Citrus Sinensis ID: 046558

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130------
Protein Sequence
EDFLAEQNNVQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEEEccEEEccccEEEEEEEEEcccccEEEEEccccccccccccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccccccHHHHHHHHHHHHHccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccHcccccccccccccccccEEEEEEcccEccccccEEEEEEEEcccccEEEEccccccccccHHHHHHHHHHHHHHHHHHcccccEEEEccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccEEEEEEEcc
Coil and Loop (DISEMBL)
EDFLAEqnnvqqsqwsppeegwlkvNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINnkrstltdtFWVIFDIIEAKKIFQNFKAQHVLRM
Flexible Loop (DISEMBL)
edflaeqnnvqqsqwsppeegWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELInnkrstltdtFWVIFDIIEAKKIFQNFKAQHVLRM
Low Complexity Region (SEG)
EDFLAEQNNVQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM
Disordered region (IsUnstruct)
********************GWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQ*****
Disordered Region (DISOPRED)
*******************EGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM
Disordered Region (DISEMBL)
*****************PEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM
Disordered Region (DISPRO)
************SQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
EDFLAEQNNVQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM
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	136
238481636	263	nucleic acid binding protein [Arabidopsi	0.705	0.365	0.302	3e-09
116830343	264	unknown [Arabidopsis thaliana]	0.705	0.363	0.302	3e-09
357129345	776	PREDICTED: putative ribonuclease H prote	0.889	0.155	0.338	4e-09
343887321	166	hypothetical protein [Citrus unshiu]	0.676	0.554	0.369	9e-09
242090371	379	hypothetical protein SORBIDRAFT_09g01895	0.882	0.316	0.309	1e-08
242085688	188	hypothetical protein SORBIDRAFT_08g01666	0.911	0.659	0.314	2e-08
253761765	821	hypothetical protein SORBIDRAFT_0011s003	0.911	0.151	0.290	2e-08
297795275	352	hypothetical protein ARALYDRAFT_917523 [	0.676	0.261	0.293	4e-08
242054685	589	hypothetical protein SORBIDRAFT_03g03719	0.904	0.208	0.292	5e-08
147777242	318	hypothetical protein VITISV_019020 [Viti	0.867	0.371	0.283	6e-08

>gi|238481636|ref|NP_001154797.1| nucleic acid binding protein [Arabidopsis thaliana] gi|98962281|gb|ABF59470.1| unknown protein [Arabidopsis thaliana] gi|332010600|gb|AED97983.1| nucleic acid binding protein [Arabidopsis thaliana]

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 51/96 (53%)

Query: 11  QQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEA 70
           + ++WSPP    LK N D +    N ++GLG +++N +G  +   +  F+     E +E 
Sbjct: 101 RNTKWSPPGRDKLKCNYDASHHERNTVSGLGWILRNSQGTVIECGMGKFQGRMTTEEAEC 160

Query: 71  KAVLWGMQAAAKAGATSVILESDSKGVIELINNKRS 106
             ++W +QA+   G   VI E D++ +  +IN K S
Sbjct: 161 STLIWAIQASYGFGHKKVIFEGDNQTITRMINTKSS 196

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116830343|gb|ABK28129.1| unknown [Arabidopsis thaliana]

 Score = 66.6 bits (161), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 51/96 (53%)

Query: 11  QQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEA 70
           + ++WSPP    LK N D +    N ++GLG +++N +G  +   +  F+     E +E 
Sbjct: 101 RNTKWSPPGRDKLKCNYDASHHERNTVSGLGWILRNSQGTVIECGMGKFQGRMTTEEAEC 160

Query: 71  KAVLWGMQAAAKAGATSVILESDSKGVIELINNKRS 106
             ++W +QA+   G   VI E D++ +  +IN K S
Sbjct: 161 STLIWAIQASYGFGHKKVIFEGDNQTITRMINTKSS 196

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357129345|ref|XP_003566324.1| PREDICTED: putative ribonuclease H protein At1g65750-like [Brachypodium distachyon]

 Score = 66.2 bits (160), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 60/121 (49%)

Query: 15  WSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVL 74
           WSPPE  W+K+NVD +       A  GAV+++  G  VA+A       G    +EAKA  
Sbjct: 431 WSPPEANWMKLNVDASFIEQTREAWWGAVLRSSDGAVVASAWGAIGPCGSATEAEAKAAR 490

Query: 75  WGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVL 134
            G+ A   A + ++ LESD K VI  + N  +  T   +VI ++  +   F  +K   V 
Sbjct: 491 NGIAALRHAASANLHLESDCKAVIASLLNPSADRTGVCFVIREVCSSLGSFDLYKCSWVC 550

Query: 135 R 135
           R
Sbjct: 551 R 551

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 65.1 bits (157), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 55/92 (59%)

Query: 37  LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKG 96
           L GLG V++N +G+ + AA  + K   +V  ++A+AV WG++ A +A   +VI+E+D   
Sbjct: 54  LTGLGVVIRNSQGQVIVAAFKSTKFEDNVTAAKAEAVKWGLEMALEARLAAVIIETDCIE 113

Query: 97  VIELINNKRSTLTDTFWVIFDIIEAKKIFQNF 128
           V  L NN+ S+  +  W I DI   K+ FQ+ 
Sbjct: 114 VANLANNETSSRKEIVWTISDIHSYKEKFQSL 145

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242090371|ref|XP_002441018.1| hypothetical protein SORBIDRAFT_09g018950 [Sorghum bicolor] gi|241946303|gb|EES19448.1| hypothetical protein SORBIDRAFT_09g018950 [Sorghum bicolor]

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 65/126 (51%), Gaps = 6/126 (4%)

Query: 10  VQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSE 69
           ++QS W  P  GW+KVNVD +       A +G V++NHKGE +  A         +  + 
Sbjct: 217 IKQS-WEVPPAGWIKVNVDASFVNATGEASVGVVIRNHKGEVLLTAWRVL-----LRCAS 270

Query: 70  AKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFK 129
           A+A + G++ A+K  A   ILESDS  ++  + + R   ++  W I +  E  ++   +K
Sbjct: 271 AEACVDGLRLASKWCAGPTILESDSARLVAALGDGREDRSELRWTILEAKEYLQLLPEWK 330

Query: 130 AQHVLR 135
            + V R
Sbjct: 331 IKKVKR 336

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242085688|ref|XP_002443269.1| hypothetical protein SORBIDRAFT_08g016660 [Sorghum bicolor] gi|241943962|gb|EES17107.1| hypothetical protein SORBIDRAFT_08g016660 [Sorghum bicolor]

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/124 (31%), Positives = 58/124 (46%)

Query: 12  QSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAK 71
           +++W  PE GW KVN D   D+       G V+++H G  V AA   F         EA 
Sbjct: 21  RARWEKPEPGWTKVNTDGGFDQQACSGRTGVVIRDHTGVVVGAAARWFDDVESALAVEAL 80

Query: 72  AVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQ 131
           A   G++ A++ G   VILE D + +   + +  S  +    +  DIIE  K F +F+  
Sbjct: 81  AAREGLELASELGLGKVILEVDCQVLARFLLDPNSVYSTIGSLCLDIIELGKGFSDFQVC 140

Query: 132 HVLR 135
            V R
Sbjct: 141 WVGR 144

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|253761765|ref|XP_002489257.1| hypothetical protein SORBIDRAFT_0011s003210 [Sorghum bicolor] gi|241947006|gb|EES20151.1| hypothetical protein SORBIDRAFT_0011s003210 [Sorghum bicolor]

 Score = 63.5 bits (153), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/124 (29%), Positives = 60/124 (48%)

Query: 12  QSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAK 71
           +++W  P  GW K+N D   DR +     G V++N  G     +    ++  D   +EA 
Sbjct: 654 KAKWEKPSPGWFKINTDAGFDRESNSGSAGVVIRNEAGLVAGGSARWIENVPDTLTAEAM 713

Query: 72  AVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQ 131
           A   G++   + G   VILE D + + +L+ ++ S  +    + FDIIE  K+F  F  +
Sbjct: 714 AAREGLELVVELGLDRVILEVDCQELSKLLLSQNSISSCIEGLCFDIIELGKMFSEFCIR 773

Query: 132 HVLR 135
            V R
Sbjct: 774 WVRR 777

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297795275|ref|XP_002865522.1| hypothetical protein ARALYDRAFT_917523 [Arabidopsis lyrata subsp. lyrata] gi|297311357|gb|EFH41781.1| hypothetical protein ARALYDRAFT_917523 [Arabidopsis lyrata subsp. lyrata]

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 49/92 (53%)

Query: 11  QQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEA 70
           + S+W  PE G++K N D +    N  +GLG ++++  G  +   +  F+    +E +E 
Sbjct: 187 RSSKWCKPERGYVKCNFDASHYEGNQSSGLGRIIRDSNGTCLDCGMGKFQGRQTIEEAEC 246

Query: 71  KAVLWGMQAAAKAGATSVILESDSKGVIELIN 102
            A++W +QA+   G   V  E D+  ++ LIN
Sbjct: 247 SALIWAIQASWALGYRHVEFEGDNANIVNLIN 278

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 = 62.8 bits (151), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 36/123 (29%), Positives = 63/123 (51%)

Query: 13  SQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKA 72
           ++WSPP  G LK+N D A  +       GAVV++  G   AA+       G V ++EA+A
Sbjct: 426 TRWSPPAPGMLKINSDGAFLQDRGTGAAGAVVRDSSGNFCAASARWLGPVGSVLIAEAEA 485

Query: 73  VLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQH 132
           +  G++   +     +I E+D++ V+ L  N+    ++   ++ +I E    F +F+  H
Sbjct: 486 IRDGLRLIPQGTMEHIIGETDAREVVALWKNRTRQRSEIAAILKEIEEIVSAFTSFELIH 545

Query: 133 VLR 135
           V R
Sbjct: 546 VRR 548

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777242|emb|CAN72157.1| hypothetical protein VITISV_019020 [Vitis vinifera]

 Score = 62.4 bits (150), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 36/127 (28%), Positives = 64/127 (50%), Gaps = 9/127 (7%)

Query: 9   NVQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELS 68
           +++   W  PE GW K+N D ++DR N  AG G + ++H G+ + A  S      D+ L 
Sbjct: 149 SIRWYSWEKPEFGWTKLNTDGSIDRGN--AGFGGLFRDHNGDPICAYASK-AHQNDIFLV 205

Query: 69  EAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKR------STLTDTFWVIFDIIEAK 122
           E  A+  G+  A+  G  ++ +ESDS  V++ IN K+       +  +  WV+    E  
Sbjct: 206 ELWAIWRGLVLASGLGIKAIWVESDSMSVVKTINRKQPYSSRAGSCLNHIWVLLGKFEKY 265

Query: 123 KIFQNFK 129
           ++   ++
Sbjct: 266 RVSHTWR 272

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	136
TAIR|locus:5019474881	263	AT5G65005 [Arabidopsis thalian	0.705	0.365	0.302	2.2e-10
TAIR|locus:2119886	575	AT4G29090 [Arabidopsis thalian	0.845	0.2	0.314	2.2e-09
TAIR|locus:2039129	160	AT2G46460 [Arabidopsis thalian	0.808	0.687	0.294	9.7e-09
TAIR|locus:2090215	343	AT3G25270 [Arabidopsis thalian	0.801	0.317	0.284	3.7e-08
TAIR|locus:2065330	365	AT2G02650 [Arabidopsis thalian	0.764	0.284	0.336	7e-08
TAIR|locus:2058379	221	AT2G04420 [Arabidopsis thalian	0.786	0.484	0.293	8.3e-08
TAIR|locus:2011571	313	AT1G52990 [Arabidopsis thalian	0.602	0.261	0.317	2.3e-07
TAIR|locus:2090950	191	AT3G23320 [Arabidopsis thalian	0.845	0.602	0.258	6.6e-07
TAIR|locus:2040899	292	AT2G34320 [Arabidopsis thalian	0.691	0.321	0.25	1.2e-06
TAIR|locus:2163391	108	AT5G44470 "AT5G44470" [Arabido	0.492	0.620	0.313	1.3e-06

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

 Score = 149 (57.5 bits), Expect = 2.2e-10, P = 2.2e-10
 Identities = 29/96 (30%), Positives = 51/96 (53%)

Query:    11 QQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEA 70
             + ++WSPP    LK N D +    N ++GLG +++N +G  +   +  F+     E +E 
Sbjct:   101 RNTKWSPPGRDKLKCNYDASHHERNTVSGLGWILRNSQGTVIECGMGKFQGRMTTEEAEC 160

Query:    71 KAVLWGMQAAAKAGATSVILESDSKGVIELINNKRS 106
               ++W +QA+   G   VI E D++ +  +IN K S
Sbjct:   161 STLIWAIQASYGFGHKKVIFEGDNQTITRMINTKSS 196

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 147 (56.8 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 40/127 (31%), Positives = 63/127 (49%)

Query:     8 NNVQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETV---AAAVSTFKSSGD 64
             N     +W PP   W+K N D   +R N   G+G V++N KGE     A A+   KS  +
Sbjct:   413 NRSSCGRWRPPPHQWVKCNTDATWNRDNERCGIGWVLRNEKGEVKWMGARALPKLKSVLE 472

Query:    65 VELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNK------RSTLTDTFWVIFDI 118
              EL   +A+ W + + ++     VI ESDS+ +IE++NN       + T+ D   ++   
Sbjct:   473 AEL---EAMRWAVLSLSRFQYNYVIFESDSQVLIEILNNDEIWPSLKPTIQDLQRLLSQF 529

Query:   119 IEAKKIF 125
              E K +F
Sbjct:   530 TEVKFVF 536

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=ISM

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

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

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 33/112 (29%), Positives = 59/112 (52%)

Query:    15 WSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVL 74
             W+ P  GW K N D + +R    +  G ++++  G+ V+A  +T   + +   SE +A+L
Sbjct:     3 WTRPPHGWKKCNYDGSYNR-EMPSKAGWIIRDESGQFVSAGQATGNHTSNALESEFQALL 61

Query:    75 WGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQ 126
               MQ+    G   +  E D++ V+E++N ++S   D F  I D+   K+ FQ
Sbjct:    62 ITMQSCWSHGHRKIWFEGDNREVMEILNRRKSRF-DIFNWIRDVQAWKQRFQ 112

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 132 (51.5 bits), Expect = 3.7e-08, P = 3.7e-08
 Identities = 31/109 (28%), Positives = 54/109 (49%)

Query:     6 EQNNVQQSQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDV 65
             +Q  + +++W  P   W+K N D A +     A  G ++++  G  + +  +   ++ D 
Sbjct:   177 QQPTMARTKWQRPPSTWIKYNYDGAFNHQTRNAKAGWLMRDENGVYMGSGQAIGSTTSDS 236

Query:    66 ELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWV 114
               SE +A++  MQ A   G   VI E DSK V EL+NN++       W+
Sbjct:   237 LESEFQALIIAMQHAWSQGYRKVIFEGDSKQVEELMNNEKLNFGRFNWI 285

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 130 (50.8 bits), Expect = 7.0e-08, P = 7.0e-08
 Identities = 36/107 (33%), Positives = 51/107 (47%)

Query:    13 SQWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKA 72
             SQW+PP EGW+K N D    + +     G  ++   G  V    +  +SS     +EA  
Sbjct:   204 SQWNPPPEGWVKCNFDSGYTQGSPYTRSGWTIRECNGHIVLCGNAKLQSSTCSLHAEALG 263

Query:    73 VLWGMQAAAKAGATSVILESDSKGVIELINNKRS-TLTDTFWVIFDI 118
              L  +Q     G   V  ESDSK ++ LINN    +L  T  +I+DI
Sbjct:   264 FLHALQVIWAHGLRYVWFESDSKSLVTLINNGEDHSLLGT--LIYDI 308

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 124 (48.7 bits), Expect = 8.3e-08, P = 8.3e-08
 Identities = 32/109 (29%), Positives = 51/109 (46%)

Query:     8 NNVQQS--QWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDV 65
             NN + +  +W  P  GW+K N D + +        G ++++ KG    AA +   +  + 
Sbjct:    54 NNRESTHQKWEQPPMGWIKCNYDGSFNYRTQQTNSGWLIRDDKGFYKGAAQAVGGTMNNA 113

Query:    66 ELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWV 114
               SE +A++  MQ     G   VI E DSK V EL+N K+       W+
Sbjct:   114 LESELQALVMAMQHTWSQGYRKVIFEGDSKQVEELLNRKQMHFGAFNWI 162

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

TAIR|locus:2011571 AT1G52990 [Arabidopsis thaliana (taxid:3702)]

 Score = 124 (48.7 bits), Expect = 2.3e-07, P = 2.3e-07
 Identities = 26/82 (31%), Positives = 44/82 (53%)

Query:    23 LKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAK 82
             +K N D +    + ++GLG +++N +G  +   +  F+     E +E  A++W +QA + 
Sbjct:    48 VKCNYDASHHEGDVVSGLGWLIRNSQGTVLECGMGKFQGRMTPEEAECSALIWAIQATSA 107

Query:    83 AGATSVILESDSKGVIELINNK 104
              G T VI E D+  V  LIN K
Sbjct:   108 FGYTKVIFEGDNSNVNRLINTK 129

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006662 "glycerol ether metabolic process" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

GO:0015035 "protein disulfide oxidoreductase activity" evidence=IEA

GO:0045454 "cell redox homeostasis" evidence=IEA

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

 Score = 114 (45.2 bits), Expect = 6.6e-07, P = 6.6e-07
 Identities = 30/116 (25%), Positives = 52/116 (44%)

Query:    14 QWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAV 73
             +W  P   W+K N D +       +GL  +++N +G  +      F+    ++ +E  A+
Sbjct:    29 KWQKPGAEWVKCNYDVSNHAGRQDSGLRWIIRNSQGTCLDCGCGKFQGRQTIKEAECTAL 88

Query:    74 LWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFK 129
             +W +Q A   G   V  E D+  V  LI NK +     +++ F I +  K F   K
Sbjct:    89 IWAIQCAWDLGYRRVEFEGDNITVNRLIRNKETNPRLRYYLEF-IQQWSKAFTTVK 143

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 = 117 (46.2 bits), Expect = 1.2e-06, P = 1.2e-06
 Identities = 25/100 (25%), Positives = 46/100 (46%)

Query:    14 QWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAV 73
             QW  P   W+K N D      N   G+G +++N  G  +         + +V  +E +A+
Sbjct:   136 QWKAPPYQWVKCNTDATWQLENPRCGIGWILRNESGGVLWMGARALPRTKNVLEAELEAL 195

Query:    74 LWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFW 113
              W +   ++     +I ESD++ ++ L+N+      D FW
Sbjct:   196 RWAVLTMSRFNYKRIIFESDAQALVNLLNS------DDFW 229

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2163391 AT5G44470 "AT5G44470" [Arabidopsis thaliana (taxid:3702)]

 Score = 111 (44.1 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 21/67 (31%), Positives = 37/67 (55%)

Query:    38 AGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGV 97
             +GLG +++N  G  +   +S F+    VE SE  A++W +Q++   G   +  + D+  +
Sbjct:    32 SGLGWIIRNSHGTFMECGMSKFQGRAPVEESECTALIWALQSSWNLGYIKIEFDGDNLSI 91

Query:    98 IELINNK 104
             I LIN K
Sbjct:    92 IRLINGK 98

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	136
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-11
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	4e-09
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	3e-04
PRK07238	372	PRK07238, PRK07238, bifunctional RNase H/acid phos	0.002

>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 = 57.4 bits (139), Expect = 1e-11
 Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 1/110 (0%)

Query: 26  NVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGA 85
           N D +       AG G V+++H+G  + A  S    +     +E  A+L  ++ A   G 
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAG-SLSIPAATNNEAELLALLEALELALDLGL 59

Query: 86  TSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR 135
             +I+E+DSK V++LIN+          +++DI+     F + + +HV R
Sbjct: 60  KKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR 109

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 21/71 (29%), Positives = 38/71 (53%)

Query: 65  VELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKI 124
              +EA+A+L G+Q A + G   +I+ESDS+ V++ I  +    +    ++ +I +  K 
Sbjct: 2   PLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKK 61

Query: 125 FQNFKAQHVLR 135
           F +    HV R
Sbjct: 62  FDSVSVSHVPR 72

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

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

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 22/114 (19%), Positives = 46/114 (40%), Gaps = 2/114 (1%)

Query: 23  LKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAK 82
             +  D A       AG G V+K+  GE +  ++           +E +A++ G++ A +
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSI-PLGFPATNNEAEYEALIAGLELALE 59

Query: 83  AGATSVILESDSKGVIELINNKRSTLTDTFWVIFD-IIEAKKIFQNFKAQHVLR 135
            G   + +  DS+ V+  I  +     +      +   E  K F+  + + + R
Sbjct: 60  LGIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKWIPR 113

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

>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase; Provisional

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 38 AGLGAVVKNHKGETVAAAVSTF--KSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSK 95
          AG GAVV +     V A  +    +++ +V  +E + ++ G++AAA+ GAT V +  DSK
Sbjct: 18 AGYGAVVWDADRGEVLAERAEAIGRATNNV--AEYRGLIAGLEAAAELGATEVEVRMDSK 75

Query: 96 GVIE 99
           V+E
Sbjct: 76 LVVE 79

Length = 372

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	136
PRK13907	128	rnhA ribonuclease H; Provisional	99.94
PRK07708	219	hypothetical protein; Validated	99.88
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.87
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.84
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.83
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.8
PRK08719	147	ribonuclease H; Reviewed	99.69
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.66
PRK06548	161	ribonuclease H; Provisional	99.65
PRK00203	150	rnhA ribonuclease H; Reviewed	99.65
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	99.13
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	96.88
COG0295	134	Cdd Cytidine deaminase [Nucleotide transport and m	92.54
COG0590	152	CumB Cytosine/adenosine deaminases [Nucleotide tra	88.02
cd01285	109	nucleoside_deaminase Nucleoside deaminases include	87.84
cd01284	115	Riboflavin_deaminase-reductase Riboflavin-specific	87.68
TIGR01354	127	cyt_deam_tetra cytidine deaminase, homotetrameric.	86.67
cd00786	96	cytidine_deaminase-like Cytidine and deoxycytidyla	86.39
COG3981	174	Predicted acetyltransferase [General function pred	83.67
cd01283	112	cytidine_deaminase Cytidine deaminase zinc-binding	81.72
TIGR02571	151	ComEB ComE operon protein 2. This protein is found	81.57

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.94  E-value=1.9e-26  Score=150.37  Aligned_cols=112  Identities=14%  Similarity=0.108  Sum_probs=100.8

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      ++++|||||+..+++.+|+|+|||+..|.+...+  .. ...|+++||++|+++||++|.+.|+++|+|+|||+.|++++
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--PL-GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAV   77 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEe--cc-cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHH
Confidence            4789999999999999999999999988765443  22 34799999999999999999999999999999999999999


Q ss_pred             hcCCCCCCchHHHHHHHHHHhhcCCceEEEEEeCC
Q 046558          102 NNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM  136 (136)
Q Consensus       102 ~~~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~Re  136 (136)
                      ++.+.....+..++++++.++..|..+.+.||||+
T Consensus        78 ~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~  112 (128)
T PRK13907         78 EKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS  112 (128)
T ss_pred             hHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch
Confidence            99776556789999999999999999999999995

>PRK07708 hypothetical protein; Validated

Probab=99.88  E-value=1.6e-21  Score=137.12  Aligned_cols=118  Identities=20%  Similarity=0.206  Sum_probs=100.1

Q ss_pred             CCCcEEEEeceeEecCCCeeeEeEEEecCCCcEE--EeecccccccCCHHHHHHHHHHHHHHHHHHcCCCe--EEEeech
Q 046558           19 EEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETV--AAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATS--VILESDS   94 (136)
Q Consensus        19 ~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~--~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~--v~iesDs   94 (136)
                      .+..+++|||||+..+++.+|+|+||+++.|...  ......+....|+++||+.|++.||+.|.++|+++  |.|++||
T Consensus        70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS  149 (219)
T PRK07708         70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS  149 (219)
T ss_pred             CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence            3457999999999999999999999999887543  23344566668999999999999999999999976  8999999


Q ss_pred             HHHHHHHhcCCCCC-CchHHHHHHHHHHhhcCC-ceEEEEEeCC
Q 046558           95 KGVIELINNKRSTL-TDTFWVIFDIIEAKKIFQ-NFKAQHVLRM  136 (136)
Q Consensus        95 ~~vv~~i~~~~~~~-~~~~~~i~~i~~l~~~~~-~~~~~~v~Re  136 (136)
                      +.|++++++.+... ..+..++++++.+++.|. .+.+.||+|+
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~  193 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK  193 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch
Confidence            99999999987653 356778899999988876 4889999995

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.87  E-value=1.9e-21  Score=146.87  Aligned_cols=114  Identities=24%  Similarity=0.227  Sum_probs=101.4

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCc-EEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGE-TVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIEL  100 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~-~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~  100 (136)
                      .+.+|+|||+.++++.+|+|++|+++.|. ++...+..++ ..|++.||+.|++.||+++.+.|.++|.|++||+.|++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            47899999999999999999999999764 5555555565 468899999999999999999999999999999999999


Q ss_pred             HhcCCCC-CCchHHHHHHHHHHhhcCCceEEEEEeCC
Q 046558          101 INNKRST-LTDTFWVIFDIIEAKKIFQNFKAQHVLRM  136 (136)
Q Consensus       101 i~~~~~~-~~~~~~~i~~i~~l~~~~~~~~~~~v~Re  136 (136)
                      +++.+.. ...+..++.+++.+++.|..+.+.||+|+
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~  117 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRA  117 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCch
Confidence            9998754 45788899999999999999999999995

>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=99.84  E-value=2.1e-19  Score=114.89  Aligned_cols=111  Identities=17%  Similarity=0.143  Sum_probs=99.5

Q ss_pred             EEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHHhc
Q 046558           24 KVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINN  103 (136)
Q Consensus        24 k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i~~  103 (136)
                      +||+|||+..+.+.+|+|+++++..+.......... ...+++++|+.|++.||+.+...+.+++.|++||+.+++.+++
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            589999999888899999999999998877766544 4579999999999999999999999999999999999999998


Q ss_pred             CCC-CCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558          104 KRS-TLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus       104 ~~~-~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      ... .......++.+++.++..+..+.|.||+|
T Consensus        80 ~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~  112 (130)
T cd06222          80 WYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPG  112 (130)
T ss_pred             cccCCChhhHHHHHHHHHHHhCCCeEEEEEcCC
Confidence            765 34578889999999998899999999998

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

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

Probab=99.83  E-value=1.1e-19  Score=120.55  Aligned_cols=110  Identities=22%  Similarity=0.114  Sum_probs=92.8

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      .+.+|+|||+.++++.+|+|+|++...+..-.  +.... ..|++.+|++|+++||+.+.+.+...|.++|||++|++.|
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 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKEL--SGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGI   79 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEE--eeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHH
Confidence            57899999999999999999999977776622  22233 4899999999999999999999999999999999999999


Q ss_pred             hcCC----CC---------CCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558          102 NNKR----ST---------LTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus       102 ~~~~----~~---------~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      + .+    ..         +-+...+++++..+++.|..+.+.||+.
T Consensus        80 ~-~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkg  125 (154)
T COG0328          80 T-RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKG  125 (154)
T ss_pred             H-HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeC
Confidence            8 33    11         2234578999999999999999999983

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

Probab=99.80  E-value=3.3e-19  Score=108.24  Aligned_cols=72  Identities=32%  Similarity=0.312  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHHhcCCCCCCchHHHHHHHHHHhhcCCceEEEEEeCC
Q 046558           65 VELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLRM  136 (136)
Q Consensus        65 ~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i~~~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~Re  136 (136)
                      |++||++|++.||++|.++|+++|++||||+.+++++++....++++..++.+|+.+++.|+++.|.||+||
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~   72 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPRE   72 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GG
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChH
Confidence            579999999999999999999999999999999999999877767999999999999999999999999996

>PRK08719 ribonuclease H; Reviewed

Probab=99.69  E-value=8.4e-16  Score=102.25  Aligned_cols=110  Identities=18%  Similarity=0.130  Sum_probs=86.0

Q ss_pred             CcEEEEeceeEecCCC---eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHH
Q 046558           21 GWLKVNVDDAMDRVNY---LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGV   97 (136)
Q Consensus        21 ~~~k~n~Dgs~~~~~~---~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~v   97 (136)
                      ..+++|+|||+..+++   .+|+|+++.+..|..+...+..+....|++.||++|++.||+.+.+.    ..|.|||+++
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            3578999999987765   68999999998887654444445555799999999999999998764    3799999999


Q ss_pred             HHHHh--------cCCCC----CCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           98 IELIN--------NKRST----LTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        98 v~~i~--------~~~~~----~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      ++.++        +.+..    +-....+++.|..+.+ ..+++|.||++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~Vkg  127 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTA  127 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecC
Confidence            99994        33321    2235678888877776 57899999986

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

Probab=99.66  E-value=1.9e-15  Score=98.38  Aligned_cols=105  Identities=15%  Similarity=0.067  Sum_probs=80.6

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      -+.+|+|||+..+++.+|+|+++.+.  .   .....++ ..|++.+|++|+.+||+ +.. . ++|.|+|||+.+++.+
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-H-RKVTIYTDSQYVLNAL   73 (132)
T ss_dssp             SEEEEEEEEECTTTTEEEEEEEEETT--E---EEEEEEE-SECHHHHHHHHHHHHHH-THS-T-SEEEEEES-HHHHHHH
T ss_pred             cEEEEEeCCccCCCCceEEEEEEECC--e---EEEeccc-ccchhhhheehHHHHHH-Hhh-c-ccccccccHHHHHHHH
Confidence            47899999999999999999977433  2   2233344 57999999999999999 552 2 9999999999999988


Q ss_pred             hc-----CCCCCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558          102 NN-----KRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus       102 ~~-----~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      +.     ..........++.++..++.....+.|.|||.
T Consensus        74 ~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~  112 (132)
T PF00075_consen   74 NKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPG  112 (132)
T ss_dssp             HTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSS
T ss_pred             HHhccccccccccccccchhheeeccccceEEeeeeccC
Confidence            87     44332222246678888888888999999986

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

>PRK06548 ribonuclease H; Provisional

Probab=99.65  E-value=9.1e-15  Score=98.34  Aligned_cols=105  Identities=17%  Similarity=0.051  Sum_probs=81.8

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      .+.+||||++.++++.+|+|+++.+. + ..   .... ...|++.||++|+++||+.+. .+..+|.|.|||+++++.+
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~~-~-~~---~g~~-~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i   77 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDEN-T-WD---SGGW-DIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSL   77 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeCC-c-EE---ccCC-CCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHH
Confidence            48999999999999999999998752 2 22   1222 347999999999999998554 4556899999999999999


Q ss_pred             hc--------CCC----CCCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          102 NN--------KRS----TLTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       102 ~~--------~~~----~~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      +.        .+.    .+-....++++|..++.. ..++|.||+
T Consensus        78 ~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVk  121 (161)
T PRK06548         78 TKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVN  121 (161)
T ss_pred             HHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEe
Confidence            94        222    122467899999998876 479999996

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.65  E-value=5.4e-15  Score=98.78  Aligned_cols=107  Identities=19%  Similarity=0.058  Sum_probs=82.4

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      .+.+|||||+..+++.+|+|+++....+....  ..... ..|++.||++|++.||+.+.+  ...|.|.|||+.+++.|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~--~~~~~-~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKEL--SGGEA-LTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEE--ecCCC-CCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHH
Confidence            48899999999999999999999865543322  22233 478999999999999998865  35899999999999988


Q ss_pred             hc--------CCCC----CCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          102 NN--------KRST----LTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       102 ~~--------~~~~----~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      +.        .+..    +-....++++|..++.. ..+.|.|||
T Consensus        78 ~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~  121 (150)
T PRK00203         78 TEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVK  121 (150)
T ss_pred             HHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEec
Confidence            85        1211    22346788888888765 689999997

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

Probab=99.13  E-value=1.2e-09  Score=81.21  Aligned_cols=118  Identities=14%  Similarity=0.062  Sum_probs=84.2

Q ss_pred             CCcCC-CCCcEEEEeceeEecCC---CeeeEeEEEecCCCcEEEeeccccc-ccCCHHHHHHHHHHHHHHHHHHcCCCeE
Q 046558           14 QWSPP-EEGWLKVNVDDAMDRVN---YLAGLGAVVKNHKGETVAAAVSTFK-SSGDVELSEAKAVLWGMQAAAKAGATSV   88 (136)
Q Consensus        14 ~W~~P-~~~~~k~n~Dgs~~~~~---~~~g~G~vird~~G~~~~~~~~~~~-~~~s~~~aE~~Al~~aL~~a~~~g~~~v   88 (136)
                      .|..+ +.+...+++|||+..+.   ..+|+|+.+=  .|.-.-.+ .++. +..|++.||+.|+.+||+.|++.+..+|
T Consensus       203 ~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg--~~~e~N~s-~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv  279 (371)
T KOG3752|consen  203 LENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWG--PGHELNVS-GPLAGGRQTNNRAELIAAIEALKKARSKNINKV  279 (371)
T ss_pred             cccccccccceEEEecCccccCCCCCCcceeEEeeC--CCCccccc-ccCCCCcccccHHHHHHHHHHHHHHHhcCCCcE
Confidence            34443 35568899999999854   3467777663  34333333 3444 7789999999999999999999999999


Q ss_pred             EEeechHHHHHHHhc--------CCC--CC-------CchHHHHHHHHHHhhc--CCceEEEEEe
Q 046558           89 ILESDSKGVIELINN--------KRS--TL-------TDTFWVIFDIIEAKKI--FQNFKAQHVL  134 (136)
Q Consensus        89 ~iesDs~~vv~~i~~--------~~~--~~-------~~~~~~i~~i~~l~~~--~~~~~~~~v~  134 (136)
                      .|.|||..++++|+.        .+.  ..       -.....+.++-.|.+.  -.++++.||+
T Consensus       280 ~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~  344 (371)
T KOG3752|consen  280 VIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVG  344 (371)
T ss_pred             EEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEec
Confidence            999999999999874        110  01       1234566667777665  3778888875

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

Probab=96.88  E-value=0.0014  Score=50.28  Aligned_cols=94  Identities=13%  Similarity=0.159  Sum_probs=66.8

Q ss_pred             CCeeeEeEEEecC-CCcEEEeecccccc--cCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHHhcCCCCCC--
Q 046558           35 NYLAGLGAVVKNH-KGETVAAAVSTFKS--SGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELINNKRSTLT--  109 (136)
Q Consensus        35 ~~~~g~G~vird~-~G~~~~~~~~~~~~--~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i~~~~~~~~--  109 (136)
                      ...+|.|+.+.|. +.............  ..++..||++|+..+|..+..+|+.++.+.+|...+...+.++.....  
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            3568899999886 44433333333321  267999999999999999999999999999998888887777655422  


Q ss_pred             chHHHHHHHHHHhhcCCce
Q 046558          110 DTFWVIFDIIEAKKIFQNF  128 (136)
Q Consensus       110 ~~~~~i~~i~~l~~~~~~~  128 (136)
                      ....++.+.+.+...+...
T Consensus        96 ~~~~l~~~v~~~r~~l~~~  114 (384)
T KOG1812|consen   96 KIVLLVELVQRIREQLTSS  114 (384)
T ss_pred             HHHHHHHHHHHHHHHhhcc
Confidence            4556666665555544433

>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]

Probab=92.54  E-value=0.94  Score=29.70  Aligned_cols=57  Identities=19%  Similarity=0.229  Sum_probs=44.8

Q ss_pred             eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeech
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDS   94 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs   94 (136)
                      +--+|.+++..+|++..+..-.........-||-.|+..++.. -...+..|.+.+|.
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            3457889999999888877655556677889999999988876 55567888898885

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

Probab=88.02  E-value=1.9  Score=28.83  Aligned_cols=57  Identities=16%  Similarity=0.112  Sum_probs=38.8

Q ss_pred             CeeeEeEEEecCCCcEEEeeccccccc-CCHHHHHHHHHHHHHHHHHHcCCCeEEEee
Q 046558           36 YLAGLGAVVKNHKGETVAAAVSTFKSS-GDVELSEAKAVLWGMQAAAKAGATSVILES   92 (136)
Q Consensus        36 ~~~g~G~vird~~G~~~~~~~~~~~~~-~s~~~aE~~Al~~aL~~a~~~g~~~v~ies   92 (136)
                      +...+|.||-+.+|.++..+....... .-..+||..|+..|-+......+....+++
T Consensus        26 ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyv   83 (152)
T COG0590          26 GEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYV   83 (152)
T ss_pred             CCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEE
Confidence            456789999888898888665544332 234599999999999888654444444433

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

Probab=87.84  E-value=2.6  Score=26.27  Aligned_cols=58  Identities=14%  Similarity=0.120  Sum_probs=37.3

Q ss_pred             CeeeEeEEEecCCCcEEEeeccccc-ccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           36 YLAGLGAVVKNHKGETVAAAVSTFK-SSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        36 ~~~g~G~vird~~G~~~~~~~~~~~-~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      +...+|.+|.+.+|+++..+..... ......+||..|+..+.+.-....+....+++.
T Consensus        15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t   73 (109)
T cd01285          15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTT   73 (109)
T ss_pred             CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEe
Confidence            4556788888888988776554432 234678999999988776533222444445443

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

>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase

Probab=87.68  E-value=2.5  Score=26.84  Aligned_cols=41  Identities=17%  Similarity=0.134  Sum_probs=30.8

Q ss_pred             CeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHH
Q 046558           36 YLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQA   79 (136)
Q Consensus        36 ~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~   79 (136)
                      +...+|.||-+.+|+++..+.....   ...+||..|+..+.+.
T Consensus        17 ~~~pvGaviv~~~g~iv~~g~n~~~---~~~HAE~~ai~~a~~~   57 (115)
T cd01284          17 PNPPVGCVIVDDDGEIVGEGYHRKA---GGPHAEVNALASAGEK   57 (115)
T ss_pred             CCCCEEEEEEeCCCeEEEEecCCCC---CcccHHHHHHHHHhhc
Confidence            3456888888877998886655443   5689999999988764

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

>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric

Probab=86.67  E-value=1.7  Score=28.05  Aligned_cols=57  Identities=12%  Similarity=0.039  Sum_probs=39.3

Q ss_pred             eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeech
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDS   94 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs   94 (136)
                      ...+|.++++.+|++..+.........-...||..|+..+...- +..+..|.+..+.
T Consensus        20 ~~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g-~~~i~~i~vv~~~   76 (127)
T TIGR01354        20 NFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAG-YRKFVAIAVADSA   76 (127)
T ss_pred             CCeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcC-CCCeEEEEEEeCC
Confidence            34578888888999888655444344556789999988877542 2356777776654

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

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

Probab=86.39  E-value=5  Score=24.39  Aligned_cols=43  Identities=16%  Similarity=0.108  Sum_probs=27.6

Q ss_pred             CeeeEeEEEecC-CCcEEEeeccc-ccccCCHHHHHHHHHHHHHH
Q 046558           36 YLAGLGAVVKNH-KGETVAAAVST-FKSSGDVELSEAKAVLWGMQ   78 (136)
Q Consensus        36 ~~~g~G~vird~-~G~~~~~~~~~-~~~~~s~~~aE~~Al~~aL~   78 (136)
                      +...+|.++.+. +|.++..+... ........+||..|+..+.+
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 56666654332 22234678999999987654

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.

>COG3981 Predicted acetyltransferase [General function prediction only]

Probab=83.67  E-value=6  Score=27.08  Aligned_cols=27  Identities=15%  Similarity=0.313  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHcCCCeEEEeechHH
Q 046558           70 AKAVLWGMQAAAKAGATSVILESDSKG   96 (136)
Q Consensus        70 ~~Al~~aL~~a~~~g~~~v~iesDs~~   96 (136)
                      -..|..||+.|.++|+++|.+-.|...
T Consensus       116 ~emLkl~L~~ar~lgi~~Vlvtcd~dN  142 (174)
T COG3981         116 KEMLKLALEKARELGIKKVLVTCDKDN  142 (174)
T ss_pred             HHHHHHHHHHHHHcCCCeEEEEeCCCC
Confidence            356889999999999999999888543

>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain

Probab=81.72  E-value=4.7  Score=25.16  Aligned_cols=43  Identities=16%  Similarity=0.061  Sum_probs=31.6

Q ss_pred             CeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHH
Q 046558           36 YLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQ   78 (136)
Q Consensus        36 ~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~   78 (136)
                      +...+|.++...+|+++.+.............||..|+..+..
T Consensus        16 ~~~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~   58 (112)
T cd01283          16 SNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVS   58 (112)
T ss_pred             CCCeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHH
Confidence            4566788888888988866655444455678999999877764

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.

>TIGR02571 ComEB ComE operon protein 2

Probab=81.57  E-value=8.9  Score=25.60  Aligned_cols=39  Identities=15%  Similarity=0.096  Sum_probs=25.0

Q ss_pred             eeeEeEEEecCCCcEEEeeccccccc----------------CCHHHHHHHHHHHH
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTFKSS----------------GDVELSEAKAVLWG   76 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~~~~----------------~s~~~aE~~Al~~a   76 (136)
                      ...+|.||.. +|+++..+....+..                .-..+||..||+.+
T Consensus        24 ~~~VGAVIV~-d~~IIs~GyN~~~~g~~~~~~~~~~~~~~~~~~~~HAE~nAI~~a   78 (151)
T TIGR02571        24 RLSVGATIVR-DKRIIAGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQC   78 (151)
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCccccccccccccccCCccCHHHHHHHHH
Confidence            3456666664 577877665544321                12469999999876

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	136
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	9e-07
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	9e-06

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

 Score = 44.2 bits (105), Expect = 9e-07
 Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 1/99 (1%)

Query: 38  AGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGV 97
           AG GAVV      TV A            ++E + ++ G+  A K GAT   +  DSK V
Sbjct: 19  AGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLV 78

Query: 98  IELINNKRSTLTDTFWVIFD-IIEAKKIFQNFKAQHVLR 135
           +E ++ +          ++         F+    + V R
Sbjct: 79  VEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR 117

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

 Score = 41.6 bits (98), Expect = 9e-06
 Identities = 18/103 (17%), Positives = 43/103 (41%), Gaps = 6/103 (5%)

Query: 37  LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEA--KAVLWGMQAAAKAGATSVILESDS 94
           +A  G V+     +     ++    S +   + A    ++  M+   + G +S I++ DS
Sbjct: 18  IATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDS 77

Query: 95  KGVIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKA--QHVLR 135
           + VI+ +N +          +++  +A ++ +   A    V R
Sbjct: 78  QLVIKQMNGEYKVKAKRIIPLYE--KAIELKKKLNATLIWVPR 118

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	136
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.93
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.93
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.92
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.88
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.84
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.83
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.82
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.79
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.79
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.78
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.77
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.73
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.73
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.72
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.6
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.58
1uwz_A	136	Cytidine deaminase; CDD, tetramer, zinc binding, p	91.94
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	91.18
2fr5_A	146	Cytidine deaminase; tetrahydrouridine, protein-inh	91.08
2z3g_A	130	Blasticidin-S deaminase; hydrolase, cytidine deami	86.51
2d30_A	141	Cytidine deaminase; purines, pyrimidines, nucleosi	83.65
1r5t_A	142	Cytidine deaminase; zinc dependent deaminase, RNA	82.81
2b3j_A	159	TRNA adenosine deaminase; mixed alpha-beta, protei	81.47
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	81.25
2a8n_A	144	Cytidine and deoxycytidylate deaminase; RNA editin	80.23

>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=99.93  E-value=3.2e-25  Score=145.39  Aligned_cols=114  Identities=21%  Similarity=0.237  Sum_probs=101.0

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCC-CcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHK-GETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIEL  100 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~-G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~  100 (136)
                      .+++|+|||+..+++.+|+|+++++.. |..+...+..++ ..|++.||++|++.||+++.++|.++|.|+|||+.+++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            489999999999999999999999987 666666665554 479999999999999999999999999999999999999


Q ss_pred             HhcCCCC-CCchHHHHHHHHHHhhcCCceEEEEEeCC
Q 046558          101 INNKRST-LTDTFWVIFDIIEAKKIFQNFKAQHVLRM  136 (136)
Q Consensus       101 i~~~~~~-~~~~~~~i~~i~~l~~~~~~~~~~~v~Re  136 (136)
                      +++.+.. ...+..++.+|+.++..|..+.|.||||+
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~  118 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRA  118 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGG
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCc
Confidence            9997644 34577889999999999999999999985

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

Probab=99.93  E-value=3.7e-25  Score=144.67  Aligned_cols=115  Identities=16%  Similarity=0.163  Sum_probs=103.5

Q ss_pred             CcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCC----eEEEeechHH
Q 046558           21 GWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGAT----SVILESDSKG   96 (136)
Q Consensus        21 ~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~----~v~iesDs~~   96 (136)
                      ..+++|+|||+..+++.+|+|+++++..|..+...+..++. .|++.||++|+++||+.|.+.+++    +|.|+|||+.
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~-~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGE-TTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEE-ECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCC-CchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            35899999999999999999999999999887766666655 699999999999999999999999    9999999999


Q ss_pred             HHHHHhcCCCC-CCchHHHHHHHHHH-hhcCCceEEEEEeCC
Q 046558           97 VIELINNKRST-LTDTFWVIFDIIEA-KKIFQNFKAQHVLRM  136 (136)
Q Consensus        97 vv~~i~~~~~~-~~~~~~~i~~i~~l-~~~~~~~~~~~v~Re  136 (136)
                      +++.+++.+.. ...+..++.+|+.+ ++.|..++|.||||+
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~  122 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPRE  122 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGG
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCch
Confidence            99999997654 45678899999999 999999999999985

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

Probab=99.92  E-value=4.4e-24  Score=141.43  Aligned_cols=113  Identities=19%  Similarity=0.120  Sum_probs=97.8

Q ss_pred             cEEEEeceeEe-cCCCeeeE-eEEEecCCCcEEEeeccccc---ccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHH
Q 046558           22 WLKVNVDDAMD-RVNYLAGL-GAVVKNHKGETVAAAVSTFK---SSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKG   96 (136)
Q Consensus        22 ~~k~n~Dgs~~-~~~~~~g~-G~vird~~G~~~~~~~~~~~---~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~   96 (136)
                      ++++|+|||+. .+++.+|+ |+++++ .|..+.......+   ...|++.||++|++.||+.|.+.|+++|.|+|||+.
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            47999999999 78899996 999999 8887755443333   358999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCC-CCchHHHHHHHHHHhhcCCceEEEEEeCC
Q 046558           97 VIELINNKRST-LTDTFWVIFDIIEAKKIFQNFKAQHVLRM  136 (136)
Q Consensus        97 vv~~i~~~~~~-~~~~~~~i~~i~~l~~~~~~~~~~~v~Re  136 (136)
                      +++.+++.+.. ...+..++++++.+++.| ++.|.||||+
T Consensus        80 vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~~  119 (149)
T 2ehg_A           80 VIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPRE  119 (149)
T ss_dssp             HHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCGG
T ss_pred             HHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCCc
Confidence            99999987543 346889999999999988 6999999984

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

Probab=99.88  E-value=8.9e-22  Score=131.07  Aligned_cols=115  Identities=14%  Similarity=0.054  Sum_probs=94.1

Q ss_pred             CCCCCcEEEEeceeEecCCC---eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           17 PPEEGWLKVNVDDAMDRVNY---LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        17 ~P~~~~~k~n~Dgs~~~~~~---~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      +|+.+.+++|+|||+..+++   .+|+|+++++..+..+.   ..+....|++.||++|++.||+.+.+.+.++|.|+||
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            57889999999999998765   48999999986554332   2344457999999999999999999999999999999


Q ss_pred             hHHHHHHHhc--------CCC----CCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           94 SKGVIELINN--------KRS----TLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        94 s~~vv~~i~~--------~~~----~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      |+.+++.|++        .+.    .+.....++++|..++..+ .+.|.||||
T Consensus        79 S~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~-~v~~~~V~~  131 (154)
T 2qkb_A           79 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGM-DIQWMHVPG  131 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTC-EEEEEECCT
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCC-ceEEEEccC
Confidence            9999999987        111    1235678999999998876 499999996

>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=99.84  E-value=1.5e-20  Score=123.33  Aligned_cols=102  Identities=18%  Similarity=0.199  Sum_probs=81.6

Q ss_pred             cCCCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechH
Q 046558           16 SPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSK   95 (136)
Q Consensus        16 ~~P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~   95 (136)
                      .||+.+++++|+|||+..+++.+|+|+|++ ..|..+... ..++ ..|++.||++|++.||+.+.+.++ +|.|+|||+
T Consensus         5 ~~~~~~~~~iy~DGa~~gNpG~~G~G~vl~-~~g~~~~~~-~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~   80 (142)
T 1zbf_A            5 AKEEIIWESLSVDVGSQGNPGIVEYKGVDT-KTGEVLFER-EPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQ   80 (142)
T ss_dssp             ---CCCSSSEEEEEEECSSSEEEEEEEEET-TTCCEEEEC-CCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCH
T ss_pred             CCCCCCeEEEEEeeccCCCCCCeEEEEEEE-eCCEEEEEe-cccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehH
Confidence            578889999999999999999999999999 678776543 3344 379999999999999999999999 999999999


Q ss_pred             HHHHHHhcCCC-----CCCchHHHHHHHHHH
Q 046558           96 GVIELINNKRS-----TLTDTFWVIFDIIEA  121 (136)
Q Consensus        96 ~vv~~i~~~~~-----~~~~~~~~i~~i~~l  121 (136)
                      +|++++++...     .+.....+++.+..+
T Consensus        81 ~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~  111 (142)
T 1zbf_A           81 TAIKWVKDKKAKSTLVRNEETALIWKLVDEA  111 (142)
T ss_dssp             HHHHHHHHTCCCCCCCCSTTTHHHHHHHHHH
T ss_pred             HHHHHHHcCCccCCCCCCcccHHHHHHHHHH
Confidence            99999998752     123455566555544

>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=99.83  E-value=8.4e-20  Score=121.06  Aligned_cols=110  Identities=21%  Similarity=0.205  Sum_probs=88.7

Q ss_pred             cCCCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechH
Q 046558           16 SPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSK   95 (136)
Q Consensus        16 ~~P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~   95 (136)
                      ..|+.+.+++|+|||+.++++.+|+|+++++..+..+     .. ...|++.||++|++.||+.+   + .+|.|+|||+
T Consensus         6 ~~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~-----~~-~~~Tnn~aEl~A~i~AL~~~---~-~~v~i~tDS~   75 (150)
T 3qio_A            6 KEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVV-----TL-TDTTNQKTELQAIYLALQDS---G-LEVNIVTDSQ   75 (150)
T ss_dssp             SSCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EE-SSCCHHHHHHHHHHHHHHHS---C-SEEEEEESCH
T ss_pred             cCCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEE-----eC-CCCCHHHHHHHHHHHHHHhC---C-CcEEEEeCcH
Confidence            4688999999999999999999999999987554332     12 34799999999999999984   3 8999999999


Q ss_pred             HHHHHHhcC------------CCCCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           96 GVIELINNK------------RSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        96 ~vv~~i~~~------------~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      ++++.+++-            ...+-....+++++..++..+..+.|.||++
T Consensus        76 ~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~g  127 (150)
T 3qio_A           76 YALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPA  127 (150)
T ss_dssp             HHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCT
T ss_pred             HHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccC
Confidence            999999862            1112345678888888777899999999987

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

Probab=99.82  E-value=2e-20  Score=125.98  Aligned_cols=113  Identities=17%  Similarity=0.080  Sum_probs=87.7

Q ss_pred             cCCCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechH
Q 046558           16 SPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSK   95 (136)
Q Consensus        16 ~~P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~   95 (136)
                      +|||.+.+++|+|||+..+++.+|+|+++++..+.....  .... ..|++.||++|++.||+.+.+.  .+|.|+|||+
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 NPSPRKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLS--GGEA-CTTNNRMELKAAIEGLKALKEP--CEVDLYTDSH   76 (166)
T ss_dssp             ----CCCCCEEEEEEESSTTEEEEEEEEECBTTBCCEEC--CEEE-EECHHHHHHHHHHHHHHSCCSC--CEEEEECCCH
T ss_pred             CCCCCccEEEEECccccCCCCCEEEEEEEEECCEEEEEe--cCCC-CCcHHHHHHHHHHHHHHHhccC--CeEEEEeChH
Confidence            578889999999999999899999999999865543322  2233 4789999999999999988765  4999999999


Q ss_pred             HHHHHHhcC---------CCC----CCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558           96 GVIELINNK---------RST----LTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus        96 ~vv~~i~~~---------~~~----~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      ++++.|++.         +..    +.....+++++..++..+ .+.|.||+
T Consensus        77 ~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~  127 (166)
T 1ril_A           77 YLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPH-RVRFHFVK  127 (166)
T ss_dssp             HHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTS-EEECCCCC
T ss_pred             HHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcC-eEEEEEee
Confidence            999999882         221    223467899999888764 89999998

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

Probab=99.79  E-value=8.8e-19  Score=115.52  Aligned_cols=108  Identities=16%  Similarity=0.126  Sum_probs=87.0

Q ss_pred             CcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHH
Q 046558           21 GWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIEL  100 (136)
Q Consensus        21 ~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~  100 (136)
                      ..+++|+|||+..+++.+|+|+++++....  ...+...+ ..|++.||++|++.||+.+.+  ..+|.|+|||+++++.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~--~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~   77 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSR--KEISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNA   77 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEE--EEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCee--EEeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHH
Confidence            358999999999999999999999985432  23333343 479999999999999999976  5899999999999999


Q ss_pred             HhcCC-------------CCCCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          101 INNKR-------------STLTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       101 i~~~~-------------~~~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      +++.+             ..+.....+++++..++..+ .+.|.||+
T Consensus        78 i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~-~v~~~~V~  123 (146)
T 3h08_A           78 MNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLH-RVTFHKVK  123 (146)
T ss_dssp             HHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHS-EEEEEECC
T ss_pred             HHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhC-ceEEEEcC
Confidence            98721             12335678999999998876 59999998

>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=99.79  E-value=1.1e-17  Score=112.33  Aligned_cols=116  Identities=13%  Similarity=0.048  Sum_probs=90.7

Q ss_pred             CCcCCCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           14 QWSPPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        14 ~W~~P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      ...|.+...+++|+|||+.++++.+|+|+++.+ .|+.+...  ......|++.||++|++.||+.+   ...+|.|+||
T Consensus        15 ~~~P~~~~~i~iytDGs~~~npG~~g~G~vi~~-~~~~~~~~--~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tD   88 (165)
T 3p1g_A           15 TDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTT-ETEVIWAR--ALPAGTSAQRAELIALTQALKMA---EGKKLNVYTD   88 (165)
T ss_dssp             BSSCCTTCSEEEEEEEEEEEETTEEEEEEEEEC-SSCEEEEE--EECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEEC
T ss_pred             CCCCCCCCCEEEEEEcccCCCCCceEEEEEEEE-CCEEEEEe--cCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEc
Confidence            455555667999999999999999999999987 45554322  34445799999999999999998   3689999999


Q ss_pred             hHHHHHHHhcCCC-CCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           94 SKGVIELINNKRS-TLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        94 s~~vv~~i~~~~~-~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      |+++++.+-.... .+-....+++++...+..+..+.|.||++
T Consensus        89 S~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkg  131 (165)
T 3p1g_A           89 SRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPG  131 (165)
T ss_dssp             CHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCS
T ss_pred             hHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecC
Confidence            9999998843222 23345677888877666788999999986

>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=99.78  E-value=1.5e-18  Score=115.57  Aligned_cols=107  Identities=16%  Similarity=0.094  Sum_probs=85.7

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      .+++|+|||+.++++.+|+|+++++..+.....  ...+ ..|++.||++|++.||+.+.+.  .+|.|+|||+.+++.+
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~--~~~~-~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i   78 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFS--AGYT-RTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGI   78 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEE--EEEE-EECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEe--cCCC-CCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHH
Confidence            589999999999999999999999865443322  2233 3689999999999999998764  8999999999999999


Q ss_pred             hc--------CCC----CCCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          102 NN--------KRS----TLTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       102 ~~--------~~~----~~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      ++        .+.    .+.....+++++..+++. ..+.|.|||
T Consensus        79 ~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~  122 (155)
T 1jl1_A           79 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVK  122 (155)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECC
T ss_pred             HHHHHHHhhcccccccCCccCCHHHHHHHHHHHcc-CceEEEEcC
Confidence            97        221    123346788999888875 489999998

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

Probab=99.77  E-value=4.7e-18  Score=113.52  Aligned_cols=108  Identities=17%  Similarity=0.093  Sum_probs=85.8

Q ss_pred             CcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHH
Q 046558           21 GWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIEL  100 (136)
Q Consensus        21 ~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~  100 (136)
                      ..+++|+|||+.++++.+|+|+++++.. .. ...+...+ ..|++.||+.|++.||+.+.+.  .+|.|+|||+.+++.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~-~~-~~~~~~~~-~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKG-HT-KEMSDGFS-LTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQG   79 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETT-EE-EEEEEEEE-EECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECC-EE-EEEecCcC-CCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHH
Confidence            4689999999999999999999999843 22 22233333 3689999999999999998653  899999999999999


Q ss_pred             Hhc--------CCCC----CCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          101 INN--------KRST----LTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       101 i~~--------~~~~----~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      +++        .+..    +.....+++++..+++. ..+.|.|||
T Consensus        80 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~  124 (158)
T 2e4l_A           80 IMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL-HQIDWRWVK  124 (158)
T ss_dssp             HHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT-SEEEEEECC
T ss_pred             HHHHHHHHHHccccccCCCcccCHHHHHHHHHHHcc-CcEEEEEcc
Confidence            988        3321    23456788899888876 489999998

>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=99.73  E-value=3.3e-17  Score=105.95  Aligned_cols=80  Identities=18%  Similarity=0.242  Sum_probs=68.0

Q ss_pred             CcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHH
Q 046558           21 GWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIEL  100 (136)
Q Consensus        21 ~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~  100 (136)
                      ....+|+|||+.++++.+|+|+|+++ .|..+... ..++ ..|++.||++|+++||+.+.+.+.+ |.|+|||++|+++
T Consensus         4 ~~~~iytDGac~GNPGp~G~ggV~~~-~g~~~~~~-g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~w   79 (134)
T 4htu_A            4 IWESLSVDVGSQGNPGIVEYKGVDTK-TGEVLFER-EPIP-IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKW   79 (134)
T ss_dssp             CSSSEEEEEEEETTTEEEEEEEEETT-TCCEEEEE-EEEE-EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHH
T ss_pred             cceEEEEeeccCCCCCCeEEEEEEEE-CCEEEEEe-cCCC-CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHH
Confidence            45679999999999999999888887 67655444 3344 4799999999999999999998876 8999999999999


Q ss_pred             HhcC
Q 046558          101 INNK  104 (136)
Q Consensus       101 i~~~  104 (136)
                      +++.
T Consensus        80 i~~~   83 (134)
T 4htu_A           80 VKDK   83 (134)
T ss_dssp             HHHT
T ss_pred             HHcC
Confidence            9864

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

Probab=99.73  E-value=2.2e-16  Score=105.97  Aligned_cols=112  Identities=19%  Similarity=0.081  Sum_probs=86.9

Q ss_pred             CcEEEEeceeEecCCCe-----eeEeEEEecCCC--cEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           21 GWLKVNVDDAMDRVNYL-----AGLGAVVKNHKG--ETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        21 ~~~k~n~Dgs~~~~~~~-----~g~G~vird~~G--~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      .-+.+|||||+..+++.     +|+|++++....  +......... ...+.+.||+.||..+|+.+.+.+. +|.|.||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~t-nn~te~~Aei~Al~~al~~al~~~~-~v~I~TD   83 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPL-GNHTAQMAEIAAVEFACKKALKIPG-PVLVITD   83 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEE-SSCCHHHHHHHHHHHHHHHHHHSSS-CEEEEES
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCc-hHHHHHHHHHHHHHHHHHHHhcCCC-eEEEEeC
Confidence            35789999999998775     999999985433  3444333333 3468899999999999999988774 7999999


Q ss_pred             hHHHHHHHhc--------CC----CCCCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558           94 SKGVIELINN--------KR----STLTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus        94 s~~vv~~i~~--------~~----~~~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      |+++++.++.        .+    ..+-....+++++..++..+.++.|.||+
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~Vk  136 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEK  136 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECC
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEe
Confidence            9999999974        11    11234578999999998888999999997

>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=99.72  E-value=2.7e-18  Score=113.46  Aligned_cols=111  Identities=12%  Similarity=0.079  Sum_probs=80.3

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEE-ee-cccccc--cCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           18 PEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVA-AA-VSTFKS--SGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        18 P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~-~~-~~~~~~--~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      .|.+.+++|+|||+.+  +.+|+|+++++ .|.... .. ....+.  ..|++.||++|++.||++|.+.+. +|.|+||
T Consensus         2 ~~~~~i~iytDGs~~~--g~~G~G~vi~~-~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tD   77 (147)
T 2kq2_A            2 DDRTEYDVYTDGSYVN--GQYAWAYAFVK-DGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHD   77 (147)
T ss_dssp             CTTSCCEEECCCCCBT--TBCEEEEEEEE-TTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSC
T ss_pred             CCCCeEEEEECCCCCC--CCcEEEEEEEE-CCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEEC
Confidence            3567899999999987  89999999998 565322 22 111122  368999999999999999999999 9999999


Q ss_pred             hHHHHHHHhcCCCCCCchHHHHHHHHHHhhcC-CceEEEEEeC
Q 046558           94 SKGVIELINNKRSTLTDTFWVIFDIIEAKKIF-QNFKAQHVLR  135 (136)
Q Consensus        94 s~~vv~~i~~~~~~~~~~~~~i~~i~~l~~~~-~~~~~~~v~R  135 (136)
                      |+.+++++++.+......   ....+.+.+.+ ..+.|.|||+
T Consensus        78 S~~i~~w~~~~w~~~~~~---~~~~~~l~~~l~~~v~~~wV~g  117 (147)
T 2kq2_A           78 YAGIAFWATGEWKAKNEF---TQAYAKLMNQYRGIYSFEKVKA  117 (147)
T ss_dssp             CSTHHHHTTSSSSCCHHH---HHHHHCGGGGGSTTCCBCCCCC
T ss_pred             cHHHHHHHhCCCccCCcc---hHHHHHHHHHhcCCeeEEEecC
Confidence            999999988865543321   12222233222 2788999874

>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=99.60  E-value=7.4e-15  Score=115.00  Aligned_cols=107  Identities=20%  Similarity=0.198  Sum_probs=85.8

Q ss_pred             CCCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHH
Q 046558           17 PPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKG   96 (136)
Q Consensus        17 ~P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~   96 (136)
                      .|..+.+++|+|||+..+++.+|+|+++.+.....+     .. ...|++.||+.|++.||+.+    ..+|.|.|||++
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            366788999999999999999999999974332222     12 24799999999999999998    689999999999


Q ss_pred             HHHHHhcCCCCCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           97 VIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        97 vv~~i~~~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      +++.+++....  ....+++++...+..+..+.+.||+|
T Consensus       504 vi~~i~~~~~~--~~~~l~~~~~~~l~~~~~v~~~wV~~  540 (557)
T 2zd1_A          504 ALGIIQAQPDK--SESELVNQIIEQLIKKEKVYLAWVPA  540 (557)
T ss_dssp             HHHHHTTCCSE--ESSHHHHHHHHHHHHCSEEEEEECCS
T ss_pred             HHHHHhcCCcc--CCHHHHHHHHHHHhcCCCEEEEEcCC
Confidence            99999984332  23456777776666778999999997

>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=99.58  E-value=1.6e-14  Score=113.02  Aligned_cols=107  Identities=18%  Similarity=0.166  Sum_probs=86.5

Q ss_pred             CCCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHH
Q 046558           17 PPEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKG   96 (136)
Q Consensus        17 ~P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~   96 (136)
                      .|..+.+++|+|||+..+++.+|+|+++++..+.     ..... ..|++.||++|++.||+.    +..+|.|+|||++
T Consensus       431 ~p~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-----~~~~~-~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~  500 (555)
T 1mu2_A          431 DPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-----VKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQY  500 (555)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEE-----EEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHH
T ss_pred             CCCCCceEEEEcccccCCCCCceEEEEEEeCCEe-----eccCC-CCCHHHHHHHHHHHHHHc----CCCeEEEEEehHH
Confidence            4567889999999999999999999999874432     11222 479999999999999998    7799999999999


Q ss_pred             HHHHHhcCCCCCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           97 VIELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        97 vv~~i~~~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      +++.+++- .. .....+++++..++..+..+.+.||++
T Consensus       501 v~~~i~~~-~~-~~~~~l~~~~~~~~~~~~~v~~~wV~~  537 (555)
T 1mu2_A          501 VMGIVASQ-PT-ESESKIVNQIIEEMIKKEAIYVAWVPA  537 (555)
T ss_dssp             HHHHHHTC-CS-EESCHHHHHHHHHHHHCSEEEEEECCS
T ss_pred             HHHHHhcc-cc-cccHHHHHHHHHHhccCCcEEEEEEEC
Confidence            99999972 21 233457777777777789999999986

>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=91.94  E-value=0.29  Score=31.14  Aligned_cols=57  Identities=12%  Similarity=0.109  Sum_probs=41.3

Q ss_pred             CeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           36 YLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        36 ~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      +...+|.++++.+|+++.+.........-...||..|+..|... -...+..+.+.+|
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            34568999999999988655544333344688999999988865 4455788888876

>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=91.18  E-value=1.6  Score=32.97  Aligned_cols=79  Identities=3%  Similarity=-0.146  Sum_probs=50.2

Q ss_pred             CCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHH-HHHHHHHHHH--cC--CCeEEEeech
Q 046558           20 EGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKA-VLWGMQAAAK--AG--ATSVILESDS   94 (136)
Q Consensus        20 ~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~A-l~~aL~~a~~--~g--~~~v~iesDs   94 (136)
                      ..-+.+.+|+|-     .+.+|+++....|....+..-.-.......+-|.+| +..||+.-..  .|  ...+++.||.
T Consensus       322 ~~~~~l~~das~-----~g~~g~vl~q~~~~~~~s~~~~~~~~y~~~~~e~la~vv~al~~~r~yl~G~~~~~~i~~td~  396 (428)
T 2zd1_B          322 SKDLIAEIQKQG-----QGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKE  396 (428)
T ss_dssp             TSCCEEEEEEEE-----TTEEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHHHSSCCEEEESSCHH
T ss_pred             CCCEEEEEecCC-----CCcEEEEEecCCCceeeecccchhhhcccchHHHHHHHHHHhhccceEEECCCCcEECCccHH
Confidence            334789999973     236788887766654433332222334566778888 9999985432  34  3567889999


Q ss_pred             HHHHHHHhc
Q 046558           95 KGVIELINN  103 (136)
Q Consensus        95 ~~vv~~i~~  103 (136)
                      +.+..+.+.
T Consensus       397 ~~~~~~~~~  405 (428)
T 2zd1_B          397 TWETWWTEY  405 (428)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            887655543

>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=91.08  E-value=0.31  Score=31.44  Aligned_cols=56  Identities=13%  Similarity=0.048  Sum_probs=40.8

Q ss_pred             eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      ...+|.++++.+|+++.+.........-...||..|+..|... -...+..+.+.+|
T Consensus        35 ~f~VGAal~~~dG~i~~G~NvEnas~~~t~cAE~~Ai~~A~~~-G~~~l~~i~v~~~   90 (146)
T 2fr5_A           35 RFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISE-GYKDFRAIAISSD   90 (146)
T ss_dssp             CCCEEEEEEETTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEES
T ss_pred             CCCEEEEEEeCCCcEEEEEeccccCCCCCcCHHHHHHHHHHhC-CCCceEEEEEEeC
Confidence            4568999998899988755533333334688999999988864 4455788888877

>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=86.51  E-value=1.2  Score=28.08  Aligned_cols=55  Identities=9%  Similarity=-0.031  Sum_probs=39.4

Q ss_pred             CeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeec
Q 046558           36 YLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESD   93 (136)
Q Consensus        36 ~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesD   93 (136)
                      +...+|.++++.+|+++.+....  .......||-.|+..+... -...+..+.+.+|
T Consensus        25 s~f~VGAal~~~dG~i~~G~NvE--~~~~t~cAE~~Ai~~A~~~-G~~~~~~i~vv~~   79 (130)
T 2z3g_A           25 EDYSVASAALSSDGRIFTGVNVY--HFTGGPCAELVVLGTAAAA-AAGNLTCIVAIGN   79 (130)
T ss_dssp             SSSCEEEEEEETTSCEEEEECCC--CTTTCCCHHHHHHHHHHHT-TCCCEEEEEEEET
T ss_pred             CCCCEEEEEEecCCeEEEEeccc--cCCcccCHHHHHHHHHHHc-CCCceEEEEEEEC
Confidence            44568899998999988755433  3445788999999888763 2345677778776

>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=83.65  E-value=1.6  Score=27.93  Aligned_cols=57  Identities=14%  Similarity=0.168  Sum_probs=40.1

Q ss_pred             eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeech
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDS   94 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs   94 (136)
                      ....|..+++.+|++..+..-........+-||-.|+..+... -...+..|.+.+|.
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            4468889999999888766543333345688999999887753 23446788888763

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

Probab=82.81  E-value=2.8  Score=26.73  Aligned_cols=57  Identities=14%  Similarity=0.106  Sum_probs=39.4

Q ss_pred             eeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcC-CCeEEEeech
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAG-ATSVILESDS   94 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g-~~~v~iesDs   94 (136)
                      ....|..+++.+|++..+..-........+.||-.|+..+... -... +..+.+.+|.
T Consensus        31 ~f~VGAAl~~~dG~i~~G~NvEnasy~~t~cAEr~Ai~~a~~~-G~~~~i~~i~vv~~~   88 (142)
T 1r5t_A           31 HFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMA-GHRSGWKCMVICGDS   88 (142)
T ss_dssp             CCCEEEEEECTTSCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCSCCCEEEEEESC
T ss_pred             CCCEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHc-CCCCceEEEEEEeCC
Confidence            4568899999999988766543333334678899998887753 2223 7788888763

>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=81.47  E-value=1.8  Score=28.16  Aligned_cols=54  Identities=15%  Similarity=0.089  Sum_probs=31.4

Q ss_pred             eeeEeEEEecCCCcEEEeecccc-cccCCHHHHHHHHHHHHHHHHHHcCCCeEEEe
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTF-KSSGDVELSEAKAVLWGMQAAAKAGATSVILE   91 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~-~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~ie   91 (136)
                      ..-+|.||.+ +|+++..+.... .......+||..||..+.+......+....++
T Consensus        26 ~~pVGAviv~-~g~Ii~~G~N~~~~~~~~~~HAE~~Ai~~a~~~~~~~~l~~~tly   80 (159)
T 2b3j_A           26 EVPIGAIITK-DDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLY   80 (159)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSCCTTEEEE
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCCccCHHHHHHHHHHHHcCCCCcceeEEE
Confidence            4456777776 788885444322 11234578999999987664322233344444

>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=81.25  E-value=0.71  Score=34.95  Aligned_cols=77  Identities=14%  Similarity=0.117  Sum_probs=48.7

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCC--CcEEEeecccccc---cCCHHHHHHHHHHHHHHHHHH-cCCCeEEEeechH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHK--GETVAAAVSTFKS---SGDVELSEAKAVLWGMQAAAK-AGATSVILESDSK   95 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~--G~~~~~~~~~~~~---~~s~~~aE~~Al~~aL~~a~~-~g~~~v~iesDs~   95 (136)
                      -+.+++|||-..     +.|++.....  +..+...++.+..   ..+..+.|+.|+..|++.... +.-.++.|.||++
T Consensus       346 ~~~l~~DAS~~~-----~gavL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~  420 (455)
T 1rw3_A          346 PFELFVDEKQGY-----AKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA  420 (455)
T ss_dssp             TTSCEEEEEECS-----SSBEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC
T ss_pred             cEEEEEeccCCc-----ceeEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh
Confidence            467889986431     1133333332  3444444444332   345678899999999988765 3337999999997


Q ss_pred             HHHHHHhcC
Q 046558           96 GVIELINNK  104 (136)
Q Consensus        96 ~vv~~i~~~  104 (136)
                       +...+++.
T Consensus       421 -~~~~l~~~  428 (455)
T 1rw3_A          421 -VEALVKQP  428 (455)
T ss_dssp             -TTTTSSST
T ss_pred             -HHHHhCCC
Confidence             66666654

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

Probab=80.23  E-value=1.5  Score=27.87  Aligned_cols=42  Identities=17%  Similarity=0.154  Sum_probs=27.5

Q ss_pred             eeeEeEEEecCCCcEEEeecccc-cccCCHHHHHHHHHHHHHHH
Q 046558           37 LAGLGAVVKNHKGETVAAAVSTF-KSSGDVELSEAKAVLWGMQA   79 (136)
Q Consensus        37 ~~g~G~vird~~G~~~~~~~~~~-~~~~s~~~aE~~Al~~aL~~   79 (136)
                      ..-+|.+|.+ +|+++..+.... .......+||..|+..+.+.
T Consensus        23 ~~~VGAviv~-~g~Ii~~G~N~~~~~~~~~~HAE~~Ai~~a~~~   65 (144)
T 2a8n_A           23 EVPIGAVLVL-DGRVIARSGNRTRELNDVTAHAEIAVIRMACEA   65 (144)
T ss_dssp             SCCCEEEEEE-TTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             CCCEEEEEEE-CCEEEEEEECCCCCCCCCcCCHHHHHHHHHHHH
Confidence            4456777777 788885444322 22233678999999988764

---

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	136
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.75
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.7
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.63
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.52
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.5
d2g84a1	189	Putative deaminase NE0047 {Nitrosomonas europaea [	82.63
d2d30a1	124	mono-domain cytidine deaminase {Bacillus anthracis	81.75

>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=99.75  E-value=1.4e-17  Score=103.36  Aligned_cols=106  Identities=21%  Similarity=0.199  Sum_probs=84.3

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHH
Q 046558           18 PEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGV   97 (136)
Q Consensus        18 P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~v   97 (136)
                      |-.+-..+|+|||+..+++.+|+|+++-+......     .+. ..|++.||++|+++||+    .+..+|.|.|||+++
T Consensus         4 Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~-----~~~-~~TNn~aEl~Avi~aL~----~~~~~v~I~TDS~yv   73 (110)
T d1s1ta1           4 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVV-----TLT-DTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYA   73 (110)
T ss_dssp             CCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEE-----EES-SCCHHHHHHHHHHHHHH----HSCSEEEEEECCHHH
T ss_pred             CCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEE-----ecc-cCcHHHHHHHHHHHHHH----hCCCeEEEEEehHHH
Confidence            56677789999999999999999988865432221     233 36999999999999986    367899999999999


Q ss_pred             HHHHhcCCCCCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           98 IELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        98 v~~i~~~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      ++.+++....  ....++.++...+..+..+.+.|||.
T Consensus        74 i~~i~~~~~~--~~~~l~~~il~~l~~~~~v~i~WVpg  109 (110)
T d1s1ta1          74 LGIIQAQPDQ--SESELVNQIIEQLIKKEKVYLAWVPA  109 (110)
T ss_dssp             HHHHHHCCSE--ESCHHHHHHHHHHHHCSEEEEEECCS
T ss_pred             HHHHhcCccc--cchHHHHHHHHHHhcCCceEEEEeCC
Confidence            9999986543  23457778888888899999999984

>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=99.70  E-value=4e-17  Score=103.54  Aligned_cols=78  Identities=14%  Similarity=0.150  Sum_probs=64.9

Q ss_pred             EEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHHh
Q 046558           23 LKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELIN  102 (136)
Q Consensus        23 ~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i~  102 (136)
                      -.+++|||+.+++|.+|+|+|+.+... .+. .+..++. .|++.||++|++.||+++.+.+ .++.|+|||++++++++
T Consensus         5 ~sIy~DGa~~GNPGp~g~g~v~~~~~~-~~~-~sg~~~~-~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~   80 (132)
T d1zbfa1           5 ESLSVDVGSQGNPGIVEYKGVDTKTGE-VLF-EREPIPI-GTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVK   80 (132)
T ss_dssp             SSEEEEEEECSSSEEEEEEEEETTTCC-EEE-ECCCEEE-ECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHH
T ss_pred             eeEEEeecCCCCCchheEEEEEEcCCE-EEE-EEcCcCc-cchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHH
Confidence            358999999999999999999976444 443 2334543 7999999999999999999987 57999999999999997


Q ss_pred             cC
Q 046558          103 NK  104 (136)
Q Consensus       103 ~~  104 (136)
                      +.
T Consensus        81 ~~   82 (132)
T d1zbfa1          81 DK   82 (132)
T ss_dssp             HT
T ss_pred             hC
Confidence            63

>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=99.63  E-value=5e-15  Score=93.72  Aligned_cols=106  Identities=16%  Similarity=0.106  Sum_probs=78.1

Q ss_pred             CCCCcEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHH
Q 046558           18 PEEGWLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGV   97 (136)
Q Consensus        18 P~~~~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~v   97 (136)
                      |-.|...+|+|||+..+++.+|+|+++.+......     .++ ..|++.||++|++.||+.    ...+|.|.|||+.+
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~-----~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v   72 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVK-----KLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYV   72 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEE-----ecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHH
Confidence            55677899999999998889999988865433221     233 368999999999998874    56899999999999


Q ss_pred             HHHHhcCCCCCCchHHHHHHHHHHhhcCCceEEEEEeC
Q 046558           98 IELINNKRSTLTDTFWVIFDIIEAKKIFQNFKAQHVLR  135 (136)
Q Consensus        98 v~~i~~~~~~~~~~~~~i~~i~~l~~~~~~~~~~~v~R  135 (136)
                      ++.+++..... ....+...+..+ .....+.|.|||.
T Consensus        73 ~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~v~~~wV~g  108 (126)
T d1mu2a1          73 MGIVASQPTES-ESKIVNQIIEEM-IKKEAIYVAWVPA  108 (126)
T ss_dssp             HHHHHTCCSEE-SCHHHHHHHHHH-HHCSEEEEEECCS
T ss_pred             HHHHhcCCccc-cchHHHHHHHHh-hhcceeEEEEEeC
Confidence            99999865432 222233344444 4456899999984

>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=99.52  E-value=1.1e-13  Score=89.60  Aligned_cols=107  Identities=16%  Similarity=0.077  Sum_probs=80.3

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      .+++|+|||+.++++.+|+|+++.+........  ...+ ..|++.||++|++.||+++.  ....+.+.+|++.++..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~--~~~~-~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFS--AGYT-RTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEE--EEEE-EECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEec--cccC-cccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcc
Confidence            379999999999999999999998765544332  2233 36899999999999998653  457899999999999887


Q ss_pred             hcCC------------CCCCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          102 NNKR------------STLTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       102 ~~~~------------~~~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      +...            ..+.....++.++..++.. .+++|.|||
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~-~~V~~~wV~  120 (152)
T d1jl1a_          77 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVK  120 (152)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECC
T ss_pred             cchhhHhHhccchhcccCeeecHHHHHHHHHHhhc-ceeEEEEec
Confidence            6421            1122345677778777654 589999998

>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=99.50  E-value=3.5e-14  Score=91.85  Aligned_cols=107  Identities=16%  Similarity=0.050  Sum_probs=80.5

Q ss_pred             cEEEEeceeEecCCCeeeEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeechHHHHHHH
Q 046558           22 WLKVNVDDAMDRVNYLAGLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDSKGVIELI  101 (136)
Q Consensus        22 ~~k~n~Dgs~~~~~~~~g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs~~vv~~i  101 (136)
                      .+.+|+|||+.++++.+|+|+++.+.........  ... ..|++.||+.|+++||+.+.  ....+.+.+||+.+++.+
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~--~~~-~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~   77 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSG--GEA-CTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAF   77 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECC--EEE-EECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHH
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEec--ccc-cccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccc
Confidence            3679999999998899999999987665544332  222 36999999999999998653  356899999999999887


Q ss_pred             hcCC-------------CCCCchHHHHHHHHHHhhcCCceEEEEEe
Q 046558          102 NNKR-------------STLTDTFWVIFDIIEAKKIFQNFKAQHVL  134 (136)
Q Consensus       102 ~~~~-------------~~~~~~~~~i~~i~~l~~~~~~~~~~~v~  134 (136)
                      ....             ..+-....++.++..++. ..++.|.|||
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~-~~~v~~~wVk  122 (147)
T d1rila_          78 TEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVK  122 (147)
T ss_dssp             HSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCC
T ss_pred             cccchhhhhhccccccccccchhHHHHHHHHHHhh-hcccceEEcc
Confidence            6521             112234668888877765 4578999987

>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=82.63  E-value=1.5  Score=27.89  Aligned_cols=45  Identities=16%  Similarity=0.048  Sum_probs=30.2

Q ss_pred             CeeeEeEEEecC-CCcEEEeeccccc-ccCCHHHHHHHHHHHHHHHH
Q 046558           36 YLAGLGAVVKNH-KGETVAAAVSTFK-SSGDVELSEAKAVLWGMQAA   80 (136)
Q Consensus        36 ~~~g~G~vird~-~G~~~~~~~~~~~-~~~s~~~aE~~Al~~aL~~a   80 (136)
                      +..-+|.||.+. .|+++..+..... ......+||..|+..|-+..
T Consensus        44 g~~P~GaviV~~~~g~Iia~g~N~~~~~~dpt~HAEi~AI~~A~~~~   90 (189)
T d2g84a1          44 DGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKL   90 (189)
T ss_dssp             TCCSCEEEEEETTTCBEEEEEECCTTTTTCTTCCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECCCCEEEEEEcCCcCcCCCCcccHHHHHHHHHHHHh
Confidence            344588888876 4888887654432 22334699999998876543

>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=81.75  E-value=0.91  Score=26.85  Aligned_cols=55  Identities=15%  Similarity=0.200  Sum_probs=39.9

Q ss_pred             eEeEEEecCCCcEEEeecccccccCCHHHHHHHHHHHHHHHHHHcCCCeEEEeech
Q 046558           39 GLGAVVKNHKGETVAAAVSTFKSSGDVELSEAKAVLWGMQAAAKAGATSVILESDS   94 (136)
Q Consensus        39 g~G~vird~~G~~~~~~~~~~~~~~s~~~aE~~Al~~aL~~a~~~g~~~v~iesDs   94 (136)
                      -+|..++..+|++..+..-.........-||..|+..++.. -+..+..|.+-+|+
T Consensus        25 ~VGAal~~~~G~i~~G~NvEn~s~~~~~CAEr~Ai~~a~~~-g~~~~~~i~v~~~~   79 (124)
T d2d30a1          25 QVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVADT   79 (124)
T ss_dssp             CEEEEEEETTCCEEEEECBCCSSGGGCBCHHHHHHHHHHHT-TCCCEEEEEEEESC
T ss_pred             cEEEEEEeCCCCEEEEEeeccccCCcccCHHHHHHHHHHhc-CCceeEEEEEEcCC
Confidence            47888889999988776654444445568999999887763 44567788887765