECTTTTBCTTTCCBCTTS-CEEECSSCEEEHHHHH
T ss_pred             CCcCCCcccCCEeCcc-eEEECccccccCcCEECCCCCCCCCC-ccEeECCEEECHHHhH
Confidence            4578999999999875 68899999999999999999999864 4678999999999985

>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=99.78  E-value=2e-19  Score=82.16  Aligned_cols=58  Identities=28%  Similarity=0.619  Sum_probs=51.7

Q ss_pred             CCccccccCccccCc-eeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.|..|+++|.+. +.+.+.++.||++||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~~~~yC~~cy~   62 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRS-FVPDKGAHYCVPCYE   62 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSC-EEEETTEEEEHHHHH
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCc-cCCcCCeEECHHHHH
Confidence            467999999999963 6788999999999999999999998764 678999999999985

>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=99.78  E-value=2.8e-19  Score=81.65  Aligned_cols=58  Identities=26%  Similarity=0.566  Sum_probs=51.6

Q ss_pred             CCccccccCccccCc-eeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.|..|+++|.+. ..+.+.++.||++||+|..|+++|.+. .++.+++.+||+.||.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~   62 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTK-SFIPKDNQNFCVPCYE   62 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSS-SEEEETTEEEEHHHHH
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCC-ccCccCCeEECHHHHh
Confidence            357899999999975 478899999999999999999999876 4678999999999985

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

Probab=99.78  E-value=2.4e-19  Score=82.71  Aligned_cols=56  Identities=23%  Similarity=0.513  Sum_probs=50.4

Q ss_pred             ccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecch-hhhc
Q psy10221         10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK-QDYA   66 (67)
Q Consensus        10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~-~~y~   66 (67)
                      +.|.+|+++|.+.+.+.+.++.||++||+|..|+++|.+.. ++.+++.+||+ .||.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~cy~   57 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGG-HAEHEGKPYCNHPCYS   57 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTT-EEEETTEEEETTTHHH
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCc-eECcCCeEeeCHHHHH
Confidence            57999999999667889999999999999999999998864 67899999999 6985

>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=99.78  E-value=1.5e-19  Score=85.95  Aligned_cols=58  Identities=22%  Similarity=0.535  Sum_probs=52.6

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ....|..|+++|.+.+.+.+.++.||+.||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~y~   71 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGT-YASLHGRIYCKPHFN   71 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTT-CCCSSSCCCCHHHHH
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCC-cEeECCEEECHHHHH
Confidence            4679999999999877889999999999999999999998865 578999999999985

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

Probab=99.78  E-value=3.6e-19  Score=82.26  Aligned_cols=58  Identities=26%  Similarity=0.625  Sum_probs=51.5

Q ss_pred             CCccccccCccccC----ceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITD----KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~----~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .++.|++|+++|.+    .+.+.+.++.||+.||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~~~~~yC~~cy~   75 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKR-FVFHQEQVYCPDCAK   75 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSC-CCEETTEECCHHHHH
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCc-cEeECCEEEChHHhc
Confidence            45899999999994    56789999999999999999999998754 578999999999985

>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=99.77  E-value=2.6e-19  Score=81.61  Aligned_cols=59  Identities=17%  Similarity=0.484  Sum_probs=51.7

Q ss_pred             cCCccccccCccccCce-eeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .....|.+|+++|...+ ++.+.++.||++||+|..|+++|.+.. ++.++|++||+.||.
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~y~   68 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGL-FYEFEGRKYCEHDFQ   68 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGC-CEEETTEEECHHHHH
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCC-eEeECCeEeCHHHHH
Confidence            45679999999999655 467999999999999999999998764 578999999999985

>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=99.77  E-value=3.4e-19  Score=81.06  Aligned_cols=58  Identities=24%  Similarity=0.621  Sum_probs=51.0

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|..|+++|.+. .+.+.++.||++||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~~~~yC~~cy~   60 (70)
T 2d8z_A            3 SGSSGCVQCKKPITTG-GVTYREQPWHKECFVCTACRKQLSGQR-FTARDDFAYCLNCFC   60 (70)
T ss_dssp             CCCCBCSSSCCBCCSS-EEESSSSEEETTTSBCSSSCCBCTTSC-CEESSSSEECHHHHH
T ss_pred             CCCCCCcccCCeeccc-eEEECccccCCCCCccCCCCCcCCcCc-eEeeCCeEECHHHHH
Confidence            3567899999999975 588999999999999999999998654 578999999999985

>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=4e-19  Score=84.29  Aligned_cols=58  Identities=24%  Similarity=0.539  Sum_probs=51.1

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|..|+++|.+ +.+.+.++.||++||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus        23 ~~~~~C~~C~~~I~~-~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~cy~   80 (90)
T 2dar_A           23 KRTPMCAHCNQVIRG-PFLVALGKSWHPEEFNCAHCKNTMAYIG-FVEEKGALYCELCYE   80 (90)
T ss_dssp             TCCCBBSSSCCBCCS-CEEEETTEEECTTTCBCSSSCCBCSSSC-BEESSSCEECHHHHH
T ss_pred             CCCCCCccCCCEecc-eEEEECCccccccCCccCCCCCCCCCCE-eEeECCEEECHHHHH
Confidence            356789999999975 4688999999999999999999998754 578999999999985

>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=99.77  E-value=3.8e-19  Score=84.21  Aligned_cols=58  Identities=26%  Similarity=0.670  Sum_probs=51.3

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .....|..|++.|.+. .+.+.++.||++||+|..|+++|.+.. ++.+++.+||+.||.
T Consensus        23 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~y~   80 (89)
T 1x64_A           23 QRMPLCDKCGSGIVGA-VVKARDKYRHPECFVCADCNLNLKQKG-YFFVEGELYCETHAR   80 (89)
T ss_dssp             CSCCBCTTTCCBCCSC-CEESSSCEECTTTCCCSSSCCCTTTSC-CEEETTEEECHHHHH
T ss_pred             CcCCCcccCCCEeccc-EEEECCceECccCCEecCCCCCCCCCC-eEeECCEEECHHHHH
Confidence            3457899999999984 688999999999999999999998765 578899999999985

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

Probab=99.77  E-value=6.2e-19  Score=79.29  Aligned_cols=58  Identities=21%  Similarity=0.501  Sum_probs=50.7

Q ss_pred             CccccccCccccC-ceeeeecCceec--cccccccccccccCCCCceeeeCCeecc-hhhhcC
Q psy10221          9 LRYCVACGESITD-KYLLQVSDKSWH--AQCLRCCICQLVLDRHPSCFIKDEAVYC-KQDYAK   67 (67)
Q Consensus         9 ~~~C~~C~~~i~~-~~~~~~~~~~~h--~~cf~C~~C~~~l~~~~~~~~~~~~~~C-~~~y~k   67 (67)
                      ++.|.+|+++|.+ .+.+.+.++.||  ++||+|+.|+++|.+.. ++.++|++|| .+||.|
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~~C~~k   63 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQK-FMPVEGMVFCSVECKKR   63 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSC-CEEETTEEESSHHHHHT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCc-eEEECCEEecCHHHhhh
Confidence            4689999999995 367899999999  99999999999998754 5789999999 888854

>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=99.77  E-value=4.1e-19  Score=82.57  Aligned_cols=59  Identities=19%  Similarity=0.316  Sum_probs=51.5

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      ....++|..|+++|.+ +.+.+.++.||++||+|..|+++|.+. . +.+++.+||+.||.+
T Consensus        12 ~~~~~~C~~C~~~I~~-~~v~a~~~~~H~~CF~C~~C~~~L~~~-~-f~~~g~~yC~~cy~~   70 (79)
T 2cor_A           12 GLGKYICQKCHAIIDE-QPLIFKNDPYHPDHFNCANCGKELTAD-A-RELKGELYCLPCHDK   70 (79)
T ss_dssp             CCCCCBCTTTCCBCCS-CCCCCSSSCCCTTTSBCSSSCCBCCTT-C-EEETTEEECHHHHHT
T ss_pred             ccCCCCCccCCCEecc-eEEEECcceeCCCCCEeCCCCCccCCC-C-EeECCEEeCHHHHHH
Confidence            3456899999999995 468899999999999999999999875 3 589999999999864

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

Probab=99.77  E-value=2.9e-19  Score=82.54  Aligned_cols=61  Identities=16%  Similarity=0.445  Sum_probs=52.6

Q ss_pred             cccCCccccccCccccC-ceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          5 IITELRYCVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         5 ~~~~~~~C~~C~~~i~~-~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .......|.+|+++|.+ ..++.+.++.||+.||+|..|+++|.+.. ++.++|.+||+.||.
T Consensus         7 ~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~~y~   68 (77)
T 1g47_A            7 NALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGL-FYEFEGRKYCEHDFQ   68 (77)
T ss_dssp             SCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGC-SEEETTEEECHHHHH
T ss_pred             cCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCC-eEeECCeEeCHHHHH
Confidence            34556899999999984 44578999999999999999999998765 578999999999985

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

Probab=99.76  E-value=7.8e-19  Score=87.93  Aligned_cols=58  Identities=33%  Similarity=0.761  Sum_probs=52.2

Q ss_pred             CccccccCccccCceeeeecCceeccccccccccccccCC-CCceeeeCCeecchhhhc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR-HPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~   66 (67)
                      .+.|.+|+++|.+.+++.++++.||++||+|..|+++|.. +..++.++|.+||+.||.
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~   60 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL   60 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHH
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchh
Confidence            5789999999999877899999999999999999999974 345788999999999985

>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=99.76  E-value=1.9e-19  Score=89.48  Aligned_cols=60  Identities=35%  Similarity=0.872  Sum_probs=53.0

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCC-CCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR-HPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|.+|+++|.+.+++.+.++.||++||+|..|+++|.+ +..++.+++.+||+.||.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~   63 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI   63 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHH
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHH
Confidence            456899999999998877899999999999999999999973 234688999999999985

>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=99.76  E-value=1.1e-18  Score=81.49  Aligned_cols=59  Identities=31%  Similarity=0.667  Sum_probs=51.5

Q ss_pred             CCccccccCcccc-CceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          8 ELRYCVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         8 ~~~~C~~C~~~i~-~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      -.+.|.+|+++|. +..++.+.++.||+.||+|+.|+++|.+.. ++.+++++||+.||.+
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~~~~~~C~~c~~~   73 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEP-FTCQDSELLCNDCYCS   73 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCC-EEEETTEEEETTTSSC
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCc-cEeeCCEEECHHHHhh
Confidence            3578999999999 455788899999999999999999998654 6789999999999864

>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=99.75  E-value=2.5e-18  Score=82.86  Aligned_cols=60  Identities=25%  Similarity=0.606  Sum_probs=52.8

Q ss_pred             cCCccccccCcccc-CceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          7 TELRYCVACGESIT-DKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         7 ~~~~~C~~C~~~i~-~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      ...+.|.+|+++|. +.+.+.+.++.||+.||+|..|+++|.+.. ++.+++++||+.||.+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~cy~~   63 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANET-FVAKDNKILCNKCTTR   63 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSC-CEEETTEEECHHHHTT
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCe-eECcCCEEEChhHhhh
Confidence            45689999999998 467899999999999999999999997644 5789999999999864

>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=99.75  E-value=1.7e-19  Score=83.77  Aligned_cols=58  Identities=24%  Similarity=0.662  Sum_probs=51.5

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +..+.|..|+++|.+. .+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.
T Consensus        13 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~cy~   70 (79)
T 1x62_A           13 QKLPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLKQKG-HFFVEDQIYCEKHAR   70 (79)
T ss_dssp             CCCCCCSSSCCCCCSS-CEECSSCEECTTTTSCSSSCCCHHHHC-CEESSSCEECHHHHH
T ss_pred             CCCCccccCCCCccCc-EEEECcceeCcCcCeeCCCCCCCCCCC-eEeECCEEECHHHHH
Confidence            4568999999999985 789999999999999999999997644 578999999999985

>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=99.75  E-value=1.6e-18  Score=80.91  Aligned_cols=58  Identities=24%  Similarity=0.557  Sum_probs=50.9

Q ss_pred             CCccccccCccccCce-eeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.|.+|+++|.+.+ .+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~~~~yC~~cy~   72 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGS-FFPKGEDFYCVTCHE   72 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSC-EEEETTEEEEHHHHH
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCc-cEeeCCEEECHHHHH
Confidence            3579999999999543 588999999999999999999998764 678999999999985

>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=99.75  E-value=9.3e-19  Score=81.57  Aligned_cols=59  Identities=27%  Similarity=0.750  Sum_probs=50.7

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeee-CCeecchhhhc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIK-DEAVYCKQDYA   66 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~y~   66 (67)
                      ....+.|.+|+++|.+. .+.+.++.||++||+|..|+++|.+.. ++.. ++++||+.||.
T Consensus        12 ~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~~~g~~yC~~cy~   71 (81)
T 2dlo_A           12 VATLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGIP-FTVDATSQIHCIEDFH   71 (81)
T ss_dssp             CSSCCBCTTTCCBCCSC-CEEETTEEECTTTCBCSSSCCBCTTSC-EECCTTCCCEEHHHHH
T ss_pred             hcCCCccccCCCeecce-eEEECCccccHHhcCcccCCCccCCCe-eEECCCCEEECHHHHH
Confidence            35678999999999975 789999999999999999999998654 4444 78999999985

>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=99.75  E-value=8.2e-19  Score=81.74  Aligned_cols=58  Identities=16%  Similarity=0.541  Sum_probs=50.2

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCcee-eeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCF-IKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~   66 (67)
                      -.++|.+|+++|.+ +.+.+.++.||++||+|..|+++|..+..+. .+++++||+.||.
T Consensus        14 ~~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~   72 (81)
T 1x6a_A           14 FGEFCHGCSLLMTG-PFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHN   72 (81)
T ss_dssp             SSCBCTTTCCBCCS-CCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHH
T ss_pred             cCCcCccCCCCcCc-eEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHH
Confidence            45789999999995 4788999999999999999999997655555 4899999999985

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

Probab=99.75  E-value=1.5e-18  Score=86.50  Aligned_cols=57  Identities=23%  Similarity=0.521  Sum_probs=51.9

Q ss_pred             CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+.|.+|+++|.+++.+.+.++.||++||+|..|+++|.+. .++.++|++||+.||.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~cy~   59 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGE-IYVMVNDKPVCKPCYV   59 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTS-EEEEETTEEEEHHHHH
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcC-EEEeECCEEechHHhC
Confidence            57899999999987788999999999999999999999864 4678999999999985

>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=99.74  E-value=1.7e-18  Score=80.43  Aligned_cols=57  Identities=23%  Similarity=0.575  Sum_probs=51.0

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.|.+|+++|.+. .+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~~~~yC~~~y~   70 (80)
T 1x3h_A           14 FSPKCGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSFSTGS-FFELDGRPFCELHYH   70 (80)
T ss_dssp             CSCBCTTTCCBCCSS-CEEETTEEECTTTCBCSSSCCBSCSSC-CEESSSCEECHHHHH
T ss_pred             cCCccccCCCeecce-eEEECCCeEecCcCChhhCCCCCCCCc-EEeECCEEECHHHHH
Confidence            357999999999984 689999999999999999999998765 578999999999985

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

Probab=99.74  E-value=3.8e-18  Score=89.47  Aligned_cols=60  Identities=35%  Similarity=0.912  Sum_probs=53.6

Q ss_pred             cccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          5 IITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         5 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.+.|..|+++|.+.+++.+.++.||+.||+|..|+++|.+..  +.++|.+||+.||.
T Consensus        56 ~~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~--f~~~g~~yC~~~y~  115 (182)
T 2jtn_A           56 GTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC--FSRGESVYCKDDFF  115 (182)
T ss_dssp             CCCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCC--EEETTEEECHHHHH
T ss_pred             CCCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCc--eeECCEeeecCccc
Confidence            3556789999999999887788999999999999999999998754  57999999999985

>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=2.6e-18  Score=79.82  Aligned_cols=58  Identities=28%  Similarity=0.610  Sum_probs=51.3

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|.+|+++|.+. .+.+.++.||++||+|..|+++|.+. .++.+++.+||+.||.
T Consensus        13 ~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~   70 (80)
T 2cuq_A           13 KFAPRCARCSKTLTQG-GVTYRDQPWHRECLVCTGCQTPLAGQ-QFTSRDEDPYCVACFG   70 (80)
T ss_dssp             CSSCCCTTTCCCCCSC-CEESSSSEECTTTCBCSSSCCBCTTC-CEEECSSSEEEHHHHH
T ss_pred             ccCCcCCCCCCEecCc-EEEECCchhhhhhCCcccCCCcCCCC-eeEeECCEEECHHHHH
Confidence            3468999999999975 68899999999999999999999765 4678999999999985

>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=99.72  E-value=2.3e-18  Score=90.71  Aligned_cols=60  Identities=35%  Similarity=0.872  Sum_probs=53.1

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCC-CCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR-HPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~   66 (67)
                      ...+.|..|+++|.+.+++.++++.||++||+|..|+++|.. +..++.++|.+||+.||.
T Consensus         3 l~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~   63 (188)
T 1rut_X            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI   63 (188)
T ss_dssp             -CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHH
T ss_pred             CCCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccc
Confidence            346899999999998878899999999999999999999975 445788999999999985

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

Probab=99.72  E-value=1.4e-17  Score=77.55  Aligned_cols=59  Identities=17%  Similarity=0.461  Sum_probs=49.9

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      -.+.|..|+++|.+ +.+.+.++.||++||+|..|+++|..+..+...++.+||..||.+
T Consensus        14 ~~~~C~~C~~~I~~-~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~   72 (81)
T 1v6g_A           14 YGTRCFSCDQFIEG-EVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLP   72 (81)
T ss_dssp             CCCBCTTTCCBCCS-CCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSC
T ss_pred             hCCcCccccCEecc-ceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcc
Confidence            45799999999996 478999999999999999999999876654445666899999864

>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=99.71  E-value=7.2e-18  Score=87.59  Aligned_cols=58  Identities=36%  Similarity=0.973  Sum_probs=50.5

Q ss_pred             cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .+.+.|.+|+++|.+.+++.++++.||++||+|..|+++|.+..  +.++|.+||+.||.
T Consensus         4 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~--f~~~g~~yC~~~y~   61 (169)
T 2rgt_A            4 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC--FSRGESVYCKDDFF   61 (169)
T ss_dssp             ---CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC--EESSSCEECHHHHH
T ss_pred             CCCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC--cccCCeeeeccccc
Confidence            45789999999999887788999999999999999999998754  57999999999985

>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=99.69  E-value=1.5e-17  Score=87.79  Aligned_cols=60  Identities=23%  Similarity=0.545  Sum_probs=53.7

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      ..+.+.|..|+++|.+.+.+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.
T Consensus         4 ~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~cy~   63 (192)
T 1b8t_A            4 WGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTT-VAVHGDEIYCKSCYG   63 (192)
T ss_dssp             CCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSS-EEEETTEEEEHHHHH
T ss_pred             CCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCe-eEecCCEeeChhhhH
Confidence            455789999999999777888999999999999999999998864 688999999999985

>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=4.4e-17  Score=86.03  Aligned_cols=58  Identities=33%  Similarity=0.659  Sum_probs=51.8

Q ss_pred             CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +.+.|.+|+++|.+.+.+.+.++.||++||+|..|+++|.+.. ++.+++++||+.||.
T Consensus       114 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~cy~  171 (192)
T 1b8t_A          114 GSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTT-LADKDGEIYCKGCYA  171 (192)
T ss_dssp             CCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSS-EEEETTEEEEHHHHH
T ss_pred             CCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCc-ccccCCEEeCHHHHH
Confidence            3567999999999777888999999999999999999998754 678999999999985

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

Probab=99.64  E-value=2.8e-16  Score=78.60  Aligned_cols=56  Identities=25%  Similarity=0.631  Sum_probs=49.5

Q ss_pred             cccccCccccCc-eeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221         11 YCVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        11 ~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .|..|+++|.+. ..+.+.++.||++||+|..|+++|..+..++..++++||+.||.
T Consensus        68 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~  124 (131)
T 2xjy_A           68 LCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIY  124 (131)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHH
T ss_pred             ChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHH
Confidence            899999999964 46789999999999999999999965555778999999999985

>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=99.60  E-value=1.1e-15  Score=80.52  Aligned_cols=57  Identities=23%  Similarity=0.607  Sum_probs=49.8

Q ss_pred             cccccCccccCce-eeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         11 YCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        11 ~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      .|..|+++|...+ ++.+.++.||+.||+|..|+++|..+..++..++++||+.||.+
T Consensus        71 ~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~  128 (188)
T 1rut_X           71 ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPT  128 (188)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCT
T ss_pred             ccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHH
Confidence            7999999999643 57899999999999999999999765556789999999999863

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

Probab=99.58  E-value=1.9e-15  Score=75.16  Aligned_cols=58  Identities=21%  Similarity=0.519  Sum_probs=49.7

Q ss_pred             CCccccccCccccC-ceeeeecCceec--cccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITD-KYLLQVSDKSWH--AQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~-~~~~~~~~~~~h--~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      -.+.|.+|+++|.+ ...+.+.++.||  ++||+|..|+++|.+ ..++.+++++||+.+|.
T Consensus        62 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~-~~f~~~~~~~yC~~~~~  122 (126)
T 2xqn_T           62 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIG-QKFMPVEGMVFCSVECK  122 (126)
T ss_dssp             SCCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTT-SEEEEETTEEESSHHHH
T ss_pred             cCccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCC-CeeEeECCEEcchHHhh
Confidence            35789999999995 346889999999  999999999999985 44678999999997764

>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=99.54  E-value=5.8e-15  Score=76.63  Aligned_cols=58  Identities=26%  Similarity=0.618  Sum_probs=48.9

Q ss_pred             CccccccCccccCce-eeeecCceeccccccccccccccCCCCcee-eeCCeecchhhhc
Q psy10221          9 LRYCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCF-IKDEAVYCKQDYA   66 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~   66 (67)
                      .+.|.+|+++|.+.+ ++.+.++.||+.||+|..|+++|..+..++ ..++++||+.||.
T Consensus        65 ~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~  124 (169)
T 2rgt_A           65 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE  124 (169)
T ss_dssp             SCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHH
T ss_pred             cccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHH
Confidence            578999999999754 457999999999999999999998655444 4689999999985

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

Probab=99.52  E-value=6.7e-15  Score=77.13  Aligned_cols=59  Identities=25%  Similarity=0.586  Sum_probs=49.4

Q ss_pred             CCccccccCccccCce-eeeecCceeccccccccccccccCCCCcee-eeCCeecchhhhc
Q psy10221          8 ELRYCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCF-IKDEAVYCKQDYA   66 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~   66 (67)
                      -.+.|..|+++|.+.+ ++.+.++.||+.||+|..|+++|..+..++ ..++++||+.||.
T Consensus       118 f~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~  178 (182)
T 2jtn_A          118 FGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE  178 (182)
T ss_dssp             TSCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHH
T ss_pred             cccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHH
Confidence            3578999999998654 457899999999999999999998655444 4689999999985

>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=98.87  E-value=1.8e-09  Score=51.64  Aligned_cols=36  Identities=17%  Similarity=0.393  Sum_probs=31.0

Q ss_pred             CCccccccCccccCc-eeeeecCceeccccccccccc
Q psy10221          8 ELRYCVACGESITDK-YLLQVSDKSWHAQCLRCCICQ   43 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~   43 (67)
                      -.+.|.+|+++|.+. ..+.+.++.||++||+|..|+
T Consensus        65 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           65 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             CCCBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             cCCccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence            357899999999943 468899999999999999985

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

Probab=98.85  E-value=8.8e-10  Score=42.59  Aligned_cols=29  Identities=28%  Similarity=0.662  Sum_probs=26.7

Q ss_pred             CccccccCccccCceeeeecCceeccccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      .+.|..|++.|+.++.+.+.++.||..||
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            46899999999988899999999999997

>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=97.58  E-value=3.4e-05  Score=37.90  Aligned_cols=17  Identities=12%  Similarity=0.028  Sum_probs=13.6

Q ss_pred             CceeeeCCeecchhhhc
Q psy10221         50 PSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        50 ~~~~~~~~~~~C~~~y~   66 (67)
                      ..++.+++++||..||.
T Consensus        95 ~~f~~~~~~~yC~~~~~  111 (122)
T 1m3v_A           95 GEFGDEDERLITRLENT  111 (122)
T ss_dssp             CTTCCTTCCCCEECTTT
T ss_pred             CccEecCCEeEccCcch
Confidence            44567899999999875

>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=96.06  E-value=0.0028  Score=30.64  Aligned_cols=57  Identities=11%  Similarity=0.036  Sum_probs=35.0

Q ss_pred             ccccccCccccC--ceeeeecCcee---------cccccccc-----ccccccCCCCceeeeCCeecchhhhc
Q psy10221         10 RYCVACGESITD--KYLLQVSDKSW---------HAQCLRCC-----ICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        10 ~~C~~C~~~i~~--~~~~~~~~~~~---------h~~cf~C~-----~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      -.|..|++++.+  .......++.|         .+.|..|.     .|+..+..+..++.+++++||..||.
T Consensus        31 F~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~~~~~~~~~~~~~g~~f~~~~~~~~C~~~~~  103 (114)
T 1j2o_A           31 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENT  103 (114)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBSCSCCCSSCSSTTSSBCCCSSSCCCEEEECT
T ss_pred             CcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCCCceeEcCCccCCCCeeEEcCCEeecchhhh
Confidence            368889988864  22334444443         33443332     24555444555678999999999875

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=89.28  E-value=0.12  Score=23.76  Aligned_cols=33  Identities=24%  Similarity=0.527  Sum_probs=27.0

Q ss_pred             CccccccCccccCceeeeecCceeccccccccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCI   41 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~   41 (67)
                      ...|.-|.+.+++...+.--...-|..||.|+.
T Consensus        15 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr   47 (93)
T 2cs3_A           15 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSR   47 (93)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHH
T ss_pred             eeEeecchhhhccCceeeCCCccCCeeeccccH
Confidence            357899999999887777777778999999864

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.20  E-value=0.24  Score=22.26  Aligned_cols=36  Identities=14%  Similarity=0.312  Sum_probs=26.2

Q ss_pred             cccccCCccccccCccccCceeeeecCceecccccc
Q psy10221          3 KTIITELRYCVACGESITDKYLLQVSDKSWHAQCLR   38 (67)
Q Consensus         3 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~   38 (67)
                      +.|......|+.|...|.....-..=+..||..|+.
T Consensus         9 ~~y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~   44 (74)
T 2ct0_A            9 ETYPDAVKICNICHSLLIQGQSCETCGIRMHLPCVA   44 (74)
T ss_dssp             CCCSSSSCBCSSSCCBCSSSEECSSSCCEECHHHHH
T ss_pred             hhccCCCCcCcchhhHcccCCccCCCCchhhHHHHH
Confidence            456677889999999998654433445678988874

>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1

Probab=88.64  E-value=0.4  Score=20.43  Aligned_cols=26  Identities=19%  Similarity=0.423  Sum_probs=16.6

Q ss_pred             cccccccccCCCCceeeeCCeecc-hhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYC-KQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C-~~~   64 (67)
                      .|..|+...+..+ .+.++|+.|| +.|
T Consensus         9 aC~~C~c~Vs~~e-ai~~dGK~YCSe~C   35 (55)
T 1jjd_A            9 ACEPCLCNVDPSK-AIDRNGLYYCSEAC   35 (55)
T ss_dssp             SSTTCCCCBCTTT-SEESSSCEESSHHH
T ss_pred             cCCCCeeEechHH-hhhcCCeEEehHHH
Confidence            4566777666533 4678888887 444

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=87.91  E-value=0.37  Score=26.29  Aligned_cols=44  Identities=16%  Similarity=0.362  Sum_probs=30.0

Q ss_pred             cccCCccccccCccccCceeeeecCceeccccc----------cccccccccCC
Q psy10221          5 IITELRYCVACGESITDKYLLQVSDKSWHAQCL----------RCCICQLVLDR   48 (67)
Q Consensus         5 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf----------~C~~C~~~l~~   48 (67)
                      +......|..|...|..+..-..=+..||..|+          .|-.|+..+..
T Consensus       176 ~~~~i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          176 YPDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             CTTTCCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             cCCCCCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            444578999999999865332223677999987          56666666543

>2das_A Zinc finger MYM-type protein 5; trash domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.17

Probab=85.90  E-value=0.69  Score=20.03  Aligned_cols=27  Identities=15%  Similarity=0.610  Sum_probs=18.6

Q ss_pred             cccccccccccCCCCceeeeCC--eecch
Q psy10221         36 CLRCCICQLVLDRHPSCFIKDE--AVYCK   62 (67)
Q Consensus        36 cf~C~~C~~~l~~~~~~~~~~~--~~~C~   62 (67)
                      -..|+.|+++|..+...|.+.|  ++||.
T Consensus        20 ~v~C~~CKk~lqKGQtAyqrkGs~~LFCS   48 (62)
T 2das_A           20 KITCANCKKPLQKGQTAYQRKGSAHLFCS   48 (62)
T ss_dssp             SCBCTTTCCBCCTTSCCEECTTCCCEESS
T ss_pred             ccChhhccchhhcCceeeeecCchhheec
Confidence            3578888888877766666544  56663

>2gvi_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 1.87A {Thermoplasma acidophilum} SCOP: d.81.3.1 g.39.1.18

Probab=84.78  E-value=0.31  Score=25.95  Aligned_cols=30  Identities=23%  Similarity=0.415  Sum_probs=22.2

Q ss_pred             cccccccccccCCCCceeeeCCeecchhhhc
Q psy10221         36 CLRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        36 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      -..|..|+-...... ....+|+.+|..|+.
T Consensus       172 ~~~C~~CGE~~~~~~-~~~~~g~~~C~~C~~  201 (204)
T 2gvi_A          172 KVRCDVCGEYTYEAD-AKLLNGKPVCKPDYY  201 (204)
T ss_dssp             EEECTTTCCEEEGGG-CEEETTEEECHHHHH
T ss_pred             ceECCCCCCchhhcc-eeeeCCcEEChhhhc
Confidence            357888988775532 245789999999985

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=84.09  E-value=0.7  Score=19.60  Aligned_cols=42  Identities=17%  Similarity=0.417  Sum_probs=26.7

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc--------cccccccccCC
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL--------RCCICQLVLDR   48 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf--------~C~~C~~~l~~   48 (67)
                      .....|.-|...+.+...+..=+..||..|.        .|-.|..++..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            3456788898887764333344566776665        36677777654

>2ds5_A CLPX, ATP-dependent CLP protease ATP-binding subunit CLPX; treble cleft zinc finger, metal binding protein, protein binding; HET: PG4; 1.50A {Escherichia coli} SCOP: g.39.1.11 PDB: 2ds6_A 2ds8_A 2ds7_A

Probab=82.21  E-value=1.4  Score=18.34  Aligned_cols=27  Identities=11%  Similarity=0.255  Sum_probs=12.9

Q ss_pred             cccccccccCCCCceeeeCCeecchhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      +|+.|+++-..........+...|..|
T Consensus        13 ~CSFCGk~~~ev~~LIaGpgv~IC~eC   39 (51)
T 2ds5_A           13 YCSFCGKSQHEVRKLIAGPSVYICDEC   39 (51)
T ss_dssp             BCTTTCCBTTTSSCEEECSSCEEEHHH
T ss_pred             EecCCCCCHHHhcccCCCCCCEehHHH
Confidence            566666665544432222333445544

>1ovx_A ATP-dependent CLP protease ATP-binding subunit CL; treble CLEF zinc finger, homodimer, metal binding protein; NMR {Escherichia coli} SCOP: g.39.1.11

Probab=82.19  E-value=1.3  Score=19.56  Aligned_cols=11  Identities=18%  Similarity=0.528  Sum_probs=5.1

Q ss_pred             cccccccccCC
Q psy10221         38 RCCICQLVLDR   48 (67)
Q Consensus        38 ~C~~C~~~l~~   48 (67)
                      +|+.|+++-..
T Consensus        20 ~CSFCGK~e~e   30 (67)
T 1ovx_A           20 YCSFCGKSQHE   30 (67)
T ss_dssp             CCTTTCCCTTT
T ss_pred             EecCCCCCHHH
Confidence            34555544443

>2dmj_A Poly (ADP-ribose) polymerase family, member 1; zinc finger, PARP-1, ADPRT, NAD(+) ADP-ribosyltransferase 1, poly(ADP-ribose) synthetase 1; NMR {Homo sapiens}

Probab=81.76  E-value=0.82  Score=21.88  Aligned_cols=31  Identities=26%  Similarity=0.553  Sum_probs=19.5

Q ss_pred             CCccccccCccccCcee-eee----c------Cceecccccc
Q psy10221          8 ELRYCVACGESITDKYL-LQV----S------DKSWHAQCLR   38 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~-~~~----~------~~~~h~~cf~   38 (67)
                      +-..|..|++.|...++ +..    .      ...+|..||.
T Consensus        24 ~Ra~Ck~C~~kI~KgelRig~~v~~~~~~g~~~~W~H~~Cf~   65 (106)
T 2dmj_A           24 GRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFW   65 (106)
T ss_dssp             SCCBCSSSCCBCCTTCEEEEEEEEETTTTEEEEEEEETTHHH
T ss_pred             CCCcchhhCCccCCCCEEEEEEecCCCCCCCcCEeECcCccc
Confidence            34689999999985443 211    0      1346888876

>1v9x_A Poly (ADP-ribose) polymerase; PARP, DNA repair, inflammation, cell death, structural genomics; NMR {Arabidopsis thaliana}

Probab=80.38  E-value=1.6  Score=21.25  Aligned_cols=32  Identities=22%  Similarity=0.367  Sum_probs=20.0

Q ss_pred             cCCccccccCccccCcee-eeec----------Cceecccccc
Q psy10221          7 TELRYCVACGESITDKYL-LQVS----------DKSWHAQCLR   38 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~-~~~~----------~~~~h~~cf~   38 (67)
                      .+-..|..|++.|...++ +...          ...+|..||.
T Consensus        18 S~RA~Ck~Ck~kI~KgeLRiG~~v~~~~~dG~~~~W~H~~Cf~   60 (114)
T 1v9x_A           18 SSRSSCKTCKSVINKENFRLGKLVQSTHFDGIMPMWNHASCIL   60 (114)
T ss_dssp             CSCCBCSSSCCBCCSSSEEEEECCCCSSSSCCCCEEEEHHHHH
T ss_pred             CCCCCchhhCCccCCCCEEEEEEecCcccCCCcceeECccccc
Confidence            344689999999985443 2211          2245788875

---

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	67
d1rutx1	30	g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus m	4e-07
d1j2oa1	30	g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus m	5e-06

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 30

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]

 Score = 39.3 bits (92), Expect = 4e-07
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 10 RYCVACGESITDKYLLQVSDKSWHAQCL 37
          + C  CG  I D++LL   D  WH++CL
Sbjct: 3  KRCAGCGGKIADRFLLYAMDSYWHSRCL 30

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]} Length = 30

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]

 Score = 36.7 bits (85), Expect = 5e-06
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 9  LRYCVACGESITDKYLLQVSDKSWHAQC 36
          L  C  C ++I D+Y L+  D+ WH  C
Sbjct: 3  LLTCGGCQQNIGDRYFLKAIDQYWHEDC 30

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	67
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	99.22
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.18
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	99.04
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	99.01
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	99.01
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	99.0
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.97
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.96
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.96
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.91
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.86
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.84
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.84
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.83
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.74
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.74
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.66
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.64
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.63
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.63
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.56
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.55
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.55
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.5
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.45
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	98.43
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.4
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.39
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.37
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	98.35
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	98.34
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.32
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.31
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.27
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.23
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.22
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.2
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.17
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.11
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.1
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.05
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.99
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.98
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.93
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.93
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.9
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.72
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.69
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.66
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.64
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.62
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	97.58
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.55
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.45
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.43
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.42
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	97.35
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.24
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.18
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.05
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.89
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	96.55
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.34
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	96.01
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.97
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	94.32
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	91.71
d2co8a1	33	Nedd9 interacting protein with calponin homology,	90.2
d2dasa1	49	Zinc finger MYM-type protein 5 {Human (Homo sapien	89.51
d1uw0a_	117	DNA ligase III {Human (Homo sapiens) [TaxId: 9606]	88.86
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	88.53
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	86.53
d2ctda2	30	Zinc finger protein 512, ZNF512 {Human (Homo sapie	86.33
d2ds5a1	38	ClpX chaperone zinc binding domain {Escherichia co	83.83
d2d8va1	54	Zinc finger FYVE domain-containing protein 19 {Mou	80.15

>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=99.22  E-value=5.6e-12  Score=48.30  Aligned_cols=34  Identities=26%  Similarity=0.728  Sum_probs=31.1

Q ss_pred             cccccCCccccccCccccCceeeeecCceeccccc
Q psy10221          3 KTIITELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         3 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ..|+.....|..|+++|.+. ++++.|+.|||.||
T Consensus         2 ~Cy~~tlEkC~~C~~~I~dr-iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           2 GCYVATLEKCATCSQPILDR-ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCSSCCBCTTTCCBCCSC-CEEETTEEECTTTC
T ss_pred             hhHHHHHHHHHHhchHHHHH-HHHHhCCCCCCCCC
Confidence            35788899999999999997 89999999999998

>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=99.18  E-value=7.4e-12  Score=48.66  Aligned_cols=31  Identities=23%  Similarity=0.632  Sum_probs=27.3

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      +.-+++|.+|+++|.+. .++++++.||++||
T Consensus         5 ~~fapkC~~C~~~I~g~-~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           5 AMFSPKCGGCNRPVLEN-YLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCSCBCTTTCCBCCSS-CEEETTEEECTTTC
T ss_pred             HHhChhhhhcCCcccch-heeecCCccCcccC
Confidence            34468999999999986 79999999999998

>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=99.04  E-value=3.3e-11  Score=43.94  Aligned_cols=30  Identities=37%  Similarity=0.709  Sum_probs=26.2

Q ss_pred             ccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         37 LRCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      |+|+.|++.|.+.. ...+||++||+.||.|
T Consensus         1 frca~cgk~lestt-~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTT-LTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSC-SEEETTEEECHHHHHH
T ss_pred             CccccccCccccce-eeccCCcEEEeeeeec
Confidence            78999999998865 3789999999999964

>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=99.01  E-value=1.9e-10  Score=42.72  Aligned_cols=29  Identities=41%  Similarity=1.068  Sum_probs=26.6

Q ss_pred             CccccccCccccCceeeeecCceeccccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ...|++|+++|.++..+.+.++.||..|+
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            46799999999999999999999999884

>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=99.01  E-value=1.5e-10  Score=46.62  Aligned_cols=30  Identities=27%  Similarity=0.601  Sum_probs=26.7

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ...+.|..|+++|.+. .+.++++.||+++|
T Consensus        16 ~r~P~C~~C~~pI~g~-~vtAlgk~WHPEhF   45 (45)
T d2dara2          16 KRTPMCAHCNQVIRGP-FLVALGKSWHPEEF   45 (45)
T ss_dssp             TCCCBBSSSCCBCCSC-EEEETTEEECTTTC
T ss_pred             CCCeeccccCCcccCc-eeeecCCccCcCCC
Confidence            4468899999999986 78999999999987

>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=99.00  E-value=1.7e-10  Score=43.86  Aligned_cols=32  Identities=34%  Similarity=0.695  Sum_probs=29.0

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ..+...|++|++.|...+.+.++++.||.+||
T Consensus         5 ~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           5 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            35678899999999999899999999999997

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.97  E-value=1.8e-10  Score=46.48  Aligned_cols=32  Identities=25%  Similarity=0.596  Sum_probs=28.9

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ..+...|..|++.++.+|.+.+.++.||..||
T Consensus        12 ~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          12 VGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             cCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            34568899999999999999999999999998

>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=98.96  E-value=1.2e-10  Score=45.10  Aligned_cols=29  Identities=17%  Similarity=0.496  Sum_probs=25.9

Q ss_pred             ccccccccccCCCCceeeeCCeecchhhhc
Q psy10221         37 LRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      |+|+.|++++.+.. +++++|++||+.||.
T Consensus         1 F~C~~C~~~f~~~~-F~e~~G~pYCe~~Y~   29 (35)
T d1g47a2           1 FVCAQCFQQFPEGL-FYEFEGRKYCEHDFQ   29 (35)
T ss_dssp             CCCTTTCCCCGGGC-SEEETTEEECHHHHH
T ss_pred             CCCCCCcCCCCCCC-eEEECCEecChHhHH
Confidence            78999999999866 489999999999985

>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=98.96  E-value=3.8e-10  Score=41.76  Aligned_cols=29  Identities=38%  Similarity=0.950  Sum_probs=26.4

Q ss_pred             CCccccccCccccCceeeeecCceecccc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQC   36 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~c   36 (67)
                      ....|++|+++|.++.++.+.++.||..|
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            35689999999999999999999999876

>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=98.91  E-value=4.8e-10  Score=41.42  Aligned_cols=29  Identities=24%  Similarity=0.541  Sum_probs=26.5

Q ss_pred             CccccccCccccCceeeeecCceeccccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      .+.|++|+++++.+|.+..+++.||..|+
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            46899999999999999999999999884

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=1.1e-09  Score=42.19  Aligned_cols=31  Identities=19%  Similarity=0.495  Sum_probs=28.6

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      +....|..|++.++..+.+.+.++.||..||
T Consensus         5 p~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           5 PARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            4567999999999999999999999999997

>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=98.84  E-value=4.3e-10  Score=41.08  Aligned_cols=28  Identities=29%  Similarity=0.722  Sum_probs=26.2

Q ss_pred             ccccccCccccCceeeeecCceeccccc
Q psy10221         10 RYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus        10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      +.|++|++.+++.+.+.-+++.||..||
T Consensus         3 ~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcccccCCccccHHHhhhhHHHHhhccC
Confidence            6799999999999999999999999997

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.83  E-value=1.1e-09  Score=42.38  Aligned_cols=33  Identities=24%  Similarity=0.406  Sum_probs=29.9

Q ss_pred             cccCCccccccCccccCceeeeecCceeccccc
Q psy10221          5 IITELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         5 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ...+...|..|++.++..+.+.+.++.||..||
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             cCCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            345678999999999999999999999999998

>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=98.74  E-value=2.3e-09  Score=39.76  Aligned_cols=28  Identities=25%  Similarity=0.666  Sum_probs=25.2

Q ss_pred             cCCccccccCccccCceeeeecCceeccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQ   35 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~   35 (67)
                      .+.+.|+.|.++|.+. .+.++++.||++
T Consensus         3 mg~p~C~~C~~PI~~~-~vtAlgk~WHpE   30 (31)
T d1u5sb1           3 MGVPICGACRRPIEGR-VVNAMGKQWHVE   30 (31)
T ss_dssp             CCCCEETTTTEECCSC-EECCTTSBEETT
T ss_pred             cCCcchhhcCCchhhh-HhhhhccccCCC
Confidence            4678999999999996 899999999986

>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=98.74  E-value=2e-09  Score=44.21  Aligned_cols=29  Identities=41%  Similarity=0.720  Sum_probs=25.2

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      +|..|++.|++.. ..++|+++||+.||.|
T Consensus         1 KC~~C~k~Lds~t-~~ehdg~~YCk~CY~k   29 (49)
T d1b8ta4           1 RCAKCGKSLESTT-LADKDGEIYCKGCYAK   29 (49)
T ss_dssp             BCTTTCCBCCSSS-EEEETTEEEEHHHHHH
T ss_pred             ChhhcCCccCCCc-ccccCCcccchhhhhh
Confidence            5899999999865 5789999999999964

>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=98.66  E-value=8.6e-09  Score=39.13  Aligned_cols=30  Identities=27%  Similarity=0.695  Sum_probs=26.3

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      .-+..|..|+++|..+ .++..++.||.+||
T Consensus         6 kfa~~C~~Ckk~It~G-GvtY~dqpWHkeCF   35 (35)
T d2cuqa2           6 KFAPRCARCSKTLTQG-GVTYRDQPWHRECL   35 (35)
T ss_dssp             CSSCCCTTTCCCCCSC-CEESSSSEECTTTC
T ss_pred             HHHHHHhhcCCccccC-ceeecCCcchhhhC
Confidence            3468999999999976 68999999999997

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.64  E-value=6.1e-09  Score=37.34  Aligned_cols=27  Identities=30%  Similarity=0.745  Sum_probs=24.6

Q ss_pred             ccccccCccccCceeeeecCceecccc
Q psy10221         10 RYCVACGESITDKYLLQVSDKSWHAQC   36 (67)
Q Consensus        10 ~~C~~C~~~i~~~~~~~~~~~~~h~~c   36 (67)
                      ..|.+|++.++.++.+...++.||..|
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            579999999999889999999999876

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=1.7e-08  Score=39.21  Aligned_cols=31  Identities=19%  Similarity=0.558  Sum_probs=26.1

Q ss_pred             cCCccccccCccccC-ceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITD-KYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~-~~~~~~~~~~~h~~cf   37 (67)
                      .-+..|.+|+++|.+ ...+.+.++.||..||
T Consensus         6 ~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           6 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            346799999999994 4458999999999997

>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=98.56  E-value=2.2e-08  Score=36.92  Aligned_cols=27  Identities=33%  Similarity=0.835  Sum_probs=23.4

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +|..|++.|...  |..+||.|||+.+|+
T Consensus         1 kC~~C~~vL~gE--Ym~kdG~PyCe~DY~   27 (31)
T d2dj7a1           1 KCQTCSVILTGE--YISKDGVPYCESDYH   27 (31)
T ss_dssp             BCSSSCCBCSSC--CEEETTEEECTTHHH
T ss_pred             CccccCccccce--eecCCCCcccHHHHH
Confidence            588999999865  567999999999986

>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=2e-08  Score=37.64  Aligned_cols=28  Identities=21%  Similarity=0.455  Sum_probs=24.4

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .|..|.+|..+++ +++.+|++||+.+|.
T Consensus         1 VC~~C~~PF~~~~-Fy~~~g~PyCe~HyH   28 (32)
T d1x3ha2           1 VCGDCFTSFSTGS-FFELDGRPFCELHYH   28 (32)
T ss_dssp             BCSSSCCBSCSSC-CEESSSCEECHHHHH
T ss_pred             CcCccCCcCCCCC-eEeECCccchHHhhh
Confidence            4889999998876 489999999999985

>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=98.50  E-value=5e-08  Score=36.25  Aligned_cols=29  Identities=28%  Similarity=0.701  Sum_probs=24.5

Q ss_pred             CccccccCccccCce-eeeecCceeccccc
Q psy10221          9 LRYCVACGESITDKY-LLQVSDKSWHAQCL   37 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf   37 (67)
                      ...|++|++.|...+ ++++.++.||..||
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            457999999998544 47899999999998

>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=98.45  E-value=6.2e-08  Score=35.04  Aligned_cols=26  Identities=23%  Similarity=0.905  Sum_probs=22.1

Q ss_pred             ccccCcccc---CceeeeecCceeccccc
Q psy10221         12 CVACGESIT---DKYLLQVSDKSWHAQCL   37 (67)
Q Consensus        12 C~~C~~~i~---~~~~~~~~~~~~h~~cf   37 (67)
                      |..|.++|.   ....++.+++.||.+||
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            788999997   44568899999999997

>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=98.43  E-value=1.1e-07  Score=35.63  Aligned_cols=30  Identities=27%  Similarity=0.723  Sum_probs=27.0

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      +..+.|.+|+..|... ++.++++.+|++||
T Consensus         6 qklp~CdkCg~GIVG~-~VK~rDk~rHPeCf   35 (35)
T d1x62a2           6 QKLPMCDKCGTGIVGV-FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCSSSCCCCCSS-CEECSSCEECTTTT
T ss_pred             ccCccccccCCCcEeE-EEEeccccCCCCCC
Confidence            4578999999999987 78999999999997

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.40  E-value=4.7e-08  Score=35.90  Aligned_cols=28  Identities=43%  Similarity=0.846  Sum_probs=23.8

Q ss_pred             ccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      |..|.+.|++... ..+++++||+.||.|
T Consensus         2 C~~C~K~LdStTv-a~h~~eiYCKsCygk   29 (32)
T d1a7ia2           2 CMVCRKNLDSTTV-AIHDAEVYCKSCYGK   29 (32)
T ss_dssp             CSSSCCEECSSCC-EEETTEEECSHHHHH
T ss_pred             chhhhhccCccee-eeecceEEehhhccc
Confidence            6789999988654 789999999999964

>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=98.39  E-value=5.6e-08  Score=39.44  Aligned_cols=28  Identities=21%  Similarity=0.450  Sum_probs=24.2

Q ss_pred             cccccccccCCCCceeeeCCeecc-hhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYC-KQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C-~~~y~   66 (67)
                      +|..|++.|+++. ..++++++|| +.||.
T Consensus         1 kC~~C~K~L~sg~-~aeHdg~pYC~k~CY~   29 (48)
T d1imla2           1 KCEKCGKTLTSGG-HAEHEGKPYCNHPCYS   29 (48)
T ss_dssp             BCTTTCCBCCTTT-EEEETTEEEETTTHHH
T ss_pred             CchhcCcCcCCCC-hhhcCCcccccccchh
Confidence            5889999999876 4799999999 77985

>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=98.37  E-value=7e-08  Score=41.60  Aligned_cols=29  Identities=31%  Similarity=0.768  Sum_probs=24.8

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      .|..|++.|++.. ..++++++||+.||.|
T Consensus         1 ~C~~C~K~LdS~~-~~eh~~e~YCk~CY~k   29 (65)
T d1b8ta2           1 LCMVCKKNLDSTT-VAVHGDEIYCKSCYGK   29 (65)
T ss_dssp             BCTTTCCBCCSSS-EEEETTEEEEHHHHHH
T ss_pred             CchhcCCccCCCc-cccCCCcccchhhhcc
Confidence            3789999999876 5789999999999964

>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=98.35  E-value=1.6e-07  Score=33.25  Aligned_cols=26  Identities=27%  Similarity=0.773  Sum_probs=21.9

Q ss_pred             ccccCccccCce-eeeecCceeccccc
Q psy10221         12 CVACGESITDKY-LLQVSDKSWHAQCL   37 (67)
Q Consensus        12 C~~C~~~i~~~~-~~~~~~~~~h~~cf   37 (67)
                      |..|.+.|++.. .+...+..||..||
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            678999999654 48899999999997

>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=98.34  E-value=2.1e-07  Score=36.92  Aligned_cols=30  Identities=27%  Similarity=0.709  Sum_probs=26.8

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      +..+.|.+|+..|... ++.++++.+|++||
T Consensus        16 QkLP~CdkCg~GIVG~-~VK~rDK~rHPeCf   45 (45)
T d1x64a1          16 QRMPLCDKCGSGIVGA-VVKARDKYRHPECF   45 (45)
T ss_dssp             CSCCBCTTTCCBCCSC-CEESSSCEECTTTC
T ss_pred             ccCccccccCCCcEEE-EEEeccccCCCCCC
Confidence            4568999999999987 78999999999997

>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=98.32  E-value=2.6e-07  Score=33.31  Aligned_cols=26  Identities=35%  Similarity=1.000  Sum_probs=21.8

Q ss_pred             ccccCcccc---CceeeeecCceeccccc
Q psy10221         12 CVACGESIT---DKYLLQVSDKSWHAQCL   37 (67)
Q Consensus        12 C~~C~~~i~---~~~~~~~~~~~~h~~cf   37 (67)
                      |..|.++|.   ....++.+++.||.+||
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            678999997   44568899999999997

>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=98.31  E-value=1.1e-07  Score=35.22  Aligned_cols=27  Identities=22%  Similarity=0.493  Sum_probs=23.4

Q ss_pred             ccccccccCCCCceeeeCCeecchhhhc
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      |+.|+.+|.+..+ .+..|.+||+.||.
T Consensus         2 Ca~C~~sL~d~gF-VEE~g~lYCe~Cye   28 (32)
T d2dara1           2 CAHCKNTMAYIGF-VEEKGALYCELCYE   28 (32)
T ss_dssp             CSSSCCBCSSSCB-EESSSCEECHHHHH
T ss_pred             cccccccHhhcce-eeecCcEeHHHHHH
Confidence            7899999998764 77899999999985

>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=98.27  E-value=4.5e-07  Score=33.60  Aligned_cols=27  Identities=22%  Similarity=0.460  Sum_probs=22.9

Q ss_pred             cccccccccCCCCceeeeCCeecch-hhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCK-QDY   65 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~-~~y   65 (67)
                      +|..|++.|..+.. .+++|++||. .||
T Consensus         1 kCekC~ktL~~G~H-aEH~gkPYC~~PCY   28 (33)
T d2cu8a2           1 KCERCSKTLTPGGH-AEHDGKPFCHKPCY   28 (33)
T ss_dssp             BCSSSCCBCCTTSC-EEETTEEECTTTHH
T ss_pred             CchhcccccCCCCc-cccCCCcCcCcchH
Confidence            58889999998775 7899999995 577

>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=98.23  E-value=2.7e-07  Score=32.55  Aligned_cols=26  Identities=35%  Similarity=0.971  Sum_probs=21.6

Q ss_pred             ccccCccccCce-eeeecCceeccccc
Q psy10221         12 CVACGESITDKY-LLQVSDKSWHAQCL   37 (67)
Q Consensus        12 C~~C~~~i~~~~-~~~~~~~~~h~~cf   37 (67)
                      |..|.+.|++.. .+...+..||..||
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            678999999654 37889999999997

>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=98.22  E-value=3.8e-07  Score=33.97  Aligned_cols=28  Identities=21%  Similarity=0.554  Sum_probs=23.4

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .|..|.++|.+. .+..+|+.|||-.||.
T Consensus         1 ~C~~C~~~L~GQ-ry~~rd~~PyC~~Cf~   28 (32)
T d2d8za2           1 VCTACRKQLSGQ-RFTARDDFAYCLNCFC   28 (32)
T ss_dssp             BCSSSCCBCTTS-CCEESSSSEECHHHHH
T ss_pred             CcccCCccccCc-eeeecCCCeehHHhhH
Confidence            378899999874 4678999999999984

>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=98.20  E-value=1.5e-07  Score=35.30  Aligned_cols=30  Identities=23%  Similarity=0.567  Sum_probs=25.4

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      +|..|+++|.+..+....++++||-.+|+|
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHr   30 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHR   30 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHH
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhh
Confidence            488999999988765667899999999975

>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=98.17  E-value=3.5e-07  Score=36.27  Aligned_cols=28  Identities=25%  Similarity=0.560  Sum_probs=23.7

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +|..|++.|..++ +...+|.+||+.||.
T Consensus         1 rC~~C~~~Ls~~~-yas~~G~lYCkpHf~   28 (42)
T d2d8ya2           1 RCSYCNNKLSLGT-YASLHGRIYCKPHFN   28 (42)
T ss_dssp             BCTTTCCBCCTTT-CCCSSSCCCCHHHHH
T ss_pred             CcCcCCCCccCCc-chhhCCEeccHHHHH
Confidence            5889999998765 577899999999983

>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=98.11  E-value=1.4e-06  Score=32.50  Aligned_cols=29  Identities=21%  Similarity=0.599  Sum_probs=24.5

Q ss_pred             ccccccccccCCCCceeeeCCeecchhhhc
Q psy10221         37 LRCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      |.|+.|.+|.-+.. .+++.|..||+.+|.
T Consensus         1 FvCA~CekPF~G~r-hyE~~g~ayCe~Hy~   29 (35)
T d1u5sb2           1 FVCAKCEKPFLGHR-HYERKGLAYCETHYN   29 (35)
T ss_dssp             CBCTTTCCBCSSSC-CEEETTEEECHHHHH
T ss_pred             CcccccCCccCCch-hhhhcCchHHHHHHH
Confidence            68999999986644 489999999999984

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.10  E-value=1.1e-06  Score=32.62  Aligned_cols=31  Identities=19%  Similarity=0.390  Sum_probs=27.3

Q ss_pred             cCCccccccCccccCceeeeecCceeccccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      .+...|..|.+.++-++-+.-.+++||..||
T Consensus         5 ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCCceeccccceEeeeeeeeecCcccccccC
Confidence            4567899999999977778899999999997

>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=98.05  E-value=8e-07  Score=32.87  Aligned_cols=28  Identities=29%  Similarity=0.581  Sum_probs=23.8

Q ss_pred             ccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      |..|..+++..+ +..+++..||..||.+
T Consensus         2 C~~C~qPIGtks-fipk~~~~yCvpCyE~   29 (32)
T d1x4ka1           2 CHRCQQPIGTKS-FIPKDNQNFCVPCYEK   29 (32)
T ss_dssp             CSSSCCCCCSSS-EEEETTEEEEHHHHHH
T ss_pred             cccccCcccccc-cccCCCCceEeecchh
Confidence            788999998865 5789999999999963

>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=97.99  E-value=2.7e-06  Score=31.28  Aligned_cols=28  Identities=29%  Similarity=0.515  Sum_probs=23.1

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .|..|+++|.+.. +..+|..+||-.||.
T Consensus         1 vCt~Ck~~LaGqr-FTSrde~pYC~~Cfg   28 (32)
T d2cuqa1           1 VCTGCQTPLAGQQ-FTSRDEDPYCVACFG   28 (32)
T ss_dssp             BCSSSCCBCTTCC-EEECSSSEEEHHHHH
T ss_pred             CccccCccccCCc-cccCCCCccHHHHhH
Confidence            4789999998754 567999999999984

>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=97.98  E-value=3.4e-06  Score=29.59  Aligned_cols=26  Identities=31%  Similarity=0.862  Sum_probs=21.1

Q ss_pred             ccccCcccc-CceeeeecCceeccccc
Q psy10221         12 CVACGESIT-DKYLLQVSDKSWHAQCL   37 (67)
Q Consensus        12 C~~C~~~i~-~~~~~~~~~~~~h~~cf   37 (67)
                      |..|.++|. +..-+...++.||..||
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            677999997 44447788999999987

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.93  E-value=4.3e-06  Score=29.47  Aligned_cols=27  Identities=30%  Similarity=0.671  Sum_probs=24.1

Q ss_pred             cccccCccccCceeeeecCceeccccc
Q psy10221         11 YCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus        11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      .|+.|.+.++-++-+.-.+++||..||
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            688999999977778899999999987

>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=97.93  E-value=2e-06  Score=31.71  Aligned_cols=27  Identities=26%  Similarity=0.508  Sum_probs=23.3

Q ss_pred             ccccccccCCCCceeeeCCeecchhhhc
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      |..|.+|++..+ +..+++..||..||.
T Consensus         2 C~~C~qPIGtkS-Fip~~~~~yCvpCYE   28 (32)
T d1wyha1           2 CSGCEQPLGSRS-FVPDKGAHYCVPCYE   28 (32)
T ss_dssp             CTTTCCBTTTSC-EEEETTEEEEHHHHH
T ss_pred             cccccCcccccc-cccCCCcEEEEeccc
Confidence            778999998865 577999999999996

>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=97.90  E-value=4.3e-06  Score=32.76  Aligned_cols=27  Identities=22%  Similarity=0.587  Sum_probs=23.5

Q ss_pred             CccccccCccccCceeeeecCceecccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQC   36 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~c   36 (67)
                      ...|..|++.|.. +++.+.++.|||.|
T Consensus        15 G~~C~~C~~~ItG-~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          15 GTRCFSCDQFIEG-EVVSALGKTYHPDC   41 (41)
T ss_dssp             CCBCTTTCCBCCS-CCEEETTEEECTTT
T ss_pred             CcccccccCEeee-eeeEecCcccCCCC
Confidence            4689999999976 48999999999987

>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=97.72  E-value=1.6e-05  Score=28.80  Aligned_cols=26  Identities=27%  Similarity=0.713  Sum_probs=21.8

Q ss_pred             cccccccccCCCCceeeeCCeecchhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      .|+.|+..|.... ++..++++||+.+
T Consensus         1 vC~dCg~NLKqrG-~Ffv~~~lyCE~H   26 (31)
T d1x64a2           1 VCADCNLNLKQKG-YFFVEGELYCETH   26 (31)
T ss_dssp             CCSSSCCCTTTSC-CEEETTEEECHHH
T ss_pred             CccccccChhhcc-eEEeccEEeehhh
Confidence            4889999998866 4678999999876

>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=97.69  E-value=3.2e-06  Score=31.47  Aligned_cols=30  Identities=30%  Similarity=0.754  Sum_probs=24.1

Q ss_pred             cccccccccCC-CCceeeeCCeecchhhhcC
Q psy10221         38 RCCICQLVLDR-HPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        38 ~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~k   67 (67)
                      +|+.|+..|.+ +...|.+.|.++|+.+|.|
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~r   31 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIR   31 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHH
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHH
Confidence            47778888865 5567889999999999864

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.66  E-value=1.9e-05  Score=28.70  Aligned_cols=28  Identities=21%  Similarity=0.604  Sum_probs=22.8

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .|..|+..|.+.. ++-.+.+.||+.||-
T Consensus         1 vC~tC~~kLRGqp-FYAvekkayCE~CYi   28 (32)
T d1x61a2           1 VCSTCRAQLRGQH-FYAVERRAYCEGCYV   28 (32)
T ss_dssp             BCSSSCCBCTTSC-EEESSSCEEEHHHHH
T ss_pred             CeeEeCceecCCc-ceEeeccccccceee
Confidence            3788999998754 577899999999983

>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=97.64  E-value=1.7e-05  Score=28.78  Aligned_cols=29  Identities=28%  Similarity=0.681  Sum_probs=24.8

Q ss_pred             cCCccccccCccccCceeeeecCceecccc
Q psy10221          7 TELRYCVACGESITDKYLLQVSDKSWHAQC   36 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~c   36 (67)
                      .+..-|..|.+-|... ++.+.++.|||.|
T Consensus         3 sgssgC~~C~~~ItGk-VLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYITGR-VLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCCSSC-CBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhhhhh-hhhccccccCCCC
Confidence            4567799999999986 7889999999987

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.62  E-value=2e-05  Score=28.60  Aligned_cols=28  Identities=21%  Similarity=0.490  Sum_probs=22.7

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      .|..|++.|.+.. +...+++.||-.||.
T Consensus         1 vC~~C~K~Lag~r-FTa~eDq~yCVdCYK   28 (31)
T d2cura1           1 VCVTCSKKLAGQR-FTAVEDQYYCVDCYK   28 (31)
T ss_dssp             BCTTTCCBCTTSC-EEECSSCEEEHHHHH
T ss_pred             CcccccchhcCce-eEEecceEEEeeeec
Confidence            4789999998754 456899999999983

>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=97.58  E-value=3.1e-05  Score=27.95  Aligned_cols=27  Identities=22%  Similarity=0.347  Sum_probs=22.0

Q ss_pred             ccccccccCCCCceeeeCCeecchhhhcC
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~y~k   67 (67)
                      |+.|++.|...  ..+..|++||.+|+.|
T Consensus         2 C~~Cgkeltad--ArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKELTAD--ARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBCCTT--CEEETTEEECHHHHHT
T ss_pred             ccccccccchh--HHHhcCCEEEEecccc
Confidence            78899999764  3678999999998754

>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=97.55  E-value=5.4e-05  Score=27.57  Aligned_cols=28  Identities=18%  Similarity=0.467  Sum_probs=23.7

Q ss_pred             cccccccccCCCCceeeeCCeecchhhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDY   65 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y   65 (67)
                      .|+.|...|-.++.+...+|.+||+.+-
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGC
T ss_pred             CcccccccccCCceeEEecCEEEEecCC
Confidence            4889999998888777799999998763

>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=97.45  E-value=3.7e-05  Score=29.66  Aligned_cols=28  Identities=25%  Similarity=0.752  Sum_probs=21.2

Q ss_pred             cccccCccccCc-eeeeecCceecccccc
Q psy10221         11 YCVACGESITDK-YLLQVSDKSWHAQCLR   38 (67)
Q Consensus        11 ~C~~C~~~i~~~-~~~~~~~~~~h~~cf~   38 (67)
                      .|.+|++.+.+. ++....+..|||.|-.
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             CcchhhccccccceeeecCCceeCCcccc
Confidence            489999999844 3455678899998853

>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=97.43  E-value=6.5e-05  Score=27.82  Aligned_cols=30  Identities=13%  Similarity=0.527  Sum_probs=24.7

Q ss_pred             ccccccccccCCCCceeee-CCeecchhhhc
Q psy10221         37 LRCCICQLVLDRHPSCFIK-DEAVYCKQDYA   66 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~-~~~~~C~~~y~   66 (67)
                      |.|..|+..+++++.+... ..++||..||.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~   31 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHN   31 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchh
Confidence            6789999999988877654 57899999984

>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=97.42  E-value=6.3e-05  Score=25.86  Aligned_cols=26  Identities=31%  Similarity=0.742  Sum_probs=21.1

Q ss_pred             ccccCcccc-CceeeeecCceeccccc
Q psy10221         12 CVACGESIT-DKYLLQVSDKSWHAQCL   37 (67)
Q Consensus        12 C~~C~~~i~-~~~~~~~~~~~~h~~cf   37 (67)
                      |.+|++-+. +...+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            678888887 55557899999999887

>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=97.35  E-value=0.0001  Score=27.41  Aligned_cols=30  Identities=17%  Similarity=0.441  Sum_probs=23.7

Q ss_pred             cCCccccccCccccCce-eeeecCceecccc
Q psy10221          7 TELRYCVACGESITDKY-LLQVSDKSWHAQC   36 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~-~~~~~~~~~h~~c   36 (67)
                      .....|.+|+..+.+.+ ++...+..||..|
T Consensus         5 L~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           5 LASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            34578999999998554 4678899999876

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.24  E-value=9.2e-05  Score=27.44  Aligned_cols=28  Identities=18%  Similarity=0.514  Sum_probs=22.6

Q ss_pred             CCccccccCccccCceeeeecCceecccc
Q psy10221          8 ELRYCVACGESITDKYLLQVSDKSWHAQC   36 (67)
Q Consensus         8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~c   36 (67)
                      -...|.+|.+.|.. .++.+....|||+|
T Consensus         7 fge~C~~C~~~itG-pvMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMTG-PFMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCCS-CCBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhccc-ceeeecccccCCCC
Confidence            35689999997775 47778888899987

>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=97.18  E-value=1.9e-05  Score=28.67  Aligned_cols=26  Identities=23%  Similarity=0.678  Sum_probs=21.1

Q ss_pred             cccccccccCCCCceeeeCCeecchhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      .|+.|+..|.... ++..++++||+.+
T Consensus         1 vC~dCg~NLKqrG-~Ffve~~lyCE~H   26 (31)
T d1x62a1           1 VCTDCGTNLKQKG-HFFVEDQIYCEKH   26 (31)
T ss_dssp             SCSSSCCCHHHHC-CEESSSCEECHHH
T ss_pred             CccccccChhhcc-eEEeccEEehhhh
Confidence            3889999998755 4678999999876

>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=97.05  E-value=0.00011  Score=26.75  Aligned_cols=30  Identities=23%  Similarity=0.541  Sum_probs=23.1

Q ss_pred             cccccccccCC-CCceeeeCCeecchhhhcC
Q psy10221         38 RCCICQLVLDR-HPSCFIKDEAVYCKQDYAK   67 (67)
Q Consensus        38 ~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~k   67 (67)
                      +|.-|+..|+. +...|.+.+.++|+.+|.|
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            57778888876 3344678999999999864

>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=96.89  E-value=0.00065  Score=24.24  Aligned_cols=27  Identities=30%  Similarity=0.588  Sum_probs=22.2

Q ss_pred             cccccccccCCCCceeeeCCeecchhhh
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDY   65 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y   65 (67)
                      .|+.|+..++.++ ++.++...||..|+
T Consensus         1 tcs~ckq~igsgs-ffpkg~d~ycvtch   27 (32)
T d1x63a2           1 TCSNCKQVIGTGS-FFPKGEDFYCVTCH   27 (32)
T ss_dssp             CCSSSCCCCTTSC-EEEETTEEEEHHHH
T ss_pred             Ccchhhhhccccc-ccCCCCcEEEEEee
Confidence            4788999898876 57899999998875

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.55  E-value=0.00089  Score=24.20  Aligned_cols=28  Identities=25%  Similarity=0.368  Sum_probs=22.1

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +|..|...|.+..+ ....|+.+|.+|..
T Consensus         1 rC~~C~~~LAD~GF-vKnagR~LCrpch~   28 (32)
T d2d8xa1           1 RCDLCQEVLADIGF-VKNAGRHLCRPCHN   28 (32)
T ss_dssp             BCSSSCCBCSSSCC-EEETTEEECHHHHH
T ss_pred             CchHHHhHHHHhhh-hhcccccccchhhh
Confidence            58889999988653 55678999998864

>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=96.34  E-value=0.0031  Score=22.51  Aligned_cols=28  Identities=25%  Similarity=0.532  Sum_probs=21.6

Q ss_pred             cccccccccCCCCceeeeCCeecchhhhc
Q psy10221         38 RCCICQLVLDRHPSCFIKDEAVYCKQDYA   66 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   66 (67)
                      +|..|-.+|.... +.-+|++++|..|-.
T Consensus         1 RCaKC~hpLA~E~-F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANET-FVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSC-CEEETTEEECHHHHT
T ss_pred             CchhhccccccCc-ccccCCeEeeccccc
Confidence            4778888898765 467999999987743

>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=96.01  E-value=0.0023  Score=23.72  Aligned_cols=31  Identities=16%  Similarity=0.324  Sum_probs=24.3

Q ss_pred             ccCCccccccCccccCceeeeecCceeccccc
Q psy10221          6 ITELRYCVACGESITDKYLLQVSDKSWHAQCL   37 (67)
Q Consensus         6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf   37 (67)
                      ..+.-+|.+|...|.+. -+...+..||+..|
T Consensus         5 glGk~vC~KCh~iIdd~-pL~Fr~d~YHp~HF   35 (35)
T d2cora2           5 GLGKYICQKCHAIIDEQ-PLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCBCTTTCCBCCSC-CCCCSSSCCCTTTS
T ss_pred             chhhHHHHHHHhhhhcC-cceecCCCCCCCCC
Confidence            35667899999888774 57788889998765

>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=95.97  E-value=0.0047  Score=23.35  Aligned_cols=19  Identities=16%  Similarity=0.356  Sum_probs=8.7

Q ss_pred             ccccCccccCceeeeecCc
Q psy10221         12 CVACGESITDKYLLQVSDK   30 (67)
Q Consensus        12 C~~C~~~i~~~~~~~~~~~   30 (67)
                      |+.|.+++-....+...++
T Consensus         3 C~vCr~pFP~GDRVTFnGK   21 (40)
T d1v6ga2           3 CAVCRLPFPPGDRVTFNGK   21 (40)
T ss_dssp             CSSSCCCCCSSSCEEEETT
T ss_pred             ccccCCCCCCCCeEEEcCc
Confidence            4445555444334444444

>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=94.32  E-value=0.029  Score=20.12  Aligned_cols=25  Identities=16%  Similarity=0.587  Sum_probs=16.2

Q ss_pred             ccccccccCCCCceeeeCCeecchhh
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      |..|+.+|-+.. +......++|..|
T Consensus         2 cgkcsvslvg~g-fltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSLVGKG-FLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBCSSSC-EEEETTEEEETTT
T ss_pred             CccceEEEEeee-eeeccCcEEehhc
Confidence            566777776544 3556667788766

>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=91.71  E-value=0.094  Score=18.13  Aligned_cols=25  Identities=20%  Similarity=0.374  Sum_probs=15.9

Q ss_pred             ccccccccCCCCceeeeCCeecchhh
Q psy10221         39 CCICQLVLDRHPSCFIKDEAVYCKQD   64 (67)
Q Consensus        39 C~~C~~~l~~~~~~~~~~~~~~C~~~   64 (67)
                      |..|+.+|-+..+..++ ..++|..|
T Consensus         2 c~kcsvslvgrgflter-ddilc~dc   26 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTER-DDILCPDC   26 (30)
T ss_dssp             CSSSCCBCTTSCCEECS-SSEECHHH
T ss_pred             cceeeEEEEeeeccccc-cceecccc
Confidence            56777788776643333 45778766

>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=90.20  E-value=0.083  Score=18.94  Aligned_cols=28  Identities=29%  Similarity=0.430  Sum_probs=17.9

Q ss_pred             cccccccccCCCCce-eeeCCeecchhhh
Q psy10221         38 RCCICQLVLDRHPSC-FIKDEAVYCKQDY   65 (67)
Q Consensus        38 ~C~~C~~~l~~~~~~-~~~~~~~~C~~~y   65 (67)
                      +|..|...|..+... ...||..||..+.
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hl   29 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHL   29 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeecc
Confidence            466777777655421 2357888998765

>d2dasa1 g.39.1.17 (A:8-56) Zinc finger MYM-type protein 5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: TRASH domain
domain: Zinc finger MYM-type protein 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.51  E-value=0.16  Score=19.98  Aligned_cols=26  Identities=15%  Similarity=0.669  Sum_probs=18.1

Q ss_pred             ccccccccccCCCCceeeeCC--eecch
Q psy10221         37 LRCCICQLVLDRHPSCFIKDE--AVYCK   62 (67)
Q Consensus        37 f~C~~C~~~l~~~~~~~~~~~--~~~C~   62 (67)
                      ..|+.|+++|-.+...|.+.|  +++|.
T Consensus        14 v~Ca~Ckk~lqKGQTAyqrkGs~~LFCS   41 (49)
T d2dasa1          14 ITCANCKKPLQKGQTAYQRKGSAHLFCS   41 (49)
T ss_dssp             CBCTTTCCBCCTTSCCEECTTCCCEESS
T ss_pred             eEecccchHHhccchHHhhCCCcceeEc
Confidence            467888888877666677644  56774

>d1uw0a_ g.39.1.12 (A:) DNA ligase III {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: PARP-type zinc finger
domain: DNA ligase III
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.86  E-value=0.086  Score=24.58  Aligned_cols=32  Identities=19%  Similarity=0.366  Sum_probs=20.6

Q ss_pred             cCCccccccCccccCcee-eee-----c-------Cceecccccc
Q psy10221          7 TELRYCVACGESITDKYL-LQV-----S-------DKSWHAQCLR   38 (67)
Q Consensus         7 ~~~~~C~~C~~~i~~~~~-~~~-----~-------~~~~h~~cf~   38 (67)
                      ++-..|.+|++.|...++ +..     .       ...+|..||.
T Consensus        13 S~Ra~Ck~C~~~I~Kg~lRig~~~~~~~~~~~g~~~~W~H~~Cf~   57 (117)
T d1uw0a_          13 RGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMF   57 (117)
T ss_dssp             SSCEECTTSSCEECTTCEEEEEEEECTTCSSCCEECCBCCHHHHH
T ss_pred             CCCcccCCCCccccCCCeEEEEEEeCcccccCCCcCccCCccccc
Confidence            445689999999985433 221     0       2346899984

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.53  E-value=0.098  Score=22.43  Aligned_cols=33  Identities=24%  Similarity=0.527  Sum_probs=26.7

Q ss_pred             CccccccCccccCceeeeecCceeccccccccc
Q psy10221          9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCI   41 (67)
Q Consensus         9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~   41 (67)
                      ...|.-|.+.+++...+.--...-|..||.|+.
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr   40 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSR   40 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccH
Confidence            457899999999887777667778999999864

>d2gvia2 g.39.1.18 (A:169-201) Uncharacterized protein Ta1109 {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: FwdE C-terminal domain-like
domain: Uncharacterized protein Ta1109
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=86.53  E-value=0.14  Score=17.88  Aligned_cols=13  Identities=31%  Similarity=0.606  Sum_probs=9.8

Q ss_pred             eeCCeecchhhhc
Q psy10221         54 IKDEAVYCKQDYA   66 (67)
Q Consensus        54 ~~~~~~~C~~~y~   66 (67)
                      ..+|++.|+.+|.
T Consensus        20 llngkpvckpdyy   32 (33)
T d2gvia2          20 LLNGKPVCKPDYY   32 (33)
T ss_dssp             EETTEEECHHHHH
T ss_pred             hhCCCcccCcccC
Confidence            3578888988874

>d2ctda2 g.37.1.1 (A:61-90) Zinc finger protein 512, ZNF512 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 512, ZNF512
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.33  E-value=0.15  Score=17.67  Aligned_cols=12  Identities=25%  Similarity=0.562  Sum_probs=10.1

Q ss_pred             ccccccccccCC
Q psy10221         37 LRCCICQLVLDR   48 (67)
Q Consensus        37 f~C~~C~~~l~~   48 (67)
                      |.|..|++.|.+
T Consensus         3 ftc~hcgkqlks   14 (30)
T d2ctda2           3 FTCHHCGKQLRS   14 (30)
T ss_dssp             CCCSSSCCCCSS
T ss_pred             eechhHHHHHhh
Confidence            789999998865

>d2ds5a1 g.39.1.11 (A:11-48) ClpX chaperone zinc binding domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: ClpX chaperone zinc binding domain
domain: ClpX chaperone zinc binding domain
species: Escherichia coli [TaxId: 562]

Probab=83.83  E-value=0.62  Score=17.33  Aligned_cols=13  Identities=15%  Similarity=0.373  Sum_probs=6.1

Q ss_pred             cccccccccCCCC
Q psy10221         38 RCCICQLVLDRHP   50 (67)
Q Consensus        38 ~C~~C~~~l~~~~   50 (67)
                      .|+.|+++-.+..
T Consensus         3 ~CSFCgk~~~eV~   15 (38)
T d2ds5a1           3 YCSFCGKSQHEVR   15 (38)
T ss_dssp             BCTTTCCBTTTSS
T ss_pred             EeeCCCCCHHHHH
Confidence            3455555544433

>d2d8va1 g.43.1.1 (A:8-61) Zinc finger FYVE domain-containing protein 19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: B-box zinc-binding domain
superfamily: B-box zinc-binding domain
family: B-box zinc-binding domain
domain: Zinc finger FYVE domain-containing protein 19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.15  E-value=0.16  Score=20.45  Aligned_cols=12  Identities=25%  Similarity=0.567  Sum_probs=9.0

Q ss_pred             eeCCeecchhhh
Q psy10221         54 IKDEAVYCKQDY   65 (67)
Q Consensus        54 ~~~~~~~C~~~y   65 (67)
                      .=+|.+||..||
T Consensus        17 gCdgdLyC~rC~   28 (54)
T d2d8va1          17 GCDGDLYCARCF   28 (54)
T ss_dssp             TTTSEEECSSHH
T ss_pred             CCCCceehHHHH
Confidence            347788888886