Citrus Sinensis ID: 034727

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80------
Protein Sequence
MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLSI
Secondary Structure (PSIPRED)
cEEcccccEEEEEEcccccccHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEHHccHcHccccHHHHHHHHHHHHHHHHccccEEEEEcccHEEEHHcccEEEccccccHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mlraddgsliynhngvgittnnvAKYGSLILGLKYALQKGFFnfrvrgdskLVHMQVCCWlmedqtpgMAELCGEAKRLKDKFLSI
Flexible Loop (DISEMBL)
mlraddgsliynhngvgittNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLSI
Low Complexity Region (SEG)
MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLSI
Disordered region (IsUnstruct)
*******SLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELC*************
Disordered Region (DISOPRED)
ML***DGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLSI
Disordered Region (DISEMBL)
MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLSI
Disordered Region (DISPRO)
*****DGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLS*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDKFLSI
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	86
359488729	287	PREDICTED: uncharacterized protein LOC10	0.976	0.292	0.579	7e-16
255552696	255	nuclease, putative [Ricinus communis] gi	0.965	0.325	0.551	2e-15
296086505	445	unnamed protein product [Vitis vinifera]	0.988	0.191	0.528	7e-15
359473412	453	PREDICTED: uncharacterized protein LOC10	0.988	0.187	0.528	9e-15
449452100	373	PREDICTED: uncharacterized protein LOC10	0.976	0.225	0.546	9e-15
365222890	288	Hop-interacting protein THI034 [Solanum	0.965	0.288	0.528	2e-14
356565894	345	PREDICTED: uncharacterized protein LOC10	0.965	0.240	0.528	5e-14
224108115	282	predicted protein [Populus trichocarpa]	0.976	0.297	0.511	5e-14
356550140	283	PREDICTED: uncharacterized protein LOC10	0.906	0.275	0.573	6e-14
449459420	255	PREDICTED: uncharacterized protein LOC10	0.976	0.329	0.534	7e-14

>gi|359488729|ref|XP_002280233.2| PREDICTED: uncharacterized protein LOC100242330 [Vitis vinifera] gi|296087711|emb|CBI34967.3| unnamed protein product [Vitis vinifera]

 Score = 87.8 bits (216), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 51/88 (57%), Positives = 62/88 (70%), Gaps = 4/88 (4%)

Query: 1   MLRADDGS-LIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC- 58
           +LRADDGS +I+   GVGI TNNVA+Y +LILG+KYAL+KG    R RGDS+LV MQ   
Sbjct: 168 VLRADDGSAVIHLREGVGIATNNVAEYRALILGMKYALKKGIKRIRARGDSQLVCMQFQG 227

Query: 59  CWLMEDQTPGMAELCGEAKRLKDKFLSI 86
            W  ++Q   MA+LC EAK L  KFLS 
Sbjct: 228 LWKTKNQN--MADLCEEAKELGKKFLSF 253

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552696|ref|XP_002517391.1| nuclease, putative [Ricinus communis] gi|223543402|gb|EEF44933.1| nuclease, putative [Ricinus communis]

 Score = 86.3 bits (212), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 48/87 (55%), Positives = 65/87 (74%), Gaps = 4/87 (4%)

Query: 1   MLRADDGSLI-YNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV-C 58
           +LRA+DGS++     G+G  TNNVA+Y ++ILGLK+AL+KGF + RVRGDS LV MQ+  
Sbjct: 135 VLRAEDGSMVCLLREGLGTATNNVAEYRAVILGLKHALRKGFKHIRVRGDSNLVVMQIKG 194

Query: 59  CWLMEDQTPGMAELCGEAKRLKDKFLS 85
            W ++ Q   +A+LC EAK LK+KFLS
Sbjct: 195 LWKIKSQN--VADLCKEAKELKNKFLS 219

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086505|emb|CBI32094.3| unnamed protein product [Vitis vinifera]

 Score = 84.7 bits (208), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 65/87 (74%), Gaps = 2/87 (2%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC 59
           +LR+D G +I     G+G+ TNNVA+Y ++ILGLKYAL+KG+ + RV+GDSKLV MQV  
Sbjct: 311 VLRSDSGRVICRVREGLGLATNNVAEYQAMILGLKYALKKGYTSIRVQGDSKLVCMQV-Q 369

Query: 60  WLMEDQTPGMAELCGEAKRLKDKFLSI 86
            L + +   M+ LC EAK+LK++FLS+
Sbjct: 370 GLWKARNKNMSILCKEAKKLKNEFLSV 396

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473412|ref|XP_002266599.2| PREDICTED: uncharacterized protein LOC100255243 [Vitis vinifera]

 Score = 84.3 bits (207), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 65/87 (74%), Gaps = 2/87 (2%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC 59
           +LR+D G +I     G+G+ TNNVA+Y ++ILGLKYAL+KG+ + RV+GDSKLV MQV  
Sbjct: 140 VLRSDSGRVICRVREGLGLATNNVAEYQAMILGLKYALKKGYTSIRVQGDSKLVCMQV-Q 198

Query: 60  WLMEDQTPGMAELCGEAKRLKDKFLSI 86
            L + +   M+ LC EAK+LK++FLS+
Sbjct: 199 GLWKARNKNMSILCKEAKKLKNEFLSV 225

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452100|ref|XP_004143798.1| PREDICTED: uncharacterized protein LOC101210930 [Cucumis sativus]

 Score = 84.3 bits (207), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 47/86 (54%), Positives = 61/86 (70%), Gaps = 2/86 (2%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC 59
           +LRA DGS+I     G+GI TNNVA+Y +++LGLK AL+KGF    V+GDSKLV MQV  
Sbjct: 255 VLRAHDGSVICRLREGLGIATNNVAEYRAILLGLKSALKKGFTRIHVQGDSKLVCMQV-Q 313

Query: 60  WLMEDQTPGMAELCGEAKRLKDKFLS 85
            L + +   M+ELC E  +LK+KFLS
Sbjct: 314 GLWKAKHENMSELCNEVTKLKNKFLS 339

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|365222890|gb|AEW69797.1| Hop-interacting protein THI034 [Solanum lycopersicum]

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 62/87 (71%), Gaps = 4/87 (4%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC- 58
           +LRA DGS+++    GVG+ TNNVA+Y  +ILGL+YAL+KGF + +V+GDSKLV MQ   
Sbjct: 167 VLRAADGSMVFRLREGVGVATNNVAEYRGVILGLRYALEKGFKHIKVKGDSKLVCMQTQG 226

Query: 59  CWLMEDQTPGMAELCGEAKRLKDKFLS 85
            W  ++Q   MAEL    K LKD+F+S
Sbjct: 227 IWKCKNQN--MAELSKIVKELKDQFMS 251

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565894|ref|XP_003551171.1| PREDICTED: uncharacterized protein LOC100809644 [Glycine max]

 Score = 82.0 bits (201), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 62/87 (71%), Gaps = 4/87 (4%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV-C 58
           +LRA+DGSLI     GVGI TNN A+Y ++ILG+KYAL+KGF   R++GDSKLV MQ+  
Sbjct: 227 ILRANDGSLICRLREGVGIATNNAAEYRAMILGMKYALKKGFTGIRIQGDSKLVCMQIDG 286

Query: 59  CWLMEDQTPGMAELCGEAKRLKDKFLS 85
            W ++++   ++ L   AK LKDKF S
Sbjct: 287 SWKVKNEN--LSTLYNVAKELKDKFSS 311

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224108115|ref|XP_002314727.1| predicted protein [Populus trichocarpa] gi|222863767|gb|EEF00898.1| predicted protein [Populus trichocarpa]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 45/88 (51%), Positives = 62/88 (70%), Gaps = 4/88 (4%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC- 58
           +LR DDGSLI     G+GI TNN+A+Y +++LG+KYALQKG+   +V+GDSKLV MQ+  
Sbjct: 164 VLRTDDGSLICRLREGLGIATNNMAEYRAILLGMKYALQKGYTKIQVKGDSKLVCMQIQG 223

Query: 59  CWLMEDQTPGMAELCGEAKRLKDKFLSI 86
            W  + +   +  LC EAK+LK+ FLS 
Sbjct: 224 SW--KAKHVNITNLCTEAKKLKNSFLSF 249

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550140|ref|XP_003543447.1| PREDICTED: uncharacterized protein LOC100796237 [Glycine max]

 Score = 81.6 bits (200), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 47/82 (57%), Positives = 58/82 (70%), Gaps = 4/82 (4%)

Query: 6   DGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV-CCWLME 63
           DGS +Y    GVGI TNNVA+Y SLILGLK+AL+KG+ +  V+GDS LV  Q+   W ++
Sbjct: 168 DGSKVYRLREGVGIQTNNVAEYRSLILGLKHALKKGYKHIIVQGDSLLVCNQIQGLWKIK 227

Query: 64  DQTPGMAELCGEAKRLKDKFLS 85
           +Q   M  LC EAK LKDKFLS
Sbjct: 228 NQN--MGTLCAEAKELKDKFLS 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459420|ref|XP_004147444.1| PREDICTED: uncharacterized protein LOC101219107 [Cucumis sativus] gi|449517156|ref|XP_004165612.1| PREDICTED: uncharacterized LOC101219107 [Cucumis sativus]

 Score = 81.3 bits (199), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 47/88 (53%), Positives = 62/88 (70%), Gaps = 4/88 (4%)

Query: 1   MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC- 58
           +LRA+DGS +     GVGI T NVA+Y ++ILGLK+AL+ G  + RV+GDSKLV MQV  
Sbjct: 135 VLRANDGSTVCKLQEGVGIATCNVAEYRAVILGLKHALKNGIKHIRVQGDSKLVCMQVQG 194

Query: 59  CWLMEDQTPGMAELCGEAKRLKDKFLSI 86
            W +++  P MA+ C  AK LKDKF+S 
Sbjct: 195 LWKLKN--PNMAKFCKVAKELKDKFVSF 220

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	86
TAIR|locus:2096692	294	AT3G01410 [Arabidopsis thalian	0.941	0.275	0.541	1e-14
TAIR|locus:2176152	322	AT5G51080 [Arabidopsis thalian	0.965	0.257	0.471	1.1e-13

TAIR|locus:2096692 AT3G01410 [Arabidopsis thaliana (taxid:3702)]

 Score = 188 (71.2 bits), Expect = 1.0e-14, P = 1.0e-14
 Identities = 46/85 (54%), Positives = 54/85 (63%)

Query:     1 MLRADDGS-LIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC- 58
             +LRA D S L Y   GVG  TNNVA+Y +L+LGL+ AL KGF N  V GDS LV MQV  
Sbjct:   175 VLRASDNSVLFYLREGVGNATNNVAEYRALLLGLRSALDKGFKNVHVLGDSMLVCMQVQG 234

Query:    59 CWLMEDQTPGMAELCGEAKRLKDKF 83
              W  +   P MAELC +AK L + F
Sbjct:   235 AW--KTNHPKMAELCKQAKELMNSF 257

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=ISS

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0006310 "DNA recombination" evidence=RCA

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007126 "meiosis" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0010332 "response to gamma radiation" evidence=RCA

GO:0031048 "chromatin silencing by small RNA" evidence=RCA

GO:0032204 "regulation of telomere maintenance" evidence=RCA

GO:0032504 "multicellular organism reproduction" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0043247 "telomere maintenance in response to DNA damage" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

GO:0048451 "petal formation" evidence=RCA

GO:0048453 "sepal formation" evidence=RCA

TAIR|locus:2176152 AT5G51080 [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 1.1e-13, P = 1.1e-13
 Identities = 41/87 (47%), Positives = 60/87 (68%)

Query:     1 MLRADDGSLIYN-HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC 59
             +L+ +DGSLI+    G+GI TNN A+Y  LILGLK+A++KG+   +V+ DSKLV MQ+  
Sbjct:   206 VLKTEDGSLIFKMRQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKG 265

Query:    60 -WLMEDQTPGMAELCGEAKRLKDKFLS 85
              W +  +   +++L  EAK+L DK LS
Sbjct:   266 QWKVNHEV--LSKLHKEAKQLSDKCLS 290


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.324   0.140   0.433    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       86        86   0.00091  102 3  11 22  0.41    29
                                                     29  0.47    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  551 (59 KB)
  Total size of DFA:  107 KB (2072 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.50u 0.13s 8.63t   Elapsed:  00:00:01
  Total cpu time:  8.50u 0.13s 8.63t   Elapsed:  00:00:01
  Start:  Fri May 10 00:06:58 2013   End:  Fri May 10 00:06:59 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=ISS

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00020795001 SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (308 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	86
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	1e-11
PRK07238	372	PRK07238, PRK07238, bifunctional RNase H/acid phos	1e-09
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	4e-07
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	1e-04
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	0.002

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

 Score = 56.0 bits (136), Expect = 1e-11
 Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 14/91 (15%)

Query: 7   GSLIYNHNGVGI---------TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV 57
           G +I + +G  +          TNN A+Y +LI GL+ AL+ G     + GDS+LV  Q+
Sbjct: 19  GIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALELGIKKLEIYGDSQLVVNQI 78

Query: 58  CCWLMEDQT--PGMAELCGEAKRLKDKFLSI 86
                E +     +A    EA+ L  KF  +
Sbjct: 79  ---QGEYEVKNERLAPYLEEARELLKKFEEV 106

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 = 52.3 bits (126), Expect = 1e-09
 Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 16  VGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC-WLMEDQTPGMAELCG 74
           +G  TNNVA+Y  LI GL+ A + G     VR DSKLV  Q+   W ++   P M  L  
Sbjct: 40  IGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKH--PDMKPLAA 97

Query: 75  EAKRLKDKFLSI 86
           +A+ L  +F  +
Sbjct: 98  QARELASQFGRV 109

Length = 372

>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 44.3 bits (105), Expect = 4e-07
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 2  LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLV 53
          LR  DG    +  G G TTNN A+  +LI  L+   + G     +  DSK V
Sbjct: 25 LRYGDGEKELSG-GEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYV 75

Length = 154

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

 Score = 36.4 bits (85), Expect = 1e-04
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 6/66 (9%)

Query: 20 TNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTP--GMAELCGEAK 77
          +   A+  +L+ GL+ AL+ G     V  DS+L    V   +  +      +A L  E +
Sbjct: 1  SPLEAEAEALLEGLQLALELGIRRLIVESDSQL----VVQQIQGEYEARSRLAALLREIR 56

Query: 78 RLKDKF 83
          +L  KF
Sbjct: 57 KLLKKF 62

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

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

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 9/64 (14%)

Query: 7  GSLIYNHNGV---------GITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV 57
          G ++ +H G             TNN A+  +L+  L+ AL  G     +  DSK V   +
Sbjct: 16 GGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLI 75

Query: 58 CCWL 61
            W 
Sbjct: 76 NSWS 79

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	86
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.77
PRK13907	128	rnhA ribonuclease H; Provisional	99.77
PRK07708	219	hypothetical protein; Validated	99.71
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.64
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.42
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.35
PRK08719	147	ribonuclease H; Reviewed	99.2
PRK06548	161	ribonuclease H; Provisional	99.1
PRK00203	150	rnhA ribonuclease H; Reviewed	98.88
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	98.69
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.3
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	96.25
PRK14840	250	undecaprenyl pyrophosphate synthase; Provisional	81.03
KOG1602	271	consensus Cis-prenyltransferase [Lipid transport a	80.44

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.77  E-value=2e-18  Score=123.00  Aligned_cols=84  Identities=35%  Similarity=0.503  Sum_probs=77.5

Q ss_pred             CeeCCCCC-EEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHH
Q 034727            1 MLRADDGS-LIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAK   77 (86)
Q Consensus         1 v~~~~~g~-~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~   77 (86)
                      ||++++|. ++. .+..++..|||.|||.|++.||+.+.++|++++.+++||++|+++++ +|+  ++++.+..|+.+++
T Consensus        23 vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~--~~~~~l~~~~~~i~  100 (372)
T PRK07238         23 VVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWK--VKHPDMKPLAAQAR  100 (372)
T ss_pred             EEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCc--cCChHHHHHHHHHH
Confidence            57888765 555 88889999999999999999999999999999999999999999999 999  99999999999999


Q ss_pred             HHhhccCCC
Q 034727           78 RLKDKFLSI   86 (86)
Q Consensus        78 ~l~~~f~~~   86 (86)
                      .++++|+++
T Consensus       101 ~l~~~f~~~  109 (372)
T PRK07238        101 ELASQFGRV  109 (372)
T ss_pred             HHHhcCCce
Confidence            999999864

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.77  E-value=4.1e-18  Score=105.56  Aligned_cols=81  Identities=23%  Similarity=0.283  Sum_probs=71.7

Q ss_pred             CeeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHH
Q 034727            1 MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRL   79 (86)
Q Consensus         1 v~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l   79 (86)
                      ||++++|.+. .+...+.+|||.|||.|++.||+.+.++|++++.+++||++|+++++ .|.   +++.+.+++++++.+
T Consensus        22 vi~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~---~~~~~~~l~~~~~~l   97 (128)
T PRK13907         22 FIKGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYA---KNKMFAPLLEEALQY   97 (128)
T ss_pred             EEEECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHh---cChhHHHHHHHHHHH
Confidence            4677777554 44567889999999999999999999999999999999999999999 884   678899999999999


Q ss_pred             hhccCC
Q 034727           80 KDKFLS   85 (86)
Q Consensus        80 ~~~f~~   85 (86)
                      +++|+.
T Consensus        98 ~~~f~~  103 (128)
T PRK13907         98 IKSFDL  103 (128)
T ss_pred             HhcCCc
Confidence            999875

>PRK07708 hypothetical protein; Validated

Probab=99.71  E-value=6e-17  Score=109.17  Aligned_cols=82  Identities=20%  Similarity=0.275  Sum_probs=70.6

Q ss_pred             CeeCCCCCEEE---eeeccC-CCcchHHHHHHHHHHHHHHHhcCCce--EEEecchHHHHHHHh-hhhhcCCChhHHHHH
Q 034727            1 MLRADDGSLIY---NHNGVG-ITTNNVAKYGSLILGLKYALQKGFFN--FRVRGDSKLVHMQVC-CWLMEDQTPGMAELC   73 (86)
Q Consensus         1 v~~~~~g~~~~---~~~~~g-~~tnn~aEy~Ali~gL~~a~~~~~~~--v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~   73 (86)
                      ||+++.|....   .+..++ ..|||+|||.|++.||+.|.++|+++  |.+++||++|++|++ .|+  ++++.+++|+
T Consensus        94 VI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk--~~~~~l~~y~  171 (219)
T PRK07708         94 VIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWP--CYDEHLNHWL  171 (219)
T ss_pred             EEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCce--eCChhHHHHH
Confidence            46666665432   334565 68999999999999999999999976  899999999999999 999  9999999999


Q ss_pred             HHHHHHhhccC
Q 034727           74 GEAKRLKDKFL   84 (86)
Q Consensus        74 ~~i~~l~~~f~   84 (86)
                      +++..++++|.
T Consensus       172 ~~i~~l~~~~~  182 (219)
T PRK07708        172 DRIEQKLKQLK  182 (219)
T ss_pred             HHHHHHHhhCC
Confidence            99999998875

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

Probab=99.64  E-value=7.5e-16  Score=98.92  Aligned_cols=83  Identities=30%  Similarity=0.359  Sum_probs=64.6

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhhhc---------CCCh-hHHH
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLME---------DQTP-GMAE   71 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~~~---------~k~~-~l~~   71 (86)
                      |+..+++. ..+...+.+|||.|||.|+|.||+.+.+.+...+.++|||++|+++|+.|..+         .+.| ..+.
T Consensus        25 l~~~~~~~-~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~d  103 (154)
T COG0328          25 LRYGDGEK-ELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKD  103 (154)
T ss_pred             EEcCCceE-EEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHH
Confidence            44334443 35555669999999999999999999999999999999999999999866300         1122 4467


Q ss_pred             HHHHHHHHhhccCC
Q 034727           72 LCGEAKRLKDKFLS   85 (86)
Q Consensus        72 ~~~~i~~l~~~f~~   85 (86)
                      +++++..+.++|..
T Consensus       104 l~~~~~~~~~~~~~  117 (154)
T COG0328         104 LWEELDELLKRHEL  117 (154)
T ss_pred             HHHHHHHHHhhCCe
Confidence            89999999998853

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

Probab=99.42  E-value=4.4e-13  Score=76.90  Aligned_cols=63  Identities=22%  Similarity=0.246  Sum_probs=54.1

Q ss_pred             chHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHHhhccCCC
Q 034727           21 NNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRLKDKFLSI   86 (86)
Q Consensus        21 nn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l~~~f~~~   86 (86)
                      +++||+.|++.||+.|.++|++++.++|||+.|+++++ .+.  .++ .+.++...++.++++|..+
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~--~~~-~~~~~~~~i~~~~~~~~~~   64 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSS--SRS-ELRPLIQDIRSLLDRFWNV   64 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS-----S-CCHHHHHHHHHHHCCCSCE
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccc--ccc-cccccchhhhhhhccccce
Confidence            57899999999999999999999999999999999999 876  666 7999999999999998753

>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=99.35  E-value=1.2e-11  Score=73.52  Aligned_cols=82  Identities=26%  Similarity=0.234  Sum_probs=69.0

Q ss_pred             CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHH
Q 034727            1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKR   78 (86)
Q Consensus         1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~   78 (86)
                      |+++++|.... .....+..+++.+|+.|++.||+.+...+.+++.+++||+.++++++ .+.  +..+.+.+++..+..
T Consensus        20 v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~--~~~~~~~~~~~~i~~   97 (130)
T cd06222          20 VLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYE--GKPVKNVDLWQRLLA   97 (130)
T ss_pred             EEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcccc--CCChhhHHHHHHHHH
Confidence            35677777776 33333788999999999999999999999999999999999999999 776  677889999999998


Q ss_pred             HhhccC
Q 034727           79 LKDKFL   84 (86)
Q Consensus        79 l~~~f~   84 (86)
                      +.+++.
T Consensus        98 ~~~~~~  103 (130)
T cd06222          98 LLKRFH  103 (130)
T ss_pred             HHhCCC
Confidence            885554

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

>PRK08719 ribonuclease H; Reviewed

Probab=99.20  E-value=1.1e-10  Score=74.59  Aligned_cols=75  Identities=19%  Similarity=0.229  Sum_probs=55.3

Q ss_pred             eeCCCCCEEE-eeeccC-CCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHH--------h-hhhhcCCCh---
Q 034727            2 LRADDGSLIY-NHNGVG-ITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV--------C-CWLMEDQTP---   67 (86)
Q Consensus         2 ~~~~~g~~~~-~~~~~g-~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~--------~-~~~~~~k~~---   67 (86)
                      +.+++|..+. .+..++ ..|||.||+.|++.||+.+.+.    ..|++||++|++++        + .|+  ..+.   
T Consensus        29 v~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~--~s~g~~v  102 (147)
T PRK08719         29 VYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWR--KSDKKPV  102 (147)
T ss_pred             EEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcc--cCCCccc
Confidence            4566777664 555554 6899999999999999988754    37999999999999        3 443  2322   


Q ss_pred             hHHHHHHHHHHHhhc
Q 034727           68 GMAELCGEAKRLKDK   82 (86)
Q Consensus        68 ~l~~~~~~i~~l~~~   82 (86)
                      ..+.+++++..+.++
T Consensus       103 ~n~dl~~~i~~l~~~  117 (147)
T PRK08719        103 ANRDLWQQVDELRAR  117 (147)
T ss_pred             ccHHHHHHHHHHhCC
Confidence            346778888877653

>PRK06548 ribonuclease H; Provisional

Probab=99.10  E-value=5.7e-10  Score=72.31  Aligned_cols=68  Identities=25%  Similarity=0.235  Sum_probs=51.0

Q ss_pred             eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh----h-----hcCCCh-hHHHHHHHHHHHhhc
Q 034727           14 NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW----L-----MEDQTP-GMAELCGEAKRLKDK   82 (86)
Q Consensus        14 ~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~----~-----~~~k~~-~l~~~~~~i~~l~~~   82 (86)
                      ...+..|||.||+.|++.||+.+ ..+..++.|++||++|+++++.|    +     .....| ..+.+++++..++++
T Consensus        35 g~~~~~TNnraEl~Aii~aL~~~-~~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~  112 (161)
T PRK06548         35 GGWDIATNNIAELTAVRELLIAT-RHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN  112 (161)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHhh-hcCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc
Confidence            33456999999999999999754 34556899999999999999843    2     001223 458899999888765

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=98.88  E-value=8.9e-09  Score=65.53  Aligned_cols=69  Identities=19%  Similarity=0.220  Sum_probs=50.7

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhhhc--CC-------Ch-hHHHHHHHHHHHhh
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLME--DQ-------TP-GMAELCGEAKRLKD   81 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~~~--~k-------~~-~l~~~~~~i~~l~~   81 (86)
                      ++...+..|||.||+.|++.||+.+.+  ...+.|++||++++++++.|...  .+       .| ..+.+++++..+++
T Consensus        34 ~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~  111 (150)
T PRK00203         34 LSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK  111 (150)
T ss_pred             EecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc
Confidence            455567899999999999999997754  35799999999999998843200  11       12 34677888887765


Q ss_pred             c
Q 034727           82 K   82 (86)
Q Consensus        82 ~   82 (86)
                      +
T Consensus       112 ~  112 (150)
T PRK00203        112 R  112 (150)
T ss_pred             c
Confidence            4

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

Probab=98.69  E-value=4.5e-08  Score=70.16  Aligned_cols=55  Identities=27%  Similarity=0.281  Sum_probs=46.3

Q ss_pred             CCCEEEeeecc--CCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh
Q 034727            6 DGSLIYNHNGV--GITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW   60 (86)
Q Consensus         6 ~g~~~~~~~~~--g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~   60 (86)
                      +|...-.++++  |..|||.||+.|++.||+.|++.++..++|.|||+++++.|+.|
T Consensus       239 ~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~w  295 (371)
T KOG3752|consen  239 PGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLW  295 (371)
T ss_pred             CCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHH
Confidence            34444444444  68999999999999999999999999999999999999998844

>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=98.30  E-value=1.7e-06  Score=52.93  Aligned_cols=45  Identities=27%  Similarity=0.210  Sum_probs=37.2

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhh
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC   59 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~   59 (86)
                      .+..++..||+.+|+.|++.||+ +.. . +.+.|++||+.+++.++.
T Consensus        31 ~~~~~~~~s~~~aEl~Ai~~AL~-~~~-~-~~v~I~tDS~~v~~~l~~   75 (132)
T PF00075_consen   31 FSFRLGGQSNNRAELQAIIEALK-ALE-H-RKVTIYTDSQYVLNALNK   75 (132)
T ss_dssp             EEEEEESECHHHHHHHHHHHHHH-THS-T-SEEEEEES-HHHHHHHHT
T ss_pred             EEecccccchhhhheehHHHHHH-Hhh-c-ccccccccHHHHHHHHHH
Confidence            44555699999999999999999 552 2 999999999999998874

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 ....

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

Probab=96.25  E-value=0.013  Score=42.76  Aligned_cols=65  Identities=22%  Similarity=0.200  Sum_probs=53.6

Q ss_pred             CcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCCh-hHHHHHHHHHHHhhccCC
Q 034727           19 TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTP-GMAELCGEAKRLKDKFLS   85 (86)
Q Consensus        19 ~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~-~l~~~~~~i~~l~~~f~~   85 (86)
                      .|--.||+.|++.||..+..+|+.++.++.|+..++..+. ...  .+.. .+..+.+.+....++|.+
T Consensus        47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~--~~~~~~~~~l~~~v~~~r~~l~~  113 (384)
T KOG1812|consen   47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREK--PEQHRKIVLLVELVQRIREQLTS  113 (384)
T ss_pred             cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhh--HHHHHHHHHHHHHHHHHHHHhhc
Confidence            5677999999999999999999999999999988888777 765  4444 577788888777776653

>PRK14840 undecaprenyl pyrophosphate synthase; Provisional

Probab=81.03  E-value=1.5  Score=30.45  Aligned_cols=49  Identities=12%  Similarity=-0.050  Sum_probs=37.3

Q ss_pred             eeCCCCCEEE-ee--eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727            2 LRADDGSLIY-NH--NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS   50 (86)
Q Consensus         2 ~~~~~g~~~~-~~--~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS   50 (86)
                      |.|.||++-. ..  ..+.....+.+.+.++..-++.|.++|++.+.+|.=|
T Consensus        25 ImDGNrRwAk~~~~~~gl~~~~GH~~G~~~l~~v~~~c~~~GIk~lTvYaFS   76 (250)
T PRK14840         25 IMDGNRRWYRKHEQFCQKRAISGHYYGAKSLPQIVDTALHLGIEVLTLFAFS   76 (250)
T ss_pred             EcCCChHHHhhCCCccCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEee
Confidence            4455555533 11  1245667899999999999999999999999999877

>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]

Probab=80.44  E-value=2.3  Score=29.87  Aligned_cols=39  Identities=18%  Similarity=0.154  Sum_probs=34.0

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS   50 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS   50 (86)
                      ....++....+.|.+.+|..=|++|.++|++.|.+|.=|
T Consensus        52 Kk~~L~~~~GH~aGf~~l~~ile~C~~lGI~~vT~fAFS   90 (271)
T KOG1602|consen   52 KKRGLETSEGHEAGFEALKEILELCKELGIKEVTVFAFS   90 (271)
T ss_pred             HhcCCCcccchHHHHHHHHHHHHHHHHcCCcEEEEEEEe
Confidence            444566788899999999999999999999999998766

---

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	86
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	5e-16
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	4e-15
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	6e-11
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	4e-08

>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 = 66.9 bits (164), Expect = 5e-16
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 15  GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC-WLMEDQTPGMAELC 73
            +G  TNNVA+Y  LI GL  A++ G     V  DSKLV  Q+   W ++   P + +L 
Sbjct: 40  AIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKH--PDLLKLY 97

Query: 74  GEAKRLKDKFLSI 86
            +A+ L  +F  I
Sbjct: 98  VQAQALASQFRRI 110

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

 Score = 64.7 bits (158), Expect = 4e-15
 Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 15/90 (16%)

Query: 7   GSLIYNHNGV------------GITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVH 54
           G +IY  N                +TNNVA+Y  LI  ++  L+ G  +  ++GDS+LV 
Sbjct: 22  GFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI 81

Query: 55  MQVCC-WLMEDQTPGMAELCGEAKRLKDKF 83
            Q+   + ++     +  L  +A  LK K 
Sbjct: 82  KQMNGEYKVKA--KRIIPLYEKAIELKKKL 109

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Length = 140

 Score = 53.7 bits (130), Expect = 6e-11
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 2  LRADDGSLIYNHN-GVGITTNNVAKYGSLILGLKYALQKGFFNF----RVRGDSKLVHMQ 56
          +  + G+ ++  +  +G TTNNVA+Y +LI  L+     G         VR DS+L+  Q
Sbjct: 25 ITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQ 84

Query: 57 V 57
          +
Sbjct: 85 M 85

>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* Length = 142

 Score = 46.4 bits (110), Expect = 4e-08
 Identities = 10/57 (17%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 4  ADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW 60
             G +++    + I TNN+ ++ +++ GL+Y  ++      +  +S+     V   
Sbjct: 34 TKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDK 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	86
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.8
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.8
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.76
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.64
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.61
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.35
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.33
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.21
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.2
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.16
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.14
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.14
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.13
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.08
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.87
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.83
3ugs_B	225	Undecaprenyl pyrophosphate synthase; niaid, csgid,	85.44
3tue_A	219	Tryparedoxin peroxidase; thioredoxin fold, peroxir	84.84
3sbc_A	216	Peroxiredoxin TSA1; alpha-beta fold, peroxidase, c	84.13

>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=99.80  E-value=1.6e-19  Score=111.59  Aligned_cols=83  Identities=33%  Similarity=0.461  Sum_probs=75.6

Q ss_pred             CeeCCC-CCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHH
Q 034727            1 MLRADD-GSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAK   77 (86)
Q Consensus         1 v~~~~~-g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~   77 (86)
                      ||++++ |.++. .+..++..|||.||+.|++.||+.+.++|.+++.|++||++|+++++ .|+  ++++.+.+++.+++
T Consensus        24 v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~--~~~~~l~~~~~~i~  101 (141)
T 3hst_B           24 VVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWK--VKHPDLLKLYVQAQ  101 (141)
T ss_dssp             EEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSC--CCSHHHHHHHHHHH
T ss_pred             EEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcc--cCCHHHHHHHHHHH
Confidence            467776 77776 88888999999999999999999999999999999999999999999 999  99999999999999


Q ss_pred             HHhhccCC
Q 034727           78 RLKDKFLS   85 (86)
Q Consensus        78 ~l~~~f~~   85 (86)
                      .+.++|..
T Consensus       102 ~l~~~~~~  109 (141)
T 3hst_B          102 ALASQFRR  109 (141)
T ss_dssp             HHHTTSSE
T ss_pred             HHHhcCCe
Confidence            99988753

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

Probab=99.80  E-value=2e-19  Score=110.63  Aligned_cols=83  Identities=25%  Similarity=0.329  Sum_probs=76.8

Q ss_pred             CeeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCc----eEEEecchHHHHHHHh-hhhhcCCChhHHHHHH
Q 034727            1 MLRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFF----NFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCG   74 (86)
Q Consensus         1 v~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~----~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~   74 (86)
                      |+++++|+.+. .+..++..|||.||+.|++.||+.+.+.+.+    ++.|++||++|+++++ .|+  ++++.+.+++.
T Consensus        24 v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~--~~~~~l~~~~~  101 (140)
T 3u3g_D           24 VITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYK--VKEPTLKEKFA  101 (140)
T ss_dssp             EEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSC--CCCGGGHHHHH
T ss_pred             EEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCCcc--cCCHHHHHHHH
Confidence            47788999886 8888889999999999999999999999998    9999999999999999 998  89999999999


Q ss_pred             HHHHH-hhccCC
Q 034727           75 EAKRL-KDKFLS   85 (86)
Q Consensus        75 ~i~~l-~~~f~~   85 (86)
                      ++..+ +++|..
T Consensus       102 ~i~~l~~~~~~~  113 (140)
T 3u3g_D          102 KIAHIKMERVPN  113 (140)
T ss_dssp             HHHHHHHHHCTT
T ss_pred             HHHHHhhcCCCc
Confidence            99999 888754

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

Probab=99.76  E-value=2.6e-18  Score=107.68  Aligned_cols=81  Identities=28%  Similarity=0.279  Sum_probs=73.3

Q ss_pred             CeeCCCCCEEE-eeeccC----CCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHH
Q 034727            1 MLRADDGSLIY-NHNGVG----ITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCG   74 (86)
Q Consensus         1 v~~~~~g~~~~-~~~~~g----~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~   74 (86)
                      ||++ +|..+. .+...|    ..|||.|||.|++.||+.+.++|.+++.+++||++|+++++ .|+  ++++.+++|++
T Consensus        24 vi~~-~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~--~~~~~~~~l~~  100 (149)
T 2ehg_A           24 VIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYK--VKAKRIIPLYE  100 (149)
T ss_dssp             EEEC-SSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSC--CCCTTHHHHHH
T ss_pred             EEEE-CCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccc--cCCHHHHHHHH
Confidence            4677 788876 666666    89999999999999999999999999999999999999999 898  88899999999


Q ss_pred             HHHHHhhccC
Q 034727           75 EAKRLKDKFL   84 (86)
Q Consensus        75 ~i~~l~~~f~   84 (86)
                      ++..++++|+
T Consensus       101 ~i~~l~~~~~  110 (149)
T 2ehg_A          101 KAIELKKKLN  110 (149)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHhcCC
Confidence            9999999873

>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=99.64  E-value=6.4e-16  Score=96.50  Aligned_cols=79  Identities=18%  Similarity=0.228  Sum_probs=58.2

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh--hhhhc----CCChhHHHHHHH
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC--CWLME----DQTPGMAELCGE   75 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~--~~~~~----~k~~~l~~~~~~   75 (86)
                      +++ +|+.+..+.++|.+|||.|||.|++.||+.+.+.+.+ +.+++||++|+++++  .|+.+    +++..|-..+++
T Consensus        27 ~~~-~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~~~~~kt~~~~~vkN~dLw~~ld~  104 (134)
T 4htu_A           27 DTK-TGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDE  104 (134)
T ss_dssp             ETT-TCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHHHTCCCCCCCCSSTTHHHHHHHHH
T ss_pred             EEE-CCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHHcCCcccCCCCCccCHHHHHHHHH
Confidence            444 6777775567889999999999999999999998876 899999999999998  45411    234444444444


Q ss_pred             HHHHhhc
Q 034727           76 AKRLKDK   82 (86)
Q Consensus        76 i~~l~~~   82 (86)
                      +..++..
T Consensus       105 ~~~~l~~  111 (134)
T 4htu_A          105 AEEWLNT  111 (134)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            4454444

>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=99.61  E-value=1.1e-15  Score=96.25  Aligned_cols=77  Identities=14%  Similarity=0.177  Sum_probs=60.7

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhh-hc-CCChhHHHHHHHHHH
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWL-ME-DQTPGMAELCGEAKR   78 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~-~~-~k~~~l~~~~~~i~~   78 (86)
                      |+ ++|+.+..+..++.+|||.|||.|++.||+.+.+.+. ++.|++||++|+++++ .|. .. .+....+.+++.+.+
T Consensus        33 l~-~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~  110 (142)
T 1zbf_A           33 DT-KTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDE  110 (142)
T ss_dssp             ET-TTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHH
T ss_pred             EE-eCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHH
Confidence            44 6788877666678899999999999999999999998 9999999999999999 883 00 112355667766655


Q ss_pred             Hh
Q 034727           79 LK   80 (86)
Q Consensus        79 l~   80 (86)
                      +.
T Consensus       111 ~~  112 (142)
T 1zbf_A          111 AE  112 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=99.35  E-value=3.8e-12  Score=80.10  Aligned_cols=70  Identities=14%  Similarity=0.063  Sum_probs=57.0

Q ss_pred             eecc-CCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh---------hhcCCC---hhHHHHHHHHHHH
Q 034727           13 HNGV-GITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW---------LMEDQT---PGMAELCGEAKRL   79 (86)
Q Consensus        13 ~~~~-g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~---------~~~~k~---~~l~~~~~~i~~l   79 (86)
                      +..+ |..|||.||+.|++.||+.+.+.+.+++.|++||++|+++++.|         +  +.+   ...+.++.++..+
T Consensus        41 ~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~--~~~~~~~~n~~l~~~i~~l  118 (154)
T 2qkb_A           41 GIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWK--TSAGKEVINKEDFVALERL  118 (154)
T ss_dssp             EEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSB--CTTSSBCTTHHHHHHHHHH
T ss_pred             EeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhcccc--ccCCCccccHHHHHHHHHH
Confidence            3444 57999999999999999999999999999999999999999843         2  221   2457889999988


Q ss_pred             hhccC
Q 034727           80 KDKFL   84 (86)
Q Consensus        80 ~~~f~   84 (86)
                      +++|+
T Consensus       119 ~~~~~  123 (154)
T 2qkb_A          119 TQGMD  123 (154)
T ss_dssp             HTTCE
T ss_pred             HcCCc
Confidence            87653

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

Probab=99.33  E-value=1.4e-12  Score=81.35  Aligned_cols=70  Identities=20%  Similarity=0.131  Sum_probs=56.1

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhc----------CCChhHHHHHHHHHHHh
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLME----------DQTPGMAELCGEAKRLK   80 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~----------~k~~~l~~~~~~i~~l~   80 (86)
                      .+..++..|||.||+.|++.||+.+.+  .+++.|++||++|+++++ +|...          -+....+.++.++..++
T Consensus        35 ~~~~~~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~  112 (146)
T 3h08_A           35 ISGYDPATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLT  112 (146)
T ss_dssp             EEEEEEEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHH
T ss_pred             eecCCCCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHH
Confidence            666778899999999999999998876  589999999999999998 57200          01224578899998888


Q ss_pred             hcc
Q 034727           81 DKF   83 (86)
Q Consensus        81 ~~f   83 (86)
                      ++|
T Consensus       113 ~~~  115 (146)
T 3h08_A          113 TLH  115 (146)
T ss_dssp             HHS
T ss_pred             hhC
Confidence            765

>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=99.21  E-value=2.7e-12  Score=80.52  Aligned_cols=60  Identities=13%  Similarity=0.144  Sum_probs=51.9

Q ss_pred             CCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHHh
Q 034727           18 ITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRLK   80 (86)
Q Consensus        18 ~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l~   80 (86)
                      ..|||.||+.|++.||+.+.+.+. ++.|++||+.|.+++. .|+  ++++..+.+.+.++.+.
T Consensus        47 ~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~~~~w~--~~~~~~~~~~~l~~~l~  107 (147)
T 2kq2_A           47 TMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWATGEWK--AKNEFTQAYAKLMNQYR  107 (147)
T ss_dssp             GTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHTTSSSS--CCHHHHHHHHCGGGGGS
T ss_pred             cccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHHhCCCc--cCCcchHHHHHHHHHhc
Confidence            479999999999999999999998 9999999999999999 998  77777777766655543

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

Probab=99.20  E-value=2.2e-11  Score=77.14  Aligned_cols=70  Identities=19%  Similarity=0.256  Sum_probs=52.7

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh----h---hcCC--Ch-hHHHHHHHHHHHhh
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW----L---MEDQ--TP-GMAELCGEAKRLKD   81 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~----~---~~~k--~~-~l~~~~~~i~~l~~   81 (86)
                      .+..++..|||.||+.|++.||+.+.+.  +++.|++||++|+++++.|    +   .++.  .| ..+.++.++..+++
T Consensus        37 ~~~~~~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~  114 (158)
T 2e4l_A           37 MSDGFSLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ  114 (158)
T ss_dssp             EEEEEEEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT
T ss_pred             EecCcCCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc
Confidence            5566678999999999999999987543  8999999999999999853    1   0011  11 34677888888776


Q ss_pred             cc
Q 034727           82 KF   83 (86)
Q Consensus        82 ~f   83 (86)
                      ++
T Consensus       115 ~~  116 (158)
T 2e4l_A          115 LH  116 (158)
T ss_dssp             TS
T ss_pred             cC
Confidence            54

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

Probab=99.16  E-value=2.6e-11  Score=77.41  Aligned_cols=70  Identities=20%  Similarity=0.153  Sum_probs=52.6

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhc-------CCC---hhHHHHHHHHHHHh
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLME-------DQT---PGMAELCGEAKRLK   80 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~-------~k~---~~l~~~~~~i~~l~   80 (86)
                      .+...+..|||.||+.|++.||+.+.+.  .++.|++||++|+++++ .|...       +.+   ...+.++.++..++
T Consensus        39 ~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~  116 (166)
T 1ril_A           39 LSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM  116 (166)
T ss_dssp             ECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH
T ss_pred             EecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHH
Confidence            4444568899999999999999987664  48999999999999999 44200       211   13467888888887


Q ss_pred             hcc
Q 034727           81 DKF   83 (86)
Q Consensus        81 ~~f   83 (86)
                      +++
T Consensus       117 ~~~  119 (166)
T 1ril_A          117 APH  119 (166)
T ss_dssp             TTS
T ss_pred             hcC
Confidence            764

>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=99.14  E-value=3.9e-11  Score=75.66  Aligned_cols=70  Identities=19%  Similarity=0.191  Sum_probs=52.9

Q ss_pred             eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh----hh---cCC--Ch-hHHHHHHHHHHHhh
Q 034727           12 NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW----LM---EDQ--TP-GMAELCGEAKRLKD   81 (86)
Q Consensus        12 ~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~----~~---~~k--~~-~l~~~~~~i~~l~~   81 (86)
                      .+..++..|||.||+.|++.||+.+.+.  .++.|++||++|+++++.|    +.   ++.  .| ..+.++.++..+++
T Consensus        35 ~~~~~~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~  112 (155)
T 1jl1_A           35 FSAGYTRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG  112 (155)
T ss_dssp             EEEEEEEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT
T ss_pred             EecCCCCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc
Confidence            5555678999999999999999988763  8999999999999999853    10   011  12 23678888888776


Q ss_pred             cc
Q 034727           82 KF   83 (86)
Q Consensus        82 ~f   83 (86)
                      ++
T Consensus       113 ~~  114 (155)
T 1jl1_A          113 QH  114 (155)
T ss_dssp             TC
T ss_pred             cC
Confidence            53

>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=99.14  E-value=7e-11  Score=74.45  Aligned_cols=65  Identities=18%  Similarity=0.192  Sum_probs=47.2

Q ss_pred             cCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh---------hhcCCC-hhHHHHHHHHHHHhhccC
Q 034727           16 VGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW---------LMEDQT-PGMAELCGEAKRLKDKFL   84 (86)
Q Consensus        16 ~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~---------~~~~k~-~~l~~~~~~i~~l~~~f~   84 (86)
                      ++.+|||.||+.|++.||+.+   + .++.|++||++|+++++.|         +..... ...++++.++..++.++.
T Consensus        44 ~~~~Tnn~aEl~A~i~AL~~~---~-~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~  118 (150)
T 3qio_A           44 LTDTTNQKTELQAIYLALQDS---G-LEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKE  118 (150)
T ss_dssp             ESSCCHHHHHHHHHHHHHHHS---C-SEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCS
T ss_pred             CCCCCHHHHHHHHHHHHHHhC---C-CcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcC
Confidence            578999999999999999874   3 8999999999999999844         100111 144678888776555543

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

Probab=99.13  E-value=4.2e-10  Score=72.05  Aligned_cols=77  Identities=14%  Similarity=-0.055  Sum_probs=55.9

Q ss_pred             CCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhh----h-----hcCCCh-hHHHHHHH
Q 034727            7 GSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCW----L-----MEDQTP-GMAELCGE   75 (86)
Q Consensus         7 g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~----~-----~~~k~~-~l~~~~~~   75 (86)
                      .+... .....+..||+.||+.||..+|+.+++.+ .+|.|+|||++|+++++.|    +     ...+.| ..+.|+.+
T Consensus        41 ~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~  119 (165)
T 2lsn_A           41 YQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKS  119 (165)
T ss_dssp             CCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHH
T ss_pred             cEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHH
Confidence            33344 55566789999999999999999998877 4799999999999999743    2     001112 34678888


Q ss_pred             HHHHhhccC
Q 034727           76 AKRLKDKFL   84 (86)
Q Consensus        76 i~~l~~~f~   84 (86)
                      +..+++.+.
T Consensus       120 l~~~~~~~~  128 (165)
T 2lsn_A          120 IAECLSMKP  128 (165)
T ss_dssp             HHHHHHHCT
T ss_pred             HHHHHhCCC
Confidence            887776553

>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=99.08  E-value=3.7e-10  Score=72.28  Aligned_cols=49  Identities=20%  Similarity=0.132  Sum_probs=41.2

Q ss_pred             CCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHH
Q 034727            6 DGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV   57 (86)
Q Consensus         6 ~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~   57 (86)
                      +|+.+..+...+.+|||.||+.|++.||+.+   ...++.|++||++|++.+
T Consensus        48 ~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~i   96 (165)
T 3p1g_A           48 ETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATA   96 (165)
T ss_dssp             SSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHH
T ss_pred             CCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhh
Confidence            5565554444568899999999999999988   368999999999999988

>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=98.87  E-value=1.7e-09  Score=79.53  Aligned_cols=60  Identities=17%  Similarity=0.057  Sum_probs=46.7

Q ss_pred             ccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhhhcCCChhHHHHHHHHHHHhhc
Q 034727           15 GVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWLMEDQTPGMAELCGEAKRLKDK   82 (86)
Q Consensus        15 ~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~~~~k~~~l~~~~~~i~~l~~~   82 (86)
                      ..+.+|||.|||.|++.||+.    +..++.|+|||++|+++++.|.  +.  ..+++++++..++.+
T Consensus       467 ~~~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~--~~--~~~~l~~~~~~~~~~  526 (555)
T 1mu2_A          467 KLEQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQP--TE--SESKIVNQIIEEMIK  526 (555)
T ss_dssp             EESSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCC--SE--ESCHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhccc--cc--ccHHHHHHHHHHhcc
Confidence            456899999999999999986    6789999999999999999774  22  224555566555443

>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=98.83  E-value=2e-09  Score=79.28  Aligned_cols=42  Identities=17%  Similarity=0.109  Sum_probs=38.4

Q ss_pred             cCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHhhhh
Q 034727           16 VGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWL   61 (86)
Q Consensus        16 ~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~~~~   61 (86)
                      .+.+|||.|||.|++.||+.+    .+++.|+|||++|+++++.|.
T Consensus       471 ~~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~  512 (557)
T 2zd1_A          471 LTNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQP  512 (557)
T ss_dssp             ECSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCC
Confidence            468999999999999999987    589999999999999999665

>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural genomics, center for structural GEN infectious diseases; HET: FFT; 2.46A {Campylobacter jejuni} SCOP: c.101.1.0

Probab=85.44  E-value=0.88  Score=30.19  Aligned_cols=49  Identities=6%  Similarity=0.003  Sum_probs=30.9

Q ss_pred             CeeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecch
Q 034727            1 MLRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDS   50 (86)
Q Consensus         1 v~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS   50 (86)
                      +|.|.||++-. ...++....+.+...++..-++.|.++|++.+++|.=|
T Consensus        12 iIMDGNrRwAk-~rgl~r~~GH~~G~~~~~~i~~~c~~lGI~~lTlYaFS   60 (225)
T 3ugs_B           12 VVMDGNRRWAR-AKGFLAKLGYSQGVKTMQKLMEVCMEENISNLSLFAFS   60 (225)
T ss_dssp             EEECCCC---------------CHHHHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             EeccCcHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEEc
Confidence            36677777643 34566778899999999999999999999999999876

>3tue_A Tryparedoxin peroxidase; thioredoxin fold, peroxiredoxin, oxidoreductase; 3.00A {Leishmania major} PDB: 1e2y_A

Probab=84.84  E-value=2.1  Score=28.05  Aligned_cols=39  Identities=13%  Similarity=0.080  Sum_probs=30.1

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKG   40 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~   40 (86)
                      |+||+|.+.....+--....|..|..-.+++|+...++|
T Consensus       152 iIDp~g~Ir~~~~~~~~~gr~~~EvLr~l~aLQ~~~~~~  190 (219)
T 3tue_A          152 IIDPHGMLRQITVNDMPVGRSVEEVLRLLEAFQFVEKHG  190 (219)
T ss_dssp             EECTTSBEEEEEEECTTCCCCHHHHHHHHHHHHHHHHC-
T ss_pred             EECCCCeEEEEEEecCCCCCCHHHHHHHHHHhhhHHhcC
Confidence            789999988744333355568999999999999998876

>3sbc_A Peroxiredoxin TSA1; alpha-beta fold, peroxidase, cytosol, oxidoreductase; 2.80A {Saccharomyces cerevisiae}

Probab=84.13  E-value=2.4  Score=27.72  Aligned_cols=40  Identities=13%  Similarity=0.040  Sum_probs=30.2

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGF   41 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~   41 (86)
                      |.||+|.+.+...+--...-|..|...++++|+...++|.
T Consensus       148 iID~~G~Ir~~~v~~~~~grn~dEiLr~l~AlQ~~~~~~~  187 (216)
T 3sbc_A          148 IIDPKGVIRHITINDLPVGRNVDEALRLVEAFQWTDKNGT  187 (216)
T ss_dssp             EECTTSBEEEEEEECTTBCCCHHHHHHHHHHHHHHHHHCC
T ss_pred             EECCCCeEEEEEEcCCCCCCCHHHHHHHHHHhhhHhhcCC
Confidence            7899998887333322345589999999999999888763

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	86
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	0.004

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

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]

 Score = 31.5 bits (71), Expect = 0.004
 Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 4/45 (8%)

Query: 17 GITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCCWL 61
            TTN   +  ++ L    ALQ       +  DS+     +    
Sbjct: 41 TDTTNQKTELQAIYL----ALQDSGLEVNIVTDSQYALGIIQAQP 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	86
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.52
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.26
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	98.84
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	98.35
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.1
d1xcca_	219	1-Cys peroxiredoxin {Plasmodium yoelii yoelii [Tax	89.25
d1zofa1	170	Thioredoxin reductase TsaA {Helicobacter pylori [T	88.41
d1e2ya_	167	Tryparedoxin peroxidase (thioredoxin peroxidase ho	87.85
d1prxa_	220	1-Cys peroxiredoxin {Human (Homo sapiens) [TaxId:	87.56
d1uula_	194	Tryparedoxin peroxidase (thioredoxin peroxidase ho	86.69
d2zcta1	237	Peroxiredoxin {Aeropyrum pernix [TaxId: 56636]}	85.67
d1zyea1	158	Peroxiredoxin-3 (AOP-1, SP-22) {Cow (Bos taurus) [	81.39
d2h01a1	170	Thioredoxin peroxidase 2 (thioredoxin peroxidase B	80.22

>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=99.52  E-value=1.9e-14  Score=88.07  Aligned_cols=73  Identities=15%  Similarity=0.201  Sum_probs=55.2

Q ss_pred             CCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh--hhhhc-CCChhHHHHHHHHHH
Q 034727            5 DDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC--CWLME-DQTPGMAELCGEAKR   78 (86)
Q Consensus         5 ~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~--~~~~~-~k~~~l~~~~~~i~~   78 (86)
                      .+|..+..+.++|.+|||.|||.|++.||+.+.+.+ .++.|+|||++|+++++  .|+.. .+.+..+.+++.+.+
T Consensus        28 ~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~  103 (132)
T d1zbfa1          28 KTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDE  103 (132)
T ss_dssp             TTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHH
T ss_pred             cCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHH
Confidence            466666677788999999999999999999998877 57999999999999998  33210 112344555555543

>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=99.26  E-value=2.9e-12  Score=75.84  Aligned_cols=62  Identities=16%  Similarity=0.013  Sum_probs=46.6

Q ss_pred             eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhcCCChhHHHHHHHHHHHhhccC
Q 034727           14 NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLMEDQTPGMAELCGEAKRLKDKFL   84 (86)
Q Consensus        14 ~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~~k~~~l~~~~~~i~~l~~~f~   84 (86)
                      ..++.+|||.||+.|++.||+    .+.+++.|++||++|+++++ .+.  ..   .++++.++...+.+++
T Consensus        38 ~~~~~~TNn~aEl~Avi~aL~----~~~~~v~I~TDS~yvi~~i~~~~~--~~---~~~l~~~il~~l~~~~  100 (110)
T d1s1ta1          38 VTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPD--QS---ESELVNQIIEQLIKKE  100 (110)
T ss_dssp             EEESSCCHHHHHHHHHHHHHH----HSCSEEEEEECCHHHHHHHHHCCS--EE---SCHHHHHHHHHHHHCS
T ss_pred             EecccCcHHHHHHHHHHHHHH----hCCCeEEEEEehHHHHHHHhcCcc--cc---chHHHHHHHHHHhcCC
Confidence            345678999999999999986    46688999999999999999 553  22   2445666666555543

>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=98.84  E-value=4.2e-09  Score=62.62  Aligned_cols=44  Identities=20%  Similarity=0.079  Sum_probs=37.6

Q ss_pred             eccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhh
Q 034727           14 NGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWL   61 (86)
Q Consensus        14 ~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~   61 (86)
                      ..++..|||.||+.|++.+|+    ...+.+.|++||++|+++++ .|.
T Consensus        37 ~~~~~~tnn~AEl~Ai~~al~----~~~~~i~I~tDS~~v~~~~~~~~~   81 (126)
T d1mu2a1          37 KKLEQTTNQQAELEAFAMALT----DSGPKVNIIVDSQYVMGIVASQPT   81 (126)
T ss_dssp             EEESSCCHHHHHHHHHHHHHH----TSCSEEEEEESCHHHHHHHHTCCS
T ss_pred             EecCCCcchHHHHHHHHHHhc----cCCcceEEEechHHHHHHHhcCCc
Confidence            345678999999999999886    45689999999999999999 664

>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=98.35  E-value=3.7e-07  Score=54.95  Aligned_cols=69  Identities=22%  Similarity=0.188  Sum_probs=47.5

Q ss_pred             eeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhhhc-------CC--Ch-hHHHHHHHHHHHhh
Q 034727           13 HNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWLME-------DQ--TP-GMAELCGEAKRLKD   81 (86)
Q Consensus        13 ~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~~~-------~k--~~-~l~~~~~~i~~l~~   81 (86)
                      +...+..|||.||+.|++.||+.+.  ....+.+++||+++++.++ .|...       ..  .| ....++.++..+.+
T Consensus        35 ~~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~  112 (147)
T d1rila_          35 SGGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA  112 (147)
T ss_dssp             CCEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT
T ss_pred             ecccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhh
Confidence            3344567999999999999997543  4568999999999999886 43200       00  11 23567777777665


Q ss_pred             cc
Q 034727           82 KF   83 (86)
Q Consensus        82 ~f   83 (86)
                      ++
T Consensus       113 ~~  114 (147)
T d1rila_         113 PH  114 (147)
T ss_dssp             TS
T ss_pred             hc
Confidence            53

>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=98.10  E-value=3.6e-06  Score=50.31  Aligned_cols=74  Identities=16%  Similarity=0.066  Sum_probs=49.8

Q ss_pred             CCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHh-hhh---h---cC---CChhHHHHHHHH
Q 034727            7 GSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVC-CWL---M---ED---QTPGMAELCGEA   76 (86)
Q Consensus         7 g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~~~v~i~~DS~lvi~q~~-~~~---~---~~---k~~~l~~~~~~i   76 (86)
                      |....++...+..|||.||+.|++.|++.+.  ....+.+++||++++..++ .+.   .   +.   +......++.++
T Consensus        28 ~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i  105 (152)
T d1jl1a_          28 GREKTFSAGYTRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRL  105 (152)
T ss_dssp             TEEEEEEEEEEEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHH
T ss_pred             CeEEEeccccCcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHH
Confidence            3334456667789999999999999987543  3567899999999999876 221   0   01   111335567777


Q ss_pred             HHHhhc
Q 034727           77 KRLKDK   82 (86)
Q Consensus        77 ~~l~~~   82 (86)
                      ..+.++
T Consensus       106 ~~~~~~  111 (152)
T d1jl1a_         106 DAALGQ  111 (152)
T ss_dssp             HHHTTT
T ss_pred             HHHhhc
Confidence            666554

>d1xcca_ c.47.1.10 (A:) 1-Cys peroxiredoxin {Plasmodium yoelii yoelii [TaxId: 73239]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: 1-Cys peroxiredoxin
species: Plasmodium yoelii yoelii [TaxId: 73239]

Probab=89.25  E-value=0.35  Score=30.16  Aligned_cols=40  Identities=8%  Similarity=-0.013  Sum_probs=32.2

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKGF   41 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~   41 (86)
                      |.||+|.+.+...+-.....|..|...++++|+++.++|.
T Consensus       132 iIDp~g~Ir~~~~~~~~~gr~~~EiLr~l~aLQ~~~~~~~  171 (219)
T d1xcca_         132 FISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPV  171 (219)
T ss_dssp             EECTTSBEEEEEEECTTBCCCHHHHHHHHHHHHHHHHSSE
T ss_pred             EEcCcceEEEEEEeCCCcccCHHHHHHHHHHHHHHHhCCC
Confidence            7899999987444444556699999999999999998763

>d1zofa1 c.47.1.10 (A:1-170) Thioredoxin reductase TsaA {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thioredoxin reductase TsaA
species: Helicobacter pylori [TaxId: 210]

Probab=88.41  E-value=0.47  Score=27.98  Aligned_cols=39  Identities=13%  Similarity=-0.028  Sum_probs=30.2

Q ss_pred             eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727            2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGF   41 (86)
Q Consensus         2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~   41 (86)
                      |.|++|.+.. ..... ....|..|...++++|+.+.++|.
T Consensus       128 vID~~G~I~~~~~~~~-~~~~~~~eiL~~l~aLq~~~~~~~  167 (170)
T d1zofa1         128 LIDKNMKVRHAVINDL-PLGRNADEMLRMVDALLHFEEHGE  167 (170)
T ss_dssp             EEETTTEEEEEEEESS-SCCCHHHHHHHHHHHHHHHHSSCC
T ss_pred             EEcCCCeEEEEEEeCC-CCCCCHHHHHHHHHHhhhHHhcCC
Confidence            6889999987 43333 345689999999999999988763

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

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

Probab=87.85  E-value=0.63  Score=27.00  Aligned_cols=38  Identities=21%  Similarity=0.255  Sum_probs=28.6

Q ss_pred             eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727            2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKG   40 (86)
Q Consensus         2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~   40 (86)
                      |.|++|.+.+ ..... ....|..|....+.+|+...++|
T Consensus       129 vID~~G~Ir~~~~~~~-~~~~~~~evL~~l~alq~~~~~g  167 (167)
T d1e2ya_         129 IIDPNGKLRQIIINDM-PIGRNVEEVIRLVEALQFVEEHG  167 (167)
T ss_dssp             EECTTSBEEEEEEECT-TBCCCHHHHHHHHHHHHHHHHCC
T ss_pred             EECCCCEEEEEEEcCC-CCCCCHHHHHHHHHHHhHHHhcC
Confidence            7899999987 33333 23447899999999999987765

>d1prxa_ c.47.1.10 (A:) 1-Cys peroxiredoxin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: 1-Cys peroxiredoxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.56  E-value=0.56  Score=29.09  Aligned_cols=39  Identities=15%  Similarity=0.104  Sum_probs=31.4

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKG   40 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~   40 (86)
                      |+|++|.+.+...+-.....|..|...++++|+.+.+.|
T Consensus       132 IID~~g~Ir~~~~~~~~~gR~~dEiLr~l~alq~~~~~~  170 (220)
T d1prxa_         132 VFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKR  170 (220)
T ss_dssp             EECTTSBEEEEEECCTTBCCCHHHHHHHHHHHHHHHHHC
T ss_pred             EEcCccceeEEEEecCCcccchHHHHHHHHHHhhhhcCC
Confidence            789999998744444455669999999999999988765

>d1uula_ c.47.1.10 (A:) Tryparedoxin peroxidase (thioredoxin peroxidase homologue) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Tryparedoxin peroxidase (thioredoxin peroxidase homologue)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=86.69  E-value=0.71  Score=27.96  Aligned_cols=39  Identities=10%  Similarity=0.036  Sum_probs=31.2

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKG   40 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~   40 (86)
                      |.|++|.+......--....|..|...++.+|+...+.|
T Consensus       129 vID~~G~I~~~~~~~~~~~r~~~E~Lr~l~alQ~~~~~~  167 (194)
T d1uula_         129 IIDPKQNLRQITVNDLPVGRDVDEALRLVKAFQFVEKHG  167 (194)
T ss_dssp             EECTTSBEEEEEEECTTBCCCHHHHHHHHHHHHHHHHHS
T ss_pred             EECCCCeEEEEEEecCCCCcCHHHHHHHHHHhhhHhhcC
Confidence            689999998844443456679999999999999987765

>d2zcta1 c.47.1.10 (A:6-242) Peroxiredoxin {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Peroxiredoxin
species: Aeropyrum pernix [TaxId: 56636]

Probab=85.67  E-value=0.83  Score=28.69  Aligned_cols=39  Identities=10%  Similarity=-0.028  Sum_probs=29.9

Q ss_pred             eeCCCCCEEE-eeeccCCCcchHHHHHHHHHHHHHHHhcCC
Q 034727            2 LRADDGSLIY-NHNGVGITTNNVAKYGSLILGLKYALQKGF   41 (86)
Q Consensus         2 ~~~~~g~~~~-~~~~~g~~tnn~aEy~Ali~gL~~a~~~~~   41 (86)
                      |.|++|.+.+ .....+. ..|..|...++++|+++..+|+
T Consensus       125 IIDpdG~Ir~~~~~~~~~-gR~~dEiLr~l~aLQ~~~~~~~  164 (237)
T d2zcta1         125 IVDARGVIRTMLYYPMEL-GRLVDEILRIVKALKLGDSLKR  164 (237)
T ss_dssp             EECTTSBEEEEEECCTTB-CCCHHHHHHHHHHHHHHHHHTC
T ss_pred             EECCCCEEEEEEEeCCCC-CCCHHHHHHHHHHHhhhccCCc
Confidence            7899999877 4444433 3378999999999999888764

>d1zyea1 c.47.1.10 (A:6-163) Peroxiredoxin-3 (AOP-1, SP-22) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Peroxiredoxin-3 (AOP-1, SP-22)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=81.39  E-value=1.4  Score=25.40  Aligned_cols=34  Identities=9%  Similarity=0.033  Sum_probs=25.2

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHH
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKY   35 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~   35 (86)
                      |.|++|.+.+....-.....|..|...++++|+.
T Consensus       122 vID~~G~I~~~~i~~~~~~~~~~EiL~~lkalq~  155 (158)
T d1zyea1         122 IIDPNGVIKHLSVNDLPVGRSVEETLRLVKAFQF  155 (158)
T ss_dssp             EECTTSBEEEEEEECTTCCCCHHHHHHHHHHHHH
T ss_pred             EECCCCEEEEEEEeCCCCCCCHHHHHHHHHHhhh
Confidence            6899999987433333455689999999998875

>d2h01a1 c.47.1.10 (A:2-171) Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin) {Plasmodium yoelii [TaxId: 5861]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thioredoxin peroxidase 2 (thioredoxin peroxidase B, 2-cys peroxiredoxin)
species: Plasmodium yoelii [TaxId: 5861]

Probab=80.22  E-value=2.5  Score=24.57  Aligned_cols=39  Identities=18%  Similarity=0.002  Sum_probs=29.4

Q ss_pred             eeCCCCCEEEeeeccCCCcchHHHHHHHHHHHHHHHhcC
Q 034727            2 LRADDGSLIYNHNGVGITTNNVAKYGSLILGLKYALQKG   40 (86)
Q Consensus         2 ~~~~~g~~~~~~~~~g~~tnn~aEy~Ali~gL~~a~~~~   40 (86)
                      |+|++|.+.......-....|..|....+.+|+...+++
T Consensus       122 iId~~G~I~~~~~~~~~~~~~~~eil~~l~~lq~~~~~~  160 (170)
T d2h01a1         122 LIDKQGVVQHLLVNNLALGRSVDEILRLIDALQHHEKYG  160 (170)
T ss_dssp             EECTTSBEEEEEEGGGSSGGGHHHHHHHHHHHHHHHHHC
T ss_pred             EEcCCCeEEEEEEecCCCCCCHHHHHHHHHHhhhhhhcC
Confidence            678999887733333345568999999999999877765