Psyllid ID: psy14580

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------15
Protein Sequence
MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKAVAYFCLIRPLCFQNV
Secondary Structure (PSIPRED)
ccccccccccccccEEEEEcccccccccccccccccccEEEEEEEEcccccccccEEEccccHHHHHHHHHcccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccEEEEEccccccccccccHcccccEEEEEEcccccccccccccccHHHHHHHHHHccccccccccHHHcccHHHccHHHHHHHHHHHHHHHHHccccccccHcccccccHHcccccHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
msdkeepnpeddknfwvdraktgrsgckkckqkiDTGTVRIAKmgynpfgsgkmkqwHHIDCILEVFKKQRQTTAKIEvvddmggwddltpedqEEVLSRFpeslresnkdrdvperkipsssekksktpkkKAVAYFCLIrplcfqnv
Flexible Loop (DISEMBL)
msdkeepnpeddknfwvdraktgrsgckkckqkidtgtvriAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIevvddmggwddLTPEDQEEVLSrfpeslresnkdrdvperkipsssekksktpkkkaVAYFCLIRPLCFQNV
Low Complexity Region (SEG)
MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERkipsssekksktpkkkAVAYFCLIRPLCFQNV
Disordered region (IsUnstruct)
**************FWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWD**********************************************AVAYFCLIRPLCF***
Disordered Region (DISOPRED)
***************WVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSR****************************************IRPLCFQ**
Disordered Region (DISEMBL)
***********DKNFWVDRAK**********QKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQ**************************************KAVAYFCLIRPLCFQNV
Disordered Region (DISPRO)
***********DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRES********************TPKKKAVAYFCLIRPLCF***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKTPKKKAVAYFCLIRPLCFQNV
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	149	2.2.26 [Sep-21-2011]
P49916	1009	DNA ligase 3 OS=Homo sapi	yes	N/A	0.718	0.106	0.385	3e-17
P97386	1015	DNA ligase 3 OS=Mus muscu	yes	N/A	0.610	0.089	0.430	5e-16
Q11208	996	Poly [ADP-ribose] polymer	N/A	N/A	0.536	0.080	0.386	3e-09
P26446	1011	Poly [ADP-ribose] polymer	no	N/A	0.523	0.077	0.372	6e-08
P09874	1014	Poly [ADP-ribose] polymer	no	N/A	0.536	0.078	0.325	2e-07
P18493	1016	Poly [ADP-ribose] polymer	no	N/A	0.510	0.074	0.350	2e-07
P27008	1014	Poly [ADP-ribose] polymer	no	N/A	0.536	0.078	0.313	3e-07
Q9R152	1013	Poly [ADP-ribose] polymer	no	N/A	0.536	0.078	0.313	3e-07
P35875	994	Poly [ADP-ribose] polymer	yes	N/A	0.577	0.086	0.322	4e-07
P11103	1013	Poly [ADP-ribose] polymer	no	N/A	0.536	0.078	0.302	1e-06

>sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2

 Score = 87.4 bits (215), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 70/127 (55%), Gaps = 20/127 (15%)

Query: 12  DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKK 69
           ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct: 90  EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 149

Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKT 129
            R TT KIE + ++ GW++L   ++E++                   + I   S K + T
Sbjct: 150 ARATTKKIEDLTELEGWEELEDNEKEQI------------------TQHIADLSSKAAGT 191

Query: 130 PKKKAVA 136
           PKKKAV 
Sbjct: 192 PKKKAVV 198

Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 5EC: .EC: 1EC: .EC: 1

>sp|P97386|DNLI3_MOUSE DNA ligase 3 OS=Mus musculus GN=Lig3 PE=1 SV=2

 Score = 83.2 bits (204), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/93 (43%), Positives = 59/93 (63%), Gaps = 2/93 (2%)

Query: 7   PNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCIL 64
           P    ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ 
Sbjct: 86  PCAMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMF 145

Query: 65  EVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
           E  ++ R TT KIE + ++ GW++L   ++E++
Sbjct: 146 EKLERARATTKKIEDLTELEGWEELEDNEKEQI 178

The alpha isoform interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. The beta isoform does not interact with XRCC1 and may be specifically involved in the completion of homologous recombination events that occur during meiotic prophase.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

>sp|Q11208|PARP_SARPE Poly [ADP-ribose] polymerase OS=Sarcophaga peregrina PE=1 SV=1

 Score = 60.8 bits (146), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 49/88 (55%), Gaps = 8/88 (9%)

Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
          E D  F V+ +K+ R+ CK CK KI+ G +RIA M  + F  GK   W H  C    F+K
Sbjct: 2  EIDLPFKVEYSKSSRASCKGCKNKIEAGILRIAAMVQSAFHDGKQPNWFHEQCF---FQK 58

Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
          QR T+A      D+  ++++  EDQE +
Sbjct: 59 QRPTSA-----GDIENFENIRFEDQERI 81

Poly[ADP-ribose] polymerase modifies various nuclear proteins by poly(ADP-ribosyl)ation. The modification is dependent on DNA and is involved in the regulation of various important cellular processes such as differentiation, proliferation, and tumor transformation and also in the regulation of the molecular events involved in the recovery of cell from DNA damage.

Sarcophaga peregrina (taxid: 7386)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|P26446|PARP1_CHICK Poly [ADP-ribose] polymerase 1 OS=Gallus gallus GN=PARP1 PE=1 SV=2

 Score = 56.2 bits (134), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 49/86 (56%), Gaps = 8/86 (9%)

Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          DK +  + AK+GR+ CKKC + I   ++R+A M  +P   GK+  WHH  C    F K+ 
Sbjct: 6  DKPYRAEYAKSGRASCKKCGESIAKDSLRLALMVQSPMFDGKVPHWHHYSC----FWKR- 60

Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
             A+I    D+ G+ +L  EDQE++
Sbjct: 61 ---ARIVSHTDIDGFPELRWEDQEKI 83

Poly[ADP-ribose] polymerase modifies various nuclear proteins by poly(ADP-ribosyl)ation. The modification is dependent on DNA and is involved in the regulation of various important cellular processes such as differentiation, proliferation, and tumor transformation and also in the regulation of the molecular events involved in the recovery of cell from DNA damage.

Gallus gallus (taxid: 9031)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|P09874|PARP1_HUMAN Poly [ADP-ribose] polymerase 1 OS=Homo sapiens GN=PARP1 PE=1 SV=4

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 6/86 (6%)

Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V    R
Sbjct: 6  DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIR 65

Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
              +++      G+ +L  +DQ++V
Sbjct: 66 HPDVEVD------GFSELRWDDQQKV 85

Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|P18493|PARP1_BOVIN Poly [ADP-ribose] polymerase 1 OS=Bos taurus GN=PARP1 PE=2 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          DK + V+ AK+GR+ CKKCK+ I   ++R+A M  +P   GK+  W+H+ C  +V     
Sbjct: 6  DKLYRVEYAKSGRASCKKCKESIPKDSIRMAFMVESPMFDGKIPHWYHLSCFWKVGFSIW 65

Query: 72 QTTAKIEVVDDMGGWDD 88
              ++E   ++  WDD
Sbjct: 66 HPDVEVEGFSEL-RWDD 81

Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.

Bos taurus (taxid: 9913)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|P27008|PARP1_RAT Poly [ADP-ribose] polymerase 1 OS=Rattus norvegicus GN=Parp1 PE=1 SV=4

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 49/86 (56%), Gaps = 6/86 (6%)

Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          ++ + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V    R
Sbjct: 6  ERLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIR 65

Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
          Q   +++      G+ +L  +DQ++V
Sbjct: 66 QPDTEVD------GFSELRWDDQQKV 85

Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|Q9R152|PARP1_CRIGR Poly [ADP-ribose] polymerase 1 OS=Cricetulus griseus GN=PARP1 PE=2 SV=3

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 49/86 (56%), Gaps = 6/86 (6%)

Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          ++ + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V    R
Sbjct: 6  ERLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIR 65

Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
          Q   +++      G+ +L  +DQ++V
Sbjct: 66 QPDVEVD------GFSELRWDDQQKV 85

Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.

Cricetulus griseus (taxid: 10029)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|P35875|PARP_DROME Poly [ADP-ribose] polymerase OS=Drosophila melanogaster GN=Parp PE=2 SV=1

 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/93 (32%), Positives = 47/93 (50%), Gaps = 7/93 (7%)

Query: 13  KNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNP---FGSGKMKQWHHIDCILEVFKK 69
           K+F ++ AK+ RS C+ C+QKI+   VR+ K  Y+       G    WHH++C    F +
Sbjct: 109 KDFGIEYAKSSRSTCRGCEQKINKDLVRLRKTVYDTEVGMKYGGQPLWHHLEC----FAQ 164

Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFP 102
            R         +DM G+  L  +DQ +V +  P
Sbjct: 165 LRSELGWFASGEDMPGFQSLADDDQAKVKNAIP 197

Poly[ADP-ribose] polymerase modifies various nuclear proteins by poly(ADP-ribosyl)ation. The modification is dependent on DNA and is involved in the regulation of various important cellular processes such as differentiation, proliferation, and tumor transformation and also in the regulation of the molecular events involved in the recovery of cell from DNA damage. Plays a fundamental role in organizing chromatin on a global scale; isoform e autoregulates Parp transcription by influencing the chromatin structure of its heterochromatic environment.

Drosophila melanogaster (taxid: 7227)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

>sp|P11103|PARP1_MOUSE Poly [ADP-ribose] polymerase 1 OS=Mus musculus GN=Parp1 PE=1 SV=3

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 48/86 (55%), Gaps = 6/86 (6%)

Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          ++ + V  AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V +  R
Sbjct: 6  ERLYRVQYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGQSIR 65

Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
              +++      G+ +L  +DQ++V
Sbjct: 66 HPDVEVD------GFSELRWDDQQKV 85

Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production (By similarity). Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 4

EC: .

EC: 2

EC: .

EC: 3

EC: 0

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	149
242008936	927	DNA ligase, putative [Pediculus humanus	0.711	0.114	0.613	4e-33
193700124	875	PREDICTED: DNA ligase 3-like [Acyrthosip	0.704	0.12	0.504	7e-25
345489172	1031	PREDICTED: DNA ligase 3 [Nasonia vitripe	0.671	0.096	0.548	6e-23
350407883	1012	PREDICTED: DNA ligase 3-like [Bombus imp	0.872	0.128	0.418	1e-21
340721941	1013	PREDICTED: LOW QUALITY PROTEIN: DNA liga	0.671	0.098	0.519	2e-21
383847368	979	PREDICTED: DNA ligase 3 [Megachile rotun	0.664	0.101	0.519	6e-21
110761354	1009	PREDICTED: DNA ligase 3 [Apis mellifera]	0.731	0.108	0.448	2e-20
91076374	853	PREDICTED: similar to rCG33581 [Triboliu	0.798	0.139	0.456	3e-20
189234169	450	PREDICTED: similar to ligase III, DNA, A	0.651	0.215	0.494	4e-20
380019623	208	PREDICTED: DNA ligase 3-like, partial [A	0.597	0.427	0.533	6e-20

>gi|242008936|ref|XP_002425250.1| DNA ligase, putative [Pediculus humanus corporis] gi|212508998|gb|EEB12512.1| DNA ligase, putative [Pediculus humanus corporis]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 65/106 (61%), Positives = 82/106 (77%)

Query: 1   MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHI 60
           MSDKE+     +K F VDRAKTGR+GCKKCKQKI  G +R+AK+ YNPFG+G +KQWHHI
Sbjct: 1   MSDKEDEEQPSEKPFHVDRAKTGRAGCKKCKQKISQGELRMAKLAYNPFGTGTIKQWHHI 60

Query: 61  DCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLR 106
            CI +VFKKQR TT KIE  D++GGWD+L   DQ+E+++ FP  L+
Sbjct: 61  QCIFDVFKKQRATTKKIEHPDEIGGWDNLNENDQQEIINYFPPELQ 106

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193700124|ref|XP_001943689.1| PREDICTED: DNA ligase 3-like [Acyrthosiphon pisum]

 Score =  118 bits (296), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 53/105 (50%), Positives = 72/105 (68%)

Query: 9   PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFK 68
           P +DK F  +++K+ R+ CKKCK+ ++ G +RIAK+  NPFG GKM  WHH  C++ VF 
Sbjct: 4   PSEDKLFVAEKSKSNRAKCKKCKEVLNQGALRIAKVVANPFGDGKMMAWHHPQCLVTVFS 63

Query: 69  KQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
           KQR +TAKI  VDD+GGWD L+ E Q E+L  FP+  +E  K  D
Sbjct: 64  KQRASTAKITCVDDIGGWDGLSMEHQNEILMTFPDIPKEKLKTHD 108

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345489172|ref|XP_001601405.2| PREDICTED: DNA ligase 3 [Nasonia vitripennis]

 Score =  112 bits (279), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 57/104 (54%), Positives = 72/104 (69%), Gaps = 4/104 (3%)

Query: 1   MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHI 60
           MSD E+   ED+K F V+RAKTGR+ CKKCK  I+   VRIAK+  NPFG GKMK WHH+
Sbjct: 1   MSDGEQ---EDEKPFAVERAKTGRAKCKKCKCPIEKDQVRIAKLMANPFGEGKMKAWHHV 57

Query: 61  DCILEVFKKQRQTTAKIE-VVDDMGGWDDLTPEDQEEVLSRFPE 103
            C+ EVF +QR TT +IE   +D+ GWD L  ED++ VL +  E
Sbjct: 58  SCLFEVFSRQRATTKRIENPEEDISGWDSLCDEDKDVVLEKLGE 101

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350407883|ref|XP_003488227.1| PREDICTED: DNA ligase 3-like [Bombus impatiens]

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/148 (41%), Positives = 91/148 (61%), Gaps = 18/148 (12%)

Query: 1   MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHI 60
           MSD+E+   E++K F V+RAK+GR+ CKKCK  I+  TVRIAK+  NPF  GKMK WHH+
Sbjct: 3   MSDEEK---EEEKPFAVERAKSGRAKCKKCKCPIEKDTVRIAKLVANPFSDGKMKAWHHL 59

Query: 61  DCILEVFKKQRQTTAKI-EVVDDMGGWDDLTPEDQEEVLSRF-----------PESLRES 108
            C+ EVF +QR TT +I +  +D+ GW DL  ED+  +L R            P++ + +
Sbjct: 60  SCLFEVFARQRATTKRIDDPEEDVSGWQDLCDEDKTAILQRIEEFENSSPFKTPKTTQVA 119

Query: 109 NKDRDVPERKIPSSSEKK---SKTPKKK 133
           N+     +RK+  ++E     +K P+KK
Sbjct: 120 NQSSGSKKRKLTRTTESDPSPNKKPRKK 147

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721941|ref|XP_003399371.1| PREDICTED: LOW QUALITY PROTEIN: DNA ligase 3-like [Bombus terrestris]

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 54/104 (51%), Positives = 72/104 (69%), Gaps = 4/104 (3%)

Query: 1   MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHI 60
           MSD+E+   E++K F V+RAK+GR+ CKKCK  I+  TVRIAK+  NPF  GKMK WHH+
Sbjct: 3   MSDEEK---EEEKPFAVERAKSGRAKCKKCKCPIEKDTVRIAKLVANPFSDGKMKAWHHL 59

Query: 61  DCILEVFKKQRQTTAKI-EVVDDMGGWDDLTPEDQEEVLSRFPE 103
            C+ EVF +QR TT +I +  +D+ GW DL  ED+  +L R  E
Sbjct: 60  SCLFEVFARQRATTKRIDDPEEDVSGWQDLCDEDKTAILQRIEE 103

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847368|ref|XP_003699326.1| PREDICTED: DNA ligase 3 [Megachile rotundata]

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 54/104 (51%), Positives = 72/104 (69%), Gaps = 5/104 (4%)

Query: 1   MSDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHI 60
           MSD E+    ++K F V+RAK+GR+ CKKCK  I+  TVRIAK+  NPF  GKMK WHH+
Sbjct: 71  MSDDEK----EEKPFAVERAKSGRAKCKKCKCPIEKDTVRIAKLMANPFAEGKMKAWHHL 126

Query: 61  DCILEVFKKQRQTTAKIE-VVDDMGGWDDLTPEDQEEVLSRFPE 103
            C+ EVF KQR TT +IE   +D+ GW++L  ED++ VL +  E
Sbjct: 127 SCLFEVFAKQRATTKRIEDPEEDVSGWEELDEEDKKTVLQKLEE 170

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110761354|ref|XP_396537.3| PREDICTED: DNA ligase 3 [Apis mellifera]

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 57/127 (44%), Positives = 78/127 (61%), Gaps = 18/127 (14%)

Query: 10  EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
           +++K F V+RAK+GR+ CKKCK  I+  TVRIAK+  NPF  GKMK WHH+ C+ EVF K
Sbjct: 4   DEEKPFAVERAKSGRAKCKKCKCPIEKDTVRIAKLVANPFTDGKMKAWHHLTCLFEVFAK 63

Query: 70  QRQTTAKI-EVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSK 128
           QR +T +I +  +D+ GW+DL+ ED+  VL    E  ++S                 K+ 
Sbjct: 64  QRASTKRIDDPAEDVSGWEDLSKEDRAIVLRMIEEFEKDS-----------------KNH 106

Query: 129 TPKKKAV 135
           TPK KAV
Sbjct: 107 TPKGKAV 113

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91076374|ref|XP_967954.1| PREDICTED: similar to rCG33581 [Tribolium castaneum] gi|270002897|gb|EEZ99344.1| ligase III [Tribolium castaneum]

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 58/127 (45%), Positives = 77/127 (60%), Gaps = 8/127 (6%)

Query: 12  DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
           +K F V+ AK GR+ CKKCKQK   G +RIAK+  NPFG GKMK WHH++C+ EVF KQR
Sbjct: 7   EKPFLVEVAKQGRAVCKKCKQKCAQGELRIAKLVANPFGEGKMKNWHHVNCLFEVFLKQR 66

Query: 72  QTTAKI-EVVDDMGGWDDLTPEDQEEVLSRFPE--SLRESNKD-----RDVPERKIPSSS 123
            TT +I + V+D+ GW  L  E + ++L R  E  S  E+        +  P+   PS+S
Sbjct: 67  PTTKRIDDPVEDIDGWVLLDDEQKSDILKRVEECNSFFETKHGVKPSPKKTPQEAKPSTS 126

Query: 124 EKKSKTP 130
            K S  P
Sbjct: 127 SKDSSGP 133

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234169|ref|XP_001809442.1| PREDICTED: similar to ligase III, DNA, ATP-dependent [Tribolium castaneum] gi|270002458|gb|EEZ98905.1| hypothetical protein TcasGA2_TC004521 [Tribolium castaneum]

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 48/97 (49%), Positives = 66/97 (68%)

Query: 11  DDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQ 70
           ++K F V+ A+ GR+ CKKC+QK   G +RIAK+  NP GSGKMK W+H+ CI E F KQ
Sbjct: 2   EEKPFAVEVARQGRALCKKCRQKCVQGDLRIAKLIPNPLGSGKMKTWYHVSCIFETFLKQ 61

Query: 71  RQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRE 107
           RQTT +IE   D+ GW+ L P+D+  +L +  +  RE
Sbjct: 62  RQTTKRIEGPLDIDGWESLDPDDKVNILEKISQCNRE 98

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019623|ref|XP_003693702.1| PREDICTED: DNA ligase 3-like, partial [Apis florea]

 Score =  102 bits (253), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 48/90 (53%), Positives = 65/90 (72%), Gaps = 1/90 (1%)

Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
          +++K F V+RAK+GR+ CKKCK  I+  TVRIAK+  NPF  GKMK WHH+ C+ EVF +
Sbjct: 4  DEEKPFAVERAKSGRAKCKKCKCPIEKDTVRIAKLVANPFTDGKMKAWHHLTCLFEVFAR 63

Query: 70 QRQTTAKI-EVVDDMGGWDDLTPEDQEEVL 98
          QR TT +I +   D+ GW+DL+ ED+  VL
Sbjct: 64 QRATTKRIDDPAVDVSGWEDLSEEDKATVL 93

Source: Apis florea

Species: Apis florea

Genus: Apis

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	149
UNIPROTKB|K7ENR9	207	LIG3 "DNA ligase 3" [Homo sapi	0.691	0.497	0.388	9.5e-18
ZFIN|ZDB-GENE-030131-8453	752	lig3 "ligase III, DNA, ATP-dep	0.657	0.130	0.41	6.3e-17
UNIPROTKB|K7ERZ5	545	LIG3 "DNA ligase 3" [Homo sapi	0.691	0.188	0.388	7.2e-17
UNIPROTKB|I3LN18	502	LIG3 "Uncharacterized protein"	0.691	0.205	0.388	7.7e-17
UNIPROTKB|F1P394	900	LIG3 "DNA ligase" [Gallus gall	0.597	0.098	0.434	1.1e-16
UNIPROTKB|F1MQY1	943	LIG3 "DNA ligase" [Bos taurus	0.691	0.109	0.416	1.1e-16
UNIPROTKB|P49916	1009	LIG3 "DNA ligase 3" [Homo sapi	0.691	0.102	0.388	2e-16
RGD|1309875	943	Lig3 "ligase III, DNA, ATP-dep	0.577	0.091	0.443	2.4e-16
UNIPROTKB|D4A2K2	955	Lig3 "DNA ligase" [Rattus norv	0.577	0.090	0.443	2.4e-16
UNIPROTKB|D4A837	1014	Lig3 "DNA ligase" [Rattus norv	0.577	0.084	0.443	2.6e-16

UNIPROTKB|K7ENR9 LIG3 "DNA ligase 3" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 42/108 (38%), Positives = 65/108 (60%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:     3 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 62

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPER 117
              R TT KIE + ++ GW++L   ++E++     +    S+K    P++
Sbjct:    63 ARATTKKIEDLTELEGWEELEDNEKEQITQHIADL---SSKAAGTPKK 107

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-030131-8453 lig3 "ligase III, DNA, ATP-dependent" [Danio rerio (taxid:7955)]

 Score = 219 (82.2 bits), Expect = 6.3e-17, P = 6.3e-17
 Identities = 41/100 (41%), Positives = 63/100 (63%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKK 69
             ++ + V+ AK G +GCKKCK KI  G VRI K+  NPF   +G+MK+W+H+ CI E  ++
Sbjct:     3 EQRYCVEYAKRGTAGCKKCKDKIMKGLVRIGKIVPNPFSESAGEMKEWYHVKCIFEKLER 62

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESN 109
              R TT KIE + ++ GW++L  ED++ +     E   + N
Sbjct:    63 ARATTKKIEDITELEGWEELQDEDKDLINKHVSELAAKVN 102

GO:0003677 "DNA binding" evidence=IEA

GO:0003909 "DNA ligase activity" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|K7ERZ5 LIG3 "DNA ligase 3" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 7.2e-17, P = 7.2e-17
 Identities = 42/108 (38%), Positives = 65/108 (60%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    99 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 158

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPER 117
              R TT KIE + ++ GW++L   ++E++     +    S+K    P++
Sbjct:   159 ARATTKKIEDLTELEGWEELEDNEKEQITQHIADL---SSKAAGTPKK 203

GO:0003677 "DNA binding" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

UNIPROTKB|I3LN18 LIG3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 215 (80.7 bits), Expect = 7.7e-17, P = 7.7e-17
 Identities = 42/108 (38%), Positives = 65/108 (60%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    90 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 149

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPER 117
              R TT KIE + ++ GW++L   ++E++     +    S+K    P++
Sbjct:   150 ARATTKKIEDLTELEGWEELEDPEKEQISQHIADL---SSKAASTPKK 194

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1P394 LIG3 "DNA ligase" [Gallus gallus (taxid:9031)]

 Score = 218 (81.8 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 40/92 (43%), Positives = 62/92 (67%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPF--GSGKMKQWHHIDCILEVFKK 69
             ++ + VD AK G +GCKKCK+KI  G VRI K+  NPF    G MK+W+H+ C+ E  +K
Sbjct:     3 EQRYCVDYAKRGTAGCKKCKEKIVKGMVRIGKIVPNPFTESGGDMKEWYHVKCMFEKLEK 62

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRF 101
              R +T KIE + D+ GW++L  + ++E+++ F
Sbjct:    63 ARASTKKIEDITDLEGWEELQ-DGEKELITNF 93

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0000795 "synaptonemal complex" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA

GO:0043504 "mitochondrial DNA repair" evidence=IEA

GO:0045910 "negative regulation of DNA recombination" evidence=IEA

UNIPROTKB|F1MQY1 LIG3 "DNA ligase" [Bos taurus (taxid:9913)]

 Score = 218 (81.8 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 45/108 (41%), Positives = 68/108 (62%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    89 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 148

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPER 117
              R TT KIE + ++ GW++L  E+++E +S+    L  S+K    P++
Sbjct:   149 ARATTKKIEDLTELEGWEELE-ENEKEQISQHIADL--SSKATSTPKK 193

GO:0045910 "negative regulation of DNA recombination" evidence=IEA

GO:0043504 "mitochondrial DNA repair" evidence=IEA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0000795 "synaptonemal complex" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P49916 LIG3 "DNA ligase 3" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 2.0e-16, P = 2.0e-16
 Identities = 42/108 (38%), Positives = 65/108 (60%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    90 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 149

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPER 117
              R TT KIE + ++ GW++L   ++E++     +    S+K    P++
Sbjct:   150 ARATTKKIEDLTELEGWEELEDNEKEQITQHIADL---SSKAAGTPKK 194

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000795 "synaptonemal complex" evidence=IEA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA

GO:0043504 "mitochondrial DNA repair" evidence=IEA

GO:0045910 "negative regulation of DNA recombination" evidence=IEA

GO:0003909 "DNA ligase activity" evidence=IDA

GO:0003910 "DNA ligase (ATP) activity" evidence=IBA

GO:0005694 "chromosome" evidence=IBA

GO:0005739 "mitochondrion" evidence=IBA

GO:0006273 "lagging strand elongation" evidence=IBA

GO:0006289 "nucleotide-excision repair" evidence=IBA

GO:0005515 "protein binding" evidence=IPI

GO:0033151 "V(D)J recombination" evidence=IDA

GO:0007131 "reciprocal meiotic recombination" evidence=TAS

GO:0007283 "spermatogenesis" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006284 "base-excision repair" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

RGD|1309875 Lig3 "ligase III, DNA, ATP-dependent" [Rattus norvegicus (taxid:10116)]

 Score = 215 (80.7 bits), Expect = 2.4e-16, P = 2.4e-16
 Identities = 39/88 (44%), Positives = 58/88 (65%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    91 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 150

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
              R TT KIE + ++ GW++L   ++E++
Sbjct:   151 ARATTKKIEDLTELEGWEELEDNEKEQI 178

GO:0000794 "condensed nuclear chromosome" evidence=ISO

GO:0000795 "synaptonemal complex" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0003909 "DNA ligase activity" evidence=ISO

GO:0003910 "DNA ligase (ATP) activity" evidence=IBA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO;IBA

GO:0005694 "chromosome" evidence=IBA

GO:0005739 "mitochondrion" evidence=IBA

GO:0006266 "DNA ligation" evidence=IBA

GO:0006273 "lagging strand elongation" evidence=IBA

GO:0006289 "nucleotide-excision repair" evidence=IBA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA;ISO

GO:0006310 "DNA recombination" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043504 "mitochondrial DNA repair" evidence=IEA;ISO

GO:0045910 "negative regulation of DNA recombination" evidence=IEA;ISO

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

GO:0033151 "V(D)J recombination" evidence=ISO

UNIPROTKB|D4A2K2 Lig3 "DNA ligase" [Rattus norvegicus (taxid:10116)]

 Score = 215 (80.7 bits), Expect = 2.4e-16, P = 2.4e-16
 Identities = 39/88 (44%), Positives = 58/88 (65%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    91 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 150

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
              R TT KIE + ++ GW++L   ++E++
Sbjct:   151 ARATTKKIEDLTELEGWEELEDNEKEQI 178

GO:0003677 "DNA binding" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

UNIPROTKB|D4A837 Lig3 "DNA ligase" [Rattus norvegicus (taxid:10116)]

 Score = 215 (80.7 bits), Expect = 2.6e-16, P = 2.6e-16
 Identities = 39/88 (44%), Positives = 58/88 (65%)

Query:    12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
             ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct:    91 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 150

Query:    70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
              R TT KIE + ++ GW++L   ++E++
Sbjct:   151 ARATTKKIEDLTELEGWEELEDNEKEQI 178

GO:0003677 "DNA binding" evidence=IEA

GO:0003910 "DNA ligase (ATP) activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	149
pfam00645	81	pfam00645, zf-PARP, Poly(ADP-ribose) polymerase an	2e-25
PLN03123	981	PLN03123, PLN03123, poly [ADP-ribose] polymerase;	6e-16
PLN03123	981	PLN03123, PLN03123, poly [ADP-ribose] polymerase;	7e-12

>gnl|CDD|189650 pfam00645, zf-PARP, Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

 Score = 92.0 bits (229), Expect = 2e-25
 Identities = 38/83 (45%), Positives = 53/83 (63%), Gaps = 4/83 (4%)

Query: 20  AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEV 79
           AK+GR+ CKKCK+KI  G +RI K+  +PF  GKMK+W+H  C  E   + R T    E 
Sbjct: 3   AKSGRASCKKCKEKIAKGELRIGKVVPSPFFDGKMKKWYHWGCFTEKRLRNRAT----ED 58

Query: 80  VDDMGGWDDLTPEDQEEVLSRFP 102
           VDD+ G+++L PEDQE++     
Sbjct: 59  VDDLDGFEELRPEDQEKIKKALE 81

Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor. Length = 81

>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional

 Score = 73.3 bits (180), Expect = 6e-16
 Identities = 39/122 (31%), Positives = 53/122 (43%), Gaps = 19/122 (15%)

Query: 20  AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEV 79
           AKT R+ C++C +KI  G VRI+          K   WHH  C LE+             
Sbjct: 112 AKTSRATCRRCSEKILKGEVRISSKPEGQ--GYKGLAWHHAKCFLEMSPSTP-------- 161

Query: 80  VDDMGGWDDLTPEDQEEVLS---RFPESLRESNKDRDVPE------RKIPSSSEKKSKTP 130
           V+ + GWD L+  DQE VL    + P   +E   +    E      RK  +S + KSK  
Sbjct: 162 VEKLSGWDTLSDSDQEAVLPLVKKSPSEAKEEKAEERKQESKKGAKRKKDASGDDKSKKA 221

Query: 131 KK 132
           K 
Sbjct: 222 KT 223

Length = 981

>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional

 Score = 61.3 bits (149), Expect = 7e-12
 Identities = 34/103 (33%), Positives = 50/103 (48%), Gaps = 8/103 (7%)

Query: 9   PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFK 68
               K +  + AK+ RS CK CK  ID   +R+ KM  +    G M  W+H  CI    K
Sbjct: 2   AAPPKPWKAEYAKSSRSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCI---LK 58

Query: 69  KQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKD 111
           K+ Q    I+ +DD+ G D L  EDQ++ + ++ ES       
Sbjct: 59  KKNQ----IKSIDDVEGIDSLRWEDQQK-IRKYVESGGTGTGT 96

Length = 981

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	149
PF00645	82	zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligas	99.96
KOG4437|consensus	482		99.92
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	99.9
PLN03123	981	poly [ADP-ribose] polymerase; Provisional	99.84
KOG1037|consensus	531		95.24
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	87.66
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	85.66

>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.96  E-value=1.7e-29  Score=175.51  Aligned_cols=82  Identities=39%  Similarity=0.775  Sum_probs=68.4

Q ss_pred             EEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCCCCHHHHHHH
Q psy14580         18 DRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEV   97 (149)
Q Consensus        18 EyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~~eDQ~~I   97 (149)
                      ||||||||+|++|+++|++|+||||.+++++.++|.++.|||+.||+......+..+   .++++|.||+.|+++||++|
T Consensus         1 EyAks~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~~~~~~~~~~~---~~~~~i~G~~~L~~~Dq~~i   77 (82)
T PF00645_consen    1 EYAKSGRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFFKKQLRNRETT---GDIEEIKGFDELKPEDQEKI   77 (82)
T ss_dssp             EE-SSSTEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHHHTTCCTTSST---SCGGGCETCCCS-HHHHHHH
T ss_pred             CcCCCCCccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccccchhhhcccC---CCHHHCCChHHCCHHHHHHH
Confidence            899999999999999999999999999999988889999999999987432211111   47899999999999999999


Q ss_pred             HHHch
Q psy14580         98 LSRFP  102 (149)
Q Consensus        98 ~~~~~  102 (149)
                      +++|+
T Consensus        78 ~~~i~   82 (82)
T PF00645_consen   78 RKLIE   82 (82)
T ss_dssp             HHHHS
T ss_pred             HHHhC
Confidence            99875

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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....

>KOG4437|consensus

Probab=99.92  E-value=6.1e-27  Score=200.83  Aligned_cols=132  Identities=33%  Similarity=0.646  Sum_probs=110.1

Q ss_pred             CCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCC--CCccceEEecCchhhHHHhhhhcccccCccCCCCCcC
Q psy14580         10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWD   87 (149)
Q Consensus        10 ~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~--~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~   87 (149)
                      |+..+|++.|||. .|+|++|+.+|.||.+|||.++++|+.  .|.|..|||.+|+|+.+.++|+||+.|+++++|+||+
T Consensus         1 ~A~~RFC~DYAKR-~A~C~KCK~~i~KGV~R~GKi~P~~~S~~~~DMK~~~H~~C~FE~L~rAR~TTK~I~~~~EiEG~E   79 (482)
T KOG4437|consen    1 MAEQRFCVDYAKR-TAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWE   79 (482)
T ss_pred             CCCchHHHHHHHH-hhhhHHHHHHHHHhhhhhccccCCCcccCCchHHHHHHHHHHHHHHHhccccccccccchhhcchh
Confidence            5678999999997 799999999999999999999999876  3689999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHchhhhccCCCCCCCCCcCCCCCCcccCC-------------------------------Cchhhhhh
Q psy14580         88 DLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSK-------------------------------TPKKKAVA  136 (149)
Q Consensus        88 ~L~~eDQ~~I~~~~~~~~~~~~~kk~~~~~~~~~~~~~~~~-------------------------------~~~~~~~~  136 (149)
                      +|.++||+.|.++|+++. ++..|+.+++ .|.+++++.+.                               +-++  =|
T Consensus        80 ~L~~~~~~~I~~~i~~Ls-~K~sK~~~~~-~K~T~~~~~T~~~~~~~~V~sT~~RK~~N~~~~rS~R~~~~~~~Sk--FN  155 (482)
T KOG4437|consen   80 ELEDNEKEQITQHIADLS-SKAAKKAVVQ-AKLTTTGQVTSPVKGASFVTSTNPRKFSNNSPKRSLRSSKCDPRSK--FN  155 (482)
T ss_pred             hhchhhHHHHHHHHHHHH-HHhhhccccc-cccCccccccccccccCcccccCccccccccchhccccccCCcccc--ch
Confidence            999999999999998883 3334444333 44444443322                               2233  68


Q ss_pred             hhhhhhhhhc
Q psy14580        137 YFCLIRPLCF  146 (149)
Q Consensus       137 ~~~~~~~~~~  146 (149)
                      .|++|+.||+
T Consensus       156 ~F~ef~kiCS  165 (482)
T KOG4437|consen  156 LFREFRKLCS  165 (482)
T ss_pred             HHHHHHHHHH
Confidence            9999999997

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=99.90  E-value=6.5e-24  Score=201.32  Aligned_cols=88  Identities=34%  Similarity=0.544  Sum_probs=80.0

Q ss_pred             CCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCCCC
Q psy14580         11 DDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLT   90 (149)
Q Consensus        11 ~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~   90 (149)
                      ...+|.|||||||||+|++|+++|.||+||||.++++|+++|.++.|||++||+..       ...++++++|.||+.|+
T Consensus         4 ~~~~~~~EYAkS~Rs~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~~~-------~~~~~~~~~l~G~~~L~   76 (981)
T PLN03123          4 PPKPWKAEYAKSSRSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCILKK-------KNQIKSIDDVEGIDSLR   76 (981)
T ss_pred             CCCCeeEEEecCCCccccccCCcccCCCeEEEEeecccccCCCCCeeecccccccc-------ccCCCChhhcCChhhCC
Confidence            34789999999999999999999999999999999999999999999999999852       22355789999999999


Q ss_pred             HHHHHHHHHHchhhh
Q psy14580         91 PEDQEEVLSRFPESL  105 (149)
Q Consensus        91 ~eDQ~~I~~~~~~~~  105 (149)
                      ++||+.|++++++..
T Consensus        77 ~eDq~~i~~~i~~~~   91 (981)
T PLN03123         77 WEDQQKIRKYVESGG   91 (981)
T ss_pred             HHHHHHHHHHHhccC
Confidence            999999999998884

>PLN03123 poly [ADP-ribose] polymerase; Provisional

Probab=99.84  E-value=3.1e-21  Score=183.24  Aligned_cols=86  Identities=35%  Similarity=0.618  Sum_probs=75.1

Q ss_pred             CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCC
Q psy14580          9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDD   88 (149)
Q Consensus         9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~   88 (149)
                      +.....|.||||+||||+|++|+++|.||+||||..++++  +|.++.|||+.||++.+    .    ..++++|.||++
T Consensus       101 ~~~~~~~~vEyAkS~Ra~Ck~C~~kI~KgelRig~~v~~~--~g~~~~W~H~~Cf~~~~----~----~~~~e~l~Gf~~  170 (981)
T PLN03123        101 AASSFEYGIEVAKTSRATCRRCSEKILKGEVRISSKPEGQ--GYKGLAWHHAKCFLEMS----P----STPVEKLSGWDT  170 (981)
T ss_pred             ccCCcceEEEEecCCCCccccCCceecCCceEEEeeecCC--CCCcccccccccccccC----C----CCChhhCCChhh
Confidence            4456899999999999999999999999999999998877  56779999999998632    1    126899999999


Q ss_pred             CCHHHHHHHHHHchhh
Q psy14580         89 LTPEDQEEVLSRFPES  104 (149)
Q Consensus        89 L~~eDQ~~I~~~~~~~  104 (149)
                      |+++||+.|++++.+.
T Consensus       171 L~~eDqe~v~~li~~~  186 (981)
T PLN03123        171 LSDSDQEAVLPLVKKS  186 (981)
T ss_pred             CCHHHHHHHHHHHhhc
Confidence            9999999999999644

>KOG1037|consensus

Probab=95.24  E-value=0.0024  Score=58.48  Aligned_cols=89  Identities=16%  Similarity=0.185  Sum_probs=68.2

Q ss_pred             CCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCC----
Q psy14580         10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGG----   85 (149)
Q Consensus        10 ~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G----   85 (149)
                      ........+|++++++.|+.|...|.+..+|.++......+++....|+|..||++.-...+.      +..+.+|    
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~~~~~~s~~~~~~~~~~~------~~v~~~~~~~~   77 (531)
T KOG1037|consen    4 TPIALDNASVLKSEDLNSGTCEHVINKDEFRKGIKELKLIFDGDVDKWKHTSCFLKKDHLIRG------PEVKVPGLNQT   77 (531)
T ss_pred             CCcccccchhhhhhchhccCCcccccchhhhhhhhhhhhccccccCcccccccccCccccccc------ccccccccccc
Confidence            345677889999999999999988999999999998888889999999999999763211111      2233445    


Q ss_pred             -----------cCCCCHHHHHHHHHHchhh
Q psy14580         86 -----------WDDLTPEDQEEVLSRFPES  104 (149)
Q Consensus        86 -----------~~~L~~eDQ~~I~~~~~~~  104 (149)
                                 ...|.|++|+.+...++..
T Consensus        78 ~~~~~~~~~~~~~~l~~d~~~~~~~~~~~~  107 (531)
T KOG1037|consen   78 NVENENNKEYTEEELEWDEQQKKRKTVEEG  107 (531)
T ss_pred             cccccccchhhhhhhhcccccceeeeeeec
Confidence                       7788888886666666554

>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=87.66  E-value=0.58  Score=29.21  Aligned_cols=28  Identities=25%  Similarity=0.623  Sum_probs=21.0

Q ss_pred             ccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         27 CKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        27 Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      |.+|++.|..+++.|...          ...||..||.
T Consensus         1 C~~C~~~I~~~~~~~~~~----------~~~~H~~Cf~   28 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAM----------GKFWHPECFK   28 (58)
T ss_dssp             BTTTSSBESSSSEEEEET----------TEEEETTTSB
T ss_pred             CCCCCCCccCcEEEEEeC----------CcEEEccccc
Confidence            789999999888766331          2578999984

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

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

Probab=85.66  E-value=0.68  Score=26.16  Aligned_cols=29  Identities=21%  Similarity=0.543  Sum_probs=19.0

Q ss_pred             cccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         26 GCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        26 ~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      .|.+|++.|..++..+...          ..-||..||.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~----------~~~~H~~Cf~   29 (39)
T smart00132        1 KCAGCGKPIRGGELVLRAL----------GKVWHPECFK   29 (39)
T ss_pred             CccccCCcccCCcEEEEeC----------CccccccCCC
Confidence            4889999998774444321          2456888873

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	149
1uw0_A	117	Solution Structure Of The Zinc-Finger Domain From D		9e-17
3oda_A	116	Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna Lengt		3e-08
4av1_A	223	Crystal Structure Of The Human Parp-1 Dna Binding D		3e-08
2dmj_A	106	Solution Structure Of The First Zf-Parp Domain Of H		4e-08
2l30_A	108	Human Parp-1 Zinc Finger 1 Length = 108		5e-08
1v9x_A	114	Solution Structure Of The First Zn-Finger Domain Of		4e-07
3od8_A	116	Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna Lengt		9e-07
3odc_A	111	Human Parp-1 Zinc Finger 2 (Zn2) Bound To Dna Lengt		7e-05
2l31_A	112	Human Parp-1 Zinc Finger 2 Length = 112		8e-05
2cs2_A	134	Solution Structure Of The Second Zn-Finger Domain O		9e-05

>pdb|1UW0|A Chain A, Solution Structure Of The Zinc-Finger Domain From Dna Ligase Iiia Length = 117

Iteration: 1
 Score = 82.4 bits (202), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 39/94 (41%), Positives = 59/94 (62%), Gaps = 2/94 (2%)
Query: 12  DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKK 69
           ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct: 3   EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 62
Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPE 103
            R TT KIE + ++ GW++L   ++E++     +
Sbjct: 63  ARATTKKIEDLTELEGWEELEDNEKEQITQHIAD 96

>pdb|3ODA|A Chain A, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna Length = 116

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 6/88 (6%)
Query: 10  EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
             DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V   
Sbjct: 24  SSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 83
Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
            R    +++      G+ +L  +DQ++V
Sbjct: 84  IRHPDVEVD------GFSELRWDDQQKV 105

>pdb|4AV1|A Chain A, Crystal Structure Of The Human Parp-1 Dna Binding Domain In Complex With Dna Length = 223

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 6/88 (6%)
Query: 10  EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
             DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V   
Sbjct: 25  HSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 84
Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
            R    +++      G+ +L  +DQ++V
Sbjct: 85  IRHPDVEVD------GFSELRWDDQQKV 106

>pdb|2DMJ|A Chain A, Solution Structure Of The First Zf-Parp Domain Of Human Poly(Adp-Ribose)polymerase-1 Length = 106

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 6/88 (6%)
Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
            DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V   
Sbjct: 11 SSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 70
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
           R    +++      G+ +L  +DQ++V
Sbjct: 71 IRHPDVEVD------GFSELRWDDQQKV 92

>pdb|2L30|A Chain A, Human Parp-1 Zinc Finger 1 Length = 108

Iteration: 1
 Score = 53.1 bits (126), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 6/86 (6%)
Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
          DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V    R
Sbjct: 6  DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIR 65
Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
              +++      G+ +L  +DQ++V
Sbjct: 66 HPDVEVD------GFSELRWDDQQKV 85

>pdb|1V9X|A Chain A, Solution Structure Of The First Zn-Finger Domain Of Poly(Adp-Ribose) Polymerase-1 Length = 114

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 17 VDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAK 76
           + AK+ RS CK CK  I+    R+ K+  +    G M  W+H  CIL       + T +
Sbjct: 13 AEYAKSSRSSCKTCKSVINKENFRLGKLVQSTHFDGIMPMWNHASCIL-------KKTKQ 65
Query: 77 IEVVDDMGGWDDLTPEDQEEV 97
          I+ VDD+ G + L  EDQ+++
Sbjct: 66 IKSVDDVEGIESLRWEDQQKI 86

>pdb|3OD8|A Chain A, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna Length = 116

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 6/86 (6%)
Query: 12  DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
           DK + V+ AK+GR+ CKKC + I   ++R A    +P   GK+  W+H  C  +V    R
Sbjct: 26  DKLYRVEYAKSGRASCKKCSESIPKDSLRXAIXVQSPXFDGKVPHWYHFSCFWKVGHSIR 85
Query: 72  QTTAKIEVVDDMGGWDDLTPEDQEEV 97
               +++      G+ +L  +DQ++V
Sbjct: 86  HPDVEVD------GFSELRWDDQQKV 105

>pdb|3ODC|A Chain A, Human Parp-1 Zinc Finger 2 (Zn2) Bound To Dna Length = 111

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 14  NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
           +F  + AK+ RS CK C +KI+ G VR++K   +P     G + +W+H  C +   K + 
Sbjct: 9   DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 65
Query: 72  QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFP 102
           +   + E     + G+  L  ED+E +  + P
Sbjct: 66  ELGFRPEYSASQLKGFSLLATEDKEALKKQLP 97

>pdb|2L31|A Chain A, Human Parp-1 Zinc Finger 2 Length = 112

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 6/103 (5%)
Query: 14  NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
           +F  + AK+ RS CK C +KI+ G VR++K   +P     G + +W+H  C +   K + 
Sbjct: 10  DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 66
Query: 72  QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
           +   + E     + G+  L  ED+E +  + P    E  +  D
Sbjct: 67  ELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGD 109

>pdb|2CS2|A Chain A, Solution Structure Of The Second Zn-Finger Domain Of Poly(Adp-Ribose) Polymerase-1 Length = 134

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 6/103 (5%)
Query: 14  NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
           +F  + AK+ RS CK C +KI+ G VR++K   +P     G + +W+H  C +   K + 
Sbjct: 17  DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 73
Query: 72  QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
           +   + E     + G+  L  ED+E +  + P    E  +  D
Sbjct: 74  ELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGD 116
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	149
2dmj_A	106	Poly (ADP-ribose) polymerase family, member 1; zin	5e-27
3od8_A	116	Poly [ADP-ribose] polymerase 1; protein-DNA comple	6e-27
1uw0_A	117	DNA ligase III; DNA repair, zinc finger, PARP-like	1e-26
1v9x_A	114	Poly (ADP-ribose) polymerase; PARP, DNA repair, in	1e-26
3odc_A	111	Poly [ADP-ribose] polymerase 1; protein-DNA comple	1e-25
2cs2_A	134	Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repa	4e-25
4av1_A	223	Poly [ADP-ribose] polymerase 1; transferase, PARP1	5e-24
4av1_A	223	Poly [ADP-ribose] polymerase 1; transferase, PARP1	8e-20

>2dmj_A Poly (ADP-ribose) polymerase family, member 1; zinc finger, PARP-1, ADPRT, NAD(+) ADP-ribosyltransferase 1, poly(ADP-ribose) synthetase 1; NMR {Homo sapiens} Length = 106

 Score = 96.5 bits (240), Expect = 5e-27
 Identities = 29/102 (28%), Positives = 49/102 (48%), Gaps = 6/102 (5%)

Query: 2   SDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHID 61
           S         DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  
Sbjct: 3   SGSSGMAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFS 62

Query: 62  CILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPE 103
           C  +V    R    +++      G+ +L  +DQ++V      
Sbjct: 63  CFWKVGHSIRHPDVEVD------GFSELRWDDQQKVKKTAEA 98

>3od8_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc finger, DNA binding protein-D complex; 2.40A {Homo sapiens} PDB: 3oda_A Length = 116

 Score = 96.6 bits (240), Expect = 6e-27
 Identities = 28/93 (30%), Positives = 48/93 (51%), Gaps = 6/93 (6%)

Query: 9   PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFK 68
              DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V  
Sbjct: 23  ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGH 82

Query: 69  KQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRF 101
             R    +++      G+ +L  +DQ++V    
Sbjct: 83  SIRHPDVEVD------GFSELRWDDQQKVKKTA 109

>1uw0_A DNA ligase III; DNA repair, zinc finger, PARP-like finger, cell division, DNA replication, nuclear protein; HET: DNA; NMR {Homo sapiens} SCOP: g.39.1.12 Length = 117

 Score = 95.9 bits (238), Expect = 1e-26
 Identities = 43/123 (34%), Positives = 66/123 (53%), Gaps = 13/123 (10%)

Query: 12  DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKK 69
           ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  ++
Sbjct: 3   EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 62

Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKT 129
            R TT KIE + ++ GW++L   ++E++     +              K   + +KK+  
Sbjct: 63  ARATTKKIEDLTELEGWEELEDNEKEQITQHIADL-----------SSKAAGTPKKKAVV 111

Query: 130 PKK 132
             K
Sbjct: 112 QAK 114

>1v9x_A Poly (ADP-ribose) polymerase; PARP, DNA repair, inflammation, cell death, structural genomics; NMR {Arabidopsis thaliana} Length = 114

 Score = 95.4 bits (237), Expect = 1e-26
 Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 11/121 (9%)

Query: 8   NPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVF 67
                K +  + AK+ RS CK CK  I+    R+ K+  +    G M  W+H  CIL+  
Sbjct: 4   GSSGHKPWRAEYAKSSRSSCKTCKSVINKENFRLGKLVQSTHFDGIMPMWNHASCILK-- 61

Query: 68  KKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKS 127
                 T +I+ VDD+ G + L  EDQ+++                       +SS   S
Sbjct: 62  -----KTKQIKSVDDVEGIESLRWEDQQKIRKYVE----SGAGSNTSTSTGTSTSSSGPS 112

Query: 128 K 128
            
Sbjct: 113 S 113

>3odc_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc finger, DNA binding protein-D complex; 2.80A {Homo sapiens} PDB: 3ode_A 2l31_A Length = 111

 Score = 93.1 bits (231), Expect = 1e-25
 Identities = 26/106 (24%), Positives = 48/106 (45%), Gaps = 4/106 (3%)

Query: 10  EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVF 67
           +   +F  + AK+ RS CK C +KI+ G VR++K   +P     G + +W+H  C ++  
Sbjct: 5   KTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVK-- 62

Query: 68  KKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
            ++            + G+  L  ED+E +  + P    E  +   
Sbjct: 63  NREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGLEHHH 108

>2cs2_A Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repair, necrosis, apoptosis, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 134

 Score = 92.5 bits (229), Expect = 4e-25
 Identities = 32/133 (24%), Positives = 54/133 (40%), Gaps = 6/133 (4%)

Query: 2   SDKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHH 59
           S       +   +F  + AK+ RS CK C +KI+ G VR++K   +P     G + +W+H
Sbjct: 5   SSGGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYH 64

Query: 60  IDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKI 119
             C ++   ++            + G+  L  ED+E +  + P    E  +  D  E   
Sbjct: 65  PGCFVK--NREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGD--EVDG 120

Query: 120 PSSSEKKSKTPKK 132
                KK   P  
Sbjct: 121 VDEVAKKKSGPSS 133

>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation; 3.10A {Homo sapiens} PDB: 2l30_A Length = 223

 Score = 92.2 bits (228), Expect = 5e-24
 Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 6/124 (4%)

Query: 10  EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
             DK + V+ AK+GR+ CKKC + I   ++R+A M  +P   GK+  W+H  C  +V   
Sbjct: 25  HSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 84

Query: 70  QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSKT 129
            R    +++      G+ +L  +DQ++V                +  +   +  +  ++ 
Sbjct: 85  IRHPDVEVD------GFSELRWDDQQKVKKTAEAGGVTGKGQDGIGSKAEKTLGDFAAEY 138

Query: 130 PKKK 133
            K  
Sbjct: 139 AKSN 142

>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation; 3.10A {Homo sapiens} PDB: 2l30_A Length = 223

 Score = 81.0 bits (199), Expect = 8e-20
 Identities = 25/103 (24%), Positives = 46/103 (44%), Gaps = 4/103 (3%)

Query: 3   DKEEPNPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHI 60
                  +   +F  + AK+ RS CK C +KI+ G VR++K   +P     G + +W+H 
Sbjct: 122 GIGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHP 181

Query: 61  DCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPE 103
            C ++   ++            + G+  L  ED+E +  + P 
Sbjct: 182 GCFVK--NREELGFRPEYSASQLKGFSLLATEDKEALKKQLPG 222

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	149
1uw0_A	117	DNA ligase III; DNA repair, zinc finger, PARP-like	100.0
1v9x_A	114	Poly (ADP-ribose) polymerase; PARP, DNA repair, in	99.97
2dmj_A	106	Poly (ADP-ribose) polymerase family, member 1; zin	99.97
2cs2_A	134	Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repa	99.97
3odc_A	111	Poly [ADP-ribose] polymerase 1; protein-DNA comple	99.97
3od8_A	116	Poly [ADP-ribose] polymerase 1; protein-DNA comple	99.97
4av1_A	223	Poly [ADP-ribose] polymerase 1; transferase, PARP1	99.95
4av1_A	223	Poly [ADP-ribose] polymerase 1; transferase, PARP1	99.93
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	83.62
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	83.36
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	81.3
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	81.17
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	80.76
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	80.43

>1uw0_A DNA ligase III; DNA repair, zinc finger, PARP-like finger, cell division, DNA replication, nuclear protein; HET: DNA; NMR {Homo sapiens} SCOP: g.39.1.12

Probab=100.00  E-value=5.6e-38  Score=232.50  Aligned_cols=111  Identities=37%  Similarity=0.719  Sum_probs=99.4

Q ss_pred             CCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCC--CCccceEEecCchhhHHHhhhhcccccCccCCCCCcC
Q psy14580         10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWD   87 (149)
Q Consensus        10 ~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~--~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~   87 (149)
                      |++.+|.|||||||||+|++|+++|.||+||||++++++++  +|.++.|||+.||++.+.+.|.+++.+.++++|+||+
T Consensus         1 m~~~~y~vEYAkSgRA~Ck~C~~kI~KgeLRiG~~v~~~~~~~~g~~~~W~H~~Cf~~k~~~~r~~~~~~~~~~~i~G~~   80 (117)
T 1uw0_A            1 MAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWE   80 (117)
T ss_dssp             CCCCEEEEEECCSSCEECTTSSCEECTTCEEEEEEEECTTCSSCCEECCBCCHHHHHHHHHHSCSSSCCSCTTSSSBSTT
T ss_pred             CCCCceEEEEeCCCCccchhhCcccCCCCeEEEEEeccccccCCCCCCeeECcccchhHHhhhhhhccCCCChHHCcChH
Confidence            67889999999999999999999999999999999999988  7899999999999998888888888888999999999


Q ss_pred             CCCHHHHHHHHHHchhhh---ccCCCCCCCCCcCCCC
Q psy14580         88 DLTPEDQEEVLSRFPESL---RESNKDRDVPERKIPS  121 (149)
Q Consensus        88 ~L~~eDQ~~I~~~~~~~~---~~~~~kk~~~~~~~~~  121 (149)
                      +|+++||+.|+++|+++.   .++|+||.+++ .+++
T Consensus        81 ~L~~eDQ~~I~~~i~~~~~~~~~~~~~~~~~~-~~~~  116 (117)
T 1uw0_A           81 ELEDNEKEQITQHIADLSSKAAGTPKKKAVVQ-AKLT  116 (117)
T ss_dssp             TSCHHHHHHHHHHHHHHHCCSSSCCCCSCCCC-CCCC
T ss_pred             HCCHHHHHHHHHHHHHhhccCCCCCccccccc-cccC
Confidence            999999999999998886   44577766555 5554

>1v9x_A Poly (ADP-ribose) polymerase; PARP, DNA repair, inflammation, cell death, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.97  E-value=5.3e-32  Score=199.91  Aligned_cols=90  Identities=31%  Similarity=0.543  Sum_probs=81.7

Q ss_pred             CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCC
Q psy14580          9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDD   88 (149)
Q Consensus         9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~   88 (149)
                      ...+.+|.|||||||||+|++|+++|.||+||||+++++++++|.++.|||+.||++.+   +    .|.++++|+||++
T Consensus         5 ~~~~~~y~vEYAKS~RA~Ck~Ck~kI~KgeLRiG~~v~~~~~dG~~~~W~H~~Cf~~~~---~----~i~~~~~I~G~~~   77 (114)
T 1v9x_A            5 SSGHKPWRAEYAKSSRSSCKTCKSVINKENFRLGKLVQSTHFDGIMPMWNHASCILKKT---K----QIKSVDDVEGIES   77 (114)
T ss_dssp             CSCCCSEEEEECSCSCCBCSSSCCBCCSSSEEEEECCCCSSSSCCCCEEEEHHHHHTSS---S----CCSCGGGEETTTT
T ss_pred             CCCCcceEEEEeCCCCCCchhhCCccCCCCEEEEEEecCcccCCCcceeECccccchhh---c----cCCChHHCCChHH
Confidence            56678999999999999999999999999999999999999999999999999998632   1    2457899999999


Q ss_pred             CCHHHHHHHHHHchhhh
Q psy14580         89 LTPEDQEEVLSRFPESL  105 (149)
Q Consensus        89 L~~eDQ~~I~~~~~~~~  105 (149)
                      |+++||++|+++|+++.
T Consensus        78 L~~eDQ~~I~~~i~~~~   94 (114)
T 1v9x_A           78 LRWEDQQKIRKYVESGA   94 (114)
T ss_dssp             SCHHHHHHHHHHHSSCS
T ss_pred             CCHHHHHHHHHHHHHcC
Confidence            99999999999999884

>2dmj_A Poly (ADP-ribose) polymerase family, member 1; zinc finger, PARP-1, ADPRT, NAD(+) ADP-ribosyltransferase 1, poly(ADP-ribose) synthetase 1; NMR {Homo sapiens}

Probab=99.97  E-value=3.6e-32  Score=198.19  Aligned_cols=89  Identities=30%  Similarity=0.527  Sum_probs=78.4

Q ss_pred             CCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCCCC
Q psy14580         11 DDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLT   90 (149)
Q Consensus        11 ~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~   90 (149)
                      .+.+|.|||||||||+|+.|+++|.||+||||+++++++++|.++.|||+.||+..+..   .   ..+.++|+||++|+
T Consensus        12 ~~~~~~vEyAkS~Ra~Ck~C~~kI~KgelRig~~v~~~~~~g~~~~W~H~~Cf~~~~~~---~---~~~~~~i~G~~~L~   85 (106)
T 2dmj_A           12 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS---I---RHPDVEVDGFSELR   85 (106)
T ss_dssp             CCCSEECEECCSSCCBCSSSCCBCCTTCEEEEEEEEETTTTEEEEEEEETTHHHHTTCC---C---SCTTTSEETTTTSC
T ss_pred             CCCeEEEEEeCCCCCcchhhCCccCCCCEEEEEEecCCCCCCCcCEeECcCccchhhcc---C---CCChhhCCChHHCC
Confidence            45799999999999999999999999999999999999999999999999999864211   1   12567899999999


Q ss_pred             HHHHHHHHHHchhhh
Q psy14580         91 PEDQEEVLSRFPESL  105 (149)
Q Consensus        91 ~eDQ~~I~~~~~~~~  105 (149)
                      ++||++|+++|+.+.
T Consensus        86 ~eDq~~i~~~~e~g~  100 (106)
T 2dmj_A           86 WDDQQKVKKTAEAGG  100 (106)
T ss_dssp             HHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHHHhCC
Confidence            999999999998873

>2cs2_A Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repair, necrosis, apoptosis, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.97  E-value=1.3e-31  Score=202.63  Aligned_cols=97  Identities=26%  Similarity=0.442  Sum_probs=83.3

Q ss_pred             CCCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCC--CCCccceEEecCchhhHHHhhhhcccccCccCCCCC
Q psy14580          8 NPEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPF--GSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGG   85 (149)
Q Consensus         8 ~~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~--~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G   85 (149)
                      .+|++.+|.|||||||||+|+.|+++|.||+||||+++++|+  ++|.++.|||+.||+..+.  +..+..+.++++|+|
T Consensus        11 ~~~~~~~y~vEYAKSgRA~CK~C~~kI~KgeLRIG~~v~~~~~~~~G~~~~W~H~~Cf~~~~~--~~~~~~~~~~~~I~G   88 (134)
T 2cs2_A           11 AEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKNRE--ELGFRPEYSASQLKG   88 (134)
T ss_dssp             CSSCEEEEEEEECSSSCCBCSSSCCBCCTTSEEEEEEEECSSCTTTCEEEEEECHHHHHHTTT--TTTCCTTCCGGGEET
T ss_pred             cccccCceEEEEeCCCCccchhcCCcccCCCeEEEEEecccccCCCCCcceeECcCcChhhhh--ccccCCCCChHhCCC
Confidence            567889999999999999999999999999999999998874  3688999999999987532  222233457899999


Q ss_pred             cCCCCHHHHHHHHHHchhhhc
Q psy14580         86 WDDLTPEDQEEVLSRFPESLR  106 (149)
Q Consensus        86 ~~~L~~eDQ~~I~~~~~~~~~  106 (149)
                      |+.|+++||+.|+++|+++..
T Consensus        89 f~~L~~eDQe~I~~~i~~~~~  109 (134)
T 2cs2_A           89 FSLLATEDKEALKKQLPGVKS  109 (134)
T ss_dssp             TTTSCHHHHHHHHTTCCSSCC
T ss_pred             hHHCCHHHHHHHHHHHHHHhh
Confidence            999999999999999988854

>3odc_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc finger, DNA binding protein-D complex; 2.80A {Homo sapiens} PDB: 3ode_A 2l31_A

Probab=99.97  E-value=1.3e-31  Score=196.95  Aligned_cols=95  Identities=26%  Similarity=0.456  Sum_probs=80.1

Q ss_pred             CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCC--CCccceEEecCchhhHHHhhhhcccccCccCCCCCc
Q psy14580          9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGW   86 (149)
Q Consensus         9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~--~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~   86 (149)
                      +.++..|.|||||||||+|++|+++|.||+||||.++++|++  +|.++.|||+.||++.+.+.  ....+.++++|+||
T Consensus         4 ~~~~~~y~vEyAkS~Ra~Ck~C~~kI~Kg~lRig~~~~~~~~~~~G~~~~W~H~~Cf~~~~~~l--~~~~~~~~~~I~Gf   81 (111)
T 3odc_A            4 EKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKNREEL--GFRPEYSASQLKGF   81 (111)
T ss_dssp             --CCCCEEEEECSSSCCBCTTTCCBCCTTCEEEEEEEEETTEEEEEEEEEEECHHHHHHTHHHH--TCCTTTGGGGEETG
T ss_pred             cccCCcceEEEeecCCccccccCCCccCCceEEeEEecCccccCCCCcceeEChhhccchhhhc--ccCCCCCHHhCCCh
Confidence            457799999999999999999999999999999999998874  58889999999999865432  22334578999999


Q ss_pred             CCCCHHHHHHHHHHchhhh
Q psy14580         87 DDLTPEDQEEVLSRFPESL  105 (149)
Q Consensus        87 ~~L~~eDQ~~I~~~~~~~~  105 (149)
                      ++|+++||++|+++|+++.
T Consensus        82 ~~L~~eDQe~Ikk~i~~~~  100 (111)
T 3odc_A           82 SLLATEDKEALKKQLPGVK  100 (111)
T ss_dssp             GGSCHHHHHHHHHHSCC--
T ss_pred             HHCCHHHHHHHHHHHHhhc
Confidence            9999999999999997763

>3od8_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc finger, DNA binding protein-D complex; 2.40A {Homo sapiens} PDB: 3oda_A 4dqy_A*

Probab=99.97  E-value=6.8e-32  Score=199.95  Aligned_cols=89  Identities=31%  Similarity=0.569  Sum_probs=76.9

Q ss_pred             CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccC-ccCCCCCcC
Q psy14580          9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIE-VVDDMGGWD   87 (149)
Q Consensus         9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~-~~edI~G~~   87 (149)
                      +..+.+|.|||||||||+|+.|+++|.||+||||+++++++++|.++.|||+.||++.+.       .+. +.++|+||+
T Consensus        23 ~~~~~~y~vEyAkS~RA~Ck~C~~kI~KgeLRiG~~v~~~~~~G~~~~WyH~~Cf~~~~~-------~~~~~~~~I~Gfd   95 (116)
T 3od8_A           23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGH-------SIRHPDVEVDGFS   95 (116)
T ss_dssp             --CCCSEEEEECSSSCCBCTTTCCBCCTTSEEEEEEEECSSSSSEEEEEEEHHHHHHTCC-------CCSCHHHHEETGG
T ss_pred             hccCCCEEEEEeccCCccCcccCCccCCCCEEEEEEeccCCcCCCCCeeECCccChhhhh-------ccCCChhhCcChH
Confidence            345689999999999999999999999999999999999999999999999999986321       111 357899999


Q ss_pred             CCCHHHHHHHHHHchhh
Q psy14580         88 DLTPEDQEEVLSRFPES  104 (149)
Q Consensus        88 ~L~~eDQ~~I~~~~~~~  104 (149)
                      +|+++||++|+++|+++
T Consensus        96 ~L~~eDQekIkk~ie~g  112 (116)
T 3od8_A           96 ELRWDDQQKVKKTAEAG  112 (116)
T ss_dssp             GSCHHHHHHHHHHHHC-
T ss_pred             HCCHHHHHHHHHHHHcC
Confidence            99999999999999876

>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation; 3.10A {Homo sapiens} PDB: 2l30_A

Probab=99.95  E-value=1.7e-29  Score=204.97  Aligned_cols=91  Identities=30%  Similarity=0.514  Sum_probs=77.9

Q ss_pred             CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCC
Q psy14580          9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDD   88 (149)
Q Consensus         9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~   88 (149)
                      +..+.+|.|||||||||+|++|+++|.||+||||+++++++++|.++.|||+.||++.+.   .   ...++++|+||++
T Consensus        24 ~~~d~~y~vEyAkS~RA~Ck~Ck~kI~Kg~LRig~~v~~~~~dG~~~~W~H~~Cf~~~~~---~---~~~~~~~I~G~~~   97 (223)
T 4av1_A           24 SHSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGH---S---IRHPDVEVDGFSE   97 (223)
T ss_dssp             ---CCSEEEEECSSTTCBCTTTCCBCCTTCEEEEEEEEETTTTEEEEEEEEHHHHTTSCC---C---CSCHHHHEETTTS
T ss_pred             cCCCCcEEEEEecCCCccCcccCCccCCCceEEEEEecCCCCCCCCceeEChhhhhhhhc---c---cCCCHHHCCChhH
Confidence            345789999999999999999999999999999999999999999999999999986321   1   1236789999999


Q ss_pred             CCHHHHHHHHHHchhhh
Q psy14580         89 LTPEDQEEVLSRFPESL  105 (149)
Q Consensus        89 L~~eDQ~~I~~~~~~~~  105 (149)
                      |+++||++|+++|+++.
T Consensus        98 L~~eDQekIk~~ie~g~  114 (223)
T 4av1_A           98 LRWDDQQKVKKTAEAGG  114 (223)
T ss_dssp             SCHHHHHHHHHHHHC--
T ss_pred             CCHHHHHHHHHHHHhCC
Confidence            99999999999998874

>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation; 3.10A {Homo sapiens} PDB: 2l30_A

Probab=99.93  E-value=1.3e-27  Score=193.75  Aligned_cols=93  Identities=27%  Similarity=0.477  Sum_probs=0.0

Q ss_pred             CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCC--CCccceEEecCchhhHHHhhhhcccccCccCCCCCc
Q psy14580          9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGW   86 (149)
Q Consensus         9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~--~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~   86 (149)
                      .+....|.|||||||||+|++|+++|.||+||||.++++|++  +|.++.|||+.||++.+...  ....+.++++|+||
T Consensus       128 ~~~~~~y~vEYAKS~Ra~Ck~C~~kI~KgeLRig~~v~~~~~~~~G~~~~W~H~~Cf~~~~~~l--~~~~~~~~~~l~Gf  205 (223)
T 4av1_A          128 EKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKNREEL--GFRPEYSASQLKGF  205 (223)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccceEEEEeccCCccccccCCccCCCCeEEeeeecCcccccCCCcceeEChhhhhchhhhc--ccCCCCChHHCCCh
Confidence            456789999999999999999999999999999999988863  57889999999998753221  11223478999999


Q ss_pred             CCCCHHHHHHHHHHchh
Q psy14580         87 DDLTPEDQEEVLSRFPE  103 (149)
Q Consensus        87 ~~L~~eDQ~~I~~~~~~  103 (149)
                      +.|+++||++|+++|..
T Consensus       206 ~~L~~eDQ~~ikk~i~~  222 (223)
T 4av1_A          206 SLLATEDKEALKKQLPG  222 (223)
T ss_dssp             -----------------
T ss_pred             HHCCHHHHHHHHHhccC
Confidence            99999999999999854

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=83.62  E-value=0.57  Score=30.34  Aligned_cols=32  Identities=19%  Similarity=0.500  Sum_probs=23.8

Q ss_pred             ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      ..|..|++.+..+..-|+-       ++.-..|||..|+
T Consensus         9 ~~C~~C~~p~~~~~~mI~C-------D~~C~~WfH~~Cv   40 (65)
T 2vpb_A            9 YPCGICTNEVNDDQDAILC-------EASCQKWFHRICT   40 (65)
T ss_dssp             CBCTTTCSBCCTTSCEEEB-------TTTTCCEEEHHHH
T ss_pred             CcCccCCCccCCCCCeEec-------ccCccccCchhcc
Confidence            4688999988777666654       3345699999996

>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=83.36  E-value=1  Score=27.89  Aligned_cols=35  Identities=14%  Similarity=0.435  Sum_probs=23.5

Q ss_pred             ccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         20 AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        20 AKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      -......|.+|++.|..++.-|..       .   ..-||..||.
T Consensus         7 ~~~~~~~C~~C~~~i~~~e~~~~~-------~---~~~~H~~CF~   41 (72)
T 3f6q_B            7 QGSASATCERCKGGFAPAEKIVNS-------N---GELYHEQCFV   41 (72)
T ss_dssp             CCCTTCBCTTTCCBCCTTCEEEEE-------T---TEEEETTTSS
T ss_pred             cCcCCccchhcCccccCCceEEEe-------C---cCeeCcCCCc
Confidence            345567999999999987644322       1   1346899984

>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=81.30  E-value=1.3  Score=29.63  Aligned_cols=35  Identities=23%  Similarity=0.618  Sum_probs=23.0

Q ss_pred             ccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         20 AKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        20 AKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      |.++...|.+|++.|.-+...|-.          ...-||..||.
T Consensus         1 ~s~~~~~C~~C~~~I~~~~~~~~a----------~~~~~H~~CF~   35 (101)
T 2cup_A            1 GSSGSSGCVECRKPIGADSKEVHY----------KNRFWHDTCFR   35 (101)
T ss_dssp             CCSCCCBCSSSCCBCCSSSCEEEE----------TTEEEETTTCC
T ss_pred             CCCCCCcCcccCCcccCCceEEEE----------CccChhhcCCc
Confidence            456678999999999753333321          12466999984

>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=81.17  E-value=1.2  Score=27.97  Aligned_cols=30  Identities=33%  Similarity=0.698  Sum_probs=20.8

Q ss_pred             ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      ..|..|++.|.-++..|-..          ..-||..||.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~----------~~~~H~~CF~   35 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEYK----------GSSWHETCFI   35 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEET----------TEEEETTTTC
T ss_pred             CCCccCCCcccCCceEEEEC----------cCeecccCCc
Confidence            58999999998765444321          2456899984

>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=80.76  E-value=0.77  Score=28.96  Aligned_cols=34  Identities=35%  Similarity=0.627  Sum_probs=21.4

Q ss_pred             cCCCccccccccCcCC--CCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         21 KTGRSGCKKCKQKIDT--GTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        21 KS~RA~Ck~Ck~kI~K--GeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      .+....|.+|++.|..  ++..|..          ...-||..||.
T Consensus         2 s~~~~~C~~C~~~I~~~~~~~~~~a----------~~~~wH~~CF~   37 (72)
T 1x4l_A            2 SSGSSGCAGCTNPISGLGGTKYISF----------EERQWHNDCFN   37 (72)
T ss_dssp             CSCSCSBTTTTBCCCCSSSCSCEEC----------SSCEECTTTCB
T ss_pred             CCCCCCCcCCCccccCCCCcceEEE----------CCcccCcccCE
Confidence            3456789999999985  3222211          12355899984

>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=80.43  E-value=0.77  Score=30.76  Aligned_cols=34  Identities=24%  Similarity=0.451  Sum_probs=22.3

Q ss_pred             cCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580         21 KTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL   64 (149)
Q Consensus        21 KS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~   64 (149)
                      +.-..+|.+|++.|..|+..|-.          ...-||..||.
T Consensus        63 ~~~~~~C~~C~~~I~~~~~~~~a----------~~~~~H~~CF~   96 (101)
T 2cup_A           63 REDSPKCKGCFKAIVAGDQNVEY----------KGTVWHKDCFS   96 (101)
T ss_dssp             TCCCCBCSSSCCBCCSSSCEEES----------SSCEEETTTCC
T ss_pred             hhcCCccccCCCccccCCeEEEe----------CCcchHHhCCC
Confidence            33446899999999877644421          12456999983

---

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	149
d1uw0a_	117	g.39.1.12 (A:) DNA ligase III {Human (Homo sapiens	2e-27

>d1uw0a_ g.39.1.12 (A:) DNA ligase III {Human (Homo sapiens) [TaxId: 9606]} Length = 117

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: PARP-type zinc finger
domain: DNA ligase III
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.2 bits (239), Expect = 2e-27
 Identities = 49/128 (38%), Positives = 70/128 (54%), Gaps = 20/128 (15%)

Query: 11  DDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFK 68
            ++ F VD AK G +GCKKCK+KI  G  RI K+  NPF    G MK+W+HI C+ E  +
Sbjct: 2   AEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLE 61

Query: 69  KQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSK 128
           + R TT KIE + ++ GW++L   ++E++                   + I   S K + 
Sbjct: 62  RARATTKKIEDLTELEGWEELEDNEKEQIT------------------QHIADLSSKAAG 103

Query: 129 TPKKKAVA 136
           TPKKKAV 
Sbjct: 104 TPKKKAVV 111

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	149
d1uw0a_	117	DNA ligase III {Human (Homo sapiens) [TaxId: 9606]	100.0
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	93.87
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	89.91
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	88.0
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	85.08
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	85.07
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	84.9
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	81.63
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	81.14
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	80.89

>d1uw0a_ g.39.1.12 (A:) DNA ligase III {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: PARP-type zinc finger
domain: DNA ligase III
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.6e-37  Score=226.94  Aligned_cols=111  Identities=37%  Similarity=0.719  Sum_probs=97.1

Q ss_pred             CCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCC--CccceEEecCchhhHHHhhhhcccccCccCCCCCcC
Q psy14580         10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWD   87 (149)
Q Consensus        10 ~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~--g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~   87 (149)
                      |++..|.||||+||||+|++|+++|+||+||||+.+++|+++  |.++.|||++||++.+.+.+.++..+.++++|+||+
T Consensus         1 m~~~~~~vEyAkS~Ra~Ck~C~~~I~Kg~lRig~~~~~~~~~~~g~~~~W~H~~Cf~~~~~~~~~~~~~~~~~~~i~G~~   80 (117)
T d1uw0a_           1 MAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWE   80 (117)
T ss_dssp             CCCCEEEEEECCSSCEECTTSSCEECTTCEEEEEEEECTTCSSCCEECCBCCHHHHHHHHHHSCSSSCCSCTTSSSBSTT
T ss_pred             CCCcceeeEEccCCCcccCCCCccccCCCeEEEEEEeCcccccCCCcCccCCcccccchhhcccccccCCCCHHHCCChh
Confidence            678999999999999999999999999999999999999886  788999999999998888888777788899999999


Q ss_pred             CCCHHHHHHHHHHchhhh---ccCCCCCCCCCcCCCC
Q psy14580         88 DLTPEDQEEVLSRFPESL---RESNKDRDVPERKIPS  121 (149)
Q Consensus        88 ~L~~eDQ~~I~~~~~~~~---~~~~~kk~~~~~~~~~  121 (149)
                      +|+++||++|+++|++..   +.+|+|+.+.+ ++++
T Consensus        81 ~L~~eDq~~i~~~i~~~~~~~~~~~~kk~~~~-~k~~  116 (117)
T d1uw0a_          81 ELEDNEKEQITQHIADLSSKAAGTPKKKAVVQ-AKLT  116 (117)
T ss_dssp             TSCHHHHHHHHHHHHHHHCCSSSCCCCSCCCC-CCCC
T ss_pred             hCCHHHHHHHHHHHHhhccccCCCCCcccchh-cccC
Confidence            999999999999998885   33455555544 5544

>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=93.87  E-value=0.016  Score=31.74  Aligned_cols=30  Identities=20%  Similarity=0.514  Sum_probs=23.2

Q ss_pred             CccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         24 RSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        24 RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      -..|-+|.+.|...+|-+-..          ..=||+.||
T Consensus         2 ~g~Ca~C~~~I~~~e~VmRA~----------~~VyHl~CF   31 (31)
T d1rutx3           2 SGACSACGQSIPASELVMRAQ----------GNVYHLKCF   31 (31)
T ss_dssp             CEECTTTCCEECTTSEEEEET----------TEEECGGGC
T ss_pred             CcccccccCcCChhHhheecc----------cceeeeccC
Confidence            357999999999988765321          367999997

>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=89.91  E-value=0.13  Score=28.76  Aligned_cols=29  Identities=28%  Similarity=0.457  Sum_probs=23.0

Q ss_pred             CCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         23 GRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        23 ~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      .-.+|..|++.|..--||-            +-+=||+.||
T Consensus         7 tlEkC~~C~~~I~driLrA------------~Gk~yHP~CF   35 (35)
T d2dloa1           7 TLEKCATCSQPILDRILRA------------MGKAYHPGCF   35 (35)
T ss_dssp             SCCBCTTTCCBCCSCCEEE------------TTEEECTTTC
T ss_pred             HHHHHHHhchHHHHHHHHH------------hCCCCCCCCC
Confidence            3568999999999888775            1256899997

>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=88.00  E-value=0.069  Score=29.66  Aligned_cols=27  Identities=22%  Similarity=0.361  Sum_probs=18.3

Q ss_pred             ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      .-|-+|+..|.--      .|..+      ..+||+.||
T Consensus         9 p~CdkCg~GIVG~------~VK~r------Dk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVGV------FVKLR------DRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCSS------CEECS------SCEECTTTT
T ss_pred             ccccccCCCcEeE------EEEec------cccCCCCCC
Confidence            4688998877533      33322      479999997

>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=85.08  E-value=0.31  Score=27.13  Aligned_cols=31  Identities=42%  Similarity=0.901  Sum_probs=23.4

Q ss_pred             CCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         22 TGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        22 S~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      ++-+.|-+|++.|..|..=++.          ..+| |+.||
T Consensus         6 ~g~~~CagCg~eik~gQaL~AL----------dkqW-H~~CF   36 (36)
T d2dj7a2           6 RGPSHCAGCKEEIKHGQSLLAL----------DKQW-HVSCF   36 (36)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEET----------TEEE-CTTTC
T ss_pred             cCCccccccchhhhCCceeeee----------ecce-eeeeC
Confidence            4667899999999999766653          1345 88887

>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=85.07  E-value=0.3  Score=27.42  Aligned_cols=21  Identities=24%  Similarity=0.512  Sum_probs=16.5

Q ss_pred             CCCccccccccCcCCCCeEEE
Q psy14580         22 TGRSGCKKCKQKIDTGTVRIA   42 (149)
Q Consensus        22 S~RA~Ck~Ck~kI~KGeLRIG   42 (149)
                      ---.+|.+|++.|.-|+=.+-
T Consensus         6 ~~a~~C~~C~k~I~~G~k~ve   26 (37)
T d1x63a1           6 EDSPKCKGCFKAIVAGDQNVE   26 (37)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEE
T ss_pred             ccCcccccCCCccCCCCeEeE
Confidence            334689999999999976664

>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=84.90  E-value=0.13  Score=30.15  Aligned_cols=27  Identities=22%  Similarity=0.522  Sum_probs=18.6

Q ss_pred             ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      --|-+|+..|.      |..|..+      ...||++||
T Consensus        19 P~CdkCg~GIV------G~~VK~r------DK~rHPeCf   45 (45)
T d1x64a1          19 PLCDKCGSGIV------GAVVKAR------DKYRHPECF   45 (45)
T ss_dssp             CBCTTTCCBCC------SCCEESS------SCEECTTTC
T ss_pred             ccccccCCCcE------EEEEEec------cccCCCCCC
Confidence            46889987774      3344322      479999997

>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=81.63  E-value=0.24  Score=26.69  Aligned_cols=30  Identities=27%  Similarity=0.666  Sum_probs=21.7

Q ss_pred             cCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCc
Q psy14580         21 KTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDC   62 (149)
Q Consensus        21 KS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~C   62 (149)
                      .|+-+.|-.|.+-|.-..|.-|            ..-||+.|
T Consensus         2 ssgssgC~~C~~~ItGkVLEAG------------~khYHP~C   31 (32)
T d1wiga1           2 SSGSSGCDSCEKYITGRVLEAG------------EKHYHPSC   31 (32)
T ss_dssp             CCSCCSCSSSCCCCSSCCBCCS------------SCCBCTTT
T ss_pred             CCccchhhhhhhhhhhhhhhcc------------ccccCCCC
Confidence            3678899999988876655433            25688888

>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=81.14  E-value=0.62  Score=25.52  Aligned_cols=27  Identities=22%  Similarity=0.516  Sum_probs=17.5

Q ss_pred             ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      .+|.+|++.|.-..| .+           +..=||+.||
T Consensus         9 pkC~~C~~~I~g~~v-~A-----------l~~~wHpeCF   35 (35)
T d1x3ha1           9 PKCGGCNRPVLENYL-SA-----------MDTVWHPECF   35 (35)
T ss_dssp             CBCTTTCCBCCSSCE-EE-----------TTEEECTTTC
T ss_pred             hhhhhcCCcccchhe-ee-----------cCCccCcccC
Confidence            489999999963321 11           1234699997

>d2d8za1 g.39.1.3 (A:8-32) 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=80.89  E-value=0.63  Score=23.97  Aligned_cols=25  Identities=36%  Similarity=0.861  Sum_probs=16.9

Q ss_pred             ccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580         27 CKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI   63 (149)
Q Consensus        27 Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf   63 (149)
                      |-+|++.|.-|-    +.+++.       -| |-.||
T Consensus         1 C~~C~K~ItsGG----vtY~~~-------PW-H~eCF   25 (26)
T d2d8za1           1 CVQCKKPITTGG----VTYREQ-------PW-HKECF   25 (26)
T ss_dssp             CSSSCCBCCSSE----EESSSS-------EE-ETTTS
T ss_pred             CcccCcceecCc----eeecCC-------cc-hhhhc
Confidence            788999999883    333322       23 88887