Psyllid ID: psy3656

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-----
Protein Sequence
STATVGTFGDRLVVCLLLQTEPAGSPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccEEEEcccccccccccccccccccccccEEEcccccccHHHHHHHcccccccccccccccEEEEcccccccccccccccccccccccEEEc
Secondary Structure Prediction (SSPRO)
ccccccEcccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccHHccccccHHHHHEcccccccccEEEHHcccccccccEEEcccccccHHHHHHHHcHHHccccccccHHHHHHcccccccccEEEEHcccccccccEEEc
Coil and Loop (DISEMBL)
statvgtfGDRLVVCLLLqtepagspegqpvpqqlehsvtdsssvsyskpnqpvhqkgkqLDCMLDSLTAEMsrqgvtttqkgccsscdkpiVGQVITAlgktwhpehficthcnqelgtrnfferdsrpycepdyhnlfsprcsycngpilDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
Flexible Loop (DISEMBL)
statvgtfgdrLVVCLLLQTEPAGSPEGQPVPQQLEHSVTDSSSVSyskpnqpvhqkgkQLDCMLDSLTAEMSRQGVtttqkgccsscdKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
Low Complexity Region (SEG)
STATVGTFGDRLVVCLLLQTEPAGSPEGQPVPQQLEHsvtdsssvsysKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
Disordered region (IsUnstruct)
****VGTFGDRLVVCLLLQ*********************************************************VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMV***
Disordered Region (DISOPRED)
***********************************************************************************CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG***VKFI
Disordered Region (DISEMBL)
STATVGTFGDRLVVCLLLQTEPA***********************************KQLDCMLDSLTAEMS**********CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
Disordered Region (DISPRO)
****VGTFGDRLVVCLLLQTEPAGSPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
STATVGTFGDRLVVCLLLQTEPAGSPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKFI
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	185	2.2.26 [Sep-21-2011]
Q8VI36	591	Paxillin OS=Mus musculus	yes	N/A	0.805	0.252	0.616	7e-53
P49024	559	Paxillin OS=Gallus gallus	yes	N/A	0.708	0.234	0.671	2e-52
Q66H76	586	Paxillin OS=Rattus norveg	yes	N/A	0.708	0.223	0.664	4e-52
P49023	591	Paxillin OS=Homo sapiens	no	N/A	0.643	0.201	0.714	2e-51
Q5R7I1	591	Paxillin OS=Pongo abelii	yes	N/A	0.643	0.201	0.714	2e-51
Q9N261	386	Leupaxin OS=Oryctolagus c	no	N/A	0.583	0.279	0.610	9e-41
Q99N69	386	Leupaxin OS=Mus musculus	no	N/A	0.686	0.329	0.573	2e-40
O60711	386	Leupaxin OS=Homo sapiens	no	N/A	0.583	0.279	0.593	7e-40
Q2TCH4	506	Transforming growth facto	N/A	N/A	0.735	0.268	0.536	2e-37
Q3MHZ4	456	Transforming growth facto	no	N/A	0.864	0.350	0.465	6e-37

>sp|Q8VI36|PAXI_MOUSE Paxillin OS=Mus musculus GN=Pxn PE=1 SV=1

 Score =  206 bits (524), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 95/154 (61%), Positives = 114/154 (74%), Gaps = 5/154 (3%)

Query: 25  SPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGC 84
           SPEGQ     +    T SSS     P   + + G QLD ML SL +++++ GV T  KG 
Sbjct: 303 SPEGQDEGGFMAQGKTGSSS-----PPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGV 357

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
           C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC
Sbjct: 358 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRC 417

Query: 145 SYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
            YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct: 418 YYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 451

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).
Mus musculus (taxid: 10090)

>sp|P49024|PAXI_CHICK Paxillin OS=Gallus gallus GN=PXN PE=1 SV=1

 Score =  204 bits (520), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 88/131 (67%), Positives = 104/131 (79%)

Query: 48  SKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPE 107
           S P     + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPE
Sbjct: 289 SSPPSTTPKPGSQLDTMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPE 348

Query: 108 HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEH 167
           HF+CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EH
Sbjct: 349 HFVCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEH 408

Query: 168 FFCAQCGKQFG 178
           FFCAQCG  FG
Sbjct: 409 FFCAQCGVFFG 419

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion). Binds in vitro to vinculin as well as to the SH3 domain of c-SRC and, when tyrosine phosphorylated, to the SH2 domain of v-CRK.

Gallus gallus (taxid: 9031)

>sp|Q66H76|PAXI_RAT Paxillin OS=Rattus norvegicus GN=Pxn PE=1 SV=1

 Score =  203 bits (517), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 87/131 (66%), Positives = 105/131 (80%)

Query: 48  SKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPE 107
           S P   + + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPE
Sbjct: 316 SSPPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPE 375

Query: 108 HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEH 167
           HF+CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC YCNGPILDK VTAL++TWH EH
Sbjct: 376 HFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRCYYCNGPILDKVVTALDRTWHPEH 435

Query: 168 FFCAQCGKQFG 178
           FFCAQCG  FG
Sbjct: 436 FFCAQCGAFFG 446

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).

Rattus norvegicus (taxid: 10116)

>sp|P49023|PAXI_HUMAN Paxillin OS=Homo sapiens GN=PXN PE=1 SV=3

 Score =  201 bits (512), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 85/119 (71%), Positives = 100/119 (84%)

Query: 60  QLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 119
           QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G
Sbjct: 333 QLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIG 392

Query: 120 TRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           +RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct: 393 SRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 451

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).

Homo sapiens (taxid: 9606)

>sp|Q5R7I1|PAXI_PONAB Paxillin OS=Pongo abelii GN=PXN PE=2 SV=1

 Score =  201 bits (511), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 85/119 (71%), Positives = 100/119 (84%)

Query: 60  QLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 119
           QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G
Sbjct: 333 QLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIG 392

Query: 120 TRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           +RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct: 393 SRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 451

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).

Pongo abelii (taxid: 9601)

>sp|Q9N261|LPXN_RABIT Leupaxin OS=Oryctolagus cuniculus GN=LPXN PE=2 SV=1

 Score =  166 bits (420), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 72/118 (61%), Positives = 88/118 (74%)

Query: 61  LDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT 120
           LD ML  L  E+   G+ T  KG C+SC KPIVG+VI ALG++WHPEHFICTHC +E+G+
Sbjct: 128 LDSMLGGLEQELQNLGIPTVPKGHCASCQKPIVGKVIHALGQSWHPEHFICTHCKEEIGS 187

Query: 121 RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
             FFER    YC  DYH+LFSPRC+YC  PILDK +TA+ +TWH EHFFC+ CG+ FG
Sbjct: 188 SPFFERSGLAYCPKDYHHLFSPRCAYCAAPILDKVLTAMNQTWHPEHFFCSHCGEVFG 245

Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling.

Oryctolagus cuniculus (taxid: 9986)

>sp|Q99N69|LPXN_MOUSE Leupaxin OS=Mus musculus GN=Lpxn PE=1 SV=2

 Score =  165 bits (417), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/129 (57%), Positives = 90/129 (69%), Gaps = 2/129 (1%)

Query: 50  PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 109
           P+Q  H+    LD ML  L  E+   G+ T  KG C+SC KPI G+VI ALG++WHPEHF
Sbjct: 119 PDQQDHKAS--LDSMLGDLEQELQDLGIATVPKGYCASCQKPIAGKVIHALGQSWHPEHF 176

Query: 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFF 169
           +CTHC +ELG+  FFER    YC  DYH LFSPRC+YC  PI DK +TA+ KTWH EHFF
Sbjct: 177 VCTHCKEELGSSPFFERSGLAYCSKDYHRLFSPRCAYCAAPITDKVLTAMNKTWHPEHFF 236

Query: 170 CAQCGKQFG 178
           C+ CG+ FG
Sbjct: 237 CSHCGEVFG 245

Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling.

Mus musculus (taxid: 10090)

>sp|O60711|LPXN_HUMAN Leupaxin OS=Homo sapiens GN=LPXN PE=1 SV=1

 Score =  163 bits (412), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 70/118 (59%), Positives = 86/118 (72%)

Query: 61  LDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT 120
           LD ML  L  E+   G+ T  KG C+SC KPI G+VI ALG++WHPEHF+CTHC +E+G+
Sbjct: 128 LDSMLGGLEQELQDLGIATVPKGHCASCQKPIAGKVIHALGQSWHPEHFVCTHCKEEIGS 187

Query: 121 RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
             FFER    YC  DYH LFSPRC+YC  PILDK +TA+ +TWH EHFFC+ CG+ FG
Sbjct: 188 SPFFERSGLAYCPNDYHQLFSPRCAYCAAPILDKVLTAMNQTWHPEHFFCSHCGEVFG 245

Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling.

Homo sapiens (taxid: 9606)

>sp|Q2TCH4|TGFI1_XENLA Transforming growth factor beta-1-induced transcript 1 protein OS=Xenopus laevis GN=tgfb1i1 PE=1 SV=2

 Score =  155 bits (392), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 73/136 (53%), Positives = 88/136 (64%)

Query: 44  SVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKT 103
           SVS SK  +        LD ML  L + + +QG+ T  KG C SC +PI GQV+TALG T
Sbjct: 232 SVSGSKVPEATSVPRSDLDSMLVKLQSGLKQQGIETYSKGLCESCQRPIAGQVVTALGHT 291

Query: 104 WHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTW 163
           WHPEHF+C HC+  +GT NFFE+D RPYCE DY  L++PRC+ C  PI+   VTAL  TW
Sbjct: 292 WHPEHFVCAHCHTLIGTSNFFEKDGRPYCEKDYFMLYAPRCALCELPIVQNMVTALGCTW 351

Query: 164 HTEHFFCAQCGKQFGE 179
           H EHF C  C K  GE
Sbjct: 352 HPEHFCCKVCKKPIGE 367

Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. May regulate both Wnt and steroid signaling pathways and play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA-binding activity.

Xenopus laevis (taxid: 8355)

>sp|Q3MHZ4|TGFI1_BOVIN Transforming growth factor beta-1-induced transcript 1 protein OS=Bos taurus GN=TGFB1I1 PE=2 SV=2

 Score =  153 bits (387), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 81/174 (46%), Positives = 99/174 (56%), Gaps = 14/174 (8%)

Query: 10  DRLVVCL----LLQTEPAGSPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCML 65
           DRL+  L    +    PA  P   PVP          SS+S   P+ P       LD ML
Sbjct: 154 DRLMASLSDFRVQNHLPASGPTPPPVP----------SSMSEDTPSPPGPTSKGSLDTML 203

Query: 66  DSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFE 125
             L +++SR+GV T  KG C SC+KPI GQV+TALG+ WHPEHF+C  C+  LG  +FFE
Sbjct: 204 GLLQSDLSRRGVPTQAKGLCGSCNKPIAGQVVTALGRAWHPEHFVCGGCSTALGGSSFFE 263

Query: 126 RDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           +D  P+C   Y   FSPRC  CN PI  K VTAL   WH EHF C  CG+ FG+
Sbjct: 264 KDGAPFCPECYFERFSPRCGLCNQPIRHKMVTALGTHWHPEHFCCVSCGEPFGD 317

Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. Links various intracellular signaling modules to plasma membrane receptors and regulates the Wnt and TGFB signaling pathways. May also regulate SLC6A3 and SLC6A4 targeting to the plasma membrane hence regulating their activity. In the nucleus, functions as a nuclear receptor coactivator regulating glucocorticoid, androgen, mineralocorticoid and progesterone receptor transcriptional activity. May play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA-binding activity.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	185
328709648	424	PREDICTED: paxillin-like isoform 2 [Acyr	0.718	0.313	0.804	7e-64
270016014	488	hypothetical protein TcasGA2_TC010609 [T	0.945	0.358	0.664	1e-63
189242184	448	PREDICTED: similar to paxillin [Triboliu	0.945	0.390	0.664	1e-63
383863879	607	PREDICTED: paxillin-like [Megachile rotu	0.702	0.214	0.854	3e-63
328709646	474	PREDICTED: paxillin-like isoform 3 [Acyr	0.745	0.291	0.804	5e-63
380025704	572	PREDICTED: paxillin-like isoform 1 [Apis	0.702	0.227	0.854	5e-63
380025706	607	PREDICTED: paxillin-like isoform 2 [Apis	0.702	0.214	0.854	6e-63
350421197	607	PREDICTED: paxillin-like [Bombus impatie	0.702	0.214	0.854	7e-63
340714019	605	PREDICTED: paxillin-like [Bombus terrest	0.702	0.214	0.854	7e-63
312372729	286	hypothetical protein AND_19782 [Anophele	0.681	0.440	0.873	2e-62

>gi|328709648|ref|XP_003244023.1| PREDICTED: paxillin-like isoform 2 [Acyrthosiphon pisum]

 Score =  248 bits (633), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 119/138 (86%)

Query: 42  SSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALG 101
           SS V  S   +       +LDCML SLTAEM+RQGV TTQKGCC++CDK IVGQVITALG
Sbjct: 206 SSPVRASYATESADSAAPRLDCMLGSLTAEMNRQGVNTTQKGCCTACDKAIVGQVITALG 265

Query: 102 KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEK 161
           KTWHPEHF C HC+QELGTRNFFER+ RPYCEPDYHNLFSPRC+YCNGPILDKCVTALEK
Sbjct: 266 KTWHPEHFTCNHCSQELGTRNFFEREGRPYCEPDYHNLFSPRCAYCNGPILDKCVTALEK 325

Query: 162 TWHTEHFFCAQCGKQFGE 179
           TWHTEHFFCAQCGKQFGE
Sbjct: 326 TWHTEHFFCAQCGKQFGE 343

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270016014|gb|EFA12462.1| hypothetical protein TcasGA2_TC010609 [Tribolium castaneum]

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 119/179 (66%), Positives = 132/179 (73%), Gaps = 4/179 (2%)

Query: 1   STATVGTFGDRLVVCLLLQTEPAGSPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQ 60
           STA   +   R +  L+         +GQP  Q    +VTDS     +K  Q      + 
Sbjct: 231 STAPAASTATRELDDLMASLSGIKVNQGQPQHQ----TVTDSQYARPTKATQSHSAPKQN 286

Query: 61  LDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT 120
           LD ML +L A+MSRQGV T+QKGCCS+CDKPIVGQVITALGKTWHPEHF C HC QELGT
Sbjct: 287 LDSMLGNLQADMSRQGVNTSQKGCCSACDKPIVGQVITALGKTWHPEHFTCAHCTQELGT 346

Query: 121 RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           RNFFERD +PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWH EHFFCAQCGKQFGE
Sbjct: 347 RNFFERDGKPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHMEHFFCAQCGKQFGE 405

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189242184|ref|XP_969819.2| PREDICTED: similar to paxillin [Tribolium castaneum]

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 119/179 (66%), Positives = 132/179 (73%), Gaps = 4/179 (2%)

Query: 1   STATVGTFGDRLVVCLLLQTEPAGSPEGQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQ 60
           STA   +   R +  L+         +GQP  Q    +VTDS     +K  Q      + 
Sbjct: 191 STAPAASTATRELDDLMASLSGIKVNQGQPQHQ----TVTDSQYARPTKATQSHSAPKQN 246

Query: 61  LDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT 120
           LD ML +L A+MSRQGV T+QKGCCS+CDKPIVGQVITALGKTWHPEHF C HC QELGT
Sbjct: 247 LDSMLGNLQADMSRQGVNTSQKGCCSACDKPIVGQVITALGKTWHPEHFTCAHCTQELGT 306

Query: 121 RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           RNFFERD +PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWH EHFFCAQCGKQFGE
Sbjct: 307 RNFFERDGKPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHMEHFFCAQCGKQFGE 365

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383863879|ref|XP_003707407.1| PREDICTED: paxillin-like [Megachile rotundata]

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 118/131 (90%), Gaps = 1/131 (0%)

Query: 50  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 108
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 302 PTQPAAQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 361

Query: 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF 168
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWHTEHF
Sbjct: 362 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHTEHF 421

Query: 169 FCAQCGKQFGE 179
           FCAQCGKQFGE
Sbjct: 422 FCAQCGKQFGE 432

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328709646|ref|XP_001945795.2| PREDICTED: paxillin-like isoform 3 [Acyrthosiphon pisum]

 Score =  245 bits (626), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 119/138 (86%)

Query: 42  SSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALG 101
           SS V  S   +       +LDCML SLTAEM+RQGV TTQKGCC++CDK IVGQVITALG
Sbjct: 198 SSPVRASYATESADSAAPRLDCMLGSLTAEMNRQGVNTTQKGCCTACDKAIVGQVITALG 257

Query: 102 KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEK 161
           KTWHPEHF C HC+QELGTRNFFER+ RPYCEPDYHNLFSPRC+YCNGPILDKCVTALEK
Sbjct: 258 KTWHPEHFTCNHCSQELGTRNFFEREGRPYCEPDYHNLFSPRCAYCNGPILDKCVTALEK 317

Query: 162 TWHTEHFFCAQCGKQFGE 179
           TWHTEHFFCAQCGKQFGE
Sbjct: 318 TWHTEHFFCAQCGKQFGE 335

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025704|ref|XP_003696608.1| PREDICTED: paxillin-like isoform 1 [Apis florea]

 Score =  245 bits (626), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 118/131 (90%), Gaps = 1/131 (0%)

Query: 50  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 108
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 303 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 362

Query: 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF 168
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWHTEHF
Sbjct: 363 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHTEHF 422

Query: 169 FCAQCGKQFGE 179
           FCAQCGKQFGE
Sbjct: 423 FCAQCGKQFGE 433

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025706|ref|XP_003696609.1| PREDICTED: paxillin-like isoform 2 [Apis florea]

 Score =  245 bits (625), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 118/131 (90%), Gaps = 1/131 (0%)

Query: 50  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 108
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 303 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 362

Query: 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF 168
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWHTEHF
Sbjct: 363 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHTEHF 422

Query: 169 FCAQCGKQFGE 179
           FCAQCGKQFGE
Sbjct: 423 FCAQCGKQFGE 433

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350421197|ref|XP_003492766.1| PREDICTED: paxillin-like [Bombus impatiens]

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 118/131 (90%), Gaps = 1/131 (0%)

Query: 50  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 108
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 303 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 362

Query: 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF 168
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWHTEHF
Sbjct: 363 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHTEHF 422

Query: 169 FCAQCGKQFGE 179
           FCAQCGKQFGE
Sbjct: 423 FCAQCGKQFGE 433

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714019|ref|XP_003395530.1| PREDICTED: paxillin-like [Bombus terrestris]

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 118/131 (90%), Gaps = 1/131 (0%)

Query: 50  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 108
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 301 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 360

Query: 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF 168
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWHTEHF
Sbjct: 361 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHTEHF 420

Query: 169 FCAQCGKQFGE 179
           FCAQCGKQFGE
Sbjct: 421 FCAQCGKQFGE 431

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312372729|gb|EFR20625.1| hypothetical protein AND_19782 [Anopheles darlingi]

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 110/126 (87%), Positives = 115/126 (91%)

Query: 54  VHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTH 113
           V   G QLD ML +LTA+MSRQGV TTQKGCCS+CDKPIVGQVITALGKTWHPEHF C H
Sbjct: 80  VTSSGDQLDSMLGNLTADMSRQGVNTTQKGCCSACDKPIVGQVITALGKTWHPEHFTCNH 139

Query: 114 CNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQC 173
           CNQELGTRNFFERD  PYCEPDYHNLFSPRC+YCNGPILDKCVTALEKTWHTEHFFCAQC
Sbjct: 140 CNQELGTRNFFERDGNPYCEPDYHNLFSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQC 199

Query: 174 GKQFGE 179
           G+QFGE
Sbjct: 200 GQQFGE 205

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	185
FB|FBgn0041789	581	Pax "Paxillin" [Drosophila mel	0.648	0.206	0.841	3.2e-58
UNIPROTKB|F1MFD1	586	PXN "Uncharacterized protein"	0.843	0.266	0.579	2.4e-51
UNIPROTKB|E7EMK8	403	PXN "Paxillin" [Homo sapiens (	0.843	0.387	0.587	3.1e-51
UNIPROTKB|F1PUT6	590	PXN "Uncharacterized protein"	0.805	0.252	0.603	4e-51
UNIPROTKB|F1NB68	559	PXN "Paxillin" [Gallus gallus	0.697	0.230	0.674	5.1e-51
UNIPROTKB|P49024	559	PXN "Paxillin" [Gallus gallus	0.697	0.230	0.674	5.1e-51
MGI|MGI:108295	591	Pxn "paxillin" [Mus musculus (	0.805	0.252	0.597	5.1e-51
UNIPROTKB|F1M1Z5	591	Pxn "Paxillin" [Rattus norvegi	0.805	0.252	0.597	5.1e-51
UNIPROTKB|F5GZ78	589	PXN "Paxillin" [Homo sapiens (	0.691	0.217	0.682	5.1e-51
UNIPROTKB|P49023	591	PXN "Paxillin" [Homo sapiens (	0.691	0.216	0.682	5.1e-51

FB|FBgn0041789 Pax "Paxillin" [Drosophila melanogaster (taxid:7227)]

 Score = 598 (215.6 bits), Expect = 3.2e-58, P = 3.2e-58
 Identities = 101/120 (84%), Positives = 109/120 (90%)

Query:    60 QLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 119
             QLD ML +L A MSRQGV T QKGCC++C+KPIVGQVITALGKTWHPEHF C HC+QELG
Sbjct:   323 QLDSMLGNLQANMSRQGVNTVQKGCCNACEKPIVGQVITALGKTWHPEHFTCNHCSQELG 382

Query:   120 TRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
             TRNFFERD  PYCEPDYHNLFSPRC+YCNG ILDKCVTAL+KTWHTEHFFCAQCG+QFGE
Sbjct:   383 TRNFFERDGFPYCEPDYHNLFSPRCAYCNGAILDKCVTALDKTWHTEHFFCAQCGQQFGE 442

GO:0007016 "cytoskeletal anchoring at plasma membrane" evidence=ISS

GO:0005925 "focal adhesion" evidence=ISS;NAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0035218 "leg disc development" evidence=IMP

GO:0032319 "regulation of Rho GTPase activity" evidence=IGI

GO:0035220 "wing disc development" evidence=IMP

GO:0010506 "regulation of autophagy" evidence=IGI

UNIPROTKB|F1MFD1 PXN "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 91/157 (57%), Positives = 109/157 (69%)

Query:    22 PAGSPEGQPVPQQLEHXXXXXXXXXXXKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQ 81
             P    +  P  Q +              P  P  + G QLD ML SL +++++ GV T  
Sbjct:   291 PLNGRQSGPEGQDMGGFMAQGKTGSSSPPGGPP-KPGSQLDSMLGSLQSDLNKLGVATVA 349

Query:    82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
             KG C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYHNLFS
Sbjct:   350 KGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHNLFS 409

Query:   142 PRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
             PRC YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct:   410 PRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 446

GO:0060396 "growth hormone receptor signaling pathway" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0030027 "lamellipodium" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA

GO:0008013 "beta-catenin binding" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

UNIPROTKB|E7EMK8 PXN "Paxillin" [Homo sapiens (taxid:9606)]

 Score = 532 (192.3 bits), Expect = 3.1e-51, P = 3.1e-51
 Identities = 94/160 (58%), Positives = 112/160 (70%)

Query:    19 QTEPAGSPEGQPVPQQLEHXXXXXXXXXXXKPNQPVHQKGKQLDCMLDSLTAEMSRQGVT 78
             +T    SP+ QP P                 P  P  + G QLD ML SL +++++ GV 
Sbjct:   108 RTPSLRSPD-QPPP--CPQFMAQGKTGSSSPPGGPP-KPGSQLDSMLGSLQSDLNKLGVA 163

Query:    79 TTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 138
             T  KG C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYHN
Sbjct:   164 TVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHN 223

Query:   139 LFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
             LFSPRC YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct:   224 LFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 263

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1PUT6 PXN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 531 (192.0 bits), Expect = 4.0e-51, P = 4.0e-51
 Identities = 93/154 (60%), Positives = 109/154 (70%)

Query:    25 SPEGQPVPQQLEHXXXXXXXXXXXKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGC 84
             SPEGQ      E             P     + G QLD ML SL +++++ GV T  KG 
Sbjct:   302 SPEGQD-----EGGFMAQGKTGSSSPPGGPPKPGSQLDSMLGSLQSDLNKLGVATVAKGV 356

Query:    85 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
             C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC
Sbjct:   357 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRC 416

Query:   145 SYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
              YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct:   417 YYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 450

GO:0060396 "growth hormone receptor signaling pathway" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0030027 "lamellipodium" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA

GO:0008013 "beta-catenin binding" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

UNIPROTKB|F1NB68 PXN "Paxillin" [Gallus gallus (taxid:9031)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 87/129 (67%), Positives = 103/129 (79%)

Query:    50 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 109
             P     + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   291 PPSTTPKPGSQLDTMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 350

Query:   110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFF 169
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EHFF
Sbjct:   351 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFF 410

Query:   170 CAQCGKQFG 178
             CAQCG  FG
Sbjct:   411 CAQCGVFFG 419

GO:0005856 "cytoskeleton" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0008013 "beta-catenin binding" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0030027 "lamellipodium" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0060396 "growth hormone receptor signaling pathway" evidence=IEA

UNIPROTKB|P49024 PXN "Paxillin" [Gallus gallus (taxid:9031)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 87/129 (67%), Positives = 103/129 (79%)

Query:    50 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 109
             P     + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   291 PPSTTPKPGSQLDTMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 350

Query:   110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFF 169
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EHFF
Sbjct:   351 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFF 410

Query:   170 CAQCGKQFG 178
             CAQCG  FG
Sbjct:   411 CAQCGVFFG 419

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:108295 Pxn "paxillin" [Mus musculus (taxid:10090)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 92/154 (59%), Positives = 110/154 (71%)

Query:    25 SPEGQPVPQQLEHXXXXXXXXXXXKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGC 84
             SPEGQ      E             P   + + G QLD ML SL +++++ GV T  KG 
Sbjct:   303 SPEGQD-----EGGFMAQGKTGSSSPPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGV 357

Query:    85 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
             C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC
Sbjct:   358 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRC 417

Query:   145 SYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
              YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct:   418 YYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 451

GO:0000187 "activation of MAPK activity" evidence=IDA

GO:0005178 "integrin binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISO

GO:0005925 "focal adhesion" evidence=ISO;IDA;TAS

GO:0006928 "cellular component movement" evidence=IMP

GO:0007010 "cytoskeleton organization" evidence=IMP

GO:0007155 "cell adhesion" evidence=IEA

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IMP;TAS

GO:0008013 "beta-catenin binding" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017166 "vinculin binding" evidence=ISO

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IDA

GO:0019901 "protein kinase binding" evidence=ISO

GO:0030027 "lamellipodium" evidence=ISO;IDA

GO:0030032 "lamellipodium assembly" evidence=IDA

GO:0030054 "cell junction" evidence=IEA

GO:0030159 "receptor signaling complex scaffold activity" evidence=TAS

GO:0031252 "cell leading edge" evidence=IDA

GO:0032403 "protein complex binding" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IDA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IDA

GO:0051435 "BH4 domain binding" evidence=IPI

GO:0060396 "growth hormone receptor signaling pathway" evidence=ISO

UNIPROTKB|F1M1Z5 Pxn "Paxillin" [Rattus norvegicus (taxid:10116)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 92/154 (59%), Positives = 110/154 (71%)

Query:    25 SPEGQPVPQQLEHXXXXXXXXXXXKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGC 84
             SPEGQ      E             P   + + G QLD ML SL +++++ GV T  KG 
Sbjct:   303 SPEGQD-----EGGFMAQGKTGSSSPPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGV 357

Query:    85 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
             C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC
Sbjct:   358 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRC 417

Query:   145 SYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
              YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct:   418 YYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 451

GO:0005856 "cytoskeleton" evidence=IEA

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F5GZ78 PXN "Paxillin" [Homo sapiens (taxid:9606)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 88/129 (68%), Positives = 104/129 (80%)

Query:    50 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 109
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   322 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 380

Query:   110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFF 169
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EHFF
Sbjct:   381 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFF 440

Query:   170 CAQCGKQFG 178
             CAQCG  FG
Sbjct:   441 CAQCGAFFG 449

GO:0005856 "cytoskeleton" evidence=IEA

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|P49023 PXN "Paxillin" [Homo sapiens (taxid:9606)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 88/129 (68%), Positives = 104/129 (80%)

Query:    50 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 109
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   324 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 382

Query:   110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFF 169
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILDK VTAL++TWH EHFF
Sbjct:   383 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFF 442

Query:   170 CAQCGKQFG 178
             CAQCG  FG
Sbjct:   443 CAQCGAFFG 451

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0005178 "integrin binding" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0005938 "cell cortex" evidence=IEA

GO:0017166 "vinculin binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA;TAS

GO:0008013 "beta-catenin binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005875 "microtubule associated complex" evidence=TAS

GO:0007155 "cell adhesion" evidence=NAS

GO:0007172 "signal complex assembly" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0006936 "muscle contraction" evidence=TAS

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0034329 "cell junction assembly" evidence=TAS

GO:0005925 "focal adhesion" evidence=IDA

GO:0030027 "lamellipodium" evidence=IDA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEP

GO:0060396 "growth hormone receptor signaling pathway" evidence=IDA

---

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)
P49024	PAXI_CHICK	No assigned EC number	0.6717	0.7081	0.2343	yes	N/A
Q66H76	PAXI_RAT	No assigned EC number	0.6641	0.7081	0.2235	yes	N/A
Q8VI36	PAXI_MOUSE	No assigned EC number	0.6168	0.8054	0.2521	yes	N/A
Q5R7I1	PAXI_PONAB	No assigned EC number	0.7142	0.6432	0.2013	yes	N/A
Q8MML5	PAXB_DICDI	No assigned EC number	0.5204	0.5297	0.1722	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	185
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	2e-31
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	2e-26
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	9e-26
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	1e-19
pfam00412	58	pfam00412, LIM, LIM domain	7e-19
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	5e-18
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-16
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	4e-16
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	1e-15
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	3e-15
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	1e-14
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	4e-14
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	5e-13
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	8e-13
cd09339	52	cd09339, LIM4_Paxillin_like, The fourth LIM domain	8e-13
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	8e-12
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	8e-12
cd09411	52	cd09411, LIM4_Paxillin, The fourth LIM domain of P	1e-11
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	1e-11
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	8e-11
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	8e-11
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	5e-10
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	8e-10
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	9e-10
cd09455	54	cd09455, LIM1_Enigma_like_1, The first LIM domain	1e-09
cd09453	52	cd09453, LIM1_ENH, The first LIM domain of the Eni	2e-09
cd09452	52	cd09452, LIM1_Enigma, The first LIM domain of Enig	2e-09
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	2e-09
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	3e-09
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	6e-09
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	6e-09
cd09335	54	cd09335, LIM5_PINCH, The fifth LIM domain of prote	1e-08
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	2e-08
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	2e-08
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	3e-08
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	7e-08
cd09454	52	cd09454, LIM1_ZASP_Cypher, The first LIM domain of	8e-08
cd09430	52	cd09430, LIM5_LIMPETin, The fifth LIM domain of pr	9e-08
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	1e-07
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	2e-07
pfam00412	58	pfam00412, LIM, LIM domain	3e-07
cd09451	53	cd09451, LIM_RIL, The LIM domain of RIL	3e-07
cd09418	56	cd09418, LIM2_Prickle, The second LIM domain of Pr	3e-07
cd09354	60	cd09354, LIM2_LPP, The second LIM domain of lipoma	4e-07
cd09424	58	cd09424, LIM2_FHL1, The second LIM domain of Four	4e-07
cd09328	56	cd09328, LIM2_abLIM, The second LIM domain on acti	5e-07
cd09345	54	cd09345, LIM2_FHL, The second LIM domain of Four a	7e-07
cd09339	52	cd09339, LIM4_Paxillin_like, The fourth LIM domain	1e-06
cd09431	57	cd09431, LIM3_Fhl2, The third LIM domain of Four a	1e-06
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	1e-06
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	1e-06
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	1e-06
cd09355	53	cd09355, LIM2_Ajuba_like, The second LIM domain of	2e-06
cd09450	53	cd09450, LIM_ALP, This family represents the LIM d	2e-06
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	2e-06
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	4e-06
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	6e-06
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	6e-06
cd09411	52	cd09411, LIM4_Paxillin, The fourth LIM domain of P	9e-06
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	1e-05
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	1e-05
cd09372	53	cd09372, LIM2_FBLP-1, The second LIM domain of the	1e-05
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	1e-05
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-05
cd09425	54	cd09425, LIM4_LIMPETin, The fourth LIM domain of p	2e-05
cd09460	55	cd09460, LIM3_ZASP_Cypher, The third LIM domain of	2e-05
cd09335	54	cd09335, LIM5_PINCH, The fifth LIM domain of prote	3e-05
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	4e-05
cd09426	57	cd09426, LIM2_FHL2, The second LIM domain of Four	6e-05
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	9e-05
cd09417	56	cd09417, LIM2_LIMPETin_like, The second LIM domain	9e-05
cd09461	54	cd09461, LIM3_Enigma_like_1, The third LIM domain	9e-05
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	1e-04
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	1e-04
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	1e-04
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	1e-04
cd09427	58	cd09427, LIM2_FHL3, The second LIM domain of Four	1e-04
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	1e-04
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	2e-04
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	2e-04
cd09356	53	cd09356, LIM2_TRIP6, The second LIM domain of Thyr	2e-04
cd09418	56	cd09418, LIM2_Prickle, The second LIM domain of Pr	3e-04
cd09429	53	cd09429, LIM3_FHL1, The third LIM domain of Four a	3e-04
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	4e-04
cd09333	51	cd09333, LIM3_PINCH, The third LIM domain of prote	4e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	4e-04
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	5e-04
cd09455	54	cd09455, LIM1_Enigma_like_1, The first LIM domain	7e-04
cd09352	54	cd09352, LIM1_Ajuba_like, The first LIM domain of	7e-04
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	8e-04
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	9e-04
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	0.001
cd09328	56	cd09328, LIM2_abLIM, The second LIM domain on acti	0.001
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	0.001
cd09340	58	cd09340, LIM1_Testin_like, The first LIM domain of	0.001
cd09348	64	cd09348, LIM4_FHL1, The fourth LIM domain of Four	0.001
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	0.001
cd09458	55	cd09458, LIM3_Enigma, The third LIM domain of Enig	0.001
cd09448	52	cd09448, LIM_CLP36, This family represents the LIM	0.002
cd09416	56	cd09416, LIM2_Testin, The second LIM domain of Tes	0.002
cd09393	56	cd09393, LIM3_Lrg1p_like, The third LIM domain of	0.002
cd09428	54	cd09428, LIM2_FHL5, The second LIM domain of Four	0.002
cd09452	52	cd09452, LIM1_Enigma, The first LIM domain of Enig	0.003
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	0.003
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	0.003
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	0.004
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	0.004

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

 Score =  107 bits (269), Expect = 2e-31
 Identities = 40/53 (75%), Positives = 46/53 (86%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C++C KPIVGQV+TALGKTWHPEHF+C  C  ELGT+NFFERD +PYCE DYH
Sbjct: 1   CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53

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

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

 Score = 94.9 bits (236), Expect = 2e-26
 Identities = 37/55 (67%), Positives = 45/55 (81%)

Query: 83  GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           G C+SC KPI GQV+TALG+TWHPEHF+C  C +ELG+R FFER+ + YCE DYH
Sbjct: 1   GDCASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55

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

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

 Score = 93.5 bits (232), Expect = 9e-26
 Identities = 39/53 (73%), Positives = 47/53 (88%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYH
Sbjct: 2   CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 77.8 bits (192), Expect = 1e-19
 Identities = 31/36 (86%), Positives = 34/36 (94%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           C+YCNGPILDKCVTAL+KTWH EHFFCAQCGK FG+
Sbjct: 1   CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGD 36

The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 75.8 bits (187), Expect = 7e-19
 Identities = 28/58 (48%), Positives = 36/58 (62%), Gaps = 2/58 (3%)

Query: 85  CSSCDKPIVGQVIT--ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140
           C+ C KPI  + +   ALGK WHPE F C  C + LG  +FFE+D + YC+ DY  LF
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 73.6 bits (181), Expect = 5e-18
 Identities = 26/52 (50%), Positives = 34/52 (65%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C+ PI+ + +TAL KTWHPEHF C  C +  G   F E+D +PYC  DY
Sbjct: 1   CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 69.3 bits (170), Expect = 2e-16
 Identities = 27/53 (50%), Positives = 36/53 (67%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVGQVI-TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C KPI G+ +  ALGK WHPE F C+ C + LG  +F+E+D +PYCE  Y
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

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

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

 Score = 68.5 bits (168), Expect = 4e-16
 Identities = 24/53 (45%), Positives = 32/53 (60%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C  C+KPI+   I+AL   WHPE F+C  C++     +FFE +  PYCE  YH
Sbjct: 1   CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53

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

>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 67.2 bits (164), Expect = 1e-15
 Identities = 26/52 (50%), Positives = 35/52 (67%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C  PI+  V+TA+ +TWHPEHF C+HC +  G   F ERD +PYC  D+
Sbjct: 1   CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin

 Score = 66.1 bits (161), Expect = 3e-15
 Identities = 28/35 (80%), Positives = 30/35 (85%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           C YCNGPILDK VTAL++TWH EHFFCAQCG  FG
Sbjct: 1   CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFG 35

The second 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 = 52

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

 Score = 64.3 bits (157), Expect = 1e-14
 Identities = 23/52 (44%), Positives = 31/52 (59%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C +C +PI G+V+TALGK WH EHF+C  C +       +E+    YCE  Y
Sbjct: 3   CGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

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

>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin

 Score = 63.1 bits (153), Expect = 4e-14
 Identities = 25/52 (48%), Positives = 32/52 (61%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C+ PI+ +V+TAL +TWHPEHF C  C    G   F E+D + YC  DY
Sbjct: 1   CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

The second 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 = 52

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

 Score = 60.5 bits (147), Expect = 5e-13
 Identities = 25/54 (46%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 84  CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPD 135
            C+ C KPI G  +V+ ALGK WHPE F C  C + L    FFE+D + YC+  
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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

>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 59.8 bits (145), Expect = 8e-13
 Identities = 21/35 (60%), Positives = 28/35 (80%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           C+YC GPIL   +TA+++TWH EHFFC+ CG+ FG
Sbjct: 1   CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFG 35

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family

 Score = 60.0 bits (146), Expect = 8e-13
 Identities = 25/52 (48%), Positives = 36/52 (69%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C KPI G+ ITA+G+ +HPEHF+C  C ++L    F E+D +PYC P +
Sbjct: 1   CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 57.5 bits (139), Expect = 8e-12
 Identities = 24/52 (46%), Positives = 31/52 (59%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C K I+G+V+ AL +TWH   F+C  C Q +G   F   D  PYCE DY
Sbjct: 1   CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

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

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

 Score = 57.4 bits (139), Expect = 8e-12
 Identities = 22/52 (42%), Positives = 30/52 (57%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C++ I G  + ALG++WHPE F C+HC+  L    F E     YCE  Y
Sbjct: 1   CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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

>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin

 Score = 56.9 bits (137), Expect = 1e-11
 Identities = 25/49 (51%), Positives = 34/49 (69%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           CS C KPI G+ ITA+GK +HPEHF+C  C ++L    F E++ +PYC 
Sbjct: 1   CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCH 49

The fourth 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 = 52

>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin

 Score = 56.7 bits (137), Expect = 1e-11
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C SC  PI G+ I+ALG+ +HPEHF+C  C + L   +F E+  +PYC   +
Sbjct: 1   CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 54.8 bits (132), Expect = 8e-11
 Identities = 22/53 (41%), Positives = 30/53 (56%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           CS C +P+    ++A    WHPE F+C+ C +     +FFE D RP CE  YH
Sbjct: 1   CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin

 Score = 54.8 bits (132), Expect = 8e-11
 Identities = 23/53 (43%), Positives = 29/53 (54%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C  C + I+   I+AL   WHPE F+C  C       +FFE D +PYCE  YH
Sbjct: 1   CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53

The third 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 = 53

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

 Score = 52.3 bits (126), Expect = 5e-10
 Identities = 19/36 (52%), Positives = 24/36 (66%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           C+ C  PI+ + VTAL KTWH EHF CA+C  + G 
Sbjct: 1   CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGT 36

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

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

 Score = 52.0 bits (124), Expect = 8e-10
 Identities = 22/52 (42%), Positives = 29/52 (55%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C + I+G+VI AL +TWH   F+C  C+  +    F   D  PYCE DY
Sbjct: 1   CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

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

>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 52.0 bits (125), Expect = 9e-10
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT-RNFFERDSRPYCEPDY 136
           C  C   + G  ITALG+ +H EHF C+ C    G   +++E + + YC   Y
Sbjct: 1   CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma subfamily with unknown function

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 24/51 (47%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTH--CNQELGTRNFFERDSRPYCE 133
           C SC++ I G  ITALGK W P+HFIC +  C + L    F E   + YCE
Sbjct: 1   CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCE 51

The first 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|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog (ENH) family

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 22/52 (42%), Positives = 29/52 (55%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C++C++ I G  + ALGK+WHPE F C HC   +    F E     YCE  Y
Sbjct: 1   CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52

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

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

 Score = 51.0 bits (122), Expect = 2e-09
 Identities = 20/52 (38%), Positives = 30/52 (57%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C+K I G+ + ALG+++HPE F C+ C + L    FFE     +C   Y
Sbjct: 1   CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

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

>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 50.7 bits (122), Expect = 2e-09
 Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C++CD+ I  G+   A GK WH +HF C  C++ LG + +  R+ +PYC   Y 
Sbjct: 3   CAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

The second 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 = 56

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

 Score = 50.4 bits (120), Expect = 3e-09
 Identities = 21/52 (40%), Positives = 28/52 (53%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C K I G+++ AL  TWH   F C  C   +  R F+  +  PYCE DY
Sbjct: 1   CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

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

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

 Score = 49.7 bits (119), Expect = 6e-09
 Identities = 20/36 (55%), Positives = 22/36 (61%)

Query: 142 PRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQF 177
           P C  C  PI  + VTAL K WH EHF CA+C K F
Sbjct: 1   PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPF 36

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

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

 Score = 49.9 bits (119), Expect = 6e-09
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL-GTRNFFERDSRPYCEPDYHNLFSPR 143
           C+ CD+ I  +++ A GK++HP+ F C  C   L G     ++ ++P+C  DYH  ++PR
Sbjct: 1   CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60

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

>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 20/49 (40%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRN-FFERDSRPYC 132
           C  C++ I G V++AL KTW  +HF C+ C+ +L  ++ F+E D +P C
Sbjct: 1   CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVC 49

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

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

 Score = 47.9 bits (114), Expect = 2e-08
 Identities = 20/35 (57%), Positives = 24/35 (68%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           C+ C  PI  + VTAL +TWH EHF C QCGK+ G
Sbjct: 3   CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELG 37

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

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

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C + I  GQ + AL K WH   F C  C + L T  +  +D +PYCE DY
Sbjct: 1   CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVL-TGEYMGKDGKPYCERDY 52

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

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

 Score = 48.1 bits (115), Expect = 3e-08
 Identities = 15/41 (36%), Positives = 23/41 (56%)

Query: 101 GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           G+ +H + F+C  C Q      F+E + R YCE D+  LF+
Sbjct: 19  GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

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

 Score = 46.9 bits (112), Expect = 7e-08
 Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 144 CSYCNGPILDKCV-TALEKTWHTEHFFCAQCGKQFGE 179
           C+ C  PI  + +  AL K WH E F C+ CGK  G 
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGG 37

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|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher family

 Score = 46.5 bits (110), Expect = 8e-08
 Identities = 21/52 (40%), Positives = 29/52 (55%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C+  I G  + ALG++WHPE F C +C+  L   +F E  +  YCE  Y
Sbjct: 1   CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. 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|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin

 Score = 46.3 bits (110), Expect = 9e-08
 Identities = 20/48 (41%), Positives = 28/48 (58%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           CS C+K I    +T   + WH E F CT+C++ L  + F  RD +PYC
Sbjct: 1   CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 46.2 bits (110), Expect = 1e-07
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           C+ C K I    +T   + WH E F+CT C ++L  + F  RD  PYC
Sbjct: 1   CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYC 48

The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 45.4 bits (108), Expect = 2e-07
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 134
           C  C + ++G+VI A+   WHP+ F C  CN+EL    F +   R  C P
Sbjct: 1   CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

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

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

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 144 CSYCNGPILDKCVT--ALEKTWHTEHFFCAQCGKQFGE 179
           C+ C  PI D+ +   AL K WH E F CA CGK  G 
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGP 38

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

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

 Score = 44.9 bits (106), Expect = 3e-07
 Identities = 20/49 (40%), Positives = 27/49 (55%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C+ C   IVG ++ A  K +HPE F+C  C   L  R +F  D + YCE
Sbjct: 1   CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYCE 49

The LIM domain of RIL: RIL contains an N-terminal PDZ domain, a LIM domain, and a short consensus C-terminal region. It is the smallest molecule in the ALP LIM domain containing protein family. RIL was identified in rat fibroblasts and in human lymphocytes. The LIM domain interacts with the AMPA glutamate receptor in dendritic spines. The consensus C-terminus interacts with PTP-BL, a submembranous protein tyrosine phosphatase and the PDZ domain is responsible to interact with alpha-actinin molecules. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 85  CSSCDKPIVGQVIT-ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           CS+CD+ I     T A G+ WH +HF C  C  +LG + +  R+ RPYC
Sbjct: 3   CSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPDYHNLFSPR 143
           CS C KPI+ +++ A GK +HP+ F C  C + L    F  +  ++ +C  D+H  F+PR
Sbjct: 1   CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60

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

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

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140
           C  C K I+   Q +   G  WH + F C++C Q +GT++FF +    YC P +   F
Sbjct: 1   CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

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

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

 Score = 44.6 bits (106), Expect = 5e-07
 Identities = 16/32 (50%), Positives = 24/32 (75%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQ 116
           C SC   + G+V++ALGKT+HP+ F+C+ C Q
Sbjct: 4   CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQ 35

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

>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM domains protein (FHL)

 Score = 44.2 bits (105), Expect = 7e-07
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C +C K I+   + +   GK WH + F C+ C + +GT++F  +D + YC P Y
Sbjct: 1   CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 16/33 (48%), Positives = 22/33 (66%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQ 176
           C+ C  PI  +C+TA+ + +H EHF CA C KQ
Sbjct: 1   CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQ 33

The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 21/57 (36%), Positives = 30/57 (52%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           C  C KPI    +T   + WH E F+CT C ++L  + F  RD   YC   + NL++
Sbjct: 1   CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. Length = 57

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

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C KP+   +  T+LG+ WH     C  C + L      E + +PYC   Y
Sbjct: 1   CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

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

>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPY 131
           C+ C   I  G+ ++ALG  WHPE F C  C + +    F    + PY
Sbjct: 1   CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48

The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C     K +  Q + AL + WH + F C+ C+  L +  +FE+D + YC  DY
Sbjct: 1   CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL-SNWYFEKDGKLYCRKDY 52

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

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

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL-GTRNFFERDSRPYCEPDY 136
           C+ C   I+  ++ ALGK++HP  F C  CN+ L G     + ++  YC  DY
Sbjct: 1   CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53

The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 20/49 (40%), Positives = 27/49 (55%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C  C   IVG V+ A  K  HPE F+C+ CN  L  + +F  + + YCE
Sbjct: 1   CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49

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

>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 7/58 (12%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSR------PYCEPDY 136
           C+ C KPI GQ + ALG  +H + F C  C + + ++ FF  D        P CE DY
Sbjct: 1   CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASK-FFPVDDPDTSEQVPLCETDY 57

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

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

 Score = 42.0 bits (99), Expect = 4e-06
 Identities = 19/49 (38%), Positives = 24/49 (48%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C  C   IVG V+ A  K  HPE F+C  C   L  + +F  +   YCE
Sbjct: 1   CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCE 49

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

>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 41.6 bits (98), Expect = 6e-06
 Identities = 14/35 (40%), Positives = 19/35 (54%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           C  C G +    +TAL + +H EHF C+ C   FG
Sbjct: 1   CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFG 35

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 42.1 bits (99), Expect = 6e-06
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 79  TTQKGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           TTQK  C +CDK + +   ++A G  +H   F C+HC   L   N+   +   YC+P + 
Sbjct: 1   TTQK--CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFE 58

Query: 138 NLF 140
            LF
Sbjct: 59  QLF 61

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

>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin

 Score = 41.1 bits (96), Expect = 9e-06
 Identities = 19/40 (47%), Positives = 24/40 (60%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVK 183
           CS C  PI  +C+TA+ K +H EHF CA C KQ  +   K
Sbjct: 1   CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFK 40

The fourth 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 = 52

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           C  CD PI    + + ALG TWH   F+C  C+  L  + F+ +  +P C
Sbjct: 1   CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50

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

 Score = 40.7 bits (95), Expect = 1e-05
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C  C+ PI    + + ALG TWH   F+C+ C + L  + FF +  +P C+   H
Sbjct: 1   CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55

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

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPDY 136
           C+ C   I   +I ALGK +HP  F C  C + +G  +F  +  +  YC  DY
Sbjct: 1   CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 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|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIVGQV--ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C + ++G+    TA+ + +H   F C  C   L  + F+  D +PYCE DY
Sbjct: 1   CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

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

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

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 143 RCSYCNGPILD--KCVTALEKTWHTEHFFCAQCGKQFGE 179
           +C+ C  PI    + + AL K WH E F CA CGK    
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSG 39

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|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 15/36 (41%), Positives = 21/36 (58%)

Query: 101 GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           G+ WH + F C  C Q +GT++F  +D   YC P Y
Sbjct: 19  GQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher family

 Score = 40.0 bits (93), Expect = 2e-05
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 137
           C  CD P+    + I ALG TWH   FIC  C+  L  + F+ +  +P C+   H
Sbjct: 1   CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55

The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. 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 = 55

>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQF 177
           C +CN  I    V+AL KTW  +HF C+ C  + 
Sbjct: 1   CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKL 34

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

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

 Score = 39.9 bits (93), Expect = 4e-05
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+SC + I  GQ + AL   WH + F C  C   L +  ++E+D R +C+ DY
Sbjct: 22  CASCGQSIYDGQYLQALNSDWHADCFRCCECGASL-SHWYYEKDGRLFCKKDY 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|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 38.9 bits (90), Expect = 6e-05
 Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           CS C K I+   + +   G +WH   FIC  C Q +GT++F  +D++ +C P Y
Sbjct: 1   CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCY 54

The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. Length = 57

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

 Score = 38.5 bits (90), Expect = 9e-05
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIVGQV--ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C + +VG+    TA+ + +H + F C  CN +L  + F+  + + YCEP Y
Sbjct: 1   CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 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|188801 cd09417, LIM2_LIMPETin_like, The second LIM domain of protein LIMPETin and related proteins

 Score = 38.7 bits (90), Expect = 9e-05
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
              CD+ I  G+   A+ K WH  HF C  C++ L  + +  RD  PYC
Sbjct: 3   SVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYC 51

The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 38.3 bits (89), Expect = 9e-05
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C SC  PI    + + AL   +H + F CT CN  L  ++F+ +  RP+C+
Sbjct: 1   CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 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|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 17/35 (48%), Positives = 21/35 (60%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           C  C  PI  + VTA+ KTWH EHF C  C ++ G
Sbjct: 2   CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIG 36

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 37.7 bits (88), Expect = 1e-04
 Identities = 16/37 (43%), Positives = 20/37 (54%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEA 180
           C  CN PIL+  ++AL   WH E F C +C K F   
Sbjct: 1   CGGCNKPILENYISALNTQWHPECFVCRECHKPFING 37

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

>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVK 183
           C  C  PI  +C++AL + +H EHF CA C +   +   K
Sbjct: 1   CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFK 40

The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

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

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 24/52 (46%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C K   G+V+    K +H + F C  C  +L    FF ++   YC  DY
Sbjct: 1   CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52

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

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C +C K ++   + +   G+TWH   FIC  C Q +G+R+F       YC P Y
Sbjct: 4   CVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57

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

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIVGQ--VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C +P+      + ALG  +H   F C  C Q+L  + F+  + +PYCE  Y
Sbjct: 34  CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 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|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQC 173
           C++CN  I    + AL ++WH E F C+ C
Sbjct: 1   CAHCNQVIRGPFLVALGRSWHPEEFTCSHC 30

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

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

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ CD+PI+ + ++  L + WH +   C  C   L T   F R+ + YC  D+
Sbjct: 1   CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPL-TEKCFSREGKLYCRNDF 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|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 15/34 (44%), Positives = 22/34 (64%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL 118
           CS C KPI+ +++ A GK +HP  F C  C++ L
Sbjct: 1   CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSL 34

The second 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 = 53

>gnl|CDD|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 142 PRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFG 178
           PRCS C+  I  D+C  A  + WH +HF C +C  Q G
Sbjct: 1   PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQLG 38

The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           C  C+KPI    +T   + WH E F+C+ C+++L  + F   + + YC
Sbjct: 1   CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 13/37 (35%), Positives = 19/37 (51%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEA 180
           CS C  P+ +  ++A    WH E F C+ C K F + 
Sbjct: 1   CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDG 37

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 134
           C  C   I  Q +   G  +HP HF C +C +EL T +  E     YC  
Sbjct: 1   CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKEL-TADARELKGELYCLR 49

The third LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 51

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

 Score = 36.8 bits (85), Expect = 4e-04
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           C  CDK +   + +T+LGK WH     C  C + L   +  E D +PYC
Sbjct: 1   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49

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

>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 36.4 bits (85), Expect = 5e-04
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)

Query: 142 PRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQC 173
           PRC+ C+  I   +   A  K WH +HF C QC
Sbjct: 1   PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQC 33

The second 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 = 56

>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma subfamily with unknown function

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 2/34 (5%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCA--QCGK 175
           C  CN  I    +TAL K W  +HF CA   C +
Sbjct: 1   CESCNQQIRGPFITALGKIWCPDHFICANASCRR 34

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

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C K + G  Q   A+G  +H   F C  C + L  + F+  + + YCE DY
Sbjct: 1   CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54

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

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

 Score = 35.8 bits (83), Expect = 8e-04
 Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPDY 136
           C+ C + I  +  + A+ + WH     C  C   L +    F RD   YC+ DY
Sbjct: 1   CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54

The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

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

 Score = 35.7 bits (82), Expect = 9e-04
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           C  CDK +   + +++LGK WH     C  C++ L      E D +PYC
Sbjct: 1   CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

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

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 14/38 (36%), Positives = 23/38 (60%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAM 181
           C+ C+  IL + + AL++TWH   F CA C +  G ++
Sbjct: 1   CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSL 38

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

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 12/35 (34%), Positives = 20/35 (57%)

Query: 143 RCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQF 177
           +C  C   +  + V+AL KT+H + F C+ C + F
Sbjct: 3   KCDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPF 37

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

>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 13/33 (39%), Positives = 17/33 (51%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQ 176
           C+ C  PI  + V AL   +H + F C  CGK 
Sbjct: 1   CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKP 33

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

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%)

Query: 85  CSSCDKPI----VGQVITALGK--TWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C +PI    V       G+   WHP  F+C  CN+ L    +F  D + YC   Y
Sbjct: 1   CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

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

>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 85  CSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 139
           CS C  PI G      V+   G +WH   F C  C+  L  + F   + + YC      L
Sbjct: 5   CSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDCAKKL 64

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 64

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 84  CCSSCDKPIVGQVI-TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
            C+ CD PI  + I     K WH +   C  C  +L T   F R  + YC+ D+
Sbjct: 3   KCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQL-TDKCFSRGGQVYCKEDF 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|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C  CD  I    + + ALG +WH   F+C  C   L  + F+ +  +P C+
Sbjct: 1   CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCK 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

>gnl|CDD|188832 cd09448, LIM_CLP36, This family represents the LIM domain of CLP36

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 17/49 (34%), Positives = 23/49 (46%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C  C   IVG  +    K  HPE ++CT C   L  +  F  + + YCE
Sbjct: 1   CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYCE 49

This family represents the LIM domain of CLP36. CLP36 has also been named as CLIM1, Elfin, or PDLIM1. CLP36 contains a C-terminal LIM domain and an N-terminal PDZ domain. CLP36 is highly expressed in heart and is present in many other tissues including lung, liver, spleen, and blood. CLP36 has been implicated in many processes including hypoxia and regulation of actin stress fibers. CLP36 co-localizes with alpha-actinin-2 at the Z-lines in myocardium. In addition, CLP36 binds to alpha-actinin-1 and alpha-actinin-4, and associates with F-actin filaments and stress fibers. CLP36 might be involved in not only the function of sarcomeres in muscle cells, but also in actin stress fiber-mediated cellular processes, such as cell shape, migration, polarit, and cytokinesis in non-muscle cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188800 cd09416, LIM2_Testin, The second LIM domain of Testin

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVGQVIT-ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ CD+ I     T A  + WH +HF C  C+  L    +   + +P C+P Y
Sbjct: 3   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCY 55

The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. 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. Knockout mice experiments reveal that tumor repressor function of testin. 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|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG----TRNFFERDSRPYC 132
           C+SC K I  + I    K WH + F C+ C++E+        F  +D R  C
Sbjct: 1   CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILC 52

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

>gnl|CDD|188812 cd09428, LIM2_FHL5, The second LIM domain of Four and a half LIM domains protein 5 (FHL5)

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 101 GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 134
           G  WH   F+C  C Q +GT+    ++++ YC P
Sbjct: 19  GNEWHETCFVCQSCQQPIGTKPLITKENKNYCVP 52

The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. 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|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 14/36 (38%), Positives = 21/36 (58%)

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           C+ CN  I  + + AL +++H E F C+QC K   E
Sbjct: 1   CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDE 36

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

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

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C K +   + +  L K WH   F C  C   L  +N+   + +PYC   Y
Sbjct: 1   CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

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

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

 Score = 34.2 bits (78), Expect = 0.003
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C K +   + +  L KTWH   F C  C   L   N+     +PYC   Y
Sbjct: 1   CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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

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

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 85  CSSCDKPIV-GQVI-TALGKTWHPEHFICTHCNQELGTRNFFE--RDSRPYCEPDY 136
           C+ CD+ I   QV+  A    +H E F C  C ++L T + F    D R  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|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain Kinase 2)

 Score = 33.7 bits (77), Expect = 0.004
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 85  CSSC-DKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C+ C  +         + + WH   F C+ C Q+L T  ++E+D + YC   Y
Sbjct: 1   CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVC-QDLLTNWYYEKDGKLYCHKHY 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	185
KOG1701|consensus	468		99.9
KOG1701|consensus	468		99.89
KOG4577|consensus	383		99.86
KOG1044|consensus	670		99.83
KOG2272|consensus	332		99.77
KOG2272|consensus	332		99.75
KOG1703|consensus	479		99.73
KOG1703|consensus	479		99.66
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.46
KOG1044|consensus	670		99.39
KOG1700|consensus	200		99.36
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.02
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.95
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.55
KOG4577|consensus	383		98.13
KOG1700|consensus	200		98.11
KOG0490|consensus	235		97.97
KOG1702|consensus	264		97.95
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.92
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	90.48
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	86.91
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	85.56
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	85.51
KOG0320|consensus	187		84.25
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	82.93
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	82.05
KOG1813|consensus	313		80.77

>KOG1701|consensus

Probab=99.90  E-value=5e-26  Score=183.46  Aligned_cols=104  Identities=29%  Similarity=0.749  Sum_probs=96.7

Q ss_pred             CCCCccccccccccc--ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEE
Q psy3656          80 TQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVT  157 (185)
Q Consensus        80 ~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~  157 (185)
                      .+..+|.+|+|.|.+  ..+.+|++.||..||+|..|+++|.+..||..++++||+.||.... +||.+|++.|++++|+
T Consensus       272 ~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLr  350 (468)
T KOG1701|consen  272 DYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILR  350 (468)
T ss_pred             hhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHH
Confidence            345699999999964  4789999999999999999999999999999999999999998776 9999999999999999


Q ss_pred             eCCCeecccCcccccCCCccCCCCeee
Q psy3656         158 ALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       158 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      |+|+.||+.||+|..|++.|++.-|.+
T Consensus       351 A~GkayHp~CF~Cv~C~r~ldgipFtv  377 (468)
T KOG1701|consen  351 ALGKAYHPGCFTCVVCARCLDGIPFTV  377 (468)
T ss_pred             hcccccCCCceEEEEeccccCCccccc
Confidence            999999999999999999999988753

>KOG1701|consensus

Probab=99.89  E-value=1.2e-24  Score=175.63  Aligned_cols=98  Identities=36%  Similarity=0.891  Sum_probs=90.9

Q ss_pred             CcccccccccccceeeecCcccccCCccCCCCCCCCCCCCee-eeCCcCCCccchhhccCCCCCccCCcccCc-------
Q psy3656          83 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILDK-------  154 (185)
Q Consensus        83 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~-~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~-------  154 (185)
                      .+|..|++.|.++++.++|+.||..||+|..|.+.|.+..|. ..++++||-+||+++|+++|+.|+++|+++       
T Consensus       335 ekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etv  414 (468)
T KOG1701|consen  335 EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETV  414 (468)
T ss_pred             HHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceE
Confidence            478999999999999999999999999999999999888886 788999999999999999999999999842       


Q ss_pred             eEEeCCCeecccCcccccCCCccCCC
Q psy3656         155 CVTALEKTWHTEHFFCAQCGKQFGEA  180 (185)
Q Consensus       155 ~~~~~~~~~H~~Cf~C~~C~~~l~~~  180 (185)
                      .|+++|+.||.+||+|..|+.+|+.+
T Consensus       415 Rvvamdr~fHv~CY~CEDCg~~LS~e  440 (468)
T KOG1701|consen  415 RVVAMDRDFHVNCYKCEDCGLLLSSE  440 (468)
T ss_pred             EEEEccccccccceehhhcCcccccc
Confidence            46899999999999999999999743

>KOG4577|consensus

Probab=99.86  E-value=3.9e-24  Score=164.74  Aligned_cols=104  Identities=26%  Similarity=0.680  Sum_probs=94.9

Q ss_pred             CCCcccccccccccc-eeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCc-eE-E
Q psy3656          81 QKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDK-CV-T  157 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~-~~-~  157 (185)
                      ..++|++|.+.|.+. ++.++++.||..|++|+.|..+| ....+.++|.+||+++|.++||.+|..|..+|.+. +| .
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL-~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk  110 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQL-ADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK  110 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHH-HHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence            357899999999876 56799999999999999999999 45689999999999999999999999999999975 44 4


Q ss_pred             eCCCeecccCcccccCCCcc-CCCCeeeC
Q psy3656         158 ALEKTWHTEHFFCAQCGKQF-GEAMVKFI  185 (185)
Q Consensus       158 ~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~  185 (185)
                      |.+.+||.+||.|..|.++| .+|+|++|
T Consensus       111 Aqd~VYHl~CF~C~iC~R~L~TGdEFYLm  139 (383)
T KOG4577|consen  111 AQDFVYHLHCFACFICKRQLATGDEFYLM  139 (383)
T ss_pred             hhcceeehhhhhhHhhhcccccCCeeEEe
Confidence            99999999999999999999 89999986

>KOG1044|consensus

Probab=99.83  E-value=1.3e-21  Score=163.05  Aligned_cols=99  Identities=34%  Similarity=0.785  Sum_probs=93.5

Q ss_pred             CCCCccccccccc-ccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEe
Q psy3656          80 TQKGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTA  158 (185)
Q Consensus        80 ~~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~  158 (185)
                      .+...|++|++.| .++.+.++++.||..||+|..|..-| .++|...+|.+||+.||...||.+|..|.+.|.|++|.|
T Consensus       131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqa  209 (670)
T KOG1044|consen  131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQA  209 (670)
T ss_pred             cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhc
Confidence            4567899999999 68999999999999999999999988 778999999999999999999999999999999999999


Q ss_pred             CCCeecccCcccccCCCccCC
Q psy3656         159 LEKTWHTEHFFCAQCGKQFGE  179 (185)
Q Consensus       159 ~~~~~H~~Cf~C~~C~~~l~~  179 (185)
                      .|+.|||.|-+|++|+.+|++
T Consensus       210 g~kh~HPtCARCsRCgqmF~e  230 (670)
T KOG1044|consen  210 GDKHFHPTCARCSRCGQMFGE  230 (670)
T ss_pred             cCcccCcchhhhhhhcccccc
Confidence            999999999999999999943

>KOG2272|consensus

Probab=99.77  E-value=6.5e-21  Score=144.64  Aligned_cols=101  Identities=29%  Similarity=0.785  Sum_probs=93.7

Q ss_pred             Ccccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEeCC
Q psy3656          83 GCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALE  160 (185)
Q Consensus        83 ~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~  160 (185)
                      -.|..|.....  ..++...|..||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.|..|++.|.|++|.+++
T Consensus        13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVikamn   92 (332)
T KOG2272|consen   13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKAMN   92 (332)
T ss_pred             HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHhhc
Confidence            35888988773  4578899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CeecccCcccccCCCccCCCCee
Q psy3656         161 KTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       161 ~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ..|||.||+|..|++.|.+.+|+
T Consensus        93 nSwHp~CF~Cd~Cn~~Lad~gf~  115 (332)
T KOG2272|consen   93 NSWHPACFRCDLCNKHLADQGFY  115 (332)
T ss_pred             cccCcccchhHHHHHHHhhhhhH
Confidence            99999999999999999877763

>KOG2272|consensus

Probab=99.75  E-value=4.5e-20  Score=140.09  Aligned_cols=105  Identities=36%  Similarity=0.800  Sum_probs=98.0

Q ss_pred             CCCCCCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceE
Q psy3656          77 VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCV  156 (185)
Q Consensus        77 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~  156 (185)
                      ....+.++|..|.++|..+++.++|+-||.+.|+|+.|.+++.+-+.|.+.|..||+.||.++||..|..|++.|-|.++
T Consensus       190 hD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv  269 (332)
T KOG2272|consen  190 HDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVV  269 (332)
T ss_pred             ccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHH
Confidence            33456789999999999889999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EeCCCeecccCcccccCCCccCCCC
Q psy3656         157 TALEKTWHTEHFFCAQCGKQFGEAM  181 (185)
Q Consensus       157 ~~~~~~~H~~Cf~C~~C~~~l~~~~  181 (185)
                      .|.++.|.++||.|+.|++.|.-..
T Consensus       270 ~al~KawCv~cf~Cs~Cdkkl~~K~  294 (332)
T KOG2272|consen  270 SALNKAWCVECFSCSTCDKKLTQKN  294 (332)
T ss_pred             HHhhhhhcccccccccccccccccc
Confidence            9999999999999999999996544

>KOG1703|consensus

Probab=99.73  E-value=7.1e-19  Score=149.69  Aligned_cols=103  Identities=36%  Similarity=0.863  Sum_probs=98.4

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc--CceEEeC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTAL  159 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~--~~~~~~~  159 (185)
                      .+.|.+|+++|.++.|.+++..||.+||.|..|.+.|....|+..+|.+||+.||+.+++.+|..|.++|.  +..+.++
T Consensus       363 ~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~  442 (479)
T KOG1703|consen  363 RPNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEAD  442 (479)
T ss_pred             CccccccCCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhcc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999987  7899999


Q ss_pred             CCeecccCcccccCCCccCCCCeee
Q psy3656         160 EKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       160 ~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +..||.+||+|+.|.+.|.++.|++
T Consensus       443 ~~~~h~~~F~c~~c~~~l~~~~~~~  467 (479)
T KOG1703|consen  443 GSPFHGDCFRCANCMKKLTKKTFFE  467 (479)
T ss_pred             CccccccceehhhhhccccCCceee
Confidence            9999999999999999999999876

>KOG1703|consensus

Probab=99.66  E-value=2.9e-17  Score=139.89  Aligned_cols=103  Identities=40%  Similarity=0.785  Sum_probs=97.8

Q ss_pred             CCccccccccccc-ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEeCC
Q psy3656          82 KGCCSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALE  160 (185)
Q Consensus        82 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~  160 (185)
                      .+.|..|...|.+ +.+.++++.||+.+|.|..|...+..+.+...+|.+||..||...+.+.|..|+.+|.+++|.|.+
T Consensus       303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~  382 (479)
T KOG1703|consen  303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALG  382 (479)
T ss_pred             cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhcc
Confidence            4789999999988 899999999999999999999999888888999999999999999999999999999999999999


Q ss_pred             CeecccCcccccCCCccCCCCeee
Q psy3656         161 KTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       161 ~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +.||++||.|..|++.|.+..|++
T Consensus       383 ~~wH~~cf~C~~C~~~~~~~~~~~  406 (479)
T KOG1703|consen  383 RLWHPECFVCADCGKPLKNSSFFE  406 (479)
T ss_pred             CeechhceeeecccCCCCCCcccc
Confidence            999999999999999998888764

>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=99.46  E-value=3.5e-14  Score=86.94  Aligned_cols=56  Identities=45%  Similarity=1.172  Sum_probs=50.4

Q ss_pred             cccccccccc-cee-eecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656          85 CSSCDKPIVG-QVI-TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  140 (185)
Q Consensus        85 C~~C~~~i~~-~~~-~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~  140 (185)
                      |..|+++|.+ +.+ .++|+.||.+||+|..|+..|....++..+|++||+.||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            7899999964 443 6999999999999999999999888999999999999999876

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

>KOG1044|consensus

Probab=99.39  E-value=3.9e-13  Score=112.86  Aligned_cols=91  Identities=26%  Similarity=0.599  Sum_probs=79.3

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEeCCC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEK  161 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~  161 (185)
                      ...|..|.+.-.++++.+.++.||..||.|..|++.|..+.|+..++.        ++++.  ..|.+.|.+++|.++++
T Consensus        16 ~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~gevvsa~gk   85 (670)
T KOG1044|consen   16 GIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGEVVSTLGK   85 (670)
T ss_pred             ceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccceeEecccc
Confidence            457999999999999999999999999999999999998888866554        34444  67899999999999999


Q ss_pred             eecccCcccccCCCcc-CCCCe
Q psy3656         162 TWHTEHFFCAQCGKQF-GEAMV  182 (185)
Q Consensus       162 ~~H~~Cf~C~~C~~~l-~~~~~  182 (185)
                      .||++||.|+.|..++ .+++.
T Consensus        86 tyh~~cf~cs~ck~pf~~g~~v  107 (670)
T KOG1044|consen   86 TYHPKCFSCSTCKSPFKSGDKV  107 (670)
T ss_pred             eeccccceecccCCCCCCCCee
Confidence            9999999999999998 55443

>KOG1700|consensus

Probab=99.36  E-value=1.2e-13  Score=104.85  Aligned_cols=102  Identities=25%  Similarity=0.603  Sum_probs=87.9

Q ss_pred             CCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCC------------------
Q psy3656          82 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP------------------  142 (185)
Q Consensus        82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~------------------  142 (185)
                      ...|..|++.|+ .+.+..+|..||..||+|..|...|....+..+++.+||+.+|...+++                  
T Consensus         7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD   86 (200)
T ss_pred             cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence            357999999995 6777799999999999999999999988999999999999977666654                  


Q ss_pred             -----------------------CCCccCCcccC-ceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         143 -----------------------RCSYCNGPILD-KCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       143 -----------------------~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                                             .|..|.+.+.+ +.+...+..||..||+|+.|++.|....|.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~  151 (200)
T KOG1700|consen   87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYA  151 (200)
T ss_pred             cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchh
Confidence                                   39999998874 566788999999999999999999766553

>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=99.02  E-value=2.8e-10  Score=69.41  Aligned_cols=41  Identities=34%  Similarity=0.790  Sum_probs=35.4

Q ss_pred             CCccCCcccCceE--EeCCCeecccCcccccCCCccCCCCeee
Q psy3656         144 CSYCNGPILDKCV--TALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       144 C~~C~~~i~~~~~--~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      |..|+++|.+..+  .+.++.||++||+|..|++.|.+..|+.
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~   43 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYE   43 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEE
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEe
Confidence            7899999996433  5999999999999999999998887653

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

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

Probab=98.95  E-value=5.5e-10  Score=62.31  Aligned_cols=36  Identities=44%  Similarity=1.018  Sum_probs=33.0

Q ss_pred             CCCccCCcccC--ceEEeCCCeecccCcccccCCCccC
Q psy3656         143 RCSYCNGPILD--KCVTALEKTWHTEHFFCAQCGKQFG  178 (185)
Q Consensus       143 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~  178 (185)
                      +|..|+++|.+  ..+.+.++.||++||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            58999999997  6778999999999999999999985

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

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

Probab=98.55  E-value=5.4e-08  Score=54.04  Aligned_cols=36  Identities=56%  Similarity=1.238  Sum_probs=32.1

Q ss_pred             ccccccccccc--ceeeecCcccccCCccCCCCCCCCC
Q psy3656          84 CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELG  119 (185)
Q Consensus        84 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~  119 (185)
                      +|..|++.|.+  ..+.+.++.||..||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            48999999965  6788999999999999999999884

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

>KOG4577|consensus

Probab=98.13  E-value=4.6e-07  Score=70.91  Aligned_cols=64  Identities=31%  Similarity=0.644  Sum_probs=52.2

Q ss_pred             CCcccccccccc-ccee-eecCcccccCCccCCCCCCCCCCC-Cee-eeCCcCCCccchhhccCCCCC
Q psy3656          82 KGCCSSCDKPIV-GQVI-TALGKTWHPEHFICTHCNQELGTR-NFF-ERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        82 ~~~C~~C~~~i~-~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ..+|..|...|. .++| .+.+..||..||.|..|.++|..+ +|| ..++++.|+++|+..-..-|.
T Consensus        92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~  159 (383)
T KOG4577|consen   92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCN  159 (383)
T ss_pred             CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcccc
Confidence            358999999994 5554 588999999999999999999844 676 788999999999875545453

>KOG1700|consensus

Probab=98.11  E-value=7.3e-07  Score=67.84  Aligned_cols=61  Identities=30%  Similarity=0.692  Sum_probs=54.4

Q ss_pred             CCCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656          80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  140 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~  140 (185)
                      .....|..|++.++ .+.+...+..||..||+|..|+..|....+...++.+||..++..+|
T Consensus       106 g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  106 GEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             ccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence            33578999999996 68899999999999999999999999999999999999998877655

>KOG0490|consensus

Probab=97.97  E-value=1.1e-06  Score=68.16  Aligned_cols=96  Identities=30%  Similarity=0.701  Sum_probs=76.0

Q ss_pred             cccccccc-eeeecCcccccCCccCCCCCCCCC-CCCeeeeCCcCCCccchhh--ccCCCCCccCCccc--CceEEeCCC
Q psy3656          88 CDKPIVGQ-VITALGKTWHPEHFICTHCNQELG-TRNFFERDSRPYCEPDYHN--LFSPRCSYCNGPIL--DKCVTALEK  161 (185)
Q Consensus        88 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~yC~~~~~~--~~~~~C~~C~~~i~--~~~~~~~~~  161 (185)
                      |+..|.+. .+...+..||..|.+|..|...|. ....+..+|..||..+|.+  .+..+|..|...|.  ++...+.++
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~   81 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEK   81 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcC
Confidence            55666543 345669999999999999999996 2344444999999999998  78899999999985  455667788


Q ss_pred             eecccCcccccCCCcc-CCCCeee
Q psy3656         162 TWHTEHFFCAQCGKQF-GEAMVKF  184 (185)
Q Consensus       162 ~~H~~Cf~C~~C~~~l-~~~~~~~  184 (185)
                      + |-.||.|..|...+ .++++.+
T Consensus        82 ~-h~Pd~~~r~~la~~~~~~e~rV  104 (235)
T KOG0490|consen   82 V-HLPCFACRECLALLLTGDEFRV  104 (235)
T ss_pred             C-CcCccchHHHHhhcCCCCeeee
Confidence            8 99999999999866 6666544

>KOG1702|consensus

Probab=97.95  E-value=1.2e-06  Score=65.56  Aligned_cols=58  Identities=29%  Similarity=0.707  Sum_probs=51.9

Q ss_pred             Ccccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656          83 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  140 (185)
Q Consensus        83 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~  140 (185)
                      .-|..|++.++ .+.+..+++.||..||+|..|+.+|...++...+.++||..+|....
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence            45889999995 68899999999999999999999999888889999999999997543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.92  E-value=0.02  Score=33.98  Aligned_cols=38  Identities=24%  Similarity=0.581  Sum_probs=29.0

Q ss_pred             cCCCCCccCCccc--CceEE--eCCCeecccCc----cccc--CCCcc
Q psy3656         140 FSPRCSYCNGPIL--DKCVT--ALEKTWHTEHF----FCAQ--CGKQF  177 (185)
Q Consensus       140 ~~~~C~~C~~~i~--~~~~~--~~~~~~H~~Cf----~C~~--C~~~l  177 (185)
                      .+.+|..|++.|.  +.+|.  .-+..||.+|+    .|..  |+..+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence            3588999999995  45554  45799999999    4877  76654

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

Probab=90.48  E-value=0.33  Score=29.89  Aligned_cols=49  Identities=14%  Similarity=0.369  Sum_probs=23.0

Q ss_pred             ccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEE
Q psy3656         109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVT  157 (185)
Q Consensus       109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~  157 (185)
                      ++|+.|..-|..--....=...||..|-...++..|.+|+.|...+.+.
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS--
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHH
Confidence            4677777766432223555678899998888888899999987655444

>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=86.91  E-value=0.45  Score=25.96  Aligned_cols=28  Identities=29%  Similarity=0.523  Sum_probs=21.0

Q ss_pred             CCccCCcccCc--eEEeCCCeecccCcccc
Q psy3656         144 CSYCNGPILDK--CVTALEKTWHTEHFFCA  171 (185)
Q Consensus       144 C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~  171 (185)
                      |.-|++.|.++  .+...++.||--|=.|.
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~   30 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCL   30 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEEECHHHH
Confidence            77899999865  45678999996665553

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

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

Probab=85.56  E-value=0.25  Score=33.26  Aligned_cols=28  Identities=29%  Similarity=0.443  Sum_probs=21.9

Q ss_pred             CCCccCCccc-CceEEe-CCCeecccCccc
Q psy3656         143 RCSYCNGPIL-DKCVTA-LEKTWHTEHFFC  170 (185)
Q Consensus       143 ~C~~C~~~i~-~~~~~~-~~~~~H~~Cf~C  170 (185)
                      +|..|+++|. |+..++ .+..-|-+||+=
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~   33 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE   33 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence            6999999997 666664 457889999863

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

Probab=85.51  E-value=0.77  Score=30.78  Aligned_cols=28  Identities=21%  Similarity=0.373  Sum_probs=17.0

Q ss_pred             CCCCccCCcccCc-eEEe-CCCeecccCcc
Q psy3656         142 PRCSYCNGPILDK-CVTA-LEKTWHTEHFF  169 (185)
Q Consensus       142 ~~C~~C~~~i~~~-~~~~-~~~~~H~~Cf~  169 (185)
                      ..|..|+++|... ++.+ .|..+|-.|++
T Consensus        79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            5577777777643 3333 35667777753

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

>KOG0320|consensus

Probab=84.25  E-value=0.35  Score=35.90  Aligned_cols=48  Identities=13%  Similarity=0.394  Sum_probs=37.2

Q ss_pred             cCCccCCCCCCCCCCCC-eeeeCCcCCCccchhhc--cCCCCCccCCcccC
Q psy3656         106 PEHFICTHCNQELGTRN-FFERDSRPYCEPDYHNL--FSPRCSYCNGPILD  153 (185)
Q Consensus       106 ~~Cf~C~~C~~~L~~~~-~~~~~g~~yC~~~~~~~--~~~~C~~C~~~i~~  153 (185)
                      ..+|+|..|-....... +...-|++||..|-...  .+.+|..|++.|..
T Consensus       129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence            45689999977775443 55788999999998754  45899999998864

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production

Probab=82.93  E-value=0.84  Score=30.12  Aligned_cols=36  Identities=25%  Similarity=0.599  Sum_probs=25.1

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD  153 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~  153 (185)
                      +|..|...+.      ..|..||..|-.++  .+|+-|++.|++
T Consensus        46 ~C~~CK~~v~------q~g~~YCq~CAYkk--GiCamCGKki~d   81 (90)
T PF10235_consen   46 KCKICKTKVH------QPGAKYCQTCAYKK--GICAMCGKKILD   81 (90)
T ss_pred             cccccccccc------cCCCccChhhhccc--CcccccCCeecc
Confidence            5666666552      22567999995543  689999999864

This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].

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

Probab=82.05  E-value=1.3  Score=29.59  Aligned_cols=32  Identities=28%  Similarity=0.453  Sum_probs=19.8

Q ss_pred             CCCCCcccccccccccc--eeeecCcccccCCcc
Q psy3656          79 TTQKGCCSSCDKPIVGQ--VITALGKTWHPEHFI  110 (185)
Q Consensus        79 ~~~~~~C~~C~~~i~~~--~~~~~~~~~H~~Cf~  110 (185)
                      ......|..|++.|...  .+--.|..+|..|++
T Consensus        75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            34456788888888432  233446677777753

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

>KOG1813|consensus

Probab=80.77  E-value=0.83  Score=36.63  Aligned_cols=47  Identities=17%  Similarity=0.388  Sum_probs=37.0

Q ss_pred             CCccCCCCCCCCCCCCeeeeCCcCCCccchhhccC--CCCCccCCcccCc
Q psy3656         107 EHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS--PRCSYCNGPILDK  154 (185)
Q Consensus       107 ~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~--~~C~~C~~~i~~~  154 (185)
                      --|.|..|.... -..+...-+..+|+.|....|.  ++|..|++.+.|.
T Consensus       240 ~Pf~c~icr~~f-~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~  288 (313)
T KOG1813|consen  240 LPFKCFICRKYF-YRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS  288 (313)
T ss_pred             CCcccccccccc-ccchhhcCCceeehhhhccccccCCcceecccccccc
Confidence            347888998877 3456677788899999887664  7899999998874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	185
1nyp_A	66	4th Lim Domain Of Pinch Protein Length = 66		3e-10
1nyp_A	66	4th Lim Domain Of Pinch Protein Length = 66		1e-04
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		1e-09
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		3e-05
2dar_A	90	Solution Structure Of First Lim Domain Of Enigma-Li		3e-08
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		2e-05
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		3e-05
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		3e-05
1x64_A	89	Solution Structure Of The Lim Domain Of Alpha-Actin		3e-05
2d8z_A	70	Solution Structure Of The Third Lim Domain Of Four		4e-05
2d8x_A	70	Solution Structure Of The Second Lim Domain Of Part		5e-05
2dlo_A	81	Solution Structure Of The Second Lim Domain Of Huma		6e-05
2xqn_T	126	Complex Of The 2nd And 3rd Lim Domains Of Tes With		7e-05
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		7e-05
2kbx_B	70	Solution Structure Of Ilk-Pinch Complex Length = 70		8e-05
1g47_A	77	1st Lim Domain Of Pinch Protein Length = 77		1e-04
1v6g_A	81	Solution Structure Of The Lim Domain Of The Human A		1e-04
2cuq_A	80	Solution Structure Of Second Lim Domain From Human		2e-04
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		2e-04
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		2e-04
1wyh_A	72	Solution Structure Of The Lim Domain From Human Ske		2e-04
1x4k_A	72	Solution Structure Of Lim Domain In Lim-Protein 3 L		5e-04
3f6q_B	72	Crystal Structure Of Integrin-Linked Kinase Ankyrin		6e-04
2cur_A	69	Solution Structure Of Skeletal Muscle Lim-Protein 1		8e-04

>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein Length = 66

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           C +C +PI G+V+ A+GK WH EHF+C  C +       +ER    YCE  Y+ LF 
Sbjct: 8   CGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 64

>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein Length = 66

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 142 PRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQF 177
           P C  C  PI  + V A+ K WH EHF CA+C K F
Sbjct: 6   PICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPF 41

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 138
           C  C++P++   ++A+   WHPE F+C  C     T +FFE D RP+CE  YH+
Sbjct: 18  CGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHH 71

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 135 DYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQF 177
           D+  +FSP+C  CN P+L+  ++A++  WH E F C  C   F
Sbjct: 9   DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSF 51

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 30/57 (52%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           C+ C++ I G  + ALGK+WHPE F C HC   +    F E     YCE  Y   F+
Sbjct: 28  CAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFA 84

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 4/97 (4%)
Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C+ CD+ I+ + ++ AL + WH +   C+ C+  L  R F  R    YC+ D+   F  +
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTK 121
Query: 144 CSYCNGPILDKCVT--ALEKTWHTEHFFCAQCGKQFG 178
           C+ C   I    V   A +  +H   F C  C +Q  
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLA 158

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140
           C+ C + I  GQ + AL K WH   F C  C+  L T  +  +D  PYCE DYH  F
Sbjct: 18  CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVIL-TGEYISKDGVPYCESDYHAQF 73

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 4/97 (4%)
Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C+ CD+ I+ + ++ AL + WH +   C+ C+  L  R F  R    YC+ D+   F  +
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTK 67
Query: 144 CSYCNGPILDKCVT--ALEKTWHTEHFFCAQCGKQFG 178
           C+ C   I    V   A +  +H   F C  C +Q  
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLA 104

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 25/49 (51%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 133
           C  C   IVG V+ A  K  HPE F+C  CN  L  + +F  +   YCE
Sbjct: 28  CDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCE 76

>pdb|2D8Z|A Chain A, Solution Structure Of The Third Lim Domain Of Four And A Half Lim Domains Protein 2 (Fhl-2) Length = 70

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           C  C KPI    +T   + WH E F+CT C ++L  + F  RD   YC   + +L++
Sbjct: 8   CVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYA 64

>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of Particularly Interesting New Cys-His Protein (Pinch) Length = 70

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 134
           C  C + I+G+VI A+  +WHPE F C  C + L    F +   R  C P
Sbjct: 8   CHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRP 57

>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human Thyroid Receptor-Interacting Protein 6 Length = 81

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 77  VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPD 135
           V T +K  C++C +PI+ +++ A+GK +HP  F C  C++ L    F  +  S+ +C  D
Sbjct: 12  VATLEK--CATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69
Query: 136 YHNLFS 141
           +H  F+
Sbjct: 70  FHRKFA 75

>pdb|2XQN|T Chain T, Complex Of The 2nd And 3rd Lim Domains Of Tes With The Evh1 Domain Of Mena And The N-Terminal Domain Of Actin-Like Protein Arp7a Length = 126

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 44/96 (45%), Gaps = 5/96 (5%)
Query: 85  CSSCDKPIVGQVIT-ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C+ CD+ I     T A  + WH +HF C  C+  L    +   + +P C+P Y    +  
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVV 65
Query: 144 CSYCNGPILDKC--VTALEKTWH--TEHFFCAQCGK 175
           C  C+  I  +   VT    +WH  TE F C+ C K
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSK 101

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 4/97 (4%)
Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C+ C++ I+ + ++  L + WH     C  C  +L  R F  R    YC+ D+   F  +
Sbjct: 9   CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCF-SRAGSVYCKEDFFKRFGTK 67
Query: 144 CSYCNGPILDKCVT--ALEKTWHTEHFFCAQCGKQFG 178
           C+ C   I    V   A +  +H   F C  C +Q  
Sbjct: 68  CTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLA 104

>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex Length = 70

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 29/48 (60%)
Query: 95  QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
           +++ + G+ +H + F+C  C Q+     F+E + R YCE D+  LF+P
Sbjct: 22  KIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP 69

>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein Length = 77

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 29/48 (60%)
Query: 95  QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
           +++ + G+ +H + F+C  C Q+     F+E + R YCE D+  LF+P
Sbjct: 26  KIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP 73

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 24/31 (77%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCN 115
           C SCD+ I G+V++ALGKT+HP+ F+C  C 
Sbjct: 18  CFSCDQFIEGEVVSALGKTYHPDCFVCAVCR 48

>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human Skeletal Muscle Lim-Protein 2 Length = 80

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           C+ C K +    +T   + WH E  +CT C   L  + F  RD  PYC   +  LF+
Sbjct: 18  CARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFA 74

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSP 142
           C  CDK +   + +T+LGK WH     C  C + L +    E + +PYC  P Y  +F P
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62
Query: 143 R 143
           +
Sbjct: 63  K 63

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/100 (29%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLFS 141
           C  C + I  +  + A+ + WH +   C  C   LG   R  + +  R  C  DY  LF 
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64
Query: 142 PR--CSYCNGPI--LDKCVTALEKTWHTEHFFCAQCGKQF 177
               C+ C+  I   +  +   +K +H E F CA C K F
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHF 104

>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal Muscle Lim-Protein 2 Length = 72

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 24/41 (58%)
Query: 101 GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           G+TWH   F+C+ C Q LG+R+F       YC P Y N F+
Sbjct: 26  GQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA 66

>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3 Length = 72

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           C  C K I+   + +   G +WH   FIC  C Q +GT++F  +D++ +C P Y
Sbjct: 8   CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCY 61

>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat Domain In Complex With Pinch1 Lim1 Domain Length = 72

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 95  QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           +++ + G+ +H + F+C  C Q+     F+E + R YCE D+  LF+
Sbjct: 26  KIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72

>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1 Length = 69

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           C  C+K I    IT   + WH + F+C  C+++L  + F   + + YC   Y N  S
Sbjct: 8   CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	185
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-34
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-14
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-11
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-33
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-12
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	3e-33
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-10
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-07
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-32
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	8e-26
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-31
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	3e-15
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	5e-10
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	6e-29
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	9e-18
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	1e-27
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	4e-15
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	8e-27
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	2e-12
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	2e-26
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-15
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	3e-26
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-19
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	4e-26
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-11
2cuq_A	80	Four and A half LIM domains 3; structural genomics	5e-26
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-20
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	7e-26
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-18
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	5e-11
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-25
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-09
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	2e-25
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-12
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	4e-25
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	7e-10
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	6e-25
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-09
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	1e-24
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	1e-10
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	5e-24
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	7e-10
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	9e-24
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-15
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	7e-23
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	7e-12
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-22
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	6e-08
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-22
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-08
2cor_A	79	Pinch protein; LIM domain, particularly interestin	1e-21
2cor_A	79	Pinch protein; LIM domain, particularly interestin	2e-10
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-20
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-08
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	8e-20
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-05
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-19
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-08
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-19
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-08
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-19
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	6e-19
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-12
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	7e-19
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	3e-17
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	7e-19
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	2e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	7e-19
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	2e-13
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-18
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	8e-06
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-18
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	3e-17
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	3e-08
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	3e-16
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	5e-16
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	4e-16
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	1e-05
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	5e-16
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	3e-10
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	8e-16
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	8e-16
2co8_A	82	NEDD9 interacting protein with calponin homology a	5e-10
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	1e-08
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	7e-08
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	1e-05

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

 Score =  115 bits (291), Expect = 5e-34
 Identities = 30/104 (28%), Positives = 47/104 (45%), Gaps = 5/104 (4%)

Query: 80  TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 138
           ++K  C+ CD+ I   +   A  + WH +HF C  C+  L    +   + +P C+P Y  
Sbjct: 1   SEKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 60

Query: 139 LFSPRCSYCNGPILDKC--VTALEKTWH--TEHFFCAQCGKQFG 178
             +  C  C+  I  +   VT    +WH  TE F C+ C K   
Sbjct: 61  NHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI 104

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

 Score = 65.9 bits (161), Expect = 2e-14
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 85  CSSCDKPIVG--QVITALGKTWHP--EHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140
           C  C   I    Q +T    +WH   E F+C+ C++ L  + F   +   +C  +     
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

Query: 141 S 141
           S
Sbjct: 126 S 126

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

 Score = 56.3 bits (136), Expect = 5e-11
 Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 1/39 (2%)

Query: 142 PRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGE 179
           PRC+ C+  I       A  + WH +HF C  C      
Sbjct: 4   PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAG 42

>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 =  116 bits (291), Expect = 2e-33
 Identities = 33/155 (21%), Positives = 56/155 (36%), Gaps = 15/155 (9%)

Query: 28  GQPVPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSS 87
           G     + E  +T   +  +   N    + G                    T +   C+ 
Sbjct: 17  GGEFGDEDERLITRLENTQFDAANGIDDEGGSG-----------GHMGSGGTPEIPMCAG 65

Query: 88  CDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY 146
           CD+ I+ + ++ AL + WH +   C+ C+  L  R  F R    YC+ D+   F  +C+ 
Sbjct: 66  CDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER-CFSRGESVYCKDDFFKRFGTKCAA 124

Query: 147 CNGPI--LDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           C   I        A +  +H   F C  C +Q   
Sbjct: 125 CQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLAT 159

>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 = 61.5 bits (149), Expect = 2e-12
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQEL--GTRNFFERDSRPYCEPDYH 137
           C++C   I     V  A    +H   F C  C ++L  G   +   DSR  C+ DY 
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE 178

>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 =  113 bits (284), Expect = 3e-33
 Identities = 25/94 (26%), Positives = 35/94 (37%), Gaps = 4/94 (4%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
           C  C KPI    + +    + WH   F C  C   L    F  +D++  C        SP
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSP 67

Query: 143 RCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCG 174
           +C  C   I+  D+ V      WH + F     G
Sbjct: 68  KCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG 101

>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 = 54.7 bits (132), Expect = 1e-10
 Identities = 13/42 (30%), Positives = 15/42 (35%), Gaps = 2/42 (4%)

Query: 140 FSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGE 179
            S  C  C  PI    K V    + WH   F CA+C      
Sbjct: 4   GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLAN 45

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

 Score = 45.1 bits (107), Expect = 5e-07
 Identities = 10/33 (30%), Positives = 12/33 (36%), Gaps = 2/33 (6%)

Query: 84  CCSSCDKPIVG--QVITALGKTWHPEHFICTHC 114
            C  C K IV   Q +   G  WH + F     
Sbjct: 68  KCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 =  113 bits (285), Expect = 2e-32
 Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 4/105 (3%)

Query: 78  TTTQKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           +T +   C+ CD+ I+ + ++ AL + WH +   C+ C+  L  R  F R    YC+ D+
Sbjct: 2   STPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER-CFSRGESVYCKDDF 60

Query: 137 HNLFSPRCSYCNG--PILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
              F  +C+ C    P       A +  +H   F C  C +Q   
Sbjct: 61  FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLAT 105

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 96.4 bits (240), Expect = 8e-26
 Identities = 21/96 (21%), Positives = 29/96 (30%), Gaps = 4/96 (4%)

Query: 85  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQEL--GTRNFFERDSRPYCEPDYHNLF 140
           C++C   I     V  A    +H   F C  C ++L  G   +   DSR  C+ DY    
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

Query: 141 SPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQ 176
                   G      + A     H           Q
Sbjct: 128 QGGSGGSGGSGGGTPMVAASPERHDGGLQANPVEVQ 163

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

 Score =  110 bits (277), Expect = 1e-31
 Identities = 28/102 (27%), Positives = 42/102 (41%), Gaps = 7/102 (6%)

Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLFS 141
           C  C + I  +  + A+ + WH +   C  C   LG      + +  R  C  DY  LF 
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64

Query: 142 PR--CSYCNGPI--LDKCVTALEKTWHTEHFFCAQCGKQFGE 179
               C+ C+  I   +  +   +K +H E F CA C K F  
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCV 106

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

 Score = 67.8 bits (166), Expect = 3e-15
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 81  QKGCCSSCDKPIVGQ--VITALGKTWHPEHFICTHCNQELGTRN-FFERDSRPYCEPDYH 137
           Q G C+SCDK I      +    K +H E F C  C +     + +   +S   CE D +
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIY 124

Query: 138 NL 139
             
Sbjct: 125 EW 126

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

 Score = 54.0 bits (130), Expect = 5e-10
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 142 PRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGEAMVKF 184
             C  C   I D+  + A+++ WH +   C  CG + GE   + 
Sbjct: 3   LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRL 46

>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 =  101 bits (254), Expect = 6e-29
 Identities = 24/66 (36%), Positives = 32/66 (48%)

Query: 80  TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 139
            +   C+ C++ I G  + ALGK+WHPE F C HC   +    F E     YCE  Y   
Sbjct: 23  KRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKF 82

Query: 140 FSPRCS 145
           F+   S
Sbjct: 83  FASGPS 88

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

 Score = 73.2 bits (180), Expect = 9e-18
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 120 TRNFFERDSRPYCEPDYHN-LFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           + +  ++D+             +P C++CN  I    + AL K+WH E F CA C     
Sbjct: 3   SGSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMA 62

Query: 179 E 179
            
Sbjct: 63  Y 63

>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 = 98.2 bits (245), Expect = 1e-27
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 69  TAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERD 127
           ++  S +G        C++C +PI+ +++ A+GK +HP  F C  C++ L    F  +  
Sbjct: 2   SSGSSGEGCYVATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDAT 61

Query: 128 SRPYCEPDYHNLFSPRCS 145
           S+ +C  D+H  F+   S
Sbjct: 62  SQIHCIEDFHRKFASGPS 79

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

 Score = 66.2 bits (162), Expect = 4e-15
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S        +     +C+ C+ PILD+ + A+ K +H   F C  C +    
Sbjct: 2   SSGSSGEGCYVATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDG 53

>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 = 95.9 bits (239), Expect = 8e-27
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
           C  C KPI    +T   + WH E F+CT C ++L  + F  RD   YC   + +L++   
Sbjct: 8   CVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGP 67

Query: 145 S 145
           S
Sbjct: 68  S 68

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

 Score = 58.9 bits (143), Expect = 2e-12
 Identities = 16/40 (40%), Positives = 17/40 (42%)

Query: 140 FSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
            S  C  C  PI    VT  E+ WH E F C  C KQ   
Sbjct: 4   GSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSG 43

>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 = 94.7 bits (236), Expect = 2e-26
 Identities = 24/59 (40%), Positives = 33/59 (55%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
            C +C +PI G+V+ A+GK WH EHF+C  C +       +ER    YCE  Y+ LF  
Sbjct: 7   ICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD 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 = 65.8 bits (161), Expect = 3e-15
 Identities = 18/41 (43%), Positives = 23/41 (56%)

Query: 138 NLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG 178
           ++  P C  C  PI  + V A+ K WH EHF CA+C K F 
Sbjct: 2   SMGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFL 42

>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 = 94.7 bits (236), Expect = 3e-26
 Identities = 23/62 (37%), Positives = 34/62 (54%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
            C  C++P++   ++A+   WHPE F+C  C     T +FFE D RP+CE  YH+     
Sbjct: 17  KCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSG 76

Query: 144 CS 145
            S
Sbjct: 77  PS 78

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

 Score = 77.0 bits (190), Expect = 2e-19
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S      D+  +FSP+C  CN P+L+  ++A++  WH E F C  C   F  
Sbjct: 2   SSGSSGKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFST 53

>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 = 94.4 bits (235), Expect = 4e-26
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 72  MSRQGVTTTQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSR 129
           +S           C  C        +++ + G+ +H + F+C  C Q+     F+E + R
Sbjct: 1   ISEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGR 60

Query: 130 PYCEPDYHNLFSP 142
            YCE D+  LF+P
Sbjct: 61  KYCEHDFQMLFAP 73

>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 = 56.6 bits (137), Expect = 2e-11
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 132 CEPDYHNLFSPRCSYCNGPI--LDKCVTALEKTWHTEHFFCAQCGKQFG 178
            E   + L S  C  C G     +K V +  + +H + F CAQC +QF 
Sbjct: 2   SEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP 50

>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 = 94.3 bits (235), Expect = 5e-26
 Identities = 20/61 (32%), Positives = 28/61 (45%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
           C+ C K +    +T   + WH E  +CT C   L  + F  RD  PYC   +  LF+   
Sbjct: 18  CARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGP 77

Query: 145 S 145
           S
Sbjct: 78  S 78

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

 Score = 79.7 bits (197), Expect = 2e-20
 Identities = 16/52 (30%), Positives = 22/52 (42%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S     P Y N F+PRC+ C+  +    VT  ++ WH E   C  C      
Sbjct: 2   SSGSSGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAG 53

>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 = 97.0 bits (241), Expect = 7e-26
 Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 7/102 (6%)

Query: 85  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLF- 140
           C+ C   I  + ++ A+   WH     C+ C  +LG      + +     C  DY  LF 
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67

Query: 141 -SPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGE 179
            S  CS C   I   +  + A    +H + F C+ C  +   
Sbjct: 68  NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVP 109

>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 = 77.7 bits (191), Expect = 2e-18
 Identities = 21/102 (20%), Positives = 32/102 (31%), Gaps = 9/102 (8%)

Query: 82  KGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGT-RNFFERDSRPYCEPDYHN 138
            G CS+C + I     V+ A G  +H + F C+ C   L     F   +   +CE D   
Sbjct: 69  SGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPT 128

Query: 139 LFSPRCSYCNGPI-LDKCVTALEKTWHTEHFFCAQCGKQFGE 179
                     G          +              G +FG+
Sbjct: 129 ALINGHLNSGGSGGSGGSGGDVMVVGE-----PTLMGGEFGD 165

>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 = 57.7 bits (139), Expect = 5e-11
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 138 NLFSPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGEAMVKFI 185
           +L   RC+ C G I D+  + A++  WH+    C+ C  Q G+      
Sbjct: 2   SLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSY 50

>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 = 93.7 bits (233), Expect = 1e-25
 Identities = 22/62 (35%), Positives = 27/62 (43%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
            C  C   IVG V+ A  K  HPE F+C  CN  L  + +F  +   YCE       S  
Sbjct: 27  LCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGP 86

Query: 144 CS 145
            S
Sbjct: 87  SS 88

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

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 13/38 (34%), Positives = 16/38 (42%)

Query: 142 PRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           P C  C   I+   V A +K  H E F CA C     +
Sbjct: 26  PLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQ 63

>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 = 92.4 bits (230), Expect = 2e-25
 Identities = 19/61 (31%), Positives = 29/61 (47%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
           C  C+K I    IT   + WH + F+C  C+++L  + F   + + YC   Y N  S   
Sbjct: 8   CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPS 67

Query: 145 S 145
           S
Sbjct: 68  S 68

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

 Score = 58.2 bits (141), Expect = 3e-12
 Identities = 12/40 (30%), Positives = 17/40 (42%)

Query: 140 FSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
            S  C  CN  I    +T  ++ WH + F C  C K+   
Sbjct: 4   GSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAG 43

>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 = 91.7 bits (228), Expect = 4e-25
 Identities = 18/61 (29%), Positives = 25/61 (40%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
           C  C   IVG  +    +  HPE ++CT C   L  +  F  + + YCE       S   
Sbjct: 18  CDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS 77

Query: 145 S 145
           S
Sbjct: 78  S 78

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

 Score = 52.4 bits (126), Expect = 7e-10
 Identities = 10/40 (25%), Positives = 15/40 (37%)

Query: 140 FSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
             P C  C   I+   V   ++  H E + C  CG    +
Sbjct: 14  KLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQ 53

>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 = 91.3 bits (227), Expect = 6e-25
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 84  CCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
            CS+C + ++   + +   G+TWH   F+C+ C Q LG+R+F       YC P Y N F+
Sbjct: 7   GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA 66

Query: 142 PRCS 145
              S
Sbjct: 67  SGPS 70

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

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 140 FSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFG 178
            S  CS C   ++   + +    +TWH   F C+ C +  G
Sbjct: 4   GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG 44

>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 = 90.6 bits (225), Expect = 1e-24
 Identities = 20/67 (29%), Positives = 32/67 (47%)

Query: 79  TTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 138
           ++    C  C + I+G+VI A+  +WHPE F C  C + L    F +   R  C P ++ 
Sbjct: 2   SSGSSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNR 61

Query: 139 LFSPRCS 145
             +   S
Sbjct: 62  EKASGPS 68

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

 Score = 54.0 bits (130), Expect = 1e-10
 Identities = 11/39 (28%), Positives = 18/39 (46%)

Query: 141 SPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S  C  C   I+ + + A+  +WH E F C  C +   +
Sbjct: 5   SSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLAD 43

>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 = 89.0 bits (221), Expect = 5e-24
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 84  CCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
            C  C K I+   + +   G +WH   FIC  C Q +GT++F  +D++ +C P Y    +
Sbjct: 7   GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA 66

Query: 142 PRCS 145
              S
Sbjct: 67  SGPS 70

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

 Score = 52.0 bits (125), Expect = 7e-10
 Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 2/42 (4%)

Query: 140 FSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGE 179
            S  C  C   I+   + +     +WH   F C +C +  G 
Sbjct: 4   GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGT 45

>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 = 88.6 bits (220), Expect = 9e-24
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 85  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
           C  C K IV   Q +   G  WH + F C++C Q +GT +FF +    YC   +   F+ 
Sbjct: 18  CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAS 77

Query: 143 RCS 145
             S
Sbjct: 78  GPS 80

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

 Score = 66.2 bits (162), Expect = 3e-15
 Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 2/53 (3%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFG 178
           S            SP+C  C   I+  D+ V      WH + F C+ C +  G
Sbjct: 2   SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG 54

>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 = 85.9 bits (213), Expect = 7e-23
 Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 82  KGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 139
              C  C        +++ + G+ +H + F+C  C Q+     F+E + R YCE D+  L
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 140 FS 141
           F+
Sbjct: 71  FA 72

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 57.4 bits (139), Expect = 7e-12
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 135 DYHNLFSPRCSYCNGPI--LDKCVTALEKTWHTEHFFCAQCGKQFG 178
            +    S  C  C G     +K V +  + +H + F CAQC +QF 
Sbjct: 5   YFQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP 50

>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 = 84.8 bits (210), Expect = 2e-22
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 79  TTQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 136
           ++    C  C + +VG    + AL + +H   F+C+ C  +L  ++F+  + R YCE  Y
Sbjct: 2   SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61

Query: 137 HNLFSPRCSYC 147
                      
Sbjct: 62  VATLE-SGPSS 71

>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 = 47.1 bits (112), Expect = 6e-08
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 2/40 (5%)

Query: 141 SPRCSYCNGPILDKC--VTALEKTWHTEHFFCAQCGKQFG 178
           S  C  C   ++     V AL++ +H   F C+ C  Q  
Sbjct: 5   SSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR 44

>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 = 84.8 bits (210), Expect = 2e-22
 Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 72  MSRQGVTTTQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRP 130
            S + +       C+ C + I  GQ + AL K WH   F C  C+  L    +  +D  P
Sbjct: 5   SSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGE-YISKDGVP 63

Query: 131 YCEPDYHNLFSPRCS 145
           YCE DYH  F    S
Sbjct: 64  YCESDYHAQFGSGPS 78

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

 Score = 49.0 bits (117), Expect = 1e-08
 Identities = 12/53 (22%), Positives = 15/53 (28%), Gaps = 1/53 (1%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGE 179
           S               C+ C   I     + AL+K WH   F C  C      
Sbjct: 2   SSGSSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG 54

>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 = 82.9 bits (205), Expect = 1e-21
 Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 73  SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 132
           S +      K  C  C   I  Q +      +HP+HF C +C +EL   +  E     YC
Sbjct: 6   SGEKARGLGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTA-DARELKGELYC 64

Query: 133 EPDYHNLFSPRCS 145
            P +  +     S
Sbjct: 65  LPCHDKMGVSGPS 77

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

 Score = 53.6 bits (129), Expect = 2e-10
 Identities = 11/38 (28%), Positives = 18/38 (47%)

Query: 142 PRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
             C  C+  I ++ +      +H +HF CA CGK+   
Sbjct: 16  YICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTA 53

>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 = 79.1 bits (195), Expect = 4e-20
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 85  CSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140
           C+ C  PI G    + I+   + WH + F C  C+  L  R F        C     ++ 
Sbjct: 8   CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDIS 67

Query: 141 SPRC 144
            P  
Sbjct: 68  GPSS 71

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

 Score = 47.5 bits (113), Expect = 4e-08
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 138 NLFSPRCSYCNGPIL----DKCVTALEKTWHTEHFFCAQCGKQFGE 179
           +  S  C+ C  PI      K ++  E+ WH + F C +C      
Sbjct: 2   SSGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVG 47

>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 = 78.2 bits (193), Expect = 8e-20
 Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C +C + +   + +   G+++H   F+C  C + L +      D+  YC+  Y   + P+
Sbjct: 10  CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPK 69

Query: 144 CSYC 147
               
Sbjct: 70  GYGY 73

>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 = 40.1 bits (94), Expect = 2e-05
 Identities = 8/39 (20%), Positives = 13/39 (33%), Gaps = 1/39 (2%)

Query: 141 SPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFG 178
             +C  C   +     V    +++H   F C  C K   
Sbjct: 7   GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLD 45

>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 = 77.0 bits (190), Expect = 2e-19
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNLFSP 142
           C  CDK +   + +T+LGK WH     C  C + L +    E + +PYC  P Y  +F P
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62

Query: 143 RCSYCNGPILDK 154
           +     G     
Sbjct: 63  KGFGRGGAESHT 74

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

 Score = 48.9 bits (117), Expect = 1e-08
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 1/38 (2%)

Query: 142 PRCSYCNGPI-LDKCVTALEKTWHTEHFFCAQCGKQFG 178
           P+C  C+  +   + VT+L K WH     C +CGK   
Sbjct: 1   PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLT 38

>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 = 78.2 bits (192), Expect = 2e-19
 Identities = 20/100 (20%), Positives = 30/100 (30%), Gaps = 7/100 (7%)

Query: 85  CSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLFS 141
           C  C + I     + A+ + WH +   C  C   LG      + +  R  C  DY  L  
Sbjct: 6   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG 65

Query: 142 PRCSYCNGPILDKC----VTALEKTWHTEHFFCAQCGKQF 177
                 +G  +       +   E     E         QF
Sbjct: 66  SGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQF 105

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 142 PRCSYCNGPILDKCV-TALEKTWHTEHFFCAQCGKQFGEAMVKF 184
             C  C   I D+    A+++ WH +   C  CG + GE   + 
Sbjct: 4   LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRL 47

>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 = 79.7 bits (196), Expect = 4e-19
 Identities = 14/101 (13%), Positives = 28/101 (27%), Gaps = 1/101 (0%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C  C K +   + +   G ++H   F+C  C + L +          YC+  Y   + P+
Sbjct: 10  CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK 69

Query: 144 CSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF 184
                           E          +        + +  
Sbjct: 70  GKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQ 110

>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 = 79.3 bits (195), Expect = 6e-19
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C  C + +   + +   GK+WH   F C  C + L +    ++D   YC+  Y   F P+
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

Query: 144 CSYCN 148
                
Sbjct: 178 GFGFG 182

>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 = 61.2 bits (148), Expect = 3e-12
 Identities = 18/96 (18%), Positives = 24/96 (25%), Gaps = 2/96 (2%)

Query: 84  CCSSCDKPIVGQVITALG-KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
            C SC     G      G                +          +            S 
Sbjct: 57  YCKSCYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSD 116

Query: 143 RCSYCNGPILD-KCVTALEKTWHTEHFFCAQCGKQF 177
            C  C   +   + V    K+WH   F CA+CGK  
Sbjct: 117 GCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSL 152

>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 = 76.0 bits (187), Expect = 7e-19
 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL--GTRNFFERDSRPYCEPDYHNLFS 141
            C  C   + G  + A    +HPE F C  C   +  G      + +  YC   ++ + S
Sbjct: 17  FCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS 76

Query: 142 PRCS 145
              S
Sbjct: 77  GPSS 80

>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 = 71.7 bits (176), Expect = 3e-17
 Identities = 13/52 (25%), Positives = 18/52 (34%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S      DY   F   C  C+  +    + A E  +H E F C  C     +
Sbjct: 2   SSGSSGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIED 53

>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 = 76.9 bits (189), Expect = 7e-19
 Identities = 18/98 (18%), Positives = 33/98 (33%), Gaps = 5/98 (5%)

Query: 85  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLFS 141
           C+ C   I    ++ A+   WH     C+ C  +LG      + +     C  DY  LF 
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67

Query: 142 PRCSYCNGPILDKC--VTALEKTWHTEHFFCAQCGKQF 177
              +  +G  +     V  + +       F  +  +  
Sbjct: 68  NSGAGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLI 105

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 138 NLFSPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGEAMVKFI 185
           +L   RC+ C G I D+  + A++  WH+    C+ C  Q G+      
Sbjct: 2   SLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSY 50

>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 = 76.0 bits (187), Expect = 7e-19
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 84  CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
            C+ C + I    + +    + +H   F C  C + L    F  +DS   C   Y + FS
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 142 PRCS 145
              S
Sbjct: 77  SGPS 80

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

 Score = 61.4 bits (149), Expect = 2e-13
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S     P Y N F+  C+ C   I    + +   ++ +H   F C +C +   +
Sbjct: 2   SSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLAD 55

>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 = 75.1 bits (185), Expect = 1e-18
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSP 142
           C  CDK +   + +++LGK WH     C  C++ L      E D +P+C  P Y  LF  
Sbjct: 12  CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGS 71

Query: 143 RCS 145
             S
Sbjct: 72  GPS 74

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

 Score = 41.2 bits (97), Expect = 8e-06
 Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 1/39 (2%)

Query: 141 SPRCSYCNGPI-LDKCVTALEKTWHTEHFFCAQCGKQFG 178
           + +C  C+  +   + V++L K WH     C +C K   
Sbjct: 9   ASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLT 47

>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 = 75.3 bits (185), Expect = 2e-18
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 85  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 143
           C  C K +   + + A  + +H   F C++CN +L    +     R YC+P ++ LF  +
Sbjct: 18  CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77

Query: 144 CSYCNG 149
            +Y  G
Sbjct: 78  GNYDEG 83

>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 = 71.4 bits (175), Expect = 3e-17
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 84  CCSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 139
            C +C KPI G    + I      WH E F C  C+  L  + F  ++   +C+     +
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 140 FSPRCSYCNG 149
            +      +G
Sbjct: 67  DTDISGPSSG 76

>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 = 47.9 bits (114), Expect = 3e-08
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 4/45 (8%)

Query: 138 NLFSPRCSYCNGPIL----DKCVTALEKTWHTEHFFCAQCGKQFG 178
           +  S  C  C+ PI      K +   +  WH+E F C +C     
Sbjct: 2   SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV 46

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

 Score = 69.0 bits (169), Expect = 3e-16
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 5/61 (8%)

Query: 84  CCSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 138
            C+ C  PI G      V+   G++WH   F C  C+  L  + F     + YC      
Sbjct: 17  KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 139 L 139
           L
Sbjct: 77  L 77

>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 = 68.3 bits (167), Expect = 5e-16
 Identities = 13/57 (22%), Positives = 19/57 (33%), Gaps = 5/57 (8%)

Query: 128 SRPYCEPDYHNLFSPRCSYCNGPIL-----DKCVTALEKTWHTEHFFCAQCGKQFGE 179
           S       Y N  + +C+ C  PI         V    ++WH   F C +C      
Sbjct: 2   SSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLAN 58

>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 = 69.8 bits (170), Expect = 5e-16
 Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 3/73 (4%)

Query: 71  EMSRQGVTTTQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNF--FERD 127
                G        C+ C   I    ++ A+   WH     C+ C  +LG      + + 
Sbjct: 50  SGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKS 109

Query: 128 SRPYCEPDYHNLF 140
               C  DY  LF
Sbjct: 110 GMILCRNDYIRLF 122

>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 = 54.4 bits (130), Expect = 3e-10
 Identities = 14/80 (17%), Positives = 25/80 (31%), Gaps = 1/80 (1%)

Query: 106 PEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDK-CVTALEKTWH 164
            ++ +                            L   RC+ C G I D+  + A++  WH
Sbjct: 26  SQYKMDVTVIDTKDGSQSKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWH 85

Query: 165 TEHFFCAQCGKQFGEAMVKF 184
           +    C+ C  Q G+     
Sbjct: 86  SRCLKCSSCQAQLGDIGTSS 105

>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 = 67.9 bits (166), Expect = 8e-16
 Identities = 18/45 (40%), Positives = 24/45 (53%)

Query: 135 DYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGE 179
           DY  L+  RC  C+  I  + V+AL KT+H + F CA C   F  
Sbjct: 9   DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPP 53

>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 = 67.9 bits (166), Expect = 8e-16
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF-ERDSRPYCEPDYH 137
            C SCD+ I G+V++ALGKT+HP+ F+C  C       +          C+    
Sbjct: 17  RCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSL 71

>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 = 52.6 bits (126), Expect = 5e-10
 Identities = 17/82 (20%), Positives = 24/82 (29%), Gaps = 5/82 (6%)

Query: 67  SLTAEMSRQGVTTTQKGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQEL--GTRNF 123
           S  +    Q         C+ C + + V + +   G  +H   F C  C   L  G    
Sbjct: 2   SSGSSGQHQEAGAGDL--CALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQ 59

Query: 124 FERDSRPYCEPDYHNLFSPRCS 145
              D   YC        S   S
Sbjct: 60  HPGDGHFYCLQHLPQTDSGPSS 81

>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 = 48.9 bits (116), Expect = 1e-08
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT-RNFFERDSRPYC 132
           C SC+K I G+V+ A  K +HP   +C  C Q        + + S  + 
Sbjct: 8   CDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56

>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 = 46.6 bits (110), Expect = 7e-08
 Identities = 13/42 (30%), Positives = 18/42 (42%)

Query: 140 FSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAM 181
            S  C  C   I  + + A EK +H     C +CG+ F E  
Sbjct: 4   GSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGE 45

>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 = 40.6 bits (95), Expect = 1e-05
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 85  CSSCDKPIV--GQVITALGKTWH--PEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140
           C  C   I    Q +T    +WH   E F+C+ C++ L  + F   +   +C  +     
Sbjct: 5   CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 64

Query: 141 S 141
           S
Sbjct: 65  S 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	185
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.95
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.94
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.94
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.93
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.93
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.92
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.92
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.76
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.73
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.7
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.7
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.69
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.69
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.69
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.69
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.68
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.68
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.67
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.67
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.67
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.66
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.66
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.66
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.65
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.64
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.64
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.64
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.64
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.64
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.64
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.64
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.63
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.63
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.63
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.63
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.63
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.62
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.61
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.61
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.58
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.57
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.56
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.55
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.55
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.52
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.52
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.51
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.49
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.46
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.45
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.36
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.33
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.33
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.33
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.32
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.31
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.29
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.29
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.27
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.26
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.25
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.25
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.24
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.22
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.21
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.19
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.18
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.18
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.16
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.13
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.13
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.12
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.11
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.08
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.06
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.05
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.05
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.04
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.03
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.02
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.02
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.02
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.93
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.88
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.17
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	97.86
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	94.22
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	92.38
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	85.25
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	85.25
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	85.2
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	83.77
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	82.71
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	81.89
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	81.63
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	80.34

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

Probab=99.95  E-value=5.5e-28  Score=170.37  Aligned_cols=103  Identities=29%  Similarity=0.590  Sum_probs=96.4

Q ss_pred             CCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc--CceEEe
Q psy3656          82 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTA  158 (185)
Q Consensus        82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~--~~~~~~  158 (185)
                      .++|..|+++|. ++.+.++|+.||.+||+|..|+.+|.+..|+.++|++||+.||.++|+++|..|+++|.  +..|.+
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a   82 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTY   82 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSCEEEE
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCceEEEC
Confidence            467999999997 57899999999999999999999998888999999999999999999999999999999  578999


Q ss_pred             CCCeec--ccCcccccCCCccCCCCeee
Q psy3656         159 LEKTWH--TEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       159 ~~~~~H--~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +++.||  ++||+|..|+++|+++.|..
T Consensus        83 ~~~~~H~~~~CF~C~~C~~~l~~~~f~~  110 (126)
T 2xqn_T           83 NNFSWHASTECFLCSCCSKCLIGQKFMP  110 (126)
T ss_dssp             TTEEEESSTTTSBCTTTCCBCTTSEEEE
T ss_pred             CCCEeeCCCCCcCcCCCCCccCCCeeEe
Confidence            999999  99999999999999888754

>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=99.94  E-value=1e-27  Score=162.70  Aligned_cols=94  Identities=27%  Similarity=0.579  Sum_probs=88.3

Q ss_pred             CCCcccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc--CceE
Q psy3656          81 QKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DKCV  156 (185)
Q Consensus        81 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~--~~~~  156 (185)
                      ...+|..|+++|.  ++.+.++++.||.+||+|..|+.+|.+..|+.++|++||+.||.++|+++|..|+++|.  +..|
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~   83 (101)
T 2cup_A            4 GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNV   83 (101)
T ss_dssp             CCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSSCEE
T ss_pred             CCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCCeEE
Confidence            3578999999995  67899999999999999999999998878999999999999999999999999999999  5789


Q ss_pred             EeCCCeecccCcccccCC
Q psy3656         157 TALEKTWHTEHFFCAQCG  174 (185)
Q Consensus       157 ~~~~~~~H~~Cf~C~~C~  174 (185)
                      +++++.||++||+|..|+
T Consensus        84 ~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           84 EYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             ESSSCEEETTTCCCTTCC
T ss_pred             EeCCcchHHhCCCCCCCC
Confidence            999999999999999996

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

Probab=99.94  E-value=4.8e-27  Score=166.56  Aligned_cols=103  Identities=28%  Similarity=0.624  Sum_probs=93.4

Q ss_pred             CCcccccccccccc-eeeecCcccccCCccCCCCCCCCC--CCCeeeeCCcCCCccchhhccCC--CCCccCCcccC--c
Q psy3656          82 KGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLFSP--RCSYCNGPILD--K  154 (185)
Q Consensus        82 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~yC~~~~~~~~~~--~C~~C~~~i~~--~  154 (185)
                      ..+|..|+++|.+. .+.++++.||.+||+|..|+.+|.  +..|+.++|++||+.||.++|++  +|..|+++|.+  .
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~   81 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEM   81 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTSE
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccce
Confidence            35799999999866 689999999999999999999996  35799999999999999999998  99999999985  5


Q ss_pred             eEEeCCCeecccCcccccCCCcc-CCCCeee
Q psy3656         155 CVTALEKTWHTEHFFCAQCGKQF-GEAMVKF  184 (185)
Q Consensus       155 ~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~  184 (185)
                      .|.+.++.||++||+|..|+++| .++.|+.
T Consensus        82 ~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~  112 (131)
T 2xjy_A           82 TMRVKDKVYHLECFKCAACQKHFCVGDRYLL  112 (131)
T ss_dssp             EEEETTEEEEGGGCBCTTTCCBCCTTCEEEE
T ss_pred             eEeeCCceECccCcccCCCCCCCCCCCEEEE
Confidence            78999999999999999999999 4676653

>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=99.93  E-value=2.3e-26  Score=169.85  Aligned_cols=102  Identities=26%  Similarity=0.652  Sum_probs=91.0

Q ss_pred             CCcccccccccccc-eeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccC--ceEEe
Q psy3656          82 KGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD--KCVTA  158 (185)
Q Consensus        82 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~--~~~~~  158 (185)
                      ..+|..|+++|.++ ++.++|+.||.+||+|..|+.+|.+.. +.++|++||+.||.++|+++|..|+++|.+  .++.+
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~v~~a   84 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRA   84 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCTTSEEEEE
T ss_pred             CCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeecccccccccccccccccccCCCcEEEEc
Confidence            56899999999765 688999999999999999999997765 589999999999999999999999999986  35689


Q ss_pred             CCCeecccCcccccCCCccC-CCCeee
Q psy3656         159 LEKTWHTEHFFCAQCGKQFG-EAMVKF  184 (185)
Q Consensus       159 ~~~~~H~~Cf~C~~C~~~l~-~~~~~~  184 (185)
                      .++.||++||+|..|+++|. ++.|++
T Consensus        85 ~~~~~H~~CF~C~~C~~~L~~g~~f~~  111 (169)
T 2rgt_A           85 QDFVYHLHCFACVVCKRQLATGDEFYL  111 (169)
T ss_dssp             TTEEEEGGGCBCTTTCCBCCTTCEEEE
T ss_pred             CCceEeeCCCcCCCCCCCCCCCCceEE
Confidence            99999999999999999996 666643

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

Probab=99.93  E-value=5.2e-26  Score=169.84  Aligned_cols=104  Identities=26%  Similarity=0.645  Sum_probs=92.4

Q ss_pred             CCCCcccccccccccc-eeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccC--ceE
Q psy3656          80 TQKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD--KCV  156 (185)
Q Consensus        80 ~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~--~~~  156 (185)
                      ...++|..|+++|.+. ++.++++.||..||+|..|+.+|.... +.++|++||+.||.++|+++|..|+++|.+  .++
T Consensus        58 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~~v~  136 (182)
T 2jtn_A           58 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVR  136 (182)
T ss_dssp             CSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCC-EEETTEEECHHHHHHTTSCCCTTTCCCCCSSCCCC
T ss_pred             CCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCc-eeECCEeeecCccccccccccccCCCccCCCceEE
Confidence            3457899999999765 678999999999999999999997665 579999999999999999999999999985  356


Q ss_pred             EeCCCeecccCcccccCCCccC-CCCeee
Q psy3656         157 TALEKTWHTEHFFCAQCGKQFG-EAMVKF  184 (185)
Q Consensus       157 ~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~  184 (185)
                      .+.++.||++||+|..|+++|. ++.|++
T Consensus       137 ~a~~~~~H~~CF~C~~C~~~L~~g~~f~~  165 (182)
T 2jtn_A          137 RAQDFVYHLHCFACVVCKRQLATGDEFYL  165 (182)
T ss_dssp             EETTEECCTTTCCCTTTCCCCCTTCEEEE
T ss_pred             ecCCCCEEeCCCcCCCCCCCCCCCCceEE
Confidence            8999999999999999999996 566543

>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=99.92  E-value=1.6e-25  Score=168.56  Aligned_cols=104  Identities=24%  Similarity=0.651  Sum_probs=94.9

Q ss_pred             CCCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCC---------------
Q psy3656          80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR---------------  143 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~---------------  143 (185)
                      .+..+|..|+++|. ++.+.++|+.||.+||+|..|+.+|....|+.++|++||+.||.++|+++               
T Consensus         5 ~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~~~~   84 (192)
T 1b8t_A            5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTDK   84 (192)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCCCC
T ss_pred             CCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccEecCC
Confidence            34578999999995 78889999999999999999999999888999999999999999999876               


Q ss_pred             ---------------------------------CCccCCccc-CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         144 ---------------------------------CSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       144 ---------------------------------C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                                                       |..|+++|. ++.|.++++.||++||+|..|+++|.+..|+
T Consensus        85 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~  158 (192)
T 1b8t_A           85 GESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLA  158 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEE
T ss_pred             CcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCccc
Confidence                                             778999998 5788899999999999999999999877765

>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=99.92  E-value=5.5e-26  Score=170.56  Aligned_cols=103  Identities=23%  Similarity=0.594  Sum_probs=93.2

Q ss_pred             CCcccccccccccc-eeeecCcccccCCccCCCCCCCCCC--CCeeeeCCcCCCccchhhccCC--CCCccCCcccC--c
Q psy3656          82 KGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLFSP--RCSYCNGPILD--K  154 (185)
Q Consensus        82 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~--~~~~~~~g~~yC~~~~~~~~~~--~C~~C~~~i~~--~  154 (185)
                      ..+|..|+++|.+. ++.++++.||.+||+|..|+.+|..  ..|+.++|++||+.||.++|++  +|..|+++|.+  .
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e~   84 (188)
T 1rut_X            5 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASEL   84 (188)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTSE
T ss_pred             CCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCcE
Confidence            46899999999865 6899999999999999999999975  5789999999999999999998  79999999984  5


Q ss_pred             eEEeCCCeecccCcccccCCCccC-CCCeee
Q psy3656         155 CVTALEKTWHTEHFFCAQCGKQFG-EAMVKF  184 (185)
Q Consensus       155 ~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~  184 (185)
                      +|.|.++.||++||+|..|++.|. ++.|+.
T Consensus        85 ~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~  115 (188)
T 1rut_X           85 VMRAQGNVYHLKCFTCSTCRNRLVPGDRFHY  115 (188)
T ss_dssp             EEEETTEEECGGGCBCTTTCCBCCTTCEEEE
T ss_pred             EEEcCCCEEeCCCCeECCCCCCCCCCCeEEE
Confidence            789999999999999999999995 566653

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

Probab=99.76  E-value=1.2e-19  Score=126.93  Aligned_cols=80  Identities=20%  Similarity=0.429  Sum_probs=71.9

Q ss_pred             CCcccccccccccc-eeeecCcccccCCccCCCCCCCCC--CCCeeeeCCcCCCccchhhccCC--CCCccCCcccCceE
Q psy3656          82 KGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLFSP--RCSYCNGPILDKCV  156 (185)
Q Consensus        82 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~yC~~~~~~~~~~--~C~~C~~~i~~~~~  156 (185)
                      .++|..|+++|.+. ++.++++.||.+||+|..|+.+|.  +..|+.++|++||+.||.++|++  +|+.|+++|.+..+
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~   84 (122)
T 1m3v_A            5 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDV   84 (122)
T ss_dssp             CCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEES
T ss_pred             CCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchhe
Confidence            57899999999765 689999999999999999999996  35789999999999999999999  99999999998777


Q ss_pred             EeCCC
Q psy3656         157 TALEK  161 (185)
Q Consensus       157 ~~~~~  161 (185)
                      ++.++
T Consensus        85 ~~~g~   89 (122)
T 1m3v_A           85 MVVGE   89 (122)
T ss_dssp             SSSSS
T ss_pred             EEcCC
Confidence            66653

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

Probab=99.73  E-value=3e-18  Score=109.95  Aligned_cols=70  Identities=31%  Similarity=0.737  Sum_probs=65.1

Q ss_pred             Ccccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCc-cchhhccCCCCCccCCccc
Q psy3656          83 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSPRCSYCNGPIL  152 (185)
Q Consensus        83 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~-~~~~~~~~~~C~~C~~~i~  152 (185)
                      ++|..|+++|. ++.+.++++.||.+||+|..|+.+|....|+..+|++||. .||.++|+++|..|++.+.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~~~~   72 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCcee
Confidence            46999999996 8899999999999999999999999888899999999999 6999999999999997654

>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=99.70  E-value=1.1e-17  Score=107.25  Aligned_cols=67  Identities=24%  Similarity=0.558  Sum_probs=63.1

Q ss_pred             CCccccccccccc----ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccC
Q psy3656          82 KGCCSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCN  148 (185)
Q Consensus        82 ~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~  148 (185)
                      .++|..|+++|.+    +.+.++++.||.+||+|..|+.+|.+..|+..++++||+.||.++|+++|+.++
T Consensus         5 ~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             CCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             CCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            5689999999986    899999999999999999999999888899999999999999999999999875

>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=99.70  E-value=1.8e-17  Score=107.36  Aligned_cols=66  Identities=36%  Similarity=0.771  Sum_probs=60.5

Q ss_pred             CCCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ....+|..|+++|. ++.+.++++.||++||+|..|+.+|.+ .|+.+++++||+.||.++|+++|+.
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            44678999999996 788999999999999999999999974 7999999999999999999999974

>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=99.69  E-value=7e-18  Score=109.54  Aligned_cols=70  Identities=19%  Similarity=0.511  Sum_probs=56.3

Q ss_pred             CCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcc
Q psy3656          82 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI  151 (185)
Q Consensus        82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i  151 (185)
                      ..+|..|+++|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||+.||.++|+++|..|++..
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----------
T ss_pred             CCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            578999999995 7889999999999999999999999888899999999999999999999999998764

>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=99.69  E-value=2.2e-17  Score=114.03  Aligned_cols=67  Identities=24%  Similarity=0.545  Sum_probs=61.7

Q ss_pred             CCcccccccccccc-eeeecCcccccCCccCCCCCCCCCC--CCeeeeCCcCCCccchhhccCCCCCccC
Q psy3656          82 KGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLFSPRCSYCN  148 (185)
Q Consensus        82 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~--~~~~~~~g~~yC~~~~~~~~~~~C~~C~  148 (185)
                      .++|..|+++|.+. .+.++++.||.+||+|..|+.+|..  ..|+.++|++||+.||.++|+++|..|.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~   72 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGS   72 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCB
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCC
Confidence            46799999999866 8999999999999999999999974  5799999999999999999999998886

>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=99.69  E-value=1.7e-17  Score=109.84  Aligned_cols=66  Identities=36%  Similarity=0.820  Sum_probs=62.0

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...+|..|+++|.++.+.++++.||++||+|..|+..|.+..|+.+++++||+.||.++|+++|+.
T Consensus        24 ~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           24 RTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             CCCBBSSSCCBCCSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCCccCCCEecceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            357899999999999999999999999999999999998888999999999999999999999974

>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=99.69  E-value=1.6e-17  Score=104.52  Aligned_cols=66  Identities=29%  Similarity=0.624  Sum_probs=61.7

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      +.++|..|+++|.++.+.++++.||.+||+|..|+.+|.+..|+.+++++||+.||.++|+++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A            4 GSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             CCCCCSSSCCCCCTTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCCC
T ss_pred             CcCCCcccCCEeCcceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCCC
Confidence            357899999999888899999999999999999999998888999999999999999999999963

>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=99.68  E-value=2.2e-17  Score=104.14  Aligned_cols=66  Identities=32%  Similarity=0.676  Sum_probs=61.6

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...+|..|+++|.++.+.++++.||.+||+|..|+.+|.+..|+..++++||+.||.++|+++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            4 GSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CCCBCSSSCCBCCSSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCCCcccCCeeccceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            356899999999888899999999999999999999998888999999999999999999999974

>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=99.68  E-value=5.2e-17  Score=105.09  Aligned_cols=58  Identities=28%  Similarity=0.596  Sum_probs=54.6

Q ss_pred             CCcCCCccchhhccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +|++||+.||.++|+++|..|+++|.++.|.+.++.||++||+|..|+++|.++.|+.
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~   58 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTS   58 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTCBCSSSCCBCTTCCEEE
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecCcEEEECCchhhhhhCCcccCCCcCCCCeeEe
Confidence            5799999999999999999999999999999999999999999999999998877754

>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=99.67  E-value=4.7e-17  Score=104.55  Aligned_cols=57  Identities=23%  Similarity=0.532  Sum_probs=53.5

Q ss_pred             CCcCCCccchhhccCCCCCccCCcccC-----ceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPILD-----KCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~~-----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++++||+.||.++|+++|..|+++|.+     +.|.|.++.||++||+|..|+++|.+..|.
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~   62 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFV   62 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCC
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccE
Confidence            478999999999999999999999997     899999999999999999999999888764

>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=99.67  E-value=7.2e-17  Score=103.45  Aligned_cols=66  Identities=32%  Similarity=0.739  Sum_probs=61.3

Q ss_pred             CCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCc-cchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~-~~~~~~~~~~C~~  146 (185)
                      ..++|..|+++|. ++.+.++++.||.+||+|..|+.+|.+..|+.+++++||+ .||.++|+++|..
T Consensus         8 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            8 MASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             CCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            3578999999997 7899999999999999999999999988899999999999 7999999999964

>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=99.67  E-value=4.7e-17  Score=105.82  Aligned_cols=58  Identities=21%  Similarity=0.453  Sum_probs=54.1

Q ss_pred             CCcCCCccchhhccCCCCCccCCccc--CceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +|++||+.||.++|+++|..|+++|.  +.+|.|+++.||++||+|..|+++|+++.|+.
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~   60 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTC   60 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEE
T ss_pred             CCceechhHhCcccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEe
Confidence            58999999999999999999999999  67889999999999999999999999887753

>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=99.66  E-value=4.9e-17  Score=103.10  Aligned_cols=65  Identities=34%  Similarity=0.780  Sum_probs=60.7

Q ss_pred             CCcccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          82 KGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        82 ~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ..+|..|+++|.  ++.+.++++.||.+||+|..|+.+|....|+..++++||+.||.++|+++|+.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            5 SSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             CCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            568999999996  57899999999999999999999999888999999999999999999999974

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

Probab=99.66  E-value=7.8e-17  Score=106.42  Aligned_cols=64  Identities=34%  Similarity=0.645  Sum_probs=60.2

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ..+|..|++.|.++.+.++++.||.+||+|..|+..|....|+.+++++||+.||.++|++++.
T Consensus        25 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           25 MPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CCCcccCCCEecccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4679999999998899999999999999999999999888899999999999999999999875

>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=99.66  E-value=8.2e-17  Score=104.14  Aligned_cols=58  Identities=31%  Similarity=0.729  Sum_probs=54.1

Q ss_pred             CCcCCCccchhhccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +|++||+.||.++|+++|..|+++|.++.|.+.++.||++||+|..|+++|.+..|+.
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~   58 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFE   58 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTCBCSSSCCBSCSSCCEE
T ss_pred             CCCccchhHHhhhcCCccccCCCeecceeEEECCCeEecCcCChhhCCCCCCCCcEEe
Confidence            4789999999999999999999999999999999999999999999999998766653

>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=99.65  E-value=1.5e-16  Score=103.25  Aligned_cols=55  Identities=35%  Similarity=0.594  Sum_probs=51.2

Q ss_pred             CcCCCccchhhccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCe
Q psy3656         128 SRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMV  182 (185)
Q Consensus       128 g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~  182 (185)
                      ..+||+.||.++|+++|..|+++|.++.|.|.++.||++||+|..|+++|....|
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~   56 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDR   56 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTTSSCSSSCCCCCSSSC
T ss_pred             CCCcchHHHHhHhCCcCccccCEeccceEEECCceeCccCCccccCCCCCCCCCE
Confidence            5689999999999999999999999999999999999999999999999975444

>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=99.64  E-value=1.1e-16  Score=101.39  Aligned_cols=65  Identities=31%  Similarity=0.758  Sum_probs=60.3

Q ss_pred             CCcccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          82 KGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        82 ~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      .++|..|+++|.  +..+.++++.||.+||+|..|+.+|....|+..++++||+.||.++|+++|+.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            568999999996  35899999999999999999999999888999999999999999999999974

>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=99.64  E-value=1.2e-16  Score=103.71  Aligned_cols=57  Identities=23%  Similarity=0.328  Sum_probs=52.9

Q ss_pred             CCcCCCccchhhccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccC-CCCee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG-EAMVK  183 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~  183 (185)
                      ++.+||+.||.++|+++|..|+++|.++.|.|+++.||++||+|..|+++|. ++.|.
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~   58 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYA   58 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEE
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcCceEEEECCceeccccCCccCCCCccCCCCcEE
Confidence            3689999999999999999999999999999999999999999999999996 56665

>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=99.64  E-value=1.4e-16  Score=101.06  Aligned_cols=64  Identities=25%  Similarity=0.604  Sum_probs=59.0

Q ss_pred             CCCccccccccccc----ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCC
Q psy3656          81 QKGCCSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC  144 (185)
Q Consensus        81 ~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C  144 (185)
                      ...+|..|+++|.+    +++.++++.||.+||+|..|+.+|.+..|+.+++++||+.||.++|++++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            4 GSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             CSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            35789999999975    78899999999999999999999988888899999999999999999876

>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=99.64  E-value=1.7e-16  Score=102.90  Aligned_cols=56  Identities=27%  Similarity=0.515  Sum_probs=53.0

Q ss_pred             CCcCCCccchhhccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      +|++||++||. +++++|..|+++|.++.|.|.++.||++||+|..|+++|.++.|.
T Consensus         2 ~g~~yC~~~y~-~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~   57 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFT   57 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBCTTTCCBCCSCCEEETTEEECTTTCBCSSSCCBCTTSCEE
T ss_pred             cCCEECHHHhh-cCCCccccCCCeecceeEEECCccccHHhcCcccCCCccCCCeeE
Confidence            68999999999 789999999999999999999999999999999999999988775

>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=99.64  E-value=9.7e-17  Score=103.80  Aligned_cols=66  Identities=35%  Similarity=0.832  Sum_probs=61.8

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...+|..|+++|.++.+.++++.||.+||+|..|+.+|..+.|+.+++++||+.||.++|+++|+.
T Consensus        14 ~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           14 FSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CSCBCTTTCCBCCSSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             cCCccccCCCeecceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            357899999999889999999999999999999999998888999999999999999999999974

>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=99.64  E-value=7.3e-17  Score=100.60  Aligned_cols=62  Identities=39%  Similarity=0.956  Sum_probs=58.5

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR  143 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~  143 (185)
                      ..+|..|+++|.++.+.++++.||.+||+|..|+.+|.+..|+.++|++||+.||.++|+++
T Consensus         5 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            5 VPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCEETTTTEECCSCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCCcccCCEecceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            57899999999988999999999999999999999998888999999999999999999875

>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=99.64  E-value=2.5e-16  Score=104.38  Aligned_cols=69  Identities=26%  Similarity=0.641  Sum_probs=62.8

Q ss_pred             CCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCC
Q psy3656          81 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNG  149 (185)
Q Consensus        81 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~  149 (185)
                      ....|..|++.|. .+.+.++++.||.+||+|..|+..|....|+..++++||+.||.++|+++|..+..
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g   83 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEG   83 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCC
Confidence            4578999999996 47889999999999999999999998888999999999999999999999985544

>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=1.7e-16  Score=100.09  Aligned_cols=65  Identities=31%  Similarity=0.661  Sum_probs=60.1

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCC
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      +..+|..|+++|.++.+.++++.||.+||+|..|+.+|....|+.+++++||+.||.++|+++..
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            4 GSSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             CSSBCSSSCCBCCSCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCCcCccCCCEecceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            45789999999998899999999999999999999999988888999999999999999987654

>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=99.63  E-value=1.7e-16  Score=102.87  Aligned_cols=66  Identities=30%  Similarity=0.663  Sum_probs=60.2

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeee-CCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFER-DSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~-~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...+|..|+++|.++.+.++++.||++||+|..|+.+|.+..|+.. +|++||+.||.++|+++|++
T Consensus        14 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           14 TLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             SCCBCTTTCCBCCSCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CCCccccCCCeecceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            4578999999999889999999999999999999999987777765 78999999999999999974

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

Probab=99.63  E-value=1.3e-16  Score=102.39  Aligned_cols=66  Identities=27%  Similarity=0.707  Sum_probs=58.5

Q ss_pred             CCCCcccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCC
Q psy3656          80 TQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        80 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ....+|..|+++|.  +..+.++|+.||.+||+|..|+.+|..+.|+.++|++||+.||.++|+++|.
T Consensus         9 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A            9 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            34678999999995  3567899999999999999999999888899999999999999999999996

>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=99.63  E-value=3.3e-16  Score=101.76  Aligned_cols=57  Identities=25%  Similarity=0.438  Sum_probs=53.0

Q ss_pred             CCcCCCccchhhccCCCCCccCCccc--CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++.+||++||.++|+++|..|+++|.  ++.|.+.++.||++||+|..|+++|.+..|+
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   59 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFF   59 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEE
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccE
Confidence            46899999999999999999999999  6789999999999999999999999887765

>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=99.63  E-value=2.3e-16  Score=101.99  Aligned_cols=66  Identities=30%  Similarity=0.645  Sum_probs=61.7

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...+|..|+++|.++.+.++++.||.+||+|..|+.+|.+..|+.+++++||+.||.++|+++|++
T Consensus        14 ~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           14 FAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             SSCCCTTTCCCCCSCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             cCCcCCCCCCEecCcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            457899999999888999999999999999999999998778999999999999999999999974

>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=99.62  E-value=9.2e-17  Score=103.74  Aligned_cols=64  Identities=28%  Similarity=0.590  Sum_probs=59.7

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ..+|..|+++|.++.+.++++.||.+||+|..|+..|....|+.+++++||+.||.++|++++.
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCccccCCCCccCcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4679999999998899999999999999999999999877899999999999999999998864

>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=99.61  E-value=4.2e-16  Score=101.26  Aligned_cols=66  Identities=24%  Similarity=0.455  Sum_probs=60.7

Q ss_pred             CCCcccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          81 QKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        81 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...+|..|+++|.  +.++.++++.||.+||+|..|+.+|.+..|+..++++||+.||.++|+++|++
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            3568999999997  56888999999999999999999998888999999999999999999999974

>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=99.61  E-value=5.5e-16  Score=100.09  Aligned_cols=65  Identities=28%  Similarity=0.465  Sum_probs=59.0

Q ss_pred             CCCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCC
Q psy3656          80 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        80 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ....+|..|+++|.++.+.++++.||.+||+|..|+.+|... ++.++|++||..||.++|++++.
T Consensus        13 ~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           13 LGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTAD-ARELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCCBCTTTCCBCCSCCCCCSSSCCCTTTSBCSSSCCBCCTT-CEEETTEEECHHHHHTTSCCSSC
T ss_pred             cCCCCCccCCCEecceEEEECcceeCCCCCEeCCCCCccCCC-CEeECCEEeCHHHHHHhCCCCCC
Confidence            346789999999998899999999999999999999999866 46999999999999999998765

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

Probab=99.58  E-value=1.4e-15  Score=98.78  Aligned_cols=65  Identities=32%  Similarity=0.661  Sum_probs=60.1

Q ss_pred             CCCcccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCC
Q psy3656          81 QKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        81 ~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ...+|..|+++|.  ++.+.++++.||.+||+|..|+.+|....|+.+++++||+.||.++|+++|.
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            3578999999996  5679999999999999999999999988899999999999999999999886

>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=99.57  E-value=1.3e-15  Score=96.48  Aligned_cols=66  Identities=26%  Similarity=0.647  Sum_probs=58.6

Q ss_pred             CCCccccccccccc--ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCcc
Q psy3656          81 QKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYC  147 (185)
Q Consensus        81 ~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C  147 (185)
                      ...+|..|+++|.+  ..+.++++.||.+||+|..|+.+|.+..|+.+++++||+.||.++| .+|..+
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~-~~~~~~   71 (72)
T 1x61_A            4 GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL-ESGPSS   71 (72)
T ss_dssp             CCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHH-HTCSSC
T ss_pred             CCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHH-ccCCCC
Confidence            35789999999963  5889999999999999999999998778999999999999999998 566654

>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=99.56  E-value=3.1e-15  Score=97.22  Aligned_cols=64  Identities=19%  Similarity=0.353  Sum_probs=56.8

Q ss_pred             CCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCee--eeCCcCCCccchhhccCCCC
Q psy3656          81 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFF--ERDSRPYCEPDYHNLFSPRC  144 (185)
Q Consensus        81 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~--~~~g~~yC~~~~~~~~~~~C  144 (185)
                      ...+|..|++.|+ .+.+.++++.||.+||+|..|+..|....|+  .+++++||+.||.++|+..+
T Consensus        14 ~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~   80 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPS   80 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCC
T ss_pred             CCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCC
Confidence            3578999999995 6788999999999999999999999888887  47999999999999987543

>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=99.55  E-value=1.9e-15  Score=113.31  Aligned_cols=71  Identities=23%  Similarity=0.592  Sum_probs=66.2

Q ss_pred             CCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcc
Q psy3656          81 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI  151 (185)
Q Consensus        81 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i  151 (185)
                      +..+|..|+++|. ++.+.++++.||.+||+|..|+.+|....|+.+++++||+.||.++|+++|..|++++
T Consensus       114 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~  185 (192)
T 1b8t_A          114 GSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA  185 (192)
T ss_dssp             CCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             CCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCcc
Confidence            3568999999996 5788999999999999999999999888899999999999999999999999999985

>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=99.55  E-value=6.3e-15  Score=93.64  Aligned_cols=62  Identities=24%  Similarity=0.482  Sum_probs=56.6

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCC-CCCeeeeCCcCCCccchhhccCCC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG-TRNFFERDSRPYCEPDYHNLFSPR  143 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~yC~~~~~~~~~~~  143 (185)
                      .++|..|+++|.++.+.++++.||.+||+|..|+.+|. +..|+..++++||..||..++...
T Consensus         5 ~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~   67 (73)
T 1wig_A            5 SSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTED   67 (73)
T ss_dssp             CCSCSSSCCCCSSCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSS
T ss_pred             cCCcccCCCEecCeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccc
Confidence            56899999999989999999999999999999999998 667889999999999999887643

>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=99.52  E-value=6.7e-15  Score=102.75  Aligned_cols=61  Identities=25%  Similarity=0.651  Sum_probs=55.3

Q ss_pred             CCCcccccccccccc-eeeecCcccccCCccCCCCCCCCC--CCCeeeeCCcCCCccchhhccC
Q psy3656          81 QKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      ...+|..|+++|.+. ++.++++.||..||+|..|+..|.  +..|+.++|++||+.||.++||
T Consensus        60 ~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           60 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             SCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             cCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            357899999999765 699999999999999999999996  3579999999999999999985

>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=99.51  E-value=6.5e-15  Score=93.01  Aligned_cols=62  Identities=27%  Similarity=0.762  Sum_probs=55.5

Q ss_pred             CCCCcccccccccc-cc-eeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656          80 TQKGCCSSCDKPIV-GQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      ....+|..|+++|. ++ .+.++++.||.+||+|..|+.+|..+.|+..+|++||+.||.++|+
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            34678999999996 44 5689999999999999999999988889999999999999999885

>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=99.49  E-value=1.8e-14  Score=93.25  Aligned_cols=65  Identities=22%  Similarity=0.441  Sum_probs=58.3

Q ss_pred             CCCcccccccccccceeeecCcccccCCccCCCCCCCCCC-CCee-eeCCcCCCccchhhccCCCCC
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT-RNFF-ERDSRPYCEPDYHNLFSPRCS  145 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~-~~~~-~~~g~~yC~~~~~~~~~~~C~  145 (185)
                      ...+|..|+++|.++.+.++++.||.+||+|..|+..|.. ..|. ..++++||+.||.++|++.|.
T Consensus        14 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           14 FGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             SSCBCTTTCCBCCSCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             cCCcCccCCCCcCceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            3568999999999889999999999999999999999974 5566 589999999999999998775

>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=99.46  E-value=5e-14  Score=90.22  Aligned_cols=58  Identities=28%  Similarity=0.696  Sum_probs=53.5

Q ss_pred             CCCccccccccccc-----ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656          81 QKGCCSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN  138 (185)
Q Consensus        81 ~~~~C~~C~~~i~~-----~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~  138 (185)
                      ..++|..|+++|.+     +.+.++++.||.+||+|..|+.+|.+..|+.+++++||+.||.+
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            45789999999985     78999999999999999999999988889999999999999965

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

Probab=99.45  E-value=3.5e-14  Score=88.08  Aligned_cols=57  Identities=25%  Similarity=0.546  Sum_probs=52.1

Q ss_pred             Ccccccccccc--cceeeecCcccc--cCCccCCCCCCCCCCCCeeeeCCcCCC-ccchhhc
Q psy3656          83 GCCSSCDKPIV--GQVITALGKTWH--PEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNL  139 (185)
Q Consensus        83 ~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C~~C~~~L~~~~~~~~~g~~yC-~~~~~~~  139 (185)
                      ++|..|+++|.  ++.+.++++.||  .+||+|..|+.+|.+..|+.++|++|| .+||.++
T Consensus         3 ~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            3 VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             EECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             CCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            57999999997  689999999999  999999999999988889999999999 7888653

>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=99.36  E-value=3.8e-13  Score=85.33  Aligned_cols=46  Identities=26%  Similarity=0.507  Sum_probs=41.9

Q ss_pred             hccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccC-CCCee
Q psy3656         138 NLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFG-EAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~  183 (185)
                      .+|+++|..|+++|.++.|.|+++.||++||+|..|+++|. ++.|.
T Consensus         2 s~~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~   48 (73)
T 1wig_A            2 SSGSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMY   48 (73)
T ss_dssp             CCSCCSCSSSCCCCSSCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCE
T ss_pred             CcCcCCcccCCCEecCeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeE
Confidence            35789999999999999999999999999999999999998 66664

>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=99.33  E-value=5e-13  Score=86.39  Aligned_cols=60  Identities=30%  Similarity=0.579  Sum_probs=52.2

Q ss_pred             CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCC-cCCCccchhhccC
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDS-RPYCEPDYHNLFS  141 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g-~~yC~~~~~~~~~  141 (185)
                      ..+|..|+++|.++.+.++++.||.+||+|..|+.+|..+.++..++ .+||..||.+++.
T Consensus        15 ~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           15 GTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCBCTTTCCBCCSCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             CCcCccccCEeccceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            46899999999988999999999999999999999998777665555 4799999987764

>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=99.33  E-value=1.4e-12  Score=86.00  Aligned_cols=55  Identities=29%  Similarity=0.458  Sum_probs=48.0

Q ss_pred             CCCccchhhccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         130 PYCEPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       130 ~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      ..+...+...+.++|..|+++|.++.|.+.++.||++||+|..|++.|.+..|+.
T Consensus        14 ~~~~~~~~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~   68 (90)
T 2dar_A           14 QRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVE   68 (90)
T ss_dssp             BCCEEECTTTCCCBBSSSCCBCCSCEEEETTEEECTTTCBCSSSCCBCSSSCBEE
T ss_pred             hhcccCCCCCCCCCCccCCCEecceEEEECCccccccCCccCCCCCCCCCCEeEe
Confidence            3445556678889999999999999999999999999999999999998877753

>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=99.33  E-value=5.6e-13  Score=99.52  Aligned_cols=86  Identities=22%  Similarity=0.429  Sum_probs=65.7

Q ss_pred             ccccccccccc--ceeeecCcccccCCccCCCCCCCCC-CCCeeeeCCcCCCccchhhccCCCCCccCCc----------
Q psy3656          84 CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELG-TRNFFERDSRPYCEPDYHNLFSPRCSYCNGP----------  150 (185)
Q Consensus        84 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~----------  150 (185)
                      +|..|+++|..  .++.++++.||..||+|..|++.|. +..|+..++++||..||.++|+++|...+..          
T Consensus        71 ~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~~~g~~~~~~~~~~~v  150 (188)
T 1rut_X           71 ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGSGGDV  150 (188)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC----------------CCC
T ss_pred             ccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhcccccccCCCCcccccCCcc
Confidence            69999999963  4678999999999999999999996 4568899999999999999999999887752          


Q ss_pred             -ccCceEEeCCCeecccCccc
Q psy3656         151 -ILDKCVTALEKTWHTEHFFC  170 (185)
Q Consensus       151 -i~~~~~~~~~~~~H~~Cf~C  170 (185)
                       +.++ ..+++..||++..+.
T Consensus       151 ~vvge-p~l~g~~~~~~~~r~  170 (188)
T 1rut_X          151 MVVGE-PTLMGGEFGDEDERL  170 (188)
T ss_dssp             EECCC-CEETTCCCCCTTEEE
T ss_pred             cccCC-CcccCCCCCCCCCce
Confidence             2233 356788999998884

>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=99.32  E-value=1.3e-12  Score=83.38  Aligned_cols=47  Identities=26%  Similarity=0.497  Sum_probs=43.0

Q ss_pred             hccCCCCCccCCcccC----ceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         138 NLFSPRCSYCNGPILD----KCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      ++|+++|..|+++|.+    +.|.++++.||++||+|..|+++|.+..|+.
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~   52 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLT   52 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEE
T ss_pred             CccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEe
Confidence            4688999999999997    8999999999999999999999999887753

>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=99.31  E-value=8.8e-13  Score=81.86  Aligned_cols=46  Identities=39%  Similarity=0.779  Sum_probs=42.3

Q ss_pred             hccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         138 NLFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++++++|..|+++|.++.|.|.++.||++||+|..|+++|.++.|+
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   47 (66)
T 1nyp_A            2 SMGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHY   47 (66)
T ss_dssp             CCCCCEETTTTEECCSCEECCTTSBEETTTCBCTTTCCBCSSSCCE
T ss_pred             CcCCCCCcccCCEecceEEEECccccccCcCEECCCCCCCCCCceE
Confidence            3577999999999999999999999999999999999999887765

>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=99.29  E-value=2.7e-12  Score=80.29  Aligned_cols=46  Identities=26%  Similarity=0.570  Sum_probs=42.3

Q ss_pred             ccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         139 LFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      .++++|..|+++|.++.|.+.++.||++||+|..|+++|.++.|..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~   48 (69)
T 2cur_A            3 SGSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTA   48 (69)
T ss_dssp             CCCCCCSSSCCCCCTTCEEETTEEECTTTTBCTTTCCBCTTSCEEE
T ss_pred             CCcCCCcccCCEeCcceEEECccccccCcCEECCCCCCCCCCccEe
Confidence            5678999999999999999999999999999999999998887753

>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=99.29  E-value=2.9e-12  Score=80.41  Aligned_cols=46  Identities=35%  Similarity=0.608  Sum_probs=42.2

Q ss_pred             ccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         139 LFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      +++++|..|+++|.++.|.++++.||++||+|..|+++|.+..|..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~   48 (70)
T 2d8z_A            3 SGSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTA   48 (70)
T ss_dssp             CCCCBCSSSCCBCCSSEEESSSSEEETTTSBCSSSCCBCTTSCCEE
T ss_pred             CCCCCCcccCCeeccceEEECccccCCCCCccCCCCCcCCcCceEe
Confidence            5678999999999999999999999999999999999998877753

>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=99.27  E-value=3.4e-12  Score=80.51  Aligned_cols=46  Identities=26%  Similarity=0.520  Sum_probs=41.7

Q ss_pred             ccCCCCCccCCcccC----ceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         139 LFSPRCSYCNGPILD----KCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      .++++|..|+++|.+    +.|.++++.||++||+|..|+++|.+..|..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~   52 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLT   52 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEE
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEe
Confidence            467899999999996    7899999999999999999999999887763

>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=99.26  E-value=5.5e-12  Score=79.49  Aligned_cols=46  Identities=22%  Similarity=0.541  Sum_probs=41.7

Q ss_pred             hccCCCCCccCCccc--CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         138 NLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++|+++|..|+++|.  +..|.+.++.||++||+|..|+++|.+..|.
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   49 (72)
T 1x4k_A            2 SSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFI   49 (72)
T ss_dssp             CSCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEE
T ss_pred             CccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccC
Confidence            467899999999999  4689999999999999999999999887765

>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=99.25  E-value=4.8e-12  Score=79.78  Aligned_cols=46  Identities=24%  Similarity=0.577  Sum_probs=41.9

Q ss_pred             hccCCCCCccCCccc--CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         138 NLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++++++|..|+++|.  ++.|.+.++.||++||+|..|+++|.+..|+
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   49 (72)
T 1wyh_A            2 SSGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFV   49 (72)
T ss_dssp             CCCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEE
T ss_pred             CccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccC
Confidence            467899999999999  6889999999999999999999999887765

>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=99.25  E-value=5.3e-12  Score=79.19  Aligned_cols=44  Identities=25%  Similarity=0.606  Sum_probs=40.7

Q ss_pred             cCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         140 FSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       140 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      +.++|..|+++|.++.|.+.++.||++||+|..|+++|.+..|.
T Consensus         4 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~   47 (70)
T 2d8x_A            4 GSSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFV   47 (70)
T ss_dssp             CSSBCSSSCCBCCSCCEEETTEEECTTTSBCSSSCCBCSSSCCE
T ss_pred             CCCcCccCCCEecceEEEECcccccccCCEeCCCCCcCCCCccE
Confidence            45899999999999999999999999999999999999887765

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

Probab=99.24  E-value=4e-12  Score=78.67  Aligned_cols=45  Identities=29%  Similarity=0.456  Sum_probs=40.6

Q ss_pred             cCCCCCccCCccc--CceEEeCCCeec--ccCcccccCCCccCCCCeee
Q psy3656         140 FSPRCSYCNGPIL--DKCVTALEKTWH--TEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       140 ~~~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      |+++|..|+++|.  ++.|.++++.||  ++||+|..|+++|.+..|+.
T Consensus         1 fa~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~   49 (65)
T 2iyb_E            1 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMP   49 (65)
T ss_dssp             -CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEE
T ss_pred             CcCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEE
Confidence            5688999999999  689999999999  99999999999999887753

>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=99.22  E-value=1.2e-11  Score=77.95  Aligned_cols=46  Identities=24%  Similarity=0.470  Sum_probs=41.2

Q ss_pred             ccCCCCCccCCcccC--ceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         139 LFSPRCSYCNGPILD--KCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      .++++|..|+++|.+  ..|.++++.||++||+|..|+++|.++.|+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~   50 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYA   50 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEE
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEe
Confidence            467899999999984  6899999999999999999999998887754

>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=99.21  E-value=1.2e-11  Score=78.87  Aligned_cols=46  Identities=22%  Similarity=0.546  Sum_probs=41.7

Q ss_pred             hccCCCCCccCCccc-CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         138 NLFSPRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ..+.++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|.
T Consensus         6 ~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~   52 (76)
T 2cu8_A            6 SGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHA   52 (76)
T ss_dssp             CCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCE
T ss_pred             CCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceE
Confidence            356789999999998 7899999999999999999999999887765

>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=99.19  E-value=9.7e-12  Score=79.95  Aligned_cols=44  Identities=27%  Similarity=0.541  Sum_probs=40.3

Q ss_pred             ccCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCe
Q psy3656         139 LFSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMV  182 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~  182 (185)
                      .+.++|..|+++|.++.|.++++.||++||+|..|+++|.+..|
T Consensus        13 ~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f   56 (79)
T 2cor_A           13 LGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTADAR   56 (79)
T ss_dssp             CCCCBCTTTCCBCCSCCCCCSSSCCCTTTSBCSSSCCBCCTTCE
T ss_pred             cCCCCCccCCCEecceEEEECcceeCCCCCEeCCCCCccCCCCE
Confidence            44589999999999999999999999999999999999987754

>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=99.18  E-value=7.2e-12  Score=80.51  Aligned_cols=44  Identities=25%  Similarity=0.575  Sum_probs=39.9

Q ss_pred             CCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         141 SPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       141 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      .++|..|+++|.++.|.|+++.||++||+|..|+++|.+..|+.
T Consensus        15 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~   58 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFF   58 (79)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTTSCSSSCCCHHHHCCEE
T ss_pred             CCccccCCCCccCcEEEECcceeCcCcCeeCCCCCCCCCCCeEe
Confidence            47999999999999999999999999999999999997766653

>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=99.16  E-value=2.2e-11  Score=79.98  Aligned_cols=44  Identities=32%  Similarity=0.594  Sum_probs=40.4

Q ss_pred             CCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656         141 SPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF  184 (185)
Q Consensus       141 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  184 (185)
                      .++|..|+++|.++.|.|+++.||++||+|..|++.|.+..|+.
T Consensus        25 ~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~   68 (89)
T 1x64_A           25 MPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFF   68 (89)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTCCCSSSCCCTTTSCCEE
T ss_pred             CCCcccCCCEecccEEEECCceECccCCEecCCCCCCCCCCeEe
Confidence            47899999999999999999999999999999999998876653

>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=99.13  E-value=4.2e-11  Score=76.25  Aligned_cols=42  Identities=31%  Similarity=0.748  Sum_probs=38.8

Q ss_pred             CCCCccCCccc-CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         142 PRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       142 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++|..|+++|. ++.|.+.++.||++||+|..|+++|.+..|.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~   43 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHA   43 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEE
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceE
Confidence            57999999998 8899999999999999999999999887765

>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=99.13  E-value=3.2e-11  Score=75.80  Aligned_cols=47  Identities=32%  Similarity=0.595  Sum_probs=40.3

Q ss_pred             hhccCCCCCccCCcccC--ceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         137 HNLFSPRCSYCNGPILD--KCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       137 ~~~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ...++++|..|+++|.+  .+|.+.++.||++||+|..|+++|....|+
T Consensus         7 ~~~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~   55 (72)
T 3f6q_B            7 QGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFY   55 (72)
T ss_dssp             CCCTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCE
T ss_pred             cCcCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeE
Confidence            34677999999999984  367899999999999999999999766654

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

Probab=99.12  E-value=3.6e-11  Score=83.90  Aligned_cols=59  Identities=24%  Similarity=0.556  Sum_probs=53.3

Q ss_pred             CCcccccccccc--cceeeecCcccc--cCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656          82 KGCCSSCDKPIV--GQVITALGKTWH--PEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  140 (185)
Q Consensus        82 ~~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~  140 (185)
                      .++|..|+++|.  +..+.++++.||  .+||+|..|+++|.+..|+..+|++||..+|.++|
T Consensus        63 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           63 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             CCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             CccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence            467999999996  468999999999  99999999999998778889999999998888766

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

Probab=99.11  E-value=1.6e-11  Score=86.32  Aligned_cols=58  Identities=28%  Similarity=0.537  Sum_probs=52.2

Q ss_pred             ccccccccccc--ceeeecCcccccCCccCCCCCCCCC-CCCeeeeCCcCCCccchhhccC
Q psy3656          84 CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELG-TRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus        84 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      +|..|+++|.+  ..+.++++.||.+||+|..|+..|. +..|+..++++||..||.++|+
T Consensus        68 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~  128 (131)
T 2xjy_A           68 LCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTK  128 (131)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHH
T ss_pred             ChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhh
Confidence            79999999964  4788999999999999999999995 5568899999999999998875

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

Probab=99.08  E-value=5.6e-11  Score=75.79  Aligned_cols=46  Identities=35%  Similarity=0.663  Sum_probs=40.0

Q ss_pred             hccCCCCCccCCccc--CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         138 NLFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ..++++|..|+++|.  +.+|.+.++.||++||+|..|+++|.+..|+
T Consensus         8 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   55 (77)
T 1g47_A            8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFY   55 (77)
T ss_dssp             CCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSE
T ss_pred             CCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeE
Confidence            355689999999996  5678999999999999999999999776654

>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=99.06  E-value=8.8e-11  Score=75.93  Aligned_cols=42  Identities=14%  Similarity=0.328  Sum_probs=38.4

Q ss_pred             CCCCccCCccc-CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         142 PRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       142 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ++|..|+++|. .+.|.++++.||++||+|..|+++|....|.
T Consensus        16 ~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~   58 (82)
T 2co8_A           16 DLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYE   58 (82)
T ss_dssp             CBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEE
T ss_pred             CCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCcee
Confidence            78999999996 5778899999999999999999999888776

>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=99.05  E-value=1.3e-10  Score=74.86  Aligned_cols=44  Identities=20%  Similarity=0.494  Sum_probs=38.8

Q ss_pred             cCCCCCccCCccc-CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         140 FSPRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       140 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ..++|..|+++|. ++.|.+.++.||++||+|..|+++|.+..|.
T Consensus         6 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   50 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVA   50 (81)
T ss_dssp             --CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCE
T ss_pred             CCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeE
Confidence            3589999999996 7889999999999999999999999887765

>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=99.05  E-value=1.7e-10  Score=74.28  Aligned_cols=42  Identities=26%  Similarity=0.593  Sum_probs=37.6

Q ss_pred             CCCCCccCCccc-CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         141 SPRCSYCNGPIL-DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       141 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      .++|..|+++|. ++.|.++++.||++||+|..|+++|.+ .|+
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~   57 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYI   57 (80)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCE
T ss_pred             CCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeE
Confidence            378999999997 788999999999999999999999986 443

>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=99.04  E-value=1.2e-10  Score=80.98  Aligned_cols=46  Identities=30%  Similarity=0.671  Sum_probs=39.8

Q ss_pred             hccCCCCCccCCcccCc-eEEeCCCeecccCcccccCCCccC--CCCee
Q psy3656         138 NLFSPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFG--EAMVK  183 (185)
Q Consensus       138 ~~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~  183 (185)
                      ..+.++|..|+++|.+. .|.|+++.||++||+|..|++.|.  +..|+
T Consensus        58 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~  106 (123)
T 2l4z_A           58 GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSY  106 (123)
T ss_dssp             CSSCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCB
T ss_pred             CccCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceE
Confidence            34568999999999987 589999999999999999999996  45554

>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=99.03  E-value=2e-10  Score=75.70  Aligned_cols=44  Identities=16%  Similarity=0.418  Sum_probs=39.3

Q ss_pred             cCCCCCccCCcccC-ceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         140 FSPRCSYCNGPILD-KCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       140 ~~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      ...+|..|+++|.+ +.|.++++.||++||+|..|+++|....|+
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~   58 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYA   58 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcE
Confidence            45899999999985 788999999999999999999999877654

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

Probab=99.02  E-value=2.3e-10  Score=76.69  Aligned_cols=45  Identities=29%  Similarity=0.502  Sum_probs=40.8

Q ss_pred             ccCCCCCccCCccc--CceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656         139 LFSPRCSYCNGPIL--DKCVTALEKTWHTEHFFCAQCGKQFGEAMVK  183 (185)
Q Consensus       139 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~  183 (185)
                      .++++|..|+++|.  ++.|.++++.||++||+|..|+++|.+..|+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~   49 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFV   49 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCE
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeE
Confidence            46789999999997  6889999999999999999999999887765

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

Probab=99.02  E-value=2.8e-10  Score=84.33  Aligned_cols=56  Identities=25%  Similarity=0.533  Sum_probs=47.3

Q ss_pred             CCcCCCccchh---hccCCCCCccCCcccCc-eEEeCCCeecccCcccccCCCccCCCCe
Q psy3656         127 DSRPYCEPDYH---NLFSPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGEAMV  182 (185)
Q Consensus       127 ~g~~yC~~~~~---~~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~  182 (185)
                      ++..||..++.   ....++|..|+++|.+. ++.|.++.||++||+|..|+++|++..|
T Consensus        43 ~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f  102 (182)
T 2jtn_A           43 DDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF  102 (182)
T ss_dssp             SSSCSSSSSCCCCCCCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE
T ss_pred             ccccccccccccCCCCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce
Confidence            56678887765   34458999999999976 5789999999999999999999988765

>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=99.02  E-value=1.3e-10  Score=85.16  Aligned_cols=86  Identities=26%  Similarity=0.385  Sum_probs=62.4

Q ss_pred             CCccccccccccc-c-eeeecCcccccCCccCCCCCCCCCCC-Cee-eeCCcCCCccchhhccCCCCC--ccCCcccCce
Q psy3656          82 KGCCSSCDKPIVG-Q-VITALGKTWHPEHFICTHCNQELGTR-NFF-ERDSRPYCEPDYHNLFSPRCS--YCNGPILDKC  155 (185)
Q Consensus        82 ~~~C~~C~~~i~~-~-~~~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~yC~~~~~~~~~~~C~--~C~~~i~~~~  155 (185)
                      .++|..|+++|.+ + ++.++++.||.+||+|..|+..|..+ .|+ ..+|++||..||.+.+...+.  ....+.  ..
T Consensus        65 ~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~~~~~~~~rpr--t~  142 (169)
T 2rgt_A           65 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGGSGGSGGSGGG--TP  142 (169)
T ss_dssp             SCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC------------EE
T ss_pred             cccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhccCCCCCCcCCC--Cc
Confidence            4679999999964 4 56899999999999999999999744 555 568999999999988765442  222222  25


Q ss_pred             EEeCCCeecccCcc
Q psy3656         156 VTALEKTWHTEHFF  169 (185)
Q Consensus       156 ~~~~~~~~H~~Cf~  169 (185)
                      +.+....+|...|.
T Consensus       143 ~~~~q~~~l~~~f~  156 (169)
T 2rgt_A          143 MVAASPERHDGGLQ  156 (169)
T ss_dssp             EECCCCEECCSSCC
T ss_pred             ccHHHHHHHHHHHh
Confidence            56666777777765

>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=98.93  E-value=6.3e-10  Score=76.32  Aligned_cols=42  Identities=29%  Similarity=0.699  Sum_probs=37.6

Q ss_pred             CCCCccCCcccCc-eEEeCCCeecccCcccccCCCccCC--CCee
Q psy3656         142 PRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFGE--AMVK  183 (185)
Q Consensus       142 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~  183 (185)
                      ++|..|+++|.+. .|.|+++.||++||+|..|+++|+.  ..|+
T Consensus         4 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~   48 (114)
T 1j2o_A            4 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLY   48 (114)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCC
T ss_pred             CCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeE
Confidence            6899999999987 7899999999999999999999974  4553

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

Probab=98.88  E-value=4.9e-10  Score=77.80  Aligned_cols=45  Identities=31%  Similarity=0.683  Sum_probs=39.0

Q ss_pred             ccCCCCCccCCcccCc-eEEeCCCeecccCcccccCCCccC--CCCee
Q psy3656         139 LFSPRCSYCNGPILDK-CVTALEKTWHTEHFFCAQCGKQFG--EAMVK  183 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~  183 (185)
                      ++.++|..|+++|.+. .|.|+++.||++||+|..|+++|+  +..|+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~   50 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSY   50 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCE
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEE
Confidence            4568999999999987 589999999999999999999997  34453

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

Probab=98.17  E-value=6e-07  Score=46.78  Aligned_cols=28  Identities=29%  Similarity=0.684  Sum_probs=25.4

Q ss_pred             CCcccccccccc-cceeeecCcccccCCc
Q psy3656          82 KGCCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      .+.|..|++.|+ ++.+.++|+.||+.||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEEECCeEecccCC
Confidence            467999999995 7899999999999998

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

Probab=97.86  E-value=4.5e-06  Score=43.39  Aligned_cols=28  Identities=32%  Similarity=0.802  Sum_probs=25.0

Q ss_pred             CCCCCccCCccc-CceEEeCCCeecccCc
Q psy3656         141 SPRCSYCNGPIL-DKCVTALEKTWHTEHF  168 (185)
Q Consensus       141 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  168 (185)
                      .++|..|++.|. .+.|.+.|+.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEEECCeEecccCC
Confidence            578999999997 4778899999999998

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=94.22  E-value=0.02  Score=39.01  Aligned_cols=91  Identities=15%  Similarity=0.381  Sum_probs=59.2

Q ss_pred             CCcccccccccccc-------eeeecCcccccCCc--------cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCc
Q psy3656          82 KGCCSSCDKPIVGQ-------VITALGKTWHPEHF--------ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  146 (185)
Q Consensus        82 ~~~C~~C~~~i~~~-------~~~~~~~~~H~~Cf--------~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~  146 (185)
                      ...|..|...+.+.       ++..=|-.||..|+        .|..|+..+....+...    |     ...-...|..
T Consensus         7 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l----~-----i~~~~~~C~i   77 (133)
T 4ap4_A            7 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI----Y-----IGSGTVSCPI   77 (133)
T ss_dssp             SCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEEC----B-----CSSSSCBCTT
T ss_pred             CCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccccccc----c-----cCCCCCCCCC
Confidence            45699998876332       34444777777776        78999998865544321    1     1112356888


Q ss_pred             cCCcccCc-------eEEeCCCeecccCc--------ccccCCCccCCCC
Q psy3656         147 CNGPILDK-------CVTALEKTWHTEHF--------FCAQCGKQFGEAM  181 (185)
Q Consensus       147 C~~~i~~~-------~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~  181 (185)
                      |.+.+...       .+..-++.||..|.        .|-.|...|..+.
T Consensus        78 C~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           78 CMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             TCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            88776532       34456889999886        5999999886554

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=92.38  E-value=0.4  Score=31.78  Aligned_cols=75  Identities=19%  Similarity=0.243  Sum_probs=46.9

Q ss_pred             CCCcccccccccc-cceee--ecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccC-ceE
Q psy3656          81 QKGCCSSCDKPIV-GQVIT--ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD-KCV  156 (185)
Q Consensus        81 ~~~~C~~C~~~i~-~~~~~--~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~-~~~  156 (185)
                      ....|..|+..-. .+.+.  .=++.||..|+.-..  .+       ...+.-+|..|.      .|.+|++.-.+ .+|
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~--~~-------~~~~~W~C~~C~------~C~~C~~~~~~~~ll   70 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TP-------LKRAGWQCPECK------VCQNCKQSGEDSKML   70 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCC--CT-------TTSTTCCCTTTC------CCTTTCCCSCCTTEE
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCcc--cc-------ccccCccCCcCC------cccccCccCCCCCee
Confidence            4567999987542 22233  336889998865432  11       234567787773      68899887653 344


Q ss_pred             E--eCCCeecccCccc
Q psy3656         157 T--ALEKTWHTEHFFC  170 (185)
Q Consensus       157 ~--~~~~~~H~~Cf~C  170 (185)
                      .  .-++.||..|..-
T Consensus        71 ~Cd~C~~~yH~~Cl~p   86 (111)
T 2ysm_A           71 VCDTCDKGYHTFCLQP   86 (111)
T ss_dssp             ECSSSCCEEEGGGSSS
T ss_pred             ECCCCCcHHhHHhcCC
Confidence            3  3368999988763

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=85.25  E-value=0.36  Score=28.02  Aligned_cols=11  Identities=27%  Similarity=0.860  Sum_probs=5.4

Q ss_pred             cccCCCccCCC
Q psy3656         170 CAQCGKQFGEA  180 (185)
Q Consensus       170 C~~C~~~l~~~  180 (185)
                      |..|...+..+
T Consensus        47 CP~Cr~~~~~~   57 (64)
T 2xeu_A           47 CPTCRKKINHK   57 (64)
T ss_dssp             CTTTCCBCTTT
T ss_pred             CCCCCccCCcc
Confidence            55555555433

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=85.25  E-value=0.22  Score=29.77  Aligned_cols=24  Identities=13%  Similarity=0.404  Sum_probs=12.9

Q ss_pred             eCCCeecccCc--------ccccCCCccCCCC
Q psy3656         158 ALEKTWHTEHF--------FCAQCGKQFGEAM  181 (185)
Q Consensus       158 ~~~~~~H~~Cf--------~C~~C~~~l~~~~  181 (185)
                      .-++.||.+|+        +|..|...+..+.
T Consensus        34 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A           34 ECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            34555555555        4666666654443

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=85.20  E-value=1  Score=30.02  Aligned_cols=75  Identities=15%  Similarity=0.248  Sum_probs=43.5

Q ss_pred             Cccccccccc--------ccceeeec--CcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc
Q psy3656          83 GCCSSCDKPI--------VGQVITAL--GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL  152 (185)
Q Consensus        83 ~~C~~C~~~i--------~~~~~~~~--~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~  152 (185)
                      +.|..|...-        .++.+.-.  ++.||..|+.-..     .. .-....+.-+|..|      ..|.+|++.-.
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~~-----~~-~~~~~~~~W~C~~C------~~C~~C~~~~~   69 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTL-----NM-TEAVKTYKWQCIEC------KSCILCGTSEN   69 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCCH-----HH-HHHHHHTTCCCGGG------CCCTTTTCCTT
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCChh-----hh-hhccCCCccCcccc------CccCcccccCC
Confidence            3577776543        12344333  6788888753110     00 00234556778777      46999988765


Q ss_pred             C-ceEE--eCCCeecccCcc
Q psy3656         153 D-KCVT--ALEKTWHTEHFF  169 (185)
Q Consensus       153 ~-~~~~--~~~~~~H~~Cf~  169 (185)
                      + .+|.  .-++.||..|..
T Consensus        70 ~~~ll~Cd~C~~~yH~~Cl~   89 (114)
T 2kwj_A           70 DDQLLFCDDCDRGYHMYCLN   89 (114)
T ss_dssp             TTTEEECSSSCCEEETTTSS
T ss_pred             CCceEEcCCCCccccccccC
Confidence            3 4444  335899999876

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=83.77  E-value=1.2  Score=29.48  Aligned_cols=27  Identities=15%  Similarity=0.402  Sum_probs=15.5

Q ss_pred             eCCcCCCccchhhccCCCCCccCCccc
Q psy3656         126 RDSRPYCEPDYHNLFSPRCSYCNGPIL  152 (185)
Q Consensus       126 ~~g~~yC~~~~~~~~~~~C~~C~~~i~  152 (185)
                      .=|..||..|..+.+...|..|...+.
T Consensus        40 ~CgH~fC~~Ci~~~~~~~CP~Cr~~~~   66 (117)
T 1jm7_B           40 GCEHIFCSNCVSDCIGTGCPVCYTPAW   66 (117)
T ss_dssp             SSSCCBCTTTGGGGTTTBCSSSCCBCS
T ss_pred             CCCCHHHHHHHHHHhcCCCcCCCCcCc
Confidence            344555666655554456777766654

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=82.71  E-value=0.86  Score=25.51  Aligned_cols=8  Identities=13%  Similarity=0.094  Sum_probs=3.7

Q ss_pred             CCeecccC
Q psy3656         160 EKTWHTEH  167 (185)
Q Consensus       160 ~~~~H~~C  167 (185)
                      ++.||.+|
T Consensus        28 gH~fc~~C   35 (55)
T 2ecm_A           28 GHLLHRTC   35 (55)
T ss_dssp             SCEEETTH
T ss_pred             CCcccHHH
Confidence            44444444

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.89  E-value=0.51  Score=27.81  Aligned_cols=44  Identities=25%  Similarity=0.619  Sum_probs=27.2

Q ss_pred             ccCCCCCCCCCCCCeeeeCCcCCCccchhhcc---CCCCCccCCcccC
Q psy3656         109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLF---SPRCSYCNGPILD  153 (185)
Q Consensus       109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~---~~~C~~C~~~i~~  153 (185)
                      +.|..|...+.. .+...=|..||..|..+.+   ...|..|+..|..
T Consensus        16 ~~C~IC~~~~~~-p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           16 YKCEKCHLVLCS-PKQTECGHRFCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             EECTTTCCEESS-CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             CCCCCCChHhcC-eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            456666555432 2234566778888877654   2568888887763

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=81.63  E-value=1.1  Score=28.07  Aligned_cols=9  Identities=22%  Similarity=0.962  Sum_probs=5.9

Q ss_pred             ccccccccc
Q psy3656          84 CCSSCDKPI   92 (185)
Q Consensus        84 ~C~~C~~~i   92 (185)
                      .|..|+.+|
T Consensus         4 ~CP~C~~~l   12 (81)
T 2jrp_A            4 TCPVCHHAL   12 (81)
T ss_dssp             CCSSSCSCC
T ss_pred             CCCCCCCcc
Confidence            467776665

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.34  E-value=0.7  Score=27.64  Aligned_cols=43  Identities=16%  Similarity=0.373  Sum_probs=23.0

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccC-----CCCCccCCcccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS-----PRCSYCNGPILD  153 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~-----~~C~~C~~~i~~  153 (185)
                      .|..|...+. ......=|..||..|..+.+.     ..|..|.+.|..
T Consensus        22 ~C~IC~~~~~-~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   69 (73)
T 2ysl_A           22 ICPICLDILQ-KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRK   69 (73)
T ss_dssp             BCTTTCSBCS-SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCC
T ss_pred             EeccCCcccC-CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCc
Confidence            4444444332 122234556667766655442     368888877753

---

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	185
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	8e-13
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	2e-09
d1u5sb1	31	g.39.1.3 (B:72-102) Pinch (particularly interestin	5e-12
d1u5sb1	31	g.39.1.3 (B:72-102) Pinch (particularly interestin	7e-10
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	2e-11
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	7e-11
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	2e-10
d1b8ta4	49	g.39.1.3 (A:144-192) Cysteine-rich (intestinal) pr	2e-05
d1x3ha2	32	g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens)	9e-05
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	2e-04
d2d8za2	32	g.39.1.3 (A:33-64) Four and a half LIM domains pro	4e-04
d1v6ga1	41	g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abL	5e-04
d1v6ga1	41	g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abL	0.003
d2cuqa1	32	g.39.1.3 (A:43-74) Four and a half LIM domains 3,	0.001
d1x4ka1	32	g.39.1.3 (A:35-66) Four and a half LIM domains pro	0.002
d2d8xa2	26	g.39.1.3 (A:8-32) Pinch (particularly interesting	0.002

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

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

 Score = 57.7 bits (140), Expect = 8e-13
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 135 DYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF 168
           D+  +FSP+C  CN P+L+  ++A++  WH E F
Sbjct: 2   DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF 35

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

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

 Score = 48.5 bits (116), Expect = 2e-09
 Identities = 9/26 (34%), Positives = 16/26 (61%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPEHF 109
            C  C++P++   ++A+   WHPE F
Sbjct: 10  KCGGCNRPVLENYLSAMDTVWHPECF 35

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 31

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

 Score = 55.5 bits (134), Expect = 5e-12
 Identities = 12/30 (40%), Positives = 16/30 (53%)

Query: 138 NLFSPRCSYCNGPILDKCVTALEKTWHTEH 167
           ++  P C  C  PI  + V A+ K WH EH
Sbjct: 2   SMGVPICGACRRPIEGRVVNAMGKQWHVEH 31

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 31

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

 Score = 49.8 bits (119), Expect = 7e-10
 Identities = 13/24 (54%), Positives = 18/24 (75%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEH 108
           C +C +PI G+V+ A+GK WH EH
Sbjct: 8   CGACRRPIEGRVVNAMGKQWHVEH 31

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 35

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

 Score = 53.9 bits (130), Expect = 2e-11
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 142
           F+C  C Q+     F+E + R YCE D+  LF+P
Sbjct: 1   FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP 34

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

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

 Score = 52.8 bits (127), Expect = 7e-11
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHF 109
           C+ C++ I G  + ALGK+WHPE F
Sbjct: 21  CAHCNQVIRGPFLVALGKSWHPEEF 45

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

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

 Score = 51.7 bits (124), Expect = 2e-10
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 141 SPRCSYCNGPILDKCVTALEKTWHTEHF 168
           +P C++CN  I    + AL K+WH E F
Sbjct: 18  TPMCAHCNQVIRGPFLVALGKSWHPEEF 45

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 49

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

 Score = 38.2 bits (89), Expect = 2e-05
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 111 CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 144
           C  C + L +    ++D   YC+  Y   F P+ 
Sbjct: 2   CAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKG 35

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 32

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

 Score = 35.9 bits (83), Expect = 9e-05
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNL 139
           +C  C     T +FFE D RP+CE  YH+ 
Sbjct: 1   VCGDCFTSFSTGSFFELDGRPFCELHYHHR 30

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

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

 Score = 35.0 bits (81), Expect = 2e-04
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 111 CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNG 149
           C++CN +L    +     R YC+P ++ LF  + +Y  G
Sbjct: 2   CSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEG 40

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]} Length = 32

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]

 Score = 34.3 bits (79), Expect = 4e-04
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           +CT C ++L  + F  RD   YC   + +L++
Sbjct: 1   VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA 32

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

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

 Score = 34.4 bits (79), Expect = 5e-04
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 135 DYHNLFSPRCSYCNGPILDKCVTALEKTWHTE 166
           DY  L+  RC  C+  I  + V+AL KT+H +
Sbjct: 9   DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPD 40

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

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

 Score = 32.1 bits (73), Expect = 0.003
 Identities = 14/24 (58%), Positives = 20/24 (83%)

Query: 84  CCSSCDKPIVGQVITALGKTWHPE 107
            C SCD+ I G+V++ALGKT+HP+
Sbjct: 17  RCFSCDQFIEGEVVSALGKTYHPD 40

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]} Length = 32

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]

 Score = 33.2 bits (76), Expect = 0.001
 Identities = 12/32 (37%), Positives = 16/32 (50%)

Query: 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           +CT C   L  + F  RD  PYC   +  LF+
Sbjct: 1   VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA 32

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]} Length = 32

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]

 Score = 32.5 bits (74), Expect = 0.002
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 141
           IC  C Q +GT++F  +D++ +C P Y    +
Sbjct: 1   ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA 32

>d2d8xa2 g.39.1.3 (A:8-32) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 26

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

 Score = 32.2 bits (73), Expect = 0.002
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 85  CSSCDKPIVGQVITALGKTWHPEHF 109
           C  C + I+G+VI A+  +WHPE F
Sbjct: 1   CHQCGEFIIGRVIKAMNNSWHPECF 25

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	185
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.52
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	99.25
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	99.12
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	99.07
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	99.05
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	98.91
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.88
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.87
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.82
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.68
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.64
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.6
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.54
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.5
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	98.48
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.45
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.39
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	98.38
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.35
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.35
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.3
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.3
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.29
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.28
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.28
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.28
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.24
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.22
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.2
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.18
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.15
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.15
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.14
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.14
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.12
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.09
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.08
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.08
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.07
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.04
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.02
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.96
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.95
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.94
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.89
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.88
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.82
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.8
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.79
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.79
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	97.78
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.72
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.72
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.71
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.68
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.67
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.67
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.65
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.64
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.62
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.55
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.53
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.48
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.47
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.46
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.43
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.41
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.4
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.37
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.33
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.28
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.23
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.17
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.09
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.0
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.91
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.86
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.83
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	96.79
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.76
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.63
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.34
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.33
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.94
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	95.92
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	95.62
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.36
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	95.25
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.22
d2co8a1	33	Nedd9 interacting protein with calponin homology,	95.17
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	94.23
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.05
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	93.87
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	93.7
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	93.63
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	93.01
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	92.96
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	92.86
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	91.31
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	90.49
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	90.42
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	90.32
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	88.11
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	85.66

>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=99.52  E-value=2.2e-15  Score=79.71  Aligned_cols=35  Identities=40%  Similarity=1.047  Sum_probs=33.7

Q ss_pred             cchhhccCCCCCccCCcccCceEEeCCCeecccCc
Q psy3656         134 PDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       134 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      ++|.++|+++|..|+++|+|++|+|+++.||++||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccchheeecCCccCcccC
Confidence            47999999999999999999999999999999998

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

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

Probab=99.25  E-value=1.4e-12  Score=67.17  Aligned_cols=35  Identities=34%  Similarity=0.725  Sum_probs=31.5

Q ss_pred             ccchhhccCCCCCccCCcccCceEEeCCCeecccCc
Q psy3656         133 EPDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       133 ~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      +.||.... ++|.+|+++|++++|+|.|+.|||.||
T Consensus         1 E~Cy~~tl-EkC~~C~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           1 EGCYVATL-EKCATCSQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCCSSC-CBCTTTCCBCCSCCEEETTEEECTTTC
T ss_pred             ChhHHHHH-HHHHHhchHHHHHHHHHhCCCCCCCCC
Confidence            35776655 999999999999999999999999998

>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=99.12  E-value=1.9e-11  Score=65.34  Aligned_cols=34  Identities=38%  Similarity=0.706  Sum_probs=32.9

Q ss_pred             cchhhccCCCCCccCCcccCceEEeCCCeecccC
Q psy3656         134 PDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEH  167 (185)
Q Consensus       134 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~C  167 (185)
                      .+|+++|+.+|..|++.|.|++|.|.+++|||+|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeeeeeEecCcccCCCC
Confidence            5799999999999999999999999999999998

>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=99.07  E-value=3.9e-11  Score=61.35  Aligned_cols=35  Identities=37%  Similarity=0.822  Sum_probs=33.6

Q ss_pred             cchhhccCCCCCccCCcccCceEEeCCCeecccCc
Q psy3656         134 PDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       134 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      +||+++|+++|..|+++|....|..+++.||.+||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             CchHHHHHHHHhhcCCccccCceeecCCcchhhhC
Confidence            58999999999999999999999999999999998

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

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

Probab=99.05  E-value=4.8e-11  Score=64.95  Aligned_cols=28  Identities=43%  Similarity=0.883  Sum_probs=27.0

Q ss_pred             CCCCCccCCcccCceEEeCCCeecccCc
Q psy3656         141 SPRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       141 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      .++|+.|+++|.|++|+|+|+.||||||
T Consensus        18 ~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CeeccccCCcccCceeeecCCccCcCCC
Confidence            4899999999999999999999999998

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

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

Probab=98.91  E-value=2.3e-10  Score=57.64  Aligned_cols=34  Identities=26%  Similarity=0.379  Sum_probs=32.4

Q ss_pred             cchhhccCCCCCccCCcccCceEEeCCCeecccC
Q psy3656         134 PDYHNLFSPRCSYCNGPILDKCVTALEKTWHTEH  167 (185)
Q Consensus       134 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~C  167 (185)
                      .+|+.+|+..|..|.+.|+|.+|.|.+..|||||
T Consensus         1 kdYw~kfge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             CcHHHHHHHHhhhhHhhcccceeeecccccCCCC
Confidence            4799999999999999999999999999999998

>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=98.88  E-value=6.1e-10  Score=58.58  Aligned_cols=35  Identities=29%  Similarity=0.495  Sum_probs=32.6

Q ss_pred             cchhhccCCCCCccCCccc--CceEEeCCCeecccCc
Q psy3656         134 PDYHNLFSPRCSYCNGPIL--DKCVTALEKTWHTEHF  168 (185)
Q Consensus       134 ~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf  168 (185)
                      .||.+.|+.+|..|+++|.  .+.|.+.++.||.+||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CccccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            4899999999999999998  4799999999999998

>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=98.82  E-value=4.7e-10  Score=55.72  Aligned_cols=29  Identities=41%  Similarity=0.864  Sum_probs=26.5

Q ss_pred             ccCCCCCccCCcccCceEEeCCCeecccC
Q psy3656         139 LFSPRCSYCNGPILDKCVTALEKTWHTEH  167 (185)
Q Consensus       139 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~C  167 (185)
                      .+.++|+.|.+||.++++.|+++.||+|+
T Consensus         3 mg~p~C~~C~~PI~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEECCSCEECCTTSBEETTT
T ss_pred             cCCcchhhcCCchhhhHhhhhccccCCCC
Confidence            34589999999999999999999999984

>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=98.68  E-value=1.6e-09  Score=56.57  Aligned_cols=34  Identities=41%  Similarity=1.004  Sum_probs=32.5

Q ss_pred             ccCCCCCCCCCCCCeeeeCCcCCCccchhhccCC
Q psy3656         109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP  142 (185)
Q Consensus       109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~  142 (185)
                      |.|..|+++|+...|+.++|++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7899999999999999999999999999999986

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

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

Probab=98.64  E-value=6.3e-09  Score=54.36  Aligned_cols=29  Identities=31%  Similarity=0.918  Sum_probs=27.3

Q ss_pred             CCCcccccccccccceeeecCcccccCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      ..++|..|+++|.++.|.|+|+.||++||
T Consensus         7 fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           7 FSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             hChhhhhcCCcccchheeecCCccCcccC
Confidence            46789999999999999999999999998

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=98.60  E-value=8.4e-09  Score=57.40  Aligned_cols=41  Identities=22%  Similarity=0.515  Sum_probs=37.8

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCc
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGP  150 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~  150 (185)
                      +|..|++.|.......+++++||+.||.++|+|+....++.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~g   41 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQG   41 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccC
Confidence            68999999998899999999999999999999999888754

>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=98.54  E-value=1.3e-08  Score=54.81  Aligned_cols=34  Identities=29%  Similarity=0.800  Sum_probs=31.7

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR  143 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~  143 (185)
                      +|..|++.|..++|...+|.+||++||.++|.++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhh
Confidence            6999999999999999999999999999999764

>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=98.50  E-value=2.6e-08  Score=50.90  Aligned_cols=28  Identities=36%  Similarity=0.961  Sum_probs=26.5

Q ss_pred             CCcccccccccccceeeecCcccccCCc
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      -.+|..|+++|.++++.++|+.||+.||
T Consensus         8 lEkC~~C~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCSCCEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHHHHHHHhCCCCCCCCC
Confidence            4689999999999999999999999998

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

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

Probab=98.48  E-value=4.3e-08  Score=49.16  Aligned_cols=27  Identities=26%  Similarity=0.562  Sum_probs=26.3

Q ss_pred             CCCCccCCcccCceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      +.|..|+..|.|.++.++++.+||+||
T Consensus         9 p~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             ccccccCCCcEeEEEEeccccCCCCCC
Confidence            889999999999999999999999998

>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=98.45  E-value=5.5e-08  Score=52.65  Aligned_cols=29  Identities=45%  Similarity=1.064  Sum_probs=27.1

Q ss_pred             CCCcccccccccccceeeecCcccccCCc
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      ..++|+.|+++|.+..+.++|+.||+++|
T Consensus        17 r~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          17 RTPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CCeeccccCCcccCceeeecCCccCcCCC
Confidence            35789999999999999999999999998

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.38  E-value=8.7e-08  Score=51.26  Aligned_cols=27  Identities=37%  Similarity=0.655  Sum_probs=26.4

Q ss_pred             CCCCccCCcccCceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      +.|..|+..|.|.++.++++.+|||||
T Consensus        19 P~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          19 PLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             ccccccCCCcEEEEEEeccccCCCCCC
Confidence            889999999999999999999999998

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.35  E-value=8.5e-08  Score=52.61  Aligned_cols=34  Identities=32%  Similarity=0.922  Sum_probs=31.7

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCC-ccchhhccCCC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYC-EPDYHNLFSPR  143 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC-~~~~~~~~~~~  143 (185)
                      +|..|++.|..+.+.++++++|| +.||..+|+|+
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPk   35 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPK   35 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCC
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCC
Confidence            68999999999999999999999 77999999985

>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=98.35  E-value=8.1e-08  Score=47.85  Aligned_cols=27  Identities=26%  Similarity=0.505  Sum_probs=23.9

Q ss_pred             CCCCccCCccc--CceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPIL--DKCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~--~~~~~~~~~~~H~~Cf  168 (185)
                      ..|+.|++.|.  +.+++|++++||.+||
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            46999999997  4677899999999998

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

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

Probab=98.30  E-value=2.5e-07  Score=47.78  Aligned_cols=30  Identities=20%  Similarity=0.448  Sum_probs=26.9

Q ss_pred             CCCCcccccccccc-cceeeecCcccccCCc
Q psy3656          80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      +..+.|..|+|.|+ .|.+.++|+.||+.||
T Consensus         5 p~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           5 PARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            34678999999995 7999999999999998

>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=98.30  E-value=2.5e-07  Score=48.00  Aligned_cols=30  Identities=17%  Similarity=0.383  Sum_probs=27.0

Q ss_pred             CCCCcccccccccc-cceeeecCcccccCCc
Q psy3656          80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      ....+|..|+|.|+ .+.+.++|+.||+.||
T Consensus         6 g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            34678999999995 7899999999999998

>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=98.28  E-value=2.2e-07  Score=45.74  Aligned_cols=28  Identities=32%  Similarity=0.813  Sum_probs=25.2

Q ss_pred             CCccccccccc-ccceeeecCcccccCCc
Q psy3656          82 KGCCSSCDKPI-VGQVITALGKTWHPEHF  109 (185)
Q Consensus        82 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf  109 (185)
                      .+.|..|+++| .+|.+..+|+.||+.|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            46799999999 58999999999999985

>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=98.28  E-value=2e-07  Score=47.19  Aligned_cols=27  Identities=33%  Similarity=0.779  Sum_probs=25.1

Q ss_pred             CCCCccCCccc-CceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPIL-DKCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  168 (185)
                      ..|+.|++.|. |+.+.|.++.||.+||
T Consensus         9 ~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccccccchhhhCCceeeeeecceeeeeC
Confidence            46999999997 7999999999999998

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.28  E-value=2.1e-07  Score=44.87  Aligned_cols=25  Identities=36%  Similarity=0.909  Sum_probs=23.2

Q ss_pred             CCccCCcccC----ceEEeCCCeecccCc
Q psy3656         144 CSYCNGPILD----KCVTALEKTWHTEHF  168 (185)
Q Consensus       144 C~~C~~~i~~----~~~~~~~~~~H~~Cf  168 (185)
                      |+.|.+||++    ++|.+.++.||.+||
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            8899999985    799999999999998

>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=98.24  E-value=2.4e-07  Score=50.38  Aligned_cols=29  Identities=24%  Similarity=0.729  Sum_probs=26.4

Q ss_pred             CCCcccccccccc-cceeeecCcccccCCc
Q psy3656          81 QKGCCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        81 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      +.+.|..|++.|+ +|.+.++|+.||+.||
T Consensus        14 ~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          14 GSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            4578999999995 7999999999999998

>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=98.22  E-value=5.1e-07  Score=45.67  Aligned_cols=32  Identities=34%  Similarity=0.712  Sum_probs=27.8

Q ss_pred             CCCCCCccccccccc-ccceeeecCcccccCCc
Q psy3656          78 TTTQKGCCSSCDKPI-VGQVITALGKTWHPEHF  109 (185)
Q Consensus        78 ~~~~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf  109 (185)
                      ...+...|++|++.| .++.+.++++.||.+||
T Consensus         4 ~~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           4 KIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CCSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            344567799999999 58899999999999998

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.20  E-value=2.9e-07  Score=45.30  Aligned_cols=31  Identities=42%  Similarity=0.974  Sum_probs=28.2

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      +|..|++.| .++|..++|.+||+.+|...||
T Consensus         1 kC~~C~~vL-~gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVIL-TGEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBC-SSCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCccc-cceeecCCCCcccHHHHHHhcC
Confidence            588999988 7789999999999999999885

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.18  E-value=4.5e-07  Score=43.57  Aligned_cols=25  Identities=36%  Similarity=0.854  Sum_probs=23.1

Q ss_pred             CCccCCcccC----ceEEeCCCeecccCc
Q psy3656         144 CSYCNGPILD----KCVTALEKTWHTEHF  168 (185)
Q Consensus       144 C~~C~~~i~~----~~~~~~~~~~H~~Cf  168 (185)
                      |..|.+||.|    ++|.+.++.||-+||
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            7899999985    699999999999998

>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=98.15  E-value=3.5e-07  Score=44.54  Aligned_cols=26  Identities=27%  Similarity=0.494  Sum_probs=24.5

Q ss_pred             CCCCccCCcccCceEEeCCCeecccC
Q psy3656         142 PRCSYCNGPILDKCVTALEKTWHTEH  167 (185)
Q Consensus       142 ~~C~~C~~~i~~~~~~~~~~~~H~~C  167 (185)
                      .-|..|.+.|.|++|+|.++.|||.|
T Consensus         6 sgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhhhhhccccccCCCC
Confidence            45999999999999999999999998

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

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

Probab=98.14  E-value=1.8e-07  Score=45.14  Aligned_cols=30  Identities=27%  Similarity=0.738  Sum_probs=28.1

Q ss_pred             ccCCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656         109 FICTHCNQELGTRNFFERDSRPYCEPDYHN  138 (185)
Q Consensus       109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~  138 (185)
                      |+|..|++.|.......++|.+||+.||.+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            799999999999999999999999999965

>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=98.14  E-value=3.8e-07  Score=44.20  Aligned_cols=28  Identities=29%  Similarity=0.684  Sum_probs=25.3

Q ss_pred             CCcccccccccc-cceeeecCcccccCCc
Q psy3656          82 KGCCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      ++.|+.|++.|+ .|.+..+++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHHhhhhHHHHhhccC
Confidence            356999999996 7899999999999998

>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=98.12  E-value=3.5e-07  Score=45.71  Aligned_cols=32  Identities=31%  Similarity=0.800  Sum_probs=29.3

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      .|..|..+|+++.|..+++++||-.||..+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            37889999999999999999999999998874

>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=98.09  E-value=5.5e-07  Score=44.43  Aligned_cols=27  Identities=44%  Similarity=1.027  Sum_probs=25.0

Q ss_pred             CCCcccccccccccceeeecCcccccC
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPE  107 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~  107 (185)
                      +.+.|+.|.++|.++.+.++|+.||.+
T Consensus         4 g~p~C~~C~~PI~~~~vtAlgk~WHpE   30 (31)
T d1u5sb1           4 GVPICGACRRPIEGRVVNAMGKQWHVE   30 (31)
T ss_dssp             CCCEETTTTEECCSCEECCTTSBEETT
T ss_pred             CCcchhhcCCchhhhHhhhhccccCCC
Confidence            467899999999999999999999986

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.08  E-value=4.1e-07  Score=45.69  Aligned_cols=32  Identities=41%  Similarity=0.920  Sum_probs=29.0

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      .|..|.+++.++.|+..+|++||+.||.++.|
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~G   32 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRRG   32 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHHS
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhcC
Confidence            48899999999999999999999999988754

>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=98.08  E-value=1e-06  Score=43.49  Aligned_cols=27  Identities=33%  Similarity=0.849  Sum_probs=24.2

Q ss_pred             CCCCccCCcccCceE-EeCCCeecccCc
Q psy3656         142 PRCSYCNGPILDKCV-TALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~~~~~-~~~~~~~H~~Cf  168 (185)
                      ..|+.|+++|.++++ .+.++.||..|.
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            579999999999865 799999999984

>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=98.07  E-value=4.2e-07  Score=53.27  Aligned_cols=35  Identities=20%  Similarity=0.608  Sum_probs=32.1

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC  144 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C  144 (185)
                      .|..|++.|....+..+++++||+.||.++|+|+=
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG   35 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKG   35 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCc
Confidence            38899999999999999999999999999999863

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

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

Probab=98.04  E-value=6.7e-07  Score=44.64  Aligned_cols=34  Identities=32%  Similarity=0.879  Sum_probs=31.7

Q ss_pred             ccCCCCCCCCCCCCeeeeCCcCCCccchhhccCC
Q psy3656         109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP  142 (185)
Q Consensus       109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~  142 (185)
                      |.|..|.+++.+..++.+.|..||+.||.++|+.
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhcc
Confidence            7899999999888999999999999999999974

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

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

Probab=98.02  E-value=1.2e-06  Score=43.36  Aligned_cols=32  Identities=34%  Similarity=0.870  Sum_probs=29.1

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCc-cchhhccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCE-PDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~-~~~~~~~~  141 (185)
                      +|..|++.|..+.+.+++|++||. +||..+||
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            688999999999999999999997 59998885

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

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

Probab=97.96  E-value=3e-06  Score=41.60  Aligned_cols=26  Identities=27%  Similarity=0.659  Sum_probs=23.3

Q ss_pred             CCCCccCCcccCceE-EeCCCeecccC
Q psy3656         142 PRCSYCNGPILDKCV-TALEKTWHTEH  167 (185)
Q Consensus       142 ~~C~~C~~~i~~~~~-~~~~~~~H~~C  167 (185)
                      ..|+.|+++|.++++ .|.++.||.+|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            469999999999865 79999999988

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

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

Probab=97.95  E-value=1.3e-06  Score=42.29  Aligned_cols=28  Identities=32%  Similarity=0.794  Sum_probs=25.3

Q ss_pred             CCCCCccCCcccC-ceEEeCCCeecccCc
Q psy3656         141 SPRCSYCNGPILD-KCVTALEKTWHTEHF  168 (185)
Q Consensus       141 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf  168 (185)
                      .+.|++|++.+.+ +-|...++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHHhhhhHHHHhhccC
Confidence            4789999999985 788999999999998

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

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

Probab=97.94  E-value=3e-06  Score=39.80  Aligned_cols=25  Identities=24%  Similarity=0.667  Sum_probs=23.0

Q ss_pred             CCccCCcccC--ceEEeCCCeecccCc
Q psy3656         144 CSYCNGPILD--KCVTALEKTWHTEHF  168 (185)
Q Consensus       144 C~~C~~~i~~--~~~~~~~~~~H~~Cf  168 (185)
                      |..|.+.|++  +.|+..|..||..||
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            7889999995  789999999999998

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

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

Probab=97.89  E-value=4.6e-06  Score=42.89  Aligned_cols=28  Identities=18%  Similarity=0.447  Sum_probs=25.4

Q ss_pred             CCCCCccCCcccC-ceEEeCCCeecccCc
Q psy3656         141 SPRCSYCNGPILD-KCVTALEKTWHTEHF  168 (185)
Q Consensus       141 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf  168 (185)
                      ..+|..|++.+.. +.|.|.|+.||..||
T Consensus         7 ~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeEecCCeehhhccC
Confidence            3789999999985 789999999999998

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

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

Probab=97.88  E-value=1.6e-06  Score=42.63  Aligned_cols=32  Identities=38%  Similarity=0.896  Sum_probs=29.3

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      .|..|.++|.++.|..++..+||-+||..+|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            38899999999999999999999999998874

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

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

Probab=97.82  E-value=4.9e-06  Score=38.96  Aligned_cols=25  Identities=28%  Similarity=0.698  Sum_probs=22.9

Q ss_pred             CCccCCcccC--ceEEeCCCeecccCc
Q psy3656         144 CSYCNGPILD--KCVTALEKTWHTEHF  168 (185)
Q Consensus       144 C~~C~~~i~~--~~~~~~~~~~H~~Cf  168 (185)
                      |..|.+.|++  +.|+..|..||..||
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            7889999985  789999999999998

>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=97.80  E-value=2.7e-06  Score=41.52  Aligned_cols=31  Identities=23%  Similarity=0.618  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         111 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       111 C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      |..|++.|.+..+..+++.+||+.||.++||
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7889999998899999999999999999875

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

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

Probab=97.79  E-value=4.5e-06  Score=43.09  Aligned_cols=27  Identities=15%  Similarity=0.370  Sum_probs=24.9

Q ss_pred             CCCCccCCcccC-ceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPILD-KCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~~-~~~~~~~~~~H~~Cf  168 (185)
                      .+|..|++.+.+ +.|.|.|+.||..||
T Consensus         9 ~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           9 DLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CcccccCCEEeeeeEEEecCcEeccccC
Confidence            789999999985 688999999999998

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

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

Probab=97.79  E-value=3.3e-06  Score=41.67  Aligned_cols=31  Identities=32%  Similarity=0.817  Sum_probs=28.3

Q ss_pred             CCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         111 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       111 C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      |..|+.+|....|....|.+||+.||.+.|+
T Consensus         2 Ca~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           2 CAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             CSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             cccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            7899999998899999999999999988763

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

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

Probab=97.78  E-value=9.4e-06  Score=42.19  Aligned_cols=30  Identities=33%  Similarity=0.671  Sum_probs=26.1

Q ss_pred             CCCCcccccccccc--cceeeecCcccccCCc
Q psy3656          80 TQKGCCSSCDKPIV--GQVITALGKTWHPEHF  109 (185)
Q Consensus        80 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf  109 (185)
                      .....|..|+++|.  ++.++..|+.||..||
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            34678999999994  4689999999999998

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

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

Probab=97.72  E-value=5.4e-06  Score=44.86  Aligned_cols=27  Identities=26%  Similarity=0.655  Sum_probs=24.5

Q ss_pred             CCCCccCCcccC-ceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPILD-KCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~~-~~~~~~~~~~H~~Cf  168 (185)
                      ++|..|++.+.. +.+.+.|+.||..||
T Consensus        16 ~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          16 DGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            689999999974 678999999999998

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

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

Probab=97.72  E-value=6.9e-06  Score=40.44  Aligned_cols=27  Identities=22%  Similarity=0.657  Sum_probs=23.6

Q ss_pred             Ccccccccccccc-eeeecCcccccCCc
Q psy3656          83 GCCSSCDKPIVGQ-VITALGKTWHPEHF  109 (185)
Q Consensus        83 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf  109 (185)
                      ..|++|+++|.+. .+.++++.||..|+
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            4699999999887 56799999999884

>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=97.68  E-value=1e-05  Score=38.86  Aligned_cols=25  Identities=32%  Similarity=0.869  Sum_probs=22.3

Q ss_pred             ccccccccc----cceeeecCcccccCCc
Q psy3656          85 CSSCDKPIV----GQVITALGKTWHPEHF  109 (185)
Q Consensus        85 C~~C~~~i~----~~~~~~~~~~~H~~Cf  109 (185)
                      |..|.++|.    ..++.++++.||..||
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            789999994    3689999999999998

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

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

Probab=97.67  E-value=8.7e-06  Score=38.60  Aligned_cols=26  Identities=27%  Similarity=0.716  Sum_probs=23.4

Q ss_pred             Ccccccccccc-cceeeecCcccccCC
Q psy3656          83 GCCSSCDKPIV-GQVITALGKTWHPEH  108 (185)
Q Consensus        83 ~~C~~C~~~i~-~~~~~~~~~~~H~~C  108 (185)
                      .+|..|++.|+ ++.+...|+.||+.|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            46999999996 789999999999987

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

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

Probab=97.67  E-value=2e-05  Score=39.83  Aligned_cols=30  Identities=23%  Similarity=0.501  Sum_probs=26.4

Q ss_pred             CCCCcccccccccccceeeecCcccccCCc
Q psy3656          80 TQKGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        80 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      .....|..|+++|..-.|.-.++.||++||
T Consensus         6 kfa~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           6 KFAPRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CSSCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             HHHHHHhhcCCccccCceeecCCcchhhhC
Confidence            345789999999987788999999999998

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

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

Probab=97.65  E-value=2.1e-05  Score=38.42  Aligned_cols=28  Identities=25%  Similarity=0.684  Sum_probs=24.9

Q ss_pred             CCCCCccCCccc-CceEEeCCCeecccCc
Q psy3656         141 SPRCSYCNGPIL-DKCVTALEKTWHTEHF  168 (185)
Q Consensus       141 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  168 (185)
                      .++|..|++++. -+.+.+.|+.||..|.
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            478999999997 5889999999999984

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

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

Probab=97.64  E-value=1.8e-05  Score=38.72  Aligned_cols=26  Identities=23%  Similarity=0.663  Sum_probs=22.9

Q ss_pred             Ccccccccccccc-eeeecCcccccCC
Q psy3656          83 GCCSSCDKPIVGQ-VITALGKTWHPEH  108 (185)
Q Consensus        83 ~~C~~C~~~i~~~-~~~~~~~~~H~~C  108 (185)
                      ..|++|+++|.++ .+.++++.||..|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            4699999999887 5689999999887

>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=97.62  E-value=1.5e-05  Score=39.43  Aligned_cols=30  Identities=20%  Similarity=0.511  Sum_probs=26.5

Q ss_pred             CCCCcccccccccc-cceeeecCcccccCCc
Q psy3656          80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      .+..+|..|++.|+ ++-+..+|+.||+.||
T Consensus         5 ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCCceeccccceEeeeeeeeecCcccccccC
Confidence            34568999999994 8899999999999998

>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=97.53  E-value=2.3e-05  Score=36.74  Aligned_cols=26  Identities=19%  Similarity=0.625  Sum_probs=23.9

Q ss_pred             cccccccccc-cceeeecCcccccCCc
Q psy3656          84 CCSSCDKPIV-GQVITALGKTWHPEHF  109 (185)
Q Consensus        84 ~C~~C~~~i~-~~~~~~~~~~~H~~Cf  109 (185)
                      +|+.|.+.|+ ++-+..+|+.||+.||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            5999999995 8899999999999998

>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=97.48  E-value=1.6e-05  Score=39.17  Aligned_cols=31  Identities=32%  Similarity=0.920  Sum_probs=28.7

Q ss_pred             CCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         111 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       111 C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      |..|..+++...|..+++..||-.||+++|+
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCCceEeecchhhcC
Confidence            7889999999999999999999999999874

>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=97.47  E-value=2.1e-05  Score=37.65  Aligned_cols=25  Identities=40%  Similarity=0.922  Sum_probs=22.1

Q ss_pred             ccccccccc----cceeeecCcccccCCc
Q psy3656          85 CSSCDKPIV----GQVITALGKTWHPEHF  109 (185)
Q Consensus        85 C~~C~~~i~----~~~~~~~~~~~H~~Cf  109 (185)
                      |..|.|+|.    ..++.++++.||.+||
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            789999994    3689999999999998

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

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

Probab=97.46  E-value=3.3e-05  Score=36.17  Aligned_cols=25  Identities=32%  Similarity=0.841  Sum_probs=22.1

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy3656          85 CSSCDKPIV--GQVITALGKTWHPEHF  109 (185)
Q Consensus        85 C~~C~~~i~--~~~~~~~~~~~H~~Cf  109 (185)
                      |..|.+.|.  ...++..|..||..||
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            788999995  3688999999999998

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

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

Probab=97.43  E-value=1.8e-05  Score=39.10  Aligned_cols=27  Identities=37%  Similarity=0.788  Sum_probs=23.1

Q ss_pred             Ccccccccccc--cceeeecCcccccCCc
Q psy3656          83 GCCSSCDKPIV--GQVITALGKTWHPEHF  109 (185)
Q Consensus        83 ~~C~~C~~~i~--~~~~~~~~~~~H~~Cf  109 (185)
                      +.|++|++.|.  +.+..+.++.||..||
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            56999999993  4466899999999998

>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=97.41  E-value=2.1e-05  Score=38.75  Aligned_cols=31  Identities=42%  Similarity=0.958  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         111 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       111 C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      |..|..+++...|..+++..||-.||+.+|+
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCcEEEEeccccccC
Confidence            7889999999999999999999999999874

>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=97.40  E-value=2.1e-05  Score=38.21  Aligned_cols=30  Identities=30%  Similarity=0.817  Sum_probs=27.1

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhc
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNL  139 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~  139 (185)
                      .|..|+..|+++.|+..+.+.||+.||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            388999999999999999999999999753

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

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

Probab=97.37  E-value=4.5e-05  Score=35.60  Aligned_cols=25  Identities=32%  Similarity=0.868  Sum_probs=21.9

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy3656          85 CSSCDKPIV--GQVITALGKTWHPEHF  109 (185)
Q Consensus        85 C~~C~~~i~--~~~~~~~~~~~H~~Cf  109 (185)
                      |..|.|.|.  ...++-.|+.||..||
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            788999995  3688999999999998

>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=97.33  E-value=6.1e-05  Score=37.46  Aligned_cols=28  Identities=29%  Similarity=0.618  Sum_probs=26.3

Q ss_pred             CCcccccccccccceeeecCcccccCCc
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      -+.|-.|+..|.+.++.+.++.+|++||
T Consensus         8 lp~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             CccccccCCCcEeEEEEeccccCCCCCC
Confidence            4679999999999999999999999998

>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=97.28  E-value=3.3e-05  Score=37.39  Aligned_cols=29  Identities=28%  Similarity=0.744  Sum_probs=26.3

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHN  138 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~  138 (185)
                      .|..|.+.|.+.+|...+.+.||-+||.+
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeecc
Confidence            38899999999999999999999999975

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

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

Probab=97.23  E-value=8e-05  Score=39.18  Aligned_cols=28  Identities=50%  Similarity=0.891  Sum_probs=25.9

Q ss_pred             CCCcccccccccccceeeecCcccccCC
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEH  108 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~C  108 (185)
                      ...+|..|.+-|.++++.+.++.||++|
T Consensus        14 fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          14 YGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             hCcccccccCEeeeeeeEecCcccCCCC
Confidence            3578999999999999999999999988

>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=97.17  E-value=0.00011  Score=39.04  Aligned_cols=28  Identities=43%  Similarity=0.726  Sum_probs=26.3

Q ss_pred             CCcccccccccccceeeecCcccccCCc
Q psy3656          82 KGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      -+.|-.|+..|.+.++.+.++.+|++||
T Consensus        18 LP~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             CccccccCCCcEEEEEEeccccCCCCCC
Confidence            4679999999999999999999999998

>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=97.09  E-value=0.00022  Score=33.11  Aligned_cols=25  Identities=36%  Similarity=0.699  Sum_probs=22.1

Q ss_pred             CCccCCccc--CceEEeCCCeecccCc
Q psy3656         144 CSYCNGPIL--DKCVTALEKTWHTEHF  168 (185)
Q Consensus       144 C~~C~~~i~--~~~~~~~~~~~H~~Cf  168 (185)
                      |..|.+||-  .+-+...++.||-.||
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            788999996  4678899999999998

>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=97.00  E-value=0.00011  Score=36.61  Aligned_cols=32  Identities=28%  Similarity=0.607  Sum_probs=28.1

Q ss_pred             cCCCCCCCCCCCCee-eeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELGTRNFF-ERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~-~~~g~~yC~~~~~~~~~  141 (185)
                      .|..|+..|.+..|. ..++++||-++|.++|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            488899999888887 78899999999999884

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

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

Probab=96.91  E-value=0.0004  Score=32.39  Aligned_cols=26  Identities=19%  Similarity=0.511  Sum_probs=23.6

Q ss_pred             CCCccCCccc-CceEEeCCCeecccCc
Q psy3656         143 RCSYCNGPIL-DKCVTALEKTWHTEHF  168 (185)
Q Consensus       143 ~C~~C~~~i~-~~~~~~~~~~~H~~Cf  168 (185)
                      +|..|.+.+. .+-+...++.||..||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            6999999886 6889999999999998

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=96.86  E-value=6.9e-05  Score=37.18  Aligned_cols=32  Identities=28%  Similarity=0.720  Sum_probs=28.1

Q ss_pred             cCCCCCCCCC--CCCeeeeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELG--TRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~--~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      +|.-|+..|+  +...|.+.|.++|+.+|.++||
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            5888999987  5678999999999999999985

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.83  E-value=0.00048  Score=31.42  Aligned_cols=25  Identities=28%  Similarity=0.675  Sum_probs=21.5

Q ss_pred             CCccCCcccC--ceEEeCCCeecccCc
Q psy3656         144 CSYCNGPILD--KCVTALEKTWHTEHF  168 (185)
Q Consensus       144 C~~C~~~i~~--~~~~~~~~~~H~~Cf  168 (185)
                      |..|++-+.+  --+.+.+++||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            7789988874  578899999999998

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.79  E-value=0.00024  Score=35.46  Aligned_cols=27  Identities=22%  Similarity=0.495  Sum_probs=25.0

Q ss_pred             CCCCccCCcccCceEEeCCCeecccCc
Q psy3656         142 PRCSYCNGPILDKCVTALEKTWHTEHF  168 (185)
Q Consensus       142 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf  168 (185)
                      -+|..|+..|.++-|.+++..|||..|
T Consensus         9 ~vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           9 YICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CBCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             HHHHHHHhhhhcCcceecCCCCCCCCC
Confidence            579999999999999999999999887

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

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

Probab=96.76  E-value=0.00028  Score=34.75  Aligned_cols=28  Identities=18%  Similarity=0.515  Sum_probs=24.7

Q ss_pred             CCCCCccCCccc-CceEEeCCCeecccCc
Q psy3656         141 SPRCSYCNGPIL-DKCVTALEKTWHTEHF  168 (185)
Q Consensus       141 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf  168 (185)
                      +.+|..|.+.+. .+-+...++.||..||
T Consensus         7 g~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CceeccccceEeeeeeeeecCcccccccC
Confidence            368999999986 6788999999999998

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.63  E-value=0.0006  Score=31.57  Aligned_cols=25  Identities=32%  Similarity=0.768  Sum_probs=20.7

Q ss_pred             ccccccccc-c-ceeeecCcccccCCc
Q psy3656          85 CSSCDKPIV-G-QVITALGKTWHPEHF  109 (185)
Q Consensus        85 C~~C~~~i~-~-~~~~~~~~~~H~~Cf  109 (185)
                      |..|.++|- + .-+...+++||..||
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            778999993 3 457789999999998

>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=96.34  E-value=0.00061  Score=32.83  Aligned_cols=28  Identities=29%  Similarity=0.778  Sum_probs=24.6

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchh
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYH  137 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~  137 (185)
                      .|..|+..|....++..++++||+.|..
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr   28 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHAR   28 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhh
Confidence            3899999999889999999999998753

>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=96.33  E-value=0.0014  Score=31.45  Aligned_cols=28  Identities=39%  Similarity=0.725  Sum_probs=25.1

Q ss_pred             CCCcccccccccccceeeecCcccccCC
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEH  108 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~C  108 (185)
                      +..-|..|.+-|.+.++++.++-||+.|
T Consensus         4 gssgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           4 GSSGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             SCCSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             ccchhhhhhhhhhhhhhhccccccCCCC
Confidence            3456999999999999999999999988

>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=95.94  E-value=0.0023  Score=29.04  Aligned_cols=25  Identities=32%  Similarity=0.787  Sum_probs=21.5

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy3656          85 CSSCDKPIV--GQVITALGKTWHPEHF  109 (185)
Q Consensus        85 C~~C~~~i~--~~~~~~~~~~~H~~Cf  109 (185)
                      |..|++.+.  +..+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            789999985  3578899999999997

>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=95.92  E-value=0.0014  Score=31.25  Aligned_cols=32  Identities=31%  Similarity=0.728  Sum_probs=28.1

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhhccC
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  141 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~  141 (185)
                      .|+.|...++.+.|+.....+||-.|.+.+|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            47889999999999999999999999887763

>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=95.62  E-value=0.004  Score=30.83  Aligned_cols=26  Identities=23%  Similarity=0.557  Sum_probs=22.5

Q ss_pred             CCCCccCCccc--CceEEeCCCeecccC
Q psy3656         142 PRCSYCNGPIL--DKCVTALEKTWHTEH  167 (185)
Q Consensus       142 ~~C~~C~~~i~--~~~~~~~~~~~H~~C  167 (185)
                      ..|.+|+....  +++|...|..||+.|
T Consensus         8 ~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           8 ATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHccCCCchHHhhcCCCccccccC
Confidence            57999998876  578899999999987

>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=95.36  E-value=0.00056  Score=33.02  Aligned_cols=28  Identities=29%  Similarity=0.720  Sum_probs=24.2

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchh
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYH  137 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~  137 (185)
                      .|..|+..|....++..++++||+.|..
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr   28 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHAR   28 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhh
Confidence            3889999998888999999999998754

>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=95.25  E-value=0.005  Score=28.83  Aligned_cols=26  Identities=27%  Similarity=0.670  Sum_probs=20.4

Q ss_pred             CCCCccCCccc-CceEEeCCCeecccC
Q psy3656         142 PRCSYCNGPIL-DKCVTALEKTWHTEH  167 (185)
Q Consensus       142 ~~C~~C~~~i~-~~~~~~~~~~~H~~C  167 (185)
                      .+|.+|++.+. -+.+.-.|+.||..|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            46999999887 355555789999987

>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=95.22  E-value=0.0073  Score=29.73  Aligned_cols=28  Identities=25%  Similarity=0.471  Sum_probs=24.4

Q ss_pred             CCCcccccccccccceeeecCcccccCC
Q psy3656          81 QKGCCSSCDKPIVGQVITALGKTWHPEH  108 (185)
Q Consensus        81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~C  108 (185)
                      ....|..|.+.|.+.++.+....||++|
T Consensus         7 fge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhcccceeeecccccCCCC
Confidence            3568999999888888888999999998

>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=95.17  E-value=0.0046  Score=30.00  Aligned_cols=28  Identities=21%  Similarity=0.445  Sum_probs=23.6

Q ss_pred             cCCCCCCCCCCCCee--eeCCcCCCccchh
Q psy3656         110 ICTHCNQELGTRNFF--ERDSRPYCEPDYH  137 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~--~~~g~~yC~~~~~  137 (185)
                      +|..|...|..+.|.  ..+|.+||..|+.
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlp   30 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLP   30 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccC
Confidence            588999999988886  6788999988764

>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=94.23  E-value=0.011  Score=28.44  Aligned_cols=30  Identities=30%  Similarity=0.708  Sum_probs=24.5

Q ss_pred             ccCCCCCCCCC--CCCeeeeCCcCCCccchhh
Q psy3656         109 FICTHCNQELG--TRNFFERDSRPYCEPDYHN  138 (185)
Q Consensus       109 f~C~~C~~~L~--~~~~~~~~g~~yC~~~~~~  138 (185)
                      ++|.-|+..|+  +...+...+.++|+.+|.+
T Consensus         1 LkC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           1 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             CccccccccccchhhHHHhhcceeeehhhhhc
Confidence            36788888887  4567889999999999976

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.05  E-value=0.008  Score=30.85  Aligned_cols=27  Identities=15%  Similarity=0.250  Sum_probs=18.9

Q ss_pred             CCCccCCccc-CceEEe-CCCeecccCcc
Q psy3656         143 RCSYCNGPIL-DKCVTA-LEKTWHTEHFF  169 (185)
Q Consensus       143 ~C~~C~~~i~-~~~~~~-~~~~~H~~Cf~  169 (185)
                      .|++|++... |+-|-. .+..|||.|-.
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             CcchhhccccccceeeecCCceeCCcccc
Confidence            3889999775 444433 56899999853

>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=93.87  E-value=0.016  Score=27.88  Aligned_cols=27  Identities=26%  Similarity=0.605  Sum_probs=21.8

Q ss_pred             cCCCCCCCCCCC-CeeeeCCcCCCccch
Q psy3656         110 ICTHCNQELGTR-NFFERDSRPYCEPDY  136 (185)
Q Consensus       110 ~C~~C~~~L~~~-~~~~~~g~~yC~~~~  136 (185)
                      .|+.|...|-.+ .|...+|.+||+.+-
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            488999998855 566999999998763

>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=93.70  E-value=0.009  Score=29.33  Aligned_cols=31  Identities=16%  Similarity=0.495  Sum_probs=24.3

Q ss_pred             ccCCCCCCCCCCCC-ee-eeCCcCCCccchhhc
Q psy3656         109 FICTHCNQELGTRN-FF-ERDSRPYCEPDYHNL  139 (185)
Q Consensus       109 f~C~~C~~~L~~~~-~~-~~~g~~yC~~~~~~~  139 (185)
                      |.|..|+.-+++++ |. ....++||-.||.+.
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            67899999888664 54 667789999998763

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.63  E-value=0.012  Score=28.01  Aligned_cols=27  Identities=33%  Similarity=0.657  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656         111 CTHCNQELGTRNFFERDSRPYCEPDYHN  138 (185)
Q Consensus       111 C~~C~~~L~~~~~~~~~g~~yC~~~~~~  138 (185)
                      |..|++.| ...-....|.+||.+|..+
T Consensus         2 C~~Cgkel-tadArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKEL-TADARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBC-CTTCEEETTEEECHHHHHT
T ss_pred             cccccccc-chhHHHhcCCEEEEecccc
Confidence            77888888 4456788899999988653

>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=93.01  E-value=0.017  Score=27.77  Aligned_cols=17  Identities=18%  Similarity=0.600  Sum_probs=14.4

Q ss_pred             ccccCCCcc-CCCCeeeC
Q psy3656         169 FCAQCGKQF-GEAMVKFI  185 (185)
Q Consensus       169 ~C~~C~~~l-~~~~~~~~  185 (185)
                      +|++|..+| .+|+|++|
T Consensus         1 tC~tC~n~LVPGDRFHyv   18 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYI   18 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEE
T ss_pred             CcccccccccCCceeEEe
Confidence            488898888 89999885

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.96  E-value=0.052  Score=33.68  Aligned_cols=27  Identities=15%  Similarity=0.368  Sum_probs=18.4

Q ss_pred             CCcCCCccchhhccCCCCCccCCcccC
Q psy3656         127 DSRPYCEPDYHNLFSPRCSYCNGPILD  153 (185)
Q Consensus       127 ~g~~yC~~~~~~~~~~~C~~C~~~i~~  153 (185)
                      -|..||..|..+.+..+|..|+..+..
T Consensus        41 CgH~fC~~Ci~~~~~~~CP~Cr~~~~~   67 (97)
T d1jm7b_          41 CEHIFCSNCVSDCIGTGCPVCYTPAWI   67 (97)
T ss_dssp             SSCCBCTTTGGGGTTTBCSSSCCBCSC
T ss_pred             CCCchhHHHHHHHHhccccccCCcCch
Confidence            456667777666666678888877653

>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=92.86  E-value=0.035  Score=27.36  Aligned_cols=30  Identities=30%  Similarity=0.555  Sum_probs=25.7

Q ss_pred             CCCCcccccccccccceeeecCcccccCCc
Q psy3656          80 TQKGCCSSCDKPIVGQVITALGKTWHPEHF  109 (185)
Q Consensus        80 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf  109 (185)
                      .++-+|..|...|.++-+.+.|..||+..|
T Consensus         6 lGk~vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           6 LGKYICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCBCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             hhhHHHHHHHhhhhcCcceecCCCCCCCCC
Confidence            457789999999977888999999998765

>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=91.31  E-value=0.064  Score=26.34  Aligned_cols=27  Identities=15%  Similarity=0.544  Sum_probs=21.9

Q ss_pred             CCcccccccccc--cceeeecCcccccCC
Q psy3656          82 KGCCSSCDKPIV--GQVITALGKTWHPEH  108 (185)
Q Consensus        82 ~~~C~~C~~~i~--~~~~~~~~~~~H~~C  108 (185)
                      .-.|..|+....  ..+|...|..||..|
T Consensus         7 ~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           7 SATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHccCCCchHHhhcCCCccccccC
Confidence            346999998883  457889999999887

>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=90.49  E-value=0.052  Score=25.97  Aligned_cols=29  Identities=24%  Similarity=0.571  Sum_probs=25.2

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYHN  138 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~  138 (185)
                      +|..|...|.+..|.-..|+.+|.+|..+
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            58899999988889999999999998765

>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=90.42  E-value=0.056  Score=25.59  Aligned_cols=28  Identities=21%  Similarity=0.564  Sum_probs=22.1

Q ss_pred             cCCCCCCCCCCCCeeeeCCcCCCccchh
Q psy3656         110 ICTHCNQELGTRNFFERDSRPYCEPDYH  137 (185)
Q Consensus       110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~  137 (185)
                      +|..|-.+|....|...++++.|..|..
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5777788887778888888988887753

>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=90.32  E-value=0.035  Score=27.89  Aligned_cols=16  Identities=50%  Similarity=0.926  Sum_probs=14.4

Q ss_pred             cccccCCCccCCCCee
Q psy3656         168 FFCAQCGKQFGEAMVK  183 (185)
Q Consensus       168 f~C~~C~~~l~~~~~~  183 (185)
                      |+|..|+++|++..|+
T Consensus         1 F~C~~C~~~f~~~~F~   16 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFY   16 (35)
T ss_dssp             CCCTTTCCCCGGGCSE
T ss_pred             CCCCCCcCCCCCCCeE
Confidence            7899999999988875

>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=88.11  E-value=0.13  Score=24.53  Aligned_cols=26  Identities=19%  Similarity=0.588  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCCeeeeCCcCCCccch
Q psy3656         111 CTHCNQELGTRNFFERDSRPYCEPDY  136 (185)
Q Consensus       111 C~~C~~~L~~~~~~~~~g~~yC~~~~  136 (185)
                      |..|+..|-+..|...+..++|.+|-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhcC
Confidence            67788888787888888888887763

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.66  E-value=0.28  Score=27.02  Aligned_cols=42  Identities=17%  Similarity=0.364  Sum_probs=27.4

Q ss_pred             ccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc
Q psy3656         109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL  152 (185)
Q Consensus       109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~  152 (185)
                      +.|..|...+.. .....=|..||..|..+ ...+|..|++.|.
T Consensus         7 l~C~IC~~~~~~-p~~lpCgH~fC~~Ci~~-~~~~CP~Cr~~~~   48 (56)
T d1bora_           7 LRCQQCQAEAKC-PKLLPCLHTLCSGCLEA-SGMQCPICQAPWP   48 (56)
T ss_dssp             SSCSSSCSSCBC-CSCSTTSCCSBTTTCSS-SSSSCSSCCSSSS
T ss_pred             CCCcccCcccCC-CEEecCCCHHhHHHHHc-CCCcCcCCCCccc
Confidence            578888776643 23345677888888653 3467888877765