Citrus Sinensis ID: 023513

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-
Protein Sequence
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKEELT
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccHHHHHHHHccHHHHHHHHHHHccccccccccccccccccccccccccccEEEEEccccccEEEEEEcccccccEEEEccccccEEEcccccccccHHHHHHHHHHcccccccEEEEEEcccccccccccEEEccHHHHHHHHHHHHHcccEEEEccHHHHHHHccccccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccEEEEcHHHHHccccccEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccHccccccEEEEEcccccEEEEEEEccccccEEEEEcccccEEEEccEEEEEccHHHHHHHHHccccccccEEEEEEcccccccccEEEEccccHHHHHHHHHHHccccEEEccHHHHHHHHccccccccHHHHHHHHHHHcHHHHHHHcccccccHHHHHHHHHHcccEEcccccccccEEccccHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mettvkiqpqlqshcismntfVSSKIrtlctypfaqhGRTLLVRAAAAGDTTKAAVAAQMKQNwldsltfpplhvhdltanqtnadsqwalgidpdLSGALAVLKsdhngcsaevfdtphlpvlvGKRVRKRLDAKSMIMLLRSldapigttayveqsipypqdgkqgwwsggfgYGLWIGILVAsgfsvvpipsltwknwyglsggtstkddsrrVASTLFPSLCSQlkrkkdhgKADAVLIAAYGKglkldsshlsgelvpqrseVVTTAQLLQKEELT
Flexible Loop (DISEMBL)
mettvkiqpqlqshciSMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSaevfdtphlpvlvgKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLcsqlkrkkdhgkADAVLIAAYGKGLKLDSSHLsgelvpqrsevvttaqllqkeelt
Low Complexity Region (SEG)
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRaaaagdttkaavaaQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKEELT
Disordered region (IsUnstruct)
***********QSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSG**************LFPSLC**********KADAVLIAAYGKGLKL*****************************
Disordered Region (DISOPRED)
********PQLQSHCISMNTFVSSK**********************************MKQNWLDS******************DSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGL*********SRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDS********PQRSEVVTTAQLLQK****
Disordered Region (DISEMBL)
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAA**********AQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQ********KADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKEELT
Disordered Region (DISPRO)
*ETTVKIQPQLQSHCISMNTFVSSKIRTLCTYPF***********************AQ*KQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQK****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKEELT
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

No hits with e-value below 0.001 by BLAST

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	281
255580004	280	conserved hypothetical protein [Ricinus	0.711	0.714	0.706	8e-79
225435862	291	PREDICTED: uncharacterized protein LOC10	0.893	0.862	0.557	4e-76
296083889	192	unnamed protein product [Vitis vinifera]	0.629	0.921	0.723	2e-72
356528579	274	PREDICTED: uncharacterized protein LOC10	0.697	0.715	0.645	4e-71
30683279	273	uncharacterized protein [Arabidopsis tha	0.935	0.963	0.533	2e-70
3426042	286	unknown protein [Arabidopsis thaliana]	0.935	0.919	0.510	8e-68
297825913	287	hypothetical protein ARALYDRAFT_320472 [	0.935	0.916	0.505	1e-67
356555307	290	PREDICTED: uncharacterized protein LOC10	0.690	0.668	0.636	2e-67
224105997	235	predicted protein [Populus trichocarpa]	0.558	0.668	0.670	1e-58
334184493	326	uncharacterized protein [Arabidopsis tha	0.935	0.806	0.422	3e-58

>gi|255580004|ref|XP_002530836.1| conserved hypothetical protein [Ricinus communis] gi|223529600|gb|EEF31549.1| conserved hypothetical protein [Ricinus communis]

 Score =  299 bits (766), Expect = 8e-79,   Method: Compositional matrix adjust.
 Identities = 147/208 (70%), Positives = 171/208 (82%), Gaps = 8/208 (3%)

Query: 52  TKAAVAAQMKQNWLDSLTFPPLHVH-------DLTANQTNADSQWALGIDPDLSGALAVL 104
           ++A VA Q+K+NWL SL+ P            D TA  +N  S W +GIDPDLSGALA+L
Sbjct: 62  SEAEVARQLKENWLHSLSCPFNQTESSASKGVDSTA-PSNVGSNWVIGIDPDLSGALALL 120

Query: 105 KSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD 164
           K D +GCSA+VFD+PHL VLVGKR+RKRLDAKS++ LL S DAP+GTTAY+EQSIP+PQD
Sbjct: 121 KIDDSGCSAQVFDSPHLKVLVGKRIRKRLDAKSIVQLLHSFDAPLGTTAYIEQSIPFPQD 180

Query: 165 GKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPS 224
           GKQGWWSGGFGYGLWIGILVASGFSVVP+PSL WKN + LSG   +KDDSR+VASTLFPS
Sbjct: 181 GKQGWWSGGFGYGLWIGILVASGFSVVPVPSLAWKNVFELSGSKFSKDDSRKVASTLFPS 240

Query: 225 LCSQLKRKKDHGKADAVLIAAYGKGLKL 252
           L S LKRKKDHG+A+A+LIAAYGKGLKL
Sbjct: 241 LSSLLKRKKDHGRAEALLIAAYGKGLKL 268

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225435862|ref|XP_002263460.1| PREDICTED: uncharacterized protein LOC100242692 isoform 1 [Vitis vinifera]

 Score =  290 bits (742), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 146/262 (55%), Positives = 188/262 (71%), Gaps = 11/262 (4%)

Query: 1   METTVKIQPQLQSHCISMNTFVSSKIRTLCTY---PFAQHGRTLLVRAAAAGDTTKAAVA 57
           M    KI P+L         F ++ + +  T+   P      T+L    ++G        
Sbjct: 18  MNPISKITPKLALSAPKFRVFCATSLNSTNTHDPIPAPSSTDTVL---RSSGKARARVSD 74

Query: 58  AQMKQNWLDSLTFPPLHVHD-----LTANQTNADSQWALGIDPDLSGALAVLKSDHNGCS 112
            Q ++NWL SL+ P    ++     + + ++NA +Q  +GIDPD+SGALA+LK+  +GCS
Sbjct: 75  TQYRENWLASLSCPFPDENERPGIRMDSAESNAGTQCVIGIDPDISGALALLKTGDSGCS 134

Query: 113 AEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSG 172
           A+VFD+PHL +LVGKRVRKRLDAKS++ LLR  DAPIGT AY+EQSIP+PQDGKQGWWSG
Sbjct: 135 AQVFDSPHLQILVGKRVRKRLDAKSIVQLLRGFDAPIGTIAYIEQSIPFPQDGKQGWWSG 194

Query: 173 GFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRK 232
           GFGYGLWIGILVASGFSVVP+PS  WKN + LSG  ++KDDSRRVAST+FPS+ S LKRK
Sbjct: 195 GFGYGLWIGILVASGFSVVPVPSSLWKNEFKLSGNGTSKDDSRRVASTIFPSMSSLLKRK 254

Query: 233 KDHGKADAVLIAAYGKGLKLDS 254
           KDHG+A+A+LIAA+GKGLK+ S
Sbjct: 255 KDHGRAEALLIAAFGKGLKMKS 276

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083889|emb|CBI24277.3| unnamed protein product [Vitis vinifera]

 Score =  278 bits (710), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 128/177 (72%), Positives = 156/177 (88%)

Query: 78  LTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKS 137
           + + ++NA +Q  +GIDPD+SGALA+LK+  +GCSA+VFD+PHL +LVGKRVRKRLDAKS
Sbjct: 1   MDSAESNAGTQCVIGIDPDISGALALLKTGDSGCSAQVFDSPHLQILVGKRVRKRLDAKS 60

Query: 138 MIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLT 197
           ++ LLR  DAPIGT AY+EQSIP+PQDGKQGWWSGGFGYGLWIGILVASGFSVVP+PS  
Sbjct: 61  IVQLLRGFDAPIGTIAYIEQSIPFPQDGKQGWWSGGFGYGLWIGILVASGFSVVPVPSSL 120

Query: 198 WKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDS 254
           WKN + LSG  ++KDDSRRVAST+FPS+ S LKRKKDHG+A+A+LIAA+GKGLK+ S
Sbjct: 121 WKNEFKLSGNGTSKDDSRRVASTIFPSMSSLLKRKKDHGRAEALLIAAFGKGLKMKS 177

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528579|ref|XP_003532877.1| PREDICTED: uncharacterized protein LOC100775189 [Glycine max]

 Score =  274 bits (700), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 131/203 (64%), Positives = 163/203 (80%), Gaps = 7/203 (3%)

Query: 53  KAAVAAQMKQNWLDSLTFP-PLHVHDLTANQT----NADSQWALGIDPDLSGALAVLKSD 107
           KA+   Q K+NWL SL++P P   H L+        N  S+W LGIDPD+SGA+A+LK+ 
Sbjct: 52  KASSDTQFKENWLASLSYPFPEKTHLLSGEHEPTHQNDGSKWVLGIDPDVSGAVALLKTH 111

Query: 108 HNGCSAEVFDTPHLPVLVGK--RVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG 165
            + CSA+VFD+PH+ +LVGK  R R+RLDAKS++ L+R  DAPIGTTA++EQS+PYPQDG
Sbjct: 112 GSVCSAQVFDSPHVKILVGKNKRTRRRLDAKSVVELVRGFDAPIGTTAFIEQSLPYPQDG 171

Query: 166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSL 225
           KQGWWSGGFGYGLWIGILVASGFSV+P+PS TWK  + LSG  +TKDDSRR+ASTLFPS+
Sbjct: 172 KQGWWSGGFGYGLWIGILVASGFSVIPVPSFTWKAKFELSGNGTTKDDSRRIASTLFPSM 231

Query: 226 CSQLKRKKDHGKADAVLIAAYGK 248
            S L RKKDHG+A+A+LIAAYG+
Sbjct: 232 TSMLSRKKDHGRAEALLIAAYGQ 254

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30683279|ref|NP_180252.2| uncharacterized protein [Arabidopsis thaliana] gi|26452962|dbj|BAC43557.1| unknown protein [Arabidopsis thaliana] gi|28973431|gb|AAO64040.1| unknown protein [Arabidopsis thaliana] gi|330252802|gb|AEC07896.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 151/283 (53%), Positives = 192/283 (67%), Gaps = 20/283 (7%)

Query: 1   METTVKIQ---PQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVA 57
           M TTV  Q   PQ+ S    +  F+S       T PF +  R+    A     TTKA  A
Sbjct: 1   MATTVYGQASLPQMHSLFSKVRPFLSHSPS--FTAPFTRR-RSFPFSALP---TTKAIDA 54

Query: 58  AQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCS--AEV 115
           A MK+ WLDSL+   L   D      NA+S   +GIDPDLSGALA+LK DH G S  A+V
Sbjct: 55  ALMKEKWLDSLS---LTSQDEDTTPENAESSCIIGIDPDLSGALALLKFDHLGSSSFAQV 111

Query: 116 FDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFG 175
           +DTPH+PVLVGKRVRKRLDAKS++ L++SLD P G+  Y+EQS P+P+DGKQGW+SGGFG
Sbjct: 112 YDTPHIPVLVGKRVRKRLDAKSIVQLIQSLDVPSGSRVYIEQSNPFPKDGKQGWYSGGFG 171

Query: 176 YGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDH 235
           YGLWIG LVASGF V+P+ +  WK  + L+ G+ TKDDSRRVA+ LFPSL SQLKRKKDH
Sbjct: 172 YGLWIGTLVASGFCVIPVSASLWKRHFQLASGSCTKDDSRRVAAELFPSLSSQLKRKKDH 231

Query: 236 GKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKE 278
           G+A+A+LIAAYG+ LK +      +L+ Q  E+++    L+ +
Sbjct: 232 GRAEALLIAAYGEALKTE------KLLIQPKELLSQVNYLENQ 268

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3426042|gb|AAC32241.1| unknown protein [Arabidopsis thaliana]

 Score =  263 bits (671), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 151/296 (51%), Positives = 193/296 (65%), Gaps = 33/296 (11%)

Query: 1   METTVKIQ---PQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVA 57
           M TTV  Q   PQ+ S    +  F+S       T PF +  R+      +A  TTKA  A
Sbjct: 1   MATTVYGQASLPQMHSLFSKVRPFLSHSPS--FTAPFTRR-RSF---PFSALPTTKAIDA 54

Query: 58  AQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCS--AEV 115
           A MK+ WLDSL+   L   D      NA+S   +GIDPDLSGALA+LK DH G S  A+V
Sbjct: 55  ALMKEKWLDSLS---LTSQDEDTTPENAESSCIIGIDPDLSGALALLKFDHLGSSSFAQV 111

Query: 116 FDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ-------- 167
           +DTPH+PVLVGKRVRKRLDAKS++ L++SLD P G+  Y+EQS P+P+DGKQ        
Sbjct: 112 YDTPHIPVLVGKRVRKRLDAKSIVQLIQSLDVPSGSRVYIEQSNPFPKDGKQVYATAHIR 171

Query: 168 -----GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLF 222
                GW+SGGFGYGLWIG LVASGF V+P+ +  WK  + L+ G+ TKDDSRRVA+ LF
Sbjct: 172 FSSAMGWYSGGFGYGLWIGTLVASGFCVIPVSASLWKRHFQLASGSCTKDDSRRVAAELF 231

Query: 223 PSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKE 278
           PSL SQLKRKKDHG+A+A+LIAAYG+ LK +      +L+ Q  E+++    L+ +
Sbjct: 232 PSLSSQLKRKKDHGRAEALLIAAYGEALKTE------KLLIQPKELLSQVNYLENQ 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297825913|ref|XP_002880839.1| hypothetical protein ARALYDRAFT_320472 [Arabidopsis lyrata subsp. lyrata] gi|297326678|gb|EFH57098.1| hypothetical protein ARALYDRAFT_320472 [Arabidopsis lyrata subsp. lyrata]

 Score =  262 bits (669), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 150/297 (50%), Positives = 192/297 (64%), Gaps = 34/297 (11%)

Query: 1   METTVKIQPQL-QSHCISMNTFVSSKIR---TLCTYPFAQHGRTLLVRAAAAGDTTKAAV 56
           M TT   QP L Q H +       SK+R   +L +  F    R     + +A  TTKA  
Sbjct: 1   MATTAYGQPSLPQMHSLF------SKLRPFLSLSSPSFTAPFRRRRDFSFSALPTTKAID 54

Query: 57  AAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCS--AE 114
            A MK+ WLDSL+   L   D      NA+S   +GIDPDLSGALA+LK DH G S  A+
Sbjct: 55  VALMKEKWLDSLS---LTSQDEDTTPENAESSCVIGIDPDLSGALALLKFDHLGSSSSAQ 111

Query: 115 VFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ------- 167
           V+DTPH+PVLVGKRVRKRLDAKS++ L++SLD P G+  Y+EQS P+P+DGKQ       
Sbjct: 112 VYDTPHIPVLVGKRVRKRLDAKSIVQLIQSLDVPSGSRVYIEQSNPFPKDGKQVYATTHI 171

Query: 168 ------GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTL 221
                 GW+SGGFGYGLWIG LVASGF V+P+ +  WK  + L+ G+ TKDDSRRVA+ L
Sbjct: 172 HFSSVMGWYSGGFGYGLWIGTLVASGFCVIPVSASLWKRHFQLASGSCTKDDSRRVAAEL 231

Query: 222 FPSLCSQLKRKKDHGKADAVLIAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKE 278
           FPSL +QLKRKKDHG+A+A+LIAAYG+ LK +      +L+ Q  E+V+    L+ +
Sbjct: 232 FPSLSTQLKRKKDHGRAEALLIAAYGEALKTE------KLLIQPQELVSQVNYLENQ 282

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555307|ref|XP_003545975.1| PREDICTED: uncharacterized protein LOC100790125 [Glycine max]

 Score =  261 bits (667), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 128/201 (63%), Positives = 156/201 (77%), Gaps = 7/201 (3%)

Query: 55  AVAAQMKQNWLDSLTFP-PLHVHDLTANQT----NADSQWALGIDPDLSGALAVLKSDHN 109
           A   Q K+NWL SL+ P P   H L         N  S+W LGIDPD+SGA+A+LK+  +
Sbjct: 70  ASDTQFKENWLASLSNPFPEKTHLLNGEHEPTHQNDGSKWVLGIDPDVSGAVALLKTHGS 129

Query: 110 GCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ 167
            CSA+VFD+PH+ +LVGK    R+RLDAKS++ L+    APIGTTAY+EQS+PYPQDGKQ
Sbjct: 130 VCSAQVFDSPHVKILVGKNKTTRRRLDAKSVVELVCGFRAPIGTTAYIEQSLPYPQDGKQ 189

Query: 168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCS 227
           GWWSGGFGYGLWIGILVASGFSV+P+PS TWK  + LSG  +TKDDSRR+ASTLFPS+ S
Sbjct: 190 GWWSGGFGYGLWIGILVASGFSVIPVPSFTWKAKFKLSGNGTTKDDSRRLASTLFPSMTS 249

Query: 228 QLKRKKDHGKADAVLIAAYGK 248
            L RKKDHG+A+A+LIAAYG+
Sbjct: 250 MLSRKKDHGRAEALLIAAYGQ 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105997|ref|XP_002314007.1| predicted protein [Populus trichocarpa] gi|222850415|gb|EEE87962.1| predicted protein [Populus trichocarpa]

 Score =  232 bits (592), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 112/167 (67%), Positives = 131/167 (78%), Gaps = 10/167 (5%)

Query: 53  KAAVAAQMKQNWLDSLTFP--------PLHVHDLTANQTNADSQWALGIDPDLSGALAVL 104
           K A  AQ+KQNWLDSLTFP         L   DL  N  N  S W +G+DPD+SGALA+L
Sbjct: 67  KVADVAQLKQNWLDSLTFPLPNETENTNLGGDDLARN--NVGSNWVIGVDPDVSGALALL 124

Query: 105 KSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD 164
           K D +GCSA+VFD+PHL V+VGK +RKRLD KS++ L+RS DAPIGTTAYVEQS P+PQD
Sbjct: 125 KIDESGCSAQVFDSPHLKVMVGKGIRKRLDVKSIVQLIRSFDAPIGTTAYVEQSTPFPQD 184

Query: 165 GKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTK 211
           GKQGWWSGGFGYGLWIG+LVASGFSVVP+PS+TWK+   L+GG  TK
Sbjct: 185 GKQGWWSGGFGYGLWIGVLVASGFSVVPVPSMTWKSDLELAGGRCTK 231

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334184493|ref|NP_001189612.1| uncharacterized protein [Arabidopsis thaliana] gi|330252803|gb|AEC07897.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  231 bits (589), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 142/336 (42%), Positives = 187/336 (55%), Gaps = 73/336 (21%)

Query: 1   METTVKIQ---PQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVA 57
           M TTV  Q   PQ+ S    +  F+S       T PF +  R+      +A  TTKA  A
Sbjct: 1   MATTVYGQASLPQMHSLFSKVRPFLSHSPSF--TAPFTRR-RSF---PFSALPTTKAIDA 54

Query: 58  AQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPD--------------------- 96
           A MK+ WLDSL+   L   D      NA+S   +GIDPD                     
Sbjct: 55  ALMKEKWLDSLS---LTSQDEDTTPENAESSCIIGIDPDLSGALALLKFDHLGSSSFAQN 111

Query: 97  ----------------------LSGALAVLKSDHNG---CSA---------EVFDTPHLP 122
                                 L G+  + + +      C +         EV+DTPH+P
Sbjct: 112 QTYYQSWLCFEHLVLMLRNYLSLQGSYVICEKNRECEGFCESFMLLCLVQFEVYDTPHIP 171

Query: 123 VLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGI 182
           VLVGKRVRKRLDAKS++ L++SLD P G+  Y+EQS P+P+DGKQGW+SGGFGYGLWIG 
Sbjct: 172 VLVGKRVRKRLDAKSIVQLIQSLDVPSGSRVYIEQSNPFPKDGKQGWYSGGFGYGLWIGT 231

Query: 183 LVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVL 242
           LVASGF V+P+ +  WK  + L+ G+ TKDDSRRVA+ LFPSL SQLKRKKDHG+A+A+L
Sbjct: 232 LVASGFCVIPVSASLWKRHFQLASGSCTKDDSRRVAAELFPSLSSQLKRKKDHGRAEALL 291

Query: 243 IAAYGKGLKLDSSHLSGELVPQRSEVVTTAQLLQKE 278
           IAAYG+ LK +      +L+ Q  E+++    L+ +
Sbjct: 292 IAAYGEALKTE------KLLIQPKELLSQVNYLENQ 321

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	281
TAIR|locus:2097129	195	AT3G43910 "AT3G43910" [Arabido	0.629	0.907	0.418	3.5e-27
TAIR|locus:2097124	84	AT3G43900 "AT3G43900" [Arabido	0.192	0.642	0.473	5.7e-06

TAIR|locus:2097129 AT3G43910 "AT3G43910" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 80/191 (41%), Positives = 115/191 (60%)

Query:    60 MKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNG-CSAEVFDT 118
             MKQ  L+ L+    +  ++   Q N    W +GIDP+LSGALAVLK D  G C A+V+DT
Sbjct:     1 MKQKSLNPLSSSSPNYDEMI--QENFKPHWIIGIDPNLSGALAVLKFDDKGSCFAQVYDT 58

Query:   119 PHLPVLVGKRVRKR-LDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYG 177
             P L V+V + +R R  + KSM+ L+RSLD P GT A+V + I +P++    + + G G G
Sbjct:    59 PQLEVVV-QNIRTRSFNEKSMLELIRSLDVPSGTKAFVAKYI-HPENAITAY-NDGLGCG 115

Query:   178 LWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRK-KDHG 236
             LW   L+ S  SV+ +   TW   + LS    + D  R++A  +FPSL  +L  K  D+ 
Sbjct:   116 LWT--LLTSSISVIYVTPSTWDKHFNLS--IWSLDGGRKLALEMFPSL--KLTTKIDDNA 169

Query:   237 KADAVLIAAYG 247
             +A+A+LIAAYG
Sbjct:   170 RANALLIAAYG 180

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2097124 AT3G43900 "AT3G43900" [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 5.7e-06, P = 5.7e-06
 Identities = 27/57 (47%), Positives = 35/57 (61%)

Query:    60 MKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNG-CSAEV 115
             MKQ  L+ L+    +  ++   Q N    W +GIDP+LSGALAVLK D  G CSA+V
Sbjct:    27 MKQKLLNPLSSSSPNYDEMI--QENFKPHWIIGIDPNLSGALAVLKFDDKGSCSAQV 81


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.133   0.407    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      281       267   0.00095  114 3  11 22  0.49    33
                                                     32  0.39    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  212 KB (2117 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  21.32u 0.08s 21.40t   Elapsed:  00:00:01
  Total cpu time:  21.32u 0.08s 21.40t   Elapsed:  00:00:01
  Start:  Fri May 10 06:07:02 2013   End:  Fri May 10 06:07:03 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00017255001 SubName- Full=Chromosome chr6 scaffold_15, whole genome shotgun sequence; (291 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	281
TIGR00228	156	ruvC crossover junction endodeoxyribonuclease RuvC	100.0
COG0817	160	RuvC Holliday junction resolvasome, endonuclease s	100.0
PRK00039	164	ruvC Holliday junction resolvase; Reviewed	100.0
PF02075	149	RuvC: Crossover junction endodeoxyribonuclease Ruv	100.0
cd00529	154	RuvC_resolvase Holliday junction resolvases (HJRs)	100.0
PF04848	143	Pox_A22: Poxvirus A22 protein; InterPro: IPR006932	98.7
PF07066	159	DUF3882: Lactococcus phage M3 protein; InterPro: I	98.68
smart00732	99	YqgFc Likely ribonuclease with RNase H fold. YqgF	97.07
PF04312	138	DUF460: Protein of unknown function (DUF460); Inte	96.98
COG2433	652	Uncharacterized conserved protein [Function unknow	96.91
PF01548	144	DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 T	95.86
PRK00109	138	Holliday junction resolvase-like protein; Reviewed	95.68
PF03652	135	UPF0081: Uncharacterised protein family (UPF0081);	95.39
COG0816	141	Predicted endonuclease involved in recombination (	93.18
COG2410	178	Predicted nuclease (RNAse H fold) [General functio	92.49
PF11215	138	DUF3010: Protein of unknown function (DUF3010); In	90.49
TIGR00250	130	RNAse_H_YqgF RNAse H-fold protein YqgF. This prote	90.4
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	89.14
PF09159	274	Ydc2-catalyt: Mitochondrial resolvase Ydc2 / RNA s	88.39
COG2183	780	Tex Transcriptional accessory protein [Transcripti	83.82
PF14239	176	RRXRR: RRXRR protein	81.51

>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC

Probab=100.00  E-value=1.1e-43  Score=306.30  Aligned_cols=151  Identities=17%  Similarity=0.109  Sum_probs=136.5

Q ss_pred             EEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCch
Q 023513           90 ALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGKQ  167 (281)
Q Consensus        90 ILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNvq  167 (281)
                      |||||||++. |||||+.+++  .+.++++|++++. +.++.+||  ..|++.|.+++. |+||+++||++|  |++|++
T Consensus         1 ILGIDPGl~~tG~gvi~~~~~--~~~~v~~G~I~t~-~~~~~~RL--~~I~~~l~~~i~~y~P~~~aiE~~F--~~~N~~   73 (156)
T TIGR00228         1 ILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTK-VDDLPSRL--KLIYAGVTEIITQFQPNYFAIEQVF--MAKNAD   73 (156)
T ss_pred             CEeECcccccccEEEEEecCC--eEEEEEeeEEECC-CCCHHHHH--HHHHHHHHHHHHHhCCCEEEEeHHh--hccCHH
Confidence            6999999995 9999999888  8899999999876 45788866  899999999998 999999999987  999999


Q ss_pred             hhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHc
Q 023513          168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYG  247 (281)
Q Consensus       168 SA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g  247 (281)
                      |++++|++|||++++++.+||||+||+|++|||+++|+ |+|+|+||++||+++|+..+    .|+ +|+|||||||+||
T Consensus        74 sa~~lg~arGvilla~~~~~ipv~Ey~P~~vKkavtG~-G~A~KeQV~~mV~~lL~l~~----~p~-~DaaDALAiAi~h  147 (156)
T TIGR00228        74 SALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRRLLKLPA----NPQ-ADAADALAIAITH  147 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhcCC-CCCCHHHHHHHHHHHcCCCC----CCC-CCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999776 99999999999999997654    245 7899999999999


Q ss_pred             cccccC
Q 023513          248 KGLKLD  253 (281)
Q Consensus       248 ~~~~~~  253 (281)
                      ....+.
T Consensus       148 ~~~~~~  153 (156)
T TIGR00228       148 AHVSQN  153 (156)
T ss_pred             hcccCc
Confidence            865443

Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.

>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]

Probab=100.00  E-value=3.5e-43  Score=303.42  Aligned_cols=149  Identities=17%  Similarity=0.132  Sum_probs=139.1

Q ss_pred             EEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCchh
Q 023513           91 LGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGKQG  168 (281)
Q Consensus        91 LGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNvqS  168 (281)
                      ||||||++. |||||+.+++  ++..+++|+++++...++..||  +.|++.|.+++. |+||++|||++|  +.+|++|
T Consensus         1 lGIDPGl~~~G~gvI~~~~~--~l~~v~~G~I~t~~~~~l~~RL--~~l~~~l~~vl~~~~P~~~AIE~~F--~~kN~~s   74 (160)
T COG0817           1 LGIDPGLRRTGYGVIEVEGR--QLSYLASGVIRTSSDAPLAERL--KQLYDGLSEVLDEYQPDEVAIEQVF--VNKNADS   74 (160)
T ss_pred             CCcCCCccccceEEEEccCC--eEEEEeeeEEecCCCccHHHHH--HHHHHHHHHHHHHhCCCeeehhHHH--HhcChHH
Confidence            699999995 9999999998  9999999999998889999966  999999999999 999999999987  9999999


Q ss_pred             hhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHcc
Q 023513          169 WWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGK  248 (281)
Q Consensus       169 A~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~  248 (281)
                      ++++||||||+++++++.|+||+||+|+++||+|.|+ |+|+|+||+.||++||+...     ++++|+|||||||+||.
T Consensus        75 ~lklgQARGv~~la~~~~~l~v~eY~p~~VKkavvG~-G~A~K~QVq~MV~~lL~~~~-----~~~~DaADALAiAitHa  148 (160)
T COG0817          75 ALKLGQARGVALLAAARRGLPVFEYTPNQVKKAVVGN-GKADKEQVQHMVKRLLGLEE-----PPPADAADALAIAITHA  148 (160)
T ss_pred             HHHHHHHHHHHHHHHHHcCCChhhccHHHHHHHhhcC-CcccHHHHHHHHHHHhCCCC-----CCCccHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999665 99999999999999998332     67888999999999998


Q ss_pred             ccc
Q 023513          249 GLK  251 (281)
Q Consensus       249 ~~~  251 (281)
                      ...
T Consensus       149 ~~~  151 (160)
T COG0817         149 HRA  151 (160)
T ss_pred             HHH
Confidence            765

>PRK00039 ruvC Holliday junction resolvase; Reviewed

Probab=100.00  E-value=3e-41  Score=292.01  Aligned_cols=154  Identities=19%  Similarity=0.140  Sum_probs=140.4

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCC
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDG  165 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqN  165 (281)
                      |+|||||||++ .||||++.+++  .+.++++|+++++...++..|+  ..|++.|.+++. |+||.++||++|  |++|
T Consensus         2 m~iLGIDPgl~~tG~avi~~~~~--~~~~~~~G~i~t~~~~~~~~Rl--~~I~~~l~~~i~~~~Pd~vaiE~~f--~~~n   75 (164)
T PRK00039          2 MRILGIDPGLRRTGYGVIEVEGR--RLSYVASGVIRTPSDLDLPERL--KQIYDGLSELIDEYQPDEVAIEEVF--FNKN   75 (164)
T ss_pred             CEEEEEccccCceeEEEEEecCC--eEEEEEeeEEECCCCCCHHHHH--HHHHHHHHHHHHHhCCCEEEEehhh--hccC
Confidence            78999999998 59999999887  7899999999887777887865  999999999998 999999999987  8999


Q ss_pred             chhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHH
Q 023513          166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAA  245 (281)
Q Consensus       166 vqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~  245 (281)
                      .+|++++|++||++++++..+||||+||+|++|||+++|+ |+|+|+||+.||+++|+...    .|++||+|||||||+
T Consensus        76 ~~sa~~l~~arGvi~la~~~~~ipv~ey~P~~VKk~vtG~-G~A~K~qV~~mv~~~l~l~~----~~~~~D~aDAlAiA~  150 (164)
T PRK00039         76 PQSALKLGQARGVAILAAAQRGLPVAEYTPLQVKKAVVGY-GRADKEQVQHMVKRLLNLPE----IPKPDDAADALAIAI  150 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHhhhhhcCC-CCCCHHHHHHHHHHHhCCCC----CCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999776 99999999999999997654    267789999999999


Q ss_pred             Hcccccc
Q 023513          246 YGKGLKL  252 (281)
Q Consensus       246 ~g~~~~~  252 (281)
                      ||.....
T Consensus       151 ~h~~~~~  157 (164)
T PRK00039        151 CHAHRRQ  157 (164)
T ss_pred             HHHhhcc
Confidence            9987543

>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []

Probab=100.00  E-value=2.1e-41  Score=287.92  Aligned_cols=147  Identities=21%  Similarity=0.187  Sum_probs=115.5

Q ss_pred             EEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCch
Q 023513           90 ALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGKQ  167 (281)
Q Consensus        90 ILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNvq  167 (281)
                      |||||||++ +||||++.+++  .+.++++|++++....++.+|+  ..|++.|.+++. |+||.++||++|  |++|.+
T Consensus         1 ILGIDPgl~~tG~avi~~~~~--~~~~i~~G~I~t~~~~~~~~Rl--~~I~~~l~~li~~~~P~~vaiE~~f--~~~n~~   74 (149)
T PF02075_consen    1 ILGIDPGLSNTGYAVIEEDGG--KLRLIDYGTIKTSSKDSLPERL--KEIYEELEELIEEYNPDEVAIEEIF--FGKNPK   74 (149)
T ss_dssp             EEEEE--SSEEEEEEEEEETT--EEEEEEEEEEE---S--HHHHH--HHHHHHHHHHHHHH--SEEEEEE-S------HH
T ss_pred             CEEECCCCCCeeEEEEEeeCC--EEEEEEeCeEECCCCCCHHHHH--HHHHHHHHHHHHhhCCCEEEeehhh--hccCHH
Confidence            799999999 59999999888  8999999999988887888866  889999999888 999999999986  899999


Q ss_pred             hhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHc
Q 023513          168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYG  247 (281)
Q Consensus       168 SA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g  247 (281)
                      |++++|++|||+++++..+||||+||+|++|||+++|+ |+|+|+||+.||+++|+...    .++++|+|||||||+||
T Consensus        75 s~~~l~~arGvi~l~~~~~~i~v~~y~P~~vKk~vtG~-G~A~KeqV~~mv~~ll~l~~----~~~~~d~aDAlAiA~~H  149 (149)
T PF02075_consen   75 SALKLGQARGVILLAAAQRGIPVFEYTPSEVKKAVTGN-GRASKEQVAFMVRKLLGLDE----KPKPDDAADALAIALCH  149 (149)
T ss_dssp             HHHHHHHHHHHHHHHHHTTT--EEEEEHHHHHHHHTSS-TT--HHHHHHHHHHHTT--------SS-S-THHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCeEEEECHHHHHHHhhCC-CccCHHHHHHHHHHHhCCCC----CCCccchHhhHhhhhcC
Confidence            99999999999999999999999999999999999666 99999999999999997654    25668899999999998

RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.

>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination

Probab=100.00  E-value=1.9e-37  Score=263.84  Aligned_cols=150  Identities=17%  Similarity=0.118  Sum_probs=136.1

Q ss_pred             eEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCc
Q 023513           89 WALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGK  166 (281)
Q Consensus        89 iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNv  166 (281)
                      .|||||||++. ||||++.+++  .+.++++|++++..+.++..|+  ..|++.|.+++. |+||.++||++|  |++|.
T Consensus         1 rILGIDPGl~~~G~av~~~~~~--~~~~~~~g~i~t~~~~~~~~rl--~~I~~~l~~~i~~~~Pd~vaiE~~~--~~~n~   74 (154)
T cd00529           1 RILGIDPGSRNTGYGVIEQEGR--KLIYLASGVIRTSSDAPLPSRL--KTIYDGLNEVIDQFQPDVVAIERVF--FAKNP   74 (154)
T ss_pred             CEEEEccCcCceEEEEEEeeCC--eEEEEEeeEEECCCCCCHHHHH--HHHHHHHHHHHHHhCCCEEEEEEhh--cccCh
Confidence            38999999995 9999998887  8999999999887777777755  889999999988 999999999987  89999


Q ss_pred             hhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHH
Q 023513          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAY  246 (281)
Q Consensus       167 qSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~  246 (281)
                      +|++++|++||++++++..+|+||+||+|++||++++|+ |+|+|+||++||+++|+...    .|++||+|||||||+|
T Consensus        75 ~s~~~l~~~~Gvi~~~~~~~~i~v~e~~P~~vKk~~tG~-G~A~KeqV~~mv~~~l~~~~----~~~~~d~aDAlaiA~~  149 (154)
T cd00529          75 DSALKLGQARGALILALANRNLPVFEYTPNQVKKAVTGY-GKADKDQVQHMVKRLLNLSE----IPKPDDAADALAVAIT  149 (154)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEccCeeEEEEECC-CCCCHHHHHHHHHHHhCCCC----CCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999776 99999999999999997543    2577889999999999


Q ss_pred             ccc
Q 023513          247 GKG  249 (281)
Q Consensus       247 g~~  249 (281)
                      |..
T Consensus       150 ~~~  152 (154)
T cd00529         150 HAH  152 (154)
T ss_pred             HHh
Confidence            864

HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.

>PF04848 Pox_A22: Poxvirus A22 protein; InterPro: IPR006932 This family, representing the Poxvirus A22 protein, is a Holliday junction resolvase, it specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products

Probab=98.70  E-value=2.4e-07  Score=79.69  Aligned_cols=135  Identities=18%  Similarity=0.118  Sum_probs=91.0

Q ss_pred             ceEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCc
Q 023513           88 QWALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (281)
Q Consensus        88 ~iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNv  166 (281)
                      |+|++||+|... ||.+++.+++  .+.+++....+.+  .        +..+..++++..+..|.+.||++   +.+|+
T Consensus         1 mii~sIDiGikNlA~~iie~~~~--~i~~~~i~~~~~~--~--------~~~~~~~~dl~~~~~d~VlIErQ---~~r~~   65 (143)
T PF04848_consen    1 MIILSIDIGIKNLAYCIIEFEGN--KIRVIDISKVDWS--R--------DWEYRILKDLLKYEADTVLIERQ---PPRNP   65 (143)
T ss_pred             CeEEEEecCCCceeEEEEEcCCC--eEEEEEeccCCcc--c--------chHHHHHHHHhhccCCEEEEecC---CCCCc
Confidence            689999999996 9999999887  7888888876533  1        11222233333366899999998   46675


Q ss_pred             hhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCccc--ccc-cCCCCCCHHHHHHH
Q 023513          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLC--SQL-KRKKDHGKADAVLI  243 (281)
Q Consensus       167 qSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~--~~L-~~kk~ddaADALAI  243 (281)
                      ..  +   -.+-+.+-+...+..|..++|.     +++..=+.-|+.+.+.++.++..-.  ..+ ..+|-||.|||+++
T Consensus        66 ~~--~---i~~fI~~~f~~~~~kv~~v~p~-----~~~~~Y~~RKk~SVe~~~~~~~~~~~~~~i~~~kK~DDlADa~~~  135 (143)
T PF04848_consen   66 NV--K---IVHFIHGYFYIKNTKVICVSPK-----MKGWSYRERKKRSVEVFKNWIKEFGIDDFIPKSKKKDDLADAFCQ  135 (143)
T ss_pred             ch--h---HHHHHHHHhccCCceEEEECcc-----cccCCHHHHHHHHHHHHHHHHHhCCchhhchhhccchHHHHHHHH
Confidence            32  2   2235555666689999999999     5221123458888888888853311  011 22566789999999


Q ss_pred             HHHc
Q 023513          244 AAYG  247 (281)
Q Consensus       244 A~~g  247 (281)
                      |+..
T Consensus       136 al~~  139 (143)
T PF04848_consen  136 ALAY  139 (143)
T ss_pred             HHHH
Confidence            9854

; GO: 0000287 magnesium ion binding, 0000400 four-way junction DNA binding, 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination

>PF07066 DUF3882: Lactococcus phage M3 protein; InterPro: IPR009773 This family consists of several Lactococcus bacteriophage 712, middle-3 (M3) proteins of around 160 residues in length

Probab=98.68  E-value=1.6e-08  Score=87.55  Aligned_cols=143  Identities=21%  Similarity=0.216  Sum_probs=92.1

Q ss_pred             EEEEcCCCC------ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC---CCCCEEEEccccC
Q 023513           90 ALGIDPDLS------GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA---PIGTTAYVEQSIP  160 (281)
Q Consensus        90 ILGIDPGl~------gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~---~~Pd~aaVE~vf~  160 (281)
                      +|.||=.++      +|||+.+  ++    +++-.+...-++++..-+  +.+.+.+.|+.++.   -.-...+||+.  
T Consensus         4 ~LslD~STs~~~~~gTG~A~~~--~~----~~~~~si~~~~k~Ks~~E--R~k~ias~Lk~ii~~~d~~~y~i~IE~~--   73 (159)
T PF07066_consen    4 VLSLDFSTSSKKGEGTGWAFFK--GS----DLVVGSIKAKHKSKSFFE--RAKSIASELKTIIQKYDLKFYIIVIEKP--   73 (159)
T ss_pred             eEEEEEecccCCCCCceeEEec--CC----eEEEeeeeecCcccCHHH--HHHHHHHHHHHHHHHhCCCcceEEEecc--
Confidence            788888777      4999986  32    333222211123444434  23555555554433   33557899994  


Q ss_pred             CCCCCchhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHh--cCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHH
Q 023513          161 YPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWY--GLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKA  238 (281)
Q Consensus       161 ffgqNvqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaV--g~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaA  238 (281)
                      +-+.|.+|++++|.++|.+++.+-..-=.++.+.|++|.+.-  .+. -++-|+|+.+..+.. ....   ..-++||.|
T Consensus        74 vmg~Nqqs~i~l~~~~G~iLG~l~~~~n~~~fIn~s~W~kY~lis~K-~rsrK~~sl~~l~a~-~i~~---~k~~~DDeA  148 (159)
T PF07066_consen   74 VMGPNQQSSIKLGIATGIILGRLINRANGYYFINVSTWRKYWLISYK-DRSRKSMSLELLKAS-EIVD---NKVKDDDEA  148 (159)
T ss_pred             cccccccceEEEEEEeEEEeeeeecccCcEEEecHHHhhhheeeeec-hhhhhhhhHHHHHHh-cccc---ccccccchh
Confidence            489999999999999999999876442279999999999987  332 345566664432222 1111   124577899


Q ss_pred             HHHHHHHHc
Q 023513          239 DAVLIAAYG  247 (281)
Q Consensus       239 DALAIA~~g  247 (281)
                      ||++|.-|-
T Consensus       149 DAi~IgsY~  157 (159)
T PF07066_consen  149 DAILIGSYC  157 (159)
T ss_pred             hhhhhhhhh
Confidence            999998763

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The function of this family is unknown.

>smart00732 YqgFc Likely ribonuclease with RNase H fold

Probab=97.07  E-value=0.0035  Score=48.15  Aligned_cols=87  Identities=16%  Similarity=0.145  Sum_probs=47.9

Q ss_pred             eEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCch
Q 023513           89 WALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ  167 (281)
Q Consensus        89 iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvq  167 (281)
                      .+||||||.+. ++|+++.+|.  .......++   ..  +...  ..+.+.+++.+   ++|+.++|+-.+  +-++..
T Consensus         2 ~ilgiD~Ggt~i~~a~~d~~g~--~~~~~~~~~---~~--~~~~--~~~~l~~~i~~---~~~~~i~Ig~pg--~v~g~~   67 (99)
T smart00732        2 RVLGLDPGRKGIGVAVVDETGK--LADPLEVIP---RT--NKEA--DAARLKKLIKK---YQPDLIVIGLPL--NMNGTA   67 (99)
T ss_pred             cEEEEccCCCeEEEEEECCCCC--EecCEEEEE---ec--Ccch--HHHHHHHHHHH---hCCCEEEEeCCc--CCCCCc
Confidence            48999999884 9999987774  222222211   11  1111  33555566655   459999999754  223322


Q ss_pred             h-hhHHHhhHHHHHHHHHHcCCceeee
Q 023513          168 G-WWSGGFGYGLWIGILVASGFSVVPI  193 (281)
Q Consensus       168 S-A~~vG~ArGVillala~~GIPV~Ey  193 (281)
                      + .+   . +-+.-..-...++||+..
T Consensus        68 ~~~~---~-~~l~~~l~~~~~~pv~~~   90 (99)
T smart00732       68 SRET---E-EAFAELLKERFNLPVVLV   90 (99)
T ss_pred             CHHH---H-HHHHHHHHHhhCCcEEEE
Confidence            1 12   1 222223344568888754

YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.

>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function

Probab=96.98  E-value=0.001  Score=57.23  Aligned_cols=75  Identities=13%  Similarity=0.173  Sum_probs=47.4

Q ss_pred             CCCceEEEEcCCCCceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCC
Q 023513           85 ADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (281)
Q Consensus        85 ~~~~iILGIDPGl~gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgq  164 (281)
                      -...+|+|||||+++|+|+|+-+|+     +++....+         .++...+.++|.++-  .|-.+|--. .++   
T Consensus        29 ~~~~lIVGiDPG~ttgiAildL~G~-----~l~l~S~R---------~~~~~evi~~I~~~G--~PviVAtDV-~p~---   88 (138)
T PF04312_consen   29 SRRYLIVGIDPGTTTGIAILDLDGE-----LLDLKSSR---------NMSRSEVIEWISEYG--KPVIVATDV-SPP---   88 (138)
T ss_pred             CCCCEEEEECCCceeEEEEEecCCc-----EEEEEeec---------CCCHHHHHHHHHHcC--CEEEEEecC-CCC---
Confidence            3556899999999999999999994     44443332         224467888888774  355555433 222   


Q ss_pred             CchhhhHHHhhHHHHH
Q 023513          165 GKQGWWSGGFGYGLWI  180 (281)
Q Consensus       165 NvqSA~~vG~ArGVil  180 (281)
                       ..+.-++...+|+.+
T Consensus        89 -P~~V~Kia~~f~A~l  103 (138)
T PF04312_consen   89 -PETVKKIARSFNAVL  103 (138)
T ss_pred             -cHHHHHHHHHhCCcc
Confidence             334555555555443

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=96.91  E-value=0.0054  Score=63.51  Aligned_cols=53  Identities=25%  Similarity=0.409  Sum_probs=39.6

Q ss_pred             ceEEEEcCCCCceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEc
Q 023513           88 QWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVE  156 (281)
Q Consensus        88 ~iILGIDPGl~gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE  156 (281)
                      .+|+|||||+++|+|+|+-+|     .++++-...         .++...+.++|.++-  +|-.+|.-
T Consensus       244 ~lIVGIDPGiTtgiAvldldG-----evl~~~S~r---------~~~~~eVve~I~~lG--~PvvVAtD  296 (652)
T COG2433         244 SLIVGIDPGITTGIAVLDLDG-----EVLDLESRR---------GIDRSEVVEFISELG--KPVVVATD  296 (652)
T ss_pred             ceEEEeCCCceeeEEEEecCC-----cEEeeeccc---------cCCHHHHHHHHHHcC--CceEEEcc
Confidence            479999999999999999999     566655443         335577888888874  46555543

>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition

Probab=95.86  E-value=0.022  Score=46.80  Aligned_cols=107  Identities=22%  Similarity=0.227  Sum_probs=67.1

Q ss_pred             EEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCchh
Q 023513           90 ALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQG  168 (281)
Q Consensus        90 ILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvqS  168 (281)
                      ++|||=|-.. -.+++...+.  .......+..+        .  .+..+.++|..+.   +..+++|.-.. ++     
T Consensus         1 ~vGiDv~k~~~~v~v~~~~~~--~~~~~~~~~~~--------~--~~~~l~~~l~~~~---~~~v~~E~tg~-y~-----   59 (144)
T PF01548_consen    1 FVGIDVSKDTHDVCVIDPNGE--KLRRFKFENDP--------A--GLEKLLDWLASLG---PVLVVMEATGG-YW-----   59 (144)
T ss_pred             eEEEEcccCeEEEEEEcCCCc--EEEEEEEeccc--------c--chhHHhhhhcccc---ccccccccccc-cc-----
Confidence            6899999995 7777877663  22222222211        0  2245566666552   77888998431 11     


Q ss_pred             hhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHcc
Q 023513          169 WWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGK  248 (281)
Q Consensus       169 A~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~  248 (281)
                             + -+.-.|...|++|+.+.|.++|..-... |                      .+.| .|..||..||.+..
T Consensus        60 -------~-~l~~~L~~~g~~v~~vnp~~~~~~~~~~-~----------------------~~~K-tD~~DA~~ia~~~~  107 (144)
T PF01548_consen   60 -------R-PLADFLQDAGIEVVVVNPLQVKRFRKSL-G----------------------RRAK-TDKIDARAIARLLR  107 (144)
T ss_pred             -------h-hhhhheeccccccccccccccccccccc-c----------------------cccc-ccccchHHHHHHHh
Confidence                   1 2334567789999999999999987431 0                      1123 34888888888777


Q ss_pred             c
Q 023513          249 G  249 (281)
Q Consensus       249 ~  249 (281)
                      .
T Consensus       108 ~  108 (144)
T PF01548_consen  108 R  108 (144)
T ss_pred             c
Confidence            6

This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated

>PRK00109 Holliday junction resolvase-like protein; Reviewed

Probab=95.68  E-value=0.5  Score=40.10  Aligned_cols=93  Identities=17%  Similarity=0.099  Sum_probs=50.6

Q ss_pred             CceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCC
Q 023513           87 SQWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (281)
Q Consensus        87 ~~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqN  165 (281)
                      +|.|||||||.. +|+|+-+..+.      +..|...+..... ..  +.+.|.++++++.   ++..+|=-..  .-+|
T Consensus         3 ~~~iLalD~G~kriGvAv~d~~~~------~a~pl~~i~~~~~-~~--~~~~l~~~i~~~~---i~~iVvGlP~--~~~G   68 (138)
T PRK00109          3 SGRILGLDVGTKRIGVAVSDPLGG------TAQPLETIKRNNG-TP--DWDRLEKLIKEWQ---PDGLVVGLPL--NMDG   68 (138)
T ss_pred             CCcEEEEEeCCCEEEEEEecCCCC------EEcCEEEEEcCCC-ch--HHHHHHHHHHHhC---CCEEEEeccC--CCCC
Confidence            567999999999 59998876543      2233221111111 11  3466666666654   7777776532  2233


Q ss_pred             chhhhHHHhhHHHHHHHHHHcCCceeeeC
Q 023513          166 KQGWWSGGFGYGLWIGILVASGFSVVPIP  194 (281)
Q Consensus       166 vqSA~~vG~ArGVillala~~GIPV~Eyt  194 (281)
                      ..+.. .-..+-.+-......++||+.+.
T Consensus        69 ~~~~~-~~~v~~f~~~L~~~~~~~v~~~D   96 (138)
T PRK00109         69 TEGPR-TERARKFANRLEGRFGLPVVLVD   96 (138)
T ss_pred             CcCHH-HHHHHHHHHHHHHHhCCCEEEEc
Confidence            33221 12223333333445599998875

>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination

Probab=95.39  E-value=0.19  Score=42.48  Aligned_cols=99  Identities=14%  Similarity=0.042  Sum_probs=57.7

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCc-ceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCC
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNG-CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~-~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqN  165 (281)
                      |.+||||+|.. +|+||-+..+.- ..+.++.....        ..  +...|.++++++.   ++.++|=-..  .-+|
T Consensus         1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~--------~~--~~~~l~~li~~~~---i~~iVvGlP~--~~~G   65 (135)
T PF03652_consen    1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNR--------EK--DIEELKKLIEEYQ---IDGIVVGLPL--NMDG   65 (135)
T ss_dssp             -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCC--------CC--CHHHHHHHHHHCC---ECEEEEEEEB--BCTS
T ss_pred             CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCC--------ch--HHHHHHHHHHHhC---CCEEEEeCCc--ccCC
Confidence            67999999999 599999876631 02344432211        11  4577778887765   8888887754  3233


Q ss_pred             chhhhHHHhhHHHHHHHHHHc-CCceeee----ChhhHHHHh
Q 023513          166 KQGWWSGGFGYGLWIGILVAS-GFSVVPI----PSLTWKNWY  202 (281)
Q Consensus       166 vqSA~~vG~ArGVillala~~-GIPV~Ey----tP~qwKkaV  202 (281)
                      ..+.. .-..+-.+-...... ++||+.+    |..+.+..+
T Consensus        66 ~~~~~-~~~v~~f~~~L~~~~~~ipV~~~DEr~TT~~A~~~l  106 (135)
T PF03652_consen   66 SESEQ-ARRVRKFAEELKKRFPGIPVILVDERLTTKEAERRL  106 (135)
T ss_dssp             SC-CC-HHHHHHHHHHHHHHH-TSEEEEEECSCSHHCCHCCH
T ss_pred             CccHH-HHHHHHHHHHHHHhcCCCcEEEECCChhHHHHHHHH
Confidence            22211 113344444445555 9999975    444444444

The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.

>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B

Probab=93.18  E-value=3.6  Score=35.58  Aligned_cols=95  Identities=15%  Similarity=0.098  Sum_probs=59.2

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCc
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNv  166 (281)
                      |.+||+|-|+. +|.|+-+..+.      +..|.-.+.......  ++...|.+++.++.   |+.++|=-...|  +|.
T Consensus         2 ~~ilalD~G~KrIGvA~sd~~~~------~A~pl~~i~~~~~~~--~~~~~l~~li~~~~---~~~vVVGlP~~m--~g~   68 (141)
T COG0816           2 MRILALDVGTKRIGVAVSDILGS------LASPLETIKRKNGKP--QDFNALLKLVKEYQ---VDTVVVGLPLNM--DGT   68 (141)
T ss_pred             ceEEEEecCCceEEEEEecCCCc------cccchhhheeccccH--hhHHHHHHHHHHhC---CCEEEEecCcCC--CCC
Confidence            67999999999 59998876553      333332221222211  36677888887765   899988764322  222


Q ss_pred             hhhhHHHhhHHHHHHHHHHcCCceeeeChh
Q 023513          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSL  196 (281)
Q Consensus       167 qSA~~vG~ArGVillala~~GIPV~EytP~  196 (281)
                      .+- ..-.++-..-......++||+....+
T Consensus        69 ~~~-~~~~~~~f~~~L~~r~~lpv~l~DER   97 (141)
T COG0816          69 EGP-RAELARKFAERLKKRFNLPVVLWDER   97 (141)
T ss_pred             cch-hHHHHHHHHHHHHHhcCCCEEEEcCc
Confidence            222 22244555556678889999998853

subtilis) [DNA replication, recombination, and repair]

>COG2410 Predicted nuclease (RNAse H fold) [General function prediction only]

Probab=92.49  E-value=3.7  Score=37.00  Aligned_cols=66  Identities=21%  Similarity=0.236  Sum_probs=44.2

Q ss_pred             HHHHHcCCceeeeChhhH-HHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHHccccccC-----C
Q 023513          181 GILVASGFSVVPIPSLTW-KNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAYGKGLKLD-----S  254 (281)
Q Consensus       181 lala~~GIPV~EytP~qw-KkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~g~~~~~~-----~  254 (281)
                      -.+...|+||+|.=|... +++++.  ++.+-+.       .+....      --+|.-||++.|.++...+..     -
T Consensus        94 r~l~~~gv~ViEthP~aa~~~~~~l--~r~~l~~-------~ie~~~------~~~~~~dAv~ag~~a~~y~~G~~i~~~  158 (178)
T COG2410          94 RLLESEGVPVIETHPRAALAKAAGL--RRHDLDR-------IIEDVA------VSEDAVDAVLAGLAALLYSLGEAIERE  158 (178)
T ss_pred             HHHHhcCCeEEEecchHHHHHHHhh--ccchhhh-------hhhhhh------hhhhHHHHHHHHHHHHHhCcchhhccc
Confidence            457788999999999999 888776  3343321       121111      135689999999887666654     5


Q ss_pred             CCCCCcc
Q 023513          255 SHLSGEL  261 (281)
Q Consensus       255 ~~~~~~~  261 (281)
                      +.++|.+
T Consensus       159 ~~~~G~i  165 (178)
T COG2410         159 RGLSGSI  165 (178)
T ss_pred             cCCceeE
Confidence            6667765

>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria

Probab=90.49  E-value=2.1  Score=37.11  Aligned_cols=109  Identities=11%  Similarity=0.028  Sum_probs=68.5

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCC
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDG  165 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqN  165 (281)
                      |.|+||+=-.+ .=++++..+++  .+++.|+-+.+....++.. .-..+.....+.++.+ |+.|.++|=+= +-=|+.
T Consensus         1 M~vCGVELkgneaii~ll~~~~~--~~~~pdcr~~k~~l~~~~~-~~~vr~Fq~~f~kl~~dy~Vd~VvIk~R-~~KGKf   76 (138)
T PF11215_consen    1 MKVCGVELKGNEAIICLLSLDDG--LFQLPDCRVRKFSLSDDNS-TEEVRKFQFTFAKLMEDYKVDKVVIKER-ATKGKF   76 (138)
T ss_pred             CeEEEEEEecCeEEEEEEecCCC--ceECCccceeEEEcCCCcc-HHHHHHHHHHHHHHHHHcCCCEEEEEec-ccCCCc
Confidence            67888885444 24778887776  7777777777554444421 1133566667777777 88999888552 112333


Q ss_pred             chhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcC
Q 023513          166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGL  204 (281)
Q Consensus       166 vqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~  204 (281)
                      ..++.  |+---.++  ....+++|..++|.++|.....
T Consensus        77 AGga~--~FKmEaaI--QL~~~~~V~lvs~~~ik~~lKr  111 (138)
T PF11215_consen   77 AGGAV--GFKMEAAI--QLIDDVEVELVSPATIKAQLKR  111 (138)
T ss_pred             cCCch--hHHHHHHH--HhcCCCcEEEECHHHHHHHHhc
Confidence            33332  22222222  1226999999999999999954

>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF

Probab=90.40  E-value=1.5  Score=36.92  Aligned_cols=89  Identities=16%  Similarity=0.006  Sum_probs=47.4

Q ss_pred             EEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCchhh
Q 023513           91 LGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGW  169 (281)
Q Consensus        91 LGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvqSA  169 (281)
                      ||||||.. +|+|+-+..+.      +..|...+.... ...  +...|.++++++.   |+.++|=-..  .-+|..|.
T Consensus         1 laiD~G~kriGvA~~d~~~~------~a~pl~~i~~~~-~~~--~~~~l~~~i~~~~---~~~iVvGlP~--~~dG~~~~   66 (130)
T TIGR00250         1 LGLDFGTKSIGVAGQDITGW------TAQGIPTIKAQD-GEP--DWSRIEELLKEWT---PDKIVVGLPL--NMDGTEGP   66 (130)
T ss_pred             CeEccCCCeEEEEEECCCCC------EEeceEEEEecC-CcH--HHHHHHHHHHHcC---CCEEEEeccC--CCCcCcCH
Confidence            69999999 59998765442      222222111111 111  3356666666654   8777775432  22333322


Q ss_pred             hHHHhhHHHHHHHHHHcCCceeeeC
Q 023513          170 WSGGFGYGLWIGILVASGFSVVPIP  194 (281)
Q Consensus       170 ~~vG~ArGVillala~~GIPV~Eyt  194 (281)
                       ....++-.+--.....++||+.+.
T Consensus        67 -~a~~v~~f~~~L~~~~~~~v~~~D   90 (130)
T TIGR00250        67 -LTERAQKFANRLEGRFGVPVVLWD   90 (130)
T ss_pred             -HHHHHHHHHHHHHHHhCCCEEEEc
Confidence             122333333334455699998764

This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=89.14  E-value=0.47  Score=42.87  Aligned_cols=65  Identities=22%  Similarity=0.259  Sum_probs=28.2

Q ss_pred             CCCCceEEEEcCC--CCc---eEEEE-eeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEcc
Q 023513           84 NADSQWALGIDPD--LSG---ALAVL-KSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQ  157 (281)
Q Consensus        84 ~~~~~iILGIDPG--l~g---GyaVL-e~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~  157 (281)
                      +-+..+++|+|||  ..+   ++.++ ...++  ...+++.-...   +.....  -...+.++...   +.|..+++|.
T Consensus       222 ~~~~~~~~g~D~a~~~~~d~~~~~~~~~~~~~--~~~~~~~~~~~---~~~~~~--~~~~i~~~~~~---~~~~~i~~d~  291 (384)
T PF03237_consen  222 PPDWPIIIGVDPAGGKGGDYTAIVVWEIVDDD--GFYVVDDEYER---GMSPEE--WAERIRELYKK---YNPIKIYIDA  291 (384)
T ss_dssp             -TT--EEEEEE--SSCTTB-EEEEEE-E-SSS--SEEEEEEEEES---SS-TTT--HHHHHHHHHHH---TTS--EEEEE
T ss_pred             CCCceEEEEEECCCCCccCCEEEEEEcccccc--ceEEeeehhhc---CCCHHH--HHHHHHHHHhh---cCceEEEEcC
Confidence            3445678999999  443   44444 23343  44555433221   111111  22344444443   5589999999


Q ss_pred             c
Q 023513          158 S  158 (281)
Q Consensus       158 v  158 (281)
                      .
T Consensus       292 ~  292 (384)
T PF03237_consen  292 N  292 (384)
T ss_dssp             S
T ss_pred             C
Confidence            4

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PF09159 Ydc2-catalyt: Mitochondrial resolvase Ydc2 / RNA splicing MRS1; InterPro: IPR015242 This domain forms a ribonuclease H fold consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif

Probab=88.39  E-value=2.2  Score=40.07  Aligned_cols=133  Identities=14%  Similarity=0.106  Sum_probs=64.8

Q ss_pred             EEEEcCCCCc-eEEEEee------CCCcceeEEeecCCcccc---------------------cccchhhhhcHHHHHHH
Q 023513           90 ALGIDPDLSG-ALAVLKS------DHNGCSAEVFDTPHLPVL---------------------VGKRVRKRLDAKSMIML  141 (281)
Q Consensus        90 ILGIDPGl~g-GyaVLe~------~g~~~~~~vvd~p~i~~~---------------------~~~~l~~rl~~~~I~~l  141 (281)
                      ||+||-|++. +|+.+..      ....-...+.+-..+.+.                     ....+..+.-....+.+
T Consensus         1 ILSIDmGIkNfAy~~l~~~~~~~~~~~~~~p~L~~W~kl~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~a~~a~~L   80 (274)
T PF09159_consen    1 ILSIDMGIKNFAYCKLKVSSDSKKASSSSLPTLNAWDKLNLSSLFSSNWQTEPGKEYFPTEEKEKESFSPRYLAHLAYKL   80 (274)
T ss_dssp             EEEEEE-STTEEEEEEEE--------TTS-EEEEEEEEE-TT-------------SS-TT--------SHHHHHHHHHHH
T ss_pred             CceeecchhhhhhhhhhhcccccccCCCCCccccCCceeecccccccccccccccccCCCCcccCCCCCHHHHHHHHHHH
Confidence            7999999996 9999998      111101222222222111                     11112222333445567


Q ss_pred             HHhhcC-CCCCEEEEccccCCCCCCchh-----hhHHHhhHHHHHHHHHHc---------CCceeeeChhhHHHHh-cCC
Q 023513          142 LRSLDA-PIGTTAYVEQSIPYPQDGKQG-----WWSGGFGYGLWIGILVAS---------GFSVVPIPSLTWKNWY-GLS  205 (281)
Q Consensus       142 L~~l~~-~~Pd~aaVE~vf~ffgqNvqS-----A~~vG~ArGVillala~~---------GIPV~EytP~qwKkaV-g~s  205 (281)
                      +..+.. +.||++.||+.=  |.-|-.+     .+.++-==|.+..++...         +.-|..+.|+.+-..- ...
T Consensus        81 v~~Ll~~~~P~~vlIERQR--~RS~g~savlEwtLrvn~lE~mLyA~L~~~~~~~~~~~~~~~V~~v~P~rv~~fW~~~~  158 (274)
T PF09159_consen   81 VSSLLLPYKPDHVLIERQR--FRSGGSSAVLEWTLRVNILEGMLYAVLYTLRQESKGEQANYVVISVDPQRVTRFWCERF  158 (274)
T ss_dssp             HHHHHHHH--SEEEEEE------T-TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEE-CCHHHHHHHH--
T ss_pred             HHHHcccCCCCEEEEeecc--ccCCCCCccchhHHHHhHHHHHHHHHHHHHHhhcccCCCCeEEEEECHHHHHHHHhccc
Confidence            777766 779999999973  4333232     356665556655555544         3479999999987665 211


Q ss_pred             --------------CCCCCHHHHHHHHHHhCCc
Q 023513          206 --------------GGTSTKDDSRRVASTLFPS  224 (281)
Q Consensus       206 --------------~G~A~KeQVq~MV~~LLp~  224 (281)
                                    .++.+|.-=..+|+.+|..
T Consensus       159 ~~~~~~~~~~~~~~~~~~~K~~ki~Lv~~wL~~  191 (274)
T PF09159_consen  159 PIRDSLNEKKKKKKSSKNSKKIKIDLVRSWLSN  191 (274)
T ss_dssp             ---------HH-----------HHHHHHHHHHT
T ss_pred             ccchhhhhhhcccccchhhHHHHHHHHHHHHHc
Confidence                          1334566667788888743

Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. They are capable of resolving Holliday junctions and cleave DNA after 5'-CT-3, and 5'-TT-3, sequences []. This entry also includes a domain found in the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [, ].; PDB: 1KCF_A.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=83.82  E-value=2.1  Score=46.10  Aligned_cols=38  Identities=24%  Similarity=0.441  Sum_probs=25.6

Q ss_pred             CCCCceEEEEcCCCCc--eEEEEeeCCCcc-eeEEeecCCc
Q 023513           84 NADSQWALGIDPDLSG--ALAVLKSDHNGC-SAEVFDTPHL  121 (281)
Q Consensus        84 ~~~~~iILGIDPGl~g--GyaVLe~~g~~~-~~~vvd~p~i  121 (281)
                      .++++.++|+|||.++  -.||++..|.-| ...++.++..
T Consensus       326 P~~~~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~  366 (780)
T COG2183         326 PAKPKATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPV  366 (780)
T ss_pred             CCCCcceeecCCccccccEEEEEcCCCceeceeEEEcCCCc
Confidence            4666679999999995  488898876422 3444444443

>PF14239 RRXRR: RRXRR protein

Probab=81.51  E-value=1.7  Score=39.09  Aligned_cols=22  Identities=32%  Similarity=0.504  Sum_probs=17.5

Q ss_pred             CCceEEEEcCCCCc-eEEEEeeC
Q 023513           86 DSQWALGIDPDLSG-ALAVLKSD  107 (281)
Q Consensus        86 ~~~iILGIDPGl~g-GyaVLe~~  107 (281)
                      ..-+.||||||+.. |+||+...
T Consensus        49 ~qpi~lgiDpGsk~tGiav~~~~   71 (176)
T PF14239_consen   49 TQPIRLGIDPGSKTTGIAVVSEK   71 (176)
T ss_pred             ccCEEEEECCCCCeEEEEEEeCC
Confidence            34468999999995 99998654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	281
4ep4_A	166	Crossover junction endodeoxyribonuclease RUVC; res	100.0
1hjr_A	158	Holliday junction resolvase (RUVC); site-specific	100.0
1vhx_A	150	Putative holliday junction resolvase; structural g	99.19
1kcf_A	258	Hypothetical 30.2 KD protein C25G10.02 in chromoso	97.53
1iv0_A	98	Hypothetical protein; rnaseh-like, YQGF, structura	95.0
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	94.97
1nu0_A	138	Hypothetical protein YQGF; structural genomics, st	94.38
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	89.63
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	82.56
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	82.31

>4ep4_A Crossover junction endodeoxyribonuclease RUVC; resolvase, hydrolase; 1.28A {Thermus thermophilus} PDB: 4ep5_A

Probab=100.00  E-value=1.6e-43  Score=306.19  Aligned_cols=156  Identities=15%  Similarity=0.116  Sum_probs=139.2

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCc-ceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCC
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNG-CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQD  164 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~-~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgq  164 (281)
                      |+|||||||++ .||||++.++++ -.+.++++|+++++.+.++.+|+  ..|++.|.+++. |+||.++||++|  |++
T Consensus         1 MrILGIDPGl~~tG~gvi~~~g~~~~~~~~v~~G~I~t~~~~~~~~RL--~~I~~~l~~~i~~~~Pd~vaiE~~F--~~~   76 (166)
T 4ep4_A            1 MVVAGIDPGITHLGLGVVAVEGKGALKARLLHGEVVKTSPQEPAKERV--GRIHARVLEVLHRFRPEAVAVEEQF--FYR   76 (166)
T ss_dssp             CEEEEEECCSSEEEEEEEEECSSSSSCEEEEEEEEEECCTTSCHHHHH--HHHHHHHHHHHHHHCCSEEEEECCC--CSS
T ss_pred             CEEEEEccccCceEEEEEEecCCccceEEEEEeCeEECCCCCCHHHHH--HHHHHHHHHHHHHhCCCEEEEeehh--hcc
Confidence            68999999999 499999988741 14678999999888888888866  899999999888 999999999987  899


Q ss_pred             CchhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHH
Q 023513          165 GKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIA  244 (281)
Q Consensus       165 NvqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA  244 (281)
                      |++|++++||+|||++++++++||||+||+|++||++++|+ |+|+|+||+.||+++|+..+    .|++||+|||||||
T Consensus        77 n~~sal~lgqarGv~~la~~~~glpv~eytP~~vKkavtG~-G~A~K~QV~~mV~~lL~l~~----~p~~~DaADALAiA  151 (166)
T 4ep4_A           77 QNELAYKVGWALGAVLVAAFEAGVPVYAYGPMQVKQALAGH-GHAAKEEVALMVRGILGLKE----APRPSHLADALAIA  151 (166)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHTCCEEEECHHHHHHHHHSS-TTCCHHHHHHHHHHHTTCSS----CCSSHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhcCC-CCCCHHHHHHHHHHHhcCCC----CCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999666 99999999999999998754    26778899999999


Q ss_pred             HHcccccc
Q 023513          245 AYGKGLKL  252 (281)
Q Consensus       245 ~~g~~~~~  252 (281)
                      +||.....
T Consensus       152 ich~~~~~  159 (166)
T 4ep4_A          152 LTHAFYAR  159 (166)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhh
Confidence            99987533

>1hjr_A Holliday junction resolvase (RUVC); site-specific recombinase; 2.50A {Escherichia coli} SCOP: c.55.3.6

Probab=100.00  E-value=4.7e-43  Score=300.46  Aligned_cols=150  Identities=17%  Similarity=0.105  Sum_probs=136.6

Q ss_pred             ceEEEEcCCCCc-eEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCC
Q 023513           88 QWALGIDPDLSG-ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDG  165 (281)
Q Consensus        88 ~iILGIDPGl~g-GyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqN  165 (281)
                      |+|||||||++. ||||++.+|+  .+.++++|+++++ +.++..|+  ..|++.|.+++. |+||.++||++|  |++|
T Consensus         1 m~ILGIDPGl~~tG~gvi~~~g~--~~~~v~~G~i~t~-~~~~~~Rl--~~i~~~l~~~i~~~~Pd~vaiE~vf--~~~n   73 (158)
T 1hjr_A            1 AIILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTK-VDDLPSRL--KLIYAGVTEIITQFQPDYFAIEQVF--MAKN   73 (158)
T ss_dssp             CEEEEEECCSSEEEEEEEEEETT--EEEEEEEEEEECC-CSCHHHHH--HHHHHHHHHHHHHHCCSEEEEEECC--CCCC
T ss_pred             CEEEEEccCCCCeeEEEEEecCC--eEEEEEeeEEECC-CCCHHHHH--HHHHHHHHHHHHHcCCCEEEEeecc--cccC
Confidence            679999999985 9999999888  8999999999887 67777765  888888888888 889999999987  8999


Q ss_pred             chhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHH
Q 023513          166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAA  245 (281)
Q Consensus       166 vqSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~  245 (281)
                      ++|++++||+||+++++++.+||||+||+|++|||+++|+ |+|+|+||+.||+++|+..+    .|++ |+|||||||+
T Consensus        74 ~~s~~~lgqarGv~~~a~~~~~ipv~eytp~~vKkavtG~-G~A~K~qV~~mv~~ll~l~~----~p~~-DaADALAiAi  147 (158)
T 1hjr_A           74 ADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRTLLKLPA----NPQA-DAADALAIAI  147 (158)
T ss_dssp             TTTHHHHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHTSS-SSCCHHHHHHHHHHHTTCCC----CCSS-CTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhhCC-CCCcHHHHHHHHHHHcCCCC----CCCC-CHHHHHHHHH
Confidence            9999999999999999999999999999999999999666 99999999999999998764    2556 8999999999


Q ss_pred             Hcccc
Q 023513          246 YGKGL  250 (281)
Q Consensus       246 ~g~~~  250 (281)
                      ||...
T Consensus       148 ~h~~~  152 (158)
T 1hjr_A          148 THCHV  152 (158)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            99764

>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8

Probab=99.19  E-value=7.8e-11  Score=99.53  Aligned_cols=104  Identities=8%  Similarity=-0.090  Sum_probs=76.5

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCc
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNv  166 (281)
                      |.|||||||++ +||||++..+..    ....+++... ..++..  +++.|.+++.+   |+|+.++||..+   ..|-
T Consensus         3 mriLGiDpG~~riGvAv~d~~g~~----a~p~~~I~~~-~~r~~~--~~~~l~~li~~---~~~~~ivVGlP~---~~nG   69 (150)
T 1vhx_A            3 LRILGLDLGTKTLGVALSDEMGWT----AQGIETIKIN-EAEGDY--GLSRLSELIKD---YTIDKIVLGFPK---NMNG   69 (150)
T ss_dssp             EEEEEEEECSSEEEEEEECTTSSS----EEEEEEEECB-GGGTBC--CHHHHHHHHTT---SEEEEEEEECCC---CBTT
T ss_pred             CEEEEEEccCCEEEEEEEECCCCE----EeeEEEEEcC-CcchHH--HHHHHHHHHHH---cCCCEEEEeeee---cCCc
Confidence            67999999999 599999987752    1123444321 112222  44556666655   459999999974   4455


Q ss_pred             hhhhHHHhhHHHHHHHHHHcCCceee----eChhhHHHHhcC
Q 023513          167 QGWWSGGFGYGLWIGILVASGFSVVP----IPSLTWKNWYGL  204 (281)
Q Consensus       167 qSA~~vG~ArGVillala~~GIPV~E----ytP~qwKkaVg~  204 (281)
                      ++....+++++++..+....++||++    |||.+.|+.+..
T Consensus        70 t~~~~~~~ar~f~~~L~~~~~lpV~~vDEr~Ts~~Ak~~l~~  111 (150)
T 1vhx_A           70 TVGPRGEASQTFAKVLETTYNVPVVLWDERLTTMAAEKMLIA  111 (150)
T ss_dssp             BCCHHHHHHHHHHHHHHHHHCSCEEEECCSSCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHhhCCCEEEecCCCCHHHHHHHHHH
Confidence            66788999999998888888999999    999999999943

>1kcf_A Hypothetical 30.2 KD protein C25G10.02 in chromosome I; beta-alpha-beta motif, RUVC resolvase family, hydrolase; 2.30A {Schizosaccharomyces pombe} SCOP: a.140.2.1 c.55.3.7

Probab=97.53  E-value=0.00037  Score=63.76  Aligned_cols=157  Identities=13%  Similarity=0.053  Sum_probs=90.0

Q ss_pred             eEEEEcCCCCc-eEEEEeeCCCcc----eeEEeecCCcc-c--ccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEcccc
Q 023513           89 WALGIDPDLSG-ALAVLKSDHNGC----SAEVFDTPHLP-V--LVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSI  159 (281)
Q Consensus        89 iILGIDPGl~g-GyaVLe~~g~~~----~~~vvd~p~i~-~--~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf  159 (281)
                      .|++||.|+.. +|+.++..+...    ..+.++..... +  ..+............+.++..+.. +.||++.||+.-
T Consensus        41 sIlSID~GikNlAyc~l~~~~~~~p~l~~W~kl~l~~~~~~~~~~k~~~~p~~~~~~a~~Li~~ll~~~~pd~vlIErQr  120 (258)
T 1kcf_A           41 RVLGIDLGIKNFSYCFASQNEDSKVIIHNWSVENLTEKNGLDIQWTEDFQPSSMADLSIQLFNTLHEKFNPHVILMERQR  120 (258)
T ss_dssp             SEEEEEECSTTEEEEEEEECTTSCEEEEEEEEECTTSCCTTCCCCCCCCSHHHHHHHHHHHHHHHHHHHCCSEEEEEECC
T ss_pred             cEEEEecCCCceEEEEEccCCCCCCeeecceeeccccccccccccccCcChHHHHHHHHHHHHHhhccCCCCEEEEeecC
Confidence            59999999996 999998532211    34444433211 0  001222212233455666666544 779999999985


Q ss_pred             CCCCCCchhhh-----HHHhhHHHHHHHHHH----------cCCceeeeChhhHHHHhc----CCCCCCCHHHHHHHHHH
Q 023513          160 PYPQDGKQGWW-----SGGFGYGLWIGILVA----------SGFSVVPIPSLTWKNWYG----LSGGTSTKDDSRRVAST  220 (281)
Q Consensus       160 ~ffgqNvqSA~-----~vG~ArGVillala~----------~GIPV~EytP~qwKkaVg----~s~G~A~KeQVq~MV~~  220 (281)
                        +.-+ .+++     .++---|.+..++..          ....|..+.|..+-+...    ....+..|.....+|+.
T Consensus       121 --~Rs~-~s~v~e~~Lrv~ilE~ML~a~l~~~~~~~~~~~~~~~~V~~~~p~~v~~yw~~~~~~~~~~~~Kk~~i~lv~~  197 (258)
T 1kcf_A          121 --YRSG-IATIPEWTLRVNMLESMLYALHYAEKRNSIEQKIQYPFLLSLSPKSTYSYWASVLNTKASFSKKKSRVQMVKE  197 (258)
T ss_dssp             --CCTT-TCCHHHHHHHHHHHHHHHHHHHHHHHHC-------CCEEEECCHHHHHHHHHHHHC-------CCCHHHHHHH
T ss_pred             --cccC-cccccchhhhHhHHHHHHHHHHHHHHhhcccccccceeEEecCHHHHHHhhhhcccccchhHHHHHHHHHHHH
Confidence              4444 4432     333333444444432          235788899999998762    11123457777788888


Q ss_pred             hCCccccc--------------ccCCCCCCHHHHHHHHHHcc
Q 023513          221 LFPSLCSQ--------------LKRKKDHGKADAVLIAAYGK  248 (281)
Q Consensus       221 LLp~~~~~--------------L~~kk~ddaADALAIA~~g~  248 (281)
                      +|......              ...+|.||-||+|+-|+...
T Consensus       198 ~L~~~~~~~~~~e~~~~~~~~~~~~~K~DDLaDslLq~lawl  239 (258)
T 1kcf_A          198 LIDGQKILFENEEALYKWNNGSRVEFKKDDMADSALIASGWM  239 (258)
T ss_dssp             HHHTTSEEESSHHHHHHHHHCCSTTTHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCcCcCcHHHHHHHhcccccCcchHHHHHHHHHHHHHH
Confidence            87433100              13467789999999888543

>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8

Probab=95.00  E-value=0.11  Score=40.75  Aligned_cols=90  Identities=14%  Similarity=0.029  Sum_probs=47.8

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCc-ceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCC
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNG-CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~-~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqN  165 (281)
                      |.|||||+|.. +|+|+-+..+.- ..+.++..       . ....  +.+.|.+++.++.   ++.++|=-..  .-+|
T Consensus         1 mriLglD~G~kriGvAvsd~~~~~A~pl~ti~~-------~-~~~~--~~~~l~~li~e~~---v~~iVvGlP~--~mdG   65 (98)
T 1iv0_A            1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVR-------K-TLEE--DVEALLDFVRREG---LGKLVVGLPL--RTDL   65 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEEC-------C-CHHH--HHHHHHHHHHHHT---CCEEEEECCC--CCCS
T ss_pred             CcEEEEEeCCCEEEEEEEeCCCCeeeeeEEEEc-------c-CcHH--HHHHHHHHHHHcC---CCEEEEeecc--CCCC
Confidence            35899999999 599998765420 02333321       1 1112  4566777777765   8888876532  2222


Q ss_pred             chhhhHHHhhHHHHHHHHHHcCCceeeeC
Q 023513          166 KQGWWSGGFGYGLWIGILVASGFSVVPIP  194 (281)
Q Consensus       166 vqSA~~vG~ArGVillala~~GIPV~Eyt  194 (281)
                      ..+. ..-.++-.+-..... ++||+.+.
T Consensus        66 t~~~-~~~~~~~f~~~L~~~-~lpV~~~D   92 (98)
T 1iv0_A           66 KESA-QAGKVLPLVEALRAR-GVEVELWD   92 (98)
T ss_dssp             SSCC-CSSTTHHHHHHHHHT-TCEEEEEC
T ss_pred             CcCH-HHHHHHHHHHHHhcC-CCCEEEEC
Confidence            2111 111222222222334 89998764

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=94.97  E-value=0.037  Score=57.62  Aligned_cols=80  Identities=21%  Similarity=0.299  Sum_probs=48.3

Q ss_pred             HHHHhhhcccccccCCCCCCCccccccCCCCCceEEEEcCCCC-c-eEEEEeeCCCcceeEEeecCCc-ccccccchhhh
Q 023513           56 VAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLS-G-ALAVLKSDHNGCSAEVFDTPHL-PVLVGKRVRKR  132 (281)
Q Consensus        56 ~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~iILGIDPGl~-g-GyaVLe~~g~~~~~~vvd~p~i-~~~~~~~l~~r  132 (281)
                      ....+.+|.-+-|.-+|            ++.+.|||||||.+ + .+++|+..|+     ++++.++ +......... 
T Consensus       309 ai~vf~~nL~~lLl~aP------------~~~~~vlg~dpg~r~g~k~a~vd~~G~-----~l~~~~iy~~~~~~~~~~-  370 (785)
T 3bzc_A          309 AISVFARNLHDLLLAAP------------AGPRATLGLDPGLRTGVKVAVVDATGK-----LLDTATVYPHAPKNQWDQ-  370 (785)
T ss_dssp             HHHHHHHHHHHHHTSCC------------CCSCCEEEEECCSSSCEEEEEECTTSC-----EEEEEEECCSGGGCCHHH-
T ss_pred             HHHHHHHHHHHHHcCCC------------CCCCeEEEECCCCcCceEEEEECCCCC-----EEEEEEEecCCchhHHHH-
Confidence            34555666555555444            33456999999987 4 6899988884     5555554 2212221212 


Q ss_pred             hcHHHHHHHHHhhcCCCCCEEEEcc
Q 023513          133 LDAKSMIMLLRSLDAPIGTTAYVEQ  157 (281)
Q Consensus       133 l~~~~I~~lL~~l~~~~Pd~aaVE~  157 (281)
                       ....|.+++.++.   |+.++|=.
T Consensus       371 -~~~~l~~li~~~~---~~~IaIGn  391 (785)
T 3bzc_A          371 -TLAVLAALCAKHQ---VELIAIGN  391 (785)
T ss_dssp             -HHHHHHHHHHHHT---CCEEEEES
T ss_pred             -HHHHHHHHHHHcC---CCEEEECC
Confidence             3355666666654   99999854

>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A

Probab=94.38  E-value=0.3  Score=40.41  Aligned_cols=99  Identities=13%  Similarity=-0.007  Sum_probs=54.7

Q ss_pred             eEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCCCch
Q 023513           89 WALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ  167 (281)
Q Consensus        89 iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgqNvq  167 (281)
                      .|||||||.. +|+||-+..+.  .  .....+++  .. ....  +...|.+++.++.   |+.++|=-..  .-+|..
T Consensus         4 ~iLglD~G~kriGvAvsd~~~~--~--A~pl~ti~--~~-~~~~--~~~~l~~li~e~~---v~~iVvGlP~--~mdGt~   69 (138)
T 1nu0_A            4 TLMAFDFGTKSIGVAVGQRITG--T--ARPLPAIK--AQ-DGTP--DWNIIERLLKEWQ---PDEIIVGLPL--NMDGTE   69 (138)
T ss_dssp             EEEEEECCSSEEEEEEEETTTT--E--EEEEEEEE--EE-TTEE--CHHHHHHHHHHHC---CSEEEEEEEE--CTTSCB
T ss_pred             eEEEEEeCCCEEEEEEEcCCCC--E--EeeEEEEE--cC-Ccch--HHHHHHHHHHHcC---CCEEEEeccc--CCCcCc
Confidence            5899999999 59999987654  1  11122222  11 1111  5578888888876   8888876532  223322


Q ss_pred             hhhHHHhhHHHHHHHHHHcCCceeee----ChhhHHHHh
Q 023513          168 GWWSGGFGYGLWIGILVASGFSVVPI----PSLTWKNWY  202 (281)
Q Consensus       168 SA~~vG~ArGVillala~~GIPV~Ey----tP~qwKkaV  202 (281)
                      + -..-.++-.+-......++||+.+    |..+-++.+
T Consensus        70 ~-~~~~~~~~f~~~L~~~~~lpV~~~DERlTT~~A~~~l  107 (138)
T 1nu0_A           70 Q-PLTARARKFANRIHGRFGVEVKLHDERLSTVEARSGL  107 (138)
T ss_dssp             C-HHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCC----
T ss_pred             C-HHHHHHHHHHHHHHHHhCCCEEEEcCCcCHHHHHHHH
Confidence            2 222233444444444569999875    454555444

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=89.63  E-value=1  Score=44.37  Aligned_cols=23  Identities=4%  Similarity=-0.165  Sum_probs=18.5

Q ss_pred             CCCCCHHHHHHHHHHccccccCC
Q 023513          232 KKDHGKADAVLIAAYGKGLKLDS  254 (281)
Q Consensus       232 kk~ddaADALAIA~~g~~~~~~~  254 (281)
                      -.+||.+|||++|+++...-.+.
T Consensus       563 g~HdD~~dAlalA~~~~~~~~~~  585 (592)
T 3cpe_A          563 GYHDDLVMSLVIFGWLSTQSKFI  585 (592)
T ss_dssp             TCCCHHHHHHHHHHHHHHSGGGT
T ss_pred             CCCCHHHHHHHHHHHHHhhhHHH
Confidence            46889999999999988755554

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=82.56  E-value=2.5  Score=45.33  Aligned_cols=87  Identities=8%  Similarity=0.073  Sum_probs=47.9

Q ss_pred             HHHHHhhhcccccccCCCCCCCccccccCCCC-CceEEEEcCCCC-----c-eEEEEeeCCCcceeEEeecCCc-ccccc
Q 023513           55 AVAAQMKQNWLDSLTFPPLHVHDLTANQTNAD-SQWALGIDPDLS-----G-ALAVLKSDHNGCSAEVFDTPHL-PVLVG  126 (281)
Q Consensus        55 ~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~-~~iILGIDPGl~-----g-GyaVLe~~g~~~~~~vvd~p~i-~~~~~  126 (281)
                      ..+..+.+|..+-|.-+|-.-+ ..     .+ ...|||||||.+     + -+++|+..|     .++++.++ +.+.+
T Consensus       491 ~ai~~f~~nL~~lL~~aP~~p~-~~-----~g~~~~VlaldpG~~~~~~~g~k~a~vd~~G-----~~l~~~~i~~~~~~  559 (1030)
T 3psf_A          491 LVAKTVRHKFMTKLDQAPFIPN-VR-----DPKIPKILSLTCGQGRFGADAIIAVYVNRKG-----DFIRDYKIVDNPFD  559 (1030)
T ss_dssp             HHHHHHHHHHHHHHCCCCCCSC-TT-----SCCCCCEEEEECTTCCTTTSCEEEEEECTTS-----CEEEEEEECSCTTC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCC-cc-----cCCCCeEEEecCCCCCCCCCCeEEEEECCCC-----CEEEEEEEcCCCCC
Confidence            3456677777766666552111 11     11 335999999985     2 468898887     45555555 21111


Q ss_pred             cchhhhhcHHHHHHHHHhhcCCCCCEEEEc
Q 023513          127 KRVRKRLDAKSMIMLLRSLDAPIGTTAYVE  156 (281)
Q Consensus       127 ~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE  156 (281)
                      ..-+. -..+.|.+++.++   +|+.+||=
T Consensus       560 ~~~~~-~~~~~l~~li~~~---~~~~IaIG  585 (1030)
T 3psf_A          560 KTNPE-KFEDTLDNIIQSC---QPNAIGIN  585 (1030)
T ss_dssp             SSCCH-HHHHHHHHHHHHH---CCSEEEEC
T ss_pred             hhhHH-HHHHHHHHHHHHc---CCcEEEEC
Confidence            11111 1124555566555   49999983

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=82.31  E-value=2.4  Score=46.26  Aligned_cols=87  Identities=8%  Similarity=0.073  Sum_probs=48.0

Q ss_pred             HHHHHhhhcccccccCCCCCCCccccccCCCC-CceEEEEcCCCC-----c-eEEEEeeCCCcceeEEeecCCc-ccccc
Q 023513           55 AVAAQMKQNWLDSLTFPPLHVHDLTANQTNAD-SQWALGIDPDLS-----G-ALAVLKSDHNGCSAEVFDTPHL-PVLVG  126 (281)
Q Consensus        55 ~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~-~~iILGIDPGl~-----g-GyaVLe~~g~~~~~~vvd~p~i-~~~~~  126 (281)
                      ..+..+.+|..+-|.-+|-.-+ ..     .+ ...|||||||.+     + -+++|+..|     .++++.++ +.+.+
T Consensus       488 ~ai~~f~~nL~~lL~~aP~~p~-~~-----lg~~~~VlaldpG~r~~g~~g~k~a~vD~~G-----~vl~~~~i~~~~~~  556 (1219)
T 3psi_A          488 LVAKTVRHKFMTKLDQAPFIPN-VR-----DPKIPKILSLTCGQGRFGADAIIAVYVNRKG-----DFIRDYKIVDNPFD  556 (1219)
T ss_dssp             HHHHHHHHHHHHHHCBCCCCSS-SS-----SCCCCCEEEEECTTCCTTTTCEEEEEECTTS-----CEEEEEEECSCTTC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCC-cc-----cCCCCeEEEecCCCCCCCCCceEEEEECCCC-----CEEEEEEEcCCCCC
Confidence            3446677777666665552111 11     11 335899999996     2 468898887     45555555 21111


Q ss_pred             cchhhhhcHHHHHHHHHhhcCCCCCEEEEc
Q 023513          127 KRVRKRLDAKSMIMLLRSLDAPIGTTAYVE  156 (281)
Q Consensus       127 ~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE  156 (281)
                      ..-+. -..+.|.+++.++   +|+.+||=
T Consensus       557 ~~~~~-~a~~~l~~li~~~---~~~vIaIG  582 (1219)
T 3psi_A          557 KTNPE-KFEDTLDNIIQSC---QPNAIGIN  582 (1219)
T ss_dssp             SSCSH-HHHHHHHHHHHHH---CCSEEEEC
T ss_pred             hhhHH-HHHHHHHHHHHHc---CCcEEEEC
Confidence            11111 1124455566555   49999984

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	281
d1hjra_	158	RuvC resolvase {Escherichia coli [TaxId: 562]}	100.0
d3bzka5	149	Transcriptional accessory factor Tex {Pseudomonas	97.65
d1kcfa2	218	Mitochondrial resolvase ydc2 catalytic domain {Fis	96.59
d1vhxa_	140	Hypothetical protein YrrK (RuvX) {Bacillus subtili	95.28
d1nu0a_	138	Hypothetical protein YqgF (RuvX) {Escherichia coli	95.03
d1iv0a_	98	Hypothetical protein, YqgF homologue {Thermus ther	88.63

>d1hjra_ c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: RuvC resolvase
domain: RuvC resolvase
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.3e-39  Score=275.56  Aligned_cols=152  Identities=18%  Similarity=0.124  Sum_probs=135.7

Q ss_pred             eEEEEcCCCC-ceEEEEeeCCCcceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEccccCCCCCCc
Q 023513           89 WALGIDPDLS-GALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSIPYPQDGK  166 (281)
Q Consensus        89 iILGIDPGl~-gGyaVLe~~g~~~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf~ffgqNv  166 (281)
                      ||||||||++ .|||||+.+++  +..+++++++++.. .++.+|+  ..|++.|.+++. |+||.++||++|  |++|.
T Consensus         2 iILGIDPGl~~~G~avid~~~~--~~~~v~~g~i~t~~-~~~~~Rl--~~i~~~l~~li~~~~Pd~vaiE~~f--~~~n~   74 (158)
T d1hjra_           2 IILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTKV-DDLPSRL--KLIYAGVTEIITQFQPDYFAIEQVF--MAKNA   74 (158)
T ss_dssp             EEEEEECCSSEEEEEEEEEETT--EEEEEEEEEEECCC-SCHHHHH--HHHHHHHHHHHHHHCCSEEEEEECC--CCCCT
T ss_pred             EEEEEccCCCceEEEEEEeeCC--EEEEEEeeEEeCCC-CChHHHH--HHHHHHHHHHHhccCCCEEEEEeeh--hccCH
Confidence            7999999999 59999999998  89999999998754 4676755  889999999988 999999999986  99999


Q ss_pred             hhhhHHHhhHHHHHHHHHHcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHHHHHHHHHH
Q 023513          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKADAVLIAAY  246 (281)
Q Consensus       167 qSA~~vG~ArGVillala~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaADALAIA~~  246 (281)
                      +|++++|++||++++++..+|||++||+|++|||+++|+ |+|+|+||+.|++.+|+...    .+. +|.|||||||+|
T Consensus        75 ~sa~~l~~arG~i~l~a~~~~ipi~e~~P~~vKk~vtG~-G~A~K~qV~~mv~~~l~l~~----~~~-~D~aDAlAiAl~  148 (158)
T d1hjra_          75 DSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRTLLKLPA----NPQ-ADAADALAIAIT  148 (158)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHTSS-SSCCHHHHHHHHHHHTTCCC----CCS-SCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCcceeecchhhhheeecCC-CCcCHHHHHHHHHHHcCCCC----CCC-CCHHHHHHHHHH
Confidence            999999999999999999999999999999999999776 99999999999999997654    144 469999999999


Q ss_pred             ccccccC
Q 023513          247 GKGLKLD  253 (281)
Q Consensus       247 g~~~~~~  253 (281)
                      |..+...
T Consensus       149 h~~~~~~  155 (158)
T d1hjra_         149 HCHVSQN  155 (158)
T ss_dssp             HHHTTSS
T ss_pred             HHHHhcc
Confidence            8876554

>d3bzka5 c.55.3.13 (A:325-473) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Tex RuvX-like domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.65  E-value=3.4e-05  Score=63.32  Aligned_cols=125  Identities=18%  Similarity=0.193  Sum_probs=67.2

Q ss_pred             CCCceEEEEcCCCC-c-eEEEEeeCCCcceeEEeecCCc-ccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCC
Q 023513           85 ADSQWALGIDPDLS-G-ALAVLKSDHNGCSAEVFDTPHL-PVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPY  161 (281)
Q Consensus        85 ~~~~iILGIDPGl~-g-GyaVLe~~g~~~~~~vvd~p~i-~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~f  161 (281)
                      .+.+.|||||||.+ | .+|+|+.+|     +++++.++ +.....+..+  ..+.|.+++.+   |+|+.++|-.    
T Consensus         2 ~~~~~vlg~DPg~r~gck~AvlD~~G-----~vld~~viyp~~~~~~~~~--a~~~l~~li~k---~~p~vIaIGN----   67 (149)
T d3bzka5           2 AGPRATLGLDPGLRTGVKVAVVDATG-----KLLDTATVYPHAPKNQWDQ--TLAVLAALCAK---HQVELIAIGN----   67 (149)
T ss_dssp             CCSCCEEEEECCSTTCEEEEEECTTS-----CEEEEEEECCSTTTCCHHH--HHHHHHHHHHH---TTCCEEEEES----
T ss_pred             CCCceEEEECCCcccccEEEEECCCC-----CEEEEEEEecCCcHHHHHH--HHHHHHHHHHH---cCCeEEEECC----
Confidence            46778999999987 4 799999888     45665555 2111211111  22345555555   5599999932    


Q ss_pred             CCCCchhhhHHHhhHHHHHHHHH---HcCCceeeeChhhHHHHhcCCCCCCCHHHHHHHHHHhCCcccccccCCCCCCHH
Q 023513          162 PQDGKQGWWSGGFGYGLWIGILV---ASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGKA  238 (281)
Q Consensus       162 fgqNvqSA~~vG~ArGVillala---~~GIPV~EytP~qwKkaVg~s~G~A~KeQVq~MV~~LLp~~~~~L~~kk~ddaA  238 (281)
                         |..|-    +..-.+--.+.   ..+|+|..+.         .  -+|+-=+.-..++.-||+....        .=
T Consensus        68 ---gTasr----e~~~~v~~l~~~~~~~~i~~~iV~---------e--~gAsvYs~S~~A~~EfP~~~~~--------~R  121 (149)
T d3bzka5          68 ---GTASR----ETDKLAGELIKKYPGMKLTKIMVS---------E--AGASVYSASELAAKEFPELDVS--------LR  121 (149)
T ss_dssp             ---STTHH----HHHHHHHHHHHHCGGGCCEEEEEC---------C--TTHHHHHTSHHHHHHCTTSCHH--------HH
T ss_pred             ---CccHH----HHHHHHHHHHHhCCCCCcEEEEEe---------c--cchhhhhCCHHHHHHCCCCChh--------Hh
Confidence               22221    11222222222   2355554332         1  2244444445667778765421        34


Q ss_pred             HHHHHHHHccc
Q 023513          239 DAVLIAAYGKG  249 (281)
Q Consensus       239 DALAIA~~g~~  249 (281)
                      -|++||.+-+.
T Consensus       122 ~AVsiaRrlQd  132 (149)
T d3bzka5         122 GAVSIARRLQD  132 (149)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHhhC
Confidence            57888876543

>d1kcfa2 c.55.3.7 (A:39-256) Mitochondrial resolvase ydc2 catalytic domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Mitochondrial resolvase ydc2 catalytic domain
domain: Mitochondrial resolvase ydc2 catalytic domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=96.59  E-value=0.0023  Score=53.69  Aligned_cols=158  Identities=13%  Similarity=0.089  Sum_probs=78.1

Q ss_pred             eEEEEcCCCCc-eEEEEeeCCCc---c-eeEEeecCCc---ccccccchhhhhcHHHHHHHHHhhcC-CCCCEEEEcccc
Q 023513           89 WALGIDPDLSG-ALAVLKSDHNG---C-SAEVFDTPHL---PVLVGKRVRKRLDAKSMIMLLRSLDA-PIGTTAYVEQSI  159 (281)
Q Consensus        89 iILGIDPGl~g-GyaVLe~~g~~---~-~~~vvd~p~i---~~~~~~~l~~rl~~~~I~~lL~~l~~-~~Pd~aaVE~vf  159 (281)
                      .||+||-|+.. ||++++.+++.   + ...+++.-.-   .......+.........+.++..+.. +.||.+.||+.-
T Consensus         3 kIlSIDvGIkNlAyc~l~~~~~~~~~I~~W~~i~L~~~~~~~~k~~~~~~~~~~~~~~~~l~~~l~~~~~~d~vlIE~Q~   82 (218)
T d1kcfa2           3 RVLGIDLGIKNFSYCFASQNEDSKVIIHNWSVENLTEKNGLDIQWTEDFQPSSMADLSIQLFNTLHEKFNPHVILMERQR   82 (218)
T ss_dssp             SEEEEEECSTTEEEEEEEECTTSCEEEEEEEEECTTSCCTTCCCCCCCCSHHHHHHHHHHHHHHHHHHHCCSEEEEEECC
T ss_pred             eEEEEEeCccccEEEEEeeCCCCCcEEEEeeeEeecccccCcccccccCCHHHHHHHHHHHHhhhhcccCCceEEEeecc
Confidence            38999999996 99999886642   1 3333332111   10011111111122334444555444 669999999984


Q ss_pred             CCCCCCchhhhH----HHhhHHHHHHHHHH---------cCCc-eeeeChhhHHHHh----cCCCCCCCHHHHHHHHHHh
Q 023513          160 PYPQDGKQGWWS----GGFGYGLWIGILVA---------SGFS-VVPIPSLTWKNWY----GLSGGTSTKDDSRRVASTL  221 (281)
Q Consensus       160 ~ffgqNvqSA~~----vG~ArGVillala~---------~GIP-V~EytP~qwKkaV----g~s~G~A~KeQVq~MV~~L  221 (281)
                        +..|..+.+.    +.--.+.+......         ..++ |....|..+-+..    +..+-...|.....+++.+
T Consensus        83 --~r~~~~~i~~~~l~~~~le~ml~~~~~~~~~~~~~~~~~~~~v~~~~~~~v~~~~~~~~~~~~~~~~Kk~~i~~~~~~  160 (218)
T d1kcfa2          83 --YRSGIATIPEWTLRVNMLESMLYALHYAEKRNSIEQKIQYPFLLSLSPKSTYSYWASVLNTKASFSKKKSRVQMVKEL  160 (218)
T ss_dssp             --CCTTTCCHHHHHHHHHHHHHHHHHHHHHHHHC-------CCEEEECCHHHHHHHHHHHHC-------CCCHHHHHHHH
T ss_pred             --cccCccchhHHHHHHHHHHHHHHHHHHHhccccccccccceeEEEcCccceeeeccccccccccchhHHHHHHHHHHH
Confidence              2223222222    22222222222211         1222 5666777765544    1110124466666777777


Q ss_pred             CCccc--------------ccccCCCCCCHHHHHHHHHHcc
Q 023513          222 FPSLC--------------SQLKRKKDHGKADAVLIAAYGK  248 (281)
Q Consensus       222 Lp~~~--------------~~L~~kk~ddaADALAIA~~g~  248 (281)
                      +....              ..-..+|-||-||+++-|++..
T Consensus       161 L~~~~~~~~~~~~~~~~~~~~~~~kKkDDLADs~Lq~l~~l  201 (218)
T d1kcfa2         161 IDGQKILFENEEALYKWNNGSRVEFKKDDMADSALIASGWM  201 (218)
T ss_dssp             HHTTSEEESSHHHHHHHHHCCSTTTHHHHHHHHHHHHHHHH
T ss_pred             HhhCccccCcchHHHHHHHhcccCCCchhhHhHHHHHHHHH
Confidence            62210              0112355678999999999754

>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YrrK (RuvX)
species: Bacillus subtilis [TaxId: 1423]

Probab=95.28  E-value=0.046  Score=43.19  Aligned_cols=94  Identities=12%  Similarity=-0.002  Sum_probs=54.0

Q ss_pred             CceEEEEcCCCC-ceEEEEeeCCCcc-eeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCC
Q 023513           87 SQWALGIDPDLS-GALAVLKSDHNGC-SAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (281)
Q Consensus        87 ~~iILGIDPGl~-gGyaVLe~~g~~~-~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgq  164 (281)
                      +|.|||||+|.. +|+|+=+..+.-. .+.++......        .......|.+++.++.   |+..+|=-.+  .-+
T Consensus         1 ~mriLgiD~G~kriGvAisd~~~~~a~pl~~i~~~~~~--------~~~~~~~l~~ii~e~~---i~~iViGlP~--~~d   67 (140)
T d1vhxa_           1 SLRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAE--------GDYGLSRLSELIKDYT---IDKIVLGFPK--NMN   67 (140)
T ss_dssp             CEEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGG--------TBCCHHHHHHHHTTSE---EEEEEEECCC--CBT
T ss_pred             CceEEEEEeCCCEEEEEEecCCCCcccceeeEeecccc--------cchHHHHHHHHHHhhc---cceEEEeccc--ccC
Confidence            578999999999 5999876554311 23333322211        0112356677776654   7877776633  444


Q ss_pred             CchhhhHHHhhHHHHHHHHHHcCCceeeeC
Q 023513          165 GKQGWWSGGFGYGLWIGILVASGFSVVPIP  194 (281)
Q Consensus       165 NvqSA~~vG~ArGVillala~~GIPV~Eyt  194 (281)
                      |..+... ...+=.+-......++||+.+.
T Consensus        68 g~~~~~~-~~~~~f~~~l~~~~~i~V~~~D   96 (140)
T d1vhxa_          68 GTVGPRG-EASQTFAKVLETTYNVPVVLWD   96 (140)
T ss_dssp             TBCCHHH-HHHHHHHHHHHHHHCSCEEEEC
T ss_pred             CcchhHH-HHHHHHHHHhccCCCccEEEee
Confidence            4433322 2333333445677799999764

>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

Probab=95.03  E-value=0.078  Score=41.72  Aligned_cols=99  Identities=13%  Similarity=0.014  Sum_probs=56.3

Q ss_pred             CceEEEEcCCCC-ceEEEEeeCCCc-ceeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCCC
Q 023513           87 SQWALGIDPDLS-GALAVLKSDHNG-CSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (281)
Q Consensus        87 ~~iILGIDPGl~-gGyaVLe~~g~~-~~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffgq  164 (281)
                      +..|||||+|.. +|+||=+..+.- ..+.++.....        ..  ++..|.+.+.++.   |+.++|=-.+  .-+
T Consensus         2 ~griLgiD~G~kriGvAvsd~~~~~a~pl~~i~~~~~--------~~--~~~~l~~i~~e~~---~~~iVvG~P~--~~~   66 (138)
T d1nu0a_           2 SGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDG--------TP--DWNIIERLLKEWQ---PDEIIVGLPL--NMD   66 (138)
T ss_dssp             CCEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETT--------EE--CHHHHHHHHHHHC---CSEEEEEEEE--CTT
T ss_pred             CCcEEEEEeCCCEEEEEEeCCCCCccccceeeecccc--------hh--hHHHHHHHhhccC---ccEEEeeccc--ccc
Confidence            456999999999 599998766530 02233332211        11  4467778888776   9999995543  334


Q ss_pred             Cchhh-hHHHhhHHHHHHHHHHcCCceee----eChhhHHHHh
Q 023513          165 GKQGW-WSGGFGYGLWIGILVASGFSVVP----IPSLTWKNWY  202 (281)
Q Consensus       165 NvqSA-~~vG~ArGVillala~~GIPV~E----ytP~qwKkaV  202 (281)
                      |..+. -..-..++-.  .....++||+.    +|..+.+..+
T Consensus        67 g~~~~~~~~v~~f~~~--L~~~~~i~V~~~DEr~TS~eA~~~l  107 (138)
T d1nu0a_          67 GTEQPLTARARKFANR--IHGRFGVEVKLHDERLSTVEARSGL  107 (138)
T ss_dssp             SCBCHHHHHHHHHHHH--HHHHHCCCEEEEEEECCCCCC----
T ss_pred             cchHHHHHHHHHHHHH--HhhccCCCeEEEeccccHHHHHHHH
Confidence            43332 2222333333  35667999976    4555555554

>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein, YqgF homologue
species: Thermus thermophilus [TaxId: 274]

Probab=88.63  E-value=0.52  Score=34.79  Aligned_cols=89  Identities=12%  Similarity=-0.018  Sum_probs=49.2

Q ss_pred             ceEEEEcCCCC-ceEEEEeeCCCcc-eeEEeecCCcccccccchhhhhcHHHHHHHHHhhcCCCCCEEEEccccCCCC-C
Q 023513           88 QWALGIDPDLS-GALAVLKSDHNGC-SAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ-D  164 (281)
Q Consensus        88 ~iILGIDPGl~-gGyaVLe~~g~~~-~~~vvd~p~i~~~~~~~l~~rl~~~~I~~lL~~l~~~~Pd~aaVE~vf~ffg-q  164 (281)
                      |.|||||-|.. +|+|+=+..+.-. .+.+++...        ...  +...|.+++.++.   |+..+|=-...+-| .
T Consensus         1 MriLglD~G~kriGiAisd~~~~~a~pl~~i~~~~--------~~~--~~~~l~~ii~e~~---i~~iVvGlP~~~dG~~   67 (98)
T d1iv0a_           1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVRKT--------LEE--DVEALLDFVRREG---LGKLVVGLPLRTDLKE   67 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEECCC--------HHH--HHHHHHHHHHHHT---CCEEEEECCCCCCSSS
T ss_pred             CcEEEEEcCCCEEEEEEecCCCCeEcceEEEECCC--------chH--HHHHHHHHHHhhc---cceeEcccccccCCCc
Confidence            56999999999 5999876544310 233333221        112  3466777777765   88888876431111 1


Q ss_pred             CchhhhHHHhhHHHHHHHHHHcCCceeeeC
Q 023513          165 GKQGWWSGGFGYGLWIGILVASGFSVVPIP  194 (281)
Q Consensus       165 NvqSA~~vG~ArGVillala~~GIPV~Eyt  194 (281)
                      +.++...  +.++-.+   ...++||+.+.
T Consensus        68 ~~~~~~v--~~f~~~L---~~~~lpv~~~D   92 (98)
T d1iv0a_          68 SAQAGKV--LPLVEAL---RARGVEVELWD   92 (98)
T ss_dssp             CCCSSTT--HHHHHHH---HHTTCEEEEEC
T ss_pred             CHHHHHH--HHHHHHH---hhCCCCEEEEc
Confidence            2222221  2222222   45699998764