Citrus Sinensis ID: 037050

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140----
Protein Sequence
MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
Secondary Structure (PSIPRED)
cccccccEEEEEEEEcccccEEEEEcccccccccHHHHHHHHHHHHHHHHHHccccEEEEEEcHHHHHHHHHcccccccHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHHcccccEEEcccccHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEcccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHHHHHHccccccEEEcccccHHHHHHHHHccc
Coil and Loop (DISEMBL)
MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFqnfkaqhtprscnGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
Flexible Loop (DISEMBL)
MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
Low Complexity Region (SEG)
MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
Disordered region (IsUnstruct)
******VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLI*****
Disordered Region (DISOPRED)
M***KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
Disordered Region (DISEMBL)
********GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
Disordered Region (DISPRO)
*******AGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSS**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLISSSSM
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	144
343887321	166	hypothetical protein [Citrus unshiu]	0.666	0.578	0.364	5e-10
332322128	1369	hypothetical protein [Beta vulgaris subs	0.881	0.092	0.251	4e-07
255572864	437	conserved hypothetical protein [Ricinus	0.958	0.315	0.266	4e-07
222637128	185	hypothetical protein OsJ_24426 [Oryza sa	0.944	0.735	0.297	7e-06
357444467	320	Heat shock transcription factor [Medicag	0.944	0.425	0.304	1e-05
34015368	275	hypothetical protein OSJNBa0070J19.14 [O	0.715	0.374	0.298	2e-05
242054685	589	hypothetical protein SORBIDRAFT_03g03719	0.861	0.210	0.274	6e-05
332322136	1355	hypothetical protein [Beta vulgaris subs	0.875	0.092	0.259	0.0001
242052151	186	hypothetical protein SORBIDRAFT_03g00648	0.881	0.682	0.267	0.0002
222632657	205	hypothetical protein OsJ_19645 [Oryza sa	0.888	0.624	0.242	0.0002

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

 Score = 69.3 bits (168), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 58/96 (60%)

Query: 3   AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFES 62
           A++Q+ GL VVIR+ +   + AA  +T+F  NV   +A  ++ G+++AL     +V+ E+
Sbjct: 50  AEQQLTGLGVVIRNSQGQVIVAAFKSTKFEDNVTAAKAEAVKWGLEMALEARLAAVIIET 109

Query: 63  DSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNF 98
           D  EV  L NN T+S  +I+W I +I   K+ FQ+ 
Sbjct: 110 DCIEVANLANNETSSRKEIVWTISDIHSYKEKFQSL 145

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|332322128|emb|CCA66036.1| hypothetical protein [Beta vulgaris subsp. vulgaris]

 Score = 59.7 bits (143), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 63/127 (49%)

Query: 9    GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVV 68
            G+  V+RD E + + A         + AM +A ++  G++VA   G  +++ E D  ++ 
Sbjct: 1233 GMGGVVRDAEGDVLLATCCGGWAMEDPAMAEACSLRYGLKVAYEAGFRNLVVEMDCKKLF 1292

Query: 69   ELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWL 128
              +  + + ++    V+ +IL       N   +H  R CN +AH LA++     E  +WL
Sbjct: 1293 LQLRGKASDVTPFGRVVDDILYLASKCSNVVFEHVKRHCNKVAHLLAQMCKNAMEKRVWL 1352

Query: 129  DEIPTDI 135
            +E P+++
Sbjct: 1353 EEYPSEV 1359

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255572864|ref|XP_002527364.1| conserved hypothetical protein [Ricinus communis] gi|223533283|gb|EEF35036.1| conserved hypothetical protein [Ricinus communis]

 Score = 59.7 bits (143), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/139 (26%), Positives = 68/139 (48%), Gaps = 1/139 (0%)

Query: 5   KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64
           +Q AG   ++RD E N + A ++      ++ + +   I  G+ +AL +G   +  ESDS
Sbjct: 292 RQHAGFGGLLRDNEGNAICAFVSKAPL-DDIFLVELWAIWRGLVLALGLGIKVIWVESDS 350

Query: 65  HEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEI 124
              V+ +N   +   K    +  I    K F+ +K  H  R  N  A +L+K+VL++ ++
Sbjct: 351 MSAVKTINRVQSHSGKANRCLNHIWALLKKFEEYKVSHAWRETNKAADYLSKMVLERNDV 410

Query: 125 VIWLDEIPTDILYLISSSS 143
           V+W    PT +  +I   +
Sbjct: 411 VLWPVHFPTTLQNIIKDDA 429

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222637128|gb|EEE67260.1| hypothetical protein OsJ_24426 [Oryza sativa Japonica Group]

 Score = 55.5 bits (132), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 42/141 (29%), Positives = 71/141 (50%), Gaps = 5/141 (3%)

Query: 3   AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYS-VLFE 61
           A ++  G   V+RD E + + A      F  +V   +A    +   +A+SV G + V  E
Sbjct: 37  ANRKTGGWGFVLRDEEGHALLAGAGRLEFVHDVVSAEARAC-LSALLAISVQGVTEVEIE 95

Query: 62  SDSHEVVELVNNRTNSMSKIIWVIFEI-LEKKKNFQNFKAQHTPRSCNGIAHFLAKLVL- 119
           SDS  +V  V + ++S +    +  EI +  + +F N K    PRSCN +AH LAK+ + 
Sbjct: 96  SDSAILVSAVTSSSHSQAVGATIFAEIKMLLQLHFANSKVSFAPRSCNNVAHNLAKIGVS 155

Query: 120 -QKKEIVIWLDEIPTDILYLI 139
               + V+W+D +P  +  L+
Sbjct: 156 WDPDQSVVWVDPLPYFVRTLV 176

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357444467|ref|XP_003592511.1| Heat shock transcription factor [Medicago truncatula] gi|355481559|gb|AES62762.1| Heat shock transcription factor [Medicago truncatula]

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/141 (30%), Positives = 64/141 (45%), Gaps = 5/141 (3%)

Query: 2   DAKKQVAG---LAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSV 58
           DA  QV G   L  +IR+ E     +A      F N    +A  I  GM +A++ G  ++
Sbjct: 103 DANLQVPGRWGLGCIIRNSEGLASVSASCGRNGFDNAETAEAYAIFAGMHLAVNCGLRNM 162

Query: 59  LFESDSHEVV-ELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKL 117
           +FESD   +V +L    T   S + +++ EI      F       TPR  N +AH LA+L
Sbjct: 163 VFESDCESIVKKLKRQHTEDRSYLGYILKEIWMTSALFDTCTYHFTPRIGNRVAHCLAQL 222

Query: 118 VLQKKEIVIWLDEIPTDILYL 138
              +   V W D +P+    L
Sbjct: 223 AHLEPNKV-WKDNVPSQAYSL 242

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|34015368|gb|AAQ56556.1| hypothetical protein OSJNBa0070J19.14 [Oryza sativa Japonica Group]

 Score = 53.9 bits (128), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 50/104 (48%), Gaps = 1/104 (0%)

Query: 37  MTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQ 96
           M +A     G+Q+A   G   +  E+D  E+ +L     +  S +  +I + +E   +F 
Sbjct: 165 MMEALACRDGIQLAREKGVLRIQVETDCQELTKLWKQGGSQRSHVASIISDAIELSSSFH 224

Query: 97  NFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIPTDILYLIS 140
            F   +TPRSCN +AH LAK V     +  W    P  I +L++
Sbjct: 225 GFTLLYTPRSCNHVAHVLAKQVTADDRLGEW-QSAPACIEHLVT 267

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242054685|ref|XP_002456488.1| hypothetical protein SORBIDRAFT_03g037190 [Sorghum bicolor] gi|241928463|gb|EES01608.1| hypothetical protein SORBIDRAFT_03g037190 [Sorghum bicolor]

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 34/124 (27%), Positives = 56/124 (45%)

Query: 5   KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS 64
           +       V+RD   N  AA+       G+V + +A  I  G+++        ++ E+D+
Sbjct: 448 RGTGAAGAVVRDSSGNFCAASARWLGPVGSVLIAEAEAIRDGLRLIPQGTMEHIIGETDA 507

Query: 65  HEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEI 124
            EVV L  NRT   S+I  ++ EI E    F +F+  H  R  N +AH  A+      + 
Sbjct: 508 REVVALWKNRTRQRSEIAAILKEIEEIVSAFTSFELIHVRREANSVAHTCARFASSSLDS 567

Query: 125 VIWL 128
            +W 
Sbjct: 568 HVWF 571

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|332322136|emb|CCA66044.1| hypothetical protein [Beta vulgaris subsp. vulgaris]

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/127 (25%), Positives = 61/127 (48%), Gaps = 1/127 (0%)

Query: 9    GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVV 68
            GL+V+ RD     + AA+   R   +  + +A  IE+ +++    G  +++ ESD   VV
Sbjct: 1218 GLSVIARDSHGTVLFAAVRKVRAQWSAEIAEAKAIEMALRLGRRYGFAAIIVESDCQVVV 1277

Query: 69   ELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWL 128
              ++ +   ++ +  ++  I     NF +    H  R  N +AH LAKL     E  IW 
Sbjct: 1278 NRLSKQALYLADLDIILHNIFSSCINFPSVLWSHVKRDANSVAHHLAKLTPFGIE-QIWE 1336

Query: 129  DEIPTDI 135
            + +P ++
Sbjct: 1337 NHVPPEV 1343

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242052151|ref|XP_002455221.1| hypothetical protein SORBIDRAFT_03g006485 [Sorghum bicolor] gi|241927196|gb|EES00341.1| hypothetical protein SORBIDRAFT_03g006485 [Sorghum bicolor]

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/127 (26%), Positives = 55/127 (43%)

Query: 6   QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSH 65
           +     +V+RD +      +        N   T+A     GMQ A   G   +L E+D  
Sbjct: 45  RTGATGMVLRDHDGQACGVSARWYEHSLNALATEAMACRDGMQFARERGVRKLLVETDCQ 104

Query: 66  EVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIV 125
            +V L  NR    S+I   + ++ +  ++F+ F      R+CN +AH  AKLV +   + 
Sbjct: 105 VLVNLWENRAMQKSEIEPFMHQMAQLSRSFEVFSLCFVSRNCNRLAHECAKLVSRGNPVE 164

Query: 126 IWLDEIP 132
            WL   P
Sbjct: 165 EWLLAPP 171

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222632657|gb|EEE64789.1| hypothetical protein OsJ_19645 [Oryza sativa Japonica Group]

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/136 (24%), Positives = 61/136 (44%), Gaps = 8/136 (5%)

Query: 8   AGLAVVIRDWERNCVAAAI-NTTRFFGNVAMTQAATI---EIGMQVALSVGGYSVLFESD 63
            G+ VVIRD    C+   + ++ R+    +  + A +     G+ +A       V+ ESD
Sbjct: 66  CGIGVVIRD----CLGRVLLSSWRYLRRCSQAEEAELLACSEGINLAAEWIHLPVILESD 121

Query: 64  SHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKE 123
                  +  +    S+  +++ EI    +  Q     H  R CN +AH LA+L  +   
Sbjct: 122 CLMATTSIAGKDMERSRWTFLLREIKAAVRRLQEVSVHHVNRECNRVAHELAQLAKRTAH 181

Query: 124 IVIWLDEIPTDILYLI 139
             +W D+ P+ IL+++
Sbjct: 182 CAVWRDQAPSCILHVL 197

Source: Oryza sativa Japonica 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	144
TAIR|locus:4010713531	138	AT1G47497 [Arabidopsis thalian	0.826	0.862	0.308	4.8e-07
TAIR|locus:2039129	160	AT2G46460 [Arabidopsis thalian	0.826	0.743	0.3	1.3e-06

TAIR|locus:4010713531 AT1G47497 [Arabidopsis thaliana (taxid:3702)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 37/120 (30%), Positives = 52/120 (43%)

Query:    13 VIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVN 72
             VIRD     V A   T     N   ++   + I MQ   S G   + FE D+ EV+E++N
Sbjct:     8 VIRDESGQFVGAGQATGNHTSNALESEFQALLIAMQSCWSHGHRKIWFEGDNREVMEILN 67

Query:    73 NRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIP 132
              R +      W I ++   K+ FQ  +     R  N  A  LAK  L + E   + D IP
Sbjct:    68 RRKSRFDTFNW-IRDVQAWKQRFQECRFTWINRKQNKPADILAKSHLPQNEQFKFYDYIP 126

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

 Score = 111 (44.1 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 36/120 (30%), Positives = 53/120 (44%)

Query:    13 VIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVN 72
             +IRD     V+A   T     N   ++   + I MQ   S G   + FE D+ EV+E++N
Sbjct:    30 IIRDESGQFVSAGQATGNHTSNALESEFQALLITMQSCWSHGHRKIWFEGDNREVMEILN 89

Query:    73 NRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLDEIP 132
              R +      W I ++   K+ FQ  +     R  N  A  LAK  L + E   + D IP
Sbjct:    90 RRKSRFDIFNW-IRDVQAWKQRFQECRFTWINRKQNKPADILAKSHLPQNEQFKFYDYIP 148


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        0.321   0.132   0.382    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      144       144   0.00091  102 3  11 22  0.40    31
                                                     30  0.48    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  592 (63 KB)
  Total size of DFA:  140 KB (2086 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:03
  No. of threads or processors used:  24
  Search cpu time:  13.75u 0.07s 13.82t   Elapsed:  00:00:08
  Total cpu time:  13.75u 0.07s 13.82t   Elapsed:  00:00:11
  Start:  Fri May 10 20:01:15 2013   End:  Fri May 10 20:01:26 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

No confident hit detected by STRING

---

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	144
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	2e-13
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-10
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	1e-04

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

 Score = 61.4 bits (150), Expect = 2e-13
 Identities = 26/75 (34%), Positives = 41/75 (54%)

Query: 45  IGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTP 104
            G+Q+AL +G   ++ ESDS  VV+ +     + S++  ++ EI +  K F +    H P
Sbjct: 12  EGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFDSVSVSHVP 71

Query: 105 RSCNGIAHFLAKLVL 119
           R CN +A  LAKL  
Sbjct: 72  RECNRVADALAKLAS 86

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

>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 = 54.7 bits (132), Expect = 2e-10
 Identities = 29/111 (26%), Positives = 55/111 (49%), Gaps = 3/111 (2%)

Query: 8   AGLAVVIRDWERNCV-AAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHE 66
           AG   V+RD E   + A +++           +   +   +++AL +G   ++ E+DS  
Sbjct: 13  AGAGGVLRDHEGAWLFAGSLSIPA--ATNNEAELLALLEALELALDLGLKKLIIETDSKY 70

Query: 67  VVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKL 117
           VV+L+N+ +    K   ++++IL     F + + +H PR  N +A  LAK 
Sbjct: 71  VVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPREGNEVADRLAKE 121

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

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 45  IGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFE-ILEKKKNFQNFKAQHT 103
            G+++AL +G   +    DS  VV  +       ++ +    E   E  K F+  + +  
Sbjct: 52  AGLELALELGIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKWI 111

Query: 104 PRSCNGIAHFLAKLVLQ 120
           PR  N  A  LA   L 
Sbjct: 112 PREENKEADALANQALD 128

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. Length = 128

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	144
PRK13907	128	rnhA ribonuclease H; Provisional	99.95
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.93
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.9
PRK07708	219	hypothetical protein; Validated	99.9
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.86
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.83
PRK08719	147	ribonuclease H; Reviewed	99.71
PRK00203	150	rnhA ribonuclease H; Reviewed	99.68
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.66
PRK06548	161	ribonuclease H; Provisional	99.63
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	99.2
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
COG0590	152	CumB Cytosine/adenosine deaminases [Nucleotide tra	92.3
COG0295	134	Cdd Cytidine deaminase [Nucleotide transport and m	89.38
cd01285	109	nucleoside_deaminase Nucleoside deaminases include	88.88
cd01284	115	Riboflavin_deaminase-reductase Riboflavin-specific	88.5
TIGR01354	127	cyt_deam_tetra cytidine deaminase, homotetrameric.	86.01
cd00786	96	cytidine_deaminase-like Cytidine and deoxycytidyla	85.97
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	82.49

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.95  E-value=3.1e-27  Score=158.10  Aligned_cols=118  Identities=17%  Similarity=0.098  Sum_probs=105.1

Q ss_pred             CCCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchh
Q 037050            1 MDAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSK   80 (144)
Q Consensus         1 f~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~   80 (144)
                      ++++++.+|+|+|+||..|.+...+.  . +..|+++||++|++.||+.+.++|+++|+++|||+.+++++++.......
T Consensus        10 ~~~~~g~~G~G~vi~~~~~~~~~~~~--~-~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~   86 (128)
T PRK13907         10 SKGNPGPSGAGVFIKGVQPAVQLSLP--L-GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKM   86 (128)
T ss_pred             CCCCCCccEEEEEEEECCeeEEEEec--c-cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChh
Confidence            46788999999999999987665432  2 36799999999999999999999999999999999999999987655567


Q ss_pred             HHHHHHHHHHHHhcCccEEEEEecCCchHHHHHHHhhhccc
Q 037050           81 IIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQK  121 (144)
Q Consensus        81 ~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~~  121 (144)
                      +..++++++.++..|+.+.+.||||++|+.||.||+.+...
T Consensus        87 ~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         87 FAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ  127 (128)
T ss_pred             HHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHhc
Confidence            89999999999999999999999999999999999998753

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

Probab=99.93  E-value=1.6e-25  Score=139.64  Aligned_cols=86  Identities=31%  Similarity=0.382  Sum_probs=75.8

Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHHHHHHHHHHHHhcCccEEEEEecCCchHHHHHH
Q 037050           35 VAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFL  114 (144)
Q Consensus        35 ~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~L  114 (144)
                      |++||++|++.||++|+++|+++|++||||+.+++.+++....++.+..++++|+.+++.|+++++.||+|++|++||.|
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~L   80 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADAL   80 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHH
Confidence            68999999999999999999999999999999999999987666689999999999999999999999999999999999


Q ss_pred             Hhhhcc
Q 037050          115 AKLVLQ  120 (144)
Q Consensus       115 Ak~a~~  120 (144)
                      ||.+.+
T Consensus        81 A~~a~~   86 (87)
T PF13456_consen   81 AKFALS   86 (87)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            999864

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.90  E-value=3.6e-23  Score=160.46  Aligned_cols=128  Identities=19%  Similarity=0.149  Sum_probs=112.6

Q ss_pred             CCCCCCceeEEEEEeCCCCC-eeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCC-Cc
Q 037050            1 MDAKKQVAGLAVVIRDWERN-CVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTN-SM   78 (144)
Q Consensus         1 f~~~~~~~g~G~vird~~g~-~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~-~~   78 (144)
                      ++.+++.+|+|+|+|+++|. ++...+..++ ..|+++||+.|++.||+.+.++|+++|+|++||+.+++.+++... ..
T Consensus        11 ~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~   89 (372)
T PRK07238         11 SRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKH   89 (372)
T ss_pred             CCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCC
Confidence            35678899999999999764 5556666555 678899999999999999999999999999999999999998754 34


Q ss_pred             hhHHHHHHHHHHHHhcCccEEEEEecCCchHHHHHHHhhhcccCCeeeecc
Q 037050           79 SKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQKKEIVIWLD  129 (144)
Q Consensus        79 ~~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~~~~~~~~~~  129 (144)
                      ..+..++++++.+.++|+.+++.||+|++|+.||.||+.++......+|.+
T Consensus        90 ~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~~~~~~~~  140 (372)
T PRK07238         90 PDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAGGEPWG  140 (372)
T ss_pred             hHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhhccCCCcc
Confidence            578889999999999999999999999999999999999999777777875

>PRK07708 hypothetical protein; Validated

Probab=99.90  E-value=1.3e-22  Score=146.57  Aligned_cols=122  Identities=20%  Similarity=0.113  Sum_probs=102.9

Q ss_pred             CCCCCCceeEEEEEeCCCCCee--eecccccCCCCChHHHHHHHHHHHHHHHHHhCCCc--eEEeccHHHHHHHHhcCCC
Q 037050            1 MDAKKQVAGLAVVIRDWERNCV--AAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYS--VLFESDSHEVVELVNNRTN   76 (144)
Q Consensus         1 f~~~~~~~g~G~vird~~g~~~--~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~--v~~esDs~~vv~~l~~~~~   76 (144)
                      |+.+++.+|+|+|++++.|...  ......++...|+++||+.|++.||+.|.++|+++  |++++||+.|++++++...
T Consensus        82 ~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk  161 (219)
T PRK07708         82 FDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWP  161 (219)
T ss_pred             cCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCce
Confidence            4567889999999998877543  33344566678999999999999999999999976  8999999999999999753


Q ss_pred             C-chhHHHHHHHHHHHHhcCcc-EEEEEecCCchHHHHHHHhhhcccC
Q 037050           77 S-MSKIIWVIFEILEKKKNFQN-FKAQHTPRSCNGIAHFLAKLVLQKK  122 (144)
Q Consensus        77 ~-~~~~~~~~~~i~~l~~~~~~-~~~~~v~r~~N~~Ad~LAk~a~~~~  122 (144)
                      . ...+..+.+++..+.+.|.. +.+.||+|++|..||.||+.|++..
T Consensus       162 ~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~  209 (219)
T PRK07708        162 CYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGT  209 (219)
T ss_pred             eCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcC
Confidence            3 34677788999888888764 8899999999999999999999843

>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=99.86  E-value=3.1e-20  Score=121.65  Aligned_cols=115  Identities=21%  Similarity=0.162  Sum_probs=102.2

Q ss_pred             CCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCC-CchhHH
Q 037050            4 KKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTN-SMSKII   82 (144)
Q Consensus         4 ~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~-~~~~~~   82 (144)
                      +.+.+|+|+|+++..+.......... ...+++++|+.|+..||+.+...+.+++.++|||+.+++.+++... ......
T Consensus        11 ~~~~~g~g~v~~~~~~~~~~~~~~~~-~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~   89 (130)
T cd06222          11 NPGPAGAGVVLRDPGGEVLLSGGLLG-GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNV   89 (130)
T ss_pred             CCCceEEEEEEEeCCCeEEEeccccC-CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhH
Confidence            34678999999999998877777654 5789999999999999999999999999999999999999998754 455788


Q ss_pred             HHHHHHHHHHhcCccEEEEEecC----CchHHHHHHHhhhc
Q 037050           83 WVIFEILEKKKNFQNFKAQHTPR----SCNGIAHFLAKLVL  119 (144)
Q Consensus        83 ~~~~~i~~l~~~~~~~~~~~v~r----~~N~~Ad~LAk~a~  119 (144)
                      .++.+++.+...+..+++.||+|    +.|..||.|||.+.
T Consensus        90 ~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          90 DLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            88999999888999999999999    99999999999874

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

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

Probab=99.83  E-value=5.1e-20  Score=125.38  Aligned_cols=118  Identities=15%  Similarity=0.012  Sum_probs=98.0

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC---C---
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR---T---   75 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~---~---   75 (144)
                      ..+||++|+|+|++..++..-...  ... .+|++.+|++|++.||+.+++.+...|.++|||+.|++.++.-   .   
T Consensus        13 ~gNpG~gG~g~vl~~~~~~~~~s~--~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~   89 (154)
T COG0328          13 LGNPGPGGWGAVLRYGDGEKELSG--GEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKN   89 (154)
T ss_pred             CCCCCCceEEEEEEcCCceEEEee--eee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhcccc
Confidence            468899999999997666662333  233 6899999999999999999999999999999999999999831   0   


Q ss_pred             ------CCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhcccC
Q 037050           76 ------NSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQKK  122 (144)
Q Consensus        76 ------~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~~  122 (144)
                            ..+-.-..+++++..+...+..+.+.||+    +..|+.||.||+.+....
T Consensus        90 ~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          90 GWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             CccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence                  11223457799999999999999999999    778999999999998743

>PRK08719 ribonuclease H; Reviewed

Probab=99.71  E-value=2.5e-16  Score=107.62  Aligned_cols=109  Identities=16%  Similarity=0.058  Sum_probs=85.7

Q ss_pred             ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------CC---
Q 037050            7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN--------RT---   75 (144)
Q Consensus         7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~--------~~---   75 (144)
                      ++|+|+++.+..|......+..+....|++.||++|+..||+.+.+.    ..|.|||+.+++.++.        ..   
T Consensus        22 ~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s   97 (147)
T PRK08719         22 RGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKS   97 (147)
T ss_pred             CcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccC
Confidence            67999999998887654444445556899999999999999998764    4799999999999952        11   


Q ss_pred             -CCchhHHHHHHHHHHHHhcCccEEEEEecC----CchHHHHHHHhhhcc
Q 037050           76 -NSMSKIIWVIFEILEKKKNFQNFKAQHTPR----SCNGIAHFLAKLVLQ  120 (144)
Q Consensus        76 -~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r----~~N~~Ad~LAk~a~~  120 (144)
                       ..+-....+++.|..+.. ...++|.||++    .+|..||.||+.|..
T Consensus        98 ~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         98 DKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             CCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence             122334677888877766 57799999999    579999999999864

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.68  E-value=9.5e-16  Score=105.14  Aligned_cols=114  Identities=11%  Similarity=-0.014  Sum_probs=86.3

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN--------   73 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~--------   73 (144)
                      +.+++.+|+|+|+...++.....+  ..+ ..|++.||++|+..||+.+.+  ...|.|.|||+.+++.+++        
T Consensus        13 ~~n~~~~g~g~v~~~~~~~~~~~~--~~~-~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~   87 (150)
T PRK00203         13 LGNPGPGGWGAILRYKGHEKELSG--GEA-LTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKN   87 (150)
T ss_pred             cCCCCceEEEEEEEECCeeEEEec--CCC-CCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHc
Confidence            456788999999986555433322  233 578999999999999998754  3579999999999999985        


Q ss_pred             CC--C--CchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhccc
Q 037050           74 RT--N--SMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQK  121 (144)
Q Consensus        74 ~~--~--~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~  121 (144)
                      ..  .  .+-....+++++..++.. ..+.|.||+    ++.|..||.|||.+...
T Consensus        88 ~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203         88 GWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             CCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            11  1  122345678888887665 679999999    66799999999998763

>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=99.66  E-value=6.3e-16  Score=103.27  Aligned_cols=109  Identities=18%  Similarity=0.025  Sum_probs=82.1

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc-----CCC
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN-----RTN   76 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~-----~~~   76 (144)
                      +.+++.+|+|+|+.+.  .   ..+..++ ..++..+|++|+..||+ +.  .-+++.|+|||+.+++.++.     ...
T Consensus        13 ~~~~~~~~~g~v~~~~--~---~~~~~~~-~~s~~~aEl~Ai~~AL~-~~--~~~~v~I~tDS~~v~~~l~~~~~~~~~~   83 (132)
T PF00075_consen   13 RPNPGKGGAGYVVWGG--R---NFSFRLG-GQSNNRAELQAIIEALK-AL--EHRKVTIYTDSQYVLNALNKWLHGNGWK   83 (132)
T ss_dssp             CTTTTEEEEEEEEETT--E---EEEEEEE-SECHHHHHHHHHHHHHH-TH--STSEEEEEES-HHHHHHHHTHHHHTTSB
T ss_pred             cCCCCceEEEEEEECC--e---EEEeccc-ccchhhhheehHHHHHH-Hh--hcccccccccHHHHHHHHHHhccccccc
Confidence            3457788999977433  2   3333444 78999999999999999 55  22999999999999998877     332


Q ss_pred             CchhHHHHHHHHHHHHhcCccEEEEEecCC-----chHHHHHHHhhhc
Q 037050           77 SMSKIIWVIFEILEKKKNFQNFKAQHTPRS-----CNGIAHFLAKLVL  119 (144)
Q Consensus        77 ~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~-----~N~~Ad~LAk~a~  119 (144)
                      .......+..++..++.....+.|.|||.+     +|..||.|||.++
T Consensus        84 ~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   84 KTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             SCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            222222466688887777889999999998     6889999999875

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 ....

>PRK06548 ribonuclease H; Provisional

Probab=99.63  E-value=1.7e-14  Score=99.64  Aligned_cols=112  Identities=15%  Similarity=0.057  Sum_probs=84.9

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN--------   73 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~--------   73 (144)
                      ..+++++|+|+++.+. + ..   +... ...|++.||++|++.||+.+. ....+|.|.|||+.+++.+++        
T Consensus        15 ~gnpg~~G~g~~~~~~-~-~~---~g~~-~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~   87 (161)
T PRK06548         15 LANPGPSGWAWYVDEN-T-WD---SGGW-DIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLTKWVYSWKMR   87 (161)
T ss_pred             CCCCCceEEEEEEeCC-c-EE---ccCC-CCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHHHHHHHHHHHC
Confidence            4578999999999753 2 21   2212 368999999999999997553 455689999999999999994        


Q ss_pred             C----CCCchhHHHHHHHHHHHHhcCccEEEEEecCC----chHHHHHHHhhhccc
Q 037050           74 R----TNSMSKIIWVIFEILEKKKNFQNFKAQHTPRS----CNGIAHFLAKLVLQK  121 (144)
Q Consensus        74 ~----~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~----~N~~Ad~LAk~a~~~  121 (144)
                      .    ...+-.-..++++|..++.. ..++|.||+-+    .|..||.||+.+...
T Consensus        88 gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548         88 KWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             CCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            1    11122357888999888766 47999999865    599999999998763

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

Probab=99.20  E-value=4.1e-10  Score=85.81  Aligned_cols=111  Identities=14%  Similarity=-0.001  Sum_probs=83.8

Q ss_pred             CceeEEEEEeCCCCCeeeecccccC-CCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC----------
Q 037050            6 QVAGLAVVIRDWERNCVAAAINTTR-FFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR----------   74 (144)
Q Consensus         6 ~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~----------   74 (144)
                      ..+|+|+.+=+  |.-.-.. .++. +..+++.||+.|+.+||+.|++...++|+|.|||..++++++..          
T Consensus       229 ~~AGyGvywg~--~~e~N~s-~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k  305 (371)
T KOG3752|consen  229 SRAGYGVYWGP--GHELNVS-GPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWK  305 (371)
T ss_pred             CcceeEEeeCC--CCccccc-ccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccc
Confidence            57899998854  3332222 3344 78999999999999999999999999999999999999999850          


Q ss_pred             CCCc-------hhHHHHHHHHHHHHhc--CccEEEEEecCC----chHHHHHHHhhhc
Q 037050           75 TNSM-------SKIIWVIFEILEKKKN--FQNFKAQHTPRS----CNGIAHFLAKLVL  119 (144)
Q Consensus        75 ~~~~-------~~~~~~~~~i~~l~~~--~~~~~~~~v~r~----~N~~Ad~LAk~a~  119 (144)
                      ....       -.-...+.++.++.+.  ...+++.||+-.    +|..||.||+.+.
T Consensus       306 ~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  306 TSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             cccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            0111       1123446666666555  477899999875    6999999999883

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

Probab=98.11  E-value=9.7e-06  Score=63.51  Aligned_cols=117  Identities=16%  Similarity=0.163  Sum_probs=93.5

Q ss_pred             CCceeEEEEEeCC-CCCeeeecccccCC--CCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCch--
Q 037050            5 KQVAGLAVVIRDW-ERNCVAAAINTTRF--FGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMS--   79 (144)
Q Consensus         5 ~~~~g~G~vird~-~g~~~~~~~~~~~~--~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~--   79 (144)
                      ...+|.|+++.|. +....+........  ..++..||++|+..+|..+.++|+.++.+.+|+..+.+.+.+......  
T Consensus        16 ~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~   95 (384)
T KOG1812|consen   16 ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHR   95 (384)
T ss_pred             hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHH
Confidence            4578999999996 66666666655442  378999999999999999999999999999998888887776643322  


Q ss_pred             hHHHHHHHHHHHHhcCccEEEEEecCC-chHHHHHHHhhhccc
Q 037050           80 KIIWVIFEILEKKKNFQNFKAQHTPRS-CNGIAHFLAKLVLQK  121 (144)
Q Consensus        80 ~~~~~~~~i~~l~~~~~~~~~~~v~r~-~N~~Ad~LAk~a~~~  121 (144)
                      .+..++++.+.+...+....-..+++. ..+.|-.||+++...
T Consensus        96 ~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s  138 (384)
T KOG1812|consen   96 KIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIVS  138 (384)
T ss_pred             HHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhcc
Confidence            577888888888888888877788775 557799999998874

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

Probab=92.30  E-value=0.43  Score=32.74  Aligned_cols=59  Identities=12%  Similarity=-0.010  Sum_probs=42.9

Q ss_pred             CCceeEEEEEeCCCCCeeeecccccCC-CCChHHHHHHHHHHHHHHHHHhCCCceEEecc
Q 037050            5 KQVAGLAVVIRDWERNCVAAAINTTRF-FGNVAMTQAATIEIGMQVALSVGGYSVLFESD   63 (144)
Q Consensus         5 ~~~~g~G~vird~~g~~~~~~~~~~~~-~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esD   63 (144)
                      .+...+|.||.+.+|.++..+...... .....+||..||+.|-+......+...++++-
T Consensus        25 ~ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyvT   84 (152)
T COG0590          25 EGEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVT   84 (152)
T ss_pred             cCCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEEe
Confidence            345678999999899888866655432 23445899999999998886656666666654

>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]

Probab=89.38  E-value=2  Score=28.92  Aligned_cols=55  Identities=11%  Similarity=0.049  Sum_probs=42.7

Q ss_pred             eEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050            9 GLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS   64 (144)
Q Consensus         9 g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs   64 (144)
                      -+|.++|..+|.+..+..--.....--.-||-.|+..++.. -...+..|.+.+|.
T Consensus        27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~   81 (134)
T COG0295          27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT   81 (134)
T ss_pred             cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence            36899999999877776644445666778999999999876 45556888898887

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

Probab=88.88  E-value=1.5  Score=28.12  Aligned_cols=58  Identities=14%  Similarity=-0.041  Sum_probs=38.5

Q ss_pred             CCceeEEEEEeCCCCCeeeecccccC-CCCChHHHHHHHHHHHHHHHHHhCCCceEEec
Q 037050            5 KQVAGLAVVIRDWERNCVAAAINTTR-FFGNVAMTQAATIEIGMQVALSVGGYSVLFES   62 (144)
Q Consensus         5 ~~~~g~G~vird~~g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~es   62 (144)
                      .+...+|.+|.|.+|.++..+..... .......||..|+..+.+.-....+....+++
T Consensus        14 ~~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~   72 (109)
T cd01285          14 EGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYT   72 (109)
T ss_pred             cCCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEE
Confidence            34567889999988988776665432 34567899999999887653222244444444

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=88.50  E-value=1.6  Score=28.49  Aligned_cols=41  Identities=10%  Similarity=0.051  Sum_probs=31.6

Q ss_pred             CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHH
Q 037050            6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQV   49 (144)
Q Consensus         6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~   49 (144)
                      +...+|.||.+.+|.++..+.....   ...+||..|+..+.+.
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            4557888998888988887665532   6789999999998764

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=86.01  E-value=1.4  Score=29.23  Aligned_cols=57  Identities=2%  Similarity=-0.049  Sum_probs=39.5

Q ss_pred             ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050            7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS   64 (144)
Q Consensus         7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs   64 (144)
                      ...+|.++++.+|.+..+...-.........||..|+..+...-. ..+..+.+-++.
T Consensus        20 ~~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~-~~i~~i~vv~~~   76 (127)
T TIGR01354        20 NFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGY-RKFVAIAVADSA   76 (127)
T ss_pred             CCeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCC-CCeEEEEEEeCC
Confidence            345788999999998775554333455667899999999886532 256677776654

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=85.97  E-value=4  Score=25.42  Aligned_cols=44  Identities=5%  Similarity=-0.009  Sum_probs=29.5

Q ss_pred             CCceeEEEEEeCC-CCCeeeecccc-cCCCCChHHHHHHHHHHHHH
Q 037050            5 KQVAGLAVVIRDW-ERNCVAAAINT-TRFFGNVAMTQAATIEIGMQ   48 (144)
Q Consensus         5 ~~~~g~G~vird~-~g~~~~~~~~~-~~~~~~~~~aE~~Al~~aL~   48 (144)
                      .+...+|.++.+. +|.++..+... .........||..|+..+.+
T Consensus        15 ~~~~pVGaviv~~~~g~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~   60 (96)
T cd00786          15 ESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS   60 (96)
T ss_pred             CCCCCEEEEEEEeCCCCeEeeeEeccCCCCCCeeCHHHHHHHHHHH
Confidence            3566778888875 56666655433 22345678999999988754

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.

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein

Probab=82.49  E-value=4.3  Score=29.37  Aligned_cols=86  Identities=12%  Similarity=0.006  Sum_probs=53.4

Q ss_pred             CCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHHHH
Q 037050            5 KQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKIIWV   84 (144)
Q Consensus         5 ~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~~~   84 (144)
                      .-..|+|..+  ..|...+.++.    .-++..+|++|...|.    .+--.++ +-|||..|++.=.  ..-++.++..
T Consensus       101 ATpTgwgi~i--~~~~~~~Tfs~----~l~IhtaELlaaClAr----~~~~~r~-l~tDnt~Vlsrky--ts~PW~lac~  167 (245)
T PF00336_consen  101 ATPTGWGISI--TGQRMRGTFSK----PLPIHTAELLAACLAR----LMSGARC-LGTDNTVVLSRKY--TSFPWLLACA  167 (245)
T ss_pred             CCCCcceeee--cCceeeeeecc----cccchHHHHHHHHHHH----hccCCcE-EeecCcEEEeccc--ccCcHHHHHH
Confidence            3456777775  33444444443    4678999999986554    3333344 8899988754211  2345666555


Q ss_pred             HHHHHHHHhcCccEEEEEecCCchH
Q 037050           85 IFEILEKKKNFQNFKAQHTPRSCNG  109 (144)
Q Consensus        85 ~~~i~~l~~~~~~~~~~~v~r~~N~  109 (144)
                      -+.|.      ...++.|||...|-
T Consensus       168 A~wiL------rgts~~yVPS~~NP  186 (245)
T PF00336_consen  168 ANWIL------RGTSFYYVPSKYNP  186 (245)
T ss_pred             HHHhh------cCceEEEeccccCc
Confidence            55443      35679999999886

The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity

---

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	144
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	8e-05
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	6e-04

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

 Score = 39.3 bits (92), Expect = 8e-05
 Identities = 26/117 (22%), Positives = 43/117 (36%), Gaps = 6/117 (5%)

Query: 7   VAGLAVVIRDWERNCVAAAINTTRFFG----NVAMTQAATIEIGMQVALSVGGYSVLFES 62
           +A    VI    R      +    F      NVA      +   M+  L +G  S + + 
Sbjct: 18  IATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSG--LICLMETMLRLGISSPIIKG 75

Query: 63  DSHEVVELVNNRTNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVL 119
           DS  V++ +N      +K I  ++E   + K   N      PR  N  A  L+++  
Sbjct: 76  DSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVAY 132

>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 = 36.9 bits (86), Expect = 6e-04
 Identities = 25/115 (21%), Positives = 42/115 (36%), Gaps = 9/115 (7%)

Query: 8   AGLAVVIRDWERNCVAAAINTTRFFG----NVAMTQAATIEIGMQVALSVGGYSVLFESD 63
           AG   V+   + + V A     +  G    NVA  +      G+  A+ +G        D
Sbjct: 19  AGYGAVVWTADHSTVLAES--KQAIGRATNNVAEYRGLIA--GLDDAVKLGATEAAVLMD 74

Query: 64  SHEVVELVNNRTNSMSKIIWVIF-EILEKKKNFQNFKAQHTPRSCNGIAHFLAKL 117
           S  VVE ++ R       +  ++ +       F+    +  PR+ N  A  LA  
Sbjct: 75  SKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAND 129

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	144
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.94
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.94
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.93
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.86
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.82
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.8
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.8
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.79
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.79
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.73
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.73
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.71
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.56
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.53
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.48
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.44
1uwz_A	136	Cytidine deaminase; CDD, tetramer, zinc binding, p	89.66
2fr5_A	146	Cytidine deaminase; tetrahydrouridine, protein-inh	86.94
2z3g_A	130	Blasticidin-S deaminase; hydrolase, cytidine deami	81.6

>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=99.94  E-value=2.5e-26  Score=154.54  Aligned_cols=119  Identities=17%  Similarity=0.191  Sum_probs=105.0

Q ss_pred             CCCCCceeEEEEEeCCC-CCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCC-CCch
Q 037050            2 DAKKQVAGLAVVIRDWE-RNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRT-NSMS   79 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~-g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~-~~~~   79 (144)
                      +.+++.+|+|+|+++.. |.++...+..++ ..|++.||+.|++.||+.+.++|.++|.|+|||+.+++.+++.. ....
T Consensus        13 ~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~~~~~   91 (141)
T 3hst_B           13 RGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHP   91 (141)
T ss_dssp             SSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSCCCSH
T ss_pred             CCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcccCCH
Confidence            45678999999999987 666666666554 68999999999999999999999999999999999999999864 4445


Q ss_pred             hHHHHHHHHHHHHhcCccEEEEEecCCchHHHHHHHhhhccc
Q 037050           80 KIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQK  121 (144)
Q Consensus        80 ~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~~  121 (144)
                      .+..++++|+.+...|..++|.||+|++|..||.|||.|+..
T Consensus        92 ~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           92 DLLKLYVQAQALASQFRRINYEWVPRARNTYADRLANDAMDA  133 (141)
T ss_dssp             HHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHHHHHHH
Confidence            688889999999999999999999999999999999999863

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

Probab=99.94  E-value=3.5e-26  Score=153.40  Aligned_cols=118  Identities=17%  Similarity=0.121  Sum_probs=105.3

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCC----ceEEeccHHHHHHHHhcCCC-
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGY----SVLFESDSHEVVELVNNRTN-   76 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~----~v~~esDs~~vv~~l~~~~~-   76 (144)
                      ..+++.+|+|+|+++++|..+...+..++ ..|++.||++|++.||+.+.+.+.+    +|+|+|||+.+++.+++... 
T Consensus        13 ~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~   91 (140)
T 3u3g_D           13 RGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKV   91 (140)
T ss_dssp             SSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSCC
T ss_pred             CCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCCccc
Confidence            45678899999999999988777776665 5799999999999999999999999    99999999999999998653 


Q ss_pred             CchhHHHHHHHHHHH-HhcCccEEEEEecCCchHHHHHHHhhhcc
Q 037050           77 SMSKIIWVIFEILEK-KKNFQNFKAQHTPRSCNGIAHFLAKLVLQ  120 (144)
Q Consensus        77 ~~~~~~~~~~~i~~l-~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~  120 (144)
                      ....+..+++++..+ ..+|..++|.||||++|..||.|||.|+.
T Consensus        92 ~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           92 KEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAID  136 (140)
T ss_dssp             CCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHHHHHH
Confidence            344677889999999 99999999999999999999999999876

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

Probab=99.93  E-value=6.3e-25  Score=149.31  Aligned_cols=116  Identities=18%  Similarity=0.158  Sum_probs=100.4

Q ss_pred             CCCCceeE-EEEEeCCCCCeeeecccccC---CCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCC-C
Q 037050            3 AKKQVAGL-AVVIRDWERNCVAAAINTTR---FFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTN-S   77 (144)
Q Consensus         3 ~~~~~~g~-G~vird~~g~~~~~~~~~~~---~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~-~   77 (144)
                      .+++.+|+ |+|+++ +|..+...+...+   ...|+++||+.|++.||+.+.++|.++|.++|||+.+++.+++... .
T Consensus        13 ~n~g~~G~~G~vi~~-~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~~~   91 (149)
T 2ehg_A           13 KNPGGIATFGFVIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVK   91 (149)
T ss_dssp             SSSSSEEEEEEEEEC-SSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSCCC
T ss_pred             CCCChheEEEEEEEE-CCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccccC
Confidence            46789996 999999 8887755443333   3789999999999999999999999999999999999999998632 2


Q ss_pred             chhHHHHHHHHHHHHhcCccEEEEEecCCchHHHHHHHhhhcc
Q 037050           78 MSKIIWVIFEILEKKKNFQNFKAQHTPRSCNGIAHFLAKLVLQ  120 (144)
Q Consensus        78 ~~~~~~~~~~i~~l~~~~~~~~~~~v~r~~N~~Ad~LAk~a~~  120 (144)
                      ...+..+++++..++..| .++|.||||++|..||.|||.|..
T Consensus        92 ~~~~~~l~~~i~~l~~~~-~v~~~~V~~~~N~~AD~LA~~a~~  133 (149)
T 2ehg_A           92 AKRIIPLYEKAIELKKKL-NATLIWVPREENKEADRLSRVAYE  133 (149)
T ss_dssp             CTTHHHHHHHHHHHHHHH-TCEEEECCGGGCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcC-CEEEEEcCCcccHHHHHHHHHHHH
Confidence            346888999999998888 599999999999999999999987

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

Probab=99.86  E-value=9e-21  Score=129.52  Aligned_cols=111  Identities=12%  Similarity=-0.046  Sum_probs=91.0

Q ss_pred             ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC------------
Q 037050            7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR------------   74 (144)
Q Consensus         7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~------------   74 (144)
                      .+|+|+|+++.++..+   +..+.+..|++.||++|++.||+.+.+.+.++|.|+|||+.+++.+++.            
T Consensus        25 ~aG~Gvv~~~~~~~~~---~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~  101 (154)
T 2qkb_A           25 RAGIGVYWGPGHPLNV---GIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTS  101 (154)
T ss_dssp             EEEEEEECSTTCTTCE---EEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCT
T ss_pred             cEEEEEEEECCCceeE---EeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhcccccc
Confidence            4899999998655332   2334446899999999999999999999999999999999999999861            


Q ss_pred             CCCchhHHHHHHHHHHHHhcCccEEEEEecCC----chHHHHHHHhhhccc
Q 037050           75 TNSMSKIIWVIFEILEKKKNFQNFKAQHTPRS----CNGIAHFLAKLVLQK  121 (144)
Q Consensus        75 ~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~----~N~~Ad~LAk~a~~~  121 (144)
                      ...+.....++++|..++..+. +.|.||+++    +|..||.|||.+...
T Consensus       102 ~~~~~~n~~l~~~i~~l~~~~~-v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          102 AGKEVINKEDFVALERLTQGMD-IQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             TSSBCTTHHHHHHHHHHHTTCE-EEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             CCCccccHHHHHHHHHHHcCCc-eEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            1122345678999999888765 999999985    599999999999874

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

Probab=99.82  E-value=2.1e-20  Score=126.58  Aligned_cols=114  Identities=15%  Similarity=0.073  Sum_probs=90.8

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC-------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR-------   74 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~-------   74 (144)
                      ..+++.+|+|+|+++.+..  ...+...+ ..|++.||+.|++.||+.+.+  ..+|.|+|||+.+++.+++.       
T Consensus        14 ~~n~g~~g~G~v~~~~~~~--~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~   88 (146)
T 3h08_A           14 SGNPGKGGWGALLMYGSSR--KEISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEGWLKRWVK   88 (146)
T ss_dssp             SSTTEEEEEEEEEEETTEE--EEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSSHHHHHHH
T ss_pred             CCCCCceEEEEEEEECCee--EEeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHHHHHHHHH
Confidence            4567889999999986432  33333343 579999999999999999876  58999999999999999872       


Q ss_pred             ------CCCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhccc
Q 037050           75 ------TNSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQK  121 (144)
Q Consensus        75 ------~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~  121 (144)
                            ...+.....+++++..+...+ .+.|.||+    |++|..||.|||.|...
T Consensus        89 ~~w~~~~~~~v~n~~l~~~~~~~~~~~-~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           89 NGWKTAAKKPVENIDLWQEILKLTTLH-RVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             TTCC----CCCTTHHHHHHHHHHHHHS-EEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCCCCcCCHHHHHHHHHHHhhC-ceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence                  122334567888898887776 59999999    99999999999999864

>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=99.80  E-value=8.2e-20  Score=124.93  Aligned_cols=115  Identities=12%  Similarity=0.022  Sum_probs=90.1

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN--------   73 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~--------   73 (144)
                      ..+++.+|+|+|+++..+.....+  ..+ ..|++.||+.|++.||+.+.+.  .+|.|+|||+.+++.+++        
T Consensus        14 ~~n~~~~G~G~v~~~~~~~~~~~~--~~~-~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i~~w~~~W~~n   88 (155)
T 1jl1_A           14 LGNPGPGGYGAILRYRGREKTFSA--GYT-RTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGITQWIHNWKKR   88 (155)
T ss_dssp             SSTTEEEEEEEEEEETTEEEEEEE--EEE-EECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHHHTTHHHHHHT
T ss_pred             CCCCCceEEEEEEEECCeEEEEec--CCC-CCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHHHHHHHHHhhc
Confidence            356788999999998665433332  233 5789999999999999998764  899999999999999987        


Q ss_pred             CC----CCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhcccC
Q 037050           74 RT----NSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQKK  122 (144)
Q Consensus        74 ~~----~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~~  122 (144)
                      ..    ..+.....+++++..++.. ..+.|.||+    |++|..||.|||.+....
T Consensus        89 ~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  144 (155)
T 1jl1_A           89 GWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVKGHAGHPENERADELARAAAMNP  144 (155)
T ss_dssp             TTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             ccccccCCccCCHHHHHHHHHHHcc-CceEEEEcCCCCCCHHHHHHHHHHHHHHhcc
Confidence            11    1122335678888887765 489999999    889999999999998753

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

Probab=99.80  E-value=1.5e-19  Score=124.01  Aligned_cols=114  Identities=8%  Similarity=-0.001  Sum_probs=89.3

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc--------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN--------   73 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~--------   73 (144)
                      ..+++.+|+|+|+++.....  ..+...+ ..|++.||+.|++.||+.+.+.  .+|.|+|||+.+++.+++        
T Consensus        16 ~~n~g~~G~G~v~~~~~~~~--~~~~~~~-~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i~~w~~~W~~n   90 (158)
T 2e4l_A           16 LGNPGPGGYGIVMNYKGHTK--EMSDGFS-LTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGIMTWIHGWKKK   90 (158)
T ss_dssp             SSSSEEEEEEEEEEETTEEE--EEEEEEE-EECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHHHTHHHHHHHT
T ss_pred             cCCCCcEEEEEEEEECCEEE--EEecCcC-CCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHHHHHHHHHHHc
Confidence            35678899999999844322  2333333 5789999999999999988653  899999999999999987        


Q ss_pred             CC----CCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhccc
Q 037050           74 RT----NSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQK  121 (144)
Q Consensus        74 ~~----~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~  121 (144)
                      ..    ..+.....+++++..++.. ..+.|.||+    |++|..||.|||.+...
T Consensus        91 ~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           91 GWMTSNRTPVKNVDLWKRLDKAAQL-HQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             TTBCTTSSBCTTHHHHHHHHHHHTT-SEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             cccccCCCcccCHHHHHHHHHHHcc-CcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            21    1223445778888888776 489999999    77999999999999875

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

Probab=99.79  E-value=1.7e-19  Score=124.70  Aligned_cols=116  Identities=11%  Similarity=-0.022  Sum_probs=90.6

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC-------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR-------   74 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~-------   74 (144)
                      ..+++.+|+|+|+++..+.....  ... ...|++.||++|++.||+.+.+.  .+|.|+|||+.+++.+++.       
T Consensus        18 ~~n~g~~G~G~v~~~~~~~~~~~--~~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~w~~~W~~   92 (166)
T 1ril_A           18 LGNPGPGGWAALLRFHAHEKLLS--GGE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEGWLEGWRK   92 (166)
T ss_dssp             SSTTEEEEEEEEECBTTBCCEEC--CEE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSSHHHHHHH
T ss_pred             cCCCCCEEEEEEEEECCEEEEEe--cCC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhhHHHHHHh
Confidence            34668899999999865543332  223 35789999999999999988765  4899999999999999881       


Q ss_pred             --C----CCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhcccCC
Q 037050           75 --T----NSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQKKE  123 (144)
Q Consensus        75 --~----~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~~~  123 (144)
                        .    ..+.....+++++..++..+ .+.|.||+    |++|..||.|||.+.....
T Consensus        93 ~~w~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           93 RGWRTAEGKPVKNRDLWEALLLAMAPH-RVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             TTSBCTTSSBCTTHHHHHHHHHHHTTS-EEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             cccccccCCccCcHHHHHHHHHHHhcC-eEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence              1    11223456788888887764 89999999    8899999999999988543

>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=99.79  E-value=1e-18  Score=118.85  Aligned_cols=110  Identities=15%  Similarity=0.131  Sum_probs=87.2

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC-------
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR-------   74 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~-------   74 (144)
                      +.+++.+|+|+|+++..+..+     .. ..+|++.||++|++.||+.+   + .+|.|+|||+.+++.+++.       
T Consensus        22 ~~n~g~~g~G~v~~~~~~~~~-----~~-~~~Tnn~aEl~A~i~AL~~~---~-~~v~i~tDS~~v~~~i~~w~~~W~~~   91 (150)
T 3qio_A           22 NRETKLGKAGYVTNRGRQKVV-----TL-TDTTNQKTELQAIYLALQDS---G-LEVNIVTDSQYALGIITQWIHNWKKR   91 (150)
T ss_dssp             CTTTCCEEEEEEETTSCEEEE-----EE-SSCCHHHHHHHHHHHHHHHS---C-SEEEEEESCHHHHHHHHHHHHHHCC-
T ss_pred             CCCCCCeEEEEEEEcCCEEEE-----eC-CCCCHHHHHHHHHHHHHHhC---C-CcEEEEeCcHHHHHHHHHHHHHHhhc
Confidence            467888999999998654332     12 36899999999999999974   3 8999999999999999872       


Q ss_pred             -----CCCchhHHHHHHHHHHHHhcCccEEEEEecCCc----hHHHHHHHhhhccc
Q 037050           75 -----TNSMSKIIWVIFEILEKKKNFQNFKAQHTPRSC----NGIAHFLAKLVLQK  121 (144)
Q Consensus        75 -----~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~r~~----N~~Ad~LAk~a~~~  121 (144)
                           ...+.....+++++..++.++..+.|.||+++.    |..||.||+.|...
T Consensus        92 gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           92 GWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             -----------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             CcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence                 111223456788887767789999999999997    99999999999874

>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=99.73  E-value=2.7e-17  Score=113.45  Aligned_cols=113  Identities=12%  Similarity=0.033  Sum_probs=86.7

Q ss_pred             CCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCC-CCchhH
Q 037050            3 AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRT-NSMSKI   81 (144)
Q Consensus         3 ~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~-~~~~~~   81 (144)
                      .+++.+|+|+++++. |..+.. . .....+|++.||++|++.||+.+   ...+|.|+|||+.+++.+-... ..+...
T Consensus        34 ~npG~~g~G~vi~~~-~~~~~~-~-~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~~~g~~v~n  107 (165)
T 3p1g_A           34 LQEGQRRAGAAVTTE-TEVIWA-R-ALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVHSEGREIKN  107 (165)
T ss_dssp             EETTEEEEEEEEECS-SCEEEE-E-EECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSCCCSCCCSS
T ss_pred             CCCCceEEEEEEEEC-CEEEEE-e-cCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcccCCCcccC
Confidence            467899999999874 444332 2 23456799999999999999988   4789999999999999884221 122233


Q ss_pred             HHHHHHHHHHHhcCccEEEEEecCCc---------hHHHHHHHhhhccc
Q 037050           82 IWVIFEILEKKKNFQNFKAQHTPRSC---------NGIAHFLAKLVLQK  121 (144)
Q Consensus        82 ~~~~~~i~~l~~~~~~~~~~~v~r~~---------N~~Ad~LAk~a~~~  121 (144)
                      ..+++++...+..+..+.|.||+++.         |..||.|||.+...
T Consensus       108 ~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A          108 KNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMK  156 (165)
T ss_dssp             HHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhc
Confidence            45677775555578899999999876         99999999999873

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

Probab=99.73  E-value=3.1e-17  Score=113.08  Aligned_cols=111  Identities=23%  Similarity=0.137  Sum_probs=85.4

Q ss_pred             eeEEEEEeCCCC--CeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc------------
Q 037050            8 AGLAVVIRDWER--NCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN------------   73 (144)
Q Consensus         8 ~g~G~vird~~g--~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~------------   73 (144)
                      +|+|+|++..+.  .+........ +..+.+.||+.||..+|+.+...+ .+|.|.|||+.+++.+++            
T Consensus        28 aG~Gv~~~~~~~~~~~~~~~~~~t-nn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~  105 (165)
T 2lsn_A           28 AGMGIVHATYKPEYQVLNQWSIPL-GNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSFYVAESANKELPYWKSNGFVN  105 (165)
T ss_dssp             EEEEEEEECCSSSCCEEEEEEEEE-SSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCHHHHHHHHTHHHHHHHTTSCS
T ss_pred             EEEEEEEEECCCccEEeccccCCc-hHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChHHHHhhhhhhhhhheeccccc
Confidence            999999985443  3333333322 467899999999999999988776 479999999999999975            


Q ss_pred             CCCCchhHHHHHHHHHHHHhcCccEEEEEec----------CCchHHHHHHHhhhcc
Q 037050           74 RTNSMSKIIWVIFEILEKKKNFQNFKAQHTP----------RSCNGIAHFLAKLVLQ  120 (144)
Q Consensus        74 ~~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----------r~~N~~Ad~LAk~a~~  120 (144)
                      ....+-....+++++..++..+..++|.||+          |++|..||.||+++..
T Consensus       106 ~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A          106 NKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             CSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            1112223467788888888888899999998          4469999999999865

>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=99.71  E-value=6e-18  Score=114.73  Aligned_cols=112  Identities=9%  Similarity=-0.023  Sum_probs=81.2

Q ss_pred             CceeEEEEEeCCCCCe-eeec-ccccCC--CCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCch-h
Q 037050            6 QVAGLAVVIRDWERNC-VAAA-INTTRF--FGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMS-K   80 (144)
Q Consensus         6 ~~~g~G~vird~~g~~-~~~~-~~~~~~--~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~-~   80 (144)
                      +.+|+|+|+++ +|.. ...+ ....+.  ..|++.||++|++.||+.+.+.+. +|.|+|||+.+.+++++...... .
T Consensus        18 g~~G~G~vi~~-~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~~~~w~~~~~~   95 (147)
T 2kq2_A           18 GQYAWAYAFVK-DGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWATGEWKAKNEF   95 (147)
T ss_dssp             TBCEEEEEEEE-TTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHTTSSSSCCHHH
T ss_pred             CCcEEEEEEEE-CCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHHhCCCccCCcc
Confidence            78999999998 4543 2222 211222  368999999999999999999999 99999999998888877543332 2


Q ss_pred             HHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhcccC
Q 037050           81 IIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQKK  122 (144)
Q Consensus        81 ~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~~  122 (144)
                      ...+.+.++.+..   .++|.|||    +++|..||.|||.|....
T Consensus        96 ~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           96 TQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             HHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             hHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            2222333333322   78899999    467999999999998843

>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=99.56  E-value=1e-14  Score=117.25  Aligned_cols=106  Identities=11%  Similarity=0.090  Sum_probs=83.3

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhH
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKI   81 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~   81 (144)
                      +++++.+|+|+|+++.++.     .... ...|++.||+.|++.||+.    +..+|.+.|||+.+++.+++....  ..
T Consensus       446 ~~n~g~~g~G~v~~~~~~~-----~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~~~--~~  513 (555)
T 1mu2_A          446 NRQSKEGKAGYVTDRGKDK-----VKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTE--SE  513 (555)
T ss_dssp             CTTTCCEEEEEEETTSCEE-----EEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCSE--ES
T ss_pred             cCCCCCceEEEEEEeCCEe-----eccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhccccc--cc
Confidence            3567789999999875432     1122 3679999999999999987    779999999999999999974321  22


Q ss_pred             HHHHHHHHHHHhcCccEEEEEecCC----chHHHHHHHhhhc
Q 037050           82 IWVIFEILEKKKNFQNFKAQHTPRS----CNGIAHFLAKLVL  119 (144)
Q Consensus        82 ~~~~~~i~~l~~~~~~~~~~~v~r~----~N~~Ad~LAk~a~  119 (144)
                      ..+++++..++..+..+.+.||+++    +|..||.||+.|+
T Consensus       514 ~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          514 SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            3456677776667889999999985    6999999999874

>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=99.53  E-value=1.3e-14  Score=116.74  Aligned_cols=104  Identities=13%  Similarity=0.105  Sum_probs=79.1

Q ss_pred             CCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHH
Q 037050            3 AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKII   82 (144)
Q Consensus         3 ~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~   82 (144)
                      .+++.+|+|+|+++.....+     .. ...|++.||+.|++.||+.+    ..+|.+.|||+.+++.+++.....  ..
T Consensus       450 ~n~g~~g~g~v~~~~~~~~~-----~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~~~~--~~  517 (557)
T 2zd1_A          450 RETKLGKAGYVTNKGRQKVV-----PL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDKS--ES  517 (557)
T ss_dssp             TTTCCEEEEEEETTSCEEEE-----EE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCCSEE--SS
T ss_pred             CCCCceEEEEEEECCcEEEe-----cC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCCccC--CH
Confidence            56788999999985443222     12 36899999999999999988    689999999999999999864321  23


Q ss_pred             HHHHHHHHHHhcCccEEEEEecCC----chHHHHHHHhhh
Q 037050           83 WVIFEILEKKKNFQNFKAQHTPRS----CNGIAHFLAKLV  118 (144)
Q Consensus        83 ~~~~~i~~l~~~~~~~~~~~v~r~----~N~~Ad~LAk~a  118 (144)
                      .+++++...+..+..+.+.||+++    +|..||.||+.|
T Consensus       518 ~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          518 ELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            455666655555678999999995    599999999975

>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=99.48  E-value=1.7e-13  Score=92.12  Aligned_cols=70  Identities=11%  Similarity=0.086  Sum_probs=59.6

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCC
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRT   75 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~   75 (144)
                      +.+++.+|+|+|++ .+|..+.... .++ ..|++.||++|++.||+.+.+.+. +|.|+|||+.+++++++..
T Consensus        21 ~gNpG~~G~G~vl~-~~g~~~~~~~-~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~   90 (142)
T 1zbf_A           21 QGNPGIVEYKGVDT-KTGEVLFERE-PIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKK   90 (142)
T ss_dssp             CSSSEEEEEEEEET-TTCCEEEECC-CEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTC
T ss_pred             CCCCCCeEEEEEEE-eCCEEEEEec-ccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCC
Confidence            45788999999999 6777665433 344 579999999999999999999999 9999999999999998754

>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=99.44  E-value=5.3e-13  Score=88.52  Aligned_cols=69  Identities=12%  Similarity=0.115  Sum_probs=57.6

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR   74 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~   74 (144)
                      +++|+++|+|+|+++ .|..+... ..++ .+|++.||++|+++||+.+.+.+.+ |.|+|||+.|++++++.
T Consensus        15 ~GNPGp~G~ggV~~~-~g~~~~~~-g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A           15 QGNPGIVEYKGVDTK-TGEVLFER-EPIP-IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             ETTTEEEEEEEEETT-TCCEEEEE-EEEE-EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHHHT
T ss_pred             CCCCCCeEEEEEEEE-CCEEEEEe-cCCC-CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHHcC
Confidence            367899999988888 66655444 2343 6899999999999999999998876 89999999999999863

>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=89.66  E-value=0.31  Score=31.82  Aligned_cols=58  Identities=3%  Similarity=-0.062  Sum_probs=40.6

Q ss_pred             CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050            6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS   64 (144)
Q Consensus         6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs   64 (144)
                      +...+|.++++.+|.++.+.............||..|+..|... -...+..+.+.+|.
T Consensus        22 s~~~VGAal~~~dG~i~~G~Nvena~~~~t~cAE~~Ai~~A~~~-G~~~~~~~~l~~~~   79 (136)
T 1uwz_A           22 SKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEATALFKAVSE-GDTEFQMLAVAADT   79 (136)
T ss_dssp             TCCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHH-TCCCEEEEEEEESC
T ss_pred             CCCCEEEEEEeCCCeEEEEeCcccCCCCCccCHHHHHHHHHHHC-CCCCeEEEEEEeCC
Confidence            34568999999999887554433333344678999999999865 33456777777763

>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=86.94  E-value=0.46  Score=31.44  Aligned_cols=57  Identities=5%  Similarity=-0.067  Sum_probs=39.9

Q ss_pred             ceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050            7 VAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS   64 (144)
Q Consensus         7 ~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs   64 (144)
                      ...+|.++++.+|.++.+...-........-||..|+..|... -...+..+.+.+|.
T Consensus        35 ~f~VGAal~~~dG~i~~G~NvEnas~~~t~cAE~~Ai~~A~~~-G~~~l~~i~v~~~~   91 (146)
T 2fr5_A           35 RFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISE-GYKDFRAIAISSDL   91 (146)
T ss_dssp             CCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEESC
T ss_pred             CCCEEEEEEeCCCcEEEEEeccccCCCCCcCHHHHHHHHHHhC-CCCceEEEEEEeCC
Confidence            4468999998899887654433223334578999999999864 33456778888774

>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=81.60  E-value=1.4  Score=28.35  Aligned_cols=56  Identities=4%  Similarity=-0.069  Sum_probs=39.0

Q ss_pred             CceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccH
Q 037050            6 QVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDS   64 (144)
Q Consensus         6 ~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs   64 (144)
                      +...+|.++++.+|.++.+...  .......-||..|+..|... -...+..+.+.+|.
T Consensus        25 s~f~VGAal~~~dG~i~~G~Nv--E~~~~t~cAE~~Ai~~A~~~-G~~~~~~i~vv~~~   80 (130)
T 2z3g_A           25 EDYSVASAALSSDGRIFTGVNV--YHFTGGPCAELVVLGTAAAA-AAGNLTCIVAIGNE   80 (130)
T ss_dssp             SSSCEEEEEEETTSCEEEEECC--CCTTTCCCHHHHHHHHHHHT-TCCCEEEEEEEETT
T ss_pred             CCCCEEEEEEecCCeEEEEecc--ccCCcccCHHHHHHHHHHHc-CCCceEEEEEEECC
Confidence            4456899999999987764443  33455788999999988863 22346677777763

---

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	144
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.61
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.61
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.57
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.45
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.39
d2g84a1	189	Putative deaminase NE0047 {Nitrosomonas europaea [	85.74

>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=99.61  E-value=6.7e-15  Score=95.54  Aligned_cols=105  Identities=12%  Similarity=0.041  Sum_probs=76.1

Q ss_pred             CCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHH
Q 037050            3 AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKII   82 (144)
Q Consensus         3 ~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~   82 (144)
                      .+++.+|+|+++.+.....  .   .++ ..|++.||+.|++.||+    ....++.|.|||+.+++.+++....... .
T Consensus        18 ~n~~~~~~g~~~~~~~~~~--~---~~~-~~tnn~AEl~Ai~~al~----~~~~~i~I~tDS~~v~~~~~~~~~~~~~-~   86 (126)
T d1mu2a1          18 RQSKEGKAGYVTDRGKDKV--K---KLE-QTTNQQAELEAFAMALT----DSGPKVNIIVDSQYVMGIVASQPTESES-K   86 (126)
T ss_dssp             TTTCCEEEEEEETTSCEEE--E---EES-SCCHHHHHHHHHHHHHH----TSCSEEEEEESCHHHHHHHHTCCSEESC-H
T ss_pred             CCCCcEEEEEEecCCCEEE--E---ecC-CCcchHHHHHHHHHHhc----cCCcceEEEechHHHHHHHhcCCccccc-h
Confidence            4567889998886644322  1   223 47899999999999986    4568999999999999999986432221 2


Q ss_pred             HHHHHHHHHHhcCccEEEEEecCC----chHHHHHHHhhhc
Q 037050           83 WVIFEILEKKKNFQNFKAQHTPRS----CNGIAHFLAKLVL  119 (144)
Q Consensus        83 ~~~~~i~~l~~~~~~~~~~~v~r~----~N~~Ad~LAk~a~  119 (144)
                      .....++.+. +...+.|.||+.+    +|..||.||++|+
T Consensus        87 ~~~~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          87 IVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            2233344444 4568999999964    5999999999874

>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=99.61  E-value=1.7e-15  Score=100.79  Aligned_cols=113  Identities=12%  Similarity=-0.014  Sum_probs=84.7

Q ss_pred             CCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcC--------
Q 037050            3 AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNR--------   74 (144)
Q Consensus         3 ~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~--------   74 (144)
                      .+++.+|+|+|+++..........  . ..+|++.||+.|+.+||+.+.  ....+.+.|||+.+++.+...        
T Consensus        14 ~N~g~~G~g~vi~~~~~~~~~~~~--~-~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~~~~~~~~~   88 (147)
T d1rila_          14 GNPGPGGWAALLRFHAHEKLLSGG--E-ACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEGWLEGWRKR   88 (147)
T ss_dssp             STTEEEEEEEEECBTTBCCEECCE--E-EEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSSHHHHHHHT
T ss_pred             CCCCccEEEEEEEECCcceEEecc--c-ccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccccccchhhhhhc
Confidence            456789999999876665444332  2 257999999999999997643  456799999999999988651        


Q ss_pred             -----CCCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhccc
Q 037050           75 -----TNSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQK  121 (144)
Q Consensus        75 -----~~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~  121 (144)
                           ...+.....+++++..+... ..++|.|||    +++|..||.|||.|...
T Consensus        89 ~~~~~~~~~v~n~dL~~~l~~~~~~-~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~  143 (147)
T d1rila_          89 GWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQS  143 (147)
T ss_dssp             TSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             cccccccccchhHHHHHHHHHHhhh-cccceEEccCCCCCcchHHHHHHHHHHHHH
Confidence                 11122335677888776654 569999998    68899999999999874

>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=99.57  E-value=6.7e-15  Score=98.01  Aligned_cols=114  Identities=12%  Similarity=0.031  Sum_probs=84.4

Q ss_pred             CCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCC-------
Q 037050            3 AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRT-------   75 (144)
Q Consensus         3 ~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~-------   75 (144)
                      .+++++|+|+|+++..........  .+ ..|++.||++|++.||+.+  .....+.+.|||+.++..++...       
T Consensus        13 ~N~g~aG~G~vi~~~~~~~~~~~~--~~-~~tnn~aE~~Ai~~Al~~~--~~~~~i~i~tds~~~i~~~~~~~~~~~~~~   87 (152)
T d1jl1a_          13 GNPGPGGYGAILRYRGREKTFSAG--YT-RTTNNRMELMAAIVALEAL--KEHAEVILSTDSQYVRQGITQWIHNWKKRG   87 (152)
T ss_dssp             STTEEEEEEEEEEETTEEEEEEEE--EE-EECHHHHHHHHHHHHHHTC--CSCCEEEEEECCHHHHHHHHTTHHHHHHTT
T ss_pred             CCCCcEEEEEEEEECCeEEEeccc--cC-cccHHHHHHhhhhhhhhhh--cccceEEEeecceeeEEcccchhhHhHhcc
Confidence            456789999999876555443332  33 5789999999999999754  34567999999999998886421       


Q ss_pred             -----CCchhHHHHHHHHHHHHhcCccEEEEEec----CCchHHHHHHHhhhcccC
Q 037050           76 -----NSMSKIIWVIFEILEKKKNFQNFKAQHTP----RSCNGIAHFLAKLVLQKK  122 (144)
Q Consensus        76 -----~~~~~~~~~~~~i~~l~~~~~~~~~~~v~----r~~N~~Ad~LAk~a~~~~  122 (144)
                           ..+.....++.++..+... ..++|.|||    +++|..||.|||+|....
T Consensus        88 ~~~~~~~~~~n~~~~~~i~~~~~~-~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~  142 (152)
T d1jl1a_          88 WKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVKGHAGHPENERADELARAAAMNP  142 (152)
T ss_dssp             TBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             chhcccCeeecHHHHHHHHHHhhc-ceeEEEEecccCCCccHHHHHHHHHHHHhCC
Confidence                 1122334567777776554 479999999    678999999999998743

>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=99.45  E-value=8.7e-14  Score=90.32  Aligned_cols=68  Identities=12%  Similarity=0.063  Sum_probs=55.9

Q ss_pred             CCCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhc
Q 037050            2 DAKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNN   73 (144)
Q Consensus         2 ~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~   73 (144)
                      +++||++|+|+|+.+.... +. .+..++ .+|+++||++|+++||+.+.+.+ .++.|+|||+.+++++++
T Consensus        14 ~GNPGp~g~g~v~~~~~~~-~~-~sg~~~-~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~   81 (132)
T d1zbfa1          14 QGNPGIVEYKGVDTKTGEV-LF-EREPIP-IGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKD   81 (132)
T ss_dssp             CSSSEEEEEEEEETTTCCE-EE-ECCCEE-EECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHH
T ss_pred             CCCCchheEEEEEEcCCEE-EE-EEcCcC-ccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHh
Confidence            4689999999999765543 33 233344 57999999999999999999988 579999999999999976

>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=99.39  E-value=2.1e-12  Score=81.67  Aligned_cols=92  Identities=14%  Similarity=0.150  Sum_probs=69.9

Q ss_pred             CCCCceeEEEEEeCCCCCeeeecccccCCCCChHHHHHHHHHHHHHHHHHhCCCceEEeccHHHHHHHHhcCCCCchhHH
Q 037050            3 AKKQVAGLAVVIRDWERNCVAAAINTTRFFGNVAMTQAATIEIGMQVALSVGGYSVLFESDSHEVVELVNNRTNSMSKII   82 (144)
Q Consensus         3 ~~~~~~g~G~vird~~g~~~~~~~~~~~~~~~~~~aE~~Al~~aL~~a~~~g~~~v~~esDs~~vv~~l~~~~~~~~~~~   82 (144)
                      .+++.+|+|+++-+......     .+. ..|++.||++|++.||+    .+..+|.|.|||+.+++.+++......  .
T Consensus        19 ~n~~~g~~g~~~~~~~~~~~-----~~~-~~TNn~aEl~Avi~aL~----~~~~~v~I~TDS~yvi~~i~~~~~~~~--~   86 (110)
T d1s1ta1          19 RETKLGKAGYVTNRGRQKVV-----TLT-DTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDQSE--S   86 (110)
T ss_dssp             TTTTEEEEEEEETTSCEEEE-----EES-SCCHHHHHHHHHHHHHH----HSCSEEEEEECCHHHHHHHHHCCSEES--C
T ss_pred             CCCCCcEEEEEEecCCeEEE-----ecc-cCcHHHHHHHHHHHHHH----hCCCeEEEEEehHHHHHHHhcCccccc--h
Confidence            45678899988865443221     122 57999999999999996    467899999999999999998654322  3


Q ss_pred             HHHHHHHHHHhcCccEEEEEecCC
Q 037050           83 WVIFEILEKKKNFQNFKAQHTPRS  106 (144)
Q Consensus        83 ~~~~~i~~l~~~~~~~~~~~v~r~  106 (144)
                      .+++++...+..+..+.+.|||.+
T Consensus        87 ~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          87 ELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             HHHHHHHHHHhcCCceEEEEeCCC
Confidence            456777776677899999999974

>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=85.74  E-value=0.51  Score=30.92  Aligned_cols=46  Identities=11%  Similarity=-0.001  Sum_probs=31.9

Q ss_pred             CceeEEEEEeCCC-CCeeeecccccC-CCCChHHHHHHHHHHHHHHHH
Q 037050            6 QVAGLAVVIRDWE-RNCVAAAINTTR-FFGNVAMTQAATIEIGMQVAL   51 (144)
Q Consensus         6 ~~~g~G~vird~~-g~~~~~~~~~~~-~~~~~~~aE~~Al~~aL~~a~   51 (144)
                      +...+|.||.+.+ |.++..+..... ......+||..||..|.+...
T Consensus        44 g~~P~GaviV~~~~g~Iia~g~N~~~~~~dpt~HAEi~AI~~A~~~~~   91 (189)
T d2g84a1          44 DGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLD   91 (189)
T ss_dssp             TCCSCEEEEEETTTCBEEEEEECCTTTTTCTTCCHHHHHHHHHHHHHT
T ss_pred             CCCCEEEEEEECCCCEEEEEEcCCcCcCCCCcccHHHHHHHHHHHHhh
Confidence            3445899998764 788887764432 333456999999999876544