Psyllid ID: psy4359

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220
Protein Sequence
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLKM
Secondary Structure (PSIPRED)
cHHHHHHHHHHHccccEEEEEccccccccEEEEEEEccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHcccccccHHccccccccccccccccccccHHHHHHHHcHHHHccccccHHHccccHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHcccccEEEEccccccccEEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHHccccccccccEEEEcccHHHHHHHHccccccHHHHHHHHHHHccccccccccHHHHccccccccccccccccccEEEEEEEEEccccccHHHHHccccccccccccccEEEEEEEEccHHHHHHcccccHHHHHHHccHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MIKSSFLEIVSkypqstkiytdaskndssvsaafwspdfsfkvklnpllSICNAELMAILYAVYFILANCLSearnssfllCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLikeenkpwhppqtfsrrdqvTLTRLRightnlthvhlmkkeqppeceicscnltVKHLLKYCLKYqnirdpndlyaclnddttpvLDFIKKTNLKM
Flexible Loop (DISEMBL)
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKeenkpwhppqtfsrrdqvTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLKM
Low Complexity Region (SEG)
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLKM
Disordered region (IsUnstruct)
*****************************VSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIK******
Disordered Region (DISOPRED)
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLK*
Disordered Region (DISEMBL)
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLKM
Disordered Region (DISPRO)
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLKM
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDDTTPVLDFIKKTNLKM
Positional Conservation
no confident homologs detected

---

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	220
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.872	0.407	0.265	1e-16
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.945	0.523	0.276	4e-15
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.859	0.376	0.276	5e-15
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.840	0.708	0.276	4e-14
383864731	833	PREDICTED: protein toll-like [Megachile	0.55	0.145	0.346	4e-13
427791063	1035	Putative tick transposon, partial [Rhipi	0.840	0.178	0.318	5e-13
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.490	0.088	0.382	7e-13
328721829	152	PREDICTED: hypothetical protein LOC10057	0.495	0.717	0.339	2e-12
427778603	1397	Putative tick transposon [Rhipicephalus	0.813	0.128	0.278	1e-11
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.822	0.776	0.304	1e-11

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

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 108/249 (43%), Gaps = 57/249 (22%)

Query: 2   IKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLS----------- 50
           I+S F + + +YP ST  YTD SK++ SV+ +F+S     K+KL   +S           
Sbjct: 6   IRSEFADALDRYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILS 65

Query: 51  ---------------ICNAELMAILY------------AVYFILANCLSEARNSSFLLC- 82
                          IC+  L AI+              V + + +   + +   F+ C 
Sbjct: 66  ALRCVEADNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCP 125

Query: 83  ------TDSLSALQSLQDIFSPNLHTL------------RQIMSLWHEDWNYLIGNKLRL 124
                  + ++   + + + S NL  L            + I S W  +W+    NKL  
Sbjct: 126 SHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNKLHS 185

Query: 125 IKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLK 184
           I     PW P Q   RR+++ L R+RIGHT+ TH ++ + +   EC  C C LTV+H++ 
Sbjct: 186 IHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVCPLTVQHIII 245

Query: 185 YCLKYQNIR 193
            C  + +IR
Sbjct: 246 ECADFLHIR 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 87.4 bits (215), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 77/278 (27%), Positives = 119/278 (42%), Gaps = 70/278 (25%)

Query: 6   FLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYF 65
           F  ++ KYP    IYTD SK++ +V+ AF    +  +  L   +SI  AEL+AI  A+ F
Sbjct: 121 FYNLIDKYP-GINIYTDGSKSNDTVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIF 179

Query: 66  I---------------------LANC-----------------LSEARNSSFLLCTDSLS 87
           I                     L+NC                 + + +   F+ C   + 
Sbjct: 180 IETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVG 239

Query: 88  AL-------QSLQDIFSPNL-----HT-----LRQ-IMSLWHEDWNYLIGNKLRLIKEEN 129
            L       Q+ Q +  P       HT     +R  + SLW  +W+    NKL +I+   
Sbjct: 240 ILGNEVADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDGETDNKLHIIQPVI 299

Query: 130 KPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLKYCL-- 187
             W       RR ++ L   RIGH++LTH +L+++E  P C  C   LTVKH+L  C+  
Sbjct: 300 SEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDF 359

Query: 188 -----KYQNIRDPNDLYACLNDDTTP--VLDFIKKTNL 218
                KY N+     L+    +DT P  +L ++K+  L
Sbjct: 360 EISRRKYFNVFSMRQLF----EDTHPSKILLYLKEIGL 393

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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 107/246 (43%), Gaps = 57/246 (23%)

Query: 1   MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAIL 60
            +K  F  ++ KYP    IYTD SK++++V+ AF    +  +  L   +SI  AEL+AI 
Sbjct: 67  FLKQEFYNLIDKYP-GINIYTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAELIAIE 125

Query: 61  YAVYFI---------------------LANC-----------------LSEARNSSFLLC 82
            A+ FI                     L+NC                 + + +   F+ C
Sbjct: 126 QALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWC 185

Query: 83  TDSLSALQS-LQDIFS-----------PNLHT-----LRQ-IMSLWHEDWNYLIGNKLRL 124
              +  L + + D  +           P  HT     +R  + SLW  +W+    NKL  
Sbjct: 186 PSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHS 245

Query: 125 IKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLK 184
           I+     W       RR ++ L R RIGH++LTH +L+++E  P C  C   LTVKH+L 
Sbjct: 246 IQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILI 305

Query: 185 YCLKYQ 190
            C+ ++
Sbjct: 306 DCIDFK 311

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 103/242 (42%), Gaps = 57/242 (23%)

Query: 1   MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAIL 60
            +K  F  ++ KYP    IYTD SK++ +V+ AF    +  +  L   +SI  AEL+AI 
Sbjct: 21  FLKQEFYNLIDKYP-GINIYTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIE 79

Query: 61  YAVYFI---------------------LANC-----------------LSEARNSSFLLC 82
            A+ FI                     L+NC                 + + +   F+ C
Sbjct: 80  QALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWC 139

Query: 83  TDSLSALQS-LQDIFS-----------PNLHT-----LRQ-IMSLWHEDWNYLIGNKLRL 124
              +  L + + D  +           P  HT     +R  + SLW  +W+    NKL  
Sbjct: 140 PSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHS 199

Query: 125 IKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTVKHLLK 184
           I+     W       RR ++ L R RIGH++LTH +L+++E  P C  C   L+VKH+L 
Sbjct: 200 IQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHILI 259

Query: 185 YC 186
            C
Sbjct: 260 DC 261

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|383864731|ref|XP_003707831.1| PREDICTED: protein toll-like [Megachile rotundata]

 Score = 80.9 bits (198), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 44/127 (34%), Positives = 68/127 (53%), Gaps = 6/127 (4%)

Query: 100 LHTLRQIMSLWHEDWNYLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHV 159
           + T+R++   W+  W      +L  IK          +  RRDQV +TR+ IGHT +TH 
Sbjct: 54  IRTIRKLEENWNNTWIMQCKPRLTTIKGHFYKKIITSSLQRRDQVVITRITIGHTRITHQ 113

Query: 160 HLMKKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDLYACLNDD------TTPVLDFI 213
           +L+ KE+PP C++C  ++TV HL+  C KY   R   D+    ND+      T  +L+F+
Sbjct: 114 YLLTKEEPPICDLCKVSVTVDHLIIQCAKYAADRQKYDIKPAWNDNLKDDKTTQNLLNFL 173

Query: 214 KKTNLKM 220
           K T L +
Sbjct: 174 KDTKLTL 180

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791063|gb|JAA60983.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 80.5 bits (197), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 81/254 (31%), Positives = 110/254 (43%), Gaps = 69/254 (27%)

Query: 2    IKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILY 61
            I + FLE+  KY    + +TDASK +SSVS A   P FS    L+   SI  AE  AI  
Sbjct: 782  IYTYFLELQHKY-TFPEFFTDASKFNSSVSYAAVGPSFSDAGVLHQNTSIFTAEAYAIFV 840

Query: 62   AVYFILANCLSEARNSSFLLCTDSLS---ALQSLQDIFSPNLHTL-----------RQIM 107
            AV  I      + +  S ++ TDSLS   AL++L+   +P L +L           + ++
Sbjct: 841  AVKHI-----EQLKLPSAVIYTDSLSVVKALKTLKKHKNPVLASLYSLLCTVYALKQHVV 895

Query: 108  SLW--------------------HE------------DWNYLIGNKLR------------ 123
              W                    HE            D   L+  KLR            
Sbjct: 896  VCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRKLRAYWQSIWDTQTQ 955

Query: 124  ----LIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLTV 179
                 IK +   W PP + SRR ++TLTRLR GHT+ TH +L+    PP CE C   LTV
Sbjct: 956  NKLHAIKPQLGEW-PPASKSRRTEITLTRLRTGHTHTTHAYLLSGNDPPRCERCGEPLTV 1014

Query: 180  KHLLKYCLKYQNIR 193
             H+L  C +   +R
Sbjct: 1015 LHILIQCNELDAMR 1028

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 44/115 (38%), Positives = 64/115 (55%), Gaps = 7/115 (6%)

Query: 110  WHEDWNYLIGNKLRLIKEENKPWHP-PQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPP 168
            W   W     +KLR I  + + W P  +  +RR   T++RLRIGHT +TH  ++K+E+PP
Sbjct: 1105 WQNRWEAETHSKLRQIVADVR-WRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPP 1163

Query: 169  ECEICSCNLTVKHLLKYCLKYQNIR----DPNDLYACLND-DTTPVLDFIKKTNL 218
             CE C   LTV+H+L  C +YQ++R       +L    N+ D   VL FI +  L
Sbjct: 1164 LCEYCDSRLTVEHILVDCPRYQDVRAKHFRATNLKTLFNNVDPGKVLGFILEVGL 1218

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|328721829|ref|XP_003247415.1| PREDICTED: hypothetical protein LOC100572018 [Acyrthosiphon pisum]

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 67/115 (58%), Gaps = 6/115 (5%)

Query: 104 RQIMSLWHEDWN-YLIGNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLM 162
           + I++ W   W+  L  NKLR++K+    W   +  SRR+Q  + R RIGH+N+TH +L+
Sbjct: 28  KSILASWQNHWDDILTSNKLRIVKKTVSKWTYSENASRREQTIINRARIGHSNITHSYLI 87

Query: 163 KKEQPPECEICSCNLTVKHLLKYCLKYQNIR----DPNDL-YACLNDDTTPVLDF 212
            KE  P C+ C+  LT++H++  C K+ + R    +P+ L  A +  +T  + +F
Sbjct: 88  TKEPRPNCDTCNTPLTIEHIIINCPKFASSRHLLKNPSSLEEALIQVNTGNIFNF 142

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427778603|gb|JAA54753.1| Putative tick transposon [Rhipicephalus pulchellus]

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 100/248 (40%), Gaps = 69/248 (27%)

Query: 1    MIKSSFLEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAIL 60
            +I+  FL +  KY +S   ++D SK+ +SVS A +   FS    L+   SI  AE   IL
Sbjct: 1094 LIQQHFLALEHKY-RSAAFFSDGSKSQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGIL 1152

Query: 61   YAVYFILANCLSEARNSSFLLCTDSLSA------------------LQSLQDIFSPNL-- 100
              V  I  + +  +     ++ TDSLS                   L ++ + ++ NL  
Sbjct: 1153 LIVEHIKQHMIRRS-----IIYTDSLSVVTALSCGKCSKNPVFNKLLNNMHEAYNQNLSI 1207

Query: 101  ---------------------------HTL---------------RQIMSLWHEDWNYLI 118
                                       HT+               R + S W  +W+  +
Sbjct: 1208 VLCWVPGHAGITGNEMVDKNAREAASRHTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQV 1267

Query: 119  GNKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHVHLMKKEQPPECEICSCNLT 178
             NKL L+K        PQ  +R  +VTL RLRIGHT  TH HL+    PP C  C   LT
Sbjct: 1268 DNKLHLVKPHLSKV-LPQKLNRFTEVTLARLRIGHTYATHKHLLTGTDPPTCIHCGETLT 1326

Query: 179  VKHLLKYC 186
            + H+L  C
Sbjct: 1327 ILHVLIEC 1334

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443730613|gb|ELU16038.1| hypothetical protein CAPTEDRAFT_206814 [Capitella teleta]

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 94/210 (44%), Gaps = 29/210 (13%)

Query: 7   LEIVSKYPQSTKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAV--- 63
           L ++S  P    IYTD SK+++ V+    +     +V+L    SI +AEL+AI   +   
Sbjct: 4   LYVISLCPDHLPIYTDGSKSETRVACVATANRLLIQVRLPDSASIFSAELLAIYEVLTLL 63

Query: 64  -------YFILAN---------CLSE----ARNSSFLLCTDSLSALQSLQDIFSPNLHTL 103
                  Y IL N         C S         + LL  ++LS      D+  P     
Sbjct: 64  ECAAPQKYTILYNRGFDLVILWCPSHIGVVGNERADLLAKEALSFTAC--DVRIPAFDFN 121

Query: 104 RQIMSLWHEDWNYLIG----NKLRLIKEENKPWHPPQTFSRRDQVTLTRLRIGHTNLTHV 159
               S + + W  L      NKL  ++   K         RR ++ L R RIGHT+LTH 
Sbjct: 122 SVAYSFYRDKWQALWSLEQNNKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTHLTHG 181

Query: 160 HLMKKEQPPECEICSCNLTVKHLLKYCLKY 189
           +L+++E PP C  C C LTVKH+L  C+ +
Sbjct: 182 YLLRRELPPFCVHCQCPLTVKHILIECVDF 211

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)

No hits with e-value below 0.001 by BLAST

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	220
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	6e-16
pfam00075	126	pfam00075, RNase_H, RNase H	8e-05

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

 Score = 71.1 bits (175), Expect = 6e-16
 Identities = 35/113 (30%), Positives = 48/113 (42%), Gaps = 15/113 (13%)

Query: 19  IYTDASKNDSSVSAAFWSPD---FSFKVKLNPLLSICNAELMAILYAVYFILANCLSEAR 75
           IYTD SK +    A F        S   KL P  S+ +AEL+AIL A+   L       R
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE---GRR 58

Query: 76  NSSFLLCTDSLSALQSLQDIFS---PNLHTLRQIMSLWHEDWNYLIGNKLRLI 125
                + +DS +AL++L+   S     L   + I  L         G K+RL 
Sbjct: 59  ARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIREL------ANHGVKVRLH 105

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 = 40.7 bits (96), Expect = 8e-05
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 14/83 (16%)

Query: 14 PQSTKIYTDAS--KNDSSVSAAFWSPDFSFKVKLNPLLSICN--AELMAILYAVYFILAN 69
          P++  +YTD S   N     A + +     K +  PL    N  AEL+A++ A       
Sbjct: 1  PEAVTVYTDGSCNGNPGPGGAGYVTDGG--KQRSKPLPGTTNQRAELLALIEA------- 51

Query: 70 CLSEARNSSFLLCTDSLSALQSL 92
           L         + TDS   +  +
Sbjct: 52 -LEALSGQKVNIYTDSQYVIGGI 73

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	220
PRK06548	161	ribonuclease H; Provisional	99.35
PRK08719	147	ribonuclease H; Reviewed	99.28
PRK00203	150	rnhA ribonuclease H; Reviewed	99.24
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.23
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.16
PRK13907	128	rnhA ribonuclease H; Provisional	98.98
KOG3752|consensus	371		98.97
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.91
PRK07708	219	hypothetical protein; Validated	98.65
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	98.47
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.39
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.77
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	93.48
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	84.38

>PRK06548 ribonuclease H; Provisional

Probab=99.35  E-value=2.1e-12  Score=104.75  Aligned_cols=89  Identities=18%  Similarity=0.185  Sum_probs=66.4

Q ss_pred             CCceeeeecCCCCC--CcceeeeeCCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHh
Q psy4359          14 PQSTKIYTDASKND--SSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQS   91 (220)
Q Consensus        14 ~~~~~IyTDgSk~~--~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~a   91 (220)
                      +..+.||||||...  +..|+|++..+.....+.....|.+.||++|++.||+.+..      ...++.|+|||++|+++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~   76 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINS   76 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHH
Confidence            45689999999874  34778766333222334445679999999999999986543      24579999999999999


Q ss_pred             hhhhhCCChHhHHHHHHhhh-hccchhhc
Q psy4359          92 LQDIFSPNLHTLRQIMSLWH-EDWNYLIG  119 (220)
Q Consensus        92 i~~~~~P~~~Di~~I~~~Wq-~~W~~~~~  119 (220)
                      +..+           ...|+ +.|+.+.+
T Consensus        77 i~~W-----------~~~Wk~~gWk~s~G   94 (161)
T PRK06548         77 LTKW-----------VYSWKMRKWRKADG   94 (161)
T ss_pred             HHHH-----------HHHHHHCCCcccCC
Confidence            9998           88895 48876544

>PRK08719 ribonuclease H; Reviewed

Probab=99.28  E-value=7.5e-12  Score=100.11  Aligned_cols=84  Identities=15%  Similarity=0.266  Sum_probs=63.7

Q ss_pred             CceeeeecCCCCCCc-----ceeeee--CCCc----ceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEec
Q psy4359          15 QSTKIYTDASKNDSS-----VSAAFW--SPDF----SFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCT   83 (220)
Q Consensus        15 ~~~~IyTDgSk~~~~-----~G~ai~--~~~~----~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~s   83 (220)
                      ..+.||||||+..++     .|+|++  .++.    .....+.+..|.++||+.||..||+.+.+.         ..|+|
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~t   73 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIYS   73 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEEe
Confidence            568999999997543     477754  3322    123446666899999999999999997643         37999


Q ss_pred             cchHHHHhhhhhhCCChHhHHHHHHhhh-hccchhh
Q psy4359          84 DSLSALQSLQDIFSPNLHTLRQIMSLWH-EDWNYLI  118 (220)
Q Consensus        84 DS~sal~ai~~~~~P~~~Di~~I~~~Wq-~~W~~~~  118 (220)
                      ||++++++++.+           ...|+ +.|..+.
T Consensus        74 DS~yvi~~i~~~-----------~~~W~~~~w~~s~   98 (147)
T PRK08719         74 DSDYCVRGFNEW-----------LDTWKQKGWRKSD   98 (147)
T ss_pred             chHHHHHHHHHH-----------HHHHHhCCcccCC
Confidence            999999999988           88894 5887643

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.24  E-value=1.7e-11  Score=97.99  Aligned_cols=85  Identities=20%  Similarity=0.184  Sum_probs=62.6

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCcc-eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDFS-FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~-~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      +.+.||||||...+  ..|+|++  .++.. ...+..+..|...||+.||+.||+.+..       ...+.|+|||++++
T Consensus         2 ~~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi   74 (150)
T PRK00203          2 KQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVR   74 (150)
T ss_pred             ceEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHH
Confidence            35899999998743  3666644  33322 2334445788899999999999998743       35799999999999


Q ss_pred             HhhhhhhCCChHhHHHHHHhhhh-ccchh
Q psy4359          90 QSLQDIFSPNLHTLRQIMSLWHE-DWNYL  117 (220)
Q Consensus        90 ~ai~~~~~P~~~Di~~I~~~Wq~-~W~~~  117 (220)
                      ++|..+           ...|+. .|...
T Consensus        75 ~~i~~w-----------~~~Wk~~~~~~~   92 (150)
T PRK00203         75 QGITEW-----------IHGWKKNGWKTA   92 (150)
T ss_pred             HHHHHH-----------HHHHHHcCCccc
Confidence            999887           667854 68753

>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=99.23  E-value=1.6e-11  Score=94.70  Aligned_cols=72  Identities=28%  Similarity=0.242  Sum_probs=54.3

Q ss_pred             CceeeeecCCCC--CCcceee-eeCCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHh
Q psy4359          15 QSTKIYTDASKN--DSSVSAA-FWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQS   91 (220)
Q Consensus        15 ~~~~IyTDgSk~--~~~~G~a-i~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~a   91 (220)
                      +++.||||||..  .+..|+| ++..+......++ ..|++.||+.||.+||+.+  .      ..+++|+|||++++.+
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--~------~~~v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--E------HRKVTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--S------TSEEEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--h------cccccccccHHHHHHH
Confidence            578999999965  3334555 3444434445566 8999999999999999944  4      3889999999999998


Q ss_pred             hhhh
Q psy4359          92 LQDI   95 (220)
Q Consensus        92 i~~~   95 (220)
                      +..+
T Consensus        73 l~~~   76 (132)
T PF00075_consen   73 LNKW   76 (132)
T ss_dssp             HHTH
T ss_pred             HHHh
Confidence            8774

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

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

Probab=99.16  E-value=1.1e-10  Score=93.70  Aligned_cols=75  Identities=17%  Similarity=0.058  Sum_probs=59.0

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCcc--eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDFS--FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA   88 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sa   88 (220)
                      ..+.||||||+..+  -.|+|+|  +++..  .+.+.. .+|.+.||+.|+++||+++.+.     +...+.|+|||+++
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv   75 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYV   75 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHH
Confidence            46899999998743  3556644  34433  334444 8999999999999999999875     68899999999999


Q ss_pred             HHhhhhh
Q psy4359          89 LQSLQDI   95 (220)
Q Consensus        89 l~ai~~~   95 (220)
                      +++|..+
T Consensus        76 ~~~i~~w   82 (154)
T COG0328          76 VEGITRW   82 (154)
T ss_pred             HHHHHHH
Confidence            9999844

>PRK13907 rnhA ribonuclease H; Provisional

Probab=98.98  E-value=1.7e-09  Score=83.74  Aligned_cols=75  Identities=16%  Similarity=0.177  Sum_probs=57.5

Q ss_pred             eeeeecCCCCC--Ccceeeee--CCCccee-eecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHh
Q psy4359          17 TKIYTDASKND--SSVSAAFW--SPDFSFK-VKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQS   91 (220)
Q Consensus        17 ~~IyTDgSk~~--~~~G~ai~--~~~~~~~-~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~a   91 (220)
                      ++||||||...  +..|+|++  +...... .+.....|...||+.|++.||+.+...     ...++.|+|||+.++..
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~   76 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA   76 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence            57999999864  45777755  2222212 222345788999999999999999986     56789999999999999


Q ss_pred             hhhhh
Q psy4359          92 LQDIF   96 (220)
Q Consensus        92 i~~~~   96 (220)
                      +++.+
T Consensus        77 ~~~~~   81 (128)
T PRK13907         77 VEKEY   81 (128)
T ss_pred             HhHHH
Confidence            99864

>KOG3752|consensus

Probab=98.97  E-value=1.2e-09  Score=97.81  Aligned_cols=76  Identities=20%  Similarity=0.143  Sum_probs=63.2

Q ss_pred             CceeeeecCCCCCC-----cceeeeeCCC---cceeeecc-hhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccc
Q psy4359          15 QSTKIYTDASKNDS-----SVSAAFWSPD---FSFKVKLN-PLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDS   85 (220)
Q Consensus        15 ~~~~IyTDgSk~~~-----~~G~ai~~~~---~~~~~~l~-~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS   85 (220)
                      +.+++|||||...+     .+|+||+.++   ......+. .-.+.|.||+.||.+||+-+.+.     +..++.|.|||
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~~~kv~I~TDS  285 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----NINKVVIRTDS  285 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----CCCcEEEEech
Confidence            34899999999864     3899998543   24456665 77899999999999999999886     57799999999


Q ss_pred             hHHHHhhhhh
Q psy4359          86 LSALQSLQDI   95 (220)
Q Consensus        86 ~sal~ai~~~   95 (220)
                      +..+++|+.+
T Consensus       286 ~~~i~~l~~w  295 (371)
T KOG3752|consen  286 EYFINSLTLW  295 (371)
T ss_pred             HHHHHHHHHH
Confidence            9999999877

>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=98.91  E-value=3.9e-09  Score=78.48  Aligned_cols=75  Identities=24%  Similarity=0.225  Sum_probs=58.5

Q ss_pred             eeeecCCCCCC--cceeeee--CCCccee---eecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHH
Q psy4359          18 KIYTDASKNDS--SVSAAFW--SPDFSFK---VKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQ   90 (220)
Q Consensus        18 ~IyTDgSk~~~--~~G~ai~--~~~~~~~---~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~   90 (220)
                      .+|||||...+  +.|+|++  .++....   .......|++.||+.|++.||+++...     ...++.|++||+.++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~   75 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN   75 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence            48999998765  5777755  3332222   222257899999999999999999865     6899999999999999


Q ss_pred             hhhhhhC
Q psy4359          91 SLQDIFS   97 (220)
Q Consensus        91 ai~~~~~   97 (220)
                      .+.+...
T Consensus        76 ~~~~~~~   82 (130)
T cd06222          76 ALTGWYE   82 (130)
T ss_pred             Hhhcccc
Confidence            9998754

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.

>PRK07708 hypothetical protein; Validated

Probab=98.65  E-value=7.8e-08  Score=81.74  Aligned_cols=84  Identities=14%  Similarity=0.127  Sum_probs=62.3

Q ss_pred             hhCCCceeeeecCCCC--CCcceeeee--CCCc--ce----eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccC--c
Q psy4359          11 SKYPQSTKIYTDASKN--DSSVSAAFW--SPDF--SF----KVKLNPLLSICNAELMAILYAVYFILANCLSEARNS--S   78 (220)
Q Consensus        11 ~~~~~~~~IyTDgSk~--~~~~G~ai~--~~~~--~~----~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~--~   78 (220)
                      +.-|+...+|+|||..  .++.|+|++  .+..  ..    ...+....|.+.||+.|++.||+.+...     +.+  .
T Consensus        68 ~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~~~  142 (219)
T PRK07708         68 EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKHEP  142 (219)
T ss_pred             ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCcce
Confidence            3466789999999974  345777743  3322  11    1356666899999999999999999886     333  4


Q ss_pred             eEEeccchHHHHhhhhhhCCC
Q psy4359          79 FLLCTDSLSALQSLQDIFSPN   99 (220)
Q Consensus        79 ~~I~sDS~sal~ai~~~~~P~   99 (220)
                      +.|++||+.+++.+.+.|...
T Consensus       143 V~I~~DSqlVi~qi~g~wk~~  163 (219)
T PRK07708        143 VTFRGDSQVVLNQLAGEWPCY  163 (219)
T ss_pred             EEEEeccHHHHHHhCCCceeC
Confidence            899999999999999876543

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=98.47  E-value=4.1e-07  Score=82.63  Aligned_cols=80  Identities=8%  Similarity=-0.026  Sum_probs=60.2

Q ss_pred             ceeeeecCCCCCC--cceeeee--CCCc--c--eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchH
Q psy4359          16 STKIYTDASKNDS--SVSAAFW--SPDF--S--FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLS   87 (220)
Q Consensus        16 ~~~IyTDgSk~~~--~~G~ai~--~~~~--~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~s   87 (220)
                      .+.||||||...+  ..|+|++  +++.  .  ...+....+|.+.||+.|++.||+++.+.     ...++.|++||+.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~l   76 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSKL   76 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcHH
Confidence            4689999998754  4677744  4322  1  12233336788999999999999999886     5778999999999


Q ss_pred             HHHhhhhhhCCCh
Q psy4359          88 ALQSLQDIFSPNL  100 (220)
Q Consensus        88 al~ai~~~~~P~~  100 (220)
                      +++.+.+.+...+
T Consensus        77 vi~~i~~~~~~~~   89 (372)
T PRK07238         77 VVEQMSGRWKVKH   89 (372)
T ss_pred             HHHHhCCCCccCC
Confidence            9999988765444

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

Probab=97.39  E-value=0.0002  Score=50.64  Aligned_cols=42  Identities=19%  Similarity=0.175  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHhhhhhhCC
Q psy4359          52 CNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSP   98 (220)
Q Consensus        52 ~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~ai~~~~~P   98 (220)
                      ..||+.|++.||+++.+.     +..+++|.|||+.++..|++...+
T Consensus         2 ~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~i~~~~~~   43 (87)
T PF13456_consen    2 LEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDAINGRSSS   43 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHHHTTSS--
T ss_pred             cHHHHHHHHHHHHHHHHC-----CCCEEEEEecCccccccccccccc
Confidence            579999999999999887     689999999999999999988543

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

Probab=96.77  E-value=0.00023  Score=51.46  Aligned_cols=46  Identities=24%  Similarity=0.364  Sum_probs=33.7

Q ss_pred             EEeEEeeccccc-ce--eeecccCCCCccceec-ccccHHHHHHHHHhcc
Q psy4359         145 TLTRLRIGHTNL-TH--VHLMKKEQPPECEICS-CNLTVKHLLKYCLKYQ  190 (220)
Q Consensus       145 ~l~rlRtGH~~l-~h--~~~~~~~~~p~C~~Cg-~~eTv~HiL~~Cp~~~  190 (220)
                      .+.--|.-|.++ +-  +.+.+...++.|..|+ ++||++|++++||...
T Consensus        34 ~~f~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   34 KFFLWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             EEEeeeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence            344445556663 32  4556778899999999 5899999999999754

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

Probab=93.48  E-value=0.22  Score=40.00  Aligned_cols=53  Identities=26%  Similarity=0.279  Sum_probs=36.1

Q ss_pred             CceeeeecCCCCCCcceeeee---CCCcc----e-----eeecchhhhhhhHHHHHHHHHHHHHHHh
Q psy4359          15 QSTKIYTDASKNDSSVSAAFW---SPDFS----F-----KVKLNPLLSICNAELMAILYAVYFILAN   69 (220)
Q Consensus        15 ~~~~IyTDgSk~~~~~G~ai~---~~~~~----~-----~~~l~~~~si~~AEl~AI~~AL~~~~~~   69 (220)
                      ..+++|+|+|+  .+.|+.+|   ..+..    .     ........||=.-|+.|++.|.+++...
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~  144 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTV  144 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence            46899999994  45555554   12211    1     1333335599999999999999998774

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

Probab=84.38  E-value=0.74  Score=38.88  Aligned_cols=61  Identities=23%  Similarity=0.215  Sum_probs=38.7

Q ss_pred             ceeeeecCCCCCCcceeeeeCCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHH
Q psy4359          16 STKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQ   90 (220)
Q Consensus        16 ~~~IyTDgSk~~~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~   90 (220)
                      --.||+|+.-..+++  ++-.......|  ..---|.+||++|...|.-++...          .|.|||.-++.
T Consensus        94 lc~VfaDATpTgwgi--~i~~~~~~~Tf--s~~l~IhtaELlaaClAr~~~~~r----------~l~tDnt~Vls  154 (245)
T PF00336_consen   94 LCQVFADATPTGWGI--SITGQRMRGTF--SKPLPIHTAELLAACLARLMSGAR----------CLGTDNTVVLS  154 (245)
T ss_pred             CCceeccCCCCccee--eecCceeeeee--cccccchHHHHHHHHHHHhccCCc----------EEeecCcEEEe
Confidence            347899987664433  22222222222  223458999999999888776544          59999987763

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	220
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

>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 = 39.5 bits (91), Expect = 7e-04
 Identities = 30/156 (19%), Positives = 49/156 (31%), Gaps = 37/156 (23%)

Query: 61  YAVYFI-LANCLSEARNSSFLLCTDSLSALQSLQDIFSPNLHTLRQIMSLWHEDWNYLIG 119
           + ++++ L NC S             L  LQ L     PN  +     S      + +  
Sbjct: 182 FKIFWLNLKNCNSP---------ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 120 NKLRLIKEENKP---------WHPP--QTFSRRDQVTL-TRLR-----IGHTNLTHVHLM 162
              RL+K +             +      F+   ++ L TR +     +     TH+ L 
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 163 KKEQPPECEICSCNLTVKHLLKYCLKYQNIRDPNDL 198
                         LT   +    LKY + R P DL
Sbjct: 293 HHSMT---------LTPDEVKSLLLKYLDCR-PQDL 318

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	220
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.44
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.3
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.3
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.3
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.29
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.25
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.23
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.21
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.2
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.18
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.13
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.1
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.06
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.02
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.76
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.73
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	93.45
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	90.33

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

Probab=99.44  E-value=1.9e-13  Score=108.29  Aligned_cols=87  Identities=15%  Similarity=0.227  Sum_probs=68.7

Q ss_pred             CceeeeecCCCCCCc-----ceeeeeCCC--c-ceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccch
Q psy4359          15 QSTKIYTDASKNDSS-----VSAAFWSPD--F-SFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSL   86 (220)
Q Consensus        15 ~~~~IyTDgSk~~~~-----~G~ai~~~~--~-~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~   86 (220)
                      +.+.||||||...++     .|+|++..+  . .....++..+|++.||+.|++.||+.+.+.     ...++.|+|||+
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~-----~~~~v~i~tDS~   80 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQ-----NINKLVLYTNSM   80 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHT-----TCCEEEEEESCH
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhC-----CCceEEEEECcH
Confidence            568999999987432     688876332  2 234556667899999999999999999875     568999999999


Q ss_pred             HHHHhhhhhhCCChHhHHHHHHhhh-hccchh
Q psy4359          87 SALQSLQDIFSPNLHTLRQIMSLWH-EDWNYL  117 (220)
Q Consensus        87 sal~ai~~~~~P~~~Di~~I~~~Wq-~~W~~~  117 (220)
                      +++++|..+           ...|+ +.|...
T Consensus        81 ~vi~~i~~~-----------~~~w~~~~w~~~  101 (154)
T 2qkb_A           81 FTINGITNW-----------VQGWKKNGWKTS  101 (154)
T ss_dssp             HHHHHHHTH-----------HHHHHTTTSBCT
T ss_pred             HHHhhhhhh-----------HHHHHhcccccc
Confidence            999999988           77885 478753

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

Probab=99.30  E-value=1.4e-12  Score=102.11  Aligned_cols=85  Identities=16%  Similarity=0.230  Sum_probs=62.9

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      +.+.||||||...+  ..|+|++  .++... ..+..+.+|++.||+.|++.||+.+.+       ..++.|+|||++++
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~-------~~~v~I~tDS~~vi   75 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKE-------PARVQLYSDSAYLV   75 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS-------CCEEEEEESCHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCc-------cCcEEEEeChHHHH
Confidence            57899999998753  3777755  333222 233335788999999999999999753       57899999999999


Q ss_pred             Hhhhh-hhCCChHhHHHHHHhhh-hccchh
Q psy4359          90 QSLQD-IFSPNLHTLRQIMSLWH-EDWNYL  117 (220)
Q Consensus        90 ~ai~~-~~~P~~~Di~~I~~~Wq-~~W~~~  117 (220)
                      ++|.. +           ...|+ +.|..+
T Consensus        76 ~~i~~~w-----------~~~W~~~~w~~~   94 (146)
T 3h08_A           76 NAMNEGW-----------LKRWVKNGWKTA   94 (146)
T ss_dssp             HHHHSSH-----------HHHHHHTTCC--
T ss_pred             HHHHHHH-----------HHHHHHCCCccC
Confidence            99998 6           66774 467653

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

Probab=99.30  E-value=2e-12  Score=99.33  Aligned_cols=84  Identities=15%  Similarity=0.071  Sum_probs=62.6

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCc-c--eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccC----ceEEec
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDF-S--FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNS----SFLLCT   83 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~-~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~----~~~I~s   83 (220)
                      +.+.||||||...+  ..|+|++  .++. .  ...+..+.+|++.||+.|++.||+++.+.     ...    ++.|+|
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~-----~~~~~~~~v~i~t   76 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMF-----GDKLVDMEVEVRM   76 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGG-----GGGGTTCEEEEEE
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHc-----CCCCCCceEEEEe
Confidence            46899999998753  4777755  3222 1  22333345799999999999999999875     345    999999


Q ss_pred             cchHHHHhhhhhhCCChHhH
Q psy4359          84 DSLSALQSLQDIFSPNLHTL  103 (220)
Q Consensus        84 DS~sal~ai~~~~~P~~~Di  103 (220)
                      ||+++++.+++.+...+.++
T Consensus        77 DS~~vi~~i~~~~~~~~~~l   96 (140)
T 3u3g_D           77 DSELIVRQMQGVYKVKEPTL   96 (140)
T ss_dssp             SCHHHHHHHTTSSCCCCGGG
T ss_pred             ChHHHHHHhCCCcccCCHHH
Confidence            99999999998775554444

>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=3.2e-12  Score=98.71  Aligned_cols=83  Identities=10%  Similarity=-0.018  Sum_probs=63.9

Q ss_pred             ceeeeecCCCCCC--cceeeee--CCC--cc--eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchH
Q psy4359          16 STKIYTDASKNDS--SVSAAFW--SPD--FS--FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLS   87 (220)
Q Consensus        16 ~~~IyTDgSk~~~--~~G~ai~--~~~--~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~s   87 (220)
                      .+.||||||...+  ..|+|++  .++  ..  ...+..+.+|++.||+.|++.||+++.+.     ...++.|+|||+.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~-----~~~~v~i~tDS~~   77 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKL-----GATEAAVLMDSKL   77 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHH-----TCSEEEEEESCHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHC-----CCceEEEEeChHH
Confidence            5789999998743  4677754  332  11  22333347899999999999999999886     5789999999999


Q ss_pred             HHHhhhhhhCCChHhH
Q psy4359          88 ALQSLQDIFSPNLHTL  103 (220)
Q Consensus        88 al~ai~~~~~P~~~Di  103 (220)
                      +++.++..|.+.+.++
T Consensus        78 vv~~i~~~~~~~~~~l   93 (141)
T 3hst_B           78 VVEQMSGRWKVKHPDL   93 (141)
T ss_dssp             HHHHHTTSSCCCSHHH
T ss_pred             HHHHHhCCcccCCHHH
Confidence            9999998776666666

>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=99.29  E-value=7.1e-12  Score=98.70  Aligned_cols=77  Identities=16%  Similarity=0.042  Sum_probs=56.4

Q ss_pred             CCceeeeecCCCCCCcceeeee--CCCcce--ee-ec--ch--hhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEecc
Q psy4359          14 PQSTKIYTDASKNDSSVSAAFW--SPDFSF--KV-KL--NP--LLSICNAELMAILYAVYFILANCLSEARNSSFLLCTD   84 (220)
Q Consensus        14 ~~~~~IyTDgSk~~~~~G~ai~--~~~~~~--~~-~l--~~--~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sD   84 (220)
                      ++.+.||||||+..+..|+|++  ..+...  .. +.  +.  ..|++.||+.|++.||+++.+.     +. ++.|+||
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~-----~~-~v~I~tD   77 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQL-----GV-KIRILHD   77 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHH-----TC-CCCBSSC
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHC-----CC-eEEEEEC
Confidence            3568999999999877888855  333222  22 22  32  3689999999999999998776     34 9999999


Q ss_pred             chHHHHhhhhhh
Q psy4359          85 SLSALQSLQDIF   96 (220)
Q Consensus        85 S~sal~ai~~~~   96 (220)
                      |+.+.+-+.+.|
T Consensus        78 S~~i~~w~~~~w   89 (147)
T 2kq2_A           78 YAGIAFWATGEW   89 (147)
T ss_dssp             CSTHHHHTTSSS
T ss_pred             cHHHHHHHhCCC
Confidence            987766555443

>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=99.25  E-value=4.4e-12  Score=100.60  Aligned_cols=86  Identities=17%  Similarity=0.144  Sum_probs=63.8

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      ..+.||||||...+  ..|+|++  .++... ..+..+.+|++.||+.|++.||+.+.+       ..++.|+|||++++
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~~~~-------~~~v~I~tDS~~vi   75 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE-------HAEVILSTDSQYVR   75 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS-------CCEEEEEECCHHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCCCCCcHHHHHHHHHHHHHHHhCc-------CCcEEEEeCHHHHH
Confidence            46889999999753  3677755  333221 222225678999999999999998753       37899999999999


Q ss_pred             HhhhhhhCCChHhHHHHHHhhhh-ccchhh
Q psy4359          90 QSLQDIFSPNLHTLRQIMSLWHE-DWNYLI  118 (220)
Q Consensus        90 ~ai~~~~~P~~~Di~~I~~~Wq~-~W~~~~  118 (220)
                      ++|..+           ...|+. .|..+.
T Consensus        76 ~~i~~w-----------~~~W~~n~~~~~~   94 (155)
T 1jl1_A           76 QGITQW-----------IHNWKKRGWKTAD   94 (155)
T ss_dssp             HHHHTT-----------HHHHHHTTTBCTT
T ss_pred             HHHHHH-----------HHHHhhccccccc
Confidence            999997           667854 787643

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

Probab=99.23  E-value=6.5e-12  Score=100.01  Aligned_cols=85  Identities=18%  Similarity=0.156  Sum_probs=62.8

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      ..+.||||||...+  ..|+|++  .++... ..+..+.+|++.||+.|++.||+.+.+       ..++.|+|||++++
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl~A~~~AL~~~~~-------~~~v~I~tDS~~vi   77 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFSLTTNNRMELLAPIVALEALKE-------PCKIILTSDSQYMR   77 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS-------CCEEEEEECCHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCcCCCccHHHHHHHHHHHHHHhcc-------CCeEEEEeCHHHHH
Confidence            56899999999743  3677755  333221 222224688999999999999998632       37899999999999


Q ss_pred             HhhhhhhCCChHhHHHHHHhhhh-ccchh
Q psy4359          90 QSLQDIFSPNLHTLRQIMSLWHE-DWNYL  117 (220)
Q Consensus        90 ~ai~~~~~P~~~Di~~I~~~Wq~-~W~~~  117 (220)
                      ++|..+           ...|+. .|..+
T Consensus        78 ~~i~~w-----------~~~W~~n~~~~~   95 (158)
T 2e4l_A           78 QGIMTW-----------IHGWKKKGWMTS   95 (158)
T ss_dssp             HHHHTH-----------HHHHHHTTTBCT
T ss_pred             HHHHHH-----------HHHHHHcccccc
Confidence            999987           666854 78653

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

Probab=99.21  E-value=7e-12  Score=100.70  Aligned_cols=85  Identities=14%  Similarity=0.098  Sum_probs=62.9

Q ss_pred             CceeeeecCCCCCC--cceeeee--CCCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--SPDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      ..+.||||||+..+  ..|+|++  ..+... ..+..+.+|++.||+.|++.||+.+.+       ..++.|+|||++++
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~-------~~~v~I~tDS~~vi   79 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-------PCEVDLYTDSHYLK   79 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS-------CCEEEEECCCHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc-------CCeEEEEeChHHHH
Confidence            46899999999753  3677755  333221 222234688999999999999998643       35899999999999


Q ss_pred             Hhhhh-hhCCChHhHHHHHHhhhh-ccchh
Q psy4359          90 QSLQD-IFSPNLHTLRQIMSLWHE-DWNYL  117 (220)
Q Consensus        90 ~ai~~-~~~P~~~Di~~I~~~Wq~-~W~~~  117 (220)
                      ++|.. +           ...|+. .|..+
T Consensus        80 ~~i~~~w-----------~~~W~~~~w~~~   98 (166)
T 1ril_A           80 KAFTEGW-----------LEGWRKRGWRTA   98 (166)
T ss_dssp             HHHHSSH-----------HHHHHHTTSBCT
T ss_pred             HHHhhhH-----------HHHHHhcccccc
Confidence            99998 7           667854 68753

>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=99.20  E-value=2.2e-11  Score=96.33  Aligned_cols=85  Identities=21%  Similarity=0.210  Sum_probs=59.8

Q ss_pred             hCCCceeeeecCCCCCC--cceeeee-CCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHH
Q psy4359          12 KYPQSTKIYTDASKNDS--SVSAAFW-SPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA   88 (220)
Q Consensus        12 ~~~~~~~IyTDgSk~~~--~~G~ai~-~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sa   88 (220)
                      ..++.+.||||||+..+  ..|+|++ ..+....+.+ +.+|++.||+.|++.||+.+         ..++.|+|||+++
T Consensus         8 P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~---------~~~v~i~tDS~~v   77 (150)
T 3qio_A            8 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYA   77 (150)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS---------CSEEEEEESCHHH
T ss_pred             CCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeCcHHH
Confidence            44567999999998643  2566644 3333333444 57899999999999999973         3789999999999


Q ss_pred             HHhhhhhhCCChHhHHHHHHhhh-hccchh
Q psy4359          89 LQSLQDIFSPNLHTLRQIMSLWH-EDWNYL  117 (220)
Q Consensus        89 l~ai~~~~~P~~~Di~~I~~~Wq-~~W~~~  117 (220)
                      +++|+.+           ...|+ +.|..+
T Consensus        78 ~~~i~~w-----------~~~W~~~gw~~~   96 (150)
T 3qio_A           78 LGIITQW-----------IHNWKKRGWKTA   96 (150)
T ss_dssp             HHHHHHH-----------HHHHCC------
T ss_pred             HHHHHHH-----------HHHHhhcCcCcC
Confidence            9999987           66784 478764

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

Probab=99.18  E-value=2.4e-11  Score=97.76  Aligned_cols=87  Identities=18%  Similarity=0.142  Sum_probs=54.2

Q ss_pred             CceeeeecCCCCCC-c------ceeeee--CC-Ccceeeecchh----hhhhhHHHHHHHHHHHHHHHhhhhhhccCceE
Q psy4359          15 QSTKIYTDASKNDS-S------VSAAFW--SP-DFSFKVKLNPL----LSICNAELMAILYAVYFILANCLSEARNSSFL   80 (220)
Q Consensus        15 ~~~~IyTDgSk~~~-~------~G~ai~--~~-~~~~~~~l~~~----~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~   80 (220)
                      ..++||||||+..+ +      .|+||+  .. ......+-...    .+...||+.|+..||+.+.+.      ..++.
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~------~~~v~   79 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI------PGPVL   79 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS------SSCEE
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC------CCeEE
Confidence            34789999998643 2      678865  22 22222221222    333445555555555544443      56899


Q ss_pred             EeccchHHHHhhhhhhCCChHhHHHHHHhhh-hccchhh
Q psy4359          81 LCTDSLSALQSLQDIFSPNLHTLRQIMSLWH-EDWNYLI  118 (220)
Q Consensus        81 I~sDS~sal~ai~~~~~P~~~Di~~I~~~Wq-~~W~~~~  118 (220)
                      |+|||++++++|..+           ...|+ +.|..+.
T Consensus        80 I~TDS~Yvi~~it~w-----------~~~Wk~ngw~~~~  107 (165)
T 2lsn_A           80 VITDSFYVAESANKE-----------LPYWKSNGFVNNK  107 (165)
T ss_dssp             EEESCHHHHHHHHTH-----------HHHHHHTTSCSCS
T ss_pred             EEeChHHHHhhhhhh-----------hhhheeccccccC
Confidence            999999999999888           77785 4787643

>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=99.13  E-value=4.8e-11  Score=95.99  Aligned_cols=69  Identities=23%  Similarity=0.128  Sum_probs=54.1

Q ss_pred             ceeeeecCCCCC--Ccceee--eeCCCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHH
Q psy4359          16 STKIYTDASKND--SSVSAA--FWSPDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQ   90 (220)
Q Consensus        16 ~~~IyTDgSk~~--~~~G~a--i~~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~   90 (220)
                      .+.||||||+..  |..|+|  ++.++... ..+++..+|++.||+.|++.||+++  .      ..++.|+|||+++++
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~--~------~~~v~I~tDS~~vi~   94 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA--E------GKKLNVYTDSRYAFA   94 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT--B------TSEEEEEECCHHHHH
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc--c------CceEEEEEchHHHHh
Confidence            489999999973  435555  44444332 2356778899999999999999987  2      578999999999999


Q ss_pred             hh
Q psy4359          91 SL   92 (220)
Q Consensus        91 ai   92 (220)
                      +|
T Consensus        95 ~i   96 (165)
T 3p1g_A           95 TA   96 (165)
T ss_dssp             HH
T ss_pred             hh
Confidence            88

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

Probab=99.10  E-value=1.1e-10  Score=91.46  Aligned_cols=76  Identities=13%  Similarity=0.056  Sum_probs=58.0

Q ss_pred             eeeeecCCCC--C-Cccee-eee--CCCcce-eee--cc---hhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEecc
Q psy4359          17 TKIYTDASKN--D-SSVSA-AFW--SPDFSF-KVK--LN---PLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTD   84 (220)
Q Consensus        17 ~~IyTDgSk~--~-~~~G~-ai~--~~~~~~-~~~--l~---~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sD   84 (220)
                      +.||||||..  + +..|+ |++  +.+... .++  ..   +.+|++.||+.|++.||+.+.+.     ...++.|+||
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~-----g~~~v~i~tD   76 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRL-----GISSPIIKGD   76 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHH-----TCCSCEEEES
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHc-----CCCEEEEEeC
Confidence            5799999987  2 45664 643  433222 222  22   37889999999999999999886     5689999999


Q ss_pred             chHHHHhhhhhhC
Q psy4359          85 SLSALQSLQDIFS   97 (220)
Q Consensus        85 S~sal~ai~~~~~   97 (220)
                      |+.+++.++++|.
T Consensus        77 S~~vi~~i~~~w~   89 (149)
T 2ehg_A           77 SQLVIKQMNGEYK   89 (149)
T ss_dssp             CHHHHHHHTTSSC
T ss_pred             hHHHHHHHhCccc
Confidence            9999999999865

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

Probab=99.06  E-value=1.5e-10  Score=90.07  Aligned_cols=76  Identities=16%  Similarity=0.140  Sum_probs=56.2

Q ss_pred             CCceeeeecCCCCCC--ccee-eee-CCCc-ceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHH
Q psy4359          14 PQSTKIYTDASKNDS--SVSA-AFW-SPDF-SFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA   88 (220)
Q Consensus        14 ~~~~~IyTDgSk~~~--~~G~-ai~-~~~~-~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sa   88 (220)
                      +....||||||+..+  ..|+ ||+ ..+. ....+....+|++.||++|++.||+.+.+.      ..++.|+|||+.+
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~------~~~v~i~tDSqyV   76 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER------NSRKPIYSNSQTA   76 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHT------TCCCCEEESCHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhC------CCCEEEEcchHHH
Confidence            566789999998643  3667 455 3222 222333347899999999999999999775      3348999999999


Q ss_pred             HHhhhhh
Q psy4359          89 LQSLQDI   95 (220)
Q Consensus        89 l~ai~~~   95 (220)
                      ++.|.+.
T Consensus        77 i~wi~~~   83 (134)
T 4htu_A           77 IKWVKDK   83 (134)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHcC
Confidence            9988875

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

Probab=99.02  E-value=2.9e-10  Score=89.30  Aligned_cols=77  Identities=12%  Similarity=0.075  Sum_probs=57.7

Q ss_pred             CCceeeeecCCCCC--Ccceeeee-C-CCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHH
Q psy4359          14 PQSTKIYTDASKND--SSVSAAFW-S-PDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA   88 (220)
Q Consensus        14 ~~~~~IyTDgSk~~--~~~G~ai~-~-~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sa   88 (220)
                      +..+.||||||+..  +..|+|++ . .+... ..+....+|.+.||++|++.||+.+.+.     .. ++.|+|||+.+
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~-----~~-~v~i~tDS~~v   82 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER-----NS-RKPIYSNSQTA   82 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHT-----TC-CCCEEESCHHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhC-----CC-eEEEEEehHHH
Confidence            35679999999864  34677755 2 22222 1122236789999999999999999875     34 89999999999


Q ss_pred             HHhhhhhh
Q psy4359          89 LQSLQDIF   96 (220)
Q Consensus        89 l~ai~~~~   96 (220)
                      ++.+++.+
T Consensus        83 i~w~~~~~   90 (142)
T 1zbf_A           83 IKWVKDKK   90 (142)
T ss_dssp             HHHHHHTC
T ss_pred             HHHHHcCC
Confidence            99998876

>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=98.76  E-value=5.6e-09  Score=98.14  Aligned_cols=81  Identities=22%  Similarity=0.123  Sum_probs=58.9

Q ss_pred             CCCceeeeecCCCCCC-c-ceeeee-CCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          13 YPQSTKIYTDASKNDS-S-VSAAFW-SPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        13 ~~~~~~IyTDgSk~~~-~-~G~ai~-~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      ..+.+.||||||+..+ + .|+|++ ..+....++. ..+|++.||+.|++.||+.+         ..++.|+|||++++
T Consensus       436 ~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~---------~~~v~I~tDS~~vi  505 (557)
T 2zd1_A          436 IVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYAL  505 (557)
T ss_dssp             CTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS---------CSEEEEEECCHHHH
T ss_pred             CCCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeChHHHH
Confidence            4556899999998643 3 566644 3333333443 46889999999999999987         35799999999999


Q ss_pred             HhhhhhhCCChHhH
Q psy4359          90 QSLQDIFSPNLHTL  103 (220)
Q Consensus        90 ~ai~~~~~P~~~Di  103 (220)
                      ++|+.+......++
T Consensus       506 ~~i~~~~~~~~~~l  519 (557)
T 2zd1_A          506 GIIQAQPDKSESEL  519 (557)
T ss_dssp             HHHTTCCSEESSHH
T ss_pred             HHHhcCCccCCHHH
Confidence            99988644323344

>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=98.73  E-value=9e-09  Score=96.68  Aligned_cols=73  Identities=22%  Similarity=0.119  Sum_probs=55.3

Q ss_pred             CCCceeeeecCCCCCCc--ceeeee--CCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHH
Q psy4359          13 YPQSTKIYTDASKNDSS--VSAAFW--SPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA   88 (220)
Q Consensus        13 ~~~~~~IyTDgSk~~~~--~G~ai~--~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sa   88 (220)
                      .++.+.||||||+..++  .|+|++  .++ ..... ...+|++.||+.|++.||+.   .      ..++.|+|||+++
T Consensus       433 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~-~~~~~-~~~~TNn~aEl~A~i~aL~~---~------~~~v~I~tDS~~v  501 (555)
T 1mu2_A          433 IPGAETFYTDGSCNRQSKEGKAGYVTDRGK-DKVKK-LEQTTNQQAELEAFAMALTD---S------GPKVNIIVDSQYV  501 (555)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSC-EEEEE-ESSCCHHHHHHHHHHHHHHT---S------CSEEEEEESCHHH
T ss_pred             CCCceEEEEcccccCCCCCceEEEEEEeCC-Eeecc-CCCCCHHHHHHHHHHHHHHc---C------CCeEEEEEehHHH
Confidence            35568999999987432  566644  333 22333 34688999999999999997   2      5789999999999


Q ss_pred             HHhhhhhh
Q psy4359          89 LQSLQDIF   96 (220)
Q Consensus        89 l~ai~~~~   96 (220)
                      +++++++.
T Consensus       502 ~~~i~~~~  509 (555)
T 1mu2_A          502 MGIVASQP  509 (555)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHhccc
Confidence            99998753

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=93.45  E-value=0.046  Score=49.50  Aligned_cols=75  Identities=5%  Similarity=-0.054  Sum_probs=48.8

Q ss_pred             CCceeeeecCCCCCCcceeeeeCCC---c-ce------eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEec
Q psy4359          14 PQSTKIYTDASKNDSSVSAAFWSPD---F-SF------KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCT   83 (220)
Q Consensus        14 ~~~~~IyTDgSk~~~~~G~ai~~~~---~-~~------~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~s   83 (220)
                      ...+.+|||+|..  ++|+.....+   . ..      .-......+++..|++||..|++....+-    .+.+++|+|
T Consensus       344 ~~~~~l~~DAS~~--~~gavL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl----~g~~~~v~t  417 (455)
T 1rw3_A          344 TKPFELFVDEKQG--YAKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLT----MGQPLVIKA  417 (455)
T ss_dssp             CCTTSCEEEEEEC--SSSBEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGG----CSSCEEEEC
T ss_pred             CCcEEEEEeccCC--cceeEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHc----CCCcEEEEe
Confidence            3456899999853  3343222221   1 01      11222356789999999999999987752    467999999


Q ss_pred             cchHHHHhhhhh
Q psy4359          84 DSLSALQSLQDI   95 (220)
Q Consensus        84 DS~sal~ai~~~   95 (220)
                      |+. ++.-+.++
T Consensus       418 Dh~-~~~~l~~~  428 (455)
T 1rw3_A          418 PHA-VEALVKQP  428 (455)
T ss_dssp             SSC-TTTTSSST
T ss_pred             cCh-HHHHhCCC
Confidence            996 66666554

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=90.33  E-value=0.26  Score=44.39  Aligned_cols=72  Identities=4%  Similarity=-0.148  Sum_probs=43.5

Q ss_pred             CCceeeeecCCCCCCcceeeeeCCCc----ceeeecchhhhhhhHHHHH-HHHHHHHHHHhhhhhhccCceEEeccchH
Q psy4359          14 PQSTKIYTDASKNDSSVSAAFWSPDF----SFKVKLNPLLSICNAELMA-ILYAVYFILANCLSEARNSSFLLCTDSLS   87 (220)
Q Consensus        14 ~~~~~IyTDgSk~~~~~G~ai~~~~~----~~~~~l~~~~si~~AEl~A-I~~AL~~~~~~~~~~~~~~~~~I~sDS~s   87 (220)
                      ...+.+|||+|.. |.+|+.+.+++.    +..+......+.+.-|++| |+.||+....+- -......++++||.+.
T Consensus       322 ~~~~~l~~das~~-g~~g~vl~q~~~~~~~s~~~~~~~~y~~~~~e~la~vv~al~~~r~yl-~G~~~~~~i~~td~~~  398 (428)
T 2zd1_B          322 SKDLIAEIQKQGQ-GQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVI-WGKTPKFKLPIQKETW  398 (428)
T ss_dssp             TSCCEEEEEEEET-TEEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHH-HSSCCEEEESSCHHHH
T ss_pred             CCCEEEEEecCCC-CcEEEEEecCCCceeeecccchhhhcccchHHHHHHHHHHhhccceEE-ECCCCcEECCccHHHH
Confidence            3447899999953 233433334331    1224444455567788888 999999876641 1112456788999974

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	220
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.36
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.31
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.17
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.16
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.99

>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=99.36  E-value=2.8e-13  Score=100.34  Aligned_cols=74  Identities=23%  Similarity=0.137  Sum_probs=53.7

Q ss_pred             CCCceeeeecCCCCC-Cc-ceeeee-CCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          13 YPQSTKIYTDASKND-SS-VSAAFW-SPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        13 ~~~~~~IyTDgSk~~-~~-~G~ai~-~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      .++...+|||||+.. ++ .|+|++ ..+......+ ...|++.||+.||++||+.         ...++.|+|||++++
T Consensus         5 i~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~---------~~~~v~I~TDS~yvi   74 (110)
T d1s1ta1           5 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQD---------SGLEVNIVTDSQYAL   74 (110)
T ss_dssp             CTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHH---------SCSEEEEEECCHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHh---------CCCeEEEEEehHHHH
Confidence            456678999999753 34 344444 3333333444 4679999999999999863         356799999999999


Q ss_pred             Hhhhhhh
Q psy4359          90 QSLQDIF   96 (220)
Q Consensus        90 ~ai~~~~   96 (220)
                      .++...+
T Consensus        75 ~~i~~~~   81 (110)
T d1s1ta1          75 GIIQAQP   81 (110)
T ss_dssp             HHHHHCC
T ss_pred             HHHhcCc
Confidence            9998874

>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=99.31  E-value=8.7e-13  Score=99.27  Aligned_cols=75  Identities=23%  Similarity=0.144  Sum_probs=54.9

Q ss_pred             CCCceeeeecCCCCC-Cc-ceeeee-CCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          13 YPQSTKIYTDASKND-SS-VSAAFW-SPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        13 ~~~~~~IyTDgSk~~-~~-~G~ai~-~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      .+....||||||+.. ++ .|+|++ ..+......++ ..|++.||+.||++||+.         ...++.|+|||++++
T Consensus         4 ~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~---------~~~~i~I~tDS~~v~   73 (126)
T d1mu2a1           4 IPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVM   73 (126)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHH
T ss_pred             CCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc---------CCcceEEEechHHHH
Confidence            355678999999754 34 445544 33333344444 678999999999999874         356799999999999


Q ss_pred             HhhhhhhC
Q psy4359          90 QSLQDIFS   97 (220)
Q Consensus        90 ~ai~~~~~   97 (220)
                      +.+.+.+.
T Consensus        74 ~~~~~~~~   81 (126)
T d1mu2a1          74 GIVASQPT   81 (126)
T ss_dssp             HHHHTCCS
T ss_pred             HHHhcCCc
Confidence            99988754

>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=99.17  E-value=5.2e-12  Score=96.99  Aligned_cols=74  Identities=14%  Similarity=0.000  Sum_probs=55.8

Q ss_pred             CceeeeecCCCCCC--cceeeee--C-CCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359          15 QSTKIYTDASKNDS--SVSAAFW--S-PDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL   89 (220)
Q Consensus        15 ~~~~IyTDgSk~~~--~~G~ai~--~-~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal   89 (220)
                      ..++||||||+..+  ..|+|++  . +......+..+.+|+++||+.||++||+++.       ....+.|+|||++++
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~-------~~~~i~i~tds~~~~   74 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK-------EPCEVDLYTDSHYLK   74 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC-------SCCEEEEECCCHHHH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc-------CCceEEEecchhhhh
Confidence            46899999998764  3666644  2 3333344555667899999999999998753       356789999999999


Q ss_pred             Hhhhhh
Q psy4359          90 QSLQDI   95 (220)
Q Consensus        90 ~ai~~~   95 (220)
                      .++...
T Consensus        75 ~~~~~~   80 (147)
T d1rila_          75 KAFTEG   80 (147)
T ss_dssp             HHHHSS
T ss_pred             cccccc
Confidence            998775

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

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

Probab=99.16  E-value=1e-11  Score=94.45  Aligned_cols=73  Identities=16%  Similarity=0.148  Sum_probs=55.0

Q ss_pred             eeeecCCCCC--Ccceeeee--CCCc-ceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHhh
Q psy4359          18 KIYTDASKND--SSVSAAFW--SPDF-SFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSL   92 (220)
Q Consensus        18 ~IyTDgSk~~--~~~G~ai~--~~~~-~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~ai   92 (220)
                      .||||||+..  |-.|+|+|  ..+. ....+.-+..|.+.||++|++.||+++.+.      ..++.|+|||+.+++.+
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~------~~~i~I~tDS~yvi~wv   79 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER------NSRKPIYSNSQTAIKWV   79 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHT------TCCCCEEESCHHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcC------CceEEEEeccHHHHHHH
Confidence            5999999874  34676644  2222 223333457889999999999999998764      46799999999999988


Q ss_pred             hhhh
Q psy4359          93 QDIF   96 (220)
Q Consensus        93 ~~~~   96 (220)
                      ++..
T Consensus        80 ~~~~   83 (132)
T d1zbfa1          80 KDKK   83 (132)
T ss_dssp             HHTC
T ss_pred             HhCc
Confidence            7763

>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=98.99  E-value=9.7e-11  Score=89.60  Aligned_cols=73  Identities=18%  Similarity=0.056  Sum_probs=54.6

Q ss_pred             ceeeeecCCCCCC--cceeeee--CCCcce-eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHH
Q psy4359          16 STKIYTDASKNDS--SVSAAFW--SPDFSF-KVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQ   90 (220)
Q Consensus        16 ~~~IyTDgSk~~~--~~G~ai~--~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~   90 (220)
                      .+.||||||+..+  ..|+|++  .++... .....+..|.++||++||+.||+++..       ...+.|+|||+.++.
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~-------~~~i~i~tds~~~i~   74 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE-------HAEVILSTDSQYVRQ   74 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS-------CCEEEEEECCHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc-------cceEEEeecceeeEE
Confidence            4789999998754  3677754  343322 334445678899999999999987543       567899999999999


Q ss_pred             hhhhh
Q psy4359          91 SLQDI   95 (220)
Q Consensus        91 ai~~~   95 (220)
                      .+...
T Consensus        75 ~~~~~   79 (152)
T d1jl1a_          75 GITQW   79 (152)
T ss_dssp             HHHTT
T ss_pred             cccch
Confidence            88776