Citrus Sinensis ID: 025662

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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-------25
Protein Sequence
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHHL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEccccccEEEEEEcccccccEEEEccccccEEccccccccccHHHHHHHHHccccccccEEEEEEccccccccccEEEEccHHHHHHHHHHHHHcccEEEcccHHHHHHHccccccccHHHHHHHHHHHccccccccccccccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccEEccHHHHHHcccccEEEEcccccccccccccccccccccHcccHHHHHHHHHHHHHHHHHHcccccccccccccccHccccccEEEEEcccccEEEEEEEccccccEEEEEcccccEEEEccEEEEcccHHHHHHHHHHcccccccEEEEEEcccccccccEEEEcccHHHHHHHHHHHHccccEEEccHHHHHHHHccccccccHHHHHHHHHHHcHHHHHHHcccccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mettvkiqpqlqshcismntfVSSKIrtlctypfaqhGRTLLVRAAAAGDTTKAAVAAQMKQNwldsltfpplhvhdltanqtnadsqwalgidpdLSGALAVLKsdhngcsaevfdtphlpvlvGKRVRKRLDAKSMIMLLRSldapigttayveqsipypqdgkqgwwsggfgYGLWIGILVAsgfsvvpipsltwknwyglsggtstkddsrrVASTLFPSLCSQlkrkkdhgtisspycilyhhl
Flexible Loop (DISEMBL)
mettvkiqpqlqshciSMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSaevfdtphlpvlvgKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSlcsqlkrkkdhgtisspycilyhhl
Low Complexity Region (SEG)
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRaaaagdttkaavaaQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHHL
Disordered region (IsUnstruct)
***********QSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSG*************TLFPSLCS********GTISSPYCILYH**
Disordered Region (DISOPRED)
********PQLQSHCISMNTFVSS*************************************QNWLDS******************DSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLV**RVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGL*********SRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHHL
Disordered Region (DISEMBL)
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAA**********AQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHHL
Disordered Region (DISPRO)
*ETTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHG****************AVAAQ*KQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHHL
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METTVKIQPQLQSHCISMNTFVSSKIRTLCTYPFAQHGRTLLVRAAAAGDTTKAAVAAQMKQNWLDSLTFPPLHVHDLTANQTNADSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHHL
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	249
255580004	280	conserved hypothetical protein [Ricinus	0.738	0.657	0.687	7e-71
225435862	291	PREDICTED: uncharacterized protein LOC10	0.935	0.800	0.549	2e-68
356528579	274	PREDICTED: uncharacterized protein LOC10	0.738	0.671	0.643	1e-65
296083889	192	unnamed protein product [Vitis vinifera]	0.638	0.828	0.729	7e-65
30683279	273	uncharacterized protein [Arabidopsis tha	0.911	0.831	0.568	2e-63
356555307	290	PREDICTED: uncharacterized protein LOC10	0.730	0.627	0.634	6e-62
3426042	286	unknown protein [Arabidopsis thaliana]	0.911	0.793	0.539	9e-61
297825913	287	hypothetical protein ARALYDRAFT_320472 [	0.911	0.790	0.529	3e-60
224105997	235	predicted protein [Populus trichocarpa]	0.630	0.668	0.670	2e-58
359479130	261	PREDICTED: uncharacterized protein LOC10	0.907	0.865	0.483	1e-55

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

 Score =  273 bits (697), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 132/192 (68%), Positives = 158/192 (82%), Gaps = 8/192 (4%)

Query: 52  TKAAVAAQMKQNWLDSLTFPPLHVHDLTANQ-------TNADSQWALGIDPDLSGALAVL 104
           ++A VA Q+K+NWL SL+ P  +  + +A++       +N  S W +GIDPDLSGALA+L
Sbjct: 62  SEAEVARQLKENWLHSLSCP-FNQTESSASKGVDSTAPSNVGSNWVIGIDPDLSGALALL 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 LCSQLKRKKDHG 236
           L S LKRKKDHG
Sbjct: 241 LSSLLKRKKDHG 252

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 =  264 bits (675), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/244 (54%), Positives = 171/244 (70%), Gaps = 11/244 (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 KDHG 236
           KDHG
Sbjct: 255 KDHG 258

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 =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 123/191 (64%), Positives = 151/191 (79%), Gaps = 7/191 (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 CSQLKRKKDHG 236
            S L RKKDHG
Sbjct: 232 TSMLSRKKDHG 242

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  253 bits (645), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 116/159 (72%), Positives = 139/159 (87%)

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 WKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHG 236
           WKN + LSG  ++KDDSRRVAST+FPS+ S LKRKKDHG
Sbjct: 121 WKNEFKLSGNGTSKDDSRRVASTIFPSMSSLLKRKKDHG 159

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  248 bits (632), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 137/241 (56%), Positives = 166/241 (68%), Gaps = 14/241 (5%)

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 G 236
           G
Sbjct: 232 G 232

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  243 bits (619), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 120/189 (63%), Positives = 144/189 (76%), Gaps = 7/189 (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 QLKRKKDHG 236
            L RKKDHG
Sbjct: 250 MLSRKKDHG 258

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  239 bits (609), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 137/254 (53%), Positives = 166/254 (65%), Gaps = 27/254 (10%)

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 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 PSLCSQLKRKKDHG 236
           PSL SQLKRKKDHG
Sbjct: 232 PSLSSQLKRKKDHG 245

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 =  237 bits (605), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 135/255 (52%), Positives = 166/255 (65%), Gaps = 28/255 (10%)

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 FPSLCSQLKRKKDHG 236
           FPSL +QLKRKKDHG
Sbjct: 232 FPSLSTQLKRKKDHG 246

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  231 bits (589), Expect = 2e-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|359479130|ref|XP_003632222.1| PREDICTED: uncharacterized protein LOC100242692 isoform 2 [Vitis vinifera]

 Score =  222 bits (565), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 117/242 (48%), Positives = 158/242 (65%), Gaps = 16/242 (6%)

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  ++K     V  ++FP +   + R+
Sbjct: 195 GFGYGLWIGILVASGFSVVPVPSSLWKNEFKLSGNGTSK-----VFLSIFPLVFPHIFRE 249

Query: 233 KD 234
            +
Sbjct: 250 PN 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	249
TAIR|locus:2097129	195	AT3G43910 "AT3G43910" [Arabido	0.714	0.912	0.390	1.1e-23
TAIR|locus:2097124	84	AT3G43900 "AT3G43900" [Arabido	0.216	0.642	0.473	4.1e-06

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

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 75/192 (39%), Positives = 108/192 (56%)

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 LWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGT 237
             LW   L+ S  SV+ +   TW   + LS    + D  R++A  +FPSL  +L  K D   
Sbjct:   116 LWT--LLTSSISVIYVTPSTWDKHFNLS--IWSLDGGRKLALEMFPSL--KLTTKIDDNA 169

Query:   238 ISSPYCIL-YHH 248
              ++   I  Y H
Sbjct:   170 RANALLIAAYGH 181

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 = 4.1e-06, P = 4.1e-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        0.320   0.135   0.430    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      249       235   0.00088  113 3  11 22  0.40    33
                                                     32  0.43    36


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:  619 (66 KB)
  Total size of DFA:  211 KB (2116 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:  18.73u 0.08s 18.81t   Elapsed:  00:00:01
  Total cpu time:  18.73u 0.08s 18.81t   Elapsed:  00:00:01
  Start:  Fri May 10 20:31:32 2013   End:  Fri May 10 20:31:33 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

Fail to connect to STRING server

---

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	249
TIGR00228	156	ruvC crossover junction endodeoxyribonuclease RuvC	100.0
PRK00039	164	ruvC Holliday junction resolvase; Reviewed	100.0
PF02075	149	RuvC: Crossover junction endodeoxyribonuclease Ruv	100.0
COG0817	160	RuvC Holliday junction resolvasome, endonuclease s	100.0
cd00529	154	RuvC_resolvase Holliday junction resolvases (HJRs)	100.0
PF07066	159	DUF3882: Lactococcus phage M3 protein; InterPro: I	98.95
PF04848	143	Pox_A22: Poxvirus A22 protein; InterPro: IPR006932	98.74
smart00732	99	YqgFc Likely ribonuclease with RNase H fold. YqgF	97.13
PF04312	138	DUF460: Protein of unknown function (DUF460); Inte	96.78
PF01548	144	DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 T	96.61
PF11215	138	DUF3010: Protein of unknown function (DUF3010); In	96.37
COG2433	652	Uncharacterized conserved protein [Function unknow	96.23
PF03652	135	UPF0081: Uncharacterised protein family (UPF0081);	95.63
PRK00109	138	Holliday junction resolvase-like protein; Reviewed	95.21
COG0816	141	Predicted endonuclease involved in recombination (	93.06
PF07318	343	DUF1464: Protein of unknown function (DUF1464); In	89.09
TIGR00250	130	RNAse_H_YqgF RNAse H-fold protein YqgF. This prote	88.6
COG2410	178	Predicted nuclease (RNAse H fold) [General functio	88.4
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	86.8

>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC

Probab=100.00  E-value=2.8e-38  Score=268.25  Aligned_cols=145  Identities=14%  Similarity=0.113  Sum_probs=136.6

Q ss_pred             EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |||||||++.+ |||++..++  .++++|+++|++.. ..  .|+..++++|.++|++|   +|+.++||++|  +++|+
T Consensus         1 ILGIDPGl~~tG~gvi~~~~~--~~~~v~~G~I~t~~-~~~~~RL~~I~~~l~~~i~~y---~P~~~aiE~~F--~~~N~   72 (156)
T TIGR00228         1 ILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTKV-DDLPSRLKLIYAGVTEIITQF---QPNYFAIEQVF--MAKNA   72 (156)
T ss_pred             CEeECcccccccEEEEEecCC--eEEEEEeeEEECCC-CCHHHHHHHHHHHHHHHHHHh---CCCEEEEeHHh--hccCH
Confidence            69999999999 999998776  89999999999864 34  99999999999999999   99999999999  99999


Q ss_pred             cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhh
Q 025662          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILY  246 (249)
Q Consensus       167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~  246 (249)
                      +|++++|++||+++.+++..||||+||+|.+|||+++|+ |+|+|+|++.|++++|+..+.    ++ +|.|||||||+|
T Consensus        73 ~sa~~lg~arGvilla~~~~~ipv~Ey~P~~vKkavtG~-G~A~KeQV~~mV~~lL~l~~~----p~-~DaaDALAiAi~  146 (156)
T TIGR00228        73 DSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRRLLKLPAN----PQ-ADAADALAIAIT  146 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhcCC-CCCCHHHHHHHHHHHcCCCCC----CC-CCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999 999999999999999987654    55 899999999999


Q ss_pred             cc
Q 025662          247 HH  248 (249)
Q Consensus       247 h~  248 (249)
                      |+
T Consensus       147 h~  148 (156)
T TIGR00228       147 HA  148 (156)
T ss_pred             Hh
Confidence            96

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.

>PRK00039 ruvC Holliday junction resolvase; Reviewed

Probab=100.00  E-value=2.5e-37  Score=263.03  Aligned_cols=149  Identities=15%  Similarity=0.113  Sum_probs=140.4

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q  164 (249)
                      |+|||||||++.+ |||++.+++  .++++|+++|++..+..  .|+..+++.|.++|++|   +|+.++||++|  +++
T Consensus         2 m~iLGIDPgl~~tG~avi~~~~~--~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~---~Pd~vaiE~~f--~~~   74 (164)
T PRK00039          2 MRILGIDPGLRRTGYGVIEVEGR--RLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEY---QPDEVAIEEVF--FNK   74 (164)
T ss_pred             CEEEEEccccCceeEEEEEecCC--eEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh---CCCEEEEehhh--hcc
Confidence            7899999999999 999998865  79999999999876555  99999999999999999   99999999988  999


Q ss_pred             CccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHH
Q 025662          165 GKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCI  244 (249)
Q Consensus       165 gvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA  244 (249)
                      |.+|++++|+++|+++++|...||||+||+|++|||+++|+ |+|+|+|++.|++++|+....    ++++|.|||||||
T Consensus        75 n~~sa~~l~~arGvi~la~~~~~ipv~ey~P~~VKk~vtG~-G~A~K~qV~~mv~~~l~l~~~----~~~~D~aDAlAiA  149 (164)
T PRK00039         75 NPQSALKLGQARGVAILAAAQRGLPVAEYTPLQVKKAVVGY-GRADKEQVQHMVKRLLNLPEI----PKPDDAADALAIA  149 (164)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHhhhhhcCC-CCCCHHHHHHHHHHHhCCCCC----CCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999 999999999999999987754    6689999999999


Q ss_pred             hhcc
Q 025662          245 LYHH  248 (249)
Q Consensus       245 ~~h~  248 (249)
                      +||+
T Consensus       150 ~~h~  153 (164)
T PRK00039        150 ICHA  153 (164)
T ss_pred             HHHH
Confidence            9996

>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=1.8e-37  Score=259.26  Aligned_cols=146  Identities=17%  Similarity=0.141  Sum_probs=118.0

Q ss_pred             EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |||||||++.+ |||++.++.  .++++|+++|++.....  .|+..++++|.++|++|   +|+.++||++|  +++|.
T Consensus         1 ILGIDPgl~~tG~avi~~~~~--~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~---~P~~vaiE~~f--~~~n~   73 (149)
T PF02075_consen    1 ILGIDPGLSNTGYAVIEEDGG--KLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEY---NPDEVAIEEIF--FGKNP   73 (149)
T ss_dssp             EEEEE--SSEEEEEEEEEETT--EEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH-----SEEEEEE-S------H
T ss_pred             CEEECCCCCCeeEEEEEeeCC--EEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhh---CCCEEEeehhh--hccCH
Confidence            79999999999 999999765  89999999999887655  99999999999999999   99999999988  99999


Q ss_pred             cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhh
Q 025662          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILY  246 (249)
Q Consensus       167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~  246 (249)
                      +|++++|+++|++++++...||||++|+|++|||+++|+ |+|+|+|++.|++++|+..+.    ++++|.|||||||+|
T Consensus        74 ~s~~~l~~arGvi~l~~~~~~i~v~~y~P~~vKk~vtG~-G~A~KeqV~~mv~~ll~l~~~----~~~~d~aDAlAiA~~  148 (149)
T PF02075_consen   74 KSALKLGQARGVILLAAAQRGIPVFEYTPSEVKKAVTGN-GRASKEQVAFMVRKLLGLDEK----PKPDDAADALAIALC  148 (149)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTT--EEEEEHHHHHHHHTSS-TT--HHHHHHHHHHHTT--------SS-S-THHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCeEEEECHHHHHHHhhCC-CccCHHHHHHHHHHHhCCCCC----CCccchHhhHhhhhc
Confidence            999999999999999999999999999999999999999 899999999999999998865    667999999999999


Q ss_pred             c
Q 025662          247 H  247 (249)
Q Consensus       247 h  247 (249)
                      |
T Consensus       149 H  149 (149)
T PF02075_consen  149 H  149 (149)
T ss_dssp             H
T ss_pred             C
Confidence            8

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.

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

Probab=100.00  E-value=4.7e-37  Score=261.23  Aligned_cols=145  Identities=14%  Similarity=0.127  Sum_probs=138.5

Q ss_pred             EEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCcc
Q 025662           91 LGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ  167 (249)
Q Consensus        91 LGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvq  167 (249)
                      ||||||++.+ |||++.+++  ++..+++++|+++....  .|+..+++.+.++|++|   +|+.++||++|  +.+|++
T Consensus         1 lGIDPGl~~~G~gvI~~~~~--~l~~v~~G~I~t~~~~~l~~RL~~l~~~l~~vl~~~---~P~~~AIE~~F--~~kN~~   73 (160)
T COG0817           1 LGIDPGLRRTGYGVIEVEGR--QLSYLASGVIRTSSDAPLAERLKQLYDGLSEVLDEY---QPDEVAIEQVF--VNKNAD   73 (160)
T ss_pred             CCcCCCccccceEEEEccCC--eEEEEeeeEEecCCCccHHHHHHHHHHHHHHHHHHh---CCCeeehhHHH--HhcChH
Confidence            6999999999 999999987  99999999999886666  99999999999999999   99999999999  999999


Q ss_pred             ceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhhc
Q 025662          168 GWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYH  247 (249)
Q Consensus       168 Saf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~h  247 (249)
                      |++++|++||+++++++..++||.||+|++.||+++|+ |+++|+|++.|+++||+ .+.    ++++|+|||||||+||
T Consensus        74 s~lklgQARGv~~la~~~~~l~v~eY~p~~VKkavvG~-G~A~K~QVq~MV~~lL~-~~~----~~~~DaADALAiAitH  147 (160)
T COG0817          74 SALKLGQARGVALLAAARRGLPVFEYTPNQVKKAVVGN-GKADKEQVQHMVKRLLG-LEE----PPPADAADALAIAITH  147 (160)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCChhhccHHHHHHHhhcC-CcccHHHHHHHHHHHhC-CCC----CCCccHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999 99999999999999999 444    7799999999999999


Q ss_pred             c
Q 025662          248 H  248 (249)
Q Consensus       248 ~  248 (249)
                      +
T Consensus       148 a  148 (160)
T COG0817         148 A  148 (160)
T ss_pred             H
Confidence            6

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

Probab=100.00  E-value=4.8e-34  Score=238.77  Aligned_cols=148  Identities=14%  Similarity=0.095  Sum_probs=138.3

Q ss_pred             eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCC
Q 025662           89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (249)
Q Consensus        89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qg  165 (249)
                      +|||||||++.+ ||+++..++  ..+++++++|++..+..  .|+..+++.|.++|..|   +|+.++||++|  +++|
T Consensus         1 rILGIDPGl~~~G~av~~~~~~--~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~---~Pd~vaiE~~~--~~~n   73 (154)
T cd00529           1 RILGIDPGSRNTGYGVIEQEGR--KLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQF---QPDVVAIERVF--FAKN   73 (154)
T ss_pred             CEEEEccCcCceEEEEEEeeCC--eEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHh---CCCEEEEEEhh--cccC
Confidence            489999999999 999998775  89999999999875555  99999999999999999   89999999998  9999


Q ss_pred             ccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHh
Q 025662          166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCIL  245 (249)
Q Consensus       166 vqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~  245 (249)
                      .+|++++|+.+|+++++|...|+||++|+|++||++++|+ |+++|+|++.|++++|.....    +++||.|||||||+
T Consensus        74 ~~s~~~l~~~~Gvi~~~~~~~~i~v~e~~P~~vKk~~tG~-G~A~KeqV~~mv~~~l~~~~~----~~~~d~aDAlaiA~  148 (154)
T cd00529          74 PDSALKLGQARGALILALANRNLPVFEYTPNQVKKAVTGY-GKADKDQVQHMVKRLLNLSEI----PKPDDAADALAVAI  148 (154)
T ss_pred             hHHHHHHHHHHHHHHHHHHHcCCCEEEEccCeeEEEEECC-CCCCHHHHHHHHHHHhCCCCC----CCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999999 899999999999999987653    57899999999999


Q ss_pred             hcc
Q 025662          246 YHH  248 (249)
Q Consensus       246 ~h~  248 (249)
                      ||.
T Consensus       149 ~~~  151 (154)
T cd00529         149 THA  151 (154)
T ss_pred             HHH
Confidence            995

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.

>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=98.95  E-value=9.7e-10  Score=93.52  Aligned_cols=144  Identities=19%  Similarity=0.175  Sum_probs=102.9

Q ss_pred             eEEEEcCCCCc-----e-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccC
Q 025662           89 WALGIDPDLSG-----A-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIP  160 (249)
Q Consensus        89 ~ILGIDPGl~G-----a-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~  160 (249)
                      .+|.||=.+++     + ||+.+....     ++...... ...+.  +|-+.++.+|..+|.+|+-+ .-..+||+.. 
T Consensus         3 ~~LslD~STs~~~~~gTG~A~~~~~~~-----~~~si~~~-~k~Ks~~ER~k~ias~Lk~ii~~~d~~-~y~i~IE~~v-   74 (159)
T PF07066_consen    3 KVLSLDFSTSSKKGEGTGWAFFKGSDL-----VVGSIKAK-HKSKSFFERAKSIASELKTIIQKYDLK-FYIIVIEKPV-   74 (159)
T ss_pred             eeEEEEEecccCCCCCceeEEecCCeE-----EEeeeeec-CcccCHHHHHHHHHHHHHHHHHHhCCC-cceEEEeccc-
Confidence            48999999985     7 999974321     12221111 11222  99999999999999999754 5678999954 


Q ss_pred             CCCCCccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCC-CCChHHH--HHHHHHhCCcccccccCCCCCCc
Q 025662          161 YPQDGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGG-TSTKDDS--RRVASTLFPSLCSQLKRKKDHGT  237 (249)
Q Consensus       161 ~p~qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G-~AsKd~s--r~ma~~LfP~~~~~l~rkKdhgr  237 (249)
                       -|.|.||++++|...|.++|.+-..-=.++.|.|++|.+...-+|. ++.|.++  +..+..+.+      ..-++||.
T Consensus        75 -mg~Nqqs~i~l~~~~G~iLG~l~~~~n~~~fIn~s~W~kY~lis~K~rsrK~~sl~~l~a~~i~~------~k~~~DDe  147 (159)
T PF07066_consen   75 -MGPNQQSSIKLGIATGIILGRLINRANGYYFINVSTWRKYWLISYKDRSRKSMSLELLKASEIVD------NKVKDDDE  147 (159)
T ss_pred             -ccccccceEEEEEEeEEEeeeeecccCcEEEecHHHhhhheeeeechhhhhhhhHHHHHHhcccc------ccccccch
Confidence             8889999999999999999997644227999999999999875422 3334444  233333333      23568999


Q ss_pred             ccHHHHHhhc
Q 025662          238 ISSPYCILYH  247 (249)
Q Consensus       238 ADALaIA~~h  247 (249)
                      |||++|-.|-
T Consensus       148 ADAi~IgsY~  157 (159)
T PF07066_consen  148 ADAILIGSYC  157 (159)
T ss_pred             hhhhhhhhhh
Confidence            9999998773

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

>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=98.74  E-value=5.9e-08  Score=82.06  Aligned_cols=134  Identities=13%  Similarity=0.035  Sum_probs=95.2

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |+|++||+|...- |++++..++  .+++++..-.+.+.+.   .......+.+    +   ..+.+.||++.   .+|+
T Consensus         1 mii~sIDiGikNlA~~iie~~~~--~i~~~~i~~~~~~~~~---~~~~~~dl~~----~---~~d~VlIErQ~---~r~~   65 (143)
T PF04848_consen    1 MIILSIDIGIKNLAYCIIEFEGN--KIRVIDISKVDWSRDW---EYRILKDLLK----Y---EADTVLIERQP---PRNP   65 (143)
T ss_pred             CeEEEEecCCCceeEEEEEcCCC--eEEEEEeccCCcccch---HHHHHHHHhh----c---cCCEEEEecCC---CCCc
Confidence            7899999999999 999999776  6888988877765322   1222233333    5   78999999994   4454


Q ss_pred             cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccc--c-ccCCCCCCcccHHHH
Q 025662          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCS--Q-LKRKKDHGTISSPYC  243 (249)
Q Consensus       167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~--~-l~rkKdhgrADALaI  243 (249)
                      ..  +   -.+.+.+.+.-.+..|..|+|.     +++.+=+.-|+.|...+..++-....  . -+++|-||-|||+++
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            22  2   2346677777889999999999     55432356688888888877755321  1 233677999999998


Q ss_pred             Hhh
Q 025662          244 ILY  246 (249)
Q Consensus       244 A~~  246 (249)
                      |+.
T Consensus       136 al~  138 (143)
T PF04848_consen  136 ALA  138 (143)
T ss_pred             HHH
Confidence            864

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

>smart00732 YqgFc Likely ribonuclease with RNase H fold

Probab=97.13  E-value=0.0036  Score=47.12  Aligned_cols=89  Identities=17%  Similarity=0.185  Sum_probs=56.3

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |.+||||+|.+.. +|+++.++.  ..+....++.   .    +...+.+.+.++++++   .+..+.|+-.+..  +|.
T Consensus         1 ~~ilgiD~Ggt~i~~a~~d~~g~--~~~~~~~~~~---~----~~~~~~~~l~~~i~~~---~~~~i~Ig~pg~v--~g~   66 (99)
T smart00732        1 KRVLGLDPGRKGIGVAVVDETGK--LADPLEVIPR---T----NKEADAARLKKLIKKY---QPDLIVIGLPLNM--NGT   66 (99)
T ss_pred             CcEEEEccCCCeEEEEEECCCCC--EecCEEEEEe---c----CcchHHHHHHHHHHHh---CCCEEEEeCCcCC--CCC
Confidence            4689999998888 999987764  4443343332   1    3456789999999998   7888998876533  333


Q ss_pred             cc-eeechhhhHHHHHHHHHcCCceeEeC
Q 025662          167 QG-WWSGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       167 qS-af~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      .+ .|.    +-+...+-...++||+.+.
T Consensus        67 ~~~~~~----~~l~~~l~~~~~~pv~~~n   91 (99)
T smart00732       67 ASRETE----EAFAELLKERFNLPVVLVD   91 (99)
T ss_pred             cCHHHH----HHHHHHHHHhhCCcEEEEe
Confidence            21 121    2222222345678887653

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=96.78  E-value=0.0034  Score=53.22  Aligned_cols=61  Identities=16%  Similarity=0.290  Sum_probs=44.0

Q ss_pred             CCceEEEEcCCCCceEEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCC
Q 025662           86 DSQWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ  163 (249)
Q Consensus        86 ~~m~ILGIDPGl~Ga~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~  163 (249)
                      ....|+|||||++-++|+|+.+|.  .+.+...            +.++..++.++|.++.  .|-+++ =.+.++|.
T Consensus        30 ~~~lIVGiDPG~ttgiAildL~G~--~l~l~S~------------R~~~~~evi~~I~~~G--~PviVA-tDV~p~P~   90 (138)
T PF04312_consen   30 RRYLIVGIDPGTTTGIAILDLDGE--LLDLKSS------------RNMSRSEVIEWISEYG--KPVIVA-TDVSPPPE   90 (138)
T ss_pred             CCCEEEEECCCceeEEEEEecCCc--EEEEEee------------cCCCHHHHHHHHHHcC--CEEEEE-ecCCCCcH
Confidence            456799999999999999999985  4443333            4566788999999995  444433 44555654

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

Probab=96.61  E-value=0.0046  Score=49.83  Aligned_cols=105  Identities=21%  Similarity=0.229  Sum_probs=72.3

Q ss_pred             EEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccc
Q 025662           90 ALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQG  168 (249)
Q Consensus        90 ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqS  168 (249)
                      ++|||-+..-- .+++...+.  ......+++-+          -...++.+.|..+   .+..+++|.-.         
T Consensus         1 ~vGiDv~k~~~~v~v~~~~~~--~~~~~~~~~~~----------~~~~~l~~~l~~~---~~~~v~~E~tg---------   56 (144)
T PF01548_consen    1 FVGIDVSKDTHDVCVIDPNGE--KLRRFKFENDP----------AGLEKLLDWLASL---GPVLVVMEATG---------   56 (144)
T ss_pred             eEEEEcccCeEEEEEEcCCCc--EEEEEEEeccc----------cchhHHhhhhccc---ccccccccccc---------
Confidence            69999999887 777776663  33333443321          2235677777777   36788888743         


Q ss_pred             eeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcc--cCCCCChHHHHHHHHHhCC
Q 025662          169 WWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGL--SGGTSTKDDSRRVASTLFP  223 (249)
Q Consensus       169 af~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g--~~G~AsKd~sr~ma~~LfP  223 (249)
                          |+.+ -|.-.|...|++|+.+.|...|..-..  .....||.|++.+|..++-
T Consensus        57 ----~y~~-~l~~~L~~~g~~v~~vnp~~~~~~~~~~~~~~KtD~~DA~~ia~~~~~  108 (144)
T PF01548_consen   57 ----GYWR-PLADFLQDAGIEVVVVNPLQVKRFRKSLGRRAKTDKIDARAIARLLRR  108 (144)
T ss_pred             ----ccch-hhhhheeccccccccccccccccccccccccccccccchHHHHHHHhc
Confidence                1222 345677889999999999999988742  3357788888888877764

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

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

Probab=96.37  E-value=0.039  Score=46.91  Aligned_cols=106  Identities=11%  Similarity=-0.020  Sum_probs=75.8

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc---hhhhhhHHHHHHHHHhcCCCCCCEEEE-ccccCCC
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR---VRKRLDAKSMIMLLRSLDAPIGTTAYV-EQSIPYP  162 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~---~R~r~d~~~L~~lL~~~~~p~p~~a~I-E~v~~~p  162 (249)
                      |+|+||+=-.+-+ +++|+.++.  ..++.|+-+.+++-.+.   .-.|-=..++..++++|   ..+.++| |+.-  -
T Consensus         1 M~vCGVELkgneaii~ll~~~~~--~~~~pdcr~~k~~l~~~~~~~~vr~Fq~~f~kl~~dy---~Vd~VvIk~R~~--K   73 (138)
T PF11215_consen    1 MKVCGVELKGNEAIICLLSLDDG--LFQLPDCRVRKFSLSDDNSTEEVRKFQFTFAKLMEDY---KVDKVVIKERAT--K   73 (138)
T ss_pred             CeEEEEEEecCeEEEEEEecCCC--ceECCccceeEEEcCCCccHHHHHHHHHHHHHHHHHc---CCCEEEEEeccc--C
Confidence            7899999888888 999998876  78888888777655554   44555567788999999   5555555 5543  4


Q ss_pred             CCCccceeechhhhHHHHHHHHHc-CCceeEeCchhhhhhhccc
Q 025662          163 QDGKQGWWSGGFGYGLWIGILVAS-GFSVVPIPSLTWKNWYGLS  205 (249)
Q Consensus       163 ~qgvqSaf~~G~a~Gv~~gvLaa~-gIPV~eVtP~~WKkav~g~  205 (249)
                      |+.+.|+.+|     -+.+++.+. +++|..++|+++|....-+
T Consensus        74 GKfAGga~~F-----KmEaaIQL~~~~~V~lvs~~~ik~~lKrn  112 (138)
T PF11215_consen   74 GKFAGGAVGF-----KMEAAIQLIDDVEVELVSPATIKAQLKRN  112 (138)
T ss_pred             CCccCCchhH-----HHHHHHHhcCCCcEEEECHHHHHHHHhcC
Confidence            5544444432     233444444 9999999999999998654

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=96.23  E-value=0.034  Score=56.86  Aligned_cols=59  Identities=24%  Similarity=0.436  Sum_probs=44.4

Q ss_pred             ceEEEEcCCCCceEEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCC
Q 025662           88 QWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ  163 (249)
Q Consensus        88 m~ILGIDPGl~Ga~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~  163 (249)
                      -.|+|||||++-++|+|+.+|.     ++|+-..         +-++...+.++|.++.  +|-+++ =.|.|+|+
T Consensus       244 ~lIVGIDPGiTtgiAvldldGe-----vl~~~S~---------r~~~~~eVve~I~~lG--~PvvVA-tDVtp~P~  302 (652)
T COG2433         244 SLIVGIDPGITTGIAVLDLDGE-----VLDLESR---------RGIDRSEVVEFISELG--KPVVVA-TDVTPAPE  302 (652)
T ss_pred             ceEEEeCCCceeeEEEEecCCc-----EEeeecc---------ccCCHHHHHHHHHHcC--CceEEE-ccCCCChH
Confidence            4799999999999999999984     4444433         4577889999999995  444444 45676765

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

Probab=95.63  E-value=0.054  Score=45.03  Aligned_cols=92  Identities=14%  Similarity=0.052  Sum_probs=58.9

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |+|||||+|..-. +|+-+..+.  .  ....++++...     ...+.+.|.++++++   .++.++|=-...|  +|.
T Consensus         1 mriL~lD~G~kriGiAvsd~~~~--~--a~pl~~i~~~~-----~~~~~~~l~~li~~~---~i~~iVvGlP~~~--~G~   66 (135)
T PF03652_consen    1 MRILGLDYGTKRIGIAVSDPLGI--I--ASPLETIPRRN-----REKDIEELKKLIEEY---QIDGIVVGLPLNM--DGS   66 (135)
T ss_dssp             -EEEEEEECSSEEEEEEEETTTS--S--EEEEEEEEECC-----CCCCHHHHHHHHHHC---CECEEEEEEEBBC--TSS
T ss_pred             CeEEEEEeCCCeEEEEEecCCCC--e--EeeeEEEECCC-----CchHHHHHHHHHHHh---CCCEEEEeCCccc--CCC
Confidence            7899999999999 999988763  2  22344443111     257889999999999   7888888765533  333


Q ss_pred             cceeechhhhHHHHHHHHHc-CCceeEeC
Q 025662          167 QGWWSGGFGYGLWIGILVAS-GFSVVPIP  194 (249)
Q Consensus       167 qSaf~~G~a~Gv~~gvLaa~-gIPV~eVt  194 (249)
                      .+... -..+-....+.... ++||+.+.
T Consensus        67 ~~~~~-~~v~~f~~~L~~~~~~ipV~~~D   94 (135)
T PF03652_consen   67 ESEQA-RRVRKFAEELKKRFPGIPVILVD   94 (135)
T ss_dssp             C-CCH-HHHHHHHHHHHHHH-TSEEEEEE
T ss_pred             ccHHH-HHHHHHHHHHHHhcCCCcEEEEC
Confidence            22221 12233333444454 99999874

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.

>PRK00109 Holliday junction resolvase-like protein; Reviewed

Probab=95.21  E-value=0.53  Score=39.27  Aligned_cols=94  Identities=17%  Similarity=0.096  Sum_probs=55.2

Q ss_pred             CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662           86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (249)
Q Consensus        86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q  164 (249)
                      .+|.|||||+|..-. +|+-+..+.      +..|.-.+...+   ...+.+.|.++++++   .++.++|=-..  .-+
T Consensus         2 ~~~~iLalD~G~kriGvAv~d~~~~------~a~pl~~i~~~~---~~~~~~~l~~~i~~~---~i~~iVvGlP~--~~~   67 (138)
T PRK00109          2 PSGRILGLDVGTKRIGVAVSDPLGG------TAQPLETIKRNN---GTPDWDRLEKLIKEW---QPDGLVVGLPL--NMD   67 (138)
T ss_pred             CCCcEEEEEeCCCEEEEEEecCCCC------EEcCEEEEEcCC---CchHHHHHHHHHHHh---CCCEEEEeccC--CCC
Confidence            367899999999999 998876543      344543222211   124578899999999   67777775433  223


Q ss_pred             CccceeechhhhHHHHHHHHHcCCceeEeC
Q 025662          165 GKQGWWSGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       165 gvqSaf~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      |..|.-. -..+-....+-...++||+.+.
T Consensus        68 G~~~~~~-~~v~~f~~~L~~~~~~~v~~~D   96 (138)
T PRK00109         68 GTEGPRT-ERARKFANRLEGRFGLPVVLVD   96 (138)
T ss_pred             CCcCHHH-HHHHHHHHHHHHHhCCCEEEEc
Confidence            3322110 0111112222234489999886

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

Probab=93.06  E-value=0.99  Score=38.34  Aligned_cols=94  Identities=14%  Similarity=0.055  Sum_probs=62.9

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhh-hhHHHHHHHHHhcCCCCCCEEEEccccCCCCCC
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKR-LDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r-~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qg  165 (249)
                      |.+||+|-|+.-. +|+-+..+.    -....++++...     .. ++...|..++++|   .++.++|=-...|  +|
T Consensus         2 ~~ilalD~G~KrIGvA~sd~~~~----~A~pl~~i~~~~-----~~~~~~~~l~~li~~~---~~~~vVVGlP~~m--~g   67 (141)
T COG0816           2 MRILALDVGTKRIGVAVSDILGS----LASPLETIKRKN-----GKPQDFNALLKLVKEY---QVDTVVVGLPLNM--DG   67 (141)
T ss_pred             ceEEEEecCCceEEEEEecCCCc----cccchhhheecc-----ccHhhHHHHHHHHHHh---CCCEEEEecCcCC--CC
Confidence            7899999999988 888876653    222333443211     12 7999999999999   8888888665433  33


Q ss_pred             ccceeechhhhHHHHHHHHHcCCceeEeCch
Q 025662          166 KQGWWSGGFGYGLWIGILVASGFSVVPIPSL  196 (249)
Q Consensus       166 vqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~  196 (249)
                      -.+. ..-...-....+-...++||+.+..+
T Consensus        68 ~~~~-~~~~~~~f~~~L~~r~~lpv~l~DER   97 (141)
T COG0816          68 TEGP-RAELARKFAERLKKRFNLPVVLWDER   97 (141)
T ss_pred             Ccch-hHHHHHHHHHHHHHhcCCCEEEEcCc
Confidence            3222 22234444555567788999999864

subtilis) [DNA replication, recombination, and repair]

>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length

Probab=89.09  E-value=4.6  Score=39.03  Aligned_cols=56  Identities=18%  Similarity=0.138  Sum_probs=39.2

Q ss_pred             EEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcccc
Q 025662           92 GIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSI  159 (249)
Q Consensus        92 GIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~  159 (249)
                      |||||+++- +++++..+.  .+.-+..|+-.+        ..+...+.++|+++  ..+++++.=..+
T Consensus         1 GIDpGT~s~dv~~~dd~g~--v~~~~~ipt~~v--------~~~p~~iv~~l~~~--~~~dlIa~psGy   57 (343)
T PF07318_consen    1 GIDPGTKSFDVCGLDDDGK--VIFYFSIPTEEV--------AKNPSIIVEELEEF--GDIDLIAGPSGY   57 (343)
T ss_pred             CCCCCCCcEEEEEEccCCc--EEEEeeccHHHh--------hhCHHHHHHHHHhc--cCCCEEEeCCcC
Confidence            899999988 899987443  555566776654        34456688888887  366777665443

The function of this family is unknown.

>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF

Probab=88.60  E-value=3.2  Score=34.21  Aligned_cols=88  Identities=16%  Similarity=0.059  Sum_probs=50.7

Q ss_pred             EEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCccce
Q 025662           91 LGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQGW  169 (249)
Q Consensus        91 LGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvqSa  169 (249)
                      ||||+|..-. +|+-+..+.      +..|.-.+...   ....+.+.|.++++++   .++.++|=-..  ..+|..|.
T Consensus         1 laiD~G~kriGvA~~d~~~~------~a~pl~~i~~~---~~~~~~~~l~~~i~~~---~~~~iVvGlP~--~~dG~~~~   66 (130)
T TIGR00250         1 LGLDFGTKSIGVAGQDITGW------TAQGIPTIKAQ---DGEPDWSRIEELLKEW---TPDKIVVGLPL--NMDGTEGP   66 (130)
T ss_pred             CeEccCCCeEEEEEECCCCC------EEeceEEEEec---CCcHHHHHHHHHHHHc---CCCEEEEeccC--CCCcCcCH
Confidence            6999999999 997765543      23333222111   1235568899999999   67777765433  22333222


Q ss_pred             e-echhhhHHHHHHHHHcCCceeEeC
Q 025662          170 W-SGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       170 f-~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      - ..-+.|+-.  +....++||+.+.
T Consensus        67 ~a~~v~~f~~~--L~~~~~~~v~~~D   90 (130)
T TIGR00250        67 LTERAQKFANR--LEGRFGVPVVLWD   90 (130)
T ss_pred             HHHHHHHHHHH--HHHHhCCCEEEEc
Confidence            1 111233332  2344599999886

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.

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

Probab=88.40  E-value=3.6  Score=36.41  Aligned_cols=53  Identities=13%  Similarity=0.100  Sum_probs=35.3

Q ss_pred             HHHHHcCCceeEeCchhh-hhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhhcc
Q 025662          181 GILVASGFSVVPIPSLTW-KNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILYHH  248 (249)
Q Consensus       181 gvLaa~gIPV~eVtP~~W-Kkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~h~  248 (249)
                      -.|...|+||+|.-|.+- ++++.+.  +.+-+.-..       +.+      -.++.-||++.|.|+.
T Consensus        94 r~l~~~gv~ViEthP~aa~~~~~~l~--r~~l~~~ie-------~~~------~~~~~~dAv~ag~~a~  147 (178)
T COG2410          94 RLLESEGVPVIETHPRAALAKAAGLR--RHDLDRIIE-------DVA------VSEDAVDAVLAGLAAL  147 (178)
T ss_pred             HHHHhcCCeEEEecchHHHHHHHhhc--cchhhhhhh-------hhh------hhhhHHHHHHHHHHHH
Confidence            568899999999999999 8888764  333332111       111      1457778888877753

>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=86.80  E-value=1.7  Score=38.48  Aligned_cols=66  Identities=20%  Similarity=0.221  Sum_probs=30.5

Q ss_pred             CCCCceEEEEcCC--CCce---EEEE-ecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEcc
Q 025662           84 NADSQWALGIDPD--LSGA---LAVL-KSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQ  157 (249)
Q Consensus        84 ~~~~m~ILGIDPG--l~Ga---~avL-~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~  157 (249)
                      +-+..+++|+|||  ..+-   +.++ ...+.  ...+++.-...   +.  -...-.+.+.++...+   .+..+++|.
T Consensus       222 ~~~~~~~~g~D~a~~~~~d~~~~~~~~~~~~~--~~~~~~~~~~~---~~--~~~~~~~~i~~~~~~~---~~~~i~~d~  291 (384)
T PF03237_consen  222 PPDWPIIIGVDPAGGKGGDYTAIVVWEIVDDD--GFYVVDDEYER---GM--SPEEWAERIRELYKKY---NPIKIYIDA  291 (384)
T ss_dssp             -TT--EEEEEE--SSCTTB-EEEEEE-E-SSS--SEEEEEEEEES---SS---TTTHHHHHHHHHHHT---TS--EEEEE
T ss_pred             CCCceEEEEEECCCCCccCCEEEEEEcccccc--ceEEeeehhhc---CC--CHHHHHHHHHHHHhhc---CceEEEEcC
Confidence            3445568999999  4444   3333 22232  34444433221   10  1233345566677777   778889998


Q ss_pred             cc
Q 025662          158 SI  159 (249)
Q Consensus       158 v~  159 (249)
                      ..
T Consensus       292 ~~  293 (384)
T PF03237_consen  292 NG  293 (384)
T ss_dssp             SC
T ss_pred             Cc
Confidence            54

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.

---

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	249
1hjr_A	158	Holliday junction resolvase (RUVC); site-specific	100.0
4ep4_A	166	Crossover junction endodeoxyribonuclease RUVC; res	100.0
1vhx_A	150	Putative holliday junction resolvase; structural g	98.95
1kcf_A	258	Hypothetical 30.2 KD protein C25G10.02 in chromoso	96.75
1iv0_A	98	Hypothetical protein; rnaseh-like, YQGF, structura	95.46
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	93.91
1nu0_A	138	Hypothetical protein YQGF; structural genomics, st	93.41
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	92.34
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	92.3
3r6m_A	213	YEAZ, resuscitation promoting factor; actin/HSP70	86.85
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	86.05
3g25_A	501	Glycerol kinase; IDP00743, ATP-binding, glycerol m	80.19

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

Probab=100.00  E-value=2.2e-39  Score=273.01  Aligned_cols=147  Identities=14%  Similarity=0.097  Sum_probs=138.7

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q  164 (249)
                      |+|||||||++.+ |||++.+++  ..+++++++|++. +..  .|+..+++.|.++|++|   .|+.++||++|  +++
T Consensus         1 m~ILGIDPGl~~tG~gvi~~~g~--~~~~v~~G~i~t~-~~~~~~Rl~~i~~~l~~~i~~~---~Pd~vaiE~vf--~~~   72 (158)
T 1hjr_A            1 AIILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTK-VDDLPSRLKLIYAGVTEIITQF---QPDYFAIEQVF--MAK   72 (158)
T ss_dssp             CEEEEEECCSSEEEEEEEEEETT--EEEEEEEEEEECC-CSCHHHHHHHHHHHHHHHHHHH---CCSEEEEEECC--CCC
T ss_pred             CEEEEEccCCCCeeEEEEEecCC--eEEEEEeeEEECC-CCCHHHHHHHHHHHHHHHHHHc---CCCEEEEeecc--ccc
Confidence            7899999999998 999998776  8999999999987 444  99999999999999999   89999999999  999


Q ss_pred             CccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHH
Q 025662          165 GKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCI  244 (249)
Q Consensus       165 gvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA  244 (249)
                      |++|++++|++||+++++++..||||.||+|.+|||+++|+ |+|+|+|++.|++++|+..+.    +++ |+|||||||
T Consensus        73 n~~s~~~lgqarGv~~~a~~~~~ipv~eytp~~vKkavtG~-G~A~K~qV~~mv~~ll~l~~~----p~~-DaADALAiA  146 (158)
T 1hjr_A           73 NADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGI-GSAEKSQVQHMVRTLLKLPAN----PQA-DAADALAIA  146 (158)
T ss_dssp             CTTTHHHHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHTSS-SSCCHHHHHHHHHHHTTCCCC----CSS-CTHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhhCC-CCCcHHHHHHHHHHHcCCCCC----CCC-CHHHHHHHH
Confidence            99999999999999999999999999999999999999999 999999999999999999765    566 999999999


Q ss_pred             hhcc
Q 025662          245 LYHH  248 (249)
Q Consensus       245 ~~h~  248 (249)
                      +||+
T Consensus       147 i~h~  150 (158)
T 1hjr_A          147 ITHC  150 (158)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9995

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

Probab=100.00  E-value=5.7e-39  Score=273.03  Aligned_cols=151  Identities=14%  Similarity=0.132  Sum_probs=140.6

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCC-ceeeeeeCCCcccccccc--hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCC
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNG-CSAEVFDTPHLPVLVGKR--VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQ  163 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g-~~~~v~D~pti~v~~g~~--~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~  163 (249)
                      |+|||||||++.+ |||++.++++ ..++++++++|++..+..  .|+..+++.|.++|++|   +|+.++||++|  ++
T Consensus         1 MrILGIDPGl~~tG~gvi~~~g~~~~~~~~v~~G~I~t~~~~~~~~RL~~I~~~l~~~i~~~---~Pd~vaiE~~F--~~   75 (166)
T 4ep4_A            1 MVVAGIDPGITHLGLGVVAVEGKGALKARLLHGEVVKTSPQEPAKERVGRIHARVLEVLHRF---RPEAVAVEEQF--FY   75 (166)
T ss_dssp             CEEEEEECCSSEEEEEEEEECSSSSSCEEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHHHH---CCSEEEEECCC--CS
T ss_pred             CEEEEEccccCceEEEEEEecCCccceEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHHh---CCCEEEEeehh--hc
Confidence            7899999999998 9999987631 058899999999877655  99999999999999999   99999999998  99


Q ss_pred             CCccceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHH
Q 025662          164 DGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYC  243 (249)
Q Consensus       164 qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaI  243 (249)
                      +|++|++++|+++|+++++++..||||+||+|++||++++|+ |+|+|+|++.|++++|+..+.    ++++|+||||||
T Consensus        76 ~n~~sal~lgqarGv~~la~~~~glpv~eytP~~vKkavtG~-G~A~K~QV~~mV~~lL~l~~~----p~~~DaADALAi  150 (166)
T 4ep4_A           76 RQNELAYKVGWALGAVLVAAFEAGVPVYAYGPMQVKQALAGH-GHAAKEEVALMVRGILGLKEA----PRPSHLADALAI  150 (166)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHHHTCCEEEECHHHHHHHHHSS-TTCCHHHHHHHHHHHTTCSSC----CSSHHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHHHHHHHHcCCCEEEECHHHHHHHhcCC-CCCCHHHHHHHHHHHhcCCCC----CCCCCHHHHHHH
Confidence            999999999999999999999999999999999999999999 999999999999999998765    678899999999


Q ss_pred             Hhhcc
Q 025662          244 ILYHH  248 (249)
Q Consensus       244 A~~h~  248 (249)
                      |+||+
T Consensus       151 Aich~  155 (166)
T 4ep4_A          151 ALTHA  155 (166)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99996

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

Probab=98.95  E-value=2.1e-09  Score=89.21  Aligned_cols=106  Identities=8%  Similarity=-0.042  Sum_probs=86.2

Q ss_pred             CceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCC
Q 025662           87 SQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (249)
Q Consensus        87 ~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qg  165 (249)
                      .|.|||||||++-+ +||.+..+.  .  ...+++|....   .|...+++.|.++|++|   .|+.++||..+  .. |
T Consensus         2 ~mriLGiDpG~~riGvAv~d~~g~--~--a~p~~~I~~~~---~r~~~~~~~l~~li~~~---~~~~ivVGlP~--~~-n   68 (150)
T 1vhx_A            2 SLRILGLDLGTKTLGVALSDEMGW--T--AQGIETIKINE---AEGDYGLSRLSELIKDY---TIDKIVLGFPK--NM-N   68 (150)
T ss_dssp             CEEEEEEEECSSEEEEEEECTTSS--S--EEEEEEEECBG---GGTBCCHHHHHHHHTTS---EEEEEEEECCC--CB-T
T ss_pred             CCEEEEEEccCCEEEEEEEECCCC--E--EeeEEEEEcCC---cchHHHHHHHHHHHHHc---CCCEEEEeeee--cC-C
Confidence            48899999999999 999998764  2  23356665321   36788999999999999   89999999975  33 3


Q ss_pred             ccceeechhhhHHHHHHHHHcCCceeE----eCchhhhhhhccc
Q 025662          166 KQGWWSGGFGYGLWIGILVASGFSVVP----IPSLTWKNWYGLS  205 (249)
Q Consensus       166 vqSaf~~G~a~Gv~~gvLaa~gIPV~e----VtP~~WKkav~g~  205 (249)
                      -++....++.++++..+....++||++    +||.+.|+.+...
T Consensus        69 Gt~~~~~~~ar~f~~~L~~~~~lpV~~vDEr~Ts~~Ak~~l~~~  112 (150)
T 1vhx_A           69 GTVGPRGEASQTFAKVLETTYNVPVVLWDERLTTMAAEKMLIAA  112 (150)
T ss_dssp             TBCCHHHHHHHHHHHHHHHHHCSCEEEECCSSCHHHHHHHHHHT
T ss_pred             cchhHHHHHHHHHHHHHHHhhCCCEEEecCCCCHHHHHHHHHHc
Confidence            345677888899998888888999999    9999999999775

>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=96.75  E-value=0.0023  Score=57.42  Aligned_cols=151  Identities=10%  Similarity=0.032  Sum_probs=86.1

Q ss_pred             eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCccccc--c------cchhhh----hhHHHHHHHHHhcCCCCCCEEEE
Q 025662           89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLV--G------KRVRKR----LDAKSMIMLLRSLDAPIGTTAYV  155 (249)
Q Consensus        89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~--g------~~~R~r----~d~~~L~~lL~~~~~p~p~~a~I  155 (249)
                      .|++||.|++.- ||.++.++. ....+.+--.+.+..  |      ..-...    ..+.-+..++..+   .|++++|
T Consensus        41 sIlSID~GikNlAyc~l~~~~~-~~p~l~~W~kl~l~~~~~~~~~~k~~~~p~~~~~~a~~Li~~ll~~~---~pd~vlI  116 (258)
T 1kcf_A           41 RVLGIDLGIKNFSYCFASQNED-SKVIIHNWSVENLTEKNGLDIQWTEDFQPSSMADLSIQLFNTLHEKF---NPHVILM  116 (258)
T ss_dssp             SEEEEEECSTTEEEEEEEECTT-SCEEEEEEEEECTTSCCTTCCCCCCCCSHHHHHHHHHHHHHHHHHHH---CCSEEEE
T ss_pred             cEEEEecCCCceEEEEEccCCC-CCCeeecceeeccccccccccccccCcChHHHHHHHHHHHHHhhccC---CCCEEEE
Confidence            799999999998 999995421 122233322222211  1      111111    2222233334444   8999999


Q ss_pred             ccccCCCCCCcccee-----echhhhHHHHHHHHH----------cCCceeEeCchhhhhhhccc----CCCCChHHHHH
Q 025662          156 EQSIPYPQDGKQGWW-----SGGFGYGLWIGILVA----------SGFSVVPIPSLTWKNWYGLS----GGTSTKDDSRR  216 (249)
Q Consensus       156 E~v~~~p~qgvqSaf-----~~G~a~Gv~~gvLaa----------~gIPV~eVtP~~WKkav~g~----~G~AsKd~sr~  216 (249)
                      |++-  +.-+ .|+.     .++---|.+..+|..          ....|..+.|+...++....    .....|.....
T Consensus       117 ErQr--~Rs~-~s~v~e~~Lrv~ilE~ML~a~l~~~~~~~~~~~~~~~~V~~~~p~~v~~yw~~~~~~~~~~~~Kk~~i~  193 (258)
T 1kcf_A          117 ERQR--YRSG-IATIPEWTLRVNMLESMLYALHYAEKRNSIEQKIQYPFLLSLSPKSTYSYWASVLNTKASFSKKKSRVQ  193 (258)
T ss_dssp             EECC--CCTT-TCCHHHHHHHHHHHHHHHHHHHHHHHHC-------CCEEEECCHHHHHHHHHHHHC-------CCCHHH
T ss_pred             eecC--cccC-cccccchhhhHhHHHHHHHHHHHHHHhhcccccccceeEEecCHHHHHHhhhhcccccchhHHHHHHHH
Confidence            9997  4434 3332     223333455555543          23678889999998876421    12346777888


Q ss_pred             HHHHhCCccccc--------------ccCCCCCCcccHHHHHhh
Q 025662          217 VASTLFPSLCSQ--------------LKRKKDHGTISSPYCILY  246 (249)
Q Consensus       217 ma~~LfP~~~~~--------------l~rkKdhgrADALaIA~~  246 (249)
                      ++++++-.....              ...+|.||-||+|+-|+.
T Consensus       194 lv~~~L~~~~~~~~~~e~~~~~~~~~~~~~K~DDLaDslLq~la  237 (258)
T 1kcf_A          194 MVKELIDGQKILFENEEALYKWNNGSRVEFKKDDMADSALIASG  237 (258)
T ss_dssp             HHHHHHHTTSEEESSHHHHHHHHHCCSTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCcCcCcHHHHHHHhcccccCcchHHHHHHHHHHHH
Confidence            888887544110              345778999999997753

>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=95.46  E-value=0.12  Score=39.64  Aligned_cols=90  Identities=12%  Similarity=-0.055  Sum_probs=54.7

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |.|||||+|..-. +|+-+..+.      +..|.-.+...   ....+.+.|.++++++   .++.++|=-...|  +|.
T Consensus         1 mriLglD~G~kriGvAvsd~~~~------~A~pl~ti~~~---~~~~~~~~l~~li~e~---~v~~iVvGlP~~m--dGt   66 (98)
T 1iv0_A            1 MRVGALDVGEARIGLAVGEEGVP------LASGRGYLVRK---TLEEDVEALLDFVRRE---GLGKLVVGLPLRT--DLK   66 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCS------SCCCEEEEECC---CHHHHHHHHHHHHHHH---TCCEEEEECCCCC--CSS
T ss_pred             CcEEEEEeCCCEEEEEEEeCCCC------eeeeeEEEEcc---CcHHHHHHHHHHHHHc---CCCEEEEeeccCC--CCC
Confidence            5799999999999 999876543      33343222111   2457789999999999   7888887654322  222


Q ss_pred             cc-eeechhhhHHHHHHHHHcCCceeEeC
Q 025662          167 QG-WWSGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       167 qS-af~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      .+ ....-+.|+--+  -.. ++||+.+.
T Consensus        67 ~~~~~~~~~~f~~~L--~~~-~lpV~~~D   92 (98)
T 1iv0_A           67 ESAQAGKVLPLVEAL--RAR-GVEVELWD   92 (98)
T ss_dssp             SCCCSSTTHHHHHHH--HHT-TCEEEEEC
T ss_pred             cCHHHHHHHHHHHHH--hcC-CCCEEEEC
Confidence            21 122113333222  223 89998875

>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=93.91  E-value=0.079  Score=54.21  Aligned_cols=60  Identities=20%  Similarity=0.267  Sum_probs=41.4

Q ss_pred             CceEEEEcCCC-Cce-EEEEecCCCCceeeee-eCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEc
Q 025662           87 SQWALGIDPDL-SGA-LAVLKSDHNGCSAEVF-DTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVE  156 (249)
Q Consensus        87 ~m~ILGIDPGl-~Ga-~avL~~~g~g~~~~v~-D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE  156 (249)
                      ...|+|||||. +|+ +|+|+..|.  .++.. =||+-+     ..+.+-+.+.|..+|.+|   .|++++|=
T Consensus       328 ~~~vlg~dpg~r~g~k~a~vd~~G~--~l~~~~iy~~~~-----~~~~~~~~~~l~~li~~~---~~~~IaIG  390 (785)
T 3bzc_A          328 PRATLGLDPGLRTGVKVAVVDATGK--LLDTATVYPHAP-----KNQWDQTLAVLAALCAKH---QVELIAIG  390 (785)
T ss_dssp             SCCEEEEECCSSSCEEEEEECTTSC--EEEEEEECCSGG-----GCCHHHHHHHHHHHHHHH---TCCEEEEE
T ss_pred             CCeEEEECCCCcCceEEEEECCCCC--EEEEEEEecCCc-----hhHHHHHHHHHHHHHHHc---CCCEEEEC
Confidence            45799999996 788 999988774  22211 134421     123455677899999999   88888874

>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=93.41  E-value=0.34  Score=39.35  Aligned_cols=92  Identities=14%  Similarity=-0.013  Sum_probs=55.5

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      ..|||||+|..-. +|+-+..+.    ......+++..     ....+.+.|.++++++   .++.++|=-...|  +|.
T Consensus         3 ~~iLglD~G~kriGvAvsd~~~~----~A~pl~ti~~~-----~~~~~~~~l~~li~e~---~v~~iVvGlP~~m--dGt   68 (138)
T 1nu0_A            3 GTLMAFDFGTKSIGVAVGQRITG----TARPLPAIKAQ-----DGTPDWNIIERLLKEW---QPDEIIVGLPLNM--DGT   68 (138)
T ss_dssp             CEEEEEECCSSEEEEEEEETTTT----EEEEEEEEEEE-----TTEECHHHHHHHHHHH---CCSEEEEEEEECT--TSC
T ss_pred             CeEEEEEeCCCEEEEEEEcCCCC----EEeeEEEEEcC-----CcchHHHHHHHHHHHc---CCCEEEEecccCC--CcC
Confidence            4699999999988 999887653    22233444321     1245688999999999   7888887654422  332


Q ss_pred             cceeechhhhHHHHHHHHHcCCceeEeC
Q 025662          167 QGWWSGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      .+- ..-..+-....+-...++||+.+.
T Consensus        69 ~~~-~~~~~~~f~~~L~~~~~lpV~~~D   95 (138)
T 1nu0_A           69 EQP-LTARARKFANRIHGRFGVEVKLHD   95 (138)
T ss_dssp             BCH-HHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             cCH-HHHHHHHHHHHHHHHhCCCEEEEc
Confidence            220 011112222222334589998863

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

Probab=92.34  E-value=0.23  Score=53.06  Aligned_cols=83  Identities=6%  Similarity=0.045  Sum_probs=49.8

Q ss_pred             HHhhhcccccccCCCCCCCcccccccCCC-CceEEEEcCCCC-----ce-EEEEecCCCCceeeeeeCCCcc-cccccch
Q 025662           58 AQMKQNWLDSLTFPPLHVHDLTANQTNAD-SQWALGIDPDLS-----GA-LAVLKSDHNGCSAEVFDTPHLP-VLVGKRV  129 (249)
Q Consensus        58 ~~~~~~~l~~l~~~~~~~~~~~~~~~~~~-~m~ILGIDPGl~-----Ga-~avL~~~g~g~~~~v~D~pti~-v~~g~~~  129 (249)
                      ....+|..+-|.-+|-.-+ ..     .+ ...|+|||||.+     |+ +|+|+..|.     ++|+.+|. ...+...
T Consensus       491 ~~f~~nL~~lL~~aP~~p~-~~-----lg~~~~VlaldpG~r~~g~~g~k~a~vD~~G~-----vl~~~~i~~~~~~~~~  559 (1219)
T 3psi_A          491 KTVRHKFMTKLDQAPFIPN-VR-----DPKIPKILSLTCGQGRFGADAIIAVYVNRKGD-----FIRDYKIVDNPFDKTN  559 (1219)
T ss_dssp             HHHHHHHHHHHCBCCCCSS-SS-----SCCCCCEEEEECTTCCTTTTCEEEEEECTTSC-----EEEEEEECSCTTCSSC
T ss_pred             HHHHHHHHHHHhCCCCCCC-cc-----cCCCCeEEEecCCCCCCCCCceEEEEECCCCC-----EEEEEEEcCCCCChhh
Confidence            4556666555555542111 11     23 447999999986     77 889988874     33444331 1111112


Q ss_pred             hhhhhHHHHHHHHHhcCCCCCCEEEE
Q 025662          130 RKRLDAKSMIMLLRSLDAPIGTTAYV  155 (249)
Q Consensus       130 R~r~d~~~L~~lL~~~~~p~p~~a~I  155 (249)
                      | ....+.|..+|.+|   .|++++|
T Consensus       560 ~-~~a~~~l~~li~~~---~~~vIaI  581 (1219)
T 3psi_A          560 P-EKFEDTLDNIIQSC---QPNAIGI  581 (1219)
T ss_dssp             S-HHHHHHHHHHHHHH---CCSEEEE
T ss_pred             H-HHHHHHHHHHHHHc---CCcEEEE
Confidence            2 22347899999999   8999987

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

Probab=92.30  E-value=0.24  Score=52.05  Aligned_cols=83  Identities=6%  Similarity=0.045  Sum_probs=49.4

Q ss_pred             HHhhhcccccccCCCCCCCcccccccCCC-CceEEEEcCCCC-----ce-EEEEecCCCCceeeeeeCCCcc-cccccch
Q 025662           58 AQMKQNWLDSLTFPPLHVHDLTANQTNAD-SQWALGIDPDLS-----GA-LAVLKSDHNGCSAEVFDTPHLP-VLVGKRV  129 (249)
Q Consensus        58 ~~~~~~~l~~l~~~~~~~~~~~~~~~~~~-~m~ILGIDPGl~-----Ga-~avL~~~g~g~~~~v~D~pti~-v~~g~~~  129 (249)
                      ....+|..+-|.-+|-.-+ ..     .+ ...|+|||||.+     |+ +|+|+..|.     ++|+.++. ...+...
T Consensus       494 ~~f~~nL~~lL~~aP~~p~-~~-----~g~~~~VlaldpG~~~~~~~g~k~a~vd~~G~-----~l~~~~i~~~~~~~~~  562 (1030)
T 3psf_A          494 KTVRHKFMTKLDQAPFIPN-VR-----DPKIPKILSLTCGQGRFGADAIIAVYVNRKGD-----FIRDYKIVDNPFDKTN  562 (1030)
T ss_dssp             HHHHHHHHHHHCCCCCCSC-TT-----SCCCCCEEEEECTTCCTTTSCEEEEEECTTSC-----EEEEEEECSCTTCSSC
T ss_pred             HHHHHHHHHHHhCCCCCCC-cc-----cCCCCeEEEecCCCCCCCCCCeEEEEECCCCC-----EEEEEEEcCCCCChhh
Confidence            4556666655555552111 11     23 346999999985     77 889988874     33333331 1111112


Q ss_pred             hhhhhHHHHHHHHHhcCCCCCCEEEE
Q 025662          130 RKRLDAKSMIMLLRSLDAPIGTTAYV  155 (249)
Q Consensus       130 R~r~d~~~L~~lL~~~~~p~p~~a~I  155 (249)
                      | .-..+.|..+|.+|   .|++++|
T Consensus       563 ~-~~~~~~l~~li~~~---~~~~IaI  584 (1030)
T 3psf_A          563 P-EKFEDTLDNIIQSC---QPNAIGI  584 (1030)
T ss_dssp             C-HHHHHHHHHHHHHH---CCSEEEE
T ss_pred             H-HHHHHHHHHHHHHc---CCcEEEE
Confidence            2 22237899999999   8999987

>3r6m_A YEAZ, resuscitation promoting factor; actin/HSP70 nucleotide-binding fold, bacterial resuscitation BUT non-culturable state, Y YJEE; 3.10A {Vibrio parahaemolyticus}

Probab=86.85  E-value=0.67  Score=40.03  Aligned_cols=94  Identities=16%  Similarity=0.146  Sum_probs=52.5

Q ss_pred             CceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCC--CCCCEEEEccccCCCC
Q 025662           87 SQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDA--PIGTTAYVEQSIPYPQ  163 (249)
Q Consensus        87 ~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~--p~p~~a~IE~v~~~p~  163 (249)
                      +|.|||||-...-+ +|+++.+.   .+.-+     ...  .+.-.+.+...+.++|++...  ...+.+++=.-   ||
T Consensus         1 ~M~iLaIdTS~~~~svAl~~~~~---~~~~~-----~~~--~~~Hs~~L~p~i~~~L~~a~~~~~dld~Iav~~G---PG   67 (213)
T 3r6m_A            1 SAKILAIDTATENCSVALLVNDQ---VISRS-----EVA--PRDHTKKVLPMVDEVLKEAGLTLQDLDALAFGRG---PG   67 (213)
T ss_dssp             -CCEEEEECSSSEEEEEEESSSC---EEEEE-----EEC--CSCCHHHHHHHHHHHHHTTTCCTTTCSEEEEEEE---SS
T ss_pred             CCEEEEEEccCcceEEEEEECCE---EEEEE-----Eec--hHHHHHHHHHHHHHHHHHcCCCHHHccEEEEecC---CC
Confidence            58999999988777 99997532   22211     111  111123445567777776532  23344443322   32


Q ss_pred             CCccceeechhhhHHHHHHHHHcCCceeEeCchh
Q 025662          164 DGKQGWWSGGFGYGLWIGILVASGFSVVPIPSLT  197 (249)
Q Consensus       164 qgvqSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~  197 (249)
                        --+.+.  =+.+...+++.+.++|++.|+-.+
T Consensus        68 --sfTglR--ig~~~AkgLa~~~~iPl~gVstL~   97 (213)
T 3r6m_A           68 --SFTGVR--IGIGIAQGLAFGAELPMIGVSTLA   97 (213)
T ss_dssp             --CHHHHH--HHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             --chhhHH--HHHHHHHHHHHHhCCCEEEEcCHH
Confidence              112222  233455677888999999998764

>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=86.05  E-value=1.8  Score=41.71  Aligned_cols=63  Identities=14%  Similarity=0.185  Sum_probs=36.0

Q ss_pred             CCceEEEEcC--CCCc---eEEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccc
Q 025662           86 DSQWALGIDP--DLSG---ALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQS  158 (249)
Q Consensus        86 ~~m~ILGIDP--Gl~G---a~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v  158 (249)
                      +..+++|+||  |.++   +++++..++.  ...+++  ..   .+.........+.+.++.+.|   .+..+++|.-
T Consensus       418 ~~~~~~GvD~S~G~~~D~tai~v~~~~g~--~~~~v~--~~---~~~~~~~~~~~~~I~~l~~~y---~~~~I~iD~~  485 (592)
T 3cpe_A          418 DRKYIATLDCSEGRGQDYHALHIIDVTDD--VWEQVG--VL---HSNTISHLILPDIVMRYLVEY---NECPVYIELN  485 (592)
T ss_dssp             TCCEEEEEECCSSBTTBCEEEEEEECSSS--SEEEEE--EE---EESSSCTTTHHHHHHHHHHHT---TSCCEEEEES
T ss_pred             CceEEEEEecCCCCCCCceEEEEEEcCCC--ceEEEE--EE---ecCCCCHHHHHHHHHHHHHHc---CCcEEEEecC
Confidence            4567999999  4444   2556643432  223322  11   111112344567788888888   6778888874

>3g25_A Glycerol kinase; IDP00743, ATP-binding, glycerol metabolism, nucleotide-binding, transferase, struct genomics; HET: MSE; 1.90A {Staphylococcus aureus subsp} PDB: 3ge1_A*

Probab=80.19  E-value=3  Score=39.23  Aligned_cols=27  Identities=19%  Similarity=0.337  Sum_probs=22.2

Q ss_pred             cCCCCceEEEEcCCCCce-EEEEecCCC
Q 025662           83 TNADSQWALGIDPDLSGA-LAVLKSDHN  109 (249)
Q Consensus        83 ~~~~~m~ILGIDPGl~Ga-~avL~~~g~  109 (249)
                      +|++.+.+||||=|+++. .++++.++.
T Consensus         1 ~~aM~~~~lgIDiGtts~k~~l~d~~G~   28 (501)
T 3g25_A            1 SNAMEKYILSIDQGTTSSRAILFNQKGE   28 (501)
T ss_dssp             --CCCCEEEEEEECSSEEEEEEECTTSC
T ss_pred             CcccccEEEEEEeCccceEEEEEcCCCC
Confidence            478888999999999999 888887764

---

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	249
d1hjra_	158	RuvC resolvase {Escherichia coli [TaxId: 562]}	100.0
d3bzka5	149	Transcriptional accessory factor Tex {Pseudomonas	97.7
d1kcfa2	218	Mitochondrial resolvase ydc2 catalytic domain {Fis	96.68
d1vhxa_	140	Hypothetical protein YrrK (RuvX) {Bacillus subtili	95.72
d1nu0a_	138	Hypothetical protein YqgF (RuvX) {Escherichia coli	94.99
d1iv0a_	98	Hypothetical protein, YqgF homologue {Thermus ther	94.47
d2a6aa1	103	Hypothetical protein TM0874 {Thermotoga maritima [	89.08
d1zc6a1	114	Probable N-acetylglucosamine kinase CV2896 {Chromo	87.5
d2aa4a1	119	N-acetylmannosamine kinase NanK {Escherichia coli	85.69

>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=6.7e-35  Score=242.17  Aligned_cols=147  Identities=15%  Similarity=0.107  Sum_probs=135.9

Q ss_pred             eEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccc-hhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           89 WALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKR-VRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        89 ~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~-~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      +|||||||++.+ ||||+.+++  ..+++++++|++..+.. .|+..+++.|.++|++|   +|+.++||++|  +++|.
T Consensus         2 iILGIDPGl~~~G~avid~~~~--~~~~v~~g~i~t~~~~~~~Rl~~i~~~l~~li~~~---~Pd~vaiE~~f--~~~n~   74 (158)
T d1hjra_           2 IILGIDPGSRVTGYGVIRQVGR--QLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQF---QPDYFAIEQVF--MAKNA   74 (158)
T ss_dssp             EEEEEECCSSEEEEEEEEEETT--EEEEEEEEEEECCCSCHHHHHHHHHHHHHHHHHHH---CCSEEEEEECC--CCCCT
T ss_pred             EEEEEccCCCceEEEEEEeeCC--EEEEEEeeEEeCCCCChHHHHHHHHHHHHHHHhcc---CCCEEEEEeeh--hccCH
Confidence            699999999988 999999876  89999999999765432 89999999999999999   99999999998  99999


Q ss_pred             cceeechhhhHHHHHHHHHcCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCcccccccCCCCCCcccHHHHHhh
Q 025662          167 QGWWSGGFGYGLWIGILVASGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQLKRKKDHGTISSPYCILY  246 (249)
Q Consensus       167 qSaf~~G~a~Gv~~gvLaa~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~l~rkKdhgrADALaIA~~  246 (249)
                      +|++++|+.+|++++++...|||+.+|+|+++||+++|+ |+|+|+|++.|++.+|+..+.    ++ +|.+||||||+|
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-GSAEKSQVQHMVRTLLKLPAN----PQ-ADAADALAIAIT  148 (158)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHTSS-SSCCHHHHHHHHHHHTTCCCC----CS-SCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCcceeecchhhhheeecCC-CCcCHHHHHHHHHHHcCCCCC----CC-CCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999 899999999999999986654    33 579999999999


Q ss_pred             cc
Q 025662          247 HH  248 (249)
Q Consensus       247 h~  248 (249)
                      |+
T Consensus       149 h~  150 (158)
T d1hjra_         149 HC  150 (158)
T ss_dssp             HH
T ss_pred             HH
Confidence            86

>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=97.70  E-value=2.8e-05  Score=62.69  Aligned_cols=113  Identities=15%  Similarity=0.162  Sum_probs=68.3

Q ss_pred             CCCceEEEEcCC-CCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCC
Q 025662           85 ADSQWALGIDPD-LSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYP  162 (249)
Q Consensus        85 ~~~m~ILGIDPG-l~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p  162 (249)
                      ++.+.||||||| -+|+ +|+|+.+|.     ++|+.++.. .+...+.+...+.|.++|++|   +|++++|-.     
T Consensus         2 ~~~~~vlg~DPg~r~gck~AvlD~~G~-----vld~~viyp-~~~~~~~~~a~~~l~~li~k~---~p~vIaIGN-----   67 (149)
T d3bzka5           2 AGPRATLGLDPGLRTGVKVAVVDATGK-----LLDTATVYP-HAPKNQWDQTLAVLAALCAKH---QVELIAIGN-----   67 (149)
T ss_dssp             CCSCCEEEEECCSTTCEEEEEECTTSC-----EEEEEEECC-STTTCCHHHHHHHHHHHHHHT---TCCEEEEES-----
T ss_pred             CCCceEEEECCCcccccEEEEECCCCC-----EEEEEEEec-CCcHHHHHHHHHHHHHHHHHc---CCeEEEECC-----
Confidence            467889999999 5888 999998874     445444421 122234555667799999999   899999832     


Q ss_pred             CCCccceeechhhhHHHHHHHHH---cCCceeEeCchhhhhhhcccCCCCChHHHHHHHHHhCCccccc
Q 025662          163 QDGKQGWWSGGFGYGLWIGILVA---SGFSVVPIPSLTWKNWYGLSGGTSTKDDSRRVASTLFPSLCSQ  228 (249)
Q Consensus       163 ~qgvqSaf~~G~a~Gv~~gvLaa---~gIPV~eVtP~~WKkav~g~~G~AsKd~sr~ma~~LfP~~~~~  228 (249)
                        |..|    -+..-.+.-++..   .+|+|+.|.=           -+|+-=.....|+.-||+....
T Consensus        68 --gTas----re~~~~v~~l~~~~~~~~i~~~iV~e-----------~gAsvYs~S~~A~~EfP~~~~~  119 (149)
T d3bzka5          68 --GTAS----RETDKLAGELIKKYPGMKLTKIMVSE-----------AGASVYSASELAAKEFPELDVS  119 (149)
T ss_dssp             --STTH----HHHHHHHHHHHHHCGGGCCEEEEECC-----------TTHHHHHTSHHHHHHCTTSCHH
T ss_pred             --CccH----HHHHHHHHHHHHhCCCCCcEEEEEec-----------cchhhhhCCHHHHHHCCCCChh
Confidence              2222    1222333333322   3566655541           1233333445677788887653

>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=96.68  E-value=0.0011  Score=54.60  Aligned_cols=153  Identities=9%  Similarity=0.034  Sum_probs=81.3

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCccccccc--------c----hhhhhhHHHHHHHHHhcCCCCCCEEE
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGK--------R----VRKRLDAKSMIMLLRSLDAPIGTTAY  154 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~--------~----~R~r~d~~~L~~lL~~~~~p~p~~a~  154 (249)
                      ..|++||-|...- ||+++.+++ ..+.+.+-..+.+....        .    .-....+.-+..++..+   .|+.+.
T Consensus         2 ~kIlSIDvGIkNlAyc~l~~~~~-~~~~I~~W~~i~L~~~~~~~~k~~~~~~~~~~~~~~~~l~~~l~~~~---~~d~vl   77 (218)
T d1kcfa2           2 SRVLGIDLGIKNFSYCFASQNED-SKVIIHNWSVENLTEKNGLDIQWTEDFQPSSMADLSIQLFNTLHEKF---NPHVIL   77 (218)
T ss_dssp             SSEEEEEECSTTEEEEEEEECTT-SCEEEEEEEEECTTSCCTTCCCCCCCCSHHHHHHHHHHHHHHHHHHH---CCSEEE
T ss_pred             CeEEEEEeCccccEEEEEeeCCC-CCcEEEEeeeEeecccccCcccccccCCHHHHHHHHHHHHhhhhccc---CCceEE
Confidence            4699999999998 999988653 13445554443321111        1    11223333344555566   789999


Q ss_pred             EccccCCCCCCccceeechhhhHHHH----HHHHH---------cCCc-eeEeCchhhhhhh----cccCCCCChHHHHH
Q 025662          155 VEQSIPYPQDGKQGWWSGGFGYGLWI----GILVA---------SGFS-VVPIPSLTWKNWY----GLSGGTSTKDDSRR  216 (249)
Q Consensus       155 IE~v~~~p~qgvqSaf~~G~a~Gv~~----gvLaa---------~gIP-V~eVtP~~WKkav----~g~~G~AsKd~sr~  216 (249)
                      ||++-...  |..+.+..+-....+.    ..+..         ..++ |..+.|...-+++    +..+-...|.....
T Consensus        78 IE~Q~~r~--~~~~i~~~~l~~~~le~ml~~~~~~~~~~~~~~~~~~~~v~~~~~~~v~~~~~~~~~~~~~~~~Kk~~i~  155 (218)
T d1kcfa2          78 MERQRYRS--GIATIPEWTLRVNMLESMLYALHYAEKRNSIEQKIQYPFLLSLSPKSTYSYWASVLNTKASFSKKKSRVQ  155 (218)
T ss_dssp             EEECCCCT--TTCCHHHHHHHHHHHHHHHHHHHHHHHHC-------CCEEEECCHHHHHHHHHHHHC-------CCCHHH
T ss_pred             Eeeccccc--CccchhHHHHHHHHHHHHHHHHHHHhccccccccccceeEEEcCccceeeeccccccccccchhHHHHHH
Confidence            99995332  3333333333332232    22221         1222 5556666654443    21112456667778


Q ss_pred             HHHHhCCccc--------------ccccCCCCCCcccHHHHHhh
Q 025662          217 VASTLFPSLC--------------SQLKRKKDHGTISSPYCILY  246 (249)
Q Consensus       217 ma~~LfP~~~--------------~~l~rkKdhgrADALaIA~~  246 (249)
                      ++..++-...              ..-+++|-||-||++|-|++
T Consensus       156 ~~~~~L~~~~~~~~~~~~~~~~~~~~~~~kKkDDLADs~Lq~l~  199 (218)
T d1kcfa2         156 MVKELIDGQKILFENEEALYKWNNGSRVEFKKDDMADSALIASG  199 (218)
T ss_dssp             HHHHHHHTTSEEESSHHHHHHHHHCCSTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhCccccCcchHHHHHHHhcccCCCchhhHhHHHHHHH
Confidence            8887763221              11223567899999998875

>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=95.72  E-value=0.0098  Score=46.43  Aligned_cols=95  Identities=12%  Similarity=0.021  Sum_probs=57.0

Q ss_pred             CceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCC
Q 025662           87 SQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDG  165 (249)
Q Consensus        87 ~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qg  165 (249)
                      +|.|||||+|..-. +|+=+..+.  ..  .-..+++.   +........+.|.++++++   .++.++|=-..  .-+|
T Consensus         1 ~mriLgiD~G~kriGvAisd~~~~--~a--~pl~~i~~---~~~~~~~~~~~l~~ii~e~---~i~~iViGlP~--~~dg   68 (140)
T d1vhxa_           1 SLRILGLDLGTKTLGVALSDEMGW--TA--QGIETIKI---NEAEGDYGLSRLSELIKDY---TIDKIVLGFPK--NMNG   68 (140)
T ss_dssp             CEEEEEEEECSSEEEEEEECTTSS--SE--EEEEEEEC---BGGGTBCCHHHHHHHHTTS---EEEEEEEECCC--CBTT
T ss_pred             CceEEEEEeCCCEEEEEEecCCCC--cc--cceeeEee---cccccchHHHHHHHHHHhh---ccceEEEeccc--ccCC
Confidence            69999999999999 998665543  11  12223321   1112334568899999999   77777775543  3444


Q ss_pred             ccceeechhhhHHHHHHHHHcCCceeEeC
Q 025662          166 KQGWWSGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       166 vqSaf~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      ..+.... ...=....+....++||+.+.
T Consensus        69 ~~~~~~~-~~~~f~~~l~~~~~i~V~~~D   96 (140)
T d1vhxa_          69 TVGPRGE-ASQTFAKVLETTYNVPVVLWD   96 (140)
T ss_dssp             BCCHHHH-HHHHHHHHHHHHHCSCEEEEC
T ss_pred             cchhHHH-HHHHHHHHhccCCCccEEEee
Confidence            4333221 222222334566799999875

>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=94.99  E-value=0.037  Score=42.85  Aligned_cols=101  Identities=15%  Similarity=0.036  Sum_probs=60.6

Q ss_pred             CCceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCC
Q 025662           86 DSQWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQD  164 (249)
Q Consensus        86 ~~m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~q  164 (249)
                      ++..|||||+|..-. +|+=+..+.  ..  ...++++..     ....+.+.|..+++++   .++.++|=-..  .-+
T Consensus         1 m~griLgiD~G~kriGvAvsd~~~~--~a--~pl~~i~~~-----~~~~~~~~l~~i~~e~---~~~~iVvG~P~--~~~   66 (138)
T d1nu0a_           1 MSGTLMAFDFGTKSIGVAVGQRITG--TA--RPLPAIKAQ-----DGTPDWNIIERLLKEW---QPDEIIVGLPL--NMD   66 (138)
T ss_dssp             CCCEEEEEECCSSEEEEEEEETTTT--EE--EEEEEEEEE-----TTEECHHHHHHHHHHH---CCSEEEEEEEE--CTT
T ss_pred             CCCcEEEEEeCCCEEEEEEeCCCCC--cc--ccceeeecc-----cchhhHHHHHHHhhcc---CccEEEeeccc--ccc
Confidence            467899999999888 999876653  22  222344311     1234678899999999   88999995543  444


Q ss_pred             Cccc-eeechhhhHHHHHHHHHcCCceeEe----Cchhhhhhh
Q 025662          165 GKQG-WWSGGFGYGLWIGILVASGFSVVPI----PSLTWKNWY  202 (249)
Q Consensus       165 gvqS-af~~G~a~Gv~~gvLaa~gIPV~eV----tP~~WKkav  202 (249)
                      |..+ +-+.=..|+-.  +-...++||+.+    |..+-+..+
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            4444 22222333333  345569999875    444444443

>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=94.47  E-value=0.14  Score=37.36  Aligned_cols=90  Identities=13%  Similarity=-0.044  Sum_probs=57.0

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGK  166 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgv  166 (249)
                      |.|||||-|..-. +|+=+..+.      +..|.-.+...   ....+.+.|.++++++   .++.++|=-...|  +|.
T Consensus         1 MriLglD~G~kriGiAisd~~~~------~a~pl~~i~~~---~~~~~~~~l~~ii~e~---~i~~iVvGlP~~~--dG~   66 (98)
T d1iv0a_           1 MRVGALDVGEARIGLAVGEEGVP------LASGRGYLVRK---TLEEDVEALLDFVRRE---GLGKLVVGLPLRT--DLK   66 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCS------SCCCEEEEECC---CHHHHHHHHHHHHHHH---TCCEEEEECCCCC--CSS
T ss_pred             CcEEEEEcCCCEEEEEEecCCCC------eEcceEEEECC---CchHHHHHHHHHHHhh---ccceeEccccccc--CCC
Confidence            7899999999998 998865543      34443222211   1355678899999999   8888888664422  333


Q ss_pred             cc-eeechhhhHHHHHHHHHcCCceeEeC
Q 025662          167 QG-WWSGGFGYGLWIGILVASGFSVVPIP  194 (249)
Q Consensus       167 qS-af~~G~a~Gv~~gvLaa~gIPV~eVt  194 (249)
                      .| +-..=+.|+-.+   ...++||+.+.
T Consensus        67 ~~~~~~~v~~f~~~L---~~~~lpv~~~D   92 (98)
T d1iv0a_          67 ESAQAGKVLPLVEAL---RARGVEVELWD   92 (98)
T ss_dssp             SCCCSSTTHHHHHHH---HHTTCEEEEEC
T ss_pred             cCHHHHHHHHHHHHH---hhCCCCEEEEc
Confidence            22 222224444433   45699998875

>d2a6aa1 c.55.1.9 (A:1-103) Hypothetical protein TM0874 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: YeaZ-like
domain: Hypothetical protein TM0874
species: Thermotoga maritima [TaxId: 2336]

Probab=89.08  E-value=0.4  Score=34.56  Aligned_cols=95  Identities=17%  Similarity=0.178  Sum_probs=54.0

Q ss_pred             ceEEEEcCCCCceEEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhcCCCCCCEEEEccccCCCCCCcc
Q 025662           88 QWALGIDPDLSGALAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSLDAPIGTTAYVEQSIPYPQDGKQ  167 (249)
Q Consensus        88 m~ILGIDPGl~Ga~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~~~p~p~~a~IE~v~~~p~qgvq  167 (249)
                      |.||+||-...-.+++.+.+.   .....      .. .++.-.+.+...+.+++++...   +.--|+.+.  .+.|+.
T Consensus         1 M~iLaidTS~~~sval~~~~~---~~~~~------~~-~~~~hs~~l~~~i~~~l~~~~~---~~~di~~i~--v~~GPG   65 (103)
T d2a6aa1           1 MNVLALDTSQRIRIGLRKGED---LFEIS------YT-GEKKHAEILPVVVKKLLDELDL---KVKDLDVVG--VGIGPG   65 (103)
T ss_dssp             CEEEEEECSSSEEEEEEETTE---EEEEE------EE-SCGGGGGHHHHHHHHHHHHHTC---CGGGCSEEE--EECCSS
T ss_pred             CcEEEEEcCcccEEEEEECCE---EEEEe------cc-CchHHHHHHHHHHHHHHHHcCC---CHHHhHHHh--hcCCCC
Confidence            789999976432277765432   12111      11 1112245566667788888732   111234443  334444


Q ss_pred             ceeechhhhHHHHHHHHHcCCceeEeCchh
Q 025662          168 GWWSGGFGYGLWIGILVASGFSVVPIPSLT  197 (249)
Q Consensus       168 Saf~~G~a~Gv~~gvLaa~gIPV~eVtP~~  197 (249)
                      |-=.+=-+..++.++..+.++|++.|+..+
T Consensus        66 sfTglRig~s~akgla~~~~ip~~gis~l~   95 (103)
T d2a6aa1          66 GLTGLRVGIATVVGLVSPYDIPVAPLNSFE   95 (103)
T ss_dssp             CHHHHHHHHHHHHHHHGGGTCCEEEECHHH
T ss_pred             cchhHHHHHHHHHHHHHHcCCCEEEeCHHH
Confidence            433333455677788889999999998654

>d1zc6a1 c.55.1.5 (A:8-121) Probable N-acetylglucosamine kinase CV2896 {Chromobacterium violaceum [TaxId: 536]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: BadF/BadG/BcrA/BcrD-like
domain: Probable N-acetylglucosamine kinase CV2896
species: Chromobacterium violaceum [TaxId: 536]

Probab=87.50  E-value=0.72  Score=32.70  Aligned_cols=21  Identities=24%  Similarity=0.487  Sum_probs=18.7

Q ss_pred             eEEEEcCCCCce-EEEEecCCC
Q 025662           89 WALGIDPDLSGA-LAVLKSDHN  109 (249)
Q Consensus        89 ~ILGIDPGl~Ga-~avL~~~g~  109 (249)
                      .+||||=|.+.+ ++|++.++.
T Consensus         5 y~lGID~GGT~tk~~l~d~~G~   26 (114)
T d1zc6a1           5 YLIGVDGGGTGTRIRLHASDGT   26 (114)
T ss_dssp             EEEEEEECSSCEEEEEEETTCC
T ss_pred             EEEEEEcCcceEEEEEEcCCCC
Confidence            599999999999 999988764

>d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: N-acetylmannosamine kinase NanK
species: Escherichia coli [TaxId: 562]

Probab=85.69  E-value=0.61  Score=33.36  Aligned_cols=51  Identities=16%  Similarity=0.137  Sum_probs=32.7

Q ss_pred             ceEEEEcCCCCce-EEEEecCCCCceeeeeeCCCcccccccchhhhhhHHHHHHHHHhc
Q 025662           88 QWALGIDPDLSGA-LAVLKSDHNGCSAEVFDTPHLPVLVGKRVRKRLDAKSMIMLLRSL  145 (249)
Q Consensus        88 m~ILGIDPGl~Ga-~avL~~~g~g~~~~v~D~pti~v~~g~~~R~r~d~~~L~~lL~~~  145 (249)
                      |.+||||=|-+.. +++++.++.  .+.-...++-   ...  -.+...+.+.++++++
T Consensus         1 M~~lgiDiGgT~i~~~l~d~~G~--i~~~~~~~~~---~~~--~~~~~~~~i~~~i~~~   52 (119)
T d2aa4a1           1 MTTLAIDIGGTKLAAALIGADGQ--IRDRRELPTP---ASQ--TPEALRDALSALVSPL   52 (119)
T ss_dssp             CCEEEEEECSSEEEEEEECTTCC--EEEEEEEECC---SSC--CHHHHHHHHHHHHTTT
T ss_pred             CeEEEEEeCcCEEEEEEEcCCCC--EEEeEEEecc---ccC--cHHHHHHHHHHHHHHh
Confidence            7899999999999 999988764  4333333321   111  1344456677777776