Citrus Sinensis ID: 042421

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150----
Protein Sequence
VIKSTKPMREEDGKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCKR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEEcEEEEcccccEEEEEEEEcccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHcccccccHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccEEEEEEcccEEcccccEEEEEEEEcccccEEEEccccccccccHHHHHHHHHHHHHHHHHHHccccEEEEccHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEcccHcHHHHHHHHHcccc
Coil and Loop (DISEMBL)
vikstkpmreedgkedqwqsppigwlkiNVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHAlgfrvckr
Flexible Loop (DISEMBL)
vikstkpmreedgkedqwqsppigWLKINVDVVVDVQKQVVGLevvirdekdnCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSaahalgfrvckr
Low Complexity Region (SEG)
VIKSTKPMREEDGKEDQWQSPPIGWLKINvdvvvdvqkqvvglevvIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCKR
Disordered region (IsUnstruct)
*********************PIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVC**
Disordered Region (DISOPRED)
**********************IGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCKR
Disordered Region (DISEMBL)
******************QSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCKR
Disordered Region (DISPRO)
****************QWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCKR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VIKSTKPMREEDGKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCKR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	154
343887321	166	hypothetical protein [Citrus unshiu]	0.766	0.710	0.401	3e-17
332322128	1369	hypothetical protein [Beta vulgaris subs	0.954	0.107	0.288	7e-12
125561762	201	hypothetical protein OsI_29454 [Oryza sa	0.961	0.736	0.307	7e-11
242054685	589	hypothetical protein SORBIDRAFT_03g03719	0.902	0.235	0.324	9e-11
222622434	420	hypothetical protein OsJ_05904 [Oryza sa	0.831	0.304	0.318	9e-11
125557660	858	hypothetical protein OsI_25347 [Oryza sa	0.987	0.177	0.243	2e-10
222640671	201	hypothetical protein OsJ_27549 [Oryza sa	0.909	0.696	0.298	2e-10
218190326	556	hypothetical protein OsI_06384 [Oryza sa	0.831	0.230	0.318	2e-10
218190093	175	hypothetical protein OsI_05906 [Oryza sa	0.857	0.754	0.311	2e-09
399920210	1747	non-ltr retroelement reverse transcripta	0.876	0.077	0.296	2e-09

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

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/127 (40%), Positives = 73/127 (57%), Gaps = 9/127 (7%)

Query: 5   TKPMREEDGKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKY 64
           +K  RE   K+ +   PP           V  ++Q+ GL VVIR+ +   I AA  +TK+
Sbjct: 28  SKSPRERADKQARPMVPPAS---------VHAEQQLTGLGVVIRNSQGQVIVAAFKSTKF 78

Query: 65  FGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEM 124
             NV  A+A A+KWG+++AL A LA+V++E+DC+EV  L NN  SS  EI W IS+I   
Sbjct: 79  EDNVTAAKAEAVKWGLEMALEARLAAVIIETDCIEVANLANNETSSRKEIVWTISDIHSY 138

Query: 125 NNSFQNF 131
              FQ+ 
Sbjct: 139 KEKFQSL 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 = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 43/149 (28%), Positives = 79/149 (53%), Gaps = 2/149 (1%)

Query: 5    TKPMREEDGKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKY 64
            T P+   +  E+ W  PP+G +K+NVD  V  +   +G+  V+RD + + + A       
Sbjct: 1197 TSPVETLNTHENGWSVPPVGMVKLNVDAAV-FKHVGIGMGGVVRDAEGDVLLATCCGGWA 1255

Query: 65   FGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEM 124
              + AMAEA ++++G+KVA  AG  ++++E DC ++   +  + S +     ++ +IL +
Sbjct: 1256 MEDPAMAEACSLRYGLKVAYEAGFRNLVVEMDCKKLFLQLRGKASDVTPFGRVVDDILYL 1315

Query: 125  NNSFQNFRAQHTARIYNSAAHALGFRVCK 153
             +   N   +H  R  N  AH L  ++CK
Sbjct: 1316 ASKCSNVVFEHVKRHCNKVAHLLA-QMCK 1343

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125561762|gb|EAZ07210.1| hypothetical protein OsI_29454 [Oryza sativa Indica Group]

 Score = 72.0 bits (175), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 47/153 (30%), Positives = 80/153 (52%), Gaps = 5/153 (3%)

Query: 1   VIKST-KPMREEDGKED----QWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCI 55
           VI +T +  R  DG       +W+ PP GW+K NVD   D Q    G+ VVIRD +   I
Sbjct: 24  VIPATPRRCRRPDGSNPACKMRWERPPEGWMKANVDGSFDSQLLKGGIGVVIRDWEGAII 83

Query: 56  AAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEIS 115
            A+  +     +   AE  A++ G+ + L   L SV+LE+DCL  ++++ ++  + +E++
Sbjct: 84  FASCKSVCRCSSPLEAELLALREGIYLFLIWTLRSVILETDCLVALQMIQSKERATSELA 143

Query: 116 WMISEILEMNNSFQNFRAQHTARIYNSAAHALG 148
           +++ EI ++ N  + F      R  N  +H L 
Sbjct: 144 YLVREIRDLLNGSREFVLWKIRREQNMVSHFLA 176

Source: Oryza sativa Indica 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 = 71.6 bits (174), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 47/145 (32%), Positives = 73/145 (50%), Gaps = 6/145 (4%)

Query: 1   VIKSTKPMREEDGKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVN 60
           V K+T+P+        +W  P  G LKIN D      +       V+RD   N  AA+  
Sbjct: 417 VWKNTRPL------STRWSPPAPGMLKINSDGAFLQDRGTGAAGAVVRDSSGNFCAASAR 470

Query: 61  TTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISE 120
                G+V +AEA AI+ G+++  +  +  ++ E+D  EVV L  NR    +EI+ ++ E
Sbjct: 471 WLGPVGSVLIAEAEAIRDGLRLIPQGTMEHIIGETDAREVVALWKNRTRQRSEIAAILKE 530

Query: 121 ILEMNNSFQNFRAQHTARIYNSAAH 145
           I E+ ++F +F   H  R  NS AH
Sbjct: 531 IEEIVSAFTSFELIHVRREANSVAH 555

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222622434|gb|EEE56566.1| hypothetical protein OsJ_05904 [Oryza sativa Japonica Group]

 Score = 71.6 bits (174), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 70/132 (53%), Gaps = 4/132 (3%)

Query: 18  WQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFG--NVAMAEAAA 75
           W  PP G   IN D  V   ++ +G+ VVIRD+  NC+ AA   T++ G  +   AEA A
Sbjct: 262 WVPPPAGVFLINTDAAVFQAERQMGVGVVIRDQHGNCLLAA--NTRFMGITDPETAEACA 319

Query: 76  IKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQH 135
           I+  + +A   G  +V++  DCL V++ +N+     ++I  ++ +I ++   F +    H
Sbjct: 320 IRHALWLAKEEGFHNVIVACDCLSVIQKLNSPGRDRSKIGCLVEDIKKLGVEFISVSFIH 379

Query: 136 TARIYNSAAHAL 147
            +   N AAH L
Sbjct: 380 VSHCSNVAAHTL 391

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125557660|gb|EAZ03196.1| hypothetical protein OsI_25347 [Oryza sativa Indica Group]

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 37/152 (24%), Positives = 75/152 (49%)

Query: 1   VIKSTKPMREEDGKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVN 60
           V  S +  R+ +     W+ P  GW+K+NVD          G+  ++R+     + A+  
Sbjct: 684 VGHSGRHQRQPETLPYTWKKPDTGWMKLNVDGSFQEHDGSGGIGAILRNSAGEVVFASCG 743

Query: 61  TTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISE 120
           +    G    AE  A + G+ + L+  L  +++ESDCL+ ++L+ ++    ++++++I E
Sbjct: 744 SMNRCGGALEAELLACRDGLTLVLQWTLLPIVIESDCLQAIQLIQSKEEERSDLAFLIRE 803

Query: 121 ILEMNNSFQNFRAQHTARIYNSAAHALGFRVC 152
           I  +    ++       R  NS +HAL ++ C
Sbjct: 804 IKHLMAGNRDIVIMKIHRNQNSVSHALAYKGC 835

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222640671|gb|EEE68803.1| hypothetical protein OsJ_27549 [Oryza sativa Japonica Group]

 Score = 70.5 bits (171), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 74/144 (51%), Gaps = 4/144 (2%)

Query: 9   REEDGKED----QWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKY 64
           R  DG       +W+ PP GW+K NVD   D Q    G+ VVIRD +   I A+  +   
Sbjct: 33  RRPDGSNPACKMRWERPPEGWMKANVDGSFDSQLLKGGIGVVIRDWEGAIIFASCKSMCR 92

Query: 65  FGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEM 124
             +   AE  A++ G+ + L   L  V+LE+DCL  ++++ ++  + +E+++++ EI ++
Sbjct: 93  CSSPLEAELLALREGIYLFLIWTLRPVILETDCLVALQMIQSKERATSELAYLVREIRDL 152

Query: 125 NNSFQNFRAQHTARIYNSAAHALG 148
            N  + F      R  N  +H L 
Sbjct: 153 LNGSREFVLWKIRREQNMVSHFLA 176

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218190326|gb|EEC72753.1| hypothetical protein OsI_06384 [Oryza sativa Indica Group]

 Score = 70.5 bits (171), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 70/132 (53%), Gaps = 4/132 (3%)

Query: 18  WQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFG--NVAMAEAAA 75
           W  PP G   IN D  V   ++ +G+ VVIRD+  NC+ AA   T++ G  +   AEA A
Sbjct: 398 WVPPPAGVFLINTDAAVFQAERQMGVGVVIRDQHGNCLLAA--NTRFMGITDPETAEACA 455

Query: 76  IKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQH 135
           I+  + +A   G  +V++  DCL V++ +N+     ++I  ++ +I ++   F +    H
Sbjct: 456 IRHALWLAKEEGFHNVIVACDCLSVIQKLNSPGRDRSKIGCLVEDIKKLGVEFISVSFIH 515

Query: 136 TARIYNSAAHAL 147
            +   N AAH L
Sbjct: 516 VSHCSNVAAHTL 527

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218190093|gb|EEC72520.1| hypothetical protein OsI_05906 [Oryza sativa Indica Group]

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 70/135 (51%), Gaps = 3/135 (2%)

Query: 15  EDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNV-AMAEA 73
           ++ W+ PP G L INVD   D+     G  VV+RD    C+ A+     Y  +   MAEA
Sbjct: 22  QNGWKKPPEGMLMINVDAAFDIDSGSGGTGVVLRDHLGACVTASQAFLPYVLDAPTMAEA 81

Query: 74  AAIKWGMKVALRAGLASVLLESDCLEVVE-LVNNRCSSMAEISWMISEILEMNNSFQNFR 132
            A++ G+ +A   G  +V++++DC++VV  +++   S+ A +S +  +   M + F    
Sbjct: 82  FALRDGLALAQHIGAKNVIVQTDCMQVVSTMMDGGFSATAAMS-VFDDCKLMWDGFGTIS 140

Query: 133 AQHTARIYNSAAHAL 147
            +H  R  N  AH L
Sbjct: 141 IEHCNRNSNQVAHEL 155

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|399920210|gb|AFP55557.1| non-ltr retroelement reverse transcriptase [Rosa rugosa]

 Score = 67.0 bits (162), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 69/135 (51%)

Query: 13   GKEDQWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAE 72
            G   +WQ+P  G LK+N D   + + +  G   +IRDE  + I A     ++  +  +AE
Sbjct: 1485 GSLRRWQAPSSGQLKVNCDGAANFKDRCFGGGTIIRDEFGSLIVAGGKNFQHPVSSLVAE 1544

Query: 73   AAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFR 132
              AIK G+ + +   L ++++ESDCLE + L+N++   +A    ++ +I           
Sbjct: 1545 LLAIKVGLDLVVERRLRNIMVESDCLEAIHLLNSKERCLAPEGGLVEDIQNTMALVNISS 1604

Query: 133  AQHTARIYNSAAHAL 147
              H  R  N+AAHA+
Sbjct: 1605 IYHVRREGNTAAHAI 1619

Source: Rosa rugosa

Species: Rosa rugosa

Genus: Rosa

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	154
TAIR|locus:1006230762	257	AT1G04625 [Arabidopsis thalian	0.922	0.552	0.287	7.4e-10
TAIR|locus:2058379	221	AT2G04420 [Arabidopsis thalian	0.876	0.610	0.25	1.1e-07
TAIR|locus:2039129	160	AT2G46460 [Arabidopsis thalian	0.831	0.8	0.269	4.3e-06
TAIR|locus:2040899	292	AT2G34320 [Arabidopsis thalian	0.889	0.469	0.241	1.5e-05
TAIR|locus:2065330	365	AT2G02650 [Arabidopsis thalian	0.967	0.408	0.263	6.1e-05
TAIR|locus:2090950	191	AT3G23320 [Arabidopsis thalian	0.928	0.748	0.194	0.00034

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

 Score = 144 (55.7 bits), Expect = 7.4e-10, P = 7.4e-10
 Identities = 42/146 (28%), Positives = 62/146 (42%)

Query:     4 STKPMR--EEDGKEDQWQSPPIGWLKINXXXXXXXXXXXXXXXXXIRDEKDNCIAAAVNT 61
             S+KP R   ++   + W +PPIGW K N                 +RD++   + AA   
Sbjct:    66 SSKPDRVTSQEPTANLWTTPPIGWTKCNYDGTYHSNAPSKAGWL-LRDDRGTFLGAAHAI 124

Query:    62 TKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEI 121
                  N   +E  A+   M+     G   +  E D  EV E+VN R S+ A  +W I +I
Sbjct:   125 GSITTNPMESELQALVMAMQHCWSRGYRKIYFEGDNKEVSEIVNGRSSNFAVFNW-IRDI 183

Query:   122 LEMNNSFQNFRAQHTARIYNSAAHAL 147
                 + F+  +   T R  N AA AL
Sbjct:   184 SAWRSKFEECKFTWTRRFSNMAADAL 209

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 123 (48.4 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 34/136 (25%), Positives = 50/136 (36%)

Query:    12 DGKEDQWQSPPIGWLKINXXXXXXXXXXXXXXXXXIRDEKDNCIAAAVNTTKYFGNVAMA 71
             +    +W+ PP+GW+K N                 IRD+K     AA        N   +
Sbjct:    57 ESTHQKWEQPPMGWIKCNYDGSFNYRTQQTNSGWLIRDDKGFYKGAAQAVGGTMNNALES 116

Query:    72 EAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNF 131
             E  A+   M+     G   V+ E D  +V EL+N +       +W I E    +  F+  
Sbjct:   117 ELQALVMAMQHTWSQGYRKVIFEGDSKQVEELLNRKQMHFGAFNW-IREAWSWSKRFEEV 175

Query:   132 RAQHTARIYNSAAHAL 147
                 T R  N  A  L
Sbjct:   176 IFSWTPRTNNQPADML 191

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

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

 Score = 106 (42.4 bits), Expect = 4.3e-06, P = 4.3e-06
 Identities = 35/130 (26%), Positives = 48/130 (36%)

Query:    18 WQSPPIGWLKINXXXXXXXXXXXXXXXXXIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIK 77
             W  PP GW K N                 IRDE    ++A   T  +  N   +E  A+ 
Sbjct:     3 WTRPPHGWKKCNYDGSYNREMPSKAGWI-IRDESGQFVSAGQATGNHTSNALESEFQALL 61

Query:    78 WGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTA 137
               M+     G   +  E D  EV+E++N R S     +W I ++      FQ  R     
Sbjct:    62 ITMQSCWSHGHRKIWFEGDNREVMEILNRRKSRFDIFNW-IRDVQAWKQRFQECRFTWIN 120

Query:   138 RIYNSAAHAL 147
             R  N  A  L
Sbjct:   121 RKQNKPADIL 130

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 107 (42.7 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 35/145 (24%), Positives = 62/145 (42%)

Query:     3 KSTKPMREEDGKEDQWQSPPIGWLKINXXXXXXXXXXXXXXXXXIRDEKDNCI---AAAV 59
             K++ P  E +    QW++PP  W+K N                 +R+E    +   A A+
Sbjct:   123 KASGPQVERN-LSVQWKAPPYQWVKCNTDATWQLENPRCGIGWILRNESGGVLWMGARAL 181

Query:    60 NTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMIS 119
               TK   NV  AE  A++W +    R     ++ ESD   +V L+N+       +   + 
Sbjct:   182 PRTK---NVLEAELEALRWAVLTMSRFNYKRIIFESDAQALVNLLNSD-DFWPTLQPALE 237

Query:   120 EILEMNNSFQNFRAQHTARIYNSAA 144
             +I ++ + F+  + + T R  N  A
Sbjct:   238 DIQQLLHHFEEVKFEFTPRGGNKVA 262

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 103 (41.3 bits), Expect = 6.1e-05, P = 6.1e-05
 Identities = 40/152 (26%), Positives = 56/152 (36%)

Query:     4 STKPMREEDGKEDQWQSPPIGWLKINXXXXXXXXXXXXXXXXXIRDEKDNCIAAAVNTTK 63
             +T P++       QW  PP GW+K N                 IR E +  I    N   
Sbjct:   192 ATNPIQTSRRDSSQWNPPPEGWVKCNFDSGYTQGSPYTRSGWTIR-ECNGHIVLCGNAKL 250

Query:    64 YFGNVAM-AEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEIL 122
                  ++ AEA      ++V    GL  V  ESD   +V L+NN     + +  +I +I 
Sbjct:   251 QSSTCSLHAEALGFLHALQVIWAHGLRYVWFESDSKSLVTLINNG-EDHSLLGTLIYDIR 309

Query:   123 EMNNSFQNFRAQHTARIYNSAAHALGFRVCKR 154
                        +   R  NSAA AL   V  R
Sbjct:   310 HWMLKLPYCSLEFVNRERNSAADALASHVHAR 341

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2090950 AT3G23320 [Arabidopsis thaliana (taxid:3702)]

 Score = 97 (39.2 bits), Expect = 0.00034, P = 0.00034
 Identities = 28/144 (19%), Positives = 53/144 (36%)

Query:     4 STKPMREEDGKEDQWQSPPIGWLKINXXXXXXXXXXXXXXXXXIRDEKDNCIAAAVNTTK 63
             + K  + +  + D+WQ P   W+K N                 IR+ +  C+       +
Sbjct:    16 NVKGGQTKSSRTDKWQKPGAEWVKCNYDVSNHAGRQDSGLRWIIRNSQGTCLDCGCGKFQ 75

Query:    64 YFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILE 123
                 +  AE  A+ W ++ A   G   V  E D + V  L+ N+  +   + + +  I +
Sbjct:    76 GRQTIKEAECTALIWAIQCAWDLGYRRVEFEGDNITVNRLIRNK-ETNPRLRYYLEFIQQ 134

Query:   124 MNNSFQNFRAQHTARIYNSAAHAL 147
              + +F   +     R  N     L
Sbjct:   135 WSKAFTTVKFTFRHREQNVCVDVL 158


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        0.319   0.129   0.389    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      154       137   0.00091  102 3  11 22  0.40    31
                                                     30  0.45    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:  6
  No. of states in DFA:  598 (64 KB)
  Total size of DFA:  153 KB (2092 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.58u 0.13s 11.71t   Elapsed:  00:00:00
  Total cpu time:  11.58u 0.13s 11.71t   Elapsed:  00:00:00
  Start:  Fri May 10 07:15:43 2013   End:  Fri May 10 07:15:43 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

Your Input: LOC_Os08g09440.1 conserved hypothetical protein (394 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	154
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	4e-15
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-09
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	0.003

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

 Score = 66.1 bits (162), Expect = 4e-15
 Identities = 22/78 (28%), Positives = 41/78 (52%)

Query: 70  MAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQ 129
            AEA A+  G+++AL  G+  +++ESD   VV+ +     + + ++ ++ EI ++   F 
Sbjct: 4   EAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFD 63

Query: 130 NFRAQHTARIYNSAAHAL 147
           +    H  R  N  A AL
Sbjct: 64  SVSVSHVPRECNRVADAL 81

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 = 52.4 bits (126), Expect = 2e-09
 Identities = 22/82 (26%), Positives = 42/82 (51%)

Query: 66  GNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMN 125
                AE  A+   +++AL  GL  +++E+D   VV+L+N+      + + ++ +IL + 
Sbjct: 37  ATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLL 96

Query: 126 NSFQNFRAQHTARIYNSAAHAL 147
           + F + R +H  R  N  A  L
Sbjct: 97  SKFIDIRFEHVPREGNEVADRL 118

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 = 35.6 bits (83), Expect = 0.003
 Identities = 24/112 (21%), Positives = 41/112 (36%), Gaps = 12/112 (10%)

Query: 42  GLEVVIRDEKDNCIAAAVNTTKYFGNVA---MAEAAAIKWGMKVALRAGLASVLLESDCL 98
           G  +VI+      +  ++      G  A    AE  A+  G+++AL  G+  + +  D  
Sbjct: 17  GAGIVIKSPDGEVLEQSI----PLGFPATNNEAEYEALIAGLELALELGIKKLEIYGDSQ 72

Query: 99  EVVELVNNRCSSMAEISWMIS---EILEMNNSFQNFRAQHTARIYNSAAHAL 147
            VV  +        E   +     E  E+   F+    +   R  N  A AL
Sbjct: 73  LVVNQIQGEYEVKNE--RLAPYLEEARELLKKFEEVEIKWIPREENKEADAL 122

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	154
PRK13907	128	rnhA ribonuclease H; Provisional	100.0
PRK07708	219	hypothetical protein; Validated	99.96
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.94
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.93
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.92
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.92
PRK08719	147	ribonuclease H; Reviewed	99.88
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.87
PRK00203	150	rnhA ribonuclease H; Reviewed	99.86
PRK06548	161	ribonuclease H; Provisional	99.85
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	99.55
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	97.9
cd01284	115	Riboflavin_deaminase-reductase Riboflavin-specific	90.63
cd01285	109	nucleoside_deaminase Nucleoside deaminases include	90.11
COG0295	134	Cdd Cytidine deaminase [Nucleotide transport and m	89.86
COG0590	152	CumB Cytosine/adenosine deaminases [Nucleotide tra	89.71
TIGR01354	127	cyt_deam_tetra cytidine deaminase, homotetrameric.	88.48
PRK10860	172	tRNA-specific adenosine deaminase; Provisional	85.07
cd00786	96	cytidine_deaminase-like Cytidine and deoxycytidyla	84.59
TIGR02571	151	ComEB ComE operon protein 2. This protein is found	82.05
cd01283	112	cytidine_deaminase Cytidine deaminase zinc-binding	80.69

>PRK13907 rnhA ribonuclease H; Provisional

Probab=100.00  E-value=4.9e-32  Score=179.67  Aligned_cols=126  Identities=16%  Similarity=0.089  Sum_probs=113.8

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      ++++|||||+..+++.+|+|+|++++.|.+...+   ..+..|+++||+.|+++||+.+.+.|+.+|+|+|||++|++++
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~---~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~   77 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSL---PLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAV   77 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEe---cccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHH
Confidence            4789999999999999999999999988765432   2245799999999999999999999999999999999999999


Q ss_pred             hcCCCCchhHHHHHHHHHHHhhcCCceEEEEeCCCCcHHHHHHHHhhhc
Q 042421          105 NNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCK  153 (154)
Q Consensus       105 ~~~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~~N~~Ad~LA~~a~~  153 (154)
                      ++.+.....+..++++++.++..|..+.+.||+|++|..||.||+.|+-
T Consensus        78 ~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         78 EKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAIL  126 (128)
T ss_pred             hHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHh
Confidence            9976555678999999999999999999999999999999999999863

>PRK07708 hypothetical protein; Validated

Probab=99.96  E-value=6.9e-28  Score=171.92  Aligned_cols=134  Identities=16%  Similarity=0.119  Sum_probs=114.0

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEEEEEecCCCceE--eeccccccccchhHHHHHHHHHHHHHHHHHhCCce--EEEecc
Q 042421           21 PPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCI--AAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLAS--VLLESD   96 (154)
Q Consensus        21 p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~--~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~--v~iesD   96 (154)
                      +.+..+++|||||+..+++.+|+|+||+++.|...  ......+....|+++||+.|++.||+.|.++|+++  |+|++|
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            34567999999999999999999999999877543  23334566668999999999999999999999976  899999


Q ss_pred             HHHHHHHHhcCCCCch-hHHHHHHHHHHHhhcCC-ceEEEEeCCCCcHHHHHHHHhhhcC
Q 042421           97 CLEVVELVNNRCSSMA-EISWMISEILEMNNSFQ-NFRAQHTARIYNSAAHALGFRVCKR  154 (154)
Q Consensus        97 s~~vi~~i~~~~~~~~-~~~~li~~i~~l~~~~~-~~~~~~i~r~~N~~Ad~LA~~a~~~  154 (154)
                      |+.|++++++.+.... .+..++++++.++..|. .+.+.||+|+.|..||.||+.|+++
T Consensus       149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEG  208 (219)
T ss_pred             cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhc
Confidence            9999999999875543 56778888888888776 4889999999999999999999863

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.94  E-value=1.9e-26  Score=177.28  Aligned_cols=128  Identities=17%  Similarity=0.169  Sum_probs=113.9

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCc-eEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDN-CIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVEL  103 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~-~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~  103 (154)
                      .+++|||||+.++++.+|+|++|++++|. ++...+..+. ..|+++||+.|++.||+.+.++|.++|.|++||++|++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            47899999999999999999999999765 4444444444 568899999999999999999999999999999999999


Q ss_pred             HhcCCCCc-hhHHHHHHHHHHHhhcCCceEEEEeCCCCcHHHHHHHHhhhc
Q 042421          104 VNNRCSSM-AEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCK  153 (154)
Q Consensus       104 i~~~~~~~-~~~~~li~~i~~l~~~~~~~~~~~i~r~~N~~Ad~LA~~a~~  153 (154)
                      +++.+... ..+..++.+++.++++|..+++.||+|++|+.||.||+.|+.
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~  131 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMD  131 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHH
Confidence            99977544 578888999999999999999999999999999999999974

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

Probab=99.93  E-value=1.3e-25  Score=150.70  Aligned_cols=125  Identities=16%  Similarity=0.021  Sum_probs=106.3

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      .+.+|+||||.++++.+|+|+|++...+..-...  ... ..|+++||++|+++||+.+++.+...|.++|||++|++.|
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~--~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i   79 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSG--GEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGI   79 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEee--eee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHH
Confidence            5789999999999999999999997777663322  222 6799999999999999999999999999999999999999


Q ss_pred             hcCC-CC------------chhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          105 NNRC-SS------------MAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       105 ~~~~-~~------------~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      +. + ..            +-.-..+.+++..++..|..+.+.||+    +..|+.||.||+.+++
T Consensus        80 ~~-w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~  144 (154)
T COG0328          80 TR-WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR  144 (154)
T ss_pred             HH-HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence            83 2 11            112346789999999999999999999    7789999999999975

>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=99.92  E-value=3.8e-24  Score=139.86  Aligned_cols=125  Identities=18%  Similarity=0.112  Sum_probs=112.0

Q ss_pred             EEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHHhc
Q 042421           27 KINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNN  106 (154)
Q Consensus        27 k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i~~  106 (154)
                      +||||||+..+.+.+|+|++++++.+.+........ ...+++++|+.|+..||+.+...+..++.|++||+.+++++++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~-~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~   79 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLG-GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTG   79 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccC-CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhc
Confidence            589999999988999999999999988877665543 5679999999999999999999999999999999999999999


Q ss_pred             CCC-CchhHHHHHHHHHHHhhcCCceEEEEeCC----CCcHHHHHHHHhhh
Q 042421          107 RCS-SMAEISWMISEILEMNNSFQNFRAQHTAR----IYNSAAHALGFRVC  152 (154)
Q Consensus       107 ~~~-~~~~~~~li~~i~~l~~~~~~~~~~~i~r----~~N~~Ad~LA~~a~  152 (154)
                      ... .......++.+++.+...+..+++.||+|    +.|..||.||+.++
T Consensus        80 ~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          80 WYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             cccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            754 34577888899998888899999999999    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.

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

Probab=99.92  E-value=5.7e-25  Score=136.06  Aligned_cols=86  Identities=30%  Similarity=0.352  Sum_probs=76.3

Q ss_pred             hHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHHhcCCCCchhHHHHHHHHHHHhhcCCceEEEEeCCCCcHHHHHH
Q 042421           68 VAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHAL  147 (154)
Q Consensus        68 ~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i~~~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~~N~~Ad~L  147 (154)
                      |++||++|++.||++|.++|+++|+|||||+.+++++++....++.+..++.+|+.+++.|++++|.||+|++|..||.|
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            57999999999999999999999999999999999999987777799999999999999999999999999999999999


Q ss_pred             HHhhhc
Q 042421          148 GFRVCK  153 (154)
Q Consensus       148 A~~a~~  153 (154)
                      ||.|++
T Consensus        81 A~~a~~   86 (87)
T PF13456_consen   81 AKFALS   86 (87)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            999975

>PRK08719 ribonuclease H; Reviewed

Probab=99.88  E-value=7.3e-22  Score=133.31  Aligned_cols=125  Identities=16%  Similarity=0.093  Sum_probs=98.0

Q ss_pred             CcEEEEeceeEecCCC---eeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHH
Q 042421           24 GWLKINVDVVVDVQKQ---VVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEV  100 (154)
Q Consensus        24 g~~k~n~Dgs~~~~~~---~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~v  100 (154)
                      ..+++|||||+..+++   .+|+|+++.+..|......+..+....|++.||+.|++.||+.+.+.    ..|+|||+++
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            3578999999988765   68999999998887553333335445799999999999999998764    3799999999


Q ss_pred             HHHHhc--------CCC----CchhHHHHHHHHHHHhhcCCceEEEEeCC----CCcHHHHHHHHhhhc
Q 042421          101 VELVNN--------RCS----SMAEISWMISEILEMNNSFQNFRAQHTAR----IYNSAAHALGFRVCK  153 (154)
Q Consensus       101 i~~i~~--------~~~----~~~~~~~li~~i~~l~~~~~~~~~~~i~r----~~N~~Ad~LA~~a~~  153 (154)
                      ++.++.        .+.    .+-....+++.|..+.. ...++|.||++    .+|..||.||+.|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            999953        221    11234567788877766 57899999999    569999999999976

>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=99.87  E-value=3.5e-21  Score=127.88  Aligned_cols=119  Identities=18%  Similarity=0.037  Sum_probs=92.8

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      -+.+|||||+..+++.+|+|+++.+.  .   ..+..++ ..|++.||+.|+..||+ +..  -.+|.|+|||+.+++.+
T Consensus         3 ~~~iytDgS~~~~~~~~~~g~v~~~~--~---~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l   73 (132)
T PF00075_consen    3 AIIIYTDGSCRPNPGKGGAGYVVWGG--R---NFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNAL   73 (132)
T ss_dssp             SEEEEEEEEECTTTTEEEEEEEEETT--E---EEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHH
T ss_pred             cEEEEEeCCccCCCCceEEEEEEECC--e---EEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHH
Confidence            47899999999999999999977433  2   2223344 67999999999999999 552  29999999999999988


Q ss_pred             hc-----CCCCchhHHHHHHHHHHHhhcCCceEEEEeCCC-----CcHHHHHHHHhhh
Q 042421          105 NN-----RCSSMAEISWMISEILEMNNSFQNFRAQHTARI-----YNSAAHALGFRVC  152 (154)
Q Consensus       105 ~~-----~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~-----~N~~Ad~LA~~a~  152 (154)
                      +.     ..........++.++..++.....+.|.||+++     +|..||.|||.|+
T Consensus        74 ~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   74 NKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             HHhccccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            87     332222222466677777777889999999998     6889999999986

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 ....

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.86  E-value=8.5e-21  Score=128.92  Aligned_cols=123  Identities=10%  Similarity=-0.034  Sum_probs=95.4

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      .+.+|||||+..+++.+|+|+|+...++.....+  .. ...|++.||++|++.||+.+.+  ...|.|+|||+++++.|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~--~~-~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSG--GE-ALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEec--CC-CCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHH
Confidence            3789999999999999999999987554433222  22 3568999999999999998764  35899999999999999


Q ss_pred             hc--------CCCC----chhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          105 NN--------RCSS----MAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       105 ~~--------~~~~----~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      +.        ....    +-....+++++..++.. ..+.|.||+    ++.|..||.||+.|+.
T Consensus        78 ~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~  141 (150)
T PRK00203         78 TEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAE  141 (150)
T ss_pred             HHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHH
Confidence            85        1111    11235577888777765 689999999    5679999999999875

>PRK06548 ribonuclease H; Provisional

Probab=99.85  E-value=4.2e-20  Score=125.90  Aligned_cols=121  Identities=15%  Similarity=0.069  Sum_probs=94.0

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      .+.+|||||+.++++.+|+|+++.+. + ..   ... ....|++.||++|++.||+.+. ....+|.|+|||+++++.+
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~~-~-~~---~g~-~~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i   77 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDEN-T-WD---SGG-WDIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSL   77 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeCC-c-EE---ccC-CCCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHH
Confidence            48999999999999999999998753 2 21   111 2357999999999999998554 4556899999999999999


Q ss_pred             hc--------CCC----CchhHHHHHHHHHHHhhcCCceEEEEeCCC----CcHHHHHHHHhhhc
Q 042421          105 NN--------RCS----SMAEISWMISEILEMNNSFQNFRAQHTARI----YNSAAHALGFRVCK  153 (154)
Q Consensus       105 ~~--------~~~----~~~~~~~li~~i~~l~~~~~~~~~~~i~r~----~N~~Ad~LA~~a~~  153 (154)
                      +.        ...    .+-.-..+++++..++.. ..++|.||+.+    .|..||.||+.|+.
T Consensus        78 ~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~  141 (161)
T PRK06548         78 TKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN  141 (161)
T ss_pred             HHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence            94        111    111346788888888876 47999999875    59999999999874

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

Probab=99.55  E-value=9.5e-14  Score=104.11  Aligned_cols=133  Identities=14%  Similarity=0.011  Sum_probs=98.7

Q ss_pred             CcccCC-CCCcEEEEeceeEecCC---CeeeEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCce
Q 042421           16 DQWQSP-PIGWLKINVDVVVDVQK---QVVGLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLAS   90 (154)
Q Consensus        16 ~~W~~p-~~g~~k~n~Dgs~~~~~---~~~g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~   90 (154)
                      ..|..+ +.+.+.+|+|||+..+.   ..+|+|+.+-+..-.-+   +.++. +..+++.||+.|+.+||+.|++....+
T Consensus       202 k~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~---s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~k  278 (371)
T KOG3752|consen  202 KLENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNV---SGPLAGGRQTNNRAELIAAIEALKKARSKNINK  278 (371)
T ss_pred             hcccccccccceEEEecCccccCCCCCCcceeEEeeCCCCcccc---cccCCCCcccccHHHHHHHHHHHHHHHhcCCCc
Confidence            345554 34668899999999863   56888888765432222   23444 678999999999999999999999999


Q ss_pred             EEEeccHHHHHHHHhcC------------CCCc-----hhHHHHHHHHHHHhhc--CCceEEEEeCCC----CcHHHHHH
Q 042421           91 VLLESDCLEVVELVNNR------------CSSM-----AEISWMISEILEMNNS--FQNFRAQHTARI----YNSAAHAL  147 (154)
Q Consensus        91 v~iesDs~~vi~~i~~~------------~~~~-----~~~~~li~~i~~l~~~--~~~~~~~~i~r~----~N~~Ad~L  147 (154)
                      |+|.|||.+++++|+..            ....     -.-...+.++.++.+.  ...+++.||+.+    +|..||.|
T Consensus       279 v~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~l  358 (371)
T KOG3752|consen  279 VVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADAL  358 (371)
T ss_pred             EEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHH
Confidence            99999999999999760            0000     1123345566666665  478999999975    69999999


Q ss_pred             HHhh
Q 042421          148 GFRV  151 (154)
Q Consensus       148 A~~a  151 (154)
                      |+..
T Consensus       359 ARkg  362 (371)
T KOG3752|consen  359 ARKG  362 (371)
T ss_pred             Hhhh
Confidence            9987

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

Probab=97.90  E-value=3.4e-05  Score=59.97  Aligned_cols=116  Identities=19%  Similarity=0.156  Sum_probs=87.5

Q ss_pred             CCeeeEEEEEecC-CCceEeecccccc--ccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHHhcCCCCch--
Q 042421           38 KQVVGLEVVIRDE-KDNCIAAAVNTTK--YFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMA--  112 (154)
Q Consensus        38 ~~~~g~G~vird~-~g~~~~~~~~~~~--~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i~~~~~~~~--  112 (154)
                      ...+|.|+.+.|. +............  ...++..||++|+..+|..+.++|+.++.+++|...+...+.++.....  
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            3468899999886 4433332222222  2367999999999999999999999999999998888887777654433  


Q ss_pred             hHHHHHHHHHHHhhcCCceEEEEeCCC-CcHHHHHHHHhhhc
Q 042421          113 EISWMISEILEMNNSFQNFRAQHTARI-YNSAAHALGFRVCK  153 (154)
Q Consensus       113 ~~~~li~~i~~l~~~~~~~~~~~i~r~-~N~~Ad~LA~~a~~  153 (154)
                      .+..++.+.+.+...+....-..+++. ....|-.||+++..
T Consensus        96 ~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~  137 (384)
T KOG1812|consen   96 KIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIV  137 (384)
T ss_pred             HHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhc
Confidence            567788888888888877777777665 55779999998764

>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase

Probab=90.63  E-value=0.84  Score=29.49  Aligned_cols=50  Identities=14%  Similarity=0.038  Sum_probs=35.6

Q ss_pred             CeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEec
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLES   95 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~ies   95 (154)
                      +...+|+||.+++|+++..+.....   ...+||..|+..+.+.    .+...++++
T Consensus        17 ~~~pvGaviv~~~g~iv~~g~n~~~---~~~HAE~~ai~~a~~~----~l~g~tly~   66 (115)
T cd01284          17 PNPPVGCVIVDDDGEIVGEGYHRKA---GGPHAEVNALASAGEK----LARGATLYV   66 (115)
T ss_pred             CCCCEEEEEEeCCCeEEEEecCCCC---CcccHHHHHHHHHhhc----CCCCeEEEE
Confidence            3456888888888999887665443   5789999999998764    444444443

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

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

Probab=90.11  E-value=1  Score=28.56  Aligned_cols=58  Identities=24%  Similarity=0.127  Sum_probs=39.6

Q ss_pred             CeeeEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      +...+|++|.+.+|+++..+..... ......+||..|+..+.+......+....+++.
T Consensus        15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t   73 (109)
T cd01285          15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTT   73 (109)
T ss_pred             CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEe
Confidence            4557888998888998876554432 234578999999998876644334566666653

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

>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]

Probab=89.86  E-value=1.1  Score=29.83  Aligned_cols=57  Identities=16%  Similarity=0.169  Sum_probs=44.6

Q ss_pred             eeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      ..-+|++++..+|++..+..-......-...||-.|+..++.. -...+..|.+.+|.
T Consensus        25 ~F~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~   81 (134)
T COG0295          25 KFKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT   81 (134)
T ss_pred             CCcEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence            4568999999999888776554445566789999999988877 55667899998887

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

Probab=89.71  E-value=0.97  Score=30.71  Aligned_cols=58  Identities=24%  Similarity=0.103  Sum_probs=42.0

Q ss_pred             CeeeEEEEEecCCCceEeecccccccc-chhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTKYF-GNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~~~-~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      +...+|+||.+..|.++..+....... .-..+||..|+..|-+......+...++++-
T Consensus        26 ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyvT   84 (152)
T COG0590          26 GEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVT   84 (152)
T ss_pred             CCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEEe
Confidence            356789999998888888665544333 2345999999999999887666666666653

>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric

Probab=88.48  E-value=1.1  Score=29.41  Aligned_cols=57  Identities=7%  Similarity=0.078  Sum_probs=40.0

Q ss_pred             eeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      ....|+++++.+|+++.+.............||..|+..+...-. ..+..+.+.++.
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            446888889889998885544333344567999999998876532 256777776654

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

>PRK10860 tRNA-specific adenosine deaminase; Provisional

Probab=85.07  E-value=2.3  Score=29.51  Aligned_cols=41  Identities=22%  Similarity=0.163  Sum_probs=28.2

Q ss_pred             eeeEEEEEecCCCceEeeccccccc-cchhHHHHHHHHHHHHH
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTKY-FGNVAMAEAAAIKWGMK   81 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~~-~~s~~~AE~~Al~~aL~   81 (154)
                      ...+|+||.+ +|+++..+...... .....+||..|+..|.+
T Consensus        32 ~~pvGAVIV~-~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~   73 (172)
T PRK10860         32 EVPVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGL   73 (172)
T ss_pred             CCCEEEEEEe-CCEEEEEeeCCCCCCCCCccCHHHHHHHHHHH
Confidence            3467888876 58888876554322 22357899999998865

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

Probab=84.59  E-value=4.9  Score=24.81  Aligned_cols=43  Identities=9%  Similarity=0.062  Sum_probs=27.9

Q ss_pred             CeeeEEEEEecC-CCceEeeccccc-cccchhHHHHHHHHHHHHH
Q 042421           39 QVVGLEVVIRDE-KDNCIAAAVNTT-KYFGNVAMAEAAAIKWGMK   81 (154)
Q Consensus        39 ~~~g~G~vird~-~g~~~~~~~~~~-~~~~s~~~AE~~Al~~aL~   81 (154)
                      +...+|+++.+. +|.++..+.... ........||..|+..+.+
T Consensus        16 ~~~pVGaviv~~~~g~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~   60 (96)
T cd00786          16 SNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS   60 (96)
T ss_pred             CCCCEEEEEEEeCCCCeEeeeEeccCCCCCCeeCHHHHHHHHHHH
Confidence            455677777765 577766544322 2234568999999987654

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.

>TIGR02571 ComEB ComE operon protein 2

Probab=82.05  E-value=7.3  Score=26.44  Aligned_cols=40  Identities=18%  Similarity=0.021  Sum_probs=26.1

Q ss_pred             eeeEEEEEecCCCceEeecccccccc----------------chhHHHHHHHHHHHH
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTKYF----------------GNVAMAEAAAIKWGM   80 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~~~----------------~s~~~AE~~Al~~aL   80 (154)
                      ...+|+||.. +|+++..+....+.-                ....+||..|+..+.
T Consensus        24 ~~~VGAVIV~-d~~IIs~GyN~~~~g~~~~~~~~~~~~~~~~~~~~HAE~nAI~~a~   79 (151)
T TIGR02571        24 RLSVGATIVR-DKRIIAGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQCA   79 (151)
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCccccccccccccccCCccCHHHHHHHHHH
Confidence            3467777764 577887666554321                124799999999874

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

>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain

Probab=80.69  E-value=4.5  Score=25.68  Aligned_cols=45  Identities=11%  Similarity=0.083  Sum_probs=32.0

Q ss_pred             CeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHH
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVA   83 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a   83 (154)
                      +...+|+++...+|.++.+.............||..|+..+...-
T Consensus        16 ~~~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~~~   60 (112)
T cd01283          16 SNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSEG   60 (112)
T ss_pred             CCCeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHHcC
Confidence            456788888888888876544444444567899999998877533

These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	154
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.98
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.98
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.97
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.96
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.94
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.94
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.93
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.92
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.92
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.92
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.9
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.9
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.85
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.83
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.81
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.76
1uwz_A	136	Cytidine deaminase; CDD, tetramer, zinc binding, p	92.34
2fr5_A	146	Cytidine deaminase; tetrahydrouridine, protein-inh	91.43
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	91.37
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	89.85
1r5t_A	142	Cytidine deaminase; zinc dependent deaminase, RNA	85.97
2z3g_A	130	Blasticidin-S deaminase; hydrolase, cytidine deami	85.57
2d30_A	141	Cytidine deaminase; purines, pyrimidines, nucleosi	84.16
2b3j_A	159	TRNA adenosine deaminase; mixed alpha-beta, protei	82.23
2a8n_A	144	Cytidine and deoxycytidylate deaminase; RNA editin	81.65
1wwr_A	171	TRNA adenosine deaminase TADA; homodimer, riken st	80.76
2nx8_A	179	TRNA-specific adenosine deaminase; TAD, hydrolase;	80.46
4h8e_A	256	Undecaprenyl pyrophosphate synthase; alpha-helix,	80.24

>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=99.98  E-value=2.4e-31  Score=177.90  Aligned_cols=128  Identities=16%  Similarity=0.142  Sum_probs=113.6

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCC-CceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEK-DNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVEL  103 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~-g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~  103 (154)
                      .+++|||||+..+++.+|+|++++++. |.++...+..+ +..|+++||+.|++.||+.+.++|..+|.|+|||++++++
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            489999999999999999999999987 66655555444 3679999999999999999999999999999999999999


Q ss_pred             HhcCCCC-chhHHHHHHHHHHHhhcCCceEEEEeCCCCcHHHHHHHHhhhc
Q 042421          104 VNNRCSS-MAEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCK  153 (154)
Q Consensus       104 i~~~~~~-~~~~~~li~~i~~l~~~~~~~~~~~i~r~~N~~Ad~LA~~a~~  153 (154)
                      +++.+.. ...+..++.+++.++.+|..++|.||+|++|+.||.||+.|+.
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~~a~~  132 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLANDAMD  132 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHHHHHH
Confidence            9997543 3467788999999999999999999999999999999999975

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

Probab=99.98  E-value=1.9e-31  Score=177.98  Aligned_cols=129  Identities=19%  Similarity=0.105  Sum_probs=115.6

Q ss_pred             CcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCc----eEEEeccHHH
Q 042421           24 GWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLA----SVLLESDCLE   99 (154)
Q Consensus        24 g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~----~v~iesDs~~   99 (154)
                      ..+++|||||+..+++.+|+|+++++++|..+...+..+. ..|+++||+.|++.||+.+.+.+++    +|.|+|||++
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            3589999999999999999999999999988766565554 4699999999999999999999999    9999999999


Q ss_pred             HHHHHhcCCCC-chhHHHHHHHHHHH-hhcCCceEEEEeCCCCcHHHHHHHHhhhc
Q 042421          100 VVELVNNRCSS-MAEISWMISEILEM-NNSFQNFRAQHTARIYNSAAHALGFRVCK  153 (154)
Q Consensus       100 vi~~i~~~~~~-~~~~~~li~~i~~l-~~~~~~~~~~~i~r~~N~~Ad~LA~~a~~  153 (154)
                      +++.+++.+.. ...+..++.+++.+ +..|..++|.||+|++|+.||.||+.|+.
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAID  136 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHHHHHH
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHHHHHH
Confidence            99999997643 34677889999999 88999999999999999999999999975

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

Probab=99.97  E-value=2.6e-30  Score=174.56  Aligned_cols=127  Identities=17%  Similarity=0.134  Sum_probs=110.1

Q ss_pred             cEEEEeceeEe-cCCCeeeE-EEEEecCCCceEeecccccc---ccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHH
Q 042421           25 WLKINVDVVVD-VQKQVVGL-EVVIRDEKDNCIAAAVNTTK---YFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLE   99 (154)
Q Consensus        25 ~~k~n~Dgs~~-~~~~~~g~-G~vird~~g~~~~~~~~~~~---~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~   99 (154)
                      ++++|||||+. .+++.+|+ |+|+++ +|..+........   ...|+++||+.|++.||+.+.++|.++|.|+|||++
T Consensus         1 m~~iy~DGs~~~~n~g~~G~~G~vi~~-~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~   79 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGGIATFGFVIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQL   79 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEEC-SSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHH
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEE-CCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHH
Confidence            47899999999 78899996 999999 7877644333222   367899999999999999999999999999999999


Q ss_pred             HHHHHhcCCCCc-hhHHHHHHHHHHHhhcCCceEEEEeCCCCcHHHHHHHHhhhc
Q 042421          100 VVELVNNRCSSM-AEISWMISEILEMNNSFQNFRAQHTARIYNSAAHALGFRVCK  153 (154)
Q Consensus       100 vi~~i~~~~~~~-~~~~~li~~i~~l~~~~~~~~~~~i~r~~N~~Ad~LA~~a~~  153 (154)
                      +++++++.+... .....++++++.++..| .++|.||+|++|..||.||+.|++
T Consensus        80 vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~~~N~~AD~LA~~a~~  133 (149)
T 2ehg_A           80 VIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPREENKEADRLSRVAYE  133 (149)
T ss_dssp             HHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCCcccHHHHHHHHHHHH
Confidence            999999975432 46788999999999988 699999999999999999999975

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

Probab=99.96  E-value=7.5e-28  Score=163.35  Aligned_cols=131  Identities=11%  Similarity=0.025  Sum_probs=107.6

Q ss_pred             CCCCCcEEEEeceeEecCCC---eeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           20 SPPIGWLKINVDVVVDVQKQ---VVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        20 ~p~~g~~k~n~Dgs~~~~~~---~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      +|+.+++++|||||+..+++   .+|+|+++++..+..+.   ..+.+..|++.||+.|++.||+.+.+.+..+|.|+||
T Consensus         2 ~~~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~---~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tD   78 (154)
T 2qkb_A            2 SHMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVG---IRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTN   78 (154)
T ss_dssp             CEETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEE---EECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEES
T ss_pred             CCCCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEE---eecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEEC
Confidence            57789999999999998764   59999999986554332   2344457999999999999999999999999999999


Q ss_pred             HHHHHHHHhcC--------CC----CchhHHHHHHHHHHHhhcCCceEEEEeCCCC----cHHHHHHHHhhhcC
Q 042421           97 CLEVVELVNNR--------CS----SMAEISWMISEILEMNNSFQNFRAQHTARIY----NSAAHALGFRVCKR  154 (154)
Q Consensus        97 s~~vi~~i~~~--------~~----~~~~~~~li~~i~~l~~~~~~~~~~~i~r~~----N~~Ad~LA~~a~~~  154 (154)
                      |+++++.|++.        +.    .+.....+++++..++..+ .+.|.||+++.    |+.||.||+.|+++
T Consensus        79 S~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~-~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A           79 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGM-DIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTC-EEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCC-ceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            99999999871        11    1234567899999888876 49999999865    99999999999863

>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=99.94  E-value=2.2e-26  Score=155.22  Aligned_cols=125  Identities=11%  Similarity=0.042  Sum_probs=102.2

Q ss_pred             CCCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHH
Q 042421           20 SPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLE   99 (154)
Q Consensus        20 ~p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~   99 (154)
                      .|+.+.+++||||||..+++.+|+|+|+++..+..+.     . ...|++.||+.|++.||+.+    -.+|.|+|||++
T Consensus         7 ~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~-----~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~   76 (150)
T 3qio_A            7 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVT-----L-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQY   76 (150)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEE-----E-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHH
T ss_pred             CCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEe-----C-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHH
Confidence            6888999999999999999999999999886543331     2 35799999999999999984    389999999999


Q ss_pred             HHHHHhcC------------CCCchhHHHHHHHHHHHhhcCCceEEEEeCCCC----cHHHHHHHHhhhcC
Q 042421          100 VVELVNNR------------CSSMAEISWMISEILEMNNSFQNFRAQHTARIY----NSAAHALGFRVCKR  154 (154)
Q Consensus       100 vi~~i~~~------------~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~~----N~~Ad~LA~~a~~~  154 (154)
                      +++.+++.            ...+.....+++++..++.++..+.|.||+++.    |+.||.||+.|+++
T Consensus        77 v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           77 ALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            99999872            011123456778887777789999999999997    99999999999863

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

Probab=99.94  E-value=5e-27  Score=160.99  Aligned_cols=129  Identities=12%  Similarity=0.005  Sum_probs=101.9

Q ss_pred             cCCCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHH
Q 042421           19 QSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCL   98 (154)
Q Consensus        19 ~~p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~   98 (154)
                      +||+.+.+++|||||+..+++.+|+|+|+++..+.....+  .. ...|++.||+.|++.||+.+.+.  .+|.|+|||+
T Consensus         2 ~p~~m~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~--~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~   76 (166)
T 1ril_A            2 NPSPRKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSG--GE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSH   76 (166)
T ss_dssp             ----CCCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECC--EE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCH
T ss_pred             CCCCCccEEEEECccccCCCCCEEEEEEEEECCEEEEEec--CC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChH
Confidence            4788889999999999999999999999998655443332  22 35789999999999999988765  4999999999


Q ss_pred             HHHHHHhcC---------CC----CchhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421           99 EVVELVNNR---------CS----SMAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus        99 ~vi~~i~~~---------~~----~~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      ++++.|++.         +.    .......+++++..++..+ .+.|.||+    +++|..||.||+.|++
T Consensus        77 ~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~gH~g~~~Ne~AD~LAk~a~~  147 (166)
T 1ril_A           77 YLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPH-RVRFHFVKGHTGHPENERVDREARRQAQ  147 (166)
T ss_dssp             HHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTS-EEECCCCCGGGSCTHHHHHHHHHHHHHT
T ss_pred             HHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcC-eEEEEEeeCCCCchhHHHHHHHHHHHHH
Confidence            999999881         11    1123356788888888764 89999999    8899999999999986

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

Probab=99.93  E-value=1.1e-25  Score=151.42  Aligned_cols=124  Identities=19%  Similarity=0.061  Sum_probs=100.7

Q ss_pred             CcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHH
Q 042421           24 GWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVEL  103 (154)
Q Consensus        24 g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~  103 (154)
                      ..+++||||||..+++.+|+|+++++.......  +... ...|++.||+.|++.||+.+.+  ..+|.|+|||+++++.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~--~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~   77 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEI--SGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNA   77 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEE--EEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEe--ecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHH
Confidence            358999999999999999999999986533222  2233 3578999999999999999876  5899999999999999


Q ss_pred             HhcCC-------------CCchhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          104 VNNRC-------------SSMAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       104 i~~~~-------------~~~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      +++.+             ..+.....+++++..++..+ .+.|.||+    +++|+.||.||+.|++
T Consensus        78 i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~-~v~~~~V~gH~g~~~N~~AD~LA~~a~~  143 (146)
T 3h08_A           78 MNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLH-RVTFHKVKGHSDNPYNSRADELARLAIK  143 (146)
T ss_dssp             HHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHS-EEEEEECCC-CCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhC-ceEEEEcCCcCCcHhHHHHHHHHHHHHH
Confidence            98821             11224466888888888875 59999999    8999999999999985

>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=99.92  E-value=3e-25  Score=150.59  Aligned_cols=123  Identities=11%  Similarity=-0.030  Sum_probs=99.5

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      .+++|||||+..+++.+|+|+++++..+.....+  .. ...|++.||+.|++.||+.+.+.  .+|.|+|||+++++.+
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~--~~-~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i   78 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSA--GY-TRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGI   78 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEE--EE-EEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEec--CC-CCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHH
Confidence            5899999999999999999999998665433332  23 35689999999999999998764  8999999999999999


Q ss_pred             hc--------CCC----CchhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          105 NN--------RCS----SMAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       105 ~~--------~~~----~~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      ++        .+.    .+.....+++++..++.. ..+.|.||+    +++|..||.||+.|+.
T Consensus        79 ~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~  142 (155)
T 1jl1_A           79 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVKGHAGHPENERADELARAAAM  142 (155)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECCSSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccccccCCccCCHHHHHHHHHHHcc-CceEEEEcCCCCCCHHHHHHHHHHHHHHh
Confidence            97        211    112235678888888775 489999999    7799999999999985

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

Probab=99.92  E-value=6.4e-25  Score=149.42  Aligned_cols=124  Identities=9%  Similarity=-0.027  Sum_probs=99.2

Q ss_pred             CcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHH
Q 042421           24 GWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVEL  103 (154)
Q Consensus        24 g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~  103 (154)
                      ..+++|||||+..+++.+|+|+|+++.......  +... ...|++.||+.|++.||+.+.+.  .+|.|+|||+++++.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~--~~~~-~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEM--SDGF-SLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQG   79 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEE--EEEE-EEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEE--ecCc-CCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHH
Confidence            468999999999999999999999985432222  2223 34789999999999999998653  899999999999999


Q ss_pred             Hhc--------CCC----CchhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          104 VNN--------RCS----SMAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       104 i~~--------~~~----~~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      +++        .+.    .+.....+++++..++.. ..+.|.||+    +++|..||.||+.|++
T Consensus        80 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~  144 (158)
T 2e4l_A           80 IMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL-HQIDWRWVKGHAGHAENERCDQLARAAAE  144 (158)
T ss_dssp             HHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT-SEEEEEECCTTCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccccccCCCcccCHHHHHHHHHHHcc-CcEEEEEccCCCCchhHHHHHHHHHHHHH
Confidence            988        221    122345677888888876 489999999    6799999999999985

>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=99.92  E-value=7.6e-24  Score=144.72  Aligned_cols=131  Identities=14%  Similarity=-0.039  Sum_probs=102.2

Q ss_pred             cccCCCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           17 QWQSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        17 ~W~~p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      .+.|.+...+++|||||+..+++.+|+|+++.+. |..+...  ......|++.||+.|++.||+.+   ...+|.|+||
T Consensus        15 ~~~P~~~~~i~iytDGs~~~npG~~g~G~vi~~~-~~~~~~~--~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tD   88 (165)
T 3p1g_A           15 TDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTE-TEVIWAR--ALPAGTSAQRAELIALTQALKMA---EGKKLNVYTD   88 (165)
T ss_dssp             BSSCCTTCSEEEEEEEEEEEETTEEEEEEEEECS-SCEEEEE--EECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEEC
T ss_pred             CCCCCCCCCEEEEEEcccCCCCCceEEEEEEEEC-CEEEEEe--cCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEc
Confidence            4566666679999999999999999999999874 4443322  33456799999999999999998   3689999999


Q ss_pred             HHHHHHHHhcCCC-CchhHHHHHHHHHHHhhcCCceEEEEeCCCC---------cHHHHHHHHhhhc
Q 042421           97 CLEVVELVNNRCS-SMAEISWMISEILEMNNSFQNFRAQHTARIY---------NSAAHALGFRVCK  153 (154)
Q Consensus        97 s~~vi~~i~~~~~-~~~~~~~li~~i~~l~~~~~~~~~~~i~r~~---------N~~Ad~LA~~a~~  153 (154)
                      |+++++.+-.... ..-....+++++...+..+..+.|.||+++.         |+.||.||+.|+.
T Consensus        89 S~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~  155 (165)
T 3p1g_A           89 SRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAM  155 (165)
T ss_dssp             CHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHh
Confidence            9999998842211 1123345667775555578899999999986         9999999999975

>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=99.90  E-value=1.2e-24  Score=146.47  Aligned_cols=125  Identities=10%  Similarity=-0.004  Sum_probs=93.7

Q ss_pred             CCCcEEEEeceeEecCCCeeeEEEEEecCCCce-Eeec-cccccc--cchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           22 PIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNC-IAAA-VNTTKY--FGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        22 ~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~-~~~~-~~~~~~--~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      +.+.+++|||||+.+  +.+|+|+++++ +|.. .... ....+.  ..|++.||+.|++.||+.+.+.+. +|.|+|||
T Consensus         3 ~~~~i~iytDGs~~~--g~~G~G~vi~~-~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS   78 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVN--GQYAWAYAFVK-DGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDY   78 (147)
T ss_dssp             TTSCCEEECCCCCBT--TBCEEEEEEEE-TTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCC
T ss_pred             CCCeEEEEECCCCCC--CCcEEEEEEEE-CCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECc
Confidence            467899999999987  89999999998 4543 2222 111122  368999999999999999999999 99999999


Q ss_pred             HHHHHHHhcCCCCchh-HHHHHHHHHHHhhcCCceEEEEeCC----CCcHHHHHHHHhhhc
Q 042421           98 LEVVELVNNRCSSMAE-ISWMISEILEMNNSFQNFRAQHTAR----IYNSAAHALGFRVCK  153 (154)
Q Consensus        98 ~~vi~~i~~~~~~~~~-~~~li~~i~~l~~~~~~~~~~~i~r----~~N~~Ad~LA~~a~~  153 (154)
                      +.+.+++++.+..... ...+.+.++.+..   .+.|.||++    ++|+.||.||+.|++
T Consensus        79 ~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~  136 (147)
T 2kq2_A           79 AGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALG  136 (147)
T ss_dssp             STHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHh
Confidence            9999999886544332 2222222333322   788999985    579999999999986

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

Probab=99.90  E-value=6e-23  Score=140.17  Aligned_cols=128  Identities=20%  Similarity=0.059  Sum_probs=97.8

Q ss_pred             CcEEEEeceeEecCCCe-----eeEEEEEecCCCc--eEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           24 GWLKINVDVVVDVQKQV-----VGLEVVIRDEKDN--CIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        24 g~~k~n~Dgs~~~~~~~-----~g~G~vird~~g~--~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      -.+.+||||||..+++.     +|+|+++......  +..... ......+++.||+.|+..+|+.+.+.+ .+|.|+||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~-~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TD   83 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWS-IPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITD   83 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEE-EEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEES
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEecccc-CCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeC
Confidence            45789999999999775     9999999854433  332222 222456788999999999999888876 47999999


Q ss_pred             HHHHHHHHhc----------CC--CCchhHHHHHHHHHHHhhcCCceEEEEeCCC----------CcHHHHHHHHhhhc
Q 042421           97 CLEVVELVNN----------RC--SSMAEISWMISEILEMNNSFQNFRAQHTARI----------YNSAAHALGFRVCK  153 (154)
Q Consensus        97 s~~vi~~i~~----------~~--~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~----------~N~~Ad~LA~~a~~  153 (154)
                      |+++++.++.          ..  ..+-....+++++..++..+..+.|.||+.+          +|+.||.||++++.
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            9999999975          11  1112345678888888888889999999954          59999999999864

>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=99.85  E-value=6.7e-21  Score=126.91  Aligned_cols=86  Identities=17%  Similarity=0.190  Sum_probs=73.2

Q ss_pred             cCCCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHH
Q 042421           19 QSPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCL   98 (154)
Q Consensus        19 ~~p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~   98 (154)
                      .||+.+++++||||||..+++.+|+|+|++ ..|..+.... .+. ..|++.||++|++.||+.+.+.++ +|.|+|||+
T Consensus         5 ~~~~~~~~~iy~DGa~~gNpG~~G~G~vl~-~~g~~~~~~~-~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~   80 (142)
T 1zbf_A            5 AKEEIIWESLSVDVGSQGNPGIVEYKGVDT-KTGEVLFERE-PIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQ   80 (142)
T ss_dssp             ---CCCSSSEEEEEEECSSSEEEEEEEEET-TTCCEEEECC-CEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCH
T ss_pred             CCCCCCeEEEEEeeccCCCCCCeEEEEEEE-eCCEEEEEec-ccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehH
Confidence            467889999999999999999999999999 6676654432 233 579999999999999999999999 999999999


Q ss_pred             HHHHHHhcCC
Q 042421           99 EVVELVNNRC  108 (154)
Q Consensus        99 ~vi~~i~~~~  108 (154)
                      +|++++++..
T Consensus        81 ~vi~w~~~~~   90 (142)
T 1zbf_A           81 TAIKWVKDKK   90 (142)
T ss_dssp             HHHHHHHHTC
T ss_pred             HHHHHHHcCC
Confidence            9999999865

>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=99.83  E-value=4.8e-20  Score=147.22  Aligned_cols=121  Identities=16%  Similarity=0.030  Sum_probs=98.2

Q ss_pred             CCCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHH
Q 042421           20 SPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLE   99 (154)
Q Consensus        20 ~p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~   99 (154)
                      .|..+.+++|||||+..+++.+|+|+++.+..+..     ... ...|++.||+.|++.||+.    +..+|.|+|||++
T Consensus       431 ~p~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~-----~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~  500 (555)
T 1mu2_A          431 DPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKV-----KKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQY  500 (555)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEE-----EEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHH
T ss_pred             CCCCCceEEEEcccccCCCCCceEEEEEEeCCEee-----ccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHH
Confidence            45678899999999999999999999998754321     112 3568999999999999987    7789999999999


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHHhhcCCceEEEEeCCC----CcHHHHHHHHhhh
Q 042421          100 VVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARI----YNSAAHALGFRVC  152 (154)
Q Consensus       100 vi~~i~~~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~----~N~~Ad~LA~~a~  152 (154)
                      +++.+++....  ....+++++..++..+..+.+.||+++    +|+.||.||+.|+
T Consensus       501 v~~~i~~~~~~--~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          501 VMGIVASQPTE--SESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHHHHTCCSE--ESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHHhccccc--ccHHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            99999984322  224456677766666889999999985    6999999999985

>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=99.81  E-value=5.2e-20  Score=147.11  Aligned_cols=120  Identities=13%  Similarity=0.054  Sum_probs=94.3

Q ss_pred             CCCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHH
Q 042421           20 SPPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLE   99 (154)
Q Consensus        20 ~p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~   99 (154)
                      .|..+.+++|||||+..+++.+|+|+++.+......     .. ...|++.||+.|++.||+.+    ..+|.|+|||++
T Consensus       434 ep~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~-----~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~  503 (557)
T 2zd1_A          434 EPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVV-----PL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQY  503 (557)
T ss_dssp             SCCTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHH
T ss_pred             CCCCCCEEEEEccCCCCCCCceEEEEEEECCcEEEe-----cC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHH
Confidence            466788999999999999999999999985443232     12 35789999999999999998    689999999999


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHHhhcCCceEEEEeCCC----CcHHHHHHHHhh
Q 042421          100 VVELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARI----YNSAAHALGFRV  151 (154)
Q Consensus       100 vi~~i~~~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~----~N~~Ad~LA~~a  151 (154)
                      +++.+++....  ....+++++...+.++..+.+.||+++    +|+.||.||+.|
T Consensus       504 vi~~i~~~~~~--~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          504 ALGIIQAQPDK--SESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHHHHTTCCSE--ESSHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHHHhcCCcc--CCHHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            99999985432  123455666655556778999999996    599999999986

>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=99.76  E-value=4.4e-18  Score=111.53  Aligned_cols=80  Identities=18%  Similarity=0.201  Sum_probs=67.2

Q ss_pred             CcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHH
Q 042421           24 GWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVEL  103 (154)
Q Consensus        24 g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~  103 (154)
                      ....+||||||.++++.+|+|+|+++ .|..+... ..+ +..|+++||++|++.||+.+.+.+.+ |.|+|||++|+++
T Consensus         4 ~~~~iytDGac~GNPGp~G~ggV~~~-~g~~~~~~-g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~w   79 (134)
T 4htu_A            4 IWESLSVDVGSQGNPGIVEYKGVDTK-TGEVLFER-EPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKW   79 (134)
T ss_dssp             CSSSEEEEEEEETTTEEEEEEEEETT-TCCEEEEE-EEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHH
T ss_pred             cceEEEEeeccCCCCCCeEEEEEEEE-CCEEEEEe-cCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHH
Confidence            45679999999999999999988888 56544433 223 36799999999999999999998876 8999999999999


Q ss_pred             HhcC
Q 042421          104 VNNR  107 (154)
Q Consensus       104 i~~~  107 (154)
                      +++.
T Consensus        80 i~~~   83 (134)
T 4htu_A           80 VKDK   83 (134)
T ss_dssp             HHHT
T ss_pred             HHcC
Confidence            9873

>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=92.34  E-value=0.24  Score=32.03  Aligned_cols=57  Identities=9%  Similarity=0.049  Sum_probs=41.1

Q ss_pred             CeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      +...+|+++++.+|+++.+.............||..|+..+... -...+..+.+.+|
T Consensus        22 s~~~VGAal~~~dG~i~~G~Nvena~~~~t~cAE~~Ai~~A~~~-G~~~~~~~~l~~~   78 (136)
T 1uwz_A           22 SKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEATALFKAVSE-GDTEFQMLAVAAD   78 (136)
T ss_dssp             TCCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHH-TCCCEEEEEEEES
T ss_pred             CCCCEEEEEEeCCCeEEEEeCcccCCCCCccCHHHHHHHHHHHC-CCCCeEEEEEEeC
Confidence            34578999999999988654433333345689999999998875 3455788888876

>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=91.43  E-value=0.27  Score=32.23  Aligned_cols=58  Identities=10%  Similarity=0.056  Sum_probs=41.3

Q ss_pred             CeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      ....+|+++++.+|+++.+.............||..|+..|... -...+..+.+.+|.
T Consensus        34 s~f~VGAal~~~dG~i~~G~NvEnas~~~t~cAE~~Ai~~A~~~-G~~~l~~i~v~~~~   91 (146)
T 2fr5_A           34 SRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISE-GYKDFRAIAISSDL   91 (146)
T ss_dssp             TCCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEESC
T ss_pred             CCCCEEEEEEeCCCcEEEEEeccccCCCCCcCHHHHHHHHHHhC-CCCceEEEEEEeCC
Confidence            35578999998899888654433222334689999999998865 34457888888774

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

Probab=91.37  E-value=0.96  Score=34.79  Aligned_cols=81  Identities=7%  Similarity=-0.192  Sum_probs=52.0

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHH-HHHHHHHHHH--hCC--ceEEEec
Q 042421           21 PPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAA-IKWGMKVALR--AGL--ASVLLES   95 (154)
Q Consensus        21 p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~A-l~~aL~~a~~--~~~--~~v~ies   95 (154)
                      .+..-+.+++|+|-     .+.+|+|+..+.|....++...-...-...+-|++| +..+|+.-.-  .|-  ..+++.|
T Consensus       320 d~~~~~~l~~das~-----~g~~g~vl~q~~~~~~~s~~~~~~~~y~~~~~e~la~vv~al~~~r~yl~G~~~~~~i~~t  394 (428)
T 2zd1_B          320 DPSKDLIAEIQKQG-----QGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQ  394 (428)
T ss_dssp             CTTSCCEEEEEEEE-----TTEEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHHHSSCCEEEESSC
T ss_pred             CCCCCEEEEEecCC-----CCcEEEEEecCCCceeeecccchhhhcccchHHHHHHHHHHhhccceEEECCCCcEECCcc
Confidence            34455789999984     236788887766654433322222223456677778 9999987654  343  6678899


Q ss_pred             cHHHHHHHHhc
Q 042421           96 DCLEVVELVNN  106 (154)
Q Consensus        96 Ds~~vi~~i~~  106 (154)
                      |.+.+.-+.+.
T Consensus       395 d~~~~~~~~~~  405 (428)
T 2zd1_B          395 KETWETWWTEY  405 (428)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            99877655443

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=89.85  E-value=0.058  Score=41.84  Aligned_cols=78  Identities=15%  Similarity=-0.033  Sum_probs=51.1

Q ss_pred             CCcEEEEeceeEecCCCeeeEEEEEe-cCC--CceEeecccccccc---chhHHHHHHHHHHHHHHHHHh-CCceEEEec
Q 042421           23 IGWLKINVDVVVDVQKQVVGLEVVIR-DEK--DNCIAAAVNTTKYF---GNVAMAEAAAIKWGMKVALRA-GLASVLLES   95 (154)
Q Consensus        23 ~g~~k~n~Dgs~~~~~~~~g~G~vir-d~~--g~~~~~~~~~~~~~---~s~~~AE~~Al~~aL~~a~~~-~~~~v~ies   95 (154)
                      ..-+.+++|+|-.      |+|+|+. ...  +..+...++.+...   -+..+.|++|+..|++..... --+++.|.|
T Consensus       344 ~~~~~l~~DAS~~------~~gavL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~t  417 (455)
T 1rw3_A          344 TKPFELFVDEKQG------YAKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKA  417 (455)
T ss_dssp             CCTTSCEEEEEEC------SSSBEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEEC
T ss_pred             CCcEEEEEeccCC------cceeEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEe
Confidence            3446789998743      2333443 222  34555555554432   346789999999999988763 337999999


Q ss_pred             cHHHHHHHHhcC
Q 042421           96 DCLEVVELVNNR  107 (154)
Q Consensus        96 Ds~~vi~~i~~~  107 (154)
                      |+. +...++.+
T Consensus       418 Dh~-~~~~l~~~  428 (455)
T 1rw3_A          418 PHA-VEALVKQP  428 (455)
T ss_dssp             SSC-TTTTSSST
T ss_pred             cCh-HHHHhCCC
Confidence            997 66666654

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

Probab=85.97  E-value=1.2  Score=29.00  Aligned_cols=58  Identities=17%  Similarity=0.180  Sum_probs=40.2

Q ss_pred             eeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      ....|+++++.+|++..+...........+.||-.|+..+...-....+..+.+.+|.
T Consensus        31 ~f~VGAAl~~~dG~i~~G~NvEnasy~~t~cAEr~Ai~~a~~~G~~~~i~~i~vv~~~   88 (142)
T 1r5t_A           31 HFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDS   88 (142)
T ss_dssp             CCCEEEEEECTTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHTTCCSCCCEEEEEESC
T ss_pred             CCCEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCCCCceEEEEEEeCC
Confidence            5578999999999888755433323345689999999988764322227788887764

>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=85.57  E-value=0.98  Score=28.87  Aligned_cols=56  Identities=7%  Similarity=0.001  Sum_probs=39.5

Q ss_pred             CeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      +...+|+++++.+|+++.+....  .....+.||..|+..+... -...+..+.+.+|.
T Consensus        25 s~f~VGAal~~~dG~i~~G~NvE--~~~~t~cAE~~Ai~~A~~~-G~~~~~~i~vv~~~   80 (130)
T 2z3g_A           25 EDYSVASAALSSDGRIFTGVNVY--HFTGGPCAELVVLGTAAAA-AAGNLTCIVAIGNE   80 (130)
T ss_dssp             SSSCEEEEEEETTSCEEEEECCC--CTTTCCCHHHHHHHHHHHT-TCCCEEEEEEEETT
T ss_pred             CCCCEEEEEEecCCeEEEEeccc--cCCcccCHHHHHHHHHHHc-CCCceEEEEEEECC
Confidence            34678999998999888644332  3445789999999988863 22456788887763

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

Probab=84.16  E-value=1.5  Score=28.45  Aligned_cols=57  Identities=9%  Similarity=0.080  Sum_probs=40.3

Q ss_pred             eeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      ....|+++++.+|++..+..-........+-||-.|+..+... =...+..|.+.+|.
T Consensus        32 ~f~VGAAll~~dG~i~~G~NvEnasy~~t~CAEr~Ai~~Avs~-G~~~~~aiav~~~~   88 (141)
T 2d30_A           32 KFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVADT   88 (141)
T ss_dssp             CCCEEEEEEETTCCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEESC
T ss_pred             CCcEEEEEEeCCCCEEEeeccccCCCCcccCHHHHHHHHHHHC-CCCceEEEEEEeCC
Confidence            4578999999999887665433333345689999999988764 22446788888774

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

Probab=82.23  E-value=1.4  Score=29.14  Aligned_cols=55  Identities=29%  Similarity=0.193  Sum_probs=34.5

Q ss_pred             eeeEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCceEEEec
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLASVLLES   95 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~v~ies   95 (154)
                      ...+|+||.+ +|+++..+..... ......+||..|+..+.+..-...+....+++
T Consensus        26 ~~pVGAviv~-~g~Ii~~G~N~~~~~~~~~~HAE~~Ai~~a~~~~~~~~l~~~tlyv   81 (159)
T 2b3j_A           26 EVPIGAIITK-DDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYV   81 (159)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTEEEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCCccCHHHHHHHHHHHHcCCCCcceeEEEE
Confidence            4567777777 7888865543221 12335799999999887654334455555554

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

Probab=81.65  E-value=1.2  Score=28.85  Aligned_cols=54  Identities=24%  Similarity=0.142  Sum_probs=33.6

Q ss_pred             eeeEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCceEEEe
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLASVLLE   94 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~v~ie   94 (154)
                      ...+|+||.+ +|+++..+..... .......||..|+..+.+..-...+....++
T Consensus        23 ~~~VGAviv~-~g~Ii~~G~N~~~~~~~~~~HAE~~Ai~~a~~~~~~~~~~~~tly   77 (144)
T 2a8n_A           23 EVPIGAVLVL-DGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLY   77 (144)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTCEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCCcCCHHHHHHHHHHHHcCCCccCCeEEE
Confidence            4467888777 7888865544322 1223578999999998765333334444554

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

Probab=80.76  E-value=1.6  Score=29.26  Aligned_cols=56  Identities=23%  Similarity=0.110  Sum_probs=36.3

Q ss_pred             CeeeEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCceEEEec
Q 042421           39 QVVGLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLASVLLES   95 (154)
Q Consensus        39 ~~~g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~v~ies   95 (154)
                      +...+|+||.+ +|+++..+..... .......||..|+..+.+..-...+....+++
T Consensus        41 ~~~pVGAvIV~-dg~Ii~~G~N~~~~~~d~t~HAE~~AI~~a~~~~g~~~l~~~tlYv   97 (171)
T 1wwr_A           41 GEVPVGAIIVK-EGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYV   97 (171)
T ss_dssp             TSCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTEEEEE
T ss_pred             CCCCEEEEEEE-CCEEEEEEECCCCccCCcccCHHHHHHHHHHHHcCCCccCceEEEE
Confidence            35567888887 7888865543222 12235789999999887654444456666664

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

Probab=80.46  E-value=1.7  Score=29.36  Aligned_cols=55  Identities=18%  Similarity=0.041  Sum_probs=33.4

Q ss_pred             eeeEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCceEEEec
Q 042421           40 VVGLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLASVLLES   95 (154)
Q Consensus        40 ~~g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~v~ies   95 (154)
                      ...+|+||.+ +|+++..+..... ......+||..|+..+.+..-...+....+++
T Consensus        35 ~~pVGAVIV~-~g~Ii~~G~N~~~~~~d~t~HAE~~AI~~a~~~~~~~~l~g~tlYv   90 (179)
T 2nx8_A           35 EIPIGCVIVK-DGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGNWRLLDTTLFV   90 (179)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTEEEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCcCCCccCHHHHHHHHHHHHcCCCcccceEEEE
Confidence            4567887776 7888875543322 12235799999999887654333344444443

>4h8e_A Undecaprenyl pyrophosphate synthase; alpha-helix, prenyl transferase, cell WALL biosynthesis, FAR diphosphate binding; HET: FPP; 1.30A {Staphylococcus aureus subsp}

Probab=80.24  E-value=3.6  Score=29.48  Aligned_cols=89  Identities=12%  Similarity=0.078  Sum_probs=54.1

Q ss_pred             eEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHHhcCCCCchhHHHHHHHH
Q 042421           42 GLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNNRCSSMAEISWMISEI  121 (154)
Q Consensus        42 g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i~~~~~~~~~~~~li~~i  121 (154)
                      -+|+ |-|.+|++-..  ..++ ...-..+-+.++...++++.++|++.|.++.-|..      +-..+..+...++.-+
T Consensus        27 HVAi-IMDGN~RwAk~--rgl~-r~~GH~~G~~~~~~iv~~c~~lGI~~lTlYaFStE------NwkRp~~EV~~Lm~L~   96 (256)
T 4h8e_A           27 HIAI-IMDGNGRWAKK--RKMP-RIKGHYEGMQTIKKITRIASDIGVKYLTLYAFSTE------NWSRPESEVNYIMNLP   96 (256)
T ss_dssp             EEEE-ECCCHHHHHHH--TTCC-HHHHHHHHHHHHHHHHHHHHHHTCSEEEEEEEETT------GGGSCHHHHHHHHHHH
T ss_pred             EEEE-EcCCCHHHHHH--CCCC-HHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEchh------hhCCCHHHHHHHHHHH
Confidence            4544 45888876432  1222 34567888899999999999999999999988732      1112233444333322


Q ss_pred             HHHh----hc--CCceEEEEeCCCC
Q 042421          122 LEMN----NS--FQNFRAQHTARIY  140 (154)
Q Consensus       122 ~~l~----~~--~~~~~~~~i~r~~  140 (154)
                      ...+    ..  -..+++.+|.+..
T Consensus        97 ~~~l~~~~~~l~~~~vrvr~iGd~~  121 (256)
T 4h8e_A           97 VNFLKTFLPELIEKNVKVETIGFTD  121 (256)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEESCGG
T ss_pred             HHHHHHHHHHHHHcCeEEEEecCcc
Confidence            2111    11  2567888887644

---

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	154
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.85
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.85
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.8
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.75
d1z3aa1	156	tRNA adenosine deaminase TadA {Escherichia coli [T	86.12
d2g84a1	189	Putative deaminase NE0047 {Nitrosomonas europaea [	85.41
d1wkqa_	158	Guanine deaminase GuaD {Bacillus subtilis [TaxId:	82.57
d1wwra1	151	tRNA adenosine deaminase TadA {Aquifex aeolicus [T	81.84
d2d30a1	124	mono-domain cytidine deaminase {Bacillus anthracis	80.81

>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=99.87  E-value=1.3e-21  Score=126.86  Aligned_cols=120  Identities=16%  Similarity=-0.007  Sum_probs=91.2

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHH
Q 042421           21 PPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEV  100 (154)
Q Consensus        21 p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~v  100 (154)
                      |-.|...+|||||+..+++.+|+|+++.+....+..     + ...|++.||+.|++.||+.    ...++.|+|||+++
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~-----~-~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v   72 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKK-----L-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYV   72 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEE-----E-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEe-----c-CCCcchHHHHHHHHHHhcc----CCcceEEEechHHH
Confidence            556778899999999999999999988665433321     2 2468999999999998864    56799999999999


Q ss_pred             HHHHhcCCCCchhHHHHHHHHHHHhhcCCceEEEEeCCC----CcHHHHHHHHhhh
Q 042421          101 VELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARI----YNSAAHALGFRVC  152 (154)
Q Consensus       101 i~~i~~~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~----~N~~Ad~LA~~a~  152 (154)
                      ++++++...... ...+.+.+..+.. ...+.|.||+.+    +|+.||.||++|+
T Consensus        73 ~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          73 MGIVASQPTESE-SKIVNQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHHHTCCSEES-CHHHHHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHhcCCcccc-chHHHHHHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            999999654322 2223344444444 568999999965    5999999999985

>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=99.85  E-value=2.2e-21  Score=128.83  Aligned_cols=122  Identities=11%  Similarity=-0.024  Sum_probs=94.4

Q ss_pred             EEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHHh
Q 042421           26 LKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVN  105 (154)
Q Consensus        26 ~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i~  105 (154)
                      +.+|||||+.++++.+|+|+|+.+..........  . ...|++.||+.|+++||+.+.  ....+.+++||+++++.++
T Consensus         4 i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~--~-~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~   78 (147)
T d1rila_           4 VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGG--E-ACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFT   78 (147)
T ss_dssp             CCEEEEEEESSTTEEEEEEEEECBTTBCCEECCE--E-EEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHH
T ss_pred             EEEEEccCCCCCCCccEEEEEEEECCcceEEecc--c-ccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhcccc
Confidence            6799999999999999999999877665544332  2 346899999999999998643  4568999999999999886


Q ss_pred             cCCC-------------CchhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          106 NRCS-------------SMAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       106 ~~~~-------------~~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      ....             .+-....+++++..++.. ..+.|.||+    +++|+.||.||++|++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~-~~v~~~wVkgHsg~~gNe~AD~LAk~aa~  142 (147)
T d1rila_          79 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQ  142 (147)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHT
T ss_pred             ccchhhhhhccccccccccchhHHHHHHHHHHhhh-cccceEEccCCCCCcchHHHHHHHHHHHH
Confidence            5210             111234567777776654 578899888    6789999999999986

>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=99.85  E-value=7.1e-21  Score=126.77  Aligned_cols=123  Identities=11%  Similarity=-0.044  Sum_probs=94.2

Q ss_pred             cEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHH
Q 042421           25 WLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELV  104 (154)
Q Consensus        25 ~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i  104 (154)
                      .+++|||||+.++++.+|+|+|+.+..........  . ...|++.||++|++.||+.+.  ....+.+.+|+++++..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~--~-~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAG--Y-TRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEE--E-EEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccc--c-CcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcc
Confidence            37999999999999999999999876655443322  2 346899999999999998643  457899999999999988


Q ss_pred             hcCC------------CCchhHHHHHHHHHHHhhcCCceEEEEeC----CCCcHHHHHHHHhhhc
Q 042421          105 NNRC------------SSMAEISWMISEILEMNNSFQNFRAQHTA----RIYNSAAHALGFRVCK  153 (154)
Q Consensus       105 ~~~~------------~~~~~~~~li~~i~~l~~~~~~~~~~~i~----r~~N~~Ad~LA~~a~~  153 (154)
                      +...            ...-....++.++..+... ..++|.||+    +++|..||.||++|+.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~-~~V~~~wV~gH~g~~gNe~AD~LAk~aa~  140 (152)
T d1jl1a_          77 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVKGHAGHPENERADELARAAAM  140 (152)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECCSSTTCHHHHHHHHHHHHHHH
T ss_pred             cchhhHhHhccchhcccCeeecHHHHHHHHHHhhc-ceeEEEEecccCCCccHHHHHHHHHHHHh
Confidence            6521            1111234466777666654 589999999    5689999999999975

>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=99.80  E-value=7.3e-19  Score=110.83  Aligned_cols=107  Identities=12%  Similarity=0.075  Sum_probs=84.2

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHH
Q 042421           21 PPIGWLKINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEV  100 (154)
Q Consensus        21 p~~g~~k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~v  100 (154)
                      |-.+-..+|||||+..+++.+|+|+++.+.......     + ...|++.||+.|++.||+    .+..+|.|+|||+++
T Consensus         4 Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~-----~-~~~TNn~aEl~Avi~aL~----~~~~~v~I~TDS~yv   73 (110)
T d1s1ta1           4 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVT-----L-TDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYA   73 (110)
T ss_dssp             CCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEE-----E-SSCCHHHHHHHHHHHHHH----HSCSEEEEEECCHHH
T ss_pred             CCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEe-----c-ccCcHHHHHHHHHHHHHH----hCCCeEEEEEehHHH
Confidence            555666899999999999999999998664432221     2 246999999999999986    366899999999999


Q ss_pred             HHHHhcCCCCchhHHHHHHHHHHHhhcCCceEEEEeCCC
Q 042421          101 VELVNNRCSSMAEISWMISEILEMNNSFQNFRAQHTARI  139 (154)
Q Consensus       101 i~~i~~~~~~~~~~~~li~~i~~l~~~~~~~~~~~i~r~  139 (154)
                      ++.+++.....  ...+++++...+..+..+.+.|||.+
T Consensus        74 i~~i~~~~~~~--~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          74 LGIIQAQPDQS--ESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHHCCSEE--SCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             HHHHhcCcccc--chHHHHHHHHHHhcCCceEEEEeCCC
Confidence            99999975432  23456777776777899999999975

>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=99.75  E-value=6.6e-18  Score=108.60  Aligned_cols=77  Identities=17%  Similarity=0.178  Sum_probs=65.0

Q ss_pred             EEEeceeEecCCCeeeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccHHHHHHHHhc
Q 042421           27 KINVDVVVDVQKQVVGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDCLEVVELVNN  106 (154)
Q Consensus        27 k~n~Dgs~~~~~~~~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs~~vi~~i~~  106 (154)
                      .|||||||.+++|.+|+|+|+.+........+  .+ +..|+++||++|++.||+.+.+.+ .++.|+|||+++++++++
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg--~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~   81 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFERE--PI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKD   81 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECC--CE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEc--Cc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHh
Confidence            58999999999999999999977555444332  33 457999999999999999999987 579999999999999977


Q ss_pred             C
Q 042421          107 R  107 (154)
Q Consensus       107 ~  107 (154)
                      .
T Consensus        82 ~   82 (132)
T d1zbfa1          82 K   82 (132)
T ss_dssp             T
T ss_pred             C
Confidence            3

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

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

Probab=86.12  E-value=0.26  Score=30.90  Aligned_cols=53  Identities=21%  Similarity=0.124  Sum_probs=34.9

Q ss_pred             eEEEEEecCCCceEeeccccccc-cchhHHHHHHHHHHHHHHHHHhCCceEEEec
Q 042421           42 GLEVVIRDEKDNCIAAAVNTTKY-FGNVAMAEAAAIKWGMKVALRAGLASVLLES   95 (154)
Q Consensus        42 g~G~vird~~g~~~~~~~~~~~~-~~s~~~AE~~Al~~aL~~a~~~~~~~v~ies   95 (154)
                      .+|+||.+ +|+++..+...... .....+||..|+..+........+....+++
T Consensus        28 pvGaViv~-~g~Iia~g~n~~~~~~~~~~HAE~~ai~~a~~~~~~~~l~~~~lyt   81 (156)
T d1z3aa1          28 PVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYV   81 (156)
T ss_dssp             CCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTCEEEE
T ss_pred             CEEEEEEE-CCeEEEEeeccccccCcchhhHHHHhHHHHHhhcccccccCceeee
Confidence            47888877 68888876654332 2234699999999888766655444444443

>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=85.41  E-value=0.6  Score=30.28  Aligned_cols=46  Identities=17%  Similarity=-0.008  Sum_probs=31.4

Q ss_pred             CeeeEEEEEecC-CCceEeecccccc-ccchhHHHHHHHHHHHHHHHH
Q 042421           39 QVVGLEVVIRDE-KDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVAL   84 (154)
Q Consensus        39 ~~~g~G~vird~-~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~   84 (154)
                      +...+|+||.+. .|+++..+..... ......+||..|+..|.+...
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            344689888886 4788887654432 223346999999998876544

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

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

Probab=82.57  E-value=0.54  Score=29.56  Aligned_cols=45  Identities=29%  Similarity=0.203  Sum_probs=28.8

Q ss_pred             EEEEEecCCCceEeecccccccc-chhHHHHHHHHHHHHHHHHHhCC
Q 042421           43 LEVVIRDEKDNCIAAAVNTTKYF-GNVAMAEAAAIKWGMKVALRAGL   88 (154)
Q Consensus        43 ~G~vird~~g~~~~~~~~~~~~~-~s~~~AE~~Al~~aL~~a~~~~~   88 (154)
                      +|+||.++ |+++..+....... ....+||..|+..|........+
T Consensus        28 vGaviv~~-~~ii~~g~n~~~~~~~~t~HAE~~ai~~a~~~~~~~~l   73 (158)
T d1wkqa_          28 FGAVIVKD-GAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQL   73 (158)
T ss_dssp             CEEEEEET-TEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSSC
T ss_pred             EEEEEEec-ccceeeccceeeccCCCcccHHHHHHHHHHHhcCcccc
Confidence            77777764 77877665432222 22359999999998775544333

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

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

Probab=81.84  E-value=0.6  Score=29.05  Aligned_cols=54  Identities=24%  Similarity=0.126  Sum_probs=35.4

Q ss_pred             eEEEEEecCCCceEeecccccc-ccchhHHHHHHHHHHHHHHHHHhCCceEEEecc
Q 042421           42 GLEVVIRDEKDNCIAAAVNTTK-YFGNVAMAEAAAIKWGMKVALRAGLASVLLESD   96 (154)
Q Consensus        42 g~G~vird~~g~~~~~~~~~~~-~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesD   96 (154)
                      -+|+||.++ |+++..+..... ......+||..|+..|.+......+....+++-
T Consensus        24 pVGaVIV~~-~~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~~~~~~~l~~~tlY~T   78 (151)
T d1wwra1          24 PVGAIIVKE-GEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVT   78 (151)
T ss_dssp             CCEEEEEET-TEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTCSCCTTEEEEES
T ss_pred             CEEEEEEEC-CeeeeeecccccccCcchhhHHHHHHHHHHHhhCccccCCcEeeec
Confidence            378888774 666665443321 123356899999999888766555666677765

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

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

Probab=80.81  E-value=1  Score=27.06  Aligned_cols=56  Identities=9%  Similarity=0.092  Sum_probs=40.6

Q ss_pred             eeEEEEEecCCCceEeeccccccccchhHHHHHHHHHHHHHHHHHhCCceEEEeccH
Q 042421           41 VGLEVVIRDEKDNCIAAAVNTTKYFGNVAMAEAAAIKWGMKVALRAGLASVLLESDC   97 (154)
Q Consensus        41 ~g~G~vird~~g~~~~~~~~~~~~~~s~~~AE~~Al~~aL~~a~~~~~~~v~iesDs   97 (154)
                      .-.|+.++..+|++..+..-........+.||-.|+..++.. -+..+..|.+.+|+
T Consensus        24 f~VGAal~~~~G~i~~G~NvEn~s~~~~~CAEr~Ai~~a~~~-g~~~~~~i~v~~~~   79 (124)
T d2d30a1          24 FQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVADT   79 (124)
T ss_dssp             CCEEEEEEETTCCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEESC
T ss_pred             CcEEEEEEeCCCCEEEEEeeccccCCcccCHHHHHHHHHHhc-CCceeEEEEEEcCC
Confidence            458888999999987765543333445679999999988764 34556788887765