Citrus Sinensis ID: 039849

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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--
Protein Sequence
AQQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccEEEEEccccccccccccEEEEEEcccccEEEEEHHHHccccccHHHHHHHHHHHHHHHHHcccccEEEEEEHHHHHHHHHccccccccHHHHHHHHHHHHHccccEEEEEEc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcHHHcccccccccccccccccccEEEEEEEccEccccccEEEEEEEEcccccEEEEEcccccccccHHHHHHHHHHHHHHHHHHcccccEEEEccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccEEEEEcc
Coil and Loop (DISEMBL)
AQQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFegkrensqslvATTIGIVDSYLIIKILVDQIISKHQSinqqawmppssgwyeANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLArnrkgckseVFWTVVAIQASLKSLNRVQIQHVS
Flexible Loop (DISEMBL)
AQQDMLSALQELatskskkdleLIIVVCWSIWYSRNLFIFEgkrensqsLVATTIGIVDSYLIIKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVtlgiqvtkkikcLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASlkslnrvqiqhvs
Low Complexity Region (SEG)
AQQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS
Disordered region (IsUnstruct)
********************LELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNR*******
Disordered Region (DISOPRED)
*QQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLI***********************SSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS
Disordered Region (DISEMBL)
AQQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLN********
Disordered Region (DISPRO)
AQQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQI*********QAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
AQQDMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS
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	202
125536577	290	hypothetical protein OsI_38284 [Oryza sa	0.826	0.575	0.270	3e-08
357488513	278	hypothetical protein MTR_5g055270 [Medic	0.792	0.575	0.244	6e-08
255563286	421	RNA binding protein, putative [Ricinus c	0.797	0.382	0.291	1e-07
242052229	357	hypothetical protein SORBIDRAFT_03g00735	1.0	0.565	0.246	1e-07
242045790	357	hypothetical protein SORBIDRAFT_02g03460	1.0	0.565	0.251	2e-07
222641012	1256	hypothetical protein OsJ_28268 [Oryza sa	0.871	0.140	0.243	2e-07
255568641	199	hypothetical protein RCOM_0581330 [Ricin	0.816	0.829	0.286	2e-07
343887321	166	hypothetical protein [Citrus unshiu]	0.455	0.554	0.326	2e-07
218193742	1874	hypothetical protein OsI_13484 [Oryza sa	0.861	0.092	0.257	5e-07
218200673	1300	hypothetical protein OsI_28249 [Oryza sa	0.900	0.14	0.260	6e-07

>gi|125536577|gb|EAY83065.1| hypothetical protein OsI_38284 [Oryza sativa Indica Group]

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 52/192 (27%), Positives = 88/192 (45%), Gaps = 25/192 (13%)

Query: 17  SKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQ-----I 71
            K++  + +++ W IW++RN  I  GK   S + VA +   + SY+     + Q     I
Sbjct: 70  PKEEDAMFLMLMWRIWHNRN-EITHGK---SIAPVAVSQRFIFSYVSSLTTIKQYPQADI 125

Query: 72  ISKHQSINQ----------------QAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDS 115
           I   Q  +                 + W  PS+GW + NVD + + S+   G+G V+RDS
Sbjct: 126 IKGKQVAHPDRIRLPSRAPPAVSPPRRWEKPSTGWMKLNVDGSFQASDGKGGIGAVLRDS 185

Query: 116 KGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGC 175
            G  +  A    +  G+    E  A   GI +  +   LP I+E D  EV +L ++++  
Sbjct: 186 SGNVIFAACGSMLVCGSAMEAELLACKEGIAMALQWTFLPFIVETDCLEVFNLIQSKEKV 245

Query: 176 KSEVFWTVVAIQ 187
            SE+ + V  +Q
Sbjct: 246 LSELAFVVKEVQ 257

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357488513|ref|XP_003614544.1| hypothetical protein MTR_5g055270 [Medicago truncatula] gi|355515879|gb|AES97502.1| hypothetical protein MTR_5g055270 [Medicago truncatula]

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 77/184 (41%), Gaps = 24/184 (13%)

Query: 11  ELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQ 70
           ++  S+S+  +  + ++ W IW +RN  I+      S+ +  TT+     +        Q
Sbjct: 93  DICCSESRDTVGRVALLLWQIWAARNDVIWNDAHHTSKGIGMTTLDAWQQW--------Q 144

Query: 71  IISKHQSI------------NQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGK 118
            + KH S+            N   W  PS  W + NVDAA   SN +      +RDS+G+
Sbjct: 145 EVHKHPSLLVVPHGQNRVQGNNSVWEKPSETWLKCNVDAAFHDSNHLTSFACCVRDSRGQ 204

Query: 119 FVAVAIQRAIYKGNVAYVEAKAVTL--GIQVTKKIKCLPMIIELDSKEVVDLARNRKGCK 176
           F+    Q    + N+  +E +AV L   I      +   ++ E DS  +V    +     
Sbjct: 205 FIRA--QTKWQRANMTVLEGEAVALLAAIHFADVNRWDRVVFEFDSDTLVQALSSAGHGN 262

Query: 177 SEVF 180
           SE +
Sbjct: 263 SEFY 266

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563286|ref|XP_002522646.1| RNA binding protein, putative [Ricinus communis] gi|223538122|gb|EEF39733.1| RNA binding protein, putative [Ricinus communis]

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/168 (29%), Positives = 73/168 (43%), Gaps = 7/168 (4%)

Query: 4   DMLSALQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLI 63
           D+ + LQ          L   ++  W IWY+RN   FE K  +   +V  T  ++  Y+ 
Sbjct: 182 DIFAWLQHCFKVLLNSSLAQFMITVWGIWYARNQLCFENKSLSVDDIVQPTKLMLLYYVK 241

Query: 64  IKILV--DQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVA 121
              +   D I S+ QS     W  P  G  + NVDAA R +N  AG   +IRD  G  V 
Sbjct: 242 ANDVPVRDNIRSRSQSF----WRAPHVGRCKLNVDAAYR-NNIGAGFRAIIRDWNGGIVG 296

Query: 122 VAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA 169
            A     Y  +   VE + ++ G+     +    + +E+D   VV LA
Sbjct: 297 SACSFKPYFNDPEIVEFQDLSFGLTFALDLSITHLDVEVDCASVVQLA 344

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242052229|ref|XP_002455260.1| hypothetical protein SORBIDRAFT_03g007350 [Sorghum bicolor] gi|241927235|gb|EES00380.1| hypothetical protein SORBIDRAFT_03g007350 [Sorghum bicolor]

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 54/219 (24%), Positives = 95/219 (43%), Gaps = 17/219 (7%)

Query: 1   AQQDM-LSALQELATSKSKKDLELI---IVVCWSIWYSRNLFIFEGKRENSQSLVATTIG 56
           A++D+  +  Q L    S+  +E+I   +++ W +W  RN  +  GKR +  S V     
Sbjct: 99  AEEDLQYTGPQWLLALASRFPVEVIGNLLMLLWRVWSVRNSVLRAGKRLSIDSSVLFLTR 158

Query: 57  IVDSYLIIKILVDQIISKHQSIN-------------QQAWMPPSSGWYEANVDAAIRHSN 103
             DS +  ++       K +                ++ W+PP  GW + NVD A    +
Sbjct: 159 YRDSLMQCQLKSFHAEDKGKRCALIGSSQLERVARLEKKWVPPDPGWMKINVDGAFLPDS 218

Query: 104 WIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK 163
            +A +GV+IRD  G       +   +  +    EA A   GI +  +   +PMI+E D  
Sbjct: 219 GVAAIGVIIRDHGGGIKLSTWRLLRHCRDAVEAEAVACREGIILAARWPEVPMILETDCS 278

Query: 164 EVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS 202
            V    RN    +S ++ T+      ++ L RV++  +S
Sbjct: 279 VVAGKLRNSVQDRSVIWSTIQEATVGMEDLCRVEVLKIS 317

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242045790|ref|XP_002460766.1| hypothetical protein SORBIDRAFT_02g034600 [Sorghum bicolor] gi|241924143|gb|EER97287.1| hypothetical protein SORBIDRAFT_02g034600 [Sorghum bicolor]

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 98/219 (44%), Gaps = 17/219 (7%)

Query: 1   AQQDM-LSALQELATSKSKKDLELI---IVVCWSIWYSRNLFIFEGKRENSQSLVATTIG 56
           A++D+  +  Q L    S+  +E+I   +++ W +W  RN  +  GKR +  S V     
Sbjct: 99  AEEDLQYTGPQWLLALVSRFPVEVIGNLLMLLWRVWSVRNSVLRAGKRLSIDSSVLFLTR 158

Query: 57  IVDSYLIIKI-------------LVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSN 103
             DS +  ++             L+     +  +  ++ W+PP  GW + NVD A    +
Sbjct: 159 YRDSLMQCQLNSFHAEDKGKRCALIGSSQLERVARLEKKWVPPEPGWMKINVDGAFLPDS 218

Query: 104 WIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK 163
            +A +GV+IRD  G     A +   +  +    EA A   GI +  +   +PMI+E D  
Sbjct: 219 GVAAIGVIIRDHGGGIKLSAWRLLRHCRDAVEAEAVACREGIILAARWPEVPMILETDCS 278

Query: 164 EVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS 202
            V    RN    +S ++ T+      ++ L RV++  +S
Sbjct: 279 VVAGKLRNLVQHRSVIWSTIQEATVGIEDLCRVEVLKIS 317

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222641012|gb|EEE69144.1| hypothetical protein OsJ_28268 [Oryza sativa Japonica Group]

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 89/201 (44%), Gaps = 25/201 (12%)

Query: 11   ELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLII------ 64
            +L      +D  ++++V W IW++RN  I  GK       +  +   ++SY++       
Sbjct: 1007 DLLEQSQPEDQVMLLMVLWRIWHTRNE-IVHGKPAPG---ILVSKRFIESYVLSLAEIKQ 1062

Query: 65   ---------KILVDQIISKHQSINQ------QAWMPPSSGWYEANVDAAIRHSNWIAGLG 109
                     K +VD ++ K  SI +        W  P  G  + NVD + + S    G+G
Sbjct: 1063 HPQANPEKGKHVVDVVLKKSHSIKRSREPAPDKWSKPLPGSMKLNVDGSFQESEGKGGIG 1122

Query: 110  VVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA 169
             V+R+  G+ +  A     +  +   +E  A   G+ +  +   LP++IE D   +V L 
Sbjct: 1123 AVLRNCTGEVIFAACGHVDHCSSALEMELLASRDGLALALQWTLLPIVIETDCLAMVHLF 1182

Query: 170  RNRKGCKSEVFWTVVAIQASL 190
            R+  G KSE+ + +  I + L
Sbjct: 1183 RDATGAKSELAFLITEIDSLL 1203

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568641|ref|XP_002525294.1| hypothetical protein RCOM_0581330 [Ricinus communis] gi|223535452|gb|EEF37122.1| hypothetical protein RCOM_0581330 [Ricinus communis]

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 73/171 (42%), Gaps = 6/171 (3%)

Query: 24  IIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQQAW 83
           + V+ W  W+ RN FI        +  V   +  ++ Y       +         +   W
Sbjct: 4   LAVIPWRSWFRRNSFIHSRLLIPDEDFVGWAVNFLEEYN-----TENRKPARFKRDYHCW 58

Query: 84  MPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTL 143
            PP  G  + + DAA+     I+GLG+V+RD KG    V          V  VEA A+  
Sbjct: 59  KPPDYGLLKLDTDAAVHFDKNISGLGMVLRDHKGCVKLVGSYPMKQGLPVEVVEAMAIKC 118

Query: 144 GIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLN 194
           G+ V       P ++E DS +VV+   NR+   SE+   +  I A L SLN
Sbjct: 119 GLSVASSHGLWPSVVESDSLQVVNAICNREVIFSELAAVLSEIFAML-SLN 168

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|343887321|dbj|BAK61867.1| hypothetical protein [Citrus unshiu]

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 53/92 (57%)

Query: 97  AAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPM 156
           A++     + GLGVVIR+S+G+ +  A +   ++ NV   +A+AV  G+++  + +   +
Sbjct: 46  ASVHAEQQLTGLGVVIRNSQGQVIVAAFKSTKFEDNVTAAKAEAVKWGLEMALEARLAAV 105

Query: 157 IIELDSKEVVDLARNRKGCKSEVFWTVVAIQA 188
           IIE D  EV +LA N    + E+ WT+  I +
Sbjct: 106 IIETDCIEVANLANNETSSRKEIVWTISDIHS 137

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218193742|gb|EEC76169.1| hypothetical protein OsI_13484 [Oryza sativa Indica Group]

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 50/194 (25%), Positives = 86/194 (44%), Gaps = 20/194 (10%)

Query: 24   IIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSY----LIIKILVDQII------- 72
            I+ + W  WY RN  I    R +    +A ++  + SY    L  + + D I        
Sbjct: 1035 IMYMLWRAWYLRNDLIHGDGRCS----IAGSVSFLTSYEEVLLPNRQMPDDIKGKKPMYS 1090

Query: 73   ----SKHQSINQQA-WMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRA 127
                 KH +  Q + W+ P  G  + NVDA  R     A  G+VIRD +G  +  A +  
Sbjct: 1091 EGQKEKHMAEKQSSGWIAPPDGAAKINVDAGFRMETGEASAGIVIRDCRGLILLAACKTL 1150

Query: 128  IYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQ 187
                +    EA A   GI+   +   +P+I+E D+ EVV   + +   +S     ++  +
Sbjct: 1151 HPCSSAEQAEALASLEGIRCALQWIHMPVILETDNAEVVARLKTKHSSRSVWEGVIMEAK 1210

Query: 188  ASLKSLNRVQIQHV 201
            A+++ L  V++ H+
Sbjct: 1211 AAMQGLQAVEVAHI 1224

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218200673|gb|EEC83100.1| hypothetical protein OsI_28249 [Oryza sativa Indica Group]

 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 54/207 (26%), Positives = 91/207 (43%), Gaps = 25/207 (12%)

Query: 17   SKKDLELIIVVCWSIWYSRNLFIFEGKR----ENSQSLVATTIGIVDSYLIIKILVDQII 72
            SK++   ++++ W IWY RN  I  GK     E SQ  +++ I    S L I+   D  +
Sbjct: 1059 SKEERPTLLMMLWRIWYVRNE-ITHGKAAVPAEVSQRFISSYI---TSLLEIRQFPDANL 1114

Query: 73   SK---------------HQSINQQA--WMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDS 115
             K               H  +N     W+ P +GW + NVD +    +   G+G V+R+S
Sbjct: 1115 CKGKHVIRCAAAGAQVNHPRVNSVPVRWVRPQAGWMKLNVDGSYDPRDGSGGIGAVLRNS 1174

Query: 116  KGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGC 175
            +GK +  A        +    E  A   GI +  +   LP+I+E D  E+V L   +   
Sbjct: 1175 EGKLIFAACGSMCRPVSALEAELVACKEGIILALQWTFLPIIVETDCLELVKLVAEQGKV 1234

Query: 176  KSEVFWTVVAIQASLKSLNRVQIQHVS 202
             S++ + +  I+  +K    + I  V+
Sbjct: 1235 MSDLGFLIREIKDLVKGNREIVINKVT 1261

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	202
TAIR|locus:2119886	575	AT4G29090 [Arabidopsis thalian	0.747	0.262	0.246	4.7e-08
TAIR|locus:2090215	343	AT3G25270 [Arabidopsis thalian	0.816	0.481	0.25	3.3e-07
TAIR|locus:2058379	221	AT2G04420 [Arabidopsis thalian	0.702	0.642	0.253	9.6e-06
TAIR|locus:2046555	664	AT2G33160 [Arabidopsis thalian	0.821	0.25	0.247	1.5e-05
TAIR|locus:2040899	292	AT2G34320 [Arabidopsis thalian	0.896	0.619	0.209	2.1e-05
TAIR|locus:5019474881	263	AT5G65005 [Arabidopsis thalian	0.821	0.631	0.225	2.2e-05
TAIR|locus:2065330	365	AT2G02650 [Arabidopsis thalian	0.826	0.457	0.222	0.00073

TAIR|locus:2119886 AT4G29090 [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 4.7e-08, P = 4.7e-08
 Identities = 39/158 (24%), Positives = 78/158 (49%)

Query:    18 KKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQS 77
             +K  +L+  + W +W +RN  +F G+  N+Q ++      ++ + I +   +   +K Q 
Sbjct:   354 EKASQLVPWLLWRLWKNRNELVFRGREFNAQEVLRRAEDDLEEWRI-RTEAESCGTKPQ- 411

Query:    78 INQQA---WMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYK-GNV 133
             +N+ +   W PP   W + N DA     N   G+G V+R+ KG+   +   RA+ K  +V
Sbjct:   412 VNRSSCGRWRPPPHQWVKCNTDATWNRDNERCGIGWVLRNEKGEVKWMGA-RALPKLKSV 470

Query:   134 AYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARN 171
                E +A+   +    + +   +I E DS+ ++++  N
Sbjct:   471 LEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILNN 508

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0003964 "RNA-directed DNA polymerase activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISM

GO:0006278 "RNA-dependent DNA replication" evidence=ISS

TAIR|locus:2090215 AT3G25270 [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 3.3e-07, P = 3.3e-07
 Identities = 43/172 (25%), Positives = 74/172 (43%)

Query:     9 LQELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIV----DSYLII 64
             L     ++  +   L I + W +W SRN  +F+ K  + Q+ +      V    D+   +
Sbjct:   105 LSSCLANRQPQLFNLAIWILWRLWKSRNQLVFQQKSISWQNTLQRARNDVQEWEDTNTYV 164

Query:    65 KILVDQI-ISKHQ--SINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVA 121
             + L  Q+  S+HQ  ++ +  W  P S W + N D A  H    A  G ++RD  G ++ 
Sbjct:   165 QSLNQQVHSSRHQQPTMARTKWQRPPSTWIKYNYDGAFNHQTRNAKAGWLMRDENGVYMG 224

Query:   122 VAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRK 173
                       +    E +A+ + +Q         +I E DSK+V +L  N K
Sbjct:   225 SGQAIGSTTSDSLESEFQALIIAMQHAWSQGYRKVIFEGDSKQVEELMNNEK 276

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2058379 AT2G04420 [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 9.6e-06, P = 9.6e-06
 Identities = 39/154 (25%), Positives = 64/154 (41%)

Query:    29 WSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQSINQ-------- 80
             W +W SRN  +F+ +  + QS +      V  +   +  +  +   H ++ +        
Sbjct:     2 WRLWRSRNQLVFQHQNLSWQSTLKRAKDDVQEWENAQEYIQSL--NHYTVREGCNNREST 59

Query:    81 -QAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAK 139
              Q W  P  GW + N D +  +       G +IRD KG +   A        N    E +
Sbjct:    60 HQKWEQPPMGWIKCNYDGSFNYRTQQTNSGWLIRDDKGFYKGAAQAVGGTMNNALESELQ 119

Query:   140 AVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRK 173
             A+ + +Q T       +I E DSK+V +L  NRK
Sbjct:   120 ALVMAMQHTWSQGYRKVIFEGDSKQVEELL-NRK 152

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

TAIR|locus:2046555 AT2G33160 [Arabidopsis thaliana (taxid:3702)]

 Score = 126 (49.4 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 44/178 (24%), Positives = 84/178 (47%)

Query:     3 QDMLSALQELA-TSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSY 61
             +D +  + +LA T+++++  +L + + W +W SRN+  F+ +    ++ +   +  +D  
Sbjct:   421 EDKMQGIFQLANTTQTQRFHQLPLWILWRLWNSRNILYFQRRHVPWETTLQ--LAQMDLQ 478

Query:    62 LIIKILVDQIISKH-QSINQQA--WMPPSSGWYEANVDAAIRHSNWIAGLGV-VIRDSKG 117
                + +    I+ H  +I      W  P++GW + NVD +  + N I G G  ++RD  G
Sbjct:   479 EWNEAVTPSHINSHGTTIRSHIPNWRRPTNGWVKCNVDGSFINGN-IPGKGGWIVRDHNG 537

Query:   118 K--FVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRK 173
             +  F   AI   I   N    E +A+ + +Q         +  E D+KE+ DL    K
Sbjct:   538 RYEFAGQAIGNCI--DNALECEFQALLMAMQHCWSKGYRRICFEGDNKEMFDLINGLK 593

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004650 "polygalacturonase activity" evidence=IEA;ISS

GO:0005576 "extracellular region" evidence=ISM

GO:0005975 "carbohydrate metabolic process" evidence=IEA;ISS

TAIR|locus:2040899 AT2G34320 [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 2.1e-05, P = 2.1e-05
 Identities = 40/191 (20%), Positives = 81/191 (42%)

Query:    11 ELATSKSKKDLELIIVVCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQ 70
             E+   K  K   L+  + W +W SRN  +F+GK  ++  ++   +   + +   + L  +
Sbjct:    64 EVEIPKLGKIGNLVPWLLWRLWKSRNELMFKGKEYDAPEVLRRAMEDFEEWSTRRELEGK 123

Query:    71 IISKHQSINQQA-WMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIY 129
                     N    W  P   W + N DA  +  N   G+G ++R+  G  + +  +    
Sbjct:   124 ASGPQVERNLSVQWKAPPYQWVKCNTDATWQLENPRCGIGWILRNESGGVLWMGARALPR 183

Query:   130 KGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQAS 189
               NV   E +A+   +    +     +I E D++ +V+L        S+ FW    +Q +
Sbjct:   184 TKNVLEAELEALRWAVLTMSRFNYKRIIFESDAQALVNLLN------SDDFWPT--LQPA 235

Query:   190 LKSLNRVQIQH 200
             L+ + ++ + H
Sbjct:   236 LEDIQQL-LHH 245

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:5019474881 AT5G65005 [Arabidopsis thaliana (taxid:3702)]

 Score = 119 (46.9 bits), Expect = 2.2e-05, P = 2.2e-05
 Identities = 39/173 (22%), Positives = 73/173 (42%)

Query:    29 WSIWYSRNLFIFEGKRENSQSLVATTIGIVDSYLIIKILVDQIISKHQS--INQQAWMPP 86
             W IW S N  +F   R   Q+ V   +     +L   +  +Q      +       W PP
Sbjct:    49 WRIWKSGNDLVFNHTRTKFQTTVEMALNDTKEWLDNTMTNEQQNGNRNADPSRNTKWSPP 108

Query:    87 SSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTL--G 144
                  + N DA+    N ++GLG ++R+S+G  +   + +  ++G +   EA+  TL   
Sbjct:   109 GRDKLKCNYDASHHERNTVSGLGWILRNSQGTVIECGMGK--FQGRMTTEEAECSTLIWA 166

Query:   145 IQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQ 197
             IQ +       +I E D++ +  +  N K     +   +  IQ+ + S   ++
Sbjct:   167 IQASYGFGHKKVIFEGDNQTITRMI-NTKSSNPRLQHFLDTIQSWIPSFESIE 218

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2065330 AT2G02650 [Arabidopsis thaliana (taxid:3702)]

 Score = 109 (43.4 bits), Expect = 0.00073, P = 0.00073
 Identities = 40/180 (22%), Positives = 72/180 (40%)

Query:     3 QDMLSALQELATSKSKKDLELIIV--VCWSIWYSRNLFIFEGKRENSQSLVATTIGIVDS 60
             +D L+ L +L+ +++   L+  +   + W +W SRN+F+F+ K ++        I     
Sbjct:   117 EDNLNRLIQLSKTQTTNSLDRFLPFWIMWRLWKSRNVFLFQQKCQSPDYEARKGIQDATE 176

Query:    61 YLI---------IKILVDQIISKHQSINQQAWMPPSSGWYEANVDAAIRHSNWIAGLGVV 111
             +L          + +  + I +  +  +Q  W PP  GW + N D+     +     G  
Sbjct:   177 WLNANETTENTNVHVATNPIQTSRRDSSQ--WNPPPEGWVKCNFDSGYTQGSPYTRSGWT 234

Query:   112 IRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARN 171
             IR+  G  V     +        + EA      +QV        +  E DSK +V L  N
Sbjct:   235 IRECNGHIVLCGNAKLQSSTCSLHAEALGFLHALQVIWAHGLRYVWFESDSKSLVTLINN 294


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   0.132   0.383    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      202       202   0.00090  111 3  11 22  0.45    32
                                                     31  0.46    35


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:  7
  No. of states in DFA:  609 (65 KB)
  Total size of DFA:  165 KB (2096 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:  16.28u 0.18s 16.46t   Elapsed:  00:00:01
  Total cpu time:  16.28u 0.18s 16.46t   Elapsed:  00:00:01
  Start:  Thu May  9 14:12:28 2013   End:  Thu May  9 14:12:29 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: BRADI1G16250.1 annotation not avaliable (444 aa) (Brachypodium distachyon)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	202
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	4e-10
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	8e-07
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	4e-04

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 55.1 bits (133), Expect = 4e-10
 Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 1/108 (0%)

Query: 94  NVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKC 153
           N D + + +   AG G V+RD +G ++  A   +I        E  A+   +++   +  
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWL-FAGSLSIPAATNNEAELLALLEALELALDLGL 59

Query: 154 LPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHV 201
             +IIE DSK VVDL  +      +    +  I   L     ++ +HV
Sbjct: 60  KKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHV 107

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. 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 residues and have the same catalytic mechanism and functions in cells. 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 inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 44.9 bits (107), Expect = 8e-07
 Identities = 18/67 (26%), Positives = 34/67 (50%)

Query: 136 VEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNR 195
            EA+A+  G+Q+  ++    +I+E DS+ VV   +     +S +   +  I+  LK  + 
Sbjct: 5   AEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFDS 64

Query: 196 VQIQHVS 202
           V + HV 
Sbjct: 65  VSVSHVP 71

This domain is found in plants and appears to be part of a retrotransposon. Length = 88

>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI

 Score = 38.6 bits (91), Expect = 4e-04
 Identities = 26/114 (22%), Positives = 50/114 (43%), Gaps = 4/114 (3%)

Query: 91  YEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGN-VAYVEAKAVTLGIQVTK 149
           +    D A R +   AG G+VI+   G+ +  +I       N  A  E +A+  G+++  
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEA--EYEALIAGLELAL 58

Query: 150 KIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVA-IQASLKSLNRVQIQHVS 202
           ++    + I  DS+ VV+  +     K+E     +   +  LK    V+I+ + 
Sbjct: 59  ELGIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKWIP 112

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. Length = 128

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	202
PRK13907	128	rnhA ribonuclease H; Provisional	99.88
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.74
PRK07708	219	hypothetical protein; Validated	99.73
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.71
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.69
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.64
PRK08719	147	ribonuclease H; Reviewed	99.46
PRK06548	161	ribonuclease H; Provisional	99.43
PRK00203	150	rnhA ribonuclease H; Reviewed	99.41
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.4
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	98.4
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.4
COG0295	134	Cdd Cytidine deaminase [Nucleotide transport and m	87.29
COG0590	152	CumB Cytosine/adenosine deaminases [Nucleotide tra	85.06
TIGR01354	127	cyt_deam_tetra cytidine deaminase, homotetrameric.	83.26
cd01284	115	Riboflavin_deaminase-reductase Riboflavin-specific	81.42
cd01285	109	nucleoside_deaminase Nucleoside deaminases include	81.01

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.88  E-value=5.7e-22  Score=145.22  Aligned_cols=110  Identities=14%  Similarity=0.055  Sum_probs=99.1

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA  169 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l  169 (202)
                      ++++|||||+.++++.+|+|+|+||..|.+...+   ..+..++++||+.|+++||+.+.++|+.+|+|+|||+.|++.+
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~---~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~   77 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSL---PLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAV   77 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEe---cccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHH
Confidence            5789999999999999999999999998765432   2245799999999999999999999999999999999999999


Q ss_pred             hcCCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          170 RNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       170 ~~~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ++.......+..++.+++.++..|+.+.++||+
T Consensus        78 ~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~  110 (128)
T PRK13907         78 EKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIP  110 (128)
T ss_pred             hHHHhcChhHHHHHHHHHHHHhcCCceEEEEcC
Confidence            997765567999999999999999999999984

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.74  E-value=2.7e-17  Score=140.67  Aligned_cols=112  Identities=16%  Similarity=0.182  Sum_probs=98.7

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCc-EEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGK-FVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDL  168 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~-~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~  168 (202)
                      .+++|||||+.++++.+|+|+|++++.|. ++......+. ..+++.||+.||+.||+.+.++|.++|.|++||+.|++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            36899999999999999999999999765 5555555555 568899999999999999999999999999999999999


Q ss_pred             HhcCCCC-cchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          169 ARNRKGC-KSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       169 l~~~~~~-~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      +++.... ...+..++.+++.++++|+.+.|+||+
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~  115 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIP  115 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECC
Confidence            9988653 346899999999999999999999984

>PRK07708 hypothetical protein; Validated

Probab=99.73  E-value=7.9e-17  Score=127.77  Aligned_cols=116  Identities=16%  Similarity=0.090  Sum_probs=97.4

Q ss_pred             CCCCceEEEecceeeecCCeeeEEEEEeCCCCcEE--EeeeeecCccCCHHHHHHHHHHHHHHHHHHCCccc--EEEEec
Q 039849           86 PSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFV--AVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLP--MIIELD  161 (202)
Q Consensus        86 P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~--~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~--v~~esD  161 (202)
                      +..+.+++|||||+.++++.+|+|+|++++.|...  ......+....++++||+.|++.||+.|.++|.++  |.|++|
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            33457899999999999999999999999877643  33344566678999999999999999999999976  899999


Q ss_pred             hHHHHHHHhcCCCCcc-hHHHHHHHHHHHhhcCCc-eEEEee
Q 039849          162 SKEVVDLARNRKGCKS-EVFWTVVAIQASLKSLNR-VQIQHV  201 (202)
Q Consensus       162 s~~vv~~l~~~~~~~s-~~~~ii~~i~~l~~~f~~-~~~~~V  201 (202)
                      |+.|++++++...... .+..+..+++.++++|.. +.+.||
T Consensus       149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~V  190 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPI  190 (219)
T ss_pred             cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEEC
Confidence            9999999999865433 478899999999998874 777887

>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=99.71  E-value=3.2e-16  Score=112.23  Aligned_cols=110  Identities=19%  Similarity=0.130  Sum_probs=99.1

Q ss_pred             EEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHHhc
Q 039849           92 EANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARN  171 (202)
Q Consensus        92 K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l~~  171 (202)
                      +|++|||+..+.+.+|+|+++++..|.......... ...++.+||+.|++.||+.+...+.+++.|++||..+++.+++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~-~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~   79 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLG-GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTG   79 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccC-CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhc
Confidence            589999999888899999999999998887766554 5779999999999999999999999999999999999999998


Q ss_pred             CCC-CcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          172 RKG-CKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       172 ~~~-~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ... ....+..++.+++.++..+..++|.||+
T Consensus        80 ~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~  111 (130)
T cd06222          80 WYEGKPVKNVDLWQRLLALLKRFHKVRFEWVP  111 (130)
T ss_pred             cccCCChhhHHHHHHHHHHHhCCCeEEEEEcC
Confidence            865 4457899999999999889999999984

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=99.69  E-value=9.6e-16  Score=114.24  Aligned_cols=109  Identities=19%  Similarity=0.068  Sum_probs=91.8

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA  169 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l  169 (202)
                      .+.+++|||+.+++|.+|+|+|++...++.-...  ... ..|++.+|+.|+++||+.+++.+...|.++|||+.|++.|
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~--~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i   79 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSG--GEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGI   79 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEee--eee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHH
Confidence            4789999999999999999999997666662222  222 6799999999999999999999999999999999999999


Q ss_pred             hcCC-------------CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          170 RNRK-------------GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       170 ~~~~-------------~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      + ..             ..+-.-..+.+++..++..|+.+.+.||+
T Consensus        80 ~-~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVk  124 (154)
T COG0328          80 T-RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVK  124 (154)
T ss_pred             H-HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEee
Confidence            8 22             11223467899999999999999999995

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

Probab=99.64  E-value=1.5e-15  Score=103.15  Aligned_cols=70  Identities=26%  Similarity=0.290  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHHhcCCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          133 VAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       133 ~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l~~~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      |++||++|++.||++|.++|+++|++||||+.+|+.+++....++++..++.+|+.+++.|++++|.||.
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~   70 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC
Confidence            6899999999999999999999999999999999999999777779999999999999999999999984

>PRK08719 ribonuclease H; Reviewed

Probab=99.46  E-value=1.6e-12  Score=97.32  Aligned_cols=109  Identities=17%  Similarity=0.094  Sum_probs=85.2

Q ss_pred             CceEEEecceeeecCC---eeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHH
Q 039849           89 GWYEANVDAAIRHSNW---IAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEV  165 (202)
Q Consensus        89 ~~~K~n~Das~~~~~~---~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~v  165 (202)
                      ..++++||||+..+++   .+|+|+++.+..|..+......+....|++.||+.|+.+||+.+.+.    ..|.|||+.+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            3578999999987765   68999999998887654444445556799999999999999998764    3799999999


Q ss_pred             HHHHh--------cCC----CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          166 VDLAR--------NRK----GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       166 v~~l~--------~~~----~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ++.++        +..    ..+-....+++.|..++. ...++|.||+
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~Vk  126 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVT  126 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEec
Confidence            99995        221    122345778888888877 5779999985

>PRK06548 ribonuclease H; Provisional

Probab=99.43  E-value=4.4e-12  Score=95.97  Aligned_cols=104  Identities=15%  Similarity=0.081  Sum_probs=81.8

Q ss_pred             eEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHHh
Q 039849           91 YEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLAR  170 (202)
Q Consensus        91 ~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l~  170 (202)
                      +.++||||+.++++.+|+|+++.+. +. ..   . .....|++.||+.|+++||+.+ ..+..+|.|.|||+.+++.++
T Consensus         6 ~~IytDGa~~gnpg~~G~g~~~~~~-~~-~~---g-~~~~~TNnraEl~Aii~aL~~~-~~~~~~v~I~TDS~yvi~~i~   78 (161)
T PRK06548          6 IIAATDGSSLANPGPSGWAWYVDEN-TW-DS---G-GWDIATNNIAELTAVRELLIAT-RHTDRPILILSDSKYVINSLT   78 (161)
T ss_pred             EEEEEeeccCCCCCceEEEEEEeCC-cE-Ec---c-CCCCCCHHHHHHHHHHHHHHhh-hcCCceEEEEeChHHHHHHHH
Confidence            8899999999999999999999753 21 11   1 1235799999999999999855 345568999999999999998


Q ss_pred             c------------CCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          171 N------------RKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       171 ~------------~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      .            ....+-.-..++++|..++.. ..++|.|||
T Consensus        79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVk  121 (161)
T PRK06548         79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVN  121 (161)
T ss_pred             HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEe
Confidence            3            122233468899999999987 479999985

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.41  E-value=5.2e-12  Score=94.94  Aligned_cols=107  Identities=15%  Similarity=0.028  Sum_probs=82.5

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA  169 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l  169 (202)
                      .+.++||||+.++++.+|+|+|+...++.....  ... ...|+..||+.|+..||+.+.+  ...|.|.|||..+++.|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~--~~~-~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELS--GGE-ALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEe--cCC-CCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHH
Confidence            478999999999999999999998755443222  222 3568999999999999998865  35799999999999999


Q ss_pred             hc--------C--C--CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          170 RN--------R--K--GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       170 ~~--------~--~--~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ++        .  .  ..+-....+++++..++.. ..+.|.||+
T Consensus        78 ~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~  121 (150)
T PRK00203         78 TEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVK  121 (150)
T ss_pred             HHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEec
Confidence            85        1  1  1122356788999888876 678999985

>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=99.40  E-value=4.6e-12  Score=92.58  Aligned_cols=104  Identities=16%  Similarity=0.011  Sum_probs=79.5

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA  169 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l  169 (202)
                      -+.+++|||+.++++.+|+|+|+.+.  .   .....++ ..++..||+.|+.+||+ +. .. ++|.|.|||+.+++.+
T Consensus         3 ~~~iytDgS~~~~~~~~~~g~v~~~~--~---~~~~~~~-~~s~~~aEl~Ai~~AL~-~~-~~-~~v~I~tDS~~v~~~l   73 (132)
T PF00075_consen    3 AIIIYTDGSCRPNPGKGGAGYVVWGG--R---NFSFRLG-GQSNNRAELQAIIEALK-AL-EH-RKVTIYTDSQYVLNAL   73 (132)
T ss_dssp             SEEEEEEEEECTTTTEEEEEEEEETT--E---EEEEEEE-SECHHHHHHHHHHHHHH-TH-ST-SEEEEEES-HHHHHHH
T ss_pred             cEEEEEeCCccCCCCceEEEEEEECC--e---EEEeccc-ccchhhhheehHHHHHH-Hh-hc-ccccccccHHHHHHHH
Confidence            46899999999999999999977433  2   2223334 66999999999999999 55 22 9999999999999988


Q ss_pred             hc-----CCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          170 RN-----RKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       170 ~~-----~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      +.     .....+....+..++..++.....+.|.||+
T Consensus        74 ~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~  111 (132)
T PF00075_consen   74 NKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVP  111 (132)
T ss_dssp             HTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESS
T ss_pred             HHhccccccccccccccchhheeeccccceEEeeeecc
Confidence            87     3332222225777888888878899999985

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 ....

>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]

Probab=98.40  E-value=3.8e-06  Score=70.50  Aligned_cols=111  Identities=13%  Similarity=-0.004  Sum_probs=80.1

Q ss_pred             CceEEEecceeeec---CCeeeEEEEEeCCCCcEEEeeeeecC-ccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHH
Q 039849           89 GWYEANVDAAIRHS---NWIAGLGVVIRDSKGKFVAVAIQRAI-YKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKE  164 (202)
Q Consensus        89 ~~~K~n~Das~~~~---~~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~  164 (202)
                      +...+++||++..+   ..++|+|+.+-+.  .-...+ .++. +..+++.||+.|+.+||+-|++.+..+|+|.|||..
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~--~e~N~s-~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~  287 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPG--HELNVS-GPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEY  287 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCC--Cccccc-ccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHH
Confidence            44779999999975   3558999887552  222222 2333 688999999999999999999999999999999999


Q ss_pred             HHHHHhcC-------------CCC----cchHHHHHHHHHHHhhc--CCceEEEeeC
Q 039849          165 VVDLARNR-------------KGC----KSEVFWTVVAIQASLKS--LNRVQIQHVS  202 (202)
Q Consensus       165 vv~~l~~~-------------~~~----~s~~~~ii~~i~~l~~~--f~~~~~~~V~  202 (202)
                      +++.|+.-             ..+    .-.-...+.++-+|.+.  ...+++.||+
T Consensus       288 ~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~  344 (371)
T KOG3752|consen  288 FINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVG  344 (371)
T ss_pred             HHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEec
Confidence            99999411             000    01234566666677666  3677888874

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.40  E-value=0.018  Score=49.69  Aligned_cols=90  Identities=16%  Similarity=0.137  Sum_probs=64.0

Q ss_pred             CCeeeEEEEEeCC-CCcEEEeeeeecC--ccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHHhcCCCCcc--
Q 039849          103 NWIAGLGVVIRDS-KGKFVAVAIQRAI--YKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLARNRKGCKS--  177 (202)
Q Consensus       103 ~~~~g~G~vird~-~g~~~~~~~~~~~--~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l~~~~~~~s--  177 (202)
                      ...+|.|+.+.|+ +............  ...++.+||+.|+..+|..+..+|+.++.+.+|.......+.++.....  
T Consensus        16 ~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~   95 (384)
T KOG1812|consen   16 ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHR   95 (384)
T ss_pred             hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHH
Confidence            3568899999986 4444433333332  2368999999999999999999999999999998888887776654322  


Q ss_pred             hHHHHHHHHHHHhhc
Q 039849          178 EVFWTVVAIQASLKS  192 (202)
Q Consensus       178 ~~~~ii~~i~~l~~~  192 (202)
                      .+..+..+...+...
T Consensus        96 ~~~~l~~~v~~~r~~  110 (384)
T KOG1812|consen   96 KIVLLVELVQRIREQ  110 (384)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            345555555444443

>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]

Probab=87.29  E-value=4.7  Score=29.56  Aligned_cols=56  Identities=20%  Similarity=0.198  Sum_probs=43.6

Q ss_pred             eeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEech
Q 039849          106 AGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDS  162 (202)
Q Consensus       106 ~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs  162 (202)
                      --+|+++|..+|++..+..--......-..||-.|+-.++.. -...+..|.+.+|.
T Consensus        26 F~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~   81 (134)
T COG0295          26 FKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT   81 (134)
T ss_pred             CcEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence            347888888888877776654445667789999999999877 66677889998884

>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]

Probab=85.06  E-value=3  Score=31.27  Aligned_cols=56  Identities=18%  Similarity=0.140  Sum_probs=38.5

Q ss_pred             CeeeEEEEEeCCCCcEEEeeeeecC-ccCCHHHHHHHHHHHHHHHHHHCCcccEEEE
Q 039849          104 WIAGLGVVIRDSKGKFVAVAIQRAI-YKGNVAYVEAKAVTLGIQVTKKIKCLPMIIE  159 (202)
Q Consensus       104 ~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~AE~~al~~al~~a~~~~~~~v~~e  159 (202)
                      +...+|.||.+.+|.++..+..... .-....+||..|++.|-+......+....+.
T Consensus        26 ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tly   82 (152)
T COG0590          26 GEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLY   82 (152)
T ss_pred             CCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEE
Confidence            4567899999988988876654433 2334459999999999988865444433333

>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric

Probab=83.26  E-value=3.7  Score=29.74  Aligned_cols=57  Identities=11%  Similarity=0.050  Sum_probs=40.9

Q ss_pred             eeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEech
Q 039849          105 IAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDS  162 (202)
Q Consensus       105 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs  162 (202)
                      ...+|+++++.+|+++.+...-.........||..|+..+...-. ..+..|.+-++.
T Consensus        20 ~~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~-~~i~~i~vv~~~   76 (127)
T TIGR01354        20 NFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGY-RKFVAIAVADSA   76 (127)
T ss_pred             CCeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCC-CCeEEEEEEeCC
Confidence            345888999999998886655444455677999999999886533 256777776654

This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.

>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase

Probab=81.42  E-value=5.2  Score=28.44  Aligned_cols=41  Identities=22%  Similarity=0.199  Sum_probs=31.2

Q ss_pred             CeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHH
Q 039849          104 WIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQV  147 (202)
Q Consensus       104 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~  147 (202)
                      +...+|.||.+.+|+++..+.....   ...+||..|+..+.+.
T Consensus        17 ~~~pvGaviv~~~g~iv~~g~n~~~---~~~HAE~~ai~~a~~~   57 (115)
T cd01284          17 PNPPVGCVIVDDDGEIVGEGYHRKA---GGPHAEVNALASAGEK   57 (115)
T ss_pred             CCCCEEEEEEeCCCeEEEEecCCCC---CcccHHHHHHHHHhhc
Confidence            3456888888888999887655433   5789999999998764

Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.

>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases

Probab=81.01  E-value=6.9  Score=27.27  Aligned_cols=57  Identities=19%  Similarity=0.073  Sum_probs=37.0

Q ss_pred             CeeeEEEEEeCCCCcEEEeeeeec-CccCCHHHHHHHHHHHHHHHHHHCCcccEEEEe
Q 039849          104 WIAGLGVVIRDSKGKFVAVAIQRA-IYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIEL  160 (202)
Q Consensus       104 ~~~g~G~vird~~g~~~~~~~~~~-~~~~~~~~AE~~al~~al~~a~~~~~~~v~~es  160 (202)
                      +...+|.+|.|.+|+++..+.... .......+||..|+..+.+......+....+.+
T Consensus        15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~   72 (109)
T cd01285          15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYT   72 (109)
T ss_pred             CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEE
Confidence            445688899988899887665433 223467899999999987653322234444433

These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei

---

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	202
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	2e-05
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	7e-04

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis} Length = 141

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 106 AGLGVVIRDSKGKFVAVAIQRAIYKG--NVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK 163
           AG G V+  +    V    ++AI +   NVA  E + +  G+    K+      + +DSK
Sbjct: 19  AGYGAVVWTADHSTVLAESKQAIGRATNNVA--EYRGLIAGLDDAVKLGATEAAVLMDSK 76

Query: 164 EVVDLARNRKGCKSEVFWTVVA-IQASLKSLNRVQIQHV 201
            VV+    R   K      +    QA      R+  + V
Sbjct: 77  LVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWV 115

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A Length = 149

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 21/113 (18%), Positives = 35/113 (30%), Gaps = 8/113 (7%)

Query: 96  DAAIRHSN--WIAGLGVVIRDSKGKFVAVAIQRAIYKG----NVAYVEAKAVTLGIQVTK 149
           D      N   IA  G VI     K     +    +      NVA  E   +   ++   
Sbjct: 7   DGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVA--EYSGLICLMETML 64

Query: 150 KIKCLPMIIELDSKEVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS 202
           ++     II+ DS+ V+         K++    +      LK      +  V 
Sbjct: 65  RLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVP 117

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	202
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.84
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.84
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.82
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.77
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.71
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.7
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.69
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.64
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.64
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.63
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.6
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.53
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.52
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.46
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.29
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.28
1uwz_A	136	Cytidine deaminase; CDD, tetramer, zinc binding, p	88.33
2fr5_A	146	Cytidine deaminase; tetrahydrouridine, protein-inh	85.88

>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=99.84  E-value=3e-20  Score=136.75  Aligned_cols=112  Identities=20%  Similarity=0.194  Sum_probs=98.9

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCC-CcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSK-GKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDL  168 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~-g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~  168 (202)
                      .+++|||||+.++++.+|+|+|++++. |..+......++ ..+++.||+.|++.||+++.++|..+|.|+|||+.|++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            379999999999999999999999987 666655555554 679999999999999999999999999999999999999


Q ss_pred             HhcCCC-CcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          169 ARNRKG-CKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       169 l~~~~~-~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      +++... ....+..++.+|+.++.+|..++|.||+
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~  116 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP  116 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC
Confidence            998743 3345889999999999999999999995

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

Probab=99.84  E-value=3.9e-20  Score=135.68  Aligned_cols=113  Identities=16%  Similarity=0.134  Sum_probs=101.0

Q ss_pred             CceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcc----cEEEEechHH
Q 039849           89 GWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCL----PMIIELDSKE  164 (202)
Q Consensus        89 ~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~----~v~~esDs~~  164 (202)
                      ..+++|||||+.++++.+|+|+++++++|..+......++ ..+++.||+.|++.||+.+.+.+.+    +|.|+|||+.
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            3589999999999999999999999999998766666665 4699999999999999999999999    9999999999


Q ss_pred             HHHHHhcCCCC-cchHHHHHHHHHHH-hhcCCceEEEeeC
Q 039849          165 VVDLARNRKGC-KSEVFWTVVAIQAS-LKSLNRVQIQHVS  202 (202)
Q Consensus       165 vv~~l~~~~~~-~s~~~~ii~~i~~l-~~~f~~~~~~~V~  202 (202)
                      |++.+++.... ...+..++.+++.+ +.+|..++|.||+
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~  120 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP  120 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC
Confidence            99999987543 34688999999999 9999999999995

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

Probab=99.82  E-value=2.6e-19  Score=133.19  Aligned_cols=111  Identities=12%  Similarity=-0.016  Sum_probs=95.6

Q ss_pred             ceEEEecceee-ecCCeeeE-EEEEeCCCCcEEEeeeeecC---ccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHH
Q 039849           90 WYEANVDAAIR-HSNWIAGL-GVVIRDSKGKFVAVAIQRAI---YKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKE  164 (202)
Q Consensus        90 ~~K~n~Das~~-~~~~~~g~-G~vird~~g~~~~~~~~~~~---~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~  164 (202)
                      ++++|||||+. ++++.+|+ |+|+++ .|..+........   ...+++.||+.|++.||+.+.++|.++|.|+|||+.
T Consensus         1 m~~iy~DGs~~~~n~g~~G~~G~vi~~-~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~   79 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGGIATFGFVIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQL   79 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEEC-SSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHH
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEE-CCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHH
Confidence            57899999999 78899996 999999 8887754443333   367999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCC-cchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          165 VVDLARNRKGC-KSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       165 vv~~l~~~~~~-~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      |++.+++.... ...+..++++++.++++| .+.|.||+
T Consensus        80 vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~  117 (149)
T 2ehg_A           80 VIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVP  117 (149)
T ss_dssp             HHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECC
T ss_pred             HHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcC
Confidence            99999987432 235899999999999999 69999985

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

Probab=99.77  E-value=4.6e-18  Score=127.27  Aligned_cols=114  Identities=17%  Similarity=0.110  Sum_probs=94.1

Q ss_pred             CCCCCceEEEecceeeecCC---eeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEec
Q 039849           85 PPSSGWYEANVDAAIRHSNW---IAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELD  161 (202)
Q Consensus        85 ~P~~~~~K~n~Das~~~~~~---~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esD  161 (202)
                      +|+.++++++||||+.++++   .+|+|+++++..+..+.   ..+.+..+++.||+.|++.||+.+.+.+..+|.|+||
T Consensus         2 ~~~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~---~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tD   78 (154)
T 2qkb_A            2 SHMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVG---IRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTN   78 (154)
T ss_dssp             CEETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEE---EECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEES
T ss_pred             CCCCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEE---eecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEEC
Confidence            57789999999999998764   48999999986554332   3444467999999999999999999999999999999


Q ss_pred             hHHHHHHHhcC------------CCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          162 SKEVVDLARNR------------KGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       162 s~~vv~~l~~~------------~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      |+.|++.|++-            ...+.....++.+|..++..+. +.|.||+
T Consensus        79 S~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~-v~~~~V~  130 (154)
T 2qkb_A           79 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMD-IQWMHVP  130 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCE-EEEEECC
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCc-eEEEEcc
Confidence            99999999871            1123456789999999999875 9999985

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=99.71  E-value=5.4e-17  Score=119.62  Aligned_cols=102  Identities=15%  Similarity=0.097  Sum_probs=80.2

Q ss_pred             cCCCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechH
Q 039849           84 MPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK  163 (202)
Q Consensus        84 ~~P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~  163 (202)
                      .||+.++++++||||+.++++.+|+|+|++ ..|..+..+. .+. ..|++.||++|++.||+.+.+.+. +|.|+|||+
T Consensus         5 ~~~~~~~~~iy~DGa~~gNpG~~G~G~vl~-~~g~~~~~~~-~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~   80 (142)
T 1zbf_A            5 AKEEIIWESLSVDVGSQGNPGIVEYKGVDT-KTGEVLFERE-PIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQ   80 (142)
T ss_dssp             ---CCCSSSEEEEEEECSSSEEEEEEEEET-TTCCEEEECC-CEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCH
T ss_pred             CCCCCCeEEEEEeeccCCCCCCeEEEEEEE-eCCEEEEEec-ccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehH
Confidence            467789999999999999999999999999 6787665432 233 468999999999999999999999 999999999


Q ss_pred             HHHHHHhcCCC-----CcchHHHHHHHHHHH
Q 039849          164 EVVDLARNRKG-----CKSEVFWTVVAIQAS  189 (202)
Q Consensus       164 ~vv~~l~~~~~-----~~s~~~~ii~~i~~l  189 (202)
                      .|++.+++...     .+.....+.+.+..+
T Consensus        81 ~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~  111 (142)
T 1zbf_A           81 TAIKWVKDKKAKSTLVRNEETALIWKLVDEA  111 (142)
T ss_dssp             HHHHHHHHTCCCCCCCCSTTTHHHHHHHHHH
T ss_pred             HHHHHHHcCCccCCCCCCcccHHHHHHHHHH
Confidence            99999998752     122345555554443

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

Probab=99.70  E-value=5.3e-17  Score=122.98  Aligned_cols=113  Identities=15%  Similarity=0.027  Sum_probs=87.5

Q ss_pred             cCCCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechH
Q 039849           84 MPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK  163 (202)
Q Consensus        84 ~~P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~  163 (202)
                      .||+++.++++||||+.++++.+|+|+|+++..+.....+  .. ...+++.||+.|++.||+.+.+.  .+|.|+|||+
T Consensus         2 ~p~~m~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~--~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~   76 (166)
T 1ril_A            2 NPSPRKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSG--GE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSH   76 (166)
T ss_dssp             ----CCCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECC--EE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCH
T ss_pred             CCCCCccEEEEECccccCCCCCEEEEEEEEECCEEEEEec--CC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChH
Confidence            4788899999999999999999999999998655433222  22 24689999999999999998765  4999999999


Q ss_pred             HHHHHHhcC---------C----CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          164 EVVDLARNR---------K----GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       164 ~vv~~l~~~---------~----~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      .|++.|++.         .    ..+.....++.++..++..+ .+.|.||+
T Consensus        77 ~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~  127 (166)
T 1ril_A           77 YLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPH-RVRFHFVK  127 (166)
T ss_dssp             HHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTS-EEECCCCC
T ss_pred             HHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcC-eEEEEEee
Confidence            999999982         1    11233567899999999875 78888884

>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=99.69  E-value=3.3e-16  Score=116.69  Aligned_cols=109  Identities=20%  Similarity=0.146  Sum_probs=88.3

Q ss_pred             cCCCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechH
Q 039849           84 MPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK  163 (202)
Q Consensus        84 ~~P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~  163 (202)
                      ..|+.|.+++++|||+.++++.+|+|+|+++..+..+.     . ...+++.||+.|++.||+.+   + .+|.|.|||+
T Consensus         6 ~~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~-----~-~~~Tnn~aEl~A~i~AL~~~---~-~~v~i~tDS~   75 (150)
T 3qio_A            6 KEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVT-----L-TDTTNQKTELQAIYLALQDS---G-LEVNIVTDSQ   75 (150)
T ss_dssp             SSCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEE-----E-SSCCHHHHHHHHHHHHHHHS---C-SEEEEEESCH
T ss_pred             cCCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEe-----C-CCCCHHHHHHHHHHHHHHhC---C-CcEEEEeCcH
Confidence            46888999999999999999999999999986544331     2 35799999999999999985   3 8999999999


Q ss_pred             HHHHHHhcC------------CCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          164 EVVDLARNR------------KGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       164 ~vv~~l~~~------------~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      .|++.+++-            ...+.....++.++..++.++..+.|.||+
T Consensus        76 ~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~  126 (150)
T 3qio_A           76 YALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVP  126 (150)
T ss_dssp             HHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECC
T ss_pred             HHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEcc
Confidence            999999862            112334578888988888889999999995

>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=99.64  E-value=2e-15  Score=112.97  Aligned_cols=107  Identities=14%  Similarity=0.038  Sum_probs=85.8

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA  169 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l  169 (202)
                      .++++||||+.++++.+|+|+++++..+.....+  .. ...+++.||+.|++.||+.+.+.  .+|.|+|||+.|++.|
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~--~~-~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i   78 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSA--GY-TRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGI   78 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEE--EE-EEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEec--CC-CCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHH
Confidence            5899999999999999999999998665433322  22 24689999999999999999764  8999999999999999


Q ss_pred             hc--------CC----CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          170 RN--------RK----GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       170 ~~--------~~----~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ++        ..    ..+.....++.++..++..+ .+.|.||+
T Consensus        79 ~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~  122 (155)
T 1jl1_A           79 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQH-QIKWEWVK  122 (155)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTC-EEEEEECC
T ss_pred             HHHHHHHhhcccccccCCccCCHHHHHHHHHHHccC-ceEEEEcC
Confidence            97        21    12333477899999988864 89999985

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

Probab=99.64  E-value=1.8e-15  Score=112.04  Aligned_cols=108  Identities=15%  Similarity=0.012  Sum_probs=86.9

Q ss_pred             CceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHH
Q 039849           89 GWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDL  168 (202)
Q Consensus        89 ~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~  168 (202)
                      ..++++||||+.++++.+|+|+++++..+..  ......+ ..+++.||+.|++.||+.+.+  ..+|.|+|||+.|++.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~--~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~   77 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRK--EISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNA   77 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEE--EEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeE--EeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHH
Confidence            3589999999999999999999999864332  2233333 468999999999999999976  5899999999999999


Q ss_pred             HhcC-------------CCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          169 ARNR-------------KGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       169 l~~~-------------~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      +++.             ...+.....++.++..++..+ .+.|.||+
T Consensus        78 i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~-~v~~~~V~  123 (146)
T 3h08_A           78 MNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLH-RVTFHKVK  123 (146)
T ss_dssp             HHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHS-EEEEEECC
T ss_pred             HHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhC-ceEEEEcC
Confidence            9882             222345688999999999887 58999985

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

Probab=99.63  E-value=4.5e-15  Score=111.41  Aligned_cols=108  Identities=10%  Similarity=-0.026  Sum_probs=85.7

Q ss_pred             CceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHH
Q 039849           89 GWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDL  168 (202)
Q Consensus        89 ~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~  168 (202)
                      ..++++||||+.++++.+|+|+|+++......  .....+ ..+++.||+.|++.||+.+.+.  .+|.|+|||+.|++.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~--~~~~~~-~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKE--MSDGFS-LTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQG   79 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEE--EEEEEE-EECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEE--EecCcC-CCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHH
Confidence            45899999999999999999999998543222  222332 4689999999999999998654  899999999999999


Q ss_pred             Hhc--------CC----CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          169 ARN--------RK----GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       169 l~~--------~~----~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      |++        ..    ..+.....++.++..++..+ .+.|.||+
T Consensus        80 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~  124 (158)
T 2e4l_A           80 IMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLH-QIDWRWVK  124 (158)
T ss_dssp             HHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTS-EEEEEECC
T ss_pred             HHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccC-cEEEEEcc
Confidence            988        32    12344678889999998875 89999985

>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=99.60  E-value=4.9e-14  Score=106.43  Aligned_cols=116  Identities=14%  Similarity=0.060  Sum_probs=90.5

Q ss_pred             CcccCCCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEe
Q 039849           81 QAWMPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIEL  160 (202)
Q Consensus        81 ~~W~~P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~es  160 (202)
                      ....|.+...+++++|||+.++++.+|+|+++++. |..+...  ......+++.||+.|++.||+.+   ...+|.|.|
T Consensus        14 l~~~P~~~~~i~iytDGs~~~npG~~g~G~vi~~~-~~~~~~~--~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~t   87 (165)
T 3p1g_A           14 LTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTE-TEVIWAR--ALPAGTSAQRAELIALTQALKMA---EGKKLNVYT   87 (165)
T ss_dssp             CBSSCCTTCSEEEEEEEEEEEETTEEEEEEEEECS-SCEEEEE--EECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEE
T ss_pred             CCCCCCCCCCEEEEEEcccCCCCCceEEEEEEEEC-CEEEEEe--cCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEE
Confidence            34455665679999999999999999999999874 5544322  34456799999999999999998   368999999


Q ss_pred             chHHHHHHHhcCC-CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          161 DSKEVVDLARNRK-GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       161 Ds~~vv~~l~~~~-~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ||+.+++.+.... ..+.....++.++...+..+..+.|.||+
T Consensus        88 DS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVk  130 (165)
T 3p1g_A           88 DSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCP  130 (165)
T ss_dssp             CCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECC
T ss_pred             chHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEec
Confidence            9999999985322 22334567788887766678899999996

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

Probab=99.53  E-value=3.5e-13  Score=101.68  Aligned_cols=112  Identities=21%  Similarity=0.097  Sum_probs=87.0

Q ss_pred             CceEEEecceeeecCCe-----eeEEEEEeCCCC--cEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEec
Q 039849           89 GWYEANVDAAIRHSNWI-----AGLGVVIRDSKG--KFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELD  161 (202)
Q Consensus        89 ~~~K~n~Das~~~~~~~-----~g~G~vird~~g--~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esD  161 (202)
                      ..+.++||||+.++++.     +|+|++++....  ++...... ..+..+.+.||+.||..||+.+...+ .+|.|.||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~-~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TD   83 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSI-PLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITD   83 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEE-EESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEES
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccC-CchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeC
Confidence            34679999999998774     999999985433  33333322 23456889999999999999998877 47999999


Q ss_pred             hHHHHHHHhc------------CCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          162 SKEVVDLARN------------RKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       162 s~~vv~~l~~------------~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      |+.|++.+++            ....+-....++.++..++..+..+.|.|||
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~Vk  136 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEK  136 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECC
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEe
Confidence            9999999974            1122334578899999999989999999996

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=99.52  E-value=9.8e-14  Score=100.64  Aligned_cols=80  Identities=16%  Similarity=0.143  Sum_probs=68.0

Q ss_pred             CceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHH
Q 039849           89 GWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDL  168 (202)
Q Consensus        89 ~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~  168 (202)
                      ....++||||+.++++.+|+|+|+++ .|..+... ..+. ..+++.||++|++.||+.+.+.+.+ |.|.|||+.|++.
T Consensus         4 ~~~~iytDGac~GNPGp~G~ggV~~~-~g~~~~~~-g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~w   79 (134)
T 4htu_A            4 IWESLSVDVGSQGNPGIVEYKGVDTK-TGEVLFER-EPIP-IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKW   79 (134)
T ss_dssp             CSSSEEEEEEEETTTEEEEEEEEETT-TCCEEEEE-EEEE-EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHH
T ss_pred             cceEEEEeeccCCCCCCeEEEEEEEE-CCEEEEEe-cCCC-CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHH
Confidence            45679999999999999999989988 66655443 2333 5799999999999999999998876 8999999999999


Q ss_pred             HhcC
Q 039849          169 ARNR  172 (202)
Q Consensus       169 l~~~  172 (202)
                      +++.
T Consensus        80 i~~~   83 (134)
T 4htu_A           80 VKDK   83 (134)
T ss_dssp             HHHT
T ss_pred             HHcC
Confidence            9864

>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=99.46  E-value=3.4e-14  Score=105.38  Aligned_cols=109  Identities=12%  Similarity=0.004  Sum_probs=77.6

Q ss_pred             CCCceEEEecceeeecCCeeeEEEEEeCCCCcEEE-ee-eeecCc--cCCHHHHHHHHHHHHHHHHHHCCcccEEEEech
Q 039849           87 SSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVA-VA-IQRAIY--KGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDS  162 (202)
Q Consensus        87 ~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~-~~-~~~~~~--~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs  162 (202)
                      |.+.++++||||+.+  +.+|+|+++++ +|.... .+ ....+.  ..+++.||+.|++.||+.+.+.+. +|.|.|||
T Consensus         3 ~~~~i~iytDGs~~~--g~~G~G~vi~~-~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS   78 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVN--GQYAWAYAFVK-DGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDY   78 (147)
T ss_dssp             TTSCCEEECCCCCBT--TBCEEEEEEEE-TTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCC
T ss_pred             CCCeEEEEECCCCCC--CCcEEEEEEEE-CCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECc
Confidence            457899999999987  89999999998 555422 11 111122  358999999999999999999998 99999999


Q ss_pred             HHHHHHHhcCCCCcch-HHHHHHHHHHHhhcCCceEEEeeC
Q 039849          163 KEVVDLARNRKGCKSE-VFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       163 ~~vv~~l~~~~~~~s~-~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      +.+.+.+.+....... ...+.+.++.+..   .+.|.||+
T Consensus        79 ~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~  116 (147)
T 2kq2_A           79 AGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVK  116 (147)
T ss_dssp             STHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCC
T ss_pred             HHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEec
Confidence            9999888775433221 2222233333322   67888874

>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=99.29  E-value=1.6e-11  Score=108.93  Aligned_cols=107  Identities=21%  Similarity=0.154  Sum_probs=85.4

Q ss_pred             cCCCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechH
Q 039849           84 MPPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSK  163 (202)
Q Consensus        84 ~~P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~  163 (202)
                      ..|..+.+++++|||+.++++.+|+|+++++.....+     .. ...+++.||+.|++.||+.+    ..+|.|.|||+
T Consensus       433 ~ep~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~-----~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~  502 (557)
T 2zd1_A          433 KEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVV-----PL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQ  502 (557)
T ss_dssp             SSCCTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCH
T ss_pred             cCCCCCCEEEEEccCCCCCCCceEEEEEEECCcEEEe-----cC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChH
Confidence            3456788999999999999999999999985433332     12 35699999999999999998    68999999999


Q ss_pred             HHHHHHhcCCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          164 EVVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       164 ~vv~~l~~~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      .|++.+++....  ....++.++...+.++..+.|.||+
T Consensus       503 ~vi~~i~~~~~~--~~~~l~~~~~~~l~~~~~v~~~wV~  539 (557)
T 2zd1_A          503 YALGIIQAQPDK--SESELVNQIIEQLIKKEKVYLAWVP  539 (557)
T ss_dssp             HHHHHHTTCCSE--ESSHHHHHHHHHHHHCSEEEEEECC
T ss_pred             HHHHHHhcCCcc--CCHHHHHHHHHHHhcCCCEEEEEcC
Confidence            999999985432  1356667777666667789999985

>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=99.28  E-value=2.6e-11  Score=107.59  Aligned_cols=106  Identities=15%  Similarity=0.113  Sum_probs=86.0

Q ss_pred             CCCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHH
Q 039849           85 PPSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKE  164 (202)
Q Consensus        85 ~P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~  164 (202)
                      .|..|.+++++|||+.++++.+|+|+++++..+..     ... ...+++.||+.|++.||+.    +..+|.|.|||+.
T Consensus       431 ~p~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~-----~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~  500 (555)
T 1mu2_A          431 DPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKV-----KKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQY  500 (555)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEE-----EEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHH
T ss_pred             CCCCCceEEEEcccccCCCCCceEEEEEEeCCEee-----ccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHH
Confidence            45678899999999999999999999998754331     122 3568999999999999987    6789999999999


Q ss_pred             HHHHHhcCCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          165 VVDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       165 vv~~l~~~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      |++.+++-..  .....+..++..++..+..+.+.||+
T Consensus       501 v~~~i~~~~~--~~~~~l~~~~~~~~~~~~~v~~~wV~  536 (555)
T 1mu2_A          501 VMGIVASQPT--ESESKIVNQIIEEMIKKEAIYVAWVP  536 (555)
T ss_dssp             HHHHHHTCCS--EESCHHHHHHHHHHHHCSEEEEEECC
T ss_pred             HHHHHhcccc--cccHHHHHHHHHHhccCCcEEEEEEE
Confidence            9999997432  23456777887777778899999985

>1uwz_A Cytidine deaminase; CDD, tetramer, zinc binding, pyrimidine metabolism, salvage, hydrolase; HET: THU; 1.99A {Bacillus subtilis} SCOP: c.97.1.1 PDB: 1ux0_A* 1jtk_A* 1ux1_A*

Probab=88.33  E-value=0.86  Score=32.43  Aligned_cols=56  Identities=13%  Similarity=0.058  Sum_probs=42.0

Q ss_pred             eeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEec
Q 039849          105 IAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELD  161 (202)
Q Consensus       105 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esD  161 (202)
                      ...+|+++++.+|+++.+.............||..|+..|... -...+..+.+.+|
T Consensus        23 ~~~VGAal~~~dG~i~~G~Nvena~~~~t~cAE~~Ai~~A~~~-G~~~~~~~~l~~~   78 (136)
T 1uwz_A           23 KFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEATALFKAVSE-GDTEFQMLAVAAD   78 (136)
T ss_dssp             CCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHH-TCCCEEEEEEEES
T ss_pred             CCCEEEEEEeCCCeEEEEeCcccCCCCCccCHHHHHHHHHHHC-CCCCeEEEEEEeC
Confidence            4468999999999988655544433445689999999999876 4456788888876

>2fr5_A Cytidine deaminase; tetrahydrouridine, protein-inhibitor COM alternate conformation of Arg68, hydrolase; HET: TYU; 1.48A {Mus musculus} SCOP: c.97.1.1 PDB: 1zab_A* 2fr6_A* 1mq0_A*

Probab=85.88  E-value=1.1  Score=32.27  Aligned_cols=56  Identities=13%  Similarity=0.042  Sum_probs=41.5

Q ss_pred             eeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEec
Q 039849          105 IAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELD  161 (202)
Q Consensus       105 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esD  161 (202)
                      ...+|.++++.+|+++.+...-.........||..|+..|... -...+..+.+.+|
T Consensus        35 ~f~VGAal~~~dG~i~~G~NvEnas~~~t~cAE~~Ai~~A~~~-G~~~l~~i~v~~~   90 (146)
T 2fr5_A           35 RFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISE-GYKDFRAIAISSD   90 (146)
T ss_dssp             CCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEES
T ss_pred             CCCEEEEEEeCCCcEEEEEeccccCCCCCcCHHHHHHHHHHhC-CCCceEEEEEEeC
Confidence            4568999999999988655533333334588999999999865 4556788888877

---

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	202
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.56
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.51
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.36
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.26
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.25

>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=99.56  E-value=2.8e-14  Score=99.01  Aligned_cols=105  Identities=21%  Similarity=0.165  Sum_probs=84.7

Q ss_pred             CCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHH
Q 039849           86 PSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEV  165 (202)
Q Consensus        86 P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~v  165 (202)
                      |..|-..++||||+..+++.+|+|+++-+.......     +. ..|++.||+.|++.||+.    +..+|.|.|||+.+
T Consensus         4 Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~-----~~-~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yv   73 (110)
T d1s1ta1           4 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVT-----LT-DTTNQKTELQAIYLALQD----SGLEVNIVTDSQYA   73 (110)
T ss_dssp             CCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEE-----ES-SCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHH
T ss_pred             CCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEe-----cc-cCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHH
Confidence            556767899999999999999999988664433222     22 459999999999999974    56789999999999


Q ss_pred             HHHHhcCCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          166 VDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       166 v~~l~~~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ++.+++....  ....++.++...+..+..+.+.||+
T Consensus        74 i~~i~~~~~~--~~~~l~~~il~~l~~~~~v~i~WVp  108 (110)
T d1s1ta1          74 LGIIQAQPDQ--SESELVNQIIEQLIKKEKVYLAWVP  108 (110)
T ss_dssp             HHHHHHCCSE--ESCHHHHHHHHHHHHCSEEEEEECC
T ss_pred             HHHHhcCccc--cchHHHHHHHHHHhcCCceEEEEeC
Confidence            9999987542  3567788888888889999999996

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.51  E-value=2.8e-14  Score=101.28  Aligned_cols=78  Identities=14%  Similarity=0.062  Sum_probs=65.0

Q ss_pred             eEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHHh
Q 039849           91 YEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLAR  170 (202)
Q Consensus        91 ~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l~  170 (202)
                      -.++||||+.+++|.+|+|+|+.+..+.....+  .+ +..|++.||++|++.||+.+.+.+ .++.|.|||+.+++.++
T Consensus         5 ~sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg--~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~   80 (132)
T d1zbfa1           5 ESLSVDVGSQGNPGIVEYKGVDTKTGEVLFERE--PI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVK   80 (132)
T ss_dssp             SSEEEEEEECSSSEEEEEEEEETTTCCEEEECC--CE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHH
T ss_pred             eeEEEeecCCCCCchheEEEEEEcCCEEEEEEc--Cc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHH
Confidence            358999999999999999999987555443322  23 356899999999999999999987 57999999999999997


Q ss_pred             cC
Q 039849          171 NR  172 (202)
Q Consensus       171 ~~  172 (202)
                      +.
T Consensus        81 ~~   82 (132)
T d1zbfa1          81 DK   82 (132)
T ss_dssp             HT
T ss_pred             hC
Confidence            64

>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=99.36  E-value=5.3e-12  Score=89.27  Aligned_cols=105  Identities=14%  Similarity=0.075  Sum_probs=77.5

Q ss_pred             CCCCceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHH
Q 039849           86 PSSGWYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEV  165 (202)
Q Consensus        86 P~~~~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~v  165 (202)
                      |..|...++||||+..+++.+|+|+++.+.......     +. ..+++.||+.|++.||+.    ...+|.|.|||+.+
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~-----~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v   72 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKK-----LE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYV   72 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEE-----ES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEe-----cC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHH
Confidence            556777899999999998999999888765433322     22 458999999999999874    56799999999999


Q ss_pred             HHHHhcCCCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          166 VDLARNRKGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       166 v~~l~~~~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ++.+++...... -..+...+..+ .+...+.|.||+
T Consensus        73 ~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~v~~~wV~  107 (126)
T d1mu2a1          73 MGIVASQPTESE-SKIVNQIIEEM-IKKEAIYVAWVP  107 (126)
T ss_dssp             HHHHHTCCSEES-CHHHHHHHHHH-HHCSEEEEEECC
T ss_pred             HHHHhcCCcccc-chHHHHHHHHh-hhcceeEEEEEe
Confidence            999998754322 22233334444 445689999985

>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=99.26  E-value=4.8e-11  Score=86.51  Aligned_cols=107  Identities=14%  Similarity=0.042  Sum_probs=81.1

Q ss_pred             ceEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHH
Q 039849           90 WYEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLA  169 (202)
Q Consensus        90 ~~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l  169 (202)
                      .++++||||+.++++.+|+|+|+.+..........  . ...+++.||+.|++.||+++.  ....+.+.+|+..++..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~--~-~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAG--Y-TRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEE--E-EEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccc--c-CcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcc
Confidence            47899999999999999999999986655443322  2 245899999999999998753  456889999999999888


Q ss_pred             hcCC------------CCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          170 RNRK------------GCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       170 ~~~~------------~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      +...            ..+.....++.++..++.. ..++|.||+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~-~~V~~~wV~  120 (152)
T d1jl1a_          77 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVK  120 (152)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECC
T ss_pred             cchhhHhHhccchhcccCeeecHHHHHHHHHHhhc-ceeEEEEec
Confidence            5331            1223346678888777765 479999985

>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=99.25  E-value=1.7e-11  Score=88.76  Aligned_cols=106  Identities=15%  Similarity=0.035  Sum_probs=80.4

Q ss_pred             eEEEecceeeecCCeeeEEEEEeCCCCcEEEeeeeecCccCCHHHHHHHHHHHHHHHHHHCCcccEEEEechHHHHHHHh
Q 039849           91 YEANVDAAIRHSNWIAGLGVVIRDSKGKFVAVAIQRAIYKGNVAYVEAKAVTLGIQVTKKIKCLPMIIELDSKEVVDLAR  170 (202)
Q Consensus        91 ~K~n~Das~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~AE~~al~~al~~a~~~~~~~v~~esDs~~vv~~l~  170 (202)
                      +.++||||+.++++.+|+|+|+++..+........   ...+++.||+.|+++||+++.  ....+.+.+||..+++.+.
T Consensus         4 i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~---~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~   78 (147)
T d1rila_           4 VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE---ACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFT   78 (147)
T ss_dssp             CCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE---EEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHH
T ss_pred             EEEEEccCCCCCCCccEEEEEEEECCcceEEeccc---ccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhcccc
Confidence            67999999999999999999998776654433222   245899999999999998754  4468999999999999885


Q ss_pred             cC-------------CCCcchHHHHHHHHHHHhhcCCceEEEeeC
Q 039849          171 NR-------------KGCKSEVFWTVVAIQASLKSLNRVQIQHVS  202 (202)
Q Consensus       171 ~~-------------~~~~s~~~~ii~~i~~l~~~f~~~~~~~V~  202 (202)
                      ..             ...+.....++.++..++.. ..++|.||+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~-~~v~~~wVk  122 (147)
T d1rila_          79 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVK  122 (147)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCC
T ss_pred             ccchhhhhhccccccccccchhHHHHHHHHHHhhh-cccceEEcc
Confidence            42             11122346788888887765 468888885