Psyllid ID: psy15437

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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---
Protein Sequence
MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV
Secondary Structure (PSIPRED)
cccccccccccccccccccEEEEcccEEEccccccccccccccccccEEEEccEEEEccccHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccccEEcccccccccHHHHHHHHHcccEEEHHEEHHHHHHccccccEEEEEcccEEEcccHHHHHHHHccccccccccccccccccccccccccccEEccHHHHHHHHHHHHcccccHHHHHHHHHHHcccccEEEEEccccc
Coil and Loop (DISEMBL)
mlyvkkclgcseklgpdelVMKTLDNVFHVQCFVCVVcgsrlqrgeQFVIkqgqlfcrpdYEKEVEMLQGYaqgipfdlitsskshdgrrgpkrprtilTTQQRRAFKasfeispkpcrkvreglardtglSVRIVQSRPIPV
Flexible Loop (DISEMBL)
mlyvkkclgcseklgPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDlitsskshdgrrgpkrprtilttqqrrafkasfeispkpcrkvreglardtglsvrivqsrpipv
Low Complexity Region (SEG)
MLYVKKCLGCSEKLGPDELVMKTLDNvfhvqcfvcvvcGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV
Disordered region (IsUnstruct)
**YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLI***************************************************************
Disordered Region (DISOPRED)
MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKR*********RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP*
Disordered Region (DISEMBL)
MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSK*********RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV
Disordered Region (DISPRO)
*LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQ***********************KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV
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	143	2.2.26 [Sep-21-2011]
P53413	377	LIM/homeobox protein LMX-	no	N/A	0.951	0.360	0.512	8e-37
Q8UVR3	400	LIM homeobox transcriptio	N/A	N/A	0.951	0.34	0.512	2e-36
Q9JKU8	382	LIM homeobox transcriptio	yes	N/A	0.951	0.356	0.519	5e-36
Q04650	382	LIM homeobox transcriptio	N/A	N/A	0.951	0.356	0.519	5e-36
Q8TE12	382	LIM homeobox transcriptio	yes	N/A	0.951	0.356	0.519	5e-36
O88609	372	LIM homeobox transcriptio	no	N/A	0.951	0.365	0.490	9e-36
Q60564	369	LIM homeobox transcriptio	N/A	N/A	0.951	0.368	0.490	1e-35
O60663	379	LIM homeobox transcriptio	no	N/A	0.951	0.358	0.490	1e-35
Q969G2	390	LIM/homeobox protein Lhx4	no	N/A	0.818	0.3	0.352	6e-21
P53776	390	LIM/homeobox protein Lhx4	no	N/A	0.818	0.3	0.352	6e-21

>sp|P53413|LMX1B_CHICK LIM/homeobox protein LMX-1.2 OS=Gallus gallus GN=LMX1B PE=2 SV=1

 Score =  152 bits (383), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 79/154 (51%), Positives = 101/154 (65%), Gaps = 18/154 (11%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC EK+ P E VM+ L+ V+H+ CF C VC  +L++G++FV+K+GQL C+ DY
Sbjct: 87  LFAAKCSGCMEKIAPTEFVMRALECVYHLSCFCCCVCERQLRKGDEFVLKEGQLLCKSDY 146

Query: 62  EKEVEML----------------QGYAQGIPFDLITSSKSHDGR--RGPKRPRTILTTQQ 103
           EKE ++L                 G  +     +     S DG+  R PKRPRTILTTQQ
Sbjct: 147 EKEKDLLSSVSPDDSDSVKSDDEDGDVKPTKGQVTQGKGSDDGKDPRRPKRPRTILTTQQ 206

Query: 104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           RRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 207 RRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 240

Specifies dorsal cell fate during limb development.
Gallus gallus (taxid: 9031)

>sp|Q8UVR3|LMX1B_XENLA LIM homeobox transcription factor 1-beta.1 OS=Xenopus laevis GN=lmx1b.1 PE=2 SV=1

 Score =  150 bits (379), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 79/154 (51%), Positives = 102/154 (66%), Gaps = 18/154 (11%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC EK+ P E VM+ L+ V+H+ CF C VC  +L++G++FV+K+GQL C+ DY
Sbjct: 110 LFAAKCSGCMEKIAPTEFVMRALECVYHLSCFCCCVCERQLRKGDEFVLKEGQLLCKSDY 169

Query: 62  EKEVEML----------------QGYAQGIPFDLITSSKSHDGR--RGPKRPRTILTTQQ 103
           EKE ++L                +G  +     +     S DG+  R PKRPRTILTTQQ
Sbjct: 170 EKEKDLLSSGSPDDSDSVKSDDEEGDVKPGKGRVNQGKGSDDGKDPRRPKRPRTILTTQQ 229

Query: 104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           RRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 230 RRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 263

Required for early specification of the kidney glomus, lying upstream of wt1 in the pathway controlling glomus differentiation. The balance in levels and expression patterns of binding partners such as lhx1/lim-1 influences differentiation into glomus or tubule derivatives. Involved in specification of serotonergic neurons.

Xenopus laevis (taxid: 8355)

>sp|Q9JKU8|LMX1A_MOUSE LIM homeobox transcription factor 1-alpha OS=Mus musculus GN=Lmx1a PE=2 SV=1

 Score =  149 bits (376), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 79/152 (51%), Positives = 99/152 (65%), Gaps = 16/152 (10%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC E + P+E VM+   +V+H+ CF C VC  +LQ+G++FV+K+GQL C+ DY
Sbjct: 89  LFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGDY 148

Query: 62  EKEVEMLQ-----GYAQGIPFDLITSSKSHDG-----------RRGPKRPRTILTTQQRR 105
           EKE E+L          G   D  +  KS  G            + PKRPRTILTTQQRR
Sbjct: 149 EKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGASEDGKDHKRPKRPRTILTTQQRR 208

Query: 106 AFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           AFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 209 AFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 240

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Mus musculus (taxid: 10090)

>sp|Q04650|LMX1A_MESAU LIM homeobox transcription factor 1-alpha OS=Mesocricetus auratus GN=LMX1A PE=2 SV=1

 Score =  149 bits (376), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 79/152 (51%), Positives = 99/152 (65%), Gaps = 16/152 (10%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC E + P+E VM+   +V+H+ CF C VC  +LQ+G++FV+K+GQL C+ DY
Sbjct: 89  LFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGDY 148

Query: 62  EKEVEMLQ-----GYAQGIPFDLITSSKSHDG-----------RRGPKRPRTILTTQQRR 105
           EKE E+L          G   D  +  KS  G            + PKRPRTILTTQQRR
Sbjct: 149 EKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGTSEDGKDHKRPKRPRTILTTQQRR 208

Query: 106 AFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           AFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 209 AFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 240

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Mesocricetus auratus (taxid: 10036)

>sp|Q8TE12|LMX1A_HUMAN LIM homeobox transcription factor 1-alpha OS=Homo sapiens GN=LMX1A PE=2 SV=1

 Score =  149 bits (376), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 79/152 (51%), Positives = 99/152 (65%), Gaps = 16/152 (10%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC E + P+E VM+   +V+H+ CF C VC  +LQ+G++FV+K+GQL C+ DY
Sbjct: 89  LFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGDY 148

Query: 62  EKEVEMLQ-----GYAQGIPFDLITSSKSHDG-----------RRGPKRPRTILTTQQRR 105
           EKE E+L          G   D  +  KS  G            + PKRPRTILTTQQRR
Sbjct: 149 EKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGTAEEGKDHKRPKRPRTILTTQQRR 208

Query: 106 AFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           AFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 209 AFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 240

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Homo sapiens (taxid: 9606)

>sp|O88609|LMX1B_MOUSE LIM homeobox transcription factor 1-beta OS=Mus musculus GN=Lmx1b PE=2 SV=2

 Score =  148 bits (374), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 76/155 (49%), Positives = 100/155 (64%), Gaps = 19/155 (12%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC EK+ P E VM+ L+ V+H+ CF C VC  +L++G++FV+K+GQL C+ DY
Sbjct: 87  LFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDY 146

Query: 62  EKEVEMLQGYAQGIPFDLITSSKSHDGR-------------------RGPKRPRTILTTQ 102
           EKE ++L   +      + +  +  D +                   R PKRPRTILTTQ
Sbjct: 147 EKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQ 206

Query: 103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           QRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 207 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 241

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Mus musculus (taxid: 10090)

>sp|Q60564|LMX1B_MESAU LIM homeobox transcription factor 1-beta (Fragment) OS=Mesocricetus auratus GN=LMX1B PE=2 SV=1

 Score =  148 bits (374), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/155 (49%), Positives = 100/155 (64%), Gaps = 19/155 (12%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC EK+ P E VM+ L+ V+H+ CF C VC  +L++G++FV+K+GQL C+ DY
Sbjct: 77  LFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDY 136

Query: 62  EKEVEMLQGYAQGIPFDLITSSKSHDGR-------------------RGPKRPRTILTTQ 102
           EKE ++L   +      + +  +  D +                   R PKRPRTILTTQ
Sbjct: 137 EKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGGGDDGKDPRRPKRPRTILTTQ 196

Query: 103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           QRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 197 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 231

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels. Mediates physical interaction and transcriptional synergy with E47/PAN-1.

Mesocricetus auratus (taxid: 10036)

>sp|O60663|LMX1B_HUMAN LIM homeobox transcription factor 1-beta OS=Homo sapiens GN=LMX1B PE=1 SV=2

 Score =  148 bits (373), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/155 (49%), Positives = 100/155 (64%), Gaps = 19/155 (12%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+  KC GC EK+ P E VM+ L+ V+H+ CF C VC  +L++G++FV+K+GQL C+ DY
Sbjct: 87  LFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDY 146

Query: 62  EKEVEMLQGYAQGIPFDLITSSKSHDGR-------------------RGPKRPRTILTTQ 102
           EKE ++L   +      + +  +  D +                   R PKRPRTILTTQ
Sbjct: 147 EKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQ 206

Query: 103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           QRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct: 207 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 241

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Homo sapiens (taxid: 9606)

>sp|Q969G2|LHX4_HUMAN LIM/homeobox protein Lhx4 OS=Homo sapiens GN=LHX4 PE=1 SV=2

 Score = 99.4 bits (246), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 77/136 (56%), Gaps = 19/136 (13%)

Query: 3   YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPDY 61
           +  KC  C + + P ++V K  D V+H+ CF C++C  +L  G++F +++ G+L C+ DY
Sbjct: 85  FGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDY 144

Query: 62  EKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKV 121
           E                  T+ ++ D   G KRPRT +T +Q    K +++ SPKP R V
Sbjct: 145 E------------------TAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSPKPARHV 186

Query: 122 REGLARDTGLSVRIVQ 137
           RE L+ +TGL +R+VQ
Sbjct: 187 REQLSSETGLDMRVVQ 202

May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.

Homo sapiens (taxid: 9606)

>sp|P53776|LHX4_MOUSE LIM/homeobox protein Lhx4 OS=Mus musculus GN=Lhx4 PE=1 SV=4

 Score = 99.4 bits (246), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 77/136 (56%), Gaps = 19/136 (13%)

Query: 3   YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPDY 61
           +  KC  C + + P ++V K  D V+H+ CF C++C  +L  G++F +++ G+L C+ DY
Sbjct: 85  FGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDY 144

Query: 62  EKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKV 121
           E                  T+ ++ D   G KRPRT +T +Q    K +++ SPKP R V
Sbjct: 145 E------------------TAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSPKPARHV 186

Query: 122 REGLARDTGLSVRIVQ 137
           RE L+ +TGL +R+VQ
Sbjct: 187 REQLSSETGLDMRVVQ 202

May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.

Mus musculus (taxid: 10090)

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	143
242007292	396	Insulin gene enhancer protein ISL-2, put	0.951	0.343	0.811	2e-59
270002858	353	LIM homeobox transcription factor 1, bet	0.951	0.385	0.746	6e-55
189234898	368	PREDICTED: similar to lim homeobox prote	0.951	0.369	0.746	8e-55
312370934	919	hypothetical protein AND_22855 [Anophele	0.916	0.142	0.744	5e-54
157118342	387	lim homeobox protein [Aedes aegypti] gi|	0.923	0.341	0.761	7e-53
170032117	453	lim homeobox protein [Culex quinquefasci	0.923	0.291	0.746	4e-52
158292635	456	AGAP005138-PA [Anopheles gambiae str. PE	0.902	0.282	0.722	1e-51
195376251	564	GJ12228 [Drosophila virilis] gi|19415406	0.930	0.235	0.693	1e-47
195126142	586	GI12337 [Drosophila mojavensis] gi|19391	0.930	0.226	0.693	2e-47
195012862	583	GH16074 [Drosophila grimshawi] gi|193897	0.930	0.228	0.693	2e-47

>gi|242007292|ref|XP_002424475.1| Insulin gene enhancer protein ISL-2, putative [Pediculus humanus corporis] gi|212507893|gb|EEB11737.1| Insulin gene enhancer protein ISL-2, putative [Pediculus humanus corporis]

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 125/138 (90%), Gaps = 2/138 (1%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           LY KKCLGCSE++  DELVMK LD+VFH++CF+CVVCG RLQRG+QFVIKQGQLFCRPDY
Sbjct: 61  LYAKKCLGCSERISADELVMKALDSVFHLRCFICVVCGVRLQRGDQFVIKQGQLFCRPDY 120

Query: 62  EKEVEMLQGYAQG--IPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCR 119
           EKEVEMLQGYAQG     DL+ SS++ DGRRGPKRPRTILTTQQR+AFKASFE+SPKPCR
Sbjct: 121 EKEVEMLQGYAQGDFTCDDLLPSSRNQDGRRGPKRPRTILTTQQRKAFKASFEVSPKPCR 180

Query: 120 KVREGLARDTGLSVRIVQ 137
           KVRE LA+DTGLSVRIVQ
Sbjct: 181 KVREALAKDTGLSVRIVQ 198

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270002858|gb|EEZ99305.1| LIM homeobox transcription factor 1, beta 2 [Tribolium castaneum]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 103/138 (74%), Positives = 123/138 (89%), Gaps = 2/138 (1%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+VKKCL CSE++ P+ELVM+  +N+FH++CFVCVVCG RLQ+G+ +VIKQGQLFCR DY
Sbjct: 53  LFVKKCLACSERIAPEELVMRASENIFHLRCFVCVVCGIRLQKGDLYVIKQGQLFCRIDY 112

Query: 62  EKEVEMLQGYAQG--IPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCR 119
           EKEVEM+QG+  G  I  +L+ SS++HDGRRGPKRPRTILTTQQRRAFKASFE+SPKPCR
Sbjct: 113 EKEVEMMQGFGHGEFICDELLPSSRAHDGRRGPKRPRTILTTQQRRAFKASFEVSPKPCR 172

Query: 120 KVREGLARDTGLSVRIVQ 137
           KVRE LA+DTGLSVRIVQ
Sbjct: 173 KVREALAKDTGLSVRIVQ 190

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234898|ref|XP_967153.2| PREDICTED: similar to lim homeobox protein, partial [Tribolium castaneum]

 Score =  218 bits (554), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 103/138 (74%), Positives = 123/138 (89%), Gaps = 2/138 (1%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           L+VKKCL CSE++ P+ELVM+  +N+FH++CFVCVVCG RLQ+G+ +VIKQGQLFCR DY
Sbjct: 57  LFVKKCLACSERIAPEELVMRASENIFHLRCFVCVVCGIRLQKGDLYVIKQGQLFCRIDY 116

Query: 62  EKEVEMLQGYAQG--IPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCR 119
           EKEVEM+QG+  G  I  +L+ SS++HDGRRGPKRPRTILTTQQRRAFKASFE+SPKPCR
Sbjct: 117 EKEVEMMQGFGHGEFICDELLPSSRAHDGRRGPKRPRTILTTQQRRAFKASFEVSPKPCR 176

Query: 120 KVREGLARDTGLSVRIVQ 137
           KVRE LA+DTGLSVRIVQ
Sbjct: 177 KVREALAKDTGLSVRIVQ 194

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312370934|gb|EFR19232.1| hypothetical protein AND_22855 [Anopheles darlingi]

 Score =  215 bits (547), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 99/133 (74%), Positives = 116/133 (87%), Gaps = 2/133 (1%)

Query: 6   KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65
           +CLGC EK+G DELVM+ LDNVFH++CF+CVVCG RLQ+G+Q+VIKQ QLFCRPDYEKEV
Sbjct: 47  RCLGCGEKIGADELVMRALDNVFHLKCFICVVCGVRLQKGDQYVIKQSQLFCRPDYEKEV 106

Query: 66  EMLQGYA-QGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREG 124
           EM QGY+      D +  ++  DGRRGPKRPRTILTTQQRRAFKASF+ISPKPCRK+REG
Sbjct: 107 EMFQGYSYDDYCCDDMFQTRI-DGRRGPKRPRTILTTQQRRAFKASFDISPKPCRKIREG 165

Query: 125 LARDTGLSVRIVQ 137
           LA+DTGLS+RIVQ
Sbjct: 166 LAKDTGLSIRIVQ 178

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157118342|ref|XP_001653180.1| lim homeobox protein [Aedes aegypti] gi|108883303|gb|EAT47528.1| AAEL001380-PA [Aedes aegypti]

 Score =  211 bits (537), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 102/134 (76%), Positives = 116/134 (86%), Gaps = 2/134 (1%)

Query: 5   KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
            +CLGC EK+G DELVM+ LDNVFH++CF+CVVCG RLQ+G+Q+VIKQ QLFCRPDYEKE
Sbjct: 184 NRCLGCGEKIGADELVMRALDNVFHLKCFICVVCGVRLQKGDQYVIKQSQLFCRPDYEKE 243

Query: 65  VEMLQGYA-QGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVRE 123
           VEMLQGY       D I  ++  DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRK+RE
Sbjct: 244 VEMLQGYNYDDYCCDDIFQTR-IDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKIRE 302

Query: 124 GLARDTGLSVRIVQ 137
           GLA+DTGLS+RIVQ
Sbjct: 303 GLAKDTGLSIRIVQ 316

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170032117|ref|XP_001843929.1| lim homeobox protein [Culex quinquefasciatus] gi|167871878|gb|EDS35261.1| lim homeobox protein [Culex quinquefasciatus]

 Score =  209 bits (531), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 100/134 (74%), Positives = 115/134 (85%), Gaps = 2/134 (1%)

Query: 5   KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
            +CLGC EK+G DELVM+ LDNVFH++CF+CVVCG RLQ+G+Q+VIKQ QLFCRPDYEKE
Sbjct: 64  NRCLGCGEKIGADELVMRALDNVFHLKCFICVVCGIRLQKGDQYVIKQSQLFCRPDYEKE 123

Query: 65  VEMLQGYA-QGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVRE 123
           VEM QGY       D I  ++  DGRRGPKRPRTILTTQQRRAFKASFE+SPKPCRK+RE
Sbjct: 124 VEMFQGYNYDDYCCDDIFQTRI-DGRRGPKRPRTILTTQQRRAFKASFEVSPKPCRKIRE 182

Query: 124 GLARDTGLSVRIVQ 137
           GLA+DTGLS+RIVQ
Sbjct: 183 GLAKDTGLSIRIVQ 196

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158292635|ref|XP_314022.4| AGAP005138-PA [Anopheles gambiae str. PEST] gi|157017084|gb|EAA44525.4| AGAP005138-PA [Anopheles gambiae str. PEST]

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 99/137 (72%), Positives = 114/137 (83%), Gaps = 8/137 (5%)

Query: 5   KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
            +CLGC EK+G DELVM+ LDNVFH++CF+CVVCG RLQ+G+Q+VIKQ QLFCRPDYEKE
Sbjct: 208 NRCLGCGEKIGADELVMRALDNVFHLKCFICVVCGVRLQKGDQYVIKQSQLFCRPDYEKE 267

Query: 65  VEMLQGYAQGIPFDLITSSKSH----DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRK 120
           VEM QGY+    +D            DGRRGPKRPRTILTTQQRRAFKASF+ISPKPCRK
Sbjct: 268 VEMFQGYS----YDDYCCDDMFQTRIDGRRGPKRPRTILTTQQRRAFKASFDISPKPCRK 323

Query: 121 VREGLARDTGLSVRIVQ 137
           +REGLA+DTGLS+RIVQ
Sbjct: 324 IREGLAKDTGLSIRIVQ 340

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195376251|ref|XP_002046910.1| GJ12228 [Drosophila virilis] gi|194154068|gb|EDW69252.1| GJ12228 [Drosophila virilis]

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 95/137 (69%), Positives = 113/137 (82%), Gaps = 4/137 (2%)

Query: 2   LYVK-KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
           LY++ +CLGC  K+  DELVM++ +N+FH++CF CVVCG+ L++GEQ+V+KQGQLFCR D
Sbjct: 268 LYLRNRCLGCGHKIAADELVMRSQENIFHLKCFACVVCGALLKKGEQYVVKQGQLFCRFD 327

Query: 61  YEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRK 120
           YEKEVEMLQGY      DL       DGRRGPKRPRTIL TQQRRAFKASFE+SPKPCRK
Sbjct: 328 YEKEVEMLQGYDY-YGDDLFPPKM--DGRRGPKRPRTILNTQQRRAFKASFEVSPKPCRK 384

Query: 121 VREGLARDTGLSVRIVQ 137
           VRE LA+DTGLS+RIVQ
Sbjct: 385 VRENLAKDTGLSLRIVQ 401

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195126142|ref|XP_002007533.1| GI12337 [Drosophila mojavensis] gi|193919142|gb|EDW18009.1| GI12337 [Drosophila mojavensis]

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 95/137 (69%), Positives = 113/137 (82%), Gaps = 4/137 (2%)

Query: 2   LYVK-KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
           LY++ +CLGC  K+  DELVM++ +N+FH++CF CVVCG+ L++GEQ+V+KQGQLFCR D
Sbjct: 284 LYLRNRCLGCGHKIAADELVMRSQENIFHLKCFACVVCGAVLKKGEQYVVKQGQLFCRFD 343

Query: 61  YEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRK 120
           YEKEVEMLQGY      DL       DGRRGPKRPRTIL TQQRRAFKASFE+SPKPCRK
Sbjct: 344 YEKEVEMLQGYDY-YGDDLFPPKM--DGRRGPKRPRTILNTQQRRAFKASFEVSPKPCRK 400

Query: 121 VREGLARDTGLSVRIVQ 137
           VRE LA+DTGLS+RIVQ
Sbjct: 401 VRENLAKDTGLSLRIVQ 417

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195012862|ref|XP_001983762.1| GH16074 [Drosophila grimshawi] gi|193897244|gb|EDV96110.1| GH16074 [Drosophila grimshawi]

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 95/137 (69%), Positives = 113/137 (82%), Gaps = 4/137 (2%)

Query: 2   LYVK-KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
           LY++ +CLGC  K+  DELVM++ +N+FH++CF CVVCG+ L++GEQ+V+KQGQLFCR D
Sbjct: 290 LYLRNRCLGCGHKIAGDELVMRSQENIFHLKCFACVVCGALLKKGEQYVVKQGQLFCRFD 349

Query: 61  YEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRK 120
           YEKEVEMLQGY      DL       DGRRGPKRPRTIL TQQRRAFKASFE+SPKPCRK
Sbjct: 350 YEKEVEMLQGY-DFYGDDLFPPKM--DGRRGPKRPRTILNTQQRRAFKASFEVSPKPCRK 406

Query: 121 VREGLARDTGLSVRIVQ 137
           VRE LA+DTGLS+RIVQ
Sbjct: 407 VRENLAKDTGLSLRIVQ 423

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	143
FB|FBgn0036274	544	CG4328 [Drosophila melanogaste	0.930	0.244	0.635	6.1e-39
UNIPROTKB|G3V877	372	Lmx1b "LIM homeobox transcript	0.356	0.137	0.811	2.5e-30
ZFIN|ZDB-GENE-050114-2	375	lmx1bb "LIM homeobox transcrip	0.391	0.149	0.758	2.9e-30
UNIPROTKB|H9L043	280	H9L043 "Uncharacterized protei	0.944	0.482	0.5	1.3e-29
UNIPROTKB|Q8UVR3	400	lmx1b.1 "LIM homeobox transcri	0.951	0.34	0.474	2.4e-28
ZFIN|ZDB-GENE-050114-3	375	lmx1ba "LIM homeobox transcrip	0.944	0.36	0.493	3.1e-28
FB|FBgn0052105	640	CG32105 [Drosophila melanogast	0.951	0.212	0.517	3.4e-28
UNIPROTKB|F1N4F7	294	LMX1B "Uncharacterized protein	0.951	0.462	0.470	2.2e-27
UNIPROTKB|J9NU69	327	LMX1B "Uncharacterized protein	0.951	0.415	0.470	2.2e-27
UNIPROTKB|B7ZLH2	383	LMX1B "LMX1B protein" [Homo sa	0.951	0.355	0.470	2.2e-27

FB|FBgn0036274 CG4328 [Drosophila melanogaster (taxid:7227)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 87/137 (63%), Positives = 101/137 (73%)

Query:     2 LYVKK-CLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPD 60
             LY++  CLGC  K+  DELVM+  +N            G+ L++GEQ+V+KQGQLFCR D
Sbjct:   253 LYIRNHCLGCGLKIAADELVMRCHENVFHLKCFACVVCGALLKKGEQYVVKQGQLFCRFD 312

Query:    61 YEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRK 120
             YEKEVEMLQGY      D +   K  DGRRGPKRPRTIL TQQRRAFKASFE+SPKPCRK
Sbjct:   313 YEKEVEMLQGY--DFYGDELFPPKL-DGRRGPKRPRTILNTQQRRAFKASFEVSPKPCRK 369

Query:   121 VREGLARDTGLSVRIVQ 137
             VRE LA+DTGLS+RIVQ
Sbjct:   370 VRENLAKDTGLSLRIVQ 386

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

GO:0005634 "nucleus" evidence=ISS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0048813 "dendrite morphogenesis" evidence=IMP

GO:0006911 "phagocytosis, engulfment" evidence=IMP

UNIPROTKB|G3V877 Lmx1b "LIM homeobox transcription factor 1 beta" [Rattus norvegicus (taxid:10116)]

 Score = 210 (79.0 bits), Expect = 2.5e-30, Sum P(2) = 2.5e-30
 Identities = 43/53 (81%), Positives = 47/53 (88%)

Query:    87 DGR--RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             DG+  R PKRPRTILTTQQRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   189 DGKDPRRPKRPRTILTTQQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 241

GO:0001764 "neuron migration" evidence=IEA

GO:0002930 "trabecular meshwork development" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0008219 "cell death" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0021587 "cerebellum morphogenesis" evidence=IEA

GO:0021954 "central nervous system neuron development" evidence=IEA

GO:0030199 "collagen fibril organization" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0035108 "limb morphogenesis" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

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

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

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

ZFIN|ZDB-GENE-050114-2 lmx1bb "LIM homeobox transcription factor 1, beta b" [Danio rerio (taxid:7955)]

 Score = 215 (80.7 bits), Expect = 2.9e-30, Sum P(2) = 2.9e-30
 Identities = 44/58 (75%), Positives = 49/58 (84%)

Query:    82 SSKSHDGR--RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             + K  DG+  R PKRPRTILTTQQRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   182 TGKGDDGKDPRRPKRPRTILTTQQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 239

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0030917 "midbrain-hindbrain boundary development" evidence=IGI

GO:0042472 "inner ear morphogenesis" evidence=IMP

GO:0021592 "fourth ventricle development" evidence=IGI

GO:0060117 "auditory receptor cell development" evidence=IMP

GO:0032474 "otolith morphogenesis" evidence=IMP

GO:0048752 "semicircular canal morphogenesis" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0002072 "optic cup morphogenesis involved in camera-type eye development" evidence=IGI

GO:0061386 "closure of optic fissure" evidence=IGI

GO:0060041 "retina development in camera-type eye" evidence=IGI

UNIPROTKB|H9L043 H9L043 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 74/148 (50%), Positives = 93/148 (62%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPDY 61
             L+  KC  C + + P EL+M+ L+N              RLQRG++FV+K+GQL CR DY
Sbjct:     2 LFQTKCSSCLKAIAPSELIMRVLENVYHVHCFYCCECERRLQRGDEFVLKEGQLLCRSDY 61

Query:    62 EKEVEMLQGYAQGIPFDLITSSK-----SH-----DGR--RGPKRPRTILTTQQRRAFKA 109
             EKE EML   +   P + + S       SH     D +  +  KRPRTILTTQQRRAFKA
Sbjct:    62 EKEKEMLSAISPA-PTESVKSEDEDGGHSHGKGSEDSKDHKRSKRPRTILTTQQRRAFKA 120

Query:   110 SFEISPKPCRKVREGLARDTGLSVRIVQ 137
             SFE+S KPCRKVRE LA +TGL+VR+VQ
Sbjct:   121 SFEVSSKPCRKVRETLAAETGLTVRVVQ 148

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q8UVR3 lmx1b.1 "LIM homeobox transcription factor 1-beta.1" [Xenopus laevis (taxid:8355)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 73/154 (47%), Positives = 94/154 (61%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPDY 61
             L+  KC GC EK+ P E VM+ L+               +L++G++FV+K+GQL C+ DY
Sbjct:   110 LFAAKCSGCMEKIAPTEFVMRALECVYHLSCFCCCVCERQLRKGDEFVLKEGQLLCKSDY 169

Query:    62 EKEVEMLQGYA----QGIPFD-----------LITSSK-SHDGR--RGPKRPRTILTTQQ 103
             EKE ++L   +      +  D            +   K S DG+  R PKRPRTILTTQQ
Sbjct:   170 EKEKDLLSSGSPDDSDSVKSDDEEGDVKPGKGRVNQGKGSDDGKDPRRPKRPRTILTTQQ 229

Query:   104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             RRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   230 RRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 263

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

GO:0005634 "nucleus" evidence=ISS

GO:0030182 "neuron differentiation" evidence=IMP

GO:0039020 "pronephric nephron tubule development" evidence=IMP

GO:0072013 "glomus development" evidence=IEP;IMP

ZFIN|ZDB-GENE-050114-3 lmx1ba "LIM homeobox transcription factor 1, beta a" [Danio rerio (taxid:7955)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 75/152 (49%), Positives = 93/152 (61%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPDY 61
             L+  KC GC EK+ P ELVM+ L++              RL +G++FV+K+GQL C+ DY
Sbjct:    87 LFATKCSGCLEKISPTELVMRALESVYHLSCFCCCVCERRLCKGDEFVLKEGQLLCKTDY 146

Query:    62 EKEVEM----LQGYAQGIPFDLIT------------SSKSHDGRRGPKRPRTILTTQQRR 105
             E+E ++    L    +    DL              S  S D RR PKRPRTILTTQQRR
Sbjct:   147 EREKDLASPDLSDSDKSEDEDLDVKPEKGAGGQGKGSDDSKDPRR-PKRPRTILTTQQRR 205

Query:   106 AFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             AFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   206 AFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 237

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

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0030917 "midbrain-hindbrain boundary development" evidence=IGI

GO:0030902 "hindbrain development" evidence=IMP

GO:0021592 "fourth ventricle development" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0061386 "closure of optic fissure" evidence=IGI

GO:0060041 "retina development in camera-type eye" evidence=IGI

GO:0002072 "optic cup morphogenesis involved in camera-type eye development" evidence=IGI

FB|FBgn0052105 CG32105 [Drosophila melanogaster (taxid:7227)]

 Score = 322 (118.4 bits), Expect = 3.4e-28, P = 3.4e-28
 Identities = 73/141 (51%), Positives = 89/141 (63%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSR-LQRGEQFVIKQGQLFC-RP 59
             L+  KC  C   + P ELVM+ + N                LQ+GEQF+++ GQLFC R 
Sbjct:   329 LFGVKCSSCCHAILPQELVMRPIPNFVFHLPCFVCYACRLPLQKGEQFMLRDGQLFCYRH 388

Query:    60 DYEKEVEMLQGYAQGIPF---DLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPK 116
             D EKE+ +    AQ   F   D     +  DGRRGPKRPRTILT+QQR+ FKASF+ SPK
Sbjct:   389 DLEKEMFLAAAAAQHCGFVGLDEEDLLRPRDGRRGPKRPRTILTSQQRKQFKASFDQSPK 448

Query:   117 PCRKVREGLARDTGLSVRIVQ 137
             PCRKVRE LA+DTGLSVR+VQ
Sbjct:   449 PCRKVREALAKDTGLSVRVVQ 469

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1N4F7 LMX1B "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 73/155 (47%), Positives = 95/155 (61%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPDY 61
             L+  KC GC EK+ P E VM+ L+               +L++G++FV+K+GQL C+ DY
Sbjct:     2 LFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDY 61

Query:    62 EKEVEMLQGYA---------QGIPFDLI------TSSKSH--DGR--RGPKRPRTILTTQ 102
             EKE ++L   +         +    D+       + SK    DG+  R PKRPRTILTTQ
Sbjct:    62 EKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQ 121

Query:   103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             QRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   122 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 156

GO:0005634 "nucleus" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

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

GO:0035265 "organ growth" evidence=IEA

GO:0035108 "limb morphogenesis" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0030199 "collagen fibril organization" evidence=IEA

GO:0021954 "central nervous system neuron development" evidence=IEA

GO:0021587 "cerebellum morphogenesis" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0008219 "cell death" evidence=IEA

GO:0002930 "trabecular meshwork development" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|J9NU69 LMX1B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 73/155 (47%), Positives = 95/155 (61%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPDY 61
             L+  KC GC EK+ P E VM+ L+               +L++G++FV+K+GQL C+ DY
Sbjct:    42 LFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDY 101

Query:    62 EKEVEMLQGYA---------QGIPFDLI------TSSKSH--DGR--RGPKRPRTILTTQ 102
             EKE ++L   +         +    D+       + SK    DG+  R PKRPRTILTTQ
Sbjct:   102 EKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQ 161

Query:   103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             QRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   162 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 196

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|B7ZLH2 LMX1B "LMX1B protein" [Homo sapiens (taxid:9606)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 73/155 (47%), Positives = 95/155 (61%)

Query:     2 LYVKKCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPDY 61
             L+  KC GC EK+ P E VM+ L+               +L++G++FV+K+GQL C+ DY
Sbjct:    87 LFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDY 146

Query:    62 EKEVEMLQGYA---------QGIPFDLI------TSSKSH--DGR--RGPKRPRTILTTQ 102
             EKE ++L   +         +    D+       + SK    DG+  R PKRPRTILTTQ
Sbjct:   147 EKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQ 206

Query:   103 QRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             QRRAFKASFE+S KPCRKVRE LA +TGLSVR+VQ
Sbjct:   207 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ 241

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0001764 "neuron migration" evidence=IEA

GO:0002930 "trabecular meshwork development" evidence=IEA

GO:0008219 "cell death" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0021587 "cerebellum morphogenesis" evidence=IEA

GO:0021954 "central nervous system neuron development" evidence=IEA

GO:0030199 "collagen fibril organization" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0035108 "limb morphogenesis" evidence=IEA

GO:0035265 "organ growth" evidence=IEA

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

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8TE12	LMX1A_HUMAN	No assigned EC number	0.5197	0.9510	0.3560	yes	N/A
Q9JKU8	LMX1A_MOUSE	No assigned EC number	0.5197	0.9510	0.3560	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	143
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	2e-20
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	5e-16
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	2e-13
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	3e-13
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	3e-13
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-12
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-12
pfam00412	58	pfam00412, LIM, LIM domain	3e-11
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	5e-11
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	1e-10
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	3e-10
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	6e-10
cd09471	55	cd09471, LIM2_Isl2, The second LIM domain of Isl2	8e-10
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	1e-09
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	2e-09
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	6e-09
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-08
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	1e-08
cd09390	55	cd09390, LIM2_dLMO, The second LIM domain of dLMO	3e-08
smart00389	57	smart00389, HOX, Homeodomain	5e-08
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	6e-08
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	1e-07
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	2e-07
cd09352	54	cd09352, LIM1_Ajuba_like, The first LIM domain of	8e-07
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	8e-07
cd09342	57	cd09342, LIM3_Testin_like, The third LIM domain of	3e-06
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	3e-06
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	4e-06
cd09383	55	cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of	4e-06
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	5e-06
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	5e-06
cd09461	54	cd09461, LIM3_Enigma_like_1, The third LIM domain	9e-06
cd09385	56	cd09385, LIM2_LMO2, The second LIM domain of LMO2	1e-05
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	1e-05
cd09382	55	cd09382, LIM2_Lhx6, The second LIM domain of Lhx6	2e-05
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	2e-05
cd09372	53	cd09372, LIM2_FBLP-1, The second LIM domain of the	3e-05
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-05
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	6e-05
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	6e-05
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	1e-04
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	2e-04
cd09365	54	cd09365, LIM2_LIMK, The second LIM domain of LIMK	2e-04
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	2e-04
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	3e-04
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	3e-04
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	3e-04
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	6e-04
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	6e-04
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	8e-04
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	8e-04
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	8e-04
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	0.001
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	0.001
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	0.001
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	0.002
cd09464	55	cd09464, LIM2_LIMK1, The second LIM domain of LIMK	0.002
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	0.003
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	0.003
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	0.004
cd09458	55	cd09458, LIM3_Enigma, The third LIM domain of Enig	0.004

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

 Score = 78.6 bits (194), Expect = 2e-20
 Identities = 31/55 (56%), Positives = 44/55 (80%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC EK+ P ELVM+ L+NV+H++CF C VC  +LQ+G++FV+K+GQL C+ DY
Sbjct: 1  CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55

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

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

 Score = 67.3 bits (165), Expect = 5e-16
 Identities = 23/58 (39%), Positives = 33/58 (56%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          VK+C  C   +   ELVM+  D VFH+ CF C  C   L +G+ F ++ G ++CR  Y
Sbjct: 2  VKRCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 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|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family

 Score = 60.1 bits (146), Expect = 2e-13
 Identities = 21/56 (37%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPDY 61
          C GC E + P ++V +  DNV+H++CF C +C  +L+ G++F +++  +L C+ DY
Sbjct: 1  CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56

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

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

 Score = 60.1 bits (146), Expect = 3e-13
 Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQ-FVIKQGQLFCRPDY 61
          C GC + + P++LV +  D VFH+ CF C+VC  +L  GE+ +++ + +  C+ DY
Sbjct: 1  CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56

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

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

 Score = 59.8 bits (145), Expect = 3e-13
 Identities = 21/54 (38%), Positives = 31/54 (57%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
          C  C + +   ELVM+   NV+H++CF C  C ++L  G++F    G LFC  D
Sbjct: 1  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54

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

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

 Score = 57.8 bits (140), Expect = 2e-12
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
          KC GC + +   E V++ L  V+H +CF C  CG  L  G+ F  K G+L+C+  
Sbjct: 1  KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL-SGDTFFEKDGKLYCKDC 54

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

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

 Score = 57.3 bits (139), Expect = 2e-12
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC + +   E +++ L   +H +CF C VCG  L  G+ F  K G+ +C   Y
Sbjct: 1  CAGCGKPIEGRE-LLRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 53

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

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

 Score = 55.0 bits (133), Expect = 3e-11
 Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
          C GC + +   ELV + L  V+H +CF C VCG  L  G+ F  K G+L+C+ DY K
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFK 56

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

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

 Score = 54.0 bits (130), Expect = 5e-11
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C +    ++ VM+    ++H++CF C  C  +L  G++F ++   LFC+ D+
Sbjct: 1  CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55

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

>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 53.1 bits (127), Expect = 1e-10
 Identities = 21/55 (38%), Positives = 33/55 (60%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  CS+ +   E+VM+  DNV+H+ CF C +C  R   G++F +K   + C+ DY
Sbjct: 1  CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55

The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 52.4 bits (125), Expect = 3e-10
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
          V++C  C   +   E+VM+  ++V+H+ CF C  C   L  G+ F +K   ++CR
Sbjct: 2  VQRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCR 56

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

 Score = 51.3 bits (123), Expect = 6e-10
 Identities = 17/55 (30%), Positives = 30/55 (54%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  CS  +   + V +  D+V+H+ CF C  C  +L  GE+F + + ++ C+  Y
Sbjct: 1  CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

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

>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2

 Score = 51.1 bits (122), Expect = 8e-10
 Identities = 20/55 (36%), Positives = 34/55 (61%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C       +LVM+  D+V+H++CF C VC  +L  G++F +++ +L CR D+
Sbjct: 1  CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRADH 55

The second LIM domain of Isl2: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl proteins are found in the nucleus and act as transcription factors or cofactors. Isl1 and Isl2 are the two conserved members of this family. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Isl2 may be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 50.8 bits (121), Expect = 1e-09
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPDY 61
          C  C + + P ++V K  D V+H+ CF C++C  +L  G++F +++ G+L C+ DY
Sbjct: 1  CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56

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

>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C E +  +      +D VFHV CF C+ C  +L RG+ F   + + +C P Y
Sbjct: 1  CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKL-RGQPFYAVEKKAYCEPCY 54

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in 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 = 54

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

 Score = 48.9 bits (116), Expect = 6e-09
 Identities = 19/55 (34%), Positives = 30/55 (54%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
          V++C  C   +   E+VM+  D V+H+ CF C  C   L  G+ F +K   ++CR
Sbjct: 2  VQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCR 56

The second LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain

 Score = 48.2 bits (116), Expect = 1e-08
 Identities = 16/45 (35%), Positives = 24/45 (53%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +R RT  T +Q    +  FE +  P  + RE LA+  GL+ R V+
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45

Length = 57

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

 Score = 48.1 bits (114), Expect = 1e-08
 Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPDY 61
          KC  C + + P ++V +  D V+H+ CF C+VC  +L  G++F +++  +L C+ DY
Sbjct: 1  KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57

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

>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx)

 Score = 46.8 bits (111), Expect = 3e-08
 Identities = 19/55 (34%), Positives = 32/55 (58%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  CS+ +   E+VM+   NV+H++CF C  C  R   G++F + + ++ C  DY
Sbjct: 1  CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55

The second LIM domain of dLMO (Beaderx): dLMO is a nuclear protein that plays important roles in transcriptional regulation and development. In Drosophila dLMO modulates the activity of LIM-homeodomain protein Apterous (Ap), which regulates the formation of the dorsal-ventral axis of the Drosophila wing. Biochemical analysis shows that dLMO protein influences the activity of Apterous by binding of its cofactor Chip. Further studies shown that dLMO proteins might function in an evolutionarily conserved mechanism involved in patterning the appendages. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 46.5 bits (111), Expect = 5e-08
 Identities = 18/46 (39%), Positives = 26/46 (56%)

Query: 92  PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
            +R RT  T +Q    +  F+ +P P R+ RE LA+  GLS R V+
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. Length = 57

>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

 Score = 46.5 bits (111), Expect = 6e-08
 Identities = 18/45 (40%), Positives = 27/45 (60%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +R RT  T +Q    +  FE +P P R+ RE LA++ GL+ R V+
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45

Length = 59

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

 Score = 45.2 bits (107), Expect = 1e-07
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC  K+   + V   L+  +H  CF C VC   L     +  K G+L+CR DY
Sbjct: 1  CAGCRGKILDSQYVQ-ALNQDWHCDCFRCSVCSDSLS--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|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins

 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C +K   + L  +  D  FH++CF C VCG  L +G  FV K+G+ +C  DY
Sbjct: 1  CYKCGKKCKGEVL--RVQDKYFHIKCFTCKVCGCDLAQGGFFV-KEGEYYCTDDY 52

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

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

 Score = 43.2 bits (102), Expect = 8e-07
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C+ C + +       + + N++H  CF C  CG  L RG+ F    G+++C  DY
Sbjct: 1  CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL-RGKAFYNVNGKVYCEEDY 54

The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

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

 Score = 43.1 bits (102), Expect = 8e-07
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC E +  D  ++K     +HV C  C VC + L+R      +  Q++C+ DY
Sbjct: 1  CTGCGEPI-TDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54

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

>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like family

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHV--QCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
          C  C E +GPD   +      +H   +CF C  C   L  G+ F+ K GQ+FC P 
Sbjct: 1  CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLL-GQPFLPKNGQIFCSPK 55

The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 57

>gnl|CDD|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only protein 2)

 Score = 41.8 bits (98), Expect = 3e-06
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPDY 61
          C GC + +G D   +K +D  +H  C  C +CG RL + G +   K G+  CR DY
Sbjct: 1  CGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 55

The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 41.8 bits (98), Expect = 4e-06
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C + +  D   ++ L++ +H  CF C  CG+ L     +  K G+LFC+ DY
Sbjct: 22 CASCGQSI-YDGQYLQALNSDWHADCFRCCECGASLSH--WYYEKDGRLFCKKDY 73

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

>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8

 Score = 41.6 bits (97), Expect = 4e-06
 Identities = 17/55 (30%), Positives = 28/55 (50%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C   +   + V +   NV+H+ CF C  C  +L  GE+F + + ++ CR  Y
Sbjct: 1  CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55

The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 41.4 bits (97), Expect = 5e-06
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC  ++       + +   +H  CF C VC   L     +  K G+L+C   Y
Sbjct: 1  CTGCGGRIQDSFHY-RVVQEAWHNSCFQCSVCQDLLT--NWYYEKDGKLYCHKHY 52

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

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

 Score = 41.1 bits (96), Expect = 5e-06
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C  ++  D+ ++K  D  +HV+C  C VC + L R     IK   +FC+ DY
Sbjct: 2  CSSCGLEI-VDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDY 55

The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma subfamily with unknown function

 Score = 40.2 bits (94), Expect = 9e-06
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
          C+ C   +   +  ++ L+N +H QCF C  C   L+ G+ F  K G+ FC+
Sbjct: 1  CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE-GQSFYAKGGRPFCK 51

The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized 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. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. 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|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only protein 2)

 Score = 40.4 bits (94), Expect = 1e-05
 Identities = 14/54 (25%), Positives = 28/54 (51%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
          C  C +++   E+ M+  D V+H++CF C  C      G+++++    + C  D
Sbjct: 1  CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54

The second LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 40.1 bits (94), Expect = 1e-05
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C+ C EK+  +      +D V+H+ CF C  C   LQ G+ F    G+ +C  DY
Sbjct: 1  CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQ-GKPFYALDGKPYCEEDY 54

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

>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C  ++   + V +   N +H+ CF C  C  +L  GE+F + + ++ CR  Y
Sbjct: 1  CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55

The second LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQL-FCRPDYEKE 64
          C  C +K+   + ++K     +H QCF CVVC   L+ GE F++ Q     C  DY + 
Sbjct: 1  CAVCDQKI--TDRMLKATGKSYHPQCFTCVVCKCPLE-GESFIVDQANQPHCVNDYHRR 56

The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein. Length = 60

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

 Score = 38.9 bits (91), Expect = 3e-05
 Identities = 15/44 (34%), Positives = 24/44 (54%)

Query: 18 ELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          E +++ L   +H  CF CV CG R+      V +Q +++C  DY
Sbjct: 10 EHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription]

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 16/57 (28%), Positives = 23/57 (40%)

Query: 83  SKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSR 139
            +  DG   PK  R   T +Q    +  FEI+P P    R  L+    +  + VQ  
Sbjct: 42  ERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIW 98

Length = 156

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

 Score = 38.1 bits (88), Expect = 6e-05
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C  K+  +  V+  L   +HV CFVCV C + + R   F ++ G+ +C  DY
Sbjct: 1  CGRCQRKILGE--VINALKQTWHVSCFVCVACHNPI-RNNVFHLEDGEPYCETDY 52

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

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

 Score = 38.2 bits (89), Expect = 6e-05
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C +K+  +  VM  L   +HV CFVC  C   +     F ++ G+ +C  DY
Sbjct: 1  CARCHKKILGE--VMHALKQTWHVSCFVCAACKQPI-GNSLFHMEDGEPYCEKDY 52

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

>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C + L   +  ++ L ++FHV CF C  C  +LQ G+QF   +G+ +C   Y
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQ-GQQFYSLEGKPYCEECY 87

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 87

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

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C +K+  +  +M  L   +HV CF C  C + + R   F +++G  +C  DY
Sbjct: 1  CAKCKKKITGE--IMHALKMTWHVHCFTCAACKTPI-RNRAFYMEEGAPYCERDY 52

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

>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain Kinase )

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 7  CLGCSEKL-GPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQG-QLFCRPDY 61
          C GCS+ + GP   VM   D+ FH +CF C  C + +  G+ + + +  +L+C   Y
Sbjct: 1  CHGCSQIITGP---VMVAGDHKFHPECFSCSSCKAFIGDGDSYALVERSKLYCGVCY 54

The second 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 depolymerization. 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 = 54

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

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC ++   D+ ++  LD  +H +C  C  C   L   E+   ++G+L+CR D+
Sbjct: 1  CAGC-DRPILDKFLLNVLDRAWHAKCVQCCDCKCPLT--EKCFSREGKLYCRNDF 52

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

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

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQR-GEQFVIKQGQLFCRPDY 61
          C GC+ K+  D  ++K LD  +H  C  C  C  RL   G     K   + CR DY
Sbjct: 1  CAGCNRKI-KDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55

The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 36.2 bits (84), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62
          C GC ++   D  +++  +  +H +C  C VC   L     F  +  +L+C+ DY+
Sbjct: 1  CAGC-QRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYF--RDRKLYCKQDYQ 53

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

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

 Score = 36.2 bits (84), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC E +  D  ++K LD  +H +C  C  CG++L   ++   + G ++C+ D+
Sbjct: 1  CGGCQEHI-LDRFILKVLDRTWHAKCLKCNDCGAQLT--DKCFARNGHVYCKDDF 52

The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH

 Score = 35.8 bits (83), Expect = 6e-04
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C E   PDE ++ +   ++H QCFVC  C      G  F   +G+ +C  D+
Sbjct: 1  CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGL-FYEFEGRKYCEHDF 54

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH) family

 Score = 35.7 bits (82), Expect = 6e-04
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
          C GC   +   +  ++ L + +H  CFVC VC   L+ G+ F  K+ +  C+
Sbjct: 1  CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLE-GQTFFSKKDKPLCK 51

The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

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

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          + KC GC   +  D  ++K  D  +H +C  CV C ++L   ++   + GQ++C+ D+
Sbjct: 1  IPKCAGCDHPI-FDRFILKVQDKPWHSKCLKCVDCQAQLT--DKCFSRGGQVYCKEDF 55

The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 35.4 bits (81), Expect = 8e-04
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C  ++  D  ++K  + ++HV+C  C VC + L++     IK  ++FC+ DY
Sbjct: 1  CSSCGLEI-LDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54

The first LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in the brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 35.1 bits (81), Expect = 8e-04
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPDY 61
          C GC  K+  D  ++  LD  +H  C  C  C ++L + G     K G + C+ DY
Sbjct: 1  CAGCGGKIV-DRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55

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

>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like family

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
          C GC   +   +  ++ L + +H  CFVC VC   L+ G+ F  K+ +  C+
Sbjct: 1  CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLE-GQTFYSKKDKPLCK 51

The third 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 = 54

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

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C+ C + + P E ++     ++H  CF C  C ++L  G  +    G ++C+P +
Sbjct: 1  CVSCQKTVYPLERLVAN-QQIYHNSCFRCSYCNTKLSLG-TYASLHGNIYCKPHF 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|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC++ +  D+ ++K LD  +H  C  C  C  ++Q  E+   + G ++C+ D+
Sbjct: 1  CAGCNQHI-LDKFILKVLDRHWHSSCLKCADC--QMQLAERCFSRAGNVYCKEDF 52

The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|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 = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 7  CLGCSEKLGPDE-LVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C + + P E LV   L  VFH  CF C  C ++L  G  +    G+ +C+P +
Sbjct: 1  CSSCQKTVYPMERLVADKL--VFHNSCFCCKHCNAKLSLG-SYAALHGEFYCKPHF 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|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFV-IKQGQLFC 57
          C GCSE +    LVM   +  +H +CF C+ CG+ +  G+ +  ++  +L+C
Sbjct: 1  CHGCSETITTG-LVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYC 51

The second LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 34.2 bits (78), Expect = 0.003
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
             C GC  K+  D   +  +D  +H++C  C  C   L+       K G ++C+ DY
Sbjct: 8  AALCAGCGGKIS-DRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64

The first LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 64

>gnl|CDD|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9

 Score = 33.9 bits (77), Expect = 0.003
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C GC  K+  D   +  +D  +H++C  C  C   L+       K G ++C+ DY
Sbjct: 1  CAGCGGKIS-DRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54

The first LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

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

 Score = 33.6 bits (77), Expect = 0.004
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          C  C +++ P E ++      FH  CF C  C S+L  G  +    G+++C+P +
Sbjct: 1  CTVCQKRVYPMERLIAD-KQNFHKSCFRCEHCNSKLSLG-NYASLHGRIYCKPHF 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|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma

 Score = 33.5 bits (76), Expect = 0.004
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
          C GC  K+   +  ++ L   +H  CFVC +C   L+ G+ F  K+ +  C+
Sbjct: 1  CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLE-GKTFYSKKDKPLCK 51

The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
KOG4577|consensus	383		99.96
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.78
KOG0843|consensus	197		99.71
KOG0842|consensus	307		99.7
KOG0484|consensus	125		99.69
KOG0850|consensus	245		99.69
KOG0490|consensus	235		99.67
KOG0485|consensus	268		99.61
KOG0489|consensus	261		99.6
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.6
KOG0493|consensus	342		99.58
KOG0488|consensus	309		99.58
KOG0494|consensus	332		99.56
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.55
KOG0848|consensus	317		99.55
KOG2251|consensus	228		99.55
COG5576	156	Homeodomain-containing transcription factor [Trans	99.54
KOG0487|consensus	308		99.53
KOG1701|consensus	468		99.53
KOG0492|consensus	246		99.53
KOG1701|consensus	468		99.5
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.45
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.42
KOG0490|consensus	235		99.34
KOG0844|consensus	408		99.29
KOG0491|consensus	194		99.27
KOG0483|consensus	198		99.21
KOG4577|consensus	383		99.18
KOG3802|consensus	398		99.15
KOG0486|consensus	351		99.13
KOG0847|consensus	288		99.06
KOG0849|consensus	354		98.96
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.93
KOG2272|consensus	332		98.86
KOG1703|consensus	479		98.83
KOG2272|consensus	332		98.81
KOG1044|consensus	670		98.77
KOG1168|consensus	385		98.55
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.3
KOG2252|consensus	558		98.21
KOG0775|consensus	304		98.07
KOG0774|consensus	334		97.98
KOG1700|consensus	200		97.98
KOG1703|consensus	479		97.85
KOG1044|consensus	670		97.85
KOG1700|consensus	200		97.83
KOG1146|consensus	1406		97.63
KOG1702|consensus	264		97.4
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.33
KOG3623|consensus	1007		96.26
KOG0773|consensus	342		96.22
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	93.23
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	91.57
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.65
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	88.7
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	88.29
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	87.4
PRK08359	176	transcription factor; Validated	87.2
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	84.43
PF13248	26	zf-ribbon_3: zinc-ribbon domain	82.9
PF10668	60	Phage_terminase: Phage terminase small subunit; In	82.1
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	81.65

>KOG4577|consensus

Probab=99.96  E-value=1.3e-30  Score=176.23  Aligned_cols=127  Identities=36%  Similarity=0.731  Sum_probs=112.8

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEee-CCeeechhhHHHHHHHhhccCCCCCCccc
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIK-QGQLFCRPDYEKEVEMLQGYAQGIPFDLI   80 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~~~~~~~~~~~~~~~~~~~~~   80 (143)
                      .|+.+|..|...|-+...+..+.+.+||..||.|..|+++|.+|++||.. ++++.|..+|...-.  ..+.        
T Consensus        90 rfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~--k~~~--------  159 (383)
T KOG4577|consen   90 RFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ--KHCN--------  159 (383)
T ss_pred             HhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh--cccc--------
Confidence            48899999999999888778899999999999999999999999999765 789999999987433  2222        


Q ss_pred             cCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         81 TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        81 ~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                          +-++....||+||.+++.|+++|+..|...+.|....|++|+.++||..++|||||||
T Consensus       160 ----~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQN  217 (383)
T KOG4577|consen  160 ----ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQN  217 (383)
T ss_pred             ----ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhh
Confidence                2235566789999999999999999999999999999999999999999999999999

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.78  E-value=4.7e-19  Score=94.48  Aligned_cols=51  Identities=18%  Similarity=0.174  Sum_probs=49.5

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCC----CCHHHHHHHHHHhCCCcccceecccCC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPK----PCRKVREGLARDTGLSVRIVQSRPIPV  143 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~----p~~~~~~~la~~~~l~~~~vkvWFQn~  143 (143)
                      +|.||.||.+|+..|+..|+.++|    |+..++++||..+||++++|||||||.
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~   56 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN   56 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence            689999999999999999999999    999999999999999999999999994

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>KOG0843|consensus

Probab=99.71  E-value=5.5e-18  Score=108.02  Aligned_cols=52  Identities=29%  Similarity=0.232  Sum_probs=51.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +++|.||.|+.+|+..|+..|+.++|....+|++||..|+|++.||||||||
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQN  152 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQN  152 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhh
Confidence            7889999999999999999999999999999999999999999999999999

>KOG0842|consensus

Probab=99.70  E-value=2.4e-17  Score=114.65  Aligned_cols=56  Identities=20%  Similarity=0.205  Sum_probs=52.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.+++|+.|..|+..|...||+.|....|.+..+|++||..|+|++.||||||||
T Consensus       148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQN  203 (307)
T KOG0842|consen  148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQN  203 (307)
T ss_pred             cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeec
Confidence            34566677888999999999999999999999999999999999999999999999

>KOG0484|consensus

Probab=99.69  E-value=2e-18  Score=100.36  Aligned_cols=54  Identities=26%  Similarity=0.240  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.+|.||.|+..|+..|++.|.+.+||++..|++||.++.|+++.|||||||
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQN   67 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQN   67 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHh
Confidence            456778999999999999999999999999999999999999999999999999

>KOG0850|consensus

Probab=99.69  E-value=1.6e-17  Score=109.75  Aligned_cols=57  Identities=23%  Similarity=0.252  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.++.++.||+++..||+.|++.|++.+|....+|++||..|||+..||||||||
T Consensus       116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQN  172 (245)
T KOG0850|consen  116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQN  172 (245)
T ss_pred             CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhh
Confidence            456677778999999999999999999999999999999999999999999999999

>KOG0490|consensus

Probab=99.67  E-value=1.5e-17  Score=114.06  Aligned_cols=110  Identities=25%  Similarity=0.448  Sum_probs=91.5

Q ss_pred             cCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCCCCCCccccCCCCCCCC
Q psy15437         10 CSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGR   89 (143)
Q Consensus        10 C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (143)
                      |+..|. +.......+..||..|..|..|...+..+...+..++..||..++.+                       ...
T Consensus         2 ~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~-----------------------~~~   57 (235)
T KOG0490|consen    2 CGRQIL-DRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQR-----------------------EFK   57 (235)
T ss_pred             CCcccc-chHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchh-----------------------hhh
Confidence            566665 34445666889999999999999999533445444999999888865                       123


Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccCC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV  143 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn~  143 (143)
                      .+.++.|+.++..|+..|++.|+..|||+..+++.||..+++++..|+|||||.
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnr  111 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNR  111 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhh
Confidence            456789999999999999999999999999999999999999999999999995

>KOG0485|consensus

Probab=99.61  E-value=3.8e-16  Score=102.46  Aligned_cols=55  Identities=24%  Similarity=0.271  Sum_probs=52.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +..++|+.||+|+..|+..||..|+...|....+|..||.+|.|++.||||||||
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQN  154 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQN  154 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhh
Confidence            4557788999999999999999999999999999999999999999999999999

>KOG0489|consensus

Probab=99.60  E-value=2.3e-16  Score=109.42  Aligned_cols=53  Identities=23%  Similarity=0.184  Sum_probs=51.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.+|.||.||..|+..||+.|+.|.|.+...|.++|..|.|+++||||||||
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQN  209 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQN  209 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHH
Confidence            44788999999999999999999999999999999999999999999999999

>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=99.60  E-value=2.1e-15  Score=81.85  Aligned_cols=58  Identities=33%  Similarity=0.843  Sum_probs=51.7

Q ss_pred             ccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437          7 CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus         7 C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      |.+|+++|.+.+.++.+.++.||++||+|..|+.+|..+. ++..++.+||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhhhC
Confidence            7899999997777668999999999999999999996444 999999999999998764

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 ....

>KOG0493|consensus

Probab=99.58  E-value=8.5e-16  Score=103.39  Aligned_cols=51  Identities=29%  Similarity=0.363  Sum_probs=49.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      -||.||.|+.+|++.|+..|+.|.|.+...|.+||.+|+|.+.||||||||
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQN  296 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQN  296 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhh
Confidence            357899999999999999999999999999999999999999999999999

>KOG0488|consensus

Probab=99.58  E-value=1.6e-15  Score=107.02  Aligned_cols=55  Identities=20%  Similarity=0.154  Sum_probs=51.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..++.++.||+||+.|+..||+.|+...|....+|++||..|||+..|||+||||
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQN  222 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQN  222 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhh
Confidence            3466667899999999999999999999999999999999999999999999999

>KOG0494|consensus

Probab=99.56  E-value=3e-15  Score=100.69  Aligned_cols=54  Identities=28%  Similarity=0.271  Sum_probs=49.6

Q ss_pred             CCCCCCC-CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRP-RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~-R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.+++|. ||+||..|+..||..|.+.+||+...|+.||.+|.|++..|+|||||
T Consensus       137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQN  191 (332)
T KOG0494|consen  137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQN  191 (332)
T ss_pred             cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhh
Confidence            3334444 99999999999999999999999999999999999999999999999

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.55  E-value=1.5e-15  Score=82.12  Aligned_cols=50  Identities=34%  Similarity=0.492  Sum_probs=48.3

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.++.+|+..|+..|..+++|+..+++.||..+||+..+|++||||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n   50 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQN   50 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHH
Confidence            46789999999999999999999999999999999999999999999998

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>KOG0848|consensus

Probab=99.55  E-value=9.7e-16  Score=103.40  Aligned_cols=54  Identities=26%  Similarity=0.242  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.+.+.|.++|+.|+..||+.|+-++|.++..+.+||..|+|+++||||||||
T Consensus       196 tRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQN  249 (317)
T KOG0848|consen  196 TRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQN  249 (317)
T ss_pred             eecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhh
Confidence            344556788999999999999999999999999999999999999999999999

>KOG2251|consensus

Probab=99.55  E-value=4.8e-15  Score=97.67  Aligned_cols=56  Identities=30%  Similarity=0.276  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++++.+|.||.|+..|++.||..|.+..||+...|++||.+|+|++.+|||||-|
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKN   87 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKN   87 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhcc
Confidence            67788999999999999999999999999999999999999999999999999988

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.54  E-value=9e-15  Score=93.50  Aligned_cols=59  Identities=27%  Similarity=0.305  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         84 KSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        84 ~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...++....++.|+..+..|+..|++.|.++++|+...|..|+..++|+++.|||||||
T Consensus        43 ~~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQN  101 (156)
T COG5576          43 RKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQN  101 (156)
T ss_pred             hcccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhch
Confidence            34556677788899999999999999999999999999999999999999999999999

>KOG0487|consensus

Probab=99.53  E-value=4.4e-15  Score=103.51  Aligned_cols=53  Identities=21%  Similarity=0.176  Sum_probs=50.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.+++|..+|..|+..||+.|..|-|.+..-|.+|+..|+|+++||||||||
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQN  285 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQN  285 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehh
Confidence            55667889999999999999999999999999999999999999999999999

>KOG1701|consensus

Probab=99.53  E-value=2e-16  Score=112.85  Aligned_cols=105  Identities=27%  Similarity=0.594  Sum_probs=86.1

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEee-CCeeechhhHHHHHH-HhhccCCCCCCcccc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIK-QGQLFCRPDYEKEVE-MLQGYAQGIPFDLIT   81 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~~~~~~~-~~~~~~~~~~~~~~~   81 (143)
                      ..+|..|++.|.  |++++|+|+.||+.||+|..|.+.| +|..|... ++++||..||.+.|+ +|..|..+|.     
T Consensus       334 lekC~~Cg~~I~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~-----  405 (468)
T KOG1701|consen  334 LEKCNKCGEPIM--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPIL-----  405 (468)
T ss_pred             HHHHhhhhhHHH--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCcchhhccCCcc-----
Confidence            468999999998  7789999999999999999999999 68889765 789999999999997 7888888887     


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHH
Q psy15437         82 SSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARD  128 (143)
Q Consensus        82 ~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~  128 (143)
                         +.++....=|         +..|-+.||.+.|-+..++.+|+.+
T Consensus       406 ---P~~G~~etvR---------vvamdr~fHv~CY~CEDCg~~LS~e  440 (468)
T KOG1701|consen  406 ---PRDGKDETVR---------VVAMDRDFHVNCYKCEDCGLLLSSE  440 (468)
T ss_pred             ---CCCCCcceEE---------EEEccccccccceehhhcCcccccc
Confidence               2333332211         2347889999999999999888743

>KOG0492|consensus

Probab=99.53  E-value=8.7e-15  Score=95.48  Aligned_cols=52  Identities=23%  Similarity=0.165  Sum_probs=49.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+..||.||..|+..||+.|...+|..+.+|.+++..|.|++.||||||||
T Consensus       143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQN  194 (246)
T KOG0492|consen  143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQN  194 (246)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhh
Confidence            3456899999999999999999999999999999999999999999999999

>KOG1701|consensus

Probab=99.50  E-value=9.7e-16  Score=109.42  Aligned_cols=77  Identities=27%  Similarity=0.637  Sum_probs=70.5

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCCCCCCccc
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLI   80 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~   80 (143)
                      |...|.+|++.|.+++..++|+++.||..||+|..|.++| .|..||..+++.||+.||...+++|..|+..|.+.++
T Consensus       273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L-~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iL  349 (468)
T KOG1701|consen  273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQL-AGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRIL  349 (468)
T ss_pred             hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhh-ccccccccCCcccchHHHHHHHHHHhhhhhHHHHHHH
Confidence            4458999999999999999999999999999999999999 6999999999999999999999999999988775443

>smart00389 HOX Homeodomain

Probab=99.45  E-value=6.4e-14  Score=75.38  Aligned_cols=49  Identities=37%  Similarity=0.452  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.|+.++..++..|+..|..+++|+..++..||..+||+..+|+.||+|
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n   50 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQN   50 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHH
Confidence            4677899999999999999999999999999999999999999999998

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

Probab=99.42  E-value=1.4e-13  Score=74.76  Aligned_cols=49  Identities=37%  Similarity=0.488  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.|+.++..++..|+..|..+++|+..+++.||..+||+..+|++||+|
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n   50 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQN   50 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            4678899999999999999999999999999999999999999999998

>KOG0490|consensus

Probab=99.34  E-value=9e-13  Score=90.44  Aligned_cols=139  Identities=27%  Similarity=0.422  Sum_probs=103.5

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCC-eeechhhHHHHHHHhhccCCCCCCc---
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQG-QLFCRPDYEKEVEMLQGYAQGIPFD---   78 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~-~~~C~~~~~~~~~~~~~~~~~~~~~---   78 (143)
                      +..+|.+|...+...+.+..++.+. |.-||.|..|...+..+.++.+... ...|..++...-.....-..+....   
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~  136 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAP  136 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCC
Confidence            5679999999997667777788887 9999999999998878888876644 7788777654310111111111110   


Q ss_pred             ---cccCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         79 ---LITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        79 ---~~~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                         ............+.++.|+.+...++..+...|...++|+...++.|+..+|++++.|+|||||
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~  203 (235)
T KOG0490|consen  137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQN  203 (235)
T ss_pred             ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhccc
Confidence               0111112233455667899999999999999999999999999999999999999999999998

>KOG0844|consensus

Probab=99.29  E-value=1e-12  Score=90.55  Aligned_cols=54  Identities=20%  Similarity=0.106  Sum_probs=50.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....+|.||.|+.+|+..||+.|-+..|...+.|=+||..|+|++..|||||||
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQN  231 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQN  231 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhh
Confidence            344568999999999999999999999999999999999999999999999999

>KOG0491|consensus

Probab=99.27  E-value=2.3e-13  Score=85.84  Aligned_cols=50  Identities=22%  Similarity=0.233  Sum_probs=48.1

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.||+|+..|+..|++.|+...|....++.+||..|+|++.|||.||||
T Consensus       101 ~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQN  150 (194)
T KOG0491|consen  101 RKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQN  150 (194)
T ss_pred             hhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHH
Confidence            34799999999999999999999999999999999999999999999999

>KOG0483|consensus

Probab=99.21  E-value=7e-12  Score=82.96  Aligned_cols=49  Identities=27%  Similarity=0.260  Sum_probs=46.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.+..++.+|...|+..|+.+.+.....+..||.+|||.++||.|||||
T Consensus        52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQN  100 (198)
T KOG0483|consen   52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQN  100 (198)
T ss_pred             cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhh
Confidence            4456789999999999999999999999999999999999999999999

>KOG4577|consensus

Probab=99.18  E-value=6.9e-13  Score=90.72  Aligned_cols=69  Identities=28%  Similarity=0.741  Sum_probs=63.4

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCC
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIP   76 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~   76 (143)
                      +.|+.|.+.|. +.++..+.++.||..|++|+.|..+|.  +.++.+++.+||..+|.++|+ +|..|..+|+
T Consensus        34 p~CagC~q~Il-DrFilKvl~R~wHs~CLkCs~C~~qL~--drCFsR~~s~yCkedFfKrfGTKCsaC~~GIp  103 (383)
T KOG4577|consen   34 PICAGCDQHIL-DRFILKVLDRHWHSSCLKCSDCHDQLA--DRCFSREGSVYCKEDFFKRFGTKCSACQEGIP  103 (383)
T ss_pred             ccccchHHHHH-HHHHHHHHhhhhhhhhcchhhhhhHHH--HHHhhcCCceeehHHHHHHhCCcchhhcCCCC
Confidence            58999999998 677889999999999999999999994  678999999999999999997 7889999998

>KOG3802|consensus

Probab=99.15  E-value=5.7e-11  Score=84.96  Aligned_cols=52  Identities=21%  Similarity=0.270  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++|++||.+....+..||+.|.+|+.|+..++.+||.+|+|.+.+|+|||=|
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCN  344 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCN  344 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeec
Confidence            5677899999999999999999999999999999999999999999999966

>KOG0486|consensus

Probab=99.13  E-value=3e-11  Score=83.67  Aligned_cols=54  Identities=28%  Similarity=0.234  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      -++++|.||.|+..|++.||..|.+|.||++..|+++|+-++|++..|+|||-|
T Consensus       109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfkn  162 (351)
T KOG0486|consen  109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKN  162 (351)
T ss_pred             hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhccc
Confidence            446778999999999999999999999999999999999999999999999987

>KOG0847|consensus

Probab=99.06  E-value=4.9e-11  Score=78.79  Aligned_cols=51  Identities=20%  Similarity=0.164  Sum_probs=48.0

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+..|..|+..|+..|++.|+...|+-..++.+||..+|+.+.+|+|||||
T Consensus       167 rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQN  217 (288)
T KOG0847|consen  167 RKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQN  217 (288)
T ss_pred             ccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhc
Confidence            344678899999999999999999999999999999999999999999999

>KOG0849|consensus

Probab=98.96  E-value=4.8e-10  Score=81.06  Aligned_cols=55  Identities=35%  Similarity=0.401  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccCC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIPV  143 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn~  143 (143)
                      .++.+|.||.++..|+..|+..|+.++||++..|+.||.++++++..|+|||||.
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nr  227 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNR  227 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhh
Confidence            4555667999999999999999999999999999999999999999999999994

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

Probab=98.93  E-value=8.4e-10  Score=54.58  Aligned_cols=38  Identities=42%  Similarity=0.996  Sum_probs=33.8

Q ss_pred             cccccCccccCCcceEEecCcccccCCcccccCCcccc
Q psy15437          6 KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ   43 (143)
Q Consensus         6 ~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~   43 (143)
                      +|..|+++|.+.+..+.+.+..||+.||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            58999999986656788999999999999999999883

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.

>KOG2272|consensus

Probab=98.86  E-value=9.9e-10  Score=74.24  Aligned_cols=100  Identities=22%  Similarity=0.397  Sum_probs=75.7

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhc-cCCCCCCccccCC
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQG-YAQGIPFDLITSS   83 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~-~~~~~~~~~~~~~   83 (143)
                      ..|.+|.....+.|.++...+..||..||.|..|-.++. +..|+..+|+.||..||..++++++. |++=+.+.     
T Consensus        13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~-~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGr-----   86 (332)
T KOG2272|consen   13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFP-DGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGR-----   86 (332)
T ss_pred             HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCC-CceeEEecCcccccccchhhhchhhcccccchhhH-----
Confidence            469999999999999999999999999999999999994 66699999999999999999987654 33333222     


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHh
Q psy15437         84 KSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDT  129 (143)
Q Consensus        84 ~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~  129 (143)
                                         -+..+..+|+...+.+..+.++||...
T Consensus        87 -------------------VikamnnSwHp~CF~Cd~Cn~~Lad~g  113 (332)
T KOG2272|consen   87 -------------------VIKAMNNSWHPACFRCDLCNKHLADQG  113 (332)
T ss_pred             -------------------HHHhhccccCcccchhHHHHHHHhhhh
Confidence                               233345555556666666666655443

>KOG1703|consensus

Probab=98.83  E-value=8.6e-10  Score=82.97  Aligned_cols=100  Identities=22%  Similarity=0.422  Sum_probs=72.9

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCCccc
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPFDLI   80 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~~~~   80 (143)
                      .++..|.+|+.+|.  +.++.+.+..||++||.|..|.+.+ .+..|+.+++.+||..||..++. ++..+..++     
T Consensus       361 ~~~p~C~~C~~~i~--~~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~-----  432 (479)
T KOG1703|consen  361 PFRPNCKRCLLPIL--EEGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPV-----  432 (479)
T ss_pred             hhCccccccCCchH--HhHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhccccchhccchh-----
Confidence            36789999999998  3367888999999999999998888 57779999999999999999886 333332221     


Q ss_pred             cCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHH
Q psy15437         81 TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLA  126 (143)
Q Consensus        81 ~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la  126 (143)
                                       .+-..++..+...|+...|-+..+...|.
T Consensus       433 -----------------~~~~~~ie~~~~~~h~~~F~c~~c~~~l~  461 (479)
T KOG1703|consen  433 -----------------EFGSRQIEADGSPFHGDCFRCANCMKKLT  461 (479)
T ss_pred             -----------------HhhhhHhhccCccccccceehhhhhcccc
Confidence                             12233455556666666666665554443

>KOG2272|consensus

Probab=98.81  E-value=5.2e-10  Score=75.55  Aligned_cols=75  Identities=23%  Similarity=0.456  Sum_probs=63.4

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH-hhccCCCCCCcccc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM-LQGYAQGIPFDLIT   81 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~-~~~~~~~~~~~~~~   81 (143)
                      -+.|..|.++|.  +.++.++++.||.+.|.|..|.+++ -|.+.|.+.|..||..+|.++++. |=.|+..+.++++.
T Consensus       195 ipiCgaC~rpIe--ervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~  270 (332)
T KOG2272|consen  195 IPICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVS  270 (332)
T ss_pred             CcccccccCchH--HHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHH
Confidence            367899999997  6678999999999999999999999 478889999999999999999974 44666666665543

>KOG1044|consensus

Probab=98.77  E-value=1.7e-09  Score=80.59  Aligned_cols=69  Identities=29%  Similarity=0.691  Sum_probs=57.1

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCC
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIP   76 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~   76 (143)
                      ..|++|++.|..+. ++.+.++.||..||+|..|..-|.  .++..+++.+||..||...|+ +|..|..=|.
T Consensus       134 s~cagc~~~lk~gq-~llald~qwhv~cfkc~~c~~vL~--gey~skdg~pyce~dy~~~fgvkc~~c~~fis  203 (670)
T KOG1044|consen  134 STCAGCGEELKNGQ-ALLALDKQWHVSCFKCKSCSAVLN--GEYMSKDGVPYCEKDYQAKFGVKCEECEKFIS  203 (670)
T ss_pred             ccccchhhhhhccc-eeeeeccceeeeeeehhhhccccc--ceeeccCCCcchhhhhhhhcCeehHHhhhhhh
Confidence            47999999998544 678999999999999999999994  458899999999999998886 5555554443

>KOG1168|consensus

Probab=98.55  E-value=3.6e-08  Score=68.04  Aligned_cols=53  Identities=23%  Similarity=0.379  Sum_probs=49.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+||+||.+.+-....||..|...+.|....++.+|.+|+|.+-+|+|||=|
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCN  359 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCN  359 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeec
Confidence            34678999999999999999999999999999999999999999999999976

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=98.30  E-value=9.1e-08  Score=47.36  Aligned_cols=30  Identities=33%  Similarity=0.505  Sum_probs=25.4

Q ss_pred             cCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437        113 ISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus       113 ~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+|||+..+++.||.++|++..||..||=|
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~N   36 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFIN   36 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            479999999999999999999999999976

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>KOG2252|consensus

Probab=98.21  E-value=1.4e-06  Score=65.19  Aligned_cols=57  Identities=25%  Similarity=0.422  Sum_probs=52.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+..-.+|+.|.+|+..|+..|...|..+++|+..+.+.|+.+|+|....|..||=|
T Consensus       414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmN  470 (558)
T KOG2252|consen  414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMN  470 (558)
T ss_pred             ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHh
Confidence            445556777899999999999999999999999999999999999999999999977

>KOG0775|consensus

Probab=98.07  E-value=4.1e-06  Score=57.64  Aligned_cols=44  Identities=20%  Similarity=0.329  Sum_probs=39.5

Q ss_pred             CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |...-+..|+..|..++||...++.+||..|||+..||-.||-|
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKN  226 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKN  226 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhh
Confidence            44445668888999999999999999999999999999999988

>KOG0774|consensus

Probab=97.98  E-value=7.5e-06  Score=56.02  Aligned_cols=50  Identities=22%  Similarity=0.320  Sum_probs=46.2

Q ss_pred             CCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +|+|..|+....++|...|   ..|+||+..++++||.+.+++-.||-.||.|
T Consensus       189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgn  241 (334)
T KOG0774|consen  189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGN  241 (334)
T ss_pred             HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccc
Confidence            4678899999999999998   4678999999999999999999999999988

>KOG1700|consensus

Probab=97.98  E-value=1.4e-06  Score=58.47  Aligned_cols=59  Identities=27%  Similarity=0.687  Sum_probs=49.8

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      ..|.+|.+.+++.+. +...+..||..||+|..|+..|.+ ..+....+.++|..++...+
T Consensus       109 ~~c~~c~k~vy~~Ek-~~~~~~~~hk~cfrc~~~~~~ls~-~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  109 EKCARCQKTVYPLEK-VTGNGLEFHKSCFRCTHCGKKLSP-KNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             cccccccceeeehHH-HhhhhhhhhhhheeecccccccCC-cchhhcCCccccchhhheee
Confidence            579999999998876 568889999999999999999964 55888888999877776654

>KOG1703|consensus

Probab=97.85  E-value=9.6e-06  Score=61.41  Aligned_cols=78  Identities=19%  Similarity=0.352  Sum_probs=64.1

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCCcccc
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPFDLIT   81 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~~~~~   81 (143)
                      ....|..|...|... .++.++++.||+.+|.|..|...+..+. +...+|.+||..|+...+. .|..|..+|.+..+.
T Consensus       302 ~~p~c~~c~~~i~~~-~~i~~~~~~~h~~~~~c~~~~~~~~~~~-~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~  379 (479)
T KOG1703|consen  302 TRPLCLSCNQKIRSV-KVIVALGKEWHPEHFSCEVCAIVILDGG-PRELDGKILCHECFHAPFRPNCKRCLLPILEEGVC  379 (479)
T ss_pred             ccccccccccCcccc-eeEeeccccccccceeeccccccccCCC-ccccCCCccHHHHHHHhhCccccccCCchHHhHhh
Confidence            357899999999842 5788999999999999999999997554 5677899999999988775 788888888866554


Q ss_pred             C
Q psy15437         82 S   82 (143)
Q Consensus        82 ~   82 (143)
                      +
T Consensus       380 a  380 (479)
T KOG1703|consen  380 A  380 (479)
T ss_pred             h
Confidence            4

>KOG1044|consensus

Probab=97.85  E-value=4.4e-06  Score=62.92  Aligned_cols=60  Identities=22%  Similarity=0.493  Sum_probs=53.3

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~   63 (143)
                      .|+.+|..|.+-|.  ..++.+.++.||+.|-.|+.|+..+..|.+-|+.+..+|...|-+.
T Consensus       190 ~fgvkc~~c~~fis--gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa  249 (670)
T KOG1044|consen  190 KFGVKCEECEKFIS--GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQA  249 (670)
T ss_pred             hcCeehHHhhhhhh--hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccccc
Confidence            58899999999998  4478999999999999999999999999999999999988777543

>KOG1700|consensus

Probab=97.83  E-value=4.4e-06  Score=56.12  Aligned_cols=61  Identities=21%  Similarity=0.426  Sum_probs=50.6

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      ..+|..|++.++..+. +...+..||..||.|..|...|. ...+..+++.+||..+|...++
T Consensus         7 ~~kc~~c~k~vy~~e~-~~~~g~~~hk~c~~c~~~~k~l~-~~~~~~~e~~~yc~~~~~~~~~   67 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEK-VQKDGVDFHKECFKCEKCKKTLT-LSGYSEHEGVPYCKNCHVAQFG   67 (200)
T ss_pred             cchhhhccCcchHHHH-HhccCcchhhhHHhccccccccc-cccccccccccccccchHhhhC
Confidence            4589999999997775 45889999999999999999995 4557779999999997655554

>KOG1146|consensus

Probab=97.63  E-value=2.8e-05  Score=63.64  Aligned_cols=50  Identities=26%  Similarity=0.253  Sum_probs=47.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.++..|+..|+..|....+|...+.+.|...++++.++|+|||||
T Consensus       904 ~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qn  953 (1406)
T KOG1146|consen  904 RAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQN  953 (1406)
T ss_pred             hhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhh
Confidence            45799999999999999999999999999999999999999999999998

>KOG1702|consensus

Probab=97.40  E-value=6.9e-06  Score=54.35  Aligned_cols=59  Identities=36%  Similarity=0.706  Sum_probs=46.8

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .-|..|++.+++.|. +.-.+++||..||+|..|+..|.. ..+--.+.++||..+|...+
T Consensus         5 ~n~~~cgk~vYPvE~-v~cldk~whk~cfkce~c~mtlnm-KnyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEE-VKCLDKVWHKQCFKCEVCGMTLNM-KNYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             chhhhhccccccHHH-HhhHHHHHHHHhheeeeccCChhh-hhccccccCCCcCcccccce
Confidence            347789999998875 567889999999999999998863 22444578899999997653

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A

Probab=97.33  E-value=4.7e-05  Score=40.08  Aligned_cols=37  Identities=8%  Similarity=0.036  Sum_probs=28.3

Q ss_pred             HHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437        104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP  140 (143)
Q Consensus       104 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF  140 (143)
                      +..|+..|.....+.......|..+++|+..+|+.||
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WF   46 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWF   46 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHH
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHH
Confidence            4569999999999999999999999999999999999

>KOG3623|consensus

Probab=96.26  E-value=0.0023  Score=50.20  Aligned_cols=39  Identities=18%  Similarity=0.274  Sum_probs=36.7

Q ss_pred             HHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437        104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus       104 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +..|+..|..|..|...+...+|.+.|++.++||+||++
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~  606 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFED  606 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHh
Confidence            567888999999999999999999999999999999987

>KOG0773|consensus

Probab=96.22  E-value=0.0057  Score=44.56  Aligned_cols=52  Identities=27%  Similarity=0.284  Sum_probs=41.2

Q ss_pred             CCCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccCC
Q psy15437         92 PKRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIPV  143 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn~  143 (143)
                      ..|.+..+.......|+...   ...+||...++..|+.++||+..||..||-|.
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINa  293 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINA  293 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhc
Confidence            44455577777777777552   23579999999999999999999999999883

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=93.23  E-value=0.13  Score=26.97  Aligned_cols=45  Identities=24%  Similarity=0.285  Sum_probs=32.9

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|..+|.++...+-..++...     ....+|..+|++..+|.-|.-|
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHC
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHh
Confidence            46788999999988888888886     4668999999999998877543

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

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

Probab=91.57  E-value=0.11  Score=25.02  Aligned_cols=26  Identities=23%  Similarity=0.547  Sum_probs=17.4

Q ss_pred             ccccCccccCCcceEEecCcccccCC
Q psy15437          7 CLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         7 C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      |..||..|.++-.++...++.||.-|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~fCC   26 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYFCC   26 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEEEC
Confidence            67788888755455566777775443

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

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.65  E-value=0.16  Score=26.69  Aligned_cols=31  Identities=19%  Similarity=0.444  Sum_probs=22.0

Q ss_pred             CCccccccCccccCCcceE--EecCcccccCCc
Q psy15437          3 YVKKCLGCSEKLGPDELVM--KTLDNVFHVQCF   33 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~--~~~~~~~h~~cf   33 (143)
                      .+.+|..|++.+.+.+-++  ..=+..||.+|+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            4679999999996443233  345777888887

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

Probab=88.70  E-value=0.15  Score=30.32  Aligned_cols=12  Identities=25%  Similarity=0.587  Sum_probs=5.9

Q ss_pred             cccccCccccCC
Q psy15437          6 KCLGCSEKLGPD   17 (143)
Q Consensus         6 ~C~~C~~~i~~~   17 (143)
                      +|..|+++|+.+
T Consensus         4 kC~iCg~~I~~g   15 (101)
T PF09943_consen    4 KCYICGKPIYEG   15 (101)
T ss_pred             EEEecCCeeeec
Confidence            355555555533

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=88.29  E-value=0.58  Score=24.49  Aligned_cols=38  Identities=39%  Similarity=0.514  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHhhhcCCC--CCHHHHHHHHHHhCCCcccc
Q psy15437         99 LTTQQRRAFKASFEISPK--PCRKVREGLARDTGLSVRIV  136 (143)
Q Consensus        99 ~~~~q~~~L~~~f~~~~~--p~~~~~~~la~~~~l~~~~v  136 (143)
                      +|..|...|...++..-|  |-......||..+|+++..+
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~   40 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV   40 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence            467899999999888876  55556778999999998643

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

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

Probab=87.40  E-value=0.41  Score=29.95  Aligned_cols=24  Identities=38%  Similarity=0.701  Sum_probs=19.5

Q ss_pred             cccccCCccccCCCceEeeCCeeechhhHH
Q psy15437         33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYE   62 (143)
Q Consensus        33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~   62 (143)
                      -.|..|+.+|     |- ++|.+||..|-.
T Consensus        29 ~hCp~Cg~PL-----F~-KdG~v~CPvC~~   52 (131)
T COG1645          29 KHCPKCGTPL-----FR-KDGEVFCPVCGY   52 (131)
T ss_pred             hhCcccCCcc-----ee-eCCeEECCCCCc
Confidence            3588888888     65 899999988863

>PRK08359 transcription factor; Validated

Probab=87.20  E-value=0.87  Score=30.14  Aligned_cols=28  Identities=39%  Similarity=0.884  Sum_probs=17.3

Q ss_pred             ccccCCccccCCCceEe-eCCe--eechhhHH
Q psy15437         34 VCVVCGSRLQRGEQFVI-KQGQ--LFCRPDYE   62 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~-~~~~--~~C~~~~~   62 (143)
                      .|..|+..+ .|..+.. .+|.  ..|..|+.
T Consensus         8 ~CEiCG~~i-~g~~~~v~ieGael~VC~~Ca~   38 (176)
T PRK08359          8 YCEICGAEI-RGPGHRIRIEGAELLVCDRCYE   38 (176)
T ss_pred             eeecCCCcc-CCCCeEEEEcCeEEehHHHHHH
Confidence            388888888 4564533 3442  34888873

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=84.43  E-value=0.69  Score=19.70  Aligned_cols=10  Identities=20%  Similarity=0.753  Sum_probs=6.5

Q ss_pred             cccccCcccc
Q psy15437          6 KCLGCSEKLG   15 (143)
Q Consensus         6 ~C~~C~~~i~   15 (143)
                      +|..|+..|.
T Consensus         1 ~Cp~CG~~~~   10 (23)
T PF13240_consen    1 YCPNCGAEIE   10 (23)
T ss_pred             CCcccCCCCC
Confidence            3667776665

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=82.90  E-value=1  Score=19.73  Aligned_cols=11  Identities=18%  Similarity=0.634  Sum_probs=7.2

Q ss_pred             ccccccCcccc
Q psy15437          5 KKCLGCSEKLG   15 (143)
Q Consensus         5 ~~C~~C~~~i~   15 (143)
                      ..|..|+..+.
T Consensus         3 ~~Cp~Cg~~~~   13 (26)
T PF13248_consen    3 MFCPNCGAEID   13 (26)
T ss_pred             CCCcccCCcCC
Confidence            46777777554

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=82.10  E-value=0.45  Score=25.62  Aligned_cols=18  Identities=17%  Similarity=0.278  Sum_probs=16.0

Q ss_pred             HHHHHHHhCCCcccceec
Q psy15437        122 REGLARDTGLSVRIVQSR  139 (143)
Q Consensus       122 ~~~la~~~~l~~~~vkvW  139 (143)
                      ...+|.+||+++.+|+.|
T Consensus        25 lkdIA~~Lgvs~~tIr~W   42 (60)
T PF10668_consen   25 LKDIAEKLGVSESTIRKW   42 (60)
T ss_pred             HHHHHHHHCCCHHHHHHH
Confidence            457899999999999988

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

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

Probab=81.65  E-value=1.1  Score=22.05  Aligned_cols=22  Identities=32%  Similarity=0.759  Sum_probs=14.6

Q ss_pred             ccccCCccccCCCceEeeCCeeechhh
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPD   60 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~   60 (143)
                      .|..|+.+|     +-.+++..||..|
T Consensus        19 ~Cp~C~~PL-----~~~k~g~~~Cv~C   40 (41)
T PF06677_consen   19 HCPDCGTPL-----MRDKDGKIYCVSC   40 (41)
T ss_pred             ccCCCCCee-----EEecCCCEECCCC
Confidence            466777776     4456778888655

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	143
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	4e-28
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	3e-23
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	1e-10
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	3e-21
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-11
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-19
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	6e-10
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	4e-18
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	1e-09
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	8e-17
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-15
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	3e-15
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-14
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	1e-14
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-14
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	9e-11
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	3e-14
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	2e-13
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-13
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	3e-13
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	3e-13
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	8e-10
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	5e-13
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	3e-12
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	3e-12
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	5e-12
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	7e-12
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	1e-11
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	3e-11
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	3e-11
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-11
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	6e-11
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	8e-11
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	1e-10
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	2e-04
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-10
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-10
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	2e-10
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-10
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	2e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-10
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	4e-10
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	4e-10
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	5e-10
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	7e-10
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-09
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-08
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	2e-09
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-09
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-09
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-09
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	3e-09
1e3o_C	160	Octamer-binding transcription factor 1; transcript	2e-08
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	8e-08
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-07
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-07
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-07
2co8_A	82	NEDD9 interacting protein with calponin homology a	3e-07
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	3e-07
2cor_A	79	Pinch protein; LIM domain, particularly interestin	8e-07
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-06
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	8e-06
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	1e-05
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	1e-05
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	1e-04
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-04
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-04
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-04
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	8e-04

>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 = 88.9 bits (220), Expect = 3e-23
 Identities = 27/112 (24%), Positives = 44/112 (39%), Gaps = 7/112 (6%)

Query: 6   KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65
            C  C + +   ELVM+   NV+H++CF C  C +RL  G++F    G LFC  D    +
Sbjct: 71  ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTAL 130

Query: 66  EMLQGYAQGIPFDLITSSK-------SHDGRRGPKRPRTILTTQQRRAFKAS 110
                 + G      +          +  G         ++T  +   F A+
Sbjct: 131 INGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAA 182

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPD 60
          L  K+C GC  K+  D  ++  +D+ +H +C  C  C ++L   G     K G + CR D
Sbjct: 3  LSWKRCAGCGGKIA-DRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 61

Query: 61 YEK 63
          Y +
Sbjct: 62 YIR 64

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

 Score = 82.1 bits (203), Expect = 3e-21
 Identities = 14/63 (22%), Positives = 31/63 (49%)

Query: 5   KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
             C  C +++   E+ M+  D V+H++CF C  C      G+++++    + C  D  + 
Sbjct: 67  GLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEW 126

Query: 65  VEM 67
            ++
Sbjct: 127 TKI 129

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

 Score = 57.1 bits (138), Expect = 1e-11
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPDYE 62
          +  C GC + +G D   +K +D  +H  C  C +CG RL + G +   K G+  CR DY 
Sbjct: 2  LLTCGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 60

Query: 63 K 63
          +
Sbjct: 61 R 61

>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 = 78.4 bits (193), Expect = 3e-19
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPD 60
            +  KC  C   + P ++V +  D V+H+ CF CVVC  +L  G++F +++  +L C+ D
Sbjct: 117 RFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKAD 176

Query: 61  YEKEVE 66
           YE   +
Sbjct: 177 YETAKQ 182

>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 = 53.8 bits (129), Expect = 6e-10
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
             +  C GC + +  D  ++K LD  +H +C  C  C   L   E+   +   ++C+ D+
Sbjct: 58  PEIPMCAGCDQHIL-DRFILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDF 114

Query: 62  EK 63
            K
Sbjct: 115 FK 116

>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 = 75.3 bits (185), Expect = 4e-18
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQF-VIKQGQLFCRPD 60
            +  KC  C   + P ++V +  D V+H+ CF CVVC  +L  G++F +++  +L C+ D
Sbjct: 63  RFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKAD 122

Query: 61  YEKEVEML 68
           YE   +  
Sbjct: 123 YETAKQGG 130

>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 = 52.9 bits (127), Expect = 1e-09
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
          +  C GC + +  D  ++K LD  +H +C  C  C   L   E+   +   ++C+ D+ K
Sbjct: 6  IPMCAGCDQHIL-DRFILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDFFK 62

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 69.4 bits (170), Expect = 8e-17
 Identities = 15/57 (26%), Positives = 27/57 (47%)

Query: 81  TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +     +  +  KR RT +T +Q       + +   P RK+ + +A + GL  R+VQ
Sbjct: 6   SGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 65.1 bits (159), Expect = 3e-15
 Identities = 14/50 (28%), Positives = 26/50 (52%)

Query: 88  GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
                KRPRT +T  Q R  +  F+I+  P  +  + +A  +GL  ++++
Sbjct: 3   SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52

>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 = 65.2 bits (159), Expect = 3e-15
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV 65
           C GC E +  D   +  LD VFHV CFVC  C ++L+ G+ F   + + +C   Y   +
Sbjct: 7  GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVERRAYCEGCYVATL 65

Query: 66 E 66
          E
Sbjct: 66 E 66

>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 = 63.7 bits (155), Expect = 1e-14
 Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           +   C  C + +G D   +   D  FH  CF C  C   L   E F  +  +L C   Y
Sbjct: 13 TFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTCQDSELLCNDCY 71

Query: 62 EKE 64
             
Sbjct: 72 CSA 74

>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 = 63.2 bits (154), Expect = 1e-14
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
               C  C     P E ++ +   ++H QCFVC  C  +      F   +G+ +C  D+
Sbjct: 9  SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHDF 67

Query: 62 EK 63
          + 
Sbjct: 68 QM 69

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

 Score = 64.7 bits (158), Expect = 1e-14
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFH--VQCFVCVVCGSRLQRGEQFVIKQGQLFCRP 59
            +   C GC   + P+   +   +  +H   +CF+C  C   L  G++F+  +G +FC  
Sbjct: 61  NHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSV 119

Query: 60  DYEK 63
           + +K
Sbjct: 120 ECKK 123

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

 Score = 54.7 bits (132), Expect = 9e-11
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
          +C GC E +  +E   +  +  +H++ F C  C S L  GE +V+   +  C+P Y K
Sbjct: 5  RCAGCDELIFSNE-YTQAENQNWHLKHFCCFDCDSILA-GEIYVMVNDKPVCKPCYVK 60

>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 = 62.4 bits (152), Expect = 3e-14
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          L    C  C     P E ++ +   ++H QCFVC  C  +      F   +G+ +C  D+
Sbjct: 9  LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHDF 67

Query: 62 EK 63
          + 
Sbjct: 68 QM 69

>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 = 60.8 bits (148), Expect = 2e-13
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
              KC GC + +   +  ++    V+H  CF C  C   +     F  K    +C   +
Sbjct: 13 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFPKGEDFYCVTCH 71

Query: 62 EK 63
          E 
Sbjct: 72 ET 73

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

 Score = 60.5 bits (147), Expect = 2e-13
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 5  KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
            C  C + + P    M+   + +H  CF+C  C   +   + F+ K  Q FC P YEK+
Sbjct: 6  SGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPI-GTKSFIPKDNQNFCVPCYEKQ 64

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

 Score = 60.1 bits (146), Expect = 3e-13
 Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 5  KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
            C  C E + P    ++     +H  CF+C  C   L     FV  +G  +C P YE 
Sbjct: 6  SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPL-GSRSFVPDKGAHYCVPCYEN 63

>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 = 60.5 bits (147), Expect = 3e-13
 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
           C+ C + +G D   +   +  +H  CF C  C   L   E FV K  ++ C     +E
Sbjct: 7  GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCTTRE 64

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

 Score = 51.6 bits (124), Expect = 8e-10
 Identities = 9/38 (23%), Positives = 15/38 (39%)

Query: 2   LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCG 39
               KC GC + +   +  ++    V+H  CF     G
Sbjct: 64  EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG 101

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

 Score = 59.4 bits (144), Expect = 5e-13
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 1  MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQG-QLFCRP 59
            + + C GCS  +      M   +  +H +CF C+ C   ++ G+ + + Q   L+C  
Sbjct: 12 GKFGEFCHGCSLLMTG--PFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGK 69

Query: 60 DYEK 63
           + +
Sbjct: 70 CHNE 73

>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 = 57.5 bits (139), Expect = 3e-12
 Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 4/65 (6%)

Query: 2  LYVKKCLGCSE---KLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR 58
             KKC GC       G    V+      +H  CF C  C   L   ++FV  Q Q++C 
Sbjct: 13 FVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQVYCP 71

Query: 59 PDYEK 63
             +K
Sbjct: 72 DCAKK 76

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

 Score = 57.5 bits (139), Expect = 3e-12
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          LY  +C  C + +  +  V+  L   +H  CFVC VC      G++      +  C+   
Sbjct: 13 LYGTRCFSCDQFI--EGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCS 70

Query: 62 EK 63
            
Sbjct: 71 LP 72

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score = 56.6 bits (137), Expect = 5e-12
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 92  PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             R RT+L  +Q    +  +  +P+P   ++E L   TGLS R+++
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 58.1 bits (140), Expect = 7e-12
 Identities = 10/71 (14%), Positives = 26/71 (36%)

Query: 67  MLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLA 126
           +L  + +         ++        ++ RT ++   + A +  F    KP  +    +A
Sbjct: 62  ILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMA 121

Query: 127 RDTGLSVRIVQ 137
            +  L   +V+
Sbjct: 122 EELNLEKEVVR 132

>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 = 55.6 bits (134), Expect = 1e-11
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 2  LYVKKCLGCSEKLGPDEL--VMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRP 59
               C+ CS+ +        +   D+ +H +CF C  C   L  G+ F+ +  ++FC+ 
Sbjct: 3  SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV-GKGFLTQNKEIFCQK 61

Query: 60 DYEKEVEMLQGYAQG 74
                  + G + G
Sbjct: 62 CGSGMDTDISGPSSG 76

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 54.8 bits (132), Expect = 3e-11
 Identities = 18/50 (36%), Positives = 25/50 (50%)

Query: 88  GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
                KR RT     Q R  K+ F I+  P  K  + LA+ TGL+ R++Q
Sbjct: 3   SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52

>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 = 55.9 bits (134), Expect = 3e-11
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 4   VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPDYE 62
            K+C GC  K+  D  ++  +D+ +H +C  C  C ++L   G     K G + CR DY 
Sbjct: 61  WKRCAGCGGKIA-DRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 119

Query: 63  K 63
           +
Sbjct: 120 R 120

>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 = 54.4 bits (131), Expect = 4e-11
 Identities = 12/64 (18%), Positives = 22/64 (34%), Gaps = 3/64 (4%)

Query: 2  LYVKKCLGCSEKL--GPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRP 59
               C GC+  +        +   +  +H  CF C  C   L  G  F+ ++  + C  
Sbjct: 3  SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPD 61

Query: 60 DYEK 63
            + 
Sbjct: 62 CGKD 65

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

 Score = 53.8 bits (130), Expect = 6e-11
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
          + V  C  C   +  +  V+  +   +HV+ FVC  C      G +   ++G  +C   Y
Sbjct: 3  MGVPICGACRRPI--EGRVVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHY 59

Query: 62 EK 63
           +
Sbjct: 60 NQ 61

>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 = 53.5 bits (129), Expect = 8e-11
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 5  KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
            C+ C++ +    +     D  +H  CFVCV C  +L  G++F   + Q +C   Y+ 
Sbjct: 6  SGCVKCNKAITSGGIT--YQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYKN 61

>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 = 54.6 bits (131), Expect = 1e-10
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPD 60
          L  K+C GC  K+  D  ++  +D+ +H +C  C  C ++L   G     K G + CR D
Sbjct: 3  LSWKRCAGCGGKIA-DRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 61

Query: 61 YEK 63
          Y +
Sbjct: 62 YIR 64

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 6/36 (16%), Positives = 12/36 (33%)

Query: 28  FHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
                   +V G     G +F  +  +L  R +  +
Sbjct: 77  HMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQ 112

>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 = 53.2 bits (128), Expect = 1e-10
 Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 3  YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62
              C GC E++   +  +  LD  +HV CF C  C   L    +++ K G  +C  DY 
Sbjct: 14 GPSHCAGCKEEIKHGQ-SLLALDKQWHVSCFKCQTCSVIL--TGEYISKDGVPYCESDYH 70

Query: 63 K 63
           
Sbjct: 71 A 71

>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 = 53.1 bits (128), Expect = 2e-10
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 3/62 (4%)

Query: 2  LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDY 61
           +  +C  CS+ L      +   D  +H +C VC  C + L  G+QF  +    +C   +
Sbjct: 13 KFAPRCARCSKTLTQG--GVTYRDQPWHRECLVCTGCQTPL-AGQQFTSRDEDPYCVACF 69

Query: 62 EK 63
           +
Sbjct: 70 GE 71

>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 = 53.1 bits (128), Expect = 2e-10
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 3  YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62
           ++KC  CS+ +     +++ +   +H  CF CVVC   L      V    Q+ C  D+ 
Sbjct: 14 TLEKCATCSQPILDR--ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFH 71

Query: 63 K 63
          +
Sbjct: 72 R 72

>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 = 52.7 bits (127), Expect = 2e-10
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 1  MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
           ++  KC GC+  +   E  +  +D V+H +CFVC  C +       F    G+ FC   
Sbjct: 12 AMFSPKCGGCNRPV--LENYLSAMDTVWHPECFVCGDCFTSFS-TGSFFELDGRPFCELH 68

Query: 61 YEK 63
          Y  
Sbjct: 69 YHH 71

>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 = 52.3 bits (126), Expect = 2e-10
 Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 3  YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62
              C+ C + +    +     +  +H +CFVC  C  +L  G++F  +    +C   + 
Sbjct: 4  GSSGCVQCKKPITTGGVT--YREQPWHKECFVCTACRKQL-SGQRFTARDDFAYCLNCFC 60

Query: 63 K 63
           
Sbjct: 61 D 61

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 54.5 bits (130), Expect = 3e-10
 Identities = 19/98 (19%), Positives = 43/98 (43%), Gaps = 5/98 (5%)

Query: 40  SRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTIL 99
           S+L+ G +   +  +    P++++   +     +             D    PK+PR + 
Sbjct: 50  SKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKE-----QEHGKDRGNTPKKPRLVF 104

Query: 100 TTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           T  QRR   A F+ + +P ++++  +++  GL +  V 
Sbjct: 105 TDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVS 142

>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 = 52.4 bits (126), Expect = 4e-10
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
           C  C++ +      +  L   +H + F C  C + +     FV ++G L+C   YEK
Sbjct: 27 MCAHCNQVI--RGPFLVALGKSWHPEEFNCAHCKNTMA-YIGFVEEKGALYCELCYEK 81

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

 Score = 51.4 bits (123), Expect = 4e-10
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 3  YVKKCLGCSEKLGPDELVMKTLDNVFHV--QCFVCVVCGSRLQRGEQFVIKQGQLFCRPD 60
          +   C GC   + P+   +   +  +H   +CF+C  C   L  G++F+  +G +FC  +
Sbjct: 1  HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVE 59

Query: 61 YEKEV 65
           +K +
Sbjct: 60 CKKRM 64

>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 = 51.7 bits (124), Expect = 5e-10
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
             C  C E +     V+K ++N +H +CF C +C   L     FV   G+  CRP + +
Sbjct: 5  SSGCHQCGEFIIGR--VIKAMNNSWHPECFRCDLCQEVLA-DIGFVKNAGRHLCRPCHNR 61

Query: 64 E 64
          E
Sbjct: 62 E 62

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

 Score = 51.7 bits (124), Expect = 7e-10
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
           C  C   +     V+K  D   H +CFVC  C   L + + +   +G+L+C      
Sbjct: 27 LCDKCGSGI--VGAVVKARDKYRHPECFVCADCNLNL-KQKGYFFVEGELYCETHARA 81

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

 Score = 53.1 bits (127), Expect = 1e-09
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 3   YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYE 62
               C  C + +   E V+      +H  CF C  CG  L+       K G+++C+  Y 
Sbjct: 114 GSDGCPRCGQAVYAAEKVI-GAGKSWHKSCFRCAKCGKSLE-STTLADKDGEIYCKGCYA 171

Query: 63  K 63
           K
Sbjct: 172 K 172

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

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE 64
          KC  C + +   E V +   + FH  CF+C+VC   L       +   +++C+  Y K+
Sbjct: 9  KCGVCQKAVYFAEEV-QCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKK 65

>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 = 50.1 bits (120), Expect = 2e-09
 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
          KC  C   +   E V       FH  CF+C+VC   L       I   +++C+  Y K
Sbjct: 9  KCGACGRTVYHAEEVQ-CDGRSFHRCCFLCMVCRKNLDSTT-VAIHDAEVYCKSCYGK 64

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

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
           C  C   +    + +K  D   H +C+VC  CG+ L + +     + Q++C     +
Sbjct: 17 MCDKCGTGI--VGVFVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARE 71

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155

 Score = 51.7 bits (123), Expect = 2e-09
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 82  SSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
            SKS    +  KR RT +  + R + +  F  SPKP  +    +A   GL   +V+
Sbjct: 86  ISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141

>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 = 50.2 bits (120), Expect = 2e-09
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 5  KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
          + C+ C + + P E ++     VFH+ CF C  C ++L  G  +    G+++C+P + +
Sbjct: 16 ETCVECQKTVYPMERLL-ANQQVFHISCFRCSYCNNKLSLGT-YASLHGRIYCKPHFNQ 72

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 51.6 bits (123), Expect = 3e-09
 Identities = 13/57 (22%), Positives = 23/57 (40%)

Query: 81  TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           T+      +   ++ RT +    + A ++ F   PKP      GLA    L   +V+
Sbjct: 88  TNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVR 144

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 50.4 bits (120), Expect = 3e-09
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 4  VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL-QRGEQFVIKQGQLFCRPDYE 62
          +  C GC + +G D   +K +D  +H  C  C +CG RL + G +   K G+  CR DY 
Sbjct: 3  LLTCGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 61

Query: 63 K 63
          +
Sbjct: 62 R 62

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 49.2 bits (117), Expect = 2e-08
 Identities = 12/56 (21%), Positives = 25/56 (44%)

Query: 82  SSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +S   +G    ++ RT + T  R A + SF  + KP  +    +A    +   +++
Sbjct: 91  NSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR 146

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

 Score = 45.9 bits (108), Expect = 8e-08
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFC 57
           C  C + +     V++  +  +H  C +CV CG     GE+  ++   ++ 
Sbjct: 7  GCDSCEKYI--TGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 45.5 bits (108), Expect = 1e-07
 Identities = 16/51 (31%), Positives = 23/51 (45%)

Query: 87  DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
            G  G    +   + +Q  A K SF  +  P +   E L + TGLS R V+
Sbjct: 3   SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVR 53

>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 = 45.4 bits (108), Expect = 1e-07
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 3/59 (5%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFC-RPDYEK 63
          KC  C +++   E V  +L   +H  C  C  CG  L         +G+ +C  P Y  
Sbjct: 2  KCPKCDKEVYFAERVT-SLGKDWHRPCLKCEKCGKTL-TSGGHAEHEGKPYCNHPCYSA 58

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 44.7 bits (106), Expect = 2e-07
 Identities = 11/48 (22%), Positives = 18/48 (37%)

Query: 90  RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
              +  RT  T  Q R  +  F+ +  P     E L+    L  R++ 
Sbjct: 5   SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV 52

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 6/47 (12%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 92  PKRPRTILTTQQRRAFKASF-EISPKPCRKVREGLARDTGLSVRIVQ 137
             R RT ++ +     ++   ++   P ++    L+    L    + 
Sbjct: 7   GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII 53

>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 = 44.6 bits (105), Expect = 3e-07
 Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 2/60 (3%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGE-QFVIKQGQLFCRPDYEKE 64
           C  C E L   E +     + FH  CF C  C + L  G  +     G  +C     + 
Sbjct: 17 LCALCGEHLYVLERLC-VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQT 75

>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 = 44.3 bits (105), Expect = 3e-07
 Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 6  KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFC-RPDYEK 63
          KC  C + +   E V  +L   +H  C  C  C   L  G       G+ FC +P Y  
Sbjct: 11 KCPKCDKTVYFAEKVS-SLGKDWHKFCLKCERCSKTLTPGG-HAEHDGKPFCHKPCYAT 67

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

 Score = 43.2 bits (102), Expect = 8e-07
 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK 63
          C  C   +  DE  +   ++ +H   F C  CG  L         +G+L+C P ++K
Sbjct: 18 CQKCHAII--DEQPLIFKNDPYHPDHFNCANCGKEL--TADARELKGELYCLPCHDK 70

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89

 Score = 42.7 bits (100), Expect = 2e-06
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 81  TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQS 138
           + S        P++ +   T  Q +  + SF  S  P +   + L  +T LS R + S
Sbjct: 3   SGSSGAYPDFAPQKFKE-KTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDS 59

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 40.6 bits (95), Expect = 8e-06
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 87  DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQS 138
            G  GP + +     +Q RA ++SF  +P P  +  + L  +T ++ R + S
Sbjct: 3   SGSSGPTKYKE-RAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDS 53

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 12/46 (26%), Positives = 16/46 (34%)

Query: 92  PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
                   T +Q    KASF  S  P       L   TGL+   ++
Sbjct: 4   HHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIK 49

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 12/56 (21%), Positives = 21/56 (37%)

Query: 82  SSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
                      ++ RT  T Q   A  A FE +P P  +    +A++      +V+
Sbjct: 83  MEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVR 138

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 14/50 (28%), Positives = 19/50 (38%)

Query: 88  GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
                +R RT  T  Q    +A F  +  P   +RE +A    L    VQ
Sbjct: 3   SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 11/39 (28%), Positives = 17/39 (43%)

Query: 100 TTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQS 138
           T +Q R  +ASF  S     +    L   T L+ R + +
Sbjct: 19  TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDA 57

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61

 Score = 36.8 bits (86), Expect = 1e-04
 Identities = 8/49 (16%), Positives = 21/49 (42%)

Query: 89  RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +    + ++ ++ Q R   +  F        K +E +A+  G++   V+
Sbjct: 2   KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVR 50

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 37.1 bits (85), Expect = 2e-04
 Identities = 10/48 (20%), Positives = 21/48 (43%)

Query: 90  RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
            G        T +Q    K++F  +  P  +  + LA+++GL+   + 
Sbjct: 23  SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIV 70

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67

 Score = 35.0 bits (81), Expect = 8e-04
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +RPRT  T  Q    +  F ++  P   + E LA+   L +  +Q
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.85
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.79
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.79
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.77
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.76
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.76
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.76
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.75
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.75
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.75
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.75
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.75
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.75
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.74
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.74
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.74
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.74
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.74
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.74
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.74
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.73
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.73
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.73
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.73
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.73
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.73
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.73
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.73
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.73
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.73
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.73
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.73
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.72
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.72
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.71
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.71
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.71
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.71
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.7
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.7
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.7
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.7
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.7
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.69
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.69
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.68
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.68
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.68
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.68
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.68
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.68
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.68
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.68
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.67
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.67
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.67
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.67
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.67
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.67
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.67
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.67
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.65
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.65
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.65
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.65
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.64
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.64
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.64
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.64
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.64
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.63
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.63
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.63
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.63
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.63
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.63
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.63
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.62
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.62
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.62
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.62
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.62
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.62
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.61
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.61
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.61
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.61
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.61
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.61
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.61
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.61
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.61
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.6
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.6
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.6
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.59
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.59
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.59
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.59
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.58
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.58
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.58
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.58
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.58
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.56
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.56
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.55
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.54
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.54
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.54
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.53
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.5
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.49
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.47
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.46
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.46
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.44
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.43
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.42
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.4
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.4
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.4
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.33
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.27
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.14
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.86
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.35
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	96.6
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.39
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	93.3

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.85  E-value=3.2e-22  Score=107.79  Aligned_cols=56  Identities=11%  Similarity=0.041  Sum_probs=53.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhc-CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEI-SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.+.++|.||.++.+|+..|+..|+. ++||+...++.||.+|||++++|||||||
T Consensus         2 ~~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQN   58 (71)
T 1wi3_A            2 SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQN   58 (71)
T ss_dssp             CCCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhcc
Confidence            345678899999999999999999999 99999999999999999999999999999

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.79  E-value=8.2e-20  Score=104.26  Aligned_cols=55  Identities=22%  Similarity=0.230  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhc----CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEI----SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~----~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +..+.+|.||.|+.+|+..|+..|+.    ++||+..++++||..|||++++|||||||
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqN   71 (80)
T 1wh5_A           13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHN   71 (80)
T ss_dssp             CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccc
Confidence            44567889999999999999999999    99999999999999999999999999999

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.79  E-value=7.4e-20  Score=104.25  Aligned_cols=55  Identities=20%  Similarity=0.196  Sum_probs=51.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhc-----CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEI-----SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~-----~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +...+.+|.||.|+.+|+..|+ .|..     ++||+..++++||..|+|++++|||||||
T Consensus        12 ~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqN   71 (80)
T 1wh7_A           12 SSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN   71 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHT
T ss_pred             CCCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccc
Confidence            4456678899999999999999 7999     99999999999999999999999999999

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.77  E-value=4.3e-19  Score=102.55  Aligned_cols=57  Identities=14%  Similarity=0.100  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .....+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus        16 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqN   72 (84)
T 2kt0_A           16 DKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQN   72 (84)
T ss_dssp             CCCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            344566778999999999999999999999999999999999999999999999998

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=5.7e-19  Score=101.06  Aligned_cols=56  Identities=25%  Similarity=0.213  Sum_probs=52.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +...+.++.|+.|+..|+..|+..|..++||+..+++.||..|+|++.+|+|||||
T Consensus        12 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN   67 (80)
T 2dmt_A           12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQN   67 (80)
T ss_dssp             CCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHH
Confidence            34556778999999999999999999999999999999999999999999999998

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.76  E-value=3.7e-19  Score=99.38  Aligned_cols=54  Identities=15%  Similarity=0.140  Sum_probs=51.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   57 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQN   57 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHh
Confidence            345677899999999999999999999999999999999999999999999998

>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=99.76  E-value=3.2e-20  Score=120.65  Aligned_cols=100  Identities=26%  Similarity=0.613  Sum_probs=79.4

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEe-eCCeeechhhHHHHHHHhhccCCCCCCccc
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVI-KQGQLFCRPDYEKEVEMLQGYAQGIPFDLI   80 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~-~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~   80 (143)
                      +|+.+|..|+++|.+.+.++.+.++.||+.||+|..|+.+|..|..|+. .++.+||..||.+.+..             
T Consensus        63 ~f~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~-------------  129 (169)
T 2rgt_A           63 RFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQG-------------  129 (169)
T ss_dssp             HHSCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHC-------------
T ss_pred             cccccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhc-------------
Confidence            5789999999999977777899999999999999999999976777765 58899999999887752             


Q ss_pred             cCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCH
Q psy15437         81 TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCR  119 (143)
Q Consensus        81 ~~~~~~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~  119 (143)
                           .....+.+|+||.+++.|++.|+..|+.+++|..
T Consensus       130 -----~~~~~~~~rprt~~~~~q~~~l~~~f~~~~~~~~  163 (169)
T 2rgt_A          130 -----GSGGSGGSGGGTPMVAASPERHDGGLQANPVEVQ  163 (169)
T ss_dssp             -----C----------EEEECCCCEECCSSCCCCCCCCC
T ss_pred             -----cCCCCCCcCCCCcccHHHHHHHHHHHhCCCCccc
Confidence                 0011456789999999999999999999999864

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=5.8e-19  Score=98.57  Aligned_cols=54  Identities=24%  Similarity=0.241  Sum_probs=51.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   57 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQN   57 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            345678899999999999999999999999999999999999999999999998

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A

Probab=99.75  E-value=6.8e-19  Score=100.03  Aligned_cols=56  Identities=18%  Similarity=0.087  Sum_probs=52.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +...+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   59 (77)
T 1nk2_P            4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN   59 (77)
T ss_dssp             CCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHH
Confidence            44556778899999999999999999999999999999999999999999999998

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=6.3e-19  Score=98.45  Aligned_cols=53  Identities=30%  Similarity=0.290  Sum_probs=50.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...++.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   57 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKN   57 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehcccc
Confidence            44677899999999999999999999999999999999999999999999998

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.75  E-value=7.1e-19  Score=98.24  Aligned_cols=55  Identities=20%  Similarity=0.183  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   57 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQN   57 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHh
Confidence            3445677899999999999999999999999999999999999999999999998

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.75  E-value=5.4e-19  Score=101.28  Aligned_cols=56  Identities=27%  Similarity=0.386  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....+.++.|+.|+.+|+..|+..|..++||+..+++.||..|||++.+|+|||||
T Consensus        12 ~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   67 (80)
T 2da3_A           12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQN   67 (80)
T ss_dssp             CCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHH
Confidence            34566788999999999999999999999999999999999999999999999998

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A

Probab=99.74  E-value=5e-19  Score=96.25  Aligned_cols=51  Identities=24%  Similarity=0.307  Sum_probs=46.6

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   53 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKN   53 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhh
Confidence            567899999999999999999999999999999999999999999999998

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.74  E-value=6.2e-19  Score=98.49  Aligned_cols=54  Identities=26%  Similarity=0.430  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+.+|+..|+..|+.++||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   57 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN   57 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhh
Confidence            345678999999999999999999999999999999999999999999999998

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.74  E-value=1.4e-18  Score=99.44  Aligned_cols=53  Identities=28%  Similarity=0.232  Sum_probs=50.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...++.|+.|+..|+..|+..|..++||+..+++.||..|||++.+|+|||||
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqN   57 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSN   57 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHH
Confidence            45678899999999999999999999999999999999999999999999998

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.74  E-value=1.5e-18  Score=96.86  Aligned_cols=53  Identities=21%  Similarity=0.141  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   57 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQN   57 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHh
Confidence            44567899999999999999999999999999999999999999999999998

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.74  E-value=8.1e-19  Score=96.00  Aligned_cols=51  Identities=25%  Similarity=0.153  Sum_probs=48.2

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   53 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQN   53 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHh
Confidence            567899999999999999999999999999999999999999999999998

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.74  E-value=2e-18  Score=101.32  Aligned_cols=57  Identities=21%  Similarity=0.175  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+...+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN   67 (93)
T 3a01_A           11 NRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQN   67 (93)
T ss_dssp             TSCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHh
Confidence            344556778999999999999999999999999999999999999999999999998

>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=99.74  E-value=4.7e-18  Score=95.47  Aligned_cols=67  Identities=34%  Similarity=0.654  Sum_probs=60.5

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhh
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQ   69 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~   69 (143)
                      +++.+|..|+++|..++.++.++++.||+.||+|..|+.+| .+..|+.+++.+||..||.+++++++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~~~~~~   69 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQL-RGQHFYAVERRAYCEGCYVATLESGP   69 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBC-TTSCEEESSSCEEEHHHHHHHHHTCS
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcC-CcCcCEeeCCeEECHHHHHHHHccCC
Confidence            57899999999999766688999999999999999999999 57779999999999999999987544

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*

Probab=99.73  E-value=9.8e-19  Score=100.24  Aligned_cols=55  Identities=18%  Similarity=0.127  Sum_probs=46.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .....++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus        16 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqN   70 (81)
T 1b8i_A           16 TNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN   70 (81)
T ss_dssp             --------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHH
Confidence            3445678899999999999999999999999999999999999999999999998

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=1.7e-18  Score=99.08  Aligned_cols=54  Identities=26%  Similarity=0.182  Sum_probs=51.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+..|+..|+..|+.++||+..+++.||..++|++.+|+|||||
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   57 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKN   57 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHH
Confidence            355678999999999999999999999999999999999999999999999998

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.73  E-value=1.1e-18  Score=94.00  Aligned_cols=50  Identities=22%  Similarity=0.182  Sum_probs=48.4

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   50 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQN   50 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhH
Confidence            46899999999999999999999999999999999999999999999998

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.73  E-value=1.1e-18  Score=96.29  Aligned_cols=52  Identities=27%  Similarity=0.434  Sum_probs=49.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.++.|+.|+.+|+..|+..|+.++||+..+++.||..+||++.+|+|||||
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   53 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQN   53 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHH
Confidence            3577899999999999999999999999999999999999999999999998

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.73  E-value=8.3e-19  Score=95.68  Aligned_cols=52  Identities=19%  Similarity=0.145  Sum_probs=45.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   53 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQN   53 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHH
Confidence            3567899999999999999999999999999999999999999999999998

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2e-18  Score=98.89  Aligned_cols=54  Identities=33%  Similarity=0.368  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   57 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQN   57 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHH
Confidence            345678999999999999999999999999999999999999999999999998

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.73  E-value=1.5e-18  Score=93.47  Aligned_cols=51  Identities=18%  Similarity=0.178  Sum_probs=49.0

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.++..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   52 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQN   52 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHH
Confidence            456899999999999999999999999999999999999999999999998

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.73  E-value=1.6e-18  Score=96.15  Aligned_cols=51  Identities=20%  Similarity=0.151  Sum_probs=49.5

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   52 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKN   52 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHH
Confidence            567899999999999999999999999999999999999999999999998

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A

Probab=99.73  E-value=2.9e-18  Score=97.43  Aligned_cols=55  Identities=22%  Similarity=0.155  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.+..++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqN   63 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQN   63 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            3455678999999999999999999999999999999999999999999999998

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.73  E-value=2.7e-18  Score=96.56  Aligned_cols=53  Identities=17%  Similarity=0.129  Sum_probs=50.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqN   57 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQN   57 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            45677899999999999999999999999999999999999999999999998

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=8e-19  Score=100.47  Aligned_cols=55  Identities=20%  Similarity=0.311  Sum_probs=51.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcC----CCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEIS----PKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~----~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...+.++.|+.|+.+|+..|+..|+.+    +||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqN   62 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGN   62 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHH
Confidence            345677899999999999999999999    9999999999999999999999999998

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*

Probab=99.73  E-value=9.3e-19  Score=95.23  Aligned_cols=53  Identities=17%  Similarity=0.219  Sum_probs=43.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqN   55 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFIN   55 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            45677899999999999999999999999999999999999999999999998

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.72  E-value=2.9e-18  Score=97.04  Aligned_cols=55  Identities=27%  Similarity=0.230  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   59 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQN   59 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHH
Confidence            3455678899999999999999999999999999999999999999999999998

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.72  E-value=1.7e-18  Score=93.87  Aligned_cols=50  Identities=22%  Similarity=0.145  Sum_probs=48.1

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   51 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQN   51 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHH
Confidence            57899999999999999999999999999999999999999999999998

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=99.71  E-value=3.1e-18  Score=98.24  Aligned_cols=54  Identities=28%  Similarity=0.318  Sum_probs=50.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   68 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN   68 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            456778999999999999999999999999999999999999999999999998

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.71  E-value=3.9e-18  Score=95.41  Aligned_cols=48  Identities=19%  Similarity=0.009  Sum_probs=46.2

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         95 PRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        95 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .|..++.+|+..|+..|+.++||+..++++||..|||++++|+|||||
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqN   53 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGD   53 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHh
Confidence            566799999999999999999999999999999999999999999998

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

Probab=99.71  E-value=1e-17  Score=94.04  Aligned_cols=65  Identities=28%  Similarity=0.578  Sum_probs=59.0

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .+|+.+|..|+++|...+.++.+.++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   66 (72)
T 1x4k_A            2 SSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG-TKSFIPKDNQNFCVPCYEKQHA   66 (72)
T ss_dssp             CSCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCC-SSSEEEETTEEEEHHHHHHHTS
T ss_pred             CccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccC-CCccCccCCeEECHHHHhHHhC
Confidence            4789999999999997677899999999999999999999996 4579999999999999998876

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A

Probab=99.71  E-value=1.8e-18  Score=95.95  Aligned_cols=51  Identities=22%  Similarity=0.192  Sum_probs=49.1

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqN   52 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN   52 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHH
Confidence            357899999999999999999999999999999999999999999999998

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.70  E-value=4.8e-18  Score=94.27  Aligned_cols=51  Identities=18%  Similarity=0.125  Sum_probs=49.1

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   52 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN   52 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHH
Confidence            457899999999999999999999999999999999999999999999998

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

Probab=99.70  E-value=1.6e-17  Score=93.26  Aligned_cols=65  Identities=26%  Similarity=0.585  Sum_probs=58.7

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .+|+.+|..|+++|...+.++.+.++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   66 (72)
T 1wyh_A            2 SSGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG-SRSFVPDKGAHYCVPCYENKFA   66 (72)
T ss_dssp             CCCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTT-TSCEEEETTEEEEHHHHHHHTS
T ss_pred             CccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCC-CCccCCcCCeEECHHHHHHHcc
Confidence            4689999999999997666889999999999999999999995 5569999999999999998876

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.70  E-value=4.4e-18  Score=99.06  Aligned_cols=55  Identities=22%  Similarity=0.195  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .....++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus        24 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqN   78 (88)
T 2r5y_A           24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN   78 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHH
Confidence            3455678999999999999999999999999999999999999999999999998

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.70  E-value=6.3e-18  Score=93.56  Aligned_cols=50  Identities=26%  Similarity=0.337  Sum_probs=48.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.++..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   51 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQN   51 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHh
Confidence            57899999999999999999999999999999999999999999999998

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P

Probab=99.70  E-value=1.9e-18  Score=95.92  Aligned_cols=52  Identities=29%  Similarity=0.268  Sum_probs=49.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.++.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   53 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKN   53 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            4567899999999999999999999999999999999999999999999998

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

Probab=99.69  E-value=7.4e-18  Score=95.62  Aligned_cols=65  Identities=22%  Similarity=0.470  Sum_probs=58.2

Q ss_pred             CCCCccccccCccccC--CcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGP--DELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~--~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .+|+.+|..|+++|.+  ++.++.++++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~f~   68 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV-GKGFLTQNKEIFCQKCGSGMDT   68 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCS-SSCEEEETTEEEETTTTCCCCC
T ss_pred             CccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCC-CCceEeECCEEECHHHhhhhhC
Confidence            3789999999999995  445789999999999999999999995 7779999999999999988775

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=9.2e-18  Score=95.09  Aligned_cols=53  Identities=28%  Similarity=0.235  Sum_probs=49.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.+.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         6 ~~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqN   58 (76)
T 2dn0_A            6 SGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSD   58 (76)
T ss_dssp             SCCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHH
Confidence            33455689999999999999999999999999999999999999999999998

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.68  E-value=1.8e-17  Score=93.24  Aligned_cols=54  Identities=19%  Similarity=0.246  Sum_probs=50.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.++..|+..|+..|..   ++||+..+++.||..+||++.+|+|||||
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqN   60 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFIN   60 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHH
Confidence            3456778999999999999999976   99999999999999999999999999998

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.9e-17  Score=93.48  Aligned_cols=49  Identities=22%  Similarity=0.242  Sum_probs=46.8

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.|+.++..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   57 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSE   57 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHH
Confidence            4567799999999999999999999999999999999999999999998

>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=99.68  E-value=2.9e-17  Score=92.15  Aligned_cols=63  Identities=25%  Similarity=0.635  Sum_probs=57.1

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      +++.+|..|+++|.+.+.++.+.++.||+.||+|..|+.+|..+ .|+.+++.+||..||.++|
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~lf   71 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLF   71 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGG-CCEEETTEEECHHHHHHHT
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCC-CeEeECCeEeCHHHHHHhh
Confidence            56789999999999888778899999999999999999999655 6889999999999998875

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.68  E-value=1.9e-17  Score=93.38  Aligned_cols=52  Identities=19%  Similarity=0.068  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..++.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   56 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSD   56 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChh
Confidence            3567899999999999999999999999999999999999999999999998

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

Probab=99.68  E-value=1.8e-17  Score=93.11  Aligned_cols=64  Identities=19%  Similarity=0.454  Sum_probs=57.1

Q ss_pred             CCCccccccCccccC--CcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGP--DELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~--~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +++.+|..|+++|.+  ++.++.++++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~c~~~~~~   68 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLV-GRGFLTERDDILCPDCGKDISG   68 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCT-TSCCEECSSSEECHHHHHTCCC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCC-CCccEeECCEEEChhHcCcccC
Confidence            578999999999996  456789999999999999999999995 7778999999999999987664

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1

Probab=99.68  E-value=1.1e-17  Score=99.09  Aligned_cols=54  Identities=22%  Similarity=0.155  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....++.|+.|+..|+..|+..|..++||+..+++.||..|||++.+|+|||||
T Consensus        31 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqN   84 (97)
T 1b72_A           31 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQN   84 (97)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHH
Confidence            345677899999999999999999999999999999999999999999999998

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.68  E-value=9e-18  Score=90.94  Aligned_cols=48  Identities=23%  Similarity=0.183  Sum_probs=44.6

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         95 PRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        95 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .|+.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqN   49 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQN   49 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhh
Confidence            578999999999999999999999999999999999999999999998

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.68  E-value=1.2e-17  Score=98.66  Aligned_cols=54  Identities=20%  Similarity=0.197  Sum_probs=48.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....++.|+.++..|+..|+..|..++||+..+++.||..|||++.+|+|||||
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN   75 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGD   75 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchh
Confidence            444567899999999999999999999999999999999999999999999998

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

Probab=99.67  E-value=6.3e-17  Score=93.04  Aligned_cols=64  Identities=22%  Similarity=0.472  Sum_probs=58.3

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|+.+|..|+++|.+.+.++.+.++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus        13 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   76 (82)
T 1x63_A           13 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFPKGEDFYCVTCHETKFA   76 (82)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCT-TSCEEEETTEEEEHHHHHHHTS
T ss_pred             ccCCcCccCCcccccCceEEEECccccccccCchhhCCCccC-CCccEeeCCEEECHHHHHHHhC
Confidence            578999999999997777899999999999999999999996 4569999999999999998875

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.67  E-value=1.3e-17  Score=88.99  Aligned_cols=46  Identities=15%  Similarity=0.067  Sum_probs=43.5

Q ss_pred             CCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         97 TILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        97 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |.|+..|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   47 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQN   47 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHH
Confidence            5789999999999999999999999999999999999999999998

>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=99.67  E-value=4.1e-17  Score=90.05  Aligned_cols=63  Identities=22%  Similarity=0.576  Sum_probs=56.3

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .+|+.+|+.|+++|. ++ ++.++++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         2 ~~~~~~C~~C~~~I~-~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~y~~~f~   64 (66)
T 1nyp_A            2 SMGVPICGACRRPIE-GR-VVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHYNQLFG   64 (66)
T ss_dssp             CCCCCEETTTTEECC-SC-EECCTTSBEETTTCBCTTTCCBCS-SSCCEEETTEEECHHHHHHHCS
T ss_pred             CcCCCCCcccCCEec-ce-EEEECccccccCcCEECCCCCCCC-CCceEeECCcEECHHHHHHHhC
Confidence            368899999999999 44 688999999999999999999995 6679999999999999988764

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.67  E-value=2.5e-17  Score=92.56  Aligned_cols=50  Identities=16%  Similarity=0.081  Sum_probs=47.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc-CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEI-SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.|+.|+..|+..|+..|+. ++||+..+++.||..+||++.+|+|||||
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqN   53 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQ   53 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            457899999999999999995 99999999999999999999999999998

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.67  E-value=2.8e-17  Score=92.18  Aligned_cols=49  Identities=16%  Similarity=0.131  Sum_probs=47.2

Q ss_pred             CCCCCCCHHHHHHHHHhhhc-CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEI-SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.|+.|+..|+..|+..|+. ++||+...++.||..+||++.+|+|||||
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqN   52 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQ   52 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHH
Confidence            47899999999999999996 99999999999999999999999999998

>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=99.67  E-value=6.3e-17  Score=91.02  Aligned_cols=63  Identities=17%  Similarity=0.429  Sum_probs=56.5

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|+.+|+.|+++|..  .++.++++.||+.||+|..|+.+|..+..|+.+++.+||..||..+++
T Consensus         3 ~~~~~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~   65 (73)
T 1wig_A            3 SGSSGCDSCEKYITG--RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAART   65 (73)
T ss_dssp             CSCCSCSSSCCCCSS--CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSS
T ss_pred             cCcCCcccCCCEecC--eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhc
Confidence            689999999999984  367899999999999999999999658889999999999999987553

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.67  E-value=2.1e-17  Score=90.67  Aligned_cols=52  Identities=19%  Similarity=0.245  Sum_probs=49.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..++.|+.|+..|+..|+..|   ..++||+..+++.||..+||++.+|++||||
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqN   56 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN   56 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            356789999999999999999   9999999999999999999999999999998

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

Probab=99.67  E-value=4e-17  Score=92.77  Aligned_cols=65  Identities=26%  Similarity=0.634  Sum_probs=58.2

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      +++.+|..|+++|.+.+.++.+.++.||+.||+|..|+.+|..+ .|+.+++.+||..||.+++++
T Consensus         9 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~~   73 (77)
T 1g47_A            9 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFAP   73 (77)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGG-CSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCC-CeEeECCeEeCHHHHHHHhhc
Confidence            56789999999998778788999999999999999999999644 589999999999999988763

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

Probab=99.65  E-value=5.8e-17  Score=93.20  Aligned_cols=66  Identities=26%  Similarity=0.566  Sum_probs=59.1

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      .+|+.+|+.|+++|.+++.++.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.++++.
T Consensus        12 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~~~~~C~~c~~~~~~~   77 (82)
T 2ehe_A           12 NTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTCQDSELLCNDCYCSAFSS   77 (82)
T ss_dssp             CCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCS-SCCEEEETTEEEETTTSSCCGGG
T ss_pred             cccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccC-CCccEeeCCEEECHHHHhhhcCC
Confidence            3688999999999997677889999999999999999999995 66799999999999999887763

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=99.65  E-value=5.4e-17  Score=91.25  Aligned_cols=50  Identities=24%  Similarity=0.352  Sum_probs=48.5

Q ss_pred             CCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.|+..|+..|+..|   ..++||+..+++.||..+||++.+|+|||||
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqN   54 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN   54 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            5789999999999999999   9999999999999999999999999999998

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.65  E-value=1.1e-16  Score=92.05  Aligned_cols=54  Identities=15%  Similarity=0.169  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+..|+..|+..|..   ++||+..+++.||..+||++.||+|||||
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqN   60 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFIN   60 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhh
Confidence            3456678999999999999999877   69999999999999999999999999999

>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=99.65  E-value=2e-16  Score=88.00  Aligned_cols=63  Identities=27%  Similarity=0.643  Sum_probs=56.6

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .+++.+|..|+++|.. + .+.+.++.||+.||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         2 s~~~~~C~~C~~~I~~-~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   64 (69)
T 2cur_A            2 SSGSSGCVKCNKAITS-G-GITYQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYKNFVS   64 (69)
T ss_dssp             CCCCCCCSSSCCCCCT-T-CEEETTEEECTTTTBCTTTCCBCT-TSCEEECSSCEEEHHHHHHHHT
T ss_pred             CCCcCCCcccCCEeCc-c-eEEECccccccCcCEECCCCCCCC-CCccEeECCEEECHHHhHHHhc
Confidence            3678999999999984 4 578999999999999999999995 6779999999999999999886

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

Probab=99.64  E-value=2.4e-16  Score=89.56  Aligned_cols=61  Identities=30%  Similarity=0.625  Sum_probs=54.8

Q ss_pred             CCCccccccCccccC---CcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437          2 LYVKKCLGCSEKLGP---DELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~---~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~   63 (143)
                      +|+.+|+.|+++|.+   +..++.+.++.||+.||+|..|+.+|. +..|+.+++.+||..||.+
T Consensus        13 ~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           13 FVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCT-TSCCCEETTEECCHHHHHH
T ss_pred             hhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCC-CCccEeECCEEEChHHhcc
Confidence            678999999999996   446789999999999999999999995 6679999999999999864

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.64  E-value=7e-17  Score=95.22  Aligned_cols=54  Identities=13%  Similarity=0.076  Sum_probs=51.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhC---------------CCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTG---------------LSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+..|+..|+..|+.++||+..+++.||..++               |++.+|+|||||
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqN   72 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFAN   72 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHH
Confidence            355678999999999999999999999999999999999999               999999999998

>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=99.64  E-value=1.2e-16  Score=95.39  Aligned_cols=75  Identities=24%  Similarity=0.487  Sum_probs=66.2

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCC
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIP   76 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~   76 (143)
                      .+++.+|..|+++|..++.++.++++.||+.||+|..|+.+| .+..|+.+++.+||..||.++++ ++..|..+|.
T Consensus         2 s~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~   77 (101)
T 2cup_A            2 SSGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTREDSPKCKGCFKAIV   77 (101)
T ss_dssp             CSCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCT-TSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCC
T ss_pred             CCCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCC-CcCeeECcCCEEEChhHhhhhcCCccccCCCccc
Confidence            367899999999998656688999999999999999999999 46779999999999999988875 6778888776

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.3e-16  Score=93.82  Aligned_cols=55  Identities=13%  Similarity=0.144  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHh---------------------CCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDT---------------------GLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~---------------------~l~~~~vkvWFQn  142 (143)
                      ...+.+|.|+.++..|+..|+..|+.++||+..+|++||..+                     .|++.+|+|||||
T Consensus         2 ~~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqN   77 (102)
T 2da6_A            2 SSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFAN   77 (102)
T ss_dssp             TTCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecc
Confidence            345678899999999999999999999999999999999999                     7999999999998

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.64  E-value=4.2e-17  Score=88.14  Aligned_cols=44  Identities=27%  Similarity=0.114  Sum_probs=42.6

Q ss_pred             CCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         99 LTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        99 ~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.+|+..|+..|..++||+..++++||..|||++++|++||||
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqN   54 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSD   54 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhccc
Confidence            47899999999999999999999999999999999999999998

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.63  E-value=1.7e-16  Score=91.79  Aligned_cols=45  Identities=24%  Similarity=0.141  Sum_probs=44.4

Q ss_pred             CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.+|+..|+..|+.++||+...++.||..|||++++|+|||||
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqN   61 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTE   61 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccc
Confidence            789999999999999999999999999999999999999999998

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

Probab=99.63  E-value=2.9e-16  Score=86.32  Aligned_cols=60  Identities=25%  Similarity=0.649  Sum_probs=52.7

Q ss_pred             CCccccccCccccCCcceEEecCcccc--cCCcccccCCccccCCCceEeeCCeeec-hhhHHH
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFH--VQCFVCVVCGSRLQRGEQFVIKQGQLFC-RPDYEK   63 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h--~~cf~C~~C~~~l~~~~~~~~~~~~~~C-~~~~~~   63 (143)
                      |+.+|..|+++|.+++..+.++++.||  ++||+|..|+.+| .+..|+.+++.+|| ..||.+
T Consensus         1 fa~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~~C~~k   63 (65)
T 2iyb_E            1 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKR   63 (65)
T ss_dssp             -CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBC-TTSCCEEETTEEESSHHHHHT
T ss_pred             CcCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcC-CCCceEEECCEEecCHHHhhh
Confidence            678999999999975557899999999  9999999999999 47779999999999 777754

>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=99.63  E-value=2.7e-16  Score=90.19  Aligned_cols=64  Identities=22%  Similarity=0.548  Sum_probs=56.7

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEe-eCCeeechhhHHHHHH
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVI-KQGQLFCRPDYEKEVE   66 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~-~~~~~~C~~~~~~~~~   66 (143)
                      .+|+.+|..|+++|.  +.++.++++.||++||+|..|+.+|..|..|.+ +++.+||..||.++++
T Consensus        12 ~~~~~~C~~C~~~I~--~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~   76 (81)
T 1x6a_A           12 GKFGEFCHGCSLLMT--GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS   76 (81)
T ss_dssp             CCSSCBCTTTCCBCC--SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHC
T ss_pred             hhcCCcCccCCCCcC--ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhc
Confidence            368899999999999  346889999999999999999999976777874 8999999999999886

>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=2.4e-16  Score=87.91  Aligned_cols=62  Identities=19%  Similarity=0.525  Sum_probs=55.8

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +++.+|..|+++|.. + .+.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus         3 ~~~~~C~~C~~~I~~-~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   64 (70)
T 2d8z_A            3 SGSSGCVQCKKPITT-G-GVTYREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCFCDLYA   64 (70)
T ss_dssp             CCCCBCSSSCCBCCS-S-EEESSSSEEETTTSBCSSSCCBCT-TSCCEESSSSEECHHHHHHHTC
T ss_pred             CCCCCCcccCCeecc-c-eEEECccccCCCCCccCCCCCcCC-cCceEeeCCeEECHHHHHHHhc
Confidence            678999999999984 4 588999999999999999999994 6678999999999999998875

>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=99.63  E-value=5.1e-16  Score=86.60  Aligned_cols=62  Identities=31%  Similarity=0.618  Sum_probs=55.0

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .++.+|..|+++|. ++ ++.+.++.||++||+|..|+.+|.. ..|+.+++.+||..||.++++
T Consensus         3 ~~~~~C~~C~~~I~-~~-~~~a~~~~~H~~CF~C~~C~~~L~~-~~f~~~~g~~yC~~c~~~~~~   64 (70)
T 2d8x_A            3 SGSSGCHQCGEFII-GR-VIKAMNNSWHPECFRCDLCQEVLAD-IGFVKNAGRHLCRPCHNREKA   64 (70)
T ss_dssp             CCSSBCSSSCCBCC-SC-CEEETTEEECTTTSBCSSSCCBCSS-SCCEEETTEEECHHHHHHHHC
T ss_pred             CCCCcCccCCCEec-ce-EEEECcccccccCCEeCCCCCcCCC-CccEeECCeEECHHHhhhhcC
Confidence            46789999999998 33 6899999999999999999999964 468889999999999999886

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.63  E-value=7.8e-17  Score=95.14  Aligned_cols=55  Identities=16%  Similarity=0.207  Sum_probs=46.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHH------------------hC---CCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARD------------------TG---LSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~------------------~~---l~~~~vkvWFQn  142 (143)
                      ..++.++.|+.|+..|+..|+..|+.++||+...+++||..                  ||   |++.+|+|||||
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqN   80 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFAN   80 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHH
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHH
Confidence            34567789999999999999999999999999999999999                  88   999999999998

>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=99.63  E-value=1.9e-16  Score=97.55  Aligned_cols=78  Identities=24%  Similarity=0.468  Sum_probs=67.4

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCcccc-CCCceEeeCCeeechhhHHHHHH---HhhccCCCCCC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ-RGEQFVIKQGQLFCRPDYEKEVE---MLQGYAQGIPF   77 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~-~~~~~~~~~~~~~C~~~~~~~~~---~~~~~~~~~~~   77 (143)
                      +++.+|..|+++|...+ ++.++++.||+.||+|..|+.+|. .+..|+.+++.+||..||.++++   +|..|..+|..
T Consensus         3 ~~~~~C~~C~~~I~~~~-~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~   81 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRF-LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSG   81 (122)
T ss_dssp             SCCCCBSSSSSCCCSSC-CEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCC
T ss_pred             CCCCCCcccCCEeCCcE-EEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCc
Confidence            57889999999998543 578999999999999999999995 24679999999999999999997   48899998886


Q ss_pred             ccc
Q psy15437         78 DLI   80 (143)
Q Consensus        78 ~~~   80 (143)
                      +.+
T Consensus        82 ~~~   84 (122)
T 1m3v_A           82 GDV   84 (122)
T ss_dssp             EES
T ss_pred             hhe
Confidence            444

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=99.62  E-value=1.3e-16  Score=86.35  Aligned_cols=47  Identities=21%  Similarity=0.171  Sum_probs=45.8

Q ss_pred             CCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |+.|+..|+..|+..|..   ++||+..+++.||..+||++.+|++||||
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqN   51 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSN   51 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            678999999999999999   99999999999999999999999999998

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.62  E-value=1e-16  Score=103.01  Aligned_cols=55  Identities=20%  Similarity=0.226  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +..+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus        97 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN  151 (160)
T 1e3o_C           97 GLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSN  151 (160)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHH
Confidence            3456778999999999999999999999999999999999999999999999998

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=99.62  E-value=1.3e-16  Score=101.02  Aligned_cols=56  Identities=16%  Similarity=0.239  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +...+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus        82 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN  137 (146)
T 1au7_A           82 GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCN  137 (146)
T ss_dssp             -------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHh
Confidence            34456677899999999999999999999999999999999999999999999998

>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=99.62  E-value=3.1e-16  Score=89.93  Aligned_cols=70  Identities=29%  Similarity=0.604  Sum_probs=54.1

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCC
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQG   74 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~   74 (143)
                      ++.+|..|+++|...+ .+.+.++.||++||+|..|+.+|. +..|+.+++.+||..||.++++ ++.+++++
T Consensus         6 ~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g   76 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAE-EVQCDGRSFHRCCFLCMVCRKNLD-STTVAIHDAEVYCKSCYGKKYGPKGYGYGQG   76 (81)
T ss_dssp             --CBCSSSCCBCSSTT-EEEETTEEEESSSEECSSSCCEEC-SSCCEEETTEEECSHHHHHHCC---------
T ss_pred             CCCcCcCcCccccCce-eEEeCCcccccccCccCCCCCCCC-CCCeEeeCCEEECHHHHHHHhCCcccccCCc
Confidence            4679999999998666 578999999999999999999995 4568999999999999998885 45555544

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=2.6e-16  Score=85.89  Aligned_cols=45  Identities=13%  Similarity=0.151  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.+|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus         9 ~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqN   53 (64)
T 2e19_A            9 PPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEK   53 (64)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhc
Confidence            446899999999999999999999999999999999999999998

>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=99.62  E-value=6e-16  Score=87.67  Aligned_cols=63  Identities=24%  Similarity=0.480  Sum_probs=55.9

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeech-hhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR-PDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~-~~~~~~~~   66 (143)
                      .++.+|..|+++|...+ .+.++++.||+.||+|..|+.+|. +..|+.+++.+||. .||.++++
T Consensus         7 ~~~~~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~cy~~~f~   70 (76)
T 2cu8_A            7 GMASKCPKCDKTVYFAE-KVSSLGKDWHKFCLKCERCSKTLT-PGGHAEHDGKPFCHKPCYATLFG   70 (76)
T ss_dssp             CCCCBCTTTCCBCCTTT-EEEETTEEEETTTCBCSSSCCBCC-TTSCEEETTEEECTTTHHHHHSC
T ss_pred             CCCCCCcCCCCEeECCe-EEEECCeEeeCCCCCCCCCCCccC-CCceEeECCEEecchHHHHHhcc
Confidence            46789999999999666 467999999999999999999995 56799999999999 79998875

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

Probab=99.61  E-value=4.9e-16  Score=96.27  Aligned_cols=74  Identities=28%  Similarity=0.558  Sum_probs=64.9

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPF   77 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~   77 (143)
                      +|+.+|..|+++|...+ ++.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.++++ +|..|..+|..
T Consensus         1 ~~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~   75 (126)
T 2xqn_T            1 SEKPRCAGCDELIFSNE-YTQAENQNWHLKHFCCFDCDSILA-GEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDP   75 (126)
T ss_dssp             -CCCBBTTTSSBCCSSC-EEEETTEEECGGGSBCTTTCCBCT-TSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCT
T ss_pred             CcCCCCccCCCEeCCce-EEeeCCCCccCCCCCcCCCCCCCC-cCEEEeECCEEechHHhCcCcCccCcccCCcCCc
Confidence            47899999999998544 688999999999999999999994 6779999999999999998875 68888888874

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.61  E-value=2e-16  Score=91.87  Aligned_cols=50  Identities=24%  Similarity=0.352  Sum_probs=47.8

Q ss_pred             CCCCCCCCHHHHHHHHHhh---hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASF---EISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.|+..|+..|+..|   ..++||+..+++.||..+||++.+|+|||||
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqN   54 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN   54 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            5789999999999999999   9999999999999999999999999999998

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.61  E-value=6.1e-17  Score=90.49  Aligned_cols=48  Identities=19%  Similarity=0.252  Sum_probs=44.6

Q ss_pred             CCCCCCHHHHHHHHHhh-hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         95 PRTILTTQQRRAFKASF-EISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        95 ~R~~~~~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .|..++.+|+..|+..| +.++||+...++.||..+||++++|+|||||
T Consensus        11 ~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqN   59 (72)
T 2cqx_A           11 DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRH   59 (72)
T ss_dssp             CCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhh
Confidence            45566778899999999 9999999999999999999999999999998

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.61  E-value=2.5e-16  Score=91.43  Aligned_cols=53  Identities=19%  Similarity=0.120  Sum_probs=49.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+++.|+.|+..|+..|+..|..   ++||+..+++.||..+||++.+|++||||
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqN   80 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSN   80 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            345556899999999999999999   99999999999999999999999999998

>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=99.61  E-value=3.3e-16  Score=96.49  Aligned_cols=63  Identities=30%  Similarity=0.731  Sum_probs=55.3

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCcccc-CCCceEeeCCeeechhhHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQ-RGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~-~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .++.+|..|+++|.. ..++.++++.||+.||+|..|+.+|. .|..|+.+++.+||..||.++|
T Consensus        59 ~~~~~C~~C~~~I~~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~F  122 (123)
T 2l4z_A           59 LSWKRCAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF  122 (123)
T ss_dssp             SSCSBBSSSSSBCCS-SSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHC
T ss_pred             ccCCcCcCCCCCcCC-cEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhc
Confidence            456799999999984 44688999999999999999999995 3677999999999999998875

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=5.5e-16  Score=90.16  Aligned_cols=47  Identities=26%  Similarity=0.135  Sum_probs=44.8

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +..++.+|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqN   63 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSE   63 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHh
Confidence            34489999999999999999999999999999999999999999998

>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=99.61  E-value=7.5e-16  Score=88.09  Aligned_cols=62  Identities=24%  Similarity=0.596  Sum_probs=56.1

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|+.+|..|+++|.+ + .+.+.++.||++||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus        13 ~~~~~C~~C~~~I~~-~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   74 (80)
T 2cuq_A           13 KFAPRCARCSKTLTQ-G-GVTYRDQPWHRECLVCTGCQTPLA-GQQFTSRDEDPYCVACFGELFA   74 (80)
T ss_dssp             CSSCCCTTTCCCCCS-C-CEESSSSEECTTTCBCSSSCCBCT-TCCEEECSSSEEEHHHHHHHTT
T ss_pred             ccCCcCCCCCCEecC-c-EEEECCchhhhhhCCcccCCCcCC-CCeeEeECCEEECHHHHHHHcC
Confidence            578999999999984 4 688999999999999999999994 6679999999999999998876

>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=99.61  E-value=6.5e-16  Score=90.30  Aligned_cols=62  Identities=24%  Similarity=0.498  Sum_probs=55.2

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      .++.+|..|+++|. ++ ++.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.++|+
T Consensus        23 ~~~~~C~~C~~~I~-~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~f~   84 (90)
T 2dar_A           23 KRTPMCAHCNQVIR-GP-FLVALGKSWHPEEFNCAHCKNTMA-YIGFVEEKGALYCELCYEKFFA   84 (90)
T ss_dssp             TCCCBBSSSCCBCC-SC-EEEETTEEECTTTCBCSSSCCBCS-SSCBEESSSCEECHHHHHHHTS
T ss_pred             CCCCCCccCCCEec-ce-EEEECCccccccCCccCCCCCCCC-CCEeEeECCEEECHHHHHHHcC
Confidence            46789999999997 33 678999999999999999999995 5668899999999999998886

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=99.61  E-value=3.7e-16  Score=99.54  Aligned_cols=54  Identities=22%  Similarity=0.265  Sum_probs=51.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN  143 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSN  143 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHH
Confidence            456677899999999999999999999999999999999999999999999998

>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=99.60  E-value=8.7e-16  Score=87.84  Aligned_cols=62  Identities=27%  Similarity=0.668  Sum_probs=55.7

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|+.+|+.|+++|.+ + .+.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus        13 ~~~~~C~~C~~~I~~-~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~~y~~~f~   74 (80)
T 1x3h_A           13 MFSPKCGGCNRPVLE-N-YLSAMDTVWHPECFVCGDCFTSFS-TGSFFELDGRPFCELHYHHRRG   74 (80)
T ss_dssp             CCSCBCTTTCCBCCS-S-CEEETTEEECTTTCBCSSSCCBSC-SSCCEESSSCEECHHHHHHHHS
T ss_pred             hcCCccccCCCeecc-e-eEEECCCeEecCcCChhhCCCCCC-CCcEEeECCEEECHHHHHHHcC
Confidence            578999999999984 3 578999999999999999999996 4468999999999999999886

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.60  E-value=2.8e-16  Score=86.79  Aligned_cols=47  Identities=15%  Similarity=0.078  Sum_probs=45.1

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      -..++..|+..|+..|..++||+...++.||..+||++++|+|||||
T Consensus         8 ~~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqN   54 (69)
T 2l9r_A            8 HSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN   54 (69)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchh
Confidence            45789999999999999999999999999999999999999999998

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=99.60  E-value=4.6e-16  Score=99.38  Aligned_cols=53  Identities=26%  Similarity=0.335  Sum_probs=50.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         90 RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        90 ~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+++|.|+.++..|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqN  146 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSN  146 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeecccc
Confidence            56778899999999999999999999999999999999999999999999998

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.59  E-value=4.1e-16  Score=89.67  Aligned_cols=49  Identities=20%  Similarity=0.161  Sum_probs=46.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.|+.|+..|+..|+..|..   ++||+..+++.||..+||++.+|+|||||
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqN   55 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAA   55 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHH
Confidence            35666999999999999999   99999999999999999999999999998

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.59  E-value=2.6e-16  Score=101.30  Aligned_cols=54  Identities=22%  Similarity=0.293  Sum_probs=43.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..+.++.|+.|+..|+..|+..|..++||+..+++.||..+||++++|+|||||
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqN  149 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCN  149 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHH
Confidence            456677999999999999999999999999999999999999999999999998

>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=99.59  E-value=8.5e-16  Score=87.65  Aligned_cols=62  Identities=23%  Similarity=0.464  Sum_probs=53.5

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      ++..+|..|+++|. ++ ++.++++.||+.||+|..|+.+|. +.. +.+++.+||..||.+++++
T Consensus        13 ~~~~~C~~C~~~I~-~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~-f~~~g~~yC~~cy~~~f~p   74 (79)
T 2cor_A           13 LGKYICQKCHAIID-EQ-PLIFKNDPYHPDHFNCANCGKELT-ADA-RELKGELYCLPCHDKMGVS   74 (79)
T ss_dssp             CCCCBCTTTCCBCC-SC-CCCCSSSCCCTTTSBCSSSCCBCC-TTC-EEETTEEECHHHHHTTSCC
T ss_pred             cCCCCCccCCCEec-ce-EEEECcceeCCCCCEeCCCCCccC-CCC-EeECCEEeCHHHHHHhCCC
Confidence            46789999999999 44 578999999999999999999996 444 4889999999999987753

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.59  E-value=3.7e-16  Score=100.89  Aligned_cols=55  Identities=25%  Similarity=0.481  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...+.++.|+.|+..|+..|+..|+.++||+...++.||..+||++.+|+|||||
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqN  147 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN  147 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChh
Confidence            3456678999999999999999999999999999999999999999999999998

>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=99.58  E-value=1.1e-15  Score=89.48  Aligned_cols=69  Identities=23%  Similarity=0.678  Sum_probs=58.2

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCC
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQ   73 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~   73 (143)
                      ++.+|..|+++|...+. +.++++.||+.||+|..|+.+|.. ..|+.+++.+||..||.++++....+..
T Consensus        14 ~~~~C~~C~~~I~~~~~-v~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~g~~yC~~~y~~~f~~kc~~~~   82 (91)
T 2d8y_A           14 ARETCVECQKTVYPMER-LLANQQVFHISCFRCSYCNNKLSL-GTYASLHGRIYCKPHFNQLFKSKGNYDE   82 (91)
T ss_dssp             SSCBCTTTCCBCCTTSE-EECSSSEEETTTCBCTTTCCBCCT-TTCCCSSSCCCCHHHHHHHSCCCSCCCS
T ss_pred             CCCcCccCCCccCCcee-EEECCCEECCCCCeeCCCCCCCCC-CCcEeECCEEECHHHHHHHhCCCcCccC
Confidence            46799999999986664 689999999999999999999964 4588999999999999998875444433

>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=99.58  E-value=2.2e-15  Score=86.05  Aligned_cols=60  Identities=32%  Similarity=0.821  Sum_probs=53.7

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      ..+|..|+++|...+ .+.++++.||+.||+|..|+.+|. + .|+.+++.+||..||.++|+
T Consensus        15 ~~~C~~C~~~I~~~~-~v~a~~~~wH~~CF~C~~C~~~L~-~-~~~~~~g~~yC~~~y~~~fg   74 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQ-SLLALDKQWHVSCFKCQTCSVILT-G-EYISKDGVPYCESDYHAQFG   74 (80)
T ss_dssp             CSCCTTTCCCCSSSC-CEEETTEEECTTTCBCSSSCCBCS-S-CCEEETTEEECTTHHHHHTT
T ss_pred             CCCCcCcCCeeCCCe-EEEECCcccccccCCcCcCCCCcC-C-CeEEECCEEECHHHHHHHcC
Confidence            468999999998656 478999999999999999999995 5 58999999999999999886

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=3.7e-16  Score=84.81  Aligned_cols=42  Identities=14%  Similarity=0.164  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437        101 TQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus       101 ~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+|+..|+..|+++++|+..+++.||..+||++++|||||||
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqN   55 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQ   55 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhh
Confidence            467999999999999999999999999999999999999998

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.58  E-value=2.5e-16  Score=85.25  Aligned_cols=41  Identities=27%  Similarity=0.334  Sum_probs=38.8

Q ss_pred             HHHHHHHHhh-hcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437        102 QQRRAFKASF-EISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus       102 ~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++..||..| ..++||+...++.||.+|||+++||||||||
T Consensus        10 ~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqN   51 (64)
T 1x2m_A           10 QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQ   51 (64)
T ss_dssp             CHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            4789999999 6799999999999999999999999999998

>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=99.58  E-value=1.8e-15  Score=85.67  Aligned_cols=66  Identities=24%  Similarity=0.515  Sum_probs=55.7

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeech-hhHHHHHH-HhhccC
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCR-PDYEKEVE-MLQGYA   72 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~-~~~~~~~~-~~~~~~   72 (143)
                      ++|..|+++|..++ .+.++++.||+.||+|..|+.+|. +..|+.+++.+||. .||.++++ ++.+|+
T Consensus         1 p~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~   68 (76)
T 1iml_A            1 PKCPKCDKEVYFAE-RVTSLGKDWHRPCLKCEKCGKTLT-SGGHAEHEGKPYCNHPCYSAMFGPKGFGRG   68 (76)
T ss_dssp             CBCTTTSSBCCGGG-EEEETTEEEETTTCBCTTTCCBCC-TTTEEEETTEEEETTTHHHHHSSCCCSSCC
T ss_pred             CcCCCCCCEEECce-EEEECCccccCCCCCccccCccCC-CCceECcCCeEeeCHHHHHHHhCccCCCcC
Confidence            47999999998656 478999999999999999999996 44699999999999 69998886 344444

>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=99.56  E-value=3e-15  Score=87.25  Aligned_cols=61  Identities=25%  Similarity=0.573  Sum_probs=53.8

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      ...+|..|++.|..  .++.++++.||++||+|..|+.+|. +..|+.+++.+||..||.++|+
T Consensus        24 ~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~y~~~f~   84 (89)
T 1x64_A           24 RMPLCDKCGSGIVG--AVVKARDKYRHPECFVCADCNLNLK-QKGYFFVEGELYCETHARARTS   84 (89)
T ss_dssp             SCCBCTTTCCBCCS--CCEESSSCEECTTTCCCSSSCCCTT-TSCCEEETTEEECHHHHHHHSS
T ss_pred             cCCCcccCCCEecc--cEEEECCceECccCCEecCCCCCCC-CCCeEeECCEEECHHHHHHHhC
Confidence            45689999999994  3688999999999999999999995 4568889999999999998875

>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=3e-15  Score=85.77  Aligned_cols=62  Identities=29%  Similarity=0.768  Sum_probs=54.5

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEee-CCeeechhhHHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIK-QGQLFCRPDYEKEVE   66 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~~~~~~~   66 (143)
                      +++.+|..|+++|. + .++.++++.||+.||+|..|+.+|. +..|+.. ++.+||..||.++++
T Consensus        13 ~~~~~C~~C~~~I~-~-~~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~~g~~yC~~cy~~~f~   75 (81)
T 2dlo_A           13 ATLEKCATCSQPIL-D-RILRAMGKAYHPGCFTCVVCHRGLD-GIPFTVDATSQIHCIEDFHRKFA   75 (81)
T ss_dssp             SSCCBCTTTCCBCC-S-CCEEETTEEECTTTCBCSSSCCBCT-TSCEECCTTCCCEEHHHHHHHTT
T ss_pred             cCCCccccCCCeec-c-eeEEECCccccHHhcCcccCCCccC-CCeeEECCCCEEECHHHHHHHhc
Confidence            36789999999998 3 4789999999999999999999995 6667776 689999999998886

>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=99.55  E-value=1.2e-15  Score=86.98  Aligned_cols=61  Identities=23%  Similarity=0.536  Sum_probs=54.2

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      ...+|..|+++|.. + ++.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.++++
T Consensus        14 ~~~~C~~C~~~I~~-~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~~~   74 (79)
T 1x62_A           14 KLPMCDKCGTGIVG-V-FVKLRDRHRHPECYVCTDCGTNLK-QKGHFFVEDQIYCEKHARERVS   74 (79)
T ss_dssp             CCCCCSSSCCCCCS-S-CEECSSCEECTTTTSCSSSCCCHH-HHCCEESSSCEECHHHHHHHHS
T ss_pred             CCCccccCCCCccC-c-EEEECcceeCcCcCeeCCCCCCCC-CCCeEeECCEEECHHHHHHHhC
Confidence            35799999999984 3 689999999999999999999995 5568899999999999998886

>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=99.54  E-value=5.4e-15  Score=89.98  Aligned_cols=64  Identities=31%  Similarity=0.738  Sum_probs=56.3

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccC-CCceEeeCCeeechhhHHHHHHHh
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQR-GEQFVIKQGQLFCRPDYEKEVEML   68 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~~~~~~~~~   68 (143)
                      ..+|+.|+++|.. ..++.++++.||+.||+|..|+.+|.. |..|+.+++.+||..||.++|++.
T Consensus         3 ~~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~   67 (114)
T 1j2o_A            3 LLTCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSG   67 (114)
T ss_dssp             CBCBSSSCSCBCS-SEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSC
T ss_pred             CCCCcCCCCeeCC-cEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcc
Confidence            4689999999983 346889999999999999999999963 567999999999999999999854

>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=99.54  E-value=3.3e-15  Score=98.47  Aligned_cols=75  Identities=31%  Similarity=0.686  Sum_probs=65.5

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccC-CCceEeeCCeeechhhHHHHHHH---hhccCCCCCC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQR-GEQFVIKQGQLFCRPDYEKEVEM---LQGYAQGIPF   77 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~~~~~~~~---~~~~~~~~~~   77 (143)
                      ++..+|..|+++|. +..++.++++.||+.||+|..|+.+|.. |..|+.+++.+||..||.++++.   |..|..+|..
T Consensus         3 l~~~~C~~C~~~I~-~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~   81 (188)
T 1rut_X            3 LSWKRCAGCGGKIA-DRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPA   81 (188)
T ss_dssp             -CCCBBTTTCCBCC-CSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECT
T ss_pred             CCCCcCccCCCEeC-CceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCcccc
Confidence            57789999999998 3446789999999999999999999964 56799999999999999999985   8889888763

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

Probab=99.54  E-value=7.4e-15  Score=91.48  Aligned_cols=66  Identities=23%  Similarity=0.708  Sum_probs=59.5

Q ss_pred             CCCc--cccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437          2 LYVK--KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus         2 ~~~~--~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      +|+.  +|..|+++|.+.+.++.+.++.||+.||.|..|+.+|..|..|+..++.+||..||.++++.
T Consensus        62 ~~~~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~  129 (131)
T 2xjy_A           62 LFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKI  129 (131)
T ss_dssp             HHCCCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHH
T ss_pred             hCCCccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhc
Confidence            3566  89999999997777889999999999999999999997688899999999999999988863

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

Probab=99.53  E-value=1e-14  Score=90.88  Aligned_cols=73  Identities=29%  Similarity=0.698  Sum_probs=63.5

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccC-CCceEeeCCeeechhhHHHHHH---HhhccCCCCCC
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQR-GEQFVIKQGQLFCRPDYEKEVE---MLQGYAQGIPF   77 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~~~~~~~---~~~~~~~~~~~   77 (143)
                      ..+|+.|+++|.. ..++.++++.||+.||+|..|+.+|.. +..|+.+++.+||..||.++++   +|..|..+|..
T Consensus         2 ~~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~   78 (131)
T 2xjy_A            2 LLTCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRA   78 (131)
T ss_dssp             CCBBTTTCCBCCS-SEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECT
T ss_pred             cccCcCCCCEeCC-cEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCc
Confidence            4689999999984 336789999999999999999999963 5679999999999999999997   58888888764

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

Probab=99.50  E-value=2.5e-14  Score=81.91  Aligned_cols=62  Identities=26%  Similarity=0.650  Sum_probs=52.6

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      +|+.+|..|+++|. ++ ++.+.++.||++||+|..|+++|..+..+...++.+||..|+...+
T Consensus        13 ~~~~~C~~C~~~I~-~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~   74 (81)
T 1v6g_A           13 LYGTRCFSCDQFIE-GE-VVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVS   74 (81)
T ss_dssp             SCCCBCTTTCCBCC-SC-CEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCS
T ss_pred             HhCCcCccccCEec-cc-eEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccC
Confidence            68899999999998 33 6899999999999999999999976665666666789999986543

>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=99.49  E-value=2.8e-15  Score=86.07  Aligned_cols=61  Identities=23%  Similarity=0.443  Sum_probs=50.9

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceE--eeCCeeechhhHHHHHH
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFV--IKQGQLFCRPDYEKEVE   66 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~--~~~~~~~C~~~~~~~~~   66 (143)
                      ..+|..|+++|+..+. +.++++.||..||+|..|+.+|. +..|.  .+++.+||..||.++++
T Consensus        15 ~~~C~~C~~~I~~~e~-v~a~~~~wH~~CF~C~~C~~~L~-~~~~~~~~~~g~~yC~~~y~~~~~   77 (82)
T 2co8_A           15 GDLCALCGEHLYVLER-LCVNGHFFHRSCFRCHTCEATLW-PGGYEQHPGDGHFYCLQHLPQTDS   77 (82)
T ss_dssp             SCBCSSSCCBCCTTTB-CCBTTBCCBTTTCBCSSSCCBCC-TTSEECCTTTCCCEETTTCCCCCC
T ss_pred             CCCCcccCCCcccceE-EEECCCeeCCCcCEEcCCCCCcC-CCceeEeCcCCEEEChHHHHhhhc
Confidence            4689999999986665 56999999999999999999996 44465  46899999999977553

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.47  E-value=1.3e-14  Score=79.91  Aligned_cols=45  Identities=27%  Similarity=0.369  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHhhh---cCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         98 ILTTQQRRAFKASFE---ISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        98 ~~~~~q~~~L~~~f~---~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .|+.+++..|+..|.   .++||+..+++.||..+||++.+|++||||
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqN   51 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFIN   51 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHH
Confidence            689999999999999   999999999999999999999999999998

>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=99.46  E-value=1.6e-14  Score=95.22  Aligned_cols=66  Identities=35%  Similarity=0.802  Sum_probs=58.2

Q ss_pred             CCCc--cccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437          2 LYVK--KCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus         2 ~~~~--~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      +|+.  +|..|+++|...+.++.+.++.||+.||+|..|+.+|..|..|+..++.+||..||.+++..
T Consensus        65 ~~~~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~  132 (188)
T 1rut_X           65 LFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALIN  132 (188)
T ss_dssp             HHSCCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC-
T ss_pred             ccccCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhcc
Confidence            3566  79999999997777889999999999999999999997678899999999999999877653

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

Probab=99.46  E-value=5e-14  Score=87.16  Aligned_cols=62  Identities=26%  Similarity=0.662  Sum_probs=56.3

Q ss_pred             CCCccccccCccccCCcceEEecCcccc--cCCcccccCCccccCCCceEeeCCeeechhhHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFH--VQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE   64 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h--~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~   64 (143)
                      +|+++|..|+++|.+++.++.+.++.||  ++||.|..|+++|. +..|+.+++.+||..++.+.
T Consensus        61 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~-~~~f~~~~~~~yC~~~~~~~  124 (126)
T 2xqn_T           61 NHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVECKKR  124 (126)
T ss_dssp             HSCCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCT-TSEEEEETTEEESSHHHHHS
T ss_pred             CcCccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccC-CCeeEeECCEEcchHHhhhh
Confidence            5789999999999977778999999999  99999999999995 88899999999999888764

>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=99.44  E-value=1.2e-13  Score=89.55  Aligned_cols=71  Identities=24%  Similarity=0.592  Sum_probs=60.4

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCC
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPF   77 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~   77 (143)
                      ..+|..|+++|.. ..++.++++.||+.||+|..|+.+|. +.. +.+++.+||..||.++++ +|..|..+|..
T Consensus         6 ~~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~-~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~   77 (169)
T 2rgt_A            6 IPMCAGCDQHILD-RFILKALDRHWHSKCLKCSDCHVPLA-ERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPP   77 (169)
T ss_dssp             -CBBSSSSSBCCS-SSCEECSSCEECTTTSBCTTTCCBCC-SCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCT
T ss_pred             CCccccCCCccCC-cEEEEECCcEEccccCccCCCCCcCC-CCC-cccCCeeeecccccccccccccccccccCC
Confidence            5799999999984 44678999999999999999999995 443 478999999999999986 78888888874

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

Probab=99.43  E-value=2.1e-13  Score=89.36  Aligned_cols=71  Identities=24%  Similarity=0.592  Sum_probs=60.4

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCCCC
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGIPF   77 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~~~   77 (143)
                      ..+|..|+++|.. ..++.+.++.||+.||+|..|+.+|. +.. +.+++.+||..||.++++ +|..|..+|..
T Consensus        60 ~~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~-~~~-f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~  131 (182)
T 2jtn_A           60 IPMCAGCDQHILD-RFILKALDRHWHSKCLKCSDCHVPLA-ERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPP  131 (182)
T ss_dssp             CCBCBTSSSBCCC-SEEEEETTEEECSSTTSCTTTCCCCS-SCC-EEETTEEECHHHHHHTTSCCCTTTCCCCCS
T ss_pred             CCcCccCCCCccC-ceeEEecCCeEccccCccCCCCCccC-CCc-eeECCEeeecCccccccccccccCCCccCC
Confidence            4699999999984 44678999999999999999999995 444 478999999999999885 67788887764

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=99.42  E-value=1.3e-14  Score=95.33  Aligned_cols=55  Identities=15%  Similarity=0.174  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhC---------------------CCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTG---------------------LSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~vkvWFQn  142 (143)
                      ..++.+|.|+.|+..|+..|+..|+.++||+...|+.||..++                     |++.+|+|||||
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqN  186 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFAN  186 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchh
Confidence            3456678999999999999999999999999999999999999                     999999999998

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

Probab=99.40  E-value=2.5e-13  Score=89.05  Aligned_cols=63  Identities=35%  Similarity=0.883  Sum_probs=55.5

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEe-eCCeeechhhHHHH
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVI-KQGQLFCRPDYEKE   64 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~-~~~~~~C~~~~~~~   64 (143)
                      +|+++|..|+++|.+.+.++.+.++.||+.||+|..|+++|..|..|+. .++++||..||.++
T Consensus       117 ~f~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~  180 (182)
T 2jtn_A          117 RFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA  180 (182)
T ss_dssp             TTSCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHH
T ss_pred             ccccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHh
Confidence            6889999999999977777789999999999999999999976777765 57899999999764

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.40  E-value=6.8e-14  Score=92.84  Aligned_cols=55  Identities=13%  Similarity=0.187  Sum_probs=49.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhC---------------------CCcccceecccC
Q psy15437         88 GRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTG---------------------LSVRIVQSRPIP  142 (143)
Q Consensus        88 ~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~vkvWFQn  142 (143)
                      ..++.+|.|+.|+..|+..|+..|+.++||+..+|++||..++                     |++.+|++||||
T Consensus       138 ~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqN  213 (221)
T 2h8r_A          138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFAN  213 (221)
T ss_dssp             ----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHH
T ss_pred             ccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHH
Confidence            4566788999999999999999999999999999999999987                     888999999998

>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=99.40  E-value=2.2e-13  Score=90.00  Aligned_cols=69  Identities=26%  Similarity=0.615  Sum_probs=58.6

Q ss_pred             ccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHH-HhhccCCCC
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE-MLQGYAQGI   75 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~-~~~~~~~~~   75 (143)
                      .+|..|+++|...+. +.++++.||.+||+|..|+.+|. +..|+.+++.+||..||.++++ ++.+|++++
T Consensus       116 ~~C~~C~~~I~~~~~-v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~  185 (192)
T 1b8t_A          116 DGCPRCGQAVYAAEK-VIGAGKSWHKSCFRCAKCGKSLE-STTLADKDGEIYCKGCYAKNFGPKGFGFGQGA  185 (192)
T ss_dssp             EECTTTSCEECSSSC-EEETTEEECTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             CcCCCCCCEecCcEE-EecCCCccchhcCCccccCCCCC-CCcccccCCEEeCHHHHHHhcCCcCCCCCCcc
Confidence            469999999986665 56999999999999999999995 4569999999999999999886 566666553

>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=99.33  E-value=1.3e-12  Score=86.31  Aligned_cols=62  Identities=26%  Similarity=0.587  Sum_probs=54.9

Q ss_pred             CccccccCccccCCcceEEecCcccccCCcccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      +.+|..|+++|...+. +.++++.||+.||+|..|+.+|. +..|+.+++.+||..||.+++++
T Consensus         7 ~~~C~~C~~~I~~~~~-v~a~g~~wH~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~~   68 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEE-VQCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKKYGP   68 (192)
T ss_dssp             CEECTTTCCEECSSCC-EEETTEEECTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHHSC
T ss_pred             CCcCccCCCeecceeE-EEeCCceecCCCCcCcccCCcCC-CCeeEecCCEeeChhhhHhhcCc
Confidence            3689999999986664 67999999999999999999996 45699999999999999999874

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=99.27  E-value=8.3e-13  Score=75.77  Aligned_cols=47  Identities=17%  Similarity=0.143  Sum_probs=43.9

Q ss_pred             CCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...++.++...|+..|..   ++||+..+++.||..|||++.||++||||
T Consensus         9 ~~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~N   58 (89)
T 2lk2_A            9 SHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFIN   58 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            346889999999999977   99999999999999999999999999998

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.14  E-value=9.4e-12  Score=90.72  Aligned_cols=49  Identities=18%  Similarity=0.210  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.++.++..|+..|++.|+.++||+..+|++||.++||+++||||||||
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n  415 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFIN  415 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhh
Confidence            4577899999999999999999999999999999999999999999998

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

Probab=98.86  E-value=1.4e-09  Score=64.36  Aligned_cols=39  Identities=23%  Similarity=0.425  Sum_probs=35.4

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCcccccCC
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCG   39 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~   39 (143)
                      ++|+++|..|+++|.+++.++.++++.||++||.|..|+
T Consensus        63 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           63 REDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             TCCCCBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             hhcCCccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence            368899999999999777789999999999999999985

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

Probab=98.35  E-value=1.3e-07  Score=43.63  Aligned_cols=29  Identities=31%  Similarity=0.723  Sum_probs=25.6

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.+|..|++.++..|. +.+.++.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek-~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEK-VNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGC-CCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEeccee-EEECCeEecccCC
Confidence            4689999999998886 5689999999997

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

Probab=96.60  E-value=0.00018  Score=43.67  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=18.8

Q ss_pred             CCCceEeeCCeeechhhHHHHH
Q psy15437         44 RGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        44 ~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .|..|+.+++.+||..|+.+.+
T Consensus        93 ~g~~f~~~~~~~yC~~~~~~~~  114 (122)
T 1m3v_A           93 MGGEFGDEDERLITRLENTQFD  114 (122)
T ss_dssp             CSCTTCCTTCCCCEECTTTTTT
T ss_pred             CCCccEecCCEeEccCcchhch
Confidence            6888999999999999987654

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.39  E-value=0.0009  Score=36.10  Aligned_cols=37  Identities=11%  Similarity=0.027  Sum_probs=34.9

Q ss_pred             HHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437        104 RRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP  140 (143)
Q Consensus       104 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF  140 (143)
                      .+.|+..|.............|..++.|+-.+||-||
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwF   54 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWF   54 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHH
Confidence            3679999999999999999999999999999999999

>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=93.30  E-value=0.026  Score=33.54  Aligned_cols=59  Identities=19%  Similarity=0.235  Sum_probs=38.9

Q ss_pred             cccccCccccC-CcceEEecCccc---------ccCCcccc-----cCCccccCCCceEeeCCeeechhhHHHH
Q psy15437          6 KCLGCSEKLGP-DELVMKTLDNVF---------HVQCFVCV-----VCGSRLQRGEQFVIKQGQLFCRPDYEKE   64 (143)
Q Consensus         6 ~C~~C~~~i~~-~~~~~~~~~~~~---------h~~cf~C~-----~C~~~l~~~~~~~~~~~~~~C~~~~~~~   64 (143)
                      +|..|++++.. +.......++.|         .+.|..|.     .|..++..|+.|+.+++++||..|+.++
T Consensus        32 ~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~~~~~~~~~~~~~g~~f~~~~~~~~C~~~~~~~  105 (114)
T 1j2o_A           32 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQF  105 (114)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBSCSCCCSSCSSTTSSBCCCSSSCCCEEEECTTC
T ss_pred             cccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCCCceeEcCCccCCCCeeEEcCCEeecchhhhcc
Confidence            68889998863 122344445544         33444442     3555655788999999999999998654

---

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	143
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	5e-08
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-07
d1rutx3	31	g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus	2e-07
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-07
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	6e-07
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	8e-07
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-06
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-06
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	2e-06
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	6e-06
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	6e-06
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	8e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-05
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-05
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-05
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-05
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-05
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	3e-05
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-05
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	5e-05
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	8e-05
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	8e-05
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-04
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-04
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-04
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	0.001
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	0.003
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	0.003
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	0.004

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 5e-08
 Identities = 15/57 (26%), Positives = 22/57 (38%)

Query: 81  TSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           T+  S  G   P   RT  TT+Q    +  F  +    R  R  +A    L+   V+
Sbjct: 16  TAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 72

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (105), Expect = 1e-07
 Identities = 12/55 (21%), Positives = 21/55 (38%)

Query: 83  SKSHDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           + +    R  ++ R   T  Q    +  F  +    R  R  +AR   L+ R V+
Sbjct: 4   AANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK 58

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 31

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

 Score = 42.8 bits (101), Expect = 2e-07
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 7  CLGCSEKLGPDELVMKTLDNVFHVQCF 33
          C  C + +   ELVM+   NV+H++CF
Sbjct: 5  CSACGQSIPASELVMRAQGNVYHLKCF 31

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (101), Expect = 3e-07
 Identities = 15/45 (33%), Positives = 20/45 (44%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +R RT  T +Q  A +  FE +  P    RE LA    L    +Q
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 46

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (98), Expect = 6e-07
 Identities = 11/45 (24%), Positives = 17/45 (37%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           K  +   +  Q    +  FE         R+ LA+   LS R V+
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVK 45

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 41.8 bits (98), Expect = 8e-07
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 92  PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
             R RT+L  +Q    +  +  +P+P   ++E L   TGLS R+++
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.0 bits (96), Expect = 1e-06
 Identities = 12/43 (27%), Positives = 24/43 (55%)

Query: 95  PRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           PR + T  QRR   A F+ + +P ++++  +++  GL +  V 
Sbjct: 1   PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVS 43

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (96), Expect = 1e-06
 Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 93  KRPRTILTTQQRRAFKASFEIS---PKPCRKVREGLARDTGLSVRIVQ 137
           K  R +L        ++        P P    ++ +A  T L++  V 
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVN 50

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.6 bits (95), Expect = 2e-06
 Identities = 11/44 (25%), Positives = 22/44 (50%)

Query: 94  RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           RPRT  +++Q    K  F  +     + R+ L+ + GL+   ++
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 44

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.5 bits (92), Expect = 6e-06
 Identities = 14/46 (30%), Positives = 22/46 (47%)

Query: 92  PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
            +R RT  +  Q    + +FE +  P    RE LA+ T L+   +Q
Sbjct: 2   QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 47

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.2 bits (91), Expect = 6e-06
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +R RT  T+QQ +  +A+F+ +  P    RE +A  T L+   V+
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 46

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 8e-06
 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 3/48 (6%)

Query: 93  KRPRTILTTQQRRAFKASFE---ISPKPCRKVREGLARDTGLSVRIVQ 137
           +R R     Q        F     +P P  + +E LA+  G++V  V 
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVS 49

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.1 bits (91), Expect = 1e-05
 Identities = 10/46 (21%), Positives = 15/46 (32%)

Query: 92  PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           P+R RT  T+ Q    +  F             L+    L    V+
Sbjct: 1   PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK 46

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 1e-05
 Identities = 8/45 (17%), Positives = 18/45 (40%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           ++ R   +  Q R  +  +  +    +  R  ++  T LS R + 
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQIT 46

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 39.2 bits (91), Expect = 1e-05
 Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 4/61 (6%)

Query: 81  TSSKSHDGRRGPKRPRTILTTQQRRAFKASFE----ISPKPCRKVREGLARDTGLSVRIV 136
           + S         KR RT  T +Q+    A  E       K      E    +TG+  +++
Sbjct: 6   SGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVL 65

Query: 137 Q 137
           +
Sbjct: 66  K 66

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.6 bits (87), Expect = 3e-05
 Identities = 9/44 (20%), Positives = 19/44 (43%)

Query: 94  RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           + RT ++   + A +  F    KP  +    +A +  L   +V+
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVR 44

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 37.4 bits (87), Expect = 3e-05
 Identities = 9/42 (21%), Positives = 16/42 (38%)

Query: 96  RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           R   T  Q    +  F  +    R+ R  +A    L+ R ++
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 42

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.7 bits (87), Expect = 3e-05
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 90  RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           +  KR RT +  + R + +  F   PKP  +    +A   GL   +V+
Sbjct: 6   QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVR 53

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (86), Expect = 3e-05
 Identities = 10/42 (23%), Positives = 19/42 (45%)

Query: 96  RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           RT + T  R A + SF  + KP  +    +A    +   +++
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR 43

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.2 bits (86), Expect = 4e-05
 Identities = 8/42 (19%), Positives = 19/42 (45%)

Query: 96  RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           ++ ++ Q R   +  F        K +E +A+  G++   V+
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVR 42

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 5e-05
 Identities = 6/47 (12%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 92  PKRPRTILTTQQRRAFKASF-EISPKPCRKVREGLARDTGLSVRIVQ 137
             R RT ++ +     ++   ++   P ++    L+    L    + 
Sbjct: 7   GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII 53

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 36.4 bits (84), Expect = 8e-05
 Identities = 9/45 (20%), Positives = 17/45 (37%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           ++ R + +  Q    +  F+         RE LA    L+   V+
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVK 47

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 36.4 bits (84), Expect = 8e-05
 Identities = 11/44 (25%), Positives = 14/44 (31%)

Query: 94  RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           R RT  T  Q    +  F       R  R  LA    L    ++
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIK 44

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 10/48 (20%), Positives = 16/48 (33%)

Query: 90  RGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
              ++ R + T  Q    +  F          RE LA    L+   V+
Sbjct: 7   NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK 54

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 6/46 (13%), Positives = 14/46 (30%)

Query: 94  RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSR 139
             R     +     ++ F  +  P    RE +A      ++    +
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKK 47

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (81), Expect = 2e-04
 Identities = 11/45 (24%), Positives = 17/45 (37%)

Query: 93  KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
           ++PRT  TT Q  A +  F          R   +    L+   V+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK 45

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.2 bits (76), Expect = 0.001
 Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 100 TTQQRRAFKASF-EISPKPCRKVREGLARDTGLSVRIVQ 137
           T Q     +  F  I+  P  K  EGL++     VR +Q
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ 39

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.0 bits (73), Expect = 0.003
 Identities = 9/45 (20%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 94  RPRTILTTQQRRAFKASFE-ISPKPCRKVREGLARDTGLSVRIVQ 137
           +   +   +     +  F  ++  P  K  +GL++    SVR +Q
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ 47

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.1 bits (73), Expect = 0.003
 Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 93  KRPRTILTTQQRRAFKASFE---ISPKPCRKVREGLARDTGLSVRIVQ 137
           +  R   T +  R  ++ F     +P    K  E L ++T LS   ++
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIK 46

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 31.9 bits (72), Expect = 0.004
 Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 1/46 (2%)

Query: 93  KRPRTILTTQQRRAFKASFEISPK-PCRKVREGLARDTGLSVRIVQ 137
                 +T  Q    + +F    K P       +A + GL+    Q
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 47

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	143
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.83
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.82
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.81
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.81
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.8
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.8
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.8
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.8
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.79
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.79
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.79
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.77
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.77
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.77
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.77
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.77
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.76
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.75
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.75
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.75
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.74
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.73
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.71
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.68
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.65
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.62
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.6
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.57
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.54
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.54
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.52
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.52
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.12
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.83
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.82
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.81
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.66
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.59
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.55
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.39
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.37
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.35
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.35
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.34
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.33
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.32
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.3
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.3
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	98.29
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.25
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.24
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.21
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.19
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.16
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.08
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.07
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.0
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.99
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.97
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.97
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.94
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.93
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.91
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.91
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.91
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.89
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.89
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.87
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.85
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.81
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.74
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.72
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.72
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.72
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.71
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.67
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.66
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.65
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.62
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.61
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.53
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.46
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.4
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.38
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	97.38
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.29
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.24
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.8
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.42
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.38
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.9
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.78
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	95.33
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.24
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	94.01
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	93.96
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	93.88
d2co8a1	33	Nedd9 interacting protein with calponin homology,	93.8
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	89.04
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	86.91
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	84.3
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	81.45

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=9.6e-22  Score=102.21  Aligned_cols=49  Identities=22%  Similarity=0.303  Sum_probs=47.8

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |.|+.||.+|+..|+..|+.++||+..++++||..+||++.+|+|||||
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqN   49 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQN   49 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccc
Confidence            5799999999999999999999999999999999999999999999999

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.7e-21  Score=102.75  Aligned_cols=50  Identities=16%  Similarity=0.167  Sum_probs=48.6

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.||.+|+..|+..|+.++||+...++.||..+||++.+|+|||||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqN   51 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQN   51 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccc
Confidence            56789999999999999999999999999999999999999999999998

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=3.8e-21  Score=101.79  Aligned_cols=50  Identities=22%  Similarity=0.182  Sum_probs=48.5

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.|+.+|+..|+..|+.++||+...++.||..+||++.+|+|||||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqN   50 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQN   50 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcc
Confidence            46899999999999999999999999999999999999999999999999

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.81  E-value=4.7e-21  Score=100.94  Aligned_cols=49  Identities=22%  Similarity=0.129  Sum_probs=48.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |.|+.||..|+..|+..|..++||+...++.||..+||++.+|+|||||
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqN   49 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQN   49 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchh
Confidence            5799999999999999999999999999999999999999999999999

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.80  E-value=6.4e-21  Score=103.58  Aligned_cols=51  Identities=20%  Similarity=0.151  Sum_probs=49.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +++.|+.|+.+|+..|+..|..++||+...++.||..+||++.+|+|||||
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqN   51 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKN   51 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeecccc
Confidence            467899999999999999999999999999999999999999999999999

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.80  E-value=5.6e-21  Score=106.50  Aligned_cols=57  Identities=18%  Similarity=0.088  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         86 HDGRRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        86 ~~~~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .+.+.+.++.|+.|+.+|+..|+..|+.++||+..+++.||..+||++.+|+|||||
T Consensus         3 ~g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqN   59 (77)
T d1vnda_           3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN   59 (77)
T ss_dssp             SCCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchh
Confidence            345566778899999999999999999999999999999999999999999999999

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.80  E-value=6.3e-21  Score=99.53  Aligned_cols=47  Identities=19%  Similarity=0.170  Sum_probs=46.3

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ||.||.+|+..|+..|..++||+...++.||..+||++++|+|||||
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQN   47 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN   47 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeecccc
Confidence            78999999999999999999999999999999999999999999998

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2.2e-20  Score=103.88  Aligned_cols=54  Identities=22%  Similarity=0.166  Sum_probs=50.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ....++.|+.|+.+|+..|+..|+.++||+...++.||..+||++.+|+|||||
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqN   63 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQN   63 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhh
Confidence            344567899999999999999999999999999999999999999999999998

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.2e-20  Score=99.35  Aligned_cols=50  Identities=22%  Similarity=0.159  Sum_probs=48.4

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.||..|+..|+..|+.++||+...++.||..+||++.+|+|||||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqN   50 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQN   50 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhh
Confidence            46789999999999999999999999999999999999999999999998

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.8e-20  Score=102.09  Aligned_cols=50  Identities=30%  Similarity=0.255  Sum_probs=48.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +|.||.||.+|+..|+..|..++||+...++.||..+||++.+|+|||||
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqN   51 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSN   51 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcc
Confidence            56899999999999999999999999999999999999999999999998

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.79  E-value=2.5e-20  Score=100.70  Aligned_cols=51  Identities=27%  Similarity=0.295  Sum_probs=49.5

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqN   52 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN   52 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhh
Confidence            567899999999999999999999999999999999999999999999998

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.9e-20  Score=105.43  Aligned_cols=54  Identities=22%  Similarity=0.155  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         89 RRGPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        89 ~~~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ...+++.|+.|+..|+..|+..|+.++||+..+++.||..+||++++|+|||||
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqN   77 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQN   77 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHh
Confidence            345678899999999999999999999999999999999999999999999999

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.77  E-value=1.2e-19  Score=101.95  Aligned_cols=56  Identities=21%  Similarity=0.152  Sum_probs=50.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhc----CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         87 DGRRGPKRPRTILTTQQRRAFKASFEI----SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        87 ~~~~~~~r~R~~~~~~q~~~L~~~f~~----~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +...+.+|.||.|+.+|+..|+..|+.    +++|+..++++||.+|||++.+|+|||||
T Consensus        12 ~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN   71 (80)
T d1wh7a_          12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN   71 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHT
T ss_pred             CCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeeccc
Confidence            344556789999999999999888875    89999999999999999999999999999

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.77  E-value=4.5e-20  Score=100.40  Aligned_cols=51  Identities=18%  Similarity=0.125  Sum_probs=49.1

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         92 PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        92 ~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.|+.||..|+..|+..|..++||+...++.||..+||++.+|+|||||
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqN   52 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN   52 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeeccc
Confidence            356899999999999999999999999999999999999999999999998

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.77  E-value=5.4e-20  Score=99.58  Aligned_cols=52  Identities=27%  Similarity=0.434  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +++|.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|++||||
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqN   53 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQN   53 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHh
Confidence            4678999999999999999999999999999999999999999999999998

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=4.3e-20  Score=94.89  Aligned_cols=48  Identities=25%  Similarity=0.477  Sum_probs=47.0

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         95 PRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        95 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +|+.|+.+|+..|+..|+.++||+...++.||..+||++.+|++||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqN   48 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN   48 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCc
Confidence            589999999999999999999999999999999999999999999999

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.2e-19  Score=98.27  Aligned_cols=52  Identities=25%  Similarity=0.323  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..++.|+.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqN   58 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCN   58 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHH
Confidence            3467899999999999999999999999999999999999999999999998

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=2e-19  Score=98.52  Aligned_cols=50  Identities=16%  Similarity=0.129  Sum_probs=47.6

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc-CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEI-SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.||.+|+..|+..|.. ++||+...++.||..+||++++|+|||||
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqN   52 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQ   52 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            467999999999999999986 78999999999999999999999999998

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=4.4e-20  Score=98.29  Aligned_cols=50  Identities=30%  Similarity=0.277  Sum_probs=48.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.||.|+.+|+..|+..|..++||+..+++.||..+||++.+|++||||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqN   51 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKN   51 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHH
Confidence            57899999999999999999999999999999999999999999999998

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.75  E-value=2.2e-19  Score=94.79  Aligned_cols=49  Identities=18%  Similarity=0.256  Sum_probs=47.7

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        94 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +.||.|+.+|+..|+..|..++||+..+++.||..+||++.+|+|||||
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqN   49 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCN   49 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999998

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.74  E-value=2.3e-19  Score=93.04  Aligned_cols=47  Identities=19%  Similarity=0.244  Sum_probs=46.2

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |+.++.+|+..|+..|..++||+..+++.||..+||++.+|++||||
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqN   47 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFIN   47 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHh
Confidence            68999999999999999999999999999999999999999999998

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=5.8e-19  Score=97.05  Aligned_cols=52  Identities=12%  Similarity=0.090  Sum_probs=48.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhh-cCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         91 GPKRPRTILTTQQRRAFKASFE-ISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        91 ~~~r~R~~~~~~q~~~L~~~f~-~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..++.|+.++.+|+..|+..|+ .++||+..+++.||.++||++++|++||||
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqN   58 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQN   58 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHh
Confidence            3567899999999999999997 599999999999999999999999999998

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.7e-18  Score=90.98  Aligned_cols=48  Identities=21%  Similarity=0.205  Sum_probs=46.8

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         95 PRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        95 ~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .||+++.+|+..|+..|..++||+..+++.||..+||++.+|++||||
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqN   48 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSN   48 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            489999999999999999999999999999999999999999999998

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.6e-18  Score=95.84  Aligned_cols=50  Identities=14%  Similarity=0.098  Sum_probs=47.3

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhC---------------CCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTG---------------LSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------l~~~~vkvWFQn  142 (143)
                      ++.|+.|+.+|+..|+..|+.++||+...+++||..+|               |++.+|+|||||
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqN   65 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFAN   65 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhh
Confidence            46899999999999999999999999999999999875               899999999998

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.8e-17  Score=90.77  Aligned_cols=45  Identities=24%  Similarity=0.141  Sum_probs=43.5

Q ss_pred             CCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         98 ILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        98 ~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ..|.+|+..|+..|..++||+..+++.||..|||++.+|++||||
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqN   54 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTE   54 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHH
Confidence            458999999999999999999999999999999999999999998

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=9.2e-17  Score=88.58  Aligned_cols=50  Identities=24%  Similarity=0.353  Sum_probs=47.2

Q ss_pred             CCCCCCCCHHHHHHHHHhhh---cCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFE---ISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~---~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.++.+|+..|+..|.   .++||+..+++.||..+||++.+|++||||
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N   54 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN   54 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHH
Confidence            46789999999999999997   488999999999999999999999999998

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=2.4e-16  Score=87.51  Aligned_cols=47  Identities=19%  Similarity=0.006  Sum_probs=44.7

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      +..++.+|+..|+..|..++||+..+++.||..|||++.+|++||||
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~N   53 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGD   53 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHH
Confidence            34579999999999999999999999999999999999999999998

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=1.4e-16  Score=81.89  Aligned_cols=43  Identities=26%  Similarity=0.305  Sum_probs=39.9

Q ss_pred             CHHHHHHHHHhhhc-CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437        100 TTQQRRAFKASFEI-SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus       100 ~~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      |++|...|+..|.. ++||+...++.||..+||++++|+|||||
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqN   44 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQ   44 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHh
Confidence            45688999999976 78999999999999999999999999998

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=1.3e-15  Score=81.07  Aligned_cols=50  Identities=20%  Similarity=0.281  Sum_probs=46.5

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc---CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         93 KRPRTILTTQQRRAFKASFEI---SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        93 ~r~R~~~~~~q~~~L~~~f~~---~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      ++.|+.++.+++..|+..|..   ++||+..+++.||..+||+..+|++||||
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N   55 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFIN   55 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHH
Confidence            456788999999999999975   78999999999999999999999999998

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.54  E-value=6.4e-16  Score=85.71  Aligned_cols=47  Identities=15%  Similarity=0.170  Sum_probs=44.8

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhC---------------------CCcccceecccC
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTG---------------------LSVRIVQSRPIP  142 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~---------------------l~~~~vkvWFQn  142 (143)
                      |+.++..|+..|+..|+.++||+...|+.||.+++                     |++.+|++||||
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~N   68 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFAN   68 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHH
Confidence            67899999999999999999999999999999994                     888999999998

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=3.5e-16  Score=82.38  Aligned_cols=48  Identities=19%  Similarity=0.203  Sum_probs=42.8

Q ss_pred             CCCCCCHHHHHHHHHhhhc-CCCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         95 PRTILTTQQRRAFKASFEI-SPKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        95 ~R~~~~~~q~~~L~~~f~~-~~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .++.++.++...|+..|.. ++||+..+++.||..+||++++|++||||
T Consensus         4 ~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqN   52 (59)
T d2cqxa1           4 DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRH   52 (59)
T ss_dssp             CCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHh
Confidence            4556677777899999976 68999999999999999999999999998

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.52  E-value=2.6e-15  Score=79.47  Aligned_cols=45  Identities=22%  Similarity=0.189  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHhhhcC---CCCCHHHHHHHHHHhCCCcccceecccC
Q psy15437         98 ILTTQQRRAFKASFEIS---PKPCRKVREGLARDTGLSVRIVQSRPIP  142 (143)
Q Consensus        98 ~~~~~q~~~L~~~f~~~---~~p~~~~~~~la~~~~l~~~~vkvWFQn  142 (143)
                      .|+.+|+..|+..|..+   +||+..+++.||..+||++.+|++||||
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N   51 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSN   51 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHh
Confidence            48999999999999765   7999999999999999999999999998

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

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

Probab=99.12  E-value=1.4e-11  Score=57.19  Aligned_cols=31  Identities=32%  Similarity=0.801  Sum_probs=28.0

Q ss_pred             CCCCccccccCccccCCcceEEecCcccccCCc
Q psy15437          1 MLYVKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         1 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ++|+++|..|+++|.  +.++.|+++.||++||
T Consensus         5 ~~fapkC~~C~~~I~--g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           5 AMFSPKCGGCNRPVL--ENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCSCBCTTTCCBCC--SSCEEETTEEECTTTC
T ss_pred             HHhChhhhhcCCccc--chheeecCCccCcccC
Confidence            479999999999998  3378999999999998

>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=98.83  E-value=1.4e-09  Score=50.48  Aligned_cols=32  Identities=25%  Similarity=0.526  Sum_probs=30.4

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCc
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      .|+.+|..|+++|.+++..+.+.++.||..||
T Consensus         6 ~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           6 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            68999999999999999899999999999998

>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=98.82  E-value=1.2e-09  Score=49.42  Aligned_cols=29  Identities=24%  Similarity=0.770  Sum_probs=26.4

Q ss_pred             CCccccccCccccCCcceEEecCcccccCCc
Q psy15437          3 YVKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         3 ~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ...+|..|+++|.  |.+++|.|+.||+.||
T Consensus         7 tlEkC~~C~~~I~--driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           7 TLEKCATCSQPIL--DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             SCCBCTTTCCBCC--SCCEEETTEEECTTTC
T ss_pred             HHHHHHHhchHHH--HHHHHHhCCCCCCCCC
Confidence            4579999999998  6689999999999998

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

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

Probab=98.81  E-value=8.4e-10  Score=48.71  Aligned_cols=29  Identities=38%  Similarity=0.934  Sum_probs=27.6

Q ss_pred             ccccccCccccCCcceEEecCcccccCCc
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ..|++|++.|.+.|+++++.+.+||..||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            46999999999999999999999999998

>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=98.66  E-value=2.7e-09  Score=49.16  Aligned_cols=34  Identities=24%  Similarity=0.546  Sum_probs=30.5

Q ss_pred             cccccCCccccCCCceEeeCCeeechhhHHHHHHH
Q psy15437         33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEM   67 (143)
Q Consensus        33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~   67 (143)
                      |.|..|+++|. +..|+.++|++||..||..++++
T Consensus         1 F~C~~C~~~f~-~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFP-EGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCG-GGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCC-CCCeEEECCEecChHhHHhhcCC
Confidence            68999999996 66799999999999999998864

>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=98.59  E-value=1.3e-08  Score=48.65  Aligned_cols=28  Identities=18%  Similarity=0.444  Sum_probs=25.1

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ++.|+.|+++|.  +.++.++++.||++||
T Consensus        18 ~P~C~~C~~pI~--g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIR--GPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCC--SCEEEETTEEECTTTC
T ss_pred             CeeccccCCccc--CceeeecCCccCcCCC
Confidence            468999999998  5589999999999998

>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=98.55  E-value=2.6e-08  Score=44.68  Aligned_cols=30  Identities=23%  Similarity=0.589  Sum_probs=27.1

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCc
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      .|+.+|..|+++|..+  -++..+..||.+||
T Consensus         6 kfa~~C~~Ckk~It~G--GvtY~dqpWHkeCF   35 (35)
T d2cuqa2           6 KFAPRCARCSKTLTQG--GVTYRDQPWHRECL   35 (35)
T ss_dssp             CSSCCCTTTCCCCCSC--CEESSSSEECTTTC
T ss_pred             HHHHHHhhcCCccccC--ceeecCCcchhhhC
Confidence            5899999999999866  47899999999998

>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=98.39  E-value=8.5e-08  Score=43.77  Aligned_cols=29  Identities=31%  Similarity=0.766  Sum_probs=26.4

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ..+|..|++.+++.|. +.+.|+.||.+||
T Consensus         7 ~~kC~~C~K~VY~~E~-~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMER-LLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSE-EECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeee-EecCCeehhhccC
Confidence            4689999999999996 6899999999998

>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=98.37  E-value=5.5e-08  Score=41.64  Aligned_cols=29  Identities=31%  Similarity=0.723  Sum_probs=25.8

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      .+.|++|++.+++.|. +.-.++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ek-l~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEK-VNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGC-CCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHH-hhhhHHHHhhccC
Confidence            4689999999999986 5788999999998

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

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

Probab=98.35  E-value=1.1e-07  Score=41.50  Aligned_cols=28  Identities=32%  Similarity=0.969  Sum_probs=25.4

Q ss_pred             ccccccCccccCCcceEEecCcccccCCc
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ..|++|+++|. +.+++.+.++.||..|+
T Consensus         3 ~~CaGC~~~I~-DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIA-DRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCC-CSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccc-hhhhhccchhhhhhhhC
Confidence            58999999998 77889999999999984

>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=98.35  E-value=1e-07  Score=43.64  Aligned_cols=29  Identities=31%  Similarity=0.470  Sum_probs=26.4

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.+|..|++.+++.|. +.+.++.||..||
T Consensus         8 ~~~C~~C~K~VY~~Er-l~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLER-LCVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTB-CCBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeE-EEecCcEeccccC
Confidence            4689999999999996 5799999999998

>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=98.34  E-value=1.1e-07  Score=41.23  Aligned_cols=29  Identities=24%  Similarity=0.507  Sum_probs=25.6

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.+|++|+++++..|. +...|+.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk-~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEK-VSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTE-EEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHh-hccCCcccccccC
Confidence            4689999999999996 6788999999985

>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=98.33  E-value=9.2e-08  Score=45.93  Aligned_cols=29  Identities=21%  Similarity=0.493  Sum_probs=26.2

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.+|..|++.++..|. +.+.++.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~-~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEK-VIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSC-EEETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHH-hhcCCCccccCCC
Confidence            3689999999999996 5799999999998

>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=98.32  E-value=1.4e-07  Score=41.65  Aligned_cols=31  Identities=23%  Similarity=0.600  Sum_probs=27.9

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .|..|..+| .|..|..+++++||..||..++
T Consensus         1 ~C~~C~~~L-~GQry~~rd~~PyC~~Cf~~lf   31 (32)
T d2d8za2           1 VCTACRKQL-SGQRFTARDDFAYCLNCFCDLY   31 (32)
T ss_dssp             BCSSSCCBC-TTSCCEESSSSEECHHHHHHHT
T ss_pred             CcccCCccc-cCceeeecCCCeehHHhhHhhc
Confidence            378899999 6999999999999999998875

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

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

Probab=98.30  E-value=1.3e-07  Score=41.25  Aligned_cols=28  Identities=21%  Similarity=0.483  Sum_probs=24.8

Q ss_pred             CCCccccccCccccCCcceEEecCcccccC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQ   31 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~   31 (143)
                      .+.+.|+.|.++|.  +.++.++++.||++
T Consensus         3 mg~p~C~~C~~PI~--~~~vtAlgk~WHpE   30 (31)
T d1u5sb1           3 MGVPICGACRRPIE--GRVVNAMGKQWHVE   30 (31)
T ss_dssp             CCCCEETTTTEECC--SCEECCTTSBEETT
T ss_pred             cCCcchhhcCCchh--hhHhhhhccccCCC
Confidence            46789999999998  45899999999986

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

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

Probab=98.29  E-value=2e-07  Score=38.77  Aligned_cols=27  Identities=26%  Similarity=0.651  Sum_probs=25.4

Q ss_pred             ccccCccccCCcceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      |..|.+.|.++...+...|..||..||
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            788999999998889999999999998

>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=98.25  E-value=3.2e-07  Score=39.90  Aligned_cols=31  Identities=26%  Similarity=0.626  Sum_probs=28.1

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .|..|+++| .|..|..++..+||..||..+|
T Consensus         1 vCt~Ck~~L-aGqrFTSrde~pYC~~Cfg~Lf   31 (32)
T d2cuqa1           1 VCTGCQTPL-AGQQFTSRDEDPYCVACFGELF   31 (32)
T ss_dssp             BCSSSCCBC-TTCCEEECSSSEEEHHHHHHHT
T ss_pred             CccccCccc-cCCccccCCCCccHHHHhHhhc
Confidence            488999999 6999999999999999998775

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

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

Probab=98.24  E-value=2.6e-07  Score=38.27  Aligned_cols=27  Identities=26%  Similarity=0.663  Sum_probs=25.3

Q ss_pred             ccccCccccCCcceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      |..|.+.|.++...+...|..||..||
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            789999999998889999999999998

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

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

Probab=98.21  E-value=4.7e-07  Score=39.30  Aligned_cols=27  Identities=33%  Similarity=0.917  Sum_probs=24.5

Q ss_pred             ccccccCccccCCcceEEecCcccccCC
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      ..|++|+++|. +.+++.+.++.||..|
T Consensus         4 ~~CaGC~~~I~-DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIG-DRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBC-SSEEEECSSSEECTTT
T ss_pred             cccCCCCCcch-HHHHHHHHHHHHhcCC
Confidence            57999999998 7788999999999987

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

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

Probab=98.19  E-value=3.6e-07  Score=42.72  Aligned_cols=29  Identities=28%  Similarity=0.762  Sum_probs=26.1

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      +|+.+|..|++-|.  ..++.+.++.||+.|
T Consensus        13 ~fG~~C~~C~~~It--G~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          13 LYGTRCFSCDQFIE--GEVVSALGKTYHPDC   41 (41)
T ss_dssp             SCCCBCTTTCCBCC--SCCEEETTEEECTTT
T ss_pred             HhCcccccccCEee--eeeeEecCcccCCCC
Confidence            78999999999997  348899999999998

>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=98.16  E-value=2.4e-07  Score=43.85  Aligned_cols=32  Identities=22%  Similarity=0.814  Sum_probs=28.1

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|..|++.|+.+ .|+..+|.+||.+||.++|.
T Consensus         1 rC~~C~~~Ls~~-~yas~~G~lYCkpHf~qLF~   32 (42)
T d2d8ya2           1 RCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFK   32 (42)
T ss_dssp             BCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSC
T ss_pred             CcCcCCCCccCC-cchhhCCEeccHHHHHHHHH
Confidence            589999999755 48899999999999999886

>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=98.07  E-value=1.2e-06  Score=38.99  Aligned_cols=29  Identities=34%  Similarity=0.809  Sum_probs=24.7

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      ...|+.|++.|.. +..+.+.++.||..||
T Consensus         8 ~~~CagCg~eik~-gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           8 PSHCAGCKEEIKH-GQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSCCTTTCCCCSS-SCCEEETTEEECTTTC
T ss_pred             CccccccchhhhC-CceeeeeecceeeeeC
Confidence            3579999999984 4467899999999998

>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=98.00  E-value=1.8e-05  Score=40.72  Aligned_cols=48  Identities=19%  Similarity=0.582  Sum_probs=36.7

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHHHHhhccCCCCCCccccCC
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVEMLQGYAQGIPFDLITSS   83 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (143)
                      .|..|++.|. ......+++.+||..||.+.|+ ..+++-+.....+.++
T Consensus         1 ~C~~C~K~Ld-S~~~~eh~~e~YCk~CY~k~fG-PkG~G~G~gag~l~~d   48 (65)
T d1b8ta2           1 LCMVCKKNLD-STTVAVHGDEIYCKSCYGKKYG-PKGKGKGMGAGTLSTD   48 (65)
T ss_dssp             BCTTTCCBCC-SSSEEEETTEEEEHHHHHHHHS-CCCCCCCCCCCCCCCC
T ss_pred             CchhcCCccC-CCccccCCCcccchhhhccccC-CCccccccccceeeec
Confidence            3889999995 4558999999999999999997 3555555555555554

>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=97.99  E-value=2.8e-06  Score=37.53  Aligned_cols=30  Identities=27%  Similarity=0.578  Sum_probs=26.1

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE   64 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~   64 (143)
                      .|..|.+++. +..|+..++++||..+|..+
T Consensus         1 VC~~C~~PF~-~~~Fy~~~g~PyCe~HyH~~   30 (32)
T d1x3ha2           1 VCGDCFTSFS-TGSFFELDGRPFCELHYHHR   30 (32)
T ss_dssp             BCSSSCCBSC-SSCCEESSSCEECHHHHHHH
T ss_pred             CcCccCCcCC-CCCeEeECCccchHHhhhhh
Confidence            4889999995 56699999999999999865

>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=97.97  E-value=3.5e-06  Score=36.48  Aligned_cols=30  Identities=30%  Similarity=0.823  Sum_probs=25.8

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      +|..|++.|. | ++-.++|.+||..||+..|
T Consensus         1 kC~~C~~vL~-g-EYm~kdG~PyCe~DY~~~F   30 (31)
T d2dj7a1           1 KCQTCSVILT-G-EYISKDGVPYCESDYHAQF   30 (31)
T ss_dssp             BCSSSCCBCS-S-CCEEETTEEECTTHHHHHT
T ss_pred             CccccCcccc-c-eeecCCCCcccHHHHHHhc
Confidence            5889999994 4 4888999999999998876

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

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

Probab=97.97  E-value=3e-06  Score=37.00  Aligned_cols=31  Identities=29%  Similarity=0.667  Sum_probs=25.4

Q ss_pred             ccccCCccccCCCceEeeCCeeec-hhhHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFC-RPDYEKEV   65 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C-~~~~~~~~   65 (143)
                      +|..|++.|.+|. .+.++|++|| .+||..+|
T Consensus         1 kCekC~ktL~~G~-HaEH~gkPYC~~PCY~aLF   32 (33)
T d2cu8a2           1 KCERCSKTLTPGG-HAEHDGKPFCHKPCYATLF   32 (33)
T ss_dssp             BCSSSCCBCCTTS-CEEETTEEECTTTHHHHHS
T ss_pred             CchhcccccCCCC-ccccCCCcCcCcchHHhhc
Confidence            5889999997665 8999999999 45887665

>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=97.93  E-value=2.8e-06  Score=41.42  Aligned_cols=32  Identities=28%  Similarity=0.734  Sum_probs=28.2

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|..|++.|.+ .....+++.+||..||.+.|+
T Consensus         1 KC~~C~k~Lds-~t~~ehdg~~YCk~CY~k~fG   32 (49)
T d1b8ta4           1 RCAKCGKSLES-TTLADKDGEIYCKGCYAKNFG   32 (49)
T ss_dssp             BCTTTCCBCCS-SSEEEETTEEEEHHHHHHHTC
T ss_pred             ChhhcCCccCC-CcccccCCcccchhhhhhccC
Confidence            58899999964 458889999999999999987

>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=97.91  E-value=3.3e-06  Score=35.82  Aligned_cols=27  Identities=22%  Similarity=0.623  Sum_probs=23.1

Q ss_pred             ccccCccccCC--cceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPD--ELVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~--~~~~~~~~~~~h~~cf   33 (143)
                      |+.|.++|..-  ..++...++.||..||
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            88999999643  4778999999999997

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

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

Probab=97.91  E-value=5.8e-06  Score=35.03  Aligned_cols=30  Identities=33%  Similarity=0.885  Sum_probs=25.6

Q ss_pred             cccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437         33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus        33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~   63 (143)
                      |+|..|++.|. ......++|.+||..||-+
T Consensus         1 frca~cgk~le-stt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLE-STTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEEC-SSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccc-cceeeccCCcEEEeeeeec
Confidence            68999999995 5568999999999999853

>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=97.91  E-value=6.6e-06  Score=35.31  Aligned_cols=31  Identities=29%  Similarity=0.742  Sum_probs=27.4

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .|..|+..| .|..|+..+.+.||..||...+
T Consensus         1 vC~tC~~kL-RGqpFYAvekkayCE~CYi~tL   31 (32)
T d1x61a2           1 VCSTCRAQL-RGQHFYAVERRAYCEGCYVATL   31 (32)
T ss_dssp             BCSSSCCBC-TTSCEEESSSCEEEHHHHHHHH
T ss_pred             CeeEeCcee-cCCcceEeeccccccceeeeec
Confidence            378899999 5899999999999999998765

>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=97.89  E-value=3.1e-06  Score=35.44  Aligned_cols=28  Identities=25%  Similarity=0.592  Sum_probs=23.6

Q ss_pred             CccccccCccccCCcceEEecCcccccCC
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      +.+|.+|++.++..|.++ -.|+.||..|
T Consensus         1 sd~CpRC~~~VyaAEkvi-GaG~~WHk~C   28 (28)
T d1ibia1           1 AEKCSRCGDSVYAAEKVI-GAGKPWHKNC   28 (28)
T ss_dssp             CEECTTTSSEESSSSCEE-SSSSEECSSC
T ss_pred             CCcCcccchhHHHHHHHh-cCCCccccCC
Confidence            358999999999889866 5588999987

>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=97.89  E-value=5e-06  Score=36.52  Aligned_cols=33  Identities=24%  Similarity=0.675  Sum_probs=29.6

Q ss_pred             cccccCCccccCCCceEeeCCeeechhhHHHHHH
Q psy15437         33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus        33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      |.|..|.+++ -|...+.+.|..||..+|.++|+
T Consensus         1 FvCA~CekPF-~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPF-LGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBC-SSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCcc-CCchhhhhcCchHHHHHHHHHhc
Confidence            6899999999 58889999999999999998774

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=97.87  E-value=8.6e-06  Score=39.21  Aligned_cols=33  Identities=24%  Similarity=0.563  Sum_probs=28.4

Q ss_pred             ccccCCccccCCCceEeeCCeeec-hhhHHHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFC-RPDYEKEVEM   67 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C-~~~~~~~~~~   67 (143)
                      +|..|++.|.+ .....+++.+|| .+||..+|++
T Consensus         1 kC~~C~K~L~s-g~~aeHdg~pYC~k~CY~~~FGP   34 (48)
T d1imla2           1 KCEKCGKTLTS-GGHAEHEGKPYCNHPCYSAMFGP   34 (48)
T ss_dssp             BCTTTCCBCCT-TTEEEETTEEEETTTHHHHHSSC
T ss_pred             CchhcCcCcCC-CChhhcCCcccccccchhhccCC
Confidence            58899999965 459999999999 8899999873

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.85  E-value=4.8e-06  Score=34.29  Aligned_cols=27  Identities=26%  Similarity=0.753  Sum_probs=23.9

Q ss_pred             ccccCccccCCcceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      |..|.++|..+..-+....+.||..||
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            788999998777777889999999997

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

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

Probab=97.81  E-value=4.4e-06  Score=36.49  Aligned_cols=29  Identities=31%  Similarity=0.503  Sum_probs=25.5

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.+|..|.+.++..|- ++-.+++||..||
T Consensus         7 g~kcg~c~ktvy~aee-vqc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEE-VQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCC-EEETTEEECTTTC
T ss_pred             CceeccccceEeeeee-eeecCcccccccC
Confidence            5799999999997775 5789999999997

>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=97.74  E-value=8.9e-06  Score=35.78  Aligned_cols=27  Identities=22%  Similarity=0.486  Sum_probs=24.1

Q ss_pred             ccccccCccccCCcceEEecCcccccCCc
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.|.+|+-.|.  ..++.++++.+|++||
T Consensus         9 p~CdkCg~GIV--G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIV--GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCC--SSCEECSSCEECTTTT
T ss_pred             ccccccCCCcE--eEEEEeccccCCCCCC
Confidence            57999999998  4489999999999997

>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=97.72  E-value=1.1e-05  Score=33.37  Aligned_cols=28  Identities=29%  Similarity=0.552  Sum_probs=24.3

Q ss_pred             ccccccCccccCCcceEEecCcccccCCc
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      .+|+.|.+.++-.|- ++-.+++||..||
T Consensus         1 nkcg~c~ktvy~aee-vqc~grsfhk~cf   28 (28)
T d1a7ia1           1 NKCGACGRTVYHAEE-VQCDGRSFHRCCF   28 (28)
T ss_dssp             CBCSSSCCBCSSTTE-EEETTEEEESSSE
T ss_pred             CccccccceEeeeee-eeecCceeccccC
Confidence            379999999997774 6789999999997

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.72  E-value=1.9e-05  Score=33.99  Aligned_cols=28  Identities=39%  Similarity=0.873  Sum_probs=25.1

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDY   61 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~   61 (143)
                      .|+.|..+|-+|+.|...+|.+||+.+.
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            4889999999999999999999998764

>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=97.72  E-value=1.5e-05  Score=34.10  Aligned_cols=29  Identities=34%  Similarity=0.870  Sum_probs=25.9

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~   63 (143)
                      .|+.|.+.| .|.+|..++.+.||..||..
T Consensus         1 vC~~C~K~L-ag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKL-AGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBC-TTSCEEECSSCEEEHHHHHH
T ss_pred             Ccccccchh-cCceeEEecceEEEeeeecc
Confidence            488999999 68999999999999999864

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.71  E-value=8.8e-06  Score=34.37  Aligned_cols=27  Identities=26%  Similarity=0.648  Sum_probs=22.9

Q ss_pred             ccccCccccCC--cceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPD--ELVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~--~~~~~~~~~~~h~~cf   33 (143)
                      |..|.++|.+-  ..++...++.||..||
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            78999999644  4778999999999997

>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=97.67  E-value=1.8e-05  Score=34.40  Aligned_cols=30  Identities=37%  Similarity=0.737  Sum_probs=26.4

Q ss_pred             cccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      |..|..+++ ...|..+++..||.+||...|
T Consensus         2 C~~C~qPIG-tksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           2 CHRCQQPIG-TKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CSSSCCCCC-SSSEEEETTEEEEHHHHHHHT
T ss_pred             cccccCccc-ccccccCCCCceEeecchhhc
Confidence            788999996 566999999999999998865

>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=97.66  E-value=1.2e-05  Score=35.47  Aligned_cols=32  Identities=31%  Similarity=0.769  Sum_probs=27.1

Q ss_pred             ccccCCccccCCCceEee-CCeeechhhHHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIK-QGQLFCRPDYEKEVE   66 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~-~~~~~C~~~~~~~~~   66 (143)
                      .|..|+..| .|.+|... .+++||..||.+.++
T Consensus         1 tCvvC~~~L-DGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCccc-CCCcEEEcCCCCEeehhhhhhhcC
Confidence            488999999 68889776 789999999998763

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.65  E-value=1.7e-05  Score=32.08  Aligned_cols=27  Identities=48%  Similarity=0.898  Sum_probs=24.0

Q ss_pred             ccccCccccCCcceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      |..|++.+..+..-+.+.+++||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            789999998777778899999999997

>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=97.62  E-value=1.5e-05  Score=37.44  Aligned_cols=27  Identities=30%  Similarity=0.549  Sum_probs=24.2

Q ss_pred             ccccccCccccCCcceEEecCcccccCCc
Q psy15437          5 KKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         5 ~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      +.|.+|+-.|.  ..++.++++.+|++||
T Consensus        19 P~CdkCg~GIV--G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          19 PLCDKCGSGIV--GAVVKARDKYRHPECF   45 (45)
T ss_dssp             CBCTTTCCBCC--SCCEESSSCEECTTTC
T ss_pred             ccccccCCCcE--EEEEEeccccCCCCCC
Confidence            57999999998  4489999999999998

>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=97.61  E-value=2.6e-05  Score=33.87  Aligned_cols=30  Identities=33%  Similarity=0.755  Sum_probs=26.2

Q ss_pred             cccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      |..|..+++ ...|..+++..||.+||...|
T Consensus         2 C~~C~qPIG-tkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           2 CSGCEQPLG-SRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             CTTTCCBTT-TSCEEEETTEEEEHHHHHHHT
T ss_pred             cccccCccc-ccccccCCCcEEEEecccccc
Confidence            788999996 566999999999999998876

>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=97.53  E-value=2.8e-05  Score=33.77  Aligned_cols=30  Identities=33%  Similarity=0.652  Sum_probs=25.2

Q ss_pred             cccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      |..|+.+|. .-.|....|.+||..||.+.|
T Consensus         2 Ca~C~~sL~-d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           2 CAHCKNTMA-YIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             CSSSCCBCS-SSCBEESSSCEECHHHHHHHT
T ss_pred             cccccccHh-hcceeeecCcEeHHHHHHHhc
Confidence            788999994 566888899999999998754

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.46  E-value=7.8e-05  Score=32.63  Aligned_cols=32  Identities=22%  Similarity=0.654  Sum_probs=27.7

Q ss_pred             cccccCCccccCCCceEeeC-CeeechhhHHHH
Q psy15437         33 FVCVVCGSRLQRGEQFVIKQ-GQLFCRPDYEKE   64 (143)
Q Consensus        33 f~C~~C~~~l~~~~~~~~~~-~~~~C~~~~~~~   64 (143)
                      |.|..|+.-+.+|+.|+..+ .++||..||.+.
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            67999999999999998775 789999999764

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.40  E-value=5.2e-05  Score=33.19  Aligned_cols=33  Identities=30%  Similarity=0.625  Sum_probs=28.1

Q ss_pred             ccccCCcccc-CCCceEeeCCeeechhhHHHHHH
Q psy15437         34 VCVVCGSRLQ-RGEQFVIKQGQLFCRPDYEKEVE   66 (143)
Q Consensus        34 ~C~~C~~~l~-~~~~~~~~~~~~~C~~~~~~~~~   66 (143)
                      +|+.|+..|. .|...+.+.+.++|..||.++|+
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            5788888885 57778999999999999998873

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.38  E-value=8.6e-05  Score=31.36  Aligned_cols=31  Identities=23%  Similarity=0.521  Sum_probs=26.0

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      .|+.|...+++|+ |+.+....||..|+...|
T Consensus         1 tcs~ckq~igsgs-ffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGTGS-FFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTTSC-EEEETTEEEEHHHHHHHT
T ss_pred             Ccchhhhhccccc-ccCCCCcEEEEEeecccc
Confidence            4888999997655 899999999999998765

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.38  E-value=7.7e-05  Score=32.86  Aligned_cols=31  Identities=26%  Similarity=0.639  Sum_probs=27.3

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      |-...|.+|+....+.|.++...|..||..|
T Consensus         5 L~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           5 LASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            3456899999999999999999999999887

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

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

Probab=97.29  E-value=7.8e-05  Score=32.69  Aligned_cols=29  Identities=24%  Similarity=0.466  Sum_probs=25.3

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCC
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      .|+..|..|...|.  ..++.+....||++|
T Consensus         6 kfge~C~~C~~~it--GpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           6 KFGEFCHGCSLLMT--GPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CSSCBCTTTCCBCC--SCCBCCTTCCBCTTS
T ss_pred             HHHHHhhhhHhhcc--cceeeecccccCCCC
Confidence            58899999999887  568889889999998

>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=97.24  E-value=8.8e-05  Score=31.79  Aligned_cols=30  Identities=27%  Similarity=0.754  Sum_probs=25.2

Q ss_pred             cccCCccccCCCceEeeCCeeechhhHHHHH
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEKEV   65 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~~   65 (143)
                      |-.|.+.| +....+.+++.+||..||.+.+
T Consensus         2 C~~C~K~L-dStTva~h~~eiYCKsCygkky   31 (32)
T d1a7ia2           2 CMVCRKNL-DSTTVAIHDAEVYCKSCYGKKY   31 (32)
T ss_dssp             CSSSCCEE-CSSCCEEETTEEECSHHHHHHC
T ss_pred             chhhhhcc-CcceeeeecceEEehhhccccC
Confidence            67889999 4666899999999999998753

>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=96.80  E-value=0.00026  Score=30.11  Aligned_cols=27  Identities=19%  Similarity=0.513  Sum_probs=23.1

Q ss_pred             CccccccCccccCCcceEEecCcccccCC
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQC   32 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~c   32 (143)
                      ..-|..|.+-|.  ..++.+.++.||+.|
T Consensus         5 ssgC~~C~~~It--GkVLEAG~khYHP~C   31 (32)
T d1wiga1           5 SSGCDSCEKYIT--GRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CCSCSSSCCCCS--SCCBCCSSCCBCTTT
T ss_pred             cchhhhhhhhhh--hhhhhccccccCCCC
Confidence            346999999998  458899999999988

>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=96.42  E-value=0.00065  Score=30.93  Aligned_cols=26  Identities=19%  Similarity=0.588  Sum_probs=18.7

Q ss_pred             ccccCccccCCc-ceEEecCcccccCCc
Q psy15437          7 CLGCSEKLGPDE-LVMKTLDNVFHVQCF   33 (143)
Q Consensus         7 C~~C~~~i~~~~-~~~~~~~~~~h~~cf   33 (143)
                      |++|++....+| ++ ...+.+||+.|-
T Consensus         2 C~rC~~mF~EGEEMY-LQGs~IWHP~C~   28 (41)
T d1wiga2           2 CVRCGQMFAEGEEMY-LQGSSIWHPACR   28 (41)
T ss_dssp             CSSSCCCCCSSCCCE-EETTEEECTTHH
T ss_pred             cchhhccccccceee-ecCCceeCCccc
Confidence            888888886554 54 456678888874

>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=96.38  E-value=0.003  Score=26.75  Aligned_cols=28  Identities=25%  Similarity=0.742  Sum_probs=22.7

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYE   62 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~   62 (143)
                      .|+.|+..| ....+++.++.+||..+..
T Consensus         1 vC~dCg~NL-KqrG~Ffv~~~lyCE~HAr   28 (31)
T d1x64a2           1 VCADCNLNL-KQKGYFFVEGELYCETHAR   28 (31)
T ss_dssp             CCSSSCCCT-TTSCCEEETTEEECHHHHH
T ss_pred             CccccccCh-hhcceEEeccEEeehhhhh
Confidence            388999988 4666888899999988754

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.90  E-value=0.0056  Score=25.75  Aligned_cols=27  Identities=33%  Similarity=0.770  Sum_probs=21.2

Q ss_pred             cccCCccccCCCceEeeCCeeechhhHHH
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~~~~   63 (143)
                      |..|++.|. .+ -....|.+||.+|+.+
T Consensus         2 C~~Cgkelt-ad-ArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKELT-AD-ARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBCC-TT-CEEETTEEECHHHHHT
T ss_pred             ccccccccc-hh-HHHhcCCEEEEecccc
Confidence            788999884 33 5667899999999864

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.78  E-value=0.0054  Score=27.46  Aligned_cols=29  Identities=24%  Similarity=0.615  Sum_probs=25.6

Q ss_pred             cccccCCccccCCCceEeeCCeeechhhH
Q psy15437         33 FVCVVCGSRLQRGEQFVIKQGQLFCRPDY   61 (143)
Q Consensus        33 f~C~~C~~~l~~~~~~~~~~~~~~C~~~~   61 (143)
                      |.|..|..++..|+...+......|..|.
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs   29 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCS   29 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHH
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcC
Confidence            68999999999999999999999997774

>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=95.33  E-value=0.0073  Score=25.68  Aligned_cols=30  Identities=40%  Similarity=0.881  Sum_probs=23.7

Q ss_pred             ccccCCcccc-CCCceEeeCCeeechhhHHH
Q psy15437         34 VCVVCGSRLQ-RGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus        34 ~C~~C~~~l~-~~~~~~~~~~~~~C~~~~~~   63 (143)
                      +|..|+..|+ .|...+.+.+.++|..+|.+
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            5777888876 55667888899999999875

>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=95.24  E-value=0.0024  Score=27.14  Aligned_cols=29  Identities=24%  Similarity=0.697  Sum_probs=22.1

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEK   63 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~   63 (143)
                      .|+.|+..| ....++..++.+||..+...
T Consensus         1 vC~dCg~NL-KqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNL-KQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCH-HHHCCEESSSCEECHHHHHH
T ss_pred             CccccccCh-hhcceEEeccEEehhhhhhh
Confidence            378899888 34557788999999887654

>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=94.01  E-value=0.028  Score=23.54  Aligned_cols=27  Identities=30%  Similarity=0.591  Sum_probs=21.2

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDY   61 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~   61 (143)
                      +|..|-.+| ....|..++++++|..|.
T Consensus         1 RCaKC~hpL-A~E~F~aKd~kI~C~Kc~   27 (31)
T d2cupa2           1 RCAKCLHPL-ANETFVAKDNKILCNKCT   27 (31)
T ss_dssp             CCSSSCCCT-TSSCCEEETTEEECHHHH
T ss_pred             Cchhhcccc-ccCcccccCCeEeecccc
Confidence            366777788 567799999999997774

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.96  E-value=0.032  Score=23.63  Aligned_cols=25  Identities=28%  Similarity=0.747  Sum_probs=20.4

Q ss_pred             cccCCccccCCCceEeeCCeeechhh
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPD   60 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~   60 (143)
                      |..|+.+| .|..|......++|..|
T Consensus         2 cgkcsvsl-vg~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSL-VGKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBC-SSSCEEEETTEEEETTT
T ss_pred             CccceEEE-EeeeeeeccCcEEehhc
Confidence            67788888 58888888889999776

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

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

Probab=93.88  E-value=0.064  Score=22.62  Aligned_cols=30  Identities=33%  Similarity=0.662  Sum_probs=23.3

Q ss_pred             ccccCCccccCCCceEeeCCeeechhhHHHH
Q psy15437         34 VCVVCGSRLQRGEQFVIKQGQLFCRPDYEKE   64 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~~~~~~~~~C~~~~~~~   64 (143)
                      .|..|...| ....|...-|+.+|.+|+.+.
T Consensus         1 rC~~C~~~L-AD~GFvKnagR~LCrpch~re   30 (32)
T d2d8xa1           1 RCDLCQEVL-ADIGFVKNAGRHLCRPCHNRE   30 (32)
T ss_dssp             BCSSSCCBC-SSSCCEEETTEEECHHHHHHH
T ss_pred             CchHHHhHH-HHhhhhhcccccccchhhhhc
Confidence            477888888 445577778999999998763

>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=93.80  E-value=0.0083  Score=25.64  Aligned_cols=28  Identities=21%  Similarity=0.469  Sum_probs=20.6

Q ss_pred             ccccCCccccCCCce-EeeCCeeechhhH
Q psy15437         34 VCVVCGSRLQRGEQF-VIKQGQLFCRPDY   61 (143)
Q Consensus        34 ~C~~C~~~l~~~~~~-~~~~~~~~C~~~~   61 (143)
                      .|..|...|.+|..- ...+|.+||..++
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hl   29 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHL   29 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeecc
Confidence            478888899877733 3447899998775

>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=89.04  E-value=0.18  Score=20.55  Aligned_cols=26  Identities=23%  Similarity=0.579  Sum_probs=19.5

Q ss_pred             cccCCccccCCCceEeeCCeeechhhH
Q psy15437         35 CVVCGSRLQRGEQFVIKQGQLFCRPDY   61 (143)
Q Consensus        35 C~~C~~~l~~~~~~~~~~~~~~C~~~~   61 (143)
                      |..|..+| .|..|......++|..|-
T Consensus         2 c~kcsvsl-vgrgflterddilc~dcg   27 (30)
T d1x4la2           2 CKKCSLSL-VGRGFLTERDDILCPDCG   27 (30)
T ss_dssp             CSSSCCBC-TTSCCEECSSSEECHHHH
T ss_pred             cceeeEEE-EeeeccccccceeccccC
Confidence            56677788 577787777788887774

>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=86.91  E-value=0.25  Score=21.37  Aligned_cols=28  Identities=14%  Similarity=0.388  Sum_probs=20.2

Q ss_pred             CccccccCccccCCcceEEecCcccccCCc
Q psy15437          4 VKKCLGCSEKLGPDELVMKTLDNVFHVQCF   33 (143)
Q Consensus         4 ~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf   33 (143)
                      --.|.+|...|- +. -+..++-.||+..|
T Consensus         8 k~vC~KCh~iId-d~-pL~Fr~d~YHp~HF   35 (35)
T d2cora2           8 KYICQKCHAIID-EQ-PLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCBCTTTCCBCC-SC-CCCCSSSCCCTTTS
T ss_pred             hHHHHHHHhhhh-cC-cceecCCCCCCCCC
Confidence            347999988885 33 35688888888765

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=84.30  E-value=0.37  Score=22.63  Aligned_cols=40  Identities=15%  Similarity=0.132  Sum_probs=32.0

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCCHHHHHHHHHHhCCCcccceecc
Q psy15437         96 RTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQSRP  140 (143)
Q Consensus        96 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~vkvWF  140 (143)
                      +..++.+|+..+........     ...++|..+|++...|=-||
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-----s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-----PRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-----CHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHhhC
Confidence            35689999999999998764     36789999999987765555

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=81.45  E-value=0.83  Score=24.18  Aligned_cols=32  Identities=25%  Similarity=0.603  Sum_probs=17.2

Q ss_pred             CCCccccccCccccCCcceEEecCcccccCCcccccCCccc
Q psy15437          2 LYVKKCLGCSEKLGPDELVMKTLDNVFHVQCFVCVVCGSRL   42 (143)
Q Consensus         2 ~~~~~C~~C~~~i~~~~~~~~~~~~~~h~~cf~C~~C~~~l   42 (143)
                      +.++.|..|+..|.     +.+.+..|    ..|..|+-++
T Consensus        14 ~~~q~CqiCGd~VG-----~~~~Ge~F----VAC~eC~FPv   45 (93)
T d1weoa_          14 LDGQFCEICGDQIG-----LTVEGDLF----VACNECGFPA   45 (93)
T ss_dssp             CSSCBCSSSCCBCC-----BCSSSSBC----CSCSSSCCCC
T ss_pred             cccchhhhcccccc-----cCCCCCEE----EEecccCCcc
Confidence            34567777776664     23444443    3455555544