Psyllid ID: psy8593

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200----
Protein Sequence
MRKSKPILRYDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILNDEDL
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHccccHHHHccccccHHHHHHHHHHHHHHHHcccccccEEEEEEccccHHHHccHHHHHHHHHHHHHHHHccccccccccEEEEcccHHHHHHHcccccccHHHHHHHHHHHHccccEEEEEEcccccccccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEHcHEEEEEEEEccccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHEcccEEEEEcccccHHHHHccccccccHHHHHHHHHHHHHccEEEEEccccHHHHHHHHHHHHHHHcccccccccccccEEEEEEEccccccHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mrkskpilryDQFLIAKISTirntqsaetagekcsALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGhafstslaiprdelagfrsEATEFCYYVyghrnivvqtdhqpllainKKDLYKIQNNRLKRLKIklfpyqfelkylpgkyMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFeinfspekFQWFQQEILNDEDL
Flexible Loop (DISEMBL)
mrkskpilryDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILNDEDL
Low Complexity Region (SEG)
MRKSKPILRYDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILNDEDL
Disordered region (IsUnstruct)
******ILRYDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEI******
Disordered Region (DISOPRED)
******I**YDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLS***************DMVHTVNKFEINFSPEKFQWFQQEILND**L
Disordered Region (DISEMBL)
MRKSKPILRYDQFLIAKISTIR***********CSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILNDEDL
Disordered Region (DISPRO)
***SKPILRYDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILN****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRKSKPILRYDQFLIAKISTIRNTQSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILNDEDL
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	204
270003428	902	hypothetical protein TcasGA2_TC002657 [T	0.426	0.096	0.423	3e-11
391329414	1128	PREDICTED: uncharacterized protein LOC10	0.504	0.091	0.371	5e-10
391331501	1388	PREDICTED: uncharacterized protein K02A2	0.348	0.051	0.407	9e-07
391329000	1505	PREDICTED: uncharacterized protein LOC10	0.401	0.054	0.372	1e-06
291227763	1275	PREDICTED: RETRotransposon-like family m	0.490	0.078	0.357	8e-06
291227761	1273	PREDICTED: RETRotransposon-like family m	0.490	0.078	0.357	8e-06
391332295	574	PREDICTED: uncharacterized protein K02A2	0.450	0.160	0.339	3e-05
391333640	1202	PREDICTED: uncharacterized protein K02A2	0.450	0.076	0.339	3e-05
291230804	1215	PREDICTED: polyprotein-like, partial [Sa	0.387	0.065	0.380	4e-05
328701306	430	PREDICTED: hypothetical protein LOC10057	0.299	0.141	0.437	5e-05

>gi|270003428|gb|EEZ99875.1| hypothetical protein TcasGA2_TC002657 [Tribolium castaneum]

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 39/92 (42%), Positives = 65/92 (70%), Gaps = 5/92 (5%)

Query: 90  EFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMH 149
           +F YY+YG R++ VQTDH+PLLAI +K++ +    RL+R+ ++   Y F L+++ GK+M+
Sbjct: 438 KFHYYIYG-RHVTVQTDHKPLLAITRKNIGQT-TARLQRMLLRTLKYDFHLEFIQGKHMY 495

Query: 150 IAELADYLSRNLLVKNVQEDILMKDMVHTVNK 181
              LAD LSRN L   V++D  ++ +VH+++K
Sbjct: 496 ---LADTLSRNFLKDRVKDDEDLESVVHSISK 524

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391329414|ref|XP_003739169.1| PREDICTED: uncharacterized protein LOC100909341 [Metaseiulus occidentalis]

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 42/113 (37%), Positives = 70/113 (61%), Gaps = 10/113 (8%)

Query: 91  FCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHI 150
           F YYVYG  +++V+TDH+PL  I KK L++I   RL+++++ L  Y  ++ Y PG+ +HI
Sbjct: 691 FHYYVYGRSDVLVETDHRPLEQIFKKPLHQIP-LRLQQMRLSLQRYDIKVTYRPGRELHI 749

Query: 151 AELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILNDED 203
              AD+LSRN L    +E ++ K  + T+    I  + ++ Q +Q+E   DE+
Sbjct: 750 ---ADFLSRNPL----EEALVYKPRLSTIR--HIAIADQRLQEYQKETNQDEE 793

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391331501|ref|XP_003740183.1| PREDICTED: uncharacterized protein K02A2.6-like [Metaseiulus occidentalis]

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 51/76 (67%), Gaps = 5/76 (6%)

Query: 91  FCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMHI 150
           F +++ G + + ++TDH PL+AI KK+L  + + RL+++ ++L  + F+L+Y+PGKYM I
Sbjct: 803 FKFFIQGQQ-VTIETDHHPLIAIVKKEL-ALLSPRLQKMMLRLLRFDFKLQYIPGKYMFI 860

Query: 151 AELADYLSRNLLVKNV 166
              AD LSR  L K  
Sbjct: 861 ---ADALSRKPLAKTT 873

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391329000|ref|XP_003738967.1| PREDICTED: uncharacterized protein LOC100901668 [Metaseiulus occidentalis]

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 52/86 (60%), Gaps = 4/86 (4%)

Query: 75  AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLF 134
           A+   EL        +F + ++ H N+ ++TDHQPL+++ KK L+     RL+R+ + L 
Sbjct: 478 AVIEKELLAILVACKKFEHQIFAHPNVTIETDHQPLISVFKKPLHTTP-KRLQRMLLYLQ 536

Query: 135 PYQFELKYLPGKYMHIAELADYLSRN 160
            Y FEL+Y+ GK+  I   AD+LSR+
Sbjct: 537 KYNFELRYVKGKHNCI---ADWLSRD 559

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291227763|ref|XP_002733852.1| PREDICTED: RETRotransposon-like family member (retr-1)-like [Saccoglossus kowalevskii]

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 40/112 (35%), Positives = 61/112 (54%), Gaps = 12/112 (10%)

Query: 75  AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLF 134
           A+   EL        +F  Y+YG + + ++TDH+PLLAI  K ++K+ + RL+R++++L 
Sbjct: 777 AVIEKELLAICFGCAKFHNYIYG-KQVQIETDHKPLLAIMTKPIHKL-SARLQRMRMRLQ 834

Query: 135 PYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINF 186
            Y   L + PGK M    LAD LSR  +  N   D L  D +      E+NF
Sbjct: 835 CYDLSLVHRPGKEMF---LADTLSRAFIRDNSTAD-LFDDTI------EVNF 876

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|291227761|ref|XP_002733851.1| PREDICTED: RETRotransposon-like family member (retr-1)-like [Saccoglossus kowalevskii]

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 40/112 (35%), Positives = 61/112 (54%), Gaps = 12/112 (10%)

Query: 75  AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLF 134
           A+   EL        +F  Y+YG + + ++TDH+PLLAI  K ++K+ + RL+R++++L 
Sbjct: 775 AVIEKELLAICFGCAKFHNYIYG-KQVQIETDHKPLLAIMTKPIHKL-SARLQRMRMRLQ 832

Query: 135 PYQFELKYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINF 186
            Y   L + PGK M    LAD LSR  +  N   D L  D +      E+NF
Sbjct: 833 CYDLSLVHRPGKEMF---LADTLSRAFIRDNSTAD-LFDDTI------EVNF 874

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|391332295|ref|XP_003740571.1| PREDICTED: uncharacterized protein K02A2.6-like, partial [Metaseiulus occidentalis]

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 59/103 (57%), Gaps = 11/103 (10%)

Query: 75  AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLF 134
           A+   EL        +F  Y+  H++I +QTDHQPL+ I K+ LY     RL+R+ +KL 
Sbjct: 152 AVIEKELLAIVIACQKFEQYLIHHQDITIQTDHQPLIPIFKRPLYDAP-KRLQRMLLKLQ 210

Query: 135 PYQFELKYLPGKYMHIAELADYLSRNLLVK-------NVQEDI 170
            +  +++++ GK   +  +AD+LSR+L +K       +VQE +
Sbjct: 211 KFHLKVEHISGK---LNCVADWLSRDLSIKPRSGPKTDVQEQV 250

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391333640|ref|XP_003741220.1| PREDICTED: uncharacterized protein K02A2.6-like [Metaseiulus occidentalis]

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 59/103 (57%), Gaps = 11/103 (10%)

Query: 75  AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLF 134
           A+   EL        +F  Y+  H++I +QTDHQPL+ I K+ LY     RL+R+ +KL 
Sbjct: 792 AVIEKELLAIVIACQKFEQYLIHHQDITIQTDHQPLIPIFKRPLYDAP-KRLQRMLLKLQ 850

Query: 135 PYQFELKYLPGKYMHIAELADYLSRNLLVK-------NVQEDI 170
            +  +++++ GK   +  +AD+LSR+L +K       +VQE +
Sbjct: 851 KFHLKVEHISGK---LNCVADWLSRDLSIKPRSGPKTDVQEQV 890

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291230804|ref|XP_002735355.1| PREDICTED: polyprotein-like, partial [Saccoglossus kowalevskii]

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 51/84 (60%), Gaps = 5/84 (5%)

Query: 80  ELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFE 139
           E++      + F  Y++G + IV +TDH+PL+ I KK L+K+ + RL+R+++ L  Y  E
Sbjct: 745 EMSAILFGCSRFHDYIFGAKTIV-ETDHKPLVGIFKKPLHKL-SPRLQRMRMTLLRYDLE 802

Query: 140 LKYLPGKYMHIAELADYLSRNLLV 163
           + Y PGK M +    D LSR  L+
Sbjct: 803 VIYKPGKDMFV---PDMLSRAPLM 823

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|328701306|ref|XP_003241558.1| PREDICTED: hypothetical protein LOC100571516 [Acyrthosiphon pisum]

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 41/64 (64%), Gaps = 3/64 (4%)

Query: 141 KYLPGKYMHIAELADYLSRNLLVKNVQEDILMKDMVHTVNKFEINFSPEKFQWFQQEILN 200
           +YLPGKYM++A   D+LSRN + +  + + +M D+VHT+ + EI F   K   F+   LN
Sbjct: 101 QYLPGKYMYVA---DFLSRNYIKREEKSEEIMNDIVHTLGELEIKFENNKETEFRLATLN 157

Query: 201 DEDL 204
           DE L
Sbjct: 158 DEVL 161

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

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)

No hits with e-value below 0.001 by BLAST

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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 EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	204
cd09274	121	cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNas	1e-14

>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNase HI in long-term repeat retroelements

 Score = 67.1 bits (165), Expect = 1e-14
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 90  EFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFELKYLPGKYMH 149
           +F +Y+ G +   V TDH+ L  +  K   K  N RL R  + L  + FE++Y PGK   
Sbjct: 56  KFRHYLLGRK-FTVYTDHKSLKYLLTK---KDLNPRLARWLLLLQEFDFEIEYRPGKENV 111

Query: 150 IAELADYLSRN 160
           +   AD LSR 
Sbjct: 112 V---ADALSRL 119

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. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 121

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	204
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.17
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.65
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	95.93
PRK13907	128	rnhA ribonuclease H; Provisional	95.92
PRK07708	219	hypothetical protein; Validated	93.82
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	92.32
PRK06548	161	ribonuclease H; Provisional	91.6
PRK00203	150	rnhA ribonuclease H; Reviewed	91.12
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	90.94
PRK08719	147	ribonuclease H; Reviewed	82.96

>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=98.17  E-value=3e-06  Score=61.95  Aligned_cols=84  Identities=18%  Similarity=0.122  Sum_probs=65.0

Q ss_pred             hcCChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhcccc---ccchhHHHHHHHHh-cCCceEEEeeCC--
Q psy8593          72 TSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLY---KIQNNRLKRLKIKL-FPYQFELKYLPG--  145 (204)
Q Consensus        72 ~~Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~---k~~~~Rl~RW~~~L-~~yd~~I~y~~G--  145 (204)
                      ..++..+.|+.|+++|++... ...+ .++.|+||++.+...+++...   ......+..+...+ ...++.|.|++|  
T Consensus        37 ~~~s~~~aEl~al~~al~~~~-~~~~-~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~  114 (130)
T cd06222          37 GNTTNNRAELLALIEALELAL-ELGG-KKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHS  114 (130)
T ss_pred             CCCcHHHHHHHHHHHHHHHHH-hCCC-ceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCC
Confidence            468889999999999999976 4555 899999999999988875321   22223344444555 667899999999  


Q ss_pred             --CccccCCCCCccccc
Q psy8593         146 --KYMHIAELADYLSRN  160 (204)
Q Consensus       146 --k~n~vA~~~DaLSR~  160 (204)
                        ..|..|   |.|+|.
T Consensus       115 ~~~~n~~a---d~la~~  128 (130)
T cd06222         115 GIEGNERA---DALAKE  128 (130)
T ss_pred             CCcchHHH---HHHHHh
Confidence              999999   999874

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

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

Probab=97.65  E-value=6.2e-05  Score=53.20  Aligned_cols=79  Identities=15%  Similarity=0.155  Sum_probs=57.1

Q ss_pred             hHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccc--cccchhHHHHHHHHhcCC-ceEEEeeCCCccccCCC
Q psy8593          77 PRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDL--YKIQNNRLKRLKIKLFPY-QFELKYLPGKYMHIAEL  153 (204)
Q Consensus        77 ~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~--~k~~~~Rl~RW~~~L~~y-d~~I~y~~Gk~n~vA~~  153 (204)
                      .+-|++|+.+|++.-...  |.+++++.||++.+...+++..  .......+..+...+..| ++.+.|++...|..|  
T Consensus         2 ~~aE~~al~~al~~a~~~--g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A--   77 (87)
T PF13456_consen    2 LEAEALALLEALQLAWEL--GIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVA--   77 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCC--T-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHH--
T ss_pred             cHHHHHHHHHHHHHHHHC--CCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHH--
Confidence            578999999999997543  4368999999999998886431  123334455566667776 489999999999999  


Q ss_pred             CCccccc
Q psy8593         154 ADYLSRN  160 (204)
Q Consensus       154 ~DaLSR~  160 (204)
                       |.|+|.
T Consensus        78 -~~LA~~   83 (87)
T PF13456_consen   78 -DALAKF   83 (87)
T ss_dssp             -HHHHHH
T ss_pred             -HHHHHH
Confidence             999874

>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=95.93  E-value=0.0079  Score=45.73  Aligned_cols=79  Identities=22%  Similarity=0.256  Sum_probs=51.5

Q ss_pred             cCChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhc-----cccccchh-HHHH--HHHHhcCCceEEEeeC
Q psy8593          73 SLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKK-----DLYKIQNN-RLKR--LKIKLFPYQFELKYLP  144 (204)
Q Consensus        73 ~Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k-----~~~k~~~~-Rl~R--W~~~L~~yd~~I~y~~  144 (204)
                      ..+..+-|+.||+.||+.+    .. .+++|+||.+.+...+++     ........ .+..  |......-.+.|+|+|
T Consensus        37 ~~s~~~aEl~Ai~~AL~~~----~~-~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~  111 (132)
T PF00075_consen   37 GQSNNRAELQAIIEALKAL----EH-RKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVP  111 (132)
T ss_dssp             SECHHHHHHHHHHHHHHTH----ST-SEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESS
T ss_pred             ccchhhhheehHHHHHHHh----hc-ccccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeecc
Confidence            5677899999999999954    34 789999999999774432     11111112 1222  2222455679999999


Q ss_pred             CCccc-----cCCCCCcccc
Q psy8593         145 GKYMH-----IAELADYLSR  159 (204)
Q Consensus       145 Gk~n~-----vA~~~DaLSR  159 (204)
                      |..+.     .|   |-|.|
T Consensus       112 ~H~~~~~~N~~a---D~lAk  128 (132)
T PF00075_consen  112 GHSGVPQGNERA---DRLAK  128 (132)
T ss_dssp             SSSSSHHHHHHH---HHHHH
T ss_pred             CcCCCchhHHHH---HHHHH
Confidence            98655     45   77765

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 ....

>PRK13907 rnhA ribonuclease H; Provisional

Probab=95.92  E-value=0.0095  Score=45.86  Aligned_cols=82  Identities=16%  Similarity=0.177  Sum_probs=57.7

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHH----HHHHhcCCceE-EEeeCCCcc
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKR----LKIKLFPYQFE-LKYLPGKYM  148 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~R----W~~~L~~yd~~-I~y~~Gk~n  148 (204)
                      ++..+-|+.|++.||+.....=.  .++.++||.+-+...+++...+.  ..+..    -...+..|+.. +.|+|+..|
T Consensus        39 ~tn~~AE~~All~aL~~a~~~g~--~~v~i~sDS~~vi~~~~~~~~~~--~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N  114 (128)
T PRK13907         39 MSNHEAEYHALLAALKYCTEHNY--NIVSFRTDSQLVERAVEKEYAKN--KMFAPLLEEALQYIKSFDLFFIKWIPSSQN  114 (128)
T ss_pred             cCCcHHHHHHHHHHHHHHHhCCC--CEEEEEechHHHHHHHhHHHhcC--hhHHHHHHHHHHHHhcCCceEEEEcCchhc
Confidence            56678899999999998654322  47999999999988776422111  12222    22335777644 599999999


Q ss_pred             ccCCCCCcccccCc
Q psy8593         149 HIAELADYLSRNLL  162 (204)
Q Consensus       149 ~vA~~~DaLSR~~~  162 (204)
                      ..|   |.|+|.-.
T Consensus       115 ~~A---d~LA~~a~  125 (128)
T PRK13907        115 KVA---DELARKAI  125 (128)
T ss_pred             hhH---HHHHHHHH
Confidence            999   99988543

>PRK07708 hypothetical protein; Validated

Probab=93.82  E-value=0.083  Score=45.36  Aligned_cols=86  Identities=17%  Similarity=0.091  Sum_probs=60.7

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHHH----HhcCCc--eEEEeeCCCc
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKI----KLFPYQ--FELKYLPGKY  147 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~~----~L~~yd--~~I~y~~Gk~  147 (204)
                      .+..+-|..|++.|++.-...=....+++|++|.+-+...+++. .+..++.+..|..    .+.+|.  +.+.|++.+.
T Consensus       116 ~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~-wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~  194 (219)
T PRK07708        116 YDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGE-WPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQ  194 (219)
T ss_pred             ccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCC-ceeCChhHHHHHHHHHHHHhhCCceEEEEECCchh
Confidence            35567799999999998755433212489999999998777643 2333445666643    345665  5678999999


Q ss_pred             cccCCCCCcccccCcc
Q psy8593         148 MHIAELADYLSRNLLV  163 (204)
Q Consensus       148 n~vA~~~DaLSR~~~~  163 (204)
                      |..|   |.|++..+.
T Consensus       195 N~~A---D~LAk~Al~  207 (219)
T PRK07708        195 NKEA---DQLATQALE  207 (219)
T ss_pred             hhHH---HHHHHHHHh
Confidence            9999   999876544

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=92.32  E-value=0.14  Score=46.48  Aligned_cols=82  Identities=13%  Similarity=0.150  Sum_probs=58.5

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHH----HHhcCC-ceEEEeeCCCcc
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLK----IKLFPY-QFELKYLPGKYM  148 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~----~~L~~y-d~~I~y~~Gk~n  148 (204)
                      .+..+-|+.|+++||+..... -. +.++|+||.+.+...+++. .+..+..+....    ..++.| .+.|.|+++..|
T Consensus        43 ~tnn~AE~~All~gL~~a~~~-g~-~~v~i~~DS~lvi~~i~~~-~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N  119 (372)
T PRK07238         43 ATNNVAEYRGLIAGLEAAAEL-GA-TEVEVRMDSKLVVEQMSGR-WKVKHPDMKPLAAQARELASQFGRVTYTWIPRARN  119 (372)
T ss_pred             CCchHHHHHHHHHHHHHHHhC-CC-CeEEEEeCcHHHHHHhCCC-CccCChHHHHHHHHHHHHHhcCCceEEEECCchhh
Confidence            444578999999999987544 23 6899999999988777642 122233444332    334665 488999999999


Q ss_pred             ccCCCCCcccccC
Q psy8593         149 HIAELADYLSRNL  161 (204)
Q Consensus       149 ~vA~~~DaLSR~~  161 (204)
                      ..|   |.|.+..
T Consensus       120 ~~A---D~LA~~a  129 (372)
T PRK07238        120 AHA---DRLANEA  129 (372)
T ss_pred             hHH---HHHHHHH
Confidence            999   9998754

>PRK06548 ribonuclease H; Provisional

Probab=91.60  E-value=0.23  Score=40.75  Aligned_cols=81  Identities=15%  Similarity=0.123  Sum_probs=51.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhc-------cccc----c--chhHHHHHH-HHhcCCceEE
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKK-------DLYK----I--QNNRLKRLK-IKLFPYQFEL  140 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k-------~~~k----~--~~~Rl~RW~-~~L~~yd~~I  140 (204)
                      +.-+-|+.|++.|++....  .+ .++.|+||-+-+..-+++       .-.+    .  .|.-+-+.+ ..++...++|
T Consensus        41 TNnraEl~Aii~aL~~~~~--~~-~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~  117 (161)
T PRK06548         41 TNNIAELTAVRELLIATRH--TD-RPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRM  117 (161)
T ss_pred             CHHHHHHHHHHHHHHhhhc--CC-ceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEE
Confidence            3456799999999975432  23 679999999888666542       0011    1  122222222 2345668999


Q ss_pred             EeeCCCc----cccCCCCCcccccC
Q psy8593         141 KYLPGKY----MHIAELADYLSRNL  161 (204)
Q Consensus       141 ~y~~Gk~----n~vA~~~DaLSR~~  161 (204)
                      .+++|..    |-.|   |.|.|..
T Consensus       118 ~wVkgHsg~~gNe~a---D~LA~~a  139 (161)
T PRK06548        118 SWVNAHTGHPLNEAA---DSLARQA  139 (161)
T ss_pred             EEEecCCCCHHHHHH---HHHHHHH
Confidence            9999865    7677   9988753

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=91.12  E-value=0.12  Score=41.19  Aligned_cols=81  Identities=21%  Similarity=0.137  Sum_probs=48.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhc-------ccccc------chhHH-HHHHHHhcCCceEE
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKK-------DLYKI------QNNRL-KRLKIKLFPYQFEL  140 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k-------~~~k~------~~~Rl-~RW~~~L~~yd~~I  140 (204)
                      +...-|+.|++.||+...   .. ..+.|+||.+.+..-+++       ...+.      .|..+ .+-...+..-.+.+
T Consensus        42 TN~~aEL~Ai~~AL~~~~---~~-~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~  117 (150)
T PRK00203         42 TNNRMELMAAIEALEALK---EP-CEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKW  117 (150)
T ss_pred             cHHHHHHHHHHHHHHHcC---CC-CeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEE
Confidence            345689999999998653   24 679999998655433321       00011      11111 12222345567899


Q ss_pred             EeeCCCc----cccCCCCCcccccCc
Q psy8593         141 KYLPGKY----MHIAELADYLSRNLL  162 (204)
Q Consensus       141 ~y~~Gk~----n~vA~~~DaLSR~~~  162 (204)
                      .++||..    |-.|   |.|.|...
T Consensus       118 ~wV~~H~~~~~N~~A---D~lA~~a~  140 (150)
T PRK00203        118 HWVKGHAGHPENERC---DELARAGA  140 (150)
T ss_pred             EEecCCCCCHHHHHH---HHHHHHHH
Confidence            9999765    6677   98887543

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

Probab=90.94  E-value=0.24  Score=40.56  Aligned_cols=84  Identities=18%  Similarity=0.140  Sum_probs=55.2

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccc--ccc-----------chhH-HHHHHHHhcCC-ce
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDL--YKI-----------QNNR-LKRLKIKLFPY-QF  138 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~--~k~-----------~~~R-l~RW~~~L~~y-d~  138 (204)
                      -+--+-|+.|++.||+..+.  .|...++|+||.+-+..-++.=+  .+.           .|.. ..+-...+..+ .+
T Consensus        41 tTNNraEl~A~i~AL~~l~~--~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v  118 (154)
T COG0328          41 TTNNRAELRALIEALEALKE--LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELV  118 (154)
T ss_pred             ccChHHHHHHHHHHHHHHHh--cCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeE
Confidence            34457899999999999887  34488999999987754433100  000           0111 33334556778 88


Q ss_pred             EEEeeCC----CccccCCCCCcccccCc
Q psy8593         139 ELKYLPG----KYMHIAELADYLSRNLL  162 (204)
Q Consensus       139 ~I~y~~G----k~n~vA~~~DaLSR~~~  162 (204)
                      .++.++|    ..|-.|   |.|.|.-.
T Consensus       119 ~~~WVkgH~g~~~Nera---D~LA~~~~  143 (154)
T COG0328         119 FWEWVKGHAGHPENERA---DQLAREAA  143 (154)
T ss_pred             EEEEeeCCCCChHHHHH---HHHHHHHH
Confidence            9999995    456677   88877543

>PRK08719 ribonuclease H; Reviewed

Probab=82.96  E-value=1.3  Score=35.59  Aligned_cols=78  Identities=14%  Similarity=0.034  Sum_probs=48.1

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhh-------ccccc------cchhHHHHHHHHh-cCCceE
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINK-------KDLYK------IQNNRLKRLKIKL-FPYQFE  139 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~-------k~~~k------~~~~Rl~RW~~~L-~~yd~~  139 (204)
                      -+..+-|+.|++.||+...      ....|+||.+-...-++       +.-.+      ..|.-+-+.+..| +.-+++
T Consensus        48 ~Tnn~aEl~A~~~aL~~~~------~~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~  121 (147)
T PRK08719         48 TDNAELELLALIEALEYAR------DGDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVE  121 (147)
T ss_pred             ccHHHHHHHHHHHHHHHcC------CCCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEE
Confidence            3556789999999998753      23489999966544331       10011      1122233334433 445688


Q ss_pred             EEeeCC----CccccCCCCCccccc
Q psy8593         140 LKYLPG----KYMHIAELADYLSRN  160 (204)
Q Consensus       140 I~y~~G----k~n~vA~~~DaLSR~  160 (204)
                      ++|+||    ..|..|   |.|.|.
T Consensus       122 ~~~VkgH~g~~~Ne~a---D~lA~~  143 (147)
T PRK08719        122 VEKVTAHSGIEGNEAA---DMLAQA  143 (147)
T ss_pred             EEEecCCCCChhHHHH---HHHHHH
Confidence            999999    457777   888764

---

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	204
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	1e-05

>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 Length = 455

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 8/65 (12%), Positives = 21/65 (32%), Gaps = 2/65 (3%)

Query: 80  ELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPYQFE 139
            +A       +      G   +V++  H     + +     + N R+   +  L      
Sbjct: 393 MVAAIAVLTKDAGKLTMGQP-LVIKAPHAVEALVKQPPDRWLSNARMTHYQALLLDTD-R 450

Query: 140 LKYLP 144
           +++ P
Sbjct: 451 VQFGP 455

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	204
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	99.66
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	99.12
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.58
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.44
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	97.46
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	97.02
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	96.95
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	96.09
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	95.08
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	95.02
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	94.95
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	94.71
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	94.37
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	94.25
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	93.79
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	92.54
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	88.99
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	88.26

>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=99.66  E-value=5.3e-19  Score=161.93  Aligned_cols=130  Identities=14%  Similarity=0.154  Sum_probs=92.2

Q ss_pred             ccchhHHHHHHHHhhcCCCcccch-------hhhhchhhhhhhhhhhHH----------------------------hhh
Q psy8593           7 ILRYDQFLIAKISTIRNTQSAETA-------GEKCSALDQHFEFRLITM----------------------------QLI   51 (204)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~-------~~~c~~~~~~~~~~l~~~----------------------------q~~   51 (204)
                      .+.|||+|++.++.+..|...+..       .+.|+.+++.++..+...                            |..
T Consensus       287 ~~~y~r~fi~~~~~~~~pL~~llkk~~~~~W~~~~~~af~~lK~~l~~~pvL~~p~~~~~~~l~~DAS~~~~gavL~q~~  366 (455)
T 1rw3_A          287 TAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKL  366 (455)
T ss_dssp             TTCCCSSCCCCCGGGCCTTCC--------CCCCCCSSSCCHHHHHTCSSCCSCCSSSCCTTSCEEEEEECSSSBEECCBC
T ss_pred             cchHHHHHHhhhhhhcccHHHHhcCCCCcCchHHHHHHHHHHHHHhhcCcccccCCCCCcEEEEEeccCCcceeEEEEec
Confidence            467999999999998888876553       356666666655554444                            333


Q ss_pred             cCCCcchhhhHhhhccchhhhcCChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHHH
Q psy8593          52 GSAQRDLFFIIFYKLGHAFSTSLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKI  131 (204)
Q Consensus        52 ~~~~~~~~~~~~~k~~~~~~~~Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~~  131 (204)
                      ++..+++.|+ +.+++ ..+.+|+++|||++||++|+++|++||.| ++|+|+|||+.+.++.++...-..++|++||+.
T Consensus       367 ~~~~~~i~y~-Sk~l~-~~e~~ys~~ekEllAi~~a~~~~~~yl~g-~~~~v~tDh~~~~~l~~~~~~~~~~~Rl~rW~~  443 (455)
T 1rw3_A          367 GPWRRPVAYL-SKKLD-PVAAGWPPCLRMVAAIAVLTKDAGKLTMG-QPLVIKAPHAVEALVKQPPDRWLSNARMTHYQA  443 (455)
T ss_dssp             TTTTCCCCCC-CBCSC-SSCSSSCCSSHHHHHHHHHHHHHHGGGCS-SCEEEECSSCTTTTSSSTTTTTCCCCCCSCCCC
T ss_pred             CCcEEEEEEE-cccCC-ccccccchHHHHHHHHHHHHHHHHHHcCC-CcEEEEecChHHHHhCCCccccccchHHHHHHH
Confidence            3333444432 33343 44789999999999999999999999999 999999999855555443222226789999999


Q ss_pred             Hhc-CCceE
Q psy8593         132 KLF-PYQFE  139 (204)
Q Consensus       132 ~L~-~yd~~  139 (204)
                      .|+ .||++
T Consensus       444 ~L~e~~~i~  452 (455)
T 1rw3_A          444 LLLDTDRVQ  452 (455)
T ss_dssp             CCCCCCSSS
T ss_pred             HhCcCCCeE
Confidence            999 57765

>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=99.12  E-value=2.3e-12  Score=117.78  Aligned_cols=107  Identities=7%  Similarity=-0.149  Sum_probs=78.0

Q ss_pred             ccchhHHHHHHHH-----hhcCCC----cccchhhhhchhhhhhhhhhhHHhhhcCCCcchhhhH---------------
Q psy8593           7 ILRYDQFLIAKIS-----TIRNTQ----SAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFII---------------   62 (204)
Q Consensus         7 ~~~~~~~~~~~~~-----~~~~~~----~~~~~~~~c~~~~~~~~~~l~~~q~~~~~~~~~~~~~---------------   62 (204)
                      .+.|||+|++.++     .+....    ..-.++++|+.+|+.++..|...+++...+....+++               
T Consensus       263 ~~~yyrrFi~~~s~~pL~~llkk~~~~~~~~~Wt~~~~~af~~lK~~L~~~p~l~~pd~~~~~~l~~das~~g~~g~vl~  342 (428)
T 2zd1_B          263 KLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIY  342 (428)
T ss_dssp             HHHHHTTTCTTCCCHHHHHTTCSCCCTTCEECCCHHHHHHHHHHHHHTTSCCTTCCCCTTSCCEEEEEEEETTEEEEEEE
T ss_pred             hHHHHHHhcCCccHHHHHHHHccCCCCCCeecCCHHHHHHHHHHHHHHhcchhccccCCCCCEEEEEecCCCCcEEEEEe
Confidence            3679999998776     233333    2356779999999999988877766443222222221               


Q ss_pred             --------hhhccchhhhcCChhHHHHHH-HHHHHHHHHHhhcCc--cceecccCCcchhHhhh
Q psy8593          63 --------FYKLGHAFSTSLAIPRDELAG-FRSEATEFCYYVYGH--RNIVVQTDHQPLLAINK  115 (204)
Q Consensus        63 --------~~k~~~~~~~~Ys~~EkEllA-Iv~al~kfr~yL~G~--~~f~V~TDHk~L~~l~~  115 (204)
                              +.+++  .+.+|++.|+|+|| ||+|+++||+||.|.  ..|+++|||+.+.|+.+
T Consensus       343 q~~~~~~~s~~~~--~~~~y~~~~~e~la~vv~al~~~r~yl~G~~~~~~i~~td~~~~~~~~~  404 (428)
T 2zd1_B          343 QEPFKNLKTGKYA--RMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTE  404 (428)
T ss_dssp             SSTTCEEEEEEEE--CCSSCTTCHHHHHHHHHHHHHHHHHHHHSSCCEEEESSCHHHHHHHHHH
T ss_pred             cCCCceeeecccc--hhhhcccchHHHHHHHHHHhhccceEEECCCCcEECCccHHHHHHHHHh
Confidence                    11222  47899999999999 999999999999992  25788999999999875

>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=98.58  E-value=1.3e-09  Score=102.20  Aligned_cols=121  Identities=14%  Similarity=0.024  Sum_probs=83.5

Q ss_pred             ccchhHHHHHHHH-----hhcCCC----cccchhhhhchhhhhhhhhhhHHhhhcCCCcchhhhHhhh------------
Q psy8593           7 ILRYDQFLIAKIS-----TIRNTQ----SAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYK------------   65 (204)
Q Consensus         7 ~~~~~~~~~~~~~-----~~~~~~----~~~~~~~~c~~~~~~~~~~l~~~q~~~~~~~~~~~~~~~k------------   65 (204)
                      .+.|||+|++.++     .+....    ..-.++++|+.+|+.++..|.+.+++...+....|+++..            
T Consensus       263 ~~~~~rrfi~~~~~~pL~~llk~~~~~~~~~~wt~~~~~af~~lK~~L~~~p~L~~p~~~~~~~l~~das~~ga~g~vl~  342 (555)
T 1mu2_A          263 VLNWAAQLYPGIKTKHLCRLISGKMTLTEEVQWTELAEAELEENRIILSQEQEGHYYQEEKELEATVQKDQDNQWTYKIH  342 (555)
T ss_dssp             HHHHHHHHSTTCCCHHHHTTSCSSSCTTCBCCCCHHHHHHHHHHHHHHSCCEEEECBCTTSCCEEEEEECSSSCEEEEEE
T ss_pred             hhhhhhhccCccchHHHHHHhccCCCCCCcccCCHHHHHHHHHHHHHHhhCccccccCCCCCEEEEEecCCCCcEEEEEe
Confidence            3679999998874     232332    4566779999999999998888876554443333322111            


Q ss_pred             -ccc-------hhhhcCChhHHHHHH-HHHHHHHHHHhhcCccc--eecc----------cCCcchhHhhhccccccchh
Q psy8593          66 -LGH-------AFSTSLAIPRDELAG-FRSEATEFCYYVYGHRN--IVVQ----------TDHQPLLAINKKDLYKIQNN  124 (204)
Q Consensus        66 -~~~-------~~~~~Ys~~EkEllA-Iv~al~kfr~yL~G~~~--f~V~----------TDHk~L~~l~~k~~~k~~~~  124 (204)
                       -++       .-..+|.+.|+|+|| +++++++|++||.| +.  |.|.          |||.++.++.....  .+++
T Consensus       343 Q~~~~~~~~~~s~~~~~~~~~~~~la~~v~~l~~~~~~l~g-~~~~~~v~~~~~~w~~~~td~~~l~~~p~~~~--~~~~  419 (555)
T 1mu2_A          343 QEEKILKVGKYAKVKNTHTNGIRLLAQVVQKIGKEALVIWG-RIPKFHLPVEREIWEQWWDNYWQVTWIPDWDF--VSTP  419 (555)
T ss_dssp             ETTEEEEEEEECCC--CEECHHHHHHHHHHHHHHHHHHHHS-SCCEEEESBCHHHHHHHHHHCSSBCCCCSEEE--CCCS
T ss_pred             eCCcceeeeeccccccccCCHHHHHHHHHHHhchhheeeeC-CCeeEECCccHHHHHHhhhccchhhcCCcHHh--ccCC
Confidence             010       013468888999998 99999999999999 76  8888          99999998876322  1346


Q ss_pred             HHHHHH
Q psy8593         125 RLKRLK  130 (204)
Q Consensus       125 Rl~RW~  130 (204)
                      ++.||.
T Consensus       420 ~~~~~~  425 (555)
T 1mu2_A          420 PLVRLA  425 (555)
T ss_dssp             SCBCCC
T ss_pred             cccccc
Confidence            788875

>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=98.44  E-value=2.8e-08  Score=93.09  Aligned_cols=107  Identities=7%  Similarity=-0.127  Sum_probs=77.0

Q ss_pred             cchhHHHHHHHH--hhcCC-------CcccchhhhhchhhhhhhhhhhHHhhhcCCCcchhhhHhhhc------------
Q psy8593           8 LRYDQFLIAKIS--TIRNT-------QSAETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIFYKL------------   66 (204)
Q Consensus         8 ~~~~~~~~~~~~--~~~~~-------~~~~~~~~~c~~~~~~~~~~l~~~q~~~~~~~~~~~~~~~k~------------   66 (204)
                      +.|||+|++.++  .+..+       ...-.+.++|+.+|+.++..|...+++...+....|+++...            
T Consensus       266 ~~~yrrfi~~~~~~pl~~ll~~~~~~~~~~~Wt~~~~~af~~lK~~L~~~p~L~~pd~~~~~~l~~das~~g~~g~vl~q  345 (557)
T 2zd1_A          266 LNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQ  345 (557)
T ss_dssp             HHHHTTTSTTCCCHHHHGGGTTCCCTTCEECCCHHHHHHHHHHHHHTSSCCCBCCCCTTSCCEEEEEEEETTEEEEEEEE
T ss_pred             HHhhhhhccchhHHHHHHHhcccCCCCCceecCHHHHHHHHHHHHHHhCccceeecCCCCCEEEEEecCCCCcEEEEEec
Confidence            579999998775  22222       234567799999999999988877765544333333221100            


Q ss_pred             ---------cchhhhcCChhHHHHHH-HHHHHHHHHHhhcCcc--ceec-ccCCcchhHhhh
Q psy8593          67 ---------GHAFSTSLAIPRDELAG-FRSEATEFCYYVYGHR--NIVV-QTDHQPLLAINK  115 (204)
Q Consensus        67 ---------~~~~~~~Ys~~EkEllA-Iv~al~kfr~yL~G~~--~f~V-~TDHk~L~~l~~  115 (204)
                               .-+.+.+|++.|+|+|| +++++++|++||.| +  .|.| +|||+.+.++..
T Consensus       346 ~~~~~~~~~~~~~~~~y~~~e~e~la~vv~~l~~~~~~l~g-~~p~~~vp~~~~~~~~~~~~  406 (557)
T 2zd1_A          346 EPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWG-KTPKFKLPIQKETWETWWTE  406 (557)
T ss_dssp             ETTEEEEEEEEECCSCSEECHHHHHHHHHHHHHHHHHHHHS-SCCEEEESBCHHHHHHHHHH
T ss_pred             CCCceeeeeecccccccCCChHHHHHHHHHHhhhhheEEeC-CCCCEECCCcHHHHHHHhhh
Confidence                     01136789999999999 99999999999999 5  5777 899998888754

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

Probab=97.46  E-value=7.3e-05  Score=57.84  Aligned_cols=85  Identities=15%  Similarity=0.079  Sum_probs=62.0

Q ss_pred             cCChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhcccc-c-cch-hHHHHHHHHhcCCceEEEeeCCCccc
Q psy8593          73 SLAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLY-K-IQN-NRLKRLKIKLFPYQFELKYLPGKYMH  149 (204)
Q Consensus        73 ~Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~-k-~~~-~Rl~RW~~~L~~yd~~I~y~~Gk~n~  149 (204)
                      ..+..+-|+.|++.||+.....  |.++++|+||.+.+...+++.-. + ..+ .-+.++...+..|++.+.|+||..|.
T Consensus        45 ~~tnn~aEl~A~~~aL~~a~~~--g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~~~N~  122 (149)
T 2ehg_A           45 NSTNNVAEYSGLICLMETMLRL--GISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENK  122 (149)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHH--TCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCGGGCH
T ss_pred             CccHHHHHHHHHHHHHHHHHHc--CCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCCcccH
Confidence            4556789999999999987653  32689999999999887764211 1 111 22344455566778999999999999


Q ss_pred             cCCCCCcccccCc
Q psy8593         150 IAELADYLSRNLL  162 (204)
Q Consensus       150 vA~~~DaLSR~~~  162 (204)
                      .|   |.|++...
T Consensus       123 ~A---D~LA~~a~  132 (149)
T 2ehg_A          123 EA---DRLSRVAY  132 (149)
T ss_dssp             HH---HHHHHHHH
T ss_pred             HH---HHHHHHHH
Confidence            99   99988543

>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=97.02  E-value=0.00059  Score=51.58  Aligned_cols=82  Identities=15%  Similarity=0.200  Sum_probs=59.5

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHH----HHhcCC-ceEEEeeCCCcc
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLK----IKLFPY-QFELKYLPGKYM  148 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~----~~L~~y-d~~I~y~~Gk~n  148 (204)
                      -+..+-|+.|++.||+.....  |..+++|+||.+.+...+++. .+..++.+..+.    ..+..| .+.+.|+|+..|
T Consensus        44 ~tn~~aEl~A~~~aL~~a~~~--~~~~v~i~tDS~~vv~~i~~~-~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N  120 (141)
T 3hst_B           44 ATNNVAEYRGLIAGLDDAVKL--GATEAAVLMDSKLVVEQMSGR-WKVKHPDLLKLYVQAQALASQFRRINYEWVPRARN  120 (141)
T ss_dssp             ECHHHHHHHHHHHHHHHHHHH--TCSEEEEEESCHHHHHHHTTS-SCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGC
T ss_pred             CchHHHHHHHHHHHHHHHHHC--CCceEEEEeChHHHHHHHhCC-cccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCccc
Confidence            455789999999999987542  326899999999998877642 122233343332    344555 799999999999


Q ss_pred             ccCCCCCcccccC
Q psy8593         149 HIAELADYLSRNL  161 (204)
Q Consensus       149 ~vA~~~DaLSR~~  161 (204)
                      ..|   |.|.+..
T Consensus       121 ~~A---D~LA~~a  130 (141)
T 3hst_B          121 TYA---DRLANDA  130 (141)
T ss_dssp             HHH---HHHHHHH
T ss_pred             HHH---HHHHHHH
Confidence            999   9998754

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

Probab=96.95  E-value=0.0006  Score=51.17  Aligned_cols=80  Identities=11%  Similarity=0.164  Sum_probs=57.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCcc----ceecccCCcchhHhhhccccccchhH----HHHHHHH-hcCC-ceEEEeeC
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHR----NIVVQTDHQPLLAINKKDLYKIQNNR----LKRLKIK-LFPY-QFELKYLP  144 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~----~f~V~TDHk~L~~l~~k~~~k~~~~R----l~RW~~~-L~~y-d~~I~y~~  144 (204)
                      +..+-|+.|++.||+.....  |..    +++|+||.+.+...+++.- +..+..    +.+.... ++.| .+++.|+|
T Consensus        44 tn~~aEl~A~~~aL~~a~~~--~~~~~~~~v~i~tDS~~vi~~i~~~~-~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~  120 (140)
T 3u3g_D           44 TNNVAEYEALIRALEDLQMF--GDKLVDMEVEVRMDSELIVRQMQGVY-KVKEPTLKEKFAKIAHIKMERVPNLVFVHIP  120 (140)
T ss_dssp             CHHHHHHHHHHHHHHHHGGG--GGGGTTCEEEEEESCHHHHHHHTTSS-CCCCGGGHHHHHHHHHHHHHHCTTCEEEECC
T ss_pred             chHHHHHHHHHHHHHHHHHc--CCCCCCceEEEEeChHHHHHHhCCCc-ccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC
Confidence            56688999999999986432  313    8999999999988776421 111222    2233333 5666 89999999


Q ss_pred             CCccccCCCCCccccc
Q psy8593         145 GKYMHIAELADYLSRN  160 (204)
Q Consensus       145 Gk~n~vA~~~DaLSR~  160 (204)
                      +..|..|   |.|.+.
T Consensus       121 ~~~N~~A---D~LA~~  133 (140)
T 3u3g_D          121 REKNARA---DELVNE  133 (140)
T ss_dssp             GGGGHHH---HHHHHH
T ss_pred             chhhHHH---HHHHHH
Confidence            9999999   999874

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

Probab=96.09  E-value=0.0075  Score=46.82  Aligned_cols=83  Identities=16%  Similarity=0.067  Sum_probs=56.4

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccc-------cc------cchhH-HHHHHHHhcCCceE
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDL-------YK------IQNNR-LKRLKIKLFPYQFE  139 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~-------~k------~~~~R-l~RW~~~L~~yd~~  139 (204)
                      -+..+-|+.|++.||+..... -. .+++|+||.+.+...+++-.       .+      ..+.. +.+-...+..+++.
T Consensus        48 ~tn~~aEl~A~~~aL~~~~~~-~~-~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~  125 (154)
T 2qkb_A           48 QTNQRAEIHAACKAIEQAKTQ-NI-NKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQ  125 (154)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHT-TC-CEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEE
T ss_pred             CchHHHHHHHHHHHHHHHHhC-CC-ceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceE
Confidence            356688999999999987542 23 78999999987765554210       01      11222 22333446688999


Q ss_pred             EEeeCCCc----cccCCCCCcccccC
Q psy8593         140 LKYLPGKY----MHIAELADYLSRNL  161 (204)
Q Consensus       140 I~y~~Gk~----n~vA~~~DaLSR~~  161 (204)
                      +.|+||..    |..|   |.|++..
T Consensus       126 ~~~V~~H~g~~~N~~A---D~LA~~a  148 (154)
T 2qkb_A          126 WMHVPGHSGFIGNEEA---DRLAREG  148 (154)
T ss_dssp             EEECCTTSSCHHHHHH---HHHHHHH
T ss_pred             EEEccCCCCCHhHHHH---HHHHHHH
Confidence            99999965    9888   9998754

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

Probab=95.08  E-value=0.011  Score=46.34  Aligned_cols=83  Identities=19%  Similarity=0.113  Sum_probs=56.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhc--------cc-----cccchhHH-HHHHHHhcCCceEE
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKK--------DL-----YKIQNNRL-KRLKIKLFPYQFEL  140 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k--------~~-----~k~~~~Rl-~RW~~~L~~yd~~I  140 (204)
                      +..+-|+.|++.||+...   .+ .+++|+||.+.+...+++        .-     ....+..+ .+....+..+++.+
T Consensus        45 tn~~aEl~A~~~AL~~~~---~~-~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~  120 (158)
T 2e4l_A           45 TNNRMELLAPIVALEALK---EP-CKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDW  120 (158)
T ss_dssp             CHHHHHHHHHHHHHHTCS---SC-CEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEE
T ss_pred             ccHHHHHHHHHHHHHHhc---cC-CeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEE
Confidence            456789999999998753   35 789999999877655442        10     01112222 23334556789999


Q ss_pred             EeeCCC----ccccCCCCCcccccCccc
Q psy8593         141 KYLPGK----YMHIAELADYLSRNLLVK  164 (204)
Q Consensus       141 ~y~~Gk----~n~vA~~~DaLSR~~~~~  164 (204)
                      .|+||.    .|..|   |.|++.....
T Consensus       121 ~wV~gH~g~~~Ne~A---D~LAk~a~~~  145 (158)
T 2e4l_A          121 RWVKGHAGHAENERC---DQLARAAAEA  145 (158)
T ss_dssp             EECCTTCCCHHHHHH---HHHHHHHHHS
T ss_pred             EEccCCCCchhHHHH---HHHHHHHHHh
Confidence            999975    68888   9998765543

>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=95.02  E-value=0.0093  Score=46.27  Aligned_cols=82  Identities=12%  Similarity=0.127  Sum_probs=54.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHHHHhcCC--ceEEEeeCCC----cc
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFPY--QFELKYLPGK----YM  148 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~~~L~~y--d~~I~y~~Gk----~n  148 (204)
                      +..+-|+.|++.||+....  .| .+++|+||.+.+.....+. .+..++....+...++++  ++.+.++||.    .|
T Consensus        49 tNn~aEl~A~~~AL~~a~~--~~-~~v~I~tDS~~i~~w~~~~-w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~N  124 (147)
T 2kq2_A           49 RNVAGEIAAALYAVKKASQ--LG-VKIRILHDYAGIAFWATGE-WKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFN  124 (147)
T ss_dssp             CTTHHHHHHHHHHHHHHHH--HT-CCCCBSSCCSTHHHHTTSS-SSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHH
T ss_pred             cHHHHHHHHHHHHHHHHHH--CC-CeEEEEECcHHHHHHHhCC-CccCCcchHHHHHHHHHhcCCeeEEEecCcCCCcch
Confidence            4568899999999986433  36 6899999998876444321 223333344444333332  6888899985    48


Q ss_pred             ccCCCCCcccccCcc
Q psy8593         149 HIAELADYLSRNLLV  163 (204)
Q Consensus       149 ~vA~~~DaLSR~~~~  163 (204)
                      -.|   |.|+|.-..
T Consensus       125 e~A---D~LA~~a~~  136 (147)
T 2kq2_A          125 DYV---DMKAKSALG  136 (147)
T ss_dssp             HHH---HHHHHHHHT
T ss_pred             HHH---HHHHHHHHh
Confidence            888   999875443

>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=94.95  E-value=0.016  Score=45.33  Aligned_cols=79  Identities=20%  Similarity=0.215  Sum_probs=52.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccc-------cc------cchhHHHH-HHHHh-cCCceE
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDL-------YK------IQNNRLKR-LKIKL-FPYQFE  139 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~-------~k------~~~~Rl~R-W~~~L-~~yd~~  139 (204)
                      +...-|+.|++.||+.     .+ .+++|+||.+-+...+++-.       .+      ..|..+-+ -...+ +..++.
T Consensus        48 Tnn~aEl~A~i~AL~~-----~~-~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~  121 (150)
T 3qio_A           48 TNQKTELQAIYLALQD-----SG-LEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVY  121 (150)
T ss_dssp             CHHHHHHHHHHHHHHH-----SC-SEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEE
T ss_pred             CHHHHHHHHHHHHHHh-----CC-CcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceE
Confidence            3456899999999987     37 89999999887765544210       00      01112222 12234 345799


Q ss_pred             EEeeCCCc----cccCCCCCcccccCc
Q psy8593         140 LKYLPGKY----MHIAELADYLSRNLL  162 (204)
Q Consensus       140 I~y~~Gk~----n~vA~~~DaLSR~~~  162 (204)
                      +.++||..    |-.|   |.|.|.-.
T Consensus       122 ~~wV~gH~g~~~Ne~A---D~LA~~a~  145 (150)
T 3qio_A          122 LAWVPAHKGIGGNEQV---DKLVSAGI  145 (150)
T ss_dssp             EEECCTTSCCHHHHHH---HHHHHTTT
T ss_pred             EEEccCcCCChhHHHH---HHHHHHHH
Confidence            99999998    9999   99988654

>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=94.71  E-value=0.015  Score=45.40  Aligned_cols=82  Identities=21%  Similarity=0.163  Sum_probs=55.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhc--------cc-----cccchhHH-HHHHHHhcCCceEE
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKK--------DL-----YKIQNNRL-KRLKIKLFPYQFEL  140 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k--------~~-----~k~~~~Rl-~RW~~~L~~yd~~I  140 (204)
                      +..+-|+.|++.||+....   . .+++|+||.+.+...+++        .-     ....+..+ .+....+..+++.+
T Consensus        43 tn~~aEl~A~~~aL~~~~~---~-~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~  118 (155)
T 1jl1_A           43 TNNRMELMAAIVALEALKE---H-AEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKW  118 (155)
T ss_dssp             CHHHHHHHHHHHHHHTCCS---C-CEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEE
T ss_pred             cHHHHHHHHHHHHHHHhCc---C-CcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEE
Confidence            4567899999999987542   4 789999998877755542        00     01112222 22334456678999


Q ss_pred             EeeCCC----ccccCCCCCcccccCcc
Q psy8593         141 KYLPGK----YMHIAELADYLSRNLLV  163 (204)
Q Consensus       141 ~y~~Gk----~n~vA~~~DaLSR~~~~  163 (204)
                      .|+||.    .|..|   |.|++....
T Consensus       119 ~wV~gH~g~~~Ne~A---D~LA~~a~~  142 (155)
T 1jl1_A          119 EWVKGHAGHPENERA---DELARAAAM  142 (155)
T ss_dssp             EECCSSTTCHHHHHH---HHHHHHHHH
T ss_pred             EEcCCCCCCHHHHHH---HHHHHHHHh
Confidence            999975    68888   999876543

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

Probab=94.37  E-value=0.011  Score=46.76  Aligned_cols=83  Identities=14%  Similarity=0.125  Sum_probs=55.1

Q ss_pred             CChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhcc--------ccc------cchhH-HHHHHHHhcCCce
Q psy8593          74 LAIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKD--------LYK------IQNNR-LKRLKIKLFPYQF  138 (204)
Q Consensus        74 Ys~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~--------~~k------~~~~R-l~RW~~~L~~yd~  138 (204)
                      -+..+-|+.|++.||+...   .. .+++|+||.+.+...+++.        -.+      ..+.. +.+....+..+++
T Consensus        46 ~Tnn~aEl~Ai~~AL~~~~---~~-~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v  121 (166)
T 1ril_A           46 TTNNRMELKAAIEGLKALK---EP-CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRV  121 (166)
T ss_dssp             ECHHHHHHHHHHHHHHSCC---SC-CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEE
T ss_pred             CcHHHHHHHHHHHHHHHhc---cC-CeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeE
Confidence            3456789999999998643   24 6899999998776554430        000      11222 2233344667889


Q ss_pred             EEEeeCCC----ccccCCCCCcccccCcc
Q psy8593         139 ELKYLPGK----YMHIAELADYLSRNLLV  163 (204)
Q Consensus       139 ~I~y~~Gk----~n~vA~~~DaLSR~~~~  163 (204)
                      .+.|+||.    .|..|   |.|++....
T Consensus       122 ~~~wV~gH~g~~~Ne~A---D~LAk~a~~  147 (166)
T 1ril_A          122 RFHFVKGHTGHPENERV---DREARRQAQ  147 (166)
T ss_dssp             ECCCCCGGGSCTHHHHH---HHHHHHHHT
T ss_pred             EEEEeeCCCCchhHHHH---HHHHHHHHH
Confidence            99999964    78888   999875544

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

Probab=94.25  E-value=0.013  Score=44.84  Aligned_cols=80  Identities=16%  Similarity=0.090  Sum_probs=52.9

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhcc-------------c-cccchhHH-HHHHHHhcCCceE
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKD-------------L-YKIQNNRL-KRLKIKLFPYQFE  139 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~-------------~-~k~~~~Rl-~RW~~~L~~yd~~  139 (204)
                      +..+-|+.|++.||+....   + .+++|+||.+.+...+++.             . ....+..+ .+....+..+++.
T Consensus        43 Tnn~aEl~A~~~AL~~~~~---~-~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~  118 (146)
T 3h08_A           43 TNNRMELMAAIKGLEALKE---P-ARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVT  118 (146)
T ss_dssp             CHHHHHHHHHHHHHHTCSS---C-CEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEE
T ss_pred             cHHHHHHHHHHHHHHhcCc---c-CcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceE
Confidence            4557899999999998643   5 8999999999776555420             0 00111222 2233345667899


Q ss_pred             EEeeCC----CccccCCCCCcccccC
Q psy8593         140 LKYLPG----KYMHIAELADYLSRNL  161 (204)
Q Consensus       140 I~y~~G----k~n~vA~~~DaLSR~~  161 (204)
                      +.++||    ..|..|   |.|.+..
T Consensus       119 ~~~V~gH~g~~~N~~A---D~LA~~a  141 (146)
T 3h08_A          119 FHKVKGHSDNPYNSRA---DELARLA  141 (146)
T ss_dssp             EEECCC-CCSHHHHHH---HHHHHHH
T ss_pred             EEEcCCcCCcHhHHHH---HHHHHHH
Confidence            999995    467778   8887643

>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=93.79  E-value=0.1  Score=48.48  Aligned_cols=76  Identities=18%  Similarity=0.174  Sum_probs=52.7

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHH-HHHH-HHhcCCceEEEeeCCC----cc
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRL-KRLK-IKLFPYQFELKYLPGK----YM  148 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl-~RW~-~~L~~yd~~I~y~~Gk----~n  148 (204)
                      +..+-|+.|++.||+..     + +++.|+||.+-+...+++...+ .+..+ .+.. ......++.+.|++|.    .|
T Consensus       475 TNn~aEl~Ai~~aL~~~-----~-~~v~I~tDS~~vi~~i~~~~~~-~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~N  547 (557)
T 2zd1_A          475 TNQKTELQAIYLALQDS-----G-LEVNIVTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKEKVYLAWVPAHKGIGGN  547 (557)
T ss_dssp             CHHHHHHHHHHHHHHHS-----C-SEEEEEECCHHHHHHHTTCCSE-ESSHHHHHHHHHHHHCSEEEEEECCSSSCCTTC
T ss_pred             CHHHHHHHHHHHHHHhC-----C-CcEEEEeChHHHHHHHhcCCcc-CCHHHHHHHHHHHhcCCCEEEEEcCCCCCChhH
Confidence            45578999999999975     6 8999999998887766542222 12222 2333 2334568999999995    48


Q ss_pred             ccCCCCCccccc
Q psy8593         149 HIAELADYLSRN  160 (204)
Q Consensus       149 ~vA~~~DaLSR~  160 (204)
                      -.|   |.|++.
T Consensus       548 e~A---D~LA~~  556 (557)
T 2zd1_A          548 EQV---DKLVSA  556 (557)
T ss_dssp             CGG---GGCC--
T ss_pred             HHH---HHHHhc
Confidence            888   999873

>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=92.54  E-value=0.08  Score=42.07  Aligned_cols=79  Identities=23%  Similarity=0.297  Sum_probs=51.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhh--ccccccchhH-HHHHHHHh-cCCceEEEeeCCCc---
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINK--KDLYKIQNNR-LKRLKIKL-FPYQFELKYLPGKY---  147 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~--k~~~k~~~~R-l~RW~~~L-~~yd~~I~y~~Gk~---  147 (204)
                      +...-|+.|++.||+..    .+ .++.|+||.+-+...+-  +.-....|.- +.+-...+ ..-++.+.+++|..   
T Consensus        62 Tnn~aEl~Ai~~AL~~~----~~-~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~  136 (165)
T 3p1g_A           62 SAQRAELIALTQALKMA----EG-KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGN  136 (165)
T ss_dssp             CHHHHHHHHHHHHHHHT----BT-SEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSC
T ss_pred             cHHHHHHHHHHHHHHHc----cC-ceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCC
Confidence            45688999999999976    36 89999999976654331  1001111222 22222333 44579999999977   


Q ss_pred             ------cccCCCCCcccccC
Q psy8593         148 ------MHIAELADYLSRNL  161 (204)
Q Consensus       148 ------n~vA~~~DaLSR~~  161 (204)
                            |-.|   |.|.|..
T Consensus       137 ~~~~~gNe~A---D~LA~~a  153 (165)
T 3p1g_A          137 SAEARGNRMA---DQAAREA  153 (165)
T ss_dssp             SHHHHHHHHH---HHHHHHH
T ss_pred             cCcchHHHHH---HHHHHHH
Confidence                  6777   9888744

>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=88.99  E-value=0.23  Score=46.12  Aligned_cols=76  Identities=14%  Similarity=0.188  Sum_probs=51.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHH-HHHH-hcCCceEEEeeCCC----cc
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKR-LKIK-LFPYQFELKYLPGK----YM  148 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~R-W~~~-L~~yd~~I~y~~Gk----~n  148 (204)
                      +..+-|+.|++.||+.     .+ .++.|+||.+-+...+++- .+..+..+.+ .... ....++.+.|++|.    .|
T Consensus       472 TNn~aEl~A~i~aL~~-----~~-~~v~I~tDS~~v~~~i~~~-~~~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~N  544 (555)
T 1mu2_A          472 TNQQAELEAFAMALTD-----SG-PKVNIIVDSQYVMGIVASQ-PTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGN  544 (555)
T ss_dssp             CHHHHHHHHHHHHHHT-----SC-SEEEEEESCHHHHHHHHTC-CSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTH
T ss_pred             CHHHHHHHHHHHHHHc-----CC-CeEEEEEehHHHHHHHhcc-cccccHHHHHHHHHHhccCCcEEEEEEECCCCChhH
Confidence            3447799999999987     45 8999999998877666531 1112222222 2222 34567899999995    48


Q ss_pred             ccCCCCCccccc
Q psy8593         149 HIAELADYLSRN  160 (204)
Q Consensus       149 ~vA~~~DaLSR~  160 (204)
                      -.|   |.|.+.
T Consensus       545 e~A---D~LA~~  553 (555)
T 1mu2_A          545 QEV---DHLVSQ  553 (555)
T ss_dssp             HHH---HHHHHT
T ss_pred             HHH---HHHHHh
Confidence            888   998764

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

Probab=88.26  E-value=0.31  Score=38.66  Aligned_cols=75  Identities=17%  Similarity=0.102  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhc-----------cccc--cchhHH-HHHHHHhcC-CceEEEee
Q psy8593          79 DELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKK-----------DLYK--IQNNRL-KRLKIKLFP-YQFELKYL  143 (204)
Q Consensus        79 kEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k-----------~~~k--~~~~Rl-~RW~~~L~~-yd~~I~y~  143 (204)
                      -|+.|+..++++-  .-.+ .+++|+||.+-+..-+++           ...+  ..|.-+ .+....++. -++++.|+
T Consensus        59 Aei~Al~~al~~a--l~~~-~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~V  135 (165)
T 2lsn_A           59 AEIAAVEFACKKA--LKIP-GPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHE  135 (165)
T ss_dssp             HHHHHHHHHHHHH--HHSS-SCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEEC
T ss_pred             HHHHHHHHHHHHH--hcCC-CeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEE
Confidence            3455555555432  1245 789999998876544431           0000  112222 222233443 47999999


Q ss_pred             CCCc----------cccCCCCCcccc
Q psy8593         144 PGKY----------MHIAELADYLSR  159 (204)
Q Consensus       144 ~Gk~----------n~vA~~~DaLSR  159 (204)
                      +|..          |-.|   |.|.|
T Consensus       136 kgH~g~~~~~~~~gNe~A---D~LA~  158 (165)
T 2lsn_A          136 KGHQPTNTSIHTEGNALA---DKLAT  158 (165)
T ss_dssp             CSSSCSSSCHHHHHHHHH---HHHHH
T ss_pred             eCCCCccCCCCChHHHHH---HHHHH
Confidence            9874          6666   88766

---

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	204
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	95.86
d2zd1b1	424	HIV-1 reverse transcriptase {Human immunodeficienc	94.15
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	93.02
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	86.75
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	80.3

>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=95.86  E-value=0.0025  Score=46.15  Aligned_cols=76  Identities=14%  Similarity=0.148  Sum_probs=52.7

Q ss_pred             hhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccch-hHHHHHHHHhcCCceEEEeeCCCc----ccc
Q psy8593          76 IPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQN-NRLKRLKIKLFPYQFELKYLPGKY----MHI  150 (204)
Q Consensus        76 ~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~-~Rl~RW~~~L~~yd~~I~y~~Gk~----n~v  150 (204)
                      ...-|+.||+.|++.     .+ .++.|+||.+.....+++......+ .....+.......++.+.|+||..    |-.
T Consensus        44 nn~AEl~Ai~~al~~-----~~-~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~  117 (126)
T d1mu2a1          44 NQQAELEAFAMALTD-----SG-PKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQE  117 (126)
T ss_dssp             HHHHHHHHHHHHHHT-----SC-SEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHH
T ss_pred             chHHHHHHHHHHhcc-----CC-cceEEEechHHHHHHHhcCCccccchHHHHHHHHhhhcceeEEEEEeCCCCCcchHH
Confidence            346799999999974     45 8999999999887776532111111 223334455677789999999966    767


Q ss_pred             CCCCCccccc
Q psy8593         151 AELADYLSRN  160 (204)
Q Consensus       151 A~~~DaLSR~  160 (204)
                      |   |.|.+.
T Consensus       118 A---D~LA~~  124 (126)
T d1mu2a1         118 V---DHLVSQ  124 (126)
T ss_dssp             H---HHHHHT
T ss_pred             H---HHHHHh
Confidence            7   877653

>d2zd1b1 e.8.1.2 (B:5-428) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=94.15  E-value=0.0035  Score=55.21  Aligned_cols=131  Identities=8%  Similarity=-0.062  Sum_probs=81.1

Q ss_pred             ccchhHHHHHHHH--hhcCCC---cc----cchhhhhchhhhhhhhhhhHHhhhcCCCcchhhhHh-------------h
Q psy8593           7 ILRYDQFLIAKIS--TIRNTQ---SA----ETAGEKCSALDQHFEFRLITMQLIGSAQRDLFFIIF-------------Y   64 (204)
Q Consensus         7 ~~~~~~~~~~~~~--~~~~~~---~~----~~~~~~c~~~~~~~~~~l~~~q~~~~~~~~~~~~~~-------------~   64 (204)
                      .+.|||.|+|.++  .+..+.   .+    -.+.++|+.+|+.++..+...++....+....+++.             +
T Consensus       259 ~~n~~r~fIp~~s~~~L~~ll~~~~~~~~~~~Wt~e~~~af~~lK~~l~~~p~L~~~Dp~kp~~~~~das~~g~~~~~~~  338 (424)
T d2zd1b1         259 KLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIY  338 (424)
T ss_dssp             HHHHHTTTCTTCCCHHHHHTTCSCCCTTCEECCCHHHHHHHHHHHHHTTSCCTTCCCCTTSCCEEEEEEEETTEEEEEEE
T ss_pred             HHHHHHHhcccchHHHHHHHhhhhccCCCCccCCHHHHHHHHHHHHHhcccccccCCCCCCCEEEEEecCCCCceEEEEE
Confidence            3679999998765  233332   22    347799999999999888777765544433333321             0


Q ss_pred             hcc----------chhhhcCChhHH-HHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHHHHh
Q psy8593          65 KLG----------HAFSTSLAIPRD-ELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKL  133 (204)
Q Consensus        65 k~~----------~~~~~~Ys~~Ek-EllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~~~L  133 (204)
                      +.+          ....+.++.++. ++++.-.+.+-++++..+ -.|.                  .| .+..+|....
T Consensus       339 q~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~k~~~e~~~~~g~~-p~~~------------------~p-~~~~~w~~~~  398 (424)
T d2zd1b1         339 QEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKT-PKFK------------------LP-IQKETWETWW  398 (424)
T ss_dssp             SSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHHHSSC-CEEE------------------ES-SCHHHHHHHH
T ss_pred             cCCCcccceEEeccccccccCHHHHHHHHHHHHHHHHHHHhCcC-ccEE------------------CC-ccHHHHHHHH
Confidence            000          000112333444 344444455667777666 2221                  11 3566888888


Q ss_pred             cCCceEEEeeCCCccccCCCCCcccccC
Q psy8593         134 FPYQFELKYLPGKYMHIAELADYLSRNL  161 (204)
Q Consensus       134 ~~yd~~I~y~~Gk~n~vA~~~DaLSR~~  161 (204)
                      .+| ..+.|+|+-+++..   +.|+|..
T Consensus       399 ~~~-~~~~~~p~~~~~~~---~~l~~~~  422 (424)
T d2zd1b1         399 TEY-WQATWIPEWEFVNT---PPLVKLW  422 (424)
T ss_dssp             HHH-CCCSSCCEEEECCS---CCTTTGG
T ss_pred             Hhh-cccccCCCceeccC---cHHHHHh
Confidence            888 88999999999999   9999975

>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=93.02  E-value=0.06  Score=38.20  Aligned_cols=66  Identities=17%  Similarity=0.224  Sum_probs=41.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccccccchhHHHHHHHHhcC-CceEEEeeCCC
Q psy8593          75 AIPRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDLYKIQNNRLKRLKIKLFP-YQFELKYLPGK  146 (204)
Q Consensus        75 s~~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~~k~~~~Rl~RW~~~L~~-yd~~I~y~~Gk  146 (204)
                      +...-|+.||+.||+.     .. .++.|+||.+-+...+++...+....-..+-+..|.. -.+.|.++||.
T Consensus        44 TNn~aEl~Avi~aL~~-----~~-~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          44 TNQKTELQAIYLALQD-----SG-LEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             CHHHHHHHHHHHHHHH-----SC-SEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             cHHHHHHHHHHHHHHh-----CC-CeEEEEEehHHHHHHHhcCccccchHHHHHHHHHHhcCCceEEEEeCCC
Confidence            3447899999999974     33 7899999999887777532221111112222333333 46778888883

>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=86.75  E-value=0.12  Score=37.41  Aligned_cols=78  Identities=15%  Similarity=0.147  Sum_probs=48.2

Q ss_pred             hHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccc--------------cccchhH-HHHHHHHhcCCceEEE
Q psy8593          77 PRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDL--------------YKIQNNR-LKRLKIKLFPYQFELK  141 (204)
Q Consensus        77 ~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~--------------~k~~~~R-l~RW~~~L~~yd~~I~  141 (204)
                      ..-|+.|++.||+.    ......+.++||...+...++...              ....|.- +++-...+..++++++
T Consensus        44 n~aEl~Ai~~AL~~----~~~~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~  119 (147)
T d1rila_          44 NRMELKAAIEGLKA----LKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFH  119 (147)
T ss_dssp             HHHHHHHHHHHHHS----CCSCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECC
T ss_pred             HHHHHHHHHHHhhh----ccCCceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceE
Confidence            35699999999963    222267899999988765442100              0001111 1233345677889999


Q ss_pred             eeCCC----ccccCCCCCcccccC
Q psy8593         142 YLPGK----YMHIAELADYLSRNL  161 (204)
Q Consensus       142 y~~Gk----~n~vA~~~DaLSR~~  161 (204)
                      |+||.    .|-.|   |.|.+.-
T Consensus       120 wVkgHsg~~gNe~A---D~LAk~a  140 (147)
T d1rila_         120 FVKGHTGHPENERV---DREARRQ  140 (147)
T ss_dssp             CCCGGGSCTHHHHH---HHHHHHH
T ss_pred             EccCCCCCcchHHH---HHHHHHH
Confidence            99974    45567   8887643

>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=80.30  E-value=0.28  Score=35.17  Aligned_cols=82  Identities=22%  Similarity=0.187  Sum_probs=50.3

Q ss_pred             hHHHHHHHHHHHHHHHHhhcCccceecccCCcchhHhhhccc-----------ccc--ch-hHHHHHHHHhcCCceEEEe
Q psy8593          77 PRDELAGFRSEATEFCYYVYGHRNIVVQTDHQPLLAINKKDL-----------YKI--QN-NRLKRLKIKLFPYQFELKY  142 (204)
Q Consensus        77 ~EkEllAIv~al~kfr~yL~G~~~f~V~TDHk~L~~l~~k~~-----------~k~--~~-~Rl~RW~~~L~~yd~~I~y  142 (204)
                      ..-|++|++.|++..    .....+.++||.+.....+++..           ...  .+ ..+.+....+..+++.+++
T Consensus        43 n~aE~~Ai~~Al~~~----~~~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~w  118 (152)
T d1jl1a_          43 NRMELMAAIVALEAL----KEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEW  118 (152)
T ss_dssp             HHHHHHHHHHHHHTC----CSCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEE
T ss_pred             HHHHHhhhhhhhhhh----cccceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEE
Confidence            457999999998752    23156788899876655543110           000  11 1222333445777899999


Q ss_pred             eCCC----ccccCCCCCcccccCcccC
Q psy8593         143 LPGK----YMHIAELADYLSRNLLVKN  165 (204)
Q Consensus       143 ~~Gk----~n~vA~~~DaLSR~~~~~~  165 (204)
                      +||.    -|-.|   |.|.+.-....
T Consensus       119 V~gH~g~~gNe~A---D~LAk~aa~~~  142 (152)
T d1jl1a_         119 VKGHAGHPENERA---DELARAAAMNP  142 (152)
T ss_dssp             CCSSTTCHHHHHH---HHHHHHHHHSC
T ss_pred             ecccCCCccHHHH---HHHHHHHHhCC
Confidence            9985    46667   99987654433