Psyllid ID: psy2501

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130
Protein Sequence
VAPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccEEEccccccccccccccccccccccccEEcccccccHHHHHHHccccccccccccccccEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccHHHEHHcccccccccEEEHHcccccccccEEEcccccccHHHHHHHcccHHccccccccccEEccc
Coil and Loop (DISEMBL)
vapqqlehsvtdsssvsyskpnqpvhqkgkqLDCMLDSLTAEMsrqgvtttqkgccsscdkpiVGQVITAlgktwhpehficthcnqelgtrnfferdsrpycepdyhnlfsprcsycngpildvsirnt
Flexible Loop (DISEMBL)
vapqqlehsvtdsssvsyskpnqpvhqkgkQLDCMLDSLTAEMSRQGVtttqkgccsscdKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYhnlfsprcsycngpILDVSIRNT
Low Complexity Region (SEG)
VAPQQLEHsvtdsssvsysKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT
Disordered region (IsUnstruct)
***********************************************VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVS****
Disordered Region (DISOPRED)
**************************************************TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRN*
Disordered Region (DISEMBL)
*****************************KQLDCMLDSLTAEMS**********CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT
Disordered Region (DISPRO)
*********************************C*L*S**A**SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSI***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VAPQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT
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	130	2.2.26 [Sep-21-2011]
P49024	559	Paxillin OS=Gallus gallus	yes	N/A	0.8	0.186	0.650	3e-40
Q66H76	586	Paxillin OS=Rattus norveg	yes	N/A	0.8	0.177	0.641	7e-40
Q8VI36	591	Paxillin OS=Mus musculus	yes	N/A	0.930	0.204	0.569	7e-40
P49023	591	Paxillin OS=Homo sapiens	yes	N/A	0.730	0.160	0.680	3e-39
Q5R7I1	591	Paxillin OS=Pongo abelii	yes	N/A	0.730	0.160	0.680	3e-39
Q9N261	386	Leupaxin OS=Oryctolagus c	no	N/A	0.7	0.235	0.612	2e-30
Q2TCH4	506	Transforming growth facto	N/A	N/A	0.838	0.215	0.532	5e-30
Q99N69	386	Leupaxin OS=Mus musculus	no	N/A	0.784	0.264	0.557	1e-29
O60711	386	Leupaxin OS=Homo sapiens	no	N/A	0.638	0.215	0.591	2e-29
Q3MHZ4	456	Transforming growth facto	no	N/A	0.838	0.239	0.513	1e-27

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

 Score =  163 bits (412), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 69/106 (65%), Positives = 83/106 (78%)

Query: 19  SKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPE 78
           S P     + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPE
Sbjct: 289 SSPPSTTPKPGSQLDTMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPE 348

Query: 79  HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           HF+CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct: 349 HFVCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 394

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 =  162 bits (409), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 68/106 (64%), Positives = 84/106 (79%)

Query: 19  SKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPE 78
           S P   + + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPE
Sbjct: 316 SSPPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPE 375

Query: 79  HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           HF+CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC YCNGPILD
Sbjct: 376 HFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRCYYCNGPILD 421

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

Rattus norvegicus (taxid: 10116)

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

 Score =  162 bits (409), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 70/123 (56%), Positives = 87/123 (70%)

Query: 5   QLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIV 64
           Q E           S P   + + G QLD ML SL +++++ GV T  KG C +C KPI 
Sbjct: 307 QDEGGFMAQGKTGSSSPPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIA 366

Query: 65  GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           GQV+TA+GKTWHPEHF+CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC YCNGPILD
Sbjct: 367 GQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRCYYCNGPILD 426

Query: 125 VSI 127
             +
Sbjct: 427 KVV 429

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

Mus musculus (taxid: 10090)

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

 Score =  160 bits (404), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 66/97 (68%), Positives = 80/97 (82%)

Query: 31  QLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90
           QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G
Sbjct: 333 QLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIG 392

Query: 91  TRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSI 127
           +RNFFERD +PYCE DYHNLFSPRC YCNGPILD  +
Sbjct: 393 SRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVV 429

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 =  160 bits (404), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 66/97 (68%), Positives = 80/97 (82%)

Query: 31  QLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90
           QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF+CTHC +E+G
Sbjct: 333 QLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIG 392

Query: 91  TRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSI 127
           +RNFFERD +PYCE DYHNLFSPRC YCNGPILD  +
Sbjct: 393 SRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVV 429

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 =  130 bits (327), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 57/93 (61%), Positives = 68/93 (73%)

Query: 32  LDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT 91
           LD ML  L  E+   G+ T  KG C+SC KPIVG+VI ALG++WHPEHFICTHC +E+G+
Sbjct: 128 LDSMLGGLEQELQNLGIPTVPKGHCASCQKPIVGKVIHALGQSWHPEHFICTHCKEEIGS 187

Query: 92  RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             FFER    YC  DYH+LFSPRC+YC  PILD
Sbjct: 188 SPFFERSGLAYCPKDYHHLFSPRCAYCAAPILD 220

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

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 58/109 (53%), Positives = 73/109 (66%)

Query: 15  SVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKT 74
           SVS SK  +        LD ML  L + + +QG+ T  KG C SC +PI GQV+TALG T
Sbjct: 232 SVSGSKVPEATSVPRSDLDSMLVKLQSGLKQQGIETYSKGLCESCQRPIAGQVVTALGHT 291

Query: 75  WHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL 123
           WHPEHF+C HC+  +GT NFFE+D RPYCE DY  L++PRC+ C  PI+
Sbjct: 292 WHPEHFVCAHCHTLIGTSNFFEKDGRPYCEKDYFMLYAPRCALCELPIV 340

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

 Score =  128 bits (322), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 58/104 (55%), Positives = 70/104 (67%), Gaps = 2/104 (1%)

Query: 21  PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
           P+Q  H+    LD ML  L  E+   G+ T  KG C+SC KPI G+VI ALG++WHPEHF
Sbjct: 119 PDQQDHKAS--LDSMLGDLEQELQDLGIATVPKGYCASCQKPIAGKVIHALGQSWHPEHF 176

Query: 81  ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           +CTHC +ELG+  FFER    YC  DYH LFSPRC+YC  PI D
Sbjct: 177 VCTHCKEELGSSPFFERSGLAYCSKDYHRLFSPRCAYCAAPITD 220

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 =  127 bits (320), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/93 (59%), Positives = 66/93 (70%)

Query: 32  LDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT 91
           LD ML  L  E+   G+ T  KG C+SC KPI G+VI ALG++WHPEHF+CTHC +E+G+
Sbjct: 128 LDSMLGGLEQELQDLGIATVPKGHCASCQKPIAGKVIHALGQSWHPEHFVCTHCKEEIGS 187

Query: 92  RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             FFER    YC  DYH LFSPRC+YC  PILD
Sbjct: 188 SPFFERSGLAYCPNDYHQLFSPRCAYCAAPILD 220

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

 Score =  121 bits (303), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 56/109 (51%), Positives = 70/109 (64%)

Query: 14  SSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGK 73
           SS+S   P+ P       LD ML  L +++SR+GV T  KG C SC+KPI GQV+TALG+
Sbjct: 181 SSMSEDTPSPPGPTSKGSLDTMLGLLQSDLSRRGVPTQAKGLCGSCNKPIAGQVVTALGR 240

Query: 74  TWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI 122
            WHPEHF+C  C+  LG  +FFE+D  P+C   Y   FSPRC  CN PI
Sbjct: 241 AWHPEHFVCGGCSTALGGSSFFEKDGAPFCPECYFERFSPRCGLCNQPI 289

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	130
328709648	424	PREDICTED: paxillin-like isoform 2 [Acyr	0.861	0.264	0.758	1e-46
383863879	607	PREDICTED: paxillin-like [Megachile rotu	0.8	0.171	0.819	2e-46
270016014	488	hypothetical protein TcasGA2_TC010609 [T	0.9	0.239	0.726	3e-46
328709646	474	PREDICTED: paxillin-like isoform 3 [Acyr	0.861	0.236	0.758	3e-46
312372729	286	hypothetical protein AND_19782 [Anophele	0.915	0.416	0.739	4e-46
380025704	572	PREDICTED: paxillin-like isoform 1 [Apis	0.8	0.181	0.819	4e-46
189242184	448	PREDICTED: similar to paxillin [Triboliu	0.9	0.261	0.726	4e-46
380025706	607	PREDICTED: paxillin-like isoform 2 [Apis	0.8	0.171	0.819	5e-46
350421197	607	PREDICTED: paxillin-like [Bombus impatie	0.8	0.171	0.819	5e-46
340714019	605	PREDICTED: paxillin-like [Bombus terrest	0.8	0.171	0.819	6e-46

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

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 85/112 (75%), Positives = 93/112 (83%)

Query: 13  SSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALG 72
           SS V  S   +       +LDCML SLTAEM+RQGV TTQKGCC++CDK IVGQVITALG
Sbjct: 206 SSPVRASYATESADSAAPRLDCMLGSLTAEMNRQGVNTTQKGCCTACDKAIVGQVITALG 265

Query: 73  KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           KTWHPEHF C HC+QELGTRNFFER+ RPYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 266 KTWHPEHFTCNHCSQELGTRNFFEREGRPYCEPDYHNLFSPRCAYCNGPILD 317

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  189 bits (481), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 86/105 (81%), Positives = 92/105 (87%), Gaps = 1/105 (0%)

Query: 21  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 79
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 302 PTQPAAQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 361

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 362 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILD 406

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  189 bits (480), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 85/117 (72%), Positives = 94/117 (80%)

Query: 8   HSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQV 67
            +VTDS     +K  Q      + LD ML +L A+MSRQGV T+QKGCCS+CDKPIVGQV
Sbjct: 263 QTVTDSQYARPTKATQSHSAPKQNLDSMLGNLQADMSRQGVNTSQKGCCSACDKPIVGQV 322

Query: 68  ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           ITALGKTWHPEHF C HC QELGTRNFFERD +PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 323 ITALGKTWHPEHFTCAHCTQELGTRNFFERDGKPYCEPDYHNLFSPRCAYCNGPILD 379

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  189 bits (480), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 85/112 (75%), Positives = 93/112 (83%)

Query: 13  SSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALG 72
           SS V  S   +       +LDCML SLTAEM+RQGV TTQKGCC++CDK IVGQVITALG
Sbjct: 198 SSPVRASYATESADSAAPRLDCMLGSLTAEMNRQGVNTTQKGCCTACDKAIVGQVITALG 257

Query: 73  KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           KTWHPEHF C HC+QELGTRNFFER+ RPYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 258 KTWHPEHFTCNHCSQELGTRNFFEREGRPYCEPDYHNLFSPRCAYCNGPILD 309

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  189 bits (479), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 88/119 (73%), Positives = 95/119 (79%)

Query: 9   SVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVI 68
           S   + S +   P   V   G QLD ML +LTA+MSRQGV TTQKGCCS+CDKPIVGQVI
Sbjct: 64  STLTTVSTTEHLPPPVVTSSGDQLDSMLGNLTADMSRQGVNTTQKGCCSACDKPIVGQVI 123

Query: 69  TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSI 127
           TALGKTWHPEHF C HCNQELGTRNFFERD  PYCEPDYHNLFSPRC+YCNGPILD  +
Sbjct: 124 TALGKTWHPEHFTCNHCNQELGTRNFFERDGNPYCEPDYHNLFSPRCAYCNGPILDKCV 182

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  189 bits (479), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 86/105 (81%), Positives = 92/105 (87%), Gaps = 1/105 (0%)

Query: 21  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 79
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 303 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 362

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 363 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILD 407

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  189 bits (479), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 85/117 (72%), Positives = 94/117 (80%)

Query: 8   HSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQV 67
            +VTDS     +K  Q      + LD ML +L A+MSRQGV T+QKGCCS+CDKPIVGQV
Sbjct: 223 QTVTDSQYARPTKATQSHSAPKQNLDSMLGNLQADMSRQGVNTSQKGCCSACDKPIVGQV 282

Query: 68  ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           ITALGKTWHPEHF C HC QELGTRNFFERD +PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 283 ITALGKTWHPEHFTCAHCTQELGTRNFFERDGKPYCEPDYHNLFSPRCAYCNGPILD 339

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  188 bits (478), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 86/105 (81%), Positives = 92/105 (87%), Gaps = 1/105 (0%)

Query: 21  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 79
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 303 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 362

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 363 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILD 407

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 =  188 bits (478), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 86/105 (81%), Positives = 92/105 (87%), Gaps = 1/105 (0%)

Query: 21  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 79
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 303 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 362

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 363 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILD 407

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 =  188 bits (478), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 86/105 (81%), Positives = 92/105 (87%), Gaps = 1/105 (0%)

Query: 21  PNQPVHQ-KGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH 79
           P QP  Q K  QLD ML +L A+MSRQGV TTQKGCCS+C+KPIVGQVITALGKTWHPEH
Sbjct: 301 PPQPATQTKQNQLDSMLGNLQADMSRQGVNTTQKGCCSACEKPIVGQVITALGKTWHPEH 360

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
           F CTHCNQELGTRNFFER+  PYCEPDYHNLFSPRC+YCNGPILD
Sbjct: 361 FTCTHCNQELGTRNFFEREGHPYCEPDYHNLFSPRCAYCNGPILD 405

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

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	130
FB|FBgn0041789	581	Pax "Paxillin" [Drosophila mel	0.723	0.161	0.819	1.5e-42
UNIPROTKB|F1NB68	559	PXN "Paxillin" [Gallus gallus	0.8	0.186	0.653	4.8e-39
UNIPROTKB|P49024	559	PXN "Paxillin" [Gallus gallus	0.8	0.186	0.653	4.8e-39
UNIPROTKB|F1PUT6	590	PXN "Uncharacterized protein"	0.792	0.174	0.663	6.1e-39
UNIPROTKB|E7EMK8	403	PXN "Paxillin" [Homo sapiens (	0.792	0.255	0.663	6.1e-39
UNIPROTKB|F5GZ78	589	PXN "Paxillin" [Homo sapiens (	0.792	0.174	0.663	6.1e-39
UNIPROTKB|P49023	591	PXN "Paxillin" [Homo sapiens (	0.792	0.174	0.663	6.1e-39
UNIPROTKB|F1MFD1	586	PXN "Uncharacterized protein"	0.792	0.175	0.663	6.1e-39
MGI|MGI:108295	591	Pxn "paxillin" [Mus musculus (	0.8	0.175	0.644	2.1e-38
RGD|1305759	586	Pxn "paxillin" [Rattus norvegi	0.8	0.177	0.644	2.1e-38

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

 Score = 450 (163.5 bits), Expect = 1.5e-42, P = 1.5e-42
 Identities = 77/94 (81%), Positives = 83/94 (88%)

Query:    31 QLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90
             QLD ML +L A MSRQGV T QKGCC++C+KPIVGQVITALGKTWHPEHF C HC+QELG
Sbjct:   323 QLDSMLGNLQANMSRQGVNTVQKGCCNACEKPIVGQVITALGKTWHPEHFTCNHCSQELG 382

Query:    91 TRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             TRNFFERD  PYCEPDYHNLFSPRC+YCNG ILD
Sbjct:   383 TRNFFERDGFPYCEPDYHNLFSPRCAYCNGAILD 416

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

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 68/104 (65%), Positives = 82/104 (78%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P     + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   291 PPSTTPKPGSQLDTMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 350

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   351 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 394

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 = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 68/104 (65%), Positives = 82/104 (78%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P     + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   291 PPSTTPKPGSQLDTMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 350

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   351 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 394

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

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

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 69/104 (66%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   323 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 381

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   382 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 425

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 = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 69/104 (66%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   136 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 194

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   195 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 238

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 69/104 (66%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   322 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 380

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   381 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 424

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 = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 69/104 (66%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   324 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 382

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   383 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 426

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

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

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 69/104 (66%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P  P  + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   319 PGGPP-KPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 377

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYHNLFSPRC YCNGPILD
Sbjct:   378 VCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILD 421

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

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

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 67/104 (64%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P   + + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   323 PPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 382

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC YCNGPILD
Sbjct:   383 VCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRCYYCNGPILD 426

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

RGD|1305759 Pxn "paxillin" [Rattus norvegicus (taxid:10116)]

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 67/104 (64%), Positives = 83/104 (79%)

Query:    21 PNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF 80
             P   + + G QLD ML SL +++++ GV T  KG C +C KPI GQV+TA+GKTWHPEHF
Sbjct:   318 PPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHF 377

Query:    81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
             +CTHC +E+G+RNFFERD +PYCE DYH+LFSPRC YCNGPILD
Sbjct:   378 VCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRCYYCNGPILD 421

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

GO:0005178 "integrin binding" evidence=IPI

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA;ISO

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

GO:0005938 "cell cortex" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA;ISO

GO:0007010 "cytoskeleton organization" evidence=IEA;ISO

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA;ISO

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

GO:0019901 "protein kinase binding" evidence=IPI

GO:0030027 "lamellipodium" evidence=IEA;ISO

GO:0030032 "lamellipodium assembly" evidence=IEA;ISO

GO:0031252 "cell leading edge" evidence=ISO

GO:0032403 "protein complex binding" evidence=IPI

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

GO:0048041 "focal adhesion assembly" evidence=IEA;ISO

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

GO:0051435 "BH4 domain binding" evidence=IEA;ISO

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

---

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)
P49023	PAXI_HUMAN	No assigned EC number	0.6804	0.7307	0.1607	yes	N/A
P49024	PAXI_CHICK	No assigned EC number	0.6509	0.8	0.1860	yes	N/A
Q66H76	PAXI_RAT	No assigned EC number	0.6415	0.8	0.1774	yes	N/A
Q8VI36	PAXI_MOUSE	No assigned EC number	0.5691	0.9307	0.2047	yes	N/A
Q5R7I1	PAXI_PONAB	No assigned EC number	0.6804	0.7307	0.1607	yes	N/A
Q8MML5	PAXB_DICDI	No assigned EC number	0.5522	0.5153	0.1177	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	130
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	1e-32
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	1e-27
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	8e-27
pfam00412	58	pfam00412, LIM, LIM domain	1e-19
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	3e-19
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	4e-17
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	6e-17
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	1e-16
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	2e-15
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	5e-15
cd09339	52	cd09339, LIM4_Paxillin_like, The fourth LIM domain	1e-13
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-13
cd09411	52	cd09411, LIM4_Paxillin, The fourth LIM domain of P	2e-12
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	2e-12
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	2e-12
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	2e-12
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	1e-11
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	2e-11
cd09453	52	cd09453, LIM1_ENH, The first LIM domain of the Eni	2e-10
cd09455	54	cd09455, LIM1_Enigma_like_1, The first LIM domain	2e-10
cd09452	52	cd09452, LIM1_Enigma, The first LIM domain of Enig	3e-10
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-10
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	6e-10
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	6e-10
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	7e-10
cd09335	54	cd09335, LIM5_PINCH, The fifth LIM domain of prote	2e-09
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	4e-09
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	4e-09
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	4e-09
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	4e-08
cd09454	52	cd09454, LIM1_ZASP_Cypher, The first LIM domain of	4e-08
cd09430	52	cd09430, LIM5_LIMPETin, The fifth LIM domain of pr	4e-08
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	6e-08
cd09418	56	cd09418, LIM2_Prickle, The second LIM domain of Pr	9e-08
cd09424	58	cd09424, LIM2_FHL1, The second LIM domain of Four	1e-07
cd09451	53	cd09451, LIM_RIL, The LIM domain of RIL	1e-07
cd09328	56	cd09328, LIM2_abLIM, The second LIM domain on acti	1e-07
cd09354	60	cd09354, LIM2_LPP, The second LIM domain of lipoma	2e-07
cd09345	54	cd09345, LIM2_FHL, The second LIM domain of Four a	2e-07
cd09431	57	cd09431, LIM3_Fhl2, The third LIM domain of Four a	3e-07
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	4e-07
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	4e-07
cd09450	53	cd09450, LIM_ALP, This family represents the LIM d	5e-07
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	6e-07
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	6e-07
cd09355	53	cd09355, LIM2_Ajuba_like, The second LIM domain of	8e-07
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	1e-06
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	2e-06
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	2e-06
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-06
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	4e-06
cd09372	53	cd09372, LIM2_FBLP-1, The second LIM domain of the	4e-06
cd09425	54	cd09425, LIM4_LIMPETin, The fourth LIM domain of p	7e-06
cd09460	55	cd09460, LIM3_ZASP_Cypher, The third LIM domain of	9e-06
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	2e-05
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	2e-05
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	3e-05
cd09461	54	cd09461, LIM3_Enigma_like_1, The third LIM domain	4e-05
cd09426	57	cd09426, LIM2_FHL2, The second LIM domain of Four	4e-05
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	4e-05
cd09417	56	cd09417, LIM2_LIMPETin_like, The second LIM domain	5e-05
cd09427	58	cd09427, LIM2_FHL3, The second LIM domain of Four	7e-05
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	8e-05
cd09356	53	cd09356, LIM2_TRIP6, The second LIM domain of Thyr	1e-04
cd09429	53	cd09429, LIM3_FHL1, The third LIM domain of Four a	2e-04
cd09333	51	cd09333, LIM3_PINCH, The third LIM domain of prote	2e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	3e-04
cd09352	54	cd09352, LIM1_Ajuba_like, The first LIM domain of	3e-04
cd09340	58	cd09340, LIM1_Testin_like, The first LIM domain of	4e-04
cd09458	55	cd09458, LIM3_Enigma, The third LIM domain of Enig	5e-04
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	5e-04
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	5e-04
cd09348	64	cd09348, LIM4_FHL1, The fourth LIM domain of Four	6e-04
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	7e-04
cd09448	52	cd09448, LIM_CLP36, This family represents the LIM	8e-04
cd09416	56	cd09416, LIM2_Testin, The second LIM domain of Tes	0.001
cd09428	54	cd09428, LIM2_FHL5, The second LIM domain of Four	0.001
cd09841	59	cd09841, LIM1_Prickle_3, The first LIM domain of P	0.002
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	0.002
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	0.002
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	0.002
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	0.002
cd09393	56	cd09393, LIM3_Lrg1p_like, The third LIM domain of	0.002
cd09347	56	cd09347, LIM4_FHL, The fourth LIM domain of Four a	0.003
cd09397	58	cd09397, LIM1_UF1, LIM domain in proteins of unkno	0.003
cd09330	56	cd09330, LIM4_abLIM, The fourth LIM domain of acti	0.003
cd09484	59	cd09484, LIM1_Prickle_2, The first LIM domain of P	0.003

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

 Score =  108 bits (273), Expect = 1e-32
 Identities = 40/53 (75%), Positives = 46/53 (86%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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 = 96.5 bits (240), Expect = 1e-27
 Identities = 37/55 (67%), Positives = 45/55 (81%)

Query: 54  GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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 = 93.9 bits (233), Expect = 8e-27
 Identities = 39/53 (73%), Positives = 47/53 (88%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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|215907 pfam00412, LIM, LIM domain

 Score = 75.8 bits (187), Expect = 1e-19
 Identities = 28/58 (48%), Positives = 36/58 (62%), Gaps = 2/58 (3%)

Query: 56  CSSCDKPIVGQVIT--ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
           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 = 75.1 bits (185), Expect = 3e-19
 Identities = 26/52 (50%), Positives = 34/52 (65%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 4e-17
 Identities = 27/53 (50%), Positives = 36/53 (67%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVGQVI-TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 68.9 bits (169), Expect = 6e-17
 Identities = 24/53 (45%), Positives = 32/53 (60%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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 = 68.3 bits (167), Expect = 1e-16
 Identities = 26/52 (50%), Positives = 35/52 (67%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH

 Score = 65.5 bits (160), Expect = 2e-15
 Identities = 23/52 (44%), Positives = 31/52 (59%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 64.2 bits (156), Expect = 5e-15
 Identities = 25/52 (48%), Positives = 32/52 (61%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family

 Score = 60.4 bits (147), Expect = 1e-13
 Identities = 25/52 (48%), Positives = 36/52 (69%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 60.5 bits (147), Expect = 1e-13
 Identities = 25/54 (46%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 55  CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPD 106
            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|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin

 Score = 57.7 bits (139), Expect = 2e-12
 Identities = 25/49 (51%), Positives = 34/49 (69%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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 = 57.4 bits (139), Expect = 2e-12
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 57.4 bits (139), Expect = 2e-12
 Identities = 22/52 (42%), Positives = 30/52 (57%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 57.5 bits (139), Expect = 2e-12
 Identities = 24/52 (46%), Positives = 31/52 (59%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 55.2 bits (133), Expect = 1e-11
 Identities = 22/53 (41%), Positives = 30/53 (56%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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 = 55.2 bits (133), Expect = 2e-11
 Identities = 23/53 (43%), Positives = 29/53 (54%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog (ENH) family

 Score = 52.3 bits (125), Expect = 2e-10
 Identities = 22/52 (42%), Positives = 29/52 (55%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma subfamily with unknown function

 Score = 52.1 bits (125), Expect = 2e-10
 Identities = 24/51 (47%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTH--CNQELGTRNFFERDSRPYCE 104
           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|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma

 Score = 51.7 bits (124), Expect = 3e-10
 Identities = 20/52 (38%), Positives = 30/52 (57%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 51.6 bits (123), Expect = 4e-10
 Identities = 22/52 (42%), Positives = 29/52 (55%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 51.1 bits (123), Expect = 6e-10
 Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 51.2 bits (123), Expect = 6e-10
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT-RNFFERDSRPYCEPDY 107
           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|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 50.8 bits (121), Expect = 7e-10
 Identities = 21/52 (40%), Positives = 28/52 (53%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH

 Score = 49.7 bits (119), Expect = 2e-09
 Identities = 20/49 (40%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRN-FFERDSRPYC 103
           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|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 48.9 bits (117), Expect = 4e-09
 Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 49.2 bits (117), Expect = 4e-09
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL-GTRNFFERDSRPYCEPDYHNLFSPR 114
           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|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH

 Score = 48.9 bits (117), Expect = 4e-09
 Identities = 15/41 (36%), Positives = 23/41 (56%)

Query: 72  GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           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|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 46.2 bits (110), Expect = 4e-08
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher family

 Score = 46.5 bits (110), Expect = 4e-08
 Identities = 21/52 (40%), Positives = 29/52 (55%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 4e-08
 Identities = 20/48 (41%), Positives = 28/48 (58%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH

 Score = 45.8 bits (109), Expect = 6e-08
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 105
           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|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle

 Score = 45.5 bits (108), Expect = 9e-08
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 56  CSSCDKPIVGQVIT-ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 45.5 bits (108), Expect = 1e-07
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
           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|188835 cd09451, LIM_RIL, The LIM domain of RIL

 Score = 44.9 bits (106), Expect = 1e-07
 Identities = 20/49 (40%), Positives = 27/49 (55%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM (abLIM) proteins

 Score = 45.0 bits (107), Expect = 1e-07
 Identities = 16/32 (50%), Positives = 24/32 (75%)

Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQ 87
          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|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred partner (LPP)

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPDYHNLFSPR 114
           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|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM domains protein (FHL)

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 44.2 bits (104), Expect = 3e-07
 Identities = 21/57 (36%), Positives = 30/57 (52%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           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 = 43.9 bits (104), Expect = 4e-07
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 4e-07
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPY 102
           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|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP, actinin-associated LIM protein

 Score = 43.4 bits (102), Expect = 5e-07
 Identities = 20/49 (40%), Positives = 27/49 (55%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 43.2 bits (102), Expect = 6e-07
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 55  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 43.1 bits (102), Expect = 6e-07
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 7/58 (12%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSR------PYCEPDY 107
           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|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like proteins

 Score = 42.7 bits (101), Expect = 8e-07
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL-GTRNFFERDSRPYCEPDY 107
           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|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated LIM protein) family

 Score = 42.4 bits (100), Expect = 1e-06
 Identities = 19/49 (38%), Positives = 24/49 (48%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like family

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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 = 41.9 bits (98), Expect = 2e-06
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein SF3

 Score = 41.7 bits (98), Expect = 2e-06
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 50  TTQKGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           TTQK  C +CDK + +   ++A G  +H   F C+HC   L   N+   +   YC+P + 
Sbjct: 1   TTQK--CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFE 58

Query: 109 NLF 111
            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|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 41.3 bits (97), Expect = 4e-06
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIVGQV--ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1)

 Score = 40.9 bits (96), Expect = 4e-06
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPDY 107
           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|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin

 Score = 40.5 bits (95), Expect = 7e-06
 Identities = 15/36 (41%), Positives = 21/36 (58%)

Query: 72  GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 9e-06
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH 108
           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|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

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

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 38.9 bits (91), Expect = 2e-05
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIVGQV--ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIVGQ--VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma subfamily with unknown function

 Score = 38.7 bits (90), Expect = 4e-05
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 17/52 (32%), Positives = 24/52 (46%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188801 cd09417, LIM2_LIMPETin_like, The second LIM domain of protein LIMPETin and related proteins

 Score = 38.3 bits (89), Expect = 5e-05
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
              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|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM domains protein 3 (FHL3)

 Score = 37.9 bits (88), Expect = 7e-05
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 37.8 bits (88), Expect = 8e-05
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 37.2 bits (86), Expect = 1e-04
 Identities = 15/34 (44%), Positives = 22/34 (64%)

Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL 89
          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|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 105
           C  C   I  Q +   G  +HP HF C +C +EL      E     YC  
Sbjct: 1   CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYCLR 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 = 36.4 bits (84), Expect = 3e-04
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like proteins

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like family

 Score = 36.0 bits (84), Expect = 4e-04
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%)

Query: 56  CSSCDKPI----VGQVITALGK--TWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma

 Score = 35.8 bits (82), Expect = 5e-04
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPDY 107
           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 = 5e-04
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           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|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 56  CSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 110
           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 = 7e-04
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 55  CCSSCDKPIVGQVI-TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
            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|188832 cd09448, LIM_CLP36, This family represents the LIM domain of CLP36

 Score = 34.9 bits (80), Expect = 8e-04
 Identities = 17/49 (34%), Positives = 23/49 (46%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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 = 0.001
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVGQVIT-ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188812 cd09428, LIM2_FHL5, The second LIM domain of Four and a half LIM domains protein 5 (FHL5)

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 72  GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 105
           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|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 6/54 (11%)

Query: 56  CSSCDKPIVGQVIT------ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           C  C + I G  I        LG  WHP+ F C  C + L    +F +D + YC
Sbjct: 1   CQQCGRQICGGDIAVFASRAGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYC 54

The first LIM domain of Prickle 3/LIM domain only 6 (LM06): 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. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which 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. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. 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|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP)

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 56  CSSCDKPIV-GQVI-TALGKTWHPEHFICTHCNQELGTRNFFE--RDSRPYCEPDY 107
           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|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 33.8 bits (77), Expect = 0.002
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain Kinase 2)

 Score = 33.7 bits (77), Expect = 0.002
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 56  CSSC-DKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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

>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG----TRNFFERDSRPYC 103
           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|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM domains protein (FHL)

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 56  CSSCDKPIVGQ----VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           C++C KPI G      I+   + WH + F C  C+  L  + F  +     C
Sbjct: 1   CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILC 52

The fourth 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 interacts 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 = 56

>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function

 Score = 33.4 bits (77), Expect = 0.003
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 5/58 (8%)

Query: 56  CSSCDKPIVGQVIT----ALGKTWHPEHFICTHCNQELGTR-NFFERDSRPYCEPDYH 108
           C  C   I G+ I+     L   WH E F+CT C          +  D +PYC+  YH
Sbjct: 1   CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHYH 58

The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. 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 = 58

>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM (abLIM) proteins

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90
          C +CDK I G+V+ A GK +HP    C+ C Q  G
Sbjct: 1  CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMFG 35

The fourth 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|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2

 Score = 33.4 bits (76), Expect = 0.003
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 6/54 (11%)

Query: 56  CSSCDKPIVGQVITAL------GKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           C  C   I G  I         G  WHP+ F+C+ CN+ L    +F +D + YC
Sbjct: 1   CEQCGGQINGGDIAVFASRAGHGVCWHPQCFVCSVCNELLVDLIYFYQDGKIYC 54

The first LIM domain of Prickle 2: 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. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which 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. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	130
KOG1701|consensus	468		99.76
KOG2272|consensus	332		99.71
KOG1701|consensus	468		99.68
KOG1044|consensus	670		99.64
KOG2272|consensus	332		99.57
KOG1703|consensus	479		99.55
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.55
KOG4577|consensus	383		99.38
KOG1703|consensus	479		99.2
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.74
KOG4577|consensus	383		98.73
KOG1044|consensus	670		98.5
KOG1700|consensus	200		97.95
KOG1700|consensus	200		97.84
KOG1702|consensus	264		97.67
KOG0490|consensus	235		96.2
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	93.17
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	92.84
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	83.41
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	82.52

>KOG1701|consensus

Probab=99.76  E-value=9.2e-21  Score=139.75  Aligned_cols=115  Identities=26%  Similarity=0.530  Sum_probs=93.2

Q ss_pred             CCCCcccCCCCCCCCCCCchhHHHHHHHHHH------HHhhhcCCCCCCCccccccccccccceeeecCcccccCCcccC
Q psy2501          10 VTDSSSVSYSKPNQPVHQKGKQLDCMLDSLT------AEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICT   83 (130)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~   83 (130)
                      .....+.||++.+|..||.+..+...+..-.      +.+++..+. ....+|..|++.|+++++.++|+.||+.||+|.
T Consensus       286 g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq-~tlekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv  364 (468)
T KOG1701|consen  286 GQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQ-DTLEKCNKCGEPIMDRILRALGKAYHPGCFTCV  364 (468)
T ss_pred             CcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHH-HHHHHHhhhhhHHHHHHHHhcccccCCCceEEE
Confidence            3456788999999999998777776542211      111222332 122589999999999999999999999999999


Q ss_pred             CCCcccCCCCee-ccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          84 HCNQELGTRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        84 ~C~~~l~~~~~~-~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      .|.+.|.+..|. ..++.+||..||.++|+++|+.|++||+++
T Consensus       365 ~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~  407 (468)
T KOG1701|consen  365 VCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPR  407 (468)
T ss_pred             EeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCC
Confidence            999999988887 778999999999999999999999999753

>KOG2272|consensus

Probab=99.71  E-value=1.3e-18  Score=121.15  Aligned_cols=121  Identities=27%  Similarity=0.563  Sum_probs=99.2

Q ss_pred             CCCCcccCCCCCCCCCCCchhHH----HHHHHHHHHHh-hhcCCCCCCCccccccccccccceeeecCcccccCCcccCC
Q psy2501          10 VTDSSSVSYSKPNQPVHQKGKQL----DCMLDSLTAEM-SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTH   84 (130)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~-~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~   84 (130)
                      +.+..++-.+.++|+-+|.+..+    ++..-.+..++ .-..-...+.++|+.|.++|.++.+.++++.||.+.|+|+.
T Consensus       147 iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~  226 (332)
T KOG2272|consen  147 IDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAK  226 (332)
T ss_pred             cccccccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehh
Confidence            45566777789999999955444    44333333332 22222345678999999999999999999999999999999


Q ss_pred             CCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          85 CNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        85 C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      |.+++-+.+.|.+.|..||+.+|.++|+-.|+.|+..|.|.++.||
T Consensus       227 CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al  272 (332)
T KOG2272|consen  227 CEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSAL  272 (332)
T ss_pred             cCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHh
Confidence            9999988899999999999999999999999999999999998875

>KOG1701|consensus

Probab=99.68  E-value=9.7e-19  Score=129.14  Aligned_cols=79  Identities=30%  Similarity=0.800  Sum_probs=72.7

Q ss_pred             CCCcccccccccccc--ceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCcee
Q psy2501          51 TQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIR  128 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~  128 (130)
                      .++..|.+|+|.|.+  ..+++|++.||..||+|..|++.|.+..||..++++||+.||...+ ++|..|+++|+++||+
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            344599999999974  4578999999999999999999999999999999999999998876 8999999999999999


Q ss_pred             eC
Q psy2501         129 NT  130 (130)
Q Consensus       129 ~~  130 (130)
                      ||
T Consensus       351 A~  352 (468)
T KOG1701|consen  351 AL  352 (468)
T ss_pred             hc
Confidence            96

>KOG1044|consensus

Probab=99.64  E-value=4.1e-17  Score=124.33  Aligned_cols=119  Identities=24%  Similarity=0.516  Sum_probs=94.3

Q ss_pred             CCCCcccCCCCCCCCCCCchhHHHH---------------HHHHHHHHhhhcCCCCCCCcccccccccc-ccceeeecCc
Q psy2501          10 VTDSSSVSYSKPNQPVHQKGKQLDC---------------MLDSLTAEMSRQGVTTTQKGCCSSCDKPI-VGQVITALGK   73 (130)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~C~~C~~~i-~~~~~~~~~~   73 (130)
                      +....+.++++++|+.+|.+..+..               +-+.....+...+....+...|++|+..| .++.+.++++
T Consensus        75 ~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~  154 (670)
T KOG1044|consen   75 VEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDK  154 (670)
T ss_pred             ccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeecc
Confidence            4456788999999999995443321               11112222222222334567899999999 5899999999


Q ss_pred             ccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceee
Q psy2501          74 TWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRN  129 (130)
Q Consensus        74 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~  129 (130)
                      .||..||+|..|+..|. ++|+..+|.+||+.+|...|+.+|..|.+.|.|++|.|
T Consensus       155 qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqa  209 (670)
T KOG1044|consen  155 QWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQA  209 (670)
T ss_pred             ceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhc
Confidence            99999999999999996 47999999999999999999999999999999999987

>KOG2272|consensus

Probab=99.57  E-value=5.8e-16  Score=107.97  Aligned_cols=120  Identities=23%  Similarity=0.352  Sum_probs=97.7

Q ss_pred             CCCCcccCCCCCCCCCCCchhHHHHHHHHHHHHh------hhc-----CCCCCCCccccccccccccceeeecCcccccC
Q psy2501          10 VTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEM------SRQ-----GVTTTQKGCCSSCDKPIVGQVITALGKTWHPE   78 (130)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~-----~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~   78 (130)
                      +..+.+.+++..|||.+|.++.++..+.+.....      .+.     .....+..+|..|+..|.++.+...+..||+.
T Consensus        83 iiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~y  162 (332)
T KOG2272|consen   83 IIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPY  162 (332)
T ss_pred             hhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCcc
Confidence            4457788999999999999998887766544333      111     22345667899999999888899999999999


Q ss_pred             CcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          79 HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        79 Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      .|+|..|++.|.. .-....+.+||..|+.+.--|+|++|.+||++++|.||
T Consensus       163 HFkCt~C~keL~s-daRevk~eLyClrChD~mgipiCgaC~rpIeervi~am  213 (332)
T KOG2272|consen  163 HFKCTTCGKELTS-DAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAM  213 (332)
T ss_pred             ceecccccccccc-hhhhhccceeccccccccCCcccccccCchHHHHHHHh
Confidence            9999999999964 33477789999999877666999999999999999875

>KOG1703|consensus

Probab=99.55  E-value=2.5e-16  Score=121.31  Aligned_cols=122  Identities=29%  Similarity=0.657  Sum_probs=98.6

Q ss_pred             CCCC-CcccCCCCCCCCCCCchhHHHHHHHHHHHH------hhhcCCCCCCCccccccccccccceeeecCcccccCCcc
Q psy2501           9 SVTD-SSSVSYSKPNQPVHQKGKQLDCMLDSLTAE------MSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFI   81 (130)
Q Consensus         9 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~   81 (130)
                      +... ..++++++.||+.+|.+......+......      +....+.....+.|.+|+++|.++.|.++++.||++||.
T Consensus       312 ~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~  391 (479)
T KOG1703|consen  312 KIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFV  391 (479)
T ss_pred             CcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhcee
Confidence            4556 888999999999999666655443322221      122223345668999999999999999999999999999


Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccc--cCceeeC
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DVSIRNT  130 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~~~  130 (130)
                      |..|..++....|+..++.+||+.||.+++..+|..|.++|+  +..+.|+
T Consensus       392 C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~  442 (479)
T KOG1703|consen  392 CADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEAD  442 (479)
T ss_pred             eecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhcc
Confidence            999999999999999999999999999999999999999987  7666653

>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=99.55  E-value=5.4e-15  Score=82.89  Aligned_cols=56  Identities=46%  Similarity=1.178  Sum_probs=50.1

Q ss_pred             cccccccccc-ce-eeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501          56 CSSCDKPIVG-QV-ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  111 (130)
Q Consensus        56 C~~C~~~i~~-~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~  111 (130)
                      |..|+++|.+ .. +.+.++.||++||+|..|+.+|.+..++..++++||..||.++|
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            7899999974 33 36999999999999999999998888999999999999998875

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

>KOG4577|consensus

Probab=99.38  E-value=1.5e-14  Score=102.55  Aligned_cols=73  Identities=27%  Similarity=0.773  Sum_probs=66.2

Q ss_pred             CCccccccccccccce-eeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          52 QKGCCSSCDKPIVGQV-ITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        52 ~~~~C~~C~~~i~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      ..++|+.|.+.|.+.+ +.++++.||..|++|+.|..+|.+ ..+.+++.+||+.+|.++|+-+|++|++.|.+.
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPt  105 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPT  105 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChH
Confidence            5578999999998765 579999999999999999999975 578999999999999999999999999999753

>KOG1703|consensus

Probab=99.20  E-value=1.2e-11  Score=95.55  Aligned_cols=121  Identities=26%  Similarity=0.437  Sum_probs=91.4

Q ss_pred             CCCCcccCCCCCCCCCCCchhHHHHHHHHHHHH--hh-----hcCCCCCCCcccccccccccc-ceeeecCcccccCCcc
Q psy2501          10 VTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAE--MS-----RQGVTTTQKGCCSSCDKPIVG-QVITALGKTWHPEHFI   81 (130)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~-----~~~~~~~~~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~   81 (130)
                      .....+.+....|++..+...+.-.+.......  +.     ...+.....+.|..|...|.+ +.+.++++.||+.+|.
T Consensus       253 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~  332 (479)
T KOG1703|consen  253 ECQPLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGKEWHPEHFS  332 (479)
T ss_pred             ccCcceecccccccccccccccccchhhcccccccccccccccccccccccccccccccCcccceeEeecccccccccee
Confidence            333555666777777776444222222111111  11     111222344899999999998 8899999999999999


Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      |..|...+..+.+...+|.+||..||...+.+.|.+|+++|++++|.|+
T Consensus       333 c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~  381 (479)
T KOG1703|consen  333 CEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCAL  381 (479)
T ss_pred             eccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhc
Confidence            9999999988888899999999999999999999999999999999875

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

Probab=98.74  E-value=7.6e-09  Score=52.80  Aligned_cols=36  Identities=56%  Similarity=1.238  Sum_probs=32.1

Q ss_pred             ccccccccccc--ceeeecCcccccCCcccCCCCcccC
Q psy2501          55 CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELG   90 (130)
Q Consensus        55 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~   90 (130)
                      +|..|++.|.+  ..+.+.++.||+.||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            48899999975  6678999999999999999999885

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=98.73  E-value=8.8e-10  Score=78.63  Aligned_cols=100  Identities=21%  Similarity=0.360  Sum_probs=72.2

Q ss_pred             cCCCCCCCCCCCchhHHHHHHHHHHHHh-----hhcCCCCCCCccccccccccc-ccee-eecCcccccCCcccCCCCcc
Q psy2501          16 VSYSKPNQPVHQKGKQLDCMLDSLTAEM-----SRQGVTTTQKGCCSSCDKPIV-GQVI-TALGKTWHPEHFICTHCNQE   88 (130)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~C~~C~~~i~-~~~~-~~~~~~~H~~Cf~C~~C~~~   88 (130)
                      ..+++.||..|..++.+...+..--...     ++...-..++.+|..|...|. .+++ .+.+..||..||.|..|++.
T Consensus        50 Kvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~  129 (383)
T KOG4577|consen   50 KVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQ  129 (383)
T ss_pred             HHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcc
Confidence            4567899999997777765554433222     222222346679999999995 5554 47889999999999999999


Q ss_pred             cC-CCCee-ccCCcccCHHhhhhhcCCCC
Q psy2501          89 LG-TRNFF-ERDSRPYCEPDYHNLFSPRC  115 (130)
Q Consensus        89 l~-~~~~~-~~~~~~~C~~~~~~~~~~~C  115 (130)
                      |. +.+|| ..++++.|+.+|..--..-|
T Consensus       130 L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~  158 (383)
T KOG4577|consen  130 LATGDEFYLMEDARLVCKDDYETAKQKHC  158 (383)
T ss_pred             cccCCeeEEeccceeehhhhHHHHHhccc
Confidence            96 44777 67889999999985443434

>KOG1044|consensus

Probab=98.50  E-value=1.1e-08  Score=78.95  Aligned_cols=96  Identities=20%  Similarity=0.303  Sum_probs=77.6

Q ss_pred             CCcccCCCCCCCCCCCchhHHHHHHHHHHHH-----hhhcCCCCCCCccccccccccccceeeecCcccccCCcccCCCC
Q psy2501          12 DSSSVSYSKPNQPVHQKGKQLDCMLDSLTAE-----MSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCN   86 (130)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~   86 (130)
                      .++..++.+.||-.||.+..+...+......     .+...+...++.+|..|.+-|.+.++.+.++.||+.|-+|+.|+
T Consensus       146 gq~llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~kh~HPtCARCsRCg  225 (670)
T KOG1044|consen  146 GQALLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGDKHFHPTCARCSRCG  225 (670)
T ss_pred             cceeeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccCcccCcchhhhhhhc
Confidence            3677899999999999888777666543322     24555666778899999999999999999999999999999999


Q ss_pred             cccCCC-CeeccCCcccCHHhh
Q psy2501          87 QELGTR-NFFERDSRPYCEPDY  107 (130)
Q Consensus        87 ~~l~~~-~~~~~~~~~~C~~~~  107 (130)
                      ..++++ +.|..+..++-..|-
T Consensus       226 qmF~eGEEMYlQGs~iWHP~C~  247 (670)
T KOG1044|consen  226 QMFGEGEEMYLQGSEIWHPDCK  247 (670)
T ss_pred             cccccchheeeccccccCCccc
Confidence            999866 567777777776664

>KOG1700|consensus

Probab=97.95  E-value=2.4e-06  Score=59.21  Aligned_cols=61  Identities=26%  Similarity=0.614  Sum_probs=52.6

Q ss_pred             Cccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCC
Q psy2501          53 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP  113 (130)
Q Consensus        53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~  113 (130)
                      ...|..|++.++ .+.+...+..||..||+|..|...|....+...++.+||+.+|...+++
T Consensus         7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~   68 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGP   68 (200)
T ss_pred             cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCc
Confidence            358999999996 5556688999999999999999999888888999999999977777765

>KOG1700|consensus

Probab=97.84  E-value=3.8e-06  Score=58.24  Aligned_cols=59  Identities=31%  Similarity=0.712  Sum_probs=51.2

Q ss_pred             Cccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501          53 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  111 (130)
Q Consensus        53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~  111 (130)
                      ...|..|.+.++ .+.+...+..||..||+|+.|+..|+.+.+....+.+||+.++..++
T Consensus       108 ~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  108 KEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             ccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence            357999999996 46677889999999999999999999989999999999987776654

>KOG1702|consensus

Probab=97.67  E-value=3.6e-06  Score=57.77  Aligned_cols=58  Identities=29%  Similarity=0.707  Sum_probs=50.3

Q ss_pred             ccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501          54 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF  111 (130)
Q Consensus        54 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~  111 (130)
                      ..|..|++.++ .+.+..+++.||..||+|..|+.+|.-..+-..+.++||..+|.+..
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            45778999886 46688999999999999999999998777878999999999997654

>KOG0490|consensus

Probab=96.20  E-value=0.0013  Score=46.10  Aligned_cols=63  Identities=33%  Similarity=0.829  Sum_probs=50.3

Q ss_pred             cccccccce-eeecCcccccCCcccCCCCcccC--CCCeeccCCcccCHHhhhh--hcCCCCccCcccc
Q psy2501          59 CDKPIVGQV-ITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHN--LFSPRCSYCNGPI  122 (130)
Q Consensus        59 C~~~i~~~~-~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~--~~~~~C~~C~~~I  122 (130)
                      |+..|.+.+ +...+..||..|..|..|...+.  ...+.. +|..||..+|.+  .+..+|.+|...|
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~   69 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI   69 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence            555665443 45568999999999999999997  444445 999999999998  7778999998876

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

Probab=93.17  E-value=0.089  Score=25.85  Aligned_cols=37  Identities=16%  Similarity=0.471  Sum_probs=25.4

Q ss_pred             ccCCCCcccCCC-CeeccCCcccCHHhhhhhcCCCCccCccccc
Q psy2501          81 ICTHCNQELGTR-NFFERDSRPYCEPDYHNLFSPRCSYCNGPIL  123 (130)
Q Consensus        81 ~C~~C~~~l~~~-~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~  123 (130)
                      +|..|+.++.+. ......++.|...||      +|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf------~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECF------KCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCC------CCcccCCcCc
Confidence            477888888765 444556677776664      6777877764

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.

>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=92.84  E-value=0.075  Score=28.87  Aligned_cols=39  Identities=18%  Similarity=0.514  Sum_probs=30.6

Q ss_pred             cCCCCcccCCCCee-ccCCcccCHHhhhhhcCCCCccCccccccCc
Q psy2501          82 CTHCNQELGTRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILDVS  126 (130)
Q Consensus        82 C~~C~~~l~~~~~~-~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~  126 (130)
                      |..|+.++.+.... ...++.|...||      +|..|+++|.+..
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf------~C~~C~~~l~~~~   40 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECF------KCSKCGKPLNDGD   40 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTS------BETTTTCBTTTSS
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEcccc------ccCCCCCccCCCe
Confidence            67889998766655 578888888885      7999999987653

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 ....

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

Probab=83.41  E-value=1.2  Score=25.22  Aligned_cols=43  Identities=16%  Similarity=0.444  Sum_probs=18.6

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccc
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI  122 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I  122 (130)
                      .+|+.|..-|...-....=+..||..|-...++..|-.|+.|-
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Pa   50 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPA   50 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChH
Confidence            4566666665433223334567788777777777788887764

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

Probab=82.52  E-value=0.95  Score=27.39  Aligned_cols=42  Identities=24%  Similarity=0.543  Sum_probs=28.2

Q ss_pred             cccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccccc
Q psy2501          75 WHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD  124 (130)
Q Consensus        75 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~  124 (130)
                      |-..--.|..|...+..      .|.-||..|..+.  .+|+-|++.|++
T Consensus        40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d   81 (90)
T PF10235_consen   40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD   81 (90)
T ss_pred             ccccCcccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence            43333466667665532      2467899996654  799999999854

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 [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	130
1nyp_A	66	4th Lim Domain Of Pinch Protein Length = 66		1e-10
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		4e-10
2dar_A	90	Solution Structure Of First Lim Domain Of Enigma-Li		7e-09
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		8e-06
1x64_A	89	Solution Structure Of The Lim Domain Of Alpha-Actin		1e-05
2d8z_A	70	Solution Structure Of The Third Lim Domain Of Four		2e-05
2dlo_A	81	Solution Structure Of The Second Lim Domain Of Huma		2e-05
2d8x_A	70	Solution Structure Of The Second Lim Domain Of Part		2e-05
2kbx_B	70	Solution Structure Of Ilk-Pinch Complex Length = 70		3e-05
1g47_A	77	1st Lim Domain Of Pinch Protein Length = 77		4e-05
1v6g_A	81	Solution Structure Of The Lim Domain Of The Human A		5e-05
2cuq_A	80	Solution Structure Of Second Lim Domain From Human		6e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		9e-05
1wyh_A	72	Solution Structure Of The Lim Domain From Human Ske		9e-05
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		1e-04
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		2e-04
1x4k_A	72	Solution Structure Of Lim Domain In Lim-Protein 3 L		2e-04
3f6q_B	72	Crystal Structure Of Integrin-Linked Kinase Ankyrin		3e-04
2cur_A	69	Solution Structure Of Skeletal Muscle Lim-Protein 1		4e-04
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		4e-04
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		5e-04
1x63_A	82	Solution Structure Of The Second Lim Domain Of Skel		5e-04
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		6e-04
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		6e-04
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		7e-04

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 33/57 (57%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           C +C +PI G+V+ A+GK WH EHF+C  C +       +ER    YCE  Y+ LF 
Sbjct: 8   CGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 64

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 109
           C  C++P++   ++A+   WHPE F+C  C     T +FFE D RP+CE  YH+
Sbjct: 18  CGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHH 71

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 30/57 (52%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           C+ C++ I G  + ALGK+WHPE F C HC   +    F E     YCE  Y   F+
Sbjct: 28  CAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFA 84

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
           C+ C + I  GQ + AL K WH   F C  C+  L T  +  +D  PYCE DYH  F
Sbjct: 18  CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVIL-TGEYISKDGVPYCESDYHAQF 73

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 25/49 (51%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
           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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           C  C KPI    +T   + WH E F+CT C ++L  + F  RD   YC   + +L++
Sbjct: 8   CVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYA 64

>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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 48  VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPD 106
           V T +K  C++C +PI+ +++ A+GK +HP  F C  C++ L    F  +  S+ +C  D
Sbjct: 12  VATLEK--CATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69
Query: 107 YHNLFS 112
           +H  F+
Sbjct: 70  FHRKFA 75

>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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 105
           C  C + I+G+VI A+  +WHPE F C  C + L    F +   R  C P
Sbjct: 8   CHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRP 57

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 36  LDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF 95
           L S T E  + G    +K             ++ + G+ +H + F+C  C Q+     F+
Sbjct: 5   LASATCERCKGGFAPAEK-------------IVNSNGELYHEQCFVCAQCFQQFPEGLFY 51
Query: 96  ERDSRPYCEPDYHNLFSP 113
           E + R YCE D+  LF+P
Sbjct: 52  EFEGRKYCEHDFQMLFAP 69

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 36  LDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF 95
           L S T E  + G    +K             ++ + G+ +H + F+C  C Q+     F+
Sbjct: 9   LASATCERCKGGFAPAEK-------------IVNSNGELYHEQCFVCAQCFQQFPEGLFY 55
Query: 96  ERDSRPYCEPDYHNLFSP 113
           E + R YCE D+  LF+P
Sbjct: 56  EFEGRKYCEHDFQMLFAP 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 = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 17/30 (56%), Positives = 24/30 (80%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHC 85
          C SCD+ I G+V++ALGKT+HP+ F+C  C
Sbjct: 18 CFSCDQFIEGEVVSALGKTYHPDCFVCAVC 47

>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 = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNLFSP 113
           C  CDK +   + +T+LGK WH     C  C + L +    E + +PYC  P Y  +F P
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62
Query: 114 R 114
           +
Sbjct: 63  K 63

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 24/41 (58%)
Query: 72  GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           G+TWH   F+C+ C Q LG+R+F       YC P Y N F+
Sbjct: 26  GQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA 66

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C+ CD+ I+ + ++ AL + WH +   C+ C+  L  R F  R    YC+ D+   F  +
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTK 121
Query: 115 CSYCNGPI 122
           C+ C   I
Sbjct: 122 CAACQLGI 129

>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 = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C+ CD+ I+ + ++ AL + WH +   C+ C+  L  R F  R    YC+ D+   F  +
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTK 67
Query: 115 CSYCNGPI 122
           C+ C   I
Sbjct: 68  CAACQLGI 75

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           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 = 3e-04,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 66  QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           +++ + 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 = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           C  C+K I    IT   + WH + F+C  C+++L  + F   + + YC   Y N  S
Sbjct: 8   CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C  C + +   + +   GK+WH   F C  C + L +    ++D   YC+  Y   F P+
Sbjct: 11  CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 70

>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 = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C+ C++ I+ + ++  L + WH     C  C  +L  R F  R    YC+ D+   F  +
Sbjct: 9   CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCF-SRAGSVYCKEDFFKRFGTK 67
Query: 115 CSYCNGPI 122
           C+ C   I
Sbjct: 68  CTACQQGI 75

>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal Muscle Lim Protein 1 Length = 82

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           C  C K IV   Q +   G  WH + F C++C Q +GT +FF +    YC   +   F+
Sbjct: 18  CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA 76

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C  C + +   + +   GK+WH   F C  C + L +    ++D   YC+  Y   F P+
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 56  CSSC-DKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           CS+C D     + +   GK WH   F C  C + L +    E++   YC+  Y   F P+
Sbjct: 39  CSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNLF 111
           C  CDK +   + +++LGK WH     C  C++ L      E D +P+C +P Y  LF
Sbjct: 12  CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	130
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	8e-30
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-04
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	1e-28
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	5e-28
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	1e-27
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-27
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	3e-27
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-06
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	4e-27
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-15
2cuq_A	80	Four and A half LIM domains 3; structural genomics	5e-27
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-06
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-26
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	1e-26
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	3e-26
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	4e-26
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	1e-25
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-25
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	8e-25
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	4e-04
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	4e-24
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-07
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	6e-24
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-23
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	3e-23
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	9e-23
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	5e-13
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	7e-06
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-22
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	8e-19
2cor_A	79	Pinch protein; LIM domain, particularly interestin	2e-22
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-21
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	5e-16
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-21
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	5e-21
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	3e-20
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	5e-20
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-19
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	8e-04
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	9e-20
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-19
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	7e-05
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-19
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-04
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-19
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-19
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	5e-18
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	4e-17
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	6e-06
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	6e-17
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	7e-17
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	1e-16
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-16
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	4e-16
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	6e-16
2co8_A	82	NEDD9 interacting protein with calponin homology a	1e-10
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	3e-09
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	4e-06

>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 =  102 bits (255), Expect = 8e-30
 Identities = 24/66 (36%), Positives = 32/66 (48%)

Query: 51  TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 110
            +   C+ C++ I G  + ALGK+WHPE F C HC   +    F E     YCE  Y   
Sbjct: 23  KRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKF 82

Query: 111 FSPRCS 116
           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 = 37.0 bits (86), Expect = 2e-04
 Identities = 6/39 (15%), Positives = 15/39 (38%), Gaps = 1/39 (2%)

Query: 91  TRNFFERDSRPYCEPDYHN-LFSPRCSYCNGPILDVSIR 128
           + +  ++D+             +P C++CN  I    + 
Sbjct: 3   SGSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLV 41

>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 = 99.0 bits (247), Expect = 1e-28
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 40  TAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERD 98
           ++  S +G        C++C +PI+ +++ A+GK +HP  F C  C++ L    F  +  
Sbjct: 2   SSGSSGEGCYVATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDAT 61

Query: 99  SRPYCEPDYHNLFSPRCS 116
           S+ +C  D+H  F+   S
Sbjct: 62  SQIHCIEDFHRKFASGPS 79

>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 = 97.0 bits (242), Expect = 5e-28
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 115
           C  C KPI    +T   + WH E F+CT C ++L  + F  RD   YC   + +L++   
Sbjct: 8   CVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGP 67

Query: 116 S 116
           S
Sbjct: 68  S 68

>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 = 95.8 bits (239), Expect = 1e-27
 Identities = 24/59 (40%), Positives = 33/59 (55%)

Query: 55  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113
            C +C +PI G+V+ A+GK WH EHF+C  C +       +ER    YCE  Y+ LF  
Sbjct: 7   ICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD 65

>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 = 95.5 bits (238), Expect = 2e-27
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 43  MSRQGVTTTQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSR 100
           +S           C  C        +++ + G+ +H + F+C  C Q+     F+E + R
Sbjct: 1   ISEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGR 60

Query: 101 PYCEPDYHNLFSP 113
            YCE D+  LF+P
Sbjct: 61  KYCEHDFQMLFAP 73

>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 = 95.5 bits (238), Expect = 3e-27
 Identities = 23/62 (37%), Positives = 34/62 (54%)

Query: 55  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
            C  C++P++   ++A+   WHPE F+C  C     T +FFE D RP+CE  YH+     
Sbjct: 17  KCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSG 76

Query: 115 CS 116
            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 = 41.6 bits (98), Expect = 2e-06
 Identities = 10/29 (34%), Positives = 16/29 (55%)

Query: 99  SRPYCEPDYHNLFSPRCSYCNGPILDVSI 127
           S      D+  +FSP+C  CN P+L+  +
Sbjct: 2   SSGSSGKDFLAMFSPKCGGCNRPVLENYL 30

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

 Score = 96.3 bits (240), Expect = 4e-27
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 51  TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 109
           ++K  C+ CD+ I   +   A  + WH +HF C  C+  L    +   + +P C+P Y  
Sbjct: 1   SEKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 60

Query: 110 LFSPRCSYCNGPI 122
             +  C  C+  I
Sbjct: 61  NHAVVCQGCHNAI 73

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

 Score = 66.3 bits (162), Expect = 2e-15
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 56  CSSCDKPIVG--QVITALGKTWHP--EHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
           C  C   I    Q +T    +WH   E F+C+ C++ L  + F   +   +C  +     
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

Query: 112 S 112
           S
Sbjct: 126 S 126

>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 = 94.7 bits (236), Expect = 5e-27
 Identities = 20/61 (32%), Positives = 28/61 (45%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 115
           C+ C K +    +T   + WH E  +CT C   L  + F  RD  PYC   +  LF+   
Sbjct: 18  CARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGP 77

Query: 116 S 116
           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 = 42.3 bits (100), Expect = 1e-06
 Identities = 9/30 (30%), Positives = 14/30 (46%)

Query: 99  SRPYCEPDYHNLFSPRCSYCNGPILDVSIR 128
           S     P Y N F+PRC+ C+  +    + 
Sbjct: 2   SSGSSGPCYENKFAPRCARCSKTLTQGGVT 31

>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 = 94.1 bits (234), Expect = 1e-26
 Identities = 22/62 (35%), Positives = 27/62 (43%)

Query: 55  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
            C  C   IVG V+ A  K  HPE F+C  CN  L  + +F  +   YCE       S  
Sbjct: 27  LCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGP 86

Query: 115 CS 116
            S
Sbjct: 87  SS 88

>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 = 93.2 bits (232), Expect = 1e-26
 Identities = 19/61 (31%), Positives = 29/61 (47%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 115
           C  C+K I    IT   + WH + F+C  C+++L  + F   + + YC   Y N  S   
Sbjct: 8   CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPS 67

Query: 116 S 116
           S
Sbjct: 68  S 68

>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 = 92.5 bits (230), Expect = 3e-26
 Identities = 18/61 (29%), Positives = 25/61 (40%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 115
           C  C   IVG  +    +  HPE ++CT C   L  +  F  + + YCE       S   
Sbjct: 18  CDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS 77

Query: 116 S 116
           S
Sbjct: 78  S 78

>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 = 92.4 bits (230), Expect = 4e-26
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 55  CCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
            CS+C + ++   + +   G+TWH   F+C+ C Q LG+R+F       YC P Y N F+
Sbjct: 7   GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA 66

Query: 113 PRCS 116
              S
Sbjct: 67  SGPS 70

>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 = 91.0 bits (226), Expect = 1e-25
 Identities = 20/67 (29%), Positives = 32/67 (47%)

Query: 50  TTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 109
           ++    C  C + I+G+VI A+  +WHPE F C  C + L    F +   R  C P ++ 
Sbjct: 2   SSGSSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNR 61

Query: 110 LFSPRCS 116
             +   S
Sbjct: 62  EKASGPS 68

>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 = 89.8 bits (223), Expect = 3e-25
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 55  CCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
            C  C K I+   + +   G +WH   FIC  C Q +GT++F  +D++ +C P Y    +
Sbjct: 7   GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA 66

Query: 113 PRCS 116
              S
Sbjct: 67  SGPS 70

>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 = 89.3 bits (222), Expect = 8e-25
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113
           C  C K IV   Q +   G  WH + F C++C Q +GT +FF +    YC   +   F+ 
Sbjct: 18  CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAS 77

Query: 114 RCS 116
             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 = 35.8 bits (83), Expect = 4e-04
 Identities = 6/25 (24%), Positives = 8/25 (32%)

Query: 99  SRPYCEPDYHNLFSPRCSYCNGPIL 123
           S            SP+C  C   I+
Sbjct: 2   SSGSSGKCTTREDSPKCKGCFKAIV 26

>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 = 88.2 bits (219), Expect = 4e-24
 Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 56  CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113
           C  C KPI    + +    + WH   F C  C   L    F  +D++  C        SP
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSP 67

Query: 114 RCSYCNGPIL 123
           +C  C   I+
Sbjct: 68  KCKGCFKAIV 77

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

 Score = 45.9 bits (109), Expect = 1e-07
 Identities = 10/33 (30%), Positives = 12/33 (36%), Gaps = 2/33 (6%)

Query: 55  CCSSCDKPIVG--QVITALGKTWHPEHFICTHC 85
            C  C K IV   Q +   G  WH + F     
Sbjct: 68  KCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 = 86.7 bits (215), Expect = 6e-24
 Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 53  KGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 110
              C  C        +++ + G+ +H + F+C  C Q+     F+E + R YCE D+  L
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 111 FS 112
           F+
Sbjct: 71  FA 72

>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 = 85.6 bits (212), Expect = 1e-23
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 50  TTQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           ++    C  C + +VG    + AL + +H   F+C+ C  +L  ++F+  + R YCE  Y
Sbjct: 2   SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61

Query: 108 HNLFSPRCSYC 118
                      
Sbjct: 62  VATLE-SGPSS 71

>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 = 85.2 bits (211), Expect = 3e-23
 Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 43  MSRQGVTTTQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRP 101
            S + +       C+ C + I  GQ + AL K WH   F C  C+  L    +  +D  P
Sbjct: 5   SSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGE-YISKDGVP 63

Query: 102 YCEPDYHNLFSPRCS 116
           YCE DYH  F    S
Sbjct: 64  YCESDYHAQFGSGPS 78

>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 = 86.9 bits (215), Expect = 9e-23
 Identities = 26/121 (21%), Positives = 46/121 (38%), Gaps = 13/121 (10%)

Query: 3   PQQLEHSVTDSSSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKP 62
             + E  +T   +  +   N    + G                    T +   C+ CD+ 
Sbjct: 21  GDEDERLITRLENTQFDAANGIDDEGGSG-----------GHMGSGGTPEIPMCAGCDQH 69

Query: 63  IVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGP 121
           I+ + ++ AL + WH +   C+ C+  L  R  F R    YC+ D+   F  +C+ C   
Sbjct: 70  ILDRFILKALDRHWHSKCLKCSDCHVPLAER-CFSRGESVYCKDDFFKRFGTKCAACQLG 128

Query: 122 I 122
           I
Sbjct: 129 I 129

>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 = 5e-13
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQEL--GTRNFFERDSRPYCEPDYH 108
           C++C   I     V  A    +H   F C  C ++L  G   +   DSR  C+ DY 
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE 178

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

 Score = 42.2 bits (99), Expect = 7e-06
 Identities = 7/48 (14%), Positives = 10/48 (20%)

Query: 77  PEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 124
                     Q        +                P C+ C+  ILD
Sbjct: 25  ERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILD 72

>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 = 86.0 bits (213), Expect = 2e-22
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 49  TTTQKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
           +T +   C+ CD+ I+ + ++ AL + WH +   C+ C+  L  R  F R    YC+ D+
Sbjct: 2   STPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER-CFSRGESVYCKDDF 60

Query: 108 HNLFSPRCSYCNGPI 122
              F  +C+ C   I
Sbjct: 61  FKRFGTKCAACQLGI 75

>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 = 76.4 bits (188), Expect = 8e-19
 Identities = 18/77 (23%), Positives = 26/77 (33%), Gaps = 4/77 (5%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQEL--GTRNFFERDSRPYCEPDYHNLF 111
           C++C   I     V  A    +H   F C  C ++L  G   +   DSR  C+ DY    
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

Query: 112 SPRCSYCNGPILDVSIR 128
                   G      + 
Sbjct: 128 QGGSGGSGGSGGGTPMV 144

>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 = 2e-22
 Identities = 19/73 (26%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 44  SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC 103
           S +      K  C  C   I  Q +      +HP+HF C +C +EL   +  E     YC
Sbjct: 6   SGEKARGLGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTA-DARELKGELYC 64

Query: 104 EPDYHNLFSPRCS 116
            P +  +     S
Sbjct: 65  LPCHDKMGVSGPS 77

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

 Score = 82.5 bits (204), Expect = 1e-21
 Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLFS 112
           C  C + I  +  + A+ + WH +   C  C   LG      + +  R  C  DY  LF 
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64

Query: 113 PR--CSYCNGPI 122
               C+ C+  I
Sbjct: 65  QDGLCASCDKRI 76

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

 Score = 68.2 bits (167), Expect = 5e-16
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 52  QKGCCSSCDKPIVGQ--VITALGKTWHPEHFICTHCNQELGTRN-FFERDSRPYCEPDYH 108
           Q G C+SCDK I      +    K +H E F C  C +     + +   +S   CE D +
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIY 124

Query: 109 NL 110
             
Sbjct: 125 EW 126

>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 = 79.5 bits (196), Expect = 4e-21
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 56  CSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
           C+ C  PI G    + I+   + WH + F C  C+  L  R F        C     ++ 
Sbjct: 8   CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDIS 67

Query: 112 SPRC 115
            P  
Sbjct: 68  GPSS 71

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

 Score = 79.8 bits (197), Expect = 5e-21
 Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C +C + +   + +   G+++H   F+C  C + L +      D+  YC+  Y   + P+
Sbjct: 10  CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPK 69

Query: 115 CSYC 118
               
Sbjct: 70  GYGY 73

>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 = 77.8 bits (192), Expect = 3e-20
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNLFSP 113
           C  CDK +   + +T+LGK WH     C  C + L +    E + +PYC  P Y  +F P
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62

Query: 114 RCSYCNGPI 122
           +     G  
Sbjct: 63  KGFGRGGAE 71

>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 = 80.1 bits (197), Expect = 5e-20
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C  C + +   + +   GK+WH   F C  C + L +    ++D   YC+  Y   F P+
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

Query: 115 CSYCN 119
                
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 = 77.8 bits (191), Expect = 4e-19
 Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 1/68 (1%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C  C K +   + +   G ++H   F+C  C + L +          YC+  Y   + P+
Sbjct: 10  CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK 69

Query: 115 CSYCNGPI 122
                   
Sbjct: 70  GKGKGMGA 77

>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 = 36.5 bits (84), Expect = 8e-04
 Identities = 8/71 (11%), Positives = 11/71 (15%), Gaps = 1/71 (1%)

Query: 55  CCSSCDKPIVGQVITALG-KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113
            C SC     G      G                +          +            S 
Sbjct: 57  YCKSCYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSD 116

Query: 114 RCSYCNGPILD 124
            C  C   +  
Sbjct: 117 GCPRCGQAVYA 127

>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 = 76.3 bits (188), Expect = 9e-20
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSP 113
           C  CDK +   + +++LGK WH     C  C++ L      E D +P+C  P Y  LF  
Sbjct: 12  CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGS 71

Query: 114 RCS 116
             S
Sbjct: 72  GPS 74

>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 = 76.4 bits (188), Expect = 1e-19
 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 55  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL--GTRNFFERDSRPYCEPDYHNLFS 112
            C  C   + G  + A    +HPE F C  C   +  G      + +  YC   ++ + S
Sbjct: 17  FCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS 76

Query: 113 PRCS 116
              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 = 37.8 bits (88), Expect = 7e-05
 Identities = 6/30 (20%), Positives = 9/30 (30%)

Query: 99  SRPYCEPDYHNLFSPRCSYCNGPILDVSIR 128
           S      DY   F   C  C+  +    + 
Sbjct: 2   SSGSSGKDYWGKFGEFCHGCSLLMTGPFMV 31

>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 = 1e-19
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 55  CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
            C+ C + I    + +    + +H   F C  C + L    F  +DS   C   Y + FS
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 113 PRCS 116
              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 = 37.5 bits (87), Expect = 1e-04
 Identities = 8/24 (33%), Positives = 10/24 (41%)

Query: 99  SRPYCEPDYHNLFSPRCSYCNGPI 122
           S     P Y N F+  C+ C   I
Sbjct: 2   SSGSSGPCYDNTFANTCAECQQLI 25

>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 = 75.7 bits (186), Expect = 2e-19
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 56  CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
           C  C K +   + + A  + +H   F C++CN +L    +     R YC+P ++ LF  +
Sbjct: 18  CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77

Query: 115 CSYCNG 120
            +Y  G
Sbjct: 78  GNYDEG 83

>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 = 75.0 bits (184), Expect = 8e-19
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 3/70 (4%)

Query: 56  CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLFS 112
           C+ C   I    ++ A+   WH     C+ C  +LG      + +     C  DY  LF 
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67

Query: 113 PRCSYCNGPI 122
              +  +G  
Sbjct: 68  NSGAGGSGGH 77

>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 = 71.8 bits (176), Expect = 5e-18
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 55  CCSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNL 110
            C +C KPI G    + I      WH E F C  C+  L  + F  ++   +C+     +
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 111 FSPRCSYCNG 120
            +      +G
Sbjct: 67  DTDISGPSSG 76

>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 = 69.4 bits (170), Expect = 4e-17
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 5/61 (8%)

Query: 55  CCSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 109
            C+ C  PI G      V+   G++WH   F C  C+  L  + F     + YC      
Sbjct: 17  KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 110 L 110
           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 = 40.5 bits (95), Expect = 6e-06
 Identities = 7/25 (28%), Positives = 10/25 (40%)

Query: 99  SRPYCEPDYHNLFSPRCSYCNGPIL 123
           S       Y N  + +C+ C  PI 
Sbjct: 2   SSGSSGDCYKNFVAKKCAGCKNPIT 26

>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 = 72.0 bits (176), Expect = 6e-17
 Identities = 18/73 (24%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 53  KGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGT-RNFFERDSRPYCEPDYHN 109
            G CS+C + I     V+ A G  +H + F C+ C   L     F   +   +CE D   
Sbjct: 69  SGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPT 128

Query: 110 LFSPRCSYCNGPI 122
                     G  
Sbjct: 129 ALINGHLNSGGSG 141

>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 = 72.0 bits (176), Expect = 7e-17
 Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 56  CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLF- 111
           C+ C   I  + ++ A+   WH     C+ C  +LG      + +     C  DY  LF 
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67

Query: 112 -SPRCSYCNGPI 122
            S  CS C   I
Sbjct: 68  NSGACSACGQSI 79

>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 = 68.3 bits (167), Expect = 1e-16
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 55  CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF-ERDSRPYCEPDYH 108
            C SCD+ I G+V++ALGKT+HP+ F+C  C       +          C+    
Sbjct: 17  RCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSL 71

>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 = 68.9 bits (168), Expect = 2e-16
 Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 3/69 (4%)

Query: 56  CSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDYHNLFS 112
           C  C + I     + A+ + WH +   C  C   LG      + +  R  C  DY  L  
Sbjct: 6   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG 65

Query: 113 PRCSYCNGP 121
                 +G 
Sbjct: 66  SGGHMGSGG 74

>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 = 68.2 bits (166), Expect = 4e-16
 Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 3/73 (4%)

Query: 42  EMSRQGVTTTQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNF--FERD 98
                G        C+ C   I    ++ A+   WH     C+ C  +LG      + + 
Sbjct: 50  SGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKS 109

Query: 99  SRPYCEPDYHNLF 111
               C  DY  LF
Sbjct: 110 GMILCRNDYIRLF 122

>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 = 53.0 bits (127), Expect = 1e-10
 Identities = 17/82 (20%), Positives = 24/82 (29%), Gaps = 5/82 (6%)

Query: 38  SLTAEMSRQGVTTTQKGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQEL--GTRNF 94
           S  +    Q         C+ C + + V + +   G  +H   F C  C   L  G    
Sbjct: 2   SSGSSGQHQEAGAGDL--CALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQ 59

Query: 95  FERDSRPYCEPDYHNLFSPRCS 116
              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 = 3e-09
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 56  CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT-RNFFERDSRPYC 103
           C SC+K I G+V+ A  K +HP   +C  C Q        + + S  + 
Sbjct: 8   CDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56

>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 = 4e-06
 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 56  CSSCDKPIV--GQVITALGKTWHPEH--FICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
           C  C   I    Q +T    +WH     F+C+ C++ L  + F   +   +C  +     
Sbjct: 5   CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 64

Query: 112 S 112
           S
Sbjct: 65  S 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	130
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.85
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.83
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.82
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.8
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.78
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.77
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.77
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.77
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.76
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.76
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.76
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.75
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.75
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.75
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.75
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.74
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.74
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.74
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.73
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.73
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.73
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.73
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.73
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.72
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.72
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.72
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.72
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.71
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.71
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.71
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.7
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.7
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.69
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.67
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.66
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.65
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.63
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.62
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.62
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.61
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.59
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.58
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.58
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.56
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.54
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.5
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.41
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.41
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.97
2cuq_A	80	Four and A half LIM domains 3; structural genomics	98.37
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	98.36
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	98.36
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	98.33
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	98.31
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	98.31
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	98.18
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.15
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	98.11
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	97.26
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	94.85
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	94.82
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	94.55
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	94.45
2cor_A	79	Pinch protein; LIM domain, particularly interestin	93.16
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	92.87
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	92.56
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	91.78
2co8_A	82	NEDD9 interacting protein with calponin homology a	91.07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	90.28
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	90.16
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	90.03
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	89.71
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	89.54
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	89.5
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	89.44
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	89.28
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	89.16
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	89.13
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	88.94
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	88.87
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	87.98
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	87.55
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	80.04

>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=99.85  E-value=1.6e-21  Score=120.37  Aligned_cols=80  Identities=25%  Similarity=0.571  Sum_probs=73.5

Q ss_pred             CCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccc--cCc
Q psy2501          51 TQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DVS  126 (130)
Q Consensus        51 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~--~~~  126 (130)
                      .+.++|..|+++|.  ++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|..|+++|+  +.+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~   82 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQN   82 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSSCE
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCCeE
Confidence            45679999999996  67899999999999999999999998888999999999999999999999999999998  568


Q ss_pred             eeeC
Q psy2501         127 IRNT  130 (130)
Q Consensus       127 ~~~~  130 (130)
                      |+|+
T Consensus        83 ~~a~   86 (101)
T 2cup_A           83 VEYK   86 (101)
T ss_dssp             EESS
T ss_pred             EEeC
Confidence            8874

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

Probab=99.83  E-value=5.5e-21  Score=122.32  Aligned_cols=79  Identities=25%  Similarity=0.583  Sum_probs=72.6

Q ss_pred             CCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccc--cCcee
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DVSIR  128 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~  128 (130)
                      ..++|..|+++|. ++++.++++.||++||+|..|+.+|.+..|+..+|++||+.||.++|+++|.+|+++|.  +.+|+
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~   81 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVT   81 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSCEEE
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCceEEE
Confidence            3578999999997 67889999999999999999999999888999999999999999999999999999999  56787


Q ss_pred             eC
Q psy2501         129 NT  130 (130)
Q Consensus       129 ~~  130 (130)
                      |+
T Consensus        82 a~   83 (126)
T 2xqn_T           82 YN   83 (126)
T ss_dssp             ET
T ss_pred             CC
Confidence            74

>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=99.82  E-value=4.5e-21  Score=122.25  Aligned_cols=79  Identities=19%  Similarity=0.411  Sum_probs=70.9

Q ss_pred             CCCccccccccccccc-eeeecCcccccCCcccCCCCcccC--CCCeeccCCcccCHHhhhhhcCC--CCccCccccccC
Q psy2501          51 TQKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLFSP--RCSYCNGPILDV  125 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~~~~~--~C~~C~~~I~~~  125 (130)
                      ...++|..|+++|.+. ++.++++.||++||+|..|+.+|.  +..|+.+++++||+.||.++|++  +|++|+++|++.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~   82 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGG   82 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCE
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCch
Confidence            3457899999999865 589999999999999999999997  35789999999999999999999  999999999987


Q ss_pred             ceee
Q psy2501         126 SIRN  129 (130)
Q Consensus       126 ~~~~  129 (130)
                      .|+|
T Consensus        83 ~~~~   86 (122)
T 1m3v_A           83 DVMV   86 (122)
T ss_dssp             ESSS
T ss_pred             heEE
Confidence            6655

>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=99.80  E-value=8.1e-20  Score=107.24  Aligned_cols=71  Identities=31%  Similarity=0.729  Sum_probs=65.8

Q ss_pred             ccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCH-HhhhhhcCCCCccCcccccc
Q psy2501          54 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSPRCSYCNGPILD  124 (130)
Q Consensus        54 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~-~~~~~~~~~~C~~C~~~I~~  124 (130)
                      ++|..|+++|. ++.+.++++.||++||+|..|+.+|.+..|+..++++||+ .||.++|+++|.+|++.+..
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~~~~~   73 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAESH   73 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSSSC
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCceee
Confidence            47999999997 8889999999999999999999999988899999999999 69999999999999987653

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

Probab=99.78  E-value=2.6e-19  Score=115.14  Aligned_cols=77  Identities=27%  Similarity=0.678  Sum_probs=69.5

Q ss_pred             ccccccccccccc-eeeecCcccccCCcccCCCCcccC--CCCeeccCCcccCHHhhhhhcCC--CCccCcccccc--Cc
Q psy2501          54 GCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLFSP--RCSYCNGPILD--VS  126 (130)
Q Consensus        54 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~~~~~--~C~~C~~~I~~--~~  126 (130)
                      ++|..|+++|.+. .+.++++.||++||+|..|+.+|.  +..|+..+|++||+.||.++|++  +|..|+++|.+  .+
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~~   82 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMT   82 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTSEE
T ss_pred             ccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCcccee
Confidence            5799999999876 588999999999999999999996  35789999999999999999999  99999999986  46


Q ss_pred             eeeC
Q psy2501         127 IRNT  130 (130)
Q Consensus       127 ~~~~  130 (130)
                      |+|+
T Consensus        83 ~~a~   86 (131)
T 2xjy_A           83 MRVK   86 (131)
T ss_dssp             EEET
T ss_pred             EeeC
Confidence            7764

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

Probab=99.77  E-value=5.7e-19  Score=101.97  Aligned_cols=67  Identities=31%  Similarity=0.674  Sum_probs=62.3

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      .+.++|..|+++|.++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            3 SGSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CCCCBCSSSCCBCCSSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCCCCcccCCeeccceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            4567899999999988899999999999999999999998888999999999999999999999974

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

Probab=99.77  E-value=6.5e-19  Score=106.54  Aligned_cols=67  Identities=36%  Similarity=0.809  Sum_probs=62.9

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ...++|..|+++|.++++.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus        23 ~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           23 KRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             TCCCBBSSSCCBCCSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCCCccCCCEecceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            4567999999999999999999999999999999999999888999999999999999999999974

>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=99.77  E-value=3e-19  Score=104.83  Aligned_cols=69  Identities=23%  Similarity=0.545  Sum_probs=64.2

Q ss_pred             CCCcccccccccccc----ceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCc
Q psy2501          51 TQKGCCSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCN  119 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~  119 (130)
                      .+.++|..|+++|.+    +.+.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+++|+.++
T Consensus         3 ~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            3 SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             TCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             ccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            355789999999986    889999999999999999999999988899999999999999999999999875

>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=99.76  E-value=5.9e-19  Score=101.68  Aligned_cols=67  Identities=28%  Similarity=0.622  Sum_probs=62.4

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      .+.++|..|+++|.++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A            3 SGSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             CCCCCCSSSCCCCCTTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCCC
T ss_pred             CCcCCCcccCCEeCcceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCCC
Confidence            4567899999999988899999999999999999999999888999999999999999999999963

>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=99.76  E-value=1.1e-18  Score=103.25  Aligned_cols=73  Identities=32%  Similarity=0.750  Sum_probs=66.2

Q ss_pred             hcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          45 RQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        45 ~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ...+.....++|..|+++|.++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         7 ~~~y~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A            7 GKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CCCCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             hhHHhhhcCCccccCCCeecceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            4455556678999999999988899999999999999999999998888999999999999999999999974

>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=99.76  E-value=4.7e-19  Score=105.16  Aligned_cols=71  Identities=18%  Similarity=0.499  Sum_probs=56.1

Q ss_pred             CCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccc
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI  122 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I  122 (130)
                      ..++|..|+++|. ++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|..|++..
T Consensus         6 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             --CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----------
T ss_pred             CCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            3578999999995 7789999999999999999999999888899999999999999999999999998764

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

Probab=99.75  E-value=1.9e-18  Score=116.92  Aligned_cols=78  Identities=28%  Similarity=0.718  Sum_probs=69.0

Q ss_pred             CCCccccccccccccc-eeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC--ce
Q psy2501          51 TQKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV--SI  127 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~--~~  127 (130)
                      ...++|..|+++|.+. ++.++++.||++||+|..|+.+|.+.. +.++|++||+.||.++|+++|..|+++|.+.  ++
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            4568999999999865 578999999999999999999998766 4789999999999999999999999999863  55


Q ss_pred             ee
Q psy2501         128 RN  129 (130)
Q Consensus       128 ~~  129 (130)
                      +|
T Consensus       137 ~a  138 (182)
T 2jtn_A          137 RA  138 (182)
T ss_dssp             EE
T ss_pred             ec
Confidence            55

>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=99.75  E-value=1.3e-18  Score=116.43  Aligned_cols=77  Identities=29%  Similarity=0.727  Sum_probs=67.3

Q ss_pred             CCccccccccccccc-eeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC--cee
Q psy2501          52 QKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV--SIR  128 (130)
Q Consensus        52 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~--~~~  128 (130)
                      ..++|..|+++|.+. ++.++++.||++||+|..|+.+|.+.. +.++|++||+.||.++|+++|..|+++|.+.  +++
T Consensus         5 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~v~~   83 (169)
T 2rgt_A            5 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRR   83 (169)
T ss_dssp             --CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCTTSEEEE
T ss_pred             CCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeecccccccccccccccccccCCCcEEEE
Confidence            457899999999865 578999999999999999999998765 5889999999999999999999999999864  445


Q ss_pred             e
Q psy2501         129 N  129 (130)
Q Consensus       129 ~  129 (130)
                      |
T Consensus        84 a   84 (169)
T 2rgt_A           84 A   84 (169)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=99.75  E-value=1.9e-18  Score=102.27  Aligned_cols=74  Identities=28%  Similarity=0.568  Sum_probs=66.4

Q ss_pred             hhcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          44 SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        44 ~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ....+.....++|..|+++|.++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         6 C~~cy~~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A            6 SGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             CCCCCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             cHHHHccccCCcCCCCCCEecCcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            34455556678999999999888899999999999999999999998888999999999999999999999974

>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=99.75  E-value=1.8e-18  Score=100.33  Aligned_cols=67  Identities=33%  Similarity=0.760  Sum_probs=61.7

Q ss_pred             CCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      .+..+|..|+++|.  ++.+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            3 SGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             ccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            35678999999997  57889999999999999999999999888999999999999999999999974

>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=99.74  E-value=2.7e-18  Score=101.73  Aligned_cols=66  Identities=36%  Similarity=0.771  Sum_probs=60.5

Q ss_pred             CCCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ...++|..|+++|. ++++.++++.||++||+|..|+.+|.+ .|+..++++||+.||.++|+++|++
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            45678999999996 788999999999999999999999985 6889999999999999999999974

>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=99.74  E-value=3.3e-18  Score=99.23  Aligned_cols=67  Identities=30%  Similarity=0.738  Sum_probs=61.5

Q ss_pred             CCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      .+.++|..|+++|.  +..+.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            3 SGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             SCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             ccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            35678999999997  46789999999999999999999999888999999999999999999999974

>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=99.74  E-value=3.1e-18  Score=107.81  Aligned_cols=73  Identities=22%  Similarity=0.465  Sum_probs=64.1

Q ss_pred             Cccccccccccccc-eeeecCcccccCCcccCCCCcccCC--CCeeccCCcccCHHhhhhhcCCCCccCccccccCcee
Q psy2501          53 KGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVSIR  128 (130)
Q Consensus        53 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~  128 (130)
                      .++|..|+++|.+. ++.++++.||++||+|..|+.+|..  ..|+.+++++||+.||.++|+++|..|.   .|.+|+
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~---~~~~~~   78 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGS---GGDVMV   78 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCB---SCSCCC
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCC---CCceeE
Confidence            36899999999866 7899999999999999999999974  5789999999999999999999998885   344544

>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=99.73  E-value=3e-20  Score=126.78  Aligned_cols=69  Identities=23%  Similarity=0.613  Sum_probs=64.7

Q ss_pred             ccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCcccc
Q psy2501          54 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPI  122 (130)
Q Consensus        54 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I  122 (130)
                      .+|..|+++|. ++.+.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+++|..|+++|
T Consensus       116 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~  185 (192)
T 1b8t_A          116 DGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA  185 (192)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             CcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCcc
Confidence            46999999997 5778899999999999999999999888899999999999999999999999999985

>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=99.73  E-value=4.6e-18  Score=100.83  Aligned_cols=72  Identities=28%  Similarity=0.594  Sum_probs=63.3

Q ss_pred             hcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeecc-CCcccCHHhhhhhcCCCCcc
Q psy2501          45 RQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFER-DSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        45 ~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ...+. ...++|..|+++|.++++.++++.||++||+|..|+++|.+..|+.. ++++||+.||.++|+++|++
T Consensus         8 ~~~y~-~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A            8 EGCYV-ATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CCCCC-SSCCBCTTTCCBCCSCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             HHHhh-cCCCccccCCCeecceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            34444 46689999999999888999999999999999999999987777765 78999999999999999974

>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=99.73  E-value=3.7e-18  Score=97.47  Aligned_cols=64  Identities=38%  Similarity=0.918  Sum_probs=59.4

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCC
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR  114 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~  114 (130)
                      .+.++|..|+++|.++.+.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            3 MGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCCCEETTTTEECCSCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             cCCCCCcccCCEecceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            3457899999999988899999999999999999999999888999999999999999999875

>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=99.73  E-value=5.7e-18  Score=98.26  Aligned_cols=66  Identities=24%  Similarity=0.595  Sum_probs=60.0

Q ss_pred             CCCcccccccccccc----ceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCc
Q psy2501          51 TQKGCCSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      .+..+|..|+++|.+    +++.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+|++.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~g   72 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSSG   72 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSCC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCCC
Confidence            456789999999985    778899999999999999999999988888999999999999999998763

>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=99.73  E-value=5.1e-18  Score=99.48  Aligned_cols=67  Identities=31%  Similarity=0.722  Sum_probs=61.7

Q ss_pred             CCCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCH-HhhhhhcCCCCcc
Q psy2501          51 TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE-PDYHNLFSPRCSY  117 (130)
Q Consensus        51 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~-~~~~~~~~~~C~~  117 (130)
                      ...++|..|+++|. ++.+.++++.||++||+|..|+.+|.+..|+..++++||+ .||.++|+++|.+
T Consensus         7 ~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            7 GMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             CCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            34578999999997 7889999999999999999999999988899999999999 7999999999964

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

Probab=99.72  E-value=1.7e-18  Score=117.71  Aligned_cols=79  Identities=25%  Similarity=0.635  Sum_probs=70.2

Q ss_pred             CCccccccccccccc-eeeecCcccccCCcccCCCCcccCC--CCeeccCCcccCHHhhhhhcCC--CCccCcccccc--
Q psy2501          52 QKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLFSP--RCSYCNGPILD--  124 (130)
Q Consensus        52 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~~~~~~~~~--~C~~C~~~I~~--  124 (130)
                      ..++|..|+++|.+. ++.++++.||++||+|..|+.+|..  ..|+.+++++||+.||.++|++  +|..|+++|.+  
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e   83 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASE   83 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTS
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCc
Confidence            457899999999876 5789999999999999999999975  5789999999999999999998  79999999985  


Q ss_pred             CceeeC
Q psy2501         125 VSIRNT  130 (130)
Q Consensus       125 ~~~~~~  130 (130)
                      .+|+|+
T Consensus        84 ~~i~a~   89 (188)
T 1rut_X           84 LVMRAQ   89 (188)
T ss_dssp             EEEEET
T ss_pred             EEEEcC
Confidence            467763

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

Probab=99.72  E-value=6.7e-18  Score=99.11  Aligned_cols=67  Identities=27%  Similarity=0.700  Sum_probs=59.4

Q ss_pred             CCCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCc
Q psy2501          50 TTQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        50 ~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      .....+|..|+++|.  +.++.++++.||++||+|..|+++|.++.|+..++++||+.||.++|+++|.
T Consensus         8 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A            8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            345689999999995  5567899999999999999999999888899999999999999999999996

>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=99.72  E-value=1e-17  Score=96.72  Aligned_cols=66  Identities=30%  Similarity=0.658  Sum_probs=60.6

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCc
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      .+..+|..|++.|.++++.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+++..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            3 SGSSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             CCSSBCSSSCCBCCSCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCCCcCccCCCEecceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            356789999999998889999999999999999999999988888999999999999999988654

>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=99.72  E-value=3.4e-18  Score=101.63  Aligned_cols=74  Identities=24%  Similarity=0.411  Sum_probs=65.8

Q ss_pred             hhcCCCCCCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          44 SRQGVTTTQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        44 ~~~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ....+.....++|..|+++|.  +.++.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|.+
T Consensus         6 C~~~y~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A            6 SGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             CCCCCCCCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             chhHhCcccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            344555667789999999997  67788999999999999999999999888999999999999999999999974

>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=99.71  E-value=1.2e-17  Score=99.15  Aligned_cols=74  Identities=31%  Similarity=0.586  Sum_probs=65.5

Q ss_pred             hhcCCCCCCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCcc
Q psy2501          44 SRQGVTTTQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSY  117 (130)
Q Consensus        44 ~~~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~  117 (130)
                      ....+.....++|..|+++|.  +.++.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|..
T Consensus         6 C~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~   81 (82)
T 1x63_A            6 SGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS   81 (82)
T ss_dssp             CCCCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSC
T ss_pred             chhHHccccCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCCC
Confidence            344555566789999999997  66789999999999999999999998888999999999999999999998863

>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=99.71  E-value=1.2e-17  Score=100.77  Aligned_cols=65  Identities=34%  Similarity=0.642  Sum_probs=60.7

Q ss_pred             CCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCc
Q psy2501          52 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        52 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      ...+|..|++.|.++++.++++.||++||+|..|++.|.+..|+..++++||+.||.++|++++.
T Consensus        24 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           24 RMPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             SCCBCTTTCCBCCSCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             cCCCcccCCCEecccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            45789999999998889999999999999999999999888899999999999999999999875

>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=99.71  E-value=1.2e-17  Score=113.92  Aligned_cols=63  Identities=21%  Similarity=0.597  Sum_probs=58.4

Q ss_pred             CCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCC
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR  114 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~  114 (130)
                      +.++|..|+++|. ++.+.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+++
T Consensus         6 ~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~   69 (192)
T 1b8t_A            6 GGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK   69 (192)
T ss_dssp             CCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCC
T ss_pred             CCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCcc
Confidence            4578999999996 77788999999999999999999999888999999999999999999886

>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=99.70  E-value=2.2e-17  Score=97.56  Aligned_cols=66  Identities=27%  Similarity=0.452  Sum_probs=59.8

Q ss_pred             CCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCc
Q psy2501          50 TTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        50 ~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      ..+.++|..|++.|.++++.++++.||++||+|..|+.+|.+. ++.+++++||+.||.++|+|++.
T Consensus        12 ~~~~~~C~~C~~~I~~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           12 GLGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTAD-ARELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCCCBCTTTCCBCCSCCCCCSSSCCCTTTSBCSSSCCBCCTT-CEEETTEEECHHHHHTTSCCSSC
T ss_pred             ccCCCCCccCCCEecceEEEECcceeCCCCCEeCCCCCccCCC-CEeECCEEeCHHHHHHhCCCCCC
Confidence            3456899999999998889999999999999999999999876 45899999999999999998765

>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=99.70  E-value=4.3e-17  Score=98.66  Aligned_cols=70  Identities=24%  Similarity=0.604  Sum_probs=63.1

Q ss_pred             CCCCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCc
Q psy2501          50 TTQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCN  119 (130)
Q Consensus        50 ~~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~  119 (130)
                      .....+|..|++.|. .+.+.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|+++|..+.
T Consensus        12 ~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~   82 (91)
T 2d8y_A           12 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDE   82 (91)
T ss_dssp             SSSSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCS
T ss_pred             CCCCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccC
Confidence            345679999999997 4778999999999999999999999888899999999999999999999998543

>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=99.69  E-value=8.6e-18  Score=99.24  Aligned_cols=66  Identities=27%  Similarity=0.580  Sum_probs=60.8

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCc
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      ....+|..|++.|.++++.++++.||++||+|..|+.+|.+..|+..++++||+.||.++|++++.
T Consensus        13 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           13 QKLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCCCSSSCCCCCSSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCCCccccCCCCccCcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            345789999999998899999999999999999999999877899999999999999999999864

>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=99.67  E-value=6.5e-17  Score=93.72  Aligned_cols=67  Identities=25%  Similarity=0.645  Sum_probs=59.1

Q ss_pred             CCCccccccccccc--cceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccC
Q psy2501          51 TQKGCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYC  118 (130)
Q Consensus        51 ~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C  118 (130)
                      .+.++|..|+++|.  +..+.++++.||++||+|..|+++|.+..|+..++++||+.||.++| .+|..+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~-~~~~~~   71 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL-ESGPSS   71 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHH-HTCSSC
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHH-ccCCCC
Confidence            45679999999997  35789999999999999999999998888999999999999999988 556554

>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=99.66  E-value=1.2e-16  Score=92.97  Aligned_cols=64  Identities=23%  Similarity=0.470  Sum_probs=58.0

Q ss_pred             CCCccccccccccccceeeecCcccccCCcccCCCCcccC-CCCeeccCCcccCHHhhhhhcCCC
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG-TRNFFERDSRPYCEPDYHNLFSPR  114 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~~~~~C~~~~~~~~~~~  114 (130)
                      .+.++|..|+++|.++++.++++.||++||+|..|+.+|. +..|+..++++||..||.++++..
T Consensus         3 ~~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~   67 (73)
T 1wig_A            3 SGSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTED   67 (73)
T ss_dssp             CSCCSCSSSCCCCSSCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSS
T ss_pred             cCcCCcccCCCEecCeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccc
Confidence            3567999999999998999999999999999999999998 667889999999999999887653

>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=99.65  E-value=1.6e-16  Score=94.15  Aligned_cols=73  Identities=21%  Similarity=0.380  Sum_probs=63.4

Q ss_pred             hhcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCC-CCee-ccCCcccCHHhhhhhcCCCCc
Q psy2501          44 SRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGT-RNFF-ERDSRPYCEPDYHNLFSPRCS  116 (130)
Q Consensus        44 ~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~-~~~~~~~C~~~~~~~~~~~C~  116 (130)
                      ....+.....++|..|+++|.++.+.++++.||++||+|..|+++|.. ..|+ ..++++||+.||.++|++.|+
T Consensus         6 C~~~y~~~~~~~C~~C~~~I~~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A            6 SGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             CCCCSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             chhHHhhhcCCcCccCCCCcCceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            344566667789999999999888999999999999999999999964 5666 589999999999999998775

>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=99.63  E-value=2.6e-16  Score=90.98  Aligned_cols=65  Identities=26%  Similarity=0.722  Sum_probs=57.2

Q ss_pred             CCCCCCccccccccccc-cc-eeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          48 VTTTQKGCCSSCDKPIV-GQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        48 ~~~~~~~~C~~C~~~i~-~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      +......+|..|+++|. ++ .+.++++.||++||+|..|+++|.++.|+..++++||+.||.++|+
T Consensus         6 y~~~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            6 FQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CCCCTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             ccCcCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            34456789999999997 33 5689999999999999999999988888999999999999999875

>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=99.62  E-value=5.3e-16  Score=90.96  Aligned_cols=66  Identities=26%  Similarity=0.599  Sum_probs=58.4

Q ss_pred             hhcCCCCCCCcccccccccccc-----ceeeecCcccccCCcccCCCCcccCCCCeeccCCcccCHHhhhh
Q psy2501          44 SRQGVTTTQKGCCSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN  109 (130)
Q Consensus        44 ~~~~~~~~~~~~C~~C~~~i~~-----~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~  109 (130)
                      ....+.....++|..|+++|.+     +.+.++++.||++||+|..|+++|.+..|+..++++||+.||.+
T Consensus         6 C~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A            6 SGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             chhHhchhhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            3445555667899999999986     77999999999999999999999998889999999999999965

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

Probab=99.61  E-value=6.1e-16  Score=98.52  Aligned_cols=62  Identities=24%  Similarity=0.633  Sum_probs=55.6

Q ss_pred             CCCccccccccccccc-eeeecCcccccCCcccCCCCcccC--CCCeeccCCcccCHHhhhhhcC
Q psy2501          51 TQKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      ...++|..|+++|.+. ++.++++.||++||+|..|+.+|.  +..|+.+++++||+.||.++|+
T Consensus        59 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           59 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             SSCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             ccCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            3457999999999865 589999999999999999999996  4579999999999999999885

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

Probab=99.59  E-value=1e-15  Score=87.05  Aligned_cols=58  Identities=24%  Similarity=0.535  Sum_probs=53.2

Q ss_pred             Cccccccccccc--cceeeecCcccc--cCCcccCCCCcccCCCCeeccCCcccC-HHhhhhh
Q psy2501          53 KGCCSSCDKPIV--GQVITALGKTWH--PEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNL  110 (130)
Q Consensus        53 ~~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~C-~~~~~~~  110 (130)
                      .++|..|+++|.  ++.+.++++.||  ++||+|..|+++|.+..|+..++++|| .+||.++
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            468999999997  688999999999  999999999999998889999999999 8998654

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

Probab=99.58  E-value=1.4e-15  Score=90.26  Aligned_cols=64  Identities=19%  Similarity=0.353  Sum_probs=56.5

Q ss_pred             CCccccccccccc-cceeeecCcccccCCcccCCCCcccCCCCee--ccCCcccCHHhhhhhcCCCC
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFF--ERDSRPYCEPDYHNLFSPRC  115 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~--~~~~~~~C~~~~~~~~~~~C  115 (130)
                      ...+|..|++.|. .+.+.++++.||.+||+|..|+++|....|+  ..++++||+.||.++++.-+
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            4578999999995 6778899999999999999999999888877  47999999999999887643

>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=99.58  E-value=2.6e-17  Score=111.89  Aligned_cols=107  Identities=19%  Similarity=0.304  Sum_probs=75.4

Q ss_pred             cccCCCCCCCCCCCchhHHHHHHHHHHHH-h-------hhcCCCCCCCc--cccccccccc--cceeeecCcccccCCcc
Q psy2501          14 SSVSYSKPNQPVHQKGKQLDCMLDSLTAE-M-------SRQGVTTTQKG--CCSSCDKPIV--GQVITALGKTWHPEHFI   81 (130)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-------~~~~~~~~~~~--~C~~C~~~i~--~~~~~~~~~~~H~~Cf~   81 (130)
                      .+.++++.||+.||.+..+...+...... +       +...+...+.+  +|..|+++|.  +.++.++++.||++||+
T Consensus        20 ~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~   99 (188)
T 1rut_X           20 LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFT   99 (188)
T ss_dssp             EEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTSEEEEETTEEECGGGCB
T ss_pred             eEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCcEEEEcCCCEEeCCCCe
Confidence            46789999999999777666544431111 1       12222222334  7999999996  35678999999999999


Q ss_pred             cCCCCcccC-CCCeeccCCcccCHHhhhhhcCCCCccCcc
Q psy2501          82 CTHCNQELG-TRNFFERDSRPYCEPDYHNLFSPRCSYCNG  120 (130)
Q Consensus        82 C~~C~~~l~-~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~  120 (130)
                      |..|+++|. +..|+..++++||+.||.++++++|...+.
T Consensus       100 C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~~~g~  139 (188)
T 1rut_X          100 CSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGG  139 (188)
T ss_dssp             CTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC--------
T ss_pred             ECCCCCCCCCCCeEEEECCeEECHHHHHHHhcccccccCC
Confidence            999999995 556889999999999999999999987654

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

Probab=99.56  E-value=1.1e-17  Score=107.47  Aligned_cols=99  Identities=19%  Similarity=0.298  Sum_probs=73.9

Q ss_pred             cccCCCCCCCCCCCchhHHHHHHHHHHHH--------hhhcCCCCCCCc--ccccccccccc--ceeeecCcccccCCcc
Q psy2501          14 SSVSYSKPNQPVHQKGKQLDCMLDSLTAE--------MSRQGVTTTQKG--CCSSCDKPIVG--QVITALGKTWHPEHFI   81 (130)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~--~C~~C~~~i~~--~~~~~~~~~~H~~Cf~   81 (130)
                      .+.++++.||+.+|.+..++..+......        +....+.....+  +|..|+++|.+  ..+.++++.||++||+
T Consensus        17 ~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~   96 (131)
T 2xjy_A           17 FLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFK   96 (131)
T ss_dssp             EEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTSEEEEETTEEEEGGGCB
T ss_pred             EEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccceeEeeCCceECccCcc
Confidence            57899999999999776665433210000        011112222334  89999999974  5688999999999999


Q ss_pred             cCCCCcccC-CCCeeccCCcccCHHhhhhhcC
Q psy2501          82 CTHCNQELG-TRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        82 C~~C~~~l~-~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      |..|+++|. +..|+..++++||..||.++++
T Consensus        97 C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~  128 (131)
T 2xjy_A           97 CAACQKHFCVGDRYLLINSDIVCEQDIYEWTK  128 (131)
T ss_dssp             CTTTCCBCCTTCEEEEETTEEEEGGGHHHHHH
T ss_pred             cCCCCCCCCCCCEEEEECCEEEcHHHHHHHhh
Confidence            999999995 5678899999999999998875

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

Probab=99.54  E-value=3.3e-17  Score=104.62  Aligned_cols=99  Identities=17%  Similarity=0.321  Sum_probs=75.7

Q ss_pred             CcccCCCCCCCCCCCchhHHHHHHHHHH------HHhhhcCCCCCCCccccccccccc--cceeeecCcccc--cCCccc
Q psy2501          13 SSSVSYSKPNQPVHQKGKQLDCMLDSLT------AEMSRQGVTTTQKGCCSSCDKPIV--GQVITALGKTWH--PEHFIC   82 (130)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H--~~Cf~C   82 (130)
                      ..+.++++.||+.+|.+..+...+....      ..+....+.....++|..|+++|.  +..+.++++.||  ++||+|
T Consensus        17 ~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C   96 (126)
T 2xqn_T           17 EYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLC   96 (126)
T ss_dssp             CEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBC
T ss_pred             eEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCceEEECCCCEeeCCCCCcCc
Confidence            4677999999999997665554332110      001122223345679999999997  567899999999  999999


Q ss_pred             CCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501          83 THCNQELGTRNFFERDSRPYCEPDYHNLF  111 (130)
Q Consensus        83 ~~C~~~l~~~~~~~~~~~~~C~~~~~~~~  111 (130)
                      ..|+++|.+..|+..++++||..+|.++|
T Consensus        97 ~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           97 SCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             TTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             CCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence            99999999888889999999998887765

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

Probab=99.50  E-value=1.4e-14  Score=85.71  Aligned_cols=68  Identities=26%  Similarity=0.478  Sum_probs=56.4

Q ss_pred             hcCCCCCCCccccccccccccceeeecCcccccCCcccCCCCcccCCCCeeccCC-cccCHHhhhhhcC
Q psy2501          45 RQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDS-RPYCEPDYHNLFS  112 (130)
Q Consensus        45 ~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~-~~~C~~~~~~~~~  112 (130)
                      ...+...+.++|..|+++|.++.+.++++.||++||+|..|+++|..+.++..++ .+||..||.+++.
T Consensus         7 ~~dy~~~~~~~C~~C~~~I~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A            7 GLDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CSCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             hHHHHhHhCCcCccccCEeccceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            3444556678999999999988999999999999999999999998666665555 5799999987663

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

Probab=99.41  E-value=2.4e-15  Score=101.61  Aligned_cols=98  Identities=20%  Similarity=0.298  Sum_probs=71.1

Q ss_pred             cccCCCCCCCCCCCchhHHHHHHHHHHHHh-----hhcCCCCCCCcccccccccccc--ceeeecCcccccCCcccCCCC
Q psy2501          14 SSVSYSKPNQPVHQKGKQLDCMLDSLTAEM-----SRQGVTTTQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCN   86 (130)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~   86 (130)
                      .+.++++.||+.+|.+..+...+.......     +...+...+.++|..|+++|.+  ..+.+.++.||+.||+|..|+
T Consensus        75 ~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~  154 (182)
T 2jtn_A           75 ILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCK  154 (182)
T ss_dssp             EEEETTEEECSSTTSCTTTCCCCSSCCEEETTEEECHHHHHHTTSCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTC
T ss_pred             eEEecCCeEccccCccCCCCCccCCCceeECCEeeecCccccccccccccCCCccCCCceEEecCCCCEEeCCCcCCCCC
Confidence            356889999999997665554332211111     2222334566899999999963  356899999999999999999


Q ss_pred             cccCC-CCee-ccCCcccCHHhhhhhc
Q psy2501          87 QELGT-RNFF-ERDSRPYCEPDYHNLF  111 (130)
Q Consensus        87 ~~l~~-~~~~-~~~~~~~C~~~~~~~~  111 (130)
                      ++|.. ..|+ ..++++||+.||.++.
T Consensus       155 ~~L~~g~~f~~~~~g~~yC~~cy~~~~  181 (182)
T 2jtn_A          155 RQLATGDEFYLMEDSRLVCKADYETAK  181 (182)
T ss_dssp             CCCCTTCEEEECTTSCEECHHHHHHHT
T ss_pred             CCCCCCCceEEccCCEEECHHHHHHhh
Confidence            99974 4565 5689999999997653

>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=99.41  E-value=2.1e-15  Score=100.85  Aligned_cols=102  Identities=19%  Similarity=0.268  Sum_probs=72.6

Q ss_pred             cccCCCCCCCCCCCchhHHHHHHHHHHHHh-----hhcCCCCCCCcccccccccccc--ceeeecCcccccCCcccCCCC
Q psy2501          14 SSVSYSKPNQPVHQKGKQLDCMLDSLTAEM-----SRQGVTTTQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCN   86 (130)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~   86 (130)
                      .+.++++.||+.+|.+..+...+.......     +...+...+.++|..|++.|.+  .++.++++.||.+||+|..|+
T Consensus        21 ~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~  100 (169)
T 2rgt_A           21 ILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCK  100 (169)
T ss_dssp             CEECSSCEECTTTSBCTTTCCBCCSCCEESSSCEECHHHHHHHHSCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTC
T ss_pred             EEEECCcEEccccCccCCCCCcCCCCCcccCCeeeecccccccccccccccccccCCCcEEEEcCCceEeeCCCcCCCCC
Confidence            467899999999997666553332211000     1111222345789999999964  346899999999999999999


Q ss_pred             cccC-CCCee-ccCCcccCHHhhhhhcCCCC
Q psy2501          87 QELG-TRNFF-ERDSRPYCEPDYHNLFSPRC  115 (130)
Q Consensus        87 ~~l~-~~~~~-~~~~~~~C~~~~~~~~~~~C  115 (130)
                      +.|. +..|+ ..++++||+.||.+.+...+
T Consensus       101 ~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~~  131 (169)
T 2rgt_A          101 RQLATGDEFYLMEDSRLVCKADYETAKQGGS  131 (169)
T ss_dssp             CBCCTTCEEEECTTSCEEEHHHHHHHHHCC-
T ss_pred             CCCCCCCceEEccCCeEECHHHHHHHhhccC
Confidence            9997 44565 56899999999998875543

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

Probab=98.97  E-value=6.1e-12  Score=77.03  Aligned_cols=75  Identities=16%  Similarity=0.182  Sum_probs=54.9

Q ss_pred             CCcccCCCCCCCCCCCchhHHHHHHHHH------HHHhhhcCCCCCCCccccccccccc--cceeeecCcccccCCcccC
Q psy2501          12 DSSSVSYSKPNQPVHQKGKQLDCMLDSL------TAEMSRQGVTTTQKGCCSSCDKPIV--GQVITALGKTWHPEHFICT   83 (130)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~   83 (130)
                      ...+.++++.||+.+|.+..+...+...      ...+....+.....++|..|+++|.  +..+.++++.||++||+|.
T Consensus        19 ~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~   98 (101)
T 2cup_A           19 SKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGP   98 (101)
T ss_dssp             SCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSSCEEESSSCEEETTTCCCT
T ss_pred             ceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCCeEEEeCCcchHHhCCCCC
Confidence            5667889999999999665554433211      0011233345567789999999997  5689999999999999999


Q ss_pred             CCC
Q psy2501          84 HCN   86 (130)
Q Consensus        84 ~C~   86 (130)
                      .|+
T Consensus        99 ~C~  101 (101)
T 2cup_A           99 SSG  101 (101)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            985

>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=98.37  E-value=9.3e-08  Score=55.73  Aligned_cols=33  Identities=27%  Similarity=0.562  Sum_probs=30.0

Q ss_pred             CCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      +|++||+.||.++++++|..|+++|.+++|+|+
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~~~v~a~   33 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQGGVTYR   33 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCSCCEESS
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecCcEEEEC
Confidence            578999999999999999999999999988874

>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=98.36  E-value=1.3e-07  Score=54.75  Aligned_cols=33  Identities=21%  Similarity=0.427  Sum_probs=29.4

Q ss_pred             CCcccCHHhhhhhcCCCCccCcccccc-----CceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPILD-----VSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~~-----~~~~~~  130 (130)
                      ++++||+.||.++++++|.+|+++|.+     ++|+|+
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~   38 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYE   38 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEET
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCCCceeEEEC
Confidence            468999999999999999999999997     778774

>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=98.36  E-value=9.8e-08  Score=55.63  Aligned_cols=33  Identities=30%  Similarity=0.651  Sum_probs=30.2

Q ss_pred             CCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      ++++||+.||.++++++|..|+++|.+++|+|+
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~~~~v~a~   33 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVLENYLSAM   33 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCEEET
T ss_pred             CCCccchhHHhhhcCCccccCCCeecceeEEEC
Confidence            478999999999999999999999999999875

>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=98.33  E-value=1e-07  Score=55.70  Aligned_cols=33  Identities=18%  Similarity=0.202  Sum_probs=29.5

Q ss_pred             CCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      ++.+||+.||.++|+++|..|+++|.+++|+|+
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~~~~~~a~   33 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMTGPFMVAG   33 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCCSCCBCCT
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcCceEEEEC
Confidence            367899999999999999999999999998874

>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=98.31  E-value=2.2e-07  Score=54.30  Aligned_cols=32  Identities=25%  Similarity=0.409  Sum_probs=29.5

Q ss_pred             CcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          99 SRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        99 ~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      +.+||+.||.++|+++|..|+++|.+++|+|+
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~~~~v~a~   33 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIEGEVVSAL   33 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCCSCCEEET
T ss_pred             CCCcchHHHHhHhCCcCccccCEeccceEEEC
Confidence            46899999999999999999999999999885

>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=98.31  E-value=1.1e-07  Score=55.78  Aligned_cols=33  Identities=24%  Similarity=0.357  Sum_probs=29.0

Q ss_pred             CCcccCHHhhhhhcCCCCccCccccc--cCceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPIL--DVSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~~~  130 (130)
                      +|++||+.||.++|+++|..|+++|.  +.+|+|+
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~~~~~a~   35 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDSRELFYE   35 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCCBCCCS
T ss_pred             CCceechhHhCcccCCcCccCCCccccCcEEEEeC
Confidence            57899999999999999999999998  7777763

>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=98.18  E-value=4.8e-07  Score=52.81  Aligned_cols=32  Identities=31%  Similarity=0.466  Sum_probs=28.4

Q ss_pred             CCcccCHHhhhhhcCCCCccCccccccCceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      ++++||+.||. +++++|..|+++|.+++|+|+
T Consensus         2 ~g~~yC~~~y~-~~~~~C~~C~~~I~~~~~~a~   33 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKCATCSQPILDRILRAM   33 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBCTTTCCBCCSCCEEET
T ss_pred             cCCEECHHHhh-cCCCccccCCCeecceeEEEC
Confidence            67899999998 788999999999999988875

>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=98.15  E-value=2.3e-09  Score=67.78  Aligned_cols=87  Identities=11%  Similarity=0.029  Sum_probs=57.6

Q ss_pred             cccCCCCCCCCCCCchhHHHHHHHHH--------HHHhhhcCCCCCCCc--cccccccccccceeeecCcccccCCcccC
Q psy2501          14 SSVSYSKPNQPVHQKGKQLDCMLDSL--------TAEMSRQGVTTTQKG--CCSSCDKPIVGQVITALGKTWHPEHFICT   83 (130)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~--~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~   83 (130)
                      .+.++++.||+.+|.+..+...+...        ...++...+...+.+  +|..|+++|.+..+.++++          
T Consensus        20 ~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~~~~g~----------   89 (122)
T 1m3v_A           20 LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDVMVVGE----------   89 (122)
T ss_dssp             CEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEESSSSSS----------
T ss_pred             EEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchheEEcCC----------
Confidence            47789999999999666555433210        000111222223334  8999999998655555543          


Q ss_pred             CCCcccCCCCeeccCCcccCHHhhhhhcCC
Q psy2501          84 HCNQELGTRNFFERDSRPYCEPDYHNLFSP  113 (130)
Q Consensus        84 ~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~  113 (130)
                         ..|.+..|+.+++++||..||.+++.+
T Consensus        90 ---~~l~g~~f~~~~~~~yC~~~~~~~~~~  116 (122)
T 1m3v_A           90 ---PTLMGGEFGDEDERLITRLENTQFDAA  116 (122)
T ss_dssp             ---SSCCSCTTCCTTCCCCEECTTTTTTCC
T ss_pred             ---cCCCCCccEecCCEeEccCcchhchhh
Confidence               356777899999999999999887643

>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=98.11  E-value=6.2e-07  Score=52.40  Aligned_cols=33  Identities=21%  Similarity=0.251  Sum_probs=28.0

Q ss_pred             CCcccCHHhhhhhcCCCCccCccccc--cCceeeC
Q psy2501          98 DSRPYCEPDYHNLFSPRCSYCNGPIL--DVSIRNT  130 (130)
Q Consensus        98 ~~~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~~~  130 (130)
                      ++.+||+.||.++++++|..|+++|.  +++|+|+
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~   35 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYK   35 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSSCEEECS
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCceEEEEC
Confidence            46789999999999999999999998  6777764

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

Probab=98.07  E-value=1.2e-06  Score=41.92  Aligned_cols=28  Identities=29%  Similarity=0.684  Sum_probs=24.9

Q ss_pred             Cccccccccccc-cceeeecCcccccCCc
Q psy2501          53 KGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      ..+|..|++.|+ .+.+.+.++.||..||
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            468999999996 6888899999999998

>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=97.26  E-value=7.8e-05  Score=46.12  Aligned_cols=93  Identities=12%  Similarity=0.045  Sum_probs=48.9

Q ss_pred             CCCCC-cccCCCCCCCCCCCchhHHHHHHHHHHHHhhhcCCCCCCCcccccccccccccee--eecCcccccCCcccCCC
Q psy2501           9 SVTDS-SSVSYSKPNQPVHQKGKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVI--TALGKTWHPEHFICTHC   85 (130)
Q Consensus         9 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~--~~~~~~~H~~Cf~C~~C   85 (130)
                      ++.+. .+.++++.||+.+|.+..+...+....    ...+...+...|..|.....+..-  ...+..     .   .|
T Consensus        12 ~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g----~~~~~~~g~~yC~~~y~~~f~~~c~~c~~~~~-----~---~~   79 (114)
T 1j2o_A           12 NIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVG----RRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDV-----M---VV   79 (114)
T ss_dssp             CBCSSEEEECSSSEECTTTCCCSSSCSCCCCSS----SCCCCBTTBCCCHHHHHHHHTSCCSSCBSCSC-----C---CS
T ss_pred             eeCCcEEEEECchhHHHhcCcccccCCchhcCC----CeeEEECCeeechHHHHHHhCcccCcCCCCce-----e---Ec
Confidence            34444 678899999999997666554332100    001111222334443333221110  000111     1   13


Q ss_pred             Ccc-cCCCCeeccCCcccCHHhhhhhcCC
Q psy2501          86 NQE-LGTRNFFERDSRPYCEPDYHNLFSP  113 (130)
Q Consensus        86 ~~~-l~~~~~~~~~~~~~C~~~~~~~~~~  113 (130)
                      +.. |.+..|+..++++||..||.++..+
T Consensus        80 ~~~~~~g~~f~~~~~~~~C~~~~~~~~~~  108 (114)
T 1j2o_A           80 GEPTLMGGEFGDEDERLITRLENTQFDAA  108 (114)
T ss_dssp             SCSSTTSSBCCCSSSCCCEEEECTTCCCT
T ss_pred             CCccCCCCeeEEcCCEeecchhhhccccc
Confidence            344 4566888999999999999877543

>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=94.85  E-value=0.015  Score=32.06  Aligned_cols=19  Identities=32%  Similarity=0.387  Sum_probs=12.0

Q ss_pred             cCCCCccCccccccCceee
Q psy2501         111 FSPRCSYCNGPILDVSIRN  129 (130)
Q Consensus       111 ~~~~C~~C~~~I~~~~~~~  129 (130)
                      ++++|..|+++|.+++|+|
T Consensus         4 ~~~~C~~C~~~I~~~~~~a   22 (69)
T 2cur_A            4 GSSGCVKCNKAITSGGITY   22 (69)
T ss_dssp             CCCCCSSSCCCCCTTCEEE
T ss_pred             CcCCCcccCCEeCcceEEE
Confidence            4566666666666666655

>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=94.82  E-value=0.0063  Score=33.39  Aligned_cols=19  Identities=26%  Similarity=0.501  Sum_probs=10.1

Q ss_pred             cCCCCccCccccccCceee
Q psy2501         111 FSPRCSYCNGPILDVSIRN  129 (130)
Q Consensus       111 ~~~~C~~C~~~I~~~~~~~  129 (130)
                      ++++|.+|+++|.+++|+|
T Consensus         4 ~~~~C~~C~~~I~~~~~~a   22 (66)
T 1nyp_A            4 GVPICGACRRPIEGRVVNA   22 (66)
T ss_dssp             CCCEETTTTEECCSCEECC
T ss_pred             CCCCCcccCCEecceEEEE
Confidence            4455555555555555544

>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=94.55  E-value=0.013  Score=34.27  Aligned_cols=39  Identities=21%  Similarity=0.629  Sum_probs=27.9

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+..+. ..+....++.|...||      +|..|+++|.+.
T Consensus        26 ~~C~~C~~~I~-~~~v~a~~~~~H~~CF------~C~~C~~~L~~~   64 (90)
T 2dar_A           26 PMCAHCNQVIR-GPFLVALGKSWHPEEF------NCAHCKNTMAYI   64 (90)
T ss_dssp             CBBSSSCCBCC-SCEEEETTEEECTTTC------BCSSSCCBCSSS
T ss_pred             CCCccCCCEec-ceEEEECCccccccCC------ccCCCCCCCCCC
Confidence            46788888885 3455666778777775      688888887653

>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=94.45  E-value=0.035  Score=31.10  Aligned_cols=20  Identities=15%  Similarity=0.016  Sum_probs=16.1

Q ss_pred             CCCCCcccCCCCCCCCCCCc
Q psy2501           9 SVTDSSSVSYSKPNQPVHQK   28 (130)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~   28 (130)
                      ++.+..+.++++.||+++|.
T Consensus        14 ~I~~~~v~a~~~~wH~~CF~   33 (73)
T 1wig_A           14 YITGRVLEAGEKHYHPSCAL   33 (73)
T ss_dssp             CCSSCCBCCSSCCBCTTTSC
T ss_pred             EecCeeEEeCCCCCCCCcCE
Confidence            44557788999999999985

>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=93.16  E-value=0.033  Score=31.74  Aligned_cols=17  Identities=18%  Similarity=0.268  Sum_probs=8.4

Q ss_pred             CCCccCccccccCceee
Q psy2501         113 PRCSYCNGPILDVSIRN  129 (130)
Q Consensus       113 ~~C~~C~~~I~~~~~~~  129 (130)
                      ++|..|+++|.+++|+|
T Consensus        16 ~~C~~C~~~I~~~~v~a   32 (79)
T 2cor_A           16 YICQKCHAIIDEQPLIF   32 (79)
T ss_dssp             CBCTTTCCBCCSCCCCC
T ss_pred             CCCccCCCEecceEEEE
Confidence            44555555555544444

>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=92.87  E-value=0.091  Score=29.95  Aligned_cols=41  Identities=12%  Similarity=0.320  Sum_probs=30.8

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccCc
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDVS  126 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~~  126 (130)
                      .+|..|+.++....+....++.|...||      +|..|++++.+.+
T Consensus        16 ~~C~~C~~~I~~~~~v~a~~~~wH~~CF------~C~~C~~~L~~~~   56 (80)
T 2dj7_A           16 SHCAGCKEEIKHGQSLLALDKQWHVSCF------KCQTCSVILTGEY   56 (80)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTC------BCSSSCCBCSSCC
T ss_pred             CCCcCcCCeeCCCeEEEECCcccccccC------CcCcCCCCcCCCe
Confidence            4688899988755566667788887775      6888988887654

>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=92.56  E-value=0.064  Score=30.40  Aligned_cols=19  Identities=26%  Similarity=0.562  Sum_probs=14.6

Q ss_pred             CCCCccCccccccCceeeC
Q psy2501         112 SPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus       112 ~~~C~~C~~~I~~~~~~~~  130 (130)
                      .++|..|+++|.+++|+|+
T Consensus        15 ~~~C~~C~~~I~~~~~~a~   33 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFVKLR   33 (79)
T ss_dssp             CCCCSSSCCCCCSSCEECS
T ss_pred             CCccccCCCCccCcEEEEC
Confidence            4688888888888877764

>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=91.78  E-value=0.1  Score=29.20  Aligned_cols=40  Identities=10%  Similarity=0.268  Sum_probs=30.3

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+.++...+.....++.|...||      +|..|+++|.+.
T Consensus        10 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF------~C~~C~~~L~~~   49 (76)
T 2cu8_A           10 SKCPKCDKTVYFAEKVSSLGKDWHKFCL------KCERCSKTLTPG   49 (76)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTC------BCSSSCCBCCTT
T ss_pred             CCCcCCCCEeECCeEEEECCeEeeCCCC------CCCCCCCccCCC
Confidence            4788899998755666667788877775      588898888754

>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=91.07  E-value=0.16  Score=28.97  Aligned_cols=40  Identities=15%  Similarity=0.385  Sum_probs=28.8

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|++.+...+.....++.|...||      +|..|++++.+.
T Consensus        16 ~~C~~C~~~I~~~e~v~a~~~~wH~~CF------~C~~C~~~L~~~   55 (82)
T 2co8_A           16 DLCALCGEHLYVLERLCVNGHFFHRSCF------RCHTCEATLWPG   55 (82)
T ss_dssp             CBCSSSCCBCCTTTBCCBTTBCCBTTTC------BCSSSCCBCCTT
T ss_pred             CCCcccCCCcccceEEEECCCeeCCCcC------EEcCCCCCcCCC
Confidence            4688899988655555566777777774      688888887654

>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=90.28  E-value=0.13  Score=28.70  Aligned_cols=39  Identities=15%  Similarity=0.422  Sum_probs=28.9

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      +|..|+.++....+....++.|...||      +|..|++++.+.
T Consensus         2 ~C~~C~~~I~~~~~v~a~~~~~H~~CF------~C~~C~~~L~~~   40 (76)
T 1iml_A            2 KCPKCDKEVYFAERVTSLGKDWHRPCL------KCEKCGKTLTSG   40 (76)
T ss_dssp             BCTTTSSBCCGGGEEEETTEEEETTTC------BCTTTCCBCCTT
T ss_pred             cCCCCCCEEECceEEEECCccccCCCC------CccccCccCCCC
Confidence            578899988755556666788777775      588899888754

>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=90.16  E-value=0.14  Score=29.67  Aligned_cols=17  Identities=24%  Similarity=0.716  Sum_probs=9.8

Q ss_pred             CCCccCccccccCceee
Q psy2501         113 PRCSYCNGPILDVSIRN  129 (130)
Q Consensus       113 ~~C~~C~~~I~~~~~~~  129 (130)
                      ++|..|+++|.+++|+|
T Consensus        26 ~~C~~C~~~I~~~~~~a   42 (89)
T 1x64_A           26 PLCDKCGSGIVGAVVKA   42 (89)
T ss_dssp             CBCTTTCCBCCSCCEES
T ss_pred             CCcccCCCEecccEEEE
Confidence            45666666666555554

>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=90.03  E-value=0.13  Score=28.21  Aligned_cols=10  Identities=20%  Similarity=0.813  Sum_probs=5.6

Q ss_pred             ccCCCCcccC
Q psy2501          81 ICTHCNQELG   90 (130)
Q Consensus        81 ~C~~C~~~l~   90 (130)
                      +|..|+..+.
T Consensus        13 ~C~~C~~~i~   22 (72)
T 3f6q_B           13 TCERCKGGFA   22 (72)
T ss_dssp             BCTTTCCBCC
T ss_pred             cchhcCcccc
Confidence            4555666554

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

Probab=89.71  E-value=0.16  Score=27.48  Aligned_cols=39  Identities=13%  Similarity=0.438  Sum_probs=28.5

Q ss_pred             ccCCCCcccCC-CCeeccCCcccC--HHhhhhhcCCCCccCccccccC
Q psy2501          81 ICTHCNQELGT-RNFFERDSRPYC--EPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        81 ~C~~C~~~l~~-~~~~~~~~~~~C--~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      +|..|+.++.. .......++.|-  ..||      +|..|+++|.+.
T Consensus         4 ~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF------~C~~C~~~L~~~   45 (65)
T 2iyb_E            4 VCQGCHNAIDPEVQRVTYNNFSWHASTECF------LCSCCSKCLIGQ   45 (65)
T ss_dssp             ECTTTSSEECTTSCEEEETTEEEETTTTTS------BCTTTCCBCTTS
T ss_pred             CCcCCCCeeccCceEEEECCCccCCCCCCE------ECCCCCCcCCCC
Confidence            57888888864 355566677777  7775      688898888765

>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=89.54  E-value=0.13  Score=29.09  Aligned_cols=40  Identities=15%  Similarity=0.337  Sum_probs=29.3

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+.++.........++.|...||      +|..|+++|.+.
T Consensus         8 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF------~C~~C~~~L~~~   47 (81)
T 1a7i_A            8 NKCGACGRTVYHAEEVQCDGRSFHRCCF------LCMVCRKNLDST   47 (81)
T ss_dssp             CBCSSSCCBCSSTTEEEETTEEEESSSE------ECSSSCCEECSS
T ss_pred             CcCcCcCccccCceeEEeCCcccccccC------ccCCCCCCCCCC
Confidence            4788899998655556667777777775      588888887654

>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=89.50  E-value=0.25  Score=27.03  Aligned_cols=39  Identities=15%  Similarity=0.445  Sum_probs=28.7

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+..+.+ .+....++.|...||      +|..|+++|.+.
T Consensus         6 ~~C~~C~~~I~~-~~~~a~~~~~H~~CF------~C~~C~~~L~~~   44 (70)
T 2d8x_A            6 SGCHQCGEFIIG-RVIKAMNNSWHPECF------RCDLCQEVLADI   44 (70)
T ss_dssp             SBCSSSCCBCCS-CCEEETTEEECTTTS------BCSSSCCBCSSS
T ss_pred             CcCccCCCEecc-eEEEECcccccccCC------EeCCCCCcCCCC
Confidence            367888888864 455667788887775      688898888654

>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=89.44  E-value=0.25  Score=27.21  Aligned_cols=40  Identities=13%  Similarity=0.456  Sum_probs=28.7

Q ss_pred             cccCCCCcccCC---CCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGT---RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~---~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+.++.+   ..+....++.|...||      +|..|+++|.+.
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF------~C~~C~~~L~~~   48 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYISFEERQWHNDCF------NCKKCSLSLVGR   48 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEECSSCEECTTTC------BCSSSCCBCTTS
T ss_pred             CCCcCCCccccCCCCcceEEECCcccCcccC------EeccCCCcCCCC
Confidence            368888988874   3444556778877775      688888888654

>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=89.28  E-value=0.22  Score=28.85  Aligned_cols=40  Identities=20%  Similarity=0.448  Sum_probs=29.7

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+..+.........++.|...||      +|..|+++|.+.
T Consensus        16 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF------~C~~C~~~L~~~   55 (91)
T 2d8y_A           16 ETCVECQKTVYPMERLLANQQVFHISCF------RCSYCNNKLSLG   55 (91)
T ss_dssp             CBCTTTCCBCCTTSEEECSSSEEETTTC------BCTTTCCBCCTT
T ss_pred             CcCccCCCccCCceeEEECCCEECCCCC------eeCCCCCCCCCC
Confidence            4788999998765566667777777775      588888887653

>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=89.16  E-value=0.26  Score=27.05  Aligned_cols=39  Identities=21%  Similarity=0.446  Sum_probs=28.2

Q ss_pred             ccCCCCcccCCC-CeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          81 ICTHCNQELGTR-NFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        81 ~C~~C~~~l~~~-~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      +|..|+.++... ......++.|...||      +|..|+++|.+.
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF------~C~~C~~~L~~~   46 (72)
T 1wyh_A            7 GCSACGETVMPGSRKLEYGGQTWHEHCF------LCSGCEQPLGSR   46 (72)
T ss_dssp             BCSSSCCBCCSSSCEECSTTCCEETTTC------BCTTTCCBTTTS
T ss_pred             CCccCCCccccCccEEEECccccCcccC------eECCCCCcCCCC
Confidence            678888888753 455666777777775      588888888754

>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=89.13  E-value=0.31  Score=26.74  Aligned_cols=39  Identities=21%  Similarity=0.456  Sum_probs=28.5

Q ss_pred             ccCCCCcccCCC-CeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          81 ICTHCNQELGTR-NFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        81 ~C~~C~~~l~~~-~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      +|..|+.++... ......++.|...||      +|..|++++.+.
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF------~C~~C~~~L~~~   46 (72)
T 1x4k_A            7 GCQECKKTIMPGTRKMEYKGSSWHETCF------ICHRCQQPIGTK   46 (72)
T ss_dssp             CBSSSCCCCCSSSCEEEETTEEEETTTT------CCSSSCCCCCSS
T ss_pred             CCccCCCcccCCceEEEECcCeecccCC------cccccCCccCCC
Confidence            678888888754 345567788877775      588888888654

>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=88.94  E-value=0.28  Score=26.91  Aligned_cols=40  Identities=15%  Similarity=0.251  Sum_probs=28.6

Q ss_pred             cccCCCCcccCCC-CeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          80 FICTHCNQELGTR-NFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        80 f~C~~C~~~l~~~-~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      -+|..|+.++... ......++.|...||      +|..|++++.+.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF------~C~~C~~~L~~~   46 (72)
T 1x61_A            6 SGCGGCGEDVVGDGAGVVALDRVFHVGCF------VCSTCRAQLRGQ   46 (72)
T ss_dssp             CCCSSSCSCCCSSSCCEECSSSEECTTTC------BCSSSCCBCTTS
T ss_pred             CCCccCCCccCCCceEEEECCCeEcccCC------cccccCCcCCcC
Confidence            3678888888653 344566778877775      588899888654

>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=88.87  E-value=0.31  Score=27.16  Aligned_cols=39  Identities=13%  Similarity=0.443  Sum_probs=27.8

Q ss_pred             ccCCCCcccCC---CCeeccCCcccCHHhhhhhcCCCCccCccccccC
Q psy2501          81 ICTHCNQELGT---RNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDV  125 (130)
Q Consensus        81 ~C~~C~~~l~~---~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~I~~~  125 (130)
                      +|..|+.++.+   ..+....++.|...||      +|..|+.++.+.
T Consensus         7 ~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF------~C~~C~~~L~~~   48 (76)
T 1x68_A            7 GCVACSKPISGLTGAKFICFQDSQWHSECF------NCGKCSVSLVGK   48 (76)
T ss_dssp             CCTTTCCCCCTTTTCCEEEETTEEEEGGGC------BCTTTCCBCSSS
T ss_pred             CCccCCCcccCCCCceeEEECCcccCcccC------ChhhCCCcCCCC
Confidence            56778888764   3555667788877775      688888887654

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

Probab=87.98  E-value=0.28  Score=27.31  Aligned_cols=9  Identities=22%  Similarity=0.885  Sum_probs=4.0

Q ss_pred             ccCCCCccc
Q psy2501          81 ICTHCNQEL   89 (130)
Q Consensus        81 ~C~~C~~~l   89 (130)
                      +|..|+..+
T Consensus        13 ~C~~C~~~I   21 (77)
T 1g47_A           13 TCERCKGGF   21 (77)
T ss_dssp             BCSSSCCBC
T ss_pred             CchhcCCcc
Confidence            344444444

>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=87.55  E-value=0.28  Score=30.38  Aligned_cols=19  Identities=32%  Similarity=0.490  Sum_probs=11.1

Q ss_pred             cCCCCccCccccccCc-eee
Q psy2501         111 FSPRCSYCNGPILDVS-IRN  129 (130)
Q Consensus       111 ~~~~C~~C~~~I~~~~-~~~  129 (130)
                      ++++|..|+++|.+.. |+|
T Consensus        60 ~~~~C~~C~~~I~~~~~v~a   79 (123)
T 2l4z_A           60 SWKRCAGCGGKIADRFLLYA   79 (123)
T ss_dssp             SCSBBSSSSSBCCSSSEEEE
T ss_pred             cCCcCcCCCCCcCCcEEEEe
Confidence            3456666666666553 554

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.04  E-value=2.1  Score=23.16  Aligned_cols=46  Identities=15%  Similarity=0.323  Sum_probs=31.1

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcC-----CCCccCccccccCc
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFS-----PRCSYCNGPILDVS  126 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~-----~~C~~C~~~I~~~~  126 (130)
                      +.|..|...+... ....=|..||..|..+.+.     ..|-.|.++|...-
T Consensus        21 ~~C~IC~~~~~~~-~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           21 VICPICLDILQKP-VTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CBCTTTCSBCSSE-EECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             CEeccCCcccCCe-EEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            5667777666532 2234567789999877663     37999999887543

---

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	130
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	3e-12
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	3e-11
d1u5sb1	31	g.39.1.3 (B:72-102) Pinch (particularly interestin	2e-10
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	5e-10
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	5e-04
d1b8ta4	49	g.39.1.3 (A:144-192) Cysteine-rich (intestinal) pr	7e-06
d1x3ha2	32	g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens)	4e-05
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	1e-04
d2d8za2	32	g.39.1.3 (A:33-64) Four and a half LIM domains pro	2e-04
d2cuqa1	32	g.39.1.3 (A:43-74) Four and a half LIM domains 3,	5e-04
d1x4ka1	32	g.39.1.3 (A:35-66) Four and a half LIM domains pro	0.001
d2d8xa2	26	g.39.1.3 (A:8-32) Pinch (particularly interesting	0.001
d1v6ga1	41	g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abL	0.001
d1u5sb2	35	g.39.1.3 (B:103-137) Pinch (particularly interesti	0.003

>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 = 54.7 bits (132), Expect = 3e-12
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113
           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 = 52.4 bits (126), Expect = 3e-11
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 56 CSSCDKPIVGQVITALGKTWHPEHF 80
          C+ C++ I G  + ALGK+WHPE F
Sbjct: 21 CAHCNQVIRGPFLVALGKSWHPEEF 45

>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 = 50.1 bits (120), Expect = 2e-10
 Identities = 13/24 (54%), Positives = 18/24 (75%)

Query: 56 CSSCDKPIVGQVITALGKTWHPEH 79
          C +C +PI G+V+ A+GK WH EH
Sbjct: 8  CGACRRPIEGRVVNAMGKQWHVEH 31

>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 = 49.3 bits (118), Expect = 5e-10
 Identities = 9/26 (34%), Positives = 16/26 (61%)

Query: 55 CCSSCDKPIVGQVITALGKTWHPEHF 80
           C  C++P++   ++A+   WHPE F
Sbjct: 10 KCGGCNRPVLENYLSAMDTVWHPECF 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 = 33.5 bits (77), Expect = 5e-04
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 106 DYHNLFSPRCSYCNGPILD 124
           D+  +FSP+C  CN P+L+
Sbjct: 2   DFLAMFSPKCGGCNRPVLE 20

>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 = 38.6 bits (90), Expect = 7e-06
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 82  CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRC 115
           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 = 36.3 bits (84), Expect = 4e-05
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 81  ICTHCNQELGTRNFFERDSRPYCEPDYHNL 110
           +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 = 35.4 bits (82), Expect = 1e-04
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 82  CTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNG 120
           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 = 34.7 bits (80), Expect = 2e-04
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 81  ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           +CT C ++L  + F  RD   YC   + +L++
Sbjct: 1   VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA 32

>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 = 33.6 bits (77), Expect = 5e-04
 Identities = 12/32 (37%), Positives = 16/32 (50%)

Query: 81  ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           +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 = 0.001
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 81  ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           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 = 0.001
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 56 CSSCDKPIVGQVITALGKTWHPEHF 80
          C  C + I+G+VI A+  +WHPE F
Sbjct: 1  CHQCGEFIIGRVIKAMNNSWHPECF 25

>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 = 32.5 bits (74), Expect = 0.001
 Identities = 14/24 (58%), Positives = 20/24 (83%)

Query: 55 CCSSCDKPIVGQVITALGKTWHPE 78
           C SCD+ I G+V++ALGKT+HP+
Sbjct: 17 RCFSCDQFIEGEVVSALGKTYHPD 40

>d1u5sb2 g.39.1.3 (B:103-137) 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 = 31.3 bits (71), Expect = 0.003
 Identities = 11/33 (33%), Positives = 15/33 (45%)

Query: 80  FICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
           F+C  C +       +ER    YCE  Y+ LF 
Sbjct: 1   FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 33

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	130
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.04
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.97
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.79
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.71
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.63
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.62
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.59
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.5
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.48
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.38
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.36
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.35
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.35
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.33
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.33
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.32
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.3
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.3
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.27
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.26
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.24
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.23
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.17
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.15
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.12
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.1
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.1
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.09
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.06
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.02
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.0
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.98
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.98
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.95
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.93
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.92
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.9
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.89
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.88
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.8
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.8
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.79
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.79
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.75
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.68
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.67
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.64
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.61
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.6
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.59
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.57
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.54
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.42
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.38
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.23
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.18
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.11
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.09
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.05
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.9
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.77
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.56
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.53
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	96.48
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.15
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.68
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	95.63
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.42
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	94.7
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.29
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	94.12
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	94.02
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	93.64
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	91.79
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	90.92
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	90.72
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	90.25
d2co8a1	33	Nedd9 interacting protein with calponin homology,	87.4

>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=99.04  E-value=7.3e-11  Score=57.12  Aligned_cols=34  Identities=26%  Similarity=0.772  Sum_probs=30.8

Q ss_pred             CCCCCCCccccccccccccceeeecCcccccCCc
Q psy2501          47 GVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        47 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      ++.....++|..|+++|.++.|+++++.||++||
T Consensus         2 DY~~~fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           2 DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             cHHHHhChhhhhcCCcccchheeecCCccCcccC
Confidence            3455678999999999999999999999999998

>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=98.97  E-value=1.2e-10  Score=56.21  Aligned_cols=34  Identities=41%  Similarity=1.004  Sum_probs=32.7

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP  113 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~  113 (130)
                      |+|..|+++|++..|+.++|++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7899999999999999999999999999999987

>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=98.79  E-value=5.6e-10  Score=53.89  Aligned_cols=25  Identities=36%  Similarity=0.894  Sum_probs=23.9

Q ss_pred             hhhhhcCCCCccCccccccCceeeC
Q psy2501         106 DYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus       106 ~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      +|.++|+++|..|+++|+|++|+||
T Consensus         2 DY~~~fapkC~~C~~~I~g~~v~Al   26 (35)
T d1x3ha1           2 DFLAMFSPKCGGCNRPVLENYLSAM   26 (35)
T ss_dssp             CCCCCCSCBCTTTCCBCCSSCEEET
T ss_pred             cHHHHhChhhhhcCCcccchheeec
Confidence            6889999999999999999999997

>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=98.71  E-value=4.3e-09  Score=52.67  Aligned_cols=30  Identities=43%  Similarity=1.030  Sum_probs=27.6

Q ss_pred             CCCccccccccccccceeeecCcccccCCc
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      ...++|+.|+++|.+..+.++|+.||+++|
T Consensus        16 ~r~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          16 KRTPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TCCCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CCCeeccccCCcccCceeeecCCccCcCCC
Confidence            345789999999999999999999999998

>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=98.63  E-value=1.5e-08  Score=51.97  Aligned_cols=41  Identities=22%  Similarity=0.515  Sum_probs=37.0

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCCCccCccc
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGP  121 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~C~~C~~~  121 (130)
                      +|..|++.|.....+.+++++||+.||.++|+|+....++.
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            58899999988888899999999999999999998887653

>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=98.59  E-value=9.6e-09  Score=48.57  Aligned_cols=28  Identities=36%  Similarity=0.961  Sum_probs=26.3

Q ss_pred             CccccccccccccceeeecCcccccCCc
Q psy2501          53 KGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        53 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      ..+|..|+++|.++++.+.|+.||+.||
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            3589999999999999999999999998

>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=98.50  E-value=4.3e-08  Score=48.59  Aligned_cols=34  Identities=29%  Similarity=0.800  Sum_probs=31.1

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR  114 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~  114 (130)
                      +|..|+..|+-+.|+..+|.+||++||.++|.++
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            6899999999889999999999999999999763

>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=98.48  E-value=5.4e-08  Score=45.03  Aligned_cols=32  Identities=31%  Similarity=0.800  Sum_probs=29.4

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      .|..|..+|++++|..+++++||-.||..+|+
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            47889999999999999999999999999875

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

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

Probab=98.38  E-value=1.3e-07  Score=44.39  Aligned_cols=33  Identities=21%  Similarity=0.448  Sum_probs=29.1

Q ss_pred             CCCCCCccccccccccccceeeecCcccccCCc
Q psy2501          48 VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        48 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      +...+..+|..|+++|....|...++.||.+||
T Consensus         3 yE~kfa~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           3 YENKFAPRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCSSCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             hHHHHHHHHhhcCCccccCceeecCCcchhhhC
Confidence            455678899999999987778999999999998

>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=98.36  E-value=6.5e-08  Score=44.26  Aligned_cols=28  Identities=43%  Similarity=0.984  Sum_probs=25.6

Q ss_pred             CCCccccccccccccceeeecCcccccC
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPE   78 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~   78 (130)
                      .+.++|+.|.++|.++.+.++++.||++
T Consensus         3 mg~p~C~~C~~PI~~~~vtAlgk~WHpE   30 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRVVNAMGKQWHVE   30 (31)
T ss_dssp             CCCCEETTTTEECCSCEECCTTSBEETT
T ss_pred             cCCcchhhcCCchhhhHhhhhccccCCC
Confidence            3568999999999999999999999986

>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=98.35  E-value=1.7e-07  Score=43.32  Aligned_cols=34  Identities=32%  Similarity=0.879  Sum_probs=31.6

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhhhcCC
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP  113 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~  113 (130)
                      |+|+.|.+++-+...|.+.|..||+.+|.++|+.
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            7899999999888999999999999999999864

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

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

Probab=98.35  E-value=1.5e-07  Score=42.97  Aligned_cols=32  Identities=38%  Similarity=0.896  Sum_probs=29.5

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      .|..|+.+|.+++|..++.++||-.||..+|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            48899999999999999999999999998874

>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=98.33  E-value=2e-07  Score=43.61  Aligned_cols=32  Identities=34%  Similarity=0.712  Sum_probs=27.8

Q ss_pred             CCCCCcccccccccc-ccceeeecCcccccCCc
Q psy2501          49 TTTQKGCCSSCDKPI-VGQVITALGKTWHPEHF   80 (130)
Q Consensus        49 ~~~~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf   80 (130)
                      ...+...|++|+..| .++.+.++++.||.+||
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            345567899999999 58999999999999998

>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=98.33  E-value=1.8e-07  Score=43.46  Aligned_cols=31  Identities=42%  Similarity=0.945  Sum_probs=28.3

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhc
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLF  111 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~  111 (130)
                      +|..|..++.++.|+..+|++||+.+|.++.
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhc
Confidence            4889999999999999999999999998764

>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=98.32  E-value=1.4e-07  Score=47.72  Aligned_cols=34  Identities=32%  Similarity=0.922  Sum_probs=31.3

Q ss_pred             ccCCCCcccCCCCeeccCCcccC-HHhhhhhcCCC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYC-EPDYHNLFSPR  114 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C-~~~~~~~~~~~  114 (130)
                      +|..|++.|..+....+++++|| +.||.++|+|+
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            58899999998899999999999 78999999985

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

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

Probab=98.30  E-value=1.5e-07  Score=46.05  Aligned_cols=26  Identities=27%  Similarity=0.531  Sum_probs=24.2

Q ss_pred             HhhhhhcCCCCccCccccccCceeeC
Q psy2501         105 PDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus       105 ~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      .+|+++|+.+|..|++.|+|++|+|+
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~V~~Ag   33 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGEVVSAL   33 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSCCEEET
T ss_pred             ccHHHHhCcccccccCEeeeeeeEec
Confidence            46999999999999999999999985

>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=98.30  E-value=6.5e-08  Score=45.64  Aligned_cols=25  Identities=32%  Similarity=0.651  Sum_probs=21.7

Q ss_pred             HhhhhhcCCCCccCccccccCceeeC
Q psy2501         105 PDYHNLFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus       105 ~~~~~~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      .||...+ ++|+.|+++|++++|+||
T Consensus         2 ~Cy~~tl-EkC~~C~~~I~driLrA~   26 (35)
T d2dloa1           2 GCYVATL-EKCATCSQPILDRILRAM   26 (35)
T ss_dssp             CCCCSSC-CBCTTTCCBCCSCCEEET
T ss_pred             hhHHHHH-HHHHHhchHHHHHHHHHh
Confidence            4676665 899999999999999997

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

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

Probab=98.27  E-value=3.3e-07  Score=41.96  Aligned_cols=32  Identities=31%  Similarity=0.762  Sum_probs=28.9

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      .|+.|+++|.+..|...+|.+||+.||.+.|+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            37899999999999999999999999988764

>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=98.26  E-value=2.3e-07  Score=41.49  Aligned_cols=30  Identities=27%  Similarity=0.738  Sum_probs=27.6

Q ss_pred             cccCCCCcccCCCCeeccCCcccCHHhhhh
Q psy2501          80 FICTHCNQELGTRNFFERDSRPYCEPDYHN  109 (130)
Q Consensus        80 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~  109 (130)
                      |+|..|++.|.......++|.+||+.||.+
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            789999999988888899999999999964

>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=98.24  E-value=4.8e-07  Score=43.56  Aligned_cols=33  Identities=33%  Similarity=0.634  Sum_probs=28.0

Q ss_pred             CCCCCCccccccccccc--cceeeecCcccccCCc
Q psy2501          48 VTTTQKGCCSSCDKPIV--GQVITALGKTWHPEHF   80 (130)
Q Consensus        48 ~~~~~~~~C~~C~~~i~--~~~~~~~~~~~H~~Cf   80 (130)
                      +...+..+|..|+++|.  ++.|++.++.||..||
T Consensus         3 y~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           3 TTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             cccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            34456789999999995  4679999999999998

>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=98.23  E-value=1.9e-07  Score=41.89  Aligned_cols=28  Identities=29%  Similarity=0.684  Sum_probs=25.1

Q ss_pred             Cccccccccccc-cceeeecCcccccCCc
Q psy2501          53 KGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      ++.|++|++.++ .+.+..+++.||..||
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            467999999997 6789999999999998

>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=98.17  E-value=5.1e-07  Score=41.09  Aligned_cols=31  Identities=39%  Similarity=0.936  Sum_probs=27.1

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      +|..|+..|. ++|..++|.+||+.+|...|+
T Consensus         1 kC~~C~~vL~-gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILT-GEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCS-SCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCcccc-ceeecCCCCcccHHHHHHhcC
Confidence            5888999886 478999999999999998875

>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=98.15  E-value=6.9e-07  Score=40.58  Aligned_cols=28  Identities=32%  Similarity=0.799  Sum_probs=24.9

Q ss_pred             Cccccccccccc-cceeeecCcccccCCc
Q psy2501          53 KGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        53 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      .++|.+|++.++ .+.+..+|+.||..|+
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            468999999996 7889999999999884

>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=98.12  E-value=7.2e-07  Score=48.06  Aligned_cols=34  Identities=21%  Similarity=0.645  Sum_probs=31.0

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcCCC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR  114 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~  114 (130)
                      .|..|.+.|..+....+++.+||+.||.++|+|+
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPk   34 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK   34 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCC
Confidence            3788999998888999999999999999999985

>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=98.10  E-value=8.8e-07  Score=40.62  Aligned_cols=32  Identities=34%  Similarity=0.870  Sum_probs=28.5

Q ss_pred             ccCCCCcccCCCCeeccCCcccCH-HhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCE-PDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~-~~~~~~~~  112 (130)
                      +|..|++.|..+..+.++|++||. +||..+|+
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            588999999988999999999995 79988874

>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=98.10  E-value=6.6e-07  Score=39.88  Aligned_cols=25  Identities=32%  Similarity=0.869  Sum_probs=22.2

Q ss_pred             ccccccccc----cceeeecCcccccCCc
Q psy2501          56 CSSCDKPIV----GQVITALGKTWHPEHF   80 (130)
Q Consensus        56 C~~C~~~i~----~~~~~~~~~~~H~~Cf   80 (130)
                      |..|.++|.    +.+++++++.||.+||
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            789999995    3679999999999998

>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=98.06  E-value=3.2e-07  Score=41.88  Aligned_cols=21  Identities=24%  Similarity=0.488  Sum_probs=18.9

Q ss_pred             hcCCCCccCccccccCceeeC
Q psy2501         110 LFSPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus       110 ~~~~~C~~C~~~I~~~~~~~~  130 (130)
                      ++.|+|++|.+||+|++|+||
T Consensus         3 mg~p~C~~C~~PI~~~~vtAl   23 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRVVNAM   23 (31)
T ss_dssp             CCCCEETTTTEECCSCEECCT
T ss_pred             cCCcchhhcCCchhhhHhhhh
Confidence            455899999999999999997

>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=98.02  E-value=1.1e-06  Score=40.05  Aligned_cols=27  Identities=22%  Similarity=0.636  Sum_probs=23.8

Q ss_pred             ccccccccccccce-eeecCcccccCCc
Q psy2501          54 GCCSSCDKPIVGQV-ITALGKTWHPEHF   80 (130)
Q Consensus        54 ~~C~~C~~~i~~~~-~~~~~~~~H~~Cf   80 (130)
                      ..|++|+.+|.+++ +.+.++.||..|.
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            47999999999877 6899999999884

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

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

Probab=98.00  E-value=1.4e-06  Score=42.53  Aligned_cols=33  Identities=42%  Similarity=0.731  Sum_probs=29.7

Q ss_pred             CCCCCCCccccccccccccceeeecCcccccCC
Q psy2501          47 GVTTTQKGCCSSCDKPIVGQVITALGKTWHPEH   79 (130)
Q Consensus        47 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~C   79 (130)
                      +|...++.+|..|++-|.++++.+.++.||++|
T Consensus         9 DYq~~fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           9 DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CGGGSCCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             cHHHHhCcccccccCEeeeeeeEecCcccCCCC
Confidence            455677889999999999999999999999987

>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=97.98  E-value=2.1e-06  Score=38.74  Aligned_cols=30  Identities=30%  Similarity=0.817  Sum_probs=27.2

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhh
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNL  110 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~  110 (130)
                      .|..|+..|.++.||..+++.||+.||...
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            478999999999999999999999999764

>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=97.95  E-value=1.6e-06  Score=43.24  Aligned_cols=29  Identities=24%  Similarity=0.729  Sum_probs=25.9

Q ss_pred             CCccccccccccc-cceeeecCcccccCCc
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      +..+|..|++.|+ .+.+.+.++.||..||
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            3478999999996 6788999999999998

>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=97.93  E-value=3.2e-06  Score=38.65  Aligned_cols=31  Identities=32%  Similarity=0.920  Sum_probs=28.7

Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      |..|..+++...|..+++..||-.||.+.|+
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            7889999998899999999999999999874

>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=97.92  E-value=2.8e-06  Score=38.56  Aligned_cols=26  Identities=23%  Similarity=0.648  Sum_probs=23.0

Q ss_pred             ccccccccccccce-eeecCcccccCC
Q psy2501          54 GCCSSCDKPIVGQV-ITALGKTWHPEH   79 (130)
Q Consensus        54 ~~C~~C~~~i~~~~-~~~~~~~~H~~C   79 (130)
                      ..|++|+++|.+++ +.+.++.||..|
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            46999999999876 689999999887

>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=97.90  E-value=2.2e-06  Score=38.08  Aligned_cols=25  Identities=40%  Similarity=0.922  Sum_probs=22.0

Q ss_pred             ccccccccc----cceeeecCcccccCCc
Q psy2501          56 CSSCDKPIV----GQVITALGKTWHPEHF   80 (130)
Q Consensus        56 C~~C~~~i~----~~~~~~~~~~~H~~Cf   80 (130)
                      |..|.++|.    ..+++++++.||.+||
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            788999995    3679999999999998

>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=4.7e-06  Score=39.52  Aligned_cols=30  Identities=20%  Similarity=0.448  Sum_probs=26.3

Q ss_pred             CCCccccccccccc-cceeeecCcccccCCc
Q psy2501          51 TQKGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        51 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      +...+|..|++.++ .+.+.+.|+.||..||
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            34568999999996 6889999999999998

>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=97.88  E-value=4.4e-06  Score=38.11  Aligned_cols=31  Identities=42%  Similarity=0.958  Sum_probs=28.6

Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      |..|.++++...|...++..||-.||.++|+
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            7889999998899999999999999999875

>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=97.80  E-value=7.1e-06  Score=36.86  Aligned_cols=29  Identities=28%  Similarity=0.744  Sum_probs=26.6

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhh
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHN  109 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~  109 (130)
                      .|..|++.|++.+|...+++.||-+||.+
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            48899999999999999999999999975

>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=97.80  E-value=5.3e-06  Score=38.29  Aligned_cols=29  Identities=28%  Similarity=0.614  Sum_probs=26.7

Q ss_pred             CCccccccccccccceeeecCcccccCCc
Q psy2501          52 QKGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        52 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      ..+.|.+|+..|.+.++.+.++.+|++||
T Consensus         7 klp~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           7 KLPMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             cCccccccCCCcEeEEEEeccccCCCCCC
Confidence            34789999999999999999999999997

>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=97.79  E-value=5.7e-06  Score=37.36  Aligned_cols=31  Identities=23%  Similarity=0.618  Sum_probs=27.6

Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      |-.|.+.|.....+.+++.+||+.||.++|+
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            6778999988888999999999999998874

>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=9.2e-06  Score=38.65  Aligned_cols=29  Identities=17%  Similarity=0.409  Sum_probs=25.7

Q ss_pred             CCccccccccccc-cceeeecCcccccCCc
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      ...+|..|++.++ -+.+.+.++.||..||
T Consensus         7 ~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           7 AGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             SSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            3468999999996 6788999999999998

>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=97.75  E-value=7.6e-06  Score=35.55  Aligned_cols=25  Identities=32%  Similarity=0.841  Sum_probs=22.1

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy2501          56 CSSCDKPIV--GQVITALGKTWHPEHF   80 (130)
Q Consensus        56 C~~C~~~i~--~~~~~~~~~~~H~~Cf   80 (130)
                      |..|.+.|.  .+.++..|.+||..||
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            778999996  4679999999999998

>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=97.68  E-value=9.3e-06  Score=39.90  Aligned_cols=29  Identities=41%  Similarity=0.718  Sum_probs=26.8

Q ss_pred             CCccccccccccccceeeecCcccccCCc
Q psy2501          52 QKGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        52 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      ..+.|.+|+..|.+.++.+.++.+|++||
T Consensus        17 kLP~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          17 RMPLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             SCCBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             cCccccccCCCcEEEEEEeccccCCCCCC
Confidence            34789999999999999999999999998

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

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

Probab=97.67  E-value=4.2e-06  Score=38.61  Aligned_cols=24  Identities=21%  Similarity=0.329  Sum_probs=22.6

Q ss_pred             hhhhhcCCCCccCccccccCceee
Q psy2501         106 DYHNLFSPRCSYCNGPILDVSIRN  129 (130)
Q Consensus       106 ~~~~~~~~~C~~C~~~I~~~~~~~  129 (130)
                      +|+.+|+..|..|++-|+|.+|+|
T Consensus         2 dYw~kfge~C~~C~~~itGpvMvA   25 (34)
T d1x6aa1           2 DYWGKFGEFCHGCSLLMTGPFMVA   25 (34)
T ss_dssp             CSSCCSSCBCTTTCCBCCSCCBCC
T ss_pred             cHHHHHHHHhhhhHhhcccceeee
Confidence            689999999999999999999987

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

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

Probab=97.64  E-value=9.8e-06  Score=40.22  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=17.8

Q ss_pred             CCCCccCccccccCceeeC
Q psy2501         112 SPRCSYCNGPILDVSIRNT  130 (130)
Q Consensus       112 ~~~C~~C~~~I~~~~~~~~  130 (130)
                      .|+|..|+++|.|++|+||
T Consensus        18 ~P~C~~C~~pI~g~~vtAl   36 (45)
T d2dara2          18 TPMCAHCNQVIRGPFLVAL   36 (45)
T ss_dssp             CCBBSSSCCBCCSCEEEET
T ss_pred             CeeccccCCcccCceeeec
Confidence            4899999999999999997

>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=97.61  E-value=1.4e-05  Score=34.63  Aligned_cols=25  Identities=32%  Similarity=0.868  Sum_probs=21.8

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy2501          56 CSSCDKPIV--GQVITALGKTWHPEHF   80 (130)
Q Consensus        56 C~~C~~~i~--~~~~~~~~~~~H~~Cf   80 (130)
                      |..|.+.|.  .+.++..|.+||..||
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            678999996  4678999999999998

>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=97.60  E-value=1e-05  Score=36.97  Aligned_cols=27  Identities=37%  Similarity=0.788  Sum_probs=23.4

Q ss_pred             ccccccccccc--cceeeecCcccccCCc
Q psy2501          54 GCCSSCDKPIV--GQVITALGKTWHPEHF   80 (130)
Q Consensus        54 ~~C~~C~~~i~--~~~~~~~~~~~H~~Cf   80 (130)
                      ..|.+|+..|.  +..+++.+..||..||
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            46999999994  5667899999999998

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

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

Probab=97.59  E-value=2.6e-05  Score=35.92  Aligned_cols=32  Identities=22%  Similarity=0.354  Sum_probs=28.5

Q ss_pred             CCCCCCccccccccccccceeeecCcccccCC
Q psy2501          48 VTTTQKGCCSSCDKPIVGQVITALGKTWHPEH   79 (130)
Q Consensus        48 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~C   79 (130)
                      +...++..|..|...|.+.++.+.+..||++|
T Consensus         3 Yw~kfge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           3 YWGKFGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             HHHHHHHHhhhhHhhcccceeeecccccCCCC
Confidence            45577889999999999999999999999998

>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=97.57  E-value=1.7e-05  Score=36.29  Aligned_cols=29  Identities=21%  Similarity=0.541  Sum_probs=25.5

Q ss_pred             CCccccccccccc-cceeeecCcccccCCc
Q psy2501          52 QKGCCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        52 ~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      ++.+|+.|.+.++ .+-+...+++||..||
T Consensus         6 gg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           6 GGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCceeccccceEeeeeeeeecCcccccccC
Confidence            4578999999995 6778999999999998

>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=97.54  E-value=1.1e-05  Score=37.63  Aligned_cols=25  Identities=32%  Similarity=0.772  Sum_probs=21.9

Q ss_pred             HhhhhhcCCCCccCccccccCceee
Q psy2501         105 PDYHNLFSPRCSYCNGPILDVSIRN  129 (130)
Q Consensus       105 ~~~~~~~~~~C~~C~~~I~~~~~~~  129 (130)
                      +||.++|+++|..|.++|+...|++
T Consensus         1 PCyE~kfa~~C~~Ckk~It~GGvtY   25 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQGGVTY   25 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSCCEES
T ss_pred             CchHHHHHHHHhhcCCccccCceee
Confidence            4799999999999999999777764

>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=97.42  E-value=4e-05  Score=33.21  Aligned_cols=26  Identities=19%  Similarity=0.625  Sum_probs=23.4

Q ss_pred             cccccccccc-cceeeecCcccccCCc
Q psy2501          55 CCSSCDKPIV-GQVITALGKTWHPEHF   80 (130)
Q Consensus        55 ~C~~C~~~i~-~~~~~~~~~~~H~~Cf   80 (130)
                      +|+.|.+.++ .+-+...+++||..||
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            6999999995 7778999999999997

>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=97.38  E-value=7.5e-05  Score=34.40  Aligned_cols=32  Identities=28%  Similarity=0.607  Sum_probs=27.7

Q ss_pred             ccCCCCcccCCCCee-ccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFF-ERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~-~~~~~~~C~~~~~~~~~  112 (130)
                      .|..|+..|.+..|. ...+++||-.+|.++|+
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            478899999888887 67899999999999885

>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=97.23  E-value=6.6e-05  Score=32.84  Aligned_cols=26  Identities=27%  Similarity=0.716  Sum_probs=22.4

Q ss_pred             ccccccccccc-cceeeecCcccccCC
Q psy2501          54 GCCSSCDKPIV-GQVITALGKTWHPEH   79 (130)
Q Consensus        54 ~~C~~C~~~i~-~~~~~~~~~~~H~~C   79 (130)
                      .+|.+|++.++ .+.+.-.|+.||..|
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            47999999996 677888899999887

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.18  E-value=7.3e-05  Score=34.27  Aligned_cols=32  Identities=28%  Similarity=0.720  Sum_probs=27.1

Q ss_pred             ccCCCCcccC--CCCeeccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELG--TRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      +|+-|+..|+  +...|.+.+.++|+.+|.++|+
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            5778888885  5578899999999999999885

>d2d8xa2 g.39.1.3 (A:8-32) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.11  E-value=0.00013  Score=31.06  Aligned_cols=16  Identities=25%  Similarity=0.555  Sum_probs=15.0

Q ss_pred             CccCccccccCceeeC
Q psy2501         115 CSYCNGPILDVSIRNT  130 (130)
Q Consensus       115 C~~C~~~I~~~~~~~~  130 (130)
                      |..|+++|.|++|+||
T Consensus         1 c~kcgefiigrvikam   16 (26)
T d2d8xa2           1 CHQCGEFIIGRVIKAM   16 (26)
T ss_dssp             CSSSCCBCCSCCEEET
T ss_pred             CCccccchhHHHHHHH
Confidence            7889999999999996

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.09  E-value=0.00018  Score=32.16  Aligned_cols=29  Identities=38%  Similarity=0.717  Sum_probs=25.6

Q ss_pred             CCCccccccccccccceeeecCcccccCC
Q psy2501          51 TQKGCCSSCDKPIVGQVITALGKTWHPEH   79 (130)
Q Consensus        51 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~C   79 (130)
                      ++..-|..|.+-|.+..+++.++.||+.|
T Consensus         3 sgssgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             CccchhhhhhhhhhhhhhhccccccCCCC
Confidence            34456999999999999999999999988

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.05  E-value=0.00024  Score=31.42  Aligned_cols=32  Identities=31%  Similarity=0.728  Sum_probs=28.1

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhhhcC
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFS  112 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~  112 (130)
                      .|+.|...++.+.|+..+..+||-.|...+|+
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            47889999998899999999999999887764

>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=96.90  E-value=0.0003  Score=30.19  Aligned_cols=25  Identities=32%  Similarity=0.772  Sum_probs=20.5

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy2501          56 CSSCDKPIV--GQVITALGKTWHPEHF   80 (130)
Q Consensus        56 C~~C~~~i~--~~~~~~~~~~~H~~Cf   80 (130)
                      |..|.++|-  ..-+...++.||..||
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            678999994  3447789999999998

>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=96.77  E-value=0.00058  Score=30.42  Aligned_cols=28  Identities=29%  Similarity=0.778  Sum_probs=24.6

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhh
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYH  108 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~  108 (130)
                      .|+.|+..|....++..++++||+.+..
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            4889999998888999999999998854

>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=96.56  E-value=0.00083  Score=30.65  Aligned_cols=31  Identities=16%  Similarity=0.495  Sum_probs=24.9

Q ss_pred             cccCCCCcccCCCC-ee-ccCCcccCHHhhhhh
Q psy2501          80 FICTHCNQELGTRN-FF-ERDSRPYCEPDYHNL  110 (130)
Q Consensus        80 f~C~~C~~~l~~~~-~~-~~~~~~~C~~~~~~~  110 (130)
                      |.|..|+.-++++. |+ ....++||..||.+.
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            77999999998775 44 556899999999763

>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=96.53  E-value=0.00069  Score=28.58  Aligned_cols=25  Identities=32%  Similarity=0.787  Sum_probs=21.1

Q ss_pred             ccccccccc--cceeeecCcccccCCc
Q psy2501          56 CSSCDKPIV--GQVITALGKTWHPEHF   80 (130)
Q Consensus        56 C~~C~~~i~--~~~~~~~~~~~H~~Cf   80 (130)
                      |+.|++.+.  +..+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            788999885  4558899999999997

>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=96.48  E-value=0.00092  Score=30.75  Aligned_cols=31  Identities=29%  Similarity=0.525  Sum_probs=27.0

Q ss_pred             CCCCccccccccccccceeeecCcccccCCc
Q psy2501          50 TTQKGCCSSCDKPIVGQVITALGKTWHPEHF   80 (130)
Q Consensus        50 ~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf   80 (130)
                      ..++.+|..|+..|.++-+.+.+..||+..|
T Consensus         5 glGk~vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           5 GLGKYICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCBCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             chhhHHHHHHHhhhhcCcceecCCCCCCCCC
Confidence            4577899999999988888999999999866

>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=96.15  E-value=0.00054  Score=30.58  Aligned_cols=29  Identities=28%  Similarity=0.706  Sum_probs=24.5

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhh
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHN  109 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~  109 (130)
                      .|+.|+..|....++..++++||+.+...
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            47889999987788999999999988643

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=95.68  E-value=0.0027  Score=28.39  Aligned_cols=27  Identities=26%  Similarity=0.599  Sum_probs=21.9

Q ss_pred             ccCCCCcccC-CCCeeccCCcccCHHhh
Q psy2501          81 ICTHCNQELG-TRNFFERDSRPYCEPDY  107 (130)
Q Consensus        81 ~C~~C~~~l~-~~~~~~~~~~~~C~~~~  107 (130)
                      .|+.|...|. +.+|...+|.+||+.+-
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            4788998884 55788999999998763

>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=95.63  E-value=0.0014  Score=31.07  Aligned_cols=19  Identities=26%  Similarity=0.361  Sum_probs=17.3

Q ss_pred             HhhhhhcCCCCccCccccc
Q psy2501         105 PDYHNLFSPRCSYCNGPIL  123 (130)
Q Consensus       105 ~~~~~~~~~~C~~C~~~I~  123 (130)
                      .||.+.++.+|..|.++|+
T Consensus         1 kCy~~~~a~~C~~C~k~I~   19 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIV   19 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCC
T ss_pred             CccccccCcccccCCCccC
Confidence            3788999999999999997

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.42  E-value=0.0026  Score=28.25  Aligned_cols=17  Identities=18%  Similarity=0.401  Sum_probs=15.1

Q ss_pred             CCCccCccccccCceee
Q psy2501         113 PRCSYCNGPILDVSIRN  129 (130)
Q Consensus       113 ~~C~~C~~~I~~~~~~~  129 (130)
                      .-|..|.+.|+|++|.|
T Consensus         6 sgC~~C~~~ItGkVLEA   22 (32)
T d1wiga1           6 SGCDSCEKYITGRVLEA   22 (32)
T ss_dssp             CSCSSSCCCCSSCCBCC
T ss_pred             chhhhhhhhhhhhhhhc
Confidence            36999999999999987

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.70  E-value=0.015  Score=25.54  Aligned_cols=28  Identities=21%  Similarity=0.564  Sum_probs=24.0

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhh
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYH  108 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~  108 (130)
                      +|..|-.+|....|...+++++|..|..
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            4788888998888999999999988854

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.29  E-value=0.02  Score=25.17  Aligned_cols=27  Identities=30%  Similarity=0.627  Sum_probs=20.8

Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhhhh
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDYHN  109 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~~~  109 (130)
                      |..|++.|.. .-....|.+||.+|..+
T Consensus         2 C~~Cgkelta-dArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKELTA-DARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBCCT-TCEEETTEEECHHHHHT
T ss_pred             ccccccccch-hHHHhcCCEEEEecccc
Confidence            7788888864 34577899999999754

>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=94.12  E-value=0.015  Score=26.51  Aligned_cols=27  Identities=15%  Similarity=0.544  Sum_probs=22.4

Q ss_pred             Cccccccccccc--cceeeecCcccccCC
Q psy2501          53 KGCCSSCDKPIV--GQVITALGKTWHPEH   79 (130)
Q Consensus        53 ~~~C~~C~~~i~--~~~~~~~~~~~H~~C   79 (130)
                      .-.|.+|+....  ..++...|..||..|
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            457999999884  567889999999877

>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=94.02  E-value=0.03  Score=24.82  Aligned_cols=30  Identities=33%  Similarity=0.730  Sum_probs=22.8

Q ss_pred             ccCCCCcccC--CCCeeccCCcccCHHhhhhh
Q psy2501          81 ICTHCNQELG--TRNFFERDSRPYCEPDYHNL  110 (130)
Q Consensus        81 ~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~~  110 (130)
                      +|.-|+..|+  +...|...+.++|+.+|.++
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlRl   33 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   33 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhcC
Confidence            5677777776  33567888999999999763

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

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

Probab=93.64  E-value=0.036  Score=24.52  Aligned_cols=29  Identities=24%  Similarity=0.571  Sum_probs=25.4

Q ss_pred             ccCCCCcccCCCCeeccCCcccCHHhhhh
Q psy2501          81 ICTHCNQELGTRNFFERDSRPYCEPDYHN  109 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~~~~~~~~C~~~~~~  109 (130)
                      +|..|...|.+..|.--.|+.+|.+|..+
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            57889999999999988899999999765

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=91.79  E-value=0.039  Score=24.47  Aligned_cols=26  Identities=19%  Similarity=0.588  Sum_probs=20.7

Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhh
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDY  107 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~  107 (130)
                      |..|+-+|.+..|...+..++|..|-
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            67788888888888888888887773

>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=90.92  E-value=0.12  Score=29.13  Aligned_cols=25  Identities=16%  Similarity=0.490  Sum_probs=14.9

Q ss_pred             CcccCHHhhhhhcCCCCccCccccc
Q psy2501          99 SRPYCEPDYHNLFSPRCSYCNGPIL  123 (130)
Q Consensus        99 ~~~~C~~~~~~~~~~~C~~C~~~I~  123 (130)
                      |..||..|..+.+...|-.|..++.
T Consensus        42 gH~fC~~Ci~~~~~~~CP~Cr~~~~   66 (97)
T d1jm7b_          42 EHIFCSNCVSDCIGTGCPVCYTPAW   66 (97)
T ss_dssp             SCCBCTTTGGGGTTTBCSSSCCBCS
T ss_pred             CCchhHHHHHHHHhccccccCCcCc
Confidence            4555666655555556777776654

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=90.72  E-value=0.11  Score=22.20  Aligned_cols=26  Identities=23%  Similarity=0.483  Sum_probs=21.0

Q ss_pred             cCCCCcccCCCCeeccCCcccCHHhh
Q psy2501          82 CTHCNQELGTRNFFERDSRPYCEPDY  107 (130)
Q Consensus        82 C~~C~~~l~~~~~~~~~~~~~C~~~~  107 (130)
                      |..|+-+|.+..|......++|.+|-
T Consensus         2 c~kcsvslvgrgflterddilc~dcg   27 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCG   27 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccC
Confidence            66788888888888777788898884

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=90.25  E-value=0.05  Score=25.60  Aligned_cols=26  Identities=23%  Similarity=0.554  Sum_probs=17.4

Q ss_pred             ccccccccc-cce-eeecCcccccCCcc
Q psy2501          56 CSSCDKPIV-GQV-ITALGKTWHPEHFI   81 (130)
Q Consensus        56 C~~C~~~i~-~~~-~~~~~~~~H~~Cf~   81 (130)
                      |.+|+.... ++- ..-.+..||+.|-.
T Consensus         2 C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           2 CVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             cchhhccccccceeeecCCceeCCcccc
Confidence            788888884 332 23456779998854

>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=87.40  E-value=0.14  Score=22.64  Aligned_cols=27  Identities=22%  Similarity=0.475  Sum_probs=19.7

Q ss_pred             ccCCCCcccCCCCee--ccCCcccCHHhh
Q psy2501          81 ICTHCNQELGTRNFF--ERDSRPYCEPDY  107 (130)
Q Consensus        81 ~C~~C~~~l~~~~~~--~~~~~~~C~~~~  107 (130)
                      +|..|...|.-+.|.  ..+|.+||..+.
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hl   29 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHL   29 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeecc
Confidence            477888888655554  778899997664