Psyllid ID: psy1195

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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---
Protein Sequence
MLSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPWSPPI
Secondary Structure (PSIPRED)
cccEEEEEEcccccccccccccccccHHHHHHccccccccccccccccccccHHHHHHHHcccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccccEEEEccccHHHHHHHccccccHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEccccccccEcccccccHHHHHHHcccccccccccccccHEEEccHHHHHHHHcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccEEEEccccccccccHHHHHcccHHHHHHEEEEEccccEEEEEEEcccccccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHccccccccccccc
Coil and Loop (DISEMBL)
MLSWFLIIrsspepertylsglpdsewLALVLIdspryldnsgydsgiftyleeeeeeeeeddkEEERVEreeeeeeeddeEEERFEREEEEERRKVTtysenrqktveicpeavkippsaatiltkwpDDIQNFLILFLSKLdvqfvwvpshvgiagNEEADRLAKEALtsahpsvnqipipnyktyskKKILASWNSEWHnvqnnklreikpdnkpwsppi
Flexible Loop (DISEMBL)
MLSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYleeeeeeeeeddkeeervereeeeeeeddeeeerfereeeeerrkvttysenrqktveicpeavkippSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALtsahpsvnqipipnyktYSKKKILASWNSEWhnvqnnklreikpdnkpwsppi
Low Complexity Region (SEG)
MLSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLeeeeeeeeeddkeeervereeeeeeeddeeeerfereeeeerrKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPWSPPI
Disordered region (IsUnstruct)
***WFLIIR*******TYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTY********************************************************VEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNE****************VNQIPIPNYKTYSKKKILASWNSEWHNV*******************
Disordered Region (DISOPRED)
*LSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFT************************************************TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT****SVNQIPIPNYKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPWSPP*
Disordered Region (DISEMBL)
MLSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLE*************************************************NRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNVQNNKLREIKPD********
Disordered Region (DISPRO)
*LSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEE***********************************ERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPWSPPI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLSWFLIIRSSPEPERTYLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPWSPPI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.345	0.163	0.467	3e-11
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.345	0.289	0.441	1e-09
443694523	364	hypothetical protein CAPTEDRAFT_227708 [	0.331	0.203	0.430	1e-09
427791807	1212	Putative tick transposon, partial [Rhipi	0.390	0.071	0.369	4e-09
427791321	1210	Putative tick transposon, partial [Rhipi	0.390	0.071	0.369	5e-09
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.408	0.181	0.427	6e-09
328697366	891	PREDICTED: hypothetical protein LOC10057	0.340	0.085	0.435	9e-09
443730003	243	hypothetical protein CAPTEDRAFT_201116 [	0.408	0.374	0.398	9e-09
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.408	0.348	0.427	1e-08
443720278	498	hypothetical protein CAPTEDRAFT_219461 [	0.340	0.152	0.415	2e-08

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

 Score = 74.7 bits (182), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 45/77 (58%)

Query: 145 VQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNV 204
           V F+W PSHVGI GNE AD LAKEAL+S + +   +P  + +   KK I + W  EW   
Sbjct: 119 VVFMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQ 178

Query: 205 QNNKLREIKPDNKPWSP 221
            +NKL  I P   PW P
Sbjct: 179 HSNKLHSIHPTIGPWPP 195

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443713753|gb|ELU06453.1| hypothetical protein CAPTEDRAFT_215116 [Capitella teleta]

 Score = 69.3 bits (168), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 44/77 (57%)

Query: 145 VQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNV 204
           V F+W PSHVGI GNE A  LA++AL+S + +   +P  + +   KK I + W  EW   
Sbjct: 174 VVFMWCPSHVGIPGNEMAHTLAEKALSSTNLAELPVPASDLRGLIKKYIRSQWQHEWEEQ 233

Query: 205 QNNKLREIKPDNKPWSP 221
            NNKL  I P   PW P
Sbjct: 234 HNNKLHSIHPTIGPWPP 250

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443694523|gb|ELT95634.1| hypothetical protein CAPTEDRAFT_227708 [Capitella teleta]

 Score = 69.3 bits (168), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 46/79 (58%), Gaps = 5/79 (6%)

Query: 145 VQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPN--YKTYSKKKILASWNSEWH 202
           + F+W PSHVGI GNE AD LAK+AL     ++   PIP+  +K  ++  +   W SEW 
Sbjct: 66  IIFIWCPSHVGIPGNETADTLAKQALGM---NILNCPIPHTDFKPITRSFVKTQWQSEWD 122

Query: 203 NVQNNKLREIKPDNKPWSP 221
               NKL +I+PD   W P
Sbjct: 123 QETGNKLHDIQPDIGSWPP 141

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 5/92 (5%)

Query: 130  DDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIP--NYKT 187
             DI N +++    + ++F WVPSHVGI GNE+AD+ A  A   AH ++ +I IP  + + 
Sbjct: 1021 GDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLA---AHKTLTKIRIPLKDSQR 1077

Query: 188  YSKKKILASWNSEWHNVQNNKLREIKPDNKPW 219
              +  +LA W  +W +  +NKL  +KP    W
Sbjct: 1078 TIRLALLAKWQQQWDSCTSNKLHLVKPTLGEW 1109

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 5/92 (5%)

Query: 130  DDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIP--NYKT 187
             DI N +++    + ++F WVPSHVGI GNE+AD+ A  A   AH ++ +I IP  + + 
Sbjct: 1018 GDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLA---AHKTLTKIRIPLKDSQR 1074

Query: 188  YSKKKILASWNSEWHNVQNNKLREIKPDNKPW 219
              +  +LA W  +W +  +NKL  +KP    W
Sbjct: 1075 TIRLALLAKWQQQWDSCTSNKLHLVKPTLGEW 1106

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 67.0 bits (162), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 44/103 (42%), Positives = 59/103 (57%), Gaps = 12/103 (11%)

Query: 119 PSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVN 178
           P   +ILTK     QN L+    KL V F+W PSHVGI GNE ADRLAK+AL      V 
Sbjct: 161 PYLLSILTK-----QNNLVR-KGKL-VVFIWCPSHVGILGNEVADRLAKQALVMP---VT 210

Query: 179 QIPIPN--YKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPW 219
           ++P+P+  YK+  +  + + W +EW    +NKL  I+P    W
Sbjct: 211 KLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEW 253

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|328697366|ref|XP_003240318.1| PREDICTED: hypothetical protein LOC100575042 [Acyrthosiphon pisum]

 Score = 66.2 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 34/78 (43%), Positives = 53/78 (67%), Gaps = 2/78 (2%)

Query: 138 LFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL-TSAHPSVNQIPIPNYKTYSKKKILAS 196
           L  SK ++ F+WVPSH GI GNE+AD+ A++A  T  +P++N I   + K    +KIL+S
Sbjct: 237 LVQSKKNIVFMWVPSHTGIIGNEKADKHAEQATQTILNPTINNISSIDIKNSINQKILSS 296

Query: 197 WNSEWHNVQ-NNKLREIK 213
           W + W+++  +NKL+ IK
Sbjct: 297 WQNYWNSITLSNKLKNIK 314

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443730003|gb|ELU15698.1| hypothetical protein CAPTEDRAFT_201116 [Capitella teleta]

 Score = 66.2 bits (160), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 41/103 (39%), Positives = 58/103 (56%), Gaps = 12/103 (11%)

Query: 119 PSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVN 178
           P   +ILTK  + ++        KL V F+W PSHVGI GNE ADRLAK+AL      V 
Sbjct: 120 PYLLSILTKQNNLVRK------GKL-VVFIWCPSHVGILGNEVADRLAKQALVMP---VT 169

Query: 179 QIPIPN--YKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPW 219
           ++P+P+  YK+  +  + + W +EW    +NKL  I+P    W
Sbjct: 170 KLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEW 212

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/103 (42%), Positives = 59/103 (57%), Gaps = 12/103 (11%)

Query: 119 PSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVN 178
           P   +ILTK     QN L+    KL V F+W PSHVGI GNE ADRLAK+AL      V 
Sbjct: 115 PYLLSILTK-----QNNLVR-KGKL-VVFIWCPSHVGILGNEVADRLAKQALVMP---VT 164

Query: 179 QIPIPN--YKTYSKKKILASWNSEWHNVQNNKLREIKPDNKPW 219
           ++P+P+  YK+  +  + + W +EW    +NKL  I+P    W
Sbjct: 165 KLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEW 207

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443720278|gb|ELU10076.1| hypothetical protein CAPTEDRAFT_219461 [Capitella teleta]

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 145 VQFVWVPSHVGIAGNEEADRLAKEALTSAHPSVNQIPIPNYKTYSKKKILASWNSEWHNV 204
           + F+W PSHVGI GNE AD +AK+AL     + + IP  ++K  +   +   W SEW   
Sbjct: 178 IIFIWCPSHVGIPGNETADTVAKQALGMNILNCH-IPHTDFKPITCSFVKTQWQSEWDQE 236

Query: 205 QNNKLREIKPDNKPWSP 221
             NKL +I+PD   W P
Sbjct: 237 TGNKLHDIQPDIGSWPP 253

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	223
UNIPROTKB|H0YFU0	34	H0YFU0 "Uncharacterized protei	0.116	0.764	0.615	0.00037

UNIPROTKB|H0YFU0 H0YFU0 "Uncharacterized protein" [Homo sapiens (taxid:9606)]

 Score = 90 (36.7 bits), Expect = 0.00037, P = 0.00037
 Identities = 16/26 (61%), Positives = 21/26 (80%)

Query:   143 LDVQFVWVPSHVGIAGNEEADRLAKE 168
             +D+Q++ VP H G  GNEEADRLA+E
Sbjct:     5 MDIQWMHVPGHSGFIGNEEADRLARE 30


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.315   0.133   0.415    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      223       180   0.00092  109 3  11 22  0.47    32
                                                     31  0.39    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  616 (65 KB)
  Total size of DFA:  184 KB (2103 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  17.47u 0.10s 17.57t   Elapsed:  00:00:01
  Total cpu time:  17.47u 0.10s 17.57t   Elapsed:  00:00:01
  Start:  Thu Aug 15 15:06:30 2013   End:  Thu Aug 15 15:06:31 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

---

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	LOW CONFIDENCE prediction!
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	223
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	4e-12
pfam00075	126	pfam00075, RNase_H, RNase H	2e-10
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	7e-09
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	2e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-08
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	1e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	3e-05
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	2e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	2e-04
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-04
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	5e-04
pfam03985	431	pfam03985, Paf1, Paf1	6e-04
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	6e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	6e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	7e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	7e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	8e-04
pfam05285	317	pfam05285, SDA1, SDA1	8e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.001
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.001
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	0.001
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	0.001
pfam03985	431	pfam03985, Paf1, Paf1	0.002
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	0.002
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	0.002
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	0.003
pfam04147	809	pfam04147, Nop14, Nop14-like family	0.004
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.004
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	0.004
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	0.004
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.004

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

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 19/38 (50%), Positives = 22/38 (57%)

Query: 132 IQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEA 169
            +    L    + V+  WVP H GI GNE ADRLAKEA
Sbjct: 89  RKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKEA 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 = 56.1 bits (136), Expect = 2e-10
 Identities = 22/53 (41%), Positives = 26/53 (49%), Gaps = 6/53 (11%)

Query: 124 ILTKWPD-----DIQNFLI-LFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL 170
           I   WP       I+N +  L   K  V   WVP H GI GNE AD+LAK+  
Sbjct: 73  ITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQGA 125

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|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 = 52.6 bits (127), Expect = 7e-09
 Identities = 18/33 (54%), Positives = 21/33 (63%)

Query: 138 LFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL 170
           L    + V+F  VP H GI GNEEADRLAK+  
Sbjct: 117 LEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149

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|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus

 Score = 51.3 bits (124), Expect = 2e-08
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 133 QNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL 170
           + F+     K+ + FV V +H G   NE AD+LAK+AL
Sbjct: 96  KEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133

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 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. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 52.3 bits (125), Expect = 5e-08
 Identities = 29/61 (47%), Positives = 37/61 (60%)

Query: 40  DNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTT 99
           D  G D G  +   + EEEEEE+++EEE  E EEEEEEE++E EE    E  E R+K   
Sbjct: 848 DEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQAI 907

Query: 100 Y 100
           Y
Sbjct: 908 Y 908

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 16/34 (47%), Positives = 18/34 (52%)

Query: 136 LILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEA 169
           L   L+K  V + WV  H G  GNE AD LA  A
Sbjct: 104 LDALLAKHQVTWHWVKGHAGHPGNERADELANAA 137

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

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.4 bits (107), Expect = 1e-05
 Identities = 25/53 (47%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 54  EEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSENRQK 106
           +     +  D EEE  E EEEEEEE++EEEE  E EEE E      + E RQK
Sbjct: 853 DGGGGSDGGDSEEEE-EEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQK 904

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 22/55 (40%), Positives = 33/55 (60%)

Query: 49  FTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSEN 103
           F+ LE E+   E DD+EEE  E EEEE+E++   +E  + EE EE    + Y ++
Sbjct: 376 FSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDS 430

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 51  YLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTT---YSENRQKT 107
           +  EEEEEEEE D + +  E +E E ++++E E+  +REE  +++K      Y E  +K 
Sbjct: 43  FEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKKRVKTKAYKEPTKKK 102

Query: 108 VEICPEAVKIPPSAAT 123
            +  P A K P +AA 
Sbjct: 103 KKKDPTAAKSPKAAAP 118

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 19/44 (43%), Positives = 25/44 (56%)

Query: 55  EEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT 98
           E  ++EE+D E E + RE E EEE DEEE     ++   RRK  
Sbjct: 383 EARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFG 426

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 41.1 bits (97), Expect = 3e-04
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 52  LEEEEEEEEEDDKEEER--VEREEEEEEEDDEEEERFEREEEEERRKVTTYSENRQKTVE 109
           +++E+EE+++DD EEE   V+  +EEE+E+DE+ +  + EEEEE  K     ++ + T  
Sbjct: 330 VDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRS 389

Query: 110 ICPEAVKIPPS 120
             P     P S
Sbjct: 390 ELPFTFPCPKS 400

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

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

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 17/47 (36%), Positives = 22/47 (46%)

Query: 127 KWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSA 173
           K  D  +    L      V + WV  H G   NE AD+LA+EA  +A
Sbjct: 100 KNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146

Length = 154

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 21/55 (38%), Positives = 31/55 (56%)

Query: 53  EEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSENRQKT 107
           + EE +E+ED++EE+R +  EEEE ED EEE    RE+          S++  K 
Sbjct: 366 DFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKA 420

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 40.4 bits (94), Expect = 6e-04
 Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 37  RYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEE----DDEEEE 84
           R+L            +++++E+E+EDD +EE  E EEEEEEE    DDE+EE
Sbjct: 138 RHLAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEE 189

Length = 2849

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 39.9 bits (93), Expect = 6e-04
 Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 2/145 (1%)

Query: 53  EEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSENRQKTVEICP 112
           EE  EEEEE+++EEE  E+E EEEE +DEEEE     +     ++   SE      E   
Sbjct: 442 EESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEE 501

Query: 113 EAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADR--LAKEAL 170
           +A +     A I             +       + +   S    +  EE+D   LA+E+ 
Sbjct: 502 DAERRNSEMAGISRMSEGQQPRGSSVQPESPQEEPLQPESMDAESVGEESDEELLAEESP 561

Query: 171 TSAHPSVNQIPIPNYKTYSKKKILA 195
            S+H  +  +  P     S  + L 
Sbjct: 562 LSSHTELEGVATPVETKISSSRKLP 586

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 39.9 bits (93), Expect = 7e-04
 Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 24  DSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEE 83
           D    +    +SP     +  +S     +EEEEEEEEE+++EE+  E EE E+EE++EE 
Sbjct: 420 DPSKASSTSGESPSM---ASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEV 476

Query: 84  ERFEREEEEE 93
           E     EEE 
Sbjct: 477 EADNGSEEEM 486

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 39.6 bits (93), Expect = 7e-04
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 7/68 (10%)

Query: 33  IDS--PRYLDNSGYDSGIFTYLEEEEEEE-----EEDDKEEERVEREEEEEEEDDEEEER 85
           IDS  P  LDN      +  + + + EEE       DD   +  E ++++EE D+E+EE 
Sbjct: 81  IDSHRPWNLDNVFGSDQVVIFDDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEES 140

Query: 86  FEREEEEE 93
            + E++E+
Sbjct: 141 SKSEDDED 148

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 39.6 bits (93), Expect = 8e-04
 Identities = 14/50 (28%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 48  IFTYLEEEEEEEEEDDKEEERVE-REEEEEEEDDEEEERFEREEEEERRK 96
            +  LEE+++++EE D+E+E     E++E+++DD++++     E    R+
Sbjct: 119 AYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATRERSLERR 168

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 39.3 bits (92), Expect = 8e-04
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 45  DSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSENR 104
           +S       + E+EEE+D+  ++  E  +EE  E+DEEE   E E E E+ K +  +  R
Sbjct: 122 ESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEKASELATTR 181

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 52  LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSEN-RQKT 107
             EEE++E++      + + EEEEEE++ +EEE+ E EEE E  K     +  +Q T
Sbjct: 422 KREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQAT 478

Length = 482

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 22/52 (42%), Positives = 37/52 (71%)

Query: 48 IFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTT 99
          I+ ++E+E E+E  D++EEE  E ++EEEE+  ++EE  + EEE+E +K  T
Sbjct: 23 IYLWVEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKT 74

Length = 529

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 16/46 (34%), Positives = 31/46 (67%)

Query: 51  YLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRK 96
            L  +++E+EE+++EE  VE  +EEE+ D+  E+   + + E+RR+
Sbjct: 93  LLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRE 138

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 16/42 (38%), Positives = 32/42 (76%)

Query: 52  LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEE 93
           LE++ +E E +D +EE  + EEEEEEE++E+E+  + +++++
Sbjct: 156 LEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDD 197

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 15/51 (29%), Positives = 22/51 (43%)

Query: 52  LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSE 102
            E+EEEE+  D+ EEE  E  EEE  +  E+       +     +     E
Sbjct: 373 DEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKE 423

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 18/44 (40%), Positives = 25/44 (56%)

Query: 52  LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERR 95
           LE E+ E  E+D     +    E+E ED++E E  + EEEEE R
Sbjct: 406 LEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEAR 449

Length = 449

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 12/46 (26%), Positives = 25/46 (54%)

Query: 48  IFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEE 93
           + T++EE   EE E+ +  E+VE   ++   +  EE   E +++ +
Sbjct: 328 LMTFIEENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWD 373

Length = 390

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 20/43 (46%), Positives = 29/43 (67%), Gaps = 5/43 (11%)

Query: 51  YLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEE 93
            LE+ EEEEEEDD  E      E+E+EED++EEE  + +E ++
Sbjct: 282 LLEKAEEEEEEDDYSES-----EDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 11/41 (26%), Positives = 28/41 (68%)

Query: 53  EEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEE 93
           +  ++E+EEDD ++   E E+ +  +++E+EE  + ++E++
Sbjct: 328 DGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDD 368

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 37.6 bits (88), Expect = 0.004
 Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 38  YLDNSGYDSGIF--TYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERR 95
           +L  S   +        + E++ EEE  +++++    +++EEE++EE+E+ E E+EEE  
Sbjct: 401 FLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEE 460

Query: 96  KV 97
           + 
Sbjct: 461 EA 462

Length = 482

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 19/43 (44%), Positives = 29/43 (67%)

Query: 52 LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEER 94
          L EE+E++E  D+EE  +  +E++EE D EEE+ F   +EEE 
Sbjct: 16 LPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEV 58

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 18/54 (33%), Positives = 29/54 (53%)

Query: 52  LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTTYSENRQ 105
           L+E EE E+EDD  +  +   +EE+E+ + EE ++ RE     R      +N Q
Sbjct: 83  LDELEELEKEDDDLDGELVELQEEKEQLENEELQYLREYNLFDRNNLQLEDNLQ 136

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. Length = 356

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 37.5 bits (88), Expect = 0.004
 Identities = 10/44 (22%), Positives = 21/44 (47%)

Query: 53  EEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRK 96
           +   EE+      E     ++E+EEE+++E +     +E E  +
Sbjct: 175 DPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPE 218

Length = 619

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	223
PRK06548	161	ribonuclease H; Provisional	99.86
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.8
PRK00203	150	rnhA ribonuclease H; Reviewed	99.79
PRK08719	147	ribonuclease H; Reviewed	99.74
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.58
PRK13907	128	rnhA ribonuclease H; Provisional	99.2
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.11
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	98.88
KOG3752|consensus	371		98.84
PRK07708	219	hypothetical protein; Validated	98.7
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.13
PF03066	149	Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301	91.71

>PRK06548 ribonuclease H; Provisional

Probab=99.86  E-value=1.1e-21  Score=164.52  Aligned_cols=125  Identities=18%  Similarity=0.154  Sum_probs=96.3

Q ss_pred             cccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceE
Q psy1195          18 YLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKV   97 (223)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I   97 (223)
                      -|.|||||.|.|+|+.+..   ..+|...+.+++..|-           ...              -+..+......++|
T Consensus        13 a~~gnpg~~G~g~~~~~~~---~~~g~~~~~TNnraEl-----------~Ai--------------i~aL~~~~~~~~~v   64 (161)
T PRK06548         13 SSLANPGPSGWAWYVDENT---WDSGGWDIATNNIAEL-----------TAV--------------RELLIATRHTDRPI   64 (161)
T ss_pred             ccCCCCCceEEEEEEeCCc---EEccCCCCCCHHHHHH-----------HHH--------------HHHHHhhhcCCceE
Confidence            3789999999999987643   3467777777777655           222              22333333334579


Q ss_pred             EEEecChhhHhhhccC------CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195          98 TTYSENRQKTVEICPE------AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT  171 (223)
Q Consensus        98 ~IfTDSqyaI~aI~~~------~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~  171 (223)
                      .|||||+||+++|++|      .-|++++|++|.++  ++++.|.+++.. +.|+|.|||||+|++||+.||+||++|+.
T Consensus        65 ~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~--dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~  141 (161)
T PRK06548         65 LILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQ--EIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN  141 (161)
T ss_pred             EEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccH--HHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999963      11467789999874  899999998754 58999999999999999999999999987


Q ss_pred             cC
Q psy1195         172 SA  173 (223)
Q Consensus       172 ~~  173 (223)
                      ..
T Consensus       142 ~~  143 (161)
T PRK06548        142 NF  143 (161)
T ss_pred             Hh
Confidence            63

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

Probab=99.80  E-value=2.4e-19  Score=149.84  Aligned_cols=130  Identities=23%  Similarity=0.160  Sum_probs=97.6

Q ss_pred             cccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceE
Q psy1195          18 YLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKV   97 (223)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I   97 (223)
                      -|.|||||.|.|+||..+..-.+.||...-.+++-.|-           ...           =+-.+.+++  ..++.|
T Consensus        11 a~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl-----------~A~-----------i~AL~~l~~--~~~~~v   66 (154)
T COG0328          11 ACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAEL-----------RAL-----------IEALEALKE--LGACEV   66 (154)
T ss_pred             ccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHH-----------HHH-----------HHHHHHHHh--cCCceE
Confidence            38999999999999995555556777776555554443           111           001222222  578999


Q ss_pred             EEEecChhhHhhhccCCC------CCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195          98 TTYSENRQKTVEICPEAV------KIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT  171 (223)
Q Consensus        98 ~IfTDSqyaI~aI~~~~~------~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~  171 (223)
                      .|||||+||+++|..|..      |.+...+++.+  .++++++..++.....|.+.|||||+|+++|++||+||+.++.
T Consensus        67 ~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn--~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~  144 (154)
T COG0328          67 TLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKN--KDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR  144 (154)
T ss_pred             EEEecHHHHHHHHHHHHhhccccCccccccCcccc--HHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence            999999999999995411      45555667776  4899999999876669999999999999999999999999987


Q ss_pred             cC
Q psy1195         172 SA  173 (223)
Q Consensus       172 ~~  173 (223)
                      ..
T Consensus       145 ~~  146 (154)
T COG0328         145 AA  146 (154)
T ss_pred             hh
Confidence            73

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.79  E-value=6.8e-19  Score=143.73  Aligned_cols=125  Identities=18%  Similarity=0.121  Sum_probs=92.7

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.|+|++.+.|+|+.+.......+|..++.+++..|-           ...              .+..+.. ..+..|.
T Consensus        12 ~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL-----------~Ai--------------~~AL~~~-~~~~~v~   65 (150)
T PRK00203         12 CLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMEL-----------MAA--------------IEALEAL-KEPCEVT   65 (150)
T ss_pred             ccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHH-----------HHH--------------HHHHHHc-CCCCeEE
Confidence            7889999999999987766666666655555544332           111              1222222 2356899


Q ss_pred             EEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          99 TYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      |||||+|++++|..|.      -|.+++|+++.+  .++++.+.+++ ....|.|.|||||+|++||+.||+||+.|+..
T Consensus        66 I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n--~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203         66 LYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKN--VDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             EEECHHHHHHHHHHHHHHHHHcCCcccCCCcccc--HHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            9999999999999631      134567788776  37889888876 45889999999999999999999999999876

>PRK08719 ribonuclease H; Reviewed

Probab=99.74  E-value=1.2e-17  Score=137.62  Aligned_cols=122  Identities=20%  Similarity=0.046  Sum_probs=82.8

Q ss_pred             ccCCCC---ccceeEEEecCccc-c-ccCCCCC-CcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhh
Q psy1195          19 LSGLPD---SEWLALVLIDSPRY-L-DNSGYDS-GIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEE   92 (223)
Q Consensus        19 ~~~~~~---~~~~~~~~~~~~~~-~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (223)
                      |.|||+   ++|.|+|+.+.... . ..+.... ..+++..|-           ..                 ...+...
T Consensus        13 ~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl-----------~A-----------------~~~aL~~   64 (147)
T PRK08719         13 APNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELEL-----------LA-----------------LIEALEY   64 (147)
T ss_pred             cCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHH-----------HH-----------------HHHHHHH
Confidence            667887   67999999875422 1 2232222 244555443           11                 1222222


Q ss_pred             cCceEEEEecChhhHhhhccC------CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHH
Q psy1195          93 ERRKVTTYSENRQKTVEICPE------AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLA  166 (223)
Q Consensus        93 ~~~~I~IfTDSqyaI~aI~~~------~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LA  166 (223)
                      -.....|||||+||+++|+.|      .-|.++.|+++.+  .++++.+..+.. .+.|+|.|||||+|++||+.||+||
T Consensus        65 ~~~~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n--~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA  141 (147)
T PRK08719         65 ARDGDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVAN--RDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLA  141 (147)
T ss_pred             cCCCCEEEechHHHHHHHHHHHHHHHhCCcccCCCccccc--HHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHH
Confidence            223358999999999999641      1134555677766  388998888765 6779999999999999999999999


Q ss_pred             HHHHh
Q psy1195         167 KEALT  171 (223)
Q Consensus       167 k~Aa~  171 (223)
                      +.|++
T Consensus       142 ~~a~~  146 (147)
T PRK08719        142 QAAAE  146 (147)
T ss_pred             HHHhh
Confidence            99875

>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=99.58  E-value=2.5e-15  Score=116.71  Aligned_cols=115  Identities=28%  Similarity=0.287  Sum_probs=75.1

Q ss_pred             cCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEEE
Q psy1195          20 SGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTT   99 (223)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~I   99 (223)
                      .++|+..+.|+|+ .+++  ..++...+.+++..|-           ...              ....+ .. .+..|+|
T Consensus        13 ~~~~~~~~~g~v~-~~~~--~~~~~~~~~s~~~aEl-----------~Ai--------------~~AL~-~~-~~~~v~I   62 (132)
T PF00075_consen   13 RPNPGKGGAGYVV-WGGR--NFSFRLGGQSNNRAEL-----------QAI--------------IEALK-AL-EHRKVTI   62 (132)
T ss_dssp             CTTTTEEEEEEEE-ETTE--EEEEEEESECHHHHHH-----------HHH--------------HHHHH-TH-STSEEEE
T ss_pred             cCCCCceEEEEEE-ECCe--EEEecccccchhhhhe-----------ehH--------------HHHHH-Hh-hcccccc
Confidence            3457888888865 6553  3333223555555544           222              23334 22 4589999


Q ss_pred             EecChhhHhhhccC----CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCC-ccChHHHHHHHHHHh
Q psy1195         100 YSENRQKTVEICPE----AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGI-AGNEEADRLAKEALT  171 (223)
Q Consensus       100 fTDSqyaI~aI~~~----~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi-~GNE~AD~LAk~Aa~  171 (223)
                      ||||+++++.|..+    .+..+..+.       .+...+.+++..+..|.|+|||||+|+ .||+.||+|||.|+.
T Consensus        63 ~tDS~~v~~~l~~~~~~~~~~~~~~~~-------~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   63 YTDSQYVLNALNKWLHGNGWKKTSNGR-------PIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             EES-HHHHHHHHTHHHHTTSBSCTSSS-------BHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHhccccccccccccc-------cchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            99999999988872    110111111       244456666667889999999999999 699999999999974

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.20  E-value=1.9e-10  Score=90.66  Aligned_cols=117  Identities=15%  Similarity=0.074  Sum_probs=81.6

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHh-hcCceE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEE-EERRKV   97 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~I   97 (223)
                      |.|+|++.|.|+||.|.......++..+..+++..|-           ...              -...+... ....+|
T Consensus        10 ~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~-----------~Al--------------l~aL~~a~~~g~~~v   64 (128)
T PRK13907         10 SKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEY-----------HAL--------------LAALKYCTEHNYNIV   64 (128)
T ss_pred             CCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHH-----------HHH--------------HHHHHHHHhCCCCEE
Confidence            6789999999999998876656666555555544433           111              22223222 334689


Q ss_pred             EEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          98 TTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        98 ~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      .|||||+++++.+++.+.   +  ...   ...+++.+..++.....+.|.|||.    ++|..||.||+.|...
T Consensus        65 ~i~sDS~~vi~~~~~~~~---~--~~~---~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         65 SFRTDSQLVERAVEKEYA---K--NKM---FAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             EEEechHHHHHHHhHHHh---c--Chh---HHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            999999999999998441   1  111   1267778888776666778899998    4999999999998753

>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=99.11  E-value=2.7e-10  Score=83.84  Aligned_cols=73  Identities=36%  Similarity=0.427  Sum_probs=57.0

Q ss_pred             hhcCceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHH
Q psy1195          91 EEERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL  170 (223)
Q Consensus        91 ~~~~~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa  170 (223)
                      ....+++.|+|||++++..+.++..   .. ....   ..+++.+..++.....+.|.|||+|+|+.+|..||.||+.+.
T Consensus        58 ~~~~~~i~i~~Ds~~~~~~~~~~~~---~~-~~~~---~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          58 ELGGKKVNIYTDSQYVINALTGWYE---GK-PVKN---VDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             hCCCceEEEEECHHHHHHHhhcccc---CC-Chhh---HHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            3567899999999999999987541   01 1111   246666777666788999999999999999999999999873

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.

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=98.88  E-value=2.1e-08  Score=92.36  Aligned_cols=118  Identities=16%  Similarity=0.106  Sum_probs=81.6

Q ss_pred             ccCCCCccceeEEEecCc-c-c-cccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHh-hcC
Q psy1195          19 LSGLPDSEWLALVLIDSP-R-Y-LDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEE-EER   94 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~-~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~   94 (223)
                      |.||||++|+|+||.|.. . . ...++..+..+++..|-           +.-              ....+... ...
T Consensus        11 ~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~-----------~Al--------------l~gL~~a~~~g~   65 (372)
T PRK07238         11 SRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEY-----------RGL--------------IAGLEAAAELGA   65 (372)
T ss_pred             CCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHH-----------HHH--------------HHHHHHHHhCCC
Confidence            789999999999999964 2 2 35677777666765544           111              22223222 345


Q ss_pred             ceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          95 RKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        95 ~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      ++|.||+||+++++.+.+.+   +.+.. -+.   .++..+..++.....+.|.|||.    .+|..||.||+.|...
T Consensus        66 ~~v~i~~DS~lvi~~i~~~~---~~~~~-~l~---~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         66 TEVEVRMDSKLVVEQMSGRW---KVKHP-DMK---PLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             CeEEEEeCcHHHHHHhCCCC---ccCCh-HHH---HHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            78999999999999998743   11111 111   34455666666667899999997    6899999999999755

>KOG3752|consensus

Probab=98.84  E-value=4.8e-09  Score=98.28  Aligned_cols=85  Identities=22%  Similarity=0.167  Sum_probs=62.1

Q ss_pred             HHHHH-hhcCceEEEEecChhhHhhhccCCC------CCCCCchh-----hcccChhHHHHHHHHHh--cCCceEEEEec
Q psy1195          86 FEREE-EEERRKVTTYSENRQKTVEICPEAV------KIPPSAAT-----ILTKWPDDIQNFLILFL--SKLDVQFVWVP  151 (223)
Q Consensus        86 ~~~~~-~~~~~~I~IfTDSqyaI~aI~~~~~------~~~~Sgq~-----il~~~~~i~q~i~~ll~--~~~~V~~~WVP  151 (223)
                      +.+.. ..+..+|+|.|||+|+|++|+.|-.      |..+.++.     +.+  .+....+..|.+  ....|++.||+
T Consensus       267 ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n--~~~~~e~~~l~q~~~~~~vq~~~V~  344 (371)
T KOG3752|consen  267 ALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKN--QDFFNELDELEQEISNKKVQQEYVG  344 (371)
T ss_pred             HHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeec--chHHHHHHHHHhhhccCceEEEEec
Confidence            44444 3445699999999999999997522      23444454     433  244455666654  35899999999


Q ss_pred             cCCCCccChHHHHHHHHHHhc
Q psy1195         152 SHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus       152 GHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      ||.||.||++||.||++++..
T Consensus       345 Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  345 GHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             CcCCcchHHHHHHHHhhhhhh
Confidence            999999999999999998654

>PRK07708 hypothetical protein; Validated

Probab=98.70  E-value=2.1e-07  Score=81.66  Aligned_cols=121  Identities=18%  Similarity=0.113  Sum_probs=72.3

Q ss_pred             cCCCCccceeEEEecCcc---c-cccCCCCCC-cccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcC
Q psy1195          20 SGLPDSEWLALVLIDSPR---Y-LDNSGYDSG-IFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEER   94 (223)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~---~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (223)
                      .|+|+++|.|+||++.+.   + +..+.+.++ .+++..|-.           .-           -.-.+.+.+...++
T Consensus        83 ~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~-----------Al-----------i~aL~~A~e~g~~~  140 (219)
T PRK07708         83 DKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYA-----------AL-----------YYAMQELEELGVKH  140 (219)
T ss_pred             CCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHH-----------HH-----------HHHHHHHHHcCCCc
Confidence            458999999999997543   1 233444543 444444331           11           01122233333334


Q ss_pred             ceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhc-CCceEEEEeccCCCCccChHHHHHHHHHHhcC
Q psy1195          95 RKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLS-KLDVQFVWVPSHVGIAGNEEADRLAKEALTSA  173 (223)
Q Consensus        95 ~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~-~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~~  173 (223)
                      ..|.|++||+++++.+...+   +.. .+.+.   ...+.+..++.+ ...+.|.|||    -..|+.||+||+.|+...
T Consensus       141 ~~V~I~~DSqlVi~qi~g~w---k~~-~~~l~---~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~  209 (219)
T PRK07708        141 EPVTFRGDSQVVLNQLAGEW---PCY-DEHLN---HWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGT  209 (219)
T ss_pred             ceEEEEeccHHHHHHhCCCc---eeC-ChhHH---HHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcC
Confidence            45999999999999998743   111 11222   234445544432 2347778887    467999999999999863

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

Probab=98.13  E-value=1.3e-05  Score=57.45  Aligned_cols=68  Identities=26%  Similarity=0.201  Sum_probs=50.6

Q ss_pred             hcCceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195          92 EERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT  171 (223)
Q Consensus        92 ~~~~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~  171 (223)
                      .+.++|.|+|||+.+++.|++...     ....+.   .+++.+..++.....+.|.|||    -.+|..||.|||.|.+
T Consensus        19 ~g~~~i~v~sDs~~vv~~i~~~~~-----~~~~~~---~~~~~i~~~~~~~~~~~~~~i~----r~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   19 LGIRKIIVESDSQLVVDAINGRSS-----SRSELR---PLIQDIRSLLDRFWNVSVSHIP----REQNKVADALAKFALS   86 (87)
T ss_dssp             CT-SCEEEEES-HHHHHHHTTSS--------SCCH---HHHHHHHHHHCCCSCEEEEE------GGGSHHHHHHHHHHHH
T ss_pred             CCCCEEEEEecCcccccccccccc-----cccccc---ccchhhhhhhccccceEEEEEC----hHHhHHHHHHHHHHhh
Confidence            445789999999999999987531     111122   5788888888888899999999    6899999999999875

>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins

Probab=91.71  E-value=0.053  Score=45.29  Aligned_cols=9  Identities=22%  Similarity=-0.101  Sum_probs=4.4

Q ss_pred             CCCCcccch
Q psy1195          44 YDSGIFTYL   52 (223)
Q Consensus        44 ~~~~~~~~~   52 (223)
                      +.+|...+.
T Consensus       100 hisG~~~~~  108 (149)
T PF03066_consen  100 HISGQHLVA  108 (149)
T ss_dssp             EEEEEEEEE
T ss_pred             EeeCccccc
Confidence            355655433

They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	223
2qk9_A	154	Human Rnase H Catalytic Domain Mutant D210n In Comp		4e-04

>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex With 18-Mer RnaDNA HYBRID Length = 154

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 133 QNFLIL--FLSKLDVQFVWVPSHVGIAGNEEADRLAKEA 169
           ++F+ L      +D+Q++ VP H G  GNEEADRLA+E 
Sbjct: 110 EDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREG 148

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	223
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.84
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.83
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.83
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.83
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.81
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.8
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.78
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.78
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.65
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.56
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.56
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.55
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.51
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.46
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.07
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.82
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	95.24

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

Probab=99.84  E-value=1.2e-21  Score=162.57  Aligned_cols=127  Identities=14%  Similarity=0.005  Sum_probs=93.7

Q ss_pred             ccCCCCc-----cceeEEEecCccccccCCCCCCcccc----hhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHH
Q psy1195          19 LSGLPDS-----EWLALVLIDSPRYLDNSGYDSGIFTY----LEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFERE   89 (223)
Q Consensus        19 ~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (223)
                      |+|||||     +|.|+|+.+.......++.....+++    .+|-           ...              ++..+.
T Consensus        16 c~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei-----------~Al--------------~~al~~   70 (165)
T 2lsn_A           16 AIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEI-----------AAV--------------EFACKK   70 (165)
T ss_dssp             EEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHH-----------HHH--------------HHHHHH
T ss_pred             CCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHH-----------HHH--------------HHHHHH
Confidence            8999999     89999998765554544433322222    2211           111              233344


Q ss_pred             HhhcCceEEEEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCC------c
Q psy1195          90 EEEERRKVTTYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGI------A  157 (223)
Q Consensus        90 ~~~~~~~I~IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi------~  157 (223)
                      ....+++|.|||||+|++++|+.|.      -|++.+++++.+  .++++.+..++...+.|.|.|||||+|+      +
T Consensus        71 al~~~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN--~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~  148 (165)
T 2lsn_A           71 ALKIPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKH--ISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTE  148 (165)
T ss_dssp             HHHSSSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSS--HHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHH
T ss_pred             HhcCCCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccC--HHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCCh
Confidence            4566789999999999999998741      145677888877  4899999988877889999999999995      5


Q ss_pred             cChHHHHHHHHHHhc
Q psy1195         158 GNEEADRLAKEALTS  172 (223)
Q Consensus       158 GNE~AD~LAk~Aa~~  172 (223)
                      ||++||+||++|+..
T Consensus       149 gNe~AD~LA~~gA~~  163 (165)
T 2lsn_A          149 GNALADKLATQGSYV  163 (165)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhh
Confidence            899999999999864

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

Probab=99.83  E-value=2.8e-21  Score=154.11  Aligned_cols=125  Identities=22%  Similarity=0.118  Sum_probs=91.4

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.|+|++.+.|+|+.++......+|.....+++..|-           ...              .+..+.. ..+++|.
T Consensus        13 ~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl-----------~A~--------------~~AL~~~-~~~~~v~   66 (146)
T 3h08_A           13 ASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMEL-----------MAA--------------IKGLEAL-KEPARVQ   66 (146)
T ss_dssp             ESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHH-----------HHH--------------HHHHHTC-SSCCEEE
T ss_pred             CCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHH-----------HHH--------------HHHHHhc-CccCcEE
Confidence            6789999999999999887777777766556555443           111              2222222 2368999


Q ss_pred             EEecChhhHhhhcc-C------CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195          99 TYSENRQKTVEICP-E------AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT  171 (223)
Q Consensus        99 IfTDSqyaI~aI~~-~------~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~  171 (223)
                      |||||+|++++|.+ |      .-|+++++.++.+  .++++.+..++. ...|.|.|||||+|++||+.||+|||+|+.
T Consensus        67 I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n--~~l~~~~~~~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~  143 (146)
T 3h08_A           67 LYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVEN--IDLWQEILKLTT-LHRVTFHKVKGHSDNPYNSRADELARLAIK  143 (146)
T ss_dssp             EEESCHHHHHHHHSSHHHHHHHTTCC----CCCTT--HHHHHHHHHHHH-HSEEEEEECCC-CCSHHHHHHHHHHHHHHH
T ss_pred             EEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCC--HHHHHHHHHHHh-hCceEEEEcCCcCCcHhHHHHHHHHHHHHH
Confidence            99999999999987 2      1134556677665  378888888775 467999999999999999999999999987


Q ss_pred             c
Q psy1195         172 S  172 (223)
Q Consensus       172 ~  172 (223)
                      .
T Consensus       144 ~  144 (146)
T 3h08_A          144 E  144 (146)
T ss_dssp             H
T ss_pred             h
Confidence            5

>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=99.83  E-value=6.2e-21  Score=155.17  Aligned_cols=121  Identities=15%  Similarity=0.135  Sum_probs=83.3

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |+||||+.+.|+|+.++... ..+  ....+++..|-                            .-..++....+++|.
T Consensus        21 ~~~n~g~~g~G~v~~~~~~~-~~~--~~~~Tnn~aEl----------------------------~A~i~AL~~~~~~v~   69 (150)
T 3qio_A           21 ANRETKLGKAGYVTNRGRQK-VVT--LTDTTNQKTEL----------------------------QAIYLALQDSGLEVN   69 (150)
T ss_dssp             ECTTTCCEEEEEEETTSCEE-EEE--ESSCCHHHHHH----------------------------HHHHHHHHHSCSEEE
T ss_pred             CCCCCCCeEEEEEEEcCCEE-EEe--CCCCCHHHHHH----------------------------HHHHHHHHhCCCcEE
Confidence            78999999999999886432 121  23444444433                            112222222368999


Q ss_pred             EEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          99 TYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      |||||+|++++|++|.      -|++.+|+++.+  .++++.+..++.+...|.|.|||||+|++||++||+||++|+..
T Consensus        70 i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n--~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           70 IVTDSQYALGIITQWIHNWKKRGWKTADKKPVKN--VDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             EEESCHHHHHHHHHHHHHHCC------------C--HHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             EEeCcHHHHHHHHHHHHHHhhcCcCcCcCccccc--HHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            9999999999998751      134556667666  48888888777788899999999999999999999999998865

>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=9.2e-21  Score=157.01  Aligned_cols=120  Identities=15%  Similarity=0.164  Sum_probs=94.6

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.||||+.+.|+||++....+..++...+.+++..|-           ...              -...+..  +.++|.
T Consensus        32 ~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl-----------~Ai--------------~~AL~~~--~~~~v~   84 (165)
T 3p1g_A           32 SFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAEL-----------IAL--------------TQALKMA--EGKKLN   84 (165)
T ss_dssp             EEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHH-----------HHH--------------HHHHHHT--BTSEEE
T ss_pred             cCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHH-----------HHH--------------HHHHHHc--cCceEE
Confidence            7789999999999999887776666656666666655           222              2333333  478999


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCC-----CccChHHHHHHHHHHhc
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVG-----IAGNEEADRLAKEALTS  172 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsG-----i~GNE~AD~LAk~Aa~~  172 (223)
                      |||||+|++++|  |   .+++|+++.+  .++++.+...+..+..|.|.|||||+|     ++||++||+|||+|+..
T Consensus        85 I~tDS~~vi~~i--w---~~~~g~~v~n--~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A           85 VYTDSRYAFATA--H---VHSEGREIKN--KNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMK  156 (165)
T ss_dssp             EEECCHHHHHHH--H---SCCCSCCCSS--HHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEchHHHHhhh--h---cccCCCcccC--HHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhc
Confidence            999999999998  2   2566777766  477888866666788999999999999     99999999999999987

>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=99.81  E-value=3e-20  Score=150.59  Aligned_cols=126  Identities=17%  Similarity=0.071  Sum_probs=93.0

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.|||++.|.|+|+.+.......+|.....+++..|-           ...              -...+.. ..+++|.
T Consensus        13 ~~~n~~~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl-----------~A~--------------~~aL~~~-~~~~~v~   66 (155)
T 1jl1_A           13 ALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMEL-----------MAA--------------IVALEAL-KEHAEVI   66 (155)
T ss_dssp             ESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHH-----------HHH--------------HHHHHTC-CSCCEEE
T ss_pred             cCCCCCceEEEEEEEECCeEEEEecCCCCCcHHHHHH-----------HHH--------------HHHHHHh-CcCCcEE
Confidence            6789999999999998766566666554445554433           111              1222222 2247999


Q ss_pred             EEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          99 TYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      |||||+|++++|..|.      -|.+++|+++.+  .++++.+..++. ...|.|.|||||+|++||+.||+||+.|+..
T Consensus        67 I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n--~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  143 (155)
T 1jl1_A           67 LSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKN--VDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMN  143 (155)
T ss_dssp             EEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTT--HHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred             EEeCHHHHHHHHHHHHHHHhhcccccccCCccCC--HHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhc
Confidence            9999999999999741      134556777765  478888888764 5799999999999999999999999999987


Q ss_pred             C
Q psy1195         173 A  173 (223)
Q Consensus       173 ~  173 (223)
                      .
T Consensus       144 ~  144 (155)
T 1jl1_A          144 P  144 (155)
T ss_dssp             C
T ss_pred             c
Confidence            3

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

Probab=99.80  E-value=4.5e-20  Score=150.24  Aligned_cols=125  Identities=18%  Similarity=0.056  Sum_probs=92.8

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.|||++.|.|+|+.++......+|.....+++..|-           ...              ....+.. ..+++|.
T Consensus        15 ~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl-----------~A~--------------~~AL~~~-~~~~~v~   68 (158)
T 2e4l_A           15 CLGNPGPGGYGIVMNYKGHTKEMSDGFSLTTNNRMEL-----------LAP--------------IVALEAL-KEPCKII   68 (158)
T ss_dssp             ESSSSEEEEEEEEEEETTEEEEEEEEEEEECHHHHHH-----------HHH--------------HHHHHTC-SSCCEEE
T ss_pred             ccCCCCcEEEEEEEEECCEEEEEecCcCCCccHHHHH-----------HHH--------------HHHHHHh-ccCCeEE
Confidence            6789999999999998766556666555455554443           111              2222222 2347999


Q ss_pred             EEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          99 TYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      |||||+|++++|..|.      -|.+++|+++.+  .++++.+..++. ...|.|.|||||+|++||+.||+||+.|+..
T Consensus        69 I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n--~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           69 LTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKN--VDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             EEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTT--HHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             EEeCHHHHHHHHHHHHHHHHHccccccCCCcccC--HHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            9999999999999831      123556677665  478888888774 5799999999999999999999999999986

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

Probab=99.78  E-value=1.6e-19  Score=148.41  Aligned_cols=126  Identities=18%  Similarity=0.092  Sum_probs=93.1

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.|||++.+.|+||.+.......+|.....+++..|-           ...              -+..+.. ...++|.
T Consensus        17 ~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl-----------~Ai--------------~~AL~~~-~~~~~v~   70 (166)
T 1ril_A           17 CLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMEL-----------KAA--------------IEGLKAL-KEPCEVD   70 (166)
T ss_dssp             ESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHH-----------HHH--------------HHHHHSC-CSCCEEE
T ss_pred             ccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHH-----------HHH--------------HHHHHHh-ccCCeEE
Confidence            6789999999999998766566666554445554443           111              1222211 2346899


Q ss_pred             EEecChhhHhhhcc-CC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195          99 TYSENRQKTVEICP-EA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT  171 (223)
Q Consensus        99 IfTDSqyaI~aI~~-~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~  171 (223)
                      |||||+|++++|.+ |.      -|.+++|+++.+  .++++.+..++. ...|.|.|||||+|++||+.||+||+.|+.
T Consensus        71 I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n--~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~  147 (166)
T 1ril_A           71 LYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKN--RDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQ  147 (166)
T ss_dssp             EECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTT--HHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHT
T ss_pred             EEeChHHHHHHHhhhHHHHHHhcccccccCCccCc--HHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHH
Confidence            99999999999998 21      134566777765  378888888775 579999999999999999999999999998


Q ss_pred             cC
Q psy1195         172 SA  173 (223)
Q Consensus       172 ~~  173 (223)
                      ..
T Consensus       148 ~~  149 (166)
T 1ril_A          148 SQ  149 (166)
T ss_dssp             SS
T ss_pred             Hh
Confidence            74

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

Probab=99.78  E-value=7.7e-19  Score=141.50  Aligned_cols=125  Identities=20%  Similarity=0.190  Sum_probs=88.8

Q ss_pred             ccCCCCc---cceeEEEecCccccccCCCCCC-cccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHh-hc
Q psy1195          19 LSGLPDS---EWLALVLIDSPRYLDNSGYDSG-IFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEE-EE   93 (223)
Q Consensus        19 ~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~   93 (223)
                      |.|||++   +|.|+|+.|+.. ...|+...| .+++..|-           ...              ....+... ..
T Consensus        16 ~~~n~~~~~~aG~Gvv~~~~~~-~~~~~~l~~~~tn~~aEl-----------~A~--------------~~aL~~~~~~~   69 (154)
T 2qkb_A           16 CSSNGRRRPRAGIGVYWGPGHP-LNVGIRLPGRQTNQRAEI-----------HAA--------------CKAIEQAKTQN   69 (154)
T ss_dssp             EETTTSSSCEEEEEEECSTTCT-TCEEEECCSSCCHHHHHH-----------HHH--------------HHHHHHHHHTT
T ss_pred             cCCCCCCCCcEEEEEEEECCCc-eeEEeecCCCCchHHHHH-----------HHH--------------HHHHHHHHhCC
Confidence            6688876   899999998643 234444443 34444433           111              22233332 34


Q ss_pred             CceEEEEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHH
Q psy1195          94 RRKVTTYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAK  167 (223)
Q Consensus        94 ~~~I~IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk  167 (223)
                      .++|.|||||+|++++|..+.      -|++++++++.+  .++++.+..++. +..|.|.|||||+|++||+.||+||+
T Consensus        70 ~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n--~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~  146 (154)
T 2qkb_A           70 INKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVIN--KEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAR  146 (154)
T ss_dssp             CCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTT--HHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHH
T ss_pred             CceEEEEECcHHHHhhhhhhHHHHHhccccccCCCcccc--HHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHH
Confidence            579999999999999999741      134556666655  378888888774 67799999999999999999999999


Q ss_pred             HHHhc
Q psy1195         168 EALTS  172 (223)
Q Consensus       168 ~Aa~~  172 (223)
                      .|+..
T Consensus       147 ~a~~~  151 (154)
T 2qkb_A          147 EGAKQ  151 (154)
T ss_dssp             HHHTC
T ss_pred             HHHHh
Confidence            99875

>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=99.65  E-value=2.3e-16  Score=150.12  Aligned_cols=111  Identities=17%  Similarity=0.202  Sum_probs=82.1

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.||||+.+.|+|++++...   ++.....+++..|-                            +--..+.....++|.
T Consensus       445 ~~~n~g~~g~G~v~~~~~~~---~~~~~~~TNn~aEl----------------------------~A~i~aL~~~~~~v~  493 (555)
T 1mu2_A          445 CNRQSKEGKAGYVTDRGKDK---VKKLEQTTNQQAEL----------------------------EAFAMALTDSGPKVN  493 (555)
T ss_dssp             ECTTTCCEEEEEEETTSCEE---EEEESSCCHHHHHH----------------------------HHHHHHHHTSCSEEE
T ss_pred             ccCCCCCceEEEEEEeCCEe---eccCCCCCHHHHHH----------------------------HHHHHHHHcCCCeEE
Confidence            67899999999999987533   34444455555543                            122222223678999


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHH
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL  170 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa  170 (223)
                      |||||+||+++|.+|.   +.++       ..+++.+..++..+..|.|.|||||+|++||+.||+||++|+
T Consensus       494 I~tDS~~v~~~i~~~~---~~~~-------~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          494 IIVDSQYVMGIVASQP---TESE-------SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             EEESCHHHHHHHHTCC---SEES-------CHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             EEEehHHHHHHHhccc---cccc-------HHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            9999999999999843   2222       356677777666788999999999999999999999999874

>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=99.56  E-value=4.5e-16  Score=125.39  Aligned_cols=115  Identities=13%  Similarity=-0.026  Sum_probs=73.3

Q ss_pred             CccceeEEEecCccccccCC---CCC---CcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceE
Q psy1195          24 DSEWLALVLIDSPRYLDNSG---YDS---GIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKV   97 (223)
Q Consensus        24 ~~~~~~~~~~~~~~~~~~~~---~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I   97 (223)
                      |++|.|+||.+.+.....++   +..   ..+++..|-           ...              .+..+.....+.+|
T Consensus        18 g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl-----------~A~--------------~~AL~~a~~~~~~v   72 (147)
T 2kq2_A           18 GQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEI-----------AAA--------------LYAVKKASQLGVKI   72 (147)
T ss_dssp             TBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHH-----------HHH--------------HHHHHHHHHHTCCC
T ss_pred             CCcEEEEEEEECCEEEEEEeccccccccccccHHHHHH-----------HHH--------------HHHHHHHHHCCCeE
Confidence            89999999998766555554   222   135666554           222              33333222223389


Q ss_pred             EEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhcC
Q psy1195          98 TTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSA  173 (223)
Q Consensus        98 ~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~~  173 (223)
                      .|||||+.+.+-+...+  .++.+.++..  .++++   .+. .  .|.|.|||||+|++||+.||+||++|+...
T Consensus        73 ~I~tDS~~i~~w~~~~w--~~~~~~~~~~--~~l~~---~l~-~--~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           73 RILHDYAGIAFWATGEW--KAKNEFTQAY--AKLMN---QYR-G--IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             CBSSCCSTHHHHTTSSS--SCCHHHHHHH--HCGGG---GGS-T--TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             EEEECcHHHHHHHhCCC--ccCCcchHHH--HHHHH---Hhc-C--CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            99999998776554422  2222222211  12222   221 2  899999999999999999999999999874

>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=99.56  E-value=2.8e-15  Score=142.72  Aligned_cols=110  Identities=16%  Similarity=0.187  Sum_probs=76.0

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.||||+.+.|+|+.++....-  + ....+++..|-           +..              ....+.   -.++|.
T Consensus       448 ~~~n~g~~g~g~v~~~~~~~~~--~-~~~~TNn~aEl-----------~Ai--------------~~aL~~---~~~~v~  496 (557)
T 2zd1_A          448 ANRETKLGKAGYVTNKGRQKVV--P-LTNTTNQKTEL-----------QAI--------------YLALQD---SGLEVN  496 (557)
T ss_dssp             ECTTTCCEEEEEEETTSCEEEE--E-ECSCCHHHHHH-----------HHH--------------HHHHHH---SCSEEE
T ss_pred             CCCCCCceEEEEEEECCcEEEe--c-CCCCCHHHHHH-----------HHH--------------HHHHHh---CCCcEE
Confidence            6689999999999987654332  2 22344555443           121              222232   278999


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHH
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEA  169 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~A  169 (223)
                      ||||||||+++|.++.   .+++       .++++.+...+.....|.|.|||||+|++||+.||+||++|
T Consensus       497 I~tDS~~vi~~i~~~~---~~~~-------~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          497 IVTDSQYALGIIQAQP---DKSE-------SELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             EEECCHHHHHHHTTCC---SEES-------SHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             EEeChHHHHHHHhcCC---ccCC-------HHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            9999999999999853   2222       25666666555556789999999999999999999999976

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

Probab=99.55  E-value=2.1e-14  Score=110.94  Aligned_cols=118  Identities=19%  Similarity=0.233  Sum_probs=78.9

Q ss_pred             ccCCCCccceeEEEecC-cccc-ccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhh-cCc
Q psy1195          19 LSGLPDSEWLALVLIDS-PRYL-DNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEE-ERR   95 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~   95 (223)
                      |.|+||++|.|+|+.|. ++.+ ..++.....+++..|-           ...              -...+.... ..+
T Consensus        12 ~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl-----------~A~--------------~~aL~~a~~~~~~   66 (140)
T 3u3g_D           12 ARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEY-----------EAL--------------IRALEDLQMFGDK   66 (140)
T ss_dssp             ESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHH-----------HHH--------------HHHHHHHGGGGGG
T ss_pred             CCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHH-----------HHH--------------HHHHHHHHHcCCC
Confidence            67899999999999983 3333 5555554445544433           111              222333222 234


Q ss_pred             ----eEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHH-HhcCCceEEEEeccCCCCccChHHHHHHHHHH
Q psy1195          96 ----KVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLIL-FLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL  170 (223)
Q Consensus        96 ----~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~l-l~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa  170 (223)
                          +|.|||||+|+++++++++   +..... +.   .+++.+..+ +.+...|+|.|||+    +||+.||+||+.|+
T Consensus        67 ~~~~~v~i~tDS~~vi~~i~~~~---~~~~~~-l~---~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~  135 (140)
T 3u3g_D           67 LVDMEVEVRMDSELIVRQMQGVY---KVKEPT-LK---EKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAI  135 (140)
T ss_dssp             GTTCEEEEEESCHHHHHHHTTSS---CCCCGG-GH---HHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHH
T ss_pred             CCCceEEEEeChHHHHHHhCCCc---ccCCHH-HH---HHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHH
Confidence                8999999999999999853   111111 11   355666666 65557999999994    89999999999998


Q ss_pred             hc
Q psy1195         171 TS  172 (223)
Q Consensus       171 ~~  172 (223)
                      ..
T Consensus       136 ~~  137 (140)
T 3u3g_D          136 DK  137 (140)
T ss_dssp             HH
T ss_pred             Hh
Confidence            64

>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=99.51  E-value=6.4e-14  Score=109.04  Aligned_cols=118  Identities=14%  Similarity=0.101  Sum_probs=79.4

Q ss_pred             ccCCCCccceeEEEecCc--c-ccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHH-hhcC
Q psy1195          19 LSGLPDSEWLALVLIDSP--R-YLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREE-EEER   94 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~   94 (223)
                      |.|+||+.|.|+||.|..  . ....++.....+++..|-           ...              -...+.. ....
T Consensus        12 ~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl-----------~A~--------------~~aL~~a~~~~~   66 (141)
T 3hst_B           12 SRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEY-----------RGL--------------IAGLDDAVKLGA   66 (141)
T ss_dssp             ESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHH-----------HHH--------------HHHHHHHHHHTC
T ss_pred             CCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHH-----------HHH--------------HHHHHHHHHCCC
Confidence            679999999999999863  2 234555554555554443           111              1222222 2346


Q ss_pred             ceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          95 RKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        95 ~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      ++|.|||||+|+++.|++.+   +.... .+.   .+++.+..++.+...|.|.|||+    ++|+.||+||+.|+..
T Consensus        67 ~~v~i~tDS~~vv~~i~~~~---~~~~~-~l~---~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           67 TEAAVLMDSKLVVEQMSGRW---KVKHP-DLL---KLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             SEEEEEESCHHHHHHHTTSS---CCCSH-HHH---HHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             ceEEEEeChHHHHHHHhCCc---ccCCH-HHH---HHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            78999999999999999743   11111 111   34455666665678999999995    8999999999999876

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

Probab=99.46  E-value=2.1e-13  Score=108.27  Aligned_cols=117  Identities=15%  Similarity=0.115  Sum_probs=78.3

Q ss_pred             cc-CCCCccce-eEEEecCccccccCCCCC-----CcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHH-
Q psy1195          19 LS-GLPDSEWL-ALVLIDSPRYLDNSGYDS-----GIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREE-   90 (223)
Q Consensus        19 ~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   90 (223)
                      |. ||||++|. |+||.|.+..+..++...     ..+++..|-           ...              ....+.. 
T Consensus        10 ~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl-----------~A~--------------~~aL~~a~   64 (149)
T 2ehg_A           10 CEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEY-----------SGL--------------ICLMETML   64 (149)
T ss_dssp             EESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHH-----------HHH--------------HHHHHHHH
T ss_pred             cCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHH-----------HHH--------------HHHHHHHH
Confidence            55 89999998 999998666654333222     233333332           111              1222222 


Q ss_pred             hhcCceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHH
Q psy1195          91 EEERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL  170 (223)
Q Consensus        91 ~~~~~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa  170 (223)
                      ....++|.|||||+++++.|++++.  .++ . ..   ..+++.+..++... .|.|.||||    ++|+.||+||+.|+
T Consensus        65 ~~g~~~v~i~tDS~~vi~~i~~~w~--~~~-~-~~---~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~  132 (149)
T 2ehg_A           65 RLGISSPIIKGDSQLVIKQMNGEYK--VKA-K-RI---IPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAY  132 (149)
T ss_dssp             HHTCCSCEEEESCHHHHHHHTTSSC--CCC-T-TH---HHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHH
T ss_pred             HcCCCEEEEEeChHHHHHHHhCccc--cCC-H-HH---HHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHH
Confidence            2345789999999999999998641  222 1 11   25777777776543 699999999    49999999999998


Q ss_pred             hc
Q psy1195         171 TS  172 (223)
Q Consensus       171 ~~  172 (223)
                      ..
T Consensus       133 ~~  134 (149)
T 2ehg_A          133 EL  134 (149)
T ss_dssp             HH
T ss_pred             Hh
Confidence            76

>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=99.07  E-value=2.7e-11  Score=98.28  Aligned_cols=117  Identities=11%  Similarity=-0.146  Sum_probs=85.4

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |+||||+++.|+||...+..+..+|..+..+++..|-           ...              -+..+.......+|.
T Consensus        20 ~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl-----------~A~--------------i~aL~~~~~~~~~v~   74 (142)
T 1zbf_A           20 SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEF-----------LAI--------------VHGLRYLKERNSRKP   74 (142)
T ss_dssp             ECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHH-----------HHH--------------HHHHHHHHHTTCCCC
T ss_pred             cCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHH-----------HHH--------------HHHHHHHHhCCCeEE
Confidence            7899999999999997777777777765556666654           222              233333332211899


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHh--cCCceEEEEeccCCCCccChHHH
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFL--SKLDVQFVWVPSHVGIAGNEEAD  163 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~--~~~~V~~~WVPGHsGi~GNE~AD  163 (223)
                      |||||+||++-+.+.+ +++..++++.+  .++++.+.++..  +.+.++...|+.|++.-||..||
T Consensus        75 i~tDS~~vi~w~~~~~-~k~~~~~~v~n--~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           75 IYSNSQTAIKWVKDKK-AKSTLVRNEET--ALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             EEESCHHHHHHHHHTC-CCCCCCCSTTT--HHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             EEEehHHHHHHHHcCC-ccCCCCCCccc--HHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCccc
Confidence            9999999999888754 23444566655  488888877654  66788888899999999999988

>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=98.82  E-value=2.4e-09  Score=86.71  Aligned_cols=93  Identities=11%  Similarity=-0.176  Sum_probs=67.5

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |+|||||.+.|.|+++.+..+..+|.....+++..|-           ...              -+.++.......+|.
T Consensus        14 c~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl-----------~A~--------------i~aL~~l~~~~~~v~   68 (134)
T 4htu_A           14 SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEF-----------LAI--------------VHGLRYLKERNSRKP   68 (134)
T ss_dssp             EETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHH-----------HHH--------------HHHHHHHHHTTCCCC
T ss_pred             cCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHH-----------HHH--------------HHHHHHHHhCCCCEE
Confidence            8999999999888898887777777765566666654           222              334444443334589


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHH
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILF  139 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll  139 (223)
                      ||||||||++-|.++. |+++.++++.+  .++++.+.++.
T Consensus        69 i~tDSqyVi~wi~~~~-~kt~~~~~vkN--~dLw~~ld~~~  106 (134)
T 4htu_A           69 IYSNSQTAIKWVKDKK-AKSTLVRNEET--ALIWKLVDEAE  106 (134)
T ss_dssp             EEESCHHHHHHHHHTC-CCCCCCCSSTT--HHHHHHHHHHH
T ss_pred             EEcchHHHHHHHHcCC-cccCCCCCccC--HHHHHHHHHHH
Confidence            9999999999888754 45667788776  48888887554

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=95.24  E-value=0.0029  Score=55.39  Aligned_cols=9  Identities=22%  Similarity=-0.086  Sum_probs=4.2

Q ss_pred             ccccccCCC
Q psy1195          15 ERTYLSGLP   23 (223)
Q Consensus        15 ~~~~~~~~~   23 (223)
                      ....++||+
T Consensus       306 ~~L~l~~N~  314 (386)
T 2ca6_A          306 LFLELNGNR  314 (386)
T ss_dssp             CEEECTTSB
T ss_pred             eEEEccCCc
Confidence            334455554

---

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	223
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	1e-07
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	1e-06
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	2e-05

>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 = 47.2 bits (111), Expect = 1e-07
 Identities = 12/44 (27%), Positives = 20/44 (45%)

Query: 127 KWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL 170
                +   +   + K  +   WVP+H GI GN+E D L  + +
Sbjct: 83  SESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 126

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

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

 Score = 44.6 bits (104), Expect = 1e-06
 Identities = 14/46 (30%), Positives = 22/46 (47%)

Query: 131 DIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTSAHPS 176
           D+   L+L ++   V+F +V  H G   NE  DR A+    S   +
Sbjct: 102 DLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKT 147

>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 = 41.2 bits (95), Expect = 2e-05
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 145 VQFVWVPSHVGIAGNEEADRLAKEA 169
           +++ WV  H G   NE AD LA+ A
Sbjct: 114 IKWEWVKGHAGHPENERADELARAA 138

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	223
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.82
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.81
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.75
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.46
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.29

>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=99.82  E-value=5.6e-21  Score=150.32  Aligned_cols=126  Identities=18%  Similarity=0.114  Sum_probs=93.9

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.||||++|.|+|+++.......++...+.+++..|-           ...              .+.++ .......+.
T Consensus        12 ~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl-----------~Ai--------------~~AL~-~~~~~~~i~   65 (147)
T d1rila_          12 CLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMEL-----------KAA--------------IEGLK-ALKEPCEVD   65 (147)
T ss_dssp             ESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHH-----------HHH--------------HHHHH-SCCSCCEEE
T ss_pred             CCCCCCccEEEEEEEECCcceEEecccccccHHHHHH-----------HHH--------------HHHhh-hccCCceEE
Confidence            7899999999999987776666666666666655443           111              11111 123457899


Q ss_pred             EEecChhhHhhhccCCC-------CCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195          99 TYSENRQKTVEICPEAV-------KIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT  171 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~-------~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~  171 (223)
                      |||||+|++++|..++.       +.+..++++.+  .++++.+..++ ..+.|+|.|||||+|++||+.||+||++|+.
T Consensus        66 i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n--~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~  142 (147)
T d1rila_          66 LYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKN--RDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQ  142 (147)
T ss_dssp             EECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTT--HHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHT
T ss_pred             Eecchhhhhccccccchhhhhhccccccccccchh--HHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHH
Confidence            99999999999876321       24556677765  47888887765 5778999999999999999999999999987


Q ss_pred             cC
Q psy1195         172 SA  173 (223)
Q Consensus       172 ~~  173 (223)
                      ..
T Consensus       143 ~~  144 (147)
T d1rila_         143 SQ  144 (147)
T ss_dssp             SS
T ss_pred             Hh
Confidence            63

>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=99.81  E-value=1.8e-20  Score=146.41  Aligned_cols=126  Identities=18%  Similarity=0.109  Sum_probs=91.8

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |+||||++|.|+|+.+.......++..+..+++..|-           -.               ....-........+.
T Consensus        11 ~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~-----------~A---------------i~~Al~~~~~~~~i~   64 (152)
T d1jl1a_          11 ALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMEL-----------MA---------------AIVALEALKEHAEVI   64 (152)
T ss_dssp             ESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHH-----------HH---------------HHHHHHTCCSCCEEE
T ss_pred             CCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHH-----------hh---------------hhhhhhhhcccceEE
Confidence            7899999999999998877776676666555544332           11               111122234567899


Q ss_pred             EEecChhhHhhhccCCC------CCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195          99 TYSENRQKTVEICPEAV------KIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS  172 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~------~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~  172 (223)
                      |+|||++++.+++.+..      +...+++++.+  .++++.+..++ ....|+|+|||||+|++||++||+|||+|+..
T Consensus        65 i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n--~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~  141 (152)
T d1jl1a_          65 LSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKN--VDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMN  141 (152)
T ss_dssp             EEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTT--HHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred             EeecceeeEEcccchhhHhHhccchhcccCeeec--HHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHhC
Confidence            99999999998886421      23445555554  36677776664 56789999999999999999999999999986


Q ss_pred             C
Q psy1195         173 A  173 (223)
Q Consensus       173 ~  173 (223)
                      +
T Consensus       142 ~  142 (152)
T d1jl1a_         142 P  142 (152)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

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

Probab=99.75  E-value=1.9e-18  Score=133.32  Aligned_cols=110  Identities=17%  Similarity=0.226  Sum_probs=76.2

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.++|++.+.|+++.++.......   ...+++..|-                            .-..++......+|.
T Consensus        16 ~~~n~~~~~~g~~~~~~~~~~~~~---~~~tnn~AEl----------------------------~Ai~~al~~~~~~i~   64 (126)
T d1mu2a1          16 CNRQSKEGKAGYVTDRGKDKVKKL---EQTTNQQAEL----------------------------EAFAMALTDSGPKVN   64 (126)
T ss_dssp             ECTTTCCEEEEEEETTSCEEEEEE---SSCCHHHHHH----------------------------HHHHHHHHTSCSEEE
T ss_pred             CCCCCCcEEEEEEecCCCEEEEec---CCCcchHHHH----------------------------HHHHHHhccCCcceE
Confidence            678999999998887775544322   2334444432                            222334445678999


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHH
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEA  169 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~A  169 (223)
                      |||||+||++.+..++.  . +.    .   ..+..+...+.....|.|.|||||+|++|||+||+||++|
T Consensus        65 I~tDS~~v~~~~~~~~~--~-~~----~---~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          65 IIVDSQYVMGIVASQPT--E-SE----S---KIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             EEESCHHHHHHHHTCCS--E-ES----C---HHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             EEechHHHHHHHhcCCc--c-cc----c---hHHHHHHHHhhhcceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            99999999999987541  1 11    1   2333333333456799999999999999999999999986

>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=99.46  E-value=4.2e-15  Score=118.46  Aligned_cols=118  Identities=11%  Similarity=-0.156  Sum_probs=92.5

Q ss_pred             cccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceE
Q psy1195          18 YLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKV   97 (223)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I   97 (223)
                      -|+|||||.+.|.|+.++...+..||+....+++..|-           ...              -+..+.......++
T Consensus        12 a~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl-----------~A~--------------i~aL~~~~~~~~~i   66 (132)
T d1zbfa1          12 GSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEF-----------LAI--------------VHGLRYLKERNSRK   66 (132)
T ss_dssp             EECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHH-----------HHH--------------HHHHHHHHHTTCCC
T ss_pred             cCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHH-----------HHH--------------HHHHHHhhcCCceE
Confidence            38999999999999999999999999887777777665           333              34444444455789


Q ss_pred             EEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHh--cCCceEEEEeccCCCCccChHHH
Q psy1195          98 TTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFL--SKLDVQFVWVPSHVGIAGNEEAD  163 (223)
Q Consensus        98 ~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~--~~~~V~~~WVPGHsGi~GNE~AD  163 (223)
                      .|||||+|||+.+.++. |.+..++++.+  .++++.+.++..  +.+.+.+.||++|+..-||..||
T Consensus        67 ~I~tDS~yvi~wv~~~~-~kt~~~~~vkN--~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          67 PIYSNSQTAIKWVKDKK-AKSTLVRNEET--ALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CEEESCHHHHHHHHHTC-CCCCCCCSTTT--HHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             EEEeccHHHHHHHHhCc-eecCcCCCccc--HHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            99999999999998865 45556677666  377777766432  67889999999999999999887

>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=99.29  E-value=3.1e-12  Score=97.61  Aligned_cols=94  Identities=12%  Similarity=0.060  Sum_probs=66.7

Q ss_pred             ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195          19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT   98 (223)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~   98 (223)
                      |.|||++.+.|+|+-++....   ...+..+++..|-                            .--..+.....++|.
T Consensus        17 ~~~n~~~g~~g~~~~~~~~~~---~~~~~~TNn~aEl----------------------------~Avi~aL~~~~~~v~   65 (110)
T d1s1ta1          17 ANRETKLGKAGYVTNRGRQKV---VTLTDTTNQKTEL----------------------------QAIYLALQDSGLEVN   65 (110)
T ss_dssp             EETTTTEEEEEEEETTSCEEE---EEESSCCHHHHHH----------------------------HHHHHHHHHSCSEEE
T ss_pred             CCCCCCCcEEEEEEecCCeEE---EecccCcHHHHHH----------------------------HHHHHHHHhCCCeEE
Confidence            678999999999988876543   3333445655554                            122233345677899


Q ss_pred             EEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccC
Q psy1195          99 TYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSH  153 (223)
Q Consensus        99 IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGH  153 (223)
                      |||||+||+++|..+..   ..       ...+++++..++.....|.|.|||||
T Consensus        66 I~TDS~yvi~~i~~~~~---~~-------~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          66 IVTDSQYALGIIQAQPD---QS-------ESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             EEECCHHHHHHHHHCCS---EE-------SCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             EEEehHHHHHHHhcCcc---cc-------chHHHHHHHHHHhcCCceEEEEeCCC
Confidence            99999999999998652   11       12567777666667789999999999