Psyllid ID: psy9737

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------37
Protein Sequence
MRGMDPQERRLLTLPSPSLRGVGKSQQPSEYQPRETLLNFGIWDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRYSTVHKKEESREMITRPHCPK
Secondary Structure (PSIPRED)
cccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccEEEEcccccccEEccccEEEccccccccccHHHHHHHHHHHHHccccccccEEEccccccHHHHHHccccccHHHHHHHHHHHcccccEEEEEEcccccccccccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccccccHHHHHHcccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHccccccccccccccccccccccHHHHHHccHHHcccccccccEEcccccccccEcccccccccEEEcccccccccEEcccccccccEEccccccccHHccccccccccEEEEccccccccEEEccHcHHcHHcHHHHHHHcccccccHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHccccccccccccccccccHHHHHHHHHHHcccccHHHHHcccccccccHcccccccEEEEEEccHHHHHHHHHcccccHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
mrgmdpqerrlltlpspslrgvgksqqpseyqpretllnfgiwdlvgdevrgveyevgnevrggkyevgdevrgveyevgdevrggkyevgnevrggkyevgdkvrgrrrtvgnevrggkyevgdevrggkyevgdevrggkydcssfqaisnlyhpnplvKEIQErssnsqisfkflwcpshvgisgndqadaeakkatsepitnhsLLLDEIKSLTKKHFYQKWNTtwsninpsenklrrikstttpwktssqkaRLDEVCLMRMRightkithshlfkreerpicdschepltVEHIILHCnklrfrppsfleestqdilsdqygqldtvnnlnDSLTDRLCnrystvhkkeesremitrphcpk
Flexible Loop (DISEMBL)
mrgmdpqerrlltlpspslrgvgksqqpseyqprETLLNFGIWDLVGDEVRGVEyevgnevrggkyevgdevrgveyevgdevrggkyevgnevrggkyevgdkvrgrrrtvgnevrggkyevgdevrggkyevgdevrggkYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAtsepitnhslLLDEIKSLTKKHFYQKwnttwsninpsenklrrikstttpwktssqkarlDEVCLMRMRIGhtkithshlfkreERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRystvhkkeesremitrphcpk
Low Complexity Region (SEG)
MRGMDPQErrlltlpspslrGVGKSQQPSEYQPRETLLNFGIWDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRYSTVHKKEESREMITRPHCPK
Disordered region (IsUnstruct)
***********************************TLLNFGIWDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEI*******QISFKFLWCPSHVGI********************HSLLLDEIKSLTKKHFYQKWNTTWSNIN***********************RLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRY********************
Disordered Region (DISOPRED)
************************************************************************************GGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCN**********************
Disordered Region (DISEMBL)
********RRLLTLPSPSL************QPRETLLNFGIWDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISG**************PITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKS***********ARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRYSTV*****************
Disordered Region (DISPRO)
*********R******************SEYQPRETLLNFGIWDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRYSTVHKKEESREMITRP*CPK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRGMDPQERRLLTLPSPSLRGVGKSQQPSEYQPRETLLNFGIWDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTVGNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDSLTDRLCNRYSTVHKKEESREMITRPHCPK
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	368
427791321	1210	Putative tick transposon, partial [Rhipi	0.464	0.141	0.344	3e-23
427791807	1212	Putative tick transposon, partial [Rhipi	0.464	0.141	0.344	2e-22
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.426	0.312	0.376	2e-21
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.418	0.385	0.364	4e-21
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.426	0.601	0.370	1e-20
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.426	0.395	0.370	4e-20
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.353	0.276	0.392	4e-19
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.426	0.128	0.345	8e-19
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.361	0.570	0.370	3e-18
328720146	164	PREDICTED: hypothetical protein LOC10056	0.342	0.768	0.416	2e-17

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  115 bits (289), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 63/183 (34%), Positives = 95/183 (51%), Gaps = 12/183 (6%)

Query: 132  YEVGDEVRGGKY--------DCSSFQAISNLYHPNPLVKEIQERS--SNSQISFKFLWCP 181
            YE   ++  GK+          S+ +A+       PLV +I      ++  IS +F W P
Sbjct: 980  YEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVP 1039

Query: 182  SHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLR 241
            SHVGI GN++AD  A  A  + +T   + L + +   +     KW   W +   + NKL 
Sbjct: 1040 SHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSC--TSNKLH 1097

Query: 242  RIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHII 301
             +K T   WK    + R  EV L R+RIGHT +TH+ L  +EE+P+C+ C EPLT+ HI+
Sbjct: 1098 LVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHIL 1157

Query: 302  LHC 304
            + C
Sbjct: 1158 ILC 1160

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791807|gb|JAA61355.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  113 bits (282), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/183 (34%), Positives = 95/183 (51%), Gaps = 12/183 (6%)

Query: 132  YEVGDEVRGGKY--------DCSSFQAISNLYHPNPLVKEIQERS--SNSQISFKFLWCP 181
            YE   ++  GK+          S+ +A+       PLV +I      ++  IS +F W P
Sbjct: 983  YEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVP 1042

Query: 182  SHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLR 241
            SHVGI GN++AD  A  A  + +T   + L + +   +     KW   W +   + NKL 
Sbjct: 1043 SHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSC--TSNKLH 1100

Query: 242  RIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHII 301
             +K T   WK    + R  EV L R+RIGHT +TH+ L  +EE+P+C+ C EPLT+ HI+
Sbjct: 1101 LVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHIL 1160

Query: 302  LHC 304
            + C
Sbjct: 1161 ILC 1163

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 61/162 (37%), Positives = 85/162 (52%), Gaps = 5/162 (3%)

Query: 146 SSFQAISNLYHPNPLVKEIQERSSNSQISFK---FLWCPSHVGISGNDQADAEAKKATSE 202
           SS  A+SN    +P +  I  + +N     K   F+WCPSHVGI GN+ AD  AK+A   
Sbjct: 148 SSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVM 207

Query: 203 PITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEV 262
           P+T   L   + KS  + +    W   W     ++NKL  I+   + WK   Q  R  E+
Sbjct: 208 PVTKLPLPHTDYKSPIRSYVKSLWQNEWDE--ETDNKLHSIQPVISEWKQGPQIDRRGEI 265

Query: 263 CLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHC 304
            L R RIGH+ +TH +L +RE  P C  C   LTV+HI++ C
Sbjct: 266 VLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDC 307

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443733872|gb|ELU18078.1| hypothetical protein CAPTEDRAFT_197082 [Capitella teleta]

 Score =  108 bits (270), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 58/159 (36%), Positives = 87/159 (54%), Gaps = 5/159 (3%)

Query: 149 QAISNLYHPNPLVKEIQERSS---NSQISFKFLWCPSHVGISGNDQADAEAKKATSEPIT 205
           Q I N    +P V +I E+ +      I     WCPSHVG+ GN++AD  AK+A S    
Sbjct: 72  QGIGNFNIKHPYVVKILEKCTLLHKKGIDLVMTWCPSHVGVMGNERADLLAKEALSFTTC 131

Query: 206 NHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLM 265
              +   + K +T + + +KW   WS+    ENKL  I+ T   W  SS++ R +E+ L 
Sbjct: 132 TIRIPSSDFKPITHEFYKEKWQEQWSS--EQENKLYCIQPTLGKWAKSSREIRREEIVLA 189

Query: 266 RMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHC 304
           R RIGH+ +TH +L +RE  P+C  C   L+++HI + C
Sbjct: 190 RARIGHSHLTHGYLLRREMPPVCIPCQNILSIKHIFIEC 228

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]

 Score =  106 bits (265), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 60/162 (37%), Positives = 85/162 (52%), Gaps = 5/162 (3%)

Query: 146 SSFQAISNLYHPNPLVKEIQERSSNSQISFK---FLWCPSHVGISGNDQADAEAKKATSE 202
           SS  A+SN    +P +  I  + +N     K   F+WCPSHVGI GN+ AD  AK+A   
Sbjct: 102 SSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVM 161

Query: 203 PITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEV 262
           P+T   L   + KS  + +    W   W     ++NKL  I+   + WK   Q  R  E+
Sbjct: 162 PVTKLPLPHTDYKSPIRSYVKSLWQNEWDE--ETDNKLHSIQPVISEWKQGPQIDRRGEI 219

Query: 263 CLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHC 304
            L R RIGH+ +TH +L +RE  P C  C   L+V+HI++ C
Sbjct: 220 VLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHILIDC 261

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]

 Score =  105 bits (262), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 60/162 (37%), Positives = 85/162 (52%), Gaps = 5/162 (3%)

Query: 146 SSFQAISNLYHPNPLVKEIQERSSNSQISFK---FLWCPSHVGISGNDQADAEAKKATSE 202
           SS  A+SN    +P +  I  + +N     K   F+WCPSHVGI GN+ AD +AK+A   
Sbjct: 197 SSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQALVM 256

Query: 203 PITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEV 262
           P+T   L   + KS  + +    W   W     ++NKL  I+   + WK   Q  R  E+
Sbjct: 257 PVTKLPLPHTDYKSPIRSYVKSLWQNEWDG--ETDNKLHIIQPVISEWKQGPQIDRRGEI 314

Query: 263 CLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHC 304
            L   RIGH+ +TH +L +RE  P C  C   LTV+HI++ C
Sbjct: 315 VLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDC 356

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443721618|gb|ELU10867.1| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]

 Score =  102 bits (253), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 55/140 (39%), Positives = 81/140 (57%), Gaps = 10/140 (7%)

Query: 177 FLWCPSHVGISGNDQADAEAKKATSEPITNHSLL---LDEIKSLTKKHFYQKWNTTWSNI 233
           F+WCPSHVGI GN+ AD  AK+A S   TN + L     +++ L KK+   +W   W   
Sbjct: 121 FMWCPSHVGIPGNEMADTLAKEALSS--TNLAELPVPASDLRCLIKKYIRSRWQHEWDEQ 178

Query: 234 NPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHE 293
           +   NKL  I  T  PW    ++ R +E+ L R+RIGHT  TH ++ + +++  C +C  
Sbjct: 179 H--SNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVC 236

Query: 294 PLTVEHIILHCNK---LRFR 310
           PLTV+HII+ C     +R+R
Sbjct: 237 PLTVQHIIIECADFLHIRYR 256

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  100 bits (250), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 56/162 (34%), Positives = 87/162 (53%), Gaps = 5/162 (3%)

Query: 146  SSFQAISNLYHPNPLVKE---IQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSE 202
            S+ QA+  +    PLV +   + +  +  +    F+W PSHVGI GN+ AD EAK+A + 
Sbjct: 1022 SALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNH 1081

Query: 203  PITNHSLLLDEIKSLTKKHFYQKWNTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEV 262
             ++   +   +++       Y++W   W     + +KLR+I +      TS    R    
Sbjct: 1082 AVSGTQIPYSDLRQSIASATYREWQNRWEA--ETHSKLRQIVADVRWRPTSKGLTRRGST 1139

Query: 263  CLMRMRIGHTKITHSHLFKREERPICDSCHEPLTVEHIILHC 304
             + R+RIGHT ITHS + KREE P+C+ C   LTVEHI++ C
Sbjct: 1140 TMSRLRIGHTYITHSFVLKREEPPLCEYCDSRLTVEHILVDC 1181

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443730613|gb|ELU16038.1| hypothetical protein CAPTEDRAFT_206814 [Capitella teleta]

 Score = 99.0 bits (245), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 50/135 (37%), Positives = 71/135 (52%), Gaps = 2/135 (1%)

Query: 170 NSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNHSLLLDEIKSLTKKHFYQKWNTT 229
           N       LWCPSH+G+ GN++AD  AK+A S    +  +   +  S+    +  KW   
Sbjct: 76  NRGFDLVILWCPSHIGVVGNERADLLAKEALSFTACDVRIPAFDFNSVAYSFYRDKWQAL 135

Query: 230 WSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICD 289
           WS      NKL  ++        SS++ R  E+ L R RIGHT +TH +L +RE  P C 
Sbjct: 136 WSL--EQNNKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTHLTHGYLLRRELPPFCV 193

Query: 290 SCHEPLTVEHIILHC 304
            C  PLTV+HI++ C
Sbjct: 194 HCQCPLTVKHILIEC 208

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|328720146|ref|XP_003246964.1| PREDICTED: hypothetical protein LOC100568990, partial [Acyrthosiphon pisum]

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/132 (41%), Positives = 72/132 (54%), Gaps = 6/132 (4%)

Query: 177 FLWCPSHVGISGNDQADAEAKKATSEPITN--HSLLLDEIKSLTKKHFYQKWNTTWSNIN 234
           ++W P H GI GN++AD EA KA S P T   +    ++ K   K+   QKW   W N  
Sbjct: 7   YMWAPGHCGIQGNEKADLEASKAASSPDTPLLNIYTYEDKKKQIKQVLDQKWLIQWIN-- 64

Query: 235 PSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFKREERPICDSCHEP 294
               KL +IK+    WK      R +E  L R+RIGHT ITH HL ++ + PIC+ C   
Sbjct: 65  -QHTKLNQIKNNIQTWKNPGLN-RKEETILNRLRIGHTFITHRHLMEKNDPPICEMCGVD 122

Query: 295 LTVEHIILHCNK 306
           LTV+HII  C K
Sbjct: 123 LTVKHIITECRK 134

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	368
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.353	0.267	0.295	4.4e-05
GENEDB_PFALCIPARUM|MAL13P1.133	5415	MAL13P1.133 "hypothetical prot	0.228	0.015	0.391	6e-05
UNIPROTKB|Q8IE74	5415	MAL13P1.133 "Uncharacterized p	0.228	0.015	0.391	6e-05

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 127 (49.8 bits), Expect = 4.4e-05, P = 4.4e-05
 Identities = 42/142 (29%), Positives = 67/142 (47%)

Query:   173 ISFKFLWCPSHVGISGNDQADAEAKKATS-EPITNHSLLLDEIKSLTKKHFYQKWNTTWS 231
             ++  F W P+H G+ GN+QAD  AK+AT    I  H   +  I+S  K+  ++  N  W 
Sbjct:   284 LNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMT-IRSAVKRRAHEVVNARWE 342

Query:   232 NINPSENKLRRI-KSTTTPWK----TSSQKARLDEVCLMRMRIGHTKITHSHLFKR--EE 284
             N   S +  R + + T TP +          R     +++MR G   + H +L++R   +
Sbjct:   343 NDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPD 401

Query:   285 RPICD-SCHEPL-TVEHIILHC 304
              P  D  C     +V HI+L C
Sbjct:   402 VPNSDCQCGRATQSVRHILLAC 423

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GENEDB_PFALCIPARUM|MAL13P1.133 MAL13P1.133 "hypothetical protein, conserved" [Plasmodium falciparum (taxid:5833)]

 Score = 137 (53.3 bits), Expect = 6.0e-05, P = 6.0e-05
 Identities = 36/92 (39%), Positives = 53/92 (57%)

Query:    53 VEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTV 112
             +++E  N   G +Y+ GDE  G EY+ GDE  G +Y+ G+E  G +Y+ GD+  G     
Sbjct:  3744 IQHEEYNR-NGDEYD-GDEYDGDEYD-GDECDGDEYD-GDEYDGDEYD-GDEYDGDEHN- 3797

Query:   113 GNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYD 144
             G+E  G +Y  GDE  G +Y  GDE  G +Y+
Sbjct:  3798 GDEYNGDEYN-GDEYNGDEYN-GDEYNGDEYN 3827

GO:0016020 "membrane" evidence=ISS

UNIPROTKB|Q8IE74 MAL13P1.133 "Uncharacterized protein" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 137 (53.3 bits), Expect = 6.0e-05, P = 6.0e-05
 Identities = 36/92 (39%), Positives = 53/92 (57%)

Query:    53 VEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNEVRGGKYEVGDKVRGRRRTV 112
             +++E  N   G +Y+ GDE  G EY+ GDE  G +Y+ G+E  G +Y+ GD+  G     
Sbjct:  3744 IQHEEYNR-NGDEYD-GDEYDGDEYD-GDECDGDEYD-GDEYDGDEYD-GDEYDGDEHN- 3797

Query:   113 GNEVRGGKYEVGDEVRGGKYEVGDEVRGGKYD 144
             G+E  G +Y  GDE  G +Y  GDE  G +Y+
Sbjct:  3798 GDEYNGDEYN-GDEYNGDEYN-GDEYNGDEYN 3827


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        0.314   0.134   0.403    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      368       356   0.00080  117 3  11 23  0.46    34
                                                     34  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  620 (66 KB)
  Total size of DFA:  252 KB (2133 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:  31.78u 0.10s 31.88t   Elapsed:  00:00:04
  Total cpu time:  31.79u 0.10s 31.89t   Elapsed:  00:00:04
  Start:  Thu Aug 15 12:39:12 2013   End:  Thu Aug 15 12:39:16 2013

GO:0016020 "membrane" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	368
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-07
pfam00075	126	pfam00075, RNase_H, RNase H	1e-05
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-04

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 158 NPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATS 201
             + K I+E +++  +  +  W P H GI GN++AD  AK+A  
Sbjct: 86  LRIRKAIRELANH-GVKVRLHWVPGHSGIEGNERADRLAKEAAK 128

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 157 PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA 199
             P+  EI E            W P H GI GN+ AD  AK+ 
Sbjct: 83  SKPIKNEIWELLQKKH-KVYIQWVPGHSGIPGNELADKLAKQG 124

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 146 SSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATS 201
           S  + ++N      L K ++E      I  KF   P H GI GN++AD  AKK   
Sbjct: 96  SKGKPVANKDLIKELDKLLEELE-ERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	368
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.94
PRK08719	147	ribonuclease H; Reviewed	98.78
PRK00203	150	rnhA ribonuclease H; Reviewed	98.76
PRK06548	161	ribonuclease H; Provisional	98.68
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.36
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	98.16
KOG3752|consensus	371		97.6
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	96.24
PRK13907	128	rnhA ribonuclease H; Provisional	96.09
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	95.59
PRK07708	219	hypothetical protein; Validated	94.21
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	91.4

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=98.94  E-value=7.7e-10  Score=92.94  Aligned_cols=64  Identities=30%  Similarity=0.465  Sum_probs=52.8

Q ss_pred             ceeeeccccHHHHHHhHc-----cCC--C-C-HHHHHHHHHHHcCCCeEEEEEeccCCCC-CcChHHHHHHhhhc
Q psy9737         136 DEVRGGKYDCSSFQAISN-----LYH--P-N-PLVKEIQERSSNSQISFKFLWCPSHVGI-SGNDQADAEAKKAT  200 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~n-----p~~--~-s-~ii~~I~~~l~~~g~~V~l~WVPgH~gI-~GNE~AD~lAK~Aa  200 (368)
                      ..+...+||.+++..|..     .+.  . . ++..+|.+++ ..+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus        58 ~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   58 RKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             SEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             ccccccccHHHHHHHHHHhccccccccccccccchhheeecc-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            778889999999997766     332  1 2 4778898888 44899999999999999 69999999999986

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK08719 ribonuclease H; Reviewed

Probab=98.78  E-value=1.1e-08  Score=90.78  Aligned_cols=60  Identities=18%  Similarity=0.180  Sum_probs=43.1

Q ss_pred             eccccHHHHHHh--------HccCCCC--------HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcC
Q psy9737         140 GGKYDCSSFQAI--------SNLYHPN--------PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATS  201 (368)
Q Consensus       140 ~~s~SlSAL~aI--------~np~~~s--------~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~  201 (368)
                      ..+||+-++.+|        +|.|..+        ++.+.|.+++.  ...|+|.|||||+|++|||.||+||++|+.
T Consensus        71 i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         71 IYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             EEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            445565555555        4545433        24555555544  467999999999999999999999999975

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=98.76  E-value=9.6e-09  Score=90.55  Aligned_cols=66  Identities=20%  Similarity=0.240  Sum_probs=49.1

Q ss_pred             eeeeccccHHHHHHhHc--------cCCC--------CHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhc
Q psy9737         137 EVRGGKYDCSSFQAISN--------LYHP--------NPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT  200 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~n--------p~~~--------s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa  200 (368)
                      .+...+||..++.+|..        .+..        .++++.|.+++..  ..|.|.|||||+|++||+.||+|||+|+
T Consensus        63 ~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~~~~~N~~AD~lA~~a~  140 (150)
T PRK00203         63 EVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHAGHPENERCDELARAGA  140 (150)
T ss_pred             eEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCCCCHHHHHHHHHHHHHH
Confidence            46777777777666653        2322        1356777776643  7899999999999999999999999998


Q ss_pred             CCCC
Q psy9737         201 SEPI  204 (368)
Q Consensus       201 ~~~~  204 (368)
                      ....
T Consensus       141 ~~~~  144 (150)
T PRK00203        141 EEAT  144 (150)
T ss_pred             HHhh
Confidence            7543

>PRK06548 ribonuclease H; Provisional

Probab=98.68  E-value=3e-08  Score=89.68  Aligned_cols=67  Identities=18%  Similarity=0.273  Sum_probs=48.4

Q ss_pred             eeeeccccHHHHHHhH--------ccCC-CC-------HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhc
Q psy9737         137 EVRGGKYDCSSFQAIS--------NLYH-PN-------PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT  200 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~--------np~~-~s-------~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa  200 (368)
                      .|+..+||+-++.++.        |.|. ++       +|+++|..++..  ..|+|.|||||+|++|||.||+||++|+
T Consensus        63 ~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v~~~wVkgHsg~~gNe~aD~LA~~aa  140 (161)
T PRK06548         63 PILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNIRMSWVNAHTGHPLNEAADSLARQAA  140 (161)
T ss_pred             eEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc--CceEEEEEecCCCCHHHHHHHHHHHHHH
Confidence            3566666666666665        1222 21       367777777654  4799999999999999999999999998


Q ss_pred             CCCCC
Q psy9737         201 SEPIT  205 (368)
Q Consensus       201 ~~~~~  205 (368)
                      .....
T Consensus       141 ~~~~~  145 (161)
T PRK06548        141 NNFST  145 (161)
T ss_pred             HHhcc
Confidence            65443

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=98.36  E-value=1.3e-06  Score=69.67  Aligned_cols=67  Identities=28%  Similarity=0.380  Sum_probs=53.5

Q ss_pred             eccceeeeccccHHHHHHhHccCC-CC----HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhc
Q psy9737         133 EVGDEVRGGKYDCSSFQAISNLYH-PN----PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT  200 (368)
Q Consensus       133 ~~~~~v~~~s~SlSAL~aI~np~~-~s----~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa  200 (368)
                      .....+...+||..++..+.+... ..    .++..|++.+ .....+.|.|||+|+++..|+.||.+||+|.
T Consensus        59 ~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          59 LGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             CCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            445778888999999999987643 11    2566666665 4578899999999999999999999999874

One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]

Probab=98.16  E-value=2.3e-06  Score=77.11  Aligned_cols=43  Identities=26%  Similarity=0.383  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCCC
Q psy9737         160 LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEP  203 (368)
Q Consensus       160 ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~~  203 (368)
                      +.+++.+++.+ -..|.+.|||||+|.++||+||+||+.|+...
T Consensus       104 l~~~~~~~~~~-~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328         104 LWEELDELLKR-HELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHHHHHHHhh-CCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            45666665533 44899999999999999999999999998765

>KOG3752|consensus

Probab=97.60  E-value=7.7e-05  Score=75.32  Aligned_cols=42  Identities=31%  Similarity=0.415  Sum_probs=34.9

Q ss_pred             HHHHHHHHHc-CCCeEEEEEeccCCCCCcChHHHHHHhhhcCC
Q psy9737         161 VKEIQERSSN-SQISFKFLWCPSHVGISGNDQADAEAKKATSE  202 (368)
Q Consensus       161 i~~I~~~l~~-~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~  202 (368)
                      ...+.++++. ++..|++.|||||.||.|||+||.+|++.+..
T Consensus       323 ~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  323 FNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            4555566655 67999999999999999999999999988543

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B

Probab=96.24  E-value=0.0091  Score=46.12  Aligned_cols=60  Identities=22%  Similarity=0.150  Sum_probs=45.1

Q ss_pred             ceeeeccccHHHHHHhHccCCC-C---HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhc
Q psy9737         136 DEVRGGKYDCSSFQAISNLYHP-N---PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT  200 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np~~~-s---~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa  200 (368)
                      +.+..-+||+.++..|.+.... +   .++..|+.++.. -..+.|.|||    =+.|..||.|||.|.
T Consensus        22 ~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~----r~~N~~A~~LA~~a~   85 (87)
T PF13456_consen   22 RKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIP----REQNKVADALAKFAL   85 (87)
T ss_dssp             SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE------GGGSHHHHHHHHHHH
T ss_pred             CEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEC----hHHhHHHHHHHHHHh
Confidence            5788889999999999776432 2   367777777655 7789999998    679999999999885

>PRK13907 rnhA ribonuclease H; Provisional

Probab=96.09  E-value=0.014  Score=49.62  Aligned_cols=61  Identities=31%  Similarity=0.271  Sum_probs=45.7

Q ss_pred             eeeeccccHHHHHHhHccCCCC----HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCC
Q psy9737         137 EVRGGKYDCSSFQAISNLYHPN----PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSE  202 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~np~~~s----~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~  202 (368)
                      .+..-+||+-.+..+.+.+..+    +++++|..++. .-..+.|.|||.    +.|+.||.+|+.|...
T Consensus        63 ~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~-~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         63 IVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIK-SFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             EEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHh-cCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            4777788888888887655332    36677766664 355777899998    5999999999998753

>PF13966 zf-RVT: zinc-binding in reverse transcriptase

Probab=95.59  E-value=0.0074  Score=48.42  Aligned_cols=41  Identities=29%  Similarity=0.556  Sum_probs=31.3

Q ss_pred             ccCccccc---cccccCCCCCCCCCCCCC-CCCcceecccccccc
Q psy9737         268 RIGHTKIT---HSHLFKREERPICDSCHE-PLTVEHIILHCNKLR  308 (368)
Q Consensus       268 RTGHg~Ln---hLhRi~~~dsp~C~~CG~-~ETVeHIL~eCPry~  308 (368)
                      +.-|..+.   -+.+.+...++.|..|+. .||++|+|++||...
T Consensus        39 ~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   39 RALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             eeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence            34455552   366777788899999997 699999999999654

>PRK07708 hypothetical protein; Validated

Probab=94.21  E-value=0.11  Score=49.36  Aligned_cols=65  Identities=11%  Similarity=0.084  Sum_probs=48.4

Q ss_pred             eeeeccccHHHHHHhHccCCC-CH----HHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCCCCC
Q psy9737         137 EVRGGKYDCSSFQAISNLYHP-NP----LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPIT  205 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~np~~~-s~----ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~~~~  205 (368)
                      .|..-+||+-++..+.+.|.. ++    +...|.+++......+.|.|||-    .-|+.||+||+.|......
T Consensus       142 ~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR----~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        142 PVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISR----KQNKEADQLATQALEGTVI  211 (219)
T ss_pred             eEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCc----hhhhHHHHHHHHHHhcCCC
Confidence            377888999999999877643 32    45556666666566788899975    5699999999999985443

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=91.40  E-value=0.42  Score=47.96  Aligned_cols=63  Identities=22%  Similarity=0.286  Sum_probs=46.7

Q ss_pred             eeeeccccHHHHHHhHccCC-CCH----HHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCCCC
Q psy9737         137 EVRGGKYDCSSFQAISNLYH-PNP----LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPI  204 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~np~~-~s~----ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~~~  204 (368)
                      .+...+||.-++..+.+.+. .+.    ++.+|+++++ .-..+.|.|||.    ..|+.||.||+.|.....
T Consensus        67 ~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~-~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238         67 EVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELAS-QFGRVTYTWIPR----ARNAHADRLANEAMDAAA  134 (372)
T ss_pred             eEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHh-cCCceEEEECCc----hhhhHHHHHHHHHHHhhc
Confidence            47778889999998877653 332    4455666553 346799999997    689999999999876544

---

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

ID	Length	Definition	E-value
Query	368
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	8e-04

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 11/50 (22%), Positives = 18/50 (36%)

Query: 158 NPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNH 207
           N   +   +  +  +  + F    +H G   ND  D +AK A       H
Sbjct: 93  NEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRDLEH 142

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	368
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	98.92
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	98.92
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	98.9
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	98.89
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	98.87
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	98.76
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.7
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	98.69
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	98.4
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.39
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.25
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	97.79
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	97.73
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	97.68

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*

Probab=98.92  E-value=1.2e-09  Score=94.62  Aligned_cols=66  Identities=15%  Similarity=0.299  Sum_probs=52.8

Q ss_pred             ceeeeccccHHHHHHhHc--------cCC--------CCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhh
Q psy9737         136 DEVRGGKYDCSSFQAISN--------LYH--------PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA  199 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~n--------p~~--------~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~A  199 (368)
                      ..+...+||+.++..|..        .|.        .-+++++|..++.  +..|.|.|||+|+|+++||.||+|||+|
T Consensus        71 ~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~--~~~v~~~~V~~H~g~~~N~~AD~LA~~a  148 (154)
T 2qkb_A           71 NKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ--GMDIQWMHVPGHSGFIGNEEADRLAREG  148 (154)
T ss_dssp             CEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT--TCEEEEEECCTTSSCHHHHHHHHHHHHH
T ss_pred             ceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc--CCceEEEEccCCCCCHhHHHHHHHHHHH
Confidence            578888899888887765        121        1247788887765  4679999999999999999999999999


Q ss_pred             cCCC
Q psy9737         200 TSEP  203 (368)
Q Consensus       200 a~~~  203 (368)
                      +..+
T Consensus       149 ~~~~  152 (154)
T 2qkb_A          149 AKQS  152 (154)
T ss_dssp             HTCC
T ss_pred             HHhc
Confidence            8764

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}

Probab=98.92  E-value=6.9e-10  Score=95.08  Aligned_cols=65  Identities=20%  Similarity=0.097  Sum_probs=51.6

Q ss_pred             ceeeeccccHHHHHHhHcc---------C--------CCCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhh
Q psy9737         136 DEVRGGKYDCSSFQAISNL---------Y--------HPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKK  198 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np---------~--------~~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~  198 (368)
                      ..+...+||+.++..|...         |        ..-+++++|.+++..  ..|.|.|||||+|+++||.||+|||+
T Consensus        63 ~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~--~~v~~~~V~gH~g~~~N~~AD~LA~~  140 (146)
T 3h08_A           63 ARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL--HRVTFHKVKGHSDNPYNSRADELARL  140 (146)
T ss_dssp             CEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH--SEEEEEECCC-CCSHHHHHHHHHHHH
T ss_pred             CcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh--CceEEEEcCCcCCcHhHHHHHHHHHH
Confidence            5788888999888887651         1        112488888888764  57999999999999999999999999


Q ss_pred             hcCC
Q psy9737         199 ATSE  202 (368)
Q Consensus       199 Aa~~  202 (368)
                      |+..
T Consensus       141 a~~~  144 (146)
T 3h08_A          141 AIKE  144 (146)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9864

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=98.90  E-value=1.2e-09  Score=95.24  Aligned_cols=68  Identities=24%  Similarity=0.272  Sum_probs=54.2

Q ss_pred             ceeeeccccHHHHHHhHc--------cCC--------CCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhh
Q psy9737         136 DEVRGGKYDCSSFQAISN--------LYH--------PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA  199 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~n--------p~~--------~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~A  199 (368)
                      ..+...+||+.++..|..        .+.        ..++++.|.+++.  ...|.|.|||||+|+++||.||+|||+|
T Consensus        63 ~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  140 (155)
T 1jl1_A           63 AEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQIKWEWVKGHAGHPENERADELARAA  140 (155)
T ss_dssp             CEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT--TCEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred             CcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc--cCceEEEEcCCCCCCHHHHHHHHHHHHH
Confidence            578888899998888875        221        1247777777664  3689999999999999999999999999


Q ss_pred             cCCCCC
Q psy9737         200 TSEPIT  205 (368)
Q Consensus       200 a~~~~~  205 (368)
                      +..+..
T Consensus       141 ~~~~~~  146 (155)
T 1jl1_A          141 AMNPTL  146 (155)
T ss_dssp             HHSCCB
T ss_pred             Hhccch
Confidence            987553

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=98.89  E-value=1.5e-09  Score=94.66  Aligned_cols=66  Identities=24%  Similarity=0.325  Sum_probs=49.3

Q ss_pred             ceeeeccccHHHHHHhHcc--------C--------CCCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhh
Q psy9737         136 DEVRGGKYDCSSFQAISNL--------Y--------HPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA  199 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np--------~--------~~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~A  199 (368)
                      ..+...+||+.++.+|...        |        ...+++++|.+++. ....|.|.|||||+|++|||.||+||++|
T Consensus        66 ~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  144 (150)
T 3qio_A           66 LEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI-KKEKVYLAWVPAHKGIGGNEQVDKLVSAG  144 (150)
T ss_dssp             SEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHT-TCSEEEEEECCTTSCCHHHHHHHHHHHTT
T ss_pred             CcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHh-hcCceEEEEccCcCCChhHHHHHHHHHHH
Confidence            5677777777776666442        1        12236666666554 47789999999999999999999999999


Q ss_pred             cCC
Q psy9737         200 TSE  202 (368)
Q Consensus       200 a~~  202 (368)
                      +..
T Consensus       145 ~~~  147 (150)
T 3qio_A          145 IRK  147 (150)
T ss_dssp             TSC
T ss_pred             HHH
Confidence            875

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A

Probab=98.87  E-value=2e-09  Score=94.18  Aligned_cols=65  Identities=17%  Similarity=0.178  Sum_probs=53.0

Q ss_pred             ceeeeccccHHHHHHhHc--------cCC--------CCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhh
Q psy9737         136 DEVRGGKYDCSSFQAISN--------LYH--------PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA  199 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~n--------p~~--------~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~A  199 (368)
                      ..+...+||+.++..|..        .+.        .-++++.|.+++..  ..|.|.|||||+|+++||.||+|||+|
T Consensus        65 ~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~--~~v~~~wV~gH~g~~~Ne~AD~LAk~a  142 (158)
T 2e4l_A           65 CKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL--HQIDWRWVKGHAGHAENERCDQLARAA  142 (158)
T ss_dssp             CEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT--SEEEEEECCTTCCCHHHHHHHHHHHHH
T ss_pred             CeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHcc--CcEEEEEccCCCCchhHHHHHHHHHHH
Confidence            578888899888888766        221        12477888887753  689999999999999999999999999


Q ss_pred             cCC
Q psy9737         200 TSE  202 (368)
Q Consensus       200 a~~  202 (368)
                      +..
T Consensus       143 ~~~  145 (158)
T 2e4l_A          143 AEA  145 (158)
T ss_dssp             HHS
T ss_pred             HHh
Confidence            976

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A

Probab=98.76  E-value=4.9e-09  Score=92.58  Aligned_cols=67  Identities=16%  Similarity=0.178  Sum_probs=54.1

Q ss_pred             eeeeccccHHHHHHhHc---------cCC--------CCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhh
Q psy9737         137 EVRGGKYDCSSFQAISN---------LYH--------PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA  199 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~n---------p~~--------~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~A  199 (368)
                      .+...+||+.++..|..         .+.        ..++++.|.+++..  ..|.|.|||||+|+++||.||+|||+|
T Consensus        68 ~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~--~~v~~~wV~gH~g~~~Ne~AD~LAk~a  145 (166)
T 1ril_A           68 EVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP--HRVRFHFVKGHTGHPENERVDREARRQ  145 (166)
T ss_dssp             EEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT--SEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             eEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc--CeEEEEEeeCCCCchhHHHHHHHHHHH
Confidence            68888899988888866         121        12477888887754  589999999999999999999999999


Q ss_pred             cCCCCC
Q psy9737         200 TSEPIT  205 (368)
Q Consensus       200 a~~~~~  205 (368)
                      +.....
T Consensus       146 ~~~~~~  151 (166)
T 1ril_A          146 AQSQAK  151 (166)
T ss_dssp             HTSSCC
T ss_pred             HHHhhc
Confidence            987653

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=98.70  E-value=2.3e-09  Score=92.81  Aligned_cols=69  Identities=14%  Similarity=0.028  Sum_probs=51.0

Q ss_pred             eeeeccccHHHHHHhHccCCCC-HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCCCCC
Q psy9737         137 EVRGGKYDCSSFQAISNLYHPN-PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPIT  205 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~np~~~s-~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~~~~  205 (368)
                      .+...+||.+...-+.+.|..+ +.....+++++.....|.|.|||||+|+++||.||+|||+|+....+
T Consensus        71 ~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           71 KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcCCeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            5677777776655556666544 34455555554433389999999999999999999999999987665

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=98.69  E-value=9.1e-09  Score=91.44  Aligned_cols=70  Identities=16%  Similarity=0.204  Sum_probs=52.6

Q ss_pred             cceeeeccccHHHHHHhHccCC-----CCHHHHHHHHHHHcCCCeEEEEEeccCCC-----CCcChHHHHHHhhhcCCCC
Q psy9737         135 GDEVRGGKYDCSSFQAISNLYH-----PNPLVKEIQERSSNSQISFKFLWCPSHVG-----ISGNDQADAEAKKATSEPI  204 (368)
Q Consensus       135 ~~~v~~~s~SlSAL~aI~np~~-----~s~ii~~I~~~l~~~g~~V~l~WVPgH~g-----I~GNE~AD~lAK~Aa~~~~  204 (368)
                      ...+...+||+.++.+|.....     +-+++++|.+.+. .+..|.|.|||||+|     ++|||+||+|||+|+....
T Consensus        80 ~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~-~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~  158 (165)
T 3p1g_A           80 GKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALF-LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV  158 (165)
T ss_dssp             TSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTT-SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHh-cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence            4578888999998888842211     1135566655443 478999999999999     9999999999999987644


Q ss_pred             C
Q psy9737         205 T  205 (368)
Q Consensus       205 ~  205 (368)
                      .
T Consensus       159 ~  159 (165)
T 3p1g_A          159 L  159 (165)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}

Probab=98.40  E-value=2.7e-07  Score=82.05  Aligned_cols=42  Identities=24%  Similarity=0.138  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHcCCCeEEEEEeccCCCC------CcChHHHHHHhhhcC
Q psy9737         159 PLVKEIQERSSNSQISFKFLWCPSHVGI------SGNDQADAEAKKATS  201 (368)
Q Consensus       159 ~ii~~I~~~l~~~g~~V~l~WVPgH~gI------~GNE~AD~lAK~Aa~  201 (368)
                      +++++|.+++.. ...|.|.|||||+|+      +|||+||+||++|+.
T Consensus       115 dL~~~l~~~~~~-~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A          115 SKWKSIAECLSM-KPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             HHHHHHHHHHHH-CTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            477888887754 357999999999996      489999999999874

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=98.39  E-value=3.7e-07  Score=94.04  Aligned_cols=65  Identities=20%  Similarity=0.291  Sum_probs=53.1

Q ss_pred             cceeeeccccHHHHHHhHccC--CCCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhc
Q psy9737         135 GDEVRGGKYDCSSFQAISNLY--HPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT  200 (368)
Q Consensus       135 ~~~v~~~s~SlSAL~aI~np~--~~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa  200 (368)
                      ...+...+||+-++..|.+..  ...++.++|.+++.. ...|.|.|||||+|++|||.||+|||+|+
T Consensus       489 ~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          489 GPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHhcc-CCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            357888899999998887632  234677887777654 57899999999999999999999999985

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=98.25  E-value=5.4e-07  Score=92.86  Aligned_cols=64  Identities=27%  Similarity=0.335  Sum_probs=50.0

Q ss_pred             cceeeeccccHHHHHHhHccCC--CCHHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhh
Q psy9737         135 GDEVRGGKYDCSSFQAISNLYH--PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA  199 (368)
Q Consensus       135 ~~~v~~~s~SlSAL~aI~np~~--~s~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~A  199 (368)
                      ...+...+||+.++..|.+...  ..++.++|.+.+.. ...|.|.|||||+|++|||.||+||++|
T Consensus       492 ~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          492 GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            3678888999999999976443  34677887766644 3589999999999999999999999986

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A

Probab=97.79  E-value=2.1e-05  Score=67.01  Aligned_cols=61  Identities=16%  Similarity=0.206  Sum_probs=49.4

Q ss_pred             ceeeeccccHHHHHHhHccCCCC-----HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCC
Q psy9737         136 DEVRGGKYDCSSFQAISNLYHPN-----PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSE  202 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np~~~s-----~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~  202 (368)
                      ..+...+||+.++..+.+.|..+     ++++.|..++...  .|.|.|||+    ++|+.||+|||+|+..
T Consensus        69 ~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~--~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           69 SSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL--NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             CSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH--TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             CEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC--CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            57889999999999998876432     3667777776554  499999999    5999999999999864

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}

Probab=97.73  E-value=4.6e-05  Score=63.02  Aligned_cols=61  Identities=18%  Similarity=0.222  Sum_probs=47.8

Q ss_pred             eeeeccccHHHHHHhHccCC-CCH----HHHHHHHH-HHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCC
Q psy9737         137 EVRGGKYDCSSFQAISNLYH-PNP----LVKEIQER-SSNSQISFKFLWCPSHVGISGNDQADAEAKKATSE  202 (368)
Q Consensus       137 ~v~~~s~SlSAL~aI~np~~-~s~----ii~~I~~~-l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~  202 (368)
                      .+...+||+.++..+.+.+. .+.    ++.+|.++ +.. ...|.|.|||.    ++||.||+|||+|+..
T Consensus        71 ~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~-~~~v~~~~V~~----~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           71 EVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMER-VPNLVFVHIPR----EKNARADELVNEAIDK  137 (140)
T ss_dssp             EEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHH-CTTCEEEECCG----GGGHHHHHHHHHHHHH
T ss_pred             eEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcC-CCcEEEEEcCc----hhhHHHHHHHHHHHHh
Confidence            78899999999999988663 332    45566666 443 35899999994    9999999999998753

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}

Probab=97.68  E-value=8.8e-05  Score=61.79  Aligned_cols=62  Identities=19%  Similarity=0.219  Sum_probs=47.7

Q ss_pred             ceeeeccccHHHHHHhHccCC-CCH-H---HHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCC
Q psy9737         136 DEVRGGKYDCSSFQAISNLYH-PNP-L---VKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSE  202 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np~~-~s~-i---i~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~  202 (368)
                      ..+...+||+.++..|...|. .+. +   +.+|.+++ .....|.|.|||.    ++|+.||+|||+|+..
T Consensus        67 ~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~-~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           67 TEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALA-SQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             SEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHH-TTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             ceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHH-hcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            578999999999999988653 443 3   33444444 3468999999995    8999999999998754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	368
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	0.004

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 34.9 bits (79), Expect = 0.004
 Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 2/58 (3%)

Query: 142 KYDCSSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA 199
           +Y      +         + + I+E      I     W P+H GI GN + D    + 
Sbjct: 70  QYVMGIVASQPTESESKIVNQIIEEMIKKEAIYVA--WVPAHKGIGGNQEVDHLVSQG 125

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	368
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.03
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.88
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	98.83
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	95.79

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.03  E-value=7.2e-11  Score=97.27  Aligned_cols=63  Identities=17%  Similarity=0.222  Sum_probs=47.8

Q ss_pred             ceeeeccccHHHHHHhHccCC--CCH-HHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhc
Q psy9737         136 DEVRGGKYDCSSFQAISNLYH--PNP-LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT  200 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np~~--~s~-ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa  200 (368)
                      ..+...+||+.++..+.+.+.  .+. +.+.|+.+..  ...|.|.|||||+|++|||+||+||++|.
T Consensus        61 ~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~--~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          61 PKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIK--KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             SEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHH--CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cceEEEechHHHHHHHhcCCccccchHHHHHHHHhhh--cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            457778888888888877543  233 3344444444  36899999999999999999999999984

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

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

Probab=98.88  E-value=6.2e-10  Score=92.76  Aligned_cols=44  Identities=27%  Similarity=0.453  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCCCCC
Q psy9737         160 LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPIT  205 (368)
Q Consensus       160 ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~~~~  205 (368)
                      +++.|..++  ....|+|.|||||+|++|||+||+|||+|+..+..
T Consensus       101 ~~~~i~~~~--~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~  144 (152)
T d1jl1a_         101 LWQRLDAAL--GQHQIKWEWVKGHAGHPENERADELARAAAMNPTL  144 (152)
T ss_dssp             HHHHHHHHT--TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHHHHh--hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCC
Confidence            455555544  35689999999999999999999999999987665

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

Probab=98.83  E-value=1.1e-09  Score=91.78  Aligned_cols=43  Identities=19%  Similarity=0.329  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHcCCCeEEEEEeccCCCCCcChHHHHHHhhhcCCC
Q psy9737         159 PLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEP  203 (368)
Q Consensus       159 ~ii~~I~~~l~~~g~~V~l~WVPgH~gI~GNE~AD~lAK~Aa~~~  203 (368)
                      +++++|..++.  ...|.|.|||||+|++|||.||+|||+|+...
T Consensus       102 dL~~~l~~~~~--~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_         102 DLWEALLLAMA--PHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHHHHHHT--TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHhh--hcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            36677776654  56899999999999999999999999998764

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=95.79  E-value=0.0071  Score=47.97  Aligned_cols=47  Identities=21%  Similarity=0.217  Sum_probs=34.7

Q ss_pred             ceeeeccccHHHHHHhHccCC--CCHHHHHHHHHHHcCCCeEEEEEeccC
Q psy9737         136 DEVRGGKYDCSSFQAISNLYH--PNPLVKEIQERSSNSQISFKFLWCPSH  183 (368)
Q Consensus       136 ~~v~~~s~SlSAL~aI~np~~--~s~ii~~I~~~l~~~g~~V~l~WVPgH  183 (368)
                      ..+...+||+.++.++...+.  ...+.++|.+.|.. ...|.|.|||||
T Consensus        62 ~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l~~-~~~v~i~WVpgH  110 (110)
T d1s1ta1          62 LEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIK-KEKVYLAWVPAH  110 (110)
T ss_dssp             SEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred             CeEEEEEehHHHHHHHhcCccccchHHHHHHHHHHhc-CCceEEEEeCCC
Confidence            357777888888888866443  44577787776654 468999999999