Citrus Sinensis ID: 042834

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNCLSSLLSQ
Secondary Structure (PSIPRED)
cccccccEEEEEcEEEEcccccEEEEEEEEcccccEEEEEEEEEEccccHHHHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEcccEccccccEEEEEEEEcccccEEEEccccccccccHHHHHHHHHHHHHHHHHHcccccEEEEccHHHHHHHHHccccHHHHHHc
Coil and Loop (DISEMBL)
tsppngwfkvNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNCLSSLLSQ
Flexible Loop (DISEMBL)
tsppngwfKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLarnrnclssllsq
Low Complexity Region (SEG)
TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNCLSSLLSQ
Disordered region (IsUnstruct)
*****GWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA************
Disordered Region (DISOPRED)
TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNC*******
Disordered Region (DISEMBL)
TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNCLSSLLSQ
Disordered Region (DISPRO)
*SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNC*S*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNCLSSLLSQ
Positional Conservation
no confident homologs detected

---

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	98
62732851	816	retrotransposon protein, putative, uncla	0.826	0.099	0.407	2e-09
222630057	653	hypothetical protein OsJ_16976 [Oryza sa	0.826	0.124	0.407	2e-09
125550682	653	hypothetical protein OsI_18290 [Oryza sa	0.826	0.124	0.407	2e-09
125536577	290	hypothetical protein OsI_38284 [Oryza sa	0.897	0.303	0.363	6e-09
218194367	262	hypothetical protein OsI_14903 [Oryza sa	0.826	0.309	0.432	2e-07
255564892	142	conserved hypothetical protein [Ricinus	0.867	0.598	0.413	2e-07
222623392	408	hypothetical protein OsJ_07834 [Oryza sa	0.785	0.188	0.389	3e-07
255564900	145	conserved hypothetical protein [Ricinus	0.887	0.6	0.431	3e-07
125574872	183	hypothetical protein OsJ_31602 [Oryza sa	0.826	0.442	0.382	4e-07
125549569	172	hypothetical protein OsI_17229 [Oryza sa	0.836	0.476	0.373	4e-07

>gi|62732851|gb|AAX94970.1| retrotransposon protein, putative, unclassified [Oryza sativa Japonica Group] gi|77550533|gb|ABA93330.1| retrotransposon protein, putative, unclassified [Oryza sativa Japonica Group]

 Score = 66.6 bits (161), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/81 (40%), Positives = 48/81 (59%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           PP GW K+NVD A  ++D T G+GVI RDS GKA+ ++ + +    D   +E  A   G+
Sbjct: 494 PPEGWAKINVDGAFSMTDNTGGIGVIARDSEGKALLSSWKYLHRCADAEQVEILACYEGM 553

Query: 63  QVAQNAKFLPIIVESDSKEVV 83
           ++A      PII+ESD   V+
Sbjct: 554 KLAAEWIRKPIILESDCVTVI 574

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222630057|gb|EEE62189.1| hypothetical protein OsJ_16976 [Oryza sativa Japonica Group]

 Score = 66.6 bits (161), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/81 (40%), Positives = 48/81 (59%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           PP GW K+NVD A  ++D T G+GVI RDS GKA+ ++ + +    D   +E  A   G+
Sbjct: 494 PPEGWAKINVDGAFSMTDNTGGIGVIARDSEGKALLSSWKYLHRCADAEQVEILACYEGM 553

Query: 63  QVAQNAKFLPIIVESDSKEVV 83
           ++A      PII+ESD   V+
Sbjct: 554 KLAAEWIRKPIILESDCVTVI 574

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125550682|gb|EAY96391.1| hypothetical protein OsI_18290 [Oryza sativa Indica Group]

 Score = 66.2 bits (160), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/81 (40%), Positives = 48/81 (59%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           PP GW K+NVD A  ++D T G+GVI RDS GKA+ ++ + +    D   +E  A   G+
Sbjct: 494 PPEGWAKINVDGAFSMTDNTGGIGVIARDSEGKALLSSWEYLHRCADAEQVEILACYEGM 553

Query: 63  QVAQNAKFLPIIVESDSKEVV 83
           ++A      PII+ESD   V+
Sbjct: 554 KLAAEWIRKPIILESDCITVI 574

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 64.7 bits (156), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 46/88 (52%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           P  GW K+NVD + + SD   G+G ++RDS G  + A    +   G     E  A   GI
Sbjct: 156 PSTGWMKLNVDGSFQASDGKGGIGAVLRDSSGNVIFAACGSMLVCGSAMEAELLACKEGI 215

Query: 63  QVAQNAKFLPIIVESDSKEVVDLARNRN 90
            +A    FLP IVE+D  EV +L +++ 
Sbjct: 216 AMALQWTFLPFIVETDCLEVFNLIQSKE 243

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218194367|gb|EEC76794.1| hypothetical protein OsI_14903 [Oryza sativa Indica Group]

 Score = 60.1 bits (144), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 46/81 (56%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           PP G  K+NVDA        AG G+I RD RG  + A  +K+S     A  EA A   G+
Sbjct: 152 PPEGVAKINVDAGFNKEMGEAGAGIIARDCRGLVLLAACKKLSRCSSAAQAEALACLEGV 211

Query: 63  QVAQNAKFLPIIVESDSKEVV 83
           Q+A N   +PII+ESD+ +VV
Sbjct: 212 QLAANWVQMPIILESDNADVV 232

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564892|ref|XP_002523439.1| conserved hypothetical protein [Ricinus communis] gi|223537267|gb|EEF38898.1| conserved hypothetical protein [Ricinus communis]

 Score = 59.3 bits (142), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/87 (41%), Positives = 53/87 (60%), Gaps = 2/87 (2%)

Query: 4   PNGW-FKVNVDAAI-KLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLG 61
           P+GW F++N DAA+ K +   +GLG+++RDS GK +AA    ++    V  +EA AV  G
Sbjct: 42  PSGWIFQINTDAALAKPTQGLSGLGLMVRDSPGKFLAAGSHHITQLLPVDIVEAMAVKEG 101

Query: 62  IQVAQNAKFLPIIVESDSKEVVDLARN 88
           I +A +   L  IV SDS E+V L  +
Sbjct: 102 IILAAHVNCLSAIVASDSSEIVKLIHS 128

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222623392|gb|EEE57524.1| hypothetical protein OsJ_07834 [Oryza sativa Japonica Group]

 Score = 59.3 bits (142), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 45/77 (58%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           PP GW K+NVD +   S   AG+G+I+R+S G+A+    Q ++   D    E  A   G+
Sbjct: 247 PPPGWSKLNVDGSFNNSSGQAGIGMILRNSEGEAIFTGRQAIANCVDALESELLACKFGL 306

Query: 63  QVAQNAKFLPIIVESDS 79
            +A +   LPII+E+DS
Sbjct: 307 DLALHWSILPIILETDS 323

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564900|ref|XP_002523443.1| conserved hypothetical protein [Ricinus communis] gi|223537271|gb|EEF38902.1| conserved hypothetical protein [Ricinus communis]

 Score = 58.9 bits (141), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 53/88 (60%), Gaps = 1/88 (1%)

Query: 2   SPPNGWFKVNVDAAI-KLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNL 60
           +P +G FK+N DAA+ K +   +GLG+++RDS GK +AA    +S    V  +EA AV  
Sbjct: 44  APLDGSFKINTDAALAKPTQGLSGLGLMVRDSPGKFLAAGSHHISQLLPVDIVEAMAVKE 103

Query: 61  GIQVAQNAKFLPIIVESDSKEVVDLARN 88
           GI +A +   L  IV SDS EVV L  +
Sbjct: 104 GIILAAHVNCLSAIVASDSSEVVRLIHS 131

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125574872|gb|EAZ16156.1| hypothetical protein OsJ_31602 [Oryza sativa Japonica Group]

 Score = 58.5 bits (140), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 45/81 (55%)

Query: 3   PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
           PP G  KVN+DA  +     A  G+I+RD RG  + A  +K+         EA A   G+
Sbjct: 61  PPEGMAKVNIDAGFRKETGDACAGIIVRDCRGLGLLAACKKLPRCSSATQAEALACLEGV 120

Query: 63  QVAQNAKFLPIIVESDSKEVV 83
           ++A N   +PII+ESD+ +VV
Sbjct: 121 RLATNWIHMPIILESDNADVV 141

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125549569|gb|EAY95391.1| hypothetical protein OsI_17229 [Oryza sativa Indica Group]

 Score = 58.5 bits (140), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 3  PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
          PP+GW K+NVD + +  + T G+G I+R+S G  + A    V         E  A   GI
Sbjct: 16 PPSGWMKLNVDGSYQ-ENNTGGIGAILRNSTGDVIFAVYGFVEQCQSALEAEILACKEGI 74

Query: 63 QVAQNAKFLPIIVESDSKEVVDL 85
          ++A     LPII+ESD  E + L
Sbjct: 75 RLALQWTLLPIIIESDCAEAIQL 97

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	98
TAIR|locus:2090215	343	AT3G25270 [Arabidopsis thalian	0.877	0.250	0.302	7e-05
TAIR|locus:2058379	221	AT2G04420 [Arabidopsis thalian	0.877	0.389	0.298	8e-05
TAIR|locus:1006230762	257	AT1G04625 [Arabidopsis thalian	0.908	0.346	0.288	0.00019
TAIR|locus:2039129	160	AT2G46460 [Arabidopsis thalian	0.897	0.55	0.280	0.00024
TAIR|locus:2040899	292	AT2G34320 [Arabidopsis thalian	0.857	0.287	0.273	0.0004
TAIR|locus:2119886	575	AT4G29090 [Arabidopsis thalian	0.948	0.161	0.236	0.00085

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

 Score = 102 (41.0 bits), Expect = 7.0e-05, P = 7.0e-05
 Identities = 26/86 (30%), Positives = 40/86 (46%)

Query:     3 PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
             PP+ W K N D A     + A  G ++RD  G  + +     S   D    E  A+ + +
Sbjct:   189 PPSTWIKYNYDGAFNHQTRNAKAGWLMRDENGVYMGSGQAIGSTTSDSLESEFQALIIAM 248

Query:    63 QVAQNAKFLPIIVESDSKEVVDLARN 88
             Q A +  +  +I E DSK+V +L  N
Sbjct:   249 QHAWSQGYRKVIFEGDSKQVEELMNN 274

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 = 98 (39.6 bits), Expect = 8.0e-05, P = 8.0e-05
 Identities = 26/87 (29%), Positives = 38/87 (43%)

Query:     3 PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
             PP GW K N D +     Q    G +IRD +G    A         +    E  A+ + +
Sbjct:    66 PPMGWIKCNYDGSFNYRTQQTNSGWLIRDDKGFYKGAAQAVGGTMNNALESELQALVMAM 125

Query:    63 QVAQNAKFLPIIVESDSKEVVDLARNR 89
             Q   +  +  +I E DSK+V +L  NR
Sbjct:   126 QHTWSQGYRKVIFEGDSKQVEELL-NR 151

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

TAIR|locus:1006230762 AT1G04625 [Arabidopsis thaliana (taxid:3702)]

 Score = 96 (38.9 bits), Expect = 0.00019, P = 0.00019
 Identities = 26/90 (28%), Positives = 42/90 (46%)

Query:     1 TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNL 60
             T+PP GW K N D     S+  +  G ++RD RG  + A     S   +    E  A+ +
Sbjct:    83 TTPPIGWTKCNYDGTYH-SNAPSKAGWLLRDDRGTFLGAAHAIGSITTNPMESELQALVM 141

Query:    61 GIQVAQNAKFLPIIVESDSKEVVDLARNRN 90
              +Q   +  +  I  E D+KEV ++   R+
Sbjct:   142 AMQHCWSRGYRKIYFEGDNKEVSEIVNGRS 171

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2039129 AT2G46460 [Arabidopsis thaliana (taxid:3702)]

 Score = 90 (36.7 bits), Expect = 0.00024, P = 0.00024
 Identities = 25/89 (28%), Positives = 42/89 (47%)

Query:     1 TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNL 60
             T PP+GW K N D +    +  +  G IIRD  G+ V+A     +   +    E  A+ +
Sbjct:     4 TRPPHGWKKCNYDGSYN-REMPSKAGWIIRDESGQFVSAGQATGNHTSNALESEFQALLI 62

Query:    61 GIQVAQNAKFLPIIVESDSKEVVDLARNR 89
              +Q   +     I  E D++EV+++   R
Sbjct:    63 TMQSCWSHGHRKIWFEGDNREVMEILNRR 91

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 94 (38.1 bits), Expect = 0.00040, P = 0.00040
 Identities = 23/84 (27%), Positives = 40/84 (47%)

Query:     2 SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLG 61
             +PP  W K N DA  +L +   G+G I+R+  G  +    + +    +V   E  A+   
Sbjct:   139 APPYQWVKCNTDATWQLENPRCGIGWILRNESGGVLWMGARALPRTKNVLEAELEALRWA 198

Query:    62 IQVAQNAKFLPIIVESDSKEVVDL 85
             +       +  II ESD++ +V+L
Sbjct:   199 VLTMSRFNYKRIIFESDAQALVNL 222

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 95 (38.5 bits), Expect = 0.00085, P = 0.00085
 Identities = 22/93 (23%), Positives = 43/93 (46%)

Query:     3 PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGI 62
             PP+ W K N DA     ++  G+G ++R+ +G+      + +     V   E  A+   +
Sbjct:   423 PPHQWVKCNTDATWNRDNERCGIGWVLRNEKGEVKWMGARALPKLKSVLEAELEAMRWAV 482

Query:    63 QVAQNAKFLPIIVESDSKEVVDLARNRNCLSSL 95
                   ++  +I ESDS+ ++++  N     SL
Sbjct:   483 LSLSRFQYNYVIFESDSQVLIEILNNDEIWPSL 515


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        0.316   0.130   0.357    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       98        98   0.00091  102 3  11 22  0.39    30
                                                     29  0.45    31


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:  6
  No. of states in DFA:  513 (55 KB)
  Total size of DFA:  91 KB (2067 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:  8.65u 0.16s 8.81t   Elapsed:  00:00:00
  Total cpu time:  8.65u 0.16s 8.81t   Elapsed:  00:00:00
  Start:  Sat May 11 04:05:07 2013   End:  Sat May 11 04:05:07 2013

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	98
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-10
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	7e-06

>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 = 53.1 bits (128), Expect = 2e-10
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 11 NVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKF 70
          N D + K +   AG G ++RD  G  + A    +         E  A+   +++A +   
Sbjct: 1  NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIP-AATNNEAELLALLEALELALDLGL 59

Query: 71 LPIIVESDSKEVVDLARNRNCLSSL 95
            +I+E+DSK VVDL  + +     
Sbjct: 60 KKLIIETDSKYVVDLINSWSKGWKK 84

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 = 40.2 bits (95), Expect = 7e-06
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 4/49 (8%)

Query: 54 EAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARN----RNCLSSLLSQ 98
          EA A+  G+Q+A       +IVESDS+ VV   +     R+ L++LL +
Sbjct: 6  EAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLRE 54

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	98
PRK13907	128	rnhA ribonuclease H; Provisional	99.85
PRK07708	219	hypothetical protein; Validated	99.77
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.72
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.72
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.68
PRK08719	147	ribonuclease H; Reviewed	99.48
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.43
PRK00203	150	rnhA ribonuclease H; Reviewed	99.42
PRK06548	161	ribonuclease H; Provisional	99.41
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.36
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	98.93
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.28
COG0295	134	Cdd Cytidine deaminase [Nucleotide transport and m	94.89
COG0590	152	CumB Cytosine/adenosine deaminases [Nucleotide tra	93.88
cd01285	109	nucleoside_deaminase Nucleoside deaminases include	92.61
cd01284	115	Riboflavin_deaminase-reductase Riboflavin-specific	91.89
TIGR01354	127	cyt_deam_tetra cytidine deaminase, homotetrameric.	91.83
cd00786	96	cytidine_deaminase-like Cytidine and deoxycytidyla	91.46
cd01283	112	cytidine_deaminase Cytidine deaminase zinc-binding	91.23
PF00383	102	dCMP_cyt_deam_1: Cytidine and deoxycytidylate deam	87.72
TIGR02571	151	ComEB ComE operon protein 2. This protein is found	86.83
PHA02588	168	cd deoxycytidylate deaminase; Provisional	84.03
PRK10860	172	tRNA-specific adenosine deaminase; Provisional	83.58
PF05830	321	NodZ: Nodulation protein Z (NodZ); InterPro: IPR00	82.03
PRK12411	132	cytidine deaminase; Provisional	80.63

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.85  E-value=5.1e-21  Score=118.23  Aligned_cols=82  Identities=16%  Similarity=0.114  Sum_probs=72.9

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA   86 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l   86 (98)
                      ++++|+|||+..+++.+|+|+|+||..|.+...+  . ....++++||++|+++||+++.++++.+|+|+|||+.|++.+
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--P-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAV   77 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEe--c-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHH
Confidence            5899999999999999999999999998776443  2 234689999999999999999999999999999999999999


Q ss_pred             hcCCC
Q 042834           87 RNRNC   91 (98)
Q Consensus        87 ~~~~~   91 (98)
                      ++...
T Consensus        78 ~~~~~   82 (128)
T PRK13907         78 EKEYA   82 (128)
T ss_pred             hHHHh
Confidence            98553

>PRK07708 hypothetical protein; Validated

Probab=99.77  E-value=5.3e-18  Score=113.44  Aligned_cols=92  Identities=17%  Similarity=0.099  Sum_probs=77.8

Q ss_pred             CCCceEEEEecceeecCCCcceEEEEEeCCCccEE--EeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCcc--EEEEec
Q 042834            3 PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAV--AATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLP--IIVESD   78 (98)
Q Consensus         3 P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i--~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~--v~~esD   78 (98)
                      +.+..+++|+|||+..+++.+|+|+|++++.|...  ......+....++++||+.|++.||++|.++|+++  |.|++|
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            34567999999999999999999999999877643  33344566667999999999999999999999976  899999


Q ss_pred             hHHHHHHHhcCCCCCc
Q 042834           79 SKEVVDLARNRNCLSS   94 (98)
Q Consensus        79 s~~vv~~l~~~~~~~s   94 (98)
                      |+.|++++++....++
T Consensus       149 SqlVi~qi~g~wk~~~  164 (219)
T PRK07708        149 SQVVLNQLAGEWPCYD  164 (219)
T ss_pred             cHHHHHHhCCCceeCC
Confidence            9999999998765544

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

Probab=99.72  E-value=8.1e-17  Score=102.22  Aligned_cols=79  Identities=18%  Similarity=0.136  Sum_probs=69.2

Q ss_pred             ceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHH
Q 042834            6 GWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDL   85 (98)
Q Consensus         6 g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~   85 (98)
                      ..+.+++|||+..+++.+|+|+|++...+..  ..+.... ..+++.+|++|+++||+++++.+.+.|.++|||+.|++.
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~--~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~   78 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEK--ELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEG   78 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceE--EEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHH
Confidence            3578999999999999999999999777666  2222333 568999999999999999999999999999999999999


Q ss_pred             Hh
Q 042834           86 AR   87 (98)
Q Consensus        86 l~   87 (98)
                      |+
T Consensus        79 i~   80 (154)
T COG0328          79 IT   80 (154)
T ss_pred             HH
Confidence            98

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.72  E-value=7e-17  Score=114.96  Aligned_cols=86  Identities=21%  Similarity=0.231  Sum_probs=74.8

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCcc-EEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGK-AVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDL   85 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~-~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~   85 (98)
                      .+++|+|||+..+++.+|+|+++|+++|. ++...+..+. ..++++||+.||+.||+++.+++.++|.|++||+.|++.
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            47899999999999999999999999764 5555555555 457789999999999999999999999999999999999


Q ss_pred             HhcCCCCC
Q 042834           86 ARNRNCLS   93 (98)
Q Consensus        86 l~~~~~~~   93 (98)
                      ++++...+
T Consensus        81 i~~~~~~~   88 (372)
T PRK07238         81 MSGRWKVK   88 (372)
T ss_pred             hCCCCccC
Confidence            99866433

>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=99.68  E-value=4.7e-16  Score=93.26  Aligned_cols=82  Identities=17%  Similarity=0.120  Sum_probs=74.1

Q ss_pred             EEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHHhc
Q 042834            9 KVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARN   88 (98)
Q Consensus         9 k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~   88 (98)
                      +|++|||+..+.+.+|+|+++++..+.+........ ...+++++|++|+++||+++...+.+++.|++||+.+++.+++
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            589999999888999999999999998887766544 5679999999999999999999999999999999999999998


Q ss_pred             CCC
Q 042834           89 RNC   91 (98)
Q Consensus        89 ~~~   91 (98)
                      ...
T Consensus        80 ~~~   82 (130)
T cd06222          80 WYE   82 (130)
T ss_pred             ccc
Confidence            653

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.

>PRK08719 ribonuclease H; Reviewed

Probab=99.48  E-value=4e-13  Score=85.10  Aligned_cols=78  Identities=22%  Similarity=0.276  Sum_probs=64.8

Q ss_pred             ceEEEEecceeecCCC---cceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHH
Q 042834            6 GWFKVNVDAAIKLSDQ---TAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEV   82 (98)
Q Consensus         6 g~~k~n~D~s~~~~~~---~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~v   82 (98)
                      ..+++++|||+..+++   .+|+|+++.+..|..+...+..+....+++.||+.|++.||+.+.+.    ..|.|||+.+
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            4588999999987765   68999999998887665444445555699999999999999998764    3799999999


Q ss_pred             HHHHh
Q 042834           83 VDLAR   87 (98)
Q Consensus        83 v~~l~   87 (98)
                      ++.++
T Consensus        79 i~~i~   83 (147)
T PRK08719         79 VRGFN   83 (147)
T ss_pred             HHHHH
Confidence            99995

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

Probab=99.43  E-value=3.3e-13  Score=77.35  Aligned_cols=47  Identities=38%  Similarity=0.292  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHHhcCCCCCccc
Q 042834           50 VAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNRNCLSSLL   96 (98)
Q Consensus        50 ~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~s~~   96 (98)
                      |++||++|+++||++|+++|+++|+|||||+.+|++++++...++++
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~   47 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSEL   47 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCC
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccc
Confidence            68999999999999999999999999999999999999997776654

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.42  E-value=1.5e-12  Score=82.61  Aligned_cols=77  Identities=16%  Similarity=0.095  Sum_probs=62.5

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA   86 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l   86 (98)
                      .+++++|||+..+++.+|+|+|++..++.....  .... ..++..||++|+..||+.+.+.  ..|.|.|||+.+++.|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~--~~~~-~~TN~~aEL~Ai~~AL~~~~~~--~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELS--GGEA-LTTNNRMELMAAIEALEALKEP--CEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEe--cCCC-CCcHHHHHHHHHHHHHHHcCCC--CeEEEEECHHHHHHHH
Confidence            488999999999999999999998755443222  2233 4588999999999999988653  5799999999999998


Q ss_pred             hc
Q 042834           87 RN   88 (98)
Q Consensus        87 ~~   88 (98)
                      +.
T Consensus        78 ~~   79 (150)
T PRK00203         78 TE   79 (150)
T ss_pred             HH
Confidence            85

>PRK06548 ribonuclease H; Provisional

Probab=99.41  E-value=2.9e-12  Score=82.23  Aligned_cols=75  Identities=16%  Similarity=0.043  Sum_probs=60.3

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA   86 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l   86 (98)
                      .+.+++||++.++++.+|+|+++.+. + ..   +.. ....+++.||++|+++||+.+. ....+|.|.|||+.+++.+
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~~-~-~~---~g~-~~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i   77 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDEN-T-WD---SGG-WDIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSL   77 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeCC-c-EE---ccC-CCCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHH
Confidence            48999999999999999999999853 2 21   111 2346899999999999998554 4556899999999999999


Q ss_pred             hc
Q 042834           87 RN   88 (98)
Q Consensus        87 ~~   88 (98)
                      +.
T Consensus        78 ~~   79 (161)
T PRK06548         78 TK   79 (161)
T ss_pred             HH
Confidence            83

>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=99.36  E-value=1.2e-11  Score=75.92  Aligned_cols=74  Identities=12%  Similarity=0.155  Sum_probs=58.8

Q ss_pred             ceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHH
Q 042834            6 GWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDL   85 (98)
Q Consensus         6 g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~   85 (98)
                      .-+.+++|||+..+++.+|+|+|+.+.  .   ..+..++ ..++..||++|+.+||+ +. .. ++|.|.|||+.+++.
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~--~---~~~~~~~-~~s~~~aEl~Ai~~AL~-~~-~~-~~v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG--R---NFSFRLG-GQSNNRAELQAIIEALK-AL-EH-RKVTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT--E---EEEEEEE-SECHHHHHHHHHHHHHH-TH-ST-SEEEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC--e---EEEeccc-ccchhhhheehHHHHHH-Hh-hc-ccccccccHHHHHHH
Confidence            357899999999999999999977443  2   2233344 56899999999999999 55 22 999999999999998


Q ss_pred             Hhc
Q 042834           86 ARN   88 (98)
Q Consensus        86 l~~   88 (98)
                      +++
T Consensus        73 l~~   75 (132)
T PF00075_consen   73 LNK   75 (132)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            887

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=98.93  E-value=6.7e-09  Score=73.63  Aligned_cols=80  Identities=16%  Similarity=0.138  Sum_probs=63.3

Q ss_pred             ceEEEEecceeecCC---CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHH
Q 042834            6 GWFKVNVDAAIKLSD---QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEV   82 (98)
Q Consensus         6 g~~k~n~D~s~~~~~---~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~v   82 (98)
                      +...+++||++..+.   ..+|+|+.+=+  |.-........++..+++.||+.|+.+||+-|++....+|.|-|||..+
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~--~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~  288 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGP--GHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYF  288 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCC--CCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHH
Confidence            447799999999753   34777777754  3333333322336779999999999999999999999999999999999


Q ss_pred             HHHHh
Q 042834           83 VDLAR   87 (98)
Q Consensus        83 v~~l~   87 (98)
                      ++.|+
T Consensus       289 i~~l~  293 (371)
T KOG3752|consen  289 INSLT  293 (371)
T ss_pred             HHHHH
Confidence            99987

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

Probab=95.28  E-value=0.015  Score=42.23  Aligned_cols=69  Identities=19%  Similarity=0.142  Sum_probs=51.1

Q ss_pred             CcceEEEEEeCC-CccEEEeeeeeec--ccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHHhcC
Q 042834           21 QTAGLGVIIRDS-RGKAVAATVQKVS--FRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLARNR   89 (98)
Q Consensus        21 ~~~g~G~vird~-~G~~i~~~~~~~~--~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~   89 (98)
                      ..+|.|+.+.|+ +............  ...+++.||++|+..+|..+.++++.++.+.+|...+...+..+
T Consensus        17 ~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~   88 (384)
T KOG1812|consen   17 LLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGR   88 (384)
T ss_pred             hcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhh
Confidence            468899999886 4443332222222  22579999999999999999999999999999977776655544

>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]

Probab=94.89  E-value=0.24  Score=31.04  Aligned_cols=69  Identities=17%  Similarity=0.220  Sum_probs=53.3

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec----------hHHHHHHHhcCC
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD----------SKEVVDLARNRN   90 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD----------s~~vv~~l~~~~   90 (98)
                      ...-+|.++|..+|++..+..--......-..||-.|+..++.- -...+..|.+.+|          |.+++.-+....
T Consensus        24 S~F~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~~~~~sPCG~CRQ~i~Ef~~~d  102 (134)
T COG0295          24 SKFKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADTGKPVSPCGACRQVLAEFCGDD  102 (134)
T ss_pred             cCCcEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCCCCCcCCcHHHHHHHHHhcCCC
Confidence            45678999999999988876655555566789999999999887 5666788899888          677776666544

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

Probab=93.88  E-value=0.24  Score=31.52  Aligned_cols=57  Identities=16%  Similarity=0.159  Sum_probs=40.7

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeeccc-CCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFR-GDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~-~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      +...+|.||-+.+|.++.......... .-..+||..||+.|-+......+....+++
T Consensus        26 ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyv   83 (152)
T COG0590          26 GEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYV   83 (152)
T ss_pred             CCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEE
Confidence            456789999999998888665543333 233599999999999888665555555543

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

Probab=92.61  E-value=0.67  Score=27.56  Aligned_cols=44  Identities=23%  Similarity=0.252  Sum_probs=32.4

Q ss_pred             CcceEEEEEeCCCccEEEeeeeee-cccCCHHHHHHHHHHHHHHH
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKV-SFRGDVAYMEAAAVNLGIQV   64 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~aL~~   64 (98)
                      +...+|.+|.|.+|+++..+.... .......+||..|+..+.+.
T Consensus        15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~   59 (109)
T cd01285          15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARR   59 (109)
T ss_pred             CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHH
Confidence            456789999998899887655443 22345689999999887664

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

>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase

Probab=91.89  E-value=0.8  Score=27.78  Aligned_cols=41  Identities=17%  Similarity=0.204  Sum_probs=31.4

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHH
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQV   64 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~   64 (98)
                      +..-+|.||-+.+|+++........   ...+||..||..+.+.
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            4567888998888998887665433   5689999999888763

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.

>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric

Probab=91.83  E-value=0.5  Score=29.12  Aligned_cols=57  Identities=16%  Similarity=0.180  Sum_probs=40.0

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      ....+|.++++.+|+++.+...-.........||..|+..+...- +..+..|.+-.+
T Consensus        19 S~~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g-~~~i~~i~vv~~   75 (127)
T TIGR01354        19 SNFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAG-YRKFVAIAVADS   75 (127)
T ss_pred             CCCeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcC-CCCeEEEEEEeC
Confidence            356789999999999988665444334456799999998888652 235667777543

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.

>cd00786 cytidine_deaminase-like Cytidine and deoxycytidylate deaminase zinc-binding region

Probab=91.46  E-value=1.3  Score=25.67  Aligned_cols=44  Identities=11%  Similarity=0.026  Sum_probs=29.2

Q ss_pred             CCcceEEEEEeCC-CccEEEeeeee-ecccCCHHHHHHHHHHHHHH
Q 042834           20 DQTAGLGVIIRDS-RGKAVAATVQK-VSFRGDVAYMEAAAVNLGIQ   63 (98)
Q Consensus        20 ~~~~g~G~vird~-~G~~i~~~~~~-~~~~~~~~~aE~~Al~~aL~   63 (98)
                      .+...+|.++.+. +|..+..+... ........+||..|++.+..
T Consensus        15 ~~~~pVGaviv~~~~g~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~   60 (96)
T cd00786          15 ESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS   60 (96)
T ss_pred             CCCCCEEEEEEEeCCCCeEeeeEeccCCCCCCeeCHHHHHHHHHHH
Confidence            3567788888876 57776654432 22233558999999987754

The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. 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.

>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain

Probab=91.23  E-value=0.77  Score=27.32  Aligned_cols=45  Identities=11%  Similarity=0.103  Sum_probs=34.1

Q ss_pred             CCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHH
Q 042834           20 DQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQV   64 (98)
Q Consensus        20 ~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~   64 (98)
                      .+...+|.++++.+|.++.+............+||..|+..+...
T Consensus        15 ~~~~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~~   59 (112)
T cd01283          15 YSNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSE   59 (112)
T ss_pred             CCCCeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHHc
Confidence            356788999998889988766655544556789999999887753

These enzymes are Zn dependent. 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. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.

>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3

Probab=87.72  E-value=1.1  Score=25.86  Aligned_cols=46  Identities=17%  Similarity=0.154  Sum_probs=30.4

Q ss_pred             CCCcceEEEEEeCCCccEEEeeeeeec-ccCCHHHHHHHHHHHHHHH
Q 042834           19 SDQTAGLGVIIRDSRGKAVAATVQKVS-FRGDVAYMEAAAVNLGIQV   64 (98)
Q Consensus        19 ~~~~~g~G~vird~~G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~~   64 (98)
                      ..+...+|.+|.+++|..+..+..... ......+||..|+..+-+.
T Consensus        20 ~~~~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~   66 (102)
T PF00383_consen   20 PCGNFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN   66 (102)
T ss_dssp             TTTSSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT
T ss_pred             ccCCCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh
Confidence            346778999999977666665544332 2223469999998877765

5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....

>TIGR02571 ComEB ComE operon protein 2

Probab=86.83  E-value=3.3  Score=26.34  Aligned_cols=67  Identities=13%  Similarity=0.048  Sum_probs=40.7

Q ss_pred             cceEEEEEeCCCccEEEeeeeeeccc----------------CCHHHHHHHHHHHHH----------------------H
Q 042834           22 TAGLGVIIRDSRGKAVAATVQKVSFR----------------GDVAYMEAAAVNLGI----------------------Q   63 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~~~~~----------------~~~~~aE~~Al~~aL----------------------~   63 (98)
                      ...+|.||.. +|++|..+....+.-                ....+||..||+.+.                      .
T Consensus        24 ~~~VGAVIV~-d~~IIs~GyN~~~~g~~~~~~~~~~~~~~~~~~~~HAE~nAI~~a~~~~~~l~g~tlYvT~ePC~~Ca~  102 (151)
T TIGR02571        24 RLSVGATIVR-DKRIIAGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQCAKFGVSTEGAEIYVTHFPCLQCTK  102 (151)
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCccccccccccccccCCccCHHHHHHHHHHhcCCCcCCcEEEEeCCCcHHHHH
Confidence            4567777774 578887665543221                123699999998763                      3


Q ss_pred             HHHHCCCccEEEEec---hHHHHHHHhcC
Q 042834           64 VAQNAKFLPIIVESD---SKEVVDLARNR   89 (98)
Q Consensus        64 ~a~~~g~~~v~~esD---s~~vv~~l~~~   89 (98)
                      .+...|+.+|++-.+   ...-.+.|...
T Consensus       103 ai~~agI~~Vvy~~~~~~~~~~~~~l~~~  131 (151)
T TIGR02571       103 SIIQAGIKKIYYAQDYHNHPYAIELFEQA  131 (151)
T ss_pred             HHHHhCCCEEEEccCCCCcHHHHHHHHHC
Confidence            445668888887532   22344555443

This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.

>PHA02588 cd deoxycytidylate deaminase; Provisional

Probab=84.03  E-value=9.1  Score=24.74  Aligned_cols=29  Identities=7%  Similarity=0.035  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHH----------------------HHHHHCCCccEEEEec
Q 042834           50 VAYMEAAAVNLGI----------------------QVAQNAKFLPIIVESD   78 (98)
Q Consensus        50 ~~~aE~~Al~~aL----------------------~~a~~~g~~~v~~esD   78 (98)
                      ..+||..||+.+-                      ..+...|+.+|++-.+
T Consensus        81 ~~HAE~nAi~~a~~~~~~~~g~tLYvTlePC~~Ca~aI~~~gI~rVvy~~~  131 (168)
T PHA02588         81 EIHAELNAILFAARNGISIEGATMYVTASPCPDCAKAIAQSGIKKLVYCEK  131 (168)
T ss_pred             CccHHHHHHHHHhhcCCCCCCcEEEEeCCCcHHHHHHHHHhCCCEEEEeec
Confidence            5699999998873                      3445668888887654

>PRK10860 tRNA-specific adenosine deaminase; Provisional

Probab=83.58  E-value=4.4  Score=26.35  Aligned_cols=41  Identities=12%  Similarity=0.134  Sum_probs=27.7

Q ss_pred             cceEEEEEeCCCccEEEeeeeeec-ccCCHHHHHHHHHHHHHH
Q 042834           22 TAGLGVIIRDSRGKAVAATVQKVS-FRGDVAYMEAAAVNLGIQ   63 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~   63 (98)
                      ..-+|.||-+ +|++|..+..... ......+||..|++.+.+
T Consensus        32 ~~pvGAVIV~-~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~   73 (172)
T PRK10860         32 EVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGL   73 (172)
T ss_pred             CCCEEEEEEe-CCEEEEEeeCCCCCCCCCccCHHHHHHHHHHH
Confidence            4567888886 5888876554422 222346999999998865

>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation

Probab=82.03  E-value=4.4  Score=28.98  Aligned_cols=66  Identities=24%  Similarity=0.298  Sum_probs=30.9

Q ss_pred             CCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHC---CCccEEEEechHHHHHHHhcC
Q 042834           20 DQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNA---KFLPIIVESDSKEVVDLARNR   89 (98)
Q Consensus        20 ~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~---g~~~v~~esDs~~vv~~l~~~   89 (98)
                      .+..-+|+-||-.+|+-+..-...+.   +...+ +.-+..++.-++.+   .-.+|.+-|||+.|++.+++.
T Consensus       165 ~g~~~IGVHVRhGngeD~~~h~~~~~---D~e~~-L~~V~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~  233 (321)
T PF05830_consen  165 AGYSVIGVHVRHGNGEDIMDHAPYWA---DEERA-LRQVCTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKK  233 (321)
T ss_dssp             TTSEEEEEEE---------------H---HHHHH-HHHHHHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHH
T ss_pred             CCCceEEEEEeccCCcchhccCcccc---CchHH-HHHHHHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHH
Confidence            35667999999877765444332221   21111 22233455555443   346799999999999999864

NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.

>PRK12411 cytidine deaminase; Provisional

Probab=80.63  E-value=6.5  Score=24.45  Aligned_cols=57  Identities=16%  Similarity=0.190  Sum_probs=39.8

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      ....+|..++..+|++..+..--.....-..-||..|+..++.. -+..+..|.+-++
T Consensus        22 S~~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~-g~~~i~~i~v~~~   78 (132)
T PRK12411         22 SKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVAD   78 (132)
T ss_pred             cCCceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHC-CCCceEEEEEEeC
Confidence            45678999999999998876643333334578999998887643 2335677777665

---

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	98
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	6e-05

>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 = 38.4 bits (90), Expect = 6e-05
 Identities = 16/77 (20%), Positives = 27/77 (35%)

Query: 8  FKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQN 67
            +  D   + +   AG G ++  +    V A  ++   R      E   +  G+  A  
Sbjct: 4  VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63

Query: 68 AKFLPIIVESDSKEVVD 84
                 V  DSK VV+
Sbjct: 64 LGATEAAVLMDSKLVVE 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	98
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.83
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.83
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.83
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.82
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.79
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.72
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.7
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.68
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.63
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.62
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.6
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.59
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.58
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.47
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.36
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.34
1uwz_A	136	Cytidine deaminase; CDD, tetramer, zinc binding, p	94.42
2fr5_A	146	Cytidine deaminase; tetrahydrouridine, protein-inh	93.58
2b3j_A	159	TRNA adenosine deaminase; mixed alpha-beta, protei	90.86
2z3g_A	130	Blasticidin-S deaminase; hydrolase, cytidine deami	90.77
2a8n_A	144	Cytidine and deoxycytidylate deaminase; RNA editin	90.68
2nx8_A	179	TRNA-specific adenosine deaminase; TAD, hydrolase;	90.32
1wwr_A	171	TRNA adenosine deaminase TADA; homodimer, riken st	89.84
1r5t_A	142	Cytidine deaminase; zinc dependent deaminase, RNA	88.5
2d30_A	141	Cytidine deaminase; purines, pyrimidines, nucleosi	87.99
1z3a_A	168	TRNA-specific adenosine deaminase; tRNA adenosine	87.63
1wkq_A	164	Guanine deaminase; domain SWAP, the cytidine deami	86.86
3dh1_A	189	TRNA-specific adenosine deaminase 2; zinc-binding	86.47
2w4l_A	178	DCMP deaminse, deoxycytidylate deaminase; pyrimidi	86.13
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	85.79
1p6o_A	161	Cytosine deaminase; hydrolase, dimer, inhibitor bo	84.58
3r2n_A	138	Cytidine deaminase; structural genomics, seattle s	84.08
2g84_A	197	Cytidine and deoxycytidylate deaminase zinc-bindi;	82.67
3mpz_A	150	Cytidine deaminase; ssgcid, structu genomics, seat	82.29

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

Probab=99.83  E-value=5.7e-20  Score=113.17  Aligned_cols=85  Identities=18%  Similarity=0.147  Sum_probs=76.9

Q ss_pred             ceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCc----cEEEEechHH
Q 042834            6 GWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFL----PIIVESDSKE   81 (98)
Q Consensus         6 g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~----~v~~esDs~~   81 (98)
                      ..+++|+|||+..+++.+|+|+++++++|..+...+..++. .+++.||+.|++.||+++.+.+.+    +|.|+|||+.
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 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGE-TTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEE-ECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCC-CchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            36899999999999999999999999999988777776655 589999999999999999999999    9999999999


Q ss_pred             HHHHHhcCCC
Q 042834           82 VVDLARNRNC   91 (98)
Q Consensus        82 vv~~l~~~~~   91 (98)
                      +++.+++...
T Consensus        81 vi~~i~~~~~   90 (140)
T 3u3g_D           81 IVRQMQGVYK   90 (140)
T ss_dssp             HHHHHTTSSC
T ss_pred             HHHHhCCCcc
Confidence            9999998543

>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=99.83  E-value=1.1e-20  Score=118.07  Aligned_cols=86  Identities=12%  Similarity=0.142  Sum_probs=74.0

Q ss_pred             CCCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechH
Q 042834            1 TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSK   80 (98)
Q Consensus         1 ~~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~   80 (98)
                      .||+.+++++|+|||+..+++.+|+|+|++ .+|..+... ..+. ..+++.||++|++.||+.+.+.+. +|.|+|||+
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-KTGEVLFER-EPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQ   80 (142)
T ss_dssp             ---CCCSSSEEEEEEECSSSEEEEEEEEET-TTCCEEEEC-CCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCH
T ss_pred             CCCCCCeEEEEEeeccCCCCCCeEEEEEEE-eCCEEEEEe-cccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehH
Confidence            478899999999999999999999999999 678776543 3344 458999999999999999999999 999999999


Q ss_pred             HHHHHHhcCC
Q 042834           81 EVVDLARNRN   90 (98)
Q Consensus        81 ~vv~~l~~~~   90 (98)
                      .|++++++..
T Consensus        81 ~vi~w~~~~~   90 (142)
T 1zbf_A           81 TAIKWVKDKK   90 (142)
T ss_dssp             HHHHHHHHTC
T ss_pred             HHHHHHHcCC
Confidence            9999999865

>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=99.83  E-value=5.6e-20  Score=113.62  Aligned_cols=83  Identities=20%  Similarity=0.195  Sum_probs=74.4

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCC-ccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSR-GKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDL   85 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~-G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~   85 (98)
                      .+++|+|||+..+++.+|+|++++++. |.++...+...+ ..+++.||+.|++.||+++.+++.++|.|+|||+.|++.
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            589999999999999999999999987 777766666554 468999999999999999999999999999999999999


Q ss_pred             HhcCC
Q 042834           86 ARNRN   90 (98)
Q Consensus        86 l~~~~   90 (98)
                      +++..
T Consensus        82 i~~~~   86 (141)
T 3hst_B           82 MSGRW   86 (141)
T ss_dssp             HTTSS
T ss_pred             HhCCc
Confidence            99854

>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=1.1e-19  Score=113.69  Aligned_cols=85  Identities=9%  Similarity=0.021  Sum_probs=73.3

Q ss_pred             eEEEEecceee-cCCCcceE-EEEEeCCCccEEEeeeeeec---ccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHH
Q 042834            7 WFKVNVDAAIK-LSDQTAGL-GVIIRDSRGKAVAATVQKVS---FRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKE   81 (98)
Q Consensus         7 ~~k~n~D~s~~-~~~~~~g~-G~vird~~G~~i~~~~~~~~---~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~   81 (98)
                      ++++|+|||+. .+++.+|+ |+++++ +|..+........   ...++++||+.|++.||+++.+++.++|.|+|||+.
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            57999999999 68899996 999999 8888755443333   367899999999999999999999999999999999


Q ss_pred             HHHHHhcCCCC
Q 042834           82 VVDLARNRNCL   92 (98)
Q Consensus        82 vv~~l~~~~~~   92 (98)
                      +++.+++....
T Consensus        80 vi~~i~~~w~~   90 (149)
T 2ehg_A           80 VIKQMNGEYKV   90 (149)
T ss_dssp             HHHHHTTSSCC
T ss_pred             HHHHHhCcccc
Confidence            99999986443

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

Probab=99.79  E-value=7.3e-19  Score=110.74  Aligned_cols=84  Identities=18%  Similarity=0.162  Sum_probs=72.2

Q ss_pred             CCCCceEEEEecceeecCCC---cceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834            2 SPPNGWFKVNVDAAIKLSDQ---TAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus         2 ~P~~g~~k~n~D~s~~~~~~---~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      +|+.+++++|+|||+..+++   .+|+|+++++..+..+.   ..+....+++.||+.|++.||+++.+.+.++|.|+||
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            68889999999999998765   48999999987654332   2344457899999999999999999999999999999


Q ss_pred             hHHHHHHHhc
Q 042834           79 SKEVVDLARN   88 (98)
Q Consensus        79 s~~vv~~l~~   88 (98)
                      |+.+++.|++
T Consensus        79 S~~vi~~i~~   88 (154)
T 2qkb_A           79 SMFTINGITN   88 (154)
T ss_dssp             CHHHHHHHHT
T ss_pred             cHHHHhhhhh
Confidence            9999999986

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

Probab=99.72  E-value=6.8e-18  Score=107.71  Aligned_cols=83  Identities=13%  Similarity=0.081  Sum_probs=67.0

Q ss_pred             CCCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechH
Q 042834            1 TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSK   80 (98)
Q Consensus         1 ~~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~   80 (98)
                      +||+.+.+++|+|||+..+++.+|+|+|+++..+......  .. ...+++.||+.|++.||+.+.+.  .+|.|+|||+
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            5888899999999999998899999999998665443322  23 34589999999999999988765  5899999999


Q ss_pred             HHHHHHhc
Q 042834           81 EVVDLARN   88 (98)
Q Consensus        81 ~vv~~l~~   88 (98)
                      .+++.|++
T Consensus        77 ~vi~~i~~   84 (166)
T 1ril_A           77 YLKKAFTE   84 (166)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHHhh
Confidence            99999998

>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=99.70  E-value=5.9e-17  Score=100.13  Aligned_cols=81  Identities=12%  Similarity=0.144  Sum_probs=68.3

Q ss_pred             CceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHH
Q 042834            5 NGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVD   84 (98)
Q Consensus         5 ~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~   84 (98)
                      .....+|+|||+..+++.+|+|+|+++ .|..+... ..+. ..+++.||++|++.||+.+.+.+.+ |.++|||+.|++
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~-~g~~~~~~-g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~   78 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTK-TGEVLFER-EPIP-IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIK   78 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETT-TCCEEEEE-EEEE-EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEE-CCEEEEEe-cCCC-CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHH
Confidence            345678999999999999999888888 66655443 3343 4689999999999999999998876 899999999999


Q ss_pred             HHhcC
Q 042834           85 LARNR   89 (98)
Q Consensus        85 ~l~~~   89 (98)
                      .+++.
T Consensus        79 wi~~~   83 (134)
T 4htu_A           79 WVKDK   83 (134)
T ss_dssp             HHHHT
T ss_pred             HHHcC
Confidence            99974

>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=99.68  E-value=2.5e-16  Score=99.04  Aligned_cols=78  Identities=21%  Similarity=0.220  Sum_probs=67.1

Q ss_pred             CCCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechH
Q 042834            1 TSPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSK   80 (98)
Q Consensus         1 ~~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~   80 (98)
                      +.|+.+++++|+|||+..+++.+|+|+|+++..+..+.     . ...+++.||+.|++.||+.+   + .+|.|+|||+
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            36899999999999999999999999999986554331     2 34689999999999999984   3 8999999999


Q ss_pred             HHHHHHhc
Q 042834           81 EVVDLARN   88 (98)
Q Consensus        81 ~vv~~l~~   88 (98)
                      .+++.+++
T Consensus        76 ~v~~~i~~   83 (150)
T 3qio_A           76 YALGIITQ   83 (150)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999986

>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=99.63  E-value=7.9e-16  Score=97.03  Aligned_cols=77  Identities=16%  Similarity=0.155  Sum_probs=64.9

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA   86 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l   86 (98)
                      .+++|+|||+..+++.+|+|+++++..+.....  .... ..+++.||+.|++.||+++.+.  .+|.|+|||+.+++.|
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~--~~~~-~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i   78 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFS--AGYT-RTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGI   78 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEE--EEEE-EECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEe--cCCC-CCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHH
Confidence            589999999999989999999999866543332  2333 4589999999999999998764  8999999999999999


Q ss_pred             hc
Q 042834           87 RN   88 (98)
Q Consensus        87 ~~   88 (98)
                      ++
T Consensus        79 ~~   80 (155)
T 1jl1_A           79 TQ   80 (155)
T ss_dssp             HT
T ss_pred             HH
Confidence            97

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

Probab=99.62  E-value=1.7e-15  Score=94.46  Aligned_cols=78  Identities=15%  Similarity=0.118  Sum_probs=65.7

Q ss_pred             ceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHH
Q 042834            6 GWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDL   85 (98)
Q Consensus         6 g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~   85 (98)
                      ..+++|+|||+..+++.+|+|+++++....  ...+...+ ..+++.||+.|++.||+.+.+  ..+|.|+|||+.+++.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~--~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~   77 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSR--KEISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNA   77 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEE--EEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCee--EEeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHH
Confidence            468999999999999999999999986533  33333343 458999999999999999876  5899999999999999


Q ss_pred             Hhc
Q 042834           86 ARN   88 (98)
Q Consensus        86 l~~   88 (98)
                      |++
T Consensus        78 i~~   80 (146)
T 3h08_A           78 MNE   80 (146)
T ss_dssp             HHS
T ss_pred             HHH
Confidence            987

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

Probab=99.60  E-value=2.3e-15  Score=95.17  Aligned_cols=78  Identities=15%  Similarity=0.127  Sum_probs=64.5

Q ss_pred             ceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHH
Q 042834            6 GWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDL   85 (98)
Q Consensus         6 g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~   85 (98)
                      ..+++|+|||+..+++.+|+|+|+++.....  ..+...+ ..+++.||+.|++.||+.+.+.  .+|.|+|||+.+++.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~--~~~~~~~-~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTK--EMSDGFS-LTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQG   79 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEE--EEEEEEE-EECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEE--EEecCcC-CCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHH
Confidence            4689999999999889999999999854322  2333333 3589999999999999998654  899999999999999


Q ss_pred             Hhc
Q 042834           86 ARN   88 (98)
Q Consensus        86 l~~   88 (98)
                      |++
T Consensus        80 i~~   82 (158)
T 2e4l_A           80 IMT   82 (158)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            988

>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=99.59  E-value=1.4e-15  Score=95.24  Aligned_cols=83  Identities=16%  Similarity=0.031  Sum_probs=65.9

Q ss_pred             CCCceEEEEecceeecCCCcceEEEEEeCCCccEE-Eee-eeeecc--cCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834            3 PPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAV-AAT-VQKVSF--RGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus         3 P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i-~~~-~~~~~~--~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      .+.+.+++|+|||+..  +.+|+|+++++ +|... ... ....+.  ..+++.||+.|++.||+++.+.+. +|.|+||
T Consensus         2 ~~~~~i~iytDGs~~~--g~~G~G~vi~~-~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tD   77 (147)
T 2kq2_A            2 DDRTEYDVYTDGSYVN--GQYAWAYAFVK-DGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHD   77 (147)
T ss_dssp             CTTSCCEEECCCCCBT--TBCEEEEEEEE-TTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSC
T ss_pred             CCCCeEEEEECCCCCC--CCcEEEEEEEE-CCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEEC
Confidence            3567899999999987  89999999998 55532 222 111122  358999999999999999999998 9999999


Q ss_pred             hHHHHHHHhcC
Q 042834           79 SKEVVDLARNR   89 (98)
Q Consensus        79 s~~vv~~l~~~   89 (98)
                      |+.+.+++++.
T Consensus        78 S~~i~~w~~~~   88 (147)
T 2kq2_A           78 YAGIAFWATGE   88 (147)
T ss_dssp             CSTHHHHTTSS
T ss_pred             cHHHHHHHhCC
Confidence            99988887764

>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=99.58  E-value=1.8e-14  Score=91.89  Aligned_cols=80  Identities=15%  Similarity=0.128  Sum_probs=65.2

Q ss_pred             CCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHH
Q 042834            2 SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKE   81 (98)
Q Consensus         2 ~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~   81 (98)
                      |++...+++|+|||+..+++.+|+|+++++. |..+.. . ......+++.||+.|++.||+++   ...+|.|.|||+.
T Consensus        18 P~~~~~i~iytDGs~~~npG~~g~G~vi~~~-~~~~~~-~-~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~   91 (165)
T 3p1g_A           18 PIPDADYTWYTDGSSFLQEGQRRAGAAVTTE-TEVIWA-R-ALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRY   91 (165)
T ss_dssp             CCTTCSEEEEEEEEEEEETTEEEEEEEEECS-SCEEEE-E-EECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHH
T ss_pred             CCCCCCEEEEEEcccCCCCCceEEEEEEEEC-CEEEEE-e-cCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHH
Confidence            3444469999999999999999999999884 554432 2 33455689999999999999998   3689999999999


Q ss_pred             HHHHHh
Q 042834           82 VVDLAR   87 (98)
Q Consensus        82 vv~~l~   87 (98)
                      +++.+.
T Consensus        92 vi~~iw   97 (165)
T 3p1g_A           92 AFATAH   97 (165)
T ss_dssp             HHHHHH
T ss_pred             HHhhhh
Confidence            999884

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

Probab=99.47  E-value=1.1e-12  Score=83.68  Aligned_cols=82  Identities=20%  Similarity=0.109  Sum_probs=63.6

Q ss_pred             CceEEEEecceeecCCCc-----ceEEEEEeCCC--ccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834            5 NGWFKVNVDAAIKLSDQT-----AGLGVIIRDSR--GKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus         5 ~g~~k~n~D~s~~~~~~~-----~g~G~vird~~--G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      ...+.+|||||+..+++.     +|+|++++...  ..+....... ....+.+.||+.||..+|+.+...+ .+|.|.|
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~-tnn~te~~Aei~Al~~al~~al~~~-~~v~I~T   82 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIP-LGNHTAQMAEIAAVEFACKKALKIP-GPVLVIT   82 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEE-ESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEE
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCC-chHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEe
Confidence            446789999999998875     89999998543  3333333322 2345788999999999999988876 4799999


Q ss_pred             chHHHHHHHhc
Q 042834           78 DSKEVVDLARN   88 (98)
Q Consensus        78 Ds~~vv~~l~~   88 (98)
                      ||+.|++.++.
T Consensus        83 DS~Yvi~~it~   93 (165)
T 2lsn_A           83 DSFYVAESANK   93 (165)
T ss_dssp             SCHHHHHHHHT
T ss_pred             ChHHHHhhhhh
Confidence            99999999974

>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=99.36  E-value=2.3e-12  Score=94.81  Aligned_cols=78  Identities=21%  Similarity=0.212  Sum_probs=65.6

Q ss_pred             CCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHH
Q 042834            2 SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKE   81 (98)
Q Consensus         2 ~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~   81 (98)
                      .|..+.+++++|||+..+++.+|+|+++++.....+     .. ...+++.||+.|++.||+.+    .++|.+.|||+.
T Consensus       434 ep~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~-----~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~  503 (557)
T 2zd1_A          434 EPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVV-----PL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQY  503 (557)
T ss_dssp             SCCTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHH
T ss_pred             CCCCCCEEEEEccCCCCCCCceEEEEEEECCcEEEe-----cC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHH
Confidence            366788999999999999999999999986543333     12 34589999999999999998    689999999999


Q ss_pred             HHHHHhcC
Q 042834           82 VVDLARNR   89 (98)
Q Consensus        82 vv~~l~~~   89 (98)
                      |++.+++.
T Consensus       504 vi~~i~~~  511 (557)
T 2zd1_A          504 ALGIIQAQ  511 (557)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHhcC
Confidence            99999874

>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=99.34  E-value=4.5e-12  Score=93.23  Aligned_cols=77  Identities=14%  Similarity=0.141  Sum_probs=65.3

Q ss_pred             CCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHH
Q 042834            2 SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKE   81 (98)
Q Consensus         2 ~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~   81 (98)
                      .|..+.+++++|||+..+++.+|+|+++++..+..     ... ...+++.||+.|++.||+.    +.++|.+.|||+.
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            46678899999999999999999999999865431     122 2458999999999999987    6789999999999


Q ss_pred             HHHHHhc
Q 042834           82 VVDLARN   88 (98)
Q Consensus        82 vv~~l~~   88 (98)
                      |++.+++
T Consensus       501 v~~~i~~  507 (555)
T 1mu2_A          501 VMGIVAS  507 (555)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhc
Confidence            9999986

>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=94.42  E-value=0.073  Score=32.36  Aligned_cols=57  Identities=16%  Similarity=0.153  Sum_probs=42.8

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      +...+|.++++.+|+++.+.............||..|+..+... -+..+..+.+.+|
T Consensus        22 s~~~VGAal~~~dG~i~~G~Nvena~~~~t~cAE~~Ai~~A~~~-G~~~~~~~~l~~~   78 (136)
T 1uwz_A           22 SKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEATALFKAVSE-GDTEFQMLAVAAD   78 (136)
T ss_dssp             TCCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHH-TCCCEEEEEEEES
T ss_pred             CCCCEEEEEEeCCCeEEEEeCcccCCCCCccCHHHHHHHHHHHC-CCCCeEEEEEEeC
Confidence            45678999999999988655543333334589999999999875 4556788888876

>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=93.58  E-value=0.1  Score=32.20  Aligned_cols=57  Identities=16%  Similarity=0.144  Sum_probs=42.0

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      ....+|.++++.+|+++.+...-.....-...||..|+..|... -...+..+.+.+|
T Consensus        34 s~f~VGAal~~~dG~i~~G~NvEnas~~~t~cAE~~Ai~~A~~~-G~~~l~~i~v~~~   90 (146)
T 2fr5_A           34 SRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISE-GYKDFRAIAISSD   90 (146)
T ss_dssp             TCCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEES
T ss_pred             CCCCEEEEEEeCCCcEEEEEeccccCCCCCcCHHHHHHHHHHhC-CCCceEEEEEEeC
Confidence            45679999999999988655433322223589999999999875 4556788888877

>2b3j_A TRNA adenosine deaminase; mixed alpha-beta, protein-RNA complex, RNA stem-loop, hydrol complex; HET: P5P; 2.00A {Staphylococcus aureus subsp} SCOP: c.97.1.2

Probab=90.86  E-value=0.32  Score=30.12  Aligned_cols=55  Identities=15%  Similarity=0.140  Sum_probs=35.1

Q ss_pred             cceEEEEEeCCCccEEEeeeeee-cccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834           22 TAGLGVIIRDSRGKAVAATVQKV-SFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      ..-+|.||.+ +|+++..+.... .......+||..||..+.+......+....+++
T Consensus        26 ~~pVGAviv~-~g~Ii~~G~N~~~~~~~~~~HAE~~Ai~~a~~~~~~~~l~~~tlyv   81 (159)
T 2b3j_A           26 EVPIGAIITK-DDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYV   81 (159)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTEEEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCCccCHHHHHHHHHHHHcCCCCcceeEEEE
Confidence            4567888887 788886444322 112235799999999987754444455555554

>2z3g_A Blasticidin-S deaminase; hydrolase, cytidine deaminase family, zinc, tetramer; HET: TRE; 1.50A {Aspergillus terreus} SCOP: c.97.1.1 PDB: 1wn6_A* 1wn5_A* 2z3h_A* 2z3j_A 2z3i_A*

Probab=90.77  E-value=0.41  Score=28.75  Aligned_cols=55  Identities=7%  Similarity=0.026  Sum_probs=40.2

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      +...+|.++++.+|+++.+...-  .......||..|+..+... -+..+..+.+.+|
T Consensus        25 s~f~VGAal~~~dG~i~~G~NvE--~~~~t~cAE~~Ai~~A~~~-G~~~~~~i~vv~~   79 (130)
T 2z3g_A           25 EDYSVASAALSSDGRIFTGVNVY--HFTGGPCAELVVLGTAAAA-AAGNLTCIVAIGN   79 (130)
T ss_dssp             SSSCEEEEEEETTSCEEEEECCC--CTTTCCCHHHHHHHHHHHT-TCCCEEEEEEEET
T ss_pred             CCCCEEEEEEecCCeEEEEeccc--cCCcccCHHHHHHHHHHHc-CCCceEEEEEEEC
Confidence            45778999999999988654433  3344689999999988863 3345777777775

>2a8n_A Cytidine and deoxycytidylate deaminase; RNA editing, RNA binding protein; 1.60A {Agrobacterium tumefaciens} SCOP: c.97.1.2

Probab=90.68  E-value=0.26  Score=29.97  Aligned_cols=54  Identities=11%  Similarity=0.182  Sum_probs=33.3

Q ss_pred             cceEEEEEeCCCccEEEeeeeee-cccCCHHHHHHHHHHHHHHHHHHCCCccEEEE
Q 042834           22 TAGLGVIIRDSRGKAVAATVQKV-SFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVE   76 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~e   76 (98)
                      ..-+|.||.+ +|+++..+.... .......+||..||..+.+......+....++
T Consensus        23 ~~~VGAviv~-~g~Ii~~G~N~~~~~~~~~~HAE~~Ai~~a~~~~~~~~~~~~tly   77 (144)
T 2a8n_A           23 EVPIGAVLVL-DGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLY   77 (144)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTCEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCCcCCHHHHHHHHHHHHcCCCccCCeEEE
Confidence            4567888887 888885544332 22223579999999998765433334443333

>2nx8_A TRNA-specific adenosine deaminase; TAD, hydrolase; 2.00A {Streptococcus pyogenes serotype M6}

Probab=90.32  E-value=0.38  Score=30.51  Aligned_cols=55  Identities=15%  Similarity=0.126  Sum_probs=34.2

Q ss_pred             cceEEEEEeCCCccEEEeeeeee-cccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834           22 TAGLGVIIRDSRGKAVAATVQKV-SFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      ..-+|.||.+ +|+++..+.... .......+||..||..+-+......+....+++
T Consensus        35 ~~pVGAVIV~-~g~Ii~~G~N~~~~~~d~t~HAE~~AI~~a~~~~~~~~l~g~tlYv   90 (179)
T 2nx8_A           35 EIPIGCVIVK-DGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGNWRLLDTTLFV   90 (179)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTEEEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCcCCCccCHHHHHHHHHHHHcCCCcccceEEEE
Confidence            4567788876 788886554332 222235799999999987654333444444443

>1wwr_A TRNA adenosine deaminase TADA; homodimer, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.80A {Aquifex aeolicus} SCOP: c.97.1.2

Probab=89.84  E-value=0.48  Score=29.83  Aligned_cols=56  Identities=13%  Similarity=0.112  Sum_probs=36.3

Q ss_pred             CcceEEEEEeCCCccEEEeeeee-ecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQK-VSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~-~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      +..-+|.||.+ +|+++..+... ........+||..||..+.+......+....+++
T Consensus        41 ~~~pVGAvIV~-dg~Ii~~G~N~~~~~~d~t~HAE~~AI~~a~~~~g~~~l~~~tlYv   97 (171)
T 1wwr_A           41 GEVPVGAIIVK-EGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYV   97 (171)
T ss_dssp             TSCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTEEEEE
T ss_pred             CCCCEEEEEEE-CCEEEEEEECCCCccCCcccCHHHHHHHHHHHHcCCCccCceEEEE
Confidence            35567888887 89888644432 2222235799999999887754444556666664

>1r5t_A Cytidine deaminase; zinc dependent deaminase, RNA editing, apobec-1 related protein, hydrolase; 2.00A {Saccharomyces cerevisiae} SCOP: c.97.1.1

Probab=88.50  E-value=0.77  Score=27.98  Aligned_cols=57  Identities=9%  Similarity=0.065  Sum_probs=39.7

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCC-CccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAK-FLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g-~~~v~~esD   78 (98)
                      ....+|..+++.+|++..+...-.......+.||-.|+..+...- ... +..+.+-+|
T Consensus        30 S~f~VGAAl~~~dG~i~~G~NvEnasy~~t~cAEr~Ai~~a~~~G-~~~~i~~i~vv~~   87 (142)
T 1r5t_A           30 SHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAG-HRSGWKCMVICGD   87 (142)
T ss_dssp             TCCCEEEEEECTTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHTT-CCSCCCEEEEEES
T ss_pred             CCCCEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcC-CCCceEEEEEEeC
Confidence            466789999999999887654333233345889999998887642 223 677777765

>2d30_A Cytidine deaminase; purines, pyrimidines, nucleosides, nucleotides, salvage of nucleosides and nucleotides, structural genomics; 2.40A {Bacillus anthracis} SCOP: c.97.1.1

Probab=87.99  E-value=0.78  Score=28.00  Aligned_cols=66  Identities=15%  Similarity=0.166  Sum_probs=45.7

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec----------hHHHHHHHh
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD----------SKEVVDLAR   87 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD----------s~~vv~~l~   87 (98)
                      ....+|..+++.+|++..+...-.......+.||..|+..+..- -+..+..|.+-+|          |.+++.-+.
T Consensus        31 S~f~VGAAll~~dG~i~~G~NvEnasy~~t~CAEr~Ai~~Avs~-G~~~~~aiav~~~~~~~~~PCG~CRQ~l~E~~  106 (141)
T 2d30_A           31 SKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVADTKRPVPPCGACRQVMVELC  106 (141)
T ss_dssp             TCCCEEEEEEETTCCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEESCSSCCCCCHHHHHHHHHHS
T ss_pred             CCCcEEEEEEeCCCCEEEeeccccCCCCcccCHHHHHHHHHHHC-CCCceEEEEEEeCCCCccCcCHHHHHHHHHhc
Confidence            45678999999999888765533323334588999999888864 3345678888765          555665554

>1z3a_A TRNA-specific adenosine deaminase; tRNA adenosine deaminase, dimer, zinc, metalloenzyme, structural genomics, PSI, protein structure initiative; 2.03A {Escherichia coli} SCOP: c.97.1.2 PDB: 3ocq_A

Probab=87.63  E-value=0.55  Score=29.40  Aligned_cols=54  Identities=15%  Similarity=0.217  Sum_probs=32.5

Q ss_pred             cceEEEEEeCCCccEEEeeeee-ecccCCHHHHHHHHHHHHHHHHHHCCCccEEEE
Q 042834           22 TAGLGVIIRDSRGKAVAATVQK-VSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVE   76 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~-~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~e   76 (98)
                      ..-+|.||.+ +|+++..+... ........+||..||..+-+......+....++
T Consensus        28 ~~pVGAviV~-~g~Ii~~G~N~~~~~~d~t~HAE~~Ai~~a~~~~~~~~l~~~tlY   82 (168)
T 1z3a_A           28 EVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLY   82 (168)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTCEEE
T ss_pred             CCcEEEEEEE-CCEEEEEEEcccccCCCcchhHHHHHHHHHHHHcCCCcccccEEE
Confidence            4457788874 78888654433 222223479999999988765433333333333

>1wkq_A Guanine deaminase; domain SWAP, the cytidine deaminase superfamily, substrate specificity, structural plasticity, hydrolase; 1.17A {Bacillus subtilis} SCOP: c.97.1.2 PDB: 1tiy_A

Probab=86.86  E-value=0.84  Score=28.48  Aligned_cols=53  Identities=19%  Similarity=0.206  Sum_probs=31.1

Q ss_pred             ceEEEEEeCCCccEEEeeeeeec-ccCCHHHHHHHHHHHHHHHHHHCCCccEEEE
Q 042834           23 AGLGVIIRDSRGKAVAATVQKVS-FRGDVAYMEAAAVNLGIQVAQNAKFLPIIVE   76 (98)
Q Consensus        23 ~g~G~vird~~G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~e   76 (98)
                      .-+|.||.+ +|+++..+..... ......+||..||+.+-+......+....++
T Consensus        32 ~pVGAVIV~-~g~Ii~~G~N~~~~~~d~~~HAE~~AI~~a~~~~~~~~l~g~tlY   85 (164)
T 1wkq_A           32 GPFGAVIVK-DGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILY   85 (164)
T ss_dssp             SSCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSSCTTEEEE
T ss_pred             CCEEEEEEE-CCEEEEEEecCCcCCCCcccCHHHHHHHHHHHHcCCCCcCceEEE
Confidence            346667664 7888865544322 2223579999999988764333333333333

>3dh1_A TRNA-specific adenosine deaminase 2; zinc-binding protein, TRA tRNA processing, hydrolase, structural genomics, structural consortium, SGC; 2.80A {Homo sapiens}

Probab=86.47  E-value=0.82  Score=29.21  Aligned_cols=44  Identities=11%  Similarity=0.169  Sum_probs=29.5

Q ss_pred             ceEEEEEeCCCccEEEeeeeee-cccCCHHHHHHHHHHHHHHHHHH
Q 042834           23 AGLGVIIRDSRGKAVAATVQKV-SFRGDVAYMEAAAVNLGIQVAQN   67 (98)
Q Consensus        23 ~g~G~vird~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~aL~~a~~   67 (98)
                      .-+|+||-+ +|++|..+.... .......+||..||..+.+.+..
T Consensus        46 ~pVGAVIV~-~g~IIa~G~N~~~~~~~~t~HAEi~AI~~a~~~~~~   90 (189)
T 3dh1_A           46 VPVGCLMVY-NNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQ   90 (189)
T ss_dssp             CCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEE-CCEEEEEEeCCCCccCCCcCcHHHHHHHHHHHHHhh
Confidence            446777776 688887655431 11234579999999998876543

>2w4l_A DCMP deaminse, deoxycytidylate deaminase; pyrimidine metabolism, nucleotide biosynthesis, zinc, hexamer, hydrolase, metal-binding, phosphoprotein; 2.10A {Homo sapiens}

Probab=86.13  E-value=0.61  Score=29.51  Aligned_cols=40  Identities=18%  Similarity=0.096  Sum_probs=27.5

Q ss_pred             cceEEEEEeCCCccEEEeeeeeec-cc-----------CCH--------HHHHHHHHHHH
Q 042834           22 TAGLGVIIRDSRGKAVAATVQKVS-FR-----------GDV--------AYMEAAAVNLG   61 (98)
Q Consensus        22 ~~g~G~vird~~G~~i~~~~~~~~-~~-----------~~~--------~~aE~~Al~~a   61 (98)
                      ..-+|.||.+.+|+++..+..... .+           .++        .+||..||+.+
T Consensus        31 ~~~VGAvIV~~dg~Iia~G~N~~~~~~~d~~~~~~~~~g~p~~~~~~~t~HAE~~AI~~a   90 (178)
T 2w4l_A           31 NSQVGACIVNSENKIVGIGYNGMPNGCSDDVLPWRRTAENKLDTKYPYVCHAELNAIMNK   90 (178)
T ss_dssp             SCCCEEEEECTTSCEEEEEESBCCTTCCTTTSCCCSCCSSGGGSSTTTCBCHHHHHHHC-
T ss_pred             CCCEEEEEEecCCEEEEEEECCCCcCccccccccccccCCccccccCCcCCHHHHHHHHh
Confidence            456899999889999865544322 11           233        79999999875

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=85.79  E-value=3.6  Score=29.20  Aligned_cols=79  Identities=5%  Similarity=-0.189  Sum_probs=49.8

Q ss_pred             CCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHH-HHHHHHHHHH--CC--CccEEEEec
Q 042834            4 PNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAA-VNLGIQVAQN--AK--FLPIIVESD   78 (98)
Q Consensus         4 ~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~A-l~~aL~~a~~--~g--~~~v~~esD   78 (98)
                      +..-+.+.+|+|-     .+.+|.|+..+.|....++.-.-.......+-|.+| +..+|+--+.  .|  ...+++.||
T Consensus       321 ~~~~~~l~~das~-----~g~~g~vl~q~~~~~~~s~~~~~~~~y~~~~~e~la~vv~al~~~r~yl~G~~~~~~i~~td  395 (428)
T 2zd1_B          321 PSKDLIAEIQKQG-----QGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQK  395 (428)
T ss_dssp             TTSCCEEEEEEEE-----TTEEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHHHSSCCEEEESSCH
T ss_pred             CCCCEEEEEecCC-----CCcEEEEEecCCCceeeecccchhhhcccchHHHHHHHHHHhhccceEEECCCCcEECCccH
Confidence            3445678899883     346788887776654433332233334566788888 9999875432  23  356788899


Q ss_pred             hHHHHHHHh
Q 042834           79 SKEVVDLAR   87 (98)
Q Consensus        79 s~~vv~~l~   87 (98)
                      .+.+.-...
T Consensus       396 ~~~~~~~~~  404 (428)
T 2zd1_B          396 ETWETWWTE  404 (428)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            988654443

>1p6o_A Cytosine deaminase; hydrolase, dimer, inhibitor bound; 1.14A {Saccharomyces cerevisiae} SCOP: c.97.1.2 PDB: 1ox7_A 1rb7_A 1ysd_A 1ysb_A 2o3k_A 1uaq_A

Probab=84.58  E-value=0.72  Score=28.61  Aligned_cols=42  Identities=7%  Similarity=-0.054  Sum_probs=28.8

Q ss_pred             cceEEEEEe-CCCccEEEeeeeeec-ccCCHHHHHHHHHHHHHH
Q 042834           22 TAGLGVIIR-DSRGKAVAATVQKVS-FRGDVAYMEAAAVNLGIQ   63 (98)
Q Consensus        22 ~~g~G~vir-d~~G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~   63 (98)
                      ..-+|.||. +.+|+++..+..... ......+||..||..+.+
T Consensus        33 ~~pVGAviVd~~~g~Ii~~G~N~~~~~~~~t~HAE~~Ai~~a~~   76 (161)
T 1p6o_A           33 GVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGR   76 (161)
T ss_dssp             SCCCEEEEEETTTCCEEEEEECCHHHHTCSSCCHHHHHHHHHCS
T ss_pred             CCCEEEEEEEecCCEEEEEEECCCCCCCCcccCHHHHHHHHHHH
Confidence            456899999 588999865544322 122247999999988754

>3r2n_A Cytidine deaminase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, tuberculosis; 2.30A {Mycobacterium leprae} SCOP: c.97.1.0

Probab=84.08  E-value=1.1  Score=27.20  Aligned_cols=66  Identities=8%  Similarity=0.074  Sum_probs=45.0

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec----------hHHHHHHHh
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD----------SKEVVDLAR   87 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD----------s~~vv~~l~   87 (98)
                      ....+|.+++..+|++..+...-.......+.||..|+..+...- +..+..|.+-+|          |.+++.-+.
T Consensus        29 S~f~VGAAll~~dG~i~~G~NvEnasy~~t~CAEr~Ai~~Av~~G-~~~i~aiav~~~~~~~~~PCG~CRQ~l~E~~  104 (138)
T 3r2n_A           29 SNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATG-GGRLVAVYCVDGNGDSLMPCGRCRQLLYEHG  104 (138)
T ss_dssp             TCCCCEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHTT-CCCEEEEEEECTTSCBCCCCHHHHHHHHHHH
T ss_pred             CCCcEEEEEEeCCCcEEEEEcccccCCCCCcCHHHHHHHHHHHcC-CCceEEEEEEcCCCCcCCCCHHHHHHHHHhC
Confidence            456789999999999987665433333345789999999887642 345666666654          556655554

>2g84_A Cytidine and deoxycytidylate deaminase zinc-bindi; zinc-binding region, structural genomics, PSI, protein structure initiative; 1.40A {Nitrosomonas europaea} SCOP: c.97.1.2

Probab=82.67  E-value=2.8  Score=26.81  Aligned_cols=42  Identities=21%  Similarity=0.177  Sum_probs=29.1

Q ss_pred             eEEEEEeCCC-ccEEEeeeeeec-ccCCHHHHHHHHHHHHHHHH
Q 042834           24 GLGVIIRDSR-GKAVAATVQKVS-FRGDVAYMEAAAVNLGIQVA   65 (98)
Q Consensus        24 g~G~vird~~-G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~~a   65 (98)
                      -+|.||.+.+ |+++..+..... ......+||..||..+-+..
T Consensus        49 PvGAVIV~~~~g~Iia~G~N~~~~~~~~~~HAE~~Ai~~a~~~~   92 (197)
T 2g84_A           49 PFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKL   92 (197)
T ss_dssp             SCEEEEEETTTCBEEEEEECCTTTTTCTTCCHHHHHHHHHHHHH
T ss_pred             CEEEEEEEcCCCEEEEEEECCCCccCCCccCHHHHHHHHHHHHc
Confidence            3588888866 999876654321 22345799999999876643

>3mpz_A Cytidine deaminase; ssgcid, structu genomics, seattle structural genomics center for infectious hydrolase; 1.70A {Mycobacterium smegmatis} PDB: 3ijf_X 4f3w_A

Probab=82.29  E-value=1.5  Score=27.15  Aligned_cols=57  Identities=12%  Similarity=0.005  Sum_probs=40.2

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      ....+|..++..+|++..+...-.......+-||-.|+..++.- -+..+..|.+-+|
T Consensus        44 S~F~VGAAll~~dG~i~tG~NvEnasy~~t~CAEr~Ai~~Avs~-G~~~i~aiavv~~  100 (150)
T 3mpz_A           44 SGFPVGAAALVDDGRTVTGCNVENVSYGLGLCAECAVVCALHSG-GGGRLVALSCVGP  100 (150)
T ss_dssp             TCCCCEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEECT
T ss_pred             CCCCEEEEEEeCCCCEEEEEecccccCCccccHHHHHHHHHHHc-CCCceEEEEEEcC
Confidence            45678999999999998766544333334578999999888864 2345666666654

---

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	98
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.64
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.52
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.41
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.31
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.29
d1wkqa_	158	Guanine deaminase GuaD {Bacillus subtilis [TaxId:	93.37
d1z3aa1	156	tRNA adenosine deaminase TadA {Escherichia coli [T	91.72
d2g84a1	189	Putative deaminase NE0047 {Nitrosomonas europaea [	91.5
d1wwra1	151	tRNA adenosine deaminase TadA {Aquifex aeolicus [T	88.98
d2b3ja1	151	tRNA adenosine deaminase TadA {Staphylococcus aure	88.96
d2a8na1	130	Cytidine and deoxycytidylate deaminase CodA {Agrob	87.03
d2d30a1	124	mono-domain cytidine deaminase {Bacillus anthracis	84.86
d1uwza_	130	mono-domain cytidine deaminase {Bacillus subtilis	82.13
d1e2ya_	167	Tryparedoxin peroxidase (thioredoxin peroxidase ho	80.39
d1p6oa_	156	Cytosine deaminase {Baker's yeast (Saccharomyces c	80.08

>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=99.64  E-value=2.2e-16  Score=95.73  Aligned_cols=79  Identities=10%  Similarity=0.080  Sum_probs=65.4

Q ss_pred             EEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHHh
Q 042834            8 FKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLAR   87 (98)
Q Consensus         8 ~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~   87 (98)
                      -.+++|||+.++++.+|+|+|+.+.......  +..++ ..+++.||++|++.||+++.+.+ .++.|+|||+.+++.++
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 ESLSVDVGSQGNPGIVEYKGVDTKTGEVLFE--REPIP-IGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVK   80 (132)
T ss_dssp             SSEEEEEEECSSSEEEEEEEEETTTCCEEEE--CCCEE-EECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHH
T ss_pred             eeEEEeecCCCCCchheEEEEEEcCCEEEEE--EcCcC-ccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHH
Confidence            3589999999999999999999875554432  33344 35899999999999999999987 57999999999999998


Q ss_pred             cCC
Q 042834           88 NRN   90 (98)
Q Consensus        88 ~~~   90 (98)
                      +..
T Consensus        81 ~~~   83 (132)
T d1zbfa1          81 DKK   83 (132)
T ss_dssp             HTC
T ss_pred             hCc
Confidence            653

>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=99.52  E-value=8.3e-14  Score=82.04  Aligned_cols=79  Identities=20%  Similarity=0.216  Sum_probs=63.8

Q ss_pred             CCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHH
Q 042834            2 SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKE   81 (98)
Q Consensus         2 ~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~   81 (98)
                      -|-.+-..+++|||+..+++.+|+|+++.+.......     +. ..+++.||++|++.||+.    +..+|.|.|||+.
T Consensus         3 ~Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~-----~~-~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~y   72 (110)
T d1s1ta1           3 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVT-----LT-DTTNQKTELQAIYLALQD----SGLEVNIVTDSQY   72 (110)
T ss_dssp             SCCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEE-----ES-SCCHHHHHHHHHHHHHHH----SCSEEEEEECCHH
T ss_pred             CCCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEe-----cc-cCcHHHHHHHHHHHHHHh----CCCeEEEEEehHH
Confidence            4666777899999999999999999998765443222     22 358999999999999973    5678999999999


Q ss_pred             HHHHHhcCC
Q 042834           82 VVDLARNRN   90 (98)
Q Consensus        82 vv~~l~~~~   90 (98)
                      +++.+++..
T Consensus        73 vi~~i~~~~   81 (110)
T d1s1ta1          73 ALGIIQAQP   81 (110)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHHHhcCc
Confidence            999999754

>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=99.41  E-value=1.5e-12  Score=77.84  Aligned_cols=80  Identities=13%  Similarity=0.125  Sum_probs=64.7

Q ss_pred             CCCCceEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHH
Q 042834            2 SPPNGWFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKE   81 (98)
Q Consensus         2 ~P~~g~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~   81 (98)
                      .|-.+...+|+|||+..+.+.+|+|+++.+....+..     .. ..+++.||+.|++.||+.    ..++|.|.+||+.
T Consensus         2 ~p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~-----~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~   71 (126)
T d1mu2a1           2 DPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKK-----LE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQY   71 (126)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEE-----ES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHH
T ss_pred             CCCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEe-----cC-CCcchHHHHHHHHHHhcc----CCcceEEEechHH
Confidence            3677888999999999988999999988775543322     22 358999999999999874    5679999999999


Q ss_pred             HHHHHhcCCC
Q 042834           82 VVDLARNRNC   91 (98)
Q Consensus        82 vv~~l~~~~~   91 (98)
                      +++.+++...
T Consensus        72 v~~~~~~~~~   81 (126)
T d1mu2a1          72 VMGIVASQPT   81 (126)
T ss_dssp             HHHHHHTCCS
T ss_pred             HHHHHhcCCc
Confidence            9999998643

>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=99.31  E-value=7.4e-12  Score=76.33  Aligned_cols=77  Identities=16%  Similarity=0.155  Sum_probs=61.9

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA   86 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l   86 (98)
                      .|++|+|||+..+++.+|+|+|+++.........  ..+ ..++..||++|++.||+++  .....+.+.+|++.++..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~--~~~-~~tnn~aE~~Ai~~Al~~~--~~~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSA--GYT-RTTNNRMELMAAIVALEAL--KEHAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEE--EEE-EECHHHHHHHHHHHHHHTC--CSCCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEecc--ccC-cccHHHHHHhhhhhhhhhh--cccceEEEeecceeeEEcc
Confidence            4899999999999999999999998666554332  233 3478999999999999864  3457789999999999888


Q ss_pred             hc
Q 042834           87 RN   88 (98)
Q Consensus        87 ~~   88 (98)
                      +.
T Consensus        77 ~~   78 (152)
T d1jl1a_          77 TQ   78 (152)
T ss_dssp             HT
T ss_pred             cc
Confidence            64

>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=99.29  E-value=4.1e-12  Score=77.49  Aligned_cols=77  Identities=13%  Similarity=0.026  Sum_probs=62.2

Q ss_pred             eEEEEecceeecCCCcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEechHHHHHHH
Q 042834            7 WFKVNVDAAIKLSDQTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESDSKEVVDLA   86 (98)
Q Consensus         7 ~~k~n~D~s~~~~~~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l   86 (98)
                      .+.+|+|||+..+++.+|+|+|+++..........  . ...++..||+.|+++||+++.  ....+.+.+||+.+++.+
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~--~-~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~   77 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGG--E-ACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAF   77 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCE--E-EEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHH
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecc--c-ccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccc
Confidence            47899999999988999999999887766544332  2 335889999999999998753  446899999999999988


Q ss_pred             hc
Q 042834           87 RN   88 (98)
Q Consensus        87 ~~   88 (98)
                      ..
T Consensus        78 ~~   79 (147)
T d1rila_          78 TE   79 (147)
T ss_dssp             HS
T ss_pred             cc
Confidence            65

>d1wkqa_ c.97.1.2 (A:) Guanine deaminase GuaD {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: Guanine deaminase GuaD
species: Bacillus subtilis [TaxId: 1423]

Probab=93.37  E-value=0.059  Score=32.08  Aligned_cols=45  Identities=22%  Similarity=0.299  Sum_probs=29.2

Q ss_pred             EEEEEeCCCccEEEeeeeeecccCCH-HHHHHHHHHHHHHHHHHCCC
Q 042834           25 LGVIIRDSRGKAVAATVQKVSFRGDV-AYMEAAAVNLGIQVAQNAKF   70 (98)
Q Consensus        25 ~G~vird~~G~~i~~~~~~~~~~~~~-~~aE~~Al~~aL~~a~~~g~   70 (98)
                      +|.||-+ +|++|..+........++ .+||..|++.|.+......+
T Consensus        28 vGaviv~-~~~ii~~g~n~~~~~~~~t~HAE~~ai~~a~~~~~~~~l   73 (158)
T d1wkqa_          28 FGAVIVK-DGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQL   73 (158)
T ss_dssp             CEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSSC
T ss_pred             EEEEEEe-cccceeeccceeeccCCCcccHHHHHHHHHHHhcCcccc
Confidence            6777776 477777665443323333 59999999998765544333

>d1z3aa1 c.97.1.2 (A:13-168) tRNA adenosine deaminase TadA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: tRNA adenosine deaminase TadA
species: Escherichia coli [TaxId: 562]

Probab=91.72  E-value=0.1  Score=30.75  Aligned_cols=53  Identities=19%  Similarity=0.214  Sum_probs=35.0

Q ss_pred             ceEEEEEeCCCccEEEeeeeeecccCC-HHHHHHHHHHHHHHHHHHCCCccEEEE
Q 042834           23 AGLGVIIRDSRGKAVAATVQKVSFRGD-VAYMEAAAVNLGIQVAQNAKFLPIIVE   76 (98)
Q Consensus        23 ~g~G~vird~~G~~i~~~~~~~~~~~~-~~~aE~~Al~~aL~~a~~~g~~~v~~e   76 (98)
                      .-+|+||-+ +|+++..+........+ ..+||..|+..+........+....++
T Consensus        27 ~pvGaViv~-~g~Iia~g~n~~~~~~~~~~HAE~~ai~~a~~~~~~~~l~~~~ly   80 (156)
T d1z3aa1          27 VPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLY   80 (156)
T ss_dssp             CCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTCEEE
T ss_pred             CCEEEEEEE-CCeEEEEeeccccccCcchhhHHHHhHHHHHhhcccccccCceee
Confidence            347888887 78888877655433333 359999999998877665544433333

>d2g84a1 c.97.1.2 (A:1-189) Putative deaminase NE0047 {Nitrosomonas europaea [TaxId: 915]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: Putative deaminase NE0047
species: Nitrosomonas europaea [TaxId: 915]

Probab=91.50  E-value=0.21  Score=30.49  Aligned_cols=47  Identities=19%  Similarity=0.171  Sum_probs=31.7

Q ss_pred             CcceEEEEEeCC-CccEEEeeeeeec-ccCCHHHHHHHHHHHHHHHHHH
Q 042834           21 QTAGLGVIIRDS-RGKAVAATVQKVS-FRGDVAYMEAAAVNLGIQVAQN   67 (98)
Q Consensus        21 ~~~g~G~vird~-~G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~   67 (98)
                      +..-+|.||.+. .|+++..+..... ......+||..||+.+-+....
T Consensus        44 g~~P~GaviV~~~~g~Iia~g~N~~~~~~dpt~HAEi~AI~~A~~~~~~   92 (189)
T d2g84a1          44 DGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDT   92 (189)
T ss_dssp             TCCSCEEEEEETTTCBEEEEEECCTTTTTCTTCCHHHHHHHHHHHHHTC
T ss_pred             CCCCEEEEEEECCCCEEEEEEcCCcCcCCCCcccHHHHHHHHHHHHhhc
Confidence            344588888876 4888887655432 2223369999999988765543

>d1wwra1 c.97.1.2 (A:1-151) tRNA adenosine deaminase TadA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: tRNA adenosine deaminase TadA
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.98  E-value=0.48  Score=27.55  Aligned_cols=65  Identities=12%  Similarity=0.049  Sum_probs=42.7

Q ss_pred             eEEEEEeCCCccEEEeeeeee-cccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec---hHHHHHHHhcC
Q 042834           24 GLGVIIRDSRGKAVAATVQKV-SFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD---SKEVVDLARNR   89 (98)
Q Consensus        24 g~G~vird~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD---s~~vv~~l~~~   89 (98)
                      -+|+||.+. |..+..+.... .......+||..|+..|.+......+....+++-   |..-..+|...
T Consensus        24 pVGaVIV~~-~~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~~~~~~~l~~~tlY~TlEPC~mC~~ai~~~   92 (151)
T d1wwra1          24 PVGAIIVKE-GEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLS   92 (151)
T ss_dssp             CCEEEEEET-TEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTEEEEESSCCBHHHHHHHHHT
T ss_pred             CEEEEEEEC-CeeeeeecccccccCcchhhHHHHHHHHHHHhhCccccCCcEeeecccCCcHHHHHHHHh
Confidence            378888875 56665544332 2223346999999999988776666777777776   55555555443

>d2b3ja1 c.97.1.2 (A:1-151) tRNA adenosine deaminase TadA {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: tRNA adenosine deaminase TadA
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.96  E-value=0.27  Score=28.58  Aligned_cols=54  Identities=15%  Similarity=0.108  Sum_probs=34.2

Q ss_pred             eEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834           24 GLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus        24 g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      -+|+||.+..+.+..+............+||..|+..+........+....+++
T Consensus        25 PVGaViV~~~~ii~~g~~~~~~~~~~~~HAe~~a~~~~~~~~~~~~~~~~~ly~   78 (151)
T d2b3ja1          25 PIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYV   78 (151)
T ss_dssp             CCEEEEEETTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTEEEEE
T ss_pred             CEEEEEEecccchhhhhccccccCcchhhhhhhhhHHHHHHhCCCCCCCCeEEE
Confidence            378888875444444434333333344689999998888776666666666555

>d2a8na1 c.97.1.2 (A:2-131) Cytidine and deoxycytidylate deaminase CodA {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: Cytidine and deoxycytidylate deaminase CodA
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=87.03  E-value=0.32  Score=27.66  Aligned_cols=53  Identities=11%  Similarity=0.176  Sum_probs=32.5

Q ss_pred             eEEEEEeCCCccEEEeeeeeec-ccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe
Q 042834           24 GLGVIIRDSRGKAVAATVQKVS-FRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES   77 (98)
Q Consensus        24 g~G~vird~~G~~i~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   77 (98)
                      -+|.||.+ +|+++..+..... ......+||..|+..+.+......+....+++
T Consensus        24 PVGavIV~-~~~ii~~g~n~~~~~~~~~~HaE~~ai~~a~~~~~~~~l~~~tly~   77 (130)
T d2a8na1          24 PIGAVLVL-DGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLYV   77 (130)
T ss_dssp             CCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTCEEEE
T ss_pred             CEEEEEEE-CCeEEEeecccccccccccchhHHHHHHHHHHHhCCcCCCCCEEec
Confidence            37777775 4667665544322 22233499999999998876555554444443

>d2d30a1 c.97.1.1 (A:1-124) mono-domain cytidine deaminase {Bacillus anthracis [TaxId: 1392]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Cytidine deaminase
domain: mono-domain cytidine deaminase
species: Bacillus anthracis [TaxId: 1392]

Probab=84.86  E-value=0.57  Score=26.47  Aligned_cols=57  Identities=16%  Similarity=0.190  Sum_probs=41.2

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEec
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVESD   78 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   78 (98)
                      ...-+|..++..+|++..+..--.........||..|+..++.- -+..+..|.+-+|
T Consensus        22 S~f~VGAal~~~~G~i~~G~NvEn~s~~~~~CAEr~Ai~~a~~~-g~~~~~~i~v~~~   78 (124)
T d2d30a1          22 SKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVAD   78 (124)
T ss_dssp             TCCCEEEEEEETTCCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEES
T ss_pred             cCCcEEEEEEeCCCCEEEEEeeccccCCcccCHHHHHHHHHHhc-CCceeEEEEEEcC
Confidence            34568999999999988776543333334469999999988774 4556677777776

>d1uwza_ c.97.1.1 (A:) mono-domain cytidine deaminase {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Cytidine deaminase
domain: mono-domain cytidine deaminase
species: Bacillus subtilis [TaxId: 1423]

Probab=82.13  E-value=1.1  Score=25.39  Aligned_cols=67  Identities=13%  Similarity=0.134  Sum_probs=45.5

Q ss_pred             CcceEEEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCCCccEEEEe----------chHHHHHHHhc
Q 042834           21 QTAGLGVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAKFLPIIVES----------DSKEVVDLARN   88 (98)
Q Consensus        21 ~~~g~G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es----------Ds~~vv~~l~~   88 (98)
                      ...-+|..++..+|++..+...-........-||..|+..++.. -+..+..+.+.+          .|.+++.-+..
T Consensus        22 S~f~VGAa~~~~~G~i~~G~NvEnas~~~~~CAEr~Ai~~a~~~-g~~~~~~i~v~~~~~~~~sPCG~CRQ~l~E~~~   98 (130)
T d1uwza_          22 SKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEATALFKAVSE-GDTEFQMLAVAADTPGPVSPCGACRQVISELCT   98 (130)
T ss_dssp             TCCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHH-TCCCEEEEEEEESCSSSCCCCHHHHHHHHHHSC
T ss_pred             cCCcEEEEEEeCCCCEEEEeeeccccccccccceehhhHHHHHh-hhcceeeEEEEcCCCCccCcCHHHHHHHHHhCC
Confidence            34568999999999998876544333344468999998877654 344566666665          46666666643

>d1e2ya_ c.47.1.10 (A:) Tryparedoxin peroxidase (thioredoxin peroxidase homologue) {Crithidia fasciculata [TaxId: 5656]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Tryparedoxin peroxidase (thioredoxin peroxidase homologue)
species: Crithidia fasciculata [TaxId: 5656]

Probab=80.39  E-value=3.5  Score=23.52  Aligned_cols=42  Identities=19%  Similarity=0.248  Sum_probs=31.1

Q ss_pred             EEEEeCCCccEEEeeeeeecccCCHHHHHHHHHHHHHHHHHHCC
Q 042834           26 GVIIRDSRGKAVAATVQKVSFRGDVAYMEAAAVNLGIQVAQNAK   69 (98)
Q Consensus        26 G~vird~~G~~i~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g   69 (98)
                      +.+|-|.+|.+..........  ..+..|++..+++|+.....|
T Consensus       126 ~tfvID~~G~Ir~~~~~~~~~--~~~~~evL~~l~alq~~~~~g  167 (167)
T d1e2ya_         126 GVFIIDPNGKLRQIIINDMPI--GRNVEEVIRLVEALQFVEEHG  167 (167)
T ss_dssp             EEEEECTTSBEEEEEEECTTB--CCCHHHHHHHHHHHHHHHHCC
T ss_pred             EEEEECCCCEEEEEEEcCCCC--CCCHHHHHHHHHHHhHHHhcC
Confidence            578999999997765443221  235679999999999987765

>d1p6oa_ c.97.1.2 (A:) Cytosine deaminase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: Cytosine deaminase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.08  E-value=0.59  Score=27.46  Aligned_cols=38  Identities=8%  Similarity=0.001  Sum_probs=24.9

Q ss_pred             eEEEEEeC-CCccEEEeeeeee-cccCCHHHHHHHHHHHH
Q 042834           24 GLGVIIRD-SRGKAVAATVQKV-SFRGDVAYMEAAAVNLG   61 (98)
Q Consensus        24 g~G~vird-~~G~~i~~~~~~~-~~~~~~~~aE~~Al~~a   61 (98)
                      -+|.||.+ .+|+++..+.... .......+||..||..+
T Consensus        30 PvGaviV~~~~g~Iia~g~N~~~~~~~~~~HAE~~Ai~~a   69 (156)
T d1p6oa_          30 PIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENC   69 (156)
T ss_dssp             CCEEEEEETTTCCEEEEEECCHHHHTCSSCCHHHHHHHHH
T ss_pred             CEEEEEEEeCCCEEEEEEccccccccccccchHHHHHHHH
Confidence            37877764 6799888665432 22223359999999765