Citrus Sinensis ID: 040725

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160----
Protein Sequence
LKAKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFASMKRAAASVPEA
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEEcEEEEccccccccccccccccccccccccccccccEEcccccHHHHccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHccccccEEEEHEEEEEcccEEEcccEEEcccccEEEcccccccccEEEEcccHHHHHcccccccccccccccccccccccccccccccccccEEEcHEEEEEcccccccccEEEcccccEEccccHHHccccEEEcHHHHHHcccccccccc
Coil and Loop (DISEMBL)
lkaksfigtqqKYKVYEktvypveqlsddgvvyhkscfkcshckgtlklsnyssmegvlyckphfeqlfkesgninknfqsparlvekstpeltrspskaasiktvcpleKVAVESQAYHKtcfkcshggcsispsnyvaLEGNYNHLIKFASMKRAAASVPEA
Flexible Loop (DISEMBL)
lkaksfigtqqkykvyeKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVekstpeltrspskaasiktvcPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFASMKRAAASVPEA
Low Complexity Region (SEG)
LKAKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFASMKRAAASVPEA
Disordered region (IsUnstruct)
******IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE*******************************IKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFA************
Disordered Region (DISOPRED)
*****FI**QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN***NFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFA************
Disordered Region (DISEMBL)
LKAKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLV***************SIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFAS***********
Disordered Region (DISPRO)
*********QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES****************************ASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFASMKRAA******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
LKAKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNYNHLIKFASMKRAAASVPEA
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	164	2.2.26 [Sep-21-2011]
P29675	219	Pollen-specific protein S	N/A	no	0.853	0.639	0.490	2e-36
Q4KM31	128	LIM domain-containing pro	yes	no	0.384	0.492	0.523	1e-15
Q4U4S6	3784	Xin actin-binding repeat-	yes	no	0.384	0.016	0.555	1e-15
Q8BGB5	128	LIM domain-containing pro	no	no	0.384	0.492	0.507	2e-15
Q1LZA7	128	LIM domain-containing pro	no	no	0.384	0.492	0.507	4e-15
Q9BT23	127	LIM domain-containing pro	no	no	0.384	0.496	0.507	4e-15
B0KYV5	756	LIM domain and actin-bind	no	no	0.347	0.075	0.523	6e-15
Q9ERG0	753	LIM domain and actin-bind	no	no	0.347	0.075	0.523	7e-15
Q9UHB6	759	LIM domain and actin-bind	no	no	0.347	0.075	0.523	8e-15
Q8BML1	960	Protein-methionine sulfox	no	no	0.591	0.101	0.303	4e-09

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

 Score =  151 bits (382), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 75/153 (49%), Positives = 104/153 (67%), Gaps = 13/153 (8%)

Query: 4   KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 63
           KSF GT QK  V EKTVY V++L  +  VYHK+CF+C HC  TLKLSN++S +GV+YC+ 
Sbjct: 2   KSFTGTTQKCTVCEKTVYLVDKLVANQRVYHKACFRCHHCNSTLKLSNFNSFDGVVYCRH 61

Query: 64  HFEQLFKESGNINKNFQ-SPARLVEKSTPELTRSPSKAASI------------KTVCPLE 110
           HF+QLFK +G++ K+F  +P    E++  + T+S ++ +S             K V P+E
Sbjct: 62  HFDQLFKRTGSLEKSFDGTPKFKPERTFSQETQSANRLSSFFEGTRDKCNACAKIVYPIE 121

Query: 111 KVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
           +V V+  AYH+ CFKC HGGC+ISPSNY+A EG
Sbjct: 122 RVKVDGTAYHRACFKCCHGGCTISPSNYIAHEG 154

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

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

 Score = 82.4 bits (202), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  D +++H SCF C HC   L L +Y++M G  YCKPHF+QLFK  GN +
Sbjct: 45  QKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAAMHGEFYCKPHFQQLFKSKGNYD 104

Query: 77  KNF 79
           + F
Sbjct: 105 EGF 107

Rattus norvegicus (taxid: 10116)

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

 Score = 82.4 bits (202), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 35/63 (55%), Positives = 45/63 (71%)

Query: 17   EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
            +KTVYP+E L  D   +HKSCF+C HC   L L NY+S+ G +YCKPHF+QLFK  GN +
Sbjct: 3261 QKTVYPMECLIADKQNFHKSCFRCHHCSSKLSLGNYASLHGRIYCKPHFKQLFKSKGNYD 3320

Query: 77   KNF 79
            + F
Sbjct: 3321 EGF 3323

Protects actin filaments from depolymerization.

Mus musculus (taxid: 10090)

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

 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  D +++H SCF C HC   L L +Y++M G  YC+PHF+QLFK  GN +
Sbjct: 45  QKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAAMHGEFYCRPHFQQLFKSKGNYD 104

Query: 77  KNF 79
           + F
Sbjct: 105 EGF 107

Mus musculus (taxid: 10090)

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

 Score = 80.9 bits (198), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  D +++H SCF C HC   L L +Y+++ G  YCKPHF+QLFK  GN +
Sbjct: 45  QKTVYPMERLVADKLIFHSSCFCCKHCHTKLSLGSYAALHGEFYCKPHFQQLFKSKGNYD 104

Query: 77  KNF 79
           + F
Sbjct: 105 EGF 107

Bos taurus (taxid: 9913)

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

 Score = 80.9 bits (198), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  D +++H SCF C HC   L L +Y+++ G  YCKPHF+QLFK  GN +
Sbjct: 44  QKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAALHGEFYCKPHFQQLFKSKGNYD 103

Query: 77  KNF 79
           + F
Sbjct: 104 EGF 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 = 80.1 bits (196), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLFK  GN +
Sbjct: 390 QKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 449

Query: 77  KNF 79
           + F
Sbjct: 450 EGF 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|Q9ERG0|LIMA1_MOUSE LIM domain and actin-binding protein 1 OS=Mus musculus GN=Lima1 PE=1 SV=3

 Score = 79.7 bits (195), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLFK  GN +
Sbjct: 392 QKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 451

Query: 77  KNF 79
           + F
Sbjct: 452 EGF 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|Q9UHB6|LIMA1_HUMAN LIM domain and actin-binding protein 1 OS=Homo sapiens GN=LIMA1 PE=1 SV=1

 Score = 79.7 bits (195), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
           +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLFK  GN +
Sbjct: 394 QKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 453

Query: 77  KNF 79
           + F
Sbjct: 454 EGF 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|Q8BML1|MICA2_MOUSE Protein-methionine sulfoxide oxidase MICAL2 OS=Mus musculus GN=Mical2 PE=1 SV=1

 Score = 60.8 bits (146), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/99 (30%), Positives = 52/99 (52%), Gaps = 2/99 (2%)

Query: 17  EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQLFKESGN 74
           +K VY +E+LS +G  +H+ CF+CS C  TL+L+ Y+    EG  YCKPHF      S  
Sbjct: 757 KKRVYMIERLSAEGHFFHQECFRCSVCSATLRLAAYAFDCDEGKFYCKPHFVHCKTSSKQ 816

Query: 75  INKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVA 113
             +  +   +  E+ T +   +P +    ++ C +  ++
Sbjct: 817 RKRRAELNQQREEEGTWQEQEAPRRDVPTESSCAVAAIS 855

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.

Mus musculus (taxid: 10090)

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	164
225449230	189	PREDICTED: pollen-specific protein SF3 i	0.975	0.846	0.734	1e-67
449441328	189	PREDICTED: pollen-specific protein SF3-l	0.975	0.846	0.723	1e-67
260619528	189	LIM1 [Hevea brasiliensis]	0.975	0.846	0.723	2e-66
255579126	189	Pollen-specific protein SF3, putative [R	0.975	0.846	0.723	2e-66
224109388	189	predicted protein [Populus trichocarpa]	0.975	0.846	0.702	1e-65
224101093	189	predicted protein [Populus trichocarpa]	0.975	0.846	0.702	3e-65
5932420	189	LIM domain protein WLIM2 [Nicotiana taba	0.975	0.846	0.702	5e-65
117950171	189	LIM domain protein WLIM2a [Populus tremu	0.975	0.846	0.696	6e-65
388501992	189	unknown [Lotus japonicus] gi|388521363|g	0.975	0.846	0.680	1e-64
118485508	189	unknown [Populus trichocarpa]	0.975	0.846	0.691	2e-64

>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 =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 138/188 (73%), Positives = 144/188 (76%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SFIGTQQK K   KTVYPVEQLS DGVVYHKSCFKCSHC GTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFIGTQQKCKACLKTVYPVEQLSADGVVYHKSCFKCSHCNGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           FEQLFKESGN NKNFQSPA+  EK TPELTRSPSKAAS+            KT  PLEKV
Sbjct: 62  FEQLFKESGNFNKNFQSPAKSAEKLTPELTRSPSKAASMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGC ISPSNY ALE                G+YNHLIK ASMKR
Sbjct: 122 TVESQAYHKSCFKCSHGGCPISPSNYAALEGILYCKHHFAQLFKEKGSYNHLIKSASMKR 181

Query: 157 AAASVPEA 164
           +AASVP+A
Sbjct: 182 SAASVPDA 189

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  260 bits (664), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 136/188 (72%), Positives = 145/188 (77%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SFIGTQQK K  EKTVYPVEQLS DGV YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFIGTQQKCKACEKTVYPVEQLSADGVSYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           FEQLFKE+GN NKNFQSPA+  EK TPELTRSPSKAA +            KTV PLEKV
Sbjct: 62  FEQLFKETGNFNKNFQSPAKSAEKLTPELTRSPSKAAGMFSGTQDKCATCGKTVYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQ+YHK+CFKCSHGGC++SPSNY ALE                G+YNHLIK ASMKR
Sbjct: 122 TVESQSYHKSCFKCSHGGCALSPSNYAALEGILYCKHHFSQLFKEKGSYNHLIKSASMKR 181

Query: 157 AAASVPEA 164
           +AA VPEA
Sbjct: 182 SAAPVPEA 189

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 136/188 (72%), Positives = 143/188 (76%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF GTQQK K  EKTVYP+E LS DGV YHKSCFKC HCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFTGTQQKCKACEKTVYPMELLSADGVPYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           FEQLFKE+GN NKNFQSPA+  EK TPELTRSPSKAAS+            KT  PLEKV
Sbjct: 62  FEQLFKETGNFNKNFQSPAKSAEKLTPELTRSPSKAASMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGCS+SPSNY ALE                G+YNHLIK ASMKR
Sbjct: 122 TVESQAYHKSCFKCSHGGCSLSPSNYAALEGVLYCKHHFSQLFKEKGSYNHLIKCASMKR 181

Query: 157 AAASVPEA 164
           AAASVPEA
Sbjct: 182 AAASVPEA 189

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

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 =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 136/188 (72%), Positives = 143/188 (76%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF GTQQK K  EKTVYP+E LS DGV YHKSCFKC HCKGTLKLSNYSSMEGV+YCKPH
Sbjct: 2   SFTGTQQKCKACEKTVYPMELLSADGVPYHKSCFKCFHCKGTLKLSNYSSMEGVVYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           FEQLFKE+GN NKNFQSPA+  EK TPELTRSPSKAAS+            KT  PLEKV
Sbjct: 62  FEQLFKETGNFNKNFQSPAKSAEKLTPELTRSPSKAASMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGCSISPSNY ALE                G+YNHLIK ASMKR
Sbjct: 122 TVESQAYHKSCFKCSHGGCSISPSNYAALEGVLYCKHHFSQLFKEKGSYNHLIKSASMKR 181

Query: 157 AAASVPEA 164
           AAASVPEA
Sbjct: 182 AAASVPEA 189

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  254 bits (648), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 132/188 (70%), Positives = 142/188 (75%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF GTQQK K  EKTVYP+E LS DGV YHK+CFKC HCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFTGTQQKCKACEKTVYPMELLSADGVAYHKTCFKCFHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           FEQLFKE+GN NKNFQSPA+  EK  PELTRSPSKAAS+            KT  PLEKV
Sbjct: 62  FEQLFKETGNFNKNFQSPAKSAEKLNPELTRSPSKAASMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGC+I+PSNY ALE                G+YNHLIK A+MKR
Sbjct: 122 TVESQAYHKSCFKCSHGGCAITPSNYAALEGVLYCKHHFSQLFKEKGSYNHLIKSATMKR 181

Query: 157 AAASVPEA 164
           AAASVPEA
Sbjct: 182 AAASVPEA 189

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 =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 132/188 (70%), Positives = 141/188 (75%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF GTQQK K  EKTVYP+E LS DGV YHKSCFKC HCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFTGTQQKCKACEKTVYPMELLSTDGVAYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           F+QLFKE+GN NKNFQSPA+  EK TPELTRSPSKAA +            KT  PLEKV
Sbjct: 62  FDQLFKETGNFNKNFQSPAKSAEKLTPELTRSPSKAAGMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGC+I+PSNY ALE                G+YNHLIK ASMKR
Sbjct: 122 TVESQAYHKSCFKCSHGGCAITPSNYAALEGVLYCKHHFSQLFKEKGSYNHLIKCASMKR 181

Query: 157 AAASVPEA 164
           AAA VPEA
Sbjct: 182 AAAPVPEA 189

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  251 bits (642), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 132/188 (70%), Positives = 143/188 (76%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SFIGTQQK K  EKTVYPVE LS DGV YHKSCFKCSHCKGTLKLSN+SSMEGVLYCKPH
Sbjct: 2   SFIGTQQKCKACEKTVYPVELLSADGVNYHKSCFKCSHCKGTLKLSNFSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           FEQLFKESGN NKNFQSPA+  EK TPELTRSPSKAA +            KT  PLEKV
Sbjct: 62  FEQLFKESGNFNKNFQSPAKSAEKLTPELTRSPSKAAGMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVAL----------------EGNYNHLIKFASMKR 156
            VE+Q+YHKTCFKCSHGGCS+SPSNY AL                +G+YNHLIK ASMKR
Sbjct: 122 TVENQSYHKTCFKCSHGGCSLSPSNYAALNGILYCKPHFSQLFKEKGSYNHLIKSASMKR 181

Query: 157 AAASVPEA 164
            AA+VP++
Sbjct: 182 PAATVPDS 189

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  251 bits (641), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 131/188 (69%), Positives = 141/188 (75%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF GTQQK K  EKTVYP+E LS DGV YHKSCFKC HCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFTGTQQKCKACEKTVYPMELLSADGVAYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           F+QLFKE+GN NKNFQSPA+  EK TPELTRSPSKAA +            KT  PLEKV
Sbjct: 62  FDQLFKETGNFNKNFQSPAKTAEKLTPELTRSPSKAAGMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGC+I+PS+Y ALE                G+YNHLIK ASMKR
Sbjct: 122 TVESQAYHKSCFKCSHGGCAITPSSYAALEGVLYCKHHFSQLFKEKGSYNHLIKSASMKR 181

Query: 157 AAASVPEA 164
           AAA VPEA
Sbjct: 182 AAAPVPEA 189

Source: Populus tremula x Populus alba

Species: Populus tremula x Populus alba

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388501992|gb|AFK39062.1| unknown [Lotus japonicus] gi|388521363|gb|AFK48743.1| unknown [Lotus japonicus]

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 128/188 (68%), Positives = 143/188 (76%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF+GTQQK K  EKTVYPV+QLS DG  YHK+CF+CSHCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFLGTQQKCKACEKTVYPVDQLSADGTSYHKACFRCSHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
           +EQLFKE+G   KNFQSPA+L +K+TPELTRSPSKAA +            KT  PLEKV
Sbjct: 62  YEQLFKETGTFKKNFQSPAKLADKNTPELTRSPSKAAGMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
            VESQAYHK+CFKCSHGGC I+PSNY ALE                G+YNHLIK AS+KR
Sbjct: 122 TVESQAYHKSCFKCSHGGCPITPSNYAALEGILYCKHHFSQLFKEKGSYNHLIKSASIKR 181

Query: 157 AAASVPEA 164
           AAASVPE+
Sbjct: 182 AAASVPES 189

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  249 bits (636), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 130/188 (69%), Positives = 139/188 (73%), Gaps = 28/188 (14%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
           SF GTQQK K  EKTVYP+E LS DGV YHKSCFKC HCKGTLKLSNYSSMEGVLYCKPH
Sbjct: 2   SFTGTQQKCKACEKTVYPMELLSTDGVAYHKSCFKCFHCKGTLKLSNYSSMEGVLYCKPH 61

Query: 65  FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
            +QLFKE+GN NKNFQSPA+  EK TPELTRSPSKAA +            KT  PLEKV
Sbjct: 62  LDQLFKETGNFNKNFQSPAKSAEKLTPELTRSPSKAAGMFSGTQEKCATCGKTAYPLEKV 121

Query: 113 AVESQAYHKTCFKCSHGGCSISPSNYVALE----------------GNYNHLIKFASMKR 156
             ESQAYHK+CFKCSHGGC+I+PSNY ALE                G+YNHLIK ASMKR
Sbjct: 122 TAESQAYHKSCFKCSHGGCAITPSNYAALEGVLYCKHHFSQLFKEKGSYNHLIKCASMKR 181

Query: 157 AAASVPEA 164
           AAA VPEA
Sbjct: 182 AAAPVPEA 189

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	164
TAIR|locus:2061171	200	WLIM2a "WLIM2a" [Arabidopsis t	0.847	0.695	0.684	2.7e-52
TAIR|locus:2198210	205	PLIM2b "PLIM2b" [Arabidopsis t	0.817	0.653	0.586	7.3e-43
TAIR|locus:2050735	226	PLIM2a "PLIM2a" [Arabidopsis t	0.835	0.606	0.569	1.4e-41
TAIR|locus:2098871	213	PLIM2c "PLIM2c" [Arabidopsis t	0.835	0.643	0.516	6.1e-39
TAIR|locus:2012798	190	WLIM1 "AT1G10200" [Arabidopsis	0.847	0.731	0.522	4.3e-38
DICTYBASE|DDB_G0290575	472	DDB_G0290575 "LIM-type zinc fi	0.524	0.182	0.472	1.6e-22
UNIPROTKB|I3LS28	379	LIMA1 "Uncharacterized protein	0.384	0.166	0.523	1.1e-17
RGD|1309967	128	Limd2 "LIM domain containing 2	0.475	0.609	0.469	1.4e-16
UNIPROTKB|B0KYV5	756	LIMA1 "LIM domain and actin-bi	0.384	0.083	0.523	2e-16
UNIPROTKB|E2RGH6	128	LIMD2 "Uncharacterized protein	0.475	0.609	0.456	2.3e-16

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

 Score = 542 (195.9 bits), Expect = 2.7e-52, P = 2.7e-52
 Identities = 104/152 (68%), Positives = 119/152 (78%)

Query:     5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
             SF GTQQK +  EKTVYPVE LS DG+ YHK+CFKCSHCK  L+LSNYSSMEGV+YC+PH
Sbjct:     2 SFTGTQQKCRACEKTVYPVELLSADGISYHKACFKCSHCKSRLQLSNYSSMEGVVYCRPH 61

Query:    65 FEQLFKESGNINKNFQSPAR-LVEKSTPELTRSPSKAASI------------KTVCPLEK 111
             FEQLFKESG+ +KNFQSPA+ L +K TPEL R+PS+ A +            KTV P+EK
Sbjct:    62 FEQLFKESGSFSKNFQSPAKPLTDKPTPELNRTPSRLAGMFSGTQDKCATCTKTVYPIEK 121

Query:   112 VAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
             V VESQ YHK+CFKCSHGGC ISPSNY ALEG
Sbjct:   122 VTVESQCYHKSCFKCSHGGCPISPSNYAALEG 153

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 = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 88/150 (58%), Positives = 113/150 (75%)

Query:     5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
             SF GT  K  V +KTVY V+ LS +G+ YHKSCF+C+HCKGTL++SNYSSM+GVLYCK H
Sbjct:     2 SFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKTH 61

Query:    65 FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
             FEQLFKESGN +KNFQ P +  EK  PELTR+PSK +SI            KTV PLEK+
Sbjct:    62 FEQLFKESGNFSKNFQ-PGK-TEK--PELTRTPSKISSIFCGTQDKCAACEKTVYPLEKI 117

Query:   113 AVESQAYHKTCFKCSHGGCSISPSNYVALE 142
              +E + +HKTCF+C+HGGC+++ S+Y +L+
Sbjct:   118 QMEGECFHKTCFRCAHGGCTLTHSSYASLD 147

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 = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/151 (56%), Positives = 107/151 (70%)

Query:     5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
             SF GT  K K  +KTVY ++ L+ +G  YHKSCF+C+HCKGTL +SNYSSM+GVLYCKPH
Sbjct:     2 SFTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCTHCKGTLVISNYSSMDGVLYCKPH 61

Query:    65 FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
             FEQLFKESGN +KNFQ  A   EK    LTR+PSK +S             KTV PLEKV
Sbjct:    62 FEQLFKESGNYSKNFQ--AGKTEKPNDHLTRTPSKLSSFFSGTQDKCATCKKTVYPLEKV 119

Query:   113 AVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
              +E ++YHKTCF+C+H GC ++ S+Y +L G
Sbjct:   120 TMEGESYHKTCFRCTHSGCPLTHSSYASLNG 150

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 = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 78/151 (51%), Positives = 108/151 (71%)

Query:     5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
             +F GT  K K  +KTVY ++ ++ +G+ YHKSCF+CSHC GTL + NYSSM+GVLYCK H
Sbjct:     3 AFTGTTDKCKACDKTVYVMDLMTLEGMPYHKSCFRCSHCNGTLVICNYSSMDGVLYCKTH 62

Query:    65 FEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASI------------KTVCPLEKV 112
             FEQLFKESGN +KNFQ+  +  EKS  + T++P++ +S             KTV PLEK+
Sbjct:    63 FEQLFKESGNFSKNFQTAGK-TEKSN-DATKAPNRLSSFFSGTQDKCAACKKTVYPLEKM 120

Query:   113 AVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
              +E ++YHKTCF+C+H GC ++ S+Y AL+G
Sbjct:   121 TMEGESYHKTCFRCAHSGCPLTHSSYAALDG 151

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 = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 80/153 (52%), Positives = 104/153 (67%)

Query:     5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
             +F GT QK    +KTVY V++L+ D  VYHK+CF+C HCKGTLKLSNY+S EGVLYC+PH
Sbjct:     2 AFAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNYNSFEGVLYCRPH 61

Query:    65 FEQLFKESGNINKNFQS------PARLVEKSTPELTR-------SPSKAASI-KTVCPLE 110
             F+Q FK +G++ K+F+       P R +E   P  T+       +  K     KTV P+E
Sbjct:    62 FDQNFKRTGSLEKSFEGTPKIGKPDRPLEGERPAGTKVSNMFGGTREKCVGCDKTVYPIE 121

Query:   111 KVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
             KV+V    YHK+CFKC+HGGC+ISPSNY+A EG
Sbjct:   122 KVSVNGTLYHKSCFKCTHGGCTISPSNYIAHEG 154

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 = 219 (82.2 bits), Expect = 1.6e-22, Sum P(2) = 1.6e-22
 Identities = 43/91 (47%), Positives = 57/91 (62%)

Query:     8 GTQQKYKVYEKTVYPVEQL----SDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 63
             GTQ+K     KTVY  E++     +D   +HK C KC+HCK TL L NY+S+ GV YCKP
Sbjct:     6 GTQEKCTACAKTVYLTEKIVVEDKEDKKTFHKLCLKCTHCKLTLSLGNYASLNGVFYCKP 65

Query:    64 HFEQLFKESGNINKNFQSPARLVEKSTPELT 94
             HF+QLF   GN ++ F   ++  EK TP+ T
Sbjct:    66 HFKQLFATKGNYDEGF-GKSKHSEKWTPQAT 95

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|I3LS28 LIMA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 198 (74.8 bits), Expect = 1.1e-17, Sum P(2) = 1.1e-17
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query:    17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
             +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLFK  GN +
Sbjct:    14 QKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 73

Query:    77 KNF 79
             + F
Sbjct:    74 EGF 76

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

GO:0051015 "actin filament binding" evidence=IEA

GO:0031529 "ruffle organization" evidence=IEA

GO:0030835 "negative regulation of actin filament depolymerization" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003785 "actin monomer binding" evidence=IEA

GO:0001725 "stress fiber" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 38/81 (46%), Positives = 53/81 (65%)

Query:     2 KAKSF-IGTQQKYK--VYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGV 58
             ++KSF +  Q K      +KTVYP+E+L  D +++H SCF C HC   L L +Y++M G 
Sbjct:    27 RSKSFSLRAQVKETCAACQKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAAMHGE 86

Query:    59 LYCKPHFEQLFKESGNINKNF 79
              YCKPHF+QLFK  GN ++ F
Sbjct:    87 FYCKPHFQQLFKSKGNYDEGF 107

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|B0KYV5 LIMA1 "LIM domain and actin-binding protein 1" [Sus scrofa (taxid:9823)]

 Score = 198 (74.8 bits), Expect = 2.0e-16, Sum P(2) = 2.0e-16
 Identities = 33/63 (52%), Positives = 45/63 (71%)

Query:    17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
             +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLFK  GN +
Sbjct:   390 QKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 449

Query:    77 KNF 79
             + F
Sbjct:   450 EGF 452

GO:0005925 "focal adhesion" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2RGH6 LIMD2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 203 (76.5 bits), Expect = 2.3e-16, P = 2.3e-16
 Identities = 37/81 (45%), Positives = 53/81 (65%)

Query:     2 KAKSF-IGTQQKYK--VYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGV 58
             ++KSF +  Q K      +KTVYP+E+L  D +++H SCF C HC   L L +Y+++ G 
Sbjct:    27 RSKSFSLRAQVKESCAACQKTVYPMERLVADKLIFHNSCFCCKHCHTKLSLGSYAALHGE 86

Query:    59 LYCKPHFEQLFKESGNINKNF 79
              YCKPHF+QLFK  GN ++ F
Sbjct:    87 FYCKPHFQQLFKSKGNYDEGF 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	164
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	3e-37
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	1e-22
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	6e-21
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	2e-18
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	9e-16
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	2e-14
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	2e-14
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	2e-13
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	8e-13
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	4e-10
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	4e-10
pfam00412	58	pfam00412, LIM, LIM domain	6e-10
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	1e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	4e-08
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	6e-07
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	7e-07
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	1e-06
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	2e-06
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	3e-06
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	4e-06
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	9e-06
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	9e-06
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	1e-05
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	1e-05
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	2e-05
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	1e-04
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	2e-04
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	2e-04
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	3e-04
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	5e-04
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	7e-04
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	7e-04
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	8e-04
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	0.001
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	0.001
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	0.002
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	0.002
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	0.002
cd09414	58	cd09414, LIM1_LIMPETin, The first LIM domain of pr	0.003
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	0.004
cd09450	53	cd09450, LIM_ALP, This family represents the LIM d	0.004
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.004

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

 Score =  122 bits (307), Expect = 3e-37
 Identities = 54/63 (85%), Positives = 57/63 (90%)

Query: 9  TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 68
          T QK K  +KTVY V+QLS DGVVYHKSCF+CSHCKGTLKLSNYSSMEGVLYCKPHFEQL
Sbjct: 1  TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 69 FKE 71
          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 = 84.6 bits (210), Expect = 1e-22
 Identities = 33/49 (67%), Positives = 41/49 (83%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
           KTVYP+E+L  DG ++HKSCF+CSHC  TL+L NY+S+EG LYCKPHF
Sbjct: 5  GKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 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 = 80.6 bits (199), Expect = 6e-21
 Identities = 34/59 (57%), Positives = 42/59 (71%)

Query: 15 VYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG 73
             KTVYP+E+++ +G  YHKSCFKCSH   T+  SNY++ EG LYCK H  QLFKE G
Sbjct: 3  ACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEKG 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|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein SF3

 Score = 73.7 bits (181), Expect = 2e-18
 Identities = 30/40 (75%), Positives = 34/40 (85%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
           KTV P+EKV VE  +YHK+CFKCSHGGC+ISPSNY A EG
Sbjct: 6   KTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEG 45

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 = 67.1 bits (164), Expect = 9e-16
 Identities = 27/49 (55%), Positives = 35/49 (71%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          +K VYP+E+L  D   +HKSCF+C HC   L L NY+S+ G +YCKPHF
Sbjct: 5  QKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

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

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

 Score = 63.7 bits (155), Expect = 2e-14
 Identities = 26/49 (53%), Positives = 36/49 (73%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          +KTVYP+E+L  +  +YH SCF+CS+C   L L  Y+S+ G +YCKPHF
Sbjct: 5  QKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

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

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

 Score = 63.3 bits (154), Expect = 2e-14
 Identities = 24/49 (48%), Positives = 32/49 (65%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
           K VY +E++  +  +YHK+CF+C  C   LK+ NY S EG LYCK HF
Sbjct: 5  GKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 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|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting with CasL)

 Score = 61.2 bits (149), Expect = 2e-13
 Identities = 26/51 (50%), Positives = 37/51 (72%), Gaps = 2/51 (3%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHF 65
          +K VY +E+LS +G+ +H+SCFKCS+C  TL+L  Y+    +G  YCKPHF
Sbjct: 5  KKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 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 = 59.2 bits (143), Expect = 8e-13
 Identities = 26/49 (53%), Positives = 35/49 (71%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          +KTVYP+E+L  D +V+H SCF C HC   L L +Y+++ G  YCKPHF
Sbjct: 5  QKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 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|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule interacting with CasL) like family

 Score = 52.3 bits (126), Expect = 4e-10
 Identities = 17/42 (40%), Positives = 28/42 (66%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNY 145
           KTV P+E++  + + +HK+CF+CSH   ++   NY +LEG  
Sbjct: 6   KTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKL 47

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

 Score = 52.4 bits (126), Expect = 4e-10
 Identities = 21/49 (42%), Positives = 27/49 (55%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
           KTVYP E+L+    ++HK CFKC  C  TL + NY       YC  H+
Sbjct: 5  GKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 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 = 52.0 bits (125), Expect = 6e-10
 Identities = 14/38 (36%), Positives = 22/38 (57%)

Query: 32 VYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          V+H  CF+C+ C   L   ++   +G LYCK  + +LF
Sbjct: 21 VWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 50.9 bits (122), Expect = 1e-09
 Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPH 64
          KT YP E +  DG  YHK CFKC  C   L L  ++    +G +YC  H
Sbjct: 6  KTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 47.4 bits (113), Expect = 4e-08
 Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 18 KTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
          K +Y  E+ L   G V+H  CFKC+ C   L    +   +G LYCK  
Sbjct: 7  KPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 43.7 bits (104), Expect = 6e-07
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          K+VY  E++   G  +HKSCF C+ C   L  +  +  +G +YCK
Sbjct: 6  KSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 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|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein SF3

 Score = 44.0 bits (104), Expect = 7e-07
 Identities = 16/40 (40%), Positives = 28/40 (70%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
           KTV  +++++ +   YHK+CF+CSH   ++  SNY ++EG
Sbjct: 10  KTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEG 49

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

 Score = 43.1 bits (102), Expect = 1e-06
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          K +   E L   G  +H  CFKCS C   L   ++   +G  YC+  +
Sbjct: 6  KPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 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|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A

 Score = 42.5 bits (100), Expect = 2e-06
 Identities = 20/47 (42%), Positives = 25/47 (53%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 63
           K+VY  E+    G  +HK CFKC  C   L  +N +  EG LYCK 
Sbjct: 6  GKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQ 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|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

 Score = 42.2 bits (99), Expect = 3e-06
 Identities = 18/41 (43%), Positives = 25/41 (60%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           KTV PLE++    Q YH +CF+CS+    +S   Y +L GN
Sbjct: 6   KTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGN 46

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

 Score = 42.1 bits (99), Expect = 4e-06
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
           K V P+E++  + Q +HK+CF+C H    +S  NY +L G
Sbjct: 6   KRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHG 45

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

 Score = 40.7 bits (95), Expect = 9e-06
 Identities = 17/45 (37%), Positives = 27/45 (60%)

Query: 20 VYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
          VYP E+++     +HK+CF C  CK  L ++N+ S +   YC+ H
Sbjct: 8  VYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 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|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 40.7 bits (95), Expect = 9e-06
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          K VYP E+++     +HK+CF C  CK TL ++NY   +   YC  H+
Sbjct: 6  KIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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

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

 Score = 40.8 bits (95), Expect = 1e-05
 Identities = 17/46 (36%), Positives = 29/46 (63%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
           K+VY  E++   G  +HK+CF+C+ C  +L+ +  +  +G LYCK
Sbjct: 5  GKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 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|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 40.4 bits (95), Expect = 1e-05
 Identities = 18/46 (39%), Positives = 23/46 (50%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 63
          K VY  E+ +  G  +HK C +C  CK TL    +S  EG  YC  
Sbjct: 6  KPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 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|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 16/46 (34%), Positives = 29/46 (63%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
           K+VY  E++   G  +HK+CF+C+ C  +L+ +  +  +G +YCK
Sbjct: 5  GKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

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

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSME--GVLYCKPHF 65
          + V+ V++   DG +YH++CF+C  C  TL   +Y +    G   C  H 
Sbjct: 6  QHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 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|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase domains protein (Ltd-1)

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 14/35 (40%), Positives = 17/35 (48%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNY 138
           KT  P E V  +   YHK CFKC   G  +S   +
Sbjct: 6   KTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTF 40

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

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          EKTVY  E++  +G  +HKSCF C  C+  L  +  ++ E  +YCK
Sbjct: 5  EKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCK 50

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

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

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 16/44 (36%), Positives = 28/44 (63%)

Query: 19 TVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          +VY  E++   G  +HK+CF+C+ C  +L+ +  +  EG +YCK
Sbjct: 7  SVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 36.3 bits (83), Expect = 5e-04
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          EKTVY  E++  +G  +HK+CF C  C+  L  +  ++ E  +YCK
Sbjct: 6  EKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCK 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|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 20 VYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC 61
          V+  E+L  +G VYH++CFKC+ C   L   ++   E   YC
Sbjct: 12 VFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 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|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family

 Score = 35.7 bits (83), Expect = 7e-04
 Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 32 VYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF 65
          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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
            +   + +      +H  CF+CS C  +L  + Y   +G LYC+  +
Sbjct: 6  GKILDSQYVQALNQDWHCDCFRCSVCSDSLS-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|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP)

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 100 AASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNY 138
           A   KTV P EK+    + +HK CFKC   G +++  NY
Sbjct: 2   ARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNY 40

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

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 20/52 (38%), Positives = 29/52 (55%)

Query: 11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          +K  V +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|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 = 34.4 bits (79), Expect = 0.002
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           K V  +E++  E   YHK CF+C      +   NY + EGN
Sbjct: 6   KPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGN 46

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

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

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 15/46 (32%), Positives = 26/46 (56%)

Query: 100 AASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNY 145
           ++  KTV P+E++  +   +H +CF C H    +S  +Y AL G +
Sbjct: 2   SSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEF 47

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|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9

 Score = 35.1 bits (80), Expect = 0.002
 Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 32 VYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF 65
          VYH SCF C+ C  TL   ++  M + ++YC+ HF
Sbjct: 25 VYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 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|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 11/37 (29%), Positives = 22/37 (59%)

Query: 29 DGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          + +++H +CF+CS C+  L    Y   +  +YC+ H+
Sbjct: 22 ESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 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|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 110 EKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           E++ +E + YH+TCFKC+  G  ++P ++   E  
Sbjct: 16  ERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYG 50

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

 Score = 33.7 bits (77), Expect = 0.004
 Identities = 15/31 (48%), Positives = 17/31 (54%)

Query: 34 HKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
          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

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

 Score = 33.5 bits (77), Expect = 0.004
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 65
          G  +H   F CSHC  +L    +   +G LYC+  +
Sbjct: 17 GRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	164
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.82
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.79
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.76
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.73
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.69
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.64
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.6
KOG1700	200	consensus Regulatory protein MLP and related LIM p	99.59
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.59
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.49
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.46
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.01
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.59
KOG4577	383	consensus Transcription factor LIM3, contains LIM	98.4
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.28
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.01
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	97.87
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	96.71
KOG0490	235	consensus Transcription factor, contains HOX domai	95.88

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

Probab=99.82  E-value=9.3e-22  Score=155.46  Aligned_cols=115  Identities=16%  Similarity=0.325  Sum_probs=98.9

Q ss_pred             cccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccCC
Q 040725           11 QKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKS   89 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~   89 (164)
                      ..|.+|+|.|...+. +.+|++.||..||+|..|++.|....||..++++||+.||..... +|      ..|       
T Consensus       275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tle-kC------~~C-------  340 (468)
T KOG1701|consen  275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLE-KC------NKC-------  340 (468)
T ss_pred             hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHH-HH------hhh-------
Confidence            389999999965554 799999999999999999999999999999999999999987653 33      245       


Q ss_pred             CCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC-------Chhhhccccc
Q 040725           90 TPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG-------NYNHLIKFAS  153 (164)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g-------~y~~l~~~~~  153 (164)
                                    +.+|.+..+.|+|+.||+.||+|.+|++.|++..|+....       +|+..|..+=
T Consensus       341 --------------g~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrC  397 (468)
T KOG1701|consen  341 --------------GEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRC  397 (468)
T ss_pred             --------------hhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcch
Confidence                          5666666799999999999999999999999999998655       8888777653

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

Probab=99.79  E-value=7.7e-21  Score=150.29  Aligned_cols=114  Identities=22%  Similarity=0.431  Sum_probs=90.9

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeee-eCCeeeecchhhhhccCCCCcCCCCCCCccccc
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFKESGNINKNFQSPARLVE   87 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~-~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~   87 (164)
                      ...+|..|++.| ...++.++|+.||+.||+|..|.+.|.+..|.+ .++++||..||++.|+|+|.      .|.    
T Consensus       333 tlekC~~Cg~~I-~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs------~C~----  401 (468)
T KOG1701|consen  333 TLEKCNKCGEPI-MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCS------VCG----  401 (468)
T ss_pred             HHHHHhhhhhHH-HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchh------hcc----
Confidence            346899999999 566789999999999999999999999999885 78999999999999999996      352    


Q ss_pred             CCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCC----CCCeeccCC
Q 040725           88 KSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSIS----PSNYVALEG  143 (164)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~----~~~f~~~~g  143 (164)
                       .+|.....-      +.   .-+|.+|++.||.+|++|++|+.+|+    +...|..||
T Consensus       402 -~PI~P~~G~------~e---tvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~  451 (468)
T KOG1701|consen  402 -NPILPRDGK------DE---TVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDG  451 (468)
T ss_pred             -CCccCCCCC------cc---eEEEEEccccccccceehhhcCccccccCCCCcceeccC
Confidence             222211100      10   11488999999999999999999996    446777777

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

Probab=99.76  E-value=1.3e-20  Score=142.35  Aligned_cols=123  Identities=24%  Similarity=0.376  Sum_probs=97.2

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK   88 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~   88 (164)
                      ..+.|+.|.+.|.+..++.++++.||..|++|+.|..+|... .+.++|.+||+.+|.++|+++|+      .|.     
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCs------aC~-----   99 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCS------ACQ-----   99 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcch------hhc-----
Confidence            568999999999777778999999999999999999999874 56899999999999999999985      241     


Q ss_pred             CCCCccCCCCCCCCCcccccccc-ccccCccccccceeecCCCCCC-CCCCeeccCC-------Chh--------hhccc
Q 040725           89 STPELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCFKCSHGGCSI-SPSNYVALEG-------NYN--------HLIKF  151 (164)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF~C~~C~~~l-~~~~f~~~~g-------~y~--------~l~~~  151 (164)
                                     ..|.+... ..|.+..||.+||.|..|+++| +++.||.+++       +|+        +|.++
T Consensus       100 ---------------~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd  164 (383)
T KOG4577|consen  100 ---------------EGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGD  164 (383)
T ss_pred             ---------------CCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccc
Confidence                           11112222 4588999999999999999999 5667888877       554        44455


Q ss_pred             ccccccc
Q 040725          152 ASMKRAA  158 (164)
Q Consensus       152 ~~~~~~~  158 (164)
                      .++||-+
T Consensus       165 ~~nKRPR  171 (383)
T KOG4577|consen  165 ASNKRPR  171 (383)
T ss_pred             cccCCCc
Confidence            5666643

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

Probab=99.73  E-value=9e-19  Score=130.39  Aligned_cols=118  Identities=16%  Similarity=0.233  Sum_probs=98.7

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccc
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLV   86 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~   86 (164)
                      ..|.-.|..|+..| +.+.+...+..||+..|+|..|++.|.+. -....|.+||..|+.+.--|.|      +.|    
T Consensus       134 ~~g~YvC~KCh~~i-D~~~l~fr~d~yH~yHFkCt~C~keL~sd-aRevk~eLyClrChD~mgipiC------gaC----  201 (332)
T KOG2272|consen  134 GRGRYVCQKCHAHI-DEQPLTFRGDPYHPYHFKCTTCGKELTSD-AREVKGELYCLRCHDKMGIPIC------GAC----  201 (332)
T ss_pred             ccceeehhhhhhhc-ccccccccCCCCCccceecccccccccch-hhhhccceeccccccccCCccc------ccc----
Confidence            34566899999999 55889999999999999999999999764 3466779999999988755544      245    


Q ss_pred             cCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725           87 EKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~  153 (164)
                                       +.+|....|.+||+.||.++|+|++|.+++-|.+.|++.|      ||.+||++.-
T Consensus       202 -----------------~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~C  257 (332)
T KOG2272|consen  202 -----------------RRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLC  257 (332)
T ss_pred             -----------------cCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhh
Confidence                             5555555588999999999999999999999999999999      9999998753

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

Probab=99.69  E-value=3.5e-19  Score=132.55  Aligned_cols=115  Identities=18%  Similarity=0.403  Sum_probs=99.7

Q ss_pred             CCccCCCCccccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCC
Q 040725            2 KAKSFIGTQQKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQ   80 (164)
Q Consensus         2 ~~~~~~~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~   80 (164)
                      ++|+-......|.+|.....+.+. +...+..||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.|.      
T Consensus         4 ~~~~~g~~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~------   77 (332)
T KOG2272|consen    4 KQMASGLANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCG------   77 (332)
T ss_pred             hhhhhHHHHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhc------
Confidence            345544456789999999877776 6778899999999999999999999999999999999999999999884      


Q ss_pred             CCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725           81 SPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG  143 (164)
Q Consensus        81 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g  143 (164)
                      .|                     +..|-+..|.+|+..||+.||+|..|++.|....|+...|
T Consensus        78 kC---------------------~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqg  119 (332)
T KOG2272|consen   78 KC---------------------GEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQG  119 (332)
T ss_pred             cc---------------------ccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcc
Confidence            56                     4444555699999999999999999999999999998888

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

Probab=99.64  E-value=1.7e-16  Score=131.73  Aligned_cols=116  Identities=19%  Similarity=0.377  Sum_probs=103.8

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK   88 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~   88 (164)
                      ..++|..|...|.....+.+++..||+.+|.|..|...+....+...+|++||..|+.+.+.++|.      .|      
T Consensus       302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~------~C------  369 (479)
T KOG1703|consen  302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCK------RC------  369 (479)
T ss_pred             ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCcccc------cc------
Confidence            458999999999443789999999999999999999999988888899999999999999999984      56      


Q ss_pred             CCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccc
Q 040725           89 STPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKF  151 (164)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~  151 (164)
                                     ...|..+.|.++++.||++||+|..|++.|.+..|+..||      ||++++..
T Consensus       370 ---------------~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~  423 (479)
T KOG1703|consen  370 ---------------LLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTT  423 (479)
T ss_pred             ---------------CCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccc
Confidence                           4555666789999999999999999999999999999999      99999973

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

Probab=99.60  E-value=2.3e-16  Score=129.05  Aligned_cols=104  Identities=21%  Similarity=0.411  Sum_probs=89.7

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK   88 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~   88 (164)
                      +...|.+|++.|..++.+.++++.||..||+|..|+.-|. +.|..++|.+||+.||.+.|+.+|.      .|      
T Consensus       132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fgvkc~------~c------  198 (670)
T KOG1044|consen  132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFGVKCE------EC------  198 (670)
T ss_pred             CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcCeehH------Hh------
Confidence            5678999999999999999999999999999999999886 4788999999999999999998874      35      


Q ss_pred             CCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCC-CCeec
Q 040725           89 STPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISP-SNYVA  140 (164)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~-~~f~~  140 (164)
                                     ..-|.+..+.+.|+.||+.|-+|..|+..|+. +..|.
T Consensus       199 ---------------~~fisgkvLqag~kh~HPtCARCsRCgqmF~eGEEMYl  236 (670)
T KOG1044|consen  199 ---------------EKFISGKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYL  236 (670)
T ss_pred             ---------------hhhhhhhhhhccCcccCcchhhhhhhccccccchheee
Confidence                           34455566899999999999999999999854 44444

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

Probab=99.59  E-value=6.3e-16  Score=114.56  Aligned_cols=139  Identities=47%  Similarity=0.788  Sum_probs=105.9

Q ss_pred             ccCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC-cCCCCCCC
Q 040725            4 KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-INKNFQSP   82 (164)
Q Consensus         4 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~-~~~~~~~c   82 (164)
                      |++......|.+|++.++..+.+...+..||..||.|..|...|....+...++.+||..++..+++++.. +.++++. 
T Consensus         1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~-   79 (200)
T KOG1700|consen    1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQK-   79 (200)
T ss_pred             CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccc-
Confidence            45666777999999999999998899999999999999999999998888999999999988888888753 2333222 


Q ss_pred             cccc--cCCC-CCcc-----------CCCCCCCCC-ccccccccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725           83 ARLV--EKST-PELT-----------RSPSKAASI-KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG  143 (164)
Q Consensus        83 ~~~~--~~~~-~~~~-----------~~~~~~~~~-~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g  143 (164)
                      +...  ...+ ....           ....++..+ +.+++.+.+...+..||..||+|+.|+..|+...+...+|
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g  155 (200)
T KOG1700|consen   80 AGGLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEG  155 (200)
T ss_pred             cCCCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCC
Confidence            1110  0000 0000           001111112 7788899999999999999999999999999999999888

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

Probab=99.59  E-value=3.7e-16  Score=129.72  Aligned_cols=108  Identities=21%  Similarity=0.472  Sum_probs=91.8

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK   88 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~   88 (164)
                      ..+.|.+|..+| .++.|.+.+..||++||.|..|+..|....|+..++.+||..||.+++.++|.+      |.     
T Consensus       362 ~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~------~~-----  429 (479)
T KOG1703|consen  362 FRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDY------CK-----  429 (479)
T ss_pred             hCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchh------cc-----
Confidence            357899999999 677788889999999999999999999999999999999999999999877642      21     


Q ss_pred             CCCCccCCCCCCCCCccccc-cccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725           89 STPELTRSPSKAASIKTVCP-LEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG  143 (164)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~-~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g  143 (164)
                                     +.+.. ...|.+++..||..||+|..|.+.|.++.|+...+
T Consensus       430 ---------------~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~  470 (479)
T KOG1703|consen  430 ---------------KPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLD  470 (479)
T ss_pred             ---------------chhHhhhhHhhccCccccccceehhhhhccccCCceeecCC
Confidence                           11111 22389999999999999999999999999988776

>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=99.49  E-value=4e-14  Score=84.80  Aligned_cols=57  Identities=30%  Similarity=0.662  Sum_probs=52.5

Q ss_pred             cccCCceeecccEE-EeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725           13 YKVYEKTVYPVEQL-SDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   69 (164)
Q Consensus        13 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~   69 (164)
                      |.+|+++|...+.+ .++++.||.+||+|..|+.+|....++..++++||..||.++|
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            78999999877775 7999999999999999999999988889999999999998875

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 ....

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

Probab=99.46  E-value=5.3e-14  Score=115.39  Aligned_cols=138  Identities=18%  Similarity=0.325  Sum_probs=94.4

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeee-CCeeeecchh------------hhhccCCCCcCC
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHF------------EQLFKESGNINK   77 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~-~g~~~C~~c~------------~~~~~~~c~~~~   77 (164)
                      ..|..|.+.- .++++.+.+..||..||.|..|+..|..+.|+.+ +.++|+....            .+.+.++|....
T Consensus        17 i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs   95 (670)
T KOG1044|consen   17 IKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS   95 (670)
T ss_pred             eehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence            4799999998 7899999999999999999999999999998875 4467775322            122334443211


Q ss_pred             CCC----------------CCccccc--CCCCCccCCCCCCCCCccc-cccccccccCccccccceeecCCCCCCCCCCe
Q 040725           78 NFQ----------------SPARLVE--KSTPELTRSPSKAASIKTV-CPLEKVAVESQAYHKTCFKCSHGGCSISPSNY  138 (164)
Q Consensus        78 ~~~----------------~c~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f  138 (164)
                      .+.                .|..++.  ...+.....++.++.++.. +.++.+.++++.||+.||+|..|+..|.++ |
T Consensus        96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge-y  174 (670)
T KOG1044|consen   96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE-Y  174 (670)
T ss_pred             ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce-e
Confidence            110                0111110  0111112345566666444 444558899999999999999999999887 7


Q ss_pred             eccCC------Chhhhcc
Q 040725          139 VALEG------NYNHLIK  150 (164)
Q Consensus       139 ~~~~g------~y~~l~~  150 (164)
                      +..||      +|.+.|+
T Consensus       175 ~skdg~pyce~dy~~~fg  192 (670)
T KOG1044|consen  175 MSKDGVPYCEKDYQAKFG  192 (670)
T ss_pred             eccCCCcchhhhhhhhcC
Confidence            78888      7777665

>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=99.01  E-value=1.9e-10  Score=68.63  Aligned_cols=38  Identities=24%  Similarity=0.622  Sum_probs=34.2

Q ss_pred             ccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhc
Q 040725          112 VAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLI  149 (164)
Q Consensus       112 v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~  149 (164)
                      +.++|+.||++||+|..|+++|.+..|+..||      ||.++|
T Consensus        15 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen   15 IKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             EEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             EEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            35999999999999999999999999999999      777664

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 ....

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

Probab=98.59  E-value=4.4e-08  Score=53.27  Aligned_cols=37  Identities=35%  Similarity=0.531  Sum_probs=32.8

Q ss_pred             ccccCCceeecc-cEEEeCCcccCCCCcccCCCCCcCc
Q 040725           12 KYKVYEKTVYPV-EQLSDDGVVYHKSCFKCSHCKGTLK   48 (164)
Q Consensus        12 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~   48 (164)
                      +|..|++.|... ..+.+.+..||..||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            588999999766 5578899999999999999999885

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

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

Probab=98.40  E-value=3.2e-08  Score=75.65  Aligned_cols=66  Identities=24%  Similarity=0.481  Sum_probs=55.7

Q ss_pred             CccccccCCceeecccEE-EeCCcccCCCCcccCCCCCcCcCC-Cee-eeCCeeeecchhhhhccCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQL-SDDGVVYHKSCFKCSHCKGTLKLS-NYS-SMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ...+|..|.+.|.+..++ .+.+..||..||.|..|+.+|..+ .|+ ..++++.|+.+|.+.....|+
T Consensus        91 fGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~  159 (383)
T KOG4577|consen   91 FGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCN  159 (383)
T ss_pred             hCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcccc
Confidence            346899999999777765 788999999999999999999887 566 478999999999987666554

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

Probab=98.28  E-value=3.7e-07  Score=49.49  Aligned_cols=25  Identities=28%  Similarity=0.624  Sum_probs=22.3

Q ss_pred             ccccccCccccccceeecCCCCCCC
Q 040725          110 EKVAVESQAYHKTCFKCSHGGCSIS  134 (164)
Q Consensus       110 ~~v~~~~~~~H~~CF~C~~C~~~l~  134 (164)
                      ..+.++++.||++||+|..|+++|.
T Consensus        14 ~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132       14 LVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             EEEEeCCccccccCCCCcccCCcCc
Confidence            3477899999999999999999985

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=98.01  E-value=1.5e-06  Score=64.63  Aligned_cols=69  Identities=51%  Similarity=1.044  Sum_probs=60.0

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCc
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNI   75 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~   75 (164)
                      .+....|..|.+.+++.+.+...+..||..||+|+.|+..|....+....+.+||...+.+++-...++
T Consensus       105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~  173 (200)
T KOG1700|consen  105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNY  173 (200)
T ss_pred             hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcc
Confidence            345678999999999999999999999999999999999999999888899999988888776555443

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=97.87  E-value=7.4e-07  Score=65.29  Aligned_cols=60  Identities=38%  Similarity=0.737  Sum_probs=54.3

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      ..|..|++.+++.|.+.-+++.||..||.|..|+..|.-..+.+.+.++||..+|.++.+
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence            457889999999999999999999999999999999988888889999999999987653

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=96.71  E-value=0.00027  Score=52.10  Aligned_cols=40  Identities=38%  Similarity=0.737  Sum_probs=34.3

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG  143 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g  143 (164)
                      +.+++.|.|..+++.||..||+|..|+..|.-.+|-..|-
T Consensus        12 k~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~k   51 (264)
T KOG1702|consen   12 KTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDK   51 (264)
T ss_pred             cccccHHHHhhHHHHHHHHhheeeeccCChhhhhcccccc
Confidence            6778889999999999999999999999997776664443

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

Probab=95.88  E-value=0.0011  Score=49.85  Aligned_cols=100  Identities=20%  Similarity=0.415  Sum_probs=67.6

Q ss_pred             CCceeecccEEEeCCcccCCCCcccCCCCCcCc--CCCeeeeCCeeeecchhhh--hccCCCCcCCCCCCCcccccCCCC
Q 040725           16 YEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYCKPHFEQ--LFKESGNINKNFQSPARLVEKSTP   91 (164)
Q Consensus        16 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~~C~~c~~~--~~~~~c~~~~~~~~c~~~~~~~~~   91 (164)
                      |+..|.+...+.+.+..||..|..|..|...|.  ...|.. +|..||..+|..  .+..+|.      .|.        
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~------rt~--------   66 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA------RCK--------   66 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc------CCC--------
Confidence            566675555567779999999999999999997  444445 999999999987  4443332      221        


Q ss_pred             CccCCCCCCCCCcccccccc-ccccCccccccceeecCCCCCC-CCCCeeccCC
Q 040725           92 ELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCFKCSHGGCSI-SPSNYVALEG  143 (164)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF~C~~C~~~l-~~~~f~~~~g  143 (164)
                                  ..+...+. ..+..+. |..||.|..|...+ .+..+...+.
T Consensus        67 ------------~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvw  107 (235)
T KOG0490|consen   67 ------------FTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVW  107 (235)
T ss_pred             ------------CCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehh
Confidence                        11111222 3355666 99999999998864 4555555554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	164
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		9e-16
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		4e-05
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		7e-05
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		1e-04
2o10_A	60	Solution Structure Of The N-Terminal Lim Domain Of		2e-04
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		2e-04
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		3e-04
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		9e-04

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 46/65 (70%)
Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNIN 76
          +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YCKPHF QLFK  GN +
Sbjct: 22 QKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 81
Query: 77 KNFQS 81
          + F S
Sbjct: 82 EGFGS 86

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 33/52 (63%)
Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          K+VY  E++   G  +HK+CF+C+ C  +L+ +N +  +G LYCK  + + F
Sbjct: 7  KSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 7  IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFE 66
           G  +K      +VY  E++   G  +HK+CF+C+ C  +L+ +  +  EG +YCK  + 
Sbjct: 33 FGGAEKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 92
Query: 67 QLFKESG 73
          + 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 = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 3  AKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          A+ F G ++  +  + +VY  E++   G  +HK+CF+C+ C  +L+ +  +  EG +YCK
Sbjct: 30 AQKFGGAEKCSRCGD-SVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 88
Query: 63 PHFEQLFKESG 73
            + + F   G
Sbjct: 89 GCYAKNFGPKG 99

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 62
          EKTVY  E++  +G  +HK+CF C  C+  L  +  ++ E  +YCK
Sbjct: 8  EKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 53

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          + VY  E++   G  +HKSCF+C+ C  +L+ +  +  +G +YCK  + + F
Sbjct: 16 QAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNF 67

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 38/159 (23%), Positives = 62/159 (38%), Gaps = 24/159 (15%)
Query: 8   GTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ 67
           G  +K  V +K VY  E++  +G  +HKSCF C  CK  L  +  +     +YCK  + +
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGK 64
Query: 68  ---------------LFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCP---- 108
                          L  + G          +    + P  +R   K       CP    
Sbjct: 65  KYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGG-SDGCPRCGQ 123
Query: 109 ----LEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG 143
                EKV    +++HK+CF+C+  G S+  +     +G
Sbjct: 124 AVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDG 162

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 17 EKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC-KPHFEQLF 69
          +KTVY  E++S  G  +HK C KC  C  TL    ++  +G  +C KP +  LF
Sbjct: 16 DKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	164
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-25
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-14
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-04
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-24
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	5e-08
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-21
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-07
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	6e-21
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	6e-07
2co8_A	82	NEDD9 interacting protein with calponin homology a	1e-18
2co8_A	82	NEDD9 interacting protein with calponin homology a	2e-06
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-18
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-08
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-14
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	3e-12
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	8e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	1e-08
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-08
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-08
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-07
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-07
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-07
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-07
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	4e-07
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	5e-07
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	5e-07
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	5e-07
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	8e-07
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-07
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-06
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	2e-06
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-06
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-05
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-06
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-05
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	3e-06
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	3e-06
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	4e-06
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-06
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	6e-06
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	9e-06
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	1e-05
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	1e-05
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	6e-05
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-04
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	7e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	1e-04
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-04
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	5e-04

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

 Score = 95.9 bits (238), Expect = 1e-25
 Identities = 35/162 (21%), Positives = 60/162 (37%), Gaps = 22/162 (13%)

Query: 5   SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
              G  +K  V +K VY  E++  +G  +HKSCF C  CK  L  +  +     +YCK  
Sbjct: 2   PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSC 61

Query: 65  FEQLFKESGNINKNFQSPAR----------LVEKSTPELTRSPSKAASI----------- 103
           + + +   G                       E  +   T   +   +            
Sbjct: 62  YGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRC 121

Query: 104 -KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
            + V   EKV    +++HK+CF+C+  G S+  +     +G 
Sbjct: 122 GQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGE 163

>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 = 67.3 bits (164), Expect = 1e-14
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 18  KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN 74
           + VY  E++   G  +HKSCF+C+ C  +L+ +  +  +G +YCK  + + F   G 
Sbjct: 123 QAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF 179

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

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNY 145
           K V   E+V  E  ++HK+CF C     ++  +         
Sbjct: 15  KAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEI 56

>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 = 89.5 bits (222), Expect = 2e-24
 Identities = 35/82 (42%), Positives = 49/82 (59%)

Query: 2  KAKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC 61
            K     ++     +KTVYP+E+L  +  V+H SCF+CS+C   L L  Y+S+ G +YC
Sbjct: 7  GMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYC 66

Query: 62 KPHFEQLFKESGNINKNFQSPA 83
          KPHF QLFK  GN ++ F S  
Sbjct: 67 KPHFNQLFKSKGNYDEGFGSGP 88

>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 = 47.2 bits (112), Expect = 5e-08
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGNY 145
           KTV P+E++    Q +H +CF+CS+    +S   Y +L G  
Sbjct: 23  KTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRI 64

>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 = 82.1 bits (203), Expect = 1e-21
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 5  SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYC-KP 63
             G   K    +KTVY  E++S  G  +HK C KC  C  TL    ++  +G  +C KP
Sbjct: 4  GSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKP 63

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

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

 Score = 45.5 bits (108), Expect = 1e-07
 Identities = 13/41 (31%), Positives = 21/41 (51%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           KTV   EKV+   + +HK C KC     +++P  +   +G 
Sbjct: 17  KTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGK 57

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

 Score = 80.5 bits (199), Expect = 6e-21
 Identities = 18/70 (25%), Positives = 31/70 (44%)

Query: 5  SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 64
             G   K     +TVY  E++  DG  +H+ CF C  C+  L  +  +  +  +YCK  
Sbjct: 2  PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61

Query: 65 FEQLFKESGN 74
          + + +   G 
Sbjct: 62 YGKKYGPKGY 71

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

 Score = 43.9 bits (104), Expect = 6e-07
 Identities = 8/41 (19%), Positives = 19/41 (46%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           +TV   E+V  + +++H+ CF C     ++  +     +  
Sbjct: 15  RTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAE 55

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

 Score = 74.6 bits (183), Expect = 1e-18
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 3  AKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSM--EGVLY 60
               G      +  + +Y +E+L  +G  +H+SCF+C  C+ TL    Y     +G  Y
Sbjct: 8  QHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFY 67

Query: 61 CKPHFEQLFKESGN 74
          C  H  Q      +
Sbjct: 68 CLQHLPQTDSGPSS 81

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

 Score = 42.6 bits (100), Expect = 2e-06
 Identities = 10/41 (24%), Positives = 21/41 (51%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           + +  LE++ V    +H++CF+C     ++ P  Y    G+
Sbjct: 23  EHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGD 63

>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 = 74.3 bits (183), Expect = 1e-18
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFKESGN 74
          K VY  E+++  G  +H+ C KC  C  TL    ++  EG  YC  P +  +F   G 
Sbjct: 8  KEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF 65

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

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 11/41 (26%), Positives = 19/41 (46%)

Query: 104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEGN 144
           K V   E+V    + +H+ C KC   G +++   +   EG 
Sbjct: 8   KEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGK 48

>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 = 62.8 bits (153), Expect = 3e-14
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 18 KTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
              P E+ ++ +G +YH+ CF C+ C        +   EG  YC+  F+ LF
Sbjct: 19 GGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 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 = 58.2 bits (141), Expect = 3e-12
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 18 KTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
              P E+ ++ +G +YH+ CF C+ C        +   EG  YC+  F+ LF
Sbjct: 19 GGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 71

>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 = 48.9 bits (117), Expect = 8e-09
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 18 KTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          +TV P  + L   G  +H+ CF CS C+  L   ++   +G  YC P +E  F
Sbjct: 13 ETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 65

>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 = 48.5 bits (116), Expect = 1e-08
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 18 KTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          K +   +Q +   G V+HK CF CS+CK  +   ++       YC    E  F
Sbjct: 23 KAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

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

 Score = 47.3 bits (113), Expect = 3e-08
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          G  +H   F C+ C+       +   +G+ YC+ H+ QLF
Sbjct: 24 GKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

>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 = 47.0 bits (112), Expect = 4e-08
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 18 KTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          KT+ P  + +   G  +H++CF C  C+  +   ++   +   +C P +E+  
Sbjct: 13 KTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

>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 = 46.3 bits (110), Expect = 1e-07
 Identities = 10/45 (22%), Positives = 18/45 (40%)

Query: 26 LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 70
          +       H  C+ C+ C   LK   +  +E  +YC+ H  +   
Sbjct: 30 VKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVS 74

>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 = 45.9 bits (109), Expect = 1e-07
 Identities = 11/40 (27%), Positives = 20/40 (50%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
            V+H  CF CS C+  L+  ++ ++E   YC+  +    
Sbjct: 26 DRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL 65

>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 = 45.4 bits (108), Expect = 2e-07
 Identities = 9/40 (22%), Positives = 18/40 (45%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
            V+H  CF C  C  +    ++  ++G  +C+ H+    
Sbjct: 34 DTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR 73

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

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 14/40 (35%), Positives = 22/40 (55%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          G  +H   F C+HCK T+    +   +G LYC+  +E+ F
Sbjct: 44 GKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

>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 = 44.3 bits (105), Expect = 4e-07
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
             +HK CF C+ C+  L    +++ +   YC   F  L+
Sbjct: 24 EQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY 63

>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 = 44.4 bits (105), Expect = 5e-07
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 18 KTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          + +   + L      +H SCFKC  C   L    Y S +GV YC+  +   F
Sbjct: 23 EEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 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 = 44.4 bits (105), Expect = 5e-07
 Identities = 14/40 (35%), Positives = 17/40 (42%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
              H  CF C+ C   LK   Y  +EG LYC+ H     
Sbjct: 44 DKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARART 83

>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 = 43.5 bits (103), Expect = 8e-07
 Identities = 9/40 (22%), Positives = 16/40 (40%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
             +H  CF C  C   L    ++++E   YC   ++   
Sbjct: 24 DQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFV 63

>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 = 43.3 bits (102), Expect = 9e-07
 Identities = 8/44 (18%), Positives = 17/44 (38%)

Query: 26 LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          +S +   +H  CF C  C  +L    + +    + C    + + 
Sbjct: 24 ISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDIS 67

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

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
             +H+ C  C+ C+  L    ++S +   YC   F +LF
Sbjct: 34 DQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELF 73

>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 = 42.9 bits (101), Expect = 2e-06
 Identities = 10/47 (21%), Positives = 21/47 (44%)

Query: 23 VEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
            +L  +   +H+ CF+C  C+ +L    ++  +  L C   +   F
Sbjct: 29 SRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 9/37 (24%), Positives = 13/37 (35%)

Query: 33 YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
          +H   F C  C   L    Y  +     CKP + +  
Sbjct: 26 WHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNH 62

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

 Score = 40.1 bits (94), Expect = 5e-05
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 23  VEQLSDDGVVYH--KSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
           V++++ +   +H    CF CS C   L    +  +EG+++C    ++  
Sbjct: 77  VQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

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

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 30  GVVYHKSCFKCSHCKGTLKL-SNYSSMEGVLYCKPHFEQLFKESG 73
             VYH  CFKC+ C+    +   Y  +   + C+    +  K +G
Sbjct: 87  DKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 131

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

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 2/39 (5%)

Query: 33 YHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQLF 69
          +H+ C  C  C   L           G   C+  + +LF
Sbjct: 25 WHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLF 63

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

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 9/40 (22%), Positives = 15/40 (37%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
             +H  CF+C  C+  L    +    G   C+P   +  
Sbjct: 24 NNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 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 = 43.6 bits (102), Expect = 3e-06
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 33  YHKSCFKCSHCKGTLKLSNYSSME--GVLYCKPHFEQLF 69
           +H  C KCS C+  L     SS    G++ C+  + +LF
Sbjct: 84  WHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 122

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 43.0 bits (101), Expect = 4e-06
 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 33 YHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQLFKESGNINKNFQSP 82
          +H  C KCS C+  L     S  +  G++ C+  + +LF  SG         
Sbjct: 28 WHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMG 79

>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 = 42.4 bits (100), Expect = 5e-06
 Identities = 14/100 (14%), Positives = 27/100 (27%), Gaps = 27/100 (27%)

Query: 30  GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES-GNINKNFQSPARLVEK 88
              +H +CF+C+ C   L    + + +  + C     +          K   +  + VE 
Sbjct: 26  NRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVE- 84

Query: 89  STPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSH 128
                                     +   +HK CF    
Sbjct: 85  -------------------------YKGTVWHKDCFSGPS 99

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

 Score = 41.2 bits (97), Expect = 6e-06
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYS-SMEGVLYCKPHFEQLF 69
          G  YH  CF C  C   L    ++      ++C   F + F
Sbjct: 34 GKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKF 74

>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 = 40.9 bits (96), Expect = 9e-06
 Identities = 10/45 (22%), Positives = 19/45 (42%)

Query: 24 EQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 68
            ++ +G  +H  CF C  C   L    +   +  +YC    ++L
Sbjct: 33 SVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL 77

>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 = 42.5 bits (100), Expect = 1e-05
 Identities = 22/104 (21%), Positives = 31/104 (29%), Gaps = 28/104 (26%)

Query: 33  YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPE 92
           +H  C KCS C   L    + S    +YCK  F + F                       
Sbjct: 29  WHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF----------------------- 64

Query: 93  LTRSPSKAASIKTVCPLEKV-AVESQAYHKTCFKCSHGGCSISP 135
                  AA    + P + V   +   YH  CF C      ++ 
Sbjct: 65  ---GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLAT 105

>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 = 42.1 bits (99), Expect = 1e-05
 Identities = 15/100 (15%), Positives = 23/100 (23%), Gaps = 29/100 (29%)

Query: 30  GVVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVE 87
             VYH  CF C  CK  L      Y   +  L CK  +E   +                 
Sbjct: 86  DFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ----------------- 128

Query: 88  KSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCS 127
                 +     +     +             H    + +
Sbjct: 129 ----GGSGGSGGSGGGTPMVAASP------ERHDGGLQAN 158

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

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 33  YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
           +H  C KCS C   L    + S    +YCK  F + F
Sbjct: 83  WHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF 118

>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 = 38.4 bits (89), Expect = 3e-04
 Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 2/38 (5%)

Query: 32  VYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQ 67
           VYH  CF C  CK  L      Y   +  L CK  +E 
Sbjct: 142 VYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 179

>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 = 40.4 bits (94), Expect = 7e-05
 Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 30  GVVYHKSCFKCSHCKGTLKL-SNYSSMEGVLYCKPHFEQLF 69
           G VYH  CF CS C+  L     +  + G L+C+       
Sbjct: 90  GNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTAL 130

>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 = 38.2 bits (89), Expect = 1e-04
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 30 GVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 69
             YH   F C++C   L  ++   ++G LYC P  +++ 
Sbjct: 34 NDPYHPDHFNCANCGKELT-ADARELKGELYCLPCHDKMG 72

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

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 7/47 (14%), Positives = 17/47 (36%)

Query: 26 LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES 72
          +      +H  CF C  C  +L    + +    ++C+     +  + 
Sbjct: 24 ICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDI 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 = 36.3 bits (84), Expect = 5e-04
 Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 2/42 (4%)

Query: 30 GVVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLF 69
             YH  CF C  CK  ++   +        LYC     ++ 
Sbjct: 34 EFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	164
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.95
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.94
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.94
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.91
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.91
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.91
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.91
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.78
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.73
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.72
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.72
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.67
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.67
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.64
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.64
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.64
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.63
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.63
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.63
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.62
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.62
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.62
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.62
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.62
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.61
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.61
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.6
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.59
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.59
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.58
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.58
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.58
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.57
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.56
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.56
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.56
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.56
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.56
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.56
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.55
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.54
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.53
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.52
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.51
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.47
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.46
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.44
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.43
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.43
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.42
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.35
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.29
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.29
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.28
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.27
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.27
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.26
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.26
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.24
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.23
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.22
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.22
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.22
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.21
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.2
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.2
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.19
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.14
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.14
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.14
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.13
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.12
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.1
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.09
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.08
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.07
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.06
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.04
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.03
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.03
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.02
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.0
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.92
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	98.87
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.11
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	97.88

>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=99.95  E-value=7.7e-28  Score=176.78  Aligned_cols=148  Identities=23%  Similarity=0.429  Sum_probs=114.6

Q ss_pred             ccCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCc-CCCCCCC
Q 040725            4 KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNI-NKNFQSP   82 (164)
Q Consensus         4 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~-~~~~~~c   82 (164)
                      |+..++.++|..|+++|..++.+.++++.||++||+|..|+.+|....|+.+++++||..||.++|+++|.- .++.   
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~---   77 (192)
T 1b8t_A            1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGA---   77 (192)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCC---
T ss_pred             CCCCCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCcccccccccc---
Confidence            677778899999999998788889999999999999999999999988999999999999999999999741 1110   


Q ss_pred             cccccCCCC-----------C--ccCC----------CCCCCCCcccc-ccccccccCccccccceeecCCCCCCCCCCe
Q 040725           83 ARLVEKSTP-----------E--LTRS----------PSKAASIKTVC-PLEKVAVESQAYHKTCFKCSHGGCSISPSNY  138 (164)
Q Consensus        83 ~~~~~~~~~-----------~--~~~~----------~~~~~~~~~~~-~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f  138 (164)
                      .....+.+.           .  ...+          ..+.+.++..| ..+.|.++++.||++||+|..|+++|.++.|
T Consensus        78 g~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~  157 (192)
T 1b8t_A           78 GTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTL  157 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSE
T ss_pred             ccEecCCCcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcc
Confidence            000000000           0  0011          11233445554 4577899999999999999999999998899


Q ss_pred             eccCC------Chhhhcccccc
Q 040725          139 VALEG------NYNHLIKFASM  154 (164)
Q Consensus       139 ~~~~g------~y~~l~~~~~~  154 (164)
                      +.+||      ||.++|+++-.
T Consensus       158 ~~~~g~~yC~~cy~~~f~~kc~  179 (192)
T 1b8t_A          158 ADKDGEIYCKGCYAKNFGPKGF  179 (192)
T ss_dssp             EEETTEEEEHHHHHHHTCCCCC
T ss_pred             cccCCEEeCHHHHHHhcCCcCC
Confidence            99999      99999987653

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

Probab=99.94  E-value=3.2e-27  Score=162.48  Aligned_cols=113  Identities=16%  Similarity=0.343  Sum_probs=99.5

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccCC
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEKS   89 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~   89 (164)
                      .++|.+|+++|..++.+.++++.||++||+|..|+.+|....|+.++|++||..||.++++++|.      .|       
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~------~C-------   69 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQ------GC-------   69 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCT------TT-------
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCc------cc-------
Confidence            47899999999878889999999999999999999999988899999999999999999999884      56       


Q ss_pred             CCCccCCCCCCCCCcccccc--ccccccCcccc--ccceeecCCCCCCCCCCeeccCC------Chhhhc
Q 040725           90 TPELTRSPSKAASIKTVCPL--EKVAVESQAYH--KTCFKCSHGGCSISPSNYVALEG------NYNHLI  149 (164)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~--~~v~~~~~~~H--~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~  149 (164)
                                    +.+|..  ..|.++++.||  ++||+|..|+++|.++.|+..||      ||.++|
T Consensus        70 --------------~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           70 --------------HNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             --------------CSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             --------------CCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence                          333332  34889999999  99999999999999999999999      666654

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

Probab=99.94  E-value=5.8e-27  Score=162.19  Aligned_cols=116  Identities=18%  Similarity=0.312  Sum_probs=99.0

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC--CCeeeeCCeeeecchhhhhccC--CCCcCCCCCCCccc
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKE--SGNINKNFQSPARL   85 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~--~~~~~~~g~~~C~~c~~~~~~~--~c~~~~~~~~c~~~   85 (164)
                      ..+|..|+++|...+.+.++++.||++||+|..|+.+|..  ..|+.++|++||..||.+++++  +|.      .|   
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~------~C---   72 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCA------SC---   72 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECT------TT---
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChh------hc---
Confidence            4689999999976667899999999999999999999964  5788999999999999999988  663      56   


Q ss_pred             ccCCCCCccCCCCCCCCCccccc-cc-cccccCccccccceeecCCCCCC-CCCCeeccCC------Chhhhcccc
Q 040725           86 VEKSTPELTRSPSKAASIKTVCP-LE-KVAVESQAYHKTCFKCSHGGCSI-SPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~-~~-~v~~~~~~~H~~CF~C~~C~~~l-~~~~f~~~~g------~y~~l~~~~  152 (164)
                                        +.+|. .+ .|.++++.||++||+|..|+++| .++.|+..||      ||.+++++.
T Consensus        73 ------------------~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~~  130 (131)
T 2xjy_A           73 ------------------DKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN  130 (131)
T ss_dssp             ------------------CCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHHH
T ss_pred             ------------------CCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhcc
Confidence                              33333 23 37899999999999999999999 4777999999      899888754

>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=99.91  E-value=1.2e-25  Score=164.51  Aligned_cols=122  Identities=16%  Similarity=0.361  Sum_probs=98.8

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC--CCeeeeCCeeeecchhhhhccC--CCCcCCCCCCCcc
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKE--SGNINKNFQSPAR   84 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~--~~~~~~~g~~~C~~c~~~~~~~--~c~~~~~~~~c~~   84 (164)
                      ..++|..|++.|...+.+.++++.||.+||+|..|+.+|..  ..|+.++|++||..||.++|++  +|      ..|. 
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C------~~C~-   76 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAC------SACG-   76 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEEC------TTTC-
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCcc------ccCC-
Confidence            45789999999976667899999999999999999999986  5788999999999999999988  56      3562 


Q ss_pred             cccCCCCCccCCCCCCCCCcccccccc-ccccCccccccceeecCCCCCCC-CCCeeccCC------Chhhhcccccccc
Q 040725           85 LVEKSTPELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCFKCSHGGCSIS-PSNYVALEG------NYNHLIKFASMKR  156 (164)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF~C~~C~~~l~-~~~f~~~~g------~y~~l~~~~~~~~  156 (164)
                                         +.|...+. |.++++.||++||+|..|+++|. +..|+..+|      ||.+++..+.+..
T Consensus        77 -------------------~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~~~  137 (188)
T 1rut_X           77 -------------------QSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNS  137 (188)
T ss_dssp             -------------------CEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC------
T ss_pred             -------------------CccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhccccccc
Confidence                               22323343 78999999999999999999995 667999999      9999988776543

>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=99.91  E-value=8.1e-25  Score=157.63  Aligned_cols=116  Identities=18%  Similarity=0.292  Sum_probs=95.6

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccccC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLVEK   88 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~   88 (164)
                      +..+|..|++.|...+.+.++++.||.+||+|..|+.+|.... +.++|++||..||.++|+++|.      .|      
T Consensus         5 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~------~C------   71 (169)
T 2rgt_A            5 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCA------AC------   71 (169)
T ss_dssp             --CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCT------TT------
T ss_pred             CCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeeccccccccccccc------cc------
Confidence            4579999999998766789999999999999999999998876 4789999999999999999984      46      


Q ss_pred             CCCCccCCCCCCCCCccccc-ccc-ccccCccccccceeecCCCCCCC-CCCeec-cCC------Chhhhcccc
Q 040725           89 STPELTRSPSKAASIKTVCP-LEK-VAVESQAYHKTCFKCSHGGCSIS-PSNYVA-LEG------NYNHLIKFA  152 (164)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~-~~~-v~~~~~~~H~~CF~C~~C~~~l~-~~~f~~-~~g------~y~~l~~~~  152 (164)
                                     +..|. .+. +.++++.||++||+|..|+++|. ++.|+. .||      ||.++++..
T Consensus        72 ---------------~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~  130 (169)
T 2rgt_A           72 ---------------QLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG  130 (169)
T ss_dssp             ---------------CCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC
T ss_pred             ---------------ccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhcc
Confidence                           22222 233 57999999999999999999997 556654 577      898887653

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

Probab=99.91  E-value=1.8e-24  Score=157.62  Aligned_cols=115  Identities=18%  Similarity=0.322  Sum_probs=94.2

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccc
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLV   86 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~   86 (164)
                      ..+.++|..|+++|...+.+.++++.||.+||+|..|+.+|....| .++|++||..||.++|+++|.      .|    
T Consensus        57 ~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~------~C----  125 (182)
T 2jtn_A           57 TPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCA------AC----  125 (182)
T ss_dssp             CCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCT------TT----
T ss_pred             CCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccc------cC----
Confidence            3456899999999987667899999999999999999999988764 799999999999999999984      46    


Q ss_pred             cCCCCCccCCCCCCCCCccccc-ccc-ccccCccccccceeecCCCCCCC-CCCee-ccCC------Chhhhc
Q 040725           87 EKSTPELTRSPSKAASIKTVCP-LEK-VAVESQAYHKTCFKCSHGGCSIS-PSNYV-ALEG------NYNHLI  149 (164)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~-~~~-v~~~~~~~H~~CF~C~~C~~~l~-~~~f~-~~~g------~y~~l~  149 (164)
                                       +..|. .+. +.++++.||++||+|..|+++|. +..|+ ..||      ||.++.
T Consensus       126 -----------------~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~~  181 (182)
T 2jtn_A          126 -----------------QLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  181 (182)
T ss_dssp             -----------------CCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHHT
T ss_pred             -----------------CCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHhh
Confidence                             22222 232 57899999999999999999997 55665 4577      776654

>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=99.91  E-value=1.6e-24  Score=143.51  Aligned_cols=96  Identities=15%  Similarity=0.324  Sum_probs=83.6

Q ss_pred             CCccccccCCceeec-ccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccc
Q 040725            8 GTQQKYKVYEKTVYP-VEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLV   86 (164)
Q Consensus         8 ~~~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~   86 (164)
                      +...+|.+|+++|.. ++.+.++++.||.+||+|..|+++|....|+.++|++||..||.++++++|.      .|    
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~------~C----   72 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCK------GC----   72 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCS------SS----
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccc------cC----
Confidence            356899999999974 6779999999999999999999999888899999999999999999999884      56    


Q ss_pred             cCCCCCccCCCCCCCCCccccc-cc-cccccCccccccceeecCCC
Q 040725           87 EKSTPELTRSPSKAASIKTVCP-LE-KVAVESQAYHKTCFKCSHGG  130 (164)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~-~~-~v~~~~~~~H~~CF~C~~C~  130 (164)
                                       +.+|. ++ .|.++|+.||++||+|..|+
T Consensus        73 -----------------~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           73 -----------------FKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             -----------------CCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             -----------------CCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence                             33334 33 48899999999999999996

>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=99.78  E-value=1e-19  Score=124.28  Aligned_cols=107  Identities=15%  Similarity=0.269  Sum_probs=89.6

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC--CCeeeeCCeeeecchhhhhccC--CCCcCCCCCCCcc
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKE--SGNINKNFQSPAR   84 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~--~~~~~~~g~~~C~~c~~~~~~~--~c~~~~~~~~c~~   84 (164)
                      ..++|.+|+++|...+.+.++++.||++||+|..|+.+|..  ..|+.++|++||..||.++|++  +|.      .|  
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~------~C--   75 (122)
T 1m3v_A            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGG------SG--   75 (122)
T ss_dssp             CCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSS------CS--
T ss_pred             CCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccc------cC--
Confidence            45799999999987777899999999999999999999973  5788999999999999999999  663      56  


Q ss_pred             cccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccccc
Q 040725           85 LVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFASMK  155 (164)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~~~  155 (164)
                                         +.+|..+.|+++|+             ..|.++.|+.+||      ||.++++..+++
T Consensus        76 -------------------~~~I~~~~~~~~g~-------------~~l~g~~f~~~~~~~yC~~~~~~~~~~~g~~  120 (122)
T 1m3v_A           76 -------------------GHMGSGGDVMVVGE-------------PTLMGGEFGDEDERLITRLENTQFDAANGID  120 (122)
T ss_dssp             -------------------SCCSCCEESSSSSS-------------SSCCSCTTCCTTCCCCEECTTTTTTCCSCCC
T ss_pred             -------------------CCCcCchheEEcCC-------------cCCCCCccEecCCEeEccCcchhchhhcCCC
Confidence                               44445545666663             3688999999999      999999887765

>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=99.73  E-value=6.4e-18  Score=114.03  Aligned_cols=102  Identities=12%  Similarity=0.180  Sum_probs=82.3

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC--CCeeeeCCeeeecchhhhhccCCCCcCCCCCCCcccc
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL--SNYSSMEGVLYCKPHFEQLFKESGNINKNFQSPARLV   86 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~--~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~   86 (164)
                      +.++|.+|+++|...+.+.++++.||++||+|+.|+.+|..  ..|+.++|++||..||.++|+++|..      |..  
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~------c~~--   73 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHM------GSG--   73 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSS------CBS--
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCc------CCC--
Confidence            46789999999987768999999999999999999999985  47889999999999999999999852      210  


Q ss_pred             cCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCC-CCCCCeeccCC------Chhhhccccccc
Q 040725           87 EKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCS-ISPSNYVALEG------NYNHLIKFASMK  155 (164)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~-l~~~~f~~~~g------~y~~l~~~~~~~  155 (164)
                                       ..+     |.               |+.+ |.++.|++.||      ||.++.++.+++
T Consensus        74 -----------------~~~-----~~---------------~~~~~~~g~~f~~~~~~~~C~~~~~~~~~~~g~~  112 (114)
T 1j2o_A           74 -----------------GDV-----MV---------------VGEPTLMGGEFGDEDERLITRLENTQFDAANGID  112 (114)
T ss_dssp             -----------------CSC-----CC---------------SSCSSTTSSBCCCSSSCCCEEEECTTCCCTTSSC
T ss_pred             -----------------Cce-----eE---------------cCCccCCCCeeEEcCCEeecchhhhccccccCCC
Confidence                             111     11               2334 67888999999      888888877765

>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=99.72  E-value=1.2e-17  Score=104.79  Aligned_cols=72  Identities=31%  Similarity=0.570  Sum_probs=67.2

Q ss_pred             CccCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeec-chhhhhccCCCC
Q 040725            3 AKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFKESGN   74 (164)
Q Consensus         3 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~-~c~~~~~~~~c~   74 (164)
                      ++.|....++|..|+++|...+.+.++++.||.+||+|..|+.+|....|+.+++++||. .||.++|+++|.
T Consensus         2 s~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~   74 (76)
T 2cu8_A            2 SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPS   74 (76)
T ss_dssp             CCSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCS
T ss_pred             ccccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccC
Confidence            577888889999999999878899999999999999999999999988899999999999 799999999984

>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=99.72  E-value=3.7e-18  Score=108.39  Aligned_cols=71  Identities=25%  Similarity=0.555  Sum_probs=58.0

Q ss_pred             ccCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            4 KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         4 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      |+|.++.++|..|+++|...+.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
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            78888899999999999888899999999999999999999999988899999999999999999999985

>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=99.67  E-value=6.1e-17  Score=104.94  Aligned_cols=72  Identities=46%  Similarity=0.948  Sum_probs=65.5

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNFQ   80 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~~   80 (164)
                      ...+|..|++.|...+.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.+.++++
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g   85 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFG   85 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcC
Confidence            467999999999877889999999999999999999999988889999999999999999999997655544

>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=99.67  E-value=1.2e-16  Score=101.21  Aligned_cols=67  Identities=25%  Similarity=0.464  Sum_probs=61.2

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ..+..+|..|++.|..++.+.++++.||++||+|..|+.+|.. .|+.+++++||..||.++|+++|.
T Consensus        12 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~   78 (80)
T 2dj7_A           12 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPS   78 (80)
T ss_dssp             CSSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCST
T ss_pred             CCCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCC
Confidence            3456899999999987888999999999999999999999985 688999999999999999999984

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

Probab=99.64  E-value=1.8e-16  Score=99.43  Aligned_cols=72  Identities=22%  Similarity=0.451  Sum_probs=63.0

Q ss_pred             CccCCCCccccccCCceeeccc-EEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            3 AKSFIGTQQKYKVYEKTVYPVE-QLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         3 ~~~~~~~~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      .|+......+|.+|++.|...+ .+.++++.||.+||+|..|+.+|..+.|+.++|++||..||.++|+++|.
T Consensus         4 ~~~~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A            4 FMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             -CCSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             hhccCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            4666777899999999997555 47899999999999999999999988899999999999999999999873

>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=99.64  E-value=8.1e-17  Score=101.82  Aligned_cols=70  Identities=13%  Similarity=0.267  Sum_probs=60.5

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCC
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISP  135 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~  135 (164)
                      +|++||+.||.++++++|.      .|                     +.+|.++.|.++++.||++||+|..|+++|.+
T Consensus         1 gg~~yC~~cy~~~~~~~C~------~C---------------------~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~   53 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCA------RC---------------------SKTLTQGGVTYRDQPWHRECLVCTGCQTPLAG   53 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCT------TT---------------------CCCCCSCCEESSSSEECTTTCBCSSSCCBCTT
T ss_pred             CCcEEcHHHHccccCCcCC------CC---------------------CCEecCcEEEECCchhhhhhCCcccCCCcCCC
Confidence            5789999999999988874      56                     44445566899999999999999999999998


Q ss_pred             CCeeccCC------Chhhhcccc
Q 040725          136 SNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       136 ~~f~~~~g------~y~~l~~~~  152 (164)
                      +.|+..||      ||.++++++
T Consensus        54 ~~~~~~~~~~yC~~cy~~~f~~~   76 (80)
T 2cuq_A           54 QQFTSRDEDPYCVACFGELFASG   76 (80)
T ss_dssp             CCEEECSSSEEEHHHHHHHTTCS
T ss_pred             CeeEeECCEEECHHHHHHHcCCC
Confidence            89999999      999988765

>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=99.64  E-value=2.5e-16  Score=96.83  Aligned_cols=65  Identities=15%  Similarity=0.415  Sum_probs=59.9

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      +.++|..|+++|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
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            5679999999995 5678999999999999999999999988899999999999999999999873

>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=1.4e-16  Score=101.15  Aligned_cols=70  Identities=13%  Similarity=0.310  Sum_probs=58.7

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccc--cccccccCccccccceeecCCCCCC
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCP--LEKVAVESQAYHKTCFKCSHGGCSI  133 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~v~~~~~~~H~~CF~C~~C~~~l  133 (164)
                      +|++||+.||.++++++|.      .|                     +..|.  ...|.++++.||++||+|..|+++|
T Consensus         1 ~g~~yC~~~y~~~~~~~C~------~C---------------------~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L   53 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCA------EC---------------------QQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL   53 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCT------TT---------------------CCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBC
T ss_pred             CCceechhHhCcccCCcCc------cC---------------------CCccccCcEEEEeCCccccccCCeecCCCCcc
Confidence            5789999999999998874      56                     33333  3347789999999999999999999


Q ss_pred             CCCCeeccCC------Chhhhcccc
Q 040725          134 SPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       134 ~~~~f~~~~g------~y~~l~~~~  152 (164)
                      .++.|+..+|      ||.++++++
T Consensus        54 ~~~~f~~~~~~~~C~~c~~~~~~~~   78 (82)
T 2ehe_A           54 ADEPFTCQDSELLCNDCYCSAFSSG   78 (82)
T ss_dssp             SSCCEEEETTEEEETTTSSCCGGGS
T ss_pred             CCCccEeeCCEEECHHHHhhhcCCC
Confidence            9999999999      898888764

>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=99.63  E-value=3.2e-16  Score=96.57  Aligned_cols=65  Identities=18%  Similarity=0.442  Sum_probs=59.9

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ..++|..|+++|. ++.+.++++.||++||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus         4 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   68 (70)
T 2d8z_A            4 GSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPS   68 (70)
T ss_dssp             CCCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCT
T ss_pred             CCCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccC
Confidence            4578999999995 5679999999999999999999999888899999999999999999999984

>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=99.63  E-value=3.5e-16  Score=101.13  Aligned_cols=67  Identities=22%  Similarity=0.456  Sum_probs=61.5

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ....++|..|++.| .++.+.++++.||++||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus        22 ~~~~~~C~~C~~~I-~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~   88 (90)
T 2dar_A           22 GKRTPMCAHCNQVI-RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPS   88 (90)
T ss_dssp             TTCCCBBSSSCCBC-CSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCC
T ss_pred             CCCCCCCccCCCEe-cceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCC
Confidence            34567899999999 57889999999999999999999999988898999999999999999999985

>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=99.62  E-value=4.3e-16  Score=96.49  Aligned_cols=66  Identities=27%  Similarity=0.579  Sum_probs=60.7

Q ss_pred             CccccccCCceeecc-cEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            9 TQQKYKVYEKTVYPV-EQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ...+|..|+++|... +.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   70 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPS   70 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCC
Confidence            357899999999764 678999999999999999999999988899999999999999999999985

>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=99.62  E-value=1.3e-16  Score=100.90  Aligned_cols=70  Identities=17%  Similarity=0.281  Sum_probs=60.1

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCC
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISP  135 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~  135 (164)
                      +|++||+.||.++++++|.      .|                     +..|.++.|.++++.||++||+|..|+++|.+
T Consensus         1 gg~~yC~~~y~~~~~~~C~------~C---------------------~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~   53 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCG------GC---------------------NRPVLENYLSAMDTVWHPECFVCGDCFTSFST   53 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCT------TT---------------------CCBCCSSCEEETTEEECTTTCBCSSSCCBSCS
T ss_pred             CCCccchhHHhhhcCCccc------cC---------------------CCeecceeEEECCCeEecCcCChhhCCCCCCC
Confidence            4789999999999988874      56                     44445566899999999999999999999998


Q ss_pred             CCeeccCC------Chhhhcccc
Q 040725          136 SNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       136 ~~f~~~~g------~y~~l~~~~  152 (164)
                      ..|+.+||      ||.+++++.
T Consensus        54 ~~~~~~~~~~yC~~~y~~~f~~~   76 (80)
T 1x3h_A           54 GSFFELDGRPFCELHYHHRRGSG   76 (80)
T ss_dssp             SCCEESSSCEECHHHHHHHHSSS
T ss_pred             CcEEeECCEEECHHHHHHHcCCC
Confidence            88999999      999988764

>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=99.62  E-value=3.8e-16  Score=95.20  Aligned_cols=63  Identities=19%  Similarity=0.413  Sum_probs=58.2

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKES   72 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~   72 (164)
                      ..++|.+|+++|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++
T Consensus         4 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            4 GVPICGACRRPIE-GRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCCEETTTTEECC-SCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCCCcccCCEec-ceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            3578999999996 77899999999999999999999999888999999999999999999774

>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=99.62  E-value=5.6e-16  Score=97.04  Aligned_cols=64  Identities=31%  Similarity=0.646  Sum_probs=60.0

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeec-chhhhhccCCCC
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFKESGN   74 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~-~c~~~~~~~~c~   74 (164)
                      ++|.+|+++|..++.+.++++.||.+||+|..|+.+|....|+.+++++||. .||.++|+++|.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~   65 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF   65 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCC
Confidence            5799999999878899999999999999999999999988899999999999 699999999985

>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=99.62  E-value=3.7e-16  Score=97.89  Aligned_cols=65  Identities=12%  Similarity=0.311  Sum_probs=59.9

Q ss_pred             ccccccCCceeec---ccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           10 QQKYKVYEKTVYP---VEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        10 ~~~C~~C~~~i~~---~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      .++|..|+++|..   .+.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus         5 ~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~   72 (76)
T 1x68_A            5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISG   72 (76)
T ss_dssp             CCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSS
T ss_pred             CCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCC
Confidence            4789999999963   3779999999999999999999999988899999999999999999999985

>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=99.61  E-value=7e-16  Score=95.51  Aligned_cols=65  Identities=18%  Similarity=0.533  Sum_probs=60.1

Q ss_pred             ccccccCCceeecc-cEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           10 QQKYKVYEKTVYPV-EQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        10 ~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      .++|..|++.|... ..+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   70 (72)
T 1x4k_A            5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPS   70 (72)
T ss_dssp             CCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCC
T ss_pred             CCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCC
Confidence            47899999999776 468999999999999999999999988899999999999999999999984

>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=99.61  E-value=6e-16  Score=95.88  Aligned_cols=66  Identities=14%  Similarity=0.265  Sum_probs=59.4

Q ss_pred             CCccccccCCceeec---ccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCC
Q 040725            8 GTQQKYKVYEKTVYP---VEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG   73 (164)
Q Consensus         8 ~~~~~C~~C~~~i~~---~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c   73 (164)
                      .+..+|..|+++|..   .+.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+|++
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            356899999999974   366899999999999999999999998888899999999999999998874

>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=99.60  E-value=5e-16  Score=98.01  Aligned_cols=66  Identities=15%  Similarity=0.252  Sum_probs=60.0

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCC
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG   73 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c   73 (164)
                      .....+|..|++.|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+|++
T Consensus        12 ~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g   77 (79)
T 1x62_A           12 AQKLPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS   77 (79)
T ss_dssp             CCCCCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCC
T ss_pred             CCCCCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            345679999999996 468999999999999999999999988788999999999999999999886

>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=99.59  E-value=1.5e-15  Score=93.51  Aligned_cols=65  Identities=14%  Similarity=0.315  Sum_probs=59.4

Q ss_pred             CCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCC
Q 040725            8 GTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG   73 (164)
Q Consensus         8 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c   73 (164)
                      ++..+|..|++.|. ++.+.++++.||++||+|..|+.+|....|+.+++++||..||.++++++.
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   67 (70)
T 2d8x_A            3 SGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGP   67 (70)
T ss_dssp             CCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCS
T ss_pred             CCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCC
Confidence            45689999999995 677999999999999999999999999888889999999999999998764

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

Probab=99.59  E-value=3.3e-16  Score=98.25  Aligned_cols=61  Identities=16%  Similarity=0.273  Sum_probs=51.6

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCcccccc-----ccccccCccccccceeecCCC
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPL-----EKVAVESQAYHKTCFKCSHGG  130 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~v~~~~~~~H~~CF~C~~C~  130 (164)
                      ++++||..||.++++++|.      .|                     +..|..     +.|.++++.||++||+|..|+
T Consensus         1 g~~~yC~~cy~~~~~~~C~------~C---------------------~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~   53 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCA------GC---------------------KNPITGFGKGSSVVAYEGQSWHDYCFHCKKCS   53 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCS------SS---------------------CCCCCCCSSCCCEEEETTEEEETTTCBCSSSC
T ss_pred             CCCeEchhHhchhhCccCc------cc---------------------CCcccCCCCCceeEEECcceeCcccCEehhcC
Confidence            4689999999999998874      56                     333332     558899999999999999999


Q ss_pred             CCCCCCCeeccCC
Q 040725          131 CSISPSNYVALEG  143 (164)
Q Consensus       131 ~~l~~~~f~~~~g  143 (164)
                      ++|.+..|+..||
T Consensus        54 ~~L~~~~f~~~~~   66 (77)
T 2egq_A           54 VNLANKRFVFHQE   66 (77)
T ss_dssp             CBCTTSCCCEETT
T ss_pred             CCCCCCccEeECC
Confidence            9999999999999

>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=99.58  E-value=1.1e-15  Score=97.13  Aligned_cols=67  Identities=28%  Similarity=0.605  Sum_probs=59.7

Q ss_pred             cCCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCee--eeCCeeeecchhhhhccC
Q 040725            5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYS--SMEGVLYCKPHFEQLFKE   71 (164)
Q Consensus         5 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~--~~~g~~~C~~c~~~~~~~   71 (164)
                      +..++..+|.+|++.|+..+.+.++++.||.+||+|..|+.+|....|.  .+++++||+.||.+++++
T Consensus        10 ~~~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A           10 QEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             CCCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCC
T ss_pred             cCCCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcC
Confidence            4455678999999999888888999999999999999999999988887  479999999999988754

>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=99.58  E-value=2.5e-15  Score=96.91  Aligned_cols=64  Identities=22%  Similarity=0.380  Sum_probs=59.0

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG   73 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c   73 (164)
                      ...+|..|++.|. ++.+.++++.||.+||+|..|+..|....|+.+++++||..||.++|++++
T Consensus        24 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~   87 (89)
T 1x64_A           24 RMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPS   87 (89)
T ss_dssp             SCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCC
T ss_pred             cCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            4578999999996 477899999999999999999999998889999999999999999999986

>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=99.58  E-value=6.8e-16  Score=97.96  Aligned_cols=73  Identities=12%  Similarity=0.119  Sum_probs=60.1

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCcccccccc-ccccCccccccceeecCCCCCCC
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCFKCSHGGCSIS  134 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF~C~~C~~~l~  134 (164)
                      ++.+||+.||.++++++|.      .|.                    +.|.+++. |.++++.||++||+|..|+++|.
T Consensus         1 ~~~~yC~~cy~~~~~~~C~------~C~--------------------~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~   54 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCK------GCF--------------------KAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG   54 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCS------SSC--------------------CBCCSSSCEEECSSCEEETTTCCCSSSCCCCT
T ss_pred             CCCcCchhHHccccCCcCc------cCC--------------------cccccCceEEEECccccccccCchhhCCCccC
Confidence            3679999999999988874      562                    23333344 88999999999999999999999


Q ss_pred             CCCeeccCC------Chhhhcccccc
Q 040725          135 PSNYVALEG------NYNHLIKFASM  154 (164)
Q Consensus       135 ~~~f~~~~g------~y~~l~~~~~~  154 (164)
                      +..|+..||      ||.++++++..
T Consensus        55 ~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           55 TGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             TSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             CCccEeeCCEEECHHHHHHHhCCCCC
Confidence            999999999      99999987653

>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=99.57  E-value=3.4e-15  Score=94.68  Aligned_cols=65  Identities=26%  Similarity=0.513  Sum_probs=59.9

Q ss_pred             ccccccCCceeeccc-EEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           10 QQKYKVYEKTVYPVE-QLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ..+|.+|++.|..++ .+.++++.||.+||+|..|+++|....|+.+++++||..||.++|+++++
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             CCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            479999999997655 48999999999999999999999988899999999999999999999875

>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=99.56  E-value=3.7e-15  Score=94.06  Aligned_cols=67  Identities=18%  Similarity=0.295  Sum_probs=59.0

Q ss_pred             CCCCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            6 FIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         6 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      -..+.++|..|++.|. ++.+.++++.||.+||+|..|+.+|.... +.+++++||..||.++|+|+++
T Consensus        11 ~~~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           11 RGLGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCCSSC
T ss_pred             hccCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCCCCC
Confidence            3445689999999996 67789999999999999999999998775 5899999999999999988753

>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=99.56  E-value=2.6e-15  Score=95.26  Aligned_cols=65  Identities=15%  Similarity=0.428  Sum_probs=59.2

Q ss_pred             ccccccCCceeec-ccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           10 QQKYKVYEKTVYP-VEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        10 ~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      .++|..|+++|.. +..+.++++.||.+||+|+.|+.+|....|+.+++++||..||.++|+++|.
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            4689999999973 4567889999999999999999999988899999999999999999999874

>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=99.56  E-value=1.4e-15  Score=96.31  Aligned_cols=69  Identities=10%  Similarity=0.098  Sum_probs=57.1

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCC
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISP  135 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~  135 (164)
                      +|++||+.||. +++++|      ..|                     +.+|.+..|.++++.||++||+|..|+++|.+
T Consensus         2 ~g~~yC~~~y~-~~~~~C------~~C---------------------~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~   53 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKC------ATC---------------------SQPILDRILRAMGKAYHPGCFTCVVCHRGLDG   53 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBC------TTT---------------------CCBCCSCCEEETTEEECTTTCBCSSSCCBCTT
T ss_pred             cCCEECHHHhh-cCCCcc------ccC---------------------CCeecceeEEECCccccHHhcCcccCCCccCC
Confidence            67999999998 677776      356                     44445556899999999999999999999999


Q ss_pred             CCeecc-CC------Chhhhcccc
Q 040725          136 SNYVAL-EG------NYNHLIKFA  152 (164)
Q Consensus       136 ~~f~~~-~g------~y~~l~~~~  152 (164)
                      ..|+.. ||      ||.++|+++
T Consensus        54 ~~f~~~~~g~~yC~~cy~~~f~~~   77 (81)
T 2dlo_A           54 IPFTVDATSQIHCIEDFHRKFASG   77 (81)
T ss_dssp             SCEECCTTCCCEEHHHHHHHTTSS
T ss_pred             CeeEECCCCEEECHHHHHHHhcCc
Confidence            889876 67      999988764

>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=99.56  E-value=1.9e-15  Score=95.68  Aligned_cols=71  Identities=15%  Similarity=0.146  Sum_probs=58.1

Q ss_pred             CCeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCC-
Q 040725           56 EGVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSIS-  134 (164)
Q Consensus        56 ~g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~-  134 (164)
                      ++.+||+.||.++|+++|.      .|                     +.+|.++.|.++++.||++||+|..|+++|. 
T Consensus         1 g~~~yC~~~y~~~~~~~C~------~C---------------------~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~   53 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCH------GC---------------------SLLMTGPFMVAGEFKYHPECFACMSCKVIIED   53 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCT------TT---------------------CCBCCSCCBCCTTCCBCTTSCBCTTTCCBCCT
T ss_pred             CCCccchhHHhhhcCCcCc------cC---------------------CCCcCceEEEECCceeccccCCccCCCCccCC
Confidence            3579999999999998874      56                     4444566689999999999999999999996 


Q ss_pred             CCCee-ccCC------Chhhhccccc
Q 040725          135 PSNYV-ALEG------NYNHLIKFAS  153 (164)
Q Consensus       135 ~~~f~-~~~g------~y~~l~~~~~  153 (164)
                      +..|+ +.+|      ||.++++...
T Consensus        54 g~~f~~~~~~~~~C~~c~~~~~~~~~   79 (81)
T 1x6a_A           54 GDAYALVQHATLYCGKCHNEVVSGPS   79 (81)
T ss_dssp             TSCEEECSSSCEEEHHHHHHHHCTTS
T ss_pred             CCcEEEeeCCEEECHHHHHHHhcCCC
Confidence            56787 5787      8888887653

>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=99.56  E-value=3.1e-15  Score=94.45  Aligned_cols=64  Identities=20%  Similarity=0.470  Sum_probs=59.4

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      .++|.+|+++|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus        15 ~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~   78 (80)
T 1x3h_A           15 SPKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPS   78 (80)
T ss_dssp             SCBCTTTCCBCC-SSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCC
T ss_pred             CCccccCCCeec-ceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCC
Confidence            478999999996 4778999999999999999999999988899999999999999999999984

>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=99.56  E-value=4.2e-15  Score=94.13  Aligned_cols=66  Identities=21%  Similarity=0.423  Sum_probs=59.2

Q ss_pred             CCccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeee-CCeeeecchhhhhccCCCC
Q 040725            8 GTQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         8 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~-~g~~~C~~c~~~~~~~~c~   74 (164)
                      ...++|.+|+++|. ++.+.++++.||++||+|..|+.+|....|... ++++||..||.++|+++|.
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            45689999999996 567999999999999999999999987777765 7899999999999999984

>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=99.55  E-value=4e-15  Score=93.96  Aligned_cols=65  Identities=20%  Similarity=0.429  Sum_probs=59.5

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      ..++|..|++.|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   78 (80)
T 2cuq_A           14 FAPRCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPS   78 (80)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTT
T ss_pred             cCCcCCCCCCEec-CcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCC
Confidence            3578999999995 5678999999999999999999999887899999999999999999999984

>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=99.54  E-value=2.5e-15  Score=95.14  Aligned_cols=71  Identities=17%  Similarity=0.227  Sum_probs=57.8

Q ss_pred             CeeeecchhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccceeecCCCCCCCCC
Q 040725           57 GVLYCKPHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPS  136 (164)
Q Consensus        57 g~~~C~~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~  136 (164)
                      +.+||..||.++|+++|.      .|                     +..|.++.|.++++.||++||+|..|+++|..+
T Consensus         2 ~~~yC~~dy~~~~~~~C~------~C---------------------~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~   54 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCF------SC---------------------DQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPG   54 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCT------TT---------------------CCBCCSCCEEETTEEECTTTSSCSSSCCCCCSS
T ss_pred             CCCcchHHHHhHhCCcCc------cc---------------------cCEeccceEEECCceeCccCCccccCCCCCCCC
Confidence            468999999999998874      56                     444455669999999999999999999999876


Q ss_pred             CeeccCC-------Chhhhcccccc
Q 040725          137 NYVALEG-------NYNHLIKFASM  154 (164)
Q Consensus       137 ~f~~~~g-------~y~~l~~~~~~  154 (164)
                      .|+..+|       +|.+++.+.+.
T Consensus        55 ~~~~~~~~~~~C~~C~~~~~~~~~s   79 (81)
T 1v6g_A           55 DRVTFNGKECMCQKCSLPVSVSGPS   79 (81)
T ss_dssp             SCEEEETTEEEEHHHHSCCSSCCCC
T ss_pred             CEEEeCCCCEEChhhhcccCCCCCC
Confidence            6766666       78888777654

>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=99.53  E-value=8.2e-15  Score=90.67  Aligned_cols=63  Identities=19%  Similarity=0.395  Sum_probs=56.8

Q ss_pred             CccccccCCceeecc-cEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccC
Q 040725            9 TQQKYKVYEKTVYPV-EQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE   71 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~   71 (164)
                      ..++|.+|+++|... ..+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+.
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            568999999999764 468999999999999999999999877899999999999999998843

>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=99.52  E-value=1.1e-14  Score=89.87  Aligned_cols=62  Identities=26%  Similarity=0.638  Sum_probs=56.4

Q ss_pred             CccccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725            9 TQQKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      ...+|.+|++.|...+. +.++++.||.+||+|..|+.+|....|+.++|++||..||.++|+
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            45799999999987775 689999999999999999999988888899999999999999874

>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=99.51  E-value=1.7e-14  Score=89.59  Aligned_cols=63  Identities=16%  Similarity=0.182  Sum_probs=55.7

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCc-CCCeeeeCCeeeecchhhhhccCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLK-LSNYSSMEGVLYCKPHFEQLFKES   72 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~~C~~c~~~~~~~~   72 (164)
                      ..++|.+|+++|. ++.+.++++.||++||+|..|+.+|. ...|+.+++++||..||.++++..
T Consensus         4 ~~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~   67 (73)
T 1wig_A            4 GSSGCDSCEKYIT-GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTED   67 (73)
T ss_dssp             SCCSCSSSCCCCS-SCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSS
T ss_pred             CcCCcccCCCEec-CeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccc
Confidence            4578999999995 57789999999999999999999998 567888999999999999887543

>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=99.47  E-value=3.1e-14  Score=97.07  Aligned_cols=61  Identities=20%  Similarity=0.406  Sum_probs=55.2

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCc--CCCeeeeCCeeeecchhhhhcc
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      ..+|.+|+++|...+.+.++++.||..||+|..|+.+|.  ...|+.++|++||..||.++|+
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            468999999998777799999999999999999999997  3578899999999999999874

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

Probab=99.46  E-value=6e-14  Score=85.13  Aligned_cols=59  Identities=20%  Similarity=0.535  Sum_probs=53.2

Q ss_pred             ccccccCCceeec-ccEEEeCCcccC--CCCcccCCCCCcCcCCCeeeeCCeeee-cchhhhh
Q 040725           10 QQKYKVYEKTVYP-VEQLSDDGVVYH--KSCFKCSHCKGTLKLSNYSSMEGVLYC-KPHFEQL   68 (164)
Q Consensus        10 ~~~C~~C~~~i~~-~~~~~~~~~~~H--~~Cf~C~~C~~~L~~~~~~~~~g~~~C-~~c~~~~   68 (164)
                      .++|.+|+++|.. ++.+.++++.||  .+||+|..|+.+|....|+.++|++|| ..||.++
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            3689999999976 477999999999  999999999999998889999999999 8888764

>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=99.44  E-value=7.5e-14  Score=88.24  Aligned_cols=64  Identities=17%  Similarity=0.344  Sum_probs=56.3

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcC-CCee-eeCCeeeecchhhhhccCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKL-SNYS-SMEGVLYCKPHFEQLFKESG   73 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~-~~~~-~~~g~~~C~~c~~~~~~~~c   73 (164)
                      ..++|..|+++|. ++.+.++++.||.+||+|..|+++|.. ..|. .+++++||..||.++|++.+
T Consensus        14 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~   79 (81)
T 1x6a_A           14 FGEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPS   79 (81)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTS
T ss_pred             cCCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCC
Confidence            3468999999996 777899999999999999999999975 4566 58999999999999998765

>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=99.43  E-value=1.2e-13  Score=100.96  Aligned_cols=66  Identities=27%  Similarity=0.634  Sum_probs=61.2

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      +..+|.+|+++|...+.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++|+++|.
T Consensus       114 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~  179 (192)
T 1b8t_A          114 GSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF  179 (192)
T ss_dssp             CCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCC
T ss_pred             CCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCC
Confidence            356799999999878888999999999999999999999888899999999999999999999985

>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=99.43  E-value=1e-13  Score=86.81  Aligned_cols=60  Identities=18%  Similarity=0.435  Sum_probs=53.7

Q ss_pred             CccccccCCceeec----ccEEEeCCcccCCCCcccCCCCCcCcCCCeeeeCCeeeecchhhhh
Q 040725            9 TQQKYKVYEKTVYP----VEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   68 (164)
Q Consensus         9 ~~~~C~~C~~~i~~----~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~   68 (164)
                      ..++|.+|+++|..    .+.+.++++.||.+||+|..|+.+|....|+.+++++||..||.++
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            35789999999973    3779999999999999999999999988899999999999999753

>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=99.35  E-value=3.1e-13  Score=82.07  Aligned_cols=49  Identities=16%  Similarity=0.205  Sum_probs=43.1

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +..|.++.|.++|+.||++||+|..|+++|.++.|++.||      ||.++|+++
T Consensus        12 ~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A           12 RRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             TEECCSCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCEecceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            4555566799999999999999999999999999999999      999998764

>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=99.29  E-value=1.9e-12  Score=80.29  Aligned_cols=50  Identities=12%  Similarity=0.116  Sum_probs=42.6

Q ss_pred             ccccccccccccCccccccceeecCCCCCCC-CCCeeccCC------Chhhhccccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSIS-PSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~-~~~f~~~~g------~y~~l~~~~~  153 (164)
                      +..|.++.|.++++.||++||+|..|+++|. +..|+..+|      +|..++....
T Consensus        12 ~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~~   68 (73)
T 1wig_A           12 EKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTEDS   68 (73)
T ss_dssp             CCCCSSCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSSC
T ss_pred             CCEecCeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcccc
Confidence            5555566699999999999999999999998 788999998      8888877644

>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=99.29  E-value=1.6e-12  Score=81.13  Aligned_cols=43  Identities=12%  Similarity=0.313  Sum_probs=39.5

Q ss_pred             ccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          110 EKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       110 ~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +.|.++++.||++||+|..|+++|.+..|+..||      ||.+++++.
T Consensus        22 ~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~   70 (76)
T 1x68_A           22 KFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDI   70 (76)
T ss_dssp             CEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCS
T ss_pred             eeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCc
Confidence            5589999999999999999999999999999999      998888765

>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=99.28  E-value=2.3e-12  Score=82.98  Aligned_cols=50  Identities=16%  Similarity=0.311  Sum_probs=44.4

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~  153 (164)
                      +.+|.++.|.++++.||++||+|..|+++|.+..|++.||      ||.++|+++-
T Consensus        32 ~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c   87 (90)
T 2dar_A           32 NQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGP   87 (90)
T ss_dssp             CCBCCSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCC
T ss_pred             CCEecceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCC
Confidence            5566667799999999999999999999999999999999      9999998753

>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=99.27  E-value=3e-12  Score=78.52  Aligned_cols=49  Identities=22%  Similarity=0.375  Sum_probs=43.2

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +..|.++.|.++++.||++||+|..|+++|.+..|++.||      ||.++++++
T Consensus        12 ~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~   66 (70)
T 2d8z_A           12 KKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASG   66 (70)
T ss_dssp             CCBCCSSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCC
T ss_pred             CCeeccceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccc
Confidence            5555566699999999999999999999999999999999      999988765

>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=99.27  E-value=3.1e-12  Score=80.73  Aligned_cols=62  Identities=16%  Similarity=0.286  Sum_probs=52.3

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCCcccCCCCCcCcCCCeeee-CCeeeecchhhhhccCC
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHFEQLFKES   72 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~-~g~~~C~~c~~~~~~~~   72 (164)
                      .++|..|++.|. ++.+.++++.||.+||+|..|+++|..+.++.. ++.+||..||.+++...
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            468999999996 678999999999999999999999987776655 44579999998776443

>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=99.26  E-value=3.3e-12  Score=78.17  Aligned_cols=49  Identities=16%  Similarity=0.411  Sum_probs=43.1

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +..|.++.|.++++.||++||+|..|+++|.+..|++.||      ||.++++++
T Consensus        12 ~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~   66 (69)
T 2cur_A           12 NKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGP   66 (69)
T ss_dssp             CCCCCTTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCS
T ss_pred             CCEeCcceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCC
Confidence            4555566799999999999999999999999999999999      999988764

>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=99.26  E-value=4.2e-12  Score=78.31  Aligned_cols=44  Identities=16%  Similarity=0.383  Sum_probs=39.7

Q ss_pred             ccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725          110 EKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus       110 ~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~  153 (164)
                      ..|.++++.||++||+|..|+++|.+..|+..||      ||.+++++.+
T Consensus        22 ~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A           22 KYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             SCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             ceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            4488999999999999999999999999999999      9999987753

>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=99.24  E-value=5.1e-12  Score=77.53  Aligned_cols=49  Identities=14%  Similarity=0.226  Sum_probs=42.6

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +..|.++.|.++++.||++||+|..|+++|....|+..||      ||.+++++.
T Consensus        12 ~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   66 (70)
T 2d8x_A           12 GEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASG   66 (70)
T ss_dssp             CCBCCSCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCC
T ss_pred             CCEecceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCC
Confidence            4555566699999999999999999999999999999999      888888764

>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=99.23  E-value=1.1e-11  Score=90.28  Aligned_cols=63  Identities=22%  Similarity=0.516  Sum_probs=53.3

Q ss_pred             ccccCCceeeccc-EEEeCCcccCCCCcccCCCCCcCcC-CCeeeeCCeeeecchhhhhccCCCC
Q 040725           12 KYKVYEKTVYPVE-QLSDDGVVYHKSCFKCSHCKGTLKL-SNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        12 ~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~-~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      +|..|++.|...+ .+.++++.||..||+|..|+++|.. ..|+..++++||..||.+++++++.
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            7999999997666 4789999999999999999999964 4688899999999999999988874

>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=99.22  E-value=3.3e-12  Score=80.26  Aligned_cols=53  Identities=15%  Similarity=0.189  Sum_probs=45.7

Q ss_pred             CCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725          101 ASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus       101 ~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~  153 (164)
                      +.++..|.++.|.++++.||++||+|..|+++|.+..|+.+||      ||.++|+++.
T Consensus        19 ~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g   77 (79)
T 1x62_A           19 DKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS   77 (79)
T ss_dssp             SSSCCCCCSSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCC
T ss_pred             ccCCCCccCcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            3336666667799999999999999999999999888999999      9999998764

>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=99.22  E-value=5.4e-12  Score=77.75  Aligned_cols=43  Identities=23%  Similarity=0.492  Sum_probs=39.5

Q ss_pred             ccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          110 EKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       110 ~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +.|.++++.||++||+|..|+++|.+..|+..||      ||.++++++
T Consensus        20 ~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~   68 (72)
T 1wyh_A           20 RKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASG   68 (72)
T ss_dssp             CEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCC
T ss_pred             cEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCc
Confidence            4588999999999999999999999999999999      999988765

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

Probab=99.22  E-value=5.4e-12  Score=86.61  Aligned_cols=61  Identities=21%  Similarity=0.425  Sum_probs=54.2

Q ss_pred             ccccCCceeeccc-EEEeCCcccCCCCcccCCCCCcCc-CCCeeeeCCeeeecchhhhhccCC
Q 040725           12 KYKVYEKTVYPVE-QLSDDGVVYHKSCFKCSHCKGTLK-LSNYSSMEGVLYCKPHFEQLFKES   72 (164)
Q Consensus        12 ~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~~C~~c~~~~~~~~   72 (164)
                      +|..|+++|...+ .+.++++.||.+||+|..|+++|. +..|+..++++||..||.++++++
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            8999999997655 579999999999999999999995 456888999999999999988754

>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=99.21  E-value=1.8e-11  Score=77.44  Aligned_cols=52  Identities=21%  Similarity=0.424  Sum_probs=42.8

Q ss_pred             CCcccc-ccccccccCccccccceeecCCCCCCCCCCee--ccCC------Chhhhccccc
Q 040725          102 SIKTVC-PLEKVAVESQAYHKTCFKCSHGGCSISPSNYV--ALEG------NYNHLIKFAS  153 (164)
Q Consensus       102 ~~~~~~-~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~--~~~g------~y~~l~~~~~  153 (164)
                      .++..| ..+.|.++++.||++||+|..|+++|....|+  ++||      ||.+|+....
T Consensus        20 ~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~   80 (82)
T 2co8_A           20 LCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPS   80 (82)
T ss_dssp             SSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCC
T ss_pred             ccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCC
Confidence            334444 66789999999999999999999999999988  4688      9998887643

>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=99.20  E-value=9.3e-12  Score=79.96  Aligned_cols=54  Identities=17%  Similarity=0.222  Sum_probs=46.2

Q ss_pred             CCCCccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725          100 AASIKTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus       100 ~~~~~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~  153 (164)
                      .+.++..|.++.|.++++.||++||+|..|+++|.+..|+.+||      ||.++|+++.
T Consensus        28 C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~   87 (89)
T 1x64_A           28 CDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPS   87 (89)
T ss_dssp             CTTTCCBCCSCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCC
T ss_pred             cccCCCEecccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            33346666677799999999999999999999999888999999      9999998764

>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=99.20  E-value=6.5e-12  Score=77.37  Aligned_cols=42  Identities=19%  Similarity=0.475  Sum_probs=38.8

Q ss_pred             cccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          111 KVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       111 ~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      .|.++|+.||++||+|..|+++|.+..|++.||      ||.+++++.
T Consensus        21 ~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~   68 (72)
T 1x4k_A           21 KMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASG   68 (72)
T ss_dssp             EEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSC
T ss_pred             EEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCC
Confidence            588999999999999999999999999999999      999888765

>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=99.19  E-value=1.3e-11  Score=77.83  Aligned_cols=48  Identities=19%  Similarity=0.452  Sum_probs=41.4

Q ss_pred             cccc-ccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          104 KTVC-PLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~-~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +..| .++.|.++++.||++||+|..|+++|.+ .|+++||      ||.++|+++
T Consensus        22 ~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~   76 (80)
T 2dj7_A           22 KEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSG   76 (80)
T ss_dssp             CCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCC
T ss_pred             CCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCC
Confidence            4444 4667999999999999999999999986 6999999      999999875

>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=99.14  E-value=1.7e-11  Score=77.34  Aligned_cols=50  Identities=14%  Similarity=0.318  Sum_probs=41.6

Q ss_pred             cccc-ccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccccc
Q 040725          104 KTVC-PLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFAS  153 (164)
Q Consensus       104 ~~~~-~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~  153 (164)
                      +++| ..+.|.++++.||++||+|..|+++|.+..|+..||      ||.++++++-
T Consensus        14 ~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c   70 (81)
T 1a7i_A           14 GRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKG   70 (81)
T ss_dssp             CCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC---
T ss_pred             CccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcc
Confidence            4444 566799999999999999999999999999999999      9999988764

>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=99.14  E-value=2.3e-11  Score=75.72  Aligned_cols=49  Identities=24%  Similarity=0.461  Sum_probs=40.9

Q ss_pred             ccccc-cccccccCccccccceeecCCCCCCCCCCeeccCC-------Chhhhcccc
Q 040725          104 KTVCP-LEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG-------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~-~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g-------~y~~l~~~~  152 (164)
                      +..|. .+.|.++++.||++||+|..|+++|.+..|+++||       ||.++|+++
T Consensus        16 ~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~k   72 (76)
T 2cu8_A           16 DKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSG   72 (76)
T ss_dssp             CCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSS
T ss_pred             CCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccc
Confidence            34444 67799999999999999999999999989999998       566777654

>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=99.14  E-value=4.6e-11  Score=75.04  Aligned_cols=48  Identities=15%  Similarity=0.339  Sum_probs=40.9

Q ss_pred             ccccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          104 KTVCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      +..|.++.|.++|+.||++||+|..|+++|.+..| ++||      ||.++|.+.
T Consensus        22 ~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f-~~~g~~yC~~cy~~~f~p~   75 (79)
T 2cor_A           22 HAIIDEQPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMGVSG   75 (79)
T ss_dssp             CCBCCSCCCCCSSSCCCTTTSBCSSSCCBCCTTCE-EETTEEECHHHHHTTSCCS
T ss_pred             CCEecceEEEECcceeCCCCCEeCCCCCccCCCCE-eECCEEeCHHHHHHhCCCC
Confidence            55556667999999999999999999999998865 8888      998888764

>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=99.13  E-value=3.3e-11  Score=74.19  Aligned_cols=41  Identities=22%  Similarity=0.441  Sum_probs=37.5

Q ss_pred             cccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhccc
Q 040725          111 KVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKF  151 (164)
Q Consensus       111 ~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~  151 (164)
                      .|.++++.||++||+|..|+++|.+..|+.+||      ||.+++..
T Consensus        21 ~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~~   67 (72)
T 1x61_A           21 GVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES   67 (72)
T ss_dssp             CEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHHT
T ss_pred             EEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHcc
Confidence            588999999999999999999999889999999      88888753

>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=99.12  E-value=1.6e-11  Score=75.38  Aligned_cols=43  Identities=28%  Similarity=0.614  Sum_probs=37.6

Q ss_pred             cccc-ccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcc
Q 040725          108 PLEK-VAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIK  150 (164)
Q Consensus       108 ~~~~-v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~  150 (164)
                      ..+. |.++|+.||++||+|..|+++|.+..|+..||      ||.+||+
T Consensus        23 ~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           23 PAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             TTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             CCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            3454 67999999999999999999998889999999      8888874

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

Probab=99.10  E-value=7.4e-11  Score=80.36  Aligned_cols=60  Identities=18%  Similarity=0.504  Sum_probs=53.5

Q ss_pred             ccccccCCceeecc-cEEEeCCcccC--CCCcccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725           10 QQKYKVYEKTVYPV-EQLSDDGVVYH--KSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   69 (164)
Q Consensus        10 ~~~C~~C~~~i~~~-~~~~~~~~~~H--~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~   69 (164)
                      .++|.+|+++|... ..+.++++.||  .+||+|..|+++|.+..|+..++++||..++.++|
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            46899999999764 45899999999  99999999999999878889999999998888765

>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=99.09  E-value=4.9e-11  Score=76.84  Aligned_cols=49  Identities=33%  Similarity=0.695  Sum_probs=43.0

Q ss_pred             ccccccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccccc
Q 040725          106 VCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFASM  154 (164)
Q Consensus       106 ~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~~  154 (164)
                      |...+.|.++++.||++||+|..|+++|....|+.+||      ||.++++++..
T Consensus        25 I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~   79 (91)
T 2d8y_A           25 VYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGN   79 (91)
T ss_dssp             CCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSC
T ss_pred             cCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcC
Confidence            33346789999999999999999999999988999999      99999988754

>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=99.08  E-value=5.4e-11  Score=74.07  Aligned_cols=49  Identities=22%  Similarity=0.474  Sum_probs=41.2

Q ss_pred             ccccccccccCccccccceeecCCCCCCCCCCeeccCC-------Chhhhcccccc
Q 040725          106 VCPLEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG-------NYNHLIKFASM  154 (164)
Q Consensus       106 ~~~~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g-------~y~~l~~~~~~  154 (164)
                      |..++.|.++|+.||++||+|..|+++|.++.|++.||       ||.++++++-.
T Consensus        10 I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~   65 (76)
T 1iml_A           10 VYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF   65 (76)
T ss_dssp             CCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             EECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCC
Confidence            33367799999999999999999999999989999998       56777776543

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

Probab=99.07  E-value=6.7e-11  Score=73.71  Aligned_cols=44  Identities=25%  Similarity=0.517  Sum_probs=39.1

Q ss_pred             ccc-ccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          109 LEK-VAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       109 ~~~-v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      .+. +.++|+.||++||+|..|+++|.+..|+..||      ||.+++++.
T Consensus        24 ~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~   74 (77)
T 1g47_A           24 AEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPC   74 (77)
T ss_dssp             TTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC
T ss_pred             CceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcc
Confidence            444 67999999999999999999999888999999      999988764

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

Probab=99.06  E-value=4.6e-11  Score=72.20  Aligned_cols=35  Identities=23%  Similarity=0.604  Sum_probs=32.7

Q ss_pred             cccccccCcccc--ccceeecCCCCCCCCCCeeccCC
Q 040725          109 LEKVAVESQAYH--KTCFKCSHGGCSISPSNYVALEG  143 (164)
Q Consensus       109 ~~~v~~~~~~~H--~~CF~C~~C~~~l~~~~f~~~~g  143 (164)
                      ++.|.++|+.||  ++||+|..|+++|.+..|+.+||
T Consensus        16 ~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g   52 (65)
T 2iyb_E           16 VQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEG   52 (65)
T ss_dssp             SCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETT
T ss_pred             ceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECC
Confidence            356999999999  99999999999999999999999

>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=99.04  E-value=1.3e-10  Score=83.15  Aligned_cols=63  Identities=24%  Similarity=0.471  Sum_probs=53.2

Q ss_pred             ccccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCC-Cee-eeCCeeeecchhhhhccCC
Q 040725           10 QQKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLS-NYS-SMEGVLYCKPHFEQLFKES   72 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~~C~~c~~~~~~~~   72 (164)
                      .++|..|++.|...+. +.+++..||.+||+|..|+.+|..+ .|+ ..+|++||..||.+++...
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            3689999999977665 5899999999999999999999754 455 4689999999999887543

>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=99.03  E-value=1.3e-10  Score=78.01  Aligned_cols=49  Identities=18%  Similarity=0.310  Sum_probs=41.8

Q ss_pred             ccccccc-cccccCccccccceeecCCCCCCCC--CCeeccCC------Chhhhcccc
Q 040725          104 KTVCPLE-KVAVESQAYHKTCFKCSHGGCSISP--SNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       104 ~~~~~~~-~v~~~~~~~H~~CF~C~~C~~~l~~--~~f~~~~g------~y~~l~~~~  152 (164)
                      +.+|.+. .|.++++.||++||+|..|+++|..  ..|+.+||      ||.++|+++
T Consensus        10 ~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~   67 (114)
T 1j2o_A           10 QQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSG   67 (114)
T ss_dssp             CSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSC
T ss_pred             CCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcc
Confidence            4444444 6899999999999999999999974  68999999      999999887

>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=99.02  E-value=1.5e-10  Score=75.78  Aligned_cols=44  Identities=18%  Similarity=0.347  Sum_probs=39.5

Q ss_pred             cccccccCccccccceeecCCCCCCCCCCeeccCC------Chhhhcccc
Q 040725          109 LEKVAVESQAYHKTCFKCSHGGCSISPSNYVALEG------NYNHLIKFA  152 (164)
Q Consensus       109 ~~~v~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~g------~y~~l~~~~  152 (164)
                      ++.|.++|+.||++||+|..|+++|.+..|+.+||      ||.++++++
T Consensus        19 ~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~   68 (101)
T 2cup_A           19 SKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPK   68 (101)
T ss_dssp             SCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCB
T ss_pred             ceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCc
Confidence            45588999999999999999999999989999999      898887654

>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=99.00  E-value=1.5e-10  Score=78.72  Aligned_cols=52  Identities=17%  Similarity=0.300  Sum_probs=42.1

Q ss_pred             CCCCCccccccc-cccccCccccccceeecCCCCCCC--CCCeeccCC------Chhhhcc
Q 040725           99 KAASIKTVCPLE-KVAVESQAYHKTCFKCSHGGCSIS--PSNYVALEG------NYNHLIK  150 (164)
Q Consensus        99 ~~~~~~~~~~~~-~v~~~~~~~H~~CF~C~~C~~~l~--~~~f~~~~g------~y~~l~~  150 (164)
                      +.+.++.+|.+. .|.++++.||++||+|..|+++|.  +..|+.+||      ||.++|+
T Consensus        63 ~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           63 RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             BBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             cCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            334445555555 489999999999999999999996  568999999      8888874

>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=98.92  E-value=2.7e-10  Score=77.29  Aligned_cols=48  Identities=17%  Similarity=0.270  Sum_probs=40.4

Q ss_pred             ccccccc-cccccCccccccceeecCCCCCCC--CCCeeccCC------Chhhhccc
Q 040725          104 KTVCPLE-KVAVESQAYHKTCFKCSHGGCSIS--PSNYVALEG------NYNHLIKF  151 (164)
Q Consensus       104 ~~~~~~~-~v~~~~~~~H~~CF~C~~C~~~l~--~~~f~~~~g------~y~~l~~~  151 (164)
                      +.+|... .|.++++.||++||+|..|+++|.  +..|+.+||      ||.++|++
T Consensus        12 ~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~   68 (122)
T 1m3v_A           12 GGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGN   68 (122)
T ss_dssp             SSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCC
T ss_pred             CCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCC
Confidence            3444443 488999999999999999999996  467999999      99999987

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

Probab=98.87  E-value=1.2e-09  Score=79.02  Aligned_cols=60  Identities=25%  Similarity=0.489  Sum_probs=50.6

Q ss_pred             ccccccCCceeecccE-EEeCCcccCCCCcccCCCCCcCcCC-Cee-eeCCeeeecchhhhhc
Q 040725           10 QQKYKVYEKTVYPVEQ-LSDDGVVYHKSCFKCSHCKGTLKLS-NYS-SMEGVLYCKPHFEQLF   69 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~~C~~c~~~~~   69 (164)
                      .++|..|+++|...+. +.++++.||..||+|..|+++|..+ .|+ ..++++||..||.++.
T Consensus       119 ~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~~  181 (182)
T 2jtn_A          119 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  181 (182)
T ss_dssp             SCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHHT
T ss_pred             ccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHhh
Confidence            4689999999976664 5899999999999999999999754 455 4689999999998753

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

Probab=98.11  E-value=5e-07  Score=46.19  Aligned_cols=28  Identities=32%  Similarity=0.593  Sum_probs=26.6

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCc
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      .+|..|++.|+..|.+.++|+.||..||
T Consensus         4 ~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            4 PNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcCCccCCEEecceeEEECCeEecccCC
Confidence            5899999999999999999999999997

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

Probab=97.88  E-value=7.1e-06  Score=41.81  Aligned_cols=21  Identities=48%  Similarity=0.809  Sum_probs=19.9

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|++.|+|.++|+.||..||
T Consensus        11 k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A           11 KIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             SBCCGGGCCCSSSSCCCGGGC
T ss_pred             CEEecceeEEECCeEecccCC
Confidence            788999999999999999998

---

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	164
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	8e-18
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	1e-07
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	0.004
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	4e-07
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	2e-06

>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 = 70.5 bits (173), Expect = 8e-18
 Identities = 21/41 (51%), Positives = 28/41 (68%)

Query: 39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNF 79
          +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 = 43.6 bits (103), Expect = 1e-07
 Identities = 9/31 (29%), Positives = 17/31 (54%)

Query: 8  GTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF 38
          G      +  + +Y +E+L  +G  +H+SCF
Sbjct: 6  GAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

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

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

 Score = 31.3 bits (71), Expect = 0.004
 Identities = 6/21 (28%), Positives = 13/21 (61%)

Query: 104 KTVCPLEKVAVESQAYHKTCF 124
           + +  LE++ V    +H++CF
Sbjct: 16  EHLYVLERLCVNGHFFHRSCF 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 = 42.4 bits (100), Expect = 4e-07
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 4  KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF 38
          K     ++     +KTVYP+E+L  +  V+H SCF
Sbjct: 1  KFQAPARETCVECQKTVYPMERLLANQQVFHISCF 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 = 40.6 bits (95), Expect = 2e-06
 Identities = 10/37 (27%), Positives = 16/37 (43%)

Query: 2  KAKSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF 38
          +    +G         + VY  E++   G  +HKSCF
Sbjct: 7  RMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	164
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.88
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.87
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.78
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.7
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.53
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.47
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.46
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.38
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.36
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.36
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.3
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.27
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.21
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.19
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.19
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.14
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.12
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.11
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.1
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.1
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.09
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.09
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.07
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.07
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.03
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.0
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.99
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.98
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.91
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.91
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.9
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.9
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.9
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.89
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.88
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	97.86
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.86
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.83
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.82
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.81
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.8
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.79
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.78
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.77
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.75
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.75
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.7
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.69
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.68
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.68
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.67
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.66
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.59
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.59
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.44
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.44
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.44
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.44
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	97.44
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.39
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.38
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.31
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.3
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.22
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.2
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.13
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.03
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.99
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.95
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.88
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.87
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	96.84
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	96.78
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	96.77
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	96.65
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	96.61
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.48
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.46
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	96.43
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.38
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.32
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.3
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.29
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.28
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.07
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.04
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	96.02
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.84
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.6
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.56
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	95.51
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.48
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.39
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	95.28
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.28
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	94.99
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	94.9
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	94.73
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	94.72
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	94.58
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	94.41
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	94.25
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	94.22
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	94.1
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	93.79
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	93.7
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	93.14
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	92.97
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	92.17
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	90.2
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	90.05
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	89.36
d2co8a1	33	Nedd9 interacting protein with calponin homology,	88.48
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	82.5
d2ctda2	30	Zinc finger protein 512, ZNF512 {Human (Homo sapie	81.59
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	81.29

>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=98.88  E-value=1.8e-10  Score=59.31  Aligned_cols=35  Identities=14%  Similarity=0.297  Sum_probs=29.4

Q ss_pred             chhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccce
Q 040725           63 PHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus        63 ~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      .+|.++|+|+|.      .|                     +.+|.++.|+|+|+.||++||
T Consensus         1 ~DY~~~fapkC~------~C---------------------~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCG------GC---------------------NRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCT------TT---------------------CCBCCSSCEEETTEEECTTTC
T ss_pred             CcHHHHhChhhh------hc---------------------CCcccchheeecCCccCcccC
Confidence            368899999984      57                     666677779999999999998

>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=98.87  E-value=5.9e-10  Score=57.27  Aligned_cols=34  Identities=29%  Similarity=0.696  Sum_probs=32.7

Q ss_pred             cccCCCCCcCcCCCeeeeCCeeeecchhhhhccC
Q 040725           38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE   71 (164)
Q Consensus        38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~   71 (164)
                      |+|..|+++|....|++++|++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7899999999999999999999999999999987

>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=98.78  E-value=1.5e-09  Score=57.49  Aligned_cols=41  Identities=51%  Similarity=1.132  Sum_probs=38.3

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCCcCCCC
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNINKNF   79 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~~~~~~   79 (164)
                      +|..|+..|..+.|...+|.+||++||.++|.+++++++++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny~~gf   41 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF   41 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCCCCCC
Confidence            68999999999999999999999999999999999988775

>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=98.70  E-value=1.8e-09  Score=54.13  Aligned_cols=35  Identities=20%  Similarity=0.403  Sum_probs=30.6

Q ss_pred             chhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccce
Q 040725           63 PHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus        63 ~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +||.+.|+++|.      .|                     +++|+.+.|++.++.||.+||
T Consensus         1 PCyE~kfa~~C~------~C---------------------kk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCA------RC---------------------SKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCT------TT---------------------CCCCCSCCEESSSSEECTTTC
T ss_pred             CchHHHHHHHHh------hc---------------------CCccccCceeecCCcchhhhC
Confidence            478899998884      57                     788888899999999999998

>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=98.53  E-value=3.5e-08  Score=53.86  Aligned_cols=36  Identities=25%  Similarity=0.689  Sum_probs=33.6

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      +|..|++.|.+.....+++++||+.||.++|+|++.
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            589999999998888999999999999999999974

>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=98.47  E-value=2.9e-08  Score=50.84  Aligned_cols=29  Identities=28%  Similarity=0.372  Sum_probs=26.7

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCc
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      -.++|..|+++| .++.+.++++.||++||
T Consensus         7 fapkC~~C~~~I-~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           7 FSPKCGGCNRPV-LENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CSCBCTTTCCBC-CSSCEEETTEEECTTTC
T ss_pred             hChhhhhcCCcc-cchheeecCCccCcccC
Confidence            458999999999 78899999999999998

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

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

Probab=98.46  E-value=4.9e-08  Score=52.20  Aligned_cols=32  Identities=31%  Similarity=0.633  Sum_probs=29.7

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      .++..+|.+|++.++..|.+.++|+.||+.||
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            45678999999999999999999999999998

>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=98.38  E-value=9.7e-08  Score=50.77  Aligned_cols=33  Identities=12%  Similarity=0.021  Sum_probs=28.7

Q ss_pred             cCCCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            5 SFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         5 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      +-....+.|..|+++| .+..+.++|+.||+++|
T Consensus        13 p~~~r~P~C~~C~~pI-~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          13 PAGKRTPMCAHCNQVI-RGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CTTTCCCBBSSSCCBC-CSCEEEETTEEECTTTC
T ss_pred             CCCCCCeeccccCCcc-cCceeeecCCccCcCCC
Confidence            3345668999999999 78899999999999998

>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=98.36  E-value=7.7e-08  Score=49.08  Aligned_cols=33  Identities=27%  Similarity=0.587  Sum_probs=30.4

Q ss_pred             CCCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            6 FIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         6 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      ..+++.+|..|++.+++.|.+.++++.||+.||
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             cCCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            356778999999999999999999999999998

>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=98.36  E-value=2.3e-07  Score=49.98  Aligned_cols=36  Identities=33%  Similarity=0.715  Sum_probs=33.3

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeee-cchhhhhccCCCC
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYC-KPHFEQLFKESGN   74 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C-~~c~~~~~~~~c~   74 (164)
                      +|..|++.|..+...+++++||| ++||.++|+|++.
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            58999999999999999999999 8899999999863

>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=98.30  E-value=1.9e-07  Score=47.41  Aligned_cols=31  Identities=39%  Similarity=0.699  Sum_probs=28.9

Q ss_pred             CCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            8 GTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         8 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      +.+.+|..|++.++..|.+.++|+.||..||
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            4567999999999999999999999999998

>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=98.27  E-value=2.2e-07  Score=45.68  Aligned_cols=32  Identities=22%  Similarity=0.626  Sum_probs=29.4

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      .|..|..+|.++.|..++++|||-.||..+|+
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            47889999999999999999999999999874

>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=98.21  E-value=2.9e-07  Score=44.53  Aligned_cols=29  Identities=38%  Similarity=0.545  Sum_probs=26.9

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCCc
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      .++|.+|++.++..|.+..+|+.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            36899999999999999999999999985

>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=98.19  E-value=4.3e-07  Score=45.53  Aligned_cols=32  Identities=25%  Similarity=0.510  Sum_probs=28.3

Q ss_pred             CCCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            6 FIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         6 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      |..+..+|..|+++| ....+.+.|+.||+.||
T Consensus         4 y~~tlEkC~~C~~~I-~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           4 YVATLEKCATCSQPI-LDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCSSCCBCTTTCCBC-CSCCEEETTEEECTTTC
T ss_pred             HHHHHHHHHHhchHH-HHHHHHHhCCCCCCCCC
Confidence            456678999999999 67779999999999998

>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=98.19  E-value=5.4e-07  Score=43.68  Aligned_cols=32  Identities=28%  Similarity=0.635  Sum_probs=29.5

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      .|..|+++|.++.|..++.++||-.||.++|+
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            48899999999999999999999999998874

>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=98.14  E-value=6.1e-07  Score=44.27  Aligned_cols=31  Identities=16%  Similarity=0.585  Sum_probs=28.5

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   69 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~   69 (164)
                      +|..|.+++..+.|++.+|+|||+.+|.++.
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            4899999999999999999999999998864

>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=98.12  E-value=8.8e-07  Score=43.27  Aligned_cols=35  Identities=37%  Similarity=0.610  Sum_probs=32.3

Q ss_pred             ccCCCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            4 KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         4 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      ||.-++..+|..|.+.++..|-+.-.+++||..||
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            66667889999999999999999999999999998

>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=98.11  E-value=3.1e-07  Score=46.79  Aligned_cols=28  Identities=18%  Similarity=0.378  Sum_probs=26.4

Q ss_pred             eeecCCCCCCCCCCeeccCC------Chhhhccc
Q 040725          124 FKCSHGGCSISPSNYVALEG------NYNHLIKF  151 (164)
Q Consensus       124 F~C~~C~~~l~~~~f~~~~g------~y~~l~~~  151 (164)
                      |+|+.|+++|.+..|+++||      ||++||.+
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            79999999999999999999      99999975

>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=98.10  E-value=1.1e-06  Score=50.44  Aligned_cols=36  Identities=22%  Similarity=0.544  Sum_probs=33.3

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhccCCCC
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN   74 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~~~c~   74 (164)
                      .|..|++.|.+.....+++++||+.||.++|+|++.
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            388999999999999999999999999999999964

>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=98.10  E-value=1.5e-06  Score=42.03  Aligned_cols=31  Identities=35%  Similarity=0.815  Sum_probs=27.2

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      +|..|+..|. +.|..++|.|||+.+|+.+|+
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            5889999996 478899999999999999874

>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=98.09  E-value=6.8e-07  Score=42.41  Aligned_cols=30  Identities=30%  Similarity=0.848  Sum_probs=27.8

Q ss_pred             cccCCCCCcCcCCCeeeeCCeeeecchhhh
Q 040725           38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   67 (164)
Q Consensus        38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~~   67 (164)
                      |+|..|++.|.+.....++|.+||+.||-+
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            789999999999888999999999999864

>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=98.09  E-value=8.3e-07  Score=44.13  Aligned_cols=32  Identities=19%  Similarity=0.233  Sum_probs=29.1

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      ..++..|..|++.|..+..+.++++.||.+||
T Consensus         5 ~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           5 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            34677899999999989999999999999998

>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=98.07  E-value=5.2e-07  Score=46.28  Aligned_cols=35  Identities=17%  Similarity=0.264  Sum_probs=25.2

Q ss_pred             hhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCcccccccc-ccccCccccccce
Q 040725           64 HFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEK-VAVESQAYHKTCF  124 (164)
Q Consensus        64 c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-v~~~~~~~H~~CF  124 (164)
                      ||.+.++++|      ..|.                    +.|.++.+ |.+.|+.||.+||
T Consensus         2 Cy~~~~a~~C------~~C~--------------------k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           2 CTTREDSPKC------KGCF--------------------KAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCCCSCBC------SSSC--------------------CBCCSSSCEEECSSCEEETTTC
T ss_pred             ccccccCccc------ccCC--------------------CccCCCCeEeEeCCccchhccC
Confidence            6778888887      4562                    22223444 9999999999998

>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=98.07  E-value=3.1e-07  Score=43.81  Aligned_cols=28  Identities=32%  Similarity=0.593  Sum_probs=26.6

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCc
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      +.|++|++.+++.|.+.-+++.||..||
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            5799999999999999999999999998

>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=98.03  E-value=8.4e-07  Score=43.57  Aligned_cols=28  Identities=21%  Similarity=0.316  Sum_probs=26.6

Q ss_pred             eeecCCCCCCCCCCeeccCC------Chhhhccc
Q 040725          124 FKCSHGGCSISPSNYVALEG------NYNHLIKF  151 (164)
Q Consensus       124 F~C~~C~~~l~~~~f~~~~g------~y~~l~~~  151 (164)
                      |+|+.|.+++-+.+.+++.|      ||++||++
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            79999999999999999999      99999975

>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=98.00  E-value=1.1e-06  Score=46.73  Aligned_cols=21  Identities=38%  Similarity=0.738  Sum_probs=20.3

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.||+.|++.+.|+.||..||
T Consensus        23 k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          23 QAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECSSSCEEETTEEECTTTC
T ss_pred             CEeeHHHHhhcCCCccccCCC
Confidence            889999999999999999998

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

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

Probab=97.99  E-value=1.8e-06  Score=41.11  Aligned_cols=21  Identities=48%  Similarity=0.809  Sum_probs=20.0

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|++.|.+..+++.||+.||
T Consensus        10 k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_          10 KIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             SBCCGGGCCCSSSSCCCGGGC
T ss_pred             CccccHHHhhhhHHHHhhccC
Confidence            788999999999999999998

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.98  E-value=2.9e-06  Score=41.58  Aligned_cols=33  Identities=30%  Similarity=0.745  Sum_probs=30.8

Q ss_pred             cccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           38 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        38 f~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      |+|..|.+++-+...+++.|..||+.+|.++|+
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhc
Confidence            789999999988889999999999999999985

>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=97.91  E-value=2.1e-06  Score=41.60  Aligned_cols=28  Identities=7%  Similarity=0.057  Sum_probs=24.9

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCC
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSC   37 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   37 (164)
                      +.++|+.|+++| .+..+.++++.||++.
T Consensus         4 g~p~C~~C~~PI-~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           4 GVPICGACRRPI-EGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCEETTTTEEC-CSCEECCTTSBEETTT
T ss_pred             CCcchhhcCCch-hhhHhhhhccccCCCC
Confidence            568999999999 6788999999999874

>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=97.91  E-value=1.7e-06  Score=45.83  Aligned_cols=21  Identities=14%  Similarity=0.154  Sum_probs=18.8

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.+|.+..|+|+|+.||++||
T Consensus        25 ~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          25 NQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBCCSCEEEETTEEECTTTC
T ss_pred             CCcccCceeeecCCccCcCCC
Confidence            677777779999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.90  E-value=2.2e-06  Score=44.54  Aligned_cols=34  Identities=21%  Similarity=0.331  Sum_probs=28.5

Q ss_pred             chhhhhccCCCCcCCCCCCCcccccCCCCCccCCCCCCCCCccccccccccccCccccccc
Q 040725           63 PHFEQLFKESGNINKNFQSPARLVEKSTPELTRSPSKAASIKTVCPLEKVAVESQAYHKTC  123 (164)
Q Consensus        63 ~c~~~~~~~~c~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~H~~C  123 (164)
                      .+|+++|+.+|.      .|                     ...|+++.|.|.++.||++|
T Consensus         8 ~DYq~~fG~~C~------~C---------------------~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCF------SC---------------------DQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCT------TT---------------------CCBCCSCCEEETTEEECTTT
T ss_pred             ccHHHHhCcccc------cc---------------------cCEeeeeeeEecCcccCCCC
Confidence            579999998884      57                     56667777999999999998

>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=97.89  E-value=6.3e-06  Score=40.10  Aligned_cols=32  Identities=31%  Similarity=0.757  Sum_probs=28.4

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeec-chhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCK-PHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~-~c~~~~~~   70 (164)
                      +|..|++.|..+...+++|++||. +||..+|+
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            588999999999999999999994 69988873

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

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

Probab=97.88  E-value=6.4e-06  Score=40.03  Aligned_cols=32  Identities=16%  Similarity=0.558  Sum_probs=29.2

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      .|..|.++++...|..+++..||..||.+.|+
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCCceEeecchhhcC
Confidence            37899999999999999999999999999874

>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=97.86  E-value=2.8e-06  Score=43.50  Aligned_cols=30  Identities=33%  Similarity=0.538  Sum_probs=26.8

Q ss_pred             CccccccCCceeecccE-EEeCCcccCCCCc
Q 040725            9 TQQKYKVYEKTVYPVEQ-LSDDGVVYHKSCF   38 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf   38 (164)
                      ...+|..|+++|.++.. +.+.++.||..||
T Consensus         7 ~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           7 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             cCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            45789999999987765 9999999999998

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

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

Probab=97.86  E-value=3.3e-06  Score=42.67  Aligned_cols=21  Identities=43%  Similarity=0.934  Sum_probs=20.3

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|++.|++.+.|+.||.+||
T Consensus        15 K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1          15 KTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             CBCCTTSEEECSSSEEETTTC
T ss_pred             CEEeeeeeEecCCeehhhccC
Confidence            889999999999999999998

>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=97.83  E-value=3.2e-06  Score=44.41  Aligned_cols=31  Identities=29%  Similarity=0.505  Sum_probs=28.9

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhccccccc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIKFASMK  155 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~~~  155 (164)
                      +|+.|++.|+.+.|+..+|      ||+|||+++++-
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny   37 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNY   37 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCC
Confidence            6999999999999999999      999999998764

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.80  E-value=4.5e-06  Score=41.54  Aligned_cols=29  Identities=14%  Similarity=0.285  Sum_probs=25.2

Q ss_pred             CccccccCCceeecccEEEeCCcccCCCCc
Q 040725            9 TQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         9 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      ...+|..|++.| ....+...++.||.+||
T Consensus         7 fa~~C~~Ckk~I-t~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           7 FAPRCARCSKTL-TQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             SSCCCTTTCCCC-CSCCEESSSSEECTTTC
T ss_pred             HHHHHhhcCCcc-ccCceeecCCcchhhhC
Confidence            357899999999 56668999999999998

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.79  E-value=7.1e-06  Score=39.78  Aligned_cols=31  Identities=35%  Similarity=0.949  Sum_probs=28.3

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   69 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~   69 (164)
                      .|+.|+.+|....|.+..|.+||+.||.+-|
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHT
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhc
Confidence            3789999999999999999999999998866

>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=97.78  E-value=3.6e-06  Score=42.07  Aligned_cols=21  Identities=24%  Similarity=0.373  Sum_probs=18.2

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.+|.+..++|+|+.||+.||
T Consensus        15 ~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1          15 SQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCCSCCEEETTEEECTTTC
T ss_pred             chHHHHHHHHHhCCCCCCCCC
Confidence            666677779999999999998

>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=97.77  E-value=1.1e-05  Score=39.05  Aligned_cols=32  Identities=31%  Similarity=0.717  Sum_probs=29.1

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      .|..|.++++...|..+++..||.+||.++|+
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCcEEEEeccccccC
Confidence            37899999999999999999999999998874

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

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.75  E-value=9.1e-06  Score=39.17  Aligned_cols=28  Identities=11%  Similarity=0.087  Sum_probs=25.0

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCC
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSC   37 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~C   37 (164)
                      ...|++|+++|.+...+.+.++.||..|
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            4579999999987778999999999887

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

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

Probab=97.75  E-value=7.5e-06  Score=41.51  Aligned_cols=21  Identities=29%  Similarity=0.800  Sum_probs=20.2

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|++.|++.+.|+.||.+||
T Consensus        16 K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2          16 EHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CBCCTTTBCCBTTBCCBTTTC
T ss_pred             CEEeeeeEEEecCcEeccccC
Confidence            889999999999999999998

>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=97.69  E-value=1.3e-05  Score=38.41  Aligned_cols=31  Identities=19%  Similarity=0.596  Sum_probs=28.1

Q ss_pred             cCCCCCcCcCCCeeeeCCeeeecchhhhhcc
Q 040725           40 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        40 C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~~   70 (164)
                      |..|.+.|.+.....+++.+||+.||.+.|+
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7889999999999999999999999998763

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

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

Probab=97.68  E-value=7e-06  Score=39.73  Aligned_cols=28  Identities=11%  Similarity=0.129  Sum_probs=25.2

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCc
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      ..|.+|+++|.+...+.+.++.||..|+
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            5799999999888889999999999885

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

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

Probab=97.67  E-value=9.8e-06  Score=37.81  Aligned_cols=27  Identities=30%  Similarity=0.599  Sum_probs=25.2

Q ss_pred             cccccCCceeecccEEEeCCcccCCCC
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSC   37 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~C   37 (164)
                      .+|.+|++.++..|.+...|..||..|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            579999999999999999999999987

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.66  E-value=8e-06  Score=39.78  Aligned_cols=29  Identities=24%  Similarity=0.493  Sum_probs=25.8

Q ss_pred             ccccccCCceeecccE-EEeCCcccCCCCc
Q 040725           10 QQKYKVYEKTVYPVEQ-LSDDGVVYHKSCF   38 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf   38 (164)
                      +..|.+|++.|.+.|+ ..+.+..||..||
T Consensus         2 ~g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           2 SGACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             CEECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             CcccccccCcCChhHhheecccceeeeccC
Confidence            3579999999988888 5999999999998

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

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

Probab=97.59  E-value=1.2e-05  Score=38.74  Aligned_cols=21  Identities=43%  Similarity=0.593  Sum_probs=19.6

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|+++|++..+|+.||..|.
T Consensus        10 K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1          10 KTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CBCCTTTEEEETTEEEETTTC
T ss_pred             CceeeHHhhccCCcccccccC
Confidence            889999999999999999984

>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=97.59  E-value=1.7e-05  Score=39.24  Aligned_cols=21  Identities=19%  Similarity=0.420  Sum_probs=16.6

Q ss_pred             cccccccc-ccccCccccccce
Q 040725          104 KTVCPLEK-VAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~-v~~~~~~~H~~CF  124 (164)
                      +..|..++ +.++++.||.+||
T Consensus        15 g~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2          15 KEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CCCCSSSCCEEETTEEECTTTC
T ss_pred             chhhhCCceeeeeecceeeeeC
Confidence            55555554 8899999999998

>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=97.44  E-value=2.1e-05  Score=36.19  Aligned_cols=26  Identities=31%  Similarity=0.609  Sum_probs=23.5

Q ss_pred             cccCCceeecccE-EEeCCcccCCCCc
Q 040725           13 YKVYEKTVYPVEQ-LSDDGVVYHKSCF   38 (164)
Q Consensus        13 C~~C~~~i~~~~~-~~~~~~~~H~~Cf   38 (164)
                      |..|.+.|+++.+ +...|..||..||
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            7889999988876 8999999999998

>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=97.44  E-value=4.9e-05  Score=36.19  Aligned_cols=29  Identities=21%  Similarity=0.608  Sum_probs=26.6

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   67 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~   67 (164)
                      .|+.|++.|.+..|...++++||-.||..
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            48999999999999999999999999964

>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=97.44  E-value=2.6e-05  Score=35.96  Aligned_cols=28  Identities=36%  Similarity=0.730  Sum_probs=26.1

Q ss_pred             cccccCCceeecccEEEeCCcccCCCCc
Q 040725           11 QKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus        11 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      .+|+.|.+.++..+-+.-.++.||..||
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            3699999999999999999999999997

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.44  E-value=2.3e-05  Score=36.15  Aligned_cols=26  Identities=27%  Similarity=0.650  Sum_probs=23.6

Q ss_pred             cccCCceeecccE-EEeCCcccCCCCc
Q 040725           13 YKVYEKTVYPVEQ-LSDDGVVYHKSCF   38 (164)
Q Consensus        13 C~~C~~~i~~~~~-~~~~~~~~H~~Cf   38 (164)
                      |..|.+.|+++.+ +...|..||..||
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            7889999998876 8999999999998

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.44  E-value=2.7e-05  Score=38.02  Aligned_cols=26  Identities=15%  Similarity=0.280  Sum_probs=23.5

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhcc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIK  150 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~  150 (164)
                      .|..|.++|.|++|+++|+      +|++||+
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            4889999999999999999      8888874

>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=97.39  E-value=3.1e-05  Score=36.51  Aligned_cols=26  Identities=15%  Similarity=0.332  Sum_probs=21.2

Q ss_pred             cccCCceeecc---cEEEeCCcccCCCCc
Q 040725           13 YKVYEKTVYPV---EQLSDDGVVYHKSCF   38 (164)
Q Consensus        13 C~~C~~~i~~~---~~~~~~~~~~H~~Cf   38 (164)
                      |..|.++|..-   ..++..++.||..||
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            78899999322   248999999999998

>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=97.38  E-value=6.7e-05  Score=36.70  Aligned_cols=34  Identities=6%  Similarity=-0.057  Sum_probs=28.7

Q ss_pred             ccCCCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            4 KSFIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         4 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      +...+..+.|.+|+..| -+..+.+.++.+|++||
T Consensus         2 vg~~qklp~CdkCg~GI-VG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           2 IGNAQKLPMCDKCGTGI-VGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCCCCSSSCCCC-CSSCEECSSCEECTTTT
T ss_pred             CCccccCccccccCCCc-EeEEEEeccccCCCCCC
Confidence            33445668999999999 67889999999999997

>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=97.31  E-value=7.8e-05  Score=35.57  Aligned_cols=30  Identities=23%  Similarity=0.608  Sum_probs=27.1

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   68 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~   68 (164)
                      .|..|+..|.++.|+..+.+.||+.||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            488999999999999999999999999753

>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=97.30  E-value=3e-05  Score=37.45  Aligned_cols=20  Identities=10%  Similarity=0.057  Sum_probs=16.3

Q ss_pred             ccccccccccccCccccccc
Q 040725          104 KTVCPLEKVAVESQAYHKTC  123 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~C  123 (164)
                      +.+|.+..|+++|+.||+++
T Consensus        12 ~~PI~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1          12 RRPIEGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             TEECCSCEECCTTSBEETTT
T ss_pred             CCchhhhHhhhhccccCCCC
Confidence            56666767999999999985

>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=97.22  E-value=0.0001  Score=36.15  Aligned_cols=32  Identities=19%  Similarity=0.449  Sum_probs=28.2

Q ss_pred             ccCCCCCcCcCCCeee-eCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~-~~g~~~C~~c~~~~~~   70 (164)
                      +|..|+..|.+..|.. ..+++||-.+|++.|+
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            4889999999999986 6889999999999874

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

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

Probab=97.20  E-value=8e-05  Score=35.84  Aligned_cols=26  Identities=8%  Similarity=0.317  Sum_probs=23.2

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhcc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIK  150 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~  150 (164)
                      .|..|+++|.+++|+.+|.      +|.+||.
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            4899999999999999999      8888773

>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=97.13  E-value=0.00017  Score=37.60  Aligned_cols=31  Identities=10%  Similarity=0.089  Sum_probs=27.1

Q ss_pred             CCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            7 IGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         7 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      .+..+.|.+|+..| -+..+.+.++.+|++||
T Consensus        15 ~QkLP~CdkCg~GI-VG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          15 AQRMPLCDKCGSGI-VGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCSCCBCTTTCCBC-CSCCEESSSCEECTTTC
T ss_pred             cccCccccccCCCc-EEEEEEeccccCCCCCC
Confidence            34567899999999 67789999999999998

>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=97.03  E-value=0.00013  Score=35.68  Aligned_cols=25  Identities=28%  Similarity=0.531  Sum_probs=22.4

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLI  149 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~  149 (164)
                      +|..|.+++.+..|++.||      ||+++-
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            5899999999999999999      888763

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

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

Probab=96.99  E-value=0.00011  Score=34.16  Aligned_cols=20  Identities=35%  Similarity=0.627  Sum_probs=18.6

Q ss_pred             ccccccccccccCccccccc
Q 040725          104 KTVCPLEKVAVESQAYHKTC  123 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~C  123 (164)
                      +.|+.+|+|...|+.||+.|
T Consensus         9 ~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           9 DSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             SEESSSSCEESSSSEECSSC
T ss_pred             hhHHHHHHHhcCCCccccCC
Confidence            78899999999999999987

>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=96.95  E-value=0.00018  Score=37.09  Aligned_cols=27  Identities=22%  Similarity=0.367  Sum_probs=25.0

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCC
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSC   37 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~C   37 (164)
                      ..+|..|.+.| .++.+.+.++.||++|
T Consensus        15 G~~C~~C~~~I-tG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          15 GTRCFSCDQFI-EGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CCBCTTTCCBC-CSCCEEETTEEECTTT
T ss_pred             CcccccccCEe-eeeeeEecCcccCCCC
Confidence            46899999999 8999999999999988

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.88  E-value=0.00059  Score=32.04  Aligned_cols=31  Identities=26%  Similarity=0.581  Sum_probs=28.0

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhhc
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF   69 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~~   69 (164)
                      +|+.|++.+..+.|+.+...+||-.|....|
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHT
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeecccc
Confidence            4899999999999999999999999988766

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

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

Probab=96.87  E-value=0.00023  Score=34.69  Aligned_cols=20  Identities=15%  Similarity=0.242  Sum_probs=15.2

Q ss_pred             ccccccccccccCccccccc
Q 040725          104 KTVCPLEKVAVESQAYHKTC  123 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~C  123 (164)
                      ..+|++..+.+.+..||++|
T Consensus        15 ~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1          15 SLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCBCCSCCBCCTTCCBCTTS
T ss_pred             HhhcccceeeecccccCCCC
Confidence            44556555778889999998

>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=96.84  E-value=0.00025  Score=32.48  Aligned_cols=21  Identities=33%  Similarity=0.721  Sum_probs=16.5

Q ss_pred             cccccccc-ccccCccccccce
Q 040725          104 KTVCPLEK-VAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~-v~~~~~~~H~~CF  124 (164)
                      +.|.++.+ +.+.|..||..||
T Consensus         6 ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           6 ETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CBCCSSSCEECSTTCCEETTTC
T ss_pred             ceecCCcccccccCcccccccC
Confidence            44555544 8999999999998

>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=96.78  E-value=0.00027  Score=34.18  Aligned_cols=26  Identities=23%  Similarity=0.512  Sum_probs=23.4

Q ss_pred             eecCCCCCCCCCCeeccCC-------Chhhhcc
Q 040725          125 KCSHGGCSISPSNYVALEG-------NYNHLIK  150 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g-------~y~~l~~  150 (164)
                      +|+.|++.|+.+.+.++||       +|..||+
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            6999999999999999999       8888774

>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=96.77  E-value=0.00011  Score=34.56  Aligned_cols=26  Identities=15%  Similarity=0.344  Sum_probs=20.9

Q ss_pred             cccCCceeecc---cEEEeCCcccCCCCc
Q 040725           13 YKVYEKTVYPV---EQLSDDGVVYHKSCF   38 (164)
Q Consensus        13 C~~C~~~i~~~---~~~~~~~~~~H~~Cf   38 (164)
                      |..|.++|..-   ..++..++.||.+||
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            77899998322   348999999999997

>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=96.65  E-value=0.00038  Score=33.35  Aligned_cols=25  Identities=20%  Similarity=0.561  Sum_probs=21.3

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhcc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIK  150 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~  150 (164)
                      +|..|++.|.++ |..+||      +|..+|+
T Consensus         1 kC~~C~~vL~gE-Ym~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILTGE-YISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCSSC-CEEETTEEECTTHHHHHTT
T ss_pred             CccccCccccce-eecCCCCcccHHHHHHhcC
Confidence            589999999886 899999      8887764

>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=96.61  E-value=0.00048  Score=36.64  Aligned_cols=33  Identities=21%  Similarity=0.417  Sum_probs=30.3

Q ss_pred             eecCCCCCCCCCCeeccCC-------Chhhhccccccccc
Q 040725          125 KCSHGGCSISPSNYVALEG-------NYNHLIKFASMKRA  157 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g-------~y~~l~~~~~~~~~  157 (164)
                      +|..|++.|++....++||       +|..||+++.....
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~g~G   40 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRG   40 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCC
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCccccC
Confidence            6999999999999999999       89999999987765

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.48  E-value=0.00055  Score=31.20  Aligned_cols=26  Identities=15%  Similarity=0.331  Sum_probs=21.1

Q ss_pred             cccCCceeecccE-EEeCCcccCCCCc
Q 040725           13 YKVYEKTVYPVEQ-LSDDGVVYHKSCF   38 (164)
Q Consensus        13 C~~C~~~i~~~~~-~~~~~~~~H~~Cf   38 (164)
                      |..|.++|..... +...++.||..||
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            6789999954443 7889999999997

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.46  E-value=0.0013  Score=31.12  Aligned_cols=29  Identities=38%  Similarity=0.763  Sum_probs=25.4

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   67 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~   67 (164)
                      .|+.|+..|....++..++++||+.+...
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhc
Confidence            48999999998889999999999988654

>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=96.43  E-value=0.00045  Score=31.67  Aligned_cols=21  Identities=33%  Similarity=0.784  Sum_probs=16.1

Q ss_pred             cccccccc-ccccCccccccce
Q 040725          104 KTVCPLEK-VAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~-v~~~~~~~H~~CF  124 (164)
                      +.|.++.+ +.+.|..||..||
T Consensus         6 ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           6 KTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             CCCCSSSCEEEETTEEEETTTT
T ss_pred             ccccCCceeecccCCccccccC
Confidence            34445543 8999999999998

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.38  E-value=0.0011  Score=32.40  Aligned_cols=34  Identities=18%  Similarity=0.380  Sum_probs=27.4

Q ss_pred             ccCCCCccccccCCceeecccE-EEeCCcccCCCC
Q 040725            4 KSFIGTQQKYKVYEKTVYPVEQ-LSDDGVVYHKSC   37 (164)
Q Consensus         4 ~~~~~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~C   37 (164)
                      |+.......|.+|+....+.|. +...|..||..|
T Consensus         1 m~~sL~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           1 MANALASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             CchHHHHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            3444566789999999988876 788999999887

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

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

Probab=96.32  E-value=0.00064  Score=32.85  Aligned_cols=21  Identities=43%  Similarity=0.782  Sum_probs=19.7

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|+.+|.|...|+.||+.||
T Consensus        15 ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1          15 KAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECSSCCEEETTEEECTTTC
T ss_pred             ceEeeeeeeeecCcccccccC
Confidence            788889999999999999998

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

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

Probab=96.30  E-value=0.00084  Score=30.75  Aligned_cols=21  Identities=33%  Similarity=0.814  Sum_probs=19.4

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      +.|+-++.|...|+.||+.||
T Consensus         8 ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           8 RTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             CBCSSTTEEEETTEEEESSSE
T ss_pred             ceEeeeeeeeecCceeccccC
Confidence            778888889999999999998

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.29  E-value=0.00094  Score=31.61  Aligned_cols=29  Identities=24%  Similarity=0.314  Sum_probs=25.5

Q ss_pred             CCccccccCCceeecccEEEeCCcccCCCC
Q 040725            8 GTQQKYKVYEKTVYPVEQLSDDGVVYHKSC   37 (164)
Q Consensus         8 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   37 (164)
                      ++..-|..|.+.| .+..+.+.++.||+.|
T Consensus         3 sgssgC~~C~~~I-tGkVLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYI-TGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCC-SSCCBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhh-hhhhhhccccccCCCC
Confidence            4566799999999 7888999999999988

>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=96.28  E-value=0.00092  Score=35.89  Aligned_cols=33  Identities=15%  Similarity=0.300  Sum_probs=29.9

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhccccccccc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIKFASMKRA  157 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~~~~~  157 (164)
                      +|..|++.|++....++||      +|..+|+++...-.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G   39 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFG   39 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcc
Confidence            6999999999999999999      99999999887654

>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=96.07  E-value=0.00098  Score=31.24  Aligned_cols=20  Identities=30%  Similarity=0.674  Sum_probs=19.2

Q ss_pred             eeecCCCCCCCCCCeeccCC
Q 040725          124 FKCSHGGCSISPSNYVALEG  143 (164)
Q Consensus       124 F~C~~C~~~l~~~~f~~~~g  143 (164)
                      |+|+.|++.|.+.....+||
T Consensus         1 frca~cgk~lestt~adkdg   20 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEG   20 (31)
T ss_dssp             EECSSSCCEECSSCSEEETT
T ss_pred             CccccccCccccceeeccCC
Confidence            89999999999999999999

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.04  E-value=0.0021  Score=30.36  Aligned_cols=20  Identities=15%  Similarity=0.363  Sum_probs=16.3

Q ss_pred             ccccccccccccCccccccc
Q 040725          104 KTVCPLEKVAVESQAYHKTC  123 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~C  123 (164)
                      ..-|++..+.+.++.||+.|
T Consensus        12 ~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1          12 EKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CCCCSSCCBCCSSCCBCTTT
T ss_pred             hhhhhhhhhhccccccCCCC
Confidence            55566666899999999988

>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=96.02  E-value=0.0013  Score=30.74  Aligned_cols=13  Identities=31%  Similarity=0.994  Sum_probs=12.4

Q ss_pred             ccccCccccccce
Q 040725          112 VAVESQAYHKTCF  124 (164)
Q Consensus       112 v~~~~~~~H~~CF  124 (164)
                      |.+.++.||.+||
T Consensus        17 isFE~R~WH~~CF   29 (29)
T d1x4la1          17 ISFEERQWHNDCF   29 (29)
T ss_dssp             EECSSCEECTTTC
T ss_pred             EEeecccccccCC
Confidence            8899999999998

>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=95.84  E-value=0.0018  Score=30.57  Aligned_cols=19  Identities=16%  Similarity=0.352  Sum_probs=17.7

Q ss_pred             eecCCCCCCCCCCeeccCC
Q 040725          125 KCSHGGCSISPSNYVALEG  143 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g  143 (164)
                      .|..|.++|.+.+|..+++
T Consensus         1 vC~~C~K~Lag~rFTa~eD   19 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVED   19 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSS
T ss_pred             CcccccchhcCceeEEecc
Confidence            4899999999999999998

>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=95.60  E-value=0.0013  Score=31.14  Aligned_cols=29  Identities=28%  Similarity=0.599  Sum_probs=25.0

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQ   67 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~   67 (164)
                      .|+.|+..|....++..++++||+.+...
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            48999999988888889999999988654

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=95.56  E-value=0.0017  Score=31.50  Aligned_cols=32  Identities=28%  Similarity=0.659  Sum_probs=26.2

Q ss_pred             ccCCCCCcCcCC--CeeeeCCeeeecchhhhhcc
Q 040725           39 KCSHCKGTLKLS--NYSSMEGVLYCKPHFEQLFK   70 (164)
Q Consensus        39 ~C~~C~~~L~~~--~~~~~~g~~~C~~c~~~~~~   70 (164)
                      +|+.|+..|.+.  ..+.+.+.++|+.+|.++|+
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhcC
Confidence            578888888654  46789999999999999874

>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=95.51  E-value=0.0023  Score=29.84  Aligned_cols=13  Identities=23%  Similarity=0.884  Sum_probs=12.3

Q ss_pred             ccccCccccccce
Q 040725          112 VAVESQAYHKTCF  124 (164)
Q Consensus       112 v~~~~~~~H~~CF  124 (164)
                      |.+.++.||.+||
T Consensus        17 isFedR~WH~~CF   29 (29)
T d1x68a1          17 ICFQDSQWHSECF   29 (29)
T ss_dssp             EEETTEEEEGGGC
T ss_pred             EEeehhhcccccC
Confidence            8899999999998

>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=95.48  E-value=0.0052  Score=29.71  Aligned_cols=31  Identities=26%  Similarity=0.670  Sum_probs=25.0

Q ss_pred             cccCCCCCcCcCCC-ee-eeCCeeeecchhhhh
Q 040725           38 FKCSHCKGTLKLSN-YS-SMEGVLYCKPHFEQL   68 (164)
Q Consensus        38 f~C~~C~~~L~~~~-~~-~~~g~~~C~~c~~~~   68 (164)
                      |.|..|+.-++++. |. +...++||..||.+.
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            68999999998875 44 467799999999764

>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=95.39  E-value=0.0027  Score=30.54  Aligned_cols=17  Identities=29%  Similarity=0.667  Sum_probs=13.7

Q ss_pred             cccc-ccccCccccccce
Q 040725          108 PLEK-VAVESQAYHKTCF  124 (164)
Q Consensus       108 ~~~~-v~~~~~~~H~~CF  124 (164)
                      +.|. +++.++.||..||
T Consensus        14 ~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3          14 ASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             TTSEEEEETTEEECGGGC
T ss_pred             hhHhheecccceeeeccC
Confidence            3344 6799999999998

>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=95.28  E-value=0.0052  Score=29.19  Aligned_cols=20  Identities=15%  Similarity=0.227  Sum_probs=14.6

Q ss_pred             cccccccc-ccccCccccccc
Q 040725          104 KTVCPLEK-VAVESQAYHKTC  123 (164)
Q Consensus       104 ~~~~~~~~-v~~~~~~~H~~C  123 (164)
                      +..|.+.. +.++++.||.+|
T Consensus        10 ~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1          10 QQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CSCBCSSEEEECSSSEECTTT
T ss_pred             CCcchHHHHHHHHHHHHhcCC
Confidence            44444443 889999999987

>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=95.28  E-value=0.0034  Score=29.98  Aligned_cols=21  Identities=10%  Similarity=0.131  Sum_probs=15.5

Q ss_pred             cccccccc-ccccCccccccce
Q 040725          104 KTVCPLEK-VAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~-v~~~~~~~H~~CF  124 (164)
                      +..|.+.. +.++++.||..|.
T Consensus         9 ~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           9 GGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CCBCCCSEEEEETTEEECGGGC
T ss_pred             CCccchhhhhccchhhhhhhhC
Confidence            44445544 8899999999984

>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=94.99  E-value=0.0049  Score=31.87  Aligned_cols=20  Identities=20%  Similarity=0.243  Sum_probs=15.6

Q ss_pred             cccccccccccCccccccce
Q 040725          105 TVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       105 ~~~~~~~v~~~~~~~H~~CF  124 (164)
                      .-|.+-.|.+.++.+|++||
T Consensus        26 ~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          26 SGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CBCCSCCEESSSCEECTTTC
T ss_pred             CCcEEEEEEeccccCCCCCC
Confidence            33444458999999999998

>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=94.90  E-value=0.0049  Score=29.87  Aligned_cols=17  Identities=18%  Similarity=0.297  Sum_probs=14.2

Q ss_pred             ccccccccCccccccce
Q 040725          108 PLEKVAVESQAYHKTCF  124 (164)
Q Consensus       108 ~~~~v~~~~~~~H~~CF  124 (164)
                      .+..|.+.++.+|++||
T Consensus        19 VG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2          19 VGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CSSCEECSSCEECTTTT
T ss_pred             EeEEEEeccccCCCCCC
Confidence            34448899999999998

>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=94.73  E-value=0.014  Score=27.32  Aligned_cols=28  Identities=14%  Similarity=0.494  Sum_probs=24.5

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFE   66 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~   66 (164)
                      +|..|-.+|....|..++++++|..|..
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            5788999999999999999999987753

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.72  E-value=0.008  Score=26.78  Aligned_cols=26  Identities=19%  Similarity=0.234  Sum_probs=20.4

Q ss_pred             cccCCceeecc-cEEEeCCcccCCCCc
Q 040725           13 YKVYEKTVYPV-EQLSDDGVVYHKSCF   38 (164)
Q Consensus        13 C~~C~~~i~~~-~~~~~~~~~~H~~Cf   38 (164)
                      |..|++.+... ..+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            67898887433 348899999999987

>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=94.58  E-value=0.0079  Score=28.74  Aligned_cols=24  Identities=21%  Similarity=0.437  Sum_probs=21.2

Q ss_pred             ecCCCCCCCCCCeeccCC------Chhhhc
Q 040725          126 CSHGGCSISPSNYVALEG------NYNHLI  149 (164)
Q Consensus       126 C~~C~~~l~~~~f~~~~g------~y~~l~  149 (164)
                      |..|+++|....|...++      +|+..|
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcccccccccCCCcEEEEecccccc
Confidence            889999999999999998      777665

>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=94.41  E-value=0.0099  Score=28.44  Aligned_cols=24  Identities=13%  Similarity=0.357  Sum_probs=21.1

Q ss_pred             ecCCCCCCCCCCeeccCC------Chhhhc
Q 040725          126 CSHGGCSISPSNYVALEG------NYNHLI  149 (164)
Q Consensus       126 C~~C~~~l~~~~f~~~~g------~y~~l~  149 (164)
                      |..|+.+|....|+.+|+      +|+.-|
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcccccccccCCCCceEeecchhhc
Confidence            889999999999999999      777655

>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=94.25  E-value=0.027  Score=26.61  Aligned_cols=27  Identities=26%  Similarity=0.746  Sum_probs=21.8

Q ss_pred             ccCCCCCcCcCCC-eeeeCCeeeecchh
Q 040725           39 KCSHCKGTLKLSN-YSSMEGVLYCKPHF   65 (164)
Q Consensus        39 ~C~~C~~~L~~~~-~~~~~g~~~C~~c~   65 (164)
                      .|+.|..+|..+. |...+|.+||+.+-
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            4889999987774 56789999998764

>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=94.22  E-value=0.012  Score=28.07  Aligned_cols=26  Identities=19%  Similarity=0.497  Sum_probs=22.5

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhcc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIK  150 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~  150 (164)
                      .|+.|+++|..-.|.+.+|      +|++.|.
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            3899999999999999999      8888763

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

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

Probab=94.10  E-value=0.026  Score=26.61  Aligned_cols=30  Identities=20%  Similarity=0.533  Sum_probs=26.7

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   68 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~   68 (164)
                      +|..|...|.+..|....|+.+|.+|..+.
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            588999999999999999999999997654

>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=93.79  E-value=0.019  Score=27.85  Aligned_cols=32  Identities=13%  Similarity=-0.018  Sum_probs=26.1

Q ss_pred             CCCCccccccCCceeecccEEEeCCcccCCCCc
Q 040725            6 FIGTQQKYKVYEKTVYPVEQLSDDGVVYHKSCF   38 (164)
Q Consensus         6 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   38 (164)
                      -..+...|.+|...| +.+-+...+..||+..|
T Consensus         4 ~glGk~vC~KCh~iI-dd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           4 RGLGKYICQKCHAII-DEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCCBCTTTCCBC-CSCCCCCSSSCCCTTTS
T ss_pred             cchhhHHHHHHHhhh-hcCcceecCCCCCCCCC
Confidence            345678999999999 55668899999999876

>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=93.70  E-value=0.014  Score=28.19  Aligned_cols=27  Identities=11%  Similarity=0.124  Sum_probs=22.9

Q ss_pred             ccccccCCceeecccEEEeCCcccCCCC
Q 040725           10 QQKYKVYEKTVYPVEQLSDDGVVYHKSC   37 (164)
Q Consensus        10 ~~~C~~C~~~i~~~~~~~~~~~~~H~~C   37 (164)
                      ...|..|.+.| ++-.+.+.+..||++|
T Consensus         8 ge~C~~C~~~i-tGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           8 GEFCHGCSLLM-TGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SCBCTTTCCBC-CSCCBCCTTCCBCTTS
T ss_pred             HHHhhhhHhhc-ccceeeecccccCCCC
Confidence            46799999977 6777888889999998

>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=93.14  E-value=0.039  Score=25.71  Aligned_cols=29  Identities=28%  Similarity=0.802  Sum_probs=22.8

Q ss_pred             ccCCCCCcCcCCCeeeeCCeeeecchhhhh
Q 040725           39 KCSHCKGTLKLSNYSSMEGVLYCKPHFEQL   68 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~~~g~~~C~~c~~~~   68 (164)
                      .|..|++.|.. .-.+..|.+||.+|..++
T Consensus         1 nC~~Cgkelta-dArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTA-DARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCT-TCEEETTEEECHHHHHTT
T ss_pred             Cccccccccch-hHHHhcCCEEEEeccccc
Confidence            37889998865 345788999999998764

>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=92.97  E-value=0.022  Score=32.09  Aligned_cols=31  Identities=6%  Similarity=0.003  Sum_probs=27.5

Q ss_pred             eecCCCCCCCCCCeeccCC------Chhhhccccccc
Q 040725          125 KCSHGGCSISPSNYVALEG------NYNHLIKFASMK  155 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g------~y~~l~~~~~~~  155 (164)
                      .|..|++.|++..+.++||      +|..+|+++..-
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G   37 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKG   37 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccc
Confidence            3899999999999999999      999999887654

>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=92.17  E-value=0.039  Score=26.60  Aligned_cols=25  Identities=4%  Similarity=0.142  Sum_probs=19.8

Q ss_pred             eecCCCCCCCCCCeeccCC-------Chhhhc
Q 040725          125 KCSHGGCSISPSNYVALEG-------NYNHLI  149 (164)
Q Consensus       125 ~C~~C~~~l~~~~f~~~~g-------~y~~l~  149 (164)
                      +|..|++.|+|-.|+....       +|+..|
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkf   32 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKF   32 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhc
Confidence            5889999999999988655       666554

>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=90.20  E-value=0.074  Score=25.71  Aligned_cols=21  Identities=14%  Similarity=0.384  Sum_probs=17.1

Q ss_pred             ccccccccccccCccccccce
Q 040725          104 KTVCPLEKVAVESQAYHKTCF  124 (164)
Q Consensus       104 ~~~~~~~~v~~~~~~~H~~CF  124 (164)
                      ..+|..+-+.+.+..||+.+|
T Consensus        15 h~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2          15 HAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCBCCSCCCCCSSSCCCTTTS
T ss_pred             HhhhhcCcceecCCCCCCCCC
Confidence            566666669999999999887

>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=90.05  E-value=0.048  Score=27.36  Aligned_cols=27  Identities=11%  Similarity=0.197  Sum_probs=17.0

Q ss_pred             ccccCCceeecccEE-EeCCcccCCCCc
Q 040725           12 KYKVYEKTVYPVEQL-SDDGVVYHKSCF   38 (164)
Q Consensus        12 ~C~~C~~~i~~~~~~-~~~~~~~H~~Cf   38 (164)
                      .|.+|++....++-+ .-.+..||+.|-
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~   28 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACR   28 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHH
T ss_pred             CcchhhccccccceeeecCCceeCCccc
Confidence            377777777666543 344557887763

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=89.36  E-value=0.25  Score=23.13  Aligned_cols=26  Identities=15%  Similarity=0.461  Sum_probs=22.0

Q ss_pred             cCCCCCcCcCCCeeeeCCeeeecchh
Q 040725           40 CSHCKGTLKLSNYSSMEGVLYCKPHF   65 (164)
Q Consensus        40 C~~C~~~L~~~~~~~~~g~~~C~~c~   65 (164)
                      |..|+.+|....|......++|..|-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhcC
Confidence            67788899888998888899998773

>d2co8a1 g.39.1.3 (A:44-76) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=88.48  E-value=0.13  Score=24.26  Aligned_cols=29  Identities=34%  Similarity=0.800  Sum_probs=22.9

Q ss_pred             ccCCCCCcCcCCCeee--eCCeeeecchhhh
Q 040725           39 KCSHCKGTLKLSNYSS--MEGVLYCKPHFEQ   67 (164)
Q Consensus        39 ~C~~C~~~L~~~~~~~--~~g~~~C~~c~~~   67 (164)
                      +|..|...|..+.|..  .+|.+||..++.+
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlpq   31 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ   31 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccCC
Confidence            4788889998888764  6899999887643

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.50  E-value=0.39  Score=22.42  Aligned_cols=29  Identities=17%  Similarity=0.344  Sum_probs=21.6

Q ss_pred             ccCCCCCcCcCC--CeeeeCCeeeecchhhh
Q 040725           39 KCSHCKGTLKLS--NYSSMEGVLYCKPHFEQ   67 (164)
Q Consensus        39 ~C~~C~~~L~~~--~~~~~~g~~~C~~c~~~   67 (164)
                      +|.-|+..|++.  ..+.+.+.++|+.+|.+
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhc
Confidence            567777777654  45678899999999875

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

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

Probab=81.59  E-value=0.26  Score=22.40  Aligned_cols=13  Identities=31%  Similarity=0.731  Sum_probs=10.9

Q ss_pred             ceeecCCCCCCCC
Q 040725          123 CFKCSHGGCSISP  135 (164)
Q Consensus       123 CF~C~~C~~~l~~  135 (164)
                      =|+|..|+++|.+
T Consensus         2 ~ftc~hcgkqlks   14 (30)
T d2ctda2           2 MFTCHHCGKQLRS   14 (30)
T ss_dssp             CCCCSSSCCCCSS
T ss_pred             ceechhHHHHHhh
Confidence            3899999999854

>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=81.29  E-value=0.5  Score=21.35  Aligned_cols=27  Identities=15%  Similarity=0.332  Sum_probs=21.1

Q ss_pred             cCCCCCcCcCCCeeeeCCeeeecchhh
Q 040725           40 CSHCKGTLKLSNYSSMEGVLYCKPHFE   66 (164)
Q Consensus        40 C~~C~~~L~~~~~~~~~g~~~C~~c~~   66 (164)
                      |..|+.+|.+..|...-+.++|..|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            677888898888887777788988743