Psyllid ID: psy8376

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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-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------33
Protein Sequence
MDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHccccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEcccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEcccccccccccccccEEccccccccccHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEccccEEcccccccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHccccccccccccccccccHEEEEEccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MDDYKLEVRCVIKQqkeepqwllhqpkvtmlisskkdeelpsEINNKYLefkkdnkdkilcytdgsktntftggaYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISsfgsqvsflwipshvgirenEMVDRAARNAVNArltnqytssdykAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKhllerkdppacefcgqtpvylNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Flexible Loop (DISEMBL)
MDDYKLEVRCVikqqkeepqwllhqpkVTMLisskkdeelpsEINNKylefkkdnkdKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARltnqytssdykAHFKHIQFKRWEEIWRQNAVLgrqlrqiktdvrkwkssnrnirqeevvLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Low Complexity Region (SEG)
MDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDsiliskillkikeissFGSQVSFLWIPSHVGIRENEMVDraarnavnarLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Disordered region (IsUnstruct)
*****LEVRCVIKQ*****QWLLHQPKVTML***************KYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLF***
Disordered Region (DISOPRED)
**DYK***RC****QKEEPQWLLHQPKVTMLISS*********INNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Disordered Region (DISEMBL)
MDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Disordered Region (DISPRO)
***YKLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRSILQDNVETIDRCMKFLYHTKLFAKI
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	328	2.2.26 [Sep-21-2011]
P33459	1109	Pol polyprotein OS=Caprin	N/A	N/A	0.332	0.098	0.252	3e-05
P03370	1105	Pol polyprotein OS=Maedi	N/A	N/A	0.332	0.098	0.252	0.0002
P23427	1105	Pol polyprotein OS=Maedi	N/A	N/A	0.332	0.098	0.252	0.0002
P35956	1101	Pol polyprotein OS=Maedi	N/A	N/A	0.332	0.099	0.252	0.0002
P23426	1105	Pol polyprotein OS=Maedi	N/A	N/A	0.332	0.098	0.252	0.0004

>sp|P33459|POL_CAEVC Pol polyprotein OS=Caprine arthritis encephalitis virus (strain Cork) GN=pol PE=3 SV=1

 Score = 49.7 bits (117), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 59/119 (49%), Gaps = 10/119 (8%)

Query: 62  YTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDF 121
           YTDG K N      ++++ T E+F+ ++  +    EL AI+  L             +  
Sbjct: 582 YTDGGKKNKVGSLGFIVS-TGEKFRKHEEGTNQQLELRAIEEALKQ---------GPQTM 631

Query: 122 VICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDR 180
            + +DS+ + + L  N ++ ++ + I  +I EI+    ++   W+P H GI +NE +D+
Sbjct: 632 NLVTDSRYAFEFLLRNWDEEVIKNPIQARIMEIAHKKDRIGVHWVPGHKGIPQNEEIDK 690

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
Capra hircus (taxid: 9925)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2

>sp|P03370|POL_VILV Pol polyprotein OS=Maedi visna virus (strain 1514) GN=pol PE=3 SV=1

 Score = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 57/119 (47%), Gaps = 10/119 (8%)

Query: 62  YTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDF 121
           YTDG K N      Y+ + T E+F++++  +    EL AI+                +  
Sbjct: 577 YTDGGKKNGRGSLGYIAS-TGEKFRIHEEGTNQQLELRAIEEACKQ---------GPEKM 626

Query: 122 VICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDR 180
            I +DS+ + + +  N ++ ++ + I  +I E+     ++   W+P H GI +NE +DR
Sbjct: 627 NIVTDSRYAYEFMLRNWDEEVIRNPIQARIMELVHNKEKIGVHWVPGHKGIPQNEEIDR 685

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Ovis aries (taxid: 9940)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 2

EC: 3

>sp|P23427|POL_VILV2 Pol polyprotein OS=Maedi visna virus (strain 1514 / clone LV1-1KS2) GN=pol PE=3 SV=1

 Score = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 57/119 (47%), Gaps = 10/119 (8%)

Query: 62  YTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDF 121
           YTDG K N      Y+ + T E+F++++  +    EL AI+                +  
Sbjct: 577 YTDGGKKNGRGSLGYIAS-TGEKFRIHEEGTNQQLELRAIEEACKQ---------GPEKM 626

Query: 122 VICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDR 180
            I +DS+ + + +  N ++ ++ + I  +I E+     ++   W+P H GI +NE +DR
Sbjct: 627 NIVTDSRYAYEFMLRNWDEEVIRNPIQARIMELVHNKEKIGVHWVPGHKGIPQNEEIDR 685

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Ovis aries (taxid: 9940)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 2

EC: 3

>sp|P35956|POL_VILVK Pol polyprotein OS=Maedi visna virus (strain KV1772) GN=pol PE=1 SV=1

 Score = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 57/119 (47%), Gaps = 10/119 (8%)

Query: 62  YTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDF 121
           YTDG K N      Y+ + T E+F++++  +    EL AI+                +  
Sbjct: 573 YTDGGKKNGRGSLGYITS-TGEKFRIHEEGTNQQLELRAIEEACKQ---------GPEKM 622

Query: 122 VICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDR 180
            I +DS+ + + +  N ++ ++ + I  +I E+     ++   W+P H GI +NE +DR
Sbjct: 623 NIVTDSRYAYEFMLRNWDEEVIRNPIQARIMELVHNKEKIGVHWVPGHKGIPQNEEIDR 681

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Ovis aries (taxid: 9940)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 2

EC: 3

>sp|P23426|POL_VILV1 Pol polyprotein OS=Maedi visna virus (strain 1514 / clone LV1-1KS1) GN=pol PE=3 SV=1

 Score = 45.8 bits (107), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 56/119 (47%), Gaps = 10/119 (8%)

Query: 62  YTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDF 121
           YTDG K N      Y+ + T E+F++ +  +    EL AI+                +  
Sbjct: 577 YTDGGKKNGRGSLGYIAS-TGEKFRIYEEGTNQQLELRAIEEACKQ---------GPEKM 626

Query: 122 VICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDR 180
            I +DS+ + + +  N ++ ++ + I  +I E+     ++   W+P H GI +NE +DR
Sbjct: 627 NIVTDSRYAYEFMLRNWDEEVIRNPIQARIMELMHNKEKIGVHWVPGHKGIPQNEEIDR 685

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Ovis aries (taxid: 9940)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 2

EC: 3

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	328
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.926	0.248	0.334	2e-36
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.804	0.525	0.346	4e-27
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.698	0.877	0.364	2e-25
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.728	0.602	0.353	4e-24
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.625	0.331	0.339	4e-22
427791321	1210	Putative tick transposon, partial [Rhipi	0.762	0.206	0.315	4e-22
427791807	1212	Putative tick transposon, partial [Rhipi	0.762	0.206	0.315	5e-22
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.716	0.591	0.347	1e-21
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.746	0.520	0.298	2e-21
51950578	1219	putative ORF2 [Drosophila melanogaster]	0.905	0.243	0.292	5e-21

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/323 (33%), Positives = 174/323 (53%), Gaps = 19/323 (5%)

Query: 14   QQKEEPQWLLHQPKVTM-LISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFT 72
            +  + P WL+++PK+ + L++ KK+   PS +   + E ++   D    YTDGSK     
Sbjct: 911  ETPQNPPWLMNKPKLNLSLLNFKKENTDPSILQVHFRELQESYGDCGTIYTDGSKMEGKV 970

Query: 73   GGA-YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSL 131
              A    N+T+ + +L    SI+TAEL AI L L ++    ++ F     +ICSDSKS+L
Sbjct: 971  ACACSFRNKTISR-RLPDGCSIFTAELHAILLALMAVKASERSKF-----IICSDSKSAL 1024

Query: 132  QALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLT 191
            QAL     D  L+ K L  +  I++    V+F+W+PSHVGI  NE  DR A+ A+N  ++
Sbjct: 1025 QALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVS 1084

Query: 192  N-QYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNI-RQEEVVL 249
              Q   SD +       ++ W+  W   A    +LRQI  DVR W+ +++ + R+    +
Sbjct: 1085 GTQIPYSDLRQSIASATYREWQNRW--EAETHSKLRQIVADVR-WRPTSKGLTRRGSTTM 1141

Query: 250  CRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQHQRS----IL 305
             RLRIGH   TH  +L+R++PP CE+C  + + + H L +C    ++R +H R+     L
Sbjct: 1142 SRLRIGHTYITHSFVLKREEPPLCEYC-DSRLTVEHILVDCPRYQDVRAKHFRATNLKTL 1200

Query: 306  QDNVETIDRCMKFLYHTKLFAKI 328
             +NV+   + + F+    L  KI
Sbjct: 1201 FNNVDP-GKVLGFILEVGLSTKI 1222

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score =  128 bits (321), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 95/274 (34%), Positives = 135/274 (49%), Gaps = 10/274 (3%)

Query: 19  PQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLL 78
           P W L  P+V   IS    ++ P+    +      D    I  YTDGSK+N     A+  
Sbjct: 42  PPWKLRPPEVDTSISKFLKDQHPALFLKQEFYNLIDKYPGINIYTDGSKSNNAVACAFTC 101

Query: 79  NETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALK-FN 137
           +    QF L    SIYTAEL+AI+      L++I+       F ICSDS SSL AL   +
Sbjct: 102 STYQIQFGLPTQMSIYTAELIAIE----QALIFIETVKDEDQFNICSDSLSSLTALSNCD 157

Query: 138 LNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTN-QYTS 196
           +    L+S IL K   +   G  V F+W PSHVGI  NE+ DR A+ A+   +T      
Sbjct: 158 ITHPYLLS-ILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPH 216

Query: 197 SDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGH 256
           +DYK+  +      W+  W +      +L  I+  + +WK   +  R+ E+VL R RIGH
Sbjct: 217 TDYKSPIRSYVKSLWQNEWDEET--DNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGH 274

Query: 257 CLATHKHLLERKDPPACEFCGQTPVYLNHWLTEC 290
              TH +LL R+  P C  C Q+ + + H L +C
Sbjct: 275 SHLTHGYLLRREVAPFCIPC-QSLLTVKHILIDC 307

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]

 Score =  122 bits (307), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 122/239 (51%), Gaps = 10/239 (4%)

Query: 54  DNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQ 113
           D    I  YTDGSK+N     A+  +    QF L    SIYTAEL+AI+      L++I+
Sbjct: 31  DKYPGINIYTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIE----QALIFIE 86

Query: 114 NNFCFKDFVICSDSKSSLQALK-FNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGI 172
                  F ICSDS SSL AL   ++    L+S IL K   +   G  V F+W PSHVGI
Sbjct: 87  TVKDEDQFNICSDSLSSLTALSNCDITHPYLLS-ILTKQNNLVRKGKLVVFIWCPSHVGI 145

Query: 173 RENEMVDRAARNAVNARLTN-QYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTD 231
             NE+ DR A+ A+   +T      +DYK+  +      W+  W +      +L  I+  
Sbjct: 146 LGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEET--DNKLHSIQPV 203

Query: 232 VRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTEC 290
           + +WK   +  R+ E+VL R RIGH   TH +LL R+  P C  C Q+ + + H L +C
Sbjct: 204 ISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPC-QSLLSVKHILIDC 261

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]

 Score =  118 bits (295), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 88/249 (35%), Positives = 126/249 (50%), Gaps = 10/249 (4%)

Query: 54  DNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQ 113
           D    I  YTDGSK+N     A+  +    QF L    SIYTAEL+AI+      L++I+
Sbjct: 126 DKYPGINIYTDGSKSNDTVACAFTCSTYQIQFGLPAQMSIYTAELIAIE----QALIFIE 181

Query: 114 NNFCFKDFVICSDSKSSLQALK-FNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGI 172
                  F ICSDS SSL AL   ++    L+S IL K   +   G +V F+W PSHVGI
Sbjct: 182 TVKDEDQFNICSDSLSSLTALSNCDITHPYLLS-ILTKQNNLVRKGKKVVFIWCPSHVGI 240

Query: 173 RENEMVDRAARNAVNARLTN-QYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTD 231
             NE+ DR A+ A+   +T      +DYK+  +      W+  W  +     +L  I+  
Sbjct: 241 LGNEVADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEW--DGETDNKLHIIQPV 298

Query: 232 VRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECH 291
           + +WK   +  R+ E+VL   RIGH   TH +LL R+  P C  C Q+ + + H L +C 
Sbjct: 299 ISEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPC-QSLLTVKHILIDCI 357

Query: 292 ALGNLRRQH 300
                RR++
Sbjct: 358 DFEISRRKY 366

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443682433|gb|ELT87030.1| hypothetical protein CAPTEDRAFT_222606 [Capitella teleta]

 Score =  111 bits (278), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/215 (33%), Positives = 107/215 (49%), Gaps = 10/215 (4%)

Query: 64  DGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVI 123
           DGSK+    G A+   +      L    S+YTAEL+AI+  L SI +       + +FVI
Sbjct: 2   DGSKSEDAVGCAFHSRDFNLALGLPCQMSVYTAELIAINETLTSIAL-----LPYDEFVI 56

Query: 124 CSDSKSSLQALK-FNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAA 182
           C+DS SS+ A+   +L  S  +  IL K   ++    ++ F+W PSHVGI  NE  D  A
Sbjct: 57  CTDSFSSILAISSIDLIHS-YVQSILQKCTNLAGRDKRIIFIWCPSHVGIPGNETADTLA 115

Query: 183 RNAVNARLTN-QYTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRN 241
           + A    + N     +D+K   +     +W+    Q    G +L  I+ D+  W    R 
Sbjct: 116 QQASGMNILNCPIPHTDFKPITRSFVETQWQSESDQET--GNKLHDIEPDIGSWPPCQRE 173

Query: 242 IRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFC 276
            R++E+V+ RLRIGH   T+ HLL   D P C  C
Sbjct: 174 KRRDEIVIARLRIGHTFLTYSHLLSGNDAPMCYGC 208

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  111 bits (278), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 127/263 (48%), Gaps = 13/263 (4%)

Query: 41   PSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMA 100
            P  I  ++   ++  +D    YTDGSKT    G   +  E+    ++ Q  SI+TAE+ A
Sbjct: 919  PELIIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYA 978

Query: 101  IDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQ 160
            +      I+         K  +I +DS S+L+AL        L+  IL  +  I+S    
Sbjct: 979  LYEAARKIIAGKH-----KKAIIYTDSLSALKALHIKSECEPLVGDIL-NMVLINSKVIS 1032

Query: 161  VSFLWIPSHVGIRENEMVDRAARNAVNARLTN-QYTSSDYKAHFKHIQFKRWEEIWRQNA 219
            + F W+PSHVGI  NE  D+ A  A +  LT  +    D +   +     +W++ W  ++
Sbjct: 1033 MRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQW--DS 1090

Query: 220  VLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQT 279
                +L  +K  + +WK+     R  EV+LCRLRIGH   TH  LL +++ P CE C Q 
Sbjct: 1091 CTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKC-QE 1149

Query: 280  PVYLNHWLTECHALGNLRRQHQR 302
            P+ L H L  C    N+  Q Q+
Sbjct: 1150 PLTLIHILILC---PNIETQRQK 1169

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791807|gb|JAA61355.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  111 bits (277), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 127/263 (48%), Gaps = 13/263 (4%)

Query: 41   PSEINNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMA 100
            P  I  ++   ++  +D    YTDGSKT    G   +  E+    ++ Q  SI+TAE+ A
Sbjct: 922  PELIIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYA 981

Query: 101  IDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQ 160
            +      I+         K  +I +DS S+L+AL        L+  IL  +  I+S    
Sbjct: 982  LYEAARKIIAGKH-----KKAIIYTDSLSALKALHIKSECEPLVGDIL-NMVLINSKVIS 1035

Query: 161  VSFLWIPSHVGIRENEMVDRAARNAVNARLTN-QYTSSDYKAHFKHIQFKRWEEIWRQNA 219
            + F W+PSHVGI  NE  D+ A  A +  LT  +    D +   +     +W++ W  ++
Sbjct: 1036 MRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQW--DS 1093

Query: 220  VLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQT 279
                +L  +K  + +WK+     R  EV+LCRLRIGH   TH  LL +++ P CE C Q 
Sbjct: 1094 CTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKC-QE 1152

Query: 280  PVYLNHWLTECHALGNLRRQHQR 302
            P+ L H L  C    N+  Q Q+
Sbjct: 1153 PLTLIHILILC---PNIETQRQK 1172

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443724607|gb|ELU12531.1| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]

 Score =  110 bits (274), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 88/253 (34%), Positives = 126/253 (49%), Gaps = 18/253 (7%)

Query: 54  DNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQ 113
           D    I  YTDGSK+N     A+  +    QF L    SIYTAEL+AI+      L++I+
Sbjct: 126 DKYPGINIYTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIE----QALIFIE 181

Query: 114 NNFCFKDFVICSDSKSSLQALK-FNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGI 172
                  F ICSDS SSL AL   ++    L+S IL K   +   G  V F+W PSHVGI
Sbjct: 182 TMKDEDQFNICSDSLSSLTALSNCDITHPYLLS-ILTKQNNLVRKGKLVVFIWCPSHVGI 240

Query: 173 RENEMVDRAARNAVNARLTN-QYTSSDYK----AHFKHIQFKRWEEIWRQNAVLGRQLRQ 227
             NE+ DR A+ A+   +T      +DYK    ++ K ++   W+E          +L  
Sbjct: 241 LGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLRQNEWDE------ETDNKLHT 294

Query: 228 IKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWL 287
           I+  + +WK   +  R+ E+VL    IGH   TH +LL R+  P C  C Q+ + + H L
Sbjct: 295 IQPVISEWKQGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPC-QSLLTVKHIL 353

Query: 288 TECHALGNLRRQH 300
            +C      RR++
Sbjct: 354 IDCIDFEISRRKY 366

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443721618|gb|ELU10867.1| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/258 (29%), Positives = 123/258 (47%), Gaps = 13/258 (5%)

Query: 44  INNKYLEFKKDNKDKILCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDL 103
           I +++ +      D  + YTDGSK+      ++  +    + +L    S++T+E++AI  
Sbjct: 6   IRSEFADALDRYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAI-- 63

Query: 104 CLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSF 163
              S L  ++ +     FVICSDS S++ A+         + ++L  IK IS     V F
Sbjct: 64  --LSALRCVEADNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVF 121

Query: 164 LWIPSHVGIRENEMVDRAARNAVNARLTN----QYTSSDYKAHFKHIQFKRWEEIWRQNA 219
           +W PSHVGI  NEM D  A+ A+++  TN       +SD +   K     RW+  W +  
Sbjct: 122 MWCPSHVGIPGNEMADTLAKEALSS--TNLAELPVPASDLRCLIKKYIRSRWQHEWDEQH 179

Query: 220 VLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQT 279
               +L  I   +  W    R  R+EE+VL R+RIGH   TH ++    D   C  C   
Sbjct: 180 --SNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVAC-VC 236

Query: 280 PVYLNHWLTECHALGNLR 297
           P+ + H + EC    ++R
Sbjct: 237 PLTVQHIIIECADFLHIR 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|51950578|gb|AAA70222.2| putative ORF2 [Drosophila melanogaster]

 Score =  107 bits (268), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 99/338 (29%), Positives = 151/338 (44%), Gaps = 41/338 (12%)

Query: 12   IKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTF 71
            IK  K +P W L     T L   KK++  P +    Y   K + K     +TDGSK N  
Sbjct: 902  IKLHKNKPPWTLPNLIDTSLRIHKKEQTSPDQYRKLYEHTKNNLKTHNFIFTDGSKINYT 961

Query: 72   TGGAYLLNETVEQFQ-LNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSS 130
               A      V ++  L   +S+ T+E +AI   L +I +          F+ICSDS S+
Sbjct: 962  ISFAITTETDVLKYGILPPYSSVLTSETIAI---LEAIELTKNRR---GKFIICSDSLSA 1015

Query: 131  LQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARL 190
            + +++   N+S   S+I      I+    ++  +WIP H GI+ NE+ D+AA++A +  L
Sbjct: 1016 VDSIQNTNNNSFYPSRIR---SLITQHAPKIKIMWIPGHSGIKGNELADQAAKSASSMPL 1072

Query: 191  --TNQYTSSDYKAHFK-HIQFKRWEEI-----WRQ--NAVLGRQLRQIKTDVRKWKSSNR 240
              T    ++D K H K  +  K+ E I     W Q  N         +K     W     
Sbjct: 1073 ILTPNINTTDIKKHLKADLATKQKEHIINCSPWYQSINTNTSHPCDYLKQSHPNWT---- 1128

Query: 241  NIRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQH 300
              R +++ + RLR+GH   TH+H L     P C FC Q  + LNH    C +L     Q 
Sbjct: 1129 --RLDQIKIIRLRLGHTNITHQHYLNPNSIPTCPFC-QGDISLNHIFNSCPSL----LQT 1181

Query: 301  QRSILQD----------NVETIDRCMKFLYHTKLFAKI 328
            ++ I  +          N + I + + FL  TKL+ KI
Sbjct: 1182 KQDIFNNTNPLDLLSKPNPDNIQKLILFLKKTKLYHKI 1219

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	328
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.707	0.477	0.258	3.5e-08

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 153 (58.9 bits), Expect = 3.5e-08, P = 3.5e-08
 Identities = 67/259 (25%), Positives = 107/259 (41%)

Query:    59 ILCYTDGSKTNTFTGGA-----YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQ 113
             I  YTDGS  N   G A     YL++ +    Q ++ +++Y AEL  I L L  IL   Q
Sbjct:   183 IALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSE-STVYVAELQGILLALVIIL---Q 238

Query:   114 NNFCFKDFVICSDSKSSLQALKF--NLNDXXXXXXXXXXXXXXXXFGSQVSFLWIPSHVG 171
                  +  VI +D++++LQAL+   + +                  G  V F WIP+H G
Sbjct:   239 RQM--QHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRG 296

Query:   172 IRENEMVDXXXXXXXXXXLTNQYTS-----SDYKAHFKHIQFKRWEEIWRQNAVLGRQLR 226
             +  NE  D              +       S  K     +   RWE  W+ +   GR+L 
Sbjct:   297 VEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWK-SCHHGRELY 355

Query:   227 QIK-TDVRKWKSSNRNI-RQEEVVLCRLRIGHCLATHKHLLERKDPPA----CEFCGQTP 280
             ++  T  RK    ++++ R    ++ ++R G     H +L +R  P      C+ CG+  
Sbjct:   356 ELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPDVPNSDCQ-CGRAT 413

Query:   281 VYLNHWLTECHALGNLRRQ 299
               + H L  C     LR +
Sbjct:   414 QSVRHILLACPTFSGLREE 432


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.135   0.419    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      328       302   0.00097  115 3  11 22  0.49    33
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  252 KB (2135 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:02
  No. of threads or processors used:  24
  Search cpu time:  27.37u 0.10s 27.47t   Elapsed:  00:00:11
  Total cpu time:  27.37u 0.10s 27.47t   Elapsed:  00:00:13
  Start:  Thu Aug 15 11:29:53 2013   End:  Thu Aug 15 11:30:06 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	0.691
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

---

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	328
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-34
pfam00075	126	pfam00075, RNase_H, RNase H	1e-14
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-07
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	1e-06
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	4e-06
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	7e-04
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.001

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score =  122 bits (309), Expect = 1e-34
 Identities = 42/130 (32%), Positives = 65/130 (50%), Gaps = 6/130 (4%)

Query: 61  CYTDGSKTNTFTGGAYL---LNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFC 117
            YTDGSK    TG  +           ++L    S++ AEL+AI   L   L   +    
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRA-- 59

Query: 118 FKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEM 177
            +   I SDS+++L+AL+   + S L+ +I   I+E+++ G +V   W+P H GI  NE 
Sbjct: 60  -RKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNER 118

Query: 178 VDRAARNAVN 187
            DR A+ A  
Sbjct: 119 ADRLAKEAAK 128

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, 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. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 69.2 bits (170), Expect = 1e-14
 Identities = 28/129 (21%), Positives = 51/129 (39%), Gaps = 10/129 (7%)

Query: 59  ILCYTDGS--KTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNF 116
           +  YTDGS        G  Y+ +   ++ +     +   AEL+A+   L ++        
Sbjct: 4   VTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSG------ 57

Query: 117 CFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENE 176
             +   I +DS+  +  +            I  +I E+     +V   W+P H GI  NE
Sbjct: 58  --QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNE 115

Query: 177 MVDRAARNA 185
           + D+ A+  
Sbjct: 116 LADKLAKQG 124

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

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

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 30/132 (22%), Positives = 49/132 (37%), Gaps = 18/132 (13%)

Query: 62  YTDGSKTNTF---TGGAYLLNETVE----QFQLNQIASIYTAELMAIDLCLNSILMYIQN 114
            TDGS          G  L +               A+   AEL+A+   L ++ + +  
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLAL---LEALELALDL 57

Query: 115 NFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRE 174
               K  +I +DSK  +  +          + +L  I  + S    + F  +P     RE
Sbjct: 58  GL--KKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVP-----RE 110

Query: 175 -NEMVDRAARNA 185
            NE+ DR A+ A
Sbjct: 111 GNEVADRLAKEA 122

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

>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 34/143 (23%), Positives = 52/143 (36%), Gaps = 24/143 (16%)

Query: 60  LCYTDGSKTNTFTGGA-YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCF 118
             +TDGS      G A     + +E   L    S   AEL+A+   L             
Sbjct: 1   TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALEL--------AKG 52

Query: 119 KDFVICSDSK---SSLQAL-------KFNLNDSILISKILLKIKEISSFGSQVSFLWIPS 168
           K   I +DS      L AL        F     I ++ ++L++++       V+ + I +
Sbjct: 53  KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRA 112

Query: 169 HVG-----IRENEMVDRAARNAV 186
           H G        N   D+AAR A 
Sbjct: 113 HSGLPGPLALGNARADQAARQAA 135

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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 45.7 bits (109), Expect = 4e-06
 Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 19/106 (17%)

Query: 96  AELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQAL--------KFNLNDSI----- 142
           AEL A+   L  I    +        VI +DS+  +  +        K     S      
Sbjct: 46  AELRAVIHALRLI---KEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA 102

Query: 143 ---LISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNA 185
              LI ++   ++E+   G +V F  +P H GI  NE  DR A+  
Sbjct: 103 NKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKG 148

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes

 Score = 39.0 bits (92), Expect = 7e-04
 Identities = 10/26 (38%), Positives = 13/26 (50%)

Query: 160 QVSFLWIPSHVGIRENEMVDRAARNA 185
           QV++ W+  H G   NE  D  A  A
Sbjct: 112 QVTWHWVKGHAGHPGNERADELANAA 137

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Length = 139

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

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 33/154 (21%), Positives = 56/154 (36%), Gaps = 30/154 (19%)

Query: 57  DKILCYTDG-SKTNTFTGG-AYLLNETVEQFQLNQIASIYT-------AELMAIDLCLNS 107
            K+  +TDG    N   GG   +L     + +L    S          AEL A+   L +
Sbjct: 2   KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKEL----SGGEGRTTNNRAELRALIEALEA 57

Query: 108 ILMYIQNNFCFKDFVICSDSKSSLQAL------------KFNLNDSILISKILLKIKEIS 155
           +    +   C  +  + +DSK  ++ +            K      +    +  ++ E+ 
Sbjct: 58  LK---ELGAC--EVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELL 112

Query: 156 SFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189
                V + W+  H G  ENE  D+ AR A  A 
Sbjct: 113 KRHELVFWEWVKGHAGHPENERADQLAREAARAA 146

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	328
PRK06548	161	ribonuclease H; Provisional	99.91
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.89
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.89
PRK08719	147	ribonuclease H; Reviewed	99.89
PRK00203	150	rnhA ribonuclease H; Reviewed	99.89
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.79
PRK13907	128	rnhA ribonuclease H; Provisional	99.79
KOG3752|consensus	371		99.73
PRK07708	219	hypothetical protein; Validated	99.69
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.57
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.36
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.64
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	90.0

>PRK06548 ribonuclease H; Provisional

Probab=99.91  E-value=6.2e-24  Score=177.27  Aligned_cols=127  Identities=26%  Similarity=0.309  Sum_probs=96.8

Q ss_pred             CCcEEEEecCCCCC--CCceEEEEEcCeeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHHH
Q psy8376          56 KDKILCYTDGSKTN--TFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQA  133 (328)
Q Consensus        56 ~~~~~iytDgS~~~--~~~G~g~~~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~~  133 (328)
                      +..+.||||||+..  +..|+|+++.+.....+-...+|+++||+.|++.||    +.+...  ...+.|+|||++|+++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL----~~~~~~--~~~v~I~TDS~yvi~~   76 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELL----IATRHT--DRPILILSDSKYVINS   76 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHH----HhhhcC--CceEEEEeChHHHHHH
Confidence            45689999999884  347899888433222223346899999999999999    544432  4579999999999999


Q ss_pred             HHc---------cCCCH--HHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         134 LKF---------NLNDS--ILI-SKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       134 l~~---------~~~~~--~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      ++.         |...+  ++. +++++.+..+.+. ..|+|.|||||+|.+|||.||.||++|+...
T Consensus        77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            994         32222  333 6677777777655 4799999999999999999999999998654

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

Probab=99.89  E-value=1.8e-23  Score=170.21  Aligned_cols=117  Identities=32%  Similarity=0.428  Sum_probs=90.0

Q ss_pred             CcEEEEecCCCCC--CCceEEEEE-cCeeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHHH
Q psy8376          57 DKILCYTDGSKTN--TFTGGAYLL-NETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQA  133 (328)
Q Consensus        57 ~~~~iytDgS~~~--~~~G~g~~~-~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~~  133 (328)
                      +.+.||||||+..  +..|+|+++ .+......++ ..|++.||+.||..||    +.+ .   ...+.|+|||++++..
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL----~~~-~---~~~v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEAL----KAL-E---HRKVTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHH----HTH-S---TSEEEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHH----HHh-h---cccccccccHHHHHHH
Confidence            5789999999763  336788766 3433444555 8899999999999999    633 2   6899999999999998


Q ss_pred             HHc-----cCCCH----HHHHHHHHHHHHHHhcCCeEEEEEecCCCCC-ccchHHhHHHHHHh
Q psy8376         134 LKF-----NLNDS----ILISKILLKIKEISSFGSQVSFLWIPSHVGI-RENEMVDRAARNAV  186 (328)
Q Consensus       134 l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi-~gNe~AD~lAk~a~  186 (328)
                      +..     .....    ++..+|.+.    ...+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus        73 l~~~~~~~~~~~~~~~~~i~~~i~~~----~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   73 LNKWLHGNGWKKTSNGRPIKNEIWEL----LSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTHHHHTTSBSCTSSSBHTHHHHHH----HHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             HHHhccccccccccccccchhheeec----cccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            887     22211    355555553    356889999999999999 79999999999986

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=99.89  E-value=6.4e-23  Score=168.29  Aligned_cols=126  Identities=21%  Similarity=0.206  Sum_probs=101.3

Q ss_pred             CcEEEEecCCCCC--CCceEEEEEc--Cee--eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHH
Q psy8376          57 DKILCYTDGSKTN--TFTGGAYLLN--ETV--EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKS  129 (328)
Q Consensus        57 ~~~~iytDgS~~~--~~~G~g~~~~--~~~--~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~  129 (328)
                      ..+.||||||+..  |..|+|+|+.  +..  .+..+. .+||++||+.|++.||    +++.. +  ...|.|+|||++
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL----~~l~~~~--~~~v~l~tDS~y   74 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEAL----EALKELG--ACEVTLYTDSKY   74 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHH----HHHHhcC--CceEEEEecHHH
Confidence            4688999999983  4489998883  222  233344 8999999999999999    66665 5  889999999999


Q ss_pred             HHHHHHccCCC-----------HH-HHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         130 SLQALKFNLND-----------SI-LISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       130 ai~~l~~~~~~-----------~~-~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      |+++|+.+...           .| ...++++.+.++......|.+.|||||.|.++||.||+||+.|+...
T Consensus        75 v~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          75 VVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            99999944111           12 24678888888888888999999999999999999999999998765

>PRK08719 ribonuclease H; Reviewed

Probab=99.89  E-value=1.5e-22  Score=167.52  Aligned_cols=121  Identities=23%  Similarity=0.294  Sum_probs=91.9

Q ss_pred             CcEEEEecCCCCCCC-----ceEEEEE--c--Ce--eeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEe
Q psy8376          57 DKILCYTDGSKTNTF-----TGGAYLL--N--ET--VEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICS  125 (328)
Q Consensus        57 ~~~~iytDgS~~~~~-----~G~g~~~--~--~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~s  125 (328)
                      ..++||||||+..++     +|+|+++  .  +.  .....+....|+++||+.|++.||    +.+..     ...|+|
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL----~~~~~-----~~~i~t   73 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEAL----EYARD-----GDVIYS   73 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHH----HHcCC-----CCEEEe
Confidence            568999999997432     5999886  2  21  233446666899999999999999    65543     137999


Q ss_pred             cCHHHHHHHH--------ccCCCH---HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhh
Q psy8376         126 DSKSSLQALK--------FNLNDS---IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVN  187 (328)
Q Consensus       126 Ds~~ai~~l~--------~~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~  187 (328)
                      ||++|+++++        +.+..+   ++ ..++++.+..+.+ ...|+|.|||||+|++|||.||+||++|+.
T Consensus        74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            9999999984        333222   22 3567777777765 467999999999999999999999999874

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.89  E-value=2e-22  Score=167.99  Aligned_cols=124  Identities=20%  Similarity=0.211  Sum_probs=91.9

Q ss_pred             cEEEEecCCCCC--CCceEEEEE--cCee-eeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          58 KILCYTDGSKTN--TFTGGAYLL--NETV-EQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        58 ~~~iytDgS~~~--~~~G~g~~~--~~~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      .+.||||||+..  +.+|+|+++  .+.. ...+.....|+++|||.|++.||    +.+..   ...+.|+|||+++++
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL----~~~~~---~~~v~I~tDS~yvi~   75 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEAL----EALKE---PCEVTLYTDSQYVRQ   75 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHH----HHcCC---CCeEEEEECHHHHHH
Confidence            488999999984  347888887  2322 12223347899999999999999    65543   467999999999999


Q ss_pred             HHHcc---------CCCH--HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         133 ALKFN---------LNDS--IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       133 ~l~~~---------~~~~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      +|..+         ...+  ++ ..++++.+..+... ..|.|.|||||+|++||+.||+||++|+...
T Consensus        76 ~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203         76 GITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             HHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence            99863         1111  22 23444545455433 6899999999999999999999999998765

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=99.79  E-value=1.9e-18  Score=137.71  Aligned_cols=121  Identities=26%  Similarity=0.295  Sum_probs=92.7

Q ss_pred             EEEecCCCCCC--CceEEEEEcCe--e---eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHH
Q psy8376          60 LCYTDGSKTNT--FTGGAYLLNET--V---EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSL  131 (328)
Q Consensus        60 ~iytDgS~~~~--~~G~g~~~~~~--~---~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai  131 (328)
                      ++|||||...+  ++|+|+++.+.  .   .........+++.||+.|++.||    +.+.. +  ..++.|++||+.++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al----~~~~~~~--~~~i~i~~Ds~~~~   74 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEAL----ELALELG--GKKVNIYTDSQYVI   74 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHH----HHHHhCC--CceEEEEECHHHHH
Confidence            48999999865  58999888321  1   11222257899999999999999    54434 4  89999999999999


Q ss_pred             HHHHccCC-CHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHh
Q psy8376         132 QALKFNLN-DSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAV  186 (328)
Q Consensus       132 ~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~  186 (328)
                      ..++++.. .......+...+..+...+..+.|.|||+|+|..+|+.||.|||.|.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          75 NALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            99998765 22233334444445556788999999999999999999999999873

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.

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.79  E-value=2.6e-18  Score=139.34  Aligned_cols=121  Identities=21%  Similarity=0.221  Sum_probs=94.4

Q ss_pred             cEEEEecCCCCC--CCceEEEEEcCeee---eccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHH
Q psy8376          58 KILCYTDGSKTN--TFTGGAYLLNETVE---QFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSL  131 (328)
Q Consensus        58 ~~~iytDgS~~~--~~~G~g~~~~~~~~---~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai  131 (328)
                      .++||||||+..  +.+|+|+++++...   ........|++.||+.|++.||    +.+.. +  ..++.|+|||+.++
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL----~~a~~~g--~~~v~i~sDS~~vi   74 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAAL----KYCTEHN--YNIVSFRTDSQLVE   74 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHH----HHHHhCC--CCEEEEEechHHHH
Confidence            368999999884  45899999843221   1122346799999999999999    66555 4  67899999999999


Q ss_pred             HHHHccCCCHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhC
Q psy8376         132 QALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNA  188 (328)
Q Consensus       132 ~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  188 (328)
                      +.+++.....+-...+++.+..+..++..+.|.|||.    +.|+.||.||++|...
T Consensus        75 ~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         75 RAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            9999876544445666666667777888899999995    6999999999999753

>KOG3752|consensus

Probab=99.73  E-value=2.9e-17  Score=150.39  Aligned_cols=125  Identities=24%  Similarity=0.253  Sum_probs=96.0

Q ss_pred             CcEEEEecCCCCCC-----CceEEEEEcC---eeeeccCC-CCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEec
Q psy8376          57 DKILCYTDGSKTNT-----FTGGAYLLNE---TVEQFQLN-QIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSD  126 (328)
Q Consensus        57 ~~~~iytDgS~~~~-----~~G~g~~~~~---~~~~~~l~-~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sD  126 (328)
                      +..+||||||+..+     .+|+|+++++   ......+. ..+++|.||+.||..||    +.+.. +  ..+++|.||
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~AL----kka~~~~--~~kv~I~TD  284 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEAL----KKARSKN--INKVVIRTD  284 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHH----HHHHhcC--CCcEEEEec
Confidence            45899999998842     3899999943   44566665 88999999999999999    55544 4  669999999


Q ss_pred             CHHHHHHHHccCCC-----------HH----H--HHHHHHHHHHHHh--cCCeEEEEEecCCCCCccchHHhHHHHHHhh
Q psy8376         127 SKSSLQALKFNLND-----------SI----L--ISKILLKIKEISS--FGSQVSFLWIPSHVGIRENEMVDRAARNAVN  187 (328)
Q Consensus       127 s~~ai~~l~~~~~~-----------~~----~--~~~i~~~~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~  187 (328)
                      |++++++|+.|...           ++    +  .......+.+|.+  ++.+|++.|||||.|+.|||+||.||+++..
T Consensus       285 S~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  285 SEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             hHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            99999999865321           11    1  1233334444443  3689999999999999999999999998854

>PRK07708 hypothetical protein; Validated

Probab=99.69  E-value=5.6e-16  Score=136.18  Aligned_cols=129  Identities=16%  Similarity=0.161  Sum_probs=94.6

Q ss_pred             hhCCCcEEEEecCCCC--CCCceEEEEEc--C--eee----eccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceE
Q psy8376          53 KDNKDKILCYTDGSKT--NTFTGGAYLLN--E--TVE----QFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDF  121 (328)
Q Consensus        53 ~~~~~~~~iytDgS~~--~~~~G~g~~~~--~--~~~----~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i  121 (328)
                      ...++.+++|+|||..  ++++|+|+++.  +  ...    ...++...|++.||+.|++.||    +.+.. +.....|
T Consensus        68 ~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL----~~A~e~g~~~~~V  143 (219)
T PRK07708         68 EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAM----QELEELGVKHEPV  143 (219)
T ss_pred             ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHH----HHHHHcCCCcceE
Confidence            4457789999999986  45689998883  1  111    1245666899999999999999    55554 3112348


Q ss_pred             EEEecCHHHHHHHHccCCC-HHHHHHHHHHHHHHHhc-CCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         122 VICSDSKSSLQALKFNLND-SILISKILLKIKEISSF-GSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       122 ~I~sDs~~ai~~l~~~~~~-~~~~~~i~~~~~~l~~~-~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      .|++||+.+++++++.+.. ++....+++.+..+.++ ...+.|.|||    +..|+.||.||++|++..
T Consensus       144 ~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~  209 (219)
T PRK07708        144 TFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGT  209 (219)
T ss_pred             EEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcC
Confidence            9999999999999987643 34455555555544433 4568889998    778999999999999754

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.57  E-value=3.7e-14  Score=135.32  Aligned_cols=122  Identities=20%  Similarity=0.215  Sum_probs=94.4

Q ss_pred             cEEEEecCCCCCC--CceEEEEEcCe--e----eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCH
Q psy8376          58 KILCYTDGSKTNT--FTGGAYLLNET--V----EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSK  128 (328)
Q Consensus        58 ~~~iytDgS~~~~--~~G~g~~~~~~--~----~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~  128 (328)
                      .+.||||||+..+  .+|+|+++.+.  .    .........|++.||+.|++.||    +.+.. +  ...+.|++||+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL----~~a~~~g--~~~v~i~~DS~   75 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGL----EAAAELG--ATEVEVRMDSK   75 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHH----HHHHhCC--CCeEEEEeCcH
Confidence            3689999998853  48999988321  1    11222237889999999999999    55555 5  77999999999


Q ss_pred             HHHHHHHccCC-CHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         129 SSLQALKFNLN-DSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       129 ~ai~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      .+++.+++.+. +++-...+...+..+.+++..+.|.|||    ..+|+.||.||+.|+...
T Consensus        76 lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~  133 (372)
T PRK07238         76 LVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIP----RARNAHADRLANEAMDAA  133 (372)
T ss_pred             HHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECC----chhhhHHHHHHHHHHHhh
Confidence            99999988654 3444555666677788888999999999    479999999999997544

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

Probab=99.36  E-value=3.6e-12  Score=95.54  Aligned_cols=85  Identities=20%  Similarity=0.210  Sum_probs=66.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHHHHHHccCCCHHHHHHHHHHHHHHHhcCCeEEEEEecCCCC
Q psy8376          93 IYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVG  171 (328)
Q Consensus        93 ~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g  171 (328)
                      +..||+.|++.||    +.+.. +  .++|.|+|||+.+++.+++..........+...+..+.+.+..+.|.|||    
T Consensus         1 ~~~aE~~al~~al----~~a~~~g--~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----   70 (87)
T PF13456_consen    1 PLEAEALALLEAL----QLAWELG--IRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----   70 (87)
T ss_dssp             HHHHHHHHHHHHH----HHHHCCT---SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------
T ss_pred             CcHHHHHHHHHHH----HHHHHCC--CCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----
Confidence            4789999999999    76666 6  89999999999999999987544324455666666788889999999999    


Q ss_pred             CccchHHhHHHHHHhh
Q psy8376         172 IRENEMVDRAARNAVN  187 (328)
Q Consensus       172 i~gNe~AD~lAk~a~~  187 (328)
                      +++|..||.|||.|.+
T Consensus        71 r~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   71 REQNKVADALAKFALS   86 (87)
T ss_dssp             GGGSHHHHHHHHHHHH
T ss_pred             hHHhHHHHHHHHHHhh
Confidence            8999999999999874

>PF13966 zf-RVT: zinc-binding in reverse transcriptase

Probab=96.64  E-value=0.00083  Score=50.23  Aligned_cols=33  Identities=18%  Similarity=0.392  Sum_probs=27.6

Q ss_pred             cccccCCCCCccccccccccccchhhcccccch
Q psy8376         262 KHLLERKDPPACEFCGQTPVYLNHWLTECHALG  294 (328)
Q Consensus       262 ~~r~~~~~~p~C~~Cg~~~etv~Hil~~Cp~~~  294 (328)
                      +++.+...++.|..|+.+.||++|+++.||...
T Consensus        51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             hhccCCccCCccccCCCccccccceeccCcCcc
Confidence            345666778999999977999999999999754

>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family

Probab=90.00  E-value=1.7  Score=36.29  Aligned_cols=66  Identities=15%  Similarity=0.150  Sum_probs=38.7

Q ss_pred             CcEEEEecCCCCCCCceEEEEEc---Cee----e---eccC--CCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEE
Q psy8376          57 DKILCYTDGSKTNTFTGGAYLLN---ETV----E---QFQL--NQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVI  123 (328)
Q Consensus        57 ~~~~iytDgS~~~~~~G~g~~~~---~~~----~---~~~l--~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I  123 (328)
                      ..+++|+|+|..  +.|+.++++   +..    .   ..++  -...|+-+-||.|+..|.+++-..... +....++.+
T Consensus        80 ~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~  157 (159)
T PF05380_consen   80 VELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVF  157 (159)
T ss_pred             eeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEE
Confidence            368899999954  344444442   111    0   1112  124599999999999999777444333 323455554


Q ss_pred             E
Q psy8376         124 C  124 (328)
Q Consensus       124 ~  124 (328)
                      .
T Consensus       158 w  158 (159)
T PF05380_consen  158 W  158 (159)
T ss_pred             e
Confidence            4

---

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	328
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	5e-08
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-07
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	7e-04
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	7e-04

>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 Length = 147

 Score = 50.4 bits (121), Expect = 5e-08
 Identities = 22/143 (15%), Positives = 44/143 (30%), Gaps = 17/143 (11%)

Query: 54  DNKDKILCYTDGS-KTNTFTGGAYLLNETVEQFQLNQIASIYT--------AELMAIDLC 104
           D++ +   YTDGS     +      + +    ++   +              E+ A    
Sbjct: 2   DDRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAA--- 58

Query: 105 LNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFL 164
           L ++    Q         I  D                  ++   K+     +    SF 
Sbjct: 59  LYAVKKASQLG---VKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMN--QYRGIYSFE 113

Query: 165 WIPSHVGIRENEMVDRAARNAVN 187
            + +H G   N+ VD  A++A+ 
Sbjct: 114 KVKAHSGNEFNDYVDMKAKSALG 136

>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 Length = 165

 Score = 49.8 bits (119), Expect = 1e-07
 Identities = 31/136 (22%), Positives = 47/136 (34%), Gaps = 21/136 (15%)

Query: 62  YTDGS-KTNTFTGGA----YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNF 116
           YTDGS         A        E +    L    S   AEL+A+   L           
Sbjct: 27  YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG------ 80

Query: 117 CFKDFVICSDSKSSLQAL--KFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVG--- 171
             K   + +DS+ +           +    ++IL  +K +     ++S +  P H     
Sbjct: 81  --KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFL-PKRLSIIHCPGHQKGNS 137

Query: 172 --IRENEMVDRAARNA 185
              R N M D+AAR A
Sbjct: 138 AEARGNRMADQAAREA 153

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 9/28 (32%), Positives = 13/28 (46%)

Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVN 187
            + ++ +P H G   NE  DR AR    
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLAREGAK 150

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Length = 150

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 10/27 (37%), Positives = 15/27 (55%)

Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAV 186
           +V   W+P+H GI  NE VD+     +
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSAGI 145

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	328
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.91
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.91
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.91
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.89
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.89
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.89
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.89
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.88
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.86
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.84
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.84
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.81
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.8
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.78
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.43
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.27

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

Probab=99.91  E-value=2.4e-24  Score=179.27  Aligned_cols=127  Identities=18%  Similarity=0.282  Sum_probs=95.2

Q ss_pred             CCcEEEEecCCCCCCC-----ceEEEEEcCe---eeeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEec
Q psy8376          56 KDKILCYTDGSKTNTF-----TGGAYLLNET---VEQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSD  126 (328)
Q Consensus        56 ~~~~~iytDgS~~~~~-----~G~g~~~~~~---~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sD  126 (328)
                      .+.++||||||+..++     +|+|+++.+.   .....+...+|++.||+.|++.||    +.+.. +  ..+|.|+||
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL----~~~~~~~--~~~v~i~tD   78 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAI----EQAKTQN--INKLVLYTN   78 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHH----HHHHHTT--CCEEEEEES
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHH----HHHHhCC--CceEEEEEC
Confidence            4678999999987432     7899888431   233455557899999999999999    55544 4  689999999


Q ss_pred             CHHHHHHHHccC---------CCH--H-HHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         127 SKSSLQALKFNL---------NDS--I-LISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       127 s~~ai~~l~~~~---------~~~--~-~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      |++|++.|.++.         ...  + ....+++.+..+.. +..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        79 S~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           79 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            999999998741         111  1 12334444444444 45799999999999999999999999998764

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

Probab=99.91  E-value=3.3e-24  Score=176.80  Aligned_cols=120  Identities=24%  Similarity=0.217  Sum_probs=88.9

Q ss_pred             CcEEEEecCCCCCC--CceEEEEEc--Ceee-eccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHH
Q psy8376          57 DKILCYTDGSKTNT--FTGGAYLLN--ETVE-QFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSL  131 (328)
Q Consensus        57 ~~~~iytDgS~~~~--~~G~g~~~~--~~~~-~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai  131 (328)
                      ..++||||||+..+  .+|+|+++.  +... ..+....+|++.||+.|++.||    +.+..   ..++.|+|||++|+
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL----~~~~~---~~~v~I~tDS~~vi   75 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGL----EALKE---PARVQLYSDSAYLV   75 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHH----HTCSS---CCEEEEEESCHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHH----HhcCc---cCcEEEEeChHHHH
Confidence            56899999998853  389998872  2221 1112236899999999999999    65543   67999999999999


Q ss_pred             HHHHc-cC---------CC-------HHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhC
Q psy8376         132 QALKF-NL---------ND-------SILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNA  188 (328)
Q Consensus       132 ~~l~~-~~---------~~-------~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  188 (328)
                      +.|++ +.         ..       .++++.|..    +... ..|.|.|||||+|+++||.||+|||+|+..
T Consensus        76 ~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~----~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           76 NAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILK----LTTL-HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             HHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHH----HHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHH----HHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            99987 21         01       134444444    3333 479999999999999999999999999864

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=99.91  E-value=4.7e-24  Score=176.44  Aligned_cols=123  Identities=23%  Similarity=0.284  Sum_probs=92.6

Q ss_pred             CCcEEEEecCCCCC--CCceEEEEEcC-eeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          56 KDKILCYTDGSKTN--TFTGGAYLLNE-TVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        56 ~~~~~iytDgS~~~--~~~G~g~~~~~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      .+.++||||||+..  +..|+|+++.+ ......+ ..+|++.||+.|++.||    +.+     ..++.|+|||++|++
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL----~~~-----~~~v~i~tDS~~v~~   79 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLAL----QDS-----GLEVNIVTDSQYALG   79 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHH----HHS-----CSEEEEEESCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHH----HhC-----CCcEEEEeCcHHHHH
Confidence            56899999999874  33788988833 2223333 47899999999999999    542     578999999999999


Q ss_pred             HHHccC-----------CCHHH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhC
Q psy8376         133 ALKFNL-----------NDSIL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNA  188 (328)
Q Consensus       133 ~l~~~~-----------~~~~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  188 (328)
                      +|+++.           ...++ -.++++.+..+..++..|.|.|||||+|++|||.||+||++|+..
T Consensus        80 ~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           80 IITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            998762           11111 234444443444567899999999999999999999999999865

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.89  E-value=2.4e-23  Score=173.36  Aligned_cols=125  Identities=19%  Similarity=0.223  Sum_probs=92.8

Q ss_pred             CcEEEEecCCCCCC--CceEEEEEc--Cee--eeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHH
Q psy8376          57 DKILCYTDGSKTNT--FTGGAYLLN--ETV--EQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSS  130 (328)
Q Consensus        57 ~~~~iytDgS~~~~--~~G~g~~~~--~~~--~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~a  130 (328)
                      ..++||||||+..+  .+|+|+++.  +..  .+..+ ..+|++.||+.|++.||    +.+..   ..++.|+|||++|
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL----~~~~~---~~~v~I~tDS~~v   74 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVAL----EALKE---HAEVILSTDSQYV   74 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHH----HTCCS---CCEEEEEECCHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHH----HHhCc---CCcEEEEeCHHHH
Confidence            46889999999843  379998883  222  12223 46799999999999999    66543   5799999999999


Q ss_pred             HHHHHcc---------CCCH--HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCCC
Q psy8376         131 LQALKFN---------LNDS--IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARL  190 (328)
Q Consensus       131 i~~l~~~---------~~~~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~  190 (328)
                      ++.|+++         ...+  ++ ...+++.+..+.. ...|.|.|||||+|++|||.||+||++|+..+.
T Consensus        75 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  145 (155)
T 1jl1_A           75 RQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPT  145 (155)
T ss_dssp             HHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence            9999973         1111  11 1233444444544 368999999999999999999999999998764

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=99.89  E-value=1.7e-24  Score=178.74  Aligned_cols=124  Identities=19%  Similarity=0.122  Sum_probs=94.6

Q ss_pred             CCcEEEEecCCCCCCCceEEEEEc--Cee--eec-cC--CC--CCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEe
Q psy8376          56 KDKILCYTDGSKTNTFTGGAYLLN--ETV--EQF-QL--NQ--IASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICS  125 (328)
Q Consensus        56 ~~~~~iytDgS~~~~~~G~g~~~~--~~~--~~~-~l--~~--~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~s  125 (328)
                      ++.+.||||||+..+.+|+|+++.  +..  ... +.  +.  .+||+.||+.|++.||    +.+.. +  . +|.|+|
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL----~~a~~~~--~-~v~I~t   76 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAV----KKASQLG--V-KIRILH   76 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHH----HHHHHHT--C-CCCBSS
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHH----HHHHHCC--C-eEEEEE
Confidence            467899999999997799999882  222  222 22  22  3699999999999999    54433 4  4 999999


Q ss_pred             cCHHHHHHHHccCC-CHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         126 DSKSSLQALKFNLN-DSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       126 Ds~~ai~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      ||+.+.+.+.+.+. ..+....+.+.+..+..   .|.|.|||||+|++|||.||+|||+|+...
T Consensus        77 DS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           77 DYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             CCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             CcHHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            99988887776554 34444555554445433   899999999999999999999999999876

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.89  E-value=2.6e-23  Score=174.45  Aligned_cols=121  Identities=24%  Similarity=0.246  Sum_probs=91.7

Q ss_pred             CcEEEEecCCCC--CCCceEEEEE--cCee-eeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHH
Q psy8376          57 DKILCYTDGSKT--NTFTGGAYLL--NETV-EQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSL  131 (328)
Q Consensus        57 ~~~~iytDgS~~--~~~~G~g~~~--~~~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai  131 (328)
                      ..+.||||||+.  +|.+|+|+++  .+.. ...++...+|+++||+.|++.||    +.+  .  ..++.|+|||++|+
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL----~~~--~--~~~v~I~tDS~~vi   93 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQAL----KMA--E--GKKLNVYTDSRYAF   93 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHH----HHT--B--TSEEEEEECCHHHH
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHH----HHc--c--CceEEEEEchHHHH
Confidence            358999999997  4557888876  2222 22245678899999999999999    665  2  67999999999999


Q ss_pred             HHHHccCCCH-----HHHHHHHHHHHHHHhcCCeEEEEEecCCCC-----CccchHHhHHHHHHhhCC
Q psy8376         132 QALKFNLNDS-----ILISKILLKIKEISSFGSQVSFLWIPSHVG-----IRENEMVDRAARNAVNAR  189 (328)
Q Consensus       132 ~~l~~~~~~~-----~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g-----i~gNe~AD~lAk~a~~~~  189 (328)
                      +.+-......     .+++++..   .+ ..+..|.|.|||||+|     +.|||.||+|||+|+..+
T Consensus        94 ~~iw~~~~g~~v~n~dl~~~l~~---~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A           94 ATAHVHSEGREIKNKNEILALLK---AL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             HHHHSCCCSCCCSSHHHHHHHHH---HT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCcccCHHHHHHHHH---HH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            9983211111     23444433   23 3578999999999999     999999999999999765

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

Probab=99.89  E-value=4.3e-23  Score=172.34  Aligned_cols=123  Identities=22%  Similarity=0.259  Sum_probs=90.9

Q ss_pred             CcEEEEecCCCCC--CCceEEEEEc--Cee--eeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHH
Q psy8376          57 DKILCYTDGSKTN--TFTGGAYLLN--ETV--EQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSS  130 (328)
Q Consensus        57 ~~~~iytDgS~~~--~~~G~g~~~~--~~~--~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~a  130 (328)
                      ..++||||||+..  +.+|+|+++.  +..  ....+ ..+|++.||+.|++.||    +.+..   ..+|.|+|||++|
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL----~~~~~---~~~v~I~tDS~~v   76 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVAL----EALKE---PCKIILTSDSQYM   76 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHH----HTCSS---CCEEEEEECCHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHH----HHhcc---CCeEEEEeCHHHH
Confidence            4689999999984  3379998882  222  12223 35799999999999999    65543   4799999999999


Q ss_pred             HHHHHcc--------C-CCH--HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhC
Q psy8376         131 LQALKFN--------L-NDS--IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNA  188 (328)
Q Consensus       131 i~~l~~~--------~-~~~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  188 (328)
                      ++.|.++        + ...  ++ ..++++.+..+.. ...|.|.|||||+|++|||.||+||++|+..
T Consensus        77 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           77 RQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            9999882        2 111  11 1233333444444 3589999999999999999999999999987

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

Probab=99.88  E-value=2.6e-23  Score=174.98  Aligned_cols=126  Identities=21%  Similarity=0.156  Sum_probs=92.5

Q ss_pred             CcEEEEecCCCCCC--CceEEEEEc--Ceeee-ccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHH
Q psy8376          57 DKILCYTDGSKTNT--FTGGAYLLN--ETVEQ-FQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSL  131 (328)
Q Consensus        57 ~~~~iytDgS~~~~--~~G~g~~~~--~~~~~-~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai  131 (328)
                      ..++||||||+..+  .+|+|+++.  +.... .+....+|++.||+.|++.||    +.+..   ..+|.|+|||++|+
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL----~~~~~---~~~v~I~tDS~~vi   79 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGL----KALKE---PCEVDLYTDSHYLK   79 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHH----HSCCS---CCEEEEECCCHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHH----HHhcc---CCeEEEEeChHHHH
Confidence            46789999999843  379999883  21111 111236799999999999999    65543   45899999999999


Q ss_pred             HHHHc----------cCCCH--HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCCC
Q psy8376         132 QALKF----------NLNDS--IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARL  190 (328)
Q Consensus       132 ~~l~~----------~~~~~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~  190 (328)
                      +.|.+          +...+  ++ ..++++.+..+... ..|.|.|||||+|+++||.||+|||+|+....
T Consensus        80 ~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           80 KAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             HHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             HHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc-CeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            99998          22111  11 12344444444443 59999999999999999999999999998764

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

Probab=99.86  E-value=1.9e-22  Score=169.00  Aligned_cols=126  Identities=17%  Similarity=0.158  Sum_probs=86.8

Q ss_pred             CCcEEEEecCCCCC--CC-----ceEEEEEc--C----eeeeccC-CCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceE
Q psy8376          56 KDKILCYTDGSKTN--TF-----TGGAYLLN--E----TVEQFQL-NQIASIYTAELMAIDLCLNSILMYIQNNFCFKDF  121 (328)
Q Consensus        56 ~~~~~iytDgS~~~--~~-----~G~g~~~~--~----~~~~~~l-~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i  121 (328)
                      ...++||||||+..  |.     +|+|+++.  +    ....+.. ....+++.||+.|+..||    +.+...  ..+|
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al----~~al~~--~~~v   78 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFAC----KKALKI--PGPV   78 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHH----HHHHHS--SSCE
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHH----HHHhcC--CCeE
Confidence            35688999999873  22     79999872  2    1122222 245677788888888887    544433  5679


Q ss_pred             EEEecCHHHHHHHHccC---------CC--HHH-HHHHHHHHHHHHhcCCeEEEEEecCCCCC------ccchHHhHHHH
Q psy8376         122 VICSDSKSSLQALKFNL---------ND--SIL-ISKILLKIKEISSFGSQVSFLWIPSHVGI------RENEMVDRAAR  183 (328)
Q Consensus       122 ~I~sDs~~ai~~l~~~~---------~~--~~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi------~gNe~AD~lAk  183 (328)
                      .|+|||++|+++|..|.         ..  .++ -.++++.+..+......|.|.|||||+|+      +|||.||+||+
T Consensus        79 ~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~  158 (165)
T 2lsn_A           79 LVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLAT  158 (165)
T ss_dssp             EEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHH
T ss_pred             EEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHH
Confidence            99999999999997531         11  111 12344444444445568999999999995      58999999999


Q ss_pred             HHhh
Q psy8376         184 NAVN  187 (328)
Q Consensus       184 ~a~~  187 (328)
                      +|+.
T Consensus       159 ~gA~  162 (165)
T 2lsn_A          159 QGSY  162 (165)
T ss_dssp             HHHH
T ss_pred             Hhhh
Confidence            9974

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

Probab=99.84  E-value=1.5e-20  Score=153.47  Aligned_cols=122  Identities=20%  Similarity=0.203  Sum_probs=95.1

Q ss_pred             cEEEEecCCCCCC--CceEEEEEcC----e-e-eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCH
Q psy8376          58 KILCYTDGSKTNT--FTGGAYLLNE----T-V-EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSK  128 (328)
Q Consensus        58 ~~~iytDgS~~~~--~~G~g~~~~~----~-~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~  128 (328)
                      .++||||||+..+  .+|+|+++.+    . . ........+|++.||+.|++.||    +.+.. +  ..++.|+|||+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL----~~a~~~~--~~~v~i~tDS~   76 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGL----DDAVKLG--ATEAAVLMDSK   76 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHH----HHHHHHT--CSEEEEEESCH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHH----HHHHHCC--CceEEEEeChH
Confidence            5799999998843  4899988822    1 1 11122237899999999999999    55444 5  78999999999


Q ss_pred             HHHHHHHccC-CCHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         129 SSLQALKFNL-NDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       129 ~ai~~l~~~~-~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      ++++.+++.+ ..++.+..+++.+..+..++..|.|.|||    .++|+.||+||++|+...
T Consensus        77 ~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           77 LVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC----GGGCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC----CcccHHHHHHHHHHHHHh
Confidence            9999999854 34455556667777788778999999999    489999999999998653

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

Probab=99.84  E-value=1.4e-20  Score=153.36  Aligned_cols=122  Identities=21%  Similarity=0.235  Sum_probs=91.6

Q ss_pred             CcEEEEecCCCCCC--CceEEEEEcC----ee-eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcc----eEEEE
Q psy8376          57 DKILCYTDGSKTNT--FTGGAYLLNE----TV-EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFK----DFVIC  124 (328)
Q Consensus        57 ~~~~iytDgS~~~~--~~G~g~~~~~----~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~----~i~I~  124 (328)
                      ..++||||||+..+  .+|+|+++.+    .. ...+....+|++.||+.|++.||    +.+.. +  ..    ++.|+
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL----~~a~~~~--~~~~~~~v~i~   75 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRAL----EDLQMFG--DKLVDMEVEVR   75 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHH----HHHGGGG--GGGTTCEEEEE
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHH----HHHHHcC--CCCCCceEEEE
Confidence            35899999999743  4899998832    11 11122235799999999999999    65554 4  55    99999


Q ss_pred             ecCHHHHHHHHccCC-CHHHHHHHHHHHHHH-HhcCCeEEEEEecCCCCCccchHHhHHHHHHhhC
Q psy8376         125 SDSKSSLQALKFNLN-DSILISKILLKIKEI-SSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNA  188 (328)
Q Consensus       125 sDs~~ai~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  188 (328)
                      |||+++++.+++++. .++-+..++..+..+ .+++..|.|.|||    .++||.||+|||+|+..
T Consensus        76 tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           76 MDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             ESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             eChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            999999999998664 333333455555566 6666799999999    58999999999999864

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

Probab=99.81  E-value=1e-19  Score=150.23  Aligned_cols=120  Identities=18%  Similarity=0.209  Sum_probs=88.0

Q ss_pred             EEEEecCCCCC---CCceE-EEEEcC---eeeec--cCC---CCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEe
Q psy8376          59 ILCYTDGSKTN---TFTGG-AYLLNE---TVEQF--QLN---QIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICS  125 (328)
Q Consensus        59 ~~iytDgS~~~---~~~G~-g~~~~~---~~~~~--~l~---~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~s  125 (328)
                      ++||||||+.+   +.+|+ |+++.+   ....+  .++   ..+|++.||+.|++.||    +.+.. +  ..++.|+|
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL----~~a~~~g--~~~v~i~t   75 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM----ETMLRLG--ISSPIIKG   75 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHH----HHHHHHT--CCSCEEEE
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHH----HHHHHcC--CCEEEEEe
Confidence            68999999872   45785 988732   11112  222   47899999999999999    54444 4  68999999


Q ss_pred             cCHHHHHHHHccCCC-HHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         126 DSKSSLQALKFNLND-SILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       126 Ds~~ai~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      ||+++++.+++++.. ++....+++.+..+.+.. .|.|.|||+    ++|+.||+||++|+...
T Consensus        76 DS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           76 DSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             SCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            999999999997543 233334444444444444 599999998    59999999999998764

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=99.80  E-value=1e-19  Score=180.80  Aligned_cols=117  Identities=21%  Similarity=0.260  Sum_probs=91.6

Q ss_pred             CCcEEEEecCCCCCC--CceEEEEEc-CeeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          56 KDKILCYTDGSKTNT--FTGGAYLLN-ETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        56 ~~~~~iytDgS~~~~--~~G~g~~~~-~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      .+.+.||||||+..+  .+|+|+++. +......+ ..+||+.||+.|++.||    +.   +  ..++.|+|||++|++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL----~~---~--~~~v~I~tDS~~v~~  503 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMAL----TD---S--GPKVNIIVDSQYVMG  503 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHH----HT---S--CSEEEEEESCHHHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHH----Hc---C--CCeEEEEEehHHHHH
Confidence            457999999998843  378888883 22222223 46799999999999999    55   3  789999999999999


Q ss_pred             HHHccCCC--HHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHh
Q psy8376         133 ALKFNLND--SILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAV  186 (328)
Q Consensus       133 ~l~~~~~~--~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~  186 (328)
                      +++++...  .++.+++.+    +...+..|.|.|||||+|++|||.||+||++|+
T Consensus       504 ~i~~~~~~~~~~l~~~~~~----~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          504 IVASQPTESESKIVNQIIE----EMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHTCCSEESCHHHHHHHH----HHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHhcccccccHHHHHHHHH----HhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            99987643  256665554    222367899999999999999999999999874

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=99.78  E-value=2.1e-19  Score=178.61  Aligned_cols=116  Identities=26%  Similarity=0.359  Sum_probs=89.0

Q ss_pred             CCcEEEEecCCCCC-C-CceEEEEEc-CeeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          56 KDKILCYTDGSKTN-T-FTGGAYLLN-ETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        56 ~~~~~iytDgS~~~-~-~~G~g~~~~-~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      .+.+.||||||+.. + .+|+|+++. +.....+. ..+||+.||+.|++.||    +.+     ..++.|+|||++|++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL----~~~-----~~~v~I~tDS~~vi~  506 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLAL----QDS-----GLEVNIVTDSQYALG  506 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHH----HHS-----CSEEEEEECCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHH----HhC-----CCcEEEEeChHHHHH
Confidence            45699999999873 3 378888883 32233333 46899999999999999    554     568999999999999


Q ss_pred             HHHccCCCH--HHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHH
Q psy8376         133 ALKFNLNDS--ILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNA  185 (328)
Q Consensus       133 ~l~~~~~~~--~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a  185 (328)
                      +++++...+  ++.+++.+   .+.+ ...|.|.|||||+|++|||.||+||++|
T Consensus       507 ~i~~~~~~~~~~l~~~~~~---~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          507 IIQAQPDKSESELVNQIIE---QLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHTTCCSEESSHHHHHHHH---HHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHhcCCccCCHHHHHHHHH---HHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            999987652  56665554   3333 4689999999999999999999999986

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=99.43  E-value=1.2e-13  Score=112.34  Aligned_cols=115  Identities=13%  Similarity=0.009  Sum_probs=82.7

Q ss_pred             CCcEEEEecCCCCC--CCceEEEEEcC--ee--eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCH
Q psy8376          56 KDKILCYTDGSKTN--TFTGGAYLLNE--TV--EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSK  128 (328)
Q Consensus        56 ~~~~~iytDgS~~~--~~~G~g~~~~~--~~--~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~  128 (328)
                      ...+.||||||+..  |.+|+|+++..  ..  .+..++ .+|++.||++|++.||    +.+.. +  . ++.|+|||+
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL----~~~~~~~--~-~v~i~tDS~   80 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGL----RYLKERN--S-RKPIYSNSQ   80 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHH----HHHHHTT--C-CCCEEESCH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHH----HHHHhCC--C-eEEEEEehH
Confidence            45678999999873  44899999842  11  112222 5799999999999999    55554 3  4 999999999


Q ss_pred             HHHHHHHccCCC---------HHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhH
Q psy8376         129 SSLQALKFNLND---------SILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDR  180 (328)
Q Consensus       129 ~ai~~l~~~~~~---------~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~  180 (328)
                      +|++.+++...+         .++.+.|......+...  .++...|+-|++.-||..||.
T Consensus        81 ~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~--~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           81 TAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTH--TYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHC--CCCCCEEECCHHHHCSCTTCC
T ss_pred             HHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHhhC--CCceeEEEeccCccCcCcccc
Confidence            999999987621         13566665555556554  445556777888889999984

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=99.27  E-value=7.1e-12  Score=100.26  Aligned_cols=96  Identities=13%  Similarity=0.024  Sum_probs=65.3

Q ss_pred             CCcEEEEecCCCCC--CCceEEEEE-cC-e--eeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHH
Q psy8376          56 KDKILCYTDGSKTN--TFTGGAYLL-NE-T--VEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKS  129 (328)
Q Consensus        56 ~~~~~iytDgS~~~--~~~G~g~~~-~~-~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~  129 (328)
                      +....||||||+..  |.+|+|+|+ .+ .  .....+ ..+||++||++|++.||    +.+...  ..++.|+|||++
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL----~~l~~~--~~~v~i~tDSqy   75 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGL----RYLKER--NSRKPIYSNSQT   75 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHH----HHHHHT--TCCCCEEESCHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHH----HHHHhC--CCCEEEEcchHH
Confidence            56678999999883  337886666 32 1  122222 26899999999999999    555441  224899999999


Q ss_pred             HHHHHHccCCC--------H-HHHHHHHHHHHHHHhcC
Q psy8376         130 SLQALKFNLND--------S-ILISKILLKIKEISSFG  158 (328)
Q Consensus       130 ai~~l~~~~~~--------~-~~~~~i~~~~~~l~~~~  158 (328)
                      |++.|.++.-+        + .+.+.|..+...|....
T Consensus        76 Vi~wi~~~~~kt~~~~~vkN~dLw~~ld~~~~~l~~~~  113 (134)
T 4htu_A           76 AIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHT  113 (134)
T ss_dssp             HHHHHHHTCCCCCCCCSSTTHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHcCCcccCCCCCccCHHHHHHHHHHHHHHHhCC
Confidence            99999975321        1 46666666555565543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	328
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	2e-08
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-06
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	6e-04

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

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]

 Score = 49.9 bits (118), Expect = 2e-08
 Identities = 29/127 (22%), Positives = 49/127 (38%), Gaps = 13/127 (10%)

Query: 62  YTDGS-KTNTFTGGA-YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFK 119
           YTDGS    +  G A Y+ +   ++ +  +  +   AEL A           +       
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEA---------FAMALTDSGP 61

Query: 120 DFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVD 179
              I  DS+  +  +     +S   SKI+ +I E       +   W+P+H GI  N+ VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD 119

Query: 180 RAARNAV 186
                 +
Sbjct: 120 HLVSQGI 126

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147

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]

 Score = 44.9 bits (105), Expect = 2e-06
 Identities = 26/144 (18%), Positives = 52/144 (36%), Gaps = 10/144 (6%)

Query: 56  KDKILCYTDGS-KTNTFTGG-AYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQ 113
           + ++  +TDG+   N   GG A LL     +  L+   +  T   M +   +  +    +
Sbjct: 1   RKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE 60

Query: 114 NNF--CFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEI------SSFGSQVSFLW 165
                 + D      + +      +            +K +++      +    +V F +
Sbjct: 61  PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHF 120

Query: 166 IPSHVGIRENEMVDRAARNAVNAR 189
           +  H G  ENE VDR AR    ++
Sbjct: 121 VKGHTGHPENERVDREARRQAQSQ 144

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

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]

 Score = 37.3 bits (85), Expect = 6e-04
 Identities = 25/138 (18%), Positives = 39/138 (28%), Gaps = 9/138 (6%)

Query: 58  KILCYTDGS-KTNTFTGG--AYLL--NETVEQFQLNQIASIYTAELMAID--LCLNSILM 110
           ++  +T GS   N   GG  A L                +    ELMA    L       
Sbjct: 2   QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA 61

Query: 111 YIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEIS--SFGSQVSFLWIPS 168
            +  +   +               +          K +   + +       Q+ + W+  
Sbjct: 62  EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKG 121

Query: 169 HVGIRENEMVDRAARNAV 186
           H G  ENE  D  AR A 
Sbjct: 122 HAGHPENERADELARAAA 139

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	328
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.92
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.9
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.89
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.78
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.6

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.92  E-value=8.8e-26  Score=179.75  Aligned_cols=117  Identities=23%  Similarity=0.321  Sum_probs=88.1

Q ss_pred             CCcEEEEecCCCCC-CC-ceEEEEEcC-eeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          56 KDKILCYTDGSKTN-TF-TGGAYLLNE-TVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        56 ~~~~~iytDgS~~~-~~-~G~g~~~~~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      +...+||||||+.. ++ +|+|+++.. ......++ ..|+++||+.||++||    +.   .  ..++.|+|||++|++
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al----~~---~--~~~i~I~tDS~~v~~   74 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMAL----TD---S--GPKVNIIVDSQYVMG   74 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHH----HT---S--CSEEEEEESCHHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHh----cc---C--CcceEEEechHHHHH
Confidence            45678999999774 33 667777643 33333343 5799999999999999    53   2  678999999999999


Q ss_pred             HHHccCCCH--HHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHh
Q psy8376         133 ALKFNLNDS--ILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAV  186 (328)
Q Consensus       133 ~l~~~~~~~--~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~  186 (328)
                      .++++...+  .....+   +..+.. ...|.|.|||||+|++|||.||+||++|+
T Consensus        75 ~~~~~~~~~~~~~~~~~---~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          75 IVASQPTESESKIVNQI---IEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHTCCSEESCHHHHHH---HHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHhcCCccccchHHHHH---HHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            999876543  333222   223333 46899999999999999999999999874

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

Probab=99.90  E-value=2.4e-24  Score=175.83  Aligned_cols=125  Identities=21%  Similarity=0.163  Sum_probs=90.5

Q ss_pred             CcEEEEecCCCCCC--CceEEEEE--cC-eeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHH
Q psy8376          57 DKILCYTDGSKTNT--FTGGAYLL--NE-TVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSL  131 (328)
Q Consensus        57 ~~~~iytDgS~~~~--~~G~g~~~--~~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai  131 (328)
                      ..+.||||||+..+  .+|+|+++  .+ .....+....+|+++||+.|++.||    +++..   ...+.|++||++++
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL----~~~~~---~~~i~i~tds~~~~   74 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGL----KALKE---PCEVDLYTDSHYLK   74 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHH----HSCCS---CCEEEEECCCHHHH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHh----hhccC---CceEEEecchhhhh
Confidence            35889999998853  37889887  22 2222233345799999999999999    65443   67899999999999


Q ss_pred             HHHHccCCC----------H--HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376         132 QALKFNLND----------S--IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR  189 (328)
Q Consensus       132 ~~l~~~~~~----------~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  189 (328)
                      +.+......          .  ++ -.++++.+..+. ....|.|.|||||+|++|||.||+|||+|+...
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          75 KAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             ccccccchhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            988753210          0  11 122333333443 356899999999999999999999999998764

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.89  E-value=1e-23  Score=172.83  Aligned_cols=128  Identities=20%  Similarity=0.232  Sum_probs=92.7

Q ss_pred             cEEEEecCCCCCC--CceEEEEE--cCeeeec-cCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          58 KILCYTDGSKTNT--FTGGAYLL--NETVEQF-QLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        58 ~~~iytDgS~~~~--~~G~g~~~--~~~~~~~-~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      .|.||||||+..+  .+|+|+++  .+....+ .....+|+++||++|++.||    +++..   ...+.|++||++++.
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al----~~~~~---~~~i~i~tds~~~i~   74 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVAL----EALKE---HAEVILSTDSQYVRQ   74 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHH----HTCCS---CCEEEEEECCHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhh----hhhcc---cceEEEeecceeeEE
Confidence            4889999998753  38999887  3333222 22346789999999999999    65443   678999999999999


Q ss_pred             HHHccCC---------CH--H-HHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCCCCCC
Q psy8376         133 ALKFNLN---------DS--I-LISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQ  193 (328)
Q Consensus       133 ~l~~~~~---------~~--~-~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~~~~  193 (328)
                      .+..+..         ..  + ...++...+..+. ....|.|+|||||+|++|||.||+|||+|+..+...+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d  146 (152)
T d1jl1a_          75 GITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTLED  146 (152)
T ss_dssp             HHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCC
T ss_pred             cccchhhHhHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCc
Confidence            8875421         11  1 1122333333443 3568999999999999999999999999999875443

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

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=99.78  E-value=3.4e-19  Score=137.38  Aligned_cols=100  Identities=24%  Similarity=0.323  Sum_probs=75.1

Q ss_pred             CCcEEEEecCCCCC-CC-ceEEEEEcC-eeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376          56 KDKILCYTDGSKTN-TF-TGGAYLLNE-TVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ  132 (328)
Q Consensus        56 ~~~~~iytDgS~~~-~~-~G~g~~~~~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~  132 (328)
                      ++..++|||||+.. ++ .|+|++..+ ......+. .+||++||+.||+.||    +.   .  ..++.|+|||++|++
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL----~~---~--~~~v~I~TDS~yvi~   75 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QD---S--GLEVNIVTDSQYALG   75 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHH----HH---S--CSEEEEEECCHHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHH----Hh---C--CCeEEEEEehHHHHH
Confidence            46678999999774 33 667777633 33333343 5799999999999999    53   2  668999999999999


Q ss_pred             HHHccCCCH--HHHHHHHHHHHHHHhcCCeEEEEEecCC
Q psy8376         133 ALKFNLNDS--ILISKILLKIKEISSFGSQVSFLWIPSH  169 (328)
Q Consensus       133 ~l~~~~~~~--~~~~~i~~~~~~l~~~~~~v~~~Wvp~H  169 (328)
                      +++++....  ++.++|.+   .+. ....|.|.|||||
T Consensus        76 ~i~~~~~~~~~~l~~~il~---~l~-~~~~v~i~WVpgH  110 (110)
T d1s1ta1          76 IIQAQPDQSESELVNQIIE---QLI-KKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHCCSEESCHHHHHHHH---HHH-HCSEEEEEECCSS
T ss_pred             HHhcCccccchHHHHHHHH---HHh-cCCceEEEEeCCC
Confidence            999877543  56666655   333 3568999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.60  E-value=2.2e-16  Score=123.88  Aligned_cols=112  Identities=12%  Similarity=0.003  Sum_probs=80.7

Q ss_pred             EEEecCCCCC--CCceEEEEEcC--e-eeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHHHH
Q psy8376          60 LCYTDGSKTN--TFTGGAYLLNE--T-VEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQAL  134 (328)
Q Consensus        60 ~iytDgS~~~--~~~G~g~~~~~--~-~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~~l  134 (328)
                      .||||||+..  |.+|+|+|+..  . ....+--..+|+++||++|++.||    +.+...  ..++.|+|||++|++.+
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL----~~~~~~--~~~i~I~tDS~yvi~wv   79 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGL----RYLKER--NSRKPIYSNSQTAIKWV   79 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHH----HHHHHT--TCCCCEEESCHHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHH----HHhhcC--CceEEEEeccHHHHHHH
Confidence            3899999883  44899988722  2 221221246799999999999999    665542  45799999999999999


Q ss_pred             HccCCCH---------HHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHh
Q psy8376         135 KFNLNDS---------ILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVD  179 (328)
Q Consensus       135 ~~~~~~~---------~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD  179 (328)
                      .++....         ++.+.|.+....+..  ..+.+.|++.|+.--||..||
T Consensus        80 ~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk~--h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          80 KDKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             HHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTC
T ss_pred             HhCceecCcCCCcccHHHHHHHHHHHHHHHh--CCcCceeEEecCcccccCCCC
Confidence            8765221         355555544444543  458889999999999999998