Psyllid ID: psy6927

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90---
Protein Sequence
MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELISHKL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHcccccEEEEEccEEEcHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccEEEccccccccccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcccccEEEEEEEEEccccHEEHHHHccccHHHHHHHHHHHHHHHHHccHHHccEccccccccccccccccHHHHHHccc
Coil and Loop (DISEMBL)
MEMRCGKTFLILEHSLNSiqafswvtyrdgdsQVALYwisspplrwKTFVANRVSKIQELVsedkwfhvkgtenpadclsrgitpkelishkl
Flexible Loop (DISEMBL)
MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQElvsedkwfhvkgtenpadclsrgitpkelishkl
Low Complexity Region (SEG)
MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELISHKL
Disordered region (IsUnstruct)
****CGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCL**************
Disordered Region (DISOPRED)
MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS***
Disordered Region (DISEMBL)
MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELISHKL
Disordered Region (DISPRO)
*EMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKEL*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELISHKL
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	93
270012036	1210	hypothetical protein TcasGA2_TC006136 [T	0.677	0.052	0.603	2e-15
270016778	1330	hypothetical protein TcasGA2_TC010713 [T	0.677	0.047	0.603	2e-15
270016775	668	hypothetical protein TcasGA2_TC010710 [T	0.677	0.094	0.603	4e-15
307190428	511	hypothetical protein EAG_09297 [Camponot	0.795	0.144	0.518	4e-15
270016779	915	hypothetical protein TcasGA2_TC010714 [T	0.677	0.068	0.587	3e-14
307172693	699	hypothetical protein EAG_00896 [Camponot	0.795	0.105	0.518	6e-14
340380172	1811	PREDICTED: hypothetical protein LOC10064	0.956	0.049	0.439	2e-13
68697272	1726	BEL12_AG transposon polyprotein [Anophel	0.741	0.039	0.5	3e-13
322782831	788	hypothetical protein SINV_03189 [Solenop	0.677	0.079	0.539	1e-12
270015560	915	hypothetical protein TcasGA2_TC016136 [T	0.645	0.065	0.6	1e-12

>gi|270012036|gb|EFA08484.1| hypothetical protein TcasGA2_TC006136 [Tribolium castaneum]

 Score = 86.3 bits (212), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 47/63 (74%)

Query: 31  DSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS 90
           DS V L WI++ P RW TFVANRV+KIQELV    W+HV G ENPAD +SRG+TP  L++
Sbjct: 592 DSSVVLNWINASPHRWHTFVANRVAKIQELVPSVNWYHVDGKENPADPISRGLTPAHLLN 651

Query: 91  HKL 93
           H +
Sbjct: 652 HPI 654

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270016778|gb|EFA13224.1| hypothetical protein TcasGA2_TC010713 [Tribolium castaneum]

 Score = 86.3 bits (212), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 47/63 (74%)

Query: 31  DSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS 90
           DS V L WI++ P RW TFVANRV+KIQELV    W+HV G ENPAD +SRG+TP  L++
Sbjct: 738 DSSVVLNWINASPHRWHTFVANRVAKIQELVPSVNWYHVDGKENPADPISRGLTPAHLLN 797

Query: 91  HKL 93
           H +
Sbjct: 798 HPI 800

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270016775|gb|EFA13221.1| hypothetical protein TcasGA2_TC010710 [Tribolium castaneum]

 Score = 85.5 bits (210), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 47/63 (74%)

Query: 31  DSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS 90
           DS V L WI++ P RW TFVANRV+KIQELV    W+HV G ENPAD +SRG+TP  L++
Sbjct: 243 DSSVVLNWINASPHRWHTFVANRVAKIQELVPSVNWYHVDGKENPADPISRGLTPAHLLN 302

Query: 91  HKL 93
           H +
Sbjct: 303 HPI 305

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307190428|gb|EFN74469.1| hypothetical protein EAG_09297 [Camponotus floridanus]

 Score = 85.1 bits (209), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 5/79 (6%)

Query: 15  SLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTEN 74
           SL+S   F W      DS+V L+WI     RWKT+VANRVS+IQE + E +W HV G +N
Sbjct: 143 SLSSAPVFLW-----SDSKVTLHWIHGHASRWKTYVANRVSQIQERLPEARWRHVPGKDN 197

Query: 75  PADCLSRGITPKELISHKL 93
           PADC SRG+ P +L+ H L
Sbjct: 198 PADCASRGVLPSDLVGHLL 216

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270016779|gb|EFA13225.1| hypothetical protein TcasGA2_TC010714 [Tribolium castaneum]

 Score = 82.4 bits (202), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 46/63 (73%)

Query: 31  DSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS 90
           DS V L WI++   RW TFVANRV+KIQELV    WFHV G ENPAD +S+G+TP  L++
Sbjct: 807 DSLVVLNWINASSYRWHTFVANRVAKIQELVPSVNWFHVDGKENPADPISKGLTPAHLLN 866

Query: 91  HKL 93
           H +
Sbjct: 867 HPI 869

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307172693|gb|EFN64015.1| hypothetical protein EAG_00896 [Camponotus floridanus]

 Score = 81.6 bits (200), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 41/79 (51%), Positives = 50/79 (63%), Gaps = 5/79 (6%)

Query: 15  SLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTEN 74
           SL++   F W      DS+V L+WI     RWKT+VANRVS IQE + E +W HV G +N
Sbjct: 88  SLSAAPVFLW-----SDSKVTLHWIHGHASRWKTYVANRVSLIQEQLPEARWRHVPGRDN 142

Query: 75  PADCLSRGITPKELISHKL 93
           PADC SRGI P +L  H L
Sbjct: 143 PADCASRGILPDDLADHLL 161

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340380172|ref|XP_003388597.1| PREDICTED: hypothetical protein LOC100641852 [Amphimedon queenslandica]

 Score = 79.3 bits (194), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/91 (43%), Positives = 52/91 (57%), Gaps = 2/91 (2%)

Query: 5    CGKTFL--ILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVS 62
            CG   L  +L H    +Q     T+   DS + L W+   P R+KT+V NRVS I E + 
Sbjct: 1179 CGAQLLAQLLGHVREVLQLSLKDTFGWTDSTIVLNWLQGSPKRFKTYVCNRVSYIVEAIP 1238

Query: 63   EDKWFHVKGTENPADCLSRGITPKELISHKL 93
               WFHV G +NPADC SRG+ P EL+ H+L
Sbjct: 1239 STNWFHVDGADNPADCASRGMFPSELLDHEL 1269

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|68697272|emb|CAJ14165.1| BEL12_AG transposon polyprotein [Anopheles gambiae]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 45/74 (60%), Gaps = 5/74 (6%)

Query: 20   QAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCL 79
            + F W      DS   +YW+ S P RWKTFVANRVS+IQ    E +W HV G  NPAD +
Sbjct: 1118 ETFCWT-----DSSTVIYWLKSSPSRWKTFVANRVSQIQNATKEFEWRHVPGIHNPADAV 1172

Query: 80   SRGITPKELISHKL 93
            SRG  P E++  KL
Sbjct: 1173 SRGRNPAEVVEDKL 1186

Source: Anopheles gambiae

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322782831|gb|EFZ10604.1| hypothetical protein SINV_03189 [Solenopsis invicta]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/63 (53%), Positives = 44/63 (69%)

Query: 31  DSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS 90
           DS V LYWI     RWK FV NRVS+I +++  + W HVKG+ENPAD +SRG TP +L+ 
Sbjct: 515 DSMVVLYWIGGDSNRWKPFVGNRVSEITDILPAEHWRHVKGSENPADLISRGATPAQLLD 574

Query: 91  HKL 93
           + L
Sbjct: 575 NSL 577

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015560|gb|EFA12008.1| hypothetical protein TcasGA2_TC016136 [Tribolium castaneum]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/60 (60%), Positives = 42/60 (70%)

Query: 31  DSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELIS 90
           DS + L W++SPP RWKTF+ANRVS+IQ L    KW  V   +NPAD LSRGI P EL S
Sbjct: 276 DSTIVLNWLNSPPSRWKTFIANRVSEIQNLTQNAKWQLVPSNDNPADLLSRGIYPSELGS 335

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	93
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	97.2
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	96.82
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	96.7
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	94.14
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	93.28
PRK13907	128	rnhA ribonuclease H; Provisional	92.99
PRK07708	219	hypothetical protein; Validated	92.56
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	87.38
PRK06548	161	ribonuclease H; Provisional	84.2
PRK00203	150	rnhA ribonuclease H; Reviewed	81.31

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

Probab=97.20  E-value=0.00014  Score=56.41  Aligned_cols=50  Identities=30%  Similarity=0.347  Sum_probs=36.9

Q ss_pred             ceeeeeecccCCChHHHHHHHHhCCCCCchhH------HHHHHHHHHhhccCCceEecCCCCCCCcccCCCCC
Q psy6927          18 SIQAFSWVTYRDGDSQVALYWISSPPLRWKTF------VANRVSKIQELVSEDKWFHVKGTENPADCLSRGIT   84 (93)
Q Consensus        18 i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~F------VaNRV~~I~~~~~~~~W~hVps~~NPAD~aSRG~~   84 (93)
                      +..-.+-     |||++||+      +++.+|      +||-      +....++-||||+.||||..|||.-
T Consensus       140 ~~~r~l~-----tDnt~Vls------rkyts~PW~lac~A~w------iLrgts~~yVPS~~NPAD~PsR~~~  195 (245)
T PF00336_consen  140 SGARCLG-----TDNTVVLS------RKYTSFPWLLACAANW------ILRGTSFYYVPSKYNPADDPSRGKL  195 (245)
T ss_pred             cCCcEEe-----ecCcEEEe------cccccCcHHHHHHHHH------hhcCceEEEeccccCcCCCCCCCcc
Confidence            3444567     99999875      444443      3443      3668899999999999999999964

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

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

Probab=96.82  E-value=0.0022  Score=39.18  Aligned_cols=62  Identities=19%  Similarity=0.158  Sum_probs=41.7

Q ss_pred             HHHhcccceeeeeecccCCChHHHHHHHHhCCCCCchhHHHHHHHHHHhhcc---CCceEecCCCCCC-Ccc
Q psy6927          11 ILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVS---EDKWFHVKGTENP-ADC   78 (93)
Q Consensus        11 ~~e~~i~i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~FVaNRV~~I~~~~~---~~~W~hVps~~NP-AD~   78 (93)
                      ..-.++.+.++.+.     |||..+...|++...... .....+.+|+.+..   ...++|||-+.|= ||-
T Consensus        14 ~~a~~~g~~~i~v~-----sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~   79 (87)
T PF13456_consen   14 QLAWELGIRKIIVE-----SDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADA   79 (87)
T ss_dssp             HHHHCCT-SCEEEE-----ES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHH
T ss_pred             HHHHHCCCCEEEEE-----ecCccccccccccccccc-cccccchhhhhhhccccceEEEEEChHHhHHHHH
Confidence            33446778899999     999999999988743333 56667777777665   5889999999884 443

>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=96.70  E-value=0.0026  Score=39.45  Aligned_cols=62  Identities=16%  Similarity=0.131  Sum_probs=43.7

Q ss_pred             cccceeeeeecccCCChHHHHHHHHhCCCCCchhHHHHHHHHHHhhc---cCCceEecCC-----CCCCCcccCC
Q psy6927          15 SLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELV---SEDKWFHVKG-----TENPADCLSR   81 (93)
Q Consensus        15 ~i~i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~FVaNRV~~I~~~~---~~~~W~hVps-----~~NPAD~aSR   81 (93)
                      ......+.++     |||..++..+++.......=....+.+|++..   ....++|||+     .++.||.++|
T Consensus        58 ~~~~~~i~i~-----~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~  127 (130)
T cd06222          58 ELGGKKVNIY-----TDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAK  127 (130)
T ss_pred             hCCCceEEEE-----ECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHH
Confidence            5678899999     99999999999864312223444445555544   5688899999     5558887554

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.

>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=94.14  E-value=0.16  Score=33.23  Aligned_cols=52  Identities=13%  Similarity=0.050  Sum_probs=35.7

Q ss_pred             eeeeeecccCCChHHHHHHHHhC-----CCCCchh--HHHHHHHHHHhhccCCceEecCCCCCC
Q psy6927          19 IQAFSWVTYRDGDSQVALYWISS-----PPLRWKT--FVANRVSKIQELVSEDKWFHVKGTENP   75 (93)
Q Consensus        19 ~~~~~w~~~~~tDS~i~L~wI~~-----~~~~~~~--FVaNRV~~I~~~~~~~~W~hVps~~NP   75 (93)
                      ..+.++     |||+.++.+|..     ..+.-..  =+.+++.+.........++|||+..+-
T Consensus        58 ~~v~I~-----tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~  116 (132)
T PF00075_consen   58 RKVTIY-----TDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV  116 (132)
T ss_dssp             SEEEEE-----ES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred             cccccc-----ccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence            888999     999999998877     2111111  144566666655557899999999765

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 ....

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

Probab=93.28  E-value=0.24  Score=36.16  Aligned_cols=69  Identities=28%  Similarity=0.340  Sum_probs=44.4

Q ss_pred             CcchhhHHHHHHHhcccceeeeeecccCCChHHHHHH----HHhC-CCCCchh----HHHH--HHHHHHhhcc---CCce
Q psy6927           1 MEMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALY----WISS-PPLRWKT----FVAN--RVSKIQELVS---EDKW   66 (93)
Q Consensus         1 ~~~~~~~~~l~~e~~i~i~~~~~w~~~~~tDS~i~L~----wI~~-~~~~~~~----FVaN--RV~~I~~~~~---~~~W   66 (93)
                      ||++++..-|..-..+....+.++     |||+.|..    |+.+ ....|++    .|-|  .-.++.++.+   ...|
T Consensus        46 aEl~A~i~AL~~l~~~~~~~v~l~-----tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~  120 (154)
T COG0328          46 AELRALIEALEALKELGACEVTLY-----TDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFW  120 (154)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEE-----ecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEE
Confidence            455555544544445789999999     99998844    6444 3345663    3333  3555555555   4599


Q ss_pred             EecCCCCC
Q psy6927          67 FHVKGTEN   74 (93)
Q Consensus        67 ~hVps~~N   74 (93)
                      ++||+..+
T Consensus       121 ~WVkgH~g  128 (154)
T COG0328         121 EWVKGHAG  128 (154)
T ss_pred             EEeeCCCC
Confidence            99997764

>PRK13907 rnhA ribonuclease H; Provisional

Probab=92.99  E-value=0.28  Score=32.75  Aligned_cols=61  Identities=16%  Similarity=-0.002  Sum_probs=39.0

Q ss_pred             cccceeeeeecccCCChHHHHHHHHhCCCCCchhHHHHHHHHHHhh---ccCCceEecCCCCCC-CcccCC
Q psy6927          15 SLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQEL---VSEDKWFHVKGTENP-ADCLSR   81 (93)
Q Consensus        15 ~i~i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~FVaNRV~~I~~~---~~~~~W~hVps~~NP-AD~aSR   81 (93)
                      ...+..+.+.     |||+.+..++++...+- .-...-+.+++++   .+...+.|||.+.|= ||.+.|
T Consensus        58 ~~g~~~v~i~-----sDS~~vi~~~~~~~~~~-~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~  122 (128)
T PRK13907         58 EHNYNIVSFR-----TDSQLVERAVEKEYAKN-KMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELAR  122 (128)
T ss_pred             hCCCCEEEEE-----echHHHHHHHhHHHhcC-hhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHH
Confidence            3445679999     99999999998753211 1123334455444   344556899998874 775443

>PRK07708 hypothetical protein; Validated

Probab=92.56  E-value=0.27  Score=37.26  Aligned_cols=63  Identities=17%  Similarity=0.158  Sum_probs=38.7

Q ss_pred             HHHHhcccceeeeeecccCCChHHHHHHHHhCCCCC----chhHHHHHHHHHHhhcc-CCceEecCCCCCC-Ccc
Q psy6927          10 LILEHSLNSIQAFSWVTYRDGDSQVALYWISSPPLR----WKTFVANRVSKIQELVS-EDKWFHVKGTENP-ADC   78 (93)
Q Consensus        10 l~~e~~i~i~~~~~w~~~~~tDS~i~L~wI~~~~~~----~~~FVaNRV~~I~~~~~-~~~W~hVps~~NP-AD~   78 (93)
                      +..++++.-..+.+.     +||+.+..|+++.-+.    .+.+. .++.++.+... ...+.|||-++|= ||-
T Consensus       132 ~A~e~g~~~~~V~I~-----~DSqlVi~qi~g~wk~~~~~l~~y~-~~i~~l~~~~~l~~~~~~VpR~~N~~AD~  200 (219)
T PRK07708        132 ELEELGVKHEPVTFR-----GDSQVVLNQLAGEWPCYDEHLNHWL-DRIEQKLKQLKLTPVYEPISRKQNKEADQ  200 (219)
T ss_pred             HHHHcCCCcceEEEE-----eccHHHHHHhCCCceeCChhHHHHH-HHHHHHHhhCCceEEEEECCchhhhHHHH
Confidence            344556555568899     9999999999875222    22333 23332222222 2567899998884 664

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=87.38  E-value=1.4  Score=34.76  Aligned_cols=59  Identities=15%  Similarity=0.129  Sum_probs=39.8

Q ss_pred             ccceeeeeecccCCChHHHHHHHHhCCCC----CchhHHHHHHHHHHhhccCCceEecCCCCC-CCcccC
Q psy6927          16 LNSIQAFSWVTYRDGDSQVALYWISSPPL----RWKTFVANRVSKIQELVSEDKWFHVKGTEN-PADCLS   80 (93)
Q Consensus        16 i~i~~~~~w~~~~~tDS~i~L~wI~~~~~----~~~~FVaNRV~~I~~~~~~~~W~hVps~~N-PAD~aS   80 (93)
                      ..+..+.+.     |||..+..-+.+.-+    .+..+. ..+.++.+..+...++|||.++| .||.+.
T Consensus        63 ~g~~~v~i~-----~DS~lvi~~i~~~~~~~~~~l~~~~-~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA  126 (372)
T PRK07238         63 LGATEVEVR-----MDSKLVVEQMSGRWKVKHPDMKPLA-AQARELASQFGRVTYTWIPRARNAHADRLA  126 (372)
T ss_pred             CCCCeEEEE-----eCcHHHHHHhCCCCccCChHHHHHH-HHHHHHHhcCCceEEEECCchhhhHHHHHH
Confidence            445689999     999999999976421    222332 34555555566789999998766 466543

>PRK06548 ribonuclease H; Provisional

Probab=84.20  E-value=2.2  Score=30.94  Aligned_cols=65  Identities=17%  Similarity=0.284  Sum_probs=36.3

Q ss_pred             cchhhHHHHHHHhcccceeeeeecccCCChHHHHHHHHh----C-CCCCch----hHHHHH--HHHHHhhcc--CCceEe
Q psy6927           2 EMRCGKTFLILEHSLNSIQAFSWVTYRDGDSQVALYWIS----S-PPLRWK----TFVANR--VSKIQELVS--EDKWFH   68 (93)
Q Consensus         2 ~~~~~~~~l~~e~~i~i~~~~~w~~~~~tDS~i~L~wI~----~-~~~~~~----~FVaNR--V~~I~~~~~--~~~W~h   68 (93)
                      |..+....| +.+.-....+.++     |||+.|+.=|.    + ..+.|+    .-|+||  +.+|.++..  ...|.|
T Consensus        46 El~Aii~aL-~~~~~~~~~v~I~-----TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~w  119 (161)
T PRK06548         46 ELTAVRELL-IATRHTDRPILIL-----SDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSW  119 (161)
T ss_pred             HHHHHHHHH-HhhhcCCceEEEE-----eChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEE
Confidence            444444322 2333333468999     99999965443    2 112232    457776  344444432  578999


Q ss_pred             cCCC
Q psy6927          69 VKGT   72 (93)
Q Consensus        69 Vps~   72 (93)
                      |++.
T Consensus       120 VkgH  123 (161)
T PRK06548        120 VNAH  123 (161)
T ss_pred             EecC
Confidence            9874

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=81.31  E-value=2.2  Score=29.61  Aligned_cols=52  Identities=27%  Similarity=0.441  Sum_probs=32.3

Q ss_pred             ceeeeeecccCCChHHHHHH----HHhC-CCCCch----hHHHHH--HHHHHhhcc--CCceEecCCCCC
Q psy6927          18 SIQAFSWVTYRDGDSQVALY----WISS-PPLRWK----TFVANR--VSKIQELVS--EDKWFHVKGTEN   74 (93)
Q Consensus        18 i~~~~~w~~~~~tDS~i~L~----wI~~-~~~~~~----~FVaNR--V~~I~~~~~--~~~W~hVps~~N   74 (93)
                      ...+.++     |||+.++.    |+.. ..+.|+    .-|+|+  ..+|.++..  ...|.|||+-.+
T Consensus        61 ~~~v~I~-----tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~  125 (150)
T PRK00203         61 PCEVTLY-----TDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAG  125 (150)
T ss_pred             CCeEEEE-----ECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCC
Confidence            3578899     99987765    4432 112233    245665  466666544  578999997653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	93
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	96.73
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	96.4
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	96.27
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	92.58
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	88.76
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	86.43
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	83.76

>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=96.73  E-value=0.0022  Score=41.87  Aligned_cols=59  Identities=20%  Similarity=0.057  Sum_probs=39.9

Q ss_pred             ccceeeeeecccCCChHHHHHHHHhCCCCCchhHHHHHHHHHHhhc---cCCceEecCCCCC-CCccc
Q psy6927          16 LNSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELV---SEDKWFHVKGTEN-PADCL   79 (93)
Q Consensus        16 i~i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~FVaNRV~~I~~~~---~~~~W~hVps~~N-PAD~a   79 (93)
                      ..+.++.+.     |||+.++.++++.-+.-..-....+.+|+++.   ....|.|||.+.| .||-+
T Consensus        64 ~~~~~v~i~-----tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~L  126 (141)
T 3hst_B           64 LGATEAAVL-----MDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRL  126 (141)
T ss_dssp             HTCSEEEEE-----ESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHH
T ss_pred             CCCceEEEE-----eChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHH
Confidence            456789999     99999999998731111122334455555554   4689999998887 46643

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

Probab=96.40  E-value=0.0051  Score=39.70  Aligned_cols=54  Identities=19%  Similarity=0.144  Sum_probs=36.0

Q ss_pred             eeeeecccCCChHHHHHHHHhCCCC-CchhH--HHHHHHHH-HhhccCCceEecCCCCC-CCcc
Q psy6927          20 QAFSWVTYRDGDSQVALYWISSPPL-RWKTF--VANRVSKI-QELVSEDKWFHVKGTEN-PADC   78 (93)
Q Consensus        20 ~~~~w~~~~~tDS~i~L~wI~~~~~-~~~~F--VaNRV~~I-~~~~~~~~W~hVps~~N-PAD~   78 (93)
                      .+.+.     |||+.++.++++.-. +-+.+  ...++.++ .+......|.|||.+.| .||-
T Consensus        71 ~v~i~-----tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~  129 (140)
T 3u3g_D           71 EVEVR-----MDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADE  129 (140)
T ss_dssp             EEEEE-----ESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHH
T ss_pred             eEEEE-----eChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHH
Confidence            89999     999999999987321 11111  22344444 44456899999998777 3554

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

Probab=96.27  E-value=0.0041  Score=41.53  Aligned_cols=58  Identities=22%  Similarity=0.232  Sum_probs=38.7

Q ss_pred             ccceeeeeecccCCChHHHHHHHHhCCC----CCchhHHHHHHHHHHhhccCCceEecCCCCC-CCcccC
Q psy6927          16 LNSIQAFSWVTYRDGDSQVALYWISSPP----LRWKTFVANRVSKIQELVSEDKWFHVKGTEN-PADCLS   80 (93)
Q Consensus        16 i~i~~~~~w~~~~~tDS~i~L~wI~~~~----~~~~~FVaNRV~~I~~~~~~~~W~hVps~~N-PAD~aS   80 (93)
                      ..+.++.+.     |||+.+..||++.-    ...+.+ ..++.++.+.. ...|.|||.+.| .||-+.
T Consensus        66 ~g~~~v~i~-----tDS~~vi~~i~~~w~~~~~~~~~l-~~~i~~l~~~~-~v~~~~V~~~~N~~AD~LA  128 (149)
T 2ehg_A           66 LGISSPIIK-----GDSQLVIKQMNGEYKVKAKRIIPL-YEKAIELKKKL-NATLIWVPREENKEADRLS  128 (149)
T ss_dssp             HTCCSCEEE-----ESCHHHHHHHTTSSCCCCTTHHHH-HHHHHHHHHHH-TCEEEECCGGGCHHHHHHH
T ss_pred             cCCCEEEEE-----eChHHHHHHHhCccccCCHHHHHH-HHHHHHHHhcC-CEEEEEcCCcccHHHHHHH
Confidence            446789999     99999999998741    112222 22333333333 599999999988 577543

>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=92.58  E-value=0.049  Score=36.84  Aligned_cols=48  Identities=10%  Similarity=-0.008  Sum_probs=32.4

Q ss_pred             eeeeecccCCChHHHHHHHHhCCCCC-chhHHHHHHHHHHhhccCCceEecCCCC
Q psy6927          20 QAFSWVTYRDGDSQVALYWISSPPLR-WKTFVANRVSKIQELVSEDKWFHVKGTE   73 (93)
Q Consensus        20 ~~~~w~~~~~tDS~i~L~wI~~~~~~-~~~FVaNRV~~I~~~~~~~~W~hVps~~   73 (93)
                      ++.++     |||+.+..|+.+.-+. -+..+.|+ ..++++.....|.|||+-.
T Consensus        71 ~v~I~-----tDS~~i~~w~~~~w~~~~~~~~~~~-~l~~~l~~~v~~~wV~gH~  119 (147)
T 2kq2_A           71 KIRIL-----HDYAGIAFWATGEWKAKNEFTQAYA-KLMNQYRGIYSFEKVKAHS  119 (147)
T ss_dssp             CCCBS-----SCCSTHHHHTTSSSSCCHHHHHHHH-CGGGGGSTTCCBCCCCCCC
T ss_pred             eEEEE-----ECcHHHHHHHhCCCccCCcchHHHH-HHHHHhcCCeeEEEecCcC
Confidence            88999     9999999999763211 12334443 3455555578999999753

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

Probab=88.76  E-value=0.89  Score=30.34  Aligned_cols=53  Identities=23%  Similarity=0.374  Sum_probs=31.9

Q ss_pred             ccceeeeeecccCCChHHHHHHHHhCC-----CCCch----hHHHHH--HHHHHhhcc--CCceEecCCCC
Q psy6927          16 LNSIQAFSWVTYRDGDSQVALYWISSP-----PLRWK----TFVANR--VSKIQELVS--EDKWFHVKGTE   73 (93)
Q Consensus        16 i~i~~~~~w~~~~~tDS~i~L~wI~~~-----~~~~~----~FVaNR--V~~I~~~~~--~~~W~hVps~~   73 (93)
                      .....+.++     |||+.++.-|..-     .+.|+    .-|.|+  +.+|.++..  ...|.|||+..
T Consensus        68 ~~~~~v~i~-----tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~  133 (154)
T 2qkb_A           68 QNINKLVLY-----TNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHS  133 (154)
T ss_dssp             TTCCEEEEE-----ESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTS
T ss_pred             CCCceEEEE-----ECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCC
Confidence            456789999     9999888655441     11222    112332  445554443  48899999854

>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=86.43  E-value=0.22  Score=34.39  Aligned_cols=17  Identities=24%  Similarity=0.511  Sum_probs=15.3

Q ss_pred             eeeecccCCChHHHHHHHHhCC
Q psy6927          21 AFSWVTYRDGDSQVALYWISSP   42 (93)
Q Consensus        21 ~~~w~~~~~tDS~i~L~wI~~~   42 (93)
                      +.++     |||+.|..||++.
T Consensus        67 v~i~-----tDSqyVi~wi~~~   83 (134)
T 4htu_A           67 KPIY-----SNSQTAIKWVKDK   83 (134)
T ss_dssp             CCEE-----ESCHHHHHHHHHT
T ss_pred             EEEE-----cchHHHHHHHHcC
Confidence            7899     9999999999863

>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=83.76  E-value=1.5  Score=35.17  Aligned_cols=56  Identities=20%  Similarity=0.157  Sum_probs=37.3

Q ss_pred             ceeeeeecccCCChHHHHHHHHhCCCCCchhHHHHHHH-HHHhhccCCceEecCCC-----CCCCccc
Q psy6927          18 SIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVS-KIQELVSEDKWFHVKGT-----ENPADCL   79 (93)
Q Consensus        18 i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~FVaNRV~-~I~~~~~~~~W~hVps~-----~NPAD~a   79 (93)
                      ..++.++     |||+.|+..|.+....-..-+.+++- ++.+ .....|.|||+.     +.=||-+
T Consensus       492 ~~~v~I~-----tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~~-~~~v~~~wV~~H~g~~~Ne~AD~L  553 (557)
T 2zd1_A          492 GLEVNIV-----TDSQYALGIIQAQPDKSESELVNQIIEQLIK-KEKVYLAWVPAHKGIGGNEQVDKL  553 (557)
T ss_dssp             CSEEEEE-----ECCHHHHHHHTTCCSEESSHHHHHHHHHHHH-CSEEEEEECCSSSCCTTCCGGGGC
T ss_pred             CCcEEEE-----eChHHHHHHHhcCCccCCHHHHHHHHHHHhc-CCCEEEEEcCCCCCChhHHHHHHH
Confidence            6789999     99999999998854331233334443 4443 346899999984     3446653

---

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	93
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	94.31
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	88.17

>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=94.31  E-value=0.04  Score=34.40  Aligned_cols=54  Identities=13%  Similarity=0.022  Sum_probs=37.5

Q ss_pred             hcccceeeeeecccCCChHHHHHHHHhCCCCCchh-HHHHHHHHHHhhccCCceEecCCCC
Q psy6927          14 HSLNSIQAFSWVTYRDGDSQVALYWISSPPLRWKT-FVANRVSKIQELVSEDKWFHVKGTE   73 (93)
Q Consensus        14 ~~i~i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~-FVaNRV~~I~~~~~~~~W~hVps~~   73 (93)
                      +......+.++     |||+-|+.|+.+..+.++. ....++.+..+. ....+.|||+-.
T Consensus        56 l~~~~~~i~I~-----tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~~-~~v~~~wV~gH~  110 (126)
T d1mu2a1          56 LTDSGPKVNII-----VDSQYVMGIVASQPTESESKIVNQIIEEMIKK-EAIYVAWVPAHK  110 (126)
T ss_dssp             HHTSCSEEEEE-----ESCHHHHHHHHTCCSEESCHHHHHHHHHHHHC-SEEEEEECCSSS
T ss_pred             hccCCcceEEE-----echHHHHHHHhcCCccccchHHHHHHHHhhhc-ceeEEEEEeCCC
Confidence            34456789999     9999999999997555443 333444444443 367899999864

>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=88.17  E-value=0.28  Score=30.42  Aligned_cols=50  Identities=18%  Similarity=0.054  Sum_probs=32.0

Q ss_pred             cceeeeeecccCCChHHHHHHHHhCCCCCchhHHHHHHHHHHhhccCCceEecCC
Q psy6927          17 NSIQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHVKG   71 (93)
Q Consensus        17 ~i~~~~~w~~~~~tDS~i~L~wI~~~~~~~~~FVaNRV~~I~~~~~~~~W~hVps   71 (93)
                      ....+.++     |||+.|+.-+......|+.=.-.++-+....-....+.|||+
T Consensus        60 ~~~~v~I~-----TDS~yvi~~i~~~~~~~~~~l~~~il~~l~~~~~v~i~WVpg  109 (110)
T d1s1ta1          60 SGLEVNIV-----TDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPA  109 (110)
T ss_dssp             SCSEEEEE-----ECCHHHHHHHHHCCSEESCHHHHHHHHHHHHCSEEEEEECCS
T ss_pred             CCCeEEEE-----EehHHHHHHHhcCccccchHHHHHHHHHHhcCCceEEEEeCC
Confidence            45678999     999999999987655544322222222112234678899986