Psyllid ID: psy16693

---

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------
Protein Sequence
MLGIPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHHL
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHHHHHcHHcccccEEEEEccHHHHHHHHHcccccHHHHHHHHHHHHccccccEEEEEEEcccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHEEEEEEEEcccccccccEEEEcccHHHHHHHHHccccccHHHHHHHHHHHHcccccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHccccccccccccccccHHHHHHHHHHHHccHHHccHHHHcccccccccccccccEEEEEEcc
Coil and Loop (DISEMBL)
mlgipdtcdehIYYQVdltgtaeksecqvyltpdnslSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFtwvpshvgiagNEEADRLAKEalssnsppvntipindfKRFFKSKILTTWNTEWANLADNKLRQIkeenrpwnppfsmsrkeQVSItrlrigpcishgsppmlelpatkkpivspkklclqthhl
Flexible Loop (DISEMBL)
mlgipdtcdeHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEalssnsppvntipindFKRFFKSKILTTWNTEWANLADNKLRQIkeenrpwnppfsmsRKEQVSITRLRIGPCIshgsppmlelpatkkpivspKKLCLQTHHL
Low Complexity Region (SEG)
MLGIPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHHL
Disordered region (IsUnstruct)
******TCDEHIYYQVDLTGTAEKSECQVYLTPD*****************IAREIRNLLDKNKHVFSLHFTWVPSHVGIAG*******************NTIPINDFKRFFKSKILTTWNTEWANLADNKL***********************ITRLRIGPCI******************************
Disordered Region (DISOPRED)
MLGIPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHH*
Disordered Region (DISEMBL)
MLGIPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHHL
Disordered Region (DISPRO)
*LGIPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHH*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLGIPDTCDEHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHHL
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	196
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.668	0.278	0.362	4e-15
427791807	1212	Putative tick transposon, partial [Rhipi	0.653	0.105	0.364	1e-14
427791321	1210	Putative tick transposon, partial [Rhipi	0.653	0.105	0.364	1e-14
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.658	0.494	0.373	4e-14
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.709	0.276	0.372	7e-14
443694523	364	hypothetical protein CAPTEDRAFT_227708 [	0.464	0.25	0.457	1e-12
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.780	0.125	0.335	2e-12
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.709	0.350	0.359	4e-12
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.653	0.481	0.325	1e-11
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.734	0.36	0.345	1e-11

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

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 50/138 (36%), Positives = 72/138 (52%), Gaps = 7/138 (5%)

Query: 30  YLTPDNSLSALQSIQNVSSSNP----IAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           ++   +SLSA+ +I  +   +P    +   I+++  + K V    F W PSHVGI GNE 
Sbjct: 79  FVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVV---FMWCPSHVGIPGNEM 135

Query: 86  ADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNP 145
           AD LAKEALSS +     +P +D +   K  I + W  EW     NKL  I     PW P
Sbjct: 136 ADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNKLHSIHPTIGPWPP 195

Query: 146 PFSMSRKEQVSITRLRIG 163
                R+E++ + R+RIG
Sbjct: 196 CQREKRREEIVLARIRIG 213

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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/129 (36%), Positives = 68/129 (52%), Gaps = 1/129 (0%)

Query: 35   NSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
            +SLSAL+++   S   P+  +I N++  N  V S+ F WVPSHVGI GNE+AD+ A  A 
Sbjct: 1002 DSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLAA 1061

Query: 95   SSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQ 154
                  +  IP+ D +R  +  +L  W  +W +   NKL  +K     W       R  +
Sbjct: 1062 HKTLTKIR-IPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIE 1120

Query: 155  VSITRLRIG 163
            V + RLRIG
Sbjct: 1121 VILCRLRIG 1129

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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/129 (36%), Positives = 68/129 (52%), Gaps = 1/129 (0%)

Query: 35   NSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
            +SLSAL+++   S   P+  +I N++  N  V S+ F WVPSHVGI GNE+AD+ A  A 
Sbjct: 999  DSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLAA 1058

Query: 95   SSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRKEQ 154
                  +  IP+ D +R  +  +L  W  +W +   NKL  +K     W       R  +
Sbjct: 1059 HKTLTKIR-IPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIE 1117

Query: 155  VSITRLRIG 163
            V + RLRIG
Sbjct: 1118 VILCRLRIG 1126

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 53/142 (37%), Positives = 75/142 (52%), Gaps = 13/142 (9%)

Query: 35  NSLSALQSIQNVSSSNPIAREI----RNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLA 90
           +SLS+L ++ N   ++P    I     NL+ K K V    F W PSHVGI GNE ADRLA
Sbjct: 99  DSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVV---FIWCPSHVGILGNEVADRLA 155

Query: 91  KEALSSNSPPVNTIPI--NDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFS 148
           K+AL     PV  +P+   D+K   +S + + W  EW    DNKL  I+     W     
Sbjct: 156 KQALVM---PVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGPQ 212

Query: 149 MSRKEQVSITRLRIGPC-ISHG 169
           + R+ ++ + R RIG   ++HG
Sbjct: 213 IDRRGEIVLARARIGHSHLTHG 234

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 57/153 (37%), Positives = 79/153 (51%), Gaps = 14/153 (9%)

Query: 24  KSECQVYLTPDNSLSALQSIQNVSSSNPIAREI----RNLLDKNKHVFSLHFTWVPSHVG 79
           K E Q  +  D SLS+L ++ N   ++P    I     NL+ K K V    F W PSHVG
Sbjct: 135 KDEDQFNICSD-SLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVV---FIWCPSHVG 190

Query: 80  IAGNEEADRLAKEALSSNSPPVNTIPI--NDFKRFFKSKILTTWNTEWANLADNKLRQIK 137
           I GNE ADRLAK+AL     PV  +P+   D+K   +S + + W  EW    DNKL  I+
Sbjct: 191 ILGNEVADRLAKQALVM---PVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQ 247

Query: 138 EENRPWNPPFSMSRKEQVSITRLRIGPC-ISHG 169
                W     + R+ ++ + R RIG   ++HG
Sbjct: 248 PVISEWKQGPQIDRRGEIVLARARIGHSHLTHG 280

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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/94 (45%), Positives = 54/94 (57%), Gaps = 3/94 (3%)

Query: 71  FTWVPSHVGIAGNEEADRLAKEALSSNSPPVNT-IPINDFKRFFKSKILTTWNTEWANLA 129
           F W PSHVGI GNE AD LAK+AL  N   +N  IP  DFK   +S + T W +EW    
Sbjct: 68  FIWCPSHVGIPGNETADTLAKQALGMNI--LNCPIPHTDFKPITRSFVKTQWQSEWDQET 125

Query: 130 DNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIG 163
            NKL  I+ +   W P     R+E++ I R+RIG
Sbjct: 126 GNKLHDIQPDIGSWPPCQREKRREEIVIARVRIG 159

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/164 (33%), Positives = 82/164 (50%), Gaps = 11/164 (6%)

Query: 21   TAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDK-NKHVFSLHFTWVPSHVG 79
              + SE   ++   +S SALQ++  + +  P+  +   LLD        + F WVPSHVG
Sbjct: 1005 AVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVG 1064

Query: 80   IAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEE 139
            I GNE ADR AK AL +++     IP +D ++   S     W   W     +KLRQI  +
Sbjct: 1065 IEGNEAADREAKRAL-NHAVSGTQIPYSDLRQSIASATYREWQNRWEAETHSKLRQIVAD 1123

Query: 140  NRPWNPPF-SMSRKEQVSITRLRIG-PCISHG------SPPMLE 175
             R W P    ++R+   +++RLRIG   I+H        PP+ E
Sbjct: 1124 VR-WRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCE 1166

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 55/153 (35%), Positives = 77/153 (50%), Gaps = 14/153 (9%)

Query: 24  KSECQVYLTPDNSLSALQSIQNVSSSNPIAREI----RNLLDKNKHVFSLHFTWVPSHVG 79
           K E Q  +  D SLS+L ++ N   ++P    I     NL+ K K V    F W PSHVG
Sbjct: 184 KDEDQFNICSD-SLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVV---FIWCPSHVG 239

Query: 80  IAGNEEADRLAKEALSSNSPPVNTIPI--NDFKRFFKSKILTTWNTEWANLADNKLRQIK 137
           I GNE ADR AK+AL     PV  +P+   D+K   +S + + W  EW    DNKL  I+
Sbjct: 240 ILGNEVADRQAKQALVM---PVTKLPLPHTDYKSPIRSYVKSLWQNEWDGETDNKLHIIQ 296

Query: 138 EENRPWNPPFSMSRKEQVSITRLRIGPC-ISHG 169
                W     + R+ ++ +   RIG   ++HG
Sbjct: 297 PVISEWKQGPQIDRRGEIVLACARIGHSHLTHG 329

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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/135 (32%), Positives = 69/135 (51%), Gaps = 7/135 (5%)

Query: 30  YLTPDNSLSALQSIQNVSSSNP----IAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           ++   +SLSA+ +I  +   +P    +   I+++  + K V    F W PSHVGI GNE 
Sbjct: 134 FVICSDSLSAIMAIHGMDVHHPYVLQVLYAIKSISQQEKIVV---FMWCPSHVGIPGNEM 190

Query: 86  ADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNP 145
           A  LA++ALSS +     +P +D +   K  I + W  EW    +NKL  I     PW P
Sbjct: 191 AHTLAEKALSSTNLAELPVPASDLRGLIKKYIRSQWQHEWEEQHNNKLHSIHPTIGPWPP 250

Query: 146 PFSMSRKEQVSITRL 160
                R+E++ + R+
Sbjct: 251 CQREKRREEIVLVRI 265

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443733872|gb|ELU18078.1| hypothetical protein CAPTEDRAFT_197082 [Capitella teleta]

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/165 (34%), Positives = 82/165 (49%), Gaps = 21/165 (12%)

Query: 41  QSIQNVSSSNPIAREIRNLLDK----NKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSS 96
           Q I N +  +P   +I   L+K    +K    L  TW PSHVG+ GNE AD LAKEALS 
Sbjct: 72  QGIGNFNIKHPYVVKI---LEKCTLLHKKGIDLVMTWCPSHVGVMGNERADLLAKEALSF 128

Query: 97  NSPPVNTIPINDFK----RFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSMSRK 152
            +  +  IP +DFK     F+K K    W  +W++  +NKL  I+     W       R+
Sbjct: 129 TTCTIR-IPSSDFKPITHEFYKEK----WQEQWSSEQENKLYCIQPTLGKWAKSSREIRR 183

Query: 153 EQVSITRLRIGPC-ISHGSPPMLELPATKKPIVSPKKLCLQTHHL 196
           E++ + R RIG   ++HG     E+P    P+  P +  L   H+
Sbjct: 184 EEIVLARARIGHSHLTHGYLLRREMP----PVCIPCQNILSIKHI 224

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	196
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.301	0.121	0.412	0.00019

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

 Score = 115 (45.5 bits), Expect = 0.00019, P = 0.00019
 Identities = 26/63 (41%), Positives = 39/63 (61%)

Query:    34 DNSLSALQSIQNVSSSNP--IAREIRNLLDKNKHV-FSLHFTWVPSHVGIAGNEEADRLA 90
             DN  + LQ+++N  S +   I   I   L+K +    ++HF W+P+H G+ GNE+ADR A
Sbjct:   249 DNQ-ATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADRRA 307

Query:    91 KEA 93
             KEA
Sbjct:   308 KEA 310


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        0.316   0.131   0.400    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      196       196   0.00080  111 3  11 22  0.37    33
                                                     31  0.44    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:  614 (65 KB)
  Total size of DFA:  185 KB (2106 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:  19.79u 0.11s 19.90t   Elapsed:  00:00:08
  Total cpu time:  19.79u 0.11s 19.90t   Elapsed:  00:00:08
  Start:  Thu Aug 15 15:51:27 2013   End:  Thu Aug 15 15:51:35 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	196
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-17
pfam00075	126	pfam00075, RNase_H, RNase H	6e-13
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	4e-09
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-08
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-05
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	2e-05
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	3e-04
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	0.001

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

 Score = 74.2 bits (183), Expect = 2e-17
 Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 18  LTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDK-NKHVFSLHFTWVPS 76
           L       +  ++   D S +AL+++++  SS+P+   IR  + +   H   +   WVP 
Sbjct: 53  LREGRRARKITIFS--D-SQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPG 109

Query: 77  HVGIAGNEEADRLAKEALS 95
           H GI GNE ADRLAKEA  
Sbjct: 110 HSGIEGNERADRLAKEAAK 128

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

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

 Score = 62.7 bits (153), Expect = 6e-13
 Identities = 25/58 (43%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 38  SALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALS 95
                    S S PI  EI  LL K   V+     WVP H GI GNE AD+LAK+  S
Sbjct: 72  GITNGWPTKSESKPIKNEIWELLQKKHKVY---IQWVPGHSGIPGNELADKLAKQGAS 126

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

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

 Score = 52.5 bits (127), Expect = 4e-09
 Identities = 17/45 (37%), Positives = 24/45 (53%)

Query: 50  NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
               +E +  +DK K    + F  V +H G   NE AD+LAK+AL
Sbjct: 89  KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 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|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 = 51.1 bits (123), Expect = 2e-08
 Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 55  EIRNLLDK-NKHVFSLHFTWVPSHVGIAGNEEADRLAKEALS 95
           E+  LL++  +    + F  VP H GI GNEEADRLAK+   
Sbjct: 109 ELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150

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

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 54  REIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSN 97
            E+  LL +++ VF   + WV  H G   NE AD+LA+EA  + 
Sbjct: 106 EELDELLKRHELVF---WEWVKGHAGHPENERADQLAREAARAA 146

Length = 154

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

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 4/40 (10%)

Query: 54  REIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
           +E+  LL K++    + + WV  H G  GNE AD LA  A
Sbjct: 102 QELDALLAKHQ----VTWHWVKGHAGHPGNERADELANAA 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|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI

 Score = 39.0 bits (92), Expect = 3e-04
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 7/46 (15%)

Query: 50  NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALS 95
            P   E R LL K + V      W+P       N+EAD LA +AL 
Sbjct: 90  APYLEEARELLKKFEEVE---IKWIPRE----ENKEADALANQALD 128

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. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. Length = 128

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 18/60 (30%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 35  NSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
             +  + S       N +      LL          F  VP      GNE ADRLAKEA 
Sbjct: 70  YVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIR--FEHVPRE----GNEVADRLAKEAA 123

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	196
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.61
PRK06548	161	ribonuclease H; Provisional	99.6
PRK08719	147	ribonuclease H; Reviewed	99.59
PRK00203	150	rnhA ribonuclease H; Reviewed	99.56
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.47
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.33
KOG3752|consensus	371		98.9
PRK13907	128	rnhA ribonuclease H; Provisional	98.85
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.79
PRK07708	219	hypothetical protein; Validated	98.38
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	98.31

>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=99.61  E-value=2.6e-15  Score=113.29  Aligned_cols=80  Identities=36%  Similarity=0.553  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHH--hc-CCCEEEEecccHHHHHHHhc-----ccC-C--C-hHHHHHHHHHHhccCCceEEEEecCCCCCC
Q psy16693         13 YYQVDLTGTAE--KS-ECQVYLTPDNSLSALQSIQN-----VSS-S--N-PIAREIRNLLDKNKHVFSLHFTWVPSHVGI   80 (196)
Q Consensus        13 ~~~~e~~~~~~--~~-~~~~i~I~tDs~sal~~l~~-----~~~-~--~-~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi   80 (196)
                      .+.+|+.|+..  +. ....+.|+|||++++..+..     .+. .  . ++..+|.+++..   +..|.|.|||||+|+
T Consensus        40 ~~~aEl~Ai~~AL~~~~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~---~~~v~~~~V~~H~~~  116 (132)
T PF00075_consen   40 NNRAELQAIIEALKALEHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSR---GIKVRFRWVPGHSGV  116 (132)
T ss_dssp             HHHHHHHHHHHHHHTHSTSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHH---SSEEEEEESSSSSSS
T ss_pred             hhhhheehHHHHHHHhhcccccccccHHHHHHHHHHhccccccccccccccchhheeecccc---ceEEeeeeccCcCCC
Confidence            57899998752  22 45899999999999998888     332 1  2 466777777733   348999999999999


Q ss_pred             -ccchHHhHHHHHHhh
Q psy16693         81 -AGNEEADRLAKEALS   95 (196)
Q Consensus        81 -~gNe~aD~~A~~a~~   95 (196)
                       .|||.||+|||+|+.
T Consensus       117 ~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen  117 PQGNERADRLAKEAAQ  132 (132)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHhcC
Confidence             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 ....

>PRK06548 ribonuclease H; Provisional

Probab=99.60  E-value=4.1e-15  Score=117.70  Aligned_cols=84  Identities=24%  Similarity=0.368  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHH-----hcCCCEEEEecccHHHHHHHhcc---------cCCC--hHH-HH-HHHHHHhccCCceEEEEe
Q psy16693         12 IYYQVDLTGTAE-----KSECQVYLTPDNSLSALQSIQNV---------SSSN--PIA-RE-IRNLLDKNKHVFSLHFTW   73 (196)
Q Consensus        12 ~~~~~e~~~~~~-----~~~~~~i~I~tDs~sal~~l~~~---------~~~~--~~~-~~-i~~l~~~~~~~~~v~~~W   73 (196)
                      +-..+||.|+..     ......+.|+|||++++++++.|         ..++  ++. ++ |+++.....+ ..|.|.|
T Consensus        41 TNnraEl~Aii~aL~~~~~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~w  119 (161)
T PRK06548         41 TNNIAELTAVRELLIATRHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSW  119 (161)
T ss_pred             CHHHHHHHHHHHHHHhhhcCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEE
Confidence            567888888652     22345799999999999999963         1222  322 22 3333333222 3799999


Q ss_pred             cCCCCCCccchHHhHHHHHHhhc
Q psy16693         74 VPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        74 vpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      ||||+|++|||.||+||++|+..
T Consensus       120 VkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548        120 VNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             EecCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999999977

>PRK08719 ribonuclease H; Reviewed

Probab=99.59  E-value=3.9e-15  Score=116.26  Aligned_cols=84  Identities=23%  Similarity=0.245  Sum_probs=57.7

Q ss_pred             HHHHHHHHHHHH--hcCCCEEEEecccHHHHHHHhc--------ccCCC---hHH-HHHHHHHHhccCCceEEEEecCCC
Q psy16693         12 IYYQVDLTGTAE--KSECQVYLTPDNSLSALQSIQN--------VSSSN---PIA-REIRNLLDKNKHVFSLHFTWVPSH   77 (196)
Q Consensus        12 ~~~~~e~~~~~~--~~~~~~i~I~tDs~sal~~l~~--------~~~~~---~~~-~~i~~l~~~~~~~~~v~~~WvpgH   77 (196)
                      +.+++|+.|+..  +.-.....|+|||++++++++.        +|..+   ++. .++.+.+........|.|.|||||
T Consensus        49 Tnn~aEl~A~~~aL~~~~~~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH  128 (147)
T PRK08719         49 DNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAH  128 (147)
T ss_pred             cHHHHHHHHHHHHHHHcCCCCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCC
Confidence            678999998762  2222335899999999999953        33221   221 222222222112347999999999


Q ss_pred             CCCccchHHhHHHHHHhh
Q psy16693         78 VGIAGNEEADRLAKEALS   95 (196)
Q Consensus        78 ~gi~gNe~aD~~A~~a~~   95 (196)
                      +|++|||.||+||++|+.
T Consensus       129 ~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        129 SGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             CCChhHHHHHHHHHHHhh
Confidence            999999999999999975

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.56  E-value=1.2e-14  Score=113.52  Aligned_cols=81  Identities=21%  Similarity=0.303  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHH--h--cCCCEEEEecccHHHHHHHhcc--------cC-CC--h-----HHHHHHHHHHhccCCceEEE
Q psy16693         12 IYYQVDLTGTAE--K--SECQVYLTPDNSLSALQSIQNV--------SS-SN--P-----IAREIRNLLDKNKHVFSLHF   71 (196)
Q Consensus        12 ~~~~~e~~~~~~--~--~~~~~i~I~tDs~sal~~l~~~--------~~-~~--~-----~~~~i~~l~~~~~~~~~v~~   71 (196)
                      +...|||.|+..  +  .....+.|+|||++++++|..|        +. ++  +     +.++|.+++.    ...|.|
T Consensus        42 TN~~aEL~Ai~~AL~~~~~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~----~~~v~~  117 (150)
T PRK00203         42 TNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK----RHQIKW  117 (150)
T ss_pred             cHHHHHHHHHHHHHHHcCCCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc----cCceEE
Confidence            467899998752  1  3346899999999999999973        11 11  2     2333433332    247999


Q ss_pred             EecCCCCCCccchHHhHHHHHHhhc
Q psy16693         72 TWVPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        72 ~WvpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      .|||||+|++|||.||+||++|+..
T Consensus       118 ~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203        118 HWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             EEecCCCCCHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999987

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

Probab=99.47  E-value=1.4e-13  Score=107.88  Aligned_cols=83  Identities=24%  Similarity=0.355  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcc---cCCC--------h-----HHHHHHHHHHhccCCceE
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNV---SSSN--------P-----IAREIRNLLDKNKHVFSL   69 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~---~~~~--------~-----~~~~i~~l~~~~~~~~~v   69 (196)
                      |-..+|+.|+.      .+.+...|.|+|||++++++|..|   +...        |     +.+++.+++..++   .|
T Consensus        42 TNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~---~v  118 (154)
T COG0328          42 TNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHE---LV  118 (154)
T ss_pred             cChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCC---eE
Confidence            44567777654      346788999999999999999954   1111        1     2344444444443   69


Q ss_pred             EEEecCCCCCCccchHHhHHHHHHhhcC
Q psy16693         70 HFTWVPSHVGIAGNEEADRLAKEALSSN   97 (196)
Q Consensus        70 ~~~WvpgH~gi~gNe~aD~~A~~a~~~~   97 (196)
                      .+.|||||+|.++||.||+||+.|+...
T Consensus       119 ~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328         119 FWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             EEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999998873

>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=99.33  E-value=1.2e-11  Score=89.96  Aligned_cols=79  Identities=28%  Similarity=0.376  Sum_probs=61.7

Q ss_pred             HHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccC-C-C---hHHHHHHHHHHhccCCceEEEEecCCCCCCc
Q psy16693         13 YYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSS-S-N---PIAREIRNLLDKNKHVFSLHFTWVPSHVGIA   81 (196)
Q Consensus        13 ~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~-~-~---~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~   81 (196)
                      ++.+|+.|+.      ......++.|++||+.+++.+.++.. . .   .+...+++++   .+...+.|.|||+|+|+.
T Consensus        41 ~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~---~~~~~~~i~~v~~h~~~~  117 (130)
T cd06222          41 NNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALL---KRFHKVRFEWVPGHSGIE  117 (130)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHH---hCCCeEEEEEcCCCCCCc
Confidence            6788998865      24678899999999999999998754 2 2   2334444444   234479999999999999


Q ss_pred             cchHHhHHHHHHh
Q psy16693         82 GNEEADRLAKEAL   94 (196)
Q Consensus        82 gNe~aD~~A~~a~   94 (196)
                      +|+.||.+|++|.
T Consensus       118 ~n~~ad~la~~~~  130 (130)
T cd06222         118 GNERADALAKEAA  130 (130)
T ss_pred             chHHHHHHHHhhC
Confidence            9999999999874

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

>KOG3752|consensus

Probab=98.90  E-value=4.4e-09  Score=92.12  Aligned_cols=84  Identities=20%  Similarity=0.217  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhccc---CCC--------h----------HHHHHHHHHHhcc
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVS---SSN--------P----------IAREIRNLLDKNK   64 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~---~~~--------~----------~~~~i~~l~~~~~   64 (196)
                      +-..||+.|+.      .+.+..+++|.|||++++++|+.|.   .+.        +          ....+.++.+.. 
T Consensus       255 tNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~-  333 (371)
T KOG3752|consen  255 TNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI-  333 (371)
T ss_pred             cccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh-
Confidence            35678887754      3455669999999999999999872   221        1          122233333331 


Q ss_pred             CCceEEEEecCCCCCCccchHHhHHHHHHhhc
Q psy16693         65 HVFSLHFTWVPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        65 ~~~~v~~~WvpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      .+..|.+.|||||.||.|||.||.+|++....
T Consensus       334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  334 SNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             ccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            23589999999999999999999999998544

>PRK13907 rnhA ribonuclease H; Provisional

Probab=98.85  E-value=1.6e-08  Score=76.50  Aligned_cols=77  Identities=17%  Similarity=0.299  Sum_probs=57.8

Q ss_pred             HHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccCCC----hHHHHHHHHHHhccCCceEEEEecCCCCCCcc
Q psy16693         13 YYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSSSN----PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAG   82 (196)
Q Consensus        13 ~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~~~----~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~g   82 (196)
                      ...||+.|+.      ...+..++.|+|||+++++.+++.+..+    ++..++..++..+.   .+.|.|||+    ++
T Consensus        41 n~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~---~~~~~~v~r----~~  113 (128)
T PRK13907         41 NHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFD---LFFIKWIPS----SQ  113 (128)
T ss_pred             CcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCC---ceEEEEcCc----hh
Confidence            4567777643      3556678999999999999999976543    34455555555444   577899999    69


Q ss_pred             chHHhHHHHHHhhc
Q psy16693         83 NEEADRLAKEALSS   96 (196)
Q Consensus        83 Ne~aD~~A~~a~~~   96 (196)
                      |+.||.+|++|...
T Consensus       114 N~~Ad~LA~~a~~~  127 (128)
T PRK13907        114 NKVADELARKAILQ  127 (128)
T ss_pred             chhHHHHHHHHHhc
Confidence            99999999999754

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

Probab=98.79  E-value=4.1e-08  Score=68.31  Aligned_cols=74  Identities=27%  Similarity=0.346  Sum_probs=54.1

Q ss_pred             HHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccC-CC---hHHHHHHHHHHhccCCceEEEEecCCCCCCccch
Q psy16693         15 QVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSS-SN---PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE   84 (196)
Q Consensus        15 ~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~-~~---~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~gNe   84 (196)
                      .||+.|+.      .+.+..++.|.|||+.+++.|++... .+   .++..|+.+++.+.   ++.|.|||.    ++|.
T Consensus         3 ~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~---~~~~~~i~r----~~N~   75 (87)
T PF13456_consen    3 EAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFW---NVSVSHIPR----EQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCS---CEEEEE--G----GGSH
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcccc---ceEEEEECh----HHhH
Confidence            46666643      56788899999999999999998743 22   35566666666544   699999998    9999


Q ss_pred             HHhHHHHHHhh
Q psy16693         85 EADRLAKEALS   95 (196)
Q Consensus        85 ~aD~~A~~a~~   95 (196)
                      .||.|||.|..
T Consensus        76 ~A~~LA~~a~~   86 (87)
T PF13456_consen   76 VADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhh
Confidence            99999999875

>PRK07708 hypothetical protein; Validated

Probab=98.38  E-value=1.9e-06  Score=71.57  Aligned_cols=78  Identities=18%  Similarity=0.173  Sum_probs=55.8

Q ss_pred             HHHHHHHHHH------HhcCCC--EEEEecccHHHHHHHhcccC-CCh----HHHHHHHHHHhccCCceEEEEecCCCCC
Q psy16693         13 YYQVDLTGTA------EKSECQ--VYLTPDNSLSALQSIQNVSS-SNP----IAREIRNLLDKNKHVFSLHFTWVPSHVG   79 (196)
Q Consensus        13 ~~~~e~~~~~------~~~~~~--~i~I~tDs~sal~~l~~~~~-~~~----~~~~i~~l~~~~~~~~~v~~~WvpgH~g   79 (196)
                      ...||+.|..      ...+.+  .|.|++||+.+++.+.+.|. .++    +...+.+++..+.  ..+.|.|||.   
T Consensus       118 NN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~--l~~~~~~VpR---  192 (219)
T PRK07708        118 NNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLK--LTPVYEPISR---  192 (219)
T ss_pred             CcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCC--ceEEEEECCc---
Confidence            4456666543      334443  48999999999999998764 343    3444555555443  2588899987   


Q ss_pred             CccchHHhHHHHHHhhc
Q psy16693         80 IAGNEEADRLAKEALSS   96 (196)
Q Consensus        80 i~gNe~aD~~A~~a~~~   96 (196)
                       +.|+.||+||++|+..
T Consensus       193 -~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        193 -KQNKEADQLATQALEG  208 (219)
T ss_pred             -hhhhHHHHHHHHHHhc
Confidence             7899999999999987

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=98.31  E-value=2.4e-06  Score=75.74  Aligned_cols=77  Identities=23%  Similarity=0.361  Sum_probs=58.8

Q ss_pred             HHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccC-CCh----HHHHHHHHHHhccCCceEEEEecCCCCCCc
Q psy16693         13 YYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSS-SNP----IAREIRNLLDKNKHVFSLHFTWVPSHVGIA   81 (196)
Q Consensus        13 ~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~-~~~----~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~   81 (196)
                      ...||+.|+.      .+.+..++.|++||+.+++.+.+.+. +++    +..++++++..+.   .+.|.|||+    +
T Consensus        45 nn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~---~~~i~~v~r----~  117 (372)
T PRK07238         45 NNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFG---RVTYTWIPR----A  117 (372)
T ss_pred             chHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCC---ceEEEECCc----h
Confidence            3467777654      35667899999999999999988664 432    3345555555544   699999998    8


Q ss_pred             cchHHhHHHHHHhhc
Q psy16693         82 GNEEADRLAKEALSS   96 (196)
Q Consensus        82 gNe~aD~~A~~a~~~   96 (196)
                      +|+.||.||+.|...
T Consensus       118 ~N~~AD~LA~~a~~~  132 (372)
T PRK07238        118 RNAHADRLANEAMDA  132 (372)
T ss_pred             hhhHHHHHHHHHHHh
Confidence            999999999999755

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	196
4b3p_A	560	Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A		4e-04
4b3q_A	560	Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A		5e-04
4b3o_A	560	Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A		5e-04
1s1t_A	560	Crystal Structure Of L100i Mutant Hiv-1 Reverse Tra		5e-04
1s1w_A	560	Crystal Structure Of V106a Mutant Hiv-1 Reverse Tra		5e-04
3ffi_A	561	Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Len		5e-04
3drr_A	563	Hiv Reverse Transcriptase Y181c Mutant In Complex W		5e-04
2rki_A	560	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
2ynf_A	563	Hiv-1 Reverse Transcriptase Y188l Mutant In Complex		6e-04
1s1x_A	560	Crystal Structure Of V108i Mutant Hiv-1 Reverse Tra		6e-04
1eet_A	557	Hiv-1 Reverse Transcriptase In Complex With The Inh		6e-04
3med_A	560	Hiv-1 K103n Reverse Transcriptase In Complex With T		6e-04
3jsm_A	558	K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linke		6e-04
2rf2_A	563	Hiv Reverse Transcriptase In Complex With Inhibitor		6e-04
1lwe_A	560	Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse		6e-04
1hni_A	558	Structure Of Hiv-1 Reverse Transcriptase In A Compl		6e-04
1jkh_A	560	Crystal Structure Of Y181c Mutant Hiv-1 Reverse Tra		6e-04
3kle_A	562	Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr		6e-04
3di6_A	561	Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor		6e-04
1dlo_A	556	Human Immunodeficiency Virus Type 1 Length = 556		6e-04
1ikv_A	560	K103n Mutant Hiv-1 Reverse Transcriptase In Complex		6e-04
1lw0_A	560	Crystal Structure Of T215y Mutant Hiv-1 Reverse Tra		6e-04
1jlf_A	560	Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra		6e-04
1lwc_A	560	Crystal Structure Of M184v Mutant Hiv-1 Reverse Tra		6e-04
3kjv_A	560	Hiv-1 Reverse Transcriptase In Complex With Dna Len		6e-04
1hmv_A	560	The Structure Of Unliganded Reverse Transcriptase F		6e-04
1jle_A	560	Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra		6e-04
1qe1_A	558	Crystal Structure Of 3tc-Resistant M184i Mutant Of		6e-04
3klh_A	564	Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr		6e-04
2jle_A	566	Novel Indazole Nnrtis Created Using Molecular Templ		6e-04
3dmj_A	560	Crystal Structure Of Hiv-1 V106a And Y181c Mutant R		6e-04
2vg5_A	557	Crystal Structures Of Hiv-1 Reverse Transcriptase C		6e-04
1lwf_A	560	Crystal Structure Of A Mutant Hiv-1 Reverse Transcr		6e-04
1n5y_A	558	Hiv-1 Reverse Transcriptase Crosslinked To Post- Tr		6e-04
1ikw_A	560	Wild Type Hiv-1 Reverse Transcriptase In Complex Wi		6e-04
1rev_A	560	Hiv-1 Reverse Transcriptase Length = 560		6e-04
1s6p_A	560	Crystal Structure Of Human Immunodeficiency Virus T		6e-04
1rt3_A	560	Azt Drug Resistant Hiv-1 Reverse Transcriptase Comp		6e-04
2iaj_A	560	Crystal Structure Of K103nY181C MUTANT HIV-1 Revers		6e-04
1uwb_A	558	Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558		6e-04
3dm2_A	560	Crystal Structure Of Hiv-1 K103n Mutant Reverse Tra		6e-04
3hvt_A	556	Structural Basis Of Asymmetry In The Human Immunode		6e-04
1hpz_A	560	Human Immunodeficiency Virus Type 1 Length = 560		6e-04
3drs_A	563	Hiv Reverse Transcriptase K103n Mutant In Complex W		6e-04
2ykn_A	562	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
2ykm_A	562	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
3v4i_A	556	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
3ig1_A	555	Hiv-1 Reverse Transcriptase With The Inhibitor Beta		7e-04
3dlk_A	556	Crystal Structure Of An Engineered Form Of The Hiv-		7e-04
3qo9_A	557	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		7e-04
2i5j_A	552	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		7e-04
1hys_A	553	Crystal Structure Of Hiv-1 Reverse Transcriptase In		7e-04
3qlh_A	555	Hiv-1 Reverse Transcriptase In Complex With Manicol		7e-04
1hvu_A	554	Human Immunodeficiency Virus Type 1 Reverse Transcr		7e-04
3irx_A	558	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		7e-04
3klf_A	557	Crystal Structure Of Wild-Type Hiv-1 Reverse Transc		7e-04
2zd1_A	557	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		7e-04
2ze2_A	557	Crystal Structure Of L100iK103N MUTANT HIV-1 Revers		8e-04
3bgr_A	557	Crystal Structure Of K103nY181C MUTANT HIV-1 Revers		8e-04
1rtd_A	554	Structure Of A Catalytic Complex Of Hiv-1 Reverse T		8e-04

>pdb|4B3P|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique Rt Conformation And Substrate Interface Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTASQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|4B3Q|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique Rt Conformation And Substrate Interface Length = 560

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTNSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|4B3O|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique Rt Conformation And Substrate Interface Length = 560

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1S1T|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Length = 561

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 493 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 548
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 549 VDKLVSAGI 557

>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With Inhibitor R8e Length = 563

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 550
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 551 VDKLVSAGI 559

>pdb|2RKI|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Triazole Derived Nnrti Length = 560

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With Inhibitor Gsk560 Length = 563

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 550
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 551 VDKLVSAGI 559

>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1EET|A Chain A, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor Msc204 Length = 557

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3MED|A Chain A, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc125 Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3JSM|A Chain A, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To Ds-Dna And Complexed With Tenofovir-Diphosphate As The Incoming Nucleotide Substrate Length = 558

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|2RF2|A Chain A, Hiv Reverse Transcriptase In Complex With Inhibitor 7e (Nnrti) Length = 563

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 550
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 551 VDKLVSAGI 559

>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse Transcriptase (Rtmn) In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1HNI|A Chain A, Structure Of Hiv-1 Reverse Transcriptase In A Complex With The Nonnucleoside Inhibitor Alpha-Apa R 95845 At 2.8 Angstroms Resolution Length = 558

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1JKH|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse Transcriptase In Complex With Dmp-266(Efavirenz) Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3KLE|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 562

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 550 VDKLVSAGI 558

>pdb|3DI6|A Chain A, Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor Length = 561

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1 Length = 556

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1IKV|A Chain A, K103n Mutant Hiv-1 Reverse Transcriptase In Complex With Efivarenz Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1LW0|A Chain A, Crystal Structure Of T215y Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3KJV|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Dna Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1HMV|A Chain A, The Structure Of Unliganded Reverse Transcriptase From The Human Immunodeficiency Virus Type 1 Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1JLE|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1QE1|A Chain A, Crystal Structure Of 3tc-Resistant M184i Mutant Of Hiv-1 Reverse Transcriptase Length = 558

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3KLH|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To Post-Translocation Aztmp-Terminated Dna (Complex P) Length = 564

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 550 VDKLVSAGI 558

>pdb|2JLE|A Chain A, Novel Indazole Nnrtis Created Using Molecular Template Hybridization Based On Crystallographic Overlays Length = 566

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse Transcriptase In Complex With Gw564511 Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|2VG5|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase Complexes With Thiocarbamate Non-Nucleoside Inhibitors Length = 557

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1LWF|A Chain A, Crystal Structure Of A Mutant Hiv-1 Reverse Transcriptase (rtmq+m184v: M41l/d67n/k70r/m184v/t215y) In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1N5Y|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Post- Translocation Aztmp-Terminated Dna (Complex P) Length = 558

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1IKW|A Chain A, Wild Type Hiv-1 Reverse Transcriptase In Complex With Efavirenz Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1REV|A Chain A, Hiv-1 Reverse Transcriptase Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1S6P|A Chain A, Crystal Structure Of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (Rt) In Complex With Janssen-R100943 Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed With 1051u91 Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|2IAJ|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Atp Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3DM2|A Chain A, Crystal Structure Of Hiv-1 K103n Mutant Reverse Transcriptase In Complex With Gw564511. Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human Immunodeficiency Virus Type 1 Reverse Transcriptase Heterodimer Length = 556

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|1HPZ|A Chain A, Human Immunodeficiency Virus Type 1 Length = 560

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3DRS|A Chain A, Hiv Reverse Transcriptase K103n Mutant In Complex With Inhibitor R8d Length = 563

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 550
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 551 VDKLVSAGI 559

>pdb|2YKN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 562

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|2YKM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 562

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLAKEAL 94
            D+L    +
Sbjct: 548 VDKLVSAGI 556

>pdb|3V4I|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With Dna And Azttp Length = 556

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTNSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLA 90
            D+L 
Sbjct: 550 VDKLV 554

>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta- Thujaplicinol Bound At The Rnase H Active Site Length = 555

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLA 90
            D+L 
Sbjct: 548 VDKLV 552

>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1 Reverse Transcriptase, Rt69a Length = 556

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 493 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 548
Query: 86  ADRLA 90
            D+L 
Sbjct: 549 VDKLV 553

>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 557

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLA 90
            D+L 
Sbjct: 550 VDKLV 554

>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Dhbnh, An Rnase H Inhibitor Length = 552

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLA 90
            D+L 
Sbjct: 548 VDKLV 552

>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In Complex With A Polypurine Tract Rna:dna Length = 553

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLA 90
            D+L 
Sbjct: 548 VDKLV 552

>pdb|3QLH|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Manicol At The Rnase H Active Site And Tmc278 (rilpivirine) At The Nnrti Binding Pocket Length = 555

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 493 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 548
Query: 86  ADRLA 90
            D+L 
Sbjct: 549 VDKLV 553

>pdb|1HVU|A Chain A, Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed With A 33-Base Nucleotide Rna Pseudoknot Length = 554

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLA 90
            D+L 
Sbjct: 548 VDKLV 552

>pdb|3IRX|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With The Non-Nucleoside Rt Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-Oxo-2, 3-Dihydrobenzo[d]oxazol-5-Yl)-5- (5-Methyl-1,3,4-Oxadiazol-2-Yl)pent-1-Enyl)-2-Methoxy-3- Methylbenzothioate. Length = 558

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 495 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 550
Query: 86  ADRLA 90
            D+L 
Sbjct: 551 VDKLV 555

>pdb|3KLF|A Chain A, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 557

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLA 90
            D+L 
Sbjct: 550 VDKLV 554

>pdb|2ZD1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLA 90
            D+L 
Sbjct: 550 VDKLV 554

>pdb|2ZE2|A Chain A, Crystal Structure Of L100iK103N MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLA 90
            D+L 
Sbjct: 550 VDKLV 554

>pdb|3BGR|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 549
Query: 86  ADRLA 90
            D+L 
Sbjct: 550 VDKLV 554

>pdb|1RTD|A Chain A, Structure Of A Catalytic Complex Of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance Length = 554

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 26  ECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEE 85
           E  +      +L  +Q+  + S S  + + I  L+ K K    ++  WVP+H GI GNE+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDESESELVNQIIEQLIKKEK----VYLAWVPAHKGIGGNEQ 547
Query: 86  ADRLA 90
            D+L 
Sbjct: 548 VDKLV 552

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	196
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	8e-10
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	3e-06
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	7e-06
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	3e-05
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	4e-05
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	7e-05
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	7e-05
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	9e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	1e-04
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	2e-04
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	2e-04
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	6e-04
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	6e-04

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 53.9 bits (130), Expect = 8e-10
 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 50  NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
           N   +    L+++ +      F  V +H G   N+  D  AK AL
Sbjct: 93  NEFTQAYAKLMNQYRG--IYSFEKVKAHSGNEFNDYVDMKAKSAL 135

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 15/34 (44%), Positives = 20/34 (58%)

Query: 60  LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
           L++      + +  VP H G  GNEEADRLA+E 
Sbjct: 115 LERLTQGMDIQWMHVPGHSGFIGNEEADRLAREG 148

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

 Score = 42.9 bits (102), Expect = 7e-06
 Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 4/37 (10%)

Query: 59  LLDK--NKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
           ++++   K    L   WVP+H GI GNE+ D+L    
Sbjct: 110 IIEQLIKKEKVYLA--WVPAHKGIGGNEQVDKLVSAG 144

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} Length = 146

 Score = 41.3 bits (98), Expect = 3e-05
 Identities = 12/39 (30%), Positives = 17/39 (43%)

Query: 60  LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNS 98
           + K   +  + F  V  H     N  AD LA+ A+  NS
Sbjct: 108 ILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKENS 146

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A Length = 149

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 8/51 (15%)

Query: 50  NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPP 100
            P+  +   L  K     +    WVP       N+EADRL++ A       
Sbjct: 96  IPLYEKAIELKKK----LNATLIWVPR----EENKEADRLSRVAYELVRRG 138

>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 ... Length = 155

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 13/41 (31%), Positives = 18/41 (43%)

Query: 60  LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPP 100
           LD       + + WV  H G   NE AD LA+ A  + +  
Sbjct: 107 LDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLE 147

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A Length = 158

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 60  LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNT 103
           LDK   +  + + WV  H G A NE  D+LA+ A  +N   ++T
Sbjct: 109 LDKAAQLHQIDWRWVKGHAGHAENERCDQLARAAAEANPTQIDT 152

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A Length = 165

 Score = 40.2 bits (94), Expect = 9e-05
 Identities = 15/59 (25%), Positives = 19/59 (32%), Gaps = 5/59 (8%)

Query: 51  PIAREIRNLLDKNKHVFSLHFTWVPSHVG-----IAGNEEADRLAKEALSSNSPPVNTI 104
               EI  LL        L     P H         GN  AD+ A+EA        +T+
Sbjct: 106 KNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTL 164

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

 Score = 41.4 bits (96), Expect = 9e-05
 Identities = 19/148 (12%), Positives = 45/148 (30%), Gaps = 50/148 (33%)

Query: 55  EIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTI---------- 104
           + +++ D  K + S               EE D +           V+            
Sbjct: 34  DCKDVQDMPKSILS--------------KEEIDHIIMS-----KDAVSGTLRLFWTLLSK 74

Query: 105 PINDFKRFFKSK-------ILTTWNTEWANLADNKLRQIKEENRPWN-----PPFSMSRK 152
                ++F +         +++   TE    +      I++ +R +N       +++SR 
Sbjct: 75  QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL 134

Query: 153 EQV-----SITRLRIGPCIS-HGSPPML 174
           +       ++  LR    +   G   +L
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDG---VL 159

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis} Length = 141

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 7/51 (13%)

Query: 51  PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPV 101
            +  + + L  + + +   ++ WVP       N  ADRLA +A+ + +   
Sbjct: 95  KLYVQAQALASQFRRI---NYEWVPRA----RNTYADRLANDAMDAAAQSA 138

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A Length = 166

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 11/39 (28%), Positives = 15/39 (38%)

Query: 60  LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNS 98
           L        + F +V  H G   NE  DR A+    S +
Sbjct: 112 LLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQA 150

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... Length = 557

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 48  SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRL 89
           S + +  +I   L K + V   +  WVP+H GI GNE+ D+L
Sbjct: 515 SESELVNQIIEQLIKKEKV---YLAWVPAHKGIGGNEQVDKL 553

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Length = 140

 Score = 37.5 bits (88), Expect = 6e-04
 Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 6/45 (13%)

Query: 50  NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
                +I ++  +           V  H+    N  AD L  EA+
Sbjct: 97  KEKFAKIAHIKMER------VPNLVFVHIPREKNARADELVNEAI 135

>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 Length = 555

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 48  SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRL 89
           S + I  +I   + K + ++     WVP+H GI GN+E D L
Sbjct: 512 SESKIVNQIIEEMIKKEAIY---VAWVPAHKGIGGNQEVDHL 550

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	196
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.68
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.67
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.65
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.62
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.6
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.6
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.57
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.52
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.51
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.44
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.39
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.31
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.3
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.24
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	97.01
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	93.55

>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=99.68  E-value=6.5e-17  Score=125.36  Aligned_cols=85  Identities=20%  Similarity=0.319  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHH--HhcCCCEEEEecccHHHHHHHhccc---CCC--------hH--HHHHHHHHHhccCCceEEEEecCC
Q psy16693         12 IYYQVDLTGTA--EKSECQVYLTPDNSLSALQSIQNVS---SSN--------PI--AREIRNLLDKNKHVFSLHFTWVPS   76 (196)
Q Consensus        12 ~~~~~e~~~~~--~~~~~~~i~I~tDs~sal~~l~~~~---~~~--------~~--~~~i~~l~~~~~~~~~v~~~Wvpg   76 (196)
                      +...+|+.|+.  .+....++.|+|||++++++|.+|.   ..+        ++  ...++++++...+...|.|.||||
T Consensus        48 Tnn~aEl~A~i~AL~~~~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~g  127 (150)
T 3qio_A           48 TNQKTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPA  127 (150)
T ss_dssp             CHHHHHHHHHHHHHHHSCSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCT
T ss_pred             CHHHHHHHHHHHHHHhCCCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccC
Confidence            46789999875  3444689999999999999999862   111        11  122344444334456899999999


Q ss_pred             CCCCccchHHhHHHHHHhhc
Q psy16693         77 HVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        77 H~gi~gNe~aD~~A~~a~~~   96 (196)
                      |+|++|||.||+||++|+..
T Consensus       128 H~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          128 HKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             TSCCHHHHHHHHHHHTTTSC
T ss_pred             cCCChhHHHHHHHHHHHHHH
Confidence            99999999999999999875

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

Probab=99.67  E-value=2e-16  Score=122.57  Aligned_cols=81  Identities=25%  Similarity=0.361  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhccc--------C-CC-------hHHHHHHHHHHhccCCceE
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVS--------S-SN-------PIAREIRNLLDKNKHVFSL   69 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~--------~-~~-------~~~~~i~~l~~~~~~~~~v   69 (196)
                      +.+.||+.|+.      ......++.|+|||++++++|.+|.        . .+       .++++|.+++.    ++.|
T Consensus        49 tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~----~~~v  124 (154)
T 2qkb_A           49 TNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ----GMDI  124 (154)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT----TCEE
T ss_pred             chHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc----CCce
Confidence            46789999865      2355689999999999999999841        1 11       23444444433    3479


Q ss_pred             EEEecCCCCCCccchHHhHHHHHHhhc
Q psy16693         70 HFTWVPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        70 ~~~WvpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      .|.|||||+|++|||.||+||++|+..
T Consensus       125 ~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          125 QWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             EEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             EEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            999999999999999999999999876

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

Probab=99.65  E-value=2.9e-16  Score=120.43  Aligned_cols=81  Identities=19%  Similarity=0.147  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHH----hcCCCEEEEecccHHHHHHHhc-cc--------C-C-------ChHHHHHHHHHHhccCCceEE
Q psy16693         12 IYYQVDLTGTAE----KSECQVYLTPDNSLSALQSIQN-VS--------S-S-------NPIAREIRNLLDKNKHVFSLH   70 (196)
Q Consensus        12 ~~~~~e~~~~~~----~~~~~~i~I~tDs~sal~~l~~-~~--------~-~-------~~~~~~i~~l~~~~~~~~~v~   70 (196)
                      +...||+.|+..    -....++.|+|||++++++|.. |.        . +       ..+.+++.+++..    +.|.
T Consensus        43 Tnn~aEl~A~~~AL~~~~~~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~----~~v~  118 (146)
T 3h08_A           43 TNNRMELMAAIKGLEALKEPARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL----HRVT  118 (146)
T ss_dssp             CHHHHHHHHHHHHHHTCSSCCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH----SEEE
T ss_pred             cHHHHHHHHHHHHHHhcCccCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh----CceE
Confidence            367899998752    1236799999999999999998 31        0 1       1355566666554    3699


Q ss_pred             EEecCCCCCCccchHHhHHHHHHhhc
Q psy16693         71 FTWVPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        71 ~~WvpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      |.|||||+|++|||.||+||++|+..
T Consensus       119 ~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A          119 FHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             EEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             EEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            99999999999999999999999875

>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=99.62  E-value=8.8e-16  Score=120.87  Aligned_cols=85  Identities=24%  Similarity=0.179  Sum_probs=64.7

Q ss_pred             HHHHHHHHHHHH---hcCCCEEEEecccHHHHHHHhcccCCChH--HHHHHHHHHhccCCceEEEEecCCCCC-----Cc
Q psy16693         12 IYYQVDLTGTAE---KSECQVYLTPDNSLSALQSIQNVSSSNPI--AREIRNLLDKNKHVFSLHFTWVPSHVG-----IA   81 (196)
Q Consensus        12 ~~~~~e~~~~~~---~~~~~~i~I~tDs~sal~~l~~~~~~~~~--~~~i~~l~~~~~~~~~v~~~WvpgH~g-----i~   81 (196)
                      +.+.+|+.|+..   .....++.|+|||+++++++-......++  ...+++++.....+..|.|.|||||+|     ++
T Consensus        62 Tnn~aEl~Ai~~AL~~~~~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~  141 (165)
T 3p1g_A           62 SAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEAR  141 (165)
T ss_dssp             CHHHHHHHHHHHHHHHTBTSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHH
T ss_pred             cHHHHHHHHHHHHHHHccCceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcch
Confidence            478999998752   23578999999999999999211112222  233566655544566999999999999     99


Q ss_pred             cchHHhHHHHHHhhc
Q psy16693         82 GNEEADRLAKEALSS   96 (196)
Q Consensus        82 gNe~aD~~A~~a~~~   96 (196)
                      |||.||+||++|+..
T Consensus       142 gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A          142 GNRMADQAAREAAMK  156 (165)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999988

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

Probab=99.60  E-value=1.6e-15  Score=118.14  Aligned_cols=81  Identities=22%  Similarity=0.302  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHH--h--cCCCEEEEecccHHHHHHHhcc--------cC-C------C-hHHHHHHHHHHhccCCceEEE
Q psy16693         12 IYYQVDLTGTAE--K--SECQVYLTPDNSLSALQSIQNV--------SS-S------N-PIAREIRNLLDKNKHVFSLHF   71 (196)
Q Consensus        12 ~~~~~e~~~~~~--~--~~~~~i~I~tDs~sal~~l~~~--------~~-~------~-~~~~~i~~l~~~~~~~~~v~~   71 (196)
                      +...||+.|+..  +  ....++.|+|||++++++|..|        +. .      + .+.+.|.+++.    ...|.|
T Consensus        45 tn~~aEl~A~~~AL~~~~~~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~----~~~v~~  120 (158)
T 2e4l_A           45 TNNRMELLAPIVALEALKEPCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ----LHQIDW  120 (158)
T ss_dssp             CHHHHHHHHHHHHHHTCSSCCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT----TSEEEE
T ss_pred             ccHHHHHHHHHHHHHHhccCCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc----cCcEEE
Confidence            467899998752  1  2237999999999999999983        21 1      1 23444554443    248999


Q ss_pred             EecCCCCCCccchHHhHHHHHHhhc
Q psy16693         72 TWVPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        72 ~WvpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      .|||||+|++|||.||+||++|+..
T Consensus       121 ~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          121 RWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             EECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             EEccCCCCchhHHHHHHHHHHHHHh
Confidence            9999999999999999999999987

>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=99.60  E-value=1.4e-15  Score=118.15  Aligned_cols=82  Identities=22%  Similarity=0.311  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHH--h--cCCCEEEEecccHHHHHHHhcc--------c-CC------C-hHHHHHHHHHHhccCCceEEE
Q psy16693         12 IYYQVDLTGTAE--K--SECQVYLTPDNSLSALQSIQNV--------S-SS------N-PIAREIRNLLDKNKHVFSLHF   71 (196)
Q Consensus        12 ~~~~~e~~~~~~--~--~~~~~i~I~tDs~sal~~l~~~--------~-~~------~-~~~~~i~~l~~~~~~~~~v~~   71 (196)
                      +...||+.|+..  +  ....++.|+|||++++++|..|        + .+      + .+.++|.+++.    ...|.|
T Consensus        43 tn~~aEl~A~~~aL~~~~~~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~----~~~v~~  118 (155)
T 1jl1_A           43 TNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG----QHQIKW  118 (155)
T ss_dssp             CHHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT----TCEEEE
T ss_pred             cHHHHHHHHHHHHHHHhCcCCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc----cCceEE
Confidence            467899998752  1  2247999999999999999973        1 11      1 23344443332    358999


Q ss_pred             EecCCCCCCccchHHhHHHHHHhhcC
Q psy16693         72 TWVPSHVGIAGNEEADRLAKEALSSN   97 (196)
Q Consensus        72 ~WvpgH~gi~gNe~aD~~A~~a~~~~   97 (196)
                      .|||||+|++|||.||+||++|+..+
T Consensus       119 ~wV~gH~g~~~Ne~AD~LA~~a~~~~  144 (155)
T 1jl1_A          119 EWVKGHAGHPENERADELARAAAMNP  144 (155)
T ss_dssp             EECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             EEcCCCCCCHHHHHHHHHHHHHHhcc
Confidence            99999999999999999999999874

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

Probab=99.57  E-value=3.2e-15  Score=117.49  Aligned_cols=82  Identities=18%  Similarity=0.182  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHHH--h--cCCCEEEEecccHHHHHHHhc-c--------c-CCC-------hHHHHHHHHHHhccCCceEE
Q psy16693         12 IYYQVDLTGTAE--K--SECQVYLTPDNSLSALQSIQN-V--------S-SSN-------PIAREIRNLLDKNKHVFSLH   70 (196)
Q Consensus        12 ~~~~~e~~~~~~--~--~~~~~i~I~tDs~sal~~l~~-~--------~-~~~-------~~~~~i~~l~~~~~~~~~v~   70 (196)
                      +...||+.|+..  +  ....+|.|+|||++++++|.+ |        | .++       .++++|.+++..    ..|.
T Consensus        47 Tnn~aEl~Ai~~AL~~~~~~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~----~~v~  122 (166)
T 1ril_A           47 TNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP----HRVR  122 (166)
T ss_dssp             CHHHHHHHHHHHHHHSCCSCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT----SEEE
T ss_pred             cHHHHHHHHHHHHHHHhccCCeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc----CeEE
Confidence            467899998762  1  224589999999999999999 2        2 111       244455544432    4899


Q ss_pred             EEecCCCCCCccchHHhHHHHHHhhcC
Q psy16693         71 FTWVPSHVGIAGNEEADRLAKEALSSN   97 (196)
Q Consensus        71 ~~WvpgH~gi~gNe~aD~~A~~a~~~~   97 (196)
                      |.|||||+|++|||.||+||++|+...
T Consensus       123 ~~wV~gH~g~~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A          123 FHFVKGHTGHPENERVDREARRQAQSQ  149 (166)
T ss_dssp             CCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             EEEeeCCCCchhHHHHHHHHHHHHHHh
Confidence            999999999999999999999999883

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

Probab=99.52  E-value=2.8e-14  Score=112.26  Aligned_cols=68  Identities=18%  Similarity=0.103  Sum_probs=51.2

Q ss_pred             CCCEEEEecccHHHHHHHhccc--------C---CC-----hHHHHHHHHHHhccCCceEEEEecCCCCCC------ccc
Q psy16693         26 ECQVYLTPDNSLSALQSIQNVS--------S---SN-----PIAREIRNLLDKNKHVFSLHFTWVPSHVGI------AGN   83 (196)
Q Consensus        26 ~~~~i~I~tDs~sal~~l~~~~--------~---~~-----~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi------~gN   83 (196)
                      .+.+|.|+|||+|++++|..|.        .   ..     .+.+++.+++...   .+|.|.|||||+|+      +||
T Consensus        74 ~~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~---~~v~~~~VkgH~g~~~~~~~~gN  150 (165)
T 2lsn_A           74 IPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMK---PDITIQHEKGHQPTNTSIHTEGN  150 (165)
T ss_dssp             SSSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHC---TTCEEEECCSSSCSSSCHHHHHH
T ss_pred             CCCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCC---CCEEEEEEeCCCCccCCCCChHH
Confidence            4567999999999999998741        1   11     2445555555443   36999999999995      589


Q ss_pred             hHHhHHHHHHhhc
Q psy16693         84 EEADRLAKEALSS   96 (196)
Q Consensus        84 e~aD~~A~~a~~~   96 (196)
                      |.||+||++|+..
T Consensus       151 e~AD~LA~~gA~~  163 (165)
T 2lsn_A          151 ALADKLATQGSYV  163 (165)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhh
Confidence            9999999999854

>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=99.51  E-value=2.3e-15  Score=116.01  Aligned_cols=83  Identities=13%  Similarity=0.061  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccCCC-hHHHHHHHHHHhccCCceEEEEecCCCCCCccch
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSSSN-PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNE   84 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~~~-~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~gNe   84 (196)
                      +.+.||+.|+.      .+.+. +|.|+|||+++..-+.+.|..+ +....+.++++....  .|.|.|||||+|++|||
T Consensus        49 tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~--~v~~~wV~gH~g~~~Ne  125 (147)
T 2kq2_A           49 RNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG--IYSFEKVKAHSGNEFND  125 (147)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST--TCCBCCCCCCCCCHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcC--CeeEEEecCcCCCcchH
Confidence            46788888854      23344 8999999998887666655443 444555566655544  79999999999999999


Q ss_pred             HHhHHHHHHhhcC
Q psy16693         85 EADRLAKEALSSN   97 (196)
Q Consensus        85 ~aD~~A~~a~~~~   97 (196)
                      .||+||++|+...
T Consensus       126 ~AD~LA~~a~~~~  138 (147)
T 2kq2_A          126 YVDMKAKSALGIR  138 (147)
T ss_dssp             HHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHhcc
Confidence            9999999999873

>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=99.44  E-value=2.2e-13  Score=124.89  Aligned_cols=80  Identities=24%  Similarity=0.308  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHH--HhcCCCEEEEecccHHHHHHHhccc--CCChHHHHHHHHHHhccCCceEEEEecCCCCCCccchHHh
Q psy16693         12 IYYQVDLTGTA--EKSECQVYLTPDNSLSALQSIQNVS--SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEAD   87 (196)
Q Consensus        12 ~~~~~e~~~~~--~~~~~~~i~I~tDs~sal~~l~~~~--~~~~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~gNe~aD   87 (196)
                      +.+.||+.|+.  .+....++.|+|||+++++++.+|.  ...++..++.+++..   +..|.|.|||||+|++|||.||
T Consensus       472 TNn~aEl~A~i~aL~~~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~~~---~~~v~~~wV~~H~g~~~Ne~AD  548 (555)
T 1mu2_A          472 TNQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIK---KEAIYVAWVPAHKGIGGNQEVD  548 (555)
T ss_dssp             CHHHHHHHHHHHHHHTSCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHH---CSEEEEEECCSSSCCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHhcc---CCcEEEEEEECCCCChhHHHHH
Confidence            46789999875  3457789999999999999999975  344666766655544   2479999999999999999999


Q ss_pred             HHHHHHh
Q psy16693         88 RLAKEAL   94 (196)
Q Consensus        88 ~~A~~a~   94 (196)
                      +||++|+
T Consensus       549 ~LA~~a~  555 (555)
T 1mu2_A          549 HLVSQGI  555 (555)
T ss_dssp             HHHHTTC
T ss_pred             HHHHhhC
Confidence            9999884

>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=99.39  E-value=3.3e-13  Score=123.76  Aligned_cols=79  Identities=25%  Similarity=0.332  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHH--HhcCCCEEEEecccHHHHHHHhcccCC--ChHHHHHHHHHHhccCCceEEEEecCCCCCCccchHHh
Q psy16693         12 IYYQVDLTGTA--EKSECQVYLTPDNSLSALQSIQNVSSS--NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEAD   87 (196)
Q Consensus        12 ~~~~~e~~~~~--~~~~~~~i~I~tDs~sal~~l~~~~~~--~~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~gNe~aD   87 (196)
                      +.+.||+.|+.  .+.-..++.|+|||+++++++.+|...  .++..++.+.+...   ..|.|.|||||+|++|||.||
T Consensus       475 TNn~aEl~Ai~~aL~~~~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~~~---~~v~~~wV~~H~g~~~Ne~AD  551 (557)
T 2zd1_A          475 TNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKK---EKVYLAWVPAHKGIGGNEQVD  551 (557)
T ss_dssp             CHHHHHHHHHHHHHHHSCSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHHHHC---SEEEEEECCSSSCCTTCCGGG
T ss_pred             CHHHHHHHHHHHHHHhCCCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHHhcC---CCEEEEEcCCCCCChhHHHHH
Confidence            46789999875  333378999999999999999998653  46666665544432   379999999999999999999


Q ss_pred             HHHHHH
Q psy16693         88 RLAKEA   93 (196)
Q Consensus        88 ~~A~~a   93 (196)
                      +||++|
T Consensus       552 ~LA~~a  557 (557)
T 2zd1_A          552 KLVSAG  557 (557)
T ss_dssp             GCC---
T ss_pred             HHHhcC
Confidence            999986

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

Probab=99.31  E-value=6e-12  Score=94.37  Aligned_cols=78  Identities=18%  Similarity=0.249  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHH------HhcCCC----EEEEecccHHHHHHHhcccC-CCh-H---HHHHHHH-HHhccCCceEEEEecC
Q psy16693         12 IYYQVDLTGTA------EKSECQ----VYLTPDNSLSALQSIQNVSS-SNP-I---AREIRNL-LDKNKHVFSLHFTWVP   75 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~----~i~I~tDs~sal~~l~~~~~-~~~-~---~~~i~~l-~~~~~~~~~v~~~Wvp   75 (196)
                      +.+.||+.|+.      .+.+..    ++.|+|||+++++.+.+++. .++ +   ..+|.++ +..+.   .|.|.|||
T Consensus        44 tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~---~v~~~~V~  120 (140)
T 3u3g_D           44 TNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVP---NLVFVHIP  120 (140)
T ss_dssp             CHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCT---TCEEEECC
T ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCC---cEEEEEcC
Confidence            46789998865      233444    99999999999999999774 342 3   3455555 55433   69999999


Q ss_pred             CCCCCccchHHhHHHHHHhhc
Q psy16693         76 SHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        76 gH~gi~gNe~aD~~A~~a~~~   96 (196)
                      +    ++||.||+||++|+..
T Consensus       121 ~----~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D          121 R----EKNARADELVNEAIDK  137 (140)
T ss_dssp             G----GGGHHHHHHHHHHHHH
T ss_pred             c----hhhHHHHHHHHHHHHh
Confidence            6    9999999999999864

>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=99.30  E-value=1.1e-11  Score=93.34  Aligned_cols=81  Identities=19%  Similarity=0.237  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhccc-CCCh-HHHHHHHHHHhccCCceEEEEecCCCCCCccc
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVS-SSNP-IAREIRNLLDKNKHVFSLHFTWVPSHVGIAGN   83 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~-~~~~-~~~~i~~l~~~~~~~~~v~~~WvpgH~gi~gN   83 (196)
                      +.+.||+.|+.      .+.+..++.|+|||+++++.+.+.| ..++ +...+.++.....+...|.|.|||+    ++|
T Consensus        45 tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N  120 (141)
T 3hst_B           45 TNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARN  120 (141)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGC
T ss_pred             chHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----ccc
Confidence            35788888864      3456789999999999999999865 3444 3333333333333335899999997    999


Q ss_pred             hHHhHHHHHHhhc
Q psy16693         84 EEADRLAKEALSS   96 (196)
Q Consensus        84 e~aD~~A~~a~~~   96 (196)
                      |.||+||++|+..
T Consensus       121 ~~AD~LA~~a~~~  133 (141)
T 3hst_B          121 TYADRLANDAMDA  133 (141)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999999976

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

Probab=99.24  E-value=1.8e-11  Score=93.58  Aligned_cols=77  Identities=19%  Similarity=0.276  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccCC-C----hHHHHHHHHHHhccCCceEEEEecCCCCCC
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSSS-N----PIAREIRNLLDKNKHVFSLHFTWVPSHVGI   80 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~~-~----~~~~~i~~l~~~~~~~~~v~~~WvpgH~gi   80 (196)
                      +...||+.|+.      ...+..++.|+|||+++++.+.++|.. +    ++.+++.+++..+    +|.|.||||    
T Consensus        47 tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~----~v~~~~V~~----  118 (149)
T 2ehg_A           47 TNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL----NATLIWVPR----  118 (149)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH----TCEEEECCG----
T ss_pred             cHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC----CEEEEEcCC----
Confidence            36788988864      345667899999999999999998643 2    3455566666654    499999999    


Q ss_pred             ccchHHhHHHHHHhhc
Q psy16693         81 AGNEEADRLAKEALSS   96 (196)
Q Consensus        81 ~gNe~aD~~A~~a~~~   96 (196)
                      ++|+.||+||++|+..
T Consensus       119 ~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A          119 EENKEADRLSRVAYEL  134 (149)
T ss_dssp             GGCHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHh
Confidence            6999999999999977

>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=97.01  E-value=0.00012  Score=55.73  Aligned_cols=75  Identities=9%  Similarity=0.015  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHH------HhcCCCEEEEecccHHHHHHHhcccCC-C--------hHHHHHHHHHHhccCCceEEEEecCC
Q psy16693         12 IYYQVDLTGTA------EKSECQVYLTPDNSLSALQSIQNVSSS-N--------PIAREIRNLLDKNKHVFSLHFTWVPS   76 (196)
Q Consensus        12 ~~~~~e~~~~~------~~~~~~~i~I~tDs~sal~~l~~~~~~-~--------~~~~~i~~l~~~~~~~~~v~~~Wvpg   76 (196)
                      +-..+|+.|+.      .+... ++.|+|||+++++.+.+.+.+ +        .+.+.+.++..-+. .+.+....|..
T Consensus        50 TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~-~~~~~~~~~kw  127 (142)
T 1zbf_A           50 TNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN-THTYETPILKW  127 (142)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH-HCCCCCCEEEC
T ss_pred             CcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHh-hCCCceeEEEe
Confidence            35677877754      23333 899999999999999987621 1        24444444432221 23577777888


Q ss_pred             CCCCccchHHhH
Q psy16693         77 HVGIAGNEEADR   88 (196)
Q Consensus        77 H~gi~gNe~aD~   88 (196)
                      |++.-||..||-
T Consensus       128 ~~~~~ge~pad~  139 (142)
T 1zbf_A          128 QTDKWGEIKADY  139 (142)
T ss_dssp             CHHHHCSCTTCC
T ss_pred             ccCccCcCcccc
Confidence            999999999984

>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=93.55  E-value=0.16  Score=37.92  Aligned_cols=35  Identities=11%  Similarity=0.032  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHH-----hcCCCEEEEecccHHHHHHHhcc
Q psy16693         12 IYYQVDLTGTAE-----KSECQVYLTPDNSLSALQSIQNV   46 (196)
Q Consensus        12 ~~~~~e~~~~~~-----~~~~~~i~I~tDs~sal~~l~~~   46 (196)
                      +-..+|+.|+..     .....++.|+|||+++++-|.++
T Consensus        44 TNN~aEl~A~i~aL~~l~~~~~~v~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A           44 TNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHHHHHhCCCCEEEEcchHHHHHHHHcC
Confidence            346677777541     12223489999999999999875

---

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	196
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	3e-08
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	6e-07
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	5e-06

>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 = 48.4 bits (114), Expect = 3e-08
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 62  KNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
           +     +++  WVP+H GI GN+E D L  + +
Sbjct: 94  EMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 126

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

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

 Score = 44.9 bits (105), Expect = 6e-07
 Identities = 12/46 (26%), Positives = 17/46 (36%)

Query: 51  PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSS 96
              R++   L        + F +V  H G   NE  DR A+    S
Sbjct: 98  VKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQS 143

>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 = 42.7 bits (99), Expect = 5e-06
 Identities = 13/40 (32%), Positives = 18/40 (45%)

Query: 54  REIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
            ++   LD       + + WV  H G   NE AD LA+ A
Sbjct: 99  VDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAA 138

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	196
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.72
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.57
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.52
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.09
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	98.03

>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=99.72  E-value=9.1e-18  Score=124.31  Aligned_cols=79  Identities=22%  Similarity=0.330  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHH--HhcCCCEEEEecccHHHHHHHhcccC--CChHHH-HHHHHHHhccCCceEEEEecCCCCCCccchHH
Q psy16693         12 IYYQVDLTGTA--EKSECQVYLTPDNSLSALQSIQNVSS--SNPIAR-EIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEA   86 (196)
Q Consensus        12 ~~~~~e~~~~~--~~~~~~~i~I~tDs~sal~~l~~~~~--~~~~~~-~i~~l~~~~~~~~~v~~~WvpgH~gi~gNe~a   86 (196)
                      +.+.||+.|+.  .+.....+.|+|||+++++.+.+++.  .+.... .+..+..    ...|.|.|||||+|++|||.|
T Consensus        43 tnn~AEl~Ai~~al~~~~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~----~~~v~~~wV~gH~g~~gNe~A  118 (126)
T d1mu2a1          43 TNQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIK----KEAIYVAWVPAHKGIGGNQEV  118 (126)
T ss_dssp             CHHHHHHHHHHHHHHTSCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHH----CSEEEEEECCSSSCCTTHHHH
T ss_pred             cchHHHHHHHHHHhccCCcceEEEechHHHHHHHhcCCccccchHHHHHHHHhhh----cceeEEEEEeCCCCCcchHHH
Confidence            36789999876  46677899999999999999999764  333333 3333333    237999999999999999999


Q ss_pred             hHHHHHHh
Q psy16693         87 DRLAKEAL   94 (196)
Q Consensus        87 D~~A~~a~   94 (196)
                      |+||++|.
T Consensus       119 D~LA~~ai  126 (126)
T d1mu2a1         119 DHLVSQGI  126 (126)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHhhC
Confidence            99999874

>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=99.57  E-value=1.3e-15  Score=114.88  Aligned_cols=84  Identities=20%  Similarity=0.167  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHh----cCCCEEEEecccHHHHHHHhcccC----------C--ChH--HHHHHHHHHhccCCceEEEEe
Q psy16693         12 IYYQVDLTGTAEK----SECQVYLTPDNSLSALQSIQNVSS----------S--NPI--AREIRNLLDKNKHVFSLHFTW   73 (196)
Q Consensus        12 ~~~~~e~~~~~~~----~~~~~i~I~tDs~sal~~l~~~~~----------~--~~~--~~~i~~l~~~~~~~~~v~~~W   73 (196)
                      +...||+.|+...    .....+.|+|||+++++++..++.          .  .++  ...+++++... ....|.|.|
T Consensus        42 Tnn~aEl~Ai~~AL~~~~~~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~w  120 (147)
T d1rila_          42 TNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHF  120 (147)
T ss_dssp             CHHHHHHHHHHHHHHSCCSCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCC
T ss_pred             cHHHHHHHHHHHHhhhccCCceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEE
Confidence            4678999987632    345689999999999999876421          1  122  12234443332 235899999


Q ss_pred             cCCCCCCccchHHhHHHHHHhhc
Q psy16693         74 VPSHVGIAGNEEADRLAKEALSS   96 (196)
Q Consensus        74 vpgH~gi~gNe~aD~~A~~a~~~   96 (196)
                      ||||+|++|||.||+||++|+..
T Consensus       121 VkgHsg~~gNe~AD~LAk~aa~~  143 (147)
T d1rila_         121 VKGHTGHPENERVDREARRQAQS  143 (147)
T ss_dssp             CCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             ccCCCCCcchHHHHHHHHHHHHH
Confidence            99999999999999999999987

>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=99.52  E-value=1.4e-14  Score=109.13  Aligned_cols=84  Identities=21%  Similarity=0.269  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHH----hcCCCEEEEecccHHHHHHHhcccC---------C--ChH--HHHHHHHHHhccCCceEEEEecC
Q psy16693         13 YYQVDLTGTAE----KSECQVYLTPDNSLSALQSIQNVSS---------S--NPI--AREIRNLLDKNKHVFSLHFTWVP   75 (196)
Q Consensus        13 ~~~~e~~~~~~----~~~~~~i~I~tDs~sal~~l~~~~~---------~--~~~--~~~i~~l~~~~~~~~~v~~~Wvp   75 (196)
                      ...+|+.|+..    -.....+.|+|||++++..+..+..         .  .++  ...++.+.... ...+|.|+|||
T Consensus        42 nn~aE~~Ai~~Al~~~~~~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~  120 (152)
T d1jl1a_          42 NNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVK  120 (152)
T ss_dssp             HHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECC
T ss_pred             HHHHHHhhhhhhhhhhcccceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEec
Confidence            46788887652    2445678999999999998876521         1  111  12233333332 23589999999


Q ss_pred             CCCCCccchHHhHHHHHHhhcC
Q psy16693         76 SHVGIAGNEEADRLAKEALSSN   97 (196)
Q Consensus        76 gH~gi~gNe~aD~~A~~a~~~~   97 (196)
                      ||+|++|||.||+|||+|+..+
T Consensus       121 gH~g~~gNe~AD~LAk~aa~~~  142 (152)
T d1jl1a_         121 GHAGHPENERADELARAAAMNP  142 (152)
T ss_dssp             SSTTCHHHHHHHHHHHHHHHSC
T ss_pred             ccCCCccHHHHHHHHHHHHhCC
Confidence            9999999999999999999873

>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=99.09  E-value=1.2e-10  Score=83.79  Aligned_cols=63  Identities=21%  Similarity=0.247  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHH--HhcCCCEEEEecccHHHHHHHhcccC--CChHHHHHHHHHHhccCCceEEEEecCCC
Q psy16693         12 IYYQVDLTGTA--EKSECQVYLTPDNSLSALQSIQNVSS--SNPIAREIRNLLDKNKHVFSLHFTWVPSH   77 (196)
Q Consensus        12 ~~~~~e~~~~~--~~~~~~~i~I~tDs~sal~~l~~~~~--~~~~~~~i~~l~~~~~~~~~v~~~WvpgH   77 (196)
                      +...||+.|+.  .+....++.|+|||+++++++..++.  ...+..+|.+.+....   .|.|.|||||
T Consensus        44 TNn~aEl~Avi~aL~~~~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l~~~~---~v~i~WVpgH  110 (110)
T d1s1ta1          44 TNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKE---KVYLAWVPAH  110 (110)
T ss_dssp             CHHHHHHHHHHHHHHHSCSEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHHHHCS---EEEEEECCSS
T ss_pred             cHHHHHHHHHHHHHHhCCCeEEEEEehHHHHHHHhcCccccchHHHHHHHHHHhcCC---ceEEEEeCCC
Confidence            46789999875  56778899999999999999999764  4566777666555533   7999999999

>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=98.03  E-value=4.8e-07  Score=66.55  Aligned_cols=75  Identities=11%  Similarity=0.021  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHH-----hcCCCEEEEecccHHHHHHHhcccCC--------C-hHHHHHHHHHHhccCCceEEEEecCCC
Q psy16693         12 IYYQVDLTGTAE-----KSECQVYLTPDNSLSALQSIQNVSSS--------N-PIAREIRNLLDKNKHVFSLHFTWVPSH   77 (196)
Q Consensus        12 ~~~~~e~~~~~~-----~~~~~~i~I~tDs~sal~~l~~~~~~--------~-~~~~~i~~l~~~~~~~~~v~~~WvpgH   77 (196)
                      |-..+|+.|+..     .....++.|+|||+++++.+.+++..        + .+.+.+.++..... .+.+.+.|+.+|
T Consensus        43 TNN~aEl~A~i~aL~~~~~~~~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk-~h~~~~~~~KW~  121 (132)
T d1zbfa1          43 TNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN-THTYETPILKWQ  121 (132)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH-HCCCCCCEEECC
T ss_pred             chHHHHHHHHHHHHHHhhcCCceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHHH-hCCcCceeEEec
Confidence            456788887641     23346799999999999999886421        1 24444544322221 236899999999


Q ss_pred             CCCccchHHh
Q psy16693         78 VGIAGNEEAD   87 (196)
Q Consensus        78 ~gi~gNe~aD   87 (196)
                      +..-||..||
T Consensus       122 ~~~wG~i~AD  131 (132)
T d1zbfa1         122 TDKWGEIKAD  131 (132)
T ss_dssp             HHHHCSCTTC
T ss_pred             CcccccCCCC
Confidence            9999999998