Psyllid ID: psy2243

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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-------330-------340-------350-------360-------370-------380-------390-------400-----
Protein Sequence
MLDPVQNQCLRLATGAFRSSPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITLNWGLF
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccEEEEEcccccccccEEEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHcccccHHHHccHHHHHHHHHHHccccHHHHHHHHHHHHcccccEEEEEcccccccccccHHHHHHHccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccHHcccccccccccccccccEEEEEEcccccccccccccccccccccEEEccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHcccccccHHHHHccccccccHHccHHHHHHHHHHHHHHcccccEEEEccccccHHHHccccccEEEccHHHcccHccccccccccccccccccccccccccHHHHHHHHcccccHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEccHHHHcccccccccccccHHHHHHHHHHHcccccccccEEEEccHHHHHHHHHcHHcccHHHHHHHHHHHHcccccccEEEcccHHHHHHHHHHHHHHHHccccHHHHHHcHHHHHccccccEEcccccccHHHcccHHHcccccccccccEEEEccccEEEEEccccccccccEEEEccccccccccHHHccccccccccccEEEEEEccccccEEEEEccccccccccccEEEEEc
Coil and Loop (DISEMBL)
MLDPVQNQCLRlatgafrssptasleaetsepnlkIRRSILTCNYIAKVMHhnstnpnfkrinnppykvlyenstklnptvgIQREIlmndipfhkvilqrepkeswlhkkpscnlsltlykkdgmphqVFQQEFQRNMNENYGDFVQVytdgsksdssvgcafvipqlhivkkqtlnpkssifHAELLAISDAVSTIksqsigeaVIISDSLSALQAISsmshsnplvQSIHEEistipnstikffwcpshvgiagndAADLEAKSalenpishdhgigltqlsglfahtpkpqkgdntflkpaseckpieypkpdgqvSFDLLSSVAltgtnhegdqpahltlkddsvpvntnlavydgpegrfcpagklenhntqnyveslgpkndnrtLKSLYITLNWGLF
Flexible Loop (DISEMBL)
MLDPVQNQCLRLatgafrssptasleaetsepnlkiRRSILTCNYIAKVMHhnstnpnfkrinnPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQRepkeswlhkkpSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAhltlkddsvpvnTNLAVYDGPEGRFCPAGKLENHNTQNYVEslgpkndnrtlkSLYITLNWGLF
Low Complexity Region (SEG)
MLDPVQNQCLRLATGAFRSSPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITLNWGLF
Disordered region (IsUnstruct)
**********************************KIRRSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQA*********LVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADL***********HDHGIGLTQLSGLF*********************************FDLL**V*********************VPVNTNLAVYDGPEGRFCPAGKL*******************TLKSLYITLNWGL*
Disordered Region (DISOPRED)
MLDPVQNQCLRLATGAFRSSPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNPPY****ENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITLNWGLF
Disordered Region (DISEMBL)
MLDPVQNQCLRLATGAFR*************PNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITLNWGLF
Disordered Region (DISPRO)
MLDPVQNQCLRLATGAFRSSPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITLNWGLF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLDPVQNQCLRLATGAFRSSPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQREILMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITLNWGLF
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	405	2.2.26 [Sep-21-2011]
Q6UPE1	616	Electron transfer flavopr	yes	N/A	0.237	0.155	0.687	2e-31
Q921G7	616	Electron transfer flavopr	yes	N/A	0.237	0.155	0.687	2e-31
Q2KIG0	617	Electron transfer flavopr	yes	N/A	0.237	0.155	0.687	4e-31
P55931	617	Electron transfer flavopr	yes	N/A	0.237	0.155	0.687	5e-31
Q16134	617	Electron transfer flavopr	yes	N/A	0.237	0.155	0.677	7e-31
Q5RDD3	617	Electron transfer flavopr	yes	N/A	0.237	0.155	0.677	9e-31
Q11190	597	Electron transfer flavopr	yes	N/A	0.192	0.130	0.666	2e-24
Q54XM6	606	Electron transfer flavopr	yes	N/A	0.232	0.155	0.536	1e-22
Q9HZP5	551	Electron transfer flavopr	yes	N/A	0.2	0.147	0.571	2e-18
Q08822	631	Probable electron transfe	yes	N/A	0.195	0.125	0.506	1e-15

>sp|Q6UPE1|ETFD_RAT Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Rattus norvegicus GN=Etfdh PE=2 SV=1

 Score =  136 bits (343), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 471 GIFYWILRGMEPWTLKHKGSDSEQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

Accepts electrons from ETF and reduces ubiquinone.
Rattus norvegicus (taxid: 10116)
EC: 1EC: .EC: 5EC: .EC: 5EC: .EC: 1

>sp|Q921G7|ETFD_MOUSE Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Mus musculus GN=Etfdh PE=1 SV=1

 Score =  136 bits (343), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 471 GIFYWILRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

Accepts electrons from ETF and reduces ubiquinone.

Mus musculus (taxid: 10090)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q2KIG0|ETFD_BOVIN Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Bos taurus GN=ETFDH PE=2 SV=1

 Score =  136 bits (342), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 74/96 (77%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI      G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 472 GIFYWIFRGMEPWTLKHKGSDSDKLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDSVPVN NL++YDGPE RFCPAG  E
Sbjct: 532 DQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYE 567

Accepts electrons from ETF and reduces ubiquinone.

Bos taurus (taxid: 9913)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|P55931|ETFD_PIG Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Sus scrofa GN=ETFDH PE=1 SV=2

 Score =  135 bits (341), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 74/96 (77%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI      G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 472 GIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDSVPVN NL++YDGPE RFCPAG  E
Sbjct: 532 DQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYE 567

Accepts electrons from ETF and reduces ubiquinone.

Sus scrofa (taxid: 9823)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q16134|ETFD_HUMAN Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Homo sapiens GN=ETFDH PE=1 SV=2

 Score =  135 bits (339), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 65/96 (67%), Positives = 74/96 (77%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D   LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 472 GIFYWILRGMEPWTLKHKGSDFERLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTL+DDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 532 DQPAHLTLRDDSIPVNRNLSIYDGPEQRFCPAGVYE 567

Accepts electrons from ETF and reduces ubiquinone.

Homo sapiens (taxid: 9606)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q5RDD3|ETFD_PONAB Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Pongo abelii GN=ETFDH PE=2 SV=1

 Score =  134 bits (338), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 65/96 (67%), Positives = 74/96 (77%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D   LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 472 GIFYWILRGMEPWTLKHKGSDFERLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTL+DDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 532 DQPAHLTLRDDSIPVNRNLSIYDGPEQRFCPAGVYE 567

Accepts electrons from ETF and reduces ubiquinone.

Pongo abelii (taxid: 9601)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q11190|ETFD_CAEEL Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Caenorhabditis elegans GN=let-721 PE=1 SV=2

 Score =  114 bits (284), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 52/78 (66%), Positives = 62/78 (79%)

Query: 296 KGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTN 355
           K DN  L P  + K I+YPKPDG+++FDLL+SV+LTGTNH  DQPAHLTLK+D VP++ N
Sbjct: 469 KKDNEKLIPVKDAKEIDYPKPDGKLTFDLLTSVSLTGTNHTEDQPAHLTLKNDQVPLDVN 528

Query: 356 LAVYDGPEGRFCPAGKLE 373
           LAVY GPE RFCPAG  E
Sbjct: 529 LAVYGGPEARFCPAGVYE 546

Accepts electrons from ETF and reduces ubiquinone.

Caenorhabditis elegans (taxid: 6239)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q54XM6|ETFD_DICDI Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Dictyostelium discoideum GN=etfdh PE=3 SV=1

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 52/97 (53%), Positives = 64/97 (65%), Gaps = 3/97 (3%)

Query: 280 GLTQLSGLFAHTP---KPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHE 336
           G  ++     HTP      K DN  LKPA+ECK IEY KPDGQ++FDL++SV  +GTNHE
Sbjct: 461 GALEMYIFRGHTPWTLSNGKPDNERLKPAAECKKIEYKKPDGQITFDLMTSVMRSGTNHE 520

Query: 337 GDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
            +QP HL ++D  V    N  +YDGPEGRFCPAG  E
Sbjct: 521 ENQPIHLKVRDMEVAKKVNRDIYDGPEGRFCPAGVYE 557

Accepts electrons from ETF and reduces ubiquinone.

Dictyostelium discoideum (taxid: 44689)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q9HZP5|ETFD_PSEAE Electron transfer flavoprotein-ubiquinone oxidoreductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=PA2953 PE=1 SV=1

 Score = 94.0 bits (232), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/84 (57%), Positives = 56/84 (66%), Gaps = 3/84 (3%)

Query: 290 HTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDS 349
           H  KP   D   LK ASE   I+YPKPDG++SFD LSSV L+ TNHE DQP HL L D S
Sbjct: 422 HDDKP---DYACLKKASEAPKIDYPKPDGKLSFDKLSSVFLSNTNHEEDQPIHLKLADAS 478

Query: 350 VPVNTNLAVYDGPEGRFCPAGKLE 373
           +P+  NL +YD P  R+CPAG  E
Sbjct: 479 IPIEKNLPLYDEPAQRYCPAGVYE 502

Accepts electrons from ETF and reduces ubiquinone.

Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (taxid: 208964)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

>sp|Q08822|ETFD_YEAST Probable electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CIR2 PE=1 SV=1

 Score = 84.7 bits (208), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/81 (50%), Positives = 54/81 (66%), Gaps = 2/81 (2%)

Query: 295 QKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTL--KDDSVPV 352
           +K D   L+PAS+ KPIEYPKPDG +SFD+L+SV+ TGT H+ D+P HL +  +D     
Sbjct: 500 EKNDGEILEPASKYKPIEYPKPDGVISFDILTSVSRTGTYHDDDEPCHLRVPGQDMVKYA 559

Query: 353 NTNLAVYDGPEGRFCPAGKLE 373
             +  V+ G E RFCPAG  E
Sbjct: 560 ERSFPVWKGVESRFCPAGVYE 580

Accepts electrons from ETF and reduces ubiquinone.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 1

EC: .

EC: 5

EC: .

EC: 5

EC: .

EC: 1

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	405
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.666	0.220	0.394	2e-37
332372654	601	unknown [Dendroctonus ponderosae]	0.266	0.179	0.633	4e-31
345307532	612	PREDICTED: electron transfer flavoprotei	0.237	0.156	0.708	1e-30
157116302	588	electron transfer flavoprotein-ubiquinon	0.187	0.129	0.815	1e-30
417403349	617	Putative electron transfer flavoprotein	0.237	0.155	0.708	4e-30
354476085	617	PREDICTED: electron transfer flavoprotei	0.237	0.155	0.697	1e-29
26344475	616	unnamed protein product [Mus musculus]	0.237	0.155	0.687	1e-29
158294952	607	AGAP005894-PA [Anopheles gambiae str. PE	0.187	0.125	0.802	1e-29
52138635	616	electron transfer flavoprotein-ubiquinon	0.237	0.155	0.687	1e-29
52000614	616	RecName: Full=Electron transfer flavopro	0.237	0.155	0.687	1e-29

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

 Score =  163 bits (412), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 110/279 (39%), Positives = 146/279 (52%), Gaps = 9/279 (3%)

Query: 1    MLDPVQNQCLRLATGAFRSSPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFK 60
            +L+P+QN  LRL  GAFR+SP  SL  E  E  + IR   L   YI K +  N TNP F 
Sbjct: 810  ILEPIQNAALRLCLGAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVK-LKSNPTNPAFD 868

Query: 61   RINNPPYKVLYENSTKLNPTVGIQ-REILMN-DIPFHKVILQREPKE-SWLHKKPSCNLS 117
             I NP    LY     +   +G++ RE + N   P  ++     P+   WL  KP  NLS
Sbjct: 869  SIFNPTEVELYNRRPNVIQPLGLRMREPIQNLTQPIDQISKIETPQNPPWLMNKPKLNLS 928

Query: 118  LTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTL 177
            L  +KK+     + Q  F R + E+YGD   +YTDGSK +  V CA       I ++  L
Sbjct: 929  LLNFKKENTDPSILQVHF-RELQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRR--L 985

Query: 178  NPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHE--E 235
                SIF AEL AI  A+  +K+    + +I SDS SALQA+  M    PLV    +  +
Sbjct: 986  PDGCSIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLD 1045

Query: 236  ISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPIS 274
            + T     + F W PSHVGI GN+AAD EAK AL + +S
Sbjct: 1046 LITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVS 1084

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|332372654|gb|AEE61469.1| unknown [Dendroctonus ponderosae]

 Score =  141 bits (356), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 82/112 (73%), Gaps = 4/112 (3%)

Query: 266 KSALENPISHDHGIGLTQLS----GLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVS 321
           + +  NP+    G+  +  S    G    T K    D+  LKPA ECKPIEYPKPDG++S
Sbjct: 440 RPSFHNPLGLYGGLAYSGFSVVVGGREPWTLKHGDPDHKRLKPAKECKPIEYPKPDGKIS 499

Query: 322 FDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           FDLL+SVALTGTNHEGDQPAHLTLKDD+VPVN NLAV+DGPEGRFCPAG  E
Sbjct: 500 FDLLTSVALTGTNHEGDQPAHLTLKDDTVPVNHNLAVFDGPEGRFCPAGVYE 551

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345307532|ref|XP_001510390.2| PREDICTED: electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial-like [Ornithorhynchus anatinus]

 Score =  140 bits (353), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 68/96 (70%), Positives = 74/96 (77%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI      G+   T K +  D+  LKPA EC PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 467 GIFYWIFRGMEPWTLKHKGADSDQLKPAKECTPIEYPKPDGQISFDLLSSVALSGTNHEH 526

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDSVPVN NL +YDGPEGRFCPAG  E
Sbjct: 527 DQPAHLTLKDDSVPVNKNLEIYDGPEGRFCPAGVYE 562

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|157116302|ref|XP_001652814.1| electron transfer flavoprotein-ubiquinone oxidoreductase [Aedes aegypti] gi|157116304|ref|XP_001652815.1| electron transfer flavoprotein-ubiquinone oxidoreductase [Aedes aegypti] gi|108876539|gb|EAT40764.1| AAEL007526-PB [Aedes aegypti] gi|108876540|gb|EAT40765.1| AAEL007526-PA [Aedes aegypti]

 Score =  140 bits (352), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 69/76 (90%)

Query: 298 DNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLA 357
           D+T LKPA ECKPIEYPKPDG+++FDLLSSVALTGTNHEGDQPAHLTLKDD++PV  NLA
Sbjct: 463 DHTRLKPAKECKPIEYPKPDGKITFDLLSSVALTGTNHEGDQPAHLTLKDDTIPVKNNLA 522

Query: 358 VYDGPEGRFCPAGKLE 373
           +YDGPE RFCPAG  E
Sbjct: 523 IYDGPEARFCPAGVYE 538

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|417403349|gb|JAA48482.1| Putative electron transfer flavoprotein ubiquinone oxidoreductase [Desmodus rotundus]

 Score =  138 bits (348), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 68/96 (70%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 472 GIFYWILRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDSVPVN NLA+YDGPE RFCPAG  E
Sbjct: 532 DQPAHLTLKDDSVPVNRNLAIYDGPEQRFCPAGVYE 567

Source: Desmodus rotundus

Species: Desmodus rotundus

Genus: Desmodus

Family: Phyllostomidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|354476085|ref|XP_003500255.1| PREDICTED: electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial [Cricetulus griseus]

 Score =  137 bits (345), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 67/96 (69%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 472 GIFYWILRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDSVPVN NL++YDGPE RFCPAG  E
Sbjct: 532 DQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYE 567

Source: Cricetulus griseus

Species: Cricetulus griseus

Genus: Cricetulus

Family: Cricetidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|26344475|dbj|BAC35888.1| unnamed protein product [Mus musculus]

 Score =  137 bits (344), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 471 GIFYWILRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|158294952|ref|XP_315923.3| AGAP005894-PA [Anopheles gambiae str. PEST] gi|157015804|gb|EAA11780.3| AGAP005894-PA [Anopheles gambiae str. PEST]

 Score =  137 bits (344), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 61/76 (80%), Positives = 68/76 (89%)

Query: 298 DNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLA 357
           D+T LKPA +CKPIEYPKPDG+++FDLLSSVALTGTNHEGDQPAHLTLKDD+VPV  NL 
Sbjct: 482 DHTRLKPAKDCKPIEYPKPDGKLTFDLLSSVALTGTNHEGDQPAHLTLKDDTVPVKNNLT 541

Query: 358 VYDGPEGRFCPAGKLE 373
           +YDGPE RFCPAG  E
Sbjct: 542 IYDGPEARFCPAGVYE 557

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|52138635|ref|NP_942037.2| electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor [Rattus norvegicus] gi|51859484|gb|AAH81890.1| Electron-transferring-flavoprotein dehydrogenase [Rattus norvegicus] gi|149048291|gb|EDM00867.1| electron-transferring-flavoprotein dehydrogenase [Rattus norvegicus] gi|327242981|gb|AEA41109.1| electron transferring flavoprotein dehydrogenase [Rattus norvegicus] gi|327242983|gb|AEA41110.1| electron transferring flavoprotein dehydrogenase [Rattus norvegicus]

 Score =  136 bits (343), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 471 GIFYWILRGMEPWTLKHKGSDSEQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|52000614|sp|Q6UPE1.1|ETFD_RAT RecName: Full=Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial; Short=ETF-QO; Short=ETF-ubiquinone oxidoreductase; AltName: Full=Electron-transferring-flavoprotein dehydrogenase; Short=ETF dehydrogenase; Flags: Precursor gi|34419911|gb|AAQ67364.1| electron transfer flavoprotein-ubiquinone oxidoreductase precursor [Rattus norvegicus]

 Score =  136 bits (343), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 471 GIFYWILRGMEPWTLKHKGSDSEQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct: 531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

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	405
MGI|MGI:106100	616	Etfdh "electron transferring f	0.237	0.155	0.687	1.5e-30
RGD|735052	616	Etfdh "electron-transferring-f	0.237	0.155	0.687	1.5e-30
UNIPROTKB|F1RW89	616	ETFDH "Electron transfer flavo	0.217	0.142	0.727	3.2e-30
UNIPROTKB|Q2KIG0	617	ETFDH "Electron transfer flavo	0.217	0.142	0.727	3.2e-30
UNIPROTKB|P55931	617	ETFDH "Electron transfer flavo	0.217	0.142	0.727	3.2e-30
UNIPROTKB|J3KND9	570	ETFDH "Electron transfer flavo	0.237	0.168	0.677	6.3e-30
UNIPROTKB|Q16134	617	ETFDH "Electron transfer flavo	0.237	0.155	0.677	8.8e-30
UNIPROTKB|F6V7P2	617	ETFDH "Uncharacterized protein	0.217	0.142	0.693	4e-29
UNIPROTKB|E2QTI8	618	ETFDH "Uncharacterized protein	0.217	0.142	0.693	4e-29
ZFIN|ZDB-GENE-040912-168	617	etfdh "electron-transferring-f	0.204	0.134	0.734	5.2e-29

MGI|MGI:106100 Etfdh "electron transferring flavoprotein, dehydrogenase" [Mus musculus (taxid:10090)]

 Score = 343 (125.8 bits), Expect = 1.5e-30, P = 1.5e-30
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query:   278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
             GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct:   471 GIFYWILRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query:   338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct:   531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=ISO

GO:0005739 "mitochondrion" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=IDA

GO:0006810 "transport" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IDA

GO:0009055 "electron carrier activity" evidence=ISO

GO:0016020 "membrane" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=ISO

GO:0017133 "mitochondrial electron transfer flavoprotein complex" evidence=TAS

GO:0022900 "electron transport chain" evidence=ISO

GO:0031305 "integral to mitochondrial inner membrane" evidence=ISO

GO:0031966 "mitochondrial membrane" evidence=ISO

GO:0033539 "fatty acid beta-oxidation using acyl-CoA dehydrogenase" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0048038 "quinone binding" evidence=ISO

GO:0048039 "ubiquinone binding" evidence=ISO

GO:0051536 "iron-sulfur cluster binding" evidence=ISO

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=ISO

GO:0055114 "oxidation-reduction process" evidence=IEA

RGD|735052 Etfdh "electron-transferring-flavoprotein dehydrogenase" [Rattus norvegicus (taxid:10116)]

 Score = 343 (125.8 bits), Expect = 1.5e-30, P = 1.5e-30
 Identities = 66/96 (68%), Positives = 75/96 (78%)

Query:   278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
             GI    L G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct:   471 GIFYWILRGMEPWTLKHKGSDSEQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 530

Query:   338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             DQPAHLTLKDDS+PVN NL++YDGPE RFCPAG  E
Sbjct:   531 DQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE 566

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=ISO

GO:0005743 "mitochondrial inner membrane" evidence=IEA;ISO

GO:0006979 "response to oxidative stress" evidence=IEA;ISO;ISS

GO:0008150 "biological_process" evidence=ND

GO:0009055 "electron carrier activity" evidence=IEA;ISO;IDA

GO:0016491 "oxidoreductase activity" evidence=ISO

GO:0022900 "electron transport chain" evidence=IEA;ISO

GO:0031305 "integral to mitochondrial inner membrane" evidence=IEA;ISO

GO:0031966 "mitochondrial membrane" evidence=ISO;IDA

GO:0033539 "fatty acid beta-oxidation using acyl-CoA dehydrogenase" evidence=IEA;ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0048038 "quinone binding" evidence=ISO

GO:0048039 "ubiquinone binding" evidence=IEA;ISO

GO:0051536 "iron-sulfur cluster binding" evidence=IDA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA;ISO

UNIPROTKB|F1RW89 ETFDH "Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial" [Sus scrofa (taxid:9823)]

 Score = 340 (124.7 bits), Expect = 3.2e-30, P = 3.2e-30
 Identities = 64/88 (72%), Positives = 72/88 (81%)

Query:   286 GLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTL 345
             G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTL
Sbjct:   479 GMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTL 538

Query:   346 KDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             KDDSVPVN NL++YDGPE RFCPAG  E
Sbjct:   539 KDDSVPVNRNLSIYDGPEQRFCPAGVYE 566

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0048039 "ubiquinone binding" evidence=IEA

GO:0033539 "fatty acid beta-oxidation using acyl-CoA dehydrogenase" evidence=IEA

GO:0031305 "integral to mitochondrial inner membrane" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA

UNIPROTKB|Q2KIG0 ETFDH "Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 340 (124.7 bits), Expect = 3.2e-30, P = 3.2e-30
 Identities = 64/88 (72%), Positives = 72/88 (81%)

Query:   286 GLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTL 345
             G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTL
Sbjct:   480 GMEPWTLKHKGSDSDKLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTL 539

Query:   346 KDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             KDDSVPVN NL++YDGPE RFCPAG  E
Sbjct:   540 KDDSVPVNRNLSIYDGPEQRFCPAGVYE 567

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0048039 "ubiquinone binding" evidence=IEA

GO:0033539 "fatty acid beta-oxidation using acyl-CoA dehydrogenase" evidence=IEA

GO:0031305 "integral to mitochondrial inner membrane" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|P55931 ETFDH "Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial" [Sus scrofa (taxid:9823)]

 Score = 340 (124.7 bits), Expect = 3.2e-30, P = 3.2e-30
 Identities = 64/88 (72%), Positives = 72/88 (81%)

Query:   286 GLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTL 345
             G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTL
Sbjct:   480 GMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTL 539

Query:   346 KDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             KDDSVPVN NL++YDGPE RFCPAG  E
Sbjct:   540 KDDSVPVNRNLSIYDGPEQRFCPAGVYE 567

GO:0043783 "oxidoreductase activity, oxidizing metal ions with flavin as acceptor" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0048039 "ubiquinone binding" evidence=IDA

GO:0050660 "flavin adenine dinucleotide binding" evidence=IDA

GO:0051536 "iron-sulfur cluster binding" evidence=IDA

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0044429 "mitochondrial part" evidence=IDA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IDA

GO:0022900 "electron transport chain" evidence=IDA

GO:0016491 "oxidoreductase activity" evidence=IDA

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IDA

GO:0009055 "electron carrier activity" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|J3KND9 ETFDH "Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 336 (123.3 bits), Expect = 6.3e-30, P = 6.3e-30
 Identities = 65/96 (67%), Positives = 74/96 (77%)

Query:   278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
             GI    L G+   T K +  D   LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct:   425 GIFYWILRGMEPWTLKHKGSDFERLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 484

Query:   338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             DQPAHLTL+DDS+PVN NL++YDGPE RFCPAG  E
Sbjct:   485 DQPAHLTLRDDSIPVNRNLSIYDGPEQRFCPAGVYE 520

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

UNIPROTKB|Q16134 ETFDH "Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 336 (123.3 bits), Expect = 8.8e-30, P = 8.8e-30
 Identities = 65/96 (67%), Positives = 74/96 (77%)

Query:   278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
             GI    L G+   T K +  D   LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct:   472 GIFYWILRGMEPWTLKHKGSDFERLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 531

Query:   338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             DQPAHLTL+DDS+PVN NL++YDGPE RFCPAG  E
Sbjct:   532 DQPAHLTLRDDSIPVNRNLSIYDGPEQRFCPAGVYE 567

GO:0046872 "metal ion binding" evidence=IEA

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IDA

GO:0022900 "electron transport chain" evidence=IDA

GO:0043783 "oxidoreductase activity, oxidizing metal ions with flavin as acceptor" evidence=ISS

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IDA

GO:0009055 "electron carrier activity" evidence=IDA

GO:0048038 "quinone binding" evidence=IDA

GO:0048039 "ubiquinone binding" evidence=IDA

GO:0016491 "oxidoreductase activity" evidence=IDA

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0031966 "mitochondrial membrane" evidence=IDA

GO:0050660 "flavin adenine dinucleotide binding" evidence=ISS

GO:0031305 "integral to mitochondrial inner membrane" evidence=IDA

GO:0005759 "mitochondrial matrix" evidence=TAS

GO:0022904 "respiratory electron transport chain" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0033539 "fatty acid beta-oxidation using acyl-CoA dehydrogenase" evidence=IMP

UNIPROTKB|F6V7P2 ETFDH "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 330 (121.2 bits), Expect = 4.0e-29, P = 4.0e-29
 Identities = 61/88 (69%), Positives = 72/88 (81%)

Query:   286 GLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTL 345
             G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTL
Sbjct:   480 GMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTL 539

Query:   346 KDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             +DDS+PVN NL+++DGPE RFCPAG  E
Sbjct:   540 RDDSIPVNRNLSLFDGPEQRFCPAGVYE 567

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA

UNIPROTKB|E2QTI8 ETFDH "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 330 (121.2 bits), Expect = 4.0e-29, P = 4.0e-29
 Identities = 61/88 (69%), Positives = 72/88 (81%)

Query:   286 GLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTL 345
             G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTL
Sbjct:   481 GMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTL 540

Query:   346 KDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
             +DDS+PVN NL+++DGPE RFCPAG  E
Sbjct:   541 RDDSIPVNRNLSLFDGPEQRFCPAGVYE 568

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0048039 "ubiquinone binding" evidence=IEA

GO:0033539 "fatty acid beta-oxidation using acyl-CoA dehydrogenase" evidence=IEA

GO:0031305 "integral to mitochondrial inner membrane" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA

ZFIN|ZDB-GENE-040912-168 etfdh "electron-transferring-flavoprotein dehydrogenase" [Danio rerio (taxid:7955)]

 Score = 329 (120.9 bits), Expect = 5.2e-29, P = 5.2e-29
 Identities = 61/83 (73%), Positives = 68/83 (81%)

Query:   291 TPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSV 350
             T K    D   LKPA +C PIEYPKPDG++SFDLLSSVAL+GTNHE DQPAHLTLKDDS+
Sbjct:   485 TLKHSGSDYAQLKPAKDCSPIEYPKPDGKISFDLLSSVALSGTNHEHDQPAHLTLKDDSI 544

Query:   351 PVNTNLAVYDGPEGRFCPAGKLE 373
             PV+ NLA+YDGPE RFCPAG  E
Sbjct:   545 PVSKNLAIYDGPEQRFCPAGVYE 567

GO:0004174 "electron-transferring-flavoprotein dehydrogenase activity" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0022904 "respiratory electron transport chain" evidence=IMP

---

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	405
pfam05187	110	pfam05187, ETF_QO, Electron transfer flavoprotein-	8e-44
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	5e-36
pfam00075	126	pfam00075, RNase_H, RNase H	9e-17
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	2e-07
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	4e-07
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	4e-07
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	4e-07
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	0.002

>gnl|CDD|218485 pfam05187, ETF_QO, Electron transfer flavoprotein-ubiquinone oxidoreductase

 Score =  148 bits (375), Expect = 8e-44
 Identities = 53/80 (66%), Positives = 61/80 (76%)

Query: 291 TPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSV 350
           T K  K D+  LKPASECKPI+YPKPDG+++FD LSSV L+ TNHE DQP HL LKD SV
Sbjct: 23  TLKHHKPDHAALKPASECKPIDYPKPDGKLTFDRLSSVFLSNTNHEEDQPCHLKLKDPSV 82

Query: 351 PVNTNLAVYDGPEGRFCPAG 370
           P+  NL  Y GPE R+CPAG
Sbjct: 83  PIAVNLPKYAGPEQRYCPAG 102

Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64-kDa monomer. Length = 110

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

 Score =  128 bits (323), Expect = 5e-36
 Identities = 46/126 (36%), Positives = 65/126 (51%), Gaps = 5/126 (3%)

Query: 148 QVYTDGSKSDSSVGCAFVIPQLHIVKKQ-TLNPKSSIFHAELLAISDAVSTIKSQSIG-- 204
            +YTDGSK +   G  F I +   + +   L P  S+F AELLAI +A+     +     
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 205 EAVIISDSLSALQAISSMSHSNPLVQSIHEEISTI--PNSTIKFFWCPSHVGIAGNDAAD 262
           +  I SDS +AL+A+ S   S+PLV  I + I  +      ++  W P H GI GN+ AD
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 263 LEAKSA 268
             AK A
Sbjct: 121 RLAKEA 126

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 = 75.8 bits (187), Expect = 9e-17
 Identities = 37/128 (28%), Positives = 54/128 (42%), Gaps = 13/128 (10%)

Query: 149 VYTDGS--KSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA 206
           VYTDGS   +    G  +V        K    P ++   AELLA+ +A+  +  Q +   
Sbjct: 6   VYTDGSCNGNPGPGGAGYVTDGGKQRSKP--LPGTTNQRAELLALIEALEALSGQKV--- 60

Query: 207 VIISDSLSALQAISSM----SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
            I +DS   +  I++     S S P+   I E +       +   W P H GI GN+ AD
Sbjct: 61  NIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQK--KHKVYIQWVPGHSGIPGNELAD 118

Query: 263 LEAKSALE 270
             AK    
Sbjct: 119 KLAKQGAS 126

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

 Score = 50.0 bits (120), Expect = 2e-07
 Identities = 28/155 (18%), Positives = 51/155 (32%), Gaps = 29/155 (18%)

Query: 147 VQVYTDGSKSD--SSVGCAFVI--PQLHIV-----KKQTLNPKSSIFHAELLAISDAVST 197
           V+++TDG+        G   V+              + T N       AEL A+ +A+  
Sbjct: 4   VEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNN------RAELRALIEALEA 57

Query: 198 IKSQSIGEAVIISDSLSALQAISSMSHSNPL------------VQSIHEEIST--IPNST 243
           +K     E  + +DS   ++ I+                     + + EE+      +  
Sbjct: 58  LKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHEL 117

Query: 244 IKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG 278
           + + W   H G   N+ AD  A+ A          
Sbjct: 118 VFWEWVKGHAGHPENERADQLAREAARAAKKSATP 152

Length = 154

>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 = 49.1 bits (118), Expect = 4e-07
 Identities = 36/155 (23%), Positives = 56/155 (36%), Gaps = 39/155 (25%)

Query: 149 VYTDGS-----KSDSSVGCAFVIPQLHI--------VKKQTLNPKSSIFHAELLAISDAV 195
           VYTDG+     +S +  G        H            QT         AEL A+  A+
Sbjct: 2   VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQ------RAELRAVIHAL 55

Query: 196 STIKSQSIG--EAVIISDSLSALQAISSMSHS-----------NP-----LVQSIHEEIS 237
             IK    G  + VI +DS   +  ++                 P     L++ + + + 
Sbjct: 56  RLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLE 115

Query: 238 TI--PNSTIKFFWCPSHVGIAGNDAADLEAKSALE 270
            +      +KF+  P H GI GN+ AD  AK   +
Sbjct: 116 ELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150

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|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 = 48.5 bits (116), Expect = 4e-07
 Identities = 33/129 (25%), Positives = 52/129 (40%), Gaps = 15/129 (11%)

Query: 150 YTDGSKSDSS--VGCAFVIPQLH---IVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 204
            TDGS   +    G   V+       +       P ++   AELLA+ +A+       + 
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 205 EAVIISDSLSALQAISSMSHS----NPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDA 260
           + +I +DS   +  I+S S      N L+  I   +S   +  I+F   P      GN+ 
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFID--IRFEHVPRE----GNEV 114

Query: 261 ADLEAKSAL 269
           AD  AK A 
Sbjct: 115 ADRLAKEAA 123

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 = 48.4 bits (116), Expect = 4e-07
 Identities = 31/141 (21%), Positives = 50/141 (35%), Gaps = 27/141 (19%)

Query: 149 VYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI 208
           V+TDGS      G A V     +++  TL   +S   AEL+A+  A+   K + +    I
Sbjct: 2   VFTDGSSFVRKAGYAVVTGP-DVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---I 57

Query: 209 ISDSLSALQAISSMSHS---NPLVQS----IHEEISTI------PNSTIKFF--WCPSHV 253
            +DS  A   + ++         +      +   I  +      P            +H 
Sbjct: 58  YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPK---PVAVIHIRAHS 114

Query: 254 G-----IAGNDAADLEAKSAL 269
           G       GN  AD  A+ A 
Sbjct: 115 GLPGPLALGNARADQAARQAA 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|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes

 Score = 37.9 bits (89), Expect = 0.002
 Identities = 27/146 (18%), Positives = 51/146 (34%), Gaps = 34/146 (23%)

Query: 147 VQVYTDGS---KSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHA-----ELLAISDAVSTI 198
           + +YTDG+         G A ++      K+ +               EL A+ +A+  +
Sbjct: 2   ITIYTDGACLGNPGPG-GWAAILRYGDHEKELS----GGEAGTTNNRMELTAVIEALEAL 56

Query: 199 KSQSIGEAVIISDSLSALQAISS-----------MSHSNP-----LVQSIHEEISTIPNS 242
           K       ++ +DS   +  I+             +   P     L Q +   ++     
Sbjct: 57  KEPC--PVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQELDALLA---KH 111

Query: 243 TIKFFWCPSHVGIAGNDAADLEAKSA 268
            + + W   H G  GN+ AD  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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	405
KOG2415|consensus	621		100.0
PF05187	110	ETF_QO: Electron transfer flavoprotein-ubiquinone	100.0
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.84
PRK00203	150	rnhA ribonuclease H; Reviewed	99.84
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.84
PRK08719	147	ribonuclease H; Reviewed	99.82
PRK06548	161	ribonuclease H; Provisional	99.82
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.7
KOG3752|consensus	371		99.65
PRK13907	128	rnhA ribonuclease H; Provisional	99.64
PRK07708	219	hypothetical protein; Validated	99.53
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.37
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.0
COG2440	99	FixX Ferredoxin-like protein [Energy production an	95.48
PF09257	39	BCMA-Tall_bind: BCMA, TALL-1 binding; InterPro: IP	89.27
PRK15449	95	ferredoxin-like protein FixX; Provisional	81.17

>KOG2415|consensus

Probab=100.00  E-value=1e-47  Score=374.91  Aligned_cols=172  Identities=41%  Similarity=0.599  Sum_probs=152.2

Q ss_pred             cCCCCccchHHHHHHHHHHHHHHHhcCCCcEEE-EeCcHHHHHHHhccCCCChhHHHHHHHHHcCCCCceEEEEecCCCC
Q psy2243         176 TLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI-ISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVG  254 (405)
Q Consensus       176 ~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I-~sDs~~al~~l~~~~~~~~~~~~I~~~l~~lr~~~v~f~WVpgH~G  254 (405)
                      +-.|+++|.+||  +|+.||....+  .+-+.+ .++|.+.++           .+|+|++|+.+||++++|.-   -.|
T Consensus       405 HtAMKSGmlAAe--sif~ai~~~~~--~k~~~~~~~~Ye~nlk-----------ds~V~KeLysvRNirPsf~~---~lG  466 (621)
T KOG2415|consen  405 HTAMKSGMLAAE--SIFEAIKGLPQ--SKMAGLDPTTYEENLK-----------DSYVWKELYSVRNIRPSFHG---KLG  466 (621)
T ss_pred             hhhhhcchhHHH--HHHHHHhcCcc--ccccccChhhHHHhhh-----------hhHHHHHHHHhhccCccccc---ccc
Confidence            345899999999  99999965431  111122 667887777           58999999999999999952   278


Q ss_pred             CcccHHHHHHHHHHhcCCCCCCCCccccccccCCCCCCCCCCCCCccccCCccCCCCCCCCCCCCCccccccceeccCCC
Q psy2243         255 IAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTN  334 (405)
Q Consensus       255 i~gNe~AD~lAk~a~~~~~~~~~~~~~~~l~g~~pwTl~~~~~D~~~~~~a~~~~~i~ypkpdg~ltfd~~~s~~~s~t~  334 (405)
                      ..|++.     ++|+..          ++++|++||||+|.+.|++.|+||++++||.||||||+||||+||||+|||||
T Consensus       467 ~ygGmi-----ySgi~~----------~~lkG~~PwTLkh~~~D~e~l~pa~k~~pI~YPKPDg~lSFDlltSvs~sgTn  531 (621)
T KOG2415|consen  467 LYGGMI-----YSGIFS----------YVLKGKVPWTLKHGKNDHEALKPASKYKPIVYPKPDGVLSFDLLTSVSRSGTN  531 (621)
T ss_pred             cccchh-----hhhhHH----------HhhcCccceeeccCCCchhhccchhhCCCcccCCCCceEEEeecchhhccCCC
Confidence            888875     888854          89999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcceeccCCCCcccccccCcCCcccccccCceeEeecCCCc
Q psy2243         335 HEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQNY  380 (405)
Q Consensus       335 h~~~qp~hl~~~~~~~~~~~~~~~~~~~~~~~cpa~vye~~~~~~~  380 (405)
                      |+|||||||+++|++++.++|++.|+|||+|||||||||||.||.+
T Consensus       532 H~~dqP~HL~l~~~~ip~~~nf~~y~gpE~rfCPAgVYEyV~dE~~  577 (621)
T KOG2415|consen  532 HDEDQPAHLTLRDDDIPVKVNFPVYKGPESRFCPAGVYEYVPDEAG  577 (621)
T ss_pred             CCCCCCceeeecCCCcchhcCcccccChhhccCCccceeecccccC
Confidence            9999999999999999999999999999999999999999998863

>PF05187 ETF_QO: Electron transfer flavoprotein-ubiquinone oxidoreductase; InterPro: IPR007859 Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane

Probab=100.00  E-value=9e-49  Score=322.84  Aligned_cols=98  Identities=55%  Similarity=0.917  Sum_probs=62.8

Q ss_pred             ccccccCCCCCCCCCCCCCccccCCccCCCCCCCCCCCCCccccccceeccCCCCCCCCCcceeccCCCCcccccccCcC
Q psy2243         281 LTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYD  360 (405)
Q Consensus       281 ~~~l~g~~pwTl~~~~~D~~~~~~a~~~~~i~ypkpdg~ltfd~~~s~~~s~t~h~~~qp~hl~~~~~~~~~~~~~~~~~  360 (405)
                      +.+++|+.|||++|.+.|+++++|+++++||+||||||+||||||||||+|||+|||||||||+|+|+++|+++|+++|+
T Consensus        13 ~~~~~g~~p~tl~~~~~D~~~l~~a~~~~~i~YpKpDg~ltFDklssv~~SgT~HeEdQP~HL~l~d~~i~~~~~~~~y~   92 (110)
T PF05187_consen   13 QNLLKGRAPWTLKHKKPDHESLKPASKCKPIDYPKPDGKLTFDKLSSVYLSGTNHEEDQPCHLKLKDPEIPIEVNLPEYG   92 (110)
T ss_dssp             TTTTTT--S------S-GGGG---GGGS---------SSSS--HHHHHHTTT-B--SSS--SEEESSTTHHHHTHHHHHS
T ss_pred             HHHccCCCCcccCCCCccHHHHhHHHhcccCCCCCCCCCCccccccceeccccCCCCCCCCeeEECCCChhhhhhhhhhc
Confidence            38899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccccccCceeEeecCC
Q psy2243         361 GPEGRFCPAGKLENHNTQ  378 (405)
Q Consensus       361 ~~~~~~cpa~vye~~~~~  378 (405)
                      +||||||||||||||+||
T Consensus        93 ~P~qryCPAgVYE~v~~e  110 (110)
T PF05187_consen   93 GPEQRYCPAGVYEIVEDE  110 (110)
T ss_dssp             -THHHH-TTS-EEEE---
T ss_pred             ChhhhcCcceeEEEeccC
Confidence            999999999999999875

The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64 kDa monomer [].; GO: 0004174 electron-transferring-flavoprotein dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 2GMJ_B 2GMH_B.

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

Probab=99.84  E-value=8.5e-21  Score=166.38  Aligned_cols=126  Identities=21%  Similarity=0.268  Sum_probs=101.9

Q ss_pred             cEEEEecCCCC--CCCceEEEEeecCcee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc
Q psy2243         146 FVQVYTDGSKS--DSSVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  221 (405)
Q Consensus       146 ~~~iyTDGS~~--~~~~G~g~v~~~~~~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~  221 (405)
                      .+.||||||+.  +|..|+|+|+..+...  .+...+ .+|++.||++|++.||+.+.+.+...+.|+|||+.++++|+.
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~   81 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR   81 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence            58899999998  5788999998854333  333444 799999999999999999998778899999999999999994


Q ss_pred             cCCC-----------Ch-hHHHHHHHHHcCC-CC-ceEEEEecCCCCCcccHHHHHHHHHHhcCC
Q psy2243         222 MSHS-----------NP-LVQSIHEEISTIP-NS-TIKFFWCPSHVGIAGNDAADLEAKSALENP  272 (405)
Q Consensus       222 ~~~~-----------~~-~~~~I~~~l~~lr-~~-~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~~  272 (405)
                      +...           .+ ..+.+|+++.++. .. .|.+.|||||.|.++|+.||+||+.|++..
T Consensus        82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            4111           11 2356677777764 24 899999999999999999999999999753

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.84  E-value=3e-20  Score=164.35  Aligned_cols=130  Identities=22%  Similarity=0.308  Sum_probs=98.4

Q ss_pred             cEEEEecCCCC--CCCceEEEEeecCceeE--eecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc
Q psy2243         146 FVQVYTDGSKS--DSSVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  221 (405)
Q Consensus       146 ~~~iyTDGS~~--~~~~G~g~v~~~~~~~~--~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~  221 (405)
                      .+.||||||+.  ++..|+|+|+...+...  .... ...+++.||++|++.||+.+.+  ...+.|+|||++++++|+.
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~   79 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITE   79 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHH
Confidence            48899999998  45789998886544332  2222 3678999999999999998754  4579999999999999986


Q ss_pred             c--------CC---CChh-HHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcCCCCCCCC
Q psy2243         222 M--------SH---SNPL-VQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG  278 (405)
Q Consensus       222 ~--------~~---~~~~-~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~~~~~~~~  278 (405)
                      +        +.   +.++ .+.+++++.++ ....|.|.|||||+|++||+.||+||++|+..+...|.|
T Consensus        80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~~~~~  149 (150)
T PRK00203         80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTG  149 (150)
T ss_pred             HHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhhhcccC
Confidence            2        11   2233 24456666554 346799999999999999999999999999876555543

>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=99.84  E-value=1.6e-20  Score=161.22  Aligned_cols=118  Identities=31%  Similarity=0.391  Sum_probs=92.9

Q ss_pred             CcEEEEecCCCC--CCCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc-
Q psy2243         145 DFVQVYTDGSKS--DSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS-  221 (405)
Q Consensus       145 ~~~~iyTDGS~~--~~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~-  221 (405)
                      ..+.||||||+.  ++..|+|+++..+ ...+..++ ..+++.||+.||..||+.+ .  ...++|+|||+++++.|.. 
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~   76 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKW   76 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHh
Confidence            468999999987  4556888876544 44455566 8899999999999999944 3  3889999999999998877 


Q ss_pred             ----cCCC----ChhHHHHHHHHHcCCCCceEEEEecCCCCC-cccHHHHHHHHHHh
Q psy2243         222 ----MSHS----NPLVQSIHEEISTIPNSTIKFFWCPSHVGI-AGNDAADLEAKSAL  269 (405)
Q Consensus       222 ----~~~~----~~~~~~I~~~l~~lr~~~v~f~WVpgH~Gi-~gNe~AD~lAk~a~  269 (405)
                          .+..    .++...|++.+.  ++..|.|+|||||+|+ .||+.||+|||.|+
T Consensus        77 ~~~~~~~~~~~~~~i~~~i~~~~~--~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   77 LHGNGWKKTSNGRPIKNEIWELLS--RGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHHTTSBSCTSSSBHTHHHHHHHH--HSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccchhheeeccc--cceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence                3321    246667777663  3688999999999999 69999999999997

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 ....

>PRK08719 ribonuclease H; Reviewed

Probab=99.82  E-value=9.6e-20  Score=160.40  Aligned_cols=122  Identities=25%  Similarity=0.366  Sum_probs=92.5

Q ss_pred             CcEEEEecCCCCCC-----CceEEEEeecC--cee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHH
Q psy2243         145 DFVQVYTDGSKSDS-----SVGCAFVIPQL--HIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSA  215 (405)
Q Consensus       145 ~~~~iyTDGS~~~~-----~~G~g~v~~~~--~~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~a  215 (405)
                      ..++||||||+..+     ..|+|+++...  ...  .+..+....|++.||+.|+..||+.+.+.    ..|+|||+.+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            46899999999732     46999987653  222  34445556899999999999999988542    4899999999


Q ss_pred             HHHHh--------ccCC---CChh-HHHHHHHHHcCC-CCceEEEEecCCCCCcccHHHHHHHHHHhc
Q psy2243         216 LQAIS--------SMSH---SNPL-VQSIHEEISTIP-NSTIKFFWCPSHVGIAGNDAADLEAKSALE  270 (405)
Q Consensus       216 l~~l~--------~~~~---~~~~-~~~I~~~l~~lr-~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~  270 (405)
                      +++++        +.+.   +.++ ...++++|.++. ...|.|.|||||+|++||+.||+||+.|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99984        3332   1222 356677666553 356999999999999999999999999874

>PRK06548 ribonuclease H; Provisional

Probab=99.82  E-value=1.5e-19  Score=160.84  Aligned_cols=124  Identities=25%  Similarity=0.322  Sum_probs=95.4

Q ss_pred             CcEEEEecCCCC--CCCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc-
Q psy2243         145 DFVQVYTDGSKS--DSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS-  221 (405)
Q Consensus       145 ~~~~iyTDGS~~--~~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~-  221 (405)
                      ..+.||||||+.  ++..|+|+++...+.. +... ...|++.||++|++.||+.+.. ....+.|+|||++++++++. 
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~-~g~~-~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWD-SGGW-DIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEE-ccCC-CCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHH
Confidence            358999999998  4678999888653321 1111 3579999999999999986643 34569999999999999994 


Q ss_pred             --------cCC--CChh-HHHHHHHHHcCC-CCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         222 --------MSH--SNPL-VQSIHEEISTIP-NSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       222 --------~~~--~~~~-~~~I~~~l~~lr-~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                              +..  +.++ .+.++++|.++. ...|.|.|||||+|.+||+.||+||++|+..
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence                    211  3443 477777776653 3579999999999999999999999999965

>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=99.70  E-value=4e-16  Score=130.15  Aligned_cols=122  Identities=25%  Similarity=0.324  Sum_probs=93.6

Q ss_pred             EEEecCCCCC--CCceEEEEeecCceeE---eecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         148 QVYTDGSKSD--SSVGCAFVIPQLHIVK---KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       148 ~iyTDGS~~~--~~~G~g~v~~~~~~~~---~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      ++|||||...  +.+|+|+++.+.+...   ........+++.||+.|++.||+.+.......+.|++||+.+++.+.+.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            3899999984  4789999988754322   1112246789999999999999999877788999999999999999987


Q ss_pred             CC-CChhHHHHHHHHHcC--CCCceEEEEecCCCCCcccHHHHHHHHHHh
Q psy2243         223 SH-SNPLVQSIHEEISTI--PNSTIKFFWCPSHVGIAGNDAADLEAKSAL  269 (405)
Q Consensus       223 ~~-~~~~~~~I~~~l~~l--r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~  269 (405)
                      .. .......++.++.++  +...+.|.|||+|+|..+|+.||.||+.|+
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            54 222223333333332  357899999999999999999999999874

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.

>KOG3752|consensus

Probab=99.65  E-value=8.3e-16  Score=150.18  Aligned_cols=126  Identities=26%  Similarity=0.324  Sum_probs=100.6

Q ss_pred             CcEEEEecCCCCC-----CCceEEEEeecCce-eEeecCC-CCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHH
Q psy2243         145 DFVQVYTDGSKSD-----SSVGCAFVIPQLHI-VKKQTLN-PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQ  217 (405)
Q Consensus       145 ~~~~iyTDGS~~~-----~~~G~g~v~~~~~~-~~~~~l~-~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~  217 (405)
                      +..+||||||+..     ..+|+|+++..++. ..+.++. +..+++.||+.||..||+.+.+....+++|.|||+.+++
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~  290 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFIN  290 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHH
Confidence            3489999999983     36899999987654 4566765 789999999999999999998877789999999999999


Q ss_pred             HHhccCC-----------CCh----------hHHHHHHHHHcCCCCceEEEEecCCCCCcccHHHHHHHHHHhc
Q psy2243         218 AISSMSH-----------SNP----------LVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALE  270 (405)
Q Consensus       218 ~l~~~~~-----------~~~----------~~~~I~~~l~~lr~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~  270 (405)
                      .|+.+.+           .++          ....+.+.++++++..|++.||+||.|+.||++||.||+++..
T Consensus       291 ~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  291 SLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            9987632           112          1122333334445689999999999999999999999999863

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.64  E-value=3.7e-15  Score=127.99  Aligned_cols=120  Identities=22%  Similarity=0.237  Sum_probs=92.8

Q ss_pred             EEEEecCCCC--CCCceEEEEeecCcee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         147 VQVYTDGSKS--DSSVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       147 ~~iyTDGS~~--~~~~G~g~v~~~~~~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      +.||||||+.  ++..|+|+|+.+.+..  .+... ...++..||+.|++.||+.+.+.+...+.|++||+.+++.+++.
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            5799999998  4688999999764332  22223 35789999999999999999888778899999999999999986


Q ss_pred             CCCChhHHHHHHHHHcC-CCC-ceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         223 SHSNPLVQSIHEEISTI-PNS-TIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       223 ~~~~~~~~~I~~~l~~l-r~~-~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      +..+...+.+++++..+ ..+ .+.|.|||+    ..|+.||.||+.|+.+
T Consensus        81 ~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            65444445566665544 233 466799995    5899999999999853

>PRK07708 hypothetical protein; Validated

Probab=99.53  E-value=1.8e-13  Score=128.08  Aligned_cols=125  Identities=18%  Similarity=0.087  Sum_probs=93.5

Q ss_pred             CCCcEEEEecCCCC--CCCceEEEEeec--CceeE----eecCCCCccchHHHHHHHHHHHHHHHhcCCCc--EEEEeCc
Q psy2243         143 YGDFVQVYTDGSKS--DSSVGCAFVIPQ--LHIVK----KQTLNPKSSIFHAELLAISDAVSTIKSQSIGE--AVIISDS  212 (405)
Q Consensus       143 ~~~~~~iyTDGS~~--~~~~G~g~v~~~--~~~~~----~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~--i~I~sDs  212 (405)
                      .++.+++|+|||..  ++.+|+|+++..  ++...    ...++..++++.||+.|++.||+.+.+.+...  +.|++||
T Consensus        70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS  149 (219)
T PRK07708         70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS  149 (219)
T ss_pred             CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence            34579999999986  567999998864  22222    12455567999999999999999998876544  8999999


Q ss_pred             HHHHHHHhccCC-CChhHHHHHHHHHcC-C--CCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         213 LSALQAISSMSH-SNPLVQSIHEEISTI-P--NSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       213 ~~al~~l~~~~~-~~~~~~~I~~~l~~l-r--~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      +.+++.+++.+. .++..+..++++.++ .  ...+.|.|||    +..|+.||+||+.|++.
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEG  208 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence            999999999775 344444444444432 2  2346778887    57899999999999974

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.37  E-value=1.7e-11  Score=123.92  Aligned_cols=121  Identities=17%  Similarity=0.262  Sum_probs=93.0

Q ss_pred             cEEEEecCCCCC--CCceEEEEeecC--c-eeE--eecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHH
Q psy2243         146 FVQVYTDGSKSD--SSVGCAFVIPQL--H-IVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQA  218 (405)
Q Consensus       146 ~~~iyTDGS~~~--~~~G~g~v~~~~--~-~~~--~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~  218 (405)
                      .+.||||||+..  +.+|+|+++.+.  + ...  +..++ .++++.||+.|++.||+.+.+.+...+.|++||+.+++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            378999999993  578999998864  2 212  23344 678889999999999999988878899999999999999


Q ss_pred             HhccCC-CChhHHHHHHHHHcC-CC-CceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         219 ISSMSH-SNPLVQSIHEEISTI-PN-STIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       219 l~~~~~-~~~~~~~I~~~l~~l-r~-~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      +.+.+. .++-...+++++.++ .. ..+.|.|||+    .+|+.||.||+.|++.
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            988764 333334444444443 22 4689999994    7899999999999864

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

Probab=99.00  E-value=2.3e-09  Score=84.78  Aligned_cols=84  Identities=26%  Similarity=0.261  Sum_probs=62.6

Q ss_pred             chHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhccCCCChhHHHHHHHHHcC-C-CCceEEEEecCCCCCcccHH
Q psy2243         183 IFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTI-P-NSTIKFFWCPSHVGIAGNDA  260 (405)
Q Consensus       183 v~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~~~~~~~~~~I~~~l~~l-r-~~~v~f~WVpgH~Gi~gNe~  260 (405)
                      +..||+.|++.||+.+.+.+..++.+.|||+.+++.|++..........++.++..+ . -..+.|.|||    ..+|..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~   76 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV   76 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence            357999999999999999888999999999999999998754322334445555443 2 2568999998    699999


Q ss_pred             HHHHHHHHhc
Q psy2243         261 ADLEAKSALE  270 (405)
Q Consensus       261 AD~lAk~a~~  270 (405)
                      ||.|||.|.+
T Consensus        77 A~~LA~~a~~   86 (87)
T PF13456_consen   77 ADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999999873

>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]

Probab=95.48  E-value=0.0056  Score=49.52  Aligned_cols=51  Identities=18%  Similarity=0.292  Sum_probs=35.8

Q ss_pred             cccceeccCCCCCCCCCcceeccCCCCcccccccCcCCcccccccCceeEeecCCC
Q psy2243         324 LLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQN  379 (405)
Q Consensus       324 ~~~s~~~s~t~h~~~qp~hl~~~~~~~~~~~~~~~~~~~~~~~cpa~vye~~~~~~  379 (405)
                      +...+++-. .|-+.+-.|+.++|+..+.+.+    +.|+...||||+|++.++.+
T Consensus         9 iE~kL~~n~-~~vDe~~pHI~v~~~~~~~~~~----~~~l~~aCPA~~Y~~~~~g~   59 (99)
T COG2440           9 IEEKLSVNR-YNVDEDHPHIIVKDPDDCQECE----DKPLIKACPAGCYKLIDDGK   59 (99)
T ss_pred             HhHhhhhhe-eeccCCCCcEecCCchhhhhcc----chhhhhcCCHHHeeECCCCc
Confidence            334444444 4444445799999877766544    77999999999999998553

>PF09257 BCMA-Tall_bind: BCMA, TALL-1 binding; InterPro: IPR015337 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]

Probab=89.27  E-value=0.038  Score=36.02  Aligned_cols=24  Identities=33%  Similarity=0.700  Sum_probs=17.4

Q ss_pred             CCcceeccCCCCcccccccCcCCcccccccCce
Q psy2243         339 QPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGK  371 (405)
Q Consensus       339 qp~hl~~~~~~~~~~~~~~~~~~~~~~~cpa~v  371 (405)
                      .|||||-.+..-|         -+|||||-|.|
T Consensus        15 kPChLRCsn~tPP---------~~Cq~YCnas~   38 (39)
T PF09257_consen   15 KPCHLRCSNNTPP---------LPCQRYCNASV   38 (39)
T ss_dssp             EEHHHHHTSSS-----------TTTHHHHHHTC
T ss_pred             ccceeecCCCCCC---------ccchhhccccc
Confidence            5999998763332         38999998876

Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. Members of this entry, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 2KN1_A 1OQD_R 1XU2_T.

>PRK15449 ferredoxin-like protein FixX; Provisional

Probab=81.17  E-value=0.6  Score=38.03  Aligned_cols=38  Identities=18%  Similarity=0.325  Sum_probs=26.8

Q ss_pred             CCCCCCCCCcceeccCCCCcccccccCcCCcccccccCceeEee
Q psy2243         332 GTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENH  375 (405)
Q Consensus       332 ~t~h~~~qp~hl~~~~~~~~~~~~~~~~~~~~~~~cpa~vye~~  375 (405)
                      ++++-+++-+|++|++..   ..+   -..+|...||||+|..-
T Consensus        14 ~~y~vd~~~~HI~i~~~~---~~~---~~k~C~~aCPagA~~~~   51 (95)
T PRK15449         14 NKFNVDEEHPHIVVKADA---DKQ---ALELLVKACPAGLYKKQ   51 (95)
T ss_pred             ceeECCCCCCcEEEcCCC---Cch---hhhHHHHHCCHhhcEeC
Confidence            444445566999998753   222   25699999999999753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	405
2gmh_A	584	Structure Of Porcine Electron Transfer Flavoprotein		4e-32

>pdb|2GMH|A Chain A, Structure Of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase In Complexed With Ubiquinone Length = 584

Iteration: 1
 Score =  135 bits (340), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 66/96 (68%), Positives = 74/96 (77%)
Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
           GI      G+   T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE 
Sbjct: 439 GIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 498
Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
           DQPAHLTLKDDSVPVN NL++YDGPE RFCPAG  E
Sbjct: 499 DQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYE 534

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	405
2gmh_A	584	Electron transfer flavoprotein-ubiquinone oxidored	4e-41
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-09
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	7e-06
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	4e-04
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	8e-04

>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8 d.58.1.6 PDB: 2gmj_A* Length = 584

 Score =  152 bits (385), Expect = 4e-41
 Identities = 62/80 (77%), Positives = 69/80 (86%)

Query: 291 TPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSV 350
           T K +  D+  LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTLKDDSV
Sbjct: 452 TLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSV 511

Query: 351 PVNTNLAVYDGPEGRFCPAG 370
           PVN NL++YDGPE RFCPAG
Sbjct: 512 PVNRNLSIYDGPEQRFCPAG 531

>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 = 54.7 bits (132), Expect = 2e-09
 Identities = 31/152 (20%), Positives = 51/152 (33%), Gaps = 21/152 (13%)

Query: 139 MNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQ-------TLNPKSSIFHAELLAI 191
           M++       VYTDGS  +     A+   +   V  +                  E+ A 
Sbjct: 1   MDDR--TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAA 58

Query: 192 SDAVSTIKSQSIGEAVIISDSLSALQAISSMSH-----SNPLVQSIHEEISTIPNSTIKF 246
             AV       + +  I+ D       I+  +       N   Q+  + ++        F
Sbjct: 59  LYAVKKASQLGV-KIRILHDY----AGIAFWATGEWKAKNEFTQAYAKLMNQY-RGIYSF 112

Query: 247 FWCPSHVGIAGNDAADLEAKSALENP-ISHDH 277
               +H G   ND  D++AKSAL    + H H
Sbjct: 113 EKVKAHSGNEFNDYVDMKAKSALGIRDLEHHH 144

>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 = 53.3 bits (128), Expect = 1e-08
 Identities = 27/142 (19%), Positives = 48/142 (33%), Gaps = 20/142 (14%)

Query: 149 VYTDGSKSDSS----VGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 204
            YTDGS          G A       ++  + L   +S   AEL+A++ A+   + + + 
Sbjct: 26  WYTDGSSFLQEGQRRAGAAVTTET-EVIWARALPAGTSAQRAELIALTQALKMAEGKKL- 83

Query: 205 EAVIISDSLSALQAISSMSHSNP-----LVQSIHEEISTIPNSTIKFFWCPSHVG----- 254
              + +DS  A       S          + ++ + +       +    CP H       
Sbjct: 84  --NVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKR--LSIIHCPGHQKGNSAE 139

Query: 255 IAGNDAADLEAKSALENPISHD 276
             GN  AD  A+ A    +   
Sbjct: 140 ARGNRMADQAAREAAMKAVLET 161

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.6 bits (120), Expect = 7e-07
 Identities = 56/346 (16%), Positives = 98/346 (28%), Gaps = 119/346 (34%)

Query: 2   LDPVQN---------QCLRLATGAFRS----------------------SPTASLE---- 26
           L  VQN          C  L T  F+                       +P         
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309

Query: 27  ----AETSEPNLKIRRSILTCNYIAKVMH-HNSTNPNFKRINNPPYKVLYENS-TKLNPT 80
                    P   +  +    + IA+ +    +T  N+K +N      + E+S   L P 
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369

Query: 81  VGIQRE------ILMND--IP----------------------FHKV-ILQREPKES--- 106
               R+      +      IP                       HK  +++++PKES   
Sbjct: 370 --EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427

Query: 107 ----------------WLHKK--PSCNLSLTLYKKDGMPHQVFQQEFQ--------RNMN 140
                            LH+      N+  T    D +P  + Q  +             
Sbjct: 428 IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP 487

Query: 141 ENYGDFVQVYTD----GSK----SDSSVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLA 190
           E    F  V+ D      K    S +      ++  L  +K  K  +      +   + A
Sbjct: 488 ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547

Query: 191 ISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEI 236
           I D +       I E +I S     L+ I+ M+    + +  H+++
Sbjct: 548 ILDFL-----PKIEENLICSKYTDLLR-IALMAEDEAIFEEAHKQV 587

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.4 bits (96), Expect = 5e-04
 Identities = 52/347 (14%), Positives = 94/347 (27%), Gaps = 101/347 (29%)

Query: 23  ASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNP---PYKVLYENSTKLNP 79
           + ++ E  +P      S++T  YI +     + N  F + N     PY  L +   +L P
Sbjct: 96  SPIKTEQRQP------SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP 149

Query: 80  ----TV----GIQREILMND-IPFHKVILQREPKESWLH----KKPSC------NLSLTL 120
                +    G  +  +  D    +KV  + + K  WL+      P         L   +
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209

Query: 121 YKK-----DGM---PHQV--FQQEFQRNM-NENYG------DFVQ------VYTDGSK-- 155
                   D       ++   Q E +R + ++ Y         VQ       +    K  
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269

Query: 156 ---SDSSVGCAFVIPQLHIVKKQTLNPKSSIF-HAELLAISDAVSTIKSQS--------- 202
                  V     +         +L+  S      E+ ++       + Q          
Sbjct: 270 LTTRFKQV--TDFLSAAT-TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326

Query: 203 ------IGEAV--------------------IISDSLSALQAISSMSHSNPLVQSIHEEI 236
                 I E++                    II  SL+ L+        + L  S+    
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL--SVFPPS 384

Query: 237 STIPNSTIKFFWCPSHVGIAGNDAADLEAKSALE----NPISHDHGI 279
           + IP   +   W              L   S +E            I
Sbjct: 385 AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431

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

 Score = 44.9 bits (107), Expect = 7e-06
 Identities = 33/159 (20%), Positives = 56/159 (35%), Gaps = 41/159 (25%)

Query: 144 GDFVQVYTDGSKSDSS-----VGCAFVIPQLHIVKKQTLNPKSSIFH---------AELL 189
           GDFV VYTDG     S        A +      V     +P +             AE+ 
Sbjct: 5   GDFVVVYTDGC---CSSNGRRRPRAGIG-----VYWGPGHPLNVGIRLPGRQTNQRAEIH 56

Query: 190 AISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHS---------------NP-LVQSIH 233
           A   A+   K+Q+I + V+ ++S+  +  I++                   N     ++ 
Sbjct: 57  AACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALE 116

Query: 234 EEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENP 272
                +    I++   P H G  GN+ AD  A+   +  
Sbjct: 117 RLTQGM---DIQWMHVPGHSGFIGNEEADRLAREGAKQS 152

>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* ... Length = 557

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 34/120 (28%), Positives = 53/120 (44%), Gaps = 18/120 (15%)

Query: 150 YTDGSKS-DSSVGCAFVIP----QLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 204
           Y DG+ + ++ +G A  +     Q  +    T N K+ +  A  LA+ D        S  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTEL-QAIYLALQD--------SGL 493

Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
           E  I++DS  AL  I +      + LV  I E++  I    +   W P+H GI GN+  D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551

>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 = 38.7 bits (91), Expect = 8e-04
 Identities = 36/148 (24%), Positives = 54/148 (36%), Gaps = 32/148 (21%)

Query: 147 VQVYTDGS-KSDSSVG-CAFVIP---QLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQ 201
              Y DG+   ++ +G   +V     Q  +    T N K      EL AI  A+      
Sbjct: 13  ETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQK-----TELQAIYLALQDSGL- 66

Query: 202 SIGEAVIISDSLSALQAISSMSH---------------SN-PLVQSIHEEISTIPNSTIK 245
              E  I++DS  AL  I+   H                N  LV  I E++  I    + 
Sbjct: 67  ---EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQL--IKKEKVY 121

Query: 246 FFWCPSHVGIAGNDAADLEAKSALENPI 273
             W P+H GI GN+  D    + +   +
Sbjct: 122 LAWVPAHKGIGGNEQVDKLVSAGIRKVL 149

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	405
2gmh_A	584	Electron transfer flavoprotein-ubiquinone oxidored	99.95
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.88
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.87
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.86
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.85
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.84
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.84
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.83
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.8
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.76
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.75
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.73
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.72
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.7
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.68
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.25
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.98

>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8 d.58.1.6 PDB: 2gmj_A*

Probab=99.95  E-value=7.2e-30  Score=270.03  Aligned_cols=131  Identities=52%  Similarity=0.811  Sum_probs=113.7

Q ss_pred             HHHHHHHHcCCCCceEEEEecCCC-CCcccHHHHHHHHHHhcCCCCCCCCccccccccCCCCCCCCCCCCCccccCCccC
Q psy2243         230 QSIHEEISTIPNSTIKFFWCPSHV-GIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASEC  308 (405)
Q Consensus       230 ~~I~~~l~~lr~~~v~f~WVpgH~-Gi~gNe~AD~lAk~a~~~~~~~~~~~~~~~l~g~~pwTl~~~~~D~~~~~~a~~~  308 (405)
                      +|+.+++...++.+-.|.    .. |....     ++..+++.          ++++|+.||||+|.++|++++++++++
T Consensus       409 ~~v~~~l~~~r~~~~~~~----~~~g~~~~-----~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~  469 (584)
T 2gmh_A          409 SWVWKELYSVRNIRPSCH----GILGVYGG-----MIYTGIFY----------WIFRGMEPWTLKHKGSDSDQLKPAKDC  469 (584)
T ss_dssp             SHHHHHHHHTTTTTGGGG----STTTHHHH-----HHHHHHHT----------TTTTTCCSCCCCCCSCGGGCCCCGGGS
T ss_pred             hHHHHHHHHHhChhHHHH----HhhccHHH-----HHHHHHHH----------HHcCCCCCCccCCCCCCchhhhhHHhc
Confidence            578888888777654441    11 44444     34667754          778899999999999999999999999


Q ss_pred             CCCCCCCCCCCCccccccceeccCCCCCCCCCcceeccCCCCcccccccCcCCcccccccCceeEeecCCC
Q psy2243         309 KPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQN  379 (405)
Q Consensus       309 ~~i~ypkpdg~ltfd~~~s~~~s~t~h~~~qp~hl~~~~~~~~~~~~~~~~~~~~~~~cpa~vye~~~~~~  379 (405)
                      +||+||||||+||||+|||||+|||+|+|||||||+|+|.++|.+.|+++|.+||++||||||||+|++++
T Consensus       470 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hl~~~d~~~~~~~~~~~~~~~c~~~CPa~~~~~~~~~~  540 (584)
T 2gmh_A          470 TPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQ  540 (584)
T ss_dssp             CCCCCCCCCSSSSCCHHHHHHTTTCBCCSSSCCSEEESSTTHHHHTHHHHHCCTHHHHCTTCCEEEEECSS
T ss_pred             CCCCCCCccccccccccchhhhccccccCCCCCeEEEcCcccchhhchhhhcchhhhcCChhhEEEeecCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999987543

>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=99.88  E-value=4.5e-23  Score=180.53  Aligned_cols=127  Identities=20%  Similarity=0.145  Sum_probs=99.5

Q ss_pred             CCcEEEEecCCCCCCCceEEEEeecCcee--Eee-cC--CC--CccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHH
Q psy2243         144 GDFVQVYTDGSKSDSSVGCAFVIPQLHIV--KKQ-TL--NP--KSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSAL  216 (405)
Q Consensus       144 ~~~~~iyTDGS~~~~~~G~g~v~~~~~~~--~~~-~l--~~--~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al  216 (405)
                      ++.+.||||||+..+.+|+|+|+...+..  .+. ..  +.  .++++.||+.|++.||+.+.+.+. .+.|+|||+.+.
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~   82 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIA   82 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHH
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHH
Confidence            46789999999999889999998765443  233 22  21  368999999999999998877666 899999999888


Q ss_pred             HHHhccCCCC-hhHHHHHHHHHcCCCCceEEEEecCCCCCcccHHHHHHHHHHhcCC
Q psy2243         217 QAISSMSHSN-PLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENP  272 (405)
Q Consensus       217 ~~l~~~~~~~-~~~~~I~~~l~~lr~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~~  272 (405)
                      +.+.+.+..+ +......+.+.++.. .|.|.|||||+|++||+.||+||++|+...
T Consensus        83 ~w~~~~w~~~~~~~~~~~~l~~~l~~-~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           83 FWATGEWKAKNEFTQAYAKLMNQYRG-IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             HHTTSSSSCCHHHHHHHHCGGGGGST-TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             HHHhCCCccCCcchHHHHHHHHHhcC-CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            8777765533 233444445555554 899999999999999999999999999764

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

Probab=99.87  E-value=8.9e-22  Score=173.36  Aligned_cols=127  Identities=24%  Similarity=0.348  Sum_probs=100.0

Q ss_pred             CcEEEEecCCCCCC-----CceEEEEeecCce-eEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHH
Q psy2243         145 DFVQVYTDGSKSDS-----SVGCAFVIPQLHI-VKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQA  218 (405)
Q Consensus       145 ~~~~iyTDGS~~~~-----~~G~g~v~~~~~~-~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~  218 (405)
                      +.+.||||||+..+     .+|+|+++.+++. ..+..+...++++.||+.|++.||+.+.+.+...+.|+|||+.+++.
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~   85 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTING   85 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHH
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhh
Confidence            56899999999832     2799998876432 23445655689999999999999999987777899999999999999


Q ss_pred             Hhcc--------CC---CCh-hHHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         219 ISSM--------SH---SNP-LVQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       219 l~~~--------~~---~~~-~~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      |+.+        +.   +.+ ....++++|.++ .+..|.|.|||||+|+++|+.||+||++|+..
T Consensus        86 i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A           86 ITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             HHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             hhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            9873        11   111 234566666543 35789999999999999999999999999975

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

Probab=99.86  E-value=5.8e-22  Score=172.89  Aligned_cols=124  Identities=20%  Similarity=0.191  Sum_probs=93.1

Q ss_pred             CcEEEEecCCCCC--CCceEEEEeecCceeE--eecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHh
Q psy2243         145 DFVQVYTDGSKSD--SSVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  220 (405)
Q Consensus       145 ~~~~iyTDGS~~~--~~~G~g~v~~~~~~~~--~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~  220 (405)
                      ..+.||||||+..  +..|+|+++..++...  +..++ .++++.||+.|++.||+.+.+  ...+.|+|||+++++.|+
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            3689999999984  4689999987755332  22333 688999999999999999864  578999999999999998


Q ss_pred             ccC------------CCCh-hHHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         221 SMS------------HSNP-LVQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       221 ~~~------------~~~~-~~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      ..+            .+.+ ..+.+++++.++ ....|.|.|||||+|+++|+.||+||++|++.
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            721            1111 123444444433 23579999999999999999999999999964

>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=99.85  E-value=2.4e-21  Score=170.96  Aligned_cols=125  Identities=22%  Similarity=0.302  Sum_probs=96.5

Q ss_pred             cEEEEecCCCCC--CCceEEEEeecCcee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc
Q psy2243         146 FVQVYTDGSKSD--SSVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  221 (405)
Q Consensus       146 ~~~iyTDGS~~~--~~~G~g~v~~~~~~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~  221 (405)
                      .+.||||||+..  +.+|+|+++...+..  .+..++ .++++.||+.|++.||+.+.+  ...+.|+|||+.+++.|+.
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYT-RTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCCC-CCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            588999999983  468999998764432  222332 578999999999999998864  3789999999999999997


Q ss_pred             c--------CC---CChh-HHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcCCC
Q psy2243         222 M--------SH---SNPL-VQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALENPI  273 (405)
Q Consensus       222 ~--------~~---~~~~-~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~~~  273 (405)
                      +        +.   +.++ ...++++|.++ ....|.|.|||||+|+++|+.||+||+.|+..+.
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  145 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPT  145 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence            2        21   1222 24556666554 3468999999999999999999999999998653

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

Probab=99.84  E-value=5e-21  Score=169.42  Aligned_cols=124  Identities=23%  Similarity=0.291  Sum_probs=94.9

Q ss_pred             CcEEEEecCCCC--CCCceEEEEeecCceeE--eecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHh
Q psy2243         145 DFVQVYTDGSKS--DSSVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  220 (405)
Q Consensus       145 ~~~~iyTDGS~~--~~~~G~g~v~~~~~~~~--~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~  220 (405)
                      ..+.||||||+.  ++.+|+|+|+...+...  +..++ .++++.||+.|++.||+.+.+  ...+.|+|||+++++.|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFS-LTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCcC-CCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            368999999998  35679999987654322  22333 578999999999999998754  378999999999999998


Q ss_pred             c--------cCC---CChh-HHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         221 S--------MSH---SNPL-VQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       221 ~--------~~~---~~~~-~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      .        .+.   +.+. ...+++++.++ ....|.|.|||||+|+++|+.||+||++|+..
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            8        221   1222 23455554443 34689999999999999999999999999975

>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=99.84  E-value=1.2e-20  Score=165.73  Aligned_cols=122  Identities=23%  Similarity=0.283  Sum_probs=93.4

Q ss_pred             CCcEEEEecCCCC--CCCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc
Q psy2243         144 GDFVQVYTDGSKS--DSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  221 (405)
Q Consensus       144 ~~~~~iyTDGS~~--~~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~  221 (405)
                      .+.+.||||||+.  ++..|+|+++..+... ...+ ..++++.||+.|++.||+.+    ...+.|+|||+++++.|+.
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQK-VVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCEE-EEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            3568999999987  4567899888765432 2234 36899999999999999985    4789999999999999987


Q ss_pred             cC-----------CCCh-hHHHHHHHHHc-C-CCCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         222 MS-----------HSNP-LVQSIHEEIST-I-PNSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       222 ~~-----------~~~~-~~~~I~~~l~~-l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      +.           .+.+ ..+.+++++.+ + +...|.|.|||||+|++||+.||+||++|+++
T Consensus        84 w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           84 WIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            51           1112 23455555443 2 35789999999999999999999999999975

>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=99.83  E-value=1.5e-20  Score=167.41  Aligned_cols=124  Identities=21%  Similarity=0.235  Sum_probs=95.4

Q ss_pred             cEEEEecCCCC--CCCceEEEEeecCceeE-eecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         146 FVQVYTDGSKS--DSSVGCAFVIPQLHIVK-KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       146 ~~~iyTDGS~~--~~~~G~g~v~~~~~~~~-~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      .+.||||||+.  +|..|+|+++...+... ...+...++++.||++|++.||+.+   ....+.|+|||+++++.|-..
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcc
Confidence            58999999998  57789999877654332 2234457899999999999999998   267899999999999998322


Q ss_pred             CCCChh-HHHHHHHH-HcC-CCCceEEEEecCCCC-----CcccHHHHHHHHHHhcCC
Q psy2243         223 SHSNPL-VQSIHEEI-STI-PNSTIKFFWCPSHVG-----IAGNDAADLEAKSALENP  272 (405)
Q Consensus       223 ~~~~~~-~~~I~~~l-~~l-r~~~v~f~WVpgH~G-----i~gNe~AD~lAk~a~~~~  272 (405)
                      ..+.++ .+.+++++ .++ .+..|.|.|||||+|     ++|||.||+||++|+.++
T Consensus       100 ~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A          100 SEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             CCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            223332 24545555 333 357899999999999     999999999999999753

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

Probab=99.80  E-value=2.2e-20  Score=166.61  Aligned_cols=124  Identities=19%  Similarity=0.217  Sum_probs=93.6

Q ss_pred             CcEEEEecCCCCC--CCceEEEEeecCcee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHh
Q psy2243         145 DFVQVYTDGSKSD--SSVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  220 (405)
Q Consensus       145 ~~~~iyTDGS~~~--~~~G~g~v~~~~~~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~  220 (405)
                      ..+.||||||+..  +..|+|+|+...+..  .+... ..++++.||+.|++.||+.+.+  ...+.|+|||+++++.|.
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~--~~~v~I~tDS~~vi~~i~   83 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFT   83 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhcc--CCeEEEEeChHHHHHHHh
Confidence            3578999999983  467999998754322  22222 2578999999999999998754  358999999999999999


Q ss_pred             c-c--------CC---CChh-HHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         221 S-M--------SH---SNPL-VQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       221 ~-~--------~~---~~~~-~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      . +        +.   +.++ ...+++++.++ ....|.|.|||||+|+++|+.||+||++|+..
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  148 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQS  148 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEEEeeCCCCchhHHHHHHHHHHHHHH
Confidence            8 1        21   1222 23455555443 34689999999999999999999999999975

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

Probab=99.76  E-value=4.6e-18  Score=151.32  Aligned_cols=125  Identities=21%  Similarity=0.185  Sum_probs=89.0

Q ss_pred             CcEEEEecCCCC--CCC-----ceEEEEeecCc----eeEeecCC-CCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCc
Q psy2243         145 DFVQVYTDGSKS--DSS-----VGCAFVIPQLH----IVKKQTLN-PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDS  212 (405)
Q Consensus       145 ~~~~iyTDGS~~--~~~-----~G~g~v~~~~~----~~~~~~l~-~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs  212 (405)
                      ..++||||||+.  +|.     .|+|+++...+    ....+..+ ...+.+.||+.|+..||+.+.+. ..+|.|+|||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TDS   84 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITDS   84 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEESC
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeCh
Confidence            358999999998  333     79999876432    12223332 35677889999999888877654 3569999999


Q ss_pred             HHHHHHHhcc--------CC---CChh-HHHHHHHHHcC--CCCceEEEEecCCCCC------cccHHHHHHHHHHhc
Q psy2243         213 LSALQAISSM--------SH---SNPL-VQSIHEEISTI--PNSTIKFFWCPSHVGI------AGNDAADLEAKSALE  270 (405)
Q Consensus       213 ~~al~~l~~~--------~~---~~~~-~~~I~~~l~~l--r~~~v~f~WVpgH~Gi------~gNe~AD~lAk~a~~  270 (405)
                      ++++++|+.+        +.   +.++ ...++++|.++  ....|.|.|||||+|.      +||+.||+||++|+.
T Consensus        85 ~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           85 FYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             HHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            9999999753        11   2222 24455555432  1357999999999995      589999999999984

>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=99.75  E-value=5.6e-18  Score=145.91  Aligned_cols=121  Identities=20%  Similarity=0.268  Sum_probs=95.1

Q ss_pred             cEEEEecCCCC--CCCceEEEEeecC--c-ee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHH
Q psy2243         146 FVQVYTDGSKS--DSSVGCAFVIPQL--H-IV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQA  218 (405)
Q Consensus       146 ~~~iyTDGS~~--~~~~G~g~v~~~~--~-~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~  218 (405)
                      .+.||||||+.  ++.+|+|+++.+.  + ..  .+..++ .++++.||+.|++.||+.+.+.+..++.|+|||+.+++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            48899999998  4578999998763  2 22  223333 689999999999999999988778899999999999999


Q ss_pred             HhccCC-CChhHHHHHHHHHcCC--CCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         219 ISSMSH-SNPLVQSIHEEISTIP--NSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       219 l~~~~~-~~~~~~~I~~~l~~lr--~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      +++.+. .++....+++++.++.  ...|.|.|||+    .+|+.||+||++|++.
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            998654 4444444555555442  36899999994    8999999999999964

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

Probab=99.73  E-value=6.3e-18  Score=145.03  Aligned_cols=121  Identities=19%  Similarity=0.254  Sum_probs=92.4

Q ss_pred             cEEEEecCCCC--CCCceEEEEeec-Cc-ee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCC----cEEEEeCcHHH
Q psy2243         146 FVQVYTDGSKS--DSSVGCAFVIPQ-LH-IV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIG----EAVIISDSLSA  215 (405)
Q Consensus       146 ~~~iyTDGS~~--~~~~G~g~v~~~-~~-~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~----~i~I~sDs~~a  215 (405)
                      .+.||||||+.  ++.+|+|+++.+ .+ ..  .+..++ .++++.||+.|++.||+.+.+.+..    .+.|+|||+.+
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            58999999998  356899999876 22 22  222333 4789999999999999999876656    89999999999


Q ss_pred             HHHHhccCC-CChhHHHHHHHHHcC--CC-CceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         216 LQAISSMSH-SNPLVQSIHEEISTI--PN-STIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       216 l~~l~~~~~-~~~~~~~I~~~l~~l--r~-~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      ++.+++.+. .++-...+++++.++  .+ ..|.|.|||    .++|+.||+||++|++.
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            999999765 343334444444433  22 479999999    48999999999999863

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

Probab=99.72  E-value=1.9e-17  Score=144.52  Aligned_cols=121  Identities=18%  Similarity=0.190  Sum_probs=93.3

Q ss_pred             EEEEecCCCC---CCCceE-EEEeecCcee-E--eecCC---CCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHH
Q psy2243         147 VQVYTDGSKS---DSSVGC-AFVIPQLHIV-K--KQTLN---PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSAL  216 (405)
Q Consensus       147 ~~iyTDGS~~---~~~~G~-g~v~~~~~~~-~--~~~l~---~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al  216 (405)
                      +.||||||+.   ++.+|+ |+++.+.+.. .  +..++   ..++++.||+.|++.||+.+.+.+..++.|+|||+.++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            5799999997   367885 9888764433 2  22333   36889999999999999999887778899999999999


Q ss_pred             HHHhccCC-CChhHHHHHHHHHcCC-CCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         217 QAISSMSH-SNPLVQSIHEEISTIP-NSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       217 ~~l~~~~~-~~~~~~~I~~~l~~lr-~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      +.+++++. .++....+++++.++. +..|.|.|||+    .+|+.||+||++|+..
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            99999765 3334455555554431 23599999997    6899999999999964

>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=99.70  E-value=5.6e-17  Score=170.35  Aligned_cols=118  Identities=26%  Similarity=0.329  Sum_probs=94.0

Q ss_pred             CCcEEEEecCCCCC--CCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc
Q psy2243         144 GDFVQVYTDGSKSD--SSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  221 (405)
Q Consensus       144 ~~~~~iyTDGS~~~--~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~  221 (405)
                      .+.+.+|||||+..  +..|+|+++..++.. ...++ .++++.||+.|+..||+.    ....+.|+|||+.+++.+++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~~-~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~  507 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS  507 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEe-eccCC-CCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhc
Confidence            35699999999983  457899888765432 22333 678999999999999987    46789999999999999998


Q ss_pred             cCC--CChhHHHHHHHHHcCCCCceEEEEecCCCCCcccHHHHHHHHHHh
Q psy2243         222 MSH--SNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSAL  269 (405)
Q Consensus       222 ~~~--~~~~~~~I~~~l~~lr~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~  269 (405)
                      +..  ..++.+.+.+.+.+  ...|.|.|||||+|++||+.||+||++|+
T Consensus       508 ~~~~~~~~l~~~~~~~~~~--~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          508 QPTESESKIVNQIIEEMIK--KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CCSEESCHHHHHHHHHHHH--CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccccccHHHHHHHHHHhcc--CCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            653  45555555555444  46799999999999999999999999874

>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=99.68  E-value=5.1e-17  Score=170.77  Aligned_cols=117  Identities=25%  Similarity=0.300  Sum_probs=91.0

Q ss_pred             CCcEEEEecCCCC--CCCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhc
Q psy2243         144 GDFVQVYTDGSKS--DSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  221 (405)
Q Consensus       144 ~~~~~iyTDGS~~--~~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~  221 (405)
                      .+.+.||||||+.  ++..|+|+++..++.. .... ..++++.||+.|++.||+.+    ...+.|+|||+.+++.|++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~-~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~  510 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQK-VVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA  510 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEE-EEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTT
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEE-EecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhc
Confidence            3568999999987  3457888888755432 2233 36899999999999999987    5789999999999999998


Q ss_pred             cCC--CChhHHHHHHHHHcCCCCceEEEEecCCCCCcccHHHHHHHHHH
Q psy2243         222 MSH--SNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSA  268 (405)
Q Consensus       222 ~~~--~~~~~~~I~~~l~~lr~~~v~f~WVpgH~Gi~gNe~AD~lAk~a  268 (405)
                      +..  ..++.+.+.+++.+  ...|.|.|||||+|++||+.||+||++|
T Consensus       511 ~~~~~~~~l~~~~~~~l~~--~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          511 QPDKSESELVNQIIEQLIK--KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CCSEESSHHHHHHHHHHHH--CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CCccCCHHHHHHHHHHHhc--CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            654  34555555555554  3579999999999999999999999986

>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=99.25  E-value=1.1e-12  Score=113.54  Aligned_cols=116  Identities=16%  Similarity=0.053  Sum_probs=82.9

Q ss_pred             CcEEEEecCCCC--CCCceEEEEeecCceeEe--ecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHh
Q psy2243         145 DFVQVYTDGSKS--DSSVGCAFVIPQLHIVKK--QTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  220 (405)
Q Consensus       145 ~~~~iyTDGS~~--~~~~G~g~v~~~~~~~~~--~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~  220 (405)
                      ..+.||||||+.  +|.+|+|+|+...+....  ..++ .++++.||++|++.||+.+.+... .+.|+|||+.+++.+.
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~   87 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVK   87 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHH
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHH
Confidence            457799999997  467899999875443322  2233 578999999999999999987655 8999999999999999


Q ss_pred             ccCC-----CChhHHHHHHHHHcC----CCCceEEEEecCCCCCcccHHHH
Q psy2243         221 SMSH-----SNPLVQSIHEEISTI----PNSTIKFFWCPSHVGIAGNDAAD  262 (405)
Q Consensus       221 ~~~~-----~~~~~~~I~~~l~~l----r~~~v~f~WVpgH~Gi~gNe~AD  262 (405)
                      +.+.     .......++++|.++    +...+....+.-|++..||.-||
T Consensus        88 ~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           88 DKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             HTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             cCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCccc
Confidence            8762     122345666665443    22333333444478888888776

>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=98.98  E-value=3.5e-10  Score=96.51  Aligned_cols=92  Identities=15%  Similarity=0.098  Sum_probs=65.5

Q ss_pred             CcEEEEecCCCC--CCCceEEEEeecCcee--EeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHh
Q psy2243         145 DFVQVYTDGSKS--DSSVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  220 (405)
Q Consensus       145 ~~~~iyTDGS~~--~~~~G~g~v~~~~~~~--~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~  220 (405)
                      ....||||||+.  +|..|+|+|+...+..  ....++ .+|++.||++|++.||+.+.+.+.. +.|+|||+.+++.|.
T Consensus         4 ~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~   81 (134)
T 4htu_A            4 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVK   81 (134)
T ss_dssp             CSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHH
T ss_pred             cceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHH
Confidence            346799999998  4568896666554432  222333 6899999999999999999875433 899999999999998


Q ss_pred             ccCC----CCh-hHHHHHHHHHc
Q psy2243         221 SMSH----SNP-LVQSIHEEIST  238 (405)
Q Consensus       221 ~~~~----~~~-~~~~I~~~l~~  238 (405)
                      +..-    +.+ ....+|++|.+
T Consensus        82 ~~~~kt~~~~~vkN~dLw~~ld~  104 (134)
T 4htu_A           82 DKKAKSTLVRNEETALIWKLVDE  104 (134)
T ss_dssp             HTCCCCCCCCSSTTHHHHHHHHH
T ss_pred             cCCcccCCCCCccCHHHHHHHHH
Confidence            7532    122 34566665553

---

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	405
d2gmha3	102	d.58.1.6 (A:483-584) Electron transfer flavoprotei	1e-15
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	3e-09
d2gmha1	380	c.3.1.2 (A:4-236,A:336-482) Electron transfer flav	2e-08
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	9e-07
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	1e-06

>d2gmha3 d.58.1.6 (A:483-584) Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO {Pig (Sus scrofa) [TaxId: 9823]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: ETF-QO domain-like
domain: Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
species: Pig (Sus scrofa) [TaxId: 9823]

 Score = 69.9 bits (171), Expect = 1e-15
 Identities = 43/49 (87%), Positives = 46/49 (93%)

Query: 322 FDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAG 370
           FDLLSSVAL+GTNHE DQPAHLTLKDDSVPVN NL++YDGPE RFCPAG
Sbjct: 1   FDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAG 49

>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 = 52.6 bits (125), Expect = 3e-09
 Identities = 27/123 (21%), Positives = 44/123 (35%), Gaps = 8/123 (6%)

Query: 149 VYTDGSKSD--SSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA 206
            YTDGS +         +V  +     K+    +++   AEL A + A++    +     
Sbjct: 10  FYTDGSCNRQSKEGKAGYVTDRGKDKVKKL--EQTTNQQAELEAFAMALTDSGPKVN--- 64

Query: 207 VIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAK 266
            II DS   +  ++S    +            I    I   W P+H GI GN   D    
Sbjct: 65  -IIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

Query: 267 SAL 269
             +
Sbjct: 124 QGI 126

>d2gmha1 c.3.1.2 (A:4-236,A:336-482) Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO {Pig (Sus scrofa) [TaxId: 9823]} Length = 380

class: Alpha and beta proteins (a/b)
fold: FAD/NAD(P)-binding domain
superfamily: FAD/NAD(P)-binding domain
family: FAD-linked reductases, N-terminal domain
domain: Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
species: Pig (Sus scrofa) [TaxId: 9823]

 Score = 53.7 bits (128), Expect = 2e-08
 Identities = 21/44 (47%), Positives = 27/44 (61%), Gaps = 2/44 (4%)

Query: 280 GLTQ--LSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVS 321
           G+      G+   T K +  D+  LKPA +C PIEYPKPDGQ+S
Sbjct: 337 GIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQIS 380

>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 = 46.2 bits (108), Expect = 9e-07
 Identities = 27/146 (18%), Positives = 48/146 (32%), Gaps = 14/146 (9%)

Query: 147 VQVYTDGSKSD--SSVGCAFVIPQLHIVKKQTLN-PKSSIFHAELLAISDAVSTIKSQSI 203
           V+++T GS        G   ++      K  +    +++    EL+A   A+  +K  + 
Sbjct: 3   VEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAE 62

Query: 204 GEAVIISDSLSALQAISSMSHSN-----------PLVQSIHEEISTIPNSTIKFFWCPSH 252
                 S  +         +                V       + +    IK+ W   H
Sbjct: 63  VILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGH 122

Query: 253 VGIAGNDAADLEAKSALENPISHDHG 278
            G   N+ AD  A++A  NP   D G
Sbjct: 123 AGHPENERADELARAAAMNPTLEDTG 148

>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 = 45.7 bits (107), Expect = 1e-06
 Identities = 21/142 (14%), Positives = 45/142 (31%), Gaps = 19/142 (13%)

Query: 147 VQVYTDGSKSD--SSVGCAFVIP-QLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSI 203
           V ++TDG+        G A ++    H          ++    EL A  + +  +K    
Sbjct: 4   VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCE 63

Query: 204 GEAVIISDSLSALQAISSMSHSNPLVQS--------------IHEEISTIPNSTIKFFWC 249
               + +DS    +A +         +                   +  +    ++F + 
Sbjct: 64  --VDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFV 121

Query: 250 PSHVGIAGNDAADLEAKSALEN 271
             H G   N+  D EA+   ++
Sbjct: 122 KGHTGHPENERVDREARRQAQS 143

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	405
d2gmha3	102	Electron transfer flavoprotein-ubiquinone oxidored	99.94
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.85
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.83
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.65
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.45
d2gmha1	380	Electron transfer flavoprotein-ubiquinone oxidored	99.44

>d2gmha3 d.58.1.6 (A:483-584) Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: ETF-QO domain-like
domain: Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=99.94  E-value=5.9e-29  Score=199.47  Aligned_cols=58  Identities=76%  Similarity=1.155  Sum_probs=56.5

Q ss_pred             cccccceeccCCCCCCCCCcceeccCCCCcccccccCcCCcccccccCceeEeecCCC
Q psy2243         322 FDLLSSVALTGTNHEGDQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLENHNTQN  379 (405)
Q Consensus       322 fd~~~s~~~s~t~h~~~qp~hl~~~~~~~~~~~~~~~~~~~~~~~cpa~vye~~~~~~  379 (405)
                      ||||||||+|||+|||||||||+|+|+++|+++|+++|++||+||||||||||++|++
T Consensus         1 FD~lssv~~sgt~HeEdQP~HL~ikd~~i~~~~~~~~y~~Pc~r~CPAgVYE~~~~~~   58 (102)
T d2gmha3           1 FDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQ   58 (102)
T ss_dssp             CCHHHHHHTTTCBCCSSSCCSEEESSTTHHHHTHHHHHCCTHHHHCTTCCEEEEECSS
T ss_pred             CCccceeeecCCCCCCCCCceEEecCcchhhhcccccccchheeeccceEEEEeecCC
Confidence            9999999999999999999999999999999999999999999999999999998764

>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=99.87  E-value=2.5e-22  Score=169.06  Aligned_cols=117  Identities=26%  Similarity=0.340  Sum_probs=88.3

Q ss_pred             CcEEEEecCCCC-C-CCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         145 DFVQVYTDGSKS-D-SSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       145 ~~~~iyTDGS~~-~-~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      +..++|||||+. + +..|+|+++..+... ...++ ..+++.||+.||..||+.    ....+.|+|||+++++.+.+.
T Consensus         6 ~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~-~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           6 GAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCcEEEEcCCCCCCCCcEEEEEEecCCCEE-EEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            457899999987 3 345677766655432 23344 578999999999999975    367899999999999999987


Q ss_pred             CC--CChhHHHHHHHHHcCCCCceEEEEecCCCCCcccHHHHHHHHHHh
Q psy2243         223 SH--SNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSAL  269 (405)
Q Consensus       223 ~~--~~~~~~~I~~~l~~lr~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~  269 (405)
                      ..  .+.....+++++.+  ..++.|.|||||+|++|||.||+||++|+
T Consensus        80 ~~~~~~~~~~~~~~~~~~--~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESESKIVNQIIEEMIK--KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEESCHHHHHHHHHHHH--CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CccccchHHHHHHHHhhh--cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            65  23332223333333  46899999999999999999999999984

>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=99.85  E-value=5.7e-22  Score=171.28  Aligned_cols=131  Identities=24%  Similarity=0.343  Sum_probs=96.2

Q ss_pred             cEEEEecCCCCC--CCceEEEEeecCceeEeecCC-CCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         146 FVQVYTDGSKSD--SSVGCAFVIPQLHIVKKQTLN-PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       146 ~~~iyTDGS~~~--~~~G~g~v~~~~~~~~~~~l~-~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      .+.||||||+..  +.+|+|+|+...+....+..+ ...+++.||++|+..||+++..  ...+.+++||+.++..+...
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccch
Confidence            478999999874  468999998765543322222 3578899999999999987542  45689999999999888654


Q ss_pred             CC-----------CChh-HHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcCCCCCCCC
Q psy2243         223 SH-----------SNPL-VQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG  278 (405)
Q Consensus       223 ~~-----------~~~~-~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~~~~~~~~  278 (405)
                      ..           +.++ ....+.++..+ ...+|.|+|||||+|++||+.||+|||+|+..+...|.+
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~  148 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTG  148 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTT
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccC
Confidence            20           1111 23344445443 346899999999999999999999999999876555443

>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=99.83  E-value=1.1e-21  Score=169.26  Aligned_cols=124  Identities=19%  Similarity=0.220  Sum_probs=91.3

Q ss_pred             cEEEEecCCCCC--CCceEEEEeecCceeEeec-CCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         146 FVQVYTDGSKSD--SSVGCAFVIPQLHIVKKQT-LNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       146 ~~~iyTDGS~~~--~~~G~g~v~~~~~~~~~~~-l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      .++||||||+.+  +..|+|+|+...+....+. ....+|++.||+.|++.||+.+.  ....+.|++||+.+++.+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhcccccc
Confidence            478999999984  4578998876544322211 12356899999999999998753  345789999999999988763


Q ss_pred             C------------CCChh-HHHHHHHHHcC-CCCceEEEEecCCCCCcccHHHHHHHHHHhcC
Q psy2243         223 S------------HSNPL-VQSIHEEISTI-PNSTIKFFWCPSHVGIAGNDAADLEAKSALEN  271 (405)
Q Consensus       223 ~------------~~~~~-~~~I~~~l~~l-r~~~v~f~WVpgH~Gi~gNe~AD~lAk~a~~~  271 (405)
                      .            .+.++ ...++++|..+ ....|.|.|||||+|++||+.||+||++|+++
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~  143 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQS  143 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCCcchHHHHHHHHHHHHH
Confidence            2            11222 23344554433 35789999999999999999999999999975

>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=99.65  E-value=4.9e-16  Score=127.09  Aligned_cols=100  Identities=27%  Similarity=0.329  Sum_probs=75.1

Q ss_pred             CcEEEEecCCCC-C-CCceEEEEeecCceeEeecCCCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhcc
Q psy2243         145 DFVQVYTDGSKS-D-SSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  222 (405)
Q Consensus       145 ~~~~iyTDGS~~-~-~~~G~g~v~~~~~~~~~~~l~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~  222 (405)
                      +..++|||||+. + +..|+|+++.++.. ....++ ..|++.||+.||+.||+.    ....+.|+|||+++++++++.
T Consensus         7 ~~~t~ytDGs~~~n~~~g~~g~~~~~~~~-~~~~~~-~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~~   80 (110)
T d1s1ta1           7 GAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTLT-DTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQ   80 (110)
T ss_dssp             TSEEEEEEEEEETTTTEEEEEEEETTSCE-EEEEES-SCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHHC
T ss_pred             CCcEEEEeCCCCCCCCCcEEEEEEecCCe-EEEecc-cCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhcC
Confidence            457899999987 3 34566666665433 333444 579999999999999975    356799999999999999987


Q ss_pred             CC--CChhHHHHHHHHHcCCCCceEEEEecCC
Q psy2243         223 SH--SNPLVQSIHEEISTIPNSTIKFFWCPSH  252 (405)
Q Consensus       223 ~~--~~~~~~~I~~~l~~lr~~~v~f~WVpgH  252 (405)
                      ..  .++..+.|.+++.+  ...|.|.|||||
T Consensus        81 ~~~~~~~l~~~il~~l~~--~~~v~i~WVpgH  110 (110)
T d1s1ta1          81 PDQSESELVNQIIEQLIK--KEKVYLAWVPAH  110 (110)
T ss_dssp             CSEESCHHHHHHHHHHHH--CSEEEEEECCSS
T ss_pred             ccccchHHHHHHHHHHhc--CCceEEEEeCCC
Confidence            65  45555666665655  368999999999

>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=99.45  E-value=6.6e-15  Score=123.17  Aligned_cols=113  Identities=18%  Similarity=0.082  Sum_probs=85.4

Q ss_pred             EEecCCCC--CCCceEEEEeecCceeEeecCC-CCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhccCC-
Q psy2243         149 VYTDGSKS--DSSVGCAFVIPQLHIVKKQTLN-PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSH-  224 (405)
Q Consensus       149 iyTDGS~~--~~~~G~g~v~~~~~~~~~~~l~-~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~~~-  224 (405)
                      ||||||+.  +|.+|+|+|+...+.....+-+ ...|++.||++|++.||+.+.+.+ .++.|+|||+.++..+.+... 
T Consensus         7 Iy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~k   85 (132)
T d1zbfa1           7 LSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKAK   85 (132)
T ss_dssp             EEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCCC
T ss_pred             EEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCcee
Confidence            89999998  5778999888765543322222 367899999999999999987654 568999999999999987542 


Q ss_pred             ----CChhHHHHHHHHHc----CCCCceEEEEecCCCCCcccHHHH
Q psy2243         225 ----SNPLVQSIHEEIST----IPNSTIKFFWCPSHVGIAGNDAAD  262 (405)
Q Consensus       225 ----~~~~~~~I~~~l~~----lr~~~v~f~WVpgH~Gi~gNe~AD  262 (405)
                          ...-.+.+++.|.+    ++...+.|.|++.|+...||..||
T Consensus        86 t~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          86 STLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             cCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence                12234556665544    344678888999999999998887

>d2gmha1 c.3.1.2 (A:4-236,A:336-482) Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: FAD/NAD(P)-binding domain
superfamily: FAD/NAD(P)-binding domain
family: FAD-linked reductases, N-terminal domain
domain: Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=99.44  E-value=1.6e-15  Score=149.69  Aligned_cols=113  Identities=28%  Similarity=0.389  Sum_probs=82.1

Q ss_pred             CCCccchHHHHHHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHhccCCCChhHHHHHHHHHcCCCCceEEEEecCCCCCcc
Q psy2243         178 NPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAG  257 (405)
Q Consensus       178 ~~~ssv~~AEl~AI~~AL~~~~~~~~~~i~I~sDs~~al~~l~~~~~~~~~~~~I~~~l~~lr~~~v~f~WVpgH~Gi~g  257 (405)
                      ++.+++.+||  +|..||+.-......--.-.++++..++           .+||+++|++.||++..| |-+  -|..+
T Consensus       268 Am~SG~lAAe--ai~~al~~~~~~~~~~~~~~~~y~~~~~-----------~s~~~~eL~~~rn~~~~~-~~~--~g~~~  331 (380)
T d2gmha1         268 AMKSGTLAAE--SIFNQLTSENLQSKTIGLHVTEYEDNLK-----------NSWVWKELYSVRNIRPSC-HGI--LGVYG  331 (380)
T ss_dssp             HHHHHHHHHH--HHHHHHTCCCCCCSSSSCCCTHHHHHHH-----------TSHHHHHHHHTTTTTGGG-GST--TTHHH
T ss_pred             eeccHHHHHH--HHHHHHHcCCcccchhhhhhhhHHHHHH-----------hhHHHHHHHHhhCCCHHH-Hhh--chHHH
Confidence            3567778888  7777775311100000111345566665           489999999999998877 211  25555


Q ss_pred             cHHHHHHHHHHhcCCCCCCCCccccccccCCCCCCCCCCCCCccccCCccCCCCCCCCCCCCCc
Q psy2243         258 NDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVS  321 (405)
Q Consensus       258 Ne~AD~lAk~a~~~~~~~~~~~~~~~l~g~~pwTl~~~~~D~~~~~~a~~~~~i~ypkpdg~lt  321 (405)
                      +.     +..++++          ++++|+.||||+|+++||++|+|+++++||+||||||+||
T Consensus       332 g~-----~~~~~~~----------~~~~g~~p~tl~~~~~d~~~l~~~~~~~~i~y~~~d~~~~  380 (380)
T d2gmha1         332 GM-----IYTGIFY----------WIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQIS  380 (380)
T ss_dssp             HH-----HHHHHHT----------TTTTTCCSCCCCCCSCGGGCCCCGGGSCCCCCCCCCSSSS
T ss_pred             HH-----HHHHHHH----------HHhCCCCCccCCCCCCCHHHHHHHHhCCCCCCCCCCCccC
Confidence            54     3667754          7899999999999999999999999999999999999997