Citrus Sinensis ID: 034188

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100--
Protein Sequence
MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEKLTPELVNLSYNIACISN
Secondary Structure (PSIPRED)
cccccccccccccccEEEccEEEEccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEccccEEEEHEEEEEcccEEEcccEEEcccccEEEcccccccccEEEEcccHHHHHHcccccccccccccccHHcccccccccccccccccc
Coil and Loop (DISEMBL)
msfigtqqkckvcektvypveqlsadgivyhkscfkcshckgtlklsnyssmegvlyckphfeQLFKEsgnfnknfqspaksaeklTPELVNLSYNIACISN
Flexible Loop (DISEMBL)
msfigtqqkckvceKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAksaekltpelvnlsyniacisn
Low Complexity Region (SEG)
MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEKLTPELVNLSYNIACISN
Disordered region (IsUnstruct)
*****TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE*********************LVNLSYNIACI**
Disordered Region (DISOPRED)
**FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ**************************************
Disordered Region (DISEMBL)
********KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEKLTPELVNLSYNIACISN
Disordered Region (DISPRO)
******QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES*********************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEKLTPELVNLSYNIACISN
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	102	2.2.26 [Sep-21-2011]
P29675	219	Pollen-specific protein S	N/A	no	0.784	0.365	0.587	5e-23
Q4U4S6	3784	Xin actin-binding repeat-	yes	no	0.735	0.019	0.52	2e-19
Q4KM31	128	LIM domain-containing pro	yes	no	0.686	0.546	0.514	2e-18
Q8BGB5	128	LIM domain-containing pro	no	no	0.686	0.546	0.5	3e-18
Q1LZA7	128	LIM domain-containing pro	no	no	0.686	0.546	0.5	6e-18
Q9BT23	127	LIM domain-containing pro	no	no	0.686	0.551	0.5	7e-18
B0KYV5	756	LIM domain and actin-bind	no	no	0.686	0.092	0.514	3e-17
Q9UHB6	759	LIM domain and actin-bind	no	no	0.686	0.092	0.514	4e-17
Q9ERG0	753	LIM domain and actin-bind	no	no	0.686	0.092	0.514	4e-17
G3MWR8	1960	Protein-methionine sulfox	no	no	0.578	0.030	0.491	3e-13

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

 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 47/80 (58%), Positives = 61/80 (76%)

Query: 2  SFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61
          SF GT QKC VCEKTVY V++L A+  VYHK+CF+C HC  TLKLSN++S +GV+YC+ H
Sbjct: 3  SFTGTTQKCTVCEKTVYLVDKLVANQRVYHKACFRCHHCNSTLKLSNFNSFDGVVYCRHH 62

Query: 62 FEQLFKESGNFNKNFQSPAK 81
          F+QLFK +G+  K+F    K
Sbjct: 63 FDQLFKRTGSLEKSFDGTPK 82

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

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

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/75 (52%), Positives = 55/75 (73%)

Query: 2    SFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61
            +F+  ++ C +C+KTVYP+E L AD   +HKSCF+C HC   L L NY+S+ G +YCKPH
Sbjct: 3249 AFLSDKEICIICQKTVYPMECLIADKQNFHKSCFRCHHCSSKLSLGNYASLHGRIYCKPH 3308

Query: 62   FEQLFKESGNFNKNF 76
            F+QLFK  GN+++ F
Sbjct: 3309 FKQLFKSKGNYDEGF 3323

Protects actin filaments from depolymerization.

Mus musculus (taxid: 10090)

>sp|Q4KM31|LIMD2_RAT LIM domain-containing protein 2 OS=Rattus norvegicus GN=Limd2 PE=2 SV=1

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 36/70 (51%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L AD +++H SCF C HC   L L +Y++M G  YCKPHF+QLF
Sbjct: 38  KETCAACQKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAAMHGEFYCKPHFQQLF 97

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 98  KSKGNYDEGF 107

Rattus norvegicus (taxid: 10116)

>sp|Q8BGB5|LIMD2_MOUSE LIM domain-containing protein 2 OS=Mus musculus GN=Limd2 PE=2 SV=1

 Score = 90.1 bits (222), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 35/70 (50%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L AD +++H SCF C HC   L L +Y++M G  YC+PHF+QLF
Sbjct: 38  KETCAACQKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAAMHGEFYCRPHFQQLF 97

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 98  KSKGNYDEGF 107

Mus musculus (taxid: 10090)

>sp|Q1LZA7|LIMD2_BOVIN LIM domain-containing protein 2 OS=Bos taurus GN=LIMD2 PE=2 SV=1

 Score = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 35/70 (50%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L AD +++H SCF C HC   L L +Y+++ G  YCKPHF+QLF
Sbjct: 38  KETCAACQKTVYPMERLVADKLIFHSSCFCCKHCHTKLSLGSYAALHGEFYCKPHFQQLF 97

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 98  KSKGNYDEGF 107

Bos taurus (taxid: 9913)

>sp|Q9BT23|LIMD2_HUMAN LIM domain-containing protein 2 OS=Homo sapiens GN=LIMD2 PE=1 SV=1

 Score = 89.4 bits (220), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 35/70 (50%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L AD +++H SCF C HC   L L +Y+++ G  YCKPHF+QLF
Sbjct: 37  KETCAACQKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAALHGEFYCKPHFQQLF 96

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 97  KSKGNYDEGF 106

Homo sapiens (taxid: 9606)

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

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/70 (51%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L A+  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLF
Sbjct: 383 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLF 442

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 443 KSKGNYDEGF 452

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

Sus scrofa (taxid: 9823)

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

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 36/70 (51%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L A+  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLF
Sbjct: 387 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLF 446

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 447 KSKGNYDEGF 456

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

Homo sapiens (taxid: 9606)

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

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 36/70 (51%), Positives = 51/70 (72%)

Query: 7   QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           ++ C  C+KTVYP+E+L A+  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLF
Sbjct: 385 KESCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLF 444

Query: 67  KESGNFNKNF 76
           K  GN+++ F
Sbjct: 445 KSKGNYDEGF 454

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

Mus musculus (taxid: 10090)

>sp|G3MWR8|MICA3_BOVIN Protein-methionine sulfoxide oxidase MICAL3 OS=Bos taurus GN=MICAL3 PE=3 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 30/61 (49%), Positives = 41/61 (67%), Gaps = 2/61 (3%)

Query: 4   IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM--EGVLYCKPH 61
           +G    C  C+K VY +E+LSA+G  +H+SCFKC HC  TL+LS Y+    +G  YCKPH
Sbjct: 758 LGGSDTCYFCQKRVYVMERLSAEGKFFHRSCFKCEHCATTLRLSAYAYALEDGKFYCKPH 817

Query: 62  F 62
           +
Sbjct: 818 Y 818

Monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin. Acts by modifying actin subunits through the addition of oxygen to form methionine-sulfoxide, leading to promote actin filament severing and prevent repolymerization. Involved in exocytic vesicles tethering and fusion: the monooxygenase activity is required for this process.

Bos taurus (taxid: 9913)

EC: 1

EC: .

EC: 1

EC: 4

EC: .

EC: 1

EC: 3

EC: .

EC: -

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	102
449441328	189	PREDICTED: pollen-specific protein SF3-l	0.892	0.481	0.934	2e-44
225449230	189	PREDICTED: pollen-specific protein SF3 i	0.901	0.486	0.934	6e-44
5932420	189	LIM domain protein WLIM2 [Nicotiana taba	0.901	0.486	0.923	4e-43
260619528	189	LIM1 [Hevea brasiliensis]	0.901	0.486	0.891	9e-42
117950171	189	LIM domain protein WLIM2a [Populus tremu	0.892	0.481	0.869	1e-41
255579126	189	Pollen-specific protein SF3, putative [R	0.892	0.481	0.880	2e-41
449521683	195	PREDICTED: LOW QUALITY PROTEIN: pollen-s	0.901	0.471	0.858	2e-41
224109388	189	predicted protein [Populus trichocarpa]	0.892	0.481	0.869	3e-41
224101093	189	predicted protein [Populus trichocarpa]	0.901	0.486	0.869	3e-41
118485508	189	unknown [Populus trichocarpa]	0.901	0.486	0.858	1e-40

>gi|449441328|ref|XP_004138434.1| PREDICTED: pollen-specific protein SF3-like [Cucumis sativus] gi|449516649|ref|XP_004165359.1| PREDICTED: pollen-specific protein SF3-like [Cucumis sativus]

 Score =  182 bits (462), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 86/92 (93%), Positives = 88/92 (95%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSFIGTQQKCK CEKTVYPVEQLSADG+ YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFIGTQQKCKACEKTVYPVEQLSADGVSYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKE+GNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HFEQLFKETGNFNKNFQSPAKSAEKLTPELTR 92

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225449230|ref|XP_002279922.1| PREDICTED: pollen-specific protein SF3 isoform 1 [Vitis vinifera] gi|147859521|emb|CAN81425.1| hypothetical protein VITISV_014590 [Vitis vinifera] gi|296086105|emb|CBI31546.3| unnamed protein product [Vitis vinifera]

 Score =  181 bits (458), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 86/92 (93%), Positives = 87/92 (94%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSFIGTQQKCK C KTVYPVEQLSADG+VYHKSCFKCSHC GTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFIGTQQKCKACLKTVYPVEQLSADGVVYHKSCFKCSHCNGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKESGNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELTR 92

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5932420|gb|AAD56951.1|AF184886_1 LIM domain protein WLIM2 [Nicotiana tabacum] gi|1841464|emb|CAA71891.1| LIM-domain SF3 protein [Nicotiana tabacum]

 Score =  178 bits (451), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 85/92 (92%), Positives = 87/92 (94%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSFIGTQQKCK CEKTVYPVE LSADG+ YHKSCFKCSHCKGTLKLSN+SSMEGVLYCKP
Sbjct: 1  MSFIGTQQKCKACEKTVYPVELLSADGVNYHKSCFKCSHCKGTLKLSNFSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKESGNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELTR 92

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|260619528|gb|ACX47456.1| LIM1 [Hevea brasiliensis]

 Score =  173 bits (439), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 82/92 (89%), Positives = 85/92 (92%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSF GTQQKCK CEKTVYP+E LSADG+ YHKSCFKC HCKGTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFTGTQQKCKACEKTVYPMELLSADGVPYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKE+GNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HFEQLFKETGNFNKNFQSPAKSAEKLTPELTR 92

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|117950171|gb|ABK58469.1| LIM domain protein WLIM2a [Populus tremula x Populus alba]

 Score =  173 bits (438), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 80/92 (86%), Positives = 85/92 (92%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSF GTQQKCK CEKTVYP+E LSADG+ YHKSCFKC HCKGTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFTGTQQKCKACEKTVYPMELLSADGVAYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HF+QLFKE+GNFNKNFQSPAK+AEKLTPEL  
Sbjct: 61 HFDQLFKETGNFNKNFQSPAKTAEKLTPELTR 92

Source: Populus tremula x Populus alba

Species: Populus tremula x Populus alba

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579126|ref|XP_002530411.1| Pollen-specific protein SF3, putative [Ricinus communis] gi|223530060|gb|EEF31981.1| Pollen-specific protein SF3, putative [Ricinus communis]

 Score =  172 bits (437), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 81/92 (88%), Positives = 85/92 (92%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSF GTQQKCK CEKTVYP+E LSADG+ YHKSCFKC HCKGTLKLSNYSSMEGV+YCKP
Sbjct: 1  MSFTGTQQKCKACEKTVYPMELLSADGVPYHKSCFKCFHCKGTLKLSNYSSMEGVVYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKE+GNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HFEQLFKETGNFNKNFQSPAKSAEKLTPELTR 92

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449521683|ref|XP_004167859.1| PREDICTED: LOW QUALITY PROTEIN: pollen-specific protein SF3-like [Cucumis sativus]

 Score =  172 bits (436), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 79/92 (85%), Positives = 87/92 (94%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSFIGTQQKCK C+KTVYPV+QLSADG+ +HKSCFKCSHCKGTLKLSNYSSM+GVLYCKP
Sbjct: 1  MSFIGTQQKCKACDKTVYPVDQLSADGVSFHKSCFKCSHCKGTLKLSNYSSMDGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKE+GNF+KNF SPAKS+EKLTPEL  
Sbjct: 61 HFEQLFKETGNFSKNFLSPAKSSEKLTPELTR 92

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109388|ref|XP_002315180.1| predicted protein [Populus trichocarpa] gi|118488763|gb|ABK96192.1| unknown [Populus trichocarpa] gi|222864220|gb|EEF01351.1| predicted protein [Populus trichocarpa]

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 80/92 (86%), Positives = 84/92 (91%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSF GTQQKCK CEKTVYP+E LSADG+ YHK+CFKC HCKGTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFTGTQQKCKACEKTVYPMELLSADGVAYHKTCFKCFHCKGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HFEQLFKE+GNFNKNFQSPAKSAEKL PEL  
Sbjct: 61 HFEQLFKETGNFNKNFQSPAKSAEKLNPELTR 92

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101093|ref|XP_002312139.1| predicted protein [Populus trichocarpa] gi|118485190|gb|ABK94456.1| unknown [Populus trichocarpa] gi|222851959|gb|EEE89506.1| predicted protein [Populus trichocarpa]

 Score =  171 bits (434), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 80/92 (86%), Positives = 84/92 (91%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSF GTQQKCK CEKTVYP+E LS DG+ YHKSCFKC HCKGTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFTGTQQKCKACEKTVYPMELLSTDGVAYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          HF+QLFKE+GNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HFDQLFKETGNFNKNFQSPAKSAEKLTPELTR 92

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485508|gb|ABK94608.1| unknown [Populus trichocarpa]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 79/92 (85%), Positives = 83/92 (90%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          MSF GTQQKCK CEKTVYP+E LS DG+ YHKSCFKC HCKGTLKLSNYSSMEGVLYCKP
Sbjct: 1  MSFTGTQQKCKACEKTVYPMELLSTDGVAYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKP 60

Query: 61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVN 92
          H +QLFKE+GNFNKNFQSPAKSAEKLTPEL  
Sbjct: 61 HLDQLFKETGNFNKNFQSPAKSAEKLTPELTR 92

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	102
TAIR|locus:2061171	200	WLIM2a "WLIM2a" [Arabidopsis t	0.882	0.45	0.802	3e-37
TAIR|locus:2198210	205	PLIM2b "PLIM2b" [Arabidopsis t	0.941	0.468	0.67	4.7e-32
TAIR|locus:2050735	226	PLIM2a "PLIM2a" [Arabidopsis t	0.764	0.345	0.717	6.2e-30
TAIR|locus:2098871	213	PLIM2c "PLIM2c" [Arabidopsis t	0.813	0.389	0.654	1.5e-28
TAIR|locus:2012798	190	WLIM1 "AT1G10200" [Arabidopsis	0.794	0.426	0.629	5.7e-27
DICTYBASE|DDB_G0290575	472	DDB_G0290575 "LIM-type zinc fi	0.823	0.177	0.505	2.6e-20
UNIPROTKB|K7GPY2	709	XIRP2 "Uncharacterized protein	0.686	0.098	0.542	9.5e-20
RGD|1309967	128	Limd2 "LIM domain containing 2	0.686	0.546	0.514	1.2e-19
UNIPROTKB|K7GK85	786	XIRP2 "Uncharacterized protein	0.686	0.089	0.542	1.4e-19
UNIPROTKB|E1C059	128	LIMD2 "Uncharacterized protein	0.686	0.546	0.514	1.9e-19

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

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 73/91 (80%), Positives = 81/91 (89%)

Query:     1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
             MSF GTQQKC+ CEKTVYPVE LSADGI YHK+CFKCSHCK  L+LSNYSSMEGV+YC+P
Sbjct:     1 MSFTGTQQKCRACEKTVYPVELLSADGISYHKACFKCSHCKSRLQLSNYSSMEGVVYCRP 60

Query:    61 HFEQLFKESGNFNKNFQSPAKS-AEKLTPEL 90
             HFEQLFKESG+F+KNFQSPAK   +K TPEL
Sbjct:    61 HFEQLFKESGSFSKNFQSPAKPLTDKPTPEL 91

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0000271 "polysaccharide biosynthetic process" evidence=RCA

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0009825 "multidimensional cell growth" evidence=RCA

GO:0009932 "cell tip growth" evidence=RCA

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

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

GO:0048767 "root hair elongation" evidence=RCA

GO:0071555 "cell wall organization" evidence=RCA

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

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 67/100 (67%), Positives = 79/100 (79%)

Query:     1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
             MSF GT  KC VC+KTVY V+ LS +G+ YHKSCF+C+HCKGTL++SNYSSM+GVLYCK 
Sbjct:     1 MSFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKT 60

Query:    61 HFEQLFKESGNFNKNFQSPAKSAEKLTPELVNLSYNIACI 100
             HFEQLFKESGNF+KNFQ P K+ EK  PEL      I+ I
Sbjct:    61 HFEQLFKESGNFSKNFQ-PGKT-EK--PELTRTPSKISSI 96

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 56/78 (71%), Positives = 68/78 (87%)

Query:     1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
             MSF GT  KCK C+KTVY ++ L+ +G  YHKSCF+C+HCKGTL +SNYSSM+GVLYCKP
Sbjct:     1 MSFTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCTHCKGTLVISNYSSMDGVLYCKP 60

Query:    61 HFEQLFKESGNFNKNFQS 78
             HFEQLFKESGN++KNFQ+
Sbjct:    61 HFEQLFKESGNYSKNFQA 78

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 55/84 (65%), Positives = 69/84 (82%)

Query:     2 SFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61
             +F GT  KCK C+KTVY ++ ++ +G+ YHKSCF+CSHC GTL + NYSSM+GVLYCK H
Sbjct:     3 AFTGTTDKCKACDKTVYVMDLMTLEGMPYHKSCFRCSHCNGTLVICNYSSMDGVLYCKTH 62

Query:    62 FEQLFKESGNFNKNFQSPAKSAEK 85
             FEQLFKESGNF+KNFQ+  K+ EK
Sbjct:    63 FEQLFKESGNFSKNFQTAGKT-EK 85

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 51/81 (62%), Positives = 65/81 (80%)

Query:     1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
             M+F GT QKC  C+KTVY V++L+AD  VYHK+CF+C HCKGTLKLSNY+S EGVLYC+P
Sbjct:     1 MAFAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNYNSFEGVLYCRP 60

Query:    61 HFEQLFKESGNFNKNFQSPAK 81
             HF+Q FK +G+  K+F+   K
Sbjct:    61 HFDQNFKRTGSLEKSFEGTPK 81

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

GO:0051015 "actin filament binding" evidence=IDA

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

 Score = 246 (91.7 bits), Expect = 2.6e-20, P = 2.6e-20
 Identities = 45/89 (50%), Positives = 59/89 (66%)

Query:     5 GTQQKCKVCEKTVYPVEQL----SADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
             GTQ+KC  C KTVY  E++      D   +HK C KC+HCK TL L NY+S+ GV YCKP
Sbjct:     6 GTQEKCTACAKTVYLTEKIVVEDKEDKKTFHKLCLKCTHCKLTLSLGNYASLNGVFYCKP 65

Query:    61 HFEQLFKESGNFNKNFQSPAKSAEKLTPE 89
             HF+QLF   GN+++ F   +K +EK TP+
Sbjct:    66 HFKQLFATKGNYDEGF-GKSKHSEKWTPQ 93

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|K7GPY2 XIRP2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 237 (88.5 bits), Expect = 9.5e-20, Sum P(2) = 9.5e-20
 Identities = 38/70 (54%), Positives = 52/70 (74%)

Query:     7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
             ++ C +C+KTVYP+E L AD   +HKSCF+C HC   L L NY+S+ G +YCKPHF+QLF
Sbjct:   177 KETCILCQKTVYPMECLVADRQSFHKSCFRCHHCNSKLSLGNYASLHGQIYCKPHFKQLF 236

Query:    67 KESGNFNKNF 76
             K  GN+++ F
Sbjct:   237 KSKGNYDEGF 246

GO:0008270 "zinc ion binding" evidence=IEA

RGD|1309967 Limd2 "LIM domain containing 2" [Rattus norvegicus (taxid:10116)]

 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 36/70 (51%), Positives = 51/70 (72%)

Query:     7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
             ++ C  C+KTVYP+E+L AD +++H SCF C HC   L L +Y++M G  YCKPHF+QLF
Sbjct:    38 KETCAACQKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAAMHGEFYCKPHFQQLF 97

Query:    67 KESGNFNKNF 76
             K  GN+++ F
Sbjct:    98 KSKGNYDEGF 107

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|K7GK85 XIRP2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 237 (88.5 bits), Expect = 1.4e-19, Sum P(2) = 1.4e-19
 Identities = 38/70 (54%), Positives = 52/70 (74%)

Query:     7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
             ++ C +C+KTVYP+E L AD   +HKSCF+C HC   L L NY+S+ G +YCKPHF+QLF
Sbjct:   254 KETCILCQKTVYPMECLVADRQSFHKSCFRCHHCNSKLSLGNYASLHGQIYCKPHFKQLF 313

Query:    67 KESGNFNKNF 76
             K  GN+++ F
Sbjct:   314 KSKGNYDEGF 323

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E1C059 LIMD2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 36/70 (51%), Positives = 50/70 (71%)

Query:     7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
             ++ C  C+KTVYP+E+L AD  V+H SCF C HC   L L +Y+++ G  YCKPHF+QLF
Sbjct:    38 KEMCTACQKTVYPMERLVADKFVFHNSCFCCKHCHAKLSLGSYAALHGEFYCKPHFQQLF 97

Query:    67 KESGNFNKNF 76
             K  GN+++ F
Sbjct:    98 KSKGNYDEGF 107

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00018297001 SubName- Full=Putative uncharacterized protein (Chromosome chr13 scaffold_17, whole genome shotgun sequence); (189 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	102
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	5e-41
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	4e-26
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	2e-23
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	2e-19
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	3e-17
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	7e-17
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	1e-16
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	6e-16
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	2e-12
pfam00412	58	pfam00412, LIM, LIM domain	4e-12
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	8e-12
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	5e-11
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	3e-10
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	3e-10
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	1e-09
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	2e-08
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	2e-08
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	6e-08
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	1e-07
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	2e-07
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	5e-07
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	6e-07
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	7e-07
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	1e-06
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	3e-06
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	3e-06
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	3e-06
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	2e-05
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	6e-05
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	7e-05
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	3e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	4e-04
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	5e-04
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	6e-04
cd09424	58	cd09424, LIM2_FHL1, The second LIM domain of Four	8e-04
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	9e-04
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	9e-04
cd09427	58	cd09427, LIM2_FHL3, The second LIM domain of Four	0.001
cd09414	58	cd09414, LIM1_LIMPETin, The first LIM domain of pr	0.002
cd09352	54	cd09352, LIM1_Ajuba_like, The first LIM domain of	0.003
cd09450	53	cd09450, LIM_ALP, This family represents the LIM d	0.004

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

 Score =  129 bits (325), Expect = 5e-41
 Identities = 56/63 (88%), Positives = 60/63 (95%)

Query: 6  TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65
          T QKCK C+KTVY V+QLSADG+VYHKSCF+CSHCKGTLKLSNYSSMEGVLYCKPHFEQL
Sbjct: 1  TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 66 FKE 68
          FKE
Sbjct: 61 FKE 63

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

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

 Score = 90.8 bits (226), Expect = 4e-26
 Identities = 37/53 (69%), Positives = 45/53 (84%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C VC KTVYP+E+L ADG ++HKSCF+CSHC  TL+L NY+S+EG LYCKPHF
Sbjct: 1  CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53

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

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

 Score = 84.8 bits (210), Expect = 2e-23
 Identities = 36/61 (59%), Positives = 44/61 (72%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES 69
          C  C KTVYP+E+++ +G  YHKSCFKCSH   T+  SNY++ EG LYCK H  QLFKE 
Sbjct: 1  CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 70 G 70
          G
Sbjct: 61 G 61

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

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

 Score = 74.1 bits (182), Expect = 2e-19
 Identities = 31/53 (58%), Positives = 39/53 (73%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C VC+K VYP+E+L AD   +HKSCF+C HC   L L NY+S+ G +YCKPHF
Sbjct: 1  CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

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

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

 Score = 69.0 bits (169), Expect = 3e-17
 Identities = 27/53 (50%), Positives = 36/53 (67%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C+ C K VY +E++ A+  +YHK+CF+C  C   LK+ NY S EG LYCK HF
Sbjct: 1  CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53

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

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

 Score = 67.6 bits (165), Expect = 7e-17
 Identities = 29/53 (54%), Positives = 39/53 (73%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C+KTVYP+E+L A+  +YH SCF+CS+C   L L  Y+S+ G +YCKPHF
Sbjct: 1  CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

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

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

 Score = 67.3 bits (165), Expect = 1e-16
 Identities = 29/55 (52%), Positives = 40/55 (72%), Gaps = 2/55 (3%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHF 62
          C  C+K VY +E+LSA+G+ +H+SCFKCS+C  TL+L  Y+    +G  YCKPHF
Sbjct: 1  CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55

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

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

 Score = 65.4 bits (159), Expect = 6e-16
 Identities = 29/53 (54%), Positives = 38/53 (71%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C+KTVYP+E+L AD +V+H SCF C HC   L L +Y+++ G  YCKPHF
Sbjct: 1  CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53

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

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

 Score = 56.6 bits (137), Expect = 2e-12
 Identities = 23/53 (43%), Positives = 29/53 (54%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C KTVYP E+L+    ++HK CFKC  C  TL + NY       YC  H+
Sbjct: 1  CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

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

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

 Score = 55.8 bits (135), Expect = 4e-12
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 10 CKVCEKTVYPVEQLS-ADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          C  C K +Y  E +  A G V+H  CF+C+ C   L   ++   +G LYCK  + +LF
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 54.7 bits (132), Expect = 8e-12
 Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61
          KC  C K +Y  E+ L A G V+H  CFKC+ C   L    +   +G LYCK  
Sbjct: 1  KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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

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

 Score = 52.8 bits (127), Expect = 5e-11
 Identities = 23/54 (42%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPH 61
          C  C KT YP E +  DG  YHK CFKC  C   L L  ++    +G +YC  H
Sbjct: 1  CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54

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

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

 Score = 51.1 bits (123), Expect = 3e-10
 Identities = 20/50 (40%), Positives = 29/50 (58%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          C  C K+VY  E++ A G  +HKSCF C+ C   L  +  +  +G +YCK
Sbjct: 1  CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

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

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

 Score = 50.9 bits (122), Expect = 3e-10
 Identities = 24/52 (46%), Positives = 29/52 (55%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          KC  C K+VY  E+  A G  +HK CFKC  C   L  +N +  EG LYCK 
Sbjct: 1  KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQ 52

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

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

 Score = 49.2 bits (118), Expect = 1e-09
 Identities = 18/53 (33%), Positives = 25/53 (47%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C K +   E L A G  +H  CFKCS C   L   ++   +G  YC+  +
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

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

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

 Score = 46.2 bits (110), Expect = 2e-08
 Identities = 20/51 (39%), Positives = 26/51 (50%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          C  C K VY  E+ ++ G  +HK C +C  CK TL    +S  EG  YC  
Sbjct: 1  CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

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

>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 46.2 bits (110), Expect = 2e-08
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSME--GVLYCKPHF 62
          C  C + V+ V++   DG +YH++CF+C  C  TL   +Y +    G   C  H 
Sbjct: 1  CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

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

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

 Score = 45.0 bits (106), Expect = 6e-08
 Identities = 19/50 (38%), Positives = 31/50 (62%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          C  C K+VY  E++   G  +HK+CF+C+ C  +L+ +  +  +G LYCK
Sbjct: 1  CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50

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

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

 Score = 44.5 bits (105), Expect = 1e-07
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          C  C K+VY  E++   G  +HK+CF+C+ C  +L+ +  +  +G +YCK
Sbjct: 1  CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

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

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

 Score = 43.8 bits (103), Expect = 2e-07
 Identities = 21/53 (39%), Positives = 30/53 (56%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C K VYP E+++     +HK+CF C  CK TL ++NY   +   YC  H+
Sbjct: 1  CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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

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

 Score = 42.8 bits (100), Expect = 5e-07
 Identities = 21/51 (41%), Positives = 31/51 (60%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          KC  CEKTVY  E++  +G  +HK+CF C  C+  L  +  ++ E  +YCK
Sbjct: 1  KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCK 51

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

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

 Score = 42.6 bits (100), Expect = 6e-07
 Identities = 21/50 (42%), Positives = 30/50 (60%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          C  CEKTVY  E++  +G  +HKSCF C  C+  L  +  ++ E  +YCK
Sbjct: 1  CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCK 50

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

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

 Score = 42.2 bits (99), Expect = 7e-07
 Identities = 19/52 (36%), Positives = 29/52 (55%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61
          C  C   VYP E+++     +HK+CF C  CK  L ++N+ S +   YC+ H
Sbjct: 1  CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

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

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

 Score = 41.9 bits (98), Expect = 1e-06
 Identities = 22/52 (42%), Positives = 31/52 (59%)

Query: 8  QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          +KC VC+KTVY  E++  +G  +HKSCF C  CK  L  +  +     +YCK
Sbjct: 1  KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCK 52

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

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

 Score = 40.6 bits (95), Expect = 3e-06
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C   +   + + A    +H  CF+CS C  +L  + Y   +G LYC+  +
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLS-NWYFEKDGKLYCRKDY 52

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

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

 Score = 40.9 bits (96), Expect = 3e-06
 Identities = 18/50 (36%), Positives = 26/50 (52%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC 58
           C  C   V+  E+L  +G VYH++CFKC+ C   L   ++   E   YC
Sbjct: 4  PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

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

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

 Score = 40.5 bits (94), Expect = 3e-06
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          C  C  +VY  E++   G  +HK+CF+C+ C  +L+ +  +  EG +YCK
Sbjct: 1  CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

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

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

 Score = 38.4 bits (89), Expect = 2e-05
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          KC  C +TVY  E++  DG  +HK CF C  C+  L  +  +  +  +YCK
Sbjct: 1  KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCK 51

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

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

 Score = 37.3 bits (86), Expect = 6e-05
 Identities = 17/49 (34%), Positives = 26/49 (53%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC 58
          C  C K VY  E++ + G  +H+ C +C  CK TL    ++  +G  YC
Sbjct: 1  CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49

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

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

 Score = 37.3 bits (86), Expect = 7e-05
 Identities = 18/49 (36%), Positives = 27/49 (55%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC 58
          C  C+KTVY  E++S+ G  +H+ C KC  C   L    ++  +G  YC
Sbjct: 1  CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

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

>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9

 Score = 35.4 bits (81), Expect = 3e-04
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 8  QKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF 62
          Q+C  C   +   E  + A   VYH SCF C+ C  TL   ++  M + ++YC+ HF
Sbjct: 3  QRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59

The second 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 = 59

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

 Score = 35.2 bits (81), Expect = 4e-04
 Identities = 17/49 (34%), Positives = 28/49 (57%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC 58
          C  C+K VY  E++++ G  +H+ C KC  C  TL   +++  +G  YC
Sbjct: 1  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49

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

>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family

 Score = 34.9 bits (81), Expect = 5e-04
 Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 29 VYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF 62
          V+H +CF C+ C   L   ++  M +G++YC+ H+
Sbjct: 25 VFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59

The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2

 Score = 34.7 bits (79), Expect = 6e-04
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 8  QKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF 62
          Q+C  C   +   E  + A  +VYH +CF C+ C   L   ++  M + ++YC+ HF
Sbjct: 3  QRCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59

The second 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 shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 34.4 bits (79), Expect = 8e-04
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 10 CKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          CK C K +   +Q +   G V+HK CF CS+CK  +   ++       YC P  E+ F
Sbjct: 1  CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

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

 Score = 34.3 bits (79), Expect = 9e-04
 Identities = 14/40 (35%), Positives = 20/40 (50%)

Query: 23 LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          L A G  +H   F CSHC  +L    +   +G LYC+  +
Sbjct: 13 LVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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

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

 Score = 34.9 bits (80), Expect = 9e-04
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C +++Y  + L A    +H  CF+C  C  +L    Y   +G L+CK  +
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLS-HWYYEKDGRLFCKKDY 73

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

>gnl|CDD|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM domains protein 3 (FHL3)

 Score = 34.1 bits (78), Expect = 0.001
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 9  KCKVCEKTVYP-VEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFE 63
          KC  C KTV P   +L  +G  +H+ CF C  C+  +   ++   +   YC P +E
Sbjct: 3  KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58

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

>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 10 CKVCEKTVYPVEQL-----SADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C + +   E         + +++H +CF+CS C+  L    Y   +  +YC+ H+
Sbjct: 1  CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like proteins

 Score = 32.8 bits (75), Expect = 0.003
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 10 CKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
          C  C K VY   Q   A G +YH +CF C  C  TL+   + ++ G +YC+  +
Sbjct: 1  CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54

The first 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 = 54

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

 Score = 32.6 bits (74), Expect = 0.004
 Identities = 15/31 (48%), Positives = 17/31 (54%)

Query: 31 HKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61
          H  CF CS C   LK   Y  +EG LYC+ H
Sbjct: 21 HPECFVCSDCNLNLKQKGYFFVEGQLYCEAH 51

This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	102
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.58
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.48
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.37
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.14
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.13
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.07
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.01
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	98.9
KOG4577	383	consensus Transcription factor LIM3, contains LIM	98.76
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.7
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.58
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.41
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	98.16
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	98.12
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	97.17
KOG0490	235	consensus Transcription factor, contains HOX domai	93.87
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	84.84
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	83.61
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	81.15
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	80.46

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

Probab=99.58  E-value=6e-15  Score=78.09  Aligned_cols=57  Identities=35%  Similarity=0.815  Sum_probs=52.2

Q ss_pred             cccccceeecCceE-EecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHh
Q 034188           10 CKVCEKTVYPVEQL-SADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   66 (102)
Q Consensus        10 C~~C~~~i~~~~~~-~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~   66 (102)
                      |.+|++.|.+.+.+ .+.++.||.+||+|..|+.+|....++..++++||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            78999999877764 7999999999999999999999888889999999999999876

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

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

Probab=99.48  E-value=1e-15  Score=102.42  Aligned_cols=75  Identities=25%  Similarity=0.460  Sum_probs=67.6

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAK   81 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~   81 (102)
                      ..++|++|+++|.+..++.+.++.||..|++|+.|..+|.. .++.+++.+||+.+|.++|+++|+ |+.+|.+.+|
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqV  107 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQV  107 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHH
Confidence            45789999999988777899999999999999999999974 578899999999999999999998 8888887765

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

Probab=99.37  E-value=3.4e-14  Score=99.20  Aligned_cols=76  Identities=25%  Similarity=0.530  Sum_probs=65.1

Q ss_pred             cCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEe-eCCeeeeHHHHHHHhCCCCC-CCCCCCCCC
Q 034188            4 IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFKESGN-FNKNFQSPA   80 (102)
Q Consensus         4 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~-~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~   80 (102)
                      ..+..+|..|++.|++. ++.+.++.||+.||+|.+|.+.|.+..|.. .++.+||..||+++|+++|+ |.+.|.+.+
T Consensus       331 q~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~  408 (468)
T KOG1701|consen  331 QDTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRD  408 (468)
T ss_pred             HHHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCC
Confidence            34556899999999653 479999999999999999999999888776 59999999999999999999 666666655

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

Probab=99.14  E-value=1.4e-11  Score=89.06  Aligned_cols=81  Identities=26%  Similarity=0.490  Sum_probs=69.0

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAKSAE   84 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~~~~   84 (102)
                      +...|++|++.|..+..+.+.++.||..||+|..|..-|. ++|...++.+||+.+|...|+-+|. |.+-|....+.+.
T Consensus       132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag  210 (670)
T KOG1044|consen  132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAG  210 (670)
T ss_pred             CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhcc
Confidence            5668999999998888889999999999999999999886 6789999999999999999999988 5555666666665


Q ss_pred             CCC
Q 034188           85 KLT   87 (102)
Q Consensus        85 ~~~   87 (102)
                      +.+
T Consensus       211 ~kh  213 (670)
T KOG1044|consen  211 DKH  213 (670)
T ss_pred             Ccc
Confidence            543

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

Probab=99.13  E-value=4e-12  Score=84.06  Aligned_cols=81  Identities=23%  Similarity=0.538  Sum_probs=70.0

Q ss_pred             cccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCCCCCCCCCCC---C
Q 034188            8 QKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKS---A   83 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~~~~~~~~~~---~   83 (102)
                      ..|.+|..++.+.+. +...+.+||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.|.-+..|..++|.   +
T Consensus        13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVikamn   92 (332)
T KOG2272|consen   13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKAMN   92 (332)
T ss_pred             HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHhhc
Confidence            479999999988886 688899999999999999999999999999999999999999999999966677766665   4


Q ss_pred             CCCCh
Q 034188           84 EKLTP   88 (102)
Q Consensus        84 ~~~~~   88 (102)
                      ..|+|
T Consensus        93 nSwHp   97 (332)
T KOG2272|consen   93 NSWHP   97 (332)
T ss_pred             cccCc
Confidence            44443

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

Probab=99.07  E-value=1e-11  Score=82.20  Aligned_cols=78  Identities=23%  Similarity=0.413  Sum_probs=67.3

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAKSA   83 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~~~   83 (102)
                      .+.+.|..|...|. ...+.++++.||.+.|+|.+|.+|+-+...+++.|..||+.+|.++|+.-|. |+..+.++++++
T Consensus       193 mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~a  271 (332)
T KOG2272|consen  193 MGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSA  271 (332)
T ss_pred             cCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHH
Confidence            46689999999994 3347899999999999999999998877889999999999999999999998 666777777663

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

Probab=99.01  E-value=1.9e-11  Score=85.69  Aligned_cols=69  Identities=23%  Similarity=0.557  Sum_probs=58.6

Q ss_pred             cccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCC
Q 034188            8 QKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQ   77 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~   77 (102)
                      .+|.+|++.|..... .+++++.||..||.|..|.+.|....|+..++++||+.||+..+. +|. |.+.|+
T Consensus       275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tle-kC~~Cg~~I~  345 (468)
T KOG1701|consen  275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLE-KCNKCGEPIM  345 (468)
T ss_pred             hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHH-HHhhhhhHHH
Confidence            389999999977665 799999999999999999999998899999999999999987653 444 554443

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

Probab=98.90  E-value=3.9e-10  Score=81.63  Aligned_cols=68  Identities=29%  Similarity=0.679  Sum_probs=59.6

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFN   73 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~   73 (102)
                      ...+.|.+|++.|. .+.+.+.+..||++||.|..|.+++....|+..++.+||+.||..++.++|..+
T Consensus       361 ~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~  428 (479)
T KOG1703|consen  361 PFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYC  428 (479)
T ss_pred             hhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhc
Confidence            34678999999995 445677799999999999999999998899999999999999999998887644

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

Probab=98.76  E-value=2.1e-09  Score=72.50  Aligned_cols=63  Identities=29%  Similarity=0.653  Sum_probs=52.6

Q ss_pred             cccccccceeecCceE-EecCccccccCcccccccccCcCcc-eE-eeCCeeeeHHHHHHHhCCCC
Q 034188            8 QKCKVCEKTVYPVEQL-SADGIVYHKSCFKCSHCKGTLKLSN-YS-SMEGVLYCKPHFEQLFKESG   70 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~-~~~~~~~h~~Cf~C~~C~~~l~~~~-~~-~~~~~~~C~~~~~~~~~~~c   70 (102)
                      .+|..|.++|.+..++ .+.+.+||+.||.|..|.+.|..+. |+ ..++++.|+.+|+......|
T Consensus        93 TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~  158 (383)
T KOG4577|consen   93 TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC  158 (383)
T ss_pred             CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence            3899999999776654 7889999999999999999999875 44 46999999999987644444

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

Probab=98.70  E-value=1.3e-08  Score=49.11  Aligned_cols=37  Identities=43%  Similarity=0.767  Sum_probs=32.2

Q ss_pred             ccccccceeecC-ceEEecCccccccCcccccccccCc
Q 034188            9 KCKVCEKTVYPV-EQLSADGIVYHKSCFKCSHCKGTLK   45 (102)
Q Consensus         9 ~C~~C~~~i~~~-~~~~~~~~~~h~~Cf~C~~C~~~l~   45 (102)
                      +|..|++.|.+. ..+...+..||..||.|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            588999999776 4578899999999999999998874

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

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

Probab=98.58  E-value=3.1e-08  Score=64.49  Aligned_cols=77  Identities=53%  Similarity=0.966  Sum_probs=65.2

Q ss_pred             CCccCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCC
Q 034188            1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQ   77 (102)
Q Consensus         1 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~   77 (102)
                      |++.+....|..|++.++..+++...+..||..||.|..|...|....+...++.+||..+|...++++.. ...+++
T Consensus         1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~   78 (200)
T KOG1700|consen    1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQ   78 (200)
T ss_pred             CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccccc
Confidence            45556667999999999988888899999999999999999999988899999999999977788887654 555444

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

Probab=98.41  E-value=5.6e-08  Score=63.29  Aligned_cols=70  Identities=54%  Similarity=1.205  Sum_probs=61.1

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNK   74 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~~   74 (102)
                      +....|.+|.+.+++.+.+...+..||..||+|..|...|....+....+.++|..++..+|-.+.....
T Consensus       106 g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~  175 (200)
T KOG1700|consen  106 GEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNE  175 (200)
T ss_pred             ccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcccc
Confidence            4567899999999999989999999999999999999999998899999999998888887666555543

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

Probab=98.16  E-value=1.5e-06  Score=63.20  Aligned_cols=76  Identities=17%  Similarity=0.369  Sum_probs=65.4

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAKS   82 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~~   82 (102)
                      .+.|..|+..|.....+..+++.||..+|.|..|...+..+.+...+|.+||..+|...+++.|. |...+.+..+.
T Consensus       303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~  379 (479)
T KOG1703|consen  303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVC  379 (479)
T ss_pred             cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhh
Confidence            47899999999654668999999999999999999999888888889999999999999999998 55566665555

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=98.12  E-value=1e-07  Score=61.74  Aligned_cols=59  Identities=41%  Similarity=0.836  Sum_probs=52.6

Q ss_pred             cccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHh
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   66 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~   66 (102)
                      ..|..|++.+++.+.+...++.||..||.|..|+..|....+-+.+.++||..+|....
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence            46888999999999999999999999999999999998888888899999999986543

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

Probab=97.17  E-value=0.0002  Score=52.87  Aligned_cols=52  Identities=29%  Similarity=0.622  Sum_probs=44.9

Q ss_pred             ccccccceeecCceEEecCccccccCcccccccccCcCcceEee-CCeeeeHHH
Q 034188            9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPH   61 (102)
Q Consensus         9 ~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~~   61 (102)
                      .|..|.+.- .++++.+.++.||..||.|..|+..|..+.|+.. +.++|+...
T Consensus        18 ~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~   70 (670)
T KOG1044|consen   18 KCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDD   70 (670)
T ss_pred             ehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccc
Confidence            799999998 5788999999999999999999999998888775 667777643

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

Probab=93.87  E-value=0.011  Score=38.77  Aligned_cols=58  Identities=26%  Similarity=0.639  Sum_probs=44.0

Q ss_pred             ccceeecCceEEecCccccccCcccccccccCc--CcceEeeCCeeeeHHHHHH--HhCCCCC
Q 034188           13 CEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYCKPHFEQ--LFKESGN   71 (102)
Q Consensus        13 C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~--~~~~~c~   71 (102)
                      |+..|.+...+...+..||..|..|..|...+.  ...+.. ++..||..+|.+  .+..+|.
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~   63 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA   63 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc
Confidence            566665555566678999999999999999987  334555 999999999987  5544444

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

Probab=84.84  E-value=0.5  Score=27.62  Aligned_cols=32  Identities=25%  Similarity=0.540  Sum_probs=23.4

Q ss_pred             ccccccceeecCceEEe-cCccccccCcccccc
Q 034188            9 KCKVCEKTVYPVEQLSA-DGIVYHKSCFKCSHC   40 (102)
Q Consensus         9 ~C~~C~~~i~~~~~~~~-~~~~~h~~Cf~C~~C   40 (102)
                      +|..|++.|..++++.+ ...+-|..||.-..-
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~   36 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKAS   36 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence            68999999988887654 335678888875443

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=83.61  E-value=0.65  Score=24.05  Aligned_cols=28  Identities=32%  Similarity=0.702  Sum_probs=20.0

Q ss_pred             cccccccceeecCc-eE--EecCccccccCc
Q 034188            8 QKCKVCEKTVYPVE-QL--SADGIVYHKSCF   35 (102)
Q Consensus         8 ~~C~~C~~~i~~~~-~~--~~~~~~~h~~Cf   35 (102)
                      .+|..|++.|.+.+ .+  ..=+.+||.+|+
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            48999999996444 33  334667888887

>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=81.15  E-value=1.2  Score=25.55  Aligned_cols=11  Identities=45%  Similarity=0.881  Sum_probs=5.8

Q ss_pred             ccccccceeec
Q 034188            9 KCKVCEKTVYP   19 (102)
Q Consensus         9 ~C~~C~~~i~~   19 (102)
                      .|..|++.+..
T Consensus        80 ~C~vC~k~l~~   90 (109)
T PF10367_consen   80 KCSVCGKPLGN   90 (109)
T ss_pred             CccCcCCcCCC
Confidence            45555555543

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 [].

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

Probab=80.46  E-value=1.2  Score=21.22  Aligned_cols=23  Identities=17%  Similarity=0.304  Sum_probs=14.5

Q ss_pred             cccccceeecCce-EEecCccccc
Q 034188           10 CKVCEKTVYPVEQ-LSADGIVYHK   32 (102)
Q Consensus        10 C~~C~~~i~~~~~-~~~~~~~~h~   32 (102)
                      |.-|+..|..... +...++.|+.
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~f   24 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYF   24 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEE
Confidence            5667777753333 5677777763

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	102
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		2e-18
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		2e-07
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		3e-07
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		6e-07
2o10_A	60	Solution Structure Of The N-Terminal Lim Domain Of		9e-07
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		1e-06
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		2e-06
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		7e-06
1a7i_A	81	Amino-Terminal Lim Domain From Quail Cysteine And G		1e-05
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		2e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		3e-05
3ixe_B	72	Structural Basis Of Competition Between Pinch1 And		7e-04

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

Iteration: 1
 Score = 87.0 bits (214), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 53/78 (67%)
Query: 6  TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65
           ++ C  C+KTVYP+E+L A+  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QL
Sbjct: 14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQL 73
Query: 66 FKESGNFNKNFQSPAKSA 83
          FK  GN+++ F S   S 
Sbjct: 74 FKSKGNYDEGFGSGPSSG 91

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 37/67 (55%)
Query: 4  IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFE 63
           G  +KC  C  +VY  E++   G  +HK+CF+C+ C  +L+ +  +  EG +YCK  + 
Sbjct: 33 FGGAEKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 92
Query: 64 QLFKESG 70
          + F   G
Sbjct: 93 KNFGPKG 99

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 37/67 (55%)
Query: 4  IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFE 63
           G  +KC  C  +VY  E++   G  +HK+CF+C+ C  +L+ +  +  EG +YCK  + 
Sbjct: 33 FGGAEKCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 92
Query: 64 QLFKESG 70
          + F   G
Sbjct: 93 KNFGPKG 99

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          KC  C K+VY  E++   G  +HK+CF+C+ C  +L+ +N +  +G LYCK  + + F
Sbjct: 1  KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 31/51 (60%)
Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59
          KC  CEKTVY  E++  +G  +HK+CF C  C+  L  +  ++ E  +YCK
Sbjct: 3  KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 53

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 4  IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFE 63
          +G    C  C + VY  E++   G  +HKSCF+C+ C  +L+ +  +  +G +YCK  + 
Sbjct: 5  VGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYA 64
Query: 64 QLF 66
          + F
Sbjct: 65 KNF 67

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 4   IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFE 63
           +G    C  C + VY  E++   G  +HKSCF+C+ C  +L+ +  +  +G +YCK  + 
Sbjct: 112 VGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYA 171
Query: 64  QLF 66
           + F
Sbjct: 172 KNF 174

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC-KPHFEQLF 66
          KC  C+KTVY  E++S+ G  +HK C KC  C  TL    ++  +G  +C KP +  LF
Sbjct: 11 KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 34/70 (48%)
Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          M   G   KC  C +TVY  E++  DG  +H+ CF C  C+  L  +  +  +  +YCK 
Sbjct: 1  MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKS 60
Query: 61 HFEQLFKESG 70
           + + +   G
Sbjct: 61 CYGKKYGPKG 70

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 5  GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM--EGVLYCKPHF 62
          G    C +C + +Y +E+L  +G  +H+SCF+C  C+ TL    Y     +G  YC  H 
Sbjct: 13 GAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHL 72
Query: 63 EQ 64
           Q
Sbjct: 73 PQ 74

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFK 67
          KC  C+K VY  E++++ G  +H+ C KC  C  TL    ++  EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 68 ESG 70
            G
Sbjct: 62 PKG 64

>pdb|3IXE|B Chain B, Structural Basis Of Competition Between Pinch1 And Pinch2 For Binding To The Ankyrin Repeat Domain Of Integrin-Linked Kinase Length = 72

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 10 CKVCEKTVYPVEQL-SADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          C+ C+    P E++ +++G +YH+ CF C+ C        +   EG  YC+  F+ LF
Sbjct: 14 CQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEGLFYEFEGRKYCEHDFQMLF 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	102
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	1e-31
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	6e-27
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	6e-27
2co8_A	82	NEDD9 interacting protein with calponin homology a	1e-23
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-23
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	7e-23
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	6e-19
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-18
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	4e-16
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	5e-13
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	7e-13
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-12
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-11
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-10
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-10
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-10
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-09
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	6e-08
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-09
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	2e-09
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-09
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	3e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-09
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	2e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	3e-09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	3e-09
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-09
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	5e-09
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	7e-09
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	9e-09
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	3e-08
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	3e-08
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	4e-08
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	5e-08
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	9e-05
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-08
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	4e-04
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	6e-08
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	8e-08
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	7e-07
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	4e-07
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	5e-07
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	2e-06
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	8e-06
2cor_A	79	Pinch protein; LIM domain, particularly interestin	2e-05
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	6e-05

>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 =  105 bits (264), Expect = 1e-31
 Identities = 38/81 (46%), Positives = 53/81 (65%)

Query: 3  FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
              ++ C  C+KTVYP+E+L A+  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF
Sbjct: 11 QAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHF 70

Query: 63 EQLFKESGNFNKNFQSPAKSA 83
           QLFK  GN+++ F S   S 
Sbjct: 71 NQLFKSKGNYDEGFGSGPSSG 91

>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 = 93.6 bits (233), Expect = 6e-27
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          M   G   KC  C +TVY  E++  DG  +H+ CF C  C+  L  +  +  +  +YCK 
Sbjct: 1  MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKS 60

Query: 61 HFEQLFKESG-NFNKNFQS 78
           + + +   G  + +   +
Sbjct: 61 CYGKKYGPKGYGYGQGAGT 79

>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 = 93.2 bits (232), Expect = 6e-27
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 2  SFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC-KP 60
             G   KC  C+KTVY  E++S+ G  +HK C KC  C  TL    ++  +G  +C KP
Sbjct: 4  GSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKP 63

Query: 61 HFEQLFKESGN 71
           +  LF    +
Sbjct: 64 CYATLFGSGPS 74

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

 Score = 85.0 bits (210), Expect = 1e-23
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 3  FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM--EGVLYCKP 60
            G    C +C + +Y +E+L  +G  +H+SCF+C  C+ TL    Y     +G  YC  
Sbjct: 11 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQ 70

Query: 61 HFEQLFKESGN 71
          H  Q      +
Sbjct: 71 HLPQTDSGPSS 81

>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 = 84.3 bits (209), Expect = 2e-23
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFK 67
          KC  C+K VY  E++++ G  +H+ C KC  C  TL    ++  EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 68 ESGN 71
            G 
Sbjct: 62 PKGF 65

>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 = 86.2 bits (213), Expect = 7e-23
 Identities = 24/81 (29%), Positives = 36/81 (44%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60
          M   G  +KC VC+K VY  E++  +G  +HKSCF C  CK  L  +  +     +YCK 
Sbjct: 1  MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKS 60

Query: 61 HFEQLFKESGNFNKNFQSPAK 81
           + + +   G           
Sbjct: 61 CYGKKYGPKGKGKGMGAGTLS 81

>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 = 76.2 bits (187), Expect = 6e-19
 Identities = 21/69 (30%), Positives = 36/69 (52%)

Query: 3   FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62
            +G    C  C + VY  E++   G  +HKSCF+C+ C  +L+ +  +  +G +YCK  +
Sbjct: 111 KVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCY 170

Query: 63  EQLFKESGN 71
            + F   G 
Sbjct: 171 AKNFGPKGF 179

>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 = 71.3 bits (175), Expect = 3e-18
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C+ C+    P E+ ++++G +YH+ CF C+ C        +   EG  YC+  F+ LF
Sbjct: 13 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 71

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

 Score = 65.9 bits (161), Expect = 4e-16
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 6  TQQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ 64
              C+ C+    P E+ ++++G +YH+ CF C+ C        +   EG  YC+  F+ 
Sbjct: 10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 65 LF 66
          LF
Sbjct: 70 LF 71

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

 Score = 58.1 bits (141), Expect = 5e-13
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          KCK C K +   +Q +   G V+HK CF CS+CK  +   ++       YC    E  F
Sbjct: 17 KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

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

 Score = 57.8 bits (140), Expect = 7e-13
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

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

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

 Score = 55.9 bits (135), Expect = 3e-12
 Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C+ C+KT+ P  + +   G  +H++CF C  C+  +   ++   +   +C P +E+  
Sbjct: 7  GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

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

 Score = 51.7 bits (124), Expect = 1e-10
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C + V      + A   V+H  CF CS C+  L+  ++ ++E   YC+  +    
Sbjct: 7  GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL 65

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

 Score = 51.7 bits (124), Expect = 2e-10
 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C++ +   + L A    +H SCFKC  C   L    Y S +GV YC+  +   F
Sbjct: 17 HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 73

>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 = 50.7 bits (122), Expect = 3e-10
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C + +     ++A G  +H   F C+ C+       +   +G+ YC+ H+ QLF
Sbjct: 7  ICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

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

 Score = 50.9 bits (122), Expect = 1e-09
 Identities = 13/58 (22%), Positives = 23/58 (39%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          +C  C++ ++  E   A+   +H   F C  C   L    Y  +     CKP + +  
Sbjct: 5  RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNH 62

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

 Score = 46.2 bits (110), Expect = 6e-08
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 9   KCKVCEKTVYP-VEQLSADGIVYH--KSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65
            C+ C   + P V++++ +   +H    CF CS C   L    +  +EG+++C    ++ 
Sbjct: 65  VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR 124

Query: 66  F 66
            
Sbjct: 125 M 125

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

 Score = 49.4 bits (118), Expect = 1e-09
 Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C++ +    + L  +   +H+ CF+C  C+ +L    ++  +  L C   +   F
Sbjct: 17 TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

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

 Score = 48.9 bits (117), Expect = 2e-09
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C+K +     ++     +HK CF C+ C+  L    +++ +   YC   F  L+
Sbjct: 7  GCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY 63

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

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 5   GTQQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKL-SNYSSMEGVLYCKPHF 62
           G    C  C+K +   E  +     VYH  CFKC+ C+    +   Y  +   + C+   
Sbjct: 64  GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI 123

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

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

 Score = 44.4 bits (105), Expect = 3e-07
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 2/60 (3%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQLF 66
           C  C++ +     L A    +H+ C  C  C   L           G   C+  + +LF
Sbjct: 4  TCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLF 63

>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 = 49.7 bits (118), Expect = 2e-09
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

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

Query: 63  EQLF 66
            +LF
Sbjct: 119 IRLF 122

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

 Score = 48.5 bits (116), Expect = 2e-09
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C K +     ++     +H  CF C  C   L    ++++E   YC   ++   
Sbjct: 7  GCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFV 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 = 48.5 bits (116), Expect = 3e-09
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          +C  C KT+     ++     +H+ C  C+ C+  L    ++S +   YC   F +LF
Sbjct: 17 RCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELF 73

>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 = 48.2 bits (115), Expect = 3e-09
 Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 1/59 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67
           C  C   +     +       H  C+ C+ C   LK   +  +E  +YC+ H  +   
Sbjct: 17 MCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVS 74

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

 Score = 47.9 bits (114), Expect = 4e-09
 Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 3/61 (4%)

Query: 9  KCKVCEKTVYPVEQ---LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65
           C  C   +  +     +S +   +H  CF C  C  +L    + +    + C    + +
Sbjct: 7  GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 66 F 66
           
Sbjct: 67 S 67

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

 Score = 47.7 bits (114), Expect = 5e-09
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          KC  C + V     LSA   V+H  CF C  C  +    ++  ++G  +C+ H+    
Sbjct: 17 KCGGCNRPVLE-NYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR 73

>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 = 47.9 bits (114), Expect = 7e-09
 Identities = 17/58 (29%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C   +     + A     H  CF C+ C   LK   Y  +EG LYC+ H     
Sbjct: 27 LCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARART 83

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

 Score = 47.4 bits (113), Expect = 9e-09
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C + +     L A G  +H   F C+HCK T+    +   +G LYC+  +E+ F
Sbjct: 27 MCAHCNQVIRG-PFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

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

 Score = 45.9 bits (109), Expect = 3e-08
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C + +     + A    +H  CF+C  C+  L    +    G   C+P   +  
Sbjct: 7  GCHQCGEFIIG-RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 63

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

 Score = 45.9 bits (109), Expect = 3e-08
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 9  KCKVCEKTVYPV----EQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ 64
          KC  C+  +         ++ +G  +H  CF C  C   L    +   +  +YC    ++
Sbjct: 17 KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 65 L 65
          L
Sbjct: 77 L 77

>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 = 46.5 bits (110), Expect = 4e-08
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 6  TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFE 63
          + ++C  C   +     L A    +H  C KCS C+  L     S  +  G++ C+  + 
Sbjct: 4  SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 64 QLFKESG 70
          +LF  SG
Sbjct: 64 RLFGNSG 70

>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 = 47.3 bits (112), Expect = 5e-08
 Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 3   FIGTQQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKL-SNYSSMEGVLYCKP 60
             G    C  C +++   E  + A G VYH  CF CS C+  L     +  + G L+C+ 
Sbjct: 65  LFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEH 124

Query: 61  HFEQLF 66
                 
Sbjct: 125 DRPTAL 130

>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 = 38.5 bits (89), Expect = 9e-05
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 8  QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQL 65
          ++C  C   +     L A    +H  C KCS C+  L     S  +  G++ C+  + +L
Sbjct: 6  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65

Query: 66 FKESG 70
          F  SG
Sbjct: 66 FGNSG 70

>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 = 45.9 bits (109), Expect = 5e-08
 Identities = 10/61 (16%), Positives = 22/61 (36%), Gaps = 1/61 (1%)

Query: 9  KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67
           C  C K +    + +      +H +CF+C+ C   L    + + +  + C     +   
Sbjct: 7  GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 68 E 68
           
Sbjct: 67 P 67

>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 = 35.8 bits (83), Expect = 4e-04
 Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)

Query: 9   KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHC 40
           KCK C K +   +Q +   G V+HK CF     
Sbjct: 68  KCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

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

 Score = 45.1 bits (107), Expect = 6e-08
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 3  FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS-SMEGVLYCKPH 61
          ++ T +KC  C + +     L A G  YH  CF C  C   L    ++      ++C   
Sbjct: 11 YVATLEKCATCSQPILD-RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 62 FEQLF 66
          F + F
Sbjct: 70 FHRKF 74

>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 = 46.4 bits (110), Expect = 8e-08
 Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 9   KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQL 65
           KC  C+  + P +    A   VYH  CF C  CK  L      Y   +  L CK  +E  
Sbjct: 67  KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA 126

Query: 66  F 66
            
Sbjct: 127 K 127

>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 = 44.1 bits (104), Expect = 7e-07
 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
           C  C++ +     L A    +H  C KCS C   L    + S    +YCK  F + F
Sbjct: 8  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF 64

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

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 19/59 (32%), Positives = 24/59 (40%), Gaps = 3/59 (5%)

Query: 9   KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQ 64
           KC  C+  + P +    A   VYH  CF C  CK  L      Y   +  L CK  +E 
Sbjct: 121 KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 179

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

 Score = 42.2 bits (99), Expect = 3e-06
 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 9   KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
            C  C++ +     L A    +H  C KCS C   L    + S    +YCK  F + F
Sbjct: 62  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF 118

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

 Score = 42.5 bits (100), Expect = 5e-07
 Identities = 10/64 (15%), Positives = 22/64 (34%), Gaps = 3/64 (4%)

Query: 9  KCKVCEKTVYPVEQ---LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65
           C  C K +  +     +      +H  CF C  C  +L    + +    ++C+     +
Sbjct: 7  GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 66 FKES 69
            + 
Sbjct: 67 DTDI 70

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

 Score = 40.9 bits (96), Expect = 2e-06
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 3/60 (5%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLF 66
           C  C   +     + A    YH  CF C  CK  ++   +        LYC     ++ 
Sbjct: 17 FCHGCSLLMTG-PFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

>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 = 40.4 bits (94), Expect = 8e-06
 Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 2/69 (2%)

Query: 5  GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHF 62
          G+   C  C++ +     L A    +H+ C  C  C   L           G   C+  +
Sbjct: 1  GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 63 EQLFKESGN 71
           +L    G+
Sbjct: 61 LRLGGSGGH 69

>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 = 38.6 bits (90), Expect = 2e-05
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66
          C+ C   +   + L      YH   F C++C   L  ++   ++G LYC P  +++ 
Sbjct: 18 CQKCHAIIDE-QPLIFKNDPYHPDHFNCANCGKELT-ADARELKGELYCLPCHDKMG 72

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

 Score = 36.2 bits (83), Expect = 6e-05
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 8  QKCKVCEKTVYPVEQLSADGIVYHKSCF 35
            C  C K VYP E+++     +HK+CF
Sbjct: 4  PNCARCGKIVYPTEKVNCLDKFWHKACF 31

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	102
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.79
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.78
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.77
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.75
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.74
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.73
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.72
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.72
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.71
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.71
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.71
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.7
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.7
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.7
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.7
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.69
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.69
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.69
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.69
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.69
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.68
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.68
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.68
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.67
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.66
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.65
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.65
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.65
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.64
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.63
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.63
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.62
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.62
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.62
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.62
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.6
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.57
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.56
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.56
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.56
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.53
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.53
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.41
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.38
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.29
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.28
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.16
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.07
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.42
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.23
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	96.46
2cuq_A	80	Four and A half LIM domains 3; structural genomics	95.42
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	95.38
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	95.14
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	94.7
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	94.38
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	94.0
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	92.75
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	91.33

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

Probab=99.79  E-value=6.5e-20  Score=102.61  Aligned_cols=71  Identities=30%  Similarity=0.709  Sum_probs=57.5

Q ss_pred             CCccCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         1 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      |+|.++.++|..|++.|.+.+.+.+.++.||.+||+|..|.++|....|+..++++||..||.++|+++|.
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   71 (81)
T 1a7i_A            1 MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGY   71 (81)
T ss_dssp             -------CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----
T ss_pred             CCCCCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCccc
Confidence            78888899999999999878888999999999999999999999888899999999999999999999997

>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=99.78  E-value=5.1e-19  Score=97.84  Aligned_cols=71  Identities=34%  Similarity=0.679  Sum_probs=64.8

Q ss_pred             CCccCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeH-HHHHHHhCCCCC
Q 034188            1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFKESGN   71 (102)
Q Consensus         1 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~-~~~~~~~~~~c~   71 (102)
                      +.|.+.+++|..|++.|.+.+.+.+.++.||.+||+|..|..+|....|+..++.+||. .||.++|+++|.
T Consensus         3 ~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~   74 (76)
T 2cu8_A            3 SGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPS   74 (76)
T ss_dssp             CSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCS
T ss_pred             cccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccC
Confidence            35667788999999999878888999999999999999999999987899999999999 799999999885

>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=99.77  E-value=4.5e-19  Score=101.24  Aligned_cols=75  Identities=49%  Similarity=1.057  Sum_probs=68.9

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCCCCCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPA   80 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~~~~~~~~   80 (102)
                      +.++|..|++.|.+.+.+.+.++.||..||+|..|..+|....|+..++.+||..||.++|+++|.++..|....
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~~~   88 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSGP   88 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCCCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCCCC
Confidence            456999999999887888999999999999999999999987888999999999999999999999988887755

>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=99.75  E-value=2.1e-18  Score=96.35  Aligned_cols=66  Identities=29%  Similarity=0.583  Sum_probs=60.6

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      .+.++|..|++.|.+.+.+.++++.||.+||+|..|..+|.. .|+..++.+||+.||.++|+++|+
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~   78 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPS   78 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCST
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCC
Confidence            456799999999987888899999999999999999999984 688999999999999999999886

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

Probab=99.74  E-value=4.2e-18  Score=94.22  Aligned_cols=69  Identities=26%  Similarity=0.614  Sum_probs=60.4

Q ss_pred             ccCCccccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            3 FIGTQQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         3 ~~~~~~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      .....++|.+|++.|.+.+. +.+.++.||..||+|..|..+|..+.|+..++.+||+.||.++|+++|.
T Consensus         7 ~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A            7 NALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             SCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             cCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            34556799999999986564 7899999999999999999999988899999999999999999999885

>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=99.73  E-value=9.3e-18  Score=92.72  Aligned_cols=66  Identities=33%  Similarity=0.724  Sum_probs=60.7

Q ss_pred             cccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeH-HHHHHHhCCCCCCC
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFKESGNFN   73 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~-~~~~~~~~~~c~~~   73 (102)
                      ++|..|++.|.+.+.+.+.++.||..||+|..|..+|..+.|+..++.+||. .||.++|+++|.-+
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C   67 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGR   67 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSC
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCc
Confidence            4799999999877888999999999999999999999988899999999999 69999999999833

>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=99.72  E-value=1.6e-17  Score=90.82  Aligned_cols=66  Identities=21%  Similarity=0.629  Sum_probs=60.5

Q ss_pred             ccccccccceeecCc-eEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCC
Q 034188            7 QQKCKVCEKTVYPVE-QLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNF   72 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~-~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~   72 (102)
                      +++|..|++.|.+.+ .+.+.++.||.+||+|..|.++|....|+..++.+||..||.++|+++|..
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            468999999998765 589999999999999999999999888999999999999999999998863

>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=99.72  E-value=1.2e-17  Score=91.27  Aligned_cols=65  Identities=31%  Similarity=0.717  Sum_probs=59.8

Q ss_pred             ccccccccceeecC-ceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            7 QQKCKVCEKTVYPV-EQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         7 ~~~C~~C~~~i~~~-~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      .++|..|++.|.+. +.+.+.++.||..||+|..|..+|....|+..++.+||..||.++|+++|.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   70 (72)
T 1wyh_A            5 SSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPS   70 (72)
T ss_dssp             CCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCC
T ss_pred             CCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCC
Confidence            56899999999875 568899999999999999999999988889999999999999999999886

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

Probab=99.71  E-value=2.1e-17  Score=89.71  Aligned_cols=65  Identities=18%  Similarity=0.539  Sum_probs=59.2

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      +.++|..|++.|. .+.+.+.++.||.+||+|..|..+|....|+..++.+||..||.++|+++|.
T Consensus         4 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   68 (69)
T 2cur_A            4 GSSGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS   68 (69)
T ss_dssp             CCCCCSSSCCCCC-TTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCC
T ss_pred             CcCCCcccCCEeC-cceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCC
Confidence            4679999999996 4568999999999999999999999877888999999999999999999885

>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=99.71  E-value=1.7e-17  Score=99.27  Aligned_cols=78  Identities=21%  Similarity=0.407  Sum_probs=67.7

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcC--cceEeeCCeeeeHHHHHHHhCC--CCC-CCCCCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKE--SGN-FNKNFQSPA   80 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~~--~c~-~~~~~~~~~   80 (102)
                      ..++|++|++.|...+.+.+.++.||..||+|..|..+|..  ..|+.+++.+||..||.++|++  +|. |.+.|.+..
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~   83 (122)
T 1m3v_A            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGD   83 (122)
T ss_dssp             CCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEE
T ss_pred             CCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchh
Confidence            46799999999987767899999999999999999999973  4689999999999999999999  898 666777665


Q ss_pred             CCC
Q 034188           81 KSA   83 (102)
Q Consensus        81 ~~~   83 (102)
                      +.+
T Consensus        84 ~~~   86 (122)
T 1m3v_A           84 VMV   86 (122)
T ss_dssp             SSS
T ss_pred             eEE
Confidence            543

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

Probab=99.71  E-value=1.8e-17  Score=90.10  Aligned_cols=65  Identities=22%  Similarity=0.566  Sum_probs=59.2

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      ..++|..|++.|.. +.+.+.++.||++||+|..|.++|....|+..++.+||..||.++|+++|.
T Consensus         4 ~~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   68 (70)
T 2d8z_A            4 GSSGCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPS   68 (70)
T ss_dssp             CCCBCSSSCCBCCS-SEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCT
T ss_pred             CCCCCcccCCeecc-ceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccC
Confidence            45799999999964 568999999999999999999999877888999999999999999999885

>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=99.70  E-value=1.4e-17  Score=98.63  Aligned_cols=70  Identities=20%  Similarity=0.393  Sum_probs=62.4

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcC--cceEeeCCeeeeHHHHHHHhCCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKESGNFNK   74 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~~~c~~~~   74 (102)
                      ++.++|++|++.|...+.+.+.++.||..||+|..|..+|..  ..|+.+++.+||+.||.++|+++|.++.
T Consensus         1 g~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~   72 (114)
T 1j2o_A            1 GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGS   72 (114)
T ss_dssp             CCCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCB
T ss_pred             CcCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCC
Confidence            356799999999987767899999999999999999999985  4688999999999999999999987553

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

Probab=99.70  E-value=1.6e-17  Score=89.39  Aligned_cols=62  Identities=24%  Similarity=0.567  Sum_probs=57.1

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES   69 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~   69 (102)
                      +++|++|++.|. .+.+.+.++.||.+||+|..|..+|....|+..++.+||..||.++|+++
T Consensus         5 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            5 VPICGACRRPIE-GRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCEETTTTEECC-SCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCCcccCCEec-ceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            568999999997 66788999999999999999999998878999999999999999999875

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

Probab=99.70  E-value=3e-17  Score=93.44  Aligned_cols=67  Identities=27%  Similarity=0.591  Sum_probs=60.3

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNF   72 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~   72 (102)
                      ...++|..|++.|. .+.+.+.++.||++||+|..|.++|....|+..++.+||..||.++|+++|+.
T Consensus        23 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           23 KRTPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             TCCCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            34578999999994 56788999999999999999999999878888999999999999999999863

>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=99.70  E-value=3.6e-17  Score=94.73  Aligned_cols=75  Identities=15%  Similarity=0.373  Sum_probs=65.6

Q ss_pred             CCccccccccceeec-CceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYP-VEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSP   79 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~-~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~   79 (102)
                      .+.++|..|++.|.. .+.+.+.++.||..||+|..|.++|....|+..++++||..||.++|+++|. |.+.|.++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~   79 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAG   79 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSS
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccC
Confidence            346799999999975 5668999999999999999999999877799999999999999999999998 66666643

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

Probab=99.69  E-value=1.7e-17  Score=91.70  Aligned_cols=67  Identities=15%  Similarity=0.413  Sum_probs=60.5

Q ss_pred             ccccccccceeec---CceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCC
Q 034188            7 QQKCKVCEKTVYP---VEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFN   73 (102)
Q Consensus         7 ~~~C~~C~~~i~~---~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~   73 (102)
                      +++|..|++.|.+   .+.+.+.++.||.+||+|..|..+|....|+..++++||..||.++|+++|.-+
T Consensus         5 ~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~   74 (76)
T 1x68_A            5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPS   74 (76)
T ss_dssp             CCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSS
T ss_pred             CCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCC
Confidence            5689999999974   356899999999999999999999987779999999999999999999999754

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

Probab=99.69  E-value=6.7e-17  Score=87.89  Aligned_cols=66  Identities=18%  Similarity=0.446  Sum_probs=59.2

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      ++.++|..|++.|. .+.+.+.++.||++||+|..|..+|....|+..++.+||..||.++|+++..
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            3 SGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             CCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            45679999999997 4568999999999999999999999988888899999999999999988653

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

Probab=99.69  E-value=4.7e-17  Score=92.43  Aligned_cols=65  Identities=26%  Similarity=0.522  Sum_probs=58.8

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      ...+|..|++.|.. +.+.+.++.||.+||+|..|..+|....|+..++.+||+.||.++|++++.
T Consensus        24 ~~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           24 RMPLCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             SCCBCTTTCCBCCS-CCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             cCCCcccCCCEecc-cEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            34689999999975 568899999999999999999999887899999999999999999999764

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

Probab=99.69  E-value=7.5e-17  Score=96.77  Aligned_cols=72  Identities=18%  Similarity=0.404  Sum_probs=65.3

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQS   78 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~   78 (102)
                      +++|.+|++.|.+.+.+.+.++.||.+||+|..|..+|....|+..++.+||..||.++|+++|. |.+.|.+
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~   75 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDP   75 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCT
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCc
Confidence            57899999999877778999999999999999999999877788999999999999999999998 6666664

>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=99.69  E-value=7.2e-17  Score=90.24  Aligned_cols=66  Identities=30%  Similarity=0.622  Sum_probs=60.2

Q ss_pred             ccccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNF   72 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~   72 (102)
                      +++|.+|++.|.+.+. +.+.++.||.+||+|..|.++|..+.|+..++.+||..||.++|+++++.
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~   81 (82)
T 1x63_A           15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS   81 (82)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSC
T ss_pred             CCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCCC
Confidence            4699999999987665 78999999999999999999999888999999999999999999998763

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

Probab=99.68  E-value=4.3e-17  Score=89.11  Aligned_cols=66  Identities=17%  Similarity=0.395  Sum_probs=58.5

Q ss_pred             CCccccccccceeec---CceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCC
Q 034188            5 GTQQKCKVCEKTVYP---VEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG   70 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~---~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c   70 (102)
                      .++++|..|++.|..   .+.+.+.++.||.+||+|..|..+|....|+..++++||..||.++|++++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            346799999999975   245889999999999999999999987778889999999999999998865

>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=99.68  E-value=6.1e-17  Score=90.12  Aligned_cols=64  Identities=25%  Similarity=0.612  Sum_probs=59.2

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      +++|++|++.|.+ +.+.+.++.||..||+|..|..+|..+.++..++++||+.||.++|+++|.
T Consensus        15 ~~~C~~C~~~I~~-~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~   78 (80)
T 1x3h_A           15 SPKCGGCNRPVLE-NYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPS   78 (80)
T ss_dssp             SCBCTTTCCBCCS-SCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCC
T ss_pred             CCccccCCCeecc-eeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCC
Confidence            4689999999975 568999999999999999999999887899999999999999999999885

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

Probab=99.68  E-value=2.5e-17  Score=91.63  Aligned_cols=66  Identities=18%  Similarity=0.402  Sum_probs=59.2

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      ++.++|..|++.|.. +.+.+.++.||.+||+|..|..+|....|+..++.+||..||.++|++++.
T Consensus        13 ~~~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           13 QKLPMCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCCCSSSCCCCCS-SCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCCCccccCCCCccC-cEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            345799999999975 578999999999999999999999877799999999999999999999764

>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=4.6e-16  Score=99.43  Aligned_cols=71  Identities=34%  Similarity=0.729  Sum_probs=66.1

Q ss_pred             CCccCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         1 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      |+..++.++|..|++.|.+.+.+.+.++.||..||+|..|..+|....|+.+++.+||+.||.++|+++|.
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~   71 (192)
T 1b8t_A            1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGK   71 (192)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCC
T ss_pred             CCCCCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCcccc
Confidence            66778889999999999877888899999999999999999999988899999999999999999999986

>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=99.66  E-value=1.7e-16  Score=88.60  Aligned_cols=66  Identities=26%  Similarity=0.556  Sum_probs=58.1

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEee-CCeeeeHHHHHHHhCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~~~~~~~~~~c~   71 (102)
                      ...++|+.|++.|. .+.+.+.++.||+.||+|..|..+|....|... ++.+||..||.++|+++|.
T Consensus        13 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~   79 (81)
T 2dlo_A           13 ATLEKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPS   79 (81)
T ss_dssp             SSCCBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSC
T ss_pred             cCCCccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCC
Confidence            45679999999997 456899999999999999999999986666665 7899999999999999885

>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=99.65  E-value=2e-16  Score=88.02  Aligned_cols=65  Identities=23%  Similarity=0.556  Sum_probs=59.1

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNF   72 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~   72 (102)
                      +++|..|++.|.+ +.+.+.++.||..||+|..|.++|....|+..++.+||..||.++|+++|+.
T Consensus        15 ~~~C~~C~~~I~~-~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           15 APRCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             SCCCTTTCCCCCS-CCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CCcCCCCCCEecC-cEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            5789999999965 5689999999999999999999998778889999999999999999998863

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

Probab=99.65  E-value=2.7e-16  Score=85.66  Aligned_cols=62  Identities=29%  Similarity=0.766  Sum_probs=56.3

Q ss_pred             CccccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188            6 TQQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      ..++|++|++.|...+. +.+.++.||..||+|..|+.+|..+.++..++++||+.||.++|+
T Consensus        10 ~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             TTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             CCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            45699999999987775 689999999999999999999998888999999999999999875

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

Probab=99.65  E-value=3.2e-17  Score=91.90  Aligned_cols=66  Identities=32%  Similarity=0.770  Sum_probs=57.9

Q ss_pred             cCCccccccccceeecCceEEecCccccccCcccccccccCcCcceE--eeCCeeeeHHHHHHHhCCC
Q 034188            4 IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQLFKES   69 (102)
Q Consensus         4 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~--~~~~~~~C~~~~~~~~~~~   69 (102)
                      .++.++|.+|++.|++.+.+.++++.||..||+|..|..+|....|+  .+++++||+.||.++|+..
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~   79 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGP   79 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCC
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCC
Confidence            35667999999999888888899999999999999999999988777  3699999999998877653

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

Probab=99.64  E-value=3.4e-16  Score=87.12  Aligned_cols=65  Identities=22%  Similarity=0.462  Sum_probs=56.9

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      .+.++|..|++.|. .+.+.+.++.||.+||+|..|..+|... ++..++.+||..||.++|++.++
T Consensus        13 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           13 LGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTAD-ARELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTT-CEEETTEEECHHHHHTTSCCSSC
T ss_pred             cCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCC-CEeECCEEeCHHHHHHhCCCCCC
Confidence            44679999999997 5568899999999999999999999866 45889999999999999988553

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

Probab=99.63  E-value=5.8e-16  Score=84.54  Aligned_cols=63  Identities=24%  Similarity=0.529  Sum_probs=56.4

Q ss_pred             CccccccccceeecCc-eEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCC
Q 034188            6 TQQKCKVCEKTVYPVE-QLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE   68 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~-~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~   68 (102)
                      +.++|.+|++.|...+ .+.+.++.||..||+|..|..+|....|+..++.+||..||.++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~~   67 (72)
T 1x61_A            4 GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES   67 (72)
T ss_dssp             CCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHHT
T ss_pred             CCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHcc
Confidence            4579999999998654 58999999999999999999999876799999999999999999864

>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=99.63  E-value=1.1e-16  Score=89.44  Aligned_cols=65  Identities=18%  Similarity=0.552  Sum_probs=58.3

Q ss_pred             ccccccccceeec-CceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            7 QQKCKVCEKTVYP-VEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         7 ~~~C~~C~~~i~~-~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      +++|+.|++.|.+ ...+.+.++.||..||+|..|.++|....|+..++.+||..||.++|+++|.
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~   80 (82)
T 2ehe_A           15 ANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPS   80 (82)
T ss_dssp             SCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSC
T ss_pred             CCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCC
Confidence            4689999999974 3457889999999999999999999977888999999999999999999875

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

Probab=99.62  E-value=2e-15  Score=96.40  Aligned_cols=69  Identities=30%  Similarity=0.714  Sum_probs=62.6

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFN   73 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~   73 (102)
                      ++.++|..|++.|.+.+.+.+.++.||.+||+|..|..+|....|+..++++||+.||.++|+++|.-+
T Consensus       113 ~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C  181 (192)
T 1b8t_A          113 GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGF  181 (192)
T ss_dssp             CCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCC
T ss_pred             CCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCC
Confidence            345689999999987778889999999999999999999988789999999999999999999999843

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

Probab=99.62  E-value=1.5e-15  Score=96.36  Aligned_cols=74  Identities=23%  Similarity=0.380  Sum_probs=64.1

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSP   79 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~   79 (102)
                      .+.++|..|++.|...+.+.+.++.||..||+|..|..+|.... +.+++.+||..||.++|+++|. |.+.|.+.
T Consensus        58 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~  132 (182)
T 2jtn_A           58 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPT  132 (182)
T ss_dssp             CSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCC-EEETTEEECHHHHHHTTSCCCTTTCCCCCSS
T ss_pred             CCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCc-eeECCEeeecCccccccccccccCCCccCCC
Confidence            44579999999998766678999999999999999999998765 5789999999999999999998 66566553

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

Probab=99.62  E-value=1e-15  Score=92.25  Aligned_cols=72  Identities=19%  Similarity=0.379  Sum_probs=62.8

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcC--cceEeeCCeeeeHHHHHHHhCC--CCC-CCCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKE--SGN-FNKNFQS   78 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~~--~c~-~~~~~~~   78 (102)
                      .++|..|++.|.+.+.+.+.++.||.+||+|..|..+|..  ..|+..++.+||..||.++|++  +|. |.+.|.+
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~   78 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRA   78 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECT
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCc
Confidence            4689999999987656899999999999999999999964  4688999999999999999999  888 5555554

>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=99.62  E-value=8.1e-16  Score=96.53  Aligned_cols=74  Identities=23%  Similarity=0.380  Sum_probs=62.5

Q ss_pred             CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCC
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSP   79 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~   79 (102)
                      ++.++|..|++.|.+.+.+.+.++.||..||+|..|..+|.... +.+++.+||..||.++|+++|. |.+.|.+.
T Consensus         4 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~   78 (169)
T 2rgt_A            4 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPT   78 (169)
T ss_dssp             ---CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCTT
T ss_pred             CCCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeecccccccccccccccccccCCC
Confidence            45679999999998766788999999999999999999998765 5789999999999999999998 65556543

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

Probab=99.60  E-value=6.7e-16  Score=92.54  Aligned_cols=61  Identities=25%  Similarity=0.549  Sum_probs=55.0

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcC--cceEeeCCeeeeHHHHHHHhC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      +++|.+|++.|...+.+.+.++.||..||+|..|..+|..  ..|+.+++.+||+.||.++|+
T Consensus        61 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           61 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            4689999999987767899999999999999999999973  468889999999999999885

>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=99.57  E-value=2.6e-15  Score=83.69  Aligned_cols=64  Identities=22%  Similarity=0.503  Sum_probs=55.6

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCc-ceE-eeCCeeeeHHHHHHHhCCCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLS-NYS-SMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~-~~~-~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      +++|..|++.|. .+.+.+.++.||.+||+|..|.++|..+ .|. ..++.+||..||.++|++.++
T Consensus        15 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           15 GEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             SCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             CCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            468999999997 5568899999999999999999999754 455 479999999999999998764

>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=99.56  E-value=3.7e-15  Score=94.97  Aligned_cols=73  Identities=21%  Similarity=0.488  Sum_probs=63.4

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCcC--cceEeeCCeeeeHHHHHHHhCC--CCC-CCCCCCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKE--SGN-FNKNFQS   78 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~~--~c~-~~~~~~~   78 (102)
                      ..++|..|++.|...+.+.+.++.||.+||+|..|..+|..  ..|+.+++.+||..||.++|++  +|. |.+.|.+
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~   81 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPA   81 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECT
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCcccc
Confidence            35689999999987666899999999999999999999986  4688999999999999999998  687 5555654

>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=99.56  E-value=5.8e-15  Score=80.91  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=54.5

Q ss_pred             CccccccccceeecCceEEecCccccccCcccccccccCc-CcceEeeCCeeeeHHHHHHHhCC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLK-LSNYSSMEGVLYCKPHFEQLFKE   68 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~-~~~~~~~~~~~~C~~~~~~~~~~   68 (102)
                      .+++|++|++.|.. +.+.+.++.||++||+|..|..+|. ...|+..++.+||..||..+++.
T Consensus         4 ~~~~C~~C~~~I~~-~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            4 GSSGCDSCEKYITG-RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             SCCSCSSSCCCCSS-CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSS
T ss_pred             CcCCcccCCCEecC-eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcc
Confidence            35799999999965 5678999999999999999999998 45688899999999999887664

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

Probab=99.53  E-value=1.3e-14  Score=77.83  Aligned_cols=58  Identities=22%  Similarity=0.644  Sum_probs=51.8

Q ss_pred             ccccccccceeecC-ceEEecCcccc--ccCcccccccccCcCcceEeeCCeeee-HHHHHH
Q 034188            7 QQKCKVCEKTVYPV-EQLSADGIVYH--KSCFKCSHCKGTLKLSNYSSMEGVLYC-KPHFEQ   64 (102)
Q Consensus         7 ~~~C~~C~~~i~~~-~~~~~~~~~~h--~~Cf~C~~C~~~l~~~~~~~~~~~~~C-~~~~~~   64 (102)
                      +++|++|++.|.+. +.+.+.++.||  .+||+|..|+.+|....|+..++++|| ..||.+
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 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR   63 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhh
Confidence            46899999999864 56899999999  999999999999987789999999999 778754

>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=99.53  E-value=8.9e-15  Score=80.71  Aligned_cols=58  Identities=21%  Similarity=0.566  Sum_probs=52.2

Q ss_pred             ccccccccceeec----CceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHH
Q 034188            7 QQKCKVCEKTVYP----VEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   64 (102)
Q Consensus         7 ~~~C~~C~~~i~~----~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~   64 (102)
                      +++|++|++.|.+    .+.+.+.++.||..||+|..|.++|....|+..++.+||..||.+
T Consensus        15 ~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           15 AKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             CccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            4689999999984    356899999999999999999999987778899999999999865

>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=99.41  E-value=1.4e-13  Score=76.63  Aligned_cols=62  Identities=21%  Similarity=0.427  Sum_probs=51.8

Q ss_pred             ccccccccceeecCceEEecCccccccCcccccccccCcCcceEee-CCeeeeHHHHHHHhCCC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHFEQLFKES   69 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~~~~~~~~~~   69 (102)
                      +++|+.|++.|. .+.+.+.++.||.+||+|..|.++|..+.++.. ++.+||..||.+.++..
T Consensus        15 ~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~~~   77 (81)
T 1v6g_A           15 GTRCFSCDQFIE-GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVSG   77 (81)
T ss_dssp             CCBCTTTCCBCC-SCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSSCC
T ss_pred             CCcCccccCEec-cceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCCCC
Confidence            469999999997 567899999999999999999999987766654 55679999997765543

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

Probab=99.38  E-value=3.6e-13  Score=81.06  Aligned_cols=61  Identities=25%  Similarity=0.603  Sum_probs=53.9

Q ss_pred             ccccccceeecCc-eEEecCccccccCcccccccccCcC-cceEeeCCeeeeHHHHHHHhCCC
Q 034188            9 KCKVCEKTVYPVE-QLSADGIVYHKSCFKCSHCKGTLKL-SNYSSMEGVLYCKPHFEQLFKES   69 (102)
Q Consensus         9 ~C~~C~~~i~~~~-~~~~~~~~~h~~Cf~C~~C~~~l~~-~~~~~~~~~~~C~~~~~~~~~~~   69 (102)
                      +|..|++.|...+ .+.+.++.||+.||+|..|.++|.. ..|+..++++||..||.++|+++
T Consensus        68 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~~  130 (131)
T 2xjy_A           68 LCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN  130 (131)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHHH
T ss_pred             ChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhcc
Confidence            8999999997766 4789999999999999999999964 45888999999999999988754

>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=99.29  E-value=1.9e-12  Score=82.40  Aligned_cols=63  Identities=27%  Similarity=0.653  Sum_probs=53.1

Q ss_pred             ccccccceeecCce-EEecCccccccCcccccccccCcCc-ceEeeCCeeeeHHHHHHHhCCCCC
Q 034188            9 KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLS-NYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus         9 ~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      +|..|++.|...+. +.+.++.||..||+|..|.++|..+ .|+..++++||..||.++|+++|.
T Consensus        71 ~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~  135 (188)
T 1rut_X           71 ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHL  135 (188)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC----
T ss_pred             ccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhccccc
Confidence            79999999987664 7899999999999999999999644 588889999999999999988775

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

Probab=99.28  E-value=3.4e-12  Score=76.29  Aligned_cols=60  Identities=22%  Similarity=0.625  Sum_probs=52.9

Q ss_pred             ccccccccceeecCc-eEEecCcccc--ccCcccccccccCcCcceEeeCCeeeeHHHHHHHh
Q 034188            7 QQKCKVCEKTVYPVE-QLSADGIVYH--KSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   66 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~-~~~~~~~~~h--~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~   66 (102)
                      +++|.+|++.|.+.+ .+.+.++.||  ++||+|..|.++|....|+..++++||..++.++|
T Consensus        63 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           63 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             CCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             CccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence            468999999998654 4899999999  99999999999998767888999999998887765

>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=99.16  E-value=3e-11  Score=75.61  Aligned_cols=63  Identities=29%  Similarity=0.613  Sum_probs=53.2

Q ss_pred             ccccccccceeecCce-EEecCccccccCcccccccccCcCc-ceEe-eCCeeeeHHHHHHHhCCC
Q 034188            7 QQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLS-NYSS-MEGVLYCKPHFEQLFKES   69 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~-~~~~-~~~~~~C~~~~~~~~~~~   69 (102)
                      +++|..|++.|...+. +.+.++.||..||+|..|..+|..+ .|+. .++++||..||.+++...
T Consensus        65 ~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~  130 (169)
T 2rgt_A           65 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG  130 (169)
T ss_dssp             SCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC
T ss_pred             cccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhcc
Confidence            4689999999987665 5899999999999999999999855 4544 589999999999887653

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

Probab=99.07  E-value=1e-10  Score=73.92  Aligned_cols=59  Identities=31%  Similarity=0.674  Sum_probs=49.9

Q ss_pred             ccccccccceeecCce-EEecCccccccCcccccccccCcCcc-eEe-eCCeeeeHHHHHHH
Q 034188            7 QQKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSN-YSS-MEGVLYCKPHFEQL   65 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~-~~~-~~~~~~C~~~~~~~   65 (102)
                      .++|..|++.|...+. +.+.++.||..||+|..|.++|..+. |+. .++++||..||.++
T Consensus       119 ~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~  180 (182)
T 2jtn_A          119 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA  180 (182)
T ss_dssp             SCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHH
T ss_pred             ccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHh
Confidence            4689999999987664 58999999999999999999998554 544 58999999999765

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

Probab=98.42  E-value=5.1e-08  Score=44.54  Aligned_cols=29  Identities=38%  Similarity=0.894  Sum_probs=26.7

Q ss_pred             ccccccccceeecCceEEecCccccccCc
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      .++|..|++.|++.+.+.+.++.||..||
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            35899999999999999999999999997

>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=98.23  E-value=4.6e-07  Score=51.72  Aligned_cols=35  Identities=31%  Similarity=0.645  Sum_probs=30.4

Q ss_pred             ccccccccceeecCc-eEEecCccccccCccccccc
Q 034188            7 QQKCKVCEKTVYPVE-QLSADGIVYHKSCFKCSHCK   41 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~-~~~~~~~~~h~~Cf~C~~C~   41 (102)
                      .++|..|++.|.+.+ .+.+.++.||++||.|..|+
T Consensus        66 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           66 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             CCBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             CCccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence            468999999997655 58999999999999999884

>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=96.46  E-value=0.00039  Score=40.85  Aligned_cols=62  Identities=11%  Similarity=0.212  Sum_probs=37.1

Q ss_pred             ccccccceeec--CceEEecCccccccCc--------ccccccccCc-------------CcceEeeCCeeeeHHHHHHH
Q 034188            9 KCKVCEKTVYP--VEQLSADGIVYHKSCF--------KCSHCKGTLK-------------LSNYSSMEGVLYCKPHFEQL   65 (102)
Q Consensus         9 ~C~~C~~~i~~--~~~~~~~~~~~h~~Cf--------~C~~C~~~l~-------------~~~~~~~~~~~~C~~~~~~~   65 (102)
                      +|..|++.+..  ...+...++.|...||        +|..|..++.             ...|+..++++||..||.++
T Consensus        34 ~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~~~~g~~~l~g~~f~~~~~~~yC~~~~~~~  113 (122)
T 1m3v_A           34 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQF  113 (122)
T ss_dssp             CCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEESSSSSSSSCCSCTTCCTTCCCCEECTTTTT
T ss_pred             CcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchheEEcCCcCCCCCccEecCCEeEccCcchhc
Confidence            46666666631  1124555555554444        4555655544             23466778999999998877


Q ss_pred             hCCCC
Q 034188           66 FKESG   70 (102)
Q Consensus        66 ~~~~c   70 (102)
                      +...+
T Consensus       114 ~~~~g  118 (122)
T 1m3v_A          114 DAANG  118 (122)
T ss_dssp             TCCSC
T ss_pred             hhhcC
Confidence            65543

>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=95.42  E-value=0.0019  Score=34.83  Aligned_cols=18  Identities=17%  Similarity=0.174  Sum_probs=8.5

Q ss_pred             CeeeeHHHHHHHhCCCCC
Q 034188           54 GVLYCKPHFEQLFKESGN   71 (102)
Q Consensus        54 ~~~~C~~~~~~~~~~~c~   71 (102)
                      |++||+.||.++|+++|.
T Consensus         2 g~~yC~~cy~~~~~~~C~   19 (80)
T 2cuq_A            2 SSGSSGPCYENKFAPRCA   19 (80)
T ss_dssp             CCCSCCCCCCCCSSCCCT
T ss_pred             CcEEcHHHHccccCCcCC
Confidence            344444444444444444

>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=95.38  E-value=0.0025  Score=34.54  Aligned_cols=25  Identities=8%  Similarity=0.134  Sum_probs=14.1

Q ss_pred             CCeeeeHHHHHHHhCCCCC-CCCCCC
Q 034188           53 EGVLYCKPHFEQLFKESGN-FNKNFQ   77 (102)
Q Consensus        53 ~~~~~C~~~~~~~~~~~c~-~~~~~~   77 (102)
                      +|++||+.||.++|+++|. |.+.|.
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~   26 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIG   26 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCC
T ss_pred             CCceechhHhCcccCCcCccCCCccc
Confidence            3456666666666666665 444444

>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=95.14  E-value=0.0035  Score=33.88  Aligned_cols=23  Identities=9%  Similarity=-0.117  Sum_probs=11.3

Q ss_pred             eeeeHHHHHHHhCCCCC-CCCCCC
Q 034188           55 VLYCKPHFEQLFKESGN-FNKNFQ   77 (102)
Q Consensus        55 ~~~C~~~~~~~~~~~c~-~~~~~~   77 (102)
                      .+||+.||.++|+++|. |.+.|.
T Consensus         3 ~~yC~~~y~~~~~~~C~~C~~~I~   26 (81)
T 1x6a_A            3 SGSSGKDYWGKFGEFCHGCSLLMT   26 (81)
T ss_dssp             CCCCCCCSSCCSSCBCTTTCCBCC
T ss_pred             CccchhHHhhhcCCcCccCCCCcC
Confidence            44555555555555554 333343

>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=94.70  E-value=0.0028  Score=33.90  Aligned_cols=9  Identities=33%  Similarity=1.084  Sum_probs=4.9

Q ss_pred             cccccccCc
Q 034188           37 CSHCKGTLK   45 (102)
Q Consensus        37 C~~C~~~l~   45 (102)
                      |..|..++.
T Consensus        18 C~~C~~~I~   26 (77)
T 2egq_A           18 CAGCKNPIT   26 (77)
T ss_dssp             CSSSCCCCC
T ss_pred             CcccCCccc
Confidence            555555554

>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=94.38  E-value=0.0032  Score=33.89  Aligned_cols=25  Identities=24%  Similarity=0.445  Sum_probs=11.9

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPH   61 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~   61 (102)
                      +|..|..++.. .+....++.|-..|
T Consensus        17 ~C~~C~~~I~~-~~v~a~~~~~H~~C   41 (80)
T 1x3h_A           17 KCGGCNRPVLE-NYLSAMDTVWHPEC   41 (80)
T ss_dssp             BCTTTCCBCCS-SCEEETTEEECTTT
T ss_pred             ccccCCCeecc-eeEEECCCeEecCc
Confidence            45666666543 33333445544333

>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=94.00  E-value=0.0082  Score=32.38  Aligned_cols=25  Identities=20%  Similarity=0.393  Sum_probs=12.1

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPH   61 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~   61 (102)
                      +|..|..++. .......+..|-..|
T Consensus        17 ~C~~C~~~I~-~~~v~a~~~~wH~~C   41 (81)
T 1v6g_A           17 RCFSCDQFIE-GEVVSALGKTYHPDC   41 (81)
T ss_dssp             BCTTTCCBCC-SCCEEETTEEECTTT
T ss_pred             cCccccCEec-cceEEECCceeCccC
Confidence            4566666554 233333455554444

>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=92.75  E-value=0.01  Score=32.02  Aligned_cols=26  Identities=19%  Similarity=0.447  Sum_probs=13.0

Q ss_pred             ccccccccCcCcc-eEeeCCeeeeHHH
Q 034188           36 KCSHCKGTLKLSN-YSSMEGVLYCKPH   61 (102)
Q Consensus        36 ~C~~C~~~l~~~~-~~~~~~~~~C~~~   61 (102)
                      .|..|...+.... +....++.|-..|
T Consensus        17 ~C~~C~~~I~~~~~~~~a~~~~~H~~C   43 (82)
T 1x63_A           17 KCKGCFKAIVAGDQNVEYKGTVWHKDC   43 (82)
T ss_dssp             BCSSSCCBCCSSSCEEECSSCEEETTT
T ss_pred             cCccCCcccccCceEEEECcccccccc
Confidence            4666666665332 2333455554444

>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=91.33  E-value=0.03  Score=32.19  Aligned_cols=61  Identities=10%  Similarity=0.035  Sum_probs=37.2

Q ss_pred             cccccccceeec--CceEEecCccccccCc---------ccc-----cccccCc-CcceEeeCCeeeeHHHHHHHhCC
Q 034188            8 QKCKVCEKTVYP--VEQLSADGIVYHKSCF---------KCS-----HCKGTLK-LSNYSSMEGVLYCKPHFEQLFKE   68 (102)
Q Consensus         8 ~~C~~C~~~i~~--~~~~~~~~~~~h~~Cf---------~C~-----~C~~~l~-~~~~~~~~~~~~C~~~~~~~~~~   68 (102)
                      -+|..|++.+..  ...+...+++|...||         .|.     .|...+. ...|...++++||..|+.++.+.
T Consensus        31 F~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~~~~~~~~~~~~~g~~f~~~~~~~~C~~~~~~~~~~  108 (114)
T 1j2o_A           31 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAA  108 (114)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBSCSCCCSSCSSTTSSBCCCSSSCCCEEEECTTCCCT
T ss_pred             CcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCCCceeEcCCccCCCCeeEEcCCEeecchhhhccccc
Confidence            478889998853  1234556666654433         221     2333433 33577789999999998776544

---

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	102
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	2e-18
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	1e-12
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	4e-12
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	4e-11
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	3e-05
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	6e-05
d1zfoa_	30	g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 982	5e-04
d1a7ia1	28	g.39.1.3 (A:8-35) Cysteine-rich (intestinal) prote	0.002

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 42

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

 Score = 69.7 bits (171), Expect = 2e-18
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNF 76
          +CS+C   L L  Y+S+ G +YCKPHF QLFK  GN+++ F
Sbjct: 1  RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF 41

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

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

 Score = 55.2 bits (133), Expect = 1e-12
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 5  GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF 35
          G    C +C + +Y +E+L  +G  +H+SCF
Sbjct: 6  GAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 35

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

 Score = 53.6 bits (129), Expect = 4e-12
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 5  GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF 35
            ++ C  C+KTVYP+E+L A+  V+H SCF
Sbjct: 5  PARETCVECQKTVYPMERLLANQQVFHISCF 35

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 43

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

 Score = 51.4 bits (123), Expect = 4e-11
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 2  SFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF 35
            +G    C  C + VY  E++   G  +HKSCF
Sbjct: 10 QKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

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

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

 Score = 36.1 bits (83), Expect = 3e-05
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 1  MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF 35
          M   G  +KC VC+K VY  E++  +G  +HKSCF
Sbjct: 1  MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 35

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 6e-05
 Identities = 13/26 (50%), Positives = 18/26 (69%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSC 34
          KC  C+KTVY  E++S+ G  +HK C
Sbjct: 4  KCPKCDKTVYFAEKVSSLGKDWHKFC 29

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

 Score = 32.6 bits (74), Expect = 5e-04
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 8  QKCKVCEKTVYPVEQLSADGIVYHKSCF 35
            C  C K VYP E+++     +HK+CF
Sbjct: 3  PNCARCGKIVYPTEKVNCLDKFWHKACF 30

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]} Length = 28

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

 Score = 31.1 bits (70), Expect = 0.002
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 9  KCKVCEKTVYPVEQLSADGIVYHKSCF 35
          KC  C +TVY  E++  DG  +H+ CF
Sbjct: 2  KCGACGRTVYHAEEVQCDGRSFHRCCF 28

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	102
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.93
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.93
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.7
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.66
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.57
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.5
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.48
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.48
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.46
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.43
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.42
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.34
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.33
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.3
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.3
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.28
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.27
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.24
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.23
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.23
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.23
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.21
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.21
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.2
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.13
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.12
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.06
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.04
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.04
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	98.04
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.01
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.97
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.97
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.96
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.95
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.9
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.88
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.77
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.76
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.76
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.7
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.62
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.53
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.4
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.39
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.34
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.29
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.27
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.24
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	97.12
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.04
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.73
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.2
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.09
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	95.55
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.44
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.43
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.37
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.01
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.46
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.12
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	91.51
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	91.12
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	91.0
d2co8a1	33	Nedd9 interacting protein with calponin homology,	90.77
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	87.13
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	82.27

>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=98.93  E-value=4.5e-10  Score=51.53  Aligned_cols=34  Identities=29%  Similarity=0.696  Sum_probs=32.3

Q ss_pred             cccccccccCcCcceEeeCCeeeeHHHHHHHhCC
Q 034188           35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE   68 (102)
Q Consensus        35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~   68 (102)
                      |.|..|.+++....|+.++|++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            6899999999988999999999999999999987

>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=98.93  E-value=3.6e-10  Score=53.53  Aligned_cols=42  Identities=50%  Similarity=1.143  Sum_probs=38.7

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCCCCCC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQ   77 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~~~~~   77 (102)
                      +|..|+..|+.+.|+..+|.+||+.||.++|+++++++++|.
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny~~gfg   42 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFG   42 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCCCCCCC
Confidence            588999999999999999999999999999999999988763

>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=98.70  E-value=4.2e-09  Score=50.34  Aligned_cols=32  Identities=38%  Similarity=0.882  Sum_probs=29.6

Q ss_pred             cCCccccccccceeecCceEEecCccccccCc
Q 034188            4 IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         4 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      .++.++|..|++.|+..|++.+.++.||..||
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            46678999999999999999999999999997

>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=98.66  E-value=2e-08  Score=48.87  Aligned_cols=36  Identities=25%  Similarity=0.689  Sum_probs=33.3

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      +|..|++.|.......+++++||+.||.++|+|++.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~   36 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF   36 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCcc
Confidence            588999999988888899999999999999999876

>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=98.57  E-value=1.1e-08  Score=46.82  Aligned_cols=32  Identities=34%  Similarity=0.924  Sum_probs=29.5

Q ss_pred             cCCccccccccceeecCceEEecCccccccCc
Q 034188            4 IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         4 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      .++..+|..|++.|++.+++.+.++.||..||
T Consensus         5 ~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           5 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            45678999999999999999999999999997

>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=98.50  E-value=1.1e-08  Score=44.01  Aligned_cols=28  Identities=39%  Similarity=0.917  Sum_probs=26.5

Q ss_pred             cccccccceeecCceEEecCccccccCc
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      +.|++|++.+++.+.+...++.||..||
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            5799999999999999999999999997

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.48  E-value=2.8e-08  Score=45.37  Aligned_cols=29  Identities=38%  Similarity=0.698  Sum_probs=25.6

Q ss_pred             CccccccccceeecCceEEecCccccccCc
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      -+++|+.|++.|. +..+.++++.||++||
T Consensus         7 fapkC~~C~~~I~-g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           7 FSPKCGGCNRPVL-ENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CSCBCTTTCCBCC-SSCEEETTEEECTTTC
T ss_pred             hChhhhhcCCccc-chheeecCCccCcccC
Confidence            3679999999994 5679999999999997

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

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

Probab=98.48  E-value=3.9e-08  Score=44.70  Aligned_cols=31  Identities=48%  Similarity=0.981  Sum_probs=28.5

Q ss_pred             CCccccccccceeecCceEEecCccccccCc
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      +...+|..|++.+++.+++.+.++.||..||
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            4457999999999999999999999999997

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.46  E-value=3.8e-08  Score=42.76  Aligned_cols=28  Identities=46%  Similarity=0.854  Sum_probs=26.1

Q ss_pred             cccccccceeecCceEEecCccccccCc
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      ++|++|++.+++.|.+...|+.||..|+
T Consensus         3 ~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           3 SKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CcCCCCCCceeeHHhhccCCcccccccC
Confidence            5899999999999999999999999884

>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=98.43  E-value=1.3e-07  Score=41.90  Aligned_cols=31  Identities=16%  Similarity=0.585  Sum_probs=28.2

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHh
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   66 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~   66 (102)
                      .|..|.+++..+.|+..++++||+.||.++.
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhc
Confidence            4889999999999999999999999998864

>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=98.42  E-value=1.4e-07  Score=45.35  Aligned_cols=36  Identities=33%  Similarity=0.715  Sum_probs=32.9

Q ss_pred             ccccccccCcCcceEeeCCeeee-HHHHHHHhCCCCC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYC-KPHFEQLFKESGN   71 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C-~~~~~~~~~~~c~   71 (102)
                      +|..|++.|..+....+++++|| +.||..+|+|++.
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~   37 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF   37 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCcc
Confidence            58899999999999999999999 8899999999764

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

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

Probab=98.34  E-value=9.6e-08  Score=43.85  Aligned_cols=29  Identities=41%  Similarity=0.832  Sum_probs=26.7

Q ss_pred             ccccccccceeecCce-EEecCccccccCc
Q 034188            7 QQKCKVCEKTVYPVEQ-LSADGIVYHKSCF   35 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf   35 (102)
                      +++|.+|++.|.++.+ +.+.++.||..||
T Consensus         8 a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           8 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CcccccCCCccCCCCeEeEeCCccchhccC
Confidence            5799999999998886 8999999999997

>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=98.33  E-value=4.5e-07  Score=46.40  Aligned_cols=36  Identities=22%  Similarity=0.544  Sum_probs=32.9

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   71 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~   71 (102)
                      .|..|++.|.......+++++||+.||-++|+|++-
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~   36 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGK   36 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCcc
Confidence            388999999998899999999999999999999875

>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=98.30  E-value=2.5e-07  Score=40.61  Aligned_cols=35  Identities=46%  Similarity=0.919  Sum_probs=30.9

Q ss_pred             CCccCCccccccccceeecCceEEecCccccccCc
Q 034188            1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         1 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      |+--+|..+|+.|.+.++.++-+...++.||..||
T Consensus         1 mpn~ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCccCCCceeccccceEeeeeeeeecCcccccccC
Confidence            45456778999999999999999999999999987

>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=98.30  E-value=2e-07  Score=40.49  Aligned_cols=28  Identities=21%  Similarity=0.399  Sum_probs=25.2

Q ss_pred             ccccccccceeecCceEEecCccccccC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSC   34 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~C   34 (102)
                      ...|++|++.|.+...+.+.++.||..|
T Consensus         3 ~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           3 LLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            4579999999988888999999999877

>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=98.28  E-value=4e-07  Score=39.53  Aligned_cols=31  Identities=35%  Similarity=0.815  Sum_probs=27.3

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      +|..|...|. +.|-.++|.+||+.+|+..|+
T Consensus         1 kC~~C~~vL~-gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILT-GEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCS-SCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCcccc-ceeecCCCCcccHHHHHHhcC
Confidence            4788998886 689999999999999999885

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=2.3e-07  Score=41.41  Aligned_cols=31  Identities=26%  Similarity=0.479  Sum_probs=27.6

Q ss_pred             CCccccccccceeecCceEEecCccccccCc
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      .++..|++|++.|..+..+.+.++.||..||
T Consensus         6 ~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           6 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cCCccccccchhhhCCceeeeeecceeeeeC
Confidence            4567899999999887778999999999997

>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=98.24  E-value=5.1e-07  Score=39.71  Aligned_cols=32  Identities=22%  Similarity=0.626  Sum_probs=28.9

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      .|..|.++|.+..|..+++++||-.||..+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            37789999998899999999999999999875

>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=98.23  E-value=8.7e-07  Score=39.02  Aligned_cols=34  Identities=29%  Similarity=0.750  Sum_probs=30.8

Q ss_pred             cccccccccCcCcceEeeCCeeeeHHHHHHHhCC
Q 034188           35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE   68 (102)
Q Consensus        35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~   68 (102)
                      |.|..|.+++-+...+.+.|..||+.+|.++|+.
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhcc
Confidence            6899999999877899999999999999999874

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.23  E-value=3.6e-07  Score=40.99  Aligned_cols=32  Identities=34%  Similarity=0.830  Sum_probs=27.0

Q ss_pred             ccCCccccccccceeecCceEEecCccccccCc
Q 034188            3 FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         3 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      |..+..+|..|++.|.+ ..+++.++.||+.||
T Consensus         4 y~~tlEkC~~C~~~I~d-riLrA~Gk~yHP~CF   35 (35)
T d2dloa1           4 YVATLEKCATCSQPILD-RILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCSSCCBCTTTCCBCCS-CCEEETTEEECTTTC
T ss_pred             HHHHHHHHHHhchHHHH-HHHHHhCCCCCCCCC
Confidence            45567899999999964 358999999999997

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

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.23  E-value=2.7e-07  Score=40.17  Aligned_cols=28  Identities=21%  Similarity=0.437  Sum_probs=25.3

Q ss_pred             cccccccceeecCceEEecCccccccCc
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      ..|++|+..|.+...+.+.++.||..|.
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            4799999999988889999999999884

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.21  E-value=3.5e-07  Score=43.39  Aligned_cols=30  Identities=23%  Similarity=0.385  Sum_probs=25.4

Q ss_pred             CCccccccccceeecCceEEecCccccccCc
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      ...+.|+.|++.| .+..+.++++.||+++|
T Consensus        16 ~r~P~C~~C~~pI-~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          16 KRTPMCAHCNQVI-RGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TCCCBBSSSCCBC-CSCEEEETTEEECTTTC
T ss_pred             CCCeeccccCCcc-cCceeeecCCccCcCCC
Confidence            3447899999999 45568999999999987

>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=98.21  E-value=7.4e-07  Score=38.87  Aligned_cols=31  Identities=35%  Similarity=0.936  Sum_probs=28.1

Q ss_pred             cccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      |..|+.+|....|....+.+||+.||.+.|+
T Consensus         2 Ca~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           2 CAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             CSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             cccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            7789999999999999999999999988764

>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=98.20  E-value=3.9e-07  Score=39.90  Aligned_cols=28  Identities=36%  Similarity=0.818  Sum_probs=25.3

Q ss_pred             cccccccceeecCce-EEecCccccccCc
Q 034188            8 QKCKVCEKTVYPVEQ-LSADGIVYHKSCF   35 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf   35 (102)
                      ..|++|++.|.+.+. +.+++.+||+.||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            369999999998886 7999999999997

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=1.6e-06  Score=37.66  Aligned_cols=32  Identities=28%  Similarity=0.635  Sum_probs=29.0

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      .|..|+++|.+..|..++..+||..||..+|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            37889999998899999999999999998875

>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=98.12  E-value=6e-07  Score=37.77  Aligned_cols=27  Identities=37%  Similarity=0.895  Sum_probs=25.0

Q ss_pred             cccccccceeecCceEEecCccccccC
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSC   34 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~C   34 (102)
                      .+|.+|++.++..+++...++.||..|
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            589999999999999999999999876

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.06  E-value=3.9e-06  Score=36.57  Aligned_cols=31  Identities=16%  Similarity=0.598  Sum_probs=28.5

Q ss_pred             cccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      |..|..+++...|..+++..||..||+++|+
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCCceEeecchhhcC
Confidence            7889999998889999999999999999875

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

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

Probab=98.04  E-value=2.4e-06  Score=36.35  Aligned_cols=30  Identities=30%  Similarity=0.848  Sum_probs=26.7

Q ss_pred             cccccccccCcCcceEeeCCeeeeHHHHHH
Q 034188           35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   64 (102)
Q Consensus        35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~   64 (102)
                      |+|..|++.|.......++|.+||+.||.+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            789999999987778889999999999854

>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=98.04  E-value=9.5e-07  Score=36.76  Aligned_cols=26  Identities=35%  Similarity=0.954  Sum_probs=23.8

Q ss_pred             cccccceeecCce-EEecCccccccCc
Q 034188           10 CKVCEKTVYPVEQ-LSADGIVYHKSCF   35 (102)
Q Consensus        10 C~~C~~~i~~~~~-~~~~~~~~h~~Cf   35 (102)
                      |..|.+.|+++.+ +...+..||..||
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            7789999999886 8999999999997

>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=98.01  E-value=1.2e-06  Score=39.09  Aligned_cols=28  Identities=21%  Similarity=0.571  Sum_probs=24.5

Q ss_pred             ccccccccceeecCceEEecCccccccCc
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      +.+|..|++.|..+ .+...+..||.+||
T Consensus         8 a~~C~~Ckk~It~G-GvtY~dqpWHkeCF   35 (35)
T d2cuqa2           8 APRCARCSKTLTQG-GVTYRDQPWHRECL   35 (35)
T ss_dssp             SCCCTTTCCCCCSC-CEESSSSEECTTTC
T ss_pred             HHHHhhcCCccccC-ceeecCCcchhhhC
Confidence            67999999999654 47999999999997

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=3.9e-06  Score=36.63  Aligned_cols=32  Identities=34%  Similarity=0.784  Sum_probs=27.7

Q ss_pred             ccccccccCcCcceEeeCCeeee-HHHHHHHhC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYC-KPHFEQLFK   67 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C-~~~~~~~~~   67 (102)
                      +|..|++.|..+..+++++++|| ..||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            58889999999999999999999 458887764

>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=97.97  E-value=7.5e-06  Score=35.58  Aligned_cols=31  Identities=32%  Similarity=0.762  Sum_probs=28.4

Q ss_pred             cccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      |..|..+++...|...++..||..||+.+|+
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCcEEEEeccccccC
Confidence            7789999998889999999999999999885

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

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

Probab=97.96  E-value=3.2e-06  Score=36.47  Aligned_cols=31  Identities=19%  Similarity=0.596  Sum_probs=27.9

Q ss_pred             cccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      |..|.+.|.....+.+++++||+.||.++|+
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7889999998888999999999999998874

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.95  E-value=1.1e-06  Score=36.42  Aligned_cols=26  Identities=38%  Similarity=0.919  Sum_probs=23.6

Q ss_pred             cccccceeecCce-EEecCccccccCc
Q 034188           10 CKVCEKTVYPVEQ-LSADGIVYHKSCF   35 (102)
Q Consensus        10 C~~C~~~i~~~~~-~~~~~~~~h~~Cf   35 (102)
                      |..|.+.|+++.+ +...+..||..||
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            7789999999886 8999999999997

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.77  E-value=4.2e-06  Score=36.31  Aligned_cols=28  Identities=18%  Similarity=0.317  Sum_probs=23.8

Q ss_pred             CCccccccccceeecCceEEecCcccccc
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKS   33 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~   33 (102)
                      ++.++|+.|+.+|. ...+.++++.||++
T Consensus         3 mg~p~C~~C~~PI~-~~~vtAlgk~WHpE   30 (31)
T d1u5sb1           3 MGVPICGACRRPIE-GRVVNAMGKQWHVE   30 (31)
T ss_dssp             CCCCEETTTTEECC-SCEECCTTSBEETT
T ss_pred             cCCcchhhcCCchh-hhHhhhhccccCCC
Confidence            45679999999995 45689999999986

>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=97.76  E-value=6.7e-06  Score=34.15  Aligned_cols=28  Identities=43%  Similarity=1.054  Sum_probs=25.8

Q ss_pred             cccccccceeecCceEEecCccccccCc
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      ++|+.|.+.++..+-+...++.||..||
T Consensus         1 nkcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           1 NKCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             CBCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             CccccccceEeeeeeeeecCceeccccC
Confidence            4799999999999989999999999987

>d1x62a2 g.39.1.3 (A:8-42) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.76  E-value=9.8e-06  Score=35.64  Aligned_cols=31  Identities=13%  Similarity=0.279  Sum_probs=26.1

Q ss_pred             cCCccccccccceeecCceEEecCccccccCc
Q 034188            4 IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         4 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      .+..+.|..|+.+|. +..+.++++.+|++||
T Consensus         5 ~qklp~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           5 AQKLPMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             cccCccccccCCCcE-eEEEEeccccCCCCCC
Confidence            345578999999994 5578999999999997

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.70  E-value=1.4e-05  Score=37.41  Aligned_cols=30  Identities=20%  Similarity=0.400  Sum_probs=25.6

Q ss_pred             CCccccccccceeecCceEEecCccccccCc
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      +..+.|..|+.+|. +..+.++++.+|++||
T Consensus        16 QkLP~CdkCg~GIV-G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          16 QRMPLCDKCGSGIV-GAVVKARDKYRHPECF   45 (45)
T ss_dssp             CSCCBCTTTCCBCC-SCCEESSSCEECTTTC
T ss_pred             ccCccccccCCCcE-EEEEEeccccCCCCCC
Confidence            44578999999994 5568999999999997

>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=97.62  E-value=4.7e-05  Score=32.51  Aligned_cols=29  Identities=38%  Similarity=0.763  Sum_probs=25.6

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   64 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~   64 (102)
                      .|.+|...|....++..++++||+.|...
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhc
Confidence            48999999998899999999999998654

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.53  E-value=4.8e-05  Score=33.42  Aligned_cols=32  Identities=19%  Similarity=0.449  Sum_probs=27.4

Q ss_pred             ccccccccCcCcceEe-eCCeeeeHHHHHHHhC
Q 034188           36 KCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFK   67 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~-~~~~~~C~~~~~~~~~   67 (102)
                      .|.+|+..|.+..|.. ..+++||-.+|.++|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            4788999998877776 5999999999999885

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.40  E-value=0.00018  Score=30.36  Aligned_cols=32  Identities=25%  Similarity=0.559  Sum_probs=28.2

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHHhC
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~   67 (102)
                      .|+.|...+..+.|+..+...||-.|++.+|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            37889888988899999999999999988874

>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=97.39  E-value=3.7e-05  Score=31.64  Aligned_cols=26  Identities=23%  Similarity=0.640  Sum_probs=22.1

Q ss_pred             cccccceeecCce-EEecCccccccCc
Q 034188           10 CKVCEKTVYPVEQ-LSADGIVYHKSCF   35 (102)
Q Consensus        10 C~~C~~~i~~~~~-~~~~~~~~h~~Cf   35 (102)
                      |..|.++|....+ +...++.||..||
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            6789999976665 7899999999997

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=4.7e-05  Score=32.17  Aligned_cols=26  Identities=23%  Similarity=0.636  Sum_probs=20.8

Q ss_pred             cccccceeecCc---eEEecCccccccCc
Q 034188           10 CKVCEKTVYPVE---QLSADGIVYHKSCF   35 (102)
Q Consensus        10 C~~C~~~i~~~~---~~~~~~~~~h~~Cf   35 (102)
                      |+.|.++|....   .+..+++.||.+||
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            788999885433   37899999999997

>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=97.29  E-value=4.1e-05  Score=32.77  Aligned_cols=30  Identities=27%  Similarity=0.555  Sum_probs=25.9

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   65 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~   65 (102)
                      .|.+|...|....++..++++||+.|...+
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~r   30 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARER   30 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhhc
Confidence            388999999988899999999999987543

>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=97.27  E-value=0.00019  Score=30.58  Aligned_cols=29  Identities=21%  Similarity=0.608  Sum_probs=25.7

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   64 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~   64 (102)
                      .|..|.+.|.+..|...+++.||-.||..
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeecc
Confidence            47899999998889999999999999864

>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=97.24  E-value=0.00024  Score=30.34  Aligned_cols=30  Identities=23%  Similarity=0.608  Sum_probs=26.3

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   65 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~   65 (102)
                      .|.+|...|.+..|+..+.+.||+.||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            378899999988999999999999999653

>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=97.12  E-value=0.00019  Score=31.50  Aligned_cols=29  Identities=28%  Similarity=0.816  Sum_probs=25.1

Q ss_pred             CccccccccceeecCce-EEecCccccccC
Q 034188            6 TQQKCKVCEKTVYPVEQ-LSADGIVYHKSC   34 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~-~~~~~~~~h~~C   34 (102)
                      ....|.+|+.++.+.++ +...+..||..|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            34589999999999887 789999999876

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.04  E-value=0.00015  Score=30.52  Aligned_cols=26  Identities=23%  Similarity=0.652  Sum_probs=20.3

Q ss_pred             cccccceeecCc---eEEecCccccccCc
Q 034188           10 CKVCEKTVYPVE---QLSADGIVYHKSCF   35 (102)
Q Consensus        10 C~~C~~~i~~~~---~~~~~~~~~h~~Cf   35 (102)
                      |..|.++|....   .+..+++.||.+||
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            678888875433   37889999999997

>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=96.73  E-value=0.00036  Score=32.13  Aligned_cols=26  Identities=35%  Similarity=0.729  Sum_probs=23.4

Q ss_pred             cccccccceeecCceEEecCccccccC
Q 034188            8 QKCKVCEKTVYPVEQLSADGIVYHKSC   34 (102)
Q Consensus         8 ~~C~~C~~~i~~~~~~~~~~~~~h~~C   34 (102)
                      .+|..|++.| .++.|.+.++.||+.|
T Consensus        16 ~~C~~C~~~I-tG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          16 TRCFSCDQFI-EGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CBCTTTCCBC-CSCCEEETTEEECTTT
T ss_pred             cccccccCEe-eeeeeEecCcccCCCC
Confidence            4899999999 5788999999999987

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.20  E-value=0.0013  Score=26.50  Aligned_cols=26  Identities=31%  Similarity=0.560  Sum_probs=20.1

Q ss_pred             cccccceeecCc-eEEecCccccccCc
Q 034188           10 CKVCEKTVYPVE-QLSADGIVYHKSCF   35 (102)
Q Consensus        10 C~~C~~~i~~~~-~~~~~~~~~h~~Cf   35 (102)
                      |.+|++-+.... .+.+.+++||.-||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            678888764333 47899999999886

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.09  E-value=0.0024  Score=27.69  Aligned_cols=31  Identities=26%  Similarity=0.645  Sum_probs=23.9

Q ss_pred             cccccccCcCc--ceEeeCCeeeeHHHHHHHhC
Q 034188           37 CSHCKGTLKLS--NYSSMEGVLYCKPHFEQLFK   67 (102)
Q Consensus        37 C~~C~~~l~~~--~~~~~~~~~~C~~~~~~~~~   67 (102)
                      |.-|...|...  ..+.+.+-++|+.+|.++|+
T Consensus         2 CscC~~~LgeiG~s~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2           2 CSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             CTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CcchhcChhhccchheecCCEEEEchhHHHhcC
Confidence            55666666643  36778999999999999985

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

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

Probab=95.55  E-value=0.016  Score=24.47  Aligned_cols=30  Identities=20%  Similarity=0.533  Sum_probs=26.1

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   65 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~   65 (102)
                      +|..|...|.+..|....|+.+|..|+.+.
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~re   30 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNRE   30 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhhc
Confidence            588899999998999999999999998653

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.44  E-value=0.013  Score=25.27  Aligned_cols=31  Identities=26%  Similarity=0.658  Sum_probs=23.9

Q ss_pred             cccccccccCcCcc-eEe-eCCeeeeHHHHHHH
Q 034188           35 FKCSHCKGTLKLSN-YSS-MEGVLYCKPHFEQL   65 (102)
Q Consensus        35 f~C~~C~~~l~~~~-~~~-~~~~~~C~~~~~~~   65 (102)
                      |.|..|..-+.+++ |+. ...++||..||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            57888888888776 444 47889999998763

>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=95.43  E-value=0.0035  Score=26.51  Aligned_cols=28  Identities=36%  Similarity=0.632  Sum_probs=22.8

Q ss_pred             CccccccccceeecCceEEecCccccccC
Q 034188            6 TQQKCKVCEKTVYPVEQLSADGIVYHKSC   34 (102)
Q Consensus         6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~C   34 (102)
                      +..-|..|.+.| .+..+++-.+.||+.|
T Consensus         4 gssgC~~C~~~I-tGkVLEAG~khYHP~C   31 (32)
T d1wiga1           4 GSSGCDSCEKYI-TGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             SCCSCSSSCCCC-SSCCBCCSSCCBCTTT
T ss_pred             ccchhhhhhhhh-hhhhhhccccccCCCC
Confidence            345799999999 4556899999999987

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.37  E-value=0.011  Score=25.09  Aligned_cols=27  Identities=26%  Similarity=0.746  Sum_probs=21.3

Q ss_pred             ccccccccCcCcc-eEeeCCeeeeHHHH
Q 034188           36 KCSHCKGTLKLSN-YSSMEGVLYCKPHF   62 (102)
Q Consensus        36 ~C~~C~~~l~~~~-~~~~~~~~~C~~~~   62 (102)
                      .|..|...|..+. |...+|.+||+.+.
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            4788999988876 44579999998763

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.01  E-value=0.015  Score=24.34  Aligned_cols=28  Identities=14%  Similarity=0.494  Sum_probs=23.7

Q ss_pred             ccccccccCcCcceEeeCCeeeeHHHHH
Q 034188           36 KCSHCKGTLKLSNYSSMEGVLYCKPHFE   63 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~   63 (102)
                      +|..|-.+|....|...++++.|..|..
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5788889999888999999999977753

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.46  E-value=0.007  Score=27.30  Aligned_cols=28  Identities=18%  Similarity=0.437  Sum_probs=20.8

Q ss_pred             ccccccceeecCce-EEecCccccccCcc
Q 034188            9 KCKVCEKTVYPVEQ-LSADGIVYHKSCFK   36 (102)
Q Consensus         9 ~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~   36 (102)
                      .|.+|+..+..++- ...-+.+||+.|-.
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            38899998887775 35567789987743

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.12  E-value=0.035  Score=23.20  Aligned_cols=27  Identities=30%  Similarity=0.817  Sum_probs=20.1

Q ss_pred             cccccccCcCcceEeeCCeeeeHHHHHH
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQ   64 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~~~~   64 (102)
                      |..|++.|.. .--...+.+||..|+.+
T Consensus         2 C~~Cgkelta-dArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKELTA-DARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBCCT-TCEEETTEEECHHHHHT
T ss_pred             ccccccccch-hHHHhcCCEEEEecccc
Confidence            6778887753 45567899999998754

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=91.51  E-value=0.039  Score=23.92  Aligned_cols=30  Identities=20%  Similarity=0.322  Sum_probs=22.6

Q ss_pred             CCccccccccceeecCceEEecCccccccCc
Q 034188            5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCF   35 (102)
Q Consensus         5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf   35 (102)
                      .|...|..|...|. .+-+.+++.+||+..|
T Consensus         6 lGk~vC~KCh~iId-d~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           6 LGKYICQKCHAIID-EQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCBCTTTCCBCC-SCCCCCSSSCCCTTTS
T ss_pred             hhhHHHHHHHhhhh-cCcceecCCCCCCCCC
Confidence            35568999999984 3457888999998654

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.12  E-value=0.11  Score=21.86  Aligned_cols=25  Identities=16%  Similarity=0.549  Sum_probs=19.4

Q ss_pred             cccccccCcCcceEeeCCeeeeHHH
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPH   61 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~   61 (102)
                      |..|+.+|....|......++|..|
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhc
Confidence            6677778877778888888998554

>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=91.00  E-value=0.066  Score=23.00  Aligned_cols=27  Identities=22%  Similarity=0.439  Sum_probs=20.7

Q ss_pred             ccccccccceeecCceEEecCccccccC
Q 034188            7 QQKCKVCEKTVYPVEQLSADGIVYHKSC   34 (102)
Q Consensus         7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~C   34 (102)
                      ...|..|.+.|. +..|.+-..-||++|
T Consensus         8 ge~C~~C~~~it-GpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           8 GEFCHGCSLLMT-GPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SCBCTTTCCBCC-SCCBCCTTCCBCTTS
T ss_pred             HHHhhhhHhhcc-cceeeecccccCCCC
Confidence            347999999774 556777777799987

>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=90.77  E-value=0.064  Score=22.72  Aligned_cols=27  Identities=33%  Similarity=0.832  Sum_probs=20.5

Q ss_pred             ccccccccCcCcceEe--eCCeeeeHHHH
Q 034188           36 KCSHCKGTLKLSNYSS--MEGVLYCKPHF   62 (102)
Q Consensus        36 ~C~~C~~~l~~~~~~~--~~~~~~C~~~~   62 (102)
                      +|..|...|..+.|..  .+|.+||..++
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            4677877888777765  48999997764

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.13  E-value=0.29  Score=19.86  Aligned_cols=26  Identities=15%  Similarity=0.330  Sum_probs=19.1

Q ss_pred             cccccccCcCcceEeeCCeeeeHHHH
Q 034188           37 CSHCKGTLKLSNYSSMEGVLYCKPHF   62 (102)
Q Consensus        37 C~~C~~~l~~~~~~~~~~~~~C~~~~   62 (102)
                      |..|..+|....|......++|..|-
T Consensus         2 c~kcsvslvgrgflterddilc~dcg   27 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCG   27 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccC
Confidence            66777788777777776677887763

>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=82.27  E-value=1.1  Score=19.61  Aligned_cols=28  Identities=14%  Similarity=0.320  Sum_probs=15.4

Q ss_pred             cccccccccCcCcceEe-eCCeeeeHHHH
Q 034188           35 FKCSHCKGTLKLSNYSS-MEGVLYCKPHF   62 (102)
Q Consensus        35 f~C~~C~~~l~~~~~~~-~~~~~~C~~~~   62 (102)
                      |.|..|..++..++..- .+..-.|..|-
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs   29 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCS   29 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHH
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcC
Confidence            45667777666554333 34455565553