Psyllid ID: psy16749

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-
Protein Sequence
AKLASDNHVENSVSNVDKPVSNLFEISTEETSYNEKPQEHDDLTFETKESSFQEETHTETKVESSFQETHVALETNLDDFTSQETKLDDFISAHTEKTPEVSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPTNTEEN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccHHHHHHccccHHccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHHHHHHHHHHHHHHccccEEEEcccccccccEEEEEEccccccEEEEEcccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccEEEEEEEccccccccHHHHHHHHHHHHHcccccEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHEEEEEEccccccccHHHHHHHHHHHHHHHHccccEEEccccHHHHHHccHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHccccccHHHHHHcccccccccccccccccccHHEEEEccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccEEEEccccccccEEEEEEEccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccccHHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccEEEEcccccccc
Coil and Loop (DISEMBL)
aklasdnhvensvsnvdkpvsnlfeisteetsynekpqehddltfetkessfqeethtetkveSSFQETHVALETnlddftsqetkLDDFISahtektpevsepkeeVLDDLvsvptsvpdvvpnqdaneespspavdltqdiveekeavvtptdetnsetaeketplsevpvipqeaqtvesaeestasSDLAAKVAGALVVGAAAAGAAVAVKKATaakktdkpgpaakpaskplakttttktttaakpaispvkktatttakpapkpatkpapkpttaapkstttapkpapvrkpvaSTITKTatstvsaapkpsapkpaapkkpvaapapkprpataapapkpltngvtkrpvsatttasrtssssvtsasaakpaaprvplsqrtsaakpatkpatakpsttskpttaskpatatrpatttskpatttstdiedemnqpftpEELEAAIKSglittpgrdnihypmienlpdcNKYLNIMKMICNkhwgmnptiglNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVecrenpmskrtpqLVDRFVLKVISSQTALAAKLNTLTVTHmtskycktkptppivnsycnishqygrelityekpiiynydydigkvslqsetfneyrkhpdslqDAALSSEIQEKCPNAICIYTdaskknekvgaawfcptykskacfklhpatstytAEVIGIWEALKYSASLKNNEILILTDSKSACQKLsknclnttpthLELEILSSYKHLQNTCKTVKLAWIKghegikgnvEVDRLAKYATvhgeastivisptnteen
Flexible Loop (DISEMBL)
aklasdnhvensvsnvdkpvsnLFEISTeetsynekpqehdDLTFETKESSFQEETHTETKVESSFQETHVALETNLDDFTSQETKLDDFISAhtektpevsepkeeVLDDLVSVPTSVPDvvpnqdaneespspavdltqdiVEEKeavvtptdetnsetaeketplsevpviPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKAtaakktdkpgpaakpaskplakttttktttaakpaispvkktatttakpapkpatkpapkpttaapkstttapkpapvrkpVASTITKtatstvsaapkpsapkpaapkKPVAAPAPKPRPataapapkpltngvtkrpvsatttasrtssssvtsasaakpaaprvplsqrtsaakpatkpatakpsttskpttaskpatatrpatttskpatttstdiedemnqPFTPEELEAAIKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVThmtskycktkptppivnsYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYAtvhgeastivisptnteen
Low Complexity Region (SEG)
AKLASDNHVENSVSNVDKPVSNLFEISTEETSYNEKPQEHDDLTFETKESSFQEETHTETKVESSFQETHVALETNLDDFTSQETKLDDFISAHTEKTPEVSEPKEEVLddlvsvptsvpdvvpNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPqeaqtvesaeestassdlaakvagalvvgaaaagaavavkkataakktdkpgpaakpaskplakttttktttaakpaISPVkktatttakpapkpatkpapkpttaapkstttapkpapvrkpvastitktatstvsaapkpsapkpaapkkpvaapapkprpataapapkpLTNGVTKrpvsatttasrtssssvtsasaakpaaprvPLSQRtsaakpatkpatakpsttskpttaskpatatrpatttskpatttstDIEDEMNQPFTPEELEAAIKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPTNTEEN
Disordered region (IsUnstruct)
**************************************************************************************************************************************************************************************************AKVAGALVVGAAAAGAAVAV***********************************************************************************************************************************************************************************************************************************************IKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETF*******************QEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVI********
Disordered Region (DISOPRED)
************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************YPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSK*****TPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEAS************
Disordered Region (DISEMBL)
************VSNVDKPVSNLFEISTE************DLTF*********************QETHVALETNLDDFTSQETKLDDFISAHT************VLDDLVSVPTSVPDVVPNQ**********VDLTQDIVEEKEA********************EVPVIPQE**************DLAAKVAGALVVGAAA*********************************************ISPVK************************************************************************************APAPKPLTNGV**********************************************************************************TDIEDEMNQPFTPEELEAAIKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPTNTEEN
Disordered Region (DISPRO)
*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************NIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPT*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
AKLASDNHVENSVSNVDKPVSNLFEISTEETSYNEKPQEHDDLTFETKESSFQEETHTETKVESSFQETHVALETNLDDFTSQETKLDDFISAHTEKTPEVSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTLTVTHMTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPTNTEEN
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	821	2.2.26 [Sep-21-2011]
Q28824	1176	Myosin light chain kinase	yes	N/A	0.277	0.193	0.344	0.0002

>sp|Q28824|MYLK_BOVIN Myosin light chain kinase, smooth muscle OS=Bos taurus GN=MYLK PE=1 SV=1

 Score = 48.1 bits (113), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 99/287 (34%), Positives = 119/287 (41%), Gaps = 59/287 (20%)

Query: 193 LAAKVAGAL--VVGAAAAGAAVAVKKATAAKKTDKPGPAAKPAS--KPLAKTT---TTKT 245
           L AK A  L  V  A  +G    V  A  A  T KP  + KPA   KPL       T K 
Sbjct: 81  LNAKAAEGLKPVGNAQPSGFLKPVGNAKLAD-TPKPLSSTKPAETPKPLGNVKPAETPKP 139

Query: 246 TTAAKPAISPVKKTATTTAK-PAPKPATKPA--PKPTTAAPKSTTTAP----KPAPVRKP 298
             + KPA +P    +T  A+ P P    KPA  PKP      + T  P    KPA   KP
Sbjct: 140 LGSTKPAETPKPLGSTKPAETPKPLGNVKPAETPKPLGNIKPTETPKPLGSTKPAETPKP 199

Query: 299 VASTITKTATSTVSAAPKPS-APKPAAPKKPVAAPAPKPRPATAAPA--PKPLTN---GV 352
           + ST             KP+  PKP    KP   P P        PA  PKPL N     
Sbjct: 200 LGST-------------KPAETPKPLGNVKPAETPKPL---GNVKPAETPKPLGNVKPAE 243

Query: 353 TKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKP---ATAKPSTTSK 409
           T +PVS    A      ++     AKPA    PLS      KPA  P     AKP+ TSK
Sbjct: 244 TPKPVSNAKPA-----ETLKPVGNAKPAETPKPLSN----VKPAETPKLVGNAKPAETSK 294

Query: 410 PTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKS 456
           P   +KPA A +P    +KPA         E+ +P   EEL+  IK+
Sbjct: 295 PLDNAKPAEAPKP-LGNAKPA---------EIPKPTGKEELKKEIKN 331

Calcium/calmodulin-dependent myosin light chain kinase implicated in smooth muscle contraction via phosphorylation of myosin light chains (MLC). Also regulates actin-myosin interaction through a non-kinase activty. Phosphorylates PTK2B/PYK2 and myosin light-chains. Involved in the inflammatory response (e.g. apoptosis, vascular permeability, leukocyte diapedesis), cell motility and morphology, airway hyperreactivity and other activities relevant to asthma. Required for tonic airway smooth muscle contraction that is necessary for physiological and asthmatic airway resistance. Necessary for gastrointestinal motility. Implicated in the regulation of endothelial as well as vascular permeability, probably via the regulation of cytoskeletal rearrangements. In the nervous system it has been shown to control the growth initiation of astrocytic processes in culture and to participate in transmitter release at synapses formed between cultured sympathetic ganglion cells. Critical participant in signaling sequences that result in fibroblast apoptosis. Plays a role in the regulation of epithelial cell survival. Required for epithelial wound healing, especially during actomyosin ring contraction during purse-string wound closure. Mediates RhoA-dependent membrane blebbing. Triggers TRPC5 channel activity in a calcium-dependent signaling, by inducing its subcellular localization at the plasma membrane. Promotes cell migration (including tumor cells) and tumor metastasis. PTK2B/PYK2 activation by phosphorylation mediates ITGB2 activation and is thus essential to trigger neutrophil transmigration during acute lung injury (ALI). May regulate optic nerve head astrocyte migration. Probably involved in mitotic cytoskeletal regulation. Regulates tight junction probably by modulating ZO-1 exchange in the perijunctional actomyosin ring. Mediates burn-induced microvascular barrier injury; triggers endothelial contraction in the development of microvascular hyperpermeability by phosphorylating MLC. Essential for intestinal barrier dysfunction. Mediates Giardia spp.-mediated reduced epithelial barrier function during giardiasis intestinal infection via reorganization of cytoskeletal F-actin and tight junctional ZO-1. Necessary for hypotonicity-induced Ca(2+) entry and subsequent activation of volume-sensitive organic osmolyte/anion channels (VSOAC) in cervical cancer cells.
Bos taurus (taxid: 9913)
EC: 2EC: .EC: 7EC: .EC: 1EC: 1EC: .EC: 1EC: 8

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	821
357621647	1133	putative pol-like protein [Danaus plexip	0.401	0.291	0.315	2e-32
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.390	0.262	0.297	5e-22
427791321	1210	Putative tick transposon, partial [Rhipi	0.375	0.254	0.271	6e-21
427791807	1212	Putative tick transposon, partial [Rhipi	0.375	0.254	0.271	6e-21
427798889	1199	Putative tick transposon, partial [Rhipi	0.378	0.259	0.280	1e-18
427798887	1199	Putative tick transposon, partial [Rhipi	0.378	0.259	0.277	1e-18
427798885	1199	Putative tick transposon, partial [Rhipi	0.378	0.259	0.274	6e-18
323450868	2778	hypothetical protein AURANDRAFT_65424 [A	0.277	0.082	0.307	2e-06
427795117	1654	Hypothetical protein, partial [Rhipiceph	0.238	0.118	0.314	0.0001
392342464	3307	PREDICTED: collagen alpha-3(VI) chain [R	0.176	0.043	0.3	0.0007

>gi|357621647|gb|EHJ73416.1| putative pol-like protein [Danaus plexippus]

 Score =  147 bits (372), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 111/352 (31%), Positives = 167/352 (47%), Gaps = 22/352 (6%)

Query: 478  CNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQA 537
            C   +NI++ +    WG +P      Y A IR+  D+GS        S L  LDK+Q + 
Sbjct: 664  CENNINILRSLSGVWWGSHPYTQKILYNAIIRSHFDYGSFLLVPCIKSALSILDKIQAKC 723

Query: 538  LRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVIS-SQTALAAKLNTLTVTHM 596
            LR+  G + S+PI+ + VEC E P+  R   L DRF LKVI  S   L  KLN+L+    
Sbjct: 724  LRIICGAMKSSPINALQVECGEAPLHLRRQYLSDRFFLKVIQFSNHPLIPKLNSLSDLIP 783

Query: 597  TSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYD-------YDIGKVSLQSETF 649
            ++KY   K  P ++ S          + +    P++ N         YD+  ++   +  
Sbjct: 784  SNKYWSHKEYPCLLTSLV--------KFLRLPCPVLQNQMFPLFATPYDV--LNFHPQIL 833

Query: 650  NEYRKHPDS-LQDAALSSEIQEKCPNAICIYTDASKKNEK--VGAAWFCPTYKSKACFKL 706
             E+     S + +    + ++E   + +CIYTDASK  ++   GAA + P Y     FK 
Sbjct: 834  LEFGIDKGSAIANVQFQNYVKEHWSDWLCIYTDASKMADQSNAGAAVWIPKYNIILNFKF 893

Query: 707  HPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTH-LELEIL 765
                S +TAE I I EA+ +  S K N  +I +DSKS  Q +++N   +   +   L+I 
Sbjct: 894  PSEISIFTAESIAILEAVSFVESHKLNNSIIFSDSKSCLQAIARNPFISKHNYPYILKIK 953

Query: 766  SSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPTN 817
                  Q++   V+LAWI  H GI GN  VD  AK AT  G      + P +
Sbjct: 954  DILFRCQSSNIQVRLAWIPSHSGIHGNETVDYYAKDATNTGCMDHFGVYPND 1005

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  113 bits (282), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 101/340 (29%), Positives = 157/340 (46%), Gaps = 19/340 (5%)

Query: 478  CNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQA 537
            C K LNI++++ +  WG +    L  Y++ IR+ LD+GS+ Y  +  S LK L+ +QN A
Sbjct: 759  CQKSLNILRVLSHTDWGADRDTLLLLYRSLIRSKLDYGSIIYGAARKSYLKILEPIQNAA 818

Query: 538  LRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQT--ALAAKLNTLTVTH 595
            LRL +G   ++PI ++ VE  E PM  R  +L  ++++K+ S+ T  A  +  N   V  
Sbjct: 819  LRLCLGAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVEL 878

Query: 596  MTSKYCKTKPTP-----PIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFN 650
               +    +P       PI N    I      ++   E P    +  +  K++L    F 
Sbjct: 879  YNRRPNVIQPLGLRMREPIQNLTQPID-----QISKIETPQNPPWLMNKPKLNLSLLNFK 933

Query: 651  EYRKHPDSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPAT 710
            +    P  LQ      E+QE   +   IYTD SK   KV  A  C         +L    
Sbjct: 934  KENTDPSILQ--VHFRELQESYGDCGTIYTDGSKMEGKVACA--CSFRNKTISRRLPDGC 989

Query: 711  STYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKH 770
            S +TAE+  I  AL    + + ++ +I +DSKSA Q L +   +    H  L++L     
Sbjct: 990  SIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDL--- 1046

Query: 771  LQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEAST 810
            +    + V   W+  H GI+GN   DR AK A  H  + T
Sbjct: 1047 ITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGT 1086

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  109 bits (273), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 91/335 (27%), Positives = 152/335 (45%), Gaps = 27/335 (8%)

Query: 479  NKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQAL 538
            NK LN++K++ +KHWG +    L  Y++ +R+ LD+G V Y  +  S ++ LD V N  L
Sbjct: 739  NKALNLLKVLSHKHWGSDRLCLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGL 798

Query: 539  RLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTL--TVTHM 596
            RL+ G   ++P++++ V+C E P+S R   L   +VL++ SS   +   + T   +  H 
Sbjct: 799  RLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHY 858

Query: 597  TSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHP 656
             +K    KP       YC         L    KP      +D+ ++   S +    +  P
Sbjct: 859  LNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTP 918

Query: 657  DSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAE 716
              L      + +QEK  +    YTD SK  + VG      T +S    ++    S +TAE
Sbjct: 919  PELIIQEFRA-LQEKYRDYAEFYTDGSKTRDHVGIG--IVTGESAFSVRVPQCISIFTAE 975

Query: 717  VIGIWEALKYSASLKNNEILILTDS---------KSACQKLSKNCLNTTPTHLELEILSS 767
            V  ++EA +   + K+ + +I TDS         KS C+ L  + LN             
Sbjct: 976  VYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMVL---------- 1025

Query: 768  YKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYA 802
               + +   +++  W+  H GI GN + D+ A  A
Sbjct: 1026 ---INSKVISMRFCWVPSHVGIPGNEKADKCASLA 1057

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  109 bits (272), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 91/335 (27%), Positives = 152/335 (45%), Gaps = 27/335 (8%)

Query: 479  NKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQAL 538
            NK LN++K++ +KHWG +    L  Y++ +R+ LD+G V Y  +  S ++ LD V N  L
Sbjct: 742  NKALNLLKVLSHKHWGSDRLCLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGL 801

Query: 539  RLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTALAAKLNTL--TVTHM 596
            RL+ G   ++P++++ V+C E P+S R   L   +VL++ SS   +   + T   +  H 
Sbjct: 802  RLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHY 861

Query: 597  TSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKHP 656
             +K    KP       YC         L    KP      +D+ ++   S +    +  P
Sbjct: 862  LNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTP 921

Query: 657  DSLQDAALSSEIQEKCPNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAE 716
              L      + +QEK  +    YTD SK  + VG      T +S    ++    S +TAE
Sbjct: 922  PELIIQEFRA-LQEKYRDYAEFYTDGSKTRDHVGIG--IVTGESAFSVRVPQCISIFTAE 978

Query: 717  VIGIWEALKYSASLKNNEILILTDS---------KSACQKLSKNCLNTTPTHLELEILSS 767
            V  ++EA +   + K+ + +I TDS         KS C+ L  + LN             
Sbjct: 979  VYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMVL---------- 1028

Query: 768  YKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYA 802
               + +   +++  W+  H GI GN + D+ A  A
Sbjct: 1029 ---INSKVISMRFCWVPSHVGIPGNEKADKCASLA 1060

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798889|gb|JAA64896.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  102 bits (253), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 97/346 (28%), Positives = 161/346 (46%), Gaps = 35/346 (10%)

Query: 468  HYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKL 527
            H   I+N   C K +NI+K++    WG +    +N YK+ IR  LD+G++ Y  +  + L
Sbjct: 757  HIKYIKN--KCLKTMNILKVLSRTTWGSDKKCLMNLYKSLIRTRLDYGAIIYQSASPTAL 814

Query: 528  KTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTA-LAA 586
            K LD V +  +RL+ G   ++P++++ VE  E  +  +   +   + +KV + +     +
Sbjct: 815  KMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYIKVNADKEHPSHS 874

Query: 587  KLNTLTVTHMTSKYCKTKPT--PPIVNSYCNISHQYGRELITYE--KPIIY--NYDYDIG 640
             +N L+     S   + +P+  PP      +++ Q G  L  +    P  Y   + + + 
Sbjct: 875  TINDLS----CSTLFENRPSLKPPYSLRVRDLAEQTGLPLFEHRLMAPAAYPPPWQWQLI 930

Query: 641  KVSLQSETFNEYRKHPDSLQDAALSSEIQEK--CPNAICIYTDASKKNEKVGAAWFCPTY 698
               +   +F E  KH           E+Q K  CP     YTDASK +  V  A   P++
Sbjct: 931  DCDV---SFMEVTKHAPIAHIRTYFLELQHKYNCP---AFYTDASKSHTSVSYAAVGPSF 984

Query: 699  KSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL-----SKNCL 753
             +     LHP TS +TAE   I  A+K+   LK  + +I TDS S  + L      +N +
Sbjct: 985  SAAG--ALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPV 1042

Query: 754  NTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLA 799
              +   L   I +S +H       V + W+ GH  I+GNV  D+LA
Sbjct: 1043 LVSLYSLLCTIYTSKQH-------VVVCWVPGHREIQGNVMADQLA 1081

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798887|gb|JAA64895.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  101 bits (252), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 96/346 (27%), Positives = 160/346 (46%), Gaps = 35/346 (10%)

Query: 468  HYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKL 527
            H   I+N   C K +NI+K++    WG +    +N YK+ IR  LD+G++ Y  +  + L
Sbjct: 757  HIKYIKN--KCLKTMNILKVLSRTTWGSDKKCLMNLYKSLIRTRLDYGAIIYQSASPTAL 814

Query: 528  KTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTA-LAA 586
            K LD V +  +RL+ G   ++P++++ VE  E  +  +   +   + LKV + +     +
Sbjct: 815  KMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYLKVNADKEHPSHS 874

Query: 587  KLNTLTVTHMTSKYCKTKPT--PPIVNSYCNISHQYGRELITYE--KPIIY--NYDYDIG 640
             +N L+    +S   + +P+  PP       ++ + G  L  +    P  Y   + + + 
Sbjct: 875  TINDLS----SSTLFENRPSLRPPYSLRVRGLAEETGLPLFEHRLMAPAAYPPPWQWQLI 930

Query: 641  KVSLQSETFNEYRKHPDSLQDAALSSEIQEK--CPNAICIYTDASKKNEKVGAAWFCPTY 698
               +   +F E  KH           E+Q K  CP     YTDASK +  V  A   P++
Sbjct: 931  DCDV---SFMEVTKHAPIAHIRTYFLELQHKYNCP---AFYTDASKSHTSVSYAAVGPSF 984

Query: 699  KSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL-----SKNCL 753
             +     LHP TS +TAE   I  A+K+   LK  + +I TDS S  + L      KN +
Sbjct: 985  SAAG--ALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI 1042

Query: 754  NTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLA 799
              +   L   + ++ +H       V + W+ GH  I+GNV  D LA
Sbjct: 1043 LVSLYSLVCTVYTAKQH-------VVVCWVPGHREIQGNVMADHLA 1081

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798885|gb|JAA64894.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 99.8 bits (247), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 159/346 (45%), Gaps = 35/346 (10%)

Query: 468  HYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFGSVFYSESCSSKL 527
            H   I+N   C K +NI+K++    WG +    +N YK+ IR  LD+G++ Y  +  + L
Sbjct: 757  HIQYIKN--KCLKTMNILKVLSRTTWGSDKKCLMNLYKSLIRTCLDYGAIIYQSASPTAL 814

Query: 528  KTLDKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLVDRFVLKVISSQTA-LAA 586
            K LD + +  +RL+ G   ++P++++ VE  E  +  +   +   + LKV + +     +
Sbjct: 815  KMLDPIHHLGIRLSTGAFCTSPVESLYVESNEWSLQLQRSYMSFLYYLKVNADKEHPSHS 874

Query: 587  KLNTLTVTHMTSKYCKTKPT--PPIVNSYCNISHQYGRELITYE--KPIIY--NYDYDIG 640
             +N L+    +S   + +P+  PP       ++ + G  L  +    P  Y   + + + 
Sbjct: 875  TINDLS----SSTLFENRPSLRPPYSLRVRGLAEETGLPLFEHRLMAPAAYPPPWQWQLI 930

Query: 641  KVSLQSETFNEYRKHPDSLQDAALSSEIQEK--CPNAICIYTDASKKNEKVGAAWFCPTY 698
               +   +F E  KH           E+Q K  CP     YTDASK +  V  A   P++
Sbjct: 931  DCDV---SFMEVTKHAPIAHIRTYFLELQHKYNCP---AFYTDASKSHTSVSYAAVGPSF 984

Query: 699  KSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL-----SKNCL 753
                   LHP TS +TAE   I  A+K+   LK  + +I TDS S  + L      KN +
Sbjct: 985  SDAGV--LHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI 1042

Query: 754  NTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLA 799
              +   L   + ++ +H       V + W+ GH  I+GNV  D LA
Sbjct: 1043 LVSLYSLVCTLYTAKQH-------VVVCWVPGHREIQGNVMADHLA 1081

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|323450868|gb|EGB06747.1| hypothetical protein AURANDRAFT_65424 [Aureococcus anophagefferens]

 Score = 61.6 bits (148), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 106/247 (42%), Gaps = 19/247 (7%)

Query: 193 LAAKVAGAL--VVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAK 250
           LAA  AGA+   +GA A    +A    +AA  T  P  +A P +   +   T   + +  
Sbjct: 14  LAAADAGAMRSSLGALACCWLLAAADESAAP-TALPSYSASP-TVAPSSPPTASPSFSHD 71

Query: 251 PAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATST 310
           P +SP     T++  P   P+  P   P+TAAP  TT AP           T + T  + 
Sbjct: 72  PTLSPSTAAPTSSFAPTTSPSYAPTYAPSTAAP--TTGAPTATH-----RPTASPTTAAP 124

Query: 311 VSAAPKPSAPKPAAPKKPVAAPAPKPR---PATAAPAPKPLTN---GVTKRPVSATTTAS 364
            +AAP  +    A  + P AAP P P    P TA+P+  P T+     + RP +  TTA 
Sbjct: 125 TTAAPSAAPSTAAPTEDPTAAPTPTPSTAAPTTASPSFSPTTSPQPTASPRPTATPTTAL 184

Query: 365 RTSSSSVTSAS-AAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATAT-RP 422
            +SS +  + S A   AAP       T A  P   P       T  PTTA+  A  + RP
Sbjct: 185 PSSSPTTAAPSYAPTTAAPSATAGPTTFAPVPRPDPGLPGSEYTEPPTTAAPSAAPSYRP 244

Query: 423 ATTTSKP 429
               + P
Sbjct: 245 TQEPTSP 251

Source: Aureococcus anophagefferens

Species: Aureococcus anophagefferens

Genus: Aureococcus

Class: Pelagophyceae

Superkingdom: Eukaryota

>gi|427795117|gb|JAA63010.1| Hypothetical protein, partial [Rhipicephalus pulchellus]

 Score = 55.1 bits (131), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 76/242 (31%), Positives = 111/242 (45%), Gaps = 46/242 (19%)

Query: 213  AVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKP---AISPVKK----------- 258
            A K   AAK +  P P A    KP  K   TKT  +AK    A SP+KK           
Sbjct: 1272 AQKTKPAAKASPAPKPRASSTDKPATKPLPTKTEASAKATPAAKSPLKKQPIAAKPTTAT 1331

Query: 259  -------TATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTV 311
                   TA+TTAK +     +P PKP ++AP +  +A KP P     +S ++  +T   
Sbjct: 1332 TTAKQSSTASTTAKASLTRKPEP-PKPKSSAPATDASAKKPVPA----SSRLSTGSTRPT 1386

Query: 312  SAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSV 371
            ++ P   +  PA+  KP A       P++ AP P+  T        SA T+AS+    + 
Sbjct: 1387 ASKPPEKSTAPASKAKPTA-------PSSTAPRPRTSTG-------SALTSASKAEVGTA 1432

Query: 372  TSASAAKPAAPRVPLSQ----RTSAAKPATKPATAKPSTTSKPTTA--SKPATATRPATT 425
                 AKPA  R P+S+     T  A  ++ P     +T S+PTTA  S+P T +R  +T
Sbjct: 1433 EKKPTAKPATTRPPISRTTPKSTQPASSSSAPRVGSSTTASRPTTAPTSRPGTTSRAGST 1492

Query: 426  TS 427
            ++
Sbjct: 1493 ST 1494

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|392342464|ref|XP_003754596.1| PREDICTED: collagen alpha-3(VI) chain [Rattus norvegicus]

 Score = 53.1 bits (126), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 54/180 (30%), Positives = 77/180 (42%), Gaps = 35/180 (19%)

Query: 265  KPAP-KPATKPAPKPTTAAPKST--------TTAPKPAPVRKPVASTITKTATSTVSAAP 315
            KPAP +P    +    TA+ K          T A KP PV+  V +            AP
Sbjct: 2985 KPAPAQPVHVQSASAQTASAKPVPAKPAPPQTAAAKPVPVKPAVPAQPAPAQPVHAQPAP 3044

Query: 316  ------KPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPL-TNGVTKRPVSATTTASRTSS 368
                  KP+A KPA+  KPVAA              KP+ TN  T RP SA       ++
Sbjct: 3045 AQPVLTKPAAMKPASANKPVAA--------------KPVATNTATVRPASAVK----PAA 3086

Query: 369  SSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSK 428
            +S  +A+   PAA R P++ +  A +P  KPA  KP+TT      S+    +     +++
Sbjct: 3087 ASKPAATRPLPAAVR-PVATKPEAPRPQAKPAATKPATTKPMARVSREVQVSEVTENSAR 3145

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	821
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.164	0.277	0.340	6.4e-09
ASPGD|ASPL0000017106	306	AN7977 [Emericella nidulans (t	0.155	0.418	0.302	3e-06
ASPGD|ASPL0000037597	666	AN2711 [Emericella nidulans (t	0.155	0.192	0.281	0.00024
ASPGD|ASPL0000010587	342	AN3980 [Emericella nidulans (t	0.147	0.353	0.285	0.0003
ASPGD|ASPL0000077547	1581	AN8648 [Emericella nidulans (t	0.155	0.080	0.295	0.0004
ASPGD|ASPL0000040226	1538	AN2661 [Emericella nidulans (t	0.153	0.081	0.285	0.00053

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

 Score = 165 (63.1 bits), Expect = 6.4e-09, P = 6.4e-09
 Identities = 47/138 (34%), Positives = 67/138 (48%)

Query:   668 IQEKCPNAICIYTDASKKNEKVGAAWFCPTYK-SKACFKLHPATST-YTAEVIGIWEALK 725
             I  + P  I +YTD S  N +VGAA  CP Y  S++ +    + ST Y AE+ GI  AL 
Sbjct:   175 ILNRAPRPIALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILLALV 234

Query:   726 YSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKG 785
                  +    +I TD+++  Q L      +    LE  I++  K  +     V   WI  
Sbjct:   235 IILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKG-RKAGLNVHFRWIPA 293

Query:   786 HEGIKGNVEVDRLAKYAT 803
             H G++GN + DR AK AT
Sbjct:   294 HRGVEGNEQADRRAKEAT 311

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

ASPGD|ASPL0000017106 AN7977 [Emericella nidulans (taxid:162425)]

 Score = 137 (53.3 bits), Expect = 3.0e-06, P = 3.0e-06
 Identities = 43/142 (30%), Positives = 68/142 (47%)

Query:   673 PNAICIYTDASKKNEKVG---AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSAS 729
             P  I +Y D S+ ++  G   A +F P   SK      P T  Y AE+IG  E L+ +  
Sbjct:    13 PLQISVYLDGSRTSQGAGYGYAIYFGPILMSKGHGPAGPRTEVYDAEIIGAVEGLRAALG 72

Query:   730 LK----NNEILILTDSKSACQKLS-------KNCLNTTPTHLELEILSSYKHLQNTCKTV 778
                   + +++IL D+ +A   L+       ++ L+ T + L  + + S   L    K +
Sbjct:    73 QPCVGYSTQLVILLDNLAAASLLASYRPTPHRHGLSETFSQLAAQWMESPSILTMQRKPL 132

Query:   779 KLAWIKGHEGIKGNVEVDRLAK 800
             ++ WI GH GI GN   D+LAK
Sbjct:   133 QVRWIPGHSGIAGNELADKLAK 154

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

ASPGD|ASPL0000037597 AN2711 [Emericella nidulans (taxid:162425)]

 Score = 125 (49.1 bits), Expect = 0.00024, P = 0.00024
 Identities = 40/142 (28%), Positives = 67/142 (47%)

Query:   673 PNAICIYTDASKKNEKVG---AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSAS 729
             P  I +Y+D S+  +  G   A +F P   +K      P T  Y AE++G  E L+ +  
Sbjct:   360 PLQISVYSDGSRTGQGAGYGYAIYFGPILVTKGHGPAGPRTEVYDAEIMGAVEGLRAALG 419

Query:   730 LK----NNEILILTDSKSACQKLS-------KNCLNTTPTHLELEILSSYKHLQNTCKTV 778
                   + +++IL D+ +A   L+       ++ L+ +   L  + L +   L    K +
Sbjct:   420 QPCVGYSTQLVILLDNLAAASLLASYRPTPHRHGLSESFGQLATQWLEAPSILTRPRKPL 479

Query:   779 KLAWIKGHEGIKGNVEVDRLAK 800
             ++ WI GH GI GN   D+LAK
Sbjct:   480 QVRWIPGHSGIAGNELADKLAK 501

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000010587 AN3980 [Emericella nidulans (taxid:162425)]

 Score = 120 (47.3 bits), Expect = 0.00030, P = 0.00030
 Identities = 38/133 (28%), Positives = 61/133 (45%)

Query:   676 ICIYTDASKKNEKVG---AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLK- 731
             I +Y D+ +  +  G     +F P   +K      P T  Y AE+IG  E L+ +     
Sbjct:    49 ISVYLDSLQTGQGAGFGYTVYFGPILVTKGHGPAGPRTEVYDAEIIGAVEGLRAALGQPC 108

Query:   732 ---NNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNT-CKTVKLAWIKGHE 787
                + +++IL D+ +A   L+    +  PT     +  S+  L     K +++ WI GH 
Sbjct:   109 MGYSTQLVILLDNLAAASLLA----SYRPTLHRHRLSESFGQLATQPWKPLQVCWIPGHS 164

Query:   788 GIKGNVEVDRLAK 800
             GI GN   D+LAK
Sbjct:   165 GIAGNKLADKLAK 177

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

ASPGD|ASPL0000077547 AN8648 [Emericella nidulans (taxid:162425)]

 Score = 135 (52.6 bits), Expect = 0.00040, Sum P(2) = 0.00040
 Identities = 42/142 (29%), Positives = 69/142 (48%)

Query:   673 PNAICIYTDASKKNEKVG---AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSAS 729
             P  I +Y+D S+ ++  G   A +F P   SK      P T  Y AE++G  E L+ +  
Sbjct:  1275 PLQISVYSDGSRTSQGAGYGYAIYFGPILVSKGHGPAGPRTEVYDAEIMGAVEGLRAALG 1334

Query:   730 LK----NNEILILTDSKSACQKLS-------KNCLNTTPTHLELEILSSYKHLQNTCKTV 778
                   + +++IL D+ +A   L+       ++ L+ T + L  + + S   L    K +
Sbjct:  1335 QPCVGYSTQLVILLDNLAAASLLASYRPTPHRHGLSETFSQLAAQWMESPSILTMQRKPL 1394

Query:   779 KLAWIKGHEGIKGNVEVDRLAK 800
             ++ WI GH GI GN   D+LAK
Sbjct:  1395 QVRWIPGHSGIAGNELADKLAK 1416

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000040226 AN2661 [Emericella nidulans (taxid:162425)]

 Score = 126 (49.4 bits), Expect = 0.00053, P = 0.00053
 Identities = 40/140 (28%), Positives = 67/140 (47%)

Query:   675 AICIYTDASKKNEKVG---AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLK 731
             AI +Y+D S+  +  G   A +F P   +K      P T  Y AE++G  E L+ +    
Sbjct:  1234 AISVYSDGSRTGQGAGYGYAIYFGPILVTKGHGPAGPRTEVYDAEIMGAVEGLRAALGQP 1293

Query:   732 ----NNEILILTDSKSACQKLS-------KNCLNTTPTHLELEILSSYKHLQNTCKTVKL 780
                 + +++IL D+ +A   L+       ++ L+ +   L  + L +   L    K +++
Sbjct:  1294 CVGYSTQLVILLDNLAAASLLASYRPTPHRHGLSESFGQLATQWLEAPSILTRPRKPLQV 1353

Query:   781 AWIKGHEGIKGNVEVDRLAK 800
              WI GH GI GN   D+LAK
Sbjct:  1354 RWIPGHSGIAGNELADKLAK 1373


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        0.310   0.127   0.360    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      821       562    0.0010  119 3  11 23  0.49    34
                                                     35  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  619 (66 KB)
  Total size of DFA:  328 KB (2167 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:03
  No. of threads or processors used:  24
  Search cpu time:  54.63u 0.08s 54.71t   Elapsed:  00:00:16
  Total cpu time:  54.63u 0.08s 54.71t   Elapsed:  00:00:19
  Start:  Thu Aug 15 11:28:07 2013   End:  Thu Aug 15 11:28:26 2013

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	821
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	3e-26
pfam00075	126	pfam00075, RNase_H, RNase H	2e-15
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	3e-15
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	4e-15
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	8e-15
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-14
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-13
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	3e-12
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-11
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	1e-11
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-11
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	7e-11
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	8e-11
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-10
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	4e-10
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-10
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-10
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	7e-10
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	1e-09
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-09
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-09
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	1e-09
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	3e-09
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	3e-09
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	4e-09
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	5e-09
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	7e-09
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-08
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	2e-08
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	2e-08
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	3e-08
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	4e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	4e-08
PRK12727	559	PRK12727, PRK12727, flagellar biosynthesis regulat	4e-08
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	4e-08
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	6e-08
PRK12372	413	PRK12372, PRK12372, ribonuclease III; Reviewed	1e-07
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-07
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-07
PRK12323	700	PRK12323, PRK12323, DNA polymerase III subunits ga	2e-07
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	2e-07
PRK14900	1052	PRK14900, valS, valyl-tRNA synthetase; Provisional	2e-07
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	3e-07
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	4e-07
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	4e-07
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	4e-07
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	4e-07
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	4e-07
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	5e-07
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	6e-07
PRK12373	400	PRK12373, PRK12373, NADH dehydrogenase subunit E;	6e-07
PRK12373	400	PRK12373, PRK12373, NADH dehydrogenase subunit E;	6e-07
PHA03378	991	PHA03378, PHA03378, EBNA-3B; Provisional	7e-07
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	7e-07
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	7e-07
PLN03209	576	PLN03209, PLN03209, translocon at the inner envelo	1e-06
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-06
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	2e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	2e-06
PRK14900	1052	PRK14900, valS, valyl-tRNA synthetase; Provisional	2e-06
PRK12373	400	PRK12373, PRK12373, NADH dehydrogenase subunit E;	2e-06
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-06
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-06
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	2e-06
PHA03378	991	PHA03378, PHA03378, EBNA-3B; Provisional	3e-06
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	3e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	4e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	5e-06
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	6e-06
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	6e-06
PRK08691	709	PRK08691, PRK08691, DNA polymerase III subunits ga	6e-06
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	7e-06
PRK12727	559	PRK12727, PRK12727, flagellar biosynthesis regulat	8e-06
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	9e-06
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-05
PRK07764	824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	1e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-05
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	1e-05
PRK14949	944	PRK14949, PRK14949, DNA polymerase III subunits ga	1e-05
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	1e-05
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-05
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	2e-05
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	2e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	2e-05
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	2e-05
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-05
pfam05109	830	pfam05109, Herpes_BLLF1, Herpes virus major outer	2e-05
pfam05109	830	pfam05109, Herpes_BLLF1, Herpes virus major outer	2e-05
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	3e-05
TIGR01347	403	TIGR01347, sucB, 2-oxoglutarate dehydrogenase comp	3e-05
PRK05704	407	PRK05704, PRK05704, dihydrolipoamide succinyltrans	4e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	5e-05
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	5e-05
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	5e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	6e-05
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	6e-05
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	6e-05
TIGR01347	403	TIGR01347, sucB, 2-oxoglutarate dehydrogenase comp	7e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	8e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	8e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	8e-05
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	8e-05
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	9e-05
PRK10118	408	PRK10118, PRK10118, flagellar hook-length control	9e-05
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	9e-05
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	1e-04
PRK07994	647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-04
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	1e-04
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	1e-04
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-04
pfam02993	238	pfam02993, MCPVI, Minor capsid protein VI	1e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-04
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	1e-04
PRK12372	413	PRK12372, PRK12372, ribonuclease III; Reviewed	2e-04
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	2e-04
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	2e-04
TIGR02813	2582	TIGR02813, omega_3_PfaA, polyketide-type polyunsat	2e-04
COG3087	264	COG3087, FtsN, Cell division protein [Cell divisio	2e-04
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	3e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	3e-04
pfam05109	830	pfam05109, Herpes_BLLF1, Herpes virus major outer	3e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	3e-04
PHA03269	566	PHA03269, PHA03269, envelope glycoprotein C; Provi	3e-04
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	4e-04
PRK14900	1052	PRK14900, valS, valyl-tRNA synthetase; Provisional	4e-04
PRK12373	400	PRK12373, PRK12373, NADH dehydrogenase subunit E;	4e-04
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	4e-04
pfam10667	245	pfam10667, DUF2486, Protein of unknown function (D	4e-04
PRK12727	559	PRK12727, PRK12727, flagellar biosynthesis regulat	5e-04
PRK05704	407	PRK05704, PRK05704, dihydrolipoamide succinyltrans	5e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	5e-04
PRK12799	421	PRK12799, motB, flagellar motor protein MotB; Revi	5e-04
TIGR02927	579	TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogena	5e-04
pfam07382	187	pfam07382, HC2, Histone H1-like nucleoprotein HC2	5e-04
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	6e-04
pfam10310	436	pfam10310, DUF2413, Protein of unknown function (D	6e-04
PRK14951	618	PRK14951, PRK14951, DNA polymerase III subunits ga	7e-04
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	7e-04
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	7e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	8e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	8e-04
PHA03379	935	PHA03379, PHA03379, EBNA-3A; Provisional	8e-04
pfam05539	408	pfam05539, Pneumo_att_G, Pneumovirinae attachment	9e-04
COG5373	931	COG5373, COG5373, Predicted membrane protein [Func	9e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.001
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	0.001
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	0.001
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	0.001
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	0.001
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	0.001
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.001
pfam07382	187	pfam07382, HC2, Histone H1-like nucleoprotein HC2	0.001
pfam07382	187	pfam07382, HC2, Histone H1-like nucleoprotein HC2	0.001
COG5373	931	COG5373, COG5373, Predicted membrane protein [Func	0.001
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.001
PRK14900	1052	PRK14900, valS, valyl-tRNA synthetase; Provisional	0.002
PRK06995	484	PRK06995, flhF, flagellar biosynthesis regulator F	0.002
PRK08691	709	PRK08691, PRK08691, DNA polymerase III subunits ga	0.002
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	0.002
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	0.002
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	0.002
PRK11901	327	PRK11901, PRK11901, hypothetical protein; Reviewed	0.002
PRK11901	327	PRK11901, PRK11901, hypothetical protein; Reviewed	0.002
PHA03291	401	PHA03291, PHA03291, envelope glycoprotein I; Provi	0.002
PTZ00449	943	PTZ00449, PTZ00449, 104 kDa microneme/rhoptry anti	0.002
pfam05283	187	pfam05283, MGC-24, Multi-glycosylated core protein	0.002
PRK14948	620	PRK14948, PRK14948, DNA polymerase III subunits ga	0.002
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	0.002
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	0.003
PRK14900	1052	PRK14900, valS, valyl-tRNA synthetase; Provisional	0.003
PRK14950	585	PRK14950, PRK14950, DNA polymerase III subunits ga	0.003
PTZ00144	418	PTZ00144, PTZ00144, dihydrolipoamide succinyltrans	0.003
PRK11855	547	PRK11855, PRK11855, dihydrolipoamide acetyltransfe	0.003
PHA03269	566	PHA03269, PHA03269, envelope glycoprotein C; Provi	0.003
PHA03269	566	PHA03269, PHA03269, envelope glycoprotein C; Provi	0.003
PRK14971	614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.003
TIGR02927	579	TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogena	0.003
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	0.003
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	0.003
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	0.003
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	0.003
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	0.003
PRK14959	624	PRK14959, PRK14959, DNA polymerase III subunits ga	0.003
PHA03247	3151	PHA03247, PHA03247, large tegument protein UL36; P	0.004
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	0.004
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	0.004
PRK00708	209	PRK00708, PRK00708, sec-independent translocase; P	0.004
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.004
pfam05109	830	pfam05109, Herpes_BLLF1, Herpes virus major outer	0.004
PRK10856	331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	0.004
PRK12799	421	PRK12799, motB, flagellar motor protein MotB; Revi	0.004
pfam06070	777	pfam06070, Herpes_UL32, Herpesvirus large structur	0.004
PRK11907	814	PRK11907, PRK11907, bifunctional 2',3'-cyclic nucl	0.004

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

 Score =  103 bits (260), Expect = 3e-26
 Identities = 44/130 (33%), Positives = 64/130 (49%), Gaps = 6/130 (4%)

Query: 677 CIYTDASKKNEKVGAAWFCP-TYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNN-- 733
            IYTD SK   + GA +           +KL P  S + AE++ I EAL+ +        
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 734 EILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNV 793
           +I I +DS++A + L       + + L L I  + + L N    V+L W+ GH GI+GN 
Sbjct: 61  KITIFSDSQAALKALRSP---RSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNE 117

Query: 794 EVDRLAKYAT 803
             DRLAK A 
Sbjct: 118 RADRLAKEAA 127

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 = 73.1 bits (180), Expect = 2e-15
 Identities = 40/130 (30%), Positives = 61/130 (46%), Gaps = 10/130 (7%)

Query: 673 PNAICIYTDAS-KKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLK 731
           P A+ +YTD S   N   G A +  T   K   K  P T+   AE++ + EAL+   +L 
Sbjct: 1   PEAVTVYTDGSCNGNPGPGGAGYV-TDGGKQRSKPLPGTTNQRAELLALIEALE---ALS 56

Query: 732 NNEILILTDSKSACQKLSKNCLNTT-PTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIK 790
             ++ I TDS+     ++      +    ++ EI    + LQ     V + W+ GH GI 
Sbjct: 57  GQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW---ELLQKK-HKVYIQWVPGHSGIP 112

Query: 791 GNVEVDRLAK 800
           GN   D+LAK
Sbjct: 113 GNELADKLAK 122

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|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 79.9 bits (197), Expect = 3e-15
 Identities = 62/252 (24%), Positives = 91/252 (36%), Gaps = 13/252 (5%)

Query: 184 AEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTT 243
           A  + A++ + A    A+     AAGAA+A K A AA  T    P A PA      T   
Sbjct: 382 APGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAP---PATADR 438

Query: 244 KTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTI 303
               A   A  PV   A   A    +   + A  P  +   S   +  P       A   
Sbjct: 439 GDDAADGDA--PVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRA 496

Query: 304 TKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTA 363
              + +T +A P   AP  AA ++   A A  P P    P P            +A    
Sbjct: 497 AAPSAATPAAVPDARAPA-AASREDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALDV 555

Query: 364 SRTSSSSVTS------ASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPA 417
            R +   V+S      A+AAKPAA     + + +A + A +  T +    +     +  A
Sbjct: 556 LRNAGMRVSSDRGARAAAAAKPAAAP-AAAPKPAAPRVAVQVPTPRARAATGDAPPNGAA 614

Query: 418 TATRPATTTSKP 429
            A + A +   P
Sbjct: 615 RAEQAAESRGAP 626

Length = 830

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 79.1 bits (195), Expect = 4e-15
 Identities = 64/277 (23%), Positives = 85/277 (30%), Gaps = 39/277 (14%)

Query: 167 PLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKP 226
           P   VP     A     A  + A    A     A+   A AA A  A   A A +     
Sbjct: 368 PGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATR----- 422

Query: 227 GPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKST 286
              A PA+     T       A   A  PV   A   A    +   + A  P  +   S 
Sbjct: 423 -AEAPPAAPAPPATADRGDDAADGDA--PVPAKANARASADSRCDERDAQPPADSGSASA 479

Query: 287 TTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPK 346
             +  P       A      + +T +A P   AP  AA ++   A A  P P    P P 
Sbjct: 480 PASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPA-AASREDAPAAAAPPAPEARPPTP- 537

Query: 347 PLTNGVTKRPVSATTTASRTSSSSVTSASAA----KPAAPRVPLSQRTSAAKPATKPATA 402
                           A+   ++    A+AA    + A  RV  S R + A  A KPA A
Sbjct: 538 ----------------AAAAPAARAGGAAAALDVLRNAGMRVS-SDRGARAAAAAKPAAA 580

Query: 403 KPSTTSKPTTASKPATATRPATTTSKPATTTSTDIED 439
                     A+    A R A     P    +T    
Sbjct: 581 PA--------AAPKPAAPRVAVQVPTPRARAATGDAP 609

Length = 830

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 78.4 bits (193), Expect = 8e-15
 Identities = 56/248 (22%), Positives = 78/248 (31%), Gaps = 6/248 (2%)

Query: 174 IPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPA 233
           +P       +A  ++A   + A    A    A  A AA A  +A A      P   A   
Sbjct: 380 VPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRG 439

Query: 234 SKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAP----KSTTTA 289
                          A    S   +     A+P     +  AP            +   A
Sbjct: 440 DDAADGDAPVPAKANA--RASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAA 497

Query: 290 PKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLT 349
              A     V       A S   A    + P P A     AA AP  R   AA A   L 
Sbjct: 498 APSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALDVLR 557

Query: 350 NGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSK 409
           N   +        A+  +  +   A+A KPAAPRV +   T  A+ AT  A    +  ++
Sbjct: 558 NAGMRVSSDRGARAAAAAKPAAAPAAAPKPAAPRVAVQVPTPRARAATGDAPPNGAARAE 617

Query: 410 PTTASKPA 417
               S+ A
Sbjct: 618 QAAESRGA 625

Length = 830

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 77.3 bits (190), Expect = 3e-14
 Identities = 62/283 (21%), Positives = 80/283 (28%), Gaps = 37/283 (13%)

Query: 217  ATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPAT-KPA 275
             +     D P P   P   P A  + T        A           A PA       P 
Sbjct: 2693 GSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPG 2752

Query: 276  PKPTTAAPKSTTTAPKPAPVRKPVAS-----TITKTATSTVSAAPKPSAPKPAAPKKPVA 330
                 A P +T   P PAP   P A      T    A+ + S    PS   PA P   V 
Sbjct: 2753 GPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVL 2812

Query: 331  APA-----------PKPRPATAAPAPKPLTNG-----------------VTKRPVSATTT 362
            APA           P P P +A P   P   G                 V +RP S +  
Sbjct: 2813 APAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPA 2872

Query: 363  ASRTSSSSVTSASAAKPAAPRVPLSQ---RTSAAKPATKPATAKPSTTSKPTTASKPATA 419
            A   + +       A+PA  R   S         +P    A   P    +P    +P   
Sbjct: 2873 AKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPP 2932

Query: 420  TRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKSGLITTP 462
              P      P   T+            P+    A+  G +  P
Sbjct: 2933 PPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975

Length = 3151

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 73.8 bits (181), Expect = 3e-13
 Identities = 51/233 (21%), Positives = 74/233 (31%), Gaps = 23/233 (9%)

Query: 204  GAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTK-TTTAAKPAISPVKKTATT 262
                       +   A  +  +P  A +      A +   +    AA+P +  +    T+
Sbjct: 2642 PPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSL----TS 2697

Query: 263  TAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKP 322
             A P P P T P P P      +T   P PA  R+   +          + AP      P
Sbjct: 2698 LADPPPPPPT-PEPAPHALVS-ATPLPPGPAAARQASPAL-------PAAPAPPAVPAGP 2748

Query: 323  AAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAP 382
            A P      PA   RP T A  P P              T    +S S +  S   P  P
Sbjct: 2749 ATP----GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDP 2804

Query: 383  RVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTST 435
              P +   + A  A  P  A P+    P T+++P     P      P  +   
Sbjct: 2805 ADPPAAVLAPA--AALPPAASPAGPLPPPTSAQPTA---PPPPPGPPPPSLPL 2852

Length = 3151

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 69.9 bits (171), Expect = 3e-12
 Identities = 60/231 (25%), Positives = 76/231 (32%), Gaps = 14/231 (6%)

Query: 200 ALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKT 259
           A   G +  GA  A   A AA        AA PA+   A         AA  A +  +  
Sbjct: 362 AFRPGQSGGGAGPA--TAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAV 419

Query: 260 ATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSA 319
           A   A+ +P P    A +  +A       AP PAP   P A+     A     AA   +A
Sbjct: 420 AAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAA 479

Query: 320 PKPAAPKKPVAAPAPKPR---------PATAAPAPKPLTNGVTKRPVSATTTASRTSSSS 370
           P  AA   P AAPAP            P  A+PAP             +    +      
Sbjct: 480 PARAA---PAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDD 536

Query: 371 VTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATR 421
                A  PAA   P +   +    A +P  A  S          PA A R
Sbjct: 537 AFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMFDGDWPALAAR 587

Length = 700

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 68.4 bits (167), Expect = 1e-11
 Identities = 54/257 (21%), Positives = 78/257 (30%), Gaps = 22/257 (8%)

Query: 226  PGPAAKP-ASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPK----PATKPAPKPTT 280
              PA    A +P A   + +          P      +   P       P   P+P    
Sbjct: 2578 SEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANE 2637

Query: 281  AAPKSTTTAPKPA-PVRKPVASTITKT-ATSTVSAAPKPSAPKPAAPKKPVAAPA----- 333
              P    T P P  P   P    +++      +  A + S+P P  P++  A P      
Sbjct: 2638 PDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-PQRPRRRAARPTVGSLT 2696

Query: 334  ----PKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQR 389
                P P P T  PAP  L +     P  A    + + +     A  A PA P  P    
Sbjct: 2697 SLADPPPPPPTPEPAPHALVSATPLPPGPAAARQA-SPALPAAPAPPAVPAGPATPGGPA 2755

Query: 390  TSAAKPAT----KPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPF 445
              A  P T     PA         P   ++PA A+   +  S P+     D    +  P 
Sbjct: 2756 RPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPA 2815

Query: 446  TPEELEAAIKSGLITTP 462
                  A+    L    
Sbjct: 2816 AALPPAASPAGPLPPPT 2832

Length = 3151

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 68.0 bits (166), Expect = 1e-11
 Identities = 48/214 (22%), Positives = 63/214 (29%), Gaps = 6/214 (2%)

Query: 227 GPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKST 286
           G  A PA+   A         AA  A +P    A   A PA  PA   A +   AAP   
Sbjct: 369 GGGAGPATAAAAPVAQPAPAAAAPAAAAPAP--AAPPAAPAAAPAAAAAARAVAAAPARR 426

Query: 287 TTAPKPAPV---RKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPK-PRPATAA 342
           + AP+                       +AAP  +A   AA  +PVAA A   P  A  A
Sbjct: 427 SPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPA 486

Query: 343 PAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATA 402
            AP P  +            AS   +    + +     +   P +     A     PA A
Sbjct: 487 AAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPA 546

Query: 403 KPSTTSKPTTASKPATATRPATTTSKPATTTSTD 436
                              P  + S        D
Sbjct: 547 AAPAPRAAAATEPVVAPRPPRASASGLPDMFDGD 580

Length = 700

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 68.0 bits (166), Expect = 2e-11
 Identities = 63/345 (18%), Positives = 89/345 (25%), Gaps = 38/345 (11%)

Query: 104  PKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAE 163
            P+       V   TS+ D  P     E +P   V           A   P     +  A 
Sbjct: 2683 PRRRAARPTVGSLTSLADPPPPPPTPEPAPHALV----------SATPLPPGPAAARQAS 2732

Query: 164  KETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKT 223
               P +  P                A     A            A A  A   A   ++ 
Sbjct: 2733 PALPAAPAPPAVPAGPATPGGPARPARPPTTA---------GPPAPAPPAAPAAGPPRRL 2783

Query: 224  DKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAP 283
                PA    S+      +         A+          A PA      P P PT+A P
Sbjct: 2784 --TRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAG-----PLPPPTSAQP 2836

Query: 284  KSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKP----VAAPAPKPRPA 339
             +    P P P   P+  ++            +  A KPAAP +P    +A PA      
Sbjct: 2837 TAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTE 2896

Query: 340  TAA---PAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQ-----RTS 391
            + A     P+         P                     +P  P  P +        S
Sbjct: 2897 SFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPS 2956

Query: 392  AAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTD 436
             A P        P   + P         +R A  +S P  T  + 
Sbjct: 2957 GAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001

Length = 3151

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 65.5 bits (160), Expect = 7e-11
 Identities = 50/144 (34%), Positives = 55/144 (38%), Gaps = 17/144 (11%)

Query: 205 AAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTA 264
           AAAA AA       A KKT     AA PA+ P+A+        AA  A +         A
Sbjct: 367 AAAAEAAAP-----AEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAA 421

Query: 265 KPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAA 324
            PAP  A  PA     AAP     A  PA V    A      A     A P   AP+PA 
Sbjct: 422 PPAPVAA--PAAAAPAAAP-----AAAPAAVALAPAPPA--QAAPETVAIPVRVAPEPAV 472

Query: 325 PKKPVAAPAPKPRPATAAPAPKPL 348
                AAPAP   PA A   P   
Sbjct: 473 ---ASAAPAPAAAPAAARLTPTEE 493

Length = 618

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 65.6 bits (160), Expect = 8e-11
 Identities = 50/219 (22%), Positives = 68/219 (31%), Gaps = 33/219 (15%)

Query: 202 VVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTAT 261
           V G  A G  V  + A A      P P A+ A+   A         +A PA++ V  T  
Sbjct: 362 VTGGGAPGGGVPARVAGAV-----PAPGARAAAAVGA---------SAVPAVTAV--TGA 405

Query: 262 TTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPK 321
             A  APK A   A     A P +                     A +   A+      +
Sbjct: 406 AGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDE 465

Query: 322 PAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAA 381
             A  +P A       PA+ AP               A   A+ ++++      A  PAA
Sbjct: 466 RDA--QPPADSGSASAPASDAPPDAAFE--------PAPRAAAPSAATPAAVPDARAPAA 515

Query: 382 PRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATAT 420
                  R  A   A  PA      T  P  A+  A A 
Sbjct: 516 A-----SREDAPAAAAPPAPEARPPT--PAAAAPAARAG 547

Length = 830

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 64.7 bits (158), Expect = 1e-10
 Identities = 38/146 (26%), Positives = 52/146 (35%), Gaps = 21/146 (14%)

Query: 266 PAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAP 325
            A   A  PA K T A P++   A  P              A +   AA   +A    A 
Sbjct: 367 AAAAEAAAPAEKKTPARPEAAAPAAAPVAQ----------AAAAPAPAAAPAAAASAPAA 416

Query: 326 KKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVP 385
               A PAP   PA AAPA  P           A   A+   + +  + +A +  A  V 
Sbjct: 417 PPAAAPPAPVAAPAAAAPAAAP-----------AAAPAAVALAPAPPAQAAPETVAIPVR 465

Query: 386 LSQRTSAAKPATKPATAKPSTTSKPT 411
           ++   + A  A  PA A  +    PT
Sbjct: 466 VAPEPAVASAAPAPAAAPAAARLTPT 491

Length = 618

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 63.3 bits (154), Expect = 4e-10
 Identities = 48/338 (14%), Positives = 79/338 (23%), Gaps = 41/338 (12%)

Query: 116 PTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIP 175
               P   P      E+P+     +                  S T    +        P
Sbjct: 63  DRFEPPTGPPPGPGTEAPANE-SRSTPTWSLSTLAPASPAREGSPTPPGPSSPDP---PP 118

Query: 176 QEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASK 235
                               +  G+     AA+  A     A  A        AA P S 
Sbjct: 119 PTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSS 178

Query: 236 PLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPV 295
           P               A S        +  PA      P      +A  S+   P PAP 
Sbjct: 179 P----------EETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASS---PAPAPG 225

Query: 296 RKPVASTITKTATSTVS-----------AAPKPSAPKPAAPKKPVAAPAPKPRPATA--- 341
           R         ++ S+ S             P P       P +   A       +     
Sbjct: 226 RSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPA 285

Query: 342 -------APAPKPLTNGVTKRPVSATTTASRT---SSSSVTSASAAKPAAPRVPLSQRTS 391
                    +P P  +     P  ++  AS +   S  S +S++++   + R        
Sbjct: 286 SSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGP 345

Query: 392 AAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKP 429
           +   +  P+   P             +    +   S  
Sbjct: 346 SPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAG 383

Length = 1352

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 62.9 bits (153), Expect = 5e-10
 Identities = 55/287 (19%), Positives = 99/287 (34%), Gaps = 22/287 (7%)

Query: 152 TPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAA--AG 209
           +  D           P S  P + +  + V S     A+S  AA  + A V   AA    
Sbjct: 112 SSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQ 171

Query: 210 AAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTT---KTTTAAKPAISPVKKTATTTAKP 266
           AA+ +       +     PA  P S P A  +     +++  +  A SP      + A  
Sbjct: 172 AALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADD 231

Query: 267 APKPA---TKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPA 323
           A   +   +          P++    P+PAP+  P  + I + +     ++    A   +
Sbjct: 232 AGASSSDSSSSESSGCGWGPENECPLPRPAPITLP--TRIWEASGWNGPSSRPGPASSSS 289

Query: 324 APKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAP- 382
           +P          P P+ ++P   P  +       S+++  S +SS+S +S S+   A   
Sbjct: 290 SP------RERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSP 343

Query: 383 -----RVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPAT 424
                R P   R       + P      + +  + A+     TR   
Sbjct: 344 GPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRA 390

Length = 1352

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 62.7 bits (153), Expect = 5e-10
 Identities = 48/219 (21%), Positives = 61/219 (27%), Gaps = 16/219 (7%)

Query: 226 PGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKS 285
           P P A     P A  ++     AA+PA           A PA   A  PA      A  S
Sbjct: 590 PAPGAAGGEGPPAPASSGPPEEAARPA---------APAAPAAPAAPAPAGAAAAPAEAS 640

Query: 286 TTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRP-----AT 340
              AP  A             A+      P  +    AAP  P  APAP         A 
Sbjct: 641 AAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGG--AAPAAPPPAPAPAAPAAPAGAAP 698

Query: 341 AAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPA 400
           A PAP P       +         + +  +   + AA    P  P          A    
Sbjct: 699 AQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQP 758

Query: 401 TAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIED 439
              P+       A+ P  +              S D ED
Sbjct: 759 PPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDED 797

Length = 824

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 62.6 bits (152), Expect = 7e-10
 Identities = 50/245 (20%), Positives = 74/245 (30%), Gaps = 17/245 (6%)

Query: 149 AVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAA 208
           A + P     +     E P    P  P    T +  +++ A  D            A + 
Sbjct: 408 AALAPKAAAAAAATRAEAP----PAAPAPPATADRGDDA-ADGDAPVPAKANARASADSR 462

Query: 209 GAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAP 268
                 +    +     P   A P +           + A   A+   +  A  + + AP
Sbjct: 463 CDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAP 522

Query: 269 KPATKPAPK-----PTTAAPKSTTTAPKPA-PVRKPVASTITKTATSTVSAAPKPSAPKP 322
             A  PAP+     P  AAP +       A  V +     ++    +  +AA KP+A   
Sbjct: 523 AAAAPPAPEARPPTPAAAAPAARAGGAAAALDVLRNAGMRVSSDRGARAAAAAKPAAAPA 582

Query: 323 AAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAP 382
           AAPK         PR A   P P+         P  A        S          P   
Sbjct: 583 AAPKPAA------PRVAVQVPTPRARAATGDAPPNGAARAEQAAESRGAPPPWEDIPPDD 636

Query: 383 RVPLS 387
            VPLS
Sbjct: 637 YVPLS 641

Length = 830

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 61.4 bits (149), Expect = 1e-09
 Identities = 49/182 (26%), Positives = 63/182 (34%), Gaps = 12/182 (6%)

Query: 170 EVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPA 229
                P  A    +   + A++  A  VA A    + A  A  A ++A+A      P PA
Sbjct: 392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPA 451

Query: 230 AKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPK-PATKPAPKPTTAAP--KST 286
             PA+ P A         A   A  P    A   A PA   PA  PAP      P  +  
Sbjct: 452 PAPAAAPAA--------AARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELP 503

Query: 287 TTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATA-APAP 345
                PAP +   A       +    A   P          P AAPAP+   AT    AP
Sbjct: 504 PEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAP 563

Query: 346 KP 347
           +P
Sbjct: 564 RP 565

Length = 700

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 61.3 bits (149), Expect = 1e-09
 Identities = 43/133 (32%), Positives = 53/133 (39%), Gaps = 12/133 (9%)

Query: 228 PAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTA-KPAPKPATKPAPKPTTAAPKST 286
           PAA   +   A+  T     AA PA +PV + A   A   AP  A      P  AAP   
Sbjct: 366 PAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAP--- 422

Query: 287 TTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAP---APKPRPATAAP 343
                PAPV  P A+       +  +A     AP   A  + VA P   AP+P  A+AAP
Sbjct: 423 -----PAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAP 477

Query: 344 APKPLTNGVTKRP 356
           AP          P
Sbjct: 478 APAAAPAAARLTP 490

Length = 618

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 62.2 bits (152), Expect = 1e-09
 Identities = 32/107 (29%), Positives = 43/107 (40%), Gaps = 4/107 (3%)

Query: 269 KPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKP 328
            P +  AP    AA  +  +AP  AP  K  A+       +   AAP   A   AA   P
Sbjct: 37  GPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAP 96

Query: 329 VAAPAPKPRPATAAPAPKPLTNGVTK-RPVSATTTASRTSSSSVTSA 374
            A PA       AAPA   + + VT  R  +A    +  +S  V +A
Sbjct: 97  AAPPAAAA---AAAPAAAAVEDEVTPLRGAAAAVAKNMDASLEVPTA 140

Length = 1228

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 60.3 bits (146), Expect = 1e-09
 Identities = 40/135 (29%), Positives = 48/135 (35%), Gaps = 2/135 (1%)

Query: 193 LAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPA 252
           LAA  A      A    A    KKA+A  K+     + K A+K     +  K    A  A
Sbjct: 191 LAAVGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAK--TAVSAKKAAKTAAKA 248

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVS 312
               KKTA    K A K   K A K   AA K+   A K    +        K A +   
Sbjct: 249 AKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSK 308

Query: 313 AAPKPSAPKPAAPKK 327
           A     APK  A  K
Sbjct: 309 AKATAKAPKRGAKGK 323

Length = 333

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 60.7 bits (147), Expect = 3e-09
 Identities = 64/386 (16%), Positives = 106/386 (27%), Gaps = 24/386 (6%)

Query: 96   EKTPEVSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTD 155
              TPE +         L   P +     P   A    P+                  P  
Sbjct: 2705 PPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPG-----GPARPAR 2759

Query: 156  ETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVK 215
               +       P +     P    T  +    + S +            AA    A A+ 
Sbjct: 2760 PPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

Query: 216  KATAAKKTDKPGPAAKPASKPLAK--TTTTKTTTAAKPAISPVKKTATTTAKPAPKPATK 273
             A +      P  +A+P + P        +     +      V++   + + PA KPA  
Sbjct: 2820 PAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS-PAAKPAAP 2878

Query: 274  PAPK----PTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPV 329
              P        A  +ST +   P    +                 P P  P+P  P  P 
Sbjct: 2879 ARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPR 2938

Query: 330  AAPAPKPRPATAA------PAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPR 383
              P   P    A         P+P    +    V+         + S  + +++ P    
Sbjct: 2939 PQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTG 2998

Query: 384  VPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIE----- 438
              LS+ +S A          P   S   T   P         +   + +  +D+E     
Sbjct: 2999 HSLSRVSSWASSLALHEETDPPPVSLKQTLWPPDDTEDSDADSLFDSDSERSDLEALDPL 3058

Query: 439  -DEMNQPFTPEELEAAIKSGLITTPG 463
              E + PF  E   A  ++G   +P 
Sbjct: 3059 PPEPHDPFAHEPDPATPEAGARESPS 3084

Length = 3151

>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 = 55.1 bits (133), Expect = 3e-09
 Identities = 31/135 (22%), Positives = 50/135 (37%), Gaps = 24/135 (17%)

Query: 679 YTDASKKNE--KVGAAWFCPTYKSKACFKLH-----PATSTYTAEVIGIWEALKYSASLK 731
            TD S K      GA         +  +        PA +   AE++ + EAL+ +  L 
Sbjct: 1   NTDGSCKGNPGPAGAGGVL--RDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58

Query: 732 NNEILILTDSKSACQKLSKNCLNTTPTHLELEI----LSSYKHLQNTCKTVKLAWIKGHE 787
             +++I TDSK     ++         +L L      LS +  ++          +    
Sbjct: 59  LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFE-------HVPR-- 109

Query: 788 GIKGNVEVDRLAKYA 802
             +GN   DRLAK A
Sbjct: 110 --EGNEVADRLAKEA 122

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

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 59.9 bits (145), Expect = 4e-09
 Identities = 40/200 (20%), Positives = 53/200 (26%), Gaps = 25/200 (12%)

Query: 248 AAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTA 307
           A +PA++                   P  +   A   S   A                  
Sbjct: 357 AFEPAVTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTG------------ 404

Query: 308 TSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATA----------APAPKPLTNGVTKRPV 357
                AA  P A   AA  +  A PA    PATA          AP P       +    
Sbjct: 405 --AAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSR 462

Query: 358 SATTTASRTSSSSVTSASAA-KPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKP 416
                A   + S   SA A+  P       + R +A   AT  A       +  +    P
Sbjct: 463 CDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAP 522

Query: 417 ATATRPATTTSKPATTTSTD 436
           A A  PA     P    +  
Sbjct: 523 AAAAPPAPEARPPTPAAAAP 542

Length = 830

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 59.3 bits (144), Expect = 5e-09
 Identities = 35/126 (27%), Positives = 47/126 (37%)

Query: 296 RKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKR 355
           +   A+     A     A P+ +AP  A   +  AAPAP   PA AA AP          
Sbjct: 365 KPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPA 424

Query: 356 PVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASK 415
           PV+A   A+  ++ +   A+ A   AP    +  T A      P  A  S    P  A  
Sbjct: 425 PVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPA 484

Query: 416 PATATR 421
            A  T 
Sbjct: 485 AARLTP 490

Length = 618

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 59.4 bits (144), Expect = 7e-09
 Identities = 49/209 (23%), Positives = 73/209 (34%), Gaps = 15/209 (7%)

Query: 199 GALVVGAAAAGAAVAVKKATAAKKTDKP------GPAAKPASKPLAKTTTTKTTTAAKPA 252
           G LV  +A   A   V  A A  + + P           PA++  +  T + +T A    
Sbjct: 41  GQLVSDSAELAAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASP 100

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVS 312
                 T    + P P P T P   P    P   + AP  + + +PV S     A S   
Sbjct: 101 AREGSPTPPGPSSPDPPPPTPPPASP---PP---SPAPDLSEMLRPVGSPGPPPAASPP- 153

Query: 313 AAPKPSAPKPAAPKKP--VAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSS 370
           AA    A   +        A P   P     AP+  P     +  P +A+    R SS  
Sbjct: 154 AAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPI 213

Query: 371 VTSASAAKPAAPRVPLSQRTSAAKPATKP 399
             SAS+  PA  R       +++  ++  
Sbjct: 214 SASASSPAPAPGRSAADDAGASSSDSSSS 242

Length = 1352

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 57.6 bits (139), Expect = 2e-08
 Identities = 46/206 (22%), Positives = 56/206 (27%), Gaps = 10/206 (4%)

Query: 260  ATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSA 319
            A   + P P+PA +P+    T+  +     P+ A  R PV             A P P  
Sbjct: 2563 APDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDR----GDPRGPAPPSPLP 2618

Query: 320  PKPAAPKKPVAAPAPKPRP-ATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAK 378
            P   AP      P P P P A       P T    +RP        R S           
Sbjct: 2619 PDTHAPD----PPPPSPSPAANEPDPHPPPTVPPPERPRDD-PAPGRVSRPRRARRLGRA 2673

Query: 379  PAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIE 438
              A   P   R  AA+P     T+       P T      A   AT              
Sbjct: 2674 AQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASP 2733

Query: 439  DEMNQPFTPEELEAAIKSGLITTPGR 464
                 P  P         G    P R
Sbjct: 2734 ALPAAPAPPAVPAGPATPGGPARPAR 2759

Length = 3151

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 57.4 bits (139), Expect = 2e-08
 Identities = 32/131 (24%), Positives = 45/131 (34%), Gaps = 6/131 (4%)

Query: 311 VSAAPKPSAPKPAAPKKPVAA-PAPKPRPATA-APAPKPLTNGVTKRPVSATTTASRTSS 368
            +AA   +  +   P +P AA PA  P    A APAP          P +    A     
Sbjct: 367 AAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAA----P 422

Query: 369 SSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSK 428
            +  +A AA   A     +    A  PA     A  +       A +PA A+      + 
Sbjct: 423 PAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAA 482

Query: 429 PATTTSTDIED 439
           PA    T  E+
Sbjct: 483 PAAARLTPTEE 493

Length = 618

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 56.4 bits (136), Expect = 2e-08
 Identities = 33/141 (23%), Positives = 40/141 (28%), Gaps = 7/141 (4%)

Query: 243 TKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVAST 302
            K       A S  KK +      A K + K A K   +A K+  TA K A   K  A  
Sbjct: 199 AKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKK 258

Query: 303 ITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTT 362
             K A   V  A K +A   A   K  A        A           G      S    
Sbjct: 259 ALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKA-------GKKAAAGSKAKA 311

Query: 363 ASRTSSSSVTSASAAKPAAPR 383
            ++          A K    R
Sbjct: 312 TAKAPKRGAKGKKAKKVTKKR 332

Length = 333

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 56.0 bits (135), Expect = 3e-08
 Identities = 38/136 (27%), Positives = 46/136 (33%), Gaps = 6/136 (4%)

Query: 224 DKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAP 283
            K       A     K +    + A K +    KK A  TA  A K A K A K    A 
Sbjct: 199 AKKAAKTPAAKSGAKKASAKAKSAAKKVS----KKKAAKTAVSA-KKAAKTAAKAAKKAK 253

Query: 284 KSTTTAPK-PAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAA 342
           K+   A K  A   K  A    K A      A K +  K  A KK     A   +    A
Sbjct: 254 KTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATA 313

Query: 343 PAPKPLTNGVTKRPVS 358
            APK    G   + V+
Sbjct: 314 KAPKRGAKGKKAKKVT 329

Length = 333

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 56.6 bits (137), Expect = 4e-08
 Identities = 38/138 (27%), Positives = 47/138 (34%), Gaps = 11/138 (7%)

Query: 248 AAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTA 307
           A KPA +           PA   A  PA  P   A  +   AP  AP     A+  +  A
Sbjct: 363 AFKPAAAAEAAAPAEKKTPARPEAAAPAAAP--VAQAAAAPAPAAAP-----AAAASAPA 415

Query: 308 TSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTS 367
               +A P P A   AA      A AP       AP  +     V          A   +
Sbjct: 416 APPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPV----RVAPEPA 471

Query: 368 SSSVTSASAAKPAAPRVP 385
            +S   A AA PAA R+ 
Sbjct: 472 VASAAPAPAAAPAAARLT 489

Length = 618

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 56.8 bits (138), Expect = 4e-08
 Identities = 24/99 (24%), Positives = 29/99 (29%), Gaps = 18/99 (18%)

Query: 245 TTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTIT 304
            +TAA  A +     A +    AP      AP P   A  +    PKPA           
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAA---------- 88

Query: 305 KTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAP 343
                   AA   +AP         AAPA         P
Sbjct: 89  --------AAAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119

Length = 1228

>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF; Provisional

 Score = 56.5 bits (136), Expect = 4e-08
 Identities = 49/230 (21%), Positives = 67/230 (29%), Gaps = 3/230 (1%)

Query: 173 VIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGP--AA 230
           VI    +T E  E   AS+     V  AL    +   A  A         T    P  A 
Sbjct: 27  VILSNRRTAEGIEIVAASNYDEELVQRALETARSDTPATAAAPAPAPQAPTKPAAPVHAP 86

Query: 231 KPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAP 290
              S     +   +  +AA+  I+ +      +  P   PA  P    +  +P +   A 
Sbjct: 87  LKLSANANMSQRQRVASAAEDMIAAMALRQPVSV-PRQAPAAAPVRAASIPSPAAQALAH 145

Query: 291 KPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTN 350
             A    P            + A    +AP P AP +     AP P PA AA        
Sbjct: 146 AAAVRTAPRQEHALSAVPEQLFADFLTTAPVPRAPVQAPVVAAPAPVPAIAAALAAHAAY 205

Query: 351 GVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPA 400
                            +       AA P     P +    AA  A  PA
Sbjct: 206 AQDDDEQLDDDGFDLDDALPQILPPAALPPIVVAPAAPAALAAVAAAAPA 255

Length = 559

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 56.8 bits (137), Expect = 4e-08
 Identities = 57/266 (21%), Positives = 83/266 (31%), Gaps = 25/266 (9%)

Query: 176  QEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASK 235
            ++A   E+ EE+  SS +  +    +V     AGA    KK   A   +K         K
Sbjct: 1212 KKASESETTEETYGSSAMETENVAEVVKPKGRAGA----KKKAPAAAKEKEEEDEILDLK 1267

Query: 236  PLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPV 295
                     +  A        K   T  A PA + A +  P  + +    +        V
Sbjct: 1268 DRLAAYNLDSAPAQ-----SAKMEETVKAVPARRAAARKKPLASVSVISDSDDDDDDFAV 1322

Query: 296  RKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKR 355
               +A  + K      +AA K +A  PAA KK          PAT     K LT      
Sbjct: 1323 EVSLAERLKKKGGRKPAAANKKAAKPPAAAKKRG--------PATVQSGQKLLTE----- 1369

Query: 356  PVSATTTASRTSSSSVTSASAAKPAAPRVP-LSQRTSAAKPATKPATAKPSTTSKPTTAS 414
             +     A   S         A P   +   +  R +  K          S++S+     
Sbjct: 1370 -MLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAATNKETESSENVSGSSSSEKDEID 1428

Query: 415  KPATATRPATTTSKPATTTSTDIEDE 440
              A   RP     K  T   +D E E
Sbjct: 1429 VSA-KPRPQRANRKQTTYVLSDSESE 1453

Length = 1465

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 56.1 bits (136), Expect = 6e-08
 Identities = 19/84 (22%), Positives = 23/84 (27%)

Query: 265 KPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAA 324
            P    A   A     AA  +   AP       P  +     A +        +A   A 
Sbjct: 37  GPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAP 96

Query: 325 PKKPVAAPAPKPRPATAAPAPKPL 348
              P AA A  P  A       PL
Sbjct: 97  AAPPAAAAAAAPAAAAVEDEVTPL 120

Length = 1228

>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed

 Score = 54.9 bits (132), Expect = 1e-07
 Identities = 62/241 (25%), Positives = 77/241 (31%), Gaps = 43/241 (17%)

Query: 201 LVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAK---PAI---- 253
           L V  + +GA+    +  AAKK      AA P     AK   +K   A+K   P I    
Sbjct: 194 LDVKVSGSGASRRAAEQAAAKKALDEVMAAAPML--AAKPKRSKNARASKHVEPEIVPGV 251

Query: 254 ----------SPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKP-VAST 302
                     SP +K     A+ A   A  PA     AAP         A +R   V + 
Sbjct: 252 KGVQEALDLRSPERKERAA-AREARAAAAAPAATAAAAAPAEEPAVAPMAAIRAAHVETA 310

Query: 303 ITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTT 362
             K   +   AA   +A KPA         A KP  A    A KP           A   
Sbjct: 311 ADKGERAAKPAAADKAADKPADRPDAAEKAAEKPAEAAPRAADKP--------AGQAADP 362

Query: 363 ASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRP 422
           AS ++     SA AA     R                  A P   + P  AS  A   R 
Sbjct: 363 ASSSADKPGASADAAARTPARA--------------RDAAAPDADTPPGGASLAAAQARV 408

Query: 423 A 423
           A
Sbjct: 409 A 409

Length = 413

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 54.9 bits (133), Expect = 1e-07
 Identities = 35/162 (21%), Positives = 54/162 (33%), Gaps = 14/162 (8%)

Query: 246 TTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITK 305
               +P + P       +A+    P    AP    A P    +AP+ AP           
Sbjct: 363 APLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLP------ 416

Query: 306 TATSTVSAAPKP--SAPKPAAPKKPVAAPAPKPRPATAA----PAPKPLTNGVTKRPVSA 359
             TS + AA +    A      KK   A A + RP  +A     + +P  + + K P   
Sbjct: 417 ETTSQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAKK 476

Query: 360 TTTASRTSS-SSVTSASAAKPAAPRVPLSQRTSAAKPATKPA 400
                + ++   V     A P A +  L       + A K A
Sbjct: 477 EAYRWKATNPVEVKKEPVATPKALKKALEH-EKTPELAAKLA 517

Length = 647

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 54.6 bits (131), Expect = 2e-07
 Identities = 48/239 (20%), Positives = 70/239 (29%), Gaps = 27/239 (11%)

Query: 252  AISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTI-----TKT 306
            A  P    A         P     P P+  AP      P   PV   + + I       +
Sbjct: 2486 ARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLEELAS 2545

Query: 307  ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRT 366
              +     P P A  PAAP + V  P P PRP+  A   +        +           
Sbjct: 2546 DDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDR 2605

Query: 367  SSSSVTSASAAKP---AAPRVPLSQRTSAAKPATKPATAK------------PSTTSKPT 411
                  +  +  P    AP  P    + AA                      P   S+P 
Sbjct: 2606 GDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665

Query: 412  TASKPATATRPATTT-------SKPATTTSTDIEDEMNQPFTPEELEAAIKSGLITTPG 463
             A +   A + ++         ++P   + T + D    P TPE    A+ S     PG
Sbjct: 2666 RARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPG 2724

Length = 3151

>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional

 Score = 54.1 bits (130), Expect = 2e-07
 Identities = 46/231 (19%), Positives = 64/231 (27%), Gaps = 19/231 (8%)

Query: 124 PNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVES 183
           P Q      P+ A             V  P     +  A    P +             +
Sbjct: 365 PGQSGGGAGPATAAAAP---------VAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAA 415

Query: 184 AEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTT 243
           A    A+    +    AL     A+        A A      P  AA+PA+         
Sbjct: 416 ARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAA 475

Query: 244 KTTTAAKPAISPVKKTATTTAKP---APKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVA 300
                A+ A +     A     P    P     PAP    AAP        P     P  
Sbjct: 476 AAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIP----DPAT 531

Query: 301 STITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNG 351
           +       +   A     AP+ AA  +PV AP P   P  +A     + +G
Sbjct: 532 ADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRP---PRASASGLPDMFDG 579

Length = 700

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 53.7 bits (129), Expect = 2e-07
 Identities = 36/129 (27%), Positives = 42/129 (32%), Gaps = 1/129 (0%)

Query: 207 AAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKP 266
           AA A  A K   A     K    AK A+K ++K    KT  +AK A     K A    K 
Sbjct: 196 AANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKT 255

Query: 267 APKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPK 326
           A K A K A K    A K    A   A      A+     A           +   A  K
Sbjct: 256 AKK-ALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAK 314

Query: 327 KPVAAPAPK 335
            P      K
Sbjct: 315 APKRGAKGK 323

Length = 333

>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional

 Score = 54.6 bits (131), Expect = 2e-07
 Identities = 30/126 (23%), Positives = 42/126 (33%), Gaps = 19/126 (15%)

Query: 219  AAKKTDKPGPAAKPASK-PLAKT------TTTKTTTAAKPAI-SPVKKTATTTAKPAPKP 270
                 D P   A+PA +  + ++        ++    A  A+ S ++K A    K   + 
Sbjct: 922  QKPTQDGPAAEAQPAQENTVVESAEKAVAAVSEAAQQAATAVASGIEKVAEAVRKTVRRS 981

Query: 271  ATKPAPKPTTAAPKSTTTAP-KPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPV 329
              K A        K    AP K A  +K  A            AA K    K A  KK  
Sbjct: 982  VKKAAATRAAMKKKVAKKAPAKKAAAKKAAAK----------KAAAKKKVAKKAPAKKVA 1031

Query: 330  AAPAPK 335
              PA K
Sbjct: 1032 RKPAAK 1037

Length = 1052

>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 = 50.3 bits (121), Expect = 3e-07
 Identities = 38/148 (25%), Positives = 61/148 (41%), Gaps = 24/148 (16%)

Query: 678 IYTD-ASKKNEKVGAA-----WFCPTYKSKACFKL--HPATSTYTAEVIGIWEALKYSAS 729
           +YTD A + N + GA      +F P +      +L   P T+   AE+  +  AL+    
Sbjct: 2   VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQR-AELRAVIHALRLIKE 60

Query: 730 LKNN--EILILTDSKSACQKLS-----------KNCLNTTPTHLEL--EILSSYKHLQNT 774
           +     +++I TDS+     ++           K        + +L  E+    + L+  
Sbjct: 61  VGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLEELEER 120

Query: 775 CKTVKLAWIKGHEGIKGNVEVDRLAKYA 802
              VK   + GH GI GN E DRLAK  
Sbjct: 121 GIRVKFWHVPGHSGIYGNEEADRLAKKG 148

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

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 53.5 bits (129), Expect = 4e-07
 Identities = 59/280 (21%), Positives = 84/280 (30%), Gaps = 44/280 (15%)

Query: 193 LAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPA 252
           L A++   L+  A+     +  +     ++    G A  PA+   +          A  A
Sbjct: 358 LCARM---LLPSASDDERGLLARLERLERRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAA 414

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVS 312
            +P    A     PA  P   PAP P  A P     AP       P A+  +       +
Sbjct: 415 AAPA---AAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPA 471

Query: 313 AAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNG------------VTKRPVSAT 360
           AAP+P+A    AP    A  A    PA  A                     V KR  S  
Sbjct: 472 AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILAAVPKR--SRK 529

Query: 361 TTASRTSSSSV-------------TSASAAKPAAPRVPLSQRTSAAK-----------PA 396
           T A     ++V             T   A + A+P       T+ A+             
Sbjct: 530 TWAILLPEATVLGVRGDTLVLGFSTGGLARRFASPGNAEVLVTALAEELGGDWQVEAVVG 589

Query: 397 TKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTD 436
             P  A       P ++  P  A RPA   +  A      
Sbjct: 590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAP 629

Length = 824

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 53.7 bits (130), Expect = 4e-07
 Identities = 22/84 (26%), Positives = 27/84 (32%), Gaps = 2/84 (2%)

Query: 225 KPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPK 284
            PG  A P +   A         AA  A +P        A  AP    KPA     AA  
Sbjct: 37  GPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAA--AAAA 94

Query: 285 STTTAPKPAPVRKPVASTITKTAT 308
           +    P  A    P A+ +    T
Sbjct: 95  APAAPPAAAAAAAPAAAAVEDEVT 118

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 53.4 bits (129), Expect = 4e-07
 Identities = 35/131 (26%), Positives = 38/131 (29%), Gaps = 24/131 (18%)

Query: 193 LAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPA 252
            A    G+     AAA AA A   A AA    K   A  PA              A    
Sbjct: 33  FADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPA---------AAAPAAP 83

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITK------- 305
             P    A   A  AP  A   A     A     T      P+R   A+           
Sbjct: 84  PKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVT------PLRGAAAAVAKNMDASLEV 137

Query: 306 -TATSTVSAAP 315
            TATS V A P
Sbjct: 138 PTATS-VRAVP 147

Length = 1228

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 53.3 bits (128), Expect = 4e-07
 Identities = 29/94 (30%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 260 ATTTAKPAPKPATKPAPKPTTAAPK-STTTAPKPA-----PVRKPVASTITKTATSTVSA 313
           A     PAP+PA   A  P+   P  + +T PK A     P ++PV  T T         
Sbjct: 358 ALLVPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPV 417

Query: 314 APKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKP 347
           AP       +APK   AA     +P    PAP  
Sbjct: 418 APPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPK 451

Length = 585

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 53.0 bits (128), Expect = 4e-07
 Identities = 28/141 (19%), Positives = 41/141 (29%), Gaps = 10/141 (7%)

Query: 303 ITKTATSTVSA-APKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATT 361
           I   A S ++A AP  +A   AA   P AAPA   RPA  A  P P         +    
Sbjct: 40  IVALADSDLAALAPPAAAAPAAAQPPPAAAPAAVSRPAAPAAEPAP--------WLVEHA 91

Query: 362 TASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATR 421
                    + + +AA  A      +     A           +  + P        A  
Sbjct: 92  KRLTAQREQLVARAAAPAAPEAQAPAAPAERAAAENAARRLARAAAAAPRPRVPADAAAA 151

Query: 422 PATTTSKP-ATTTSTDIEDEM 441
            A           +  +  E+
Sbjct: 152 VADAVKARIERIVNDTVMQEL 172

Length = 484

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 52.2 bits (125), Expect = 5e-07
 Identities = 31/133 (23%), Positives = 39/133 (29%)

Query: 175 PQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPAS 234
               +  ++    + +   +AK   A    +    A  AV    AAK   K    AK  +
Sbjct: 197 ANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTA 256

Query: 235 KPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAP 294
           K   K        AAK A     K A   AK     A         AA  S   A   AP
Sbjct: 257 KKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKAP 316

Query: 295 VRKPVASTITKTA 307
            R        K  
Sbjct: 317 KRGAKGKKAKKVT 329

Length = 333

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 52.9 bits (127), Expect = 6e-07
 Identities = 47/336 (13%), Positives = 97/336 (28%), Gaps = 14/336 (4%)

Query: 95  TEKTPEVSEPKEEVLDDLVSVPTSVPDVVPN-QDANEESPSPAVDLTQDIVEEKEAVVTP 153
              TP  + P      DL  +   V    P    +   + +    +  D    ++A + P
Sbjct: 117 PPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAAL-P 175

Query: 154 TDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVA 213
                       +P +E P     A         ++    +A         +AA  A  +
Sbjct: 176 LSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGAS 235

Query: 214 VKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATK 273
              +++++ +            P     T  T        +         +  +      
Sbjct: 236 SSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERS 295

Query: 274 PAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPA 333
           P+P P++       ++P+ +        + + ++TS+ S + + +A  P        + +
Sbjct: 296 PSPSPSSPGSGPAPSSPRASSSSSSSRESSS-SSTSSSSESSRGAAVSPGPS----PSRS 350

Query: 334 PKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAA 393
           P P        P        +   S   ++   S+   T   A    A R      T   
Sbjct: 351 PSPSRPPPPADPSSPR---KRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRF 407

Query: 394 KPATKPATAKPSTTSKPTTASKPATATRPATTTSKP 429
            PA +P    PS       +          T + +P
Sbjct: 408 -PAGRPR---PSPLDAGAASGAFYARYPLLTPSGEP 439

Length = 1352

>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional

 Score = 52.5 bits (126), Expect = 6e-07
 Identities = 29/136 (21%), Positives = 40/136 (29%), Gaps = 17/136 (12%)

Query: 223 TDKPGP-----AAKPASKP------LAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPA 271
             KPGP     A++PA           K     +   A+     VK+   T         
Sbjct: 176 VVKPGPQIGRYASEPAGGLTSLTEEAGKARYNASKALAEDIGDTVKRIDGTEVPLLAPWQ 235

Query: 272 TKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAA 331
              AP P + A +  +   +     K      T       +A    +           A 
Sbjct: 236 GDAAPVPPSEAARPKSADAETNAALK------TPATAPKAAAKNAKAPEAQPVSGTAAAE 289

Query: 332 PAPKPRPATAAPAPKP 347
           PAPK     AA A KP
Sbjct: 290 PAPKEAAKAAAAAAKP 305

Length = 400

>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional

 Score = 52.1 bits (125), Expect = 6e-07
 Identities = 32/162 (19%), Positives = 45/162 (27%), Gaps = 22/162 (13%)

Query: 270 PATKPAPK--PTTAAPKS-----TTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKP 322
           P  KP P+     + P       T  A K         +         +     P     
Sbjct: 175 PVVKPGPQIGRYASEPAGGLTSLTEEAGKARYNASKALAEDIGDTVKRIDGTEVPLLAPW 234

Query: 323 AAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAP 382
                PV  P+   RP +A              P +A   A    +  V+  +AA+PA  
Sbjct: 235 QGDAAPVP-PSEAARPKSADAETNAALKTPATAPKAAAKNAKAPEAQPVSGTAAAEPAPK 293

Query: 383 RVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPAT 424
                            A AKP+   KP    +P    RP  
Sbjct: 294 E----------AAKAAAAAAKPALEDKP----RPLGIARPGG 321

Length = 400

>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional

 Score = 52.8 bits (126), Expect = 7e-07
 Identities = 55/255 (21%), Positives = 76/255 (29%), Gaps = 26/255 (10%)

Query: 208 AGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKP- 266
            GA   +    A      P  A  P   P A     +   AA     P          P 
Sbjct: 679 TGANTMLPIQWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPA 738

Query: 267 -APKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAP 325
            AP  A  PA  P  A P +        P   P A T            P P AP PA  
Sbjct: 739 AAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQ----------PPPQAP-PAPQ 787

Query: 326 KKPVAAPAPKPRPAT----------AAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSAS 375
           ++P  AP P+P P            AAP  +  T  + ++ ++      R S     +  
Sbjct: 788 QRPRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLLTGGVKRGRPSLKKPAALE 847

Query: 376 AAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTST 435
               A P  P     ++ K    P    P     P    +   + R A  ++     T  
Sbjct: 848 RQAAAGPT-PSPGSGTSDKIVQAPVFYPPVLQ--PIQVMRQLGSVRAAAASTVTQAPTEY 904

Query: 436 DIEDEMNQPFTPEEL 450
             E     P  P ++
Sbjct: 905 TGERRGVGPMHPTDI 919

Length = 991

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

 Score = 48.8 bits (117), Expect = 7e-07
 Identities = 37/138 (26%), Positives = 50/138 (36%), Gaps = 18/138 (13%)

Query: 678 IYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILI 737
           ++TD S    K G A        +    L   TS   AE+I +  AL+ +     N   I
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEI-ATLPYGTSAQRAELIALIRALELAKGKPVN---I 57

Query: 738 LTDSK---SACQKL-----SKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEG- 788
            TDS         L      +  L   P  L   IL   K +Q   K V +  I+ H G 
Sbjct: 58  YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRP-KPVAVIHIRAHSGL 116

Query: 789 ----IKGNVEVDRLAKYA 802
                 GN   D+ A+ A
Sbjct: 117 PGPLALGNARADQAARQA 134

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 51.9 bits (123), Expect = 7e-07
 Identities = 56/176 (31%), Positives = 64/176 (36%), Gaps = 5/176 (2%)

Query: 176 QEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASK 235
           QE +  E   E     D AA  A      A  A A    K A AA         AK A+ 
Sbjct: 176 QELRKREKDRERARREDAAAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAP 235

Query: 236 PL-AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAP---- 290
           P  A     K   A   A +P  K A   AK A  PA   AP    AAP +   AP    
Sbjct: 236 PAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKA 295

Query: 291 KPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPK 346
             AP +   A      A +  +A P  +A  PA    P A  A  P  A AAP  K
Sbjct: 296 AAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPVGK 351

Length = 357

>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast subunit 62; Provisional

 Score = 51.5 bits (123), Expect = 1e-06
 Identities = 44/217 (20%), Positives = 73/217 (33%), Gaps = 10/217 (4%)

Query: 220 AKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAP-------KPAT 272
           +++       A    KP+     T    +      P +  A      +P       KP T
Sbjct: 325 SQRVPPKESDAADGPKPVPTKPVTPEAPSPPIEEEPPQPKAVVPRPLSPYTAYEDLKPPT 384

Query: 273 KPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAP 332
            P P P +++P S+ +    A   +P       +A++     P     K   P  P A  
Sbjct: 385 SPIPTPPSSSPASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTRPLSPYARY 444

Query: 333 APKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSA 392
                P + +P      +       S         +++ T A+A  PA  R PLS     
Sbjct: 445 EDLKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAPPPANMR-PLSPYAVY 503

Query: 393 A--KPATKPATAKPSTTSKPTTASKPATATRPATTTS 427
              KP T P+ A P     P++ ++       A  T+
Sbjct: 504 DDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTA 540

Length = 576

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 51.0 bits (123), Expect = 2e-06
 Identities = 25/99 (25%), Positives = 32/99 (32%), Gaps = 10/99 (10%)

Query: 247 TAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKT 306
            +     +     A   + PA  PA K    P  A P +   A  P P     A+     
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAA---- 94

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKP-RPATAAPA 344
                + A  P+A   AAP          P R A AA A
Sbjct: 95  -----APAAPPAAAAAAAPAAAAVEDEVTPLRGAAAAVA 128

Length = 1228

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 51.4 bits (123), Expect = 2e-06
 Identities = 44/265 (16%), Positives = 79/265 (29%), Gaps = 26/265 (9%)

Query: 205  AAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTA 264
            A A  A   +++A A  ++      ++ A K  A   TTK  + ++        +A  T 
Sbjct: 1173 AKAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSAMETE 1232

Query: 265  KPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKP-A 323
              A     K        AP     A K       +     + A   + +AP  SA     
Sbjct: 1233 NVAEVVKPKGRAGAKKKAPA----AAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEET 1288

Query: 324  APKKPVAAPAPKPRPATAAPAPKPLTN-----GVTKRPVSATTTASRTSSSSVTSASAAK 378
                P    A + +P  +        +      V                ++    +A  
Sbjct: 1289 VKAVPARRAAARKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKAAKP 1348

Query: 379  PAAPRVPLSQR----------------TSAAKPATKPATAKPSTTSKPTTASKPATATRP 422
            PAA +                           P  K    + S  +K + +     AT  
Sbjct: 1349 PAAAKKRGPATVQSGQKLLTEMLKPAEAIGISPEKKVRKMRASPFNKKSGSVLGRAATNK 1408

Query: 423  ATTTSKPATTTSTDIEDEMNQPFTP 447
             T +S+  + +S+  +DE++    P
Sbjct: 1409 ETESSENVSGSSSSEKDEIDVSAKP 1433

Length = 1465

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 51.4 bits (124), Expect = 2e-06
 Identities = 32/151 (21%), Positives = 41/151 (27%), Gaps = 11/151 (7%)

Query: 276 PKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPK 335
           P      P+    +  PA   +  A+     A     A P P A  P     P       
Sbjct: 361 PAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQA--PAVPLPET 418

Query: 336 PRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKP 395
                AA        G TK   S    ASR         ++A      V  +       P
Sbjct: 419 TSQLLAARQQLQRAQGATKAKKSEPAAASRA-----RPVNSALERLASVRPAPSALEKAP 473

Query: 396 ATKPA---TAKPSTTSKPTTASKPATATRPA 423
           A K A    A      K    + P  A + A
Sbjct: 474 AKKEAYRWKATNPVEVKKEPVATP-KALKKA 503

Length = 647

>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional

 Score = 51.5 bits (123), Expect = 2e-06
 Identities = 39/148 (26%), Positives = 55/148 (37%), Gaps = 3/148 (2%)

Query: 132  SPSPAVDLTQDIVEEKEAVVTPTDETNSET-AEKETPLSEVPVIPQEAQTVESAEESTAS 190
            S S A    +D +E +       D   +E    +E  + E       A +  + + +TA 
Sbjct: 904  SGSEANSARRDTMEIQNEQKPTQDGPAAEAQPAQENTVVESAEKAVAAVSEAAQQAATAV 963

Query: 191  SDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAK-PASKPLAKTTTTKTTTAA 249
            +    KVA A+      +    A  +A   KK  K  PA K  A K  AK    K   A 
Sbjct: 964  ASGIEKVAEAVRKTVRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAK 1023

Query: 250  KPAISPVKKTATTTAKPAPKPATKPAPK 277
            K     V +      K A KPA K A +
Sbjct: 1024 KAPAKKVARKPAAK-KAAKKPARKAAGR 1050

Length = 1052

>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional

 Score = 51.0 bits (122), Expect = 2e-06
 Identities = 27/135 (20%), Positives = 45/135 (33%), Gaps = 2/135 (1%)

Query: 203 VGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATT 262
             +  AG   ++ +     + +     A+     + +   T+    A           + 
Sbjct: 186 YASEPAGGLTSLTEEAGKARYNASKALAEDIGDTVKRIDGTEVPLLAPWQGDAAPVPPSE 245

Query: 263 TAKPAPKPA-TKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPK 321
            A+P    A T  A K    APK+       AP  +PV+ T         +A    +A K
Sbjct: 246 AARPKSADAETNAALKTPATAPKAAA-KNAKAPEAQPVSGTAAAEPAPKEAAKAAAAAAK 304

Query: 322 PAAPKKPVAAPAPKP 336
           PA   KP      +P
Sbjct: 305 PALEDKPRPLGIARP 319

Length = 400

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 51.6 bits (124), Expect = 2e-06
 Identities = 33/185 (17%), Positives = 56/185 (30%), Gaps = 7/185 (3%)

Query: 98   TPEVSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDET 157
             P+  + +E+   + V V   V +V           +P V+   ++VEE   VV      
Sbjct: 849  RPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEE-PVVVAEPQPE 907

Query: 158  NSETAEKETPLSEVPVIPQEAQTVESAEESTASSD------LAAKVAGALVVGAAAAGAA 211
                 E   P      + ++ Q +  ++ + A         +         +  AA  A 
Sbjct: 908  EVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAE 967

Query: 212  VAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPA 271
            V V +     +   P  A   A          +   A  P  +     AT     AP P 
Sbjct: 968  VVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATAPMTRAPAPE 1027

Query: 272  TKPAP 276
              P  
Sbjct: 1028 YVPEA 1032

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 51.2 bits (123), Expect = 2e-06
 Identities = 38/207 (18%), Positives = 58/207 (28%), Gaps = 18/207 (8%)

Query: 118  SVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPQE 177
              P V P     EE         Q +V E           ++   E    + E PV+  E
Sbjct: 844  RYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAE 903

Query: 178  AQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPL 237
             Q  E     T   ++ A            +  AVA + A            A+P  +P 
Sbjct: 904  PQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVA----------EHAEPVVEPQ 953

Query: 238  AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRK 297
             +T   +        +    +     A P            T   P        PA V +
Sbjct: 954  DETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEP-----EVAPAQVPE 1008

Query: 298  PVASTITKTATSTVSAAPKPS-APKPA 323
                     AT+ ++ AP P   P+  
Sbjct: 1009 ATVE--HNHATAPMTRAPAPEYVPEAP 1033

Length = 1068

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 26/108 (24%), Positives = 36/108 (33%), Gaps = 1/108 (0%)

Query: 257 KKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPK 316
           K T+ +      KPA    P      P++    P PAP     A+     A     A P+
Sbjct: 98  KATSMSEPATENKPAEVTTPVEPMGLPETPPAVPVPAPAPAVAAAAAQAAAAPKAPAKPR 157

Query: 317 PSAPKPAAPKKPVAAPA-PKPRPATAAPAPKPLTNGVTKRPVSATTTA 363
             +P+PAA   P         +    A APKP  +         T   
Sbjct: 158 AKSPRPAAKAAPKPTETITAKKAKKTAAAPKPTADKTATPAKKTTKKK 205

Length = 209

>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional

 Score = 50.5 bits (120), Expect = 3e-06
 Identities = 47/217 (21%), Positives = 65/217 (29%), Gaps = 20/217 (9%)

Query: 218 TAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAP--------- 268
           T+   +  P  A  P   P    T    TT +    +   +      +P P         
Sbjct: 582 TSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPLRMQPI 641

Query: 269 --------KPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAP 320
                    P   P  + T   P  T     P       A+T+     +  +  P P AP
Sbjct: 642 TFNVLVFPTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAP 701

Query: 321 KPAAPKKPVAAPAPKPRPATA-APAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKP 379
            P  P  P A P    RPA A   A  P       RP +A    +R  +++   A     
Sbjct: 702 TPMRP--PAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAA 759

Query: 380 AAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKP 416
           A  R         A     P  A P+   +P  A  P
Sbjct: 760 APGRARPPAAAPGAPTPQPPPQAPPAPQQRPRGAPTP 796

Length = 991

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 50.1 bits (120), Expect = 3e-06
 Identities = 29/121 (23%), Positives = 41/121 (33%)

Query: 176 QEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASK 235
           +E + +   E    S D+ A  +G +    A  G  V V    +   T    PAA PA+ 
Sbjct: 73  KEDEVICIIETDKVSVDIRAPASGVITKIFAEEGDTVEVGAPLSEIDTGGAPPAAAPAAA 132

Query: 236 PLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPV 295
             AK   T        A +P    A+    PA     +PAP             P+   V
Sbjct: 133 AAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPEPAPAAKPPPTPVARADPRETRV 192

Query: 296 R 296
            
Sbjct: 193 P 193

Length = 418

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.9 bits (120), Expect = 4e-06
 Identities = 33/151 (21%), Positives = 51/151 (33%), Gaps = 3/151 (1%)

Query: 300 ASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSA 359
           A+ + +      SAAP  SA   AAP   VA P     P   A AP+           S 
Sbjct: 362 AAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQ 421

Query: 360 TTTASR--TSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPA 417
              A +    +   T A  ++PAA        ++  + A+          +     +   
Sbjct: 422 LLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAKKEAYRW 481

Query: 418 TATRPATTTSKPATTTSTDIEDEMNQPFTPE 448
            AT P     +P  T    ++  +    TPE
Sbjct: 482 KATNPVEVKKEPVATPK-ALKKALEHEKTPE 511

Length = 647

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 50.0 bits (120), Expect = 5e-06
 Identities = 34/140 (24%), Positives = 40/140 (28%), Gaps = 2/140 (1%)

Query: 312 SAAPKPSAPKPAAPKKPV--AAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSS 369
           S+ P   A +PAAP  P   AAPAP    A  A A      GV          A   +S 
Sbjct: 605 SSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASD 664

Query: 370 SVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKP 429
                 A    A         + A PA     A       P        A  PA    + 
Sbjct: 665 GGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQA 724

Query: 430 ATTTSTDIEDEMNQPFTPEE 449
           A   S       +    P E
Sbjct: 725 AQGASAPSPAADDPVPLPPE 744

Length = 824

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.5 bits (118), Expect = 6e-06
 Identities = 28/148 (18%), Positives = 44/148 (29%), Gaps = 10/148 (6%)

Query: 313 AAPKP---SAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSS 369
           A P P   +A    A   P          A AA APK        R  +     +  +++
Sbjct: 379 AVPAPGARAAAAVGASAVPAVTAVTG--AAGAALAPKAAAAAAATRAEAPPAAPAPPATA 436

Query: 370 SVTSASAAKPAAPR----VPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATT 425
                +A   A          S  +   +   +P      + S P + + P  A  PA  
Sbjct: 437 DRGDDAADGDAPVPAKANARASADSRCDERDAQPPAD-SGSASAPASDAPPDAAFEPAPR 495

Query: 426 TSKPATTTSTDIEDEMNQPFTPEELEAA 453
            + P+  T   + D         E   A
Sbjct: 496 AAAPSAATPAAVPDARAPAAASREDAPA 523

Length = 830

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 49.8 bits (119), Expect = 6e-06
 Identities = 45/213 (21%), Positives = 71/213 (33%), Gaps = 9/213 (4%)

Query: 258 KTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKP 317
             A    +P   P   P  +      +ST T           A   + T     S  P P
Sbjct: 59  AAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPP 118

Query: 318 SAPKPAAPKKPVA---APAPKPRPA-TAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTS 373
             P PA+P    A   +   +P  +    PA  P   G +   V++   +SR ++  ++S
Sbjct: 119 PTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSS 178

Query: 374 ASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTT--SKPAT 431
                 A    P     S    A  P    P   S P +AS  + A  P  +      A+
Sbjct: 179 PEETARAPSSPPAEPPPSTPPAAASPR---PPRRSSPISASASSPAPAPGRSAADDAGAS 235

Query: 432 TTSTDIEDEMNQPFTPEELEAAIKSGLITTPGR 464
           ++ +   +     + PE      +   IT P R
Sbjct: 236 SSDSSSSESSGCGWGPENECPLPRPAPITLPTR 268

Length = 1352

>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.7 bits (118), Expect = 6e-06
 Identities = 42/164 (25%), Positives = 58/164 (35%), Gaps = 21/164 (12%)

Query: 205 AAAAGAAVAVKKAT-----AAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKT 259
           AAA+  A AV + T     +A+  +K   A KP  +P A+T  T   TA+  A+    KT
Sbjct: 362 AAASCDANAVIENTELQSPSAQTAEKETAAKKPQPRPEAETAQTPVQTASAAAMPSEGKT 421

Query: 260 ATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSA 319
           A     P         P P   AP    TA   A            T+  ++  A +   
Sbjct: 422 A----GPVSNQENNDVP-PWEDAPDEAQTAAGTAQ-----------TSAKSIQTASEAET 465

Query: 320 PKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTA 363
           P      K  AA      P +  P+  P+        V   T A
Sbjct: 466 PPENQVSKNKAADNETDAPLSEVPSENPIQATPNDEAVETETFA 509

Length = 709

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 49.1 bits (118), Expect = 7e-06
 Identities = 30/151 (19%), Positives = 50/151 (33%), Gaps = 6/151 (3%)

Query: 264 AKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPA 323
           A P P+P   P      A+ ++T           P A  +     S    AP    P+  
Sbjct: 362 AAPLPEPEVPPQSAAPAASAQATAAPTAAVAP--PQAPAVPPPPASAPQQAPAVPLPETT 419

Query: 324 APKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATT---TASRTSSSSVTSASAAKPA 380
           +          + + AT A   +P       RPV++      + R + S++  A A K A
Sbjct: 420 SQLLAARQQLQRAQGATKAKKSEPAAASRA-RPVNSALERLASVRPAPSALEKAPAKKEA 478

Query: 381 APRVPLSQRTSAAKPATKPATAKPSTTSKPT 411
                 +      +P   P   K +   + T
Sbjct: 479 YRWKATNPVEVKKEPVATPKALKKALEHEKT 509

Length = 647

>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF; Provisional

 Score = 48.8 bits (116), Expect = 8e-06
 Identities = 46/205 (22%), Positives = 57/205 (27%), Gaps = 21/205 (10%)

Query: 160 ETAEKETPLSEVPVIP-QEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKAT 218
           ETA  +TP +     P  +A T  +A         A          A+AA   +A     
Sbjct: 56  ETARSDTPATAAAPAPAPQAPTKPAAPVHAPLKLSANANMSQRQRVASAAEDMIAAMALR 115

Query: 219 AAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKP 278
                 +  PAA P     A +  +    A   A +         A  A  P    A   
Sbjct: 116 QPVSVPRQAPAAAPVR---AASIPSPAAQALAHAAAVRTAPRQEHALSA-VPEQLFADFL 171

Query: 279 TTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSA----------------APKPSAPKP 322
           TTA                PV +     A     A                A     P  
Sbjct: 172 TTAPVPRAPVQAPVVAAPAPVPAIAAALAAHAAYAQDDDEQLDDDGFDLDDALPQILPPA 231

Query: 323 AAPKKPVAAPAPKPRPATAAPAPKP 347
           A P   VA  AP    A AA AP P
Sbjct: 232 ALPPIVVAPAAPAALAAVAAAAPAP 256

Length = 559

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

 Score = 45.6 bits (109), Expect = 9e-06
 Identities = 26/101 (25%), Positives = 41/101 (40%), Gaps = 22/101 (21%)

Query: 716 EVIGIWEALKYSASLKNN-EILILTDSKSACQKLS-----------KNCLNTTPTHLEL- 762
           E+  + EAL+   +LK    +L+ TDS+     ++           K        +++L 
Sbjct: 45  ELTAVIEALE---ALKEPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLW 101

Query: 763 -EILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYA 802
            E+ +     Q     V   W+KGH G  GN   D 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|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.8 bits (117), Expect = 1e-05
 Identities = 31/187 (16%), Positives = 36/187 (19%)

Query: 172 PVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAK 231
           P           A               A    AA A A  A   A A+        A +
Sbjct: 592 PGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPE 651

Query: 232 PASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPK 291
              K +A    +                A   A     PA      P   AP    T P 
Sbjct: 652 HHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPA 711

Query: 292 PAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNG 351
                            S  S A     P P  P  P        +P             
Sbjct: 712 GQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPA 771

Query: 352 VTKRPVS 358
               P  
Sbjct: 772 AAPPPSP 778

Length = 824

>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.4 bits (116), Expect = 1e-05
 Identities = 22/130 (16%), Positives = 35/130 (26%), Gaps = 1/130 (0%)

Query: 310 TVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSS 369
            V+      A    +      A AP    A A  A          +P  A   A    S 
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAP-APAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSP 444

Query: 370 SVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKP 429
           +  + +   P+ P         A  PA  P        + P   +  A    PA   +  
Sbjct: 445 AGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPA 504

Query: 430 ATTTSTDIED 439
               +  + +
Sbjct: 505 GADDAATLRE 514

Length = 824

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 48.7 bits (117), Expect = 1e-05
 Identities = 29/95 (30%), Positives = 40/95 (42%), Gaps = 8/95 (8%)

Query: 304 TKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATA-APAPKPLTNGVTKRPVSATTT 362
                +  +AA   SAP  A   K  AAPAP P  A A A  PKP          +A   
Sbjct: 42  AAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKP-----AAAAAAAAAP 96

Query: 363 ASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPAT 397
           A+  ++++  + +AA       PL  R +AA  A 
Sbjct: 97  AAPPAAAAAAAPAAAAVEDEVTPL--RGAAAAVAK 129

Length = 1228

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 48.7 bits (117), Expect = 1e-05
 Identities = 34/147 (23%), Positives = 54/147 (36%), Gaps = 8/147 (5%)

Query: 316 KPSAPKPAAPKKPVAAPAPKPRPATAAP---APKPLTNGVTKRPVSATTTASRTSSSSVT 372
            P+AP P     P +A       ATAAP      P    V   P SA   A        T
Sbjct: 360 HPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETT 419

Query: 373 S-ASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPAT 431
           S   AA+    R   + +   ++PA   + A+P  ++    AS     +      +K   
Sbjct: 420 SQLLAARQQLQRAQGATKAKKSEPAA-ASRARPVNSALERLASVRPAPSALEKAPAKKEA 478

Query: 432 ---TTSTDIEDEMNQPFTPEELEAAIK 455
                +  +E +     TP+ L+ A++
Sbjct: 479 YRWKATNPVEVKKEPVATPKALKKALE 505

Length = 647

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 20/69 (28%), Positives = 24/69 (34%)

Query: 292 PAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNG 351
            AP     A+     A  T    PK +AP P  P      P    +P   APA KP    
Sbjct: 122 GAPPAAAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPEPAPAAKPPPTP 181

Query: 352 VTKRPVSAT 360
           V +     T
Sbjct: 182 VARADPRET 190

Length = 418

>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional

 Score = 49.0 bits (117), Expect = 1e-05
 Identities = 52/328 (15%), Positives = 89/328 (27%), Gaps = 46/328 (14%)

Query: 82  SQETKLDDFISAHTEKTPEVSEPKEEVLDDLV---------SVPTSVPDVVPNQDANEES 132
           S     +  +    + T E S     V D  V         +   +V D    +D  E +
Sbjct: 476 SSLDADNSAVPEQIDSTAEQSVVNPSVTDTQVDDTSASNNSAADNTVDDNYSAEDTLESN 535

Query: 133 PSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSD 192
                D  QD              ++               +       E+   S + S 
Sbjct: 536 GLDEGDYAQDSAPLDAYQDDYVAFSSESYNALSDDEQHSANVQSAQSAAEAQPSSQSLSP 595

Query: 193 LAAKVAGALVVGAAAAGAAV-----AVKKATAAKKTD------------KPGPAAKPASK 235
           ++A       V  AAA  A      AV  A  +  +D            K     KP + 
Sbjct: 596 ISA-------VTTAAASLADDDILDAVLAARDSLLSDLDALSPKEGDGKKSSADRKPKTP 648

Query: 236 PLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPT-------TAAPKSTTT 288
           P      + +  A+ P     + +A+    P  + AT  +            A P     
Sbjct: 649 PSRAPPASLSKPASSP--DASQTSASFDLDPDFELATHQSVPEAALASGSAPAPPPVPDP 706

Query: 289 APKP----APVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPA 344
             +P    AP            A   +S + + ++       +  A   P+ +    +PA
Sbjct: 707 YDRPPWEEAPEVASANDGPNNAAEGNLSESVEDASNSELQAVEQQATHQPQVQAEAQSPA 766

Query: 345 PKPLTNGVTKRPVSATTTASRTSSSSVT 372
                   +             SS S+T
Sbjct: 767 STTALTQTSSEVQDTELNLVLLSSGSIT 794

Length = 944

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 48.8 bits (117), Expect = 1e-05
 Identities = 44/210 (20%), Positives = 55/210 (26%), Gaps = 22/210 (10%)

Query: 194 AAKVAGALVVGAAAAGAAVAVKKAT-AAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPA 252
            A+   A    AA    AVA   A   AKK     P    A      +       A K  
Sbjct: 470 EARHKKAAEARAAKDKDAVAAALARVKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQ 529

Query: 253 ISPVKKTATTTAKPAPKPAT----------KPAPKPTTAAPKSTTTAPKPAPVRKPVAST 302
               +      A   PK A           K A +    A       PK A V   +A  
Sbjct: 530 ARARQAEKQAAAAADPKKAAVAAAIARAKAKKAAQQAANAEAEEEVDPKKAAVAAAIARA 589

Query: 303 ITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRP------ 356
             K A    ++A          PKK   A A     A  A             P      
Sbjct: 590 KAKKAAQQAASAEPEEQVAEVDPKKAAVAAAIARAKAKKAEQQANAEPEEPVDPRKAAVA 649

Query: 357 -----VSATTTASRTSSSSVTSASAAKPAA 381
                  A   A + +++    A   K AA
Sbjct: 650 AAIARAKARKAAQQQANAEPEEAEDPKKAA 679

Length = 695

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 48.4 bits (115), Expect = 2e-05
 Identities = 56/239 (23%), Positives = 72/239 (30%), Gaps = 44/239 (18%)

Query: 249 AKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTAT 308
           A PA  PV       A    + AT P P P  AAP      P        V       A 
Sbjct: 253 AAPAPPPVVGEGADRAPETARGATGPPPPPEAAAPNGAAAPPDG------VWGAALAGAP 306

Query: 309 STVSAAPKPSAPKPAAPKK---------PVAAPAPKPRPATAAPAPKPLTNGVTKRPVSA 359
             + A P P  P PA   +          V +P P+PR       PK       +RP   
Sbjct: 307 LALPAPPDPPPPAPAGDAEEEDDEDGAMEVVSPLPRPRQHYPLGFPK------RRRP--- 357

Query: 360 TTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATK------------PATAKPSTT 407
               + T  SS+   SA +    R  L  R   +                    A P   
Sbjct: 358 ----TWTPPSSLEDLSAGRHHPKRASLPTRKRRSARHAATPFARGPGGDDQTRPAAPVPA 413

Query: 408 SKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKSGLITTPGRDN 466
           S PT A  P  A+ P      PAT   +      + P  P E +    +        D+
Sbjct: 414 SVPTPAPTPVPASAPP----PPATPLPSAEPGSDDGPAPPPERQPPAPATEPAPDDPDD 468

Length = 3151

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 47.2 bits (112), Expect = 2e-05
 Identities = 32/126 (25%), Positives = 41/126 (32%), Gaps = 6/126 (4%)

Query: 293 APVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKP---RPATAAPAPKPLT 349
            P  K  A   +  A S      K  A K A   K  A  A K       TA  A K   
Sbjct: 205 TPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAA 264

Query: 350 NGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSK 409
             V K    A   A++ +     +A A K  A     + + +AA    K     P   +K
Sbjct: 265 KAVKKAAKKAAKAAAKAAKG---AAKATKGKAKAKKKAGKKAAAGSKAKATAKAPKRGAK 321

Query: 410 PTTASK 415
              A K
Sbjct: 322 GKKAKK 327

Length = 333

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 47.2 bits (112), Expect = 2e-05
 Identities = 30/146 (20%), Positives = 41/146 (28%), Gaps = 6/146 (4%)

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVS 312
           ++ V       A   P   +        A   +   + K A      A    KTA     
Sbjct: 191 LAAVGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAK 250

Query: 313 AAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVT 372
            A K +        K V   A K   A AA A K        +       A + +     
Sbjct: 251 KAKKTAKKALKKAAKAVKKAAKKAAKA-AAKAAKG-----AAKATKGKAKAKKKAGKKAA 304

Query: 373 SASAAKPAAPRVPLSQRTSAAKPATK 398
           + S AK  A       +   AK  TK
Sbjct: 305 AGSKAKATAKAPKRGAKGKKAKKVTK 330

Length = 333

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.9 bits (115), Expect = 2e-05
 Identities = 26/139 (18%), Positives = 41/139 (29%), Gaps = 4/139 (2%)

Query: 211 AVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKP 270
            +A   A    + + P  +A PA    A+ T   T   A P    V     +  + AP  
Sbjct: 356 MLAFHPAAPLPEPEVPPQSAAPA--ASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAV 413

Query: 271 ATKPAPKPTTAAPKSTTTAPKPAPVRK--PVASTITKTATSTVSAAPKPSAPKPAAPKKP 328
                     AA +    A      +K  P A++  +   S +           A  K P
Sbjct: 414 PLPETTSQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAP 473

Query: 329 VAAPAPKPRPATAAPAPKP 347
               A + +        K 
Sbjct: 474 AKKEAYRWKATNPVEVKKE 492

Length = 647

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 30/109 (27%), Positives = 36/109 (33%), Gaps = 20/109 (18%)

Query: 274 PAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPA 333
           P P P  A P    TA  P+PVR           T   S  PK +A     PK+PV   A
Sbjct: 362 PVPAPQPAKP----TAAAPSPVR----------PTPAPSTRPKAAAAANIPPKEPVRETA 407

Query: 334 PKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAP 382
             P P    P   P+         +   T  R +           PA P
Sbjct: 408 TPP-PVPPRPVAPPVP---HTPESAPKLT--RAAIPVDEKPKYTPPAPP 450

Length = 585

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 48.1 bits (115), Expect = 2e-05
 Identities = 45/250 (18%), Positives = 67/250 (26%), Gaps = 43/250 (17%)

Query: 172  PVI-PQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAA 230
            PV+ PQ+ Q  E  E               +V     A A   V  A   +        A
Sbjct: 846  PVVRPQDVQVEEQREAEEV-------QVQPVVAEVPVAAAVEPVVSAPVVE------AVA 892

Query: 231  KPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAP-KPATKPAPKPTTAAPKSTTTA 289
            +   +P+                 P    A  T +P     +     +      +     
Sbjct: 893  EVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEP 952

Query: 290  PKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVA-APAPKPRPATAAPAPKPL 348
                      A+   +   +      +P+AP  A     V    A +P  A A      +
Sbjct: 953  Q-DETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATV 1011

Query: 349  TNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRT-------------SAAKP 395
             +     P+   T A          A    P APR    QR              SA   
Sbjct: 1012 EHNHATAPM---TRA---------PAPEYVPEAPRHSDWQRPTFAFEGKGAAGGHSATHH 1059

Query: 396  ATKPATAKPS 405
            A+ PAT +P 
Sbjct: 1060 ASAPAT-RPQ 1068

Length = 1068

>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope glycoprotein (BLLF1)

 Score = 47.9 bits (113), Expect = 2e-05
 Identities = 47/214 (21%), Positives = 67/214 (31%), Gaps = 13/214 (6%)

Query: 223 TDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKT-ATTTAKPAPKPATKPAPKPTTA 281
              P  +  P       T+ T T T +         T  TT+A P     T     P   
Sbjct: 453 PSLPPASTGPTVSTADPTSGTPTGTTSSTLPEDTSPTSRTTSATPNATSPTPAVTTPNAT 512

Query: 282 APKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATA 341
           +P +  T+  P     P    I  T T+T       S P   +P+    +P         
Sbjct: 513 SPTTQKTSDTPN-ATSPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEESPVNNTNTPVV 571

Query: 342 APAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPAT 401
             AP  LT+ VT       T +S TS          +P  P    S   S +   T   T
Sbjct: 572 TSAPSVLTSAVT--TGQHGTGSSPTSQ---------QPGIPSSSHSTPRSNSTSTTPLLT 620

Query: 402 AKPSTTSKPTTASKPATATRPATTTSKPATTTST 435
           +   T  +  T   P+  +    +T  P     T
Sbjct: 621 SAHPTGGENITEETPSVPSTTHVSTLSPGPGPGT 654

This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Length = 830

>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope glycoprotein (BLLF1)

 Score = 47.9 bits (113), Expect = 2e-05
 Identities = 37/209 (17%), Positives = 61/209 (29%), Gaps = 13/209 (6%)

Query: 227 GPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKST 286
            P A   +  + +T T  TTT  K      K   TT +           P  TTA P + 
Sbjct: 396 NPVADAKTLIITRTATNATTTTHKVVFH--KAPDTTKSVIFVYTLVHVEPHKTTAVPTTP 453

Query: 287 TT-APKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAP 345
           +       P       T      +T S  P+ ++P         +A      P  A   P
Sbjct: 454 SLPPASTGPTVSTADPTSGTPTGTTSSTLPEDTSPTSRT----TSATPNATSPTPAVTTP 509

Query: 346 KPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPS 405
                     P +  T+ +  ++S           A   P    +     + +     P 
Sbjct: 510 N------ATSPTTQKTSDTPNATSPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEESPV 563

Query: 406 TTSKPTTASKPATATRPATTTSKPATTTS 434
             +     +   +    A TT +  T +S
Sbjct: 564 NNTNTPVVTSAPSVLTSAVTTGQHGTGSS 592

This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Length = 830

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 47.5 bits (113), Expect = 3e-05
 Identities = 23/146 (15%), Positives = 39/146 (26%), Gaps = 9/146 (6%)

Query: 311 VSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSS 370
           V+    P    PA     V AP  +   A  A A            V+    A+    ++
Sbjct: 362 VTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPA------VTAVTGAAGAALAPKAA 415

Query: 371 VTSASAAKPAAPR--VPLSQRTSAAKPATKPATA-KPSTTSKPTTASKPATATRPATTTS 427
             +A+    A P    P +        A   A     +       +       +P   + 
Sbjct: 416 AAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSG 475

Query: 428 KPATTTSTDIEDEMNQPFTPEELEAA 453
             +   S    D   +P       +A
Sbjct: 476 SASAPASDAPPDAAFEPAPRAAAPSA 501

Length = 830

>gnl|CDD|233365 TIGR01347, sucB, 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component)

 Score = 46.7 bits (111), Expect = 3e-05
 Identities = 24/109 (22%), Positives = 31/109 (28%), Gaps = 1/109 (0%)

Query: 236 PLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPV 295
            LA        TAA PA S  +K  T  A  A  P         + A +           
Sbjct: 70  VLAILEEGNDATAAPPAKSGEEKEETPAASAAAAPTAAANRPSLSPAARRLAKEHGIDLS 129

Query: 296 R-KPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAP 343
                  T   T    +     P++ +  AP     APA   RP     
Sbjct: 130 AVPGTGVTGRVTKEDIIKKTEAPASAQQPAPAAAAKAPANFTRPEERVK 178

This model describes the TCA cycle 2-oxoglutarate system E2 component, dihydrolipoamide succinyltransferase. It is closely related to the pyruvate dehydrogenase E2 component, dihydrolipoamide acetyltransferase. The seed for this model includes mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus. They score below the trusted cutoff, but above the noise cutoff and above all examples of dihydrolipoamide acetyltransferase [Energy metabolism, TCA cycle]. Length = 403

>gnl|CDD|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated

 Score = 46.4 bits (111), Expect = 4e-05
 Identities = 32/106 (30%), Positives = 43/106 (40%), Gaps = 11/106 (10%)

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPL--TNGVTKRPVSATTTAS 364
           A    +AA   +A   AAP +  AA A +      +PA + L   NG+    V  T    
Sbjct: 81  AAGAAAAAAAAAAAAAAAPAQAQAAAAAEQSNDALSPAARKLAAENGLDASAVKGTGKGG 140

Query: 365 RTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKP 410
           R +   V +A AA  AAP         AA  A  PA A     ++P
Sbjct: 141 RVTKEDVLAALAAAAAAP---------AAPAAAAPAAAPAPLGARP 177

Length = 407

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 46.8 bits (112), Expect = 5e-05
 Identities = 22/115 (19%), Positives = 28/115 (24%), Gaps = 33/115 (28%)

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRT 366
             ST +     +A   AA     A  A  P     AP                       
Sbjct: 38  PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAA------------------- 78

Query: 367 SSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATR 421
                  A+  KPAA          AA  A   A    +  + P  A+     T 
Sbjct: 79  -----APAAPPKPAAA---------AAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119

Length = 1228

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 46.1 bits (108), Expect = 5e-05
 Identities = 39/153 (25%), Positives = 52/153 (33%)

Query: 267 APKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPK 326
           A   A + A     AAP    +A   AP +   A        +  +AAP  +A  PA   
Sbjct: 195 AAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAA 254

Query: 327 KPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPL 386
            P A  A  P  A A PA           P +        ++++   A+AA   A   P 
Sbjct: 255 APPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPA 314

Query: 387 SQRTSAAKPATKPATAKPSTTSKPTTASKPATA 419
                 AK A  PA A           +K A A
Sbjct: 315 KAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAA 347

Length = 357

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 47.0 bits (112), Expect = 5e-05
 Identities = 28/176 (15%), Positives = 41/176 (23%), Gaps = 9/176 (5%)

Query: 253  ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVS 312
            +   +       + A +   +P       A          APV + VA          V 
Sbjct: 847  VVRPQDVQVEEQREAEEVQVQPVVAEVPVAA--AVEPVVSAPVVEAVAEV---VEEPVVV 901

Query: 313  AAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVT 372
            A P+P          P    AP     T  P     ++    + V+              
Sbjct: 902  AEPQPEEVVVVETTHPEVIAAP----VTEQPQVITESDVAVAQEVAEHAEPVVEPQDETA 957

Query: 373  SASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSK 428
                A   A  V       A   A   A       +      + A A  P  T   
Sbjct: 958  DIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVEH 1013

Length = 1068

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 46.4 bits (111), Expect = 6e-05
 Identities = 26/84 (30%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 298 PVASTITKTATSTVSAAPKPSAPKPAAPKKPVA-APAPKPRPATAAPAPKPLTNGVTKRP 356
             A+     A S  +AAP   AP   AP  P A APA  P+PA AA A            
Sbjct: 45  TAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAA 104

Query: 357 VSATTTASRTSSSSVTSASAAKPA 380
            +A   A+     +    +AA  A
Sbjct: 105 AAAPAAAAVEDEVTPLRGAAAAVA 128

Length = 1228

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 46.4 bits (111), Expect = 6e-05
 Identities = 34/174 (19%), Positives = 54/174 (31%), Gaps = 17/174 (9%)

Query: 283 PKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAA 342
           P +    P+  P     A++   TA  T + AP                PA  P+ A A 
Sbjct: 361 PAAPLPEPEVPPQSAAPAASAQATAAPTAAVAP-------PQAPAVPPPPASAPQQAPAV 413

Query: 343 PAPKPLTNGVTKRP-VSATTTASRTSSSSVTSASAAKPAA----PRVPLSQRTSAAKPAT 397
           P P+  +  +  R  +     A++   S   +AS A+P          +    SA + A 
Sbjct: 414 PLPETTSQLLAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAP 473

Query: 398 KPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELE 451
               A     + P    K      P  T          +   E+      E +E
Sbjct: 474 AKKEAYRWKATNPVEVKKE-----PVATPKALKKALEHEKTPELAAKLAAEAIE 522

Length = 647

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 46.6 bits (111), Expect = 6e-05
 Identities = 35/199 (17%), Positives = 56/199 (28%), Gaps = 14/199 (7%)

Query: 95   TEKTPEVSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPT 154
                P V    E V + +V       +VV  +  + E  +  V        E+  V+T +
Sbjct: 882  VVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVT-------EQPQVITES 934

Query: 155  DET-NSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVA 213
            D     E AE   P+ E      + +      E   +     +V         A  AA  
Sbjct: 935  DVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVA---EPEVVAQPAAPVVAEVAAEV 991

Query: 214  VKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATK 273
                    +               A   T   T A  P   P     +   +P      K
Sbjct: 992  ETVTAVEPEVAPAQVPEATVEHNHA---TAPMTRAPAPEYVPEAPRHSDWQRPTFAFEGK 1048

Query: 274  PAPKPTTAAPKSTTTAPKP 292
             A    +A   ++  A +P
Sbjct: 1049 GAAGGHSATHHASAPATRP 1067

Length = 1068

>gnl|CDD|233365 TIGR01347, sucB, 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component)

 Score = 45.5 bits (108), Expect = 7e-05
 Identities = 38/160 (23%), Positives = 52/160 (32%), Gaps = 13/160 (8%)

Query: 142 DIVEEKEAVVT-PTDETNSE-TAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAG 199
           D V+  E +V   TD+   E  +  +  L E+    +E  TVES +       LA    G
Sbjct: 26  DTVKRDENIVEIETDKVVLEVPSPADGVLQEILF--KEGDTVESGQV------LAILEEG 77

Query: 200 ALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKT 259
                A  A +    ++  AA     P  AA   S   A     K       A+     T
Sbjct: 78  NDATAAPPAKSGEEKEETPAASAAAAPTAAANRPSLSPAARRLAKEHGIDLSAVPGTGVT 137

Query: 260 ATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPV 299
              T +   K    PA       P     A  PA   +P 
Sbjct: 138 GRVTKEDIIKKTEAPAS---AQQPAPAAAAKAPANFTRPE 174

This model describes the TCA cycle 2-oxoglutarate system E2 component, dihydrolipoamide succinyltransferase. It is closely related to the pyruvate dehydrogenase E2 component, dihydrolipoamide acetyltransferase. The seed for this model includes mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus. They score below the trusted cutoff, but above the noise cutoff and above all examples of dihydrolipoamide acetyltransferase [Energy metabolism, TCA cycle]. Length = 403

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 46.0 bits (110), Expect = 8e-05
 Identities = 21/78 (26%), Positives = 34/78 (43%)

Query: 363 ASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRP 422
            S  + ++  +A+AA  +AP    + +  AA     PA A P+   KP  A+  A A   
Sbjct: 39  GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAA 98

Query: 423 ATTTSKPATTTSTDIEDE 440
               +  A   +  +EDE
Sbjct: 99  PPAAAAAAAPAAAAVEDE 116

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 46.0 bits (110), Expect = 8e-05
 Identities = 18/99 (18%), Positives = 22/99 (22%), Gaps = 13/99 (13%)

Query: 330 AAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQR 389
           A   P    A  A A              A    +         A A  P A   P    
Sbjct: 34  ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPA---------APAPAPPAAAAP---- 80

Query: 390 TSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSK 428
            +  KPA   A A          A+    A       + 
Sbjct: 81  AAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 46.0 bits (110), Expect = 8e-05
 Identities = 17/76 (22%), Positives = 29/76 (38%)

Query: 358 SATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPA 417
             +T A   ++++  +A++A  AAP        + A PA     A P   +    A+ PA
Sbjct: 38  PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPA 97

Query: 418 TATRPATTTSKPATTT 433
                A   +  A   
Sbjct: 98  APPAAAAAAAPAAAAV 113

Length = 1228

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 44.4 bits (105), Expect = 8e-05
 Identities = 22/107 (20%), Positives = 30/107 (28%), Gaps = 3/107 (2%)

Query: 241 TTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVA 300
            T+ +  A +   + V         P   PA          A  +   A  P    KP A
Sbjct: 99  ATSMSEPATENKPAEVTTPVEPMGLPETPPAVPVPAPAPAVAAAAAQAAAAPKAPAKPRA 158

Query: 301 STITKTATSTVSAAPKPSAPKP---AAPKKPVAAPAPKPRPATAAPA 344
            +    A +        +A K    AA  KP A     P   T    
Sbjct: 159 KSPRPAAKAAPKPTETITAKKAKKTAAAPKPTADKTATPAKKTTKKK 205

Length = 209

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.6 bits (108), Expect = 9e-05
 Identities = 22/100 (22%), Positives = 32/100 (32%), Gaps = 3/100 (3%)

Query: 232 PASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPK 291
           P   P     T    +  +P  +P   T    A  A  P  +P  +  T  P        
Sbjct: 362 PVPAPQPAKPTAAAPSPVRPTPAPS--TRPKAAAAANIPPKEPVRETATPPPVPPRPVAP 419

Query: 292 PAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAA 331
           P P     A  +T+ A   V   PK + P P   ++    
Sbjct: 420 PVPHTPESAPKLTRAA-IPVDEKPKYTPPAPPKEEEKALI 458

Length = 585

>gnl|CDD|236652 PRK10118, PRK10118, flagellar hook-length control protein; Provisional

 Score = 45.2 bits (107), Expect = 9e-05
 Identities = 36/197 (18%), Positives = 54/197 (27%), Gaps = 6/197 (3%)

Query: 182 ESAEESTASSDLAAKVAGALVVGAAAAG---AAVAVKKATAAKKTDKPGPAAKPASKPLA 238
           E       +  LA +    + V                 T A KT      +K A K   
Sbjct: 72  EPLVSDKLADLLAQQANLLIPVDETLPVITDEQSLSSPLTPALKTSALAALSKNAQKDEK 131

Query: 239 KTTTTKTTTAAKPAI-SPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRK 297
               +    A+  A+ + +     TT          PA KPT       +          
Sbjct: 132 ADDLSDEDLASLSALFAMLPGQDNTTPVADAPSTVLPAEKPTLLTKDMPSAPQDETHTLS 191

Query: 298 PVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPV 357
                   T+    +A P  +   PA P       A     A     P P+T   +    
Sbjct: 192 SDEHEKGLTSAQLTTAQPDDAPGTPAQP--LTPLAAEAQAKAEVISTPSPVTAAASPTIT 249

Query: 358 SATTTASRTSSSSVTSA 374
              T    T+++ V SA
Sbjct: 250 PHQTQPLPTAAAPVLSA 266

Length = 408

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 45.6 bits (109), Expect = 9e-05
 Identities = 56/260 (21%), Positives = 71/260 (27%), Gaps = 56/260 (21%)

Query: 119 VPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETP----LSEVPVI 174
                    A   + +PA            A             E + P    ++EV VI
Sbjct: 77  AAGAAAAAAAPAAAAAPAAAAAAAPAPAAAAPAAAAAAAGGGVVEVKVPDIGEITEVEVI 136

Query: 175 P---QEAQTVESAEES--TASSDLA-----AKVAGALVVGAAAAGAAVAVKKATAAKKTD 224
               +   TVE  ++S  T  +D A     + VAG +          + VK         
Sbjct: 137 EWLVKVGDTVE-EDQSLITVETDKATMEIPSPVAGVVK--------EIKVKVGDKVSVGS 187

Query: 225 KPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPK 284
                       L          AA  A +     A   A PAP PA   AP     A  
Sbjct: 188 -----------LLVVIEVAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAA 236

Query: 285 STTTAPKPA-P-VRK----------PVAST-----ITKTATSTVSAAPKPSAPKPAAPKK 327
           +       A P VR+           V  T     ITK     V A  K      AA   
Sbjct: 237 AAPGKAPHASPAVRRLARELGVDLSQVKGTGKKGRITKE---DVQAFVK--GAMSAAAAA 291

Query: 328 PVAAPAPKPRPATAAPAPKP 347
             AA A         P PK 
Sbjct: 292 AAAAAAAGGGGLGLLPWPKV 311

Length = 547

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 45.5 bits (108), Expect = 1e-04
 Identities = 35/137 (25%), Positives = 46/137 (33%), Gaps = 14/137 (10%)

Query: 156 ETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVK 215
              +  AEK+TP         EA    +A  + A++  A   A A    A AA  A A  
Sbjct: 370 AEAAAPAEKKTP------ARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPP 423

Query: 216 KATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPA 275
              AA     P  A   A   +A         A  P      +T     + AP+PA   A
Sbjct: 424 APVAAPAAAAPAAAPAAAPAAVA--------LAPAPPAQAAPETVAIPVRVAPEPAVASA 475

Query: 276 PKPTTAAPKSTTTAPKP 292
                AAP +    P  
Sbjct: 476 APAPAAAPAAARLTPTE 492

Length = 618

>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated

 Score = 45.6 bits (109), Expect = 1e-04
 Identities = 28/158 (17%), Positives = 40/158 (25%), Gaps = 5/158 (3%)

Query: 178 AQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPL 237
           A   E      +++  A+  A A    A A   A AV    A+     P       +  L
Sbjct: 363 APLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQL 422

Query: 238 AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRK 297
                              +  A + A+P      + A      +      A K A   K
Sbjct: 423 LAARQQLQRAQGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAKKEAYRWK 482

Query: 298 PVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPK 335
                 T            P A K A   +     A K
Sbjct: 483 A-----TNPVEVKKEPVATPKALKKALEHEKTPELAAK 515

Length = 647

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 29/113 (25%), Positives = 36/113 (31%), Gaps = 15/113 (13%)

Query: 216 KATAAKKTDKPGPAAKPA-SKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKP 274
             +     +KP     P     L +T       A  PA++     A    K   KP  K 
Sbjct: 101 SMSEPATENKPAEVTTPVEPMGLPETPPAVPVPAPAPAVAAAAAQAAAAPKAPAKPRAKS 160

Query: 275 APKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKK 327
                 AAPK T T       +                AAPKP+A K A P K
Sbjct: 161 PRPAAKAAPKPTETITAKKAKKTA--------------AAPKPTADKTATPAK 199

Length = 209

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 26/106 (24%), Positives = 30/106 (28%), Gaps = 6/106 (5%)

Query: 205 AAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTA 264
            A       V          +  PA  P   P           AA P      K    + 
Sbjct: 105 PATENKPAEVTTPVEPMGLPETPPAV-PVPAPAPAVAAAAAQAAAAP--KAPAKPRAKSP 161

Query: 265 KPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATST 310
           +PA K A KP    T    K T  APKP        +T  K  T  
Sbjct: 162 RPAAKAAPKPTETITAKKAKKTAAAPKPT---ADKTATPAKKTTKK 204

Length = 209

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

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 31/144 (21%), Positives = 52/144 (36%), Gaps = 14/144 (9%)

Query: 673 PNAICIYTD-ASKKNEKV---GAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSA 728
              + I+TD A   N      GA       + +        T+   AE+  + EAL+   
Sbjct: 1   MKKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNR-AELRALIEALEALK 59

Query: 729 SLKNNEILILTDSKSACQKLSKNCLN---------TTPTHLELEILSSYKHLQNTCKTVK 779
            L   E+ + TDSK   + +++  +                  ++      L    + V 
Sbjct: 60  ELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVF 119

Query: 780 LAWIKGHEGIKGNVEVDRLAKYAT 803
             W+KGH G   N   D+LA+ A 
Sbjct: 120 WEWVKGHAGHPENERADQLAREAA 143

Length = 154

>gnl|CDD|217310 pfam02993, MCPVI, Minor capsid protein VI

 Score = 44.4 bits (105), Expect = 1e-04
 Identities = 24/126 (19%), Positives = 35/126 (27%), Gaps = 22/126 (17%)

Query: 270 PATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPV 329
              +PAP+  T A       P+P P  + V           V AAP+P + +      P 
Sbjct: 111 GEEEPAPQEETVADPIQALQPRPRPDVEEVL----------VPAAPEPPSYEETIKPGPA 160

Query: 330 AAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQR 389
               P    A A PA                 T     +         +P+   V    R
Sbjct: 161 PVEEPVDSMAIAVPAI------------DTPVTLELPPAPQPPPPVVPQPSTMVVHRRSR 208

Query: 390 TSAAKP 395
               + 
Sbjct: 209 IKRTRS 214

This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. The C-terminal 11 residues may function as a protease cofactor leading to enzyme activation. Length = 238

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 45.8 bits (109), Expect = 1e-04
 Identities = 36/234 (15%), Positives = 72/234 (30%), Gaps = 16/234 (6%)

Query: 221  KKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTT 280
            K   K     KP  K   K     +   +K A S V  +    +    K   KP  K + 
Sbjct: 1161 KTKGKASKLRKPKLKKKEKKKKKSSADKSKKA-SVVGNSKRVDSDEKRKLDDKPDNKKSN 1219

Query: 281  AAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPAT 340
            ++        +     K  +    K+  +  S + + +    +        P   P+  +
Sbjct: 1220 SSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVS 1279

Query: 341  AAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPA 400
            A     P  +             S   S   +               + + AA    K +
Sbjct: 1280 AVQYSPPPPSKRPDGE-------SNGGSKPSSPTKKKVK-----KRLEGSLAALKKKKKS 1327

Query: 401  TAKPSTTSKPTTASKPATATRPATTTSKPATT---TSTDIEDEMNQPFTPEELE 451
              K +   K  T  K A+A++ +    +P      +S++ +D+     + +E +
Sbjct: 1328 EKKTARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDSEDEDD 1381

Length = 1388

>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 44.9 bits (106), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 24/68 (35%), Gaps = 1/68 (1%)

Query: 257 KKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVR-KPVASTITKTATSTVSAAP 315
           K    T     P      AP PT + P S  +    AP       S   ++AT+T   +P
Sbjct: 76  KPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESP 135

Query: 316 KPSAPKPA 323
             S P   
Sbjct: 136 STSVPSSG 143

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 378

>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 40/176 (22%), Positives = 60/176 (34%), Gaps = 7/176 (3%)

Query: 267 APKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTIT-KTATSTVSAAPKPSAPKPAAP 325
           A  P     PK +  A  S    P+  P  K V   +  ++      AA + +    AAP
Sbjct: 222 AAAPMLAAKPKRSKNARASKHVEPEIVPGVKGVQEALDLRSPERKERAAAREARAAAAAP 281

Query: 326 KKPVAAPAPKPRPATAAP-----APKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPA 380
               AA AP   PA  AP     A    T        +    A + +        AA+ A
Sbjct: 282 AATAAAAAPAEEPA-VAPMAAIRAAHVETAADKGERAAKPAAADKAADKPADRPDAAEKA 340

Query: 381 APRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTD 436
           A +   +   +A KPA + A    S+  KP  ++  A  T      +      +  
Sbjct: 341 AEKPAEAAPRAADKPAGQAADPASSSADKPGASADAAARTPARARDAAAPDADTPP 396

Length = 413

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 44.2 bits (103), Expect = 2e-04
 Identities = 46/181 (25%), Positives = 62/181 (34%), Gaps = 5/181 (2%)

Query: 146 EKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGA 205
           EK+      ++  +  A K+   ++    P   ++ ++A  + A++  A   A      A
Sbjct: 182 EKDRERARREDAAAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAA 241

Query: 206 AAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAK 265
           A A AA A  KA A        PA   A    A     K       A +P  K A   AK
Sbjct: 242 APAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAK 301

Query: 266 PAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAP 325
            A  PA   A     AAP +   AP       P      K A     AA  P   K    
Sbjct: 302 AAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPP-----AKAAAPPAKAAAAPVGKKAGGK 356

Query: 326 K 326
           K
Sbjct: 357 K 357

Length = 357

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 25/117 (21%), Positives = 41/117 (35%), Gaps = 7/117 (5%)

Query: 321 KPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPA 380
           K  +  +P     P        P       G+ + P +    A   + ++  + +AA P 
Sbjct: 98  KATSMSEPATENKP---AEVTTPVE---PMGLPETPPAVPVPAPAPAVAAAAAQAAAAPK 151

Query: 381 APRVPLSQRTSAAKPATKPATAKPST-TSKPTTASKPATATRPATTTSKPATTTSTD 436
           AP  P ++    A  A    T   +   +K T A+   TA + AT   K      T 
Sbjct: 152 APAKPRAKSPRPAAKAAPKPTETITAKKAKKTAAAPKPTADKTATPAKKTTKKKKTK 208

Length = 209

>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid synthase PfaA

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 27/97 (27%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 293  APVRKPVASTITKTATSTVSAAPKPSAPK-PAAPKKPVAAPAPKPRPATAAPAPKPLTNG 351
            APV K   S +T+     V+ +  P+AP  PA    PV + AP    ATA          
Sbjct: 1126 APVIK---SVVTQAPVVQVTISVAPAAPVLPAVVSPPVVSAAPAQSVATAVAMAP----- 1177

Query: 352  VTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQ 388
            V + P++     S     SV  A+A + +     + Q
Sbjct: 1178 VAEVPIAVPVQQSVDYMPSVAQAAAPQASVNDSAIQQ 1214

Members of the seed for this alignment are involved in omega-3 polyunsaturated fatty acid biosynthesis, such as the protein PfaA from the eicosapentaenoic acid biosynthesis operon in Photobacterium profundum strain SS9. PfaA is encoded together with PfaB, PfaC, and PfaD, and the functions of the individual polypeptides have not yet been described. More distant homologs of PfaA, also included with the reach of this model, appear to be involved in polyketide-like biosynthetic mechanisms of polyunsaturated fatty acid biosynthesis, an alternative to the more familiar iterated mechanism of chain extension and desaturation, and in most cases are encoded near genes for homologs of PfaB, PfaC, and/or PfaD. Length = 2582

>gnl|CDD|225629 COG3087, FtsN, Cell division protein [Cell division and chromosome partitioning]

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 31/173 (17%), Positives = 47/173 (27%), Gaps = 11/173 (6%)

Query: 197 VAGALVVGAAAAGAAVAVKKATAAK-KTDKPGPAAKPASK------PLAKTTTTKTTTAA 249
            A  +V            KKA          G       +         +          
Sbjct: 22  AAAVIVTFIGGLYFITHHKKAPIPFLSNQGTGSLLPNKPEEVWSYIKALEDRQIGVPQPT 81

Query: 250 KPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATS 309
           +PA     +  T    P  +   +       A P      P+ A + +   +   K  + 
Sbjct: 82  EPAAVKDAERLT----PEQRQLLEQMEVDQKAQPTQLGEQPEQARIEEQPRTQSQKAQSQ 137

Query: 310 TVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTT 362
             +   +P  PKP   K    APAP P P   AP  +       K   +A T 
Sbjct: 138 ATTVQTQPVKPKPRPEKPQPVAPAPAPEPVEKAPKAEAAPPPKPKAEDAAETR 190

Length = 264

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 43.4 bits (101), Expect = 3e-04
 Identities = 53/182 (29%), Positives = 64/182 (35%), Gaps = 22/182 (12%)

Query: 238 AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPA----TKPAPKPTTAAPKSTTTAPKPA 293
           A     K   AAK A +P  K +   A PA   A        P    AAP     AP  A
Sbjct: 194 AAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKA 253

Query: 294 PVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVT 353
                 A+     A +  + A  P A   A P K  A PA     A AAPA         
Sbjct: 254 AAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPA----KAAAAPAK-------- 301

Query: 354 KRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTA 413
               +A   A   ++ +  +A  AK AAP  P    T  AK A  PA A  +   K    
Sbjct: 302 ----AAAAPAKAAAAPAKAAAPPAKAAAP--PAKAATPPAKAAAPPAKAAAAPVGKKAGG 355

Query: 414 SK 415
            K
Sbjct: 356 KK 357

Length = 357

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 44.3 bits (105), Expect = 3e-04
 Identities = 30/197 (15%), Positives = 46/197 (23%), Gaps = 13/197 (6%)

Query: 234  SKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPA 293
              P+ +    +     +     V+         A       AP              +P 
Sbjct: 844  RYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAP----VVEAVAEVVEEPV 899

Query: 294  PVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVT 353
             V +P    +    T+        +AP    P   V   +        A   +P+     
Sbjct: 900  VVAEPQPEEVVVVETTHPEVI---AAPVTEQP--QVITESDVAVAQEVAEHAEPVVE-PQ 953

Query: 354  KRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTA 413
                     A             A+PAAP V                   P+   + T  
Sbjct: 954  DETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVA-AEVETVTAVEPEVAPAQVPEATVE 1012

Query: 414  SKPATATRPATTTSKPA 430
               ATA  P T    P 
Sbjct: 1013 HNHATA--PMTRAPAPE 1027

Length = 1068

>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope glycoprotein (BLLF1)

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 73/376 (19%), Positives = 113/376 (30%), Gaps = 43/376 (11%)

Query: 101 VSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSE 160
           V++ K  ++    +  T+    V    A + + S     T   VE  +    PT  +   
Sbjct: 398 VADAKTLIITRTATNATTTTHKVVFHKAPDTTKSVIFVYTLVHVEPHKTTAVPTTPSLPP 457

Query: 161 TAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAA 220
            +   T  +  P       T  S      S       A         A         T  
Sbjct: 458 ASTGPTVSTADPTSGTPTGTTSSTLPEDTSPTSRTTSATPNATSPTPAVTTPNATSPTTQ 517

Query: 221 KKTDKP----------GPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKP 270
           K +D P          G      S P   T+    T+      SPV  T T     AP  
Sbjct: 518 KTSDTPNATSPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEESPVNNTNTPVVTSAPSV 577

Query: 271 ATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSA----------P 320
            T  A         S+ T+ +P     P +S  T  + ST +     SA           
Sbjct: 578 LTS-AVTTGQHGTGSSPTSQQPGI---PSSSHSTPRSNSTSTTPLLTSAHPTGGENITEE 633

Query: 321 KPAAPKK-PVAAPAPKPRPAT---------AAPAPKPLTNGVTK-RPVSATTTASRTSSS 369
            P+ P    V+  +P P P T         ++ +  P    VT+  P    T+ S  S  
Sbjct: 634 TPSVPSTTHVSTLSPGPGPGTTSQVSGPGNSSTSRYPGEVHVTEGMPNPNATSPSAPSGQ 693

Query: 370 SVTSASAAKPAAPRVPLSQRTSA--AKPATKPATAKPSTTSKPTTASKPATATRPA---- 423
                +           ++ TS      +T P T + +  + P  A+     +  +    
Sbjct: 694 KTAVPTVTSTGGKANSTTKETSGSTLMASTSPHTNEGAFRTTPYNATTYLPPSTSSKLRP 753

Query: 424 --TTTSKPATTTSTDI 437
             T TS P TT    +
Sbjct: 754 RWTFTSPPVTTKQATV 769

This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Length = 830

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 43.2 bits (102), Expect = 3e-04
 Identities = 28/155 (18%), Positives = 45/155 (29%), Gaps = 7/155 (4%)

Query: 185 EESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTK 244
                   +        ++ A    A     +       ++P P  +P + P       K
Sbjct: 26  LHQEDFVGIELVPLAVFLLAAKVLEAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPK 85

Query: 245 TTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTIT 304
                +      K       KP PK   +P PK   +   +   A    P R P      
Sbjct: 86  EKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKPKKPPSKTAAKAPAAPNQPARPP------ 139

Query: 305 KTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPA 339
            +A S   AA  PSA   +  ++ +      P  A
Sbjct: 140 -SAASASGAATGPSASYLSGLRRAIRRAPRYPAQA 173

Length = 244

>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional

 Score = 43.9 bits (103), Expect = 3e-04
 Identities = 27/123 (21%), Positives = 42/123 (34%), Gaps = 7/123 (5%)

Query: 260 ATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSA 319
           AT    PAP P    +  P  A   ++  + KP   + P  +   K   +         A
Sbjct: 36  ATQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRA 95

Query: 320 PKPAAPKKPVAAPAPKPR-PATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAK 378
           P PA   +  AAP P      T+A               + T+ AS+    +  +  +  
Sbjct: 96  PDPAVAPQLAAAPKPDAAEAFTSAAQAHEAP------ADAGTSAASKKPDPAAHTQHSPP 149

Query: 379 PAA 381
           P A
Sbjct: 150 PFA 152

Length = 566

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 43.0 bits (101), Expect = 4e-04
 Identities = 30/126 (23%), Positives = 43/126 (34%), Gaps = 3/126 (2%)

Query: 311 VSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSS 370
           V AA   +  K AA      + A K      + A K       K  VSA   A   + ++
Sbjct: 190 VLAAVGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAA 249

Query: 371 VTSASAAKPAAPRVPLSQRTSA---AKPATKPATAKPSTTSKPTTASKPATATRPATTTS 427
             +   AK A  +   + + +A   AK A K A      T     A K A     A + +
Sbjct: 250 KKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKA 309

Query: 428 KPATTT 433
           K     
Sbjct: 310 KATAKA 315

Length = 333

>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional

 Score = 43.8 bits (103), Expect = 4e-04
 Identities = 33/147 (22%), Positives = 49/147 (33%), Gaps = 9/147 (6%)

Query: 241  TTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVA 300
            +  + T   +    P +      A+PA +     + +   AA          A     VA
Sbjct: 910  SARRDTMEIQNEQKPTQDGPAAEAQPAQENTVVESAEKAVAAVSEAAQQAATA-----VA 964

Query: 301  STITKTATSTVSAAPKP---SAPKPAAPKKPVAAPAP-KPRPATAAPAPKPLTNGVTKRP 356
            S I K A +      +    +A   AA KK VA  AP K   A  A A K        + 
Sbjct: 965  SGIEKVAEAVRKTVRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKK 1024

Query: 357  VSATTTASRTSSSSVTSASAAKPAAPR 383
              A   A + ++       A K A  +
Sbjct: 1025 APAKKVARKPAAKKAAKKPARKAAGRK 1051

Length = 1052

>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional

 Score = 43.3 bits (102), Expect = 4e-04
 Identities = 33/165 (20%), Positives = 47/165 (28%), Gaps = 9/165 (5%)

Query: 138 DLTQDIVEE--------KEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTA 189
           DLT + +EE        K  VV P  +     +E    L+ +     +A+   S   +  
Sbjct: 156 DLTPERLEEIIDAFAAGKGPVVKPGPQIGRYASEPAGGLTSLTEEAGKARYNASKALAED 215

Query: 190 SSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAA 249
             D   ++ G  V   A      A    + A +          A K  A         A 
Sbjct: 216 IGDTVKRIDGTEVPLLAPWQGDAAPVPPSEAARPKSADAETNAALKTPATAPKAAAKNAK 275

Query: 250 KPAISPVKKTATTTAKPAPKPATK-PAPKPTTAAPKSTTTAPKPA 293
            P   PV  TA     P         A KP            +P 
Sbjct: 276 APEAQPVSGTAAAEPAPKEAAKAAAAAAKPALEDKPRPLGIARPG 320

Length = 400

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 30/99 (30%), Positives = 35/99 (35%), Gaps = 8/99 (8%)

Query: 234 SKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPA 293
           S PL  +TTT   T   PA         TT   +  PA   AP P     ++   AP  A
Sbjct: 161 SVPLDTSTTTDPATTPAPA-----APVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQA 215

Query: 294 PVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAP 332
            V           AT    AAP P+    A    P A P
Sbjct: 216 NVDTAATPAPAAPATPD-GAAPLPTD--QAGVSTPAADP 251

Length = 331

>gnl|CDD|220840 pfam10667, DUF2486, Protein of unknown function (DUF2486)

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 28/170 (16%), Positives = 47/170 (27%), Gaps = 12/170 (7%)

Query: 247 TAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKT 306
           T A  +  P          P P  ++                  +  P  +  AS     
Sbjct: 2   TQANDSSIPTLTDVLVPGHPVPARSSSADAAGPHDDAAEPVLTDQIVPGAEQAASAAPVH 61

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRT 366
           A    +A P+  A +P       A   P    A A P   P    V     +A      +
Sbjct: 62  AAREATADPEFVAVEPVPTPHVPAVALPGDTDAPAEPGAAP---HVVAERAAAMQAPLPS 118

Query: 367 S---------SSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTT 407
           +          +  T+A A   A    P +   ++   A + A +  +  
Sbjct: 119 ALAADDPQAPPAGATAADAGDAAPDATPPAAGDASPPAAAQAAASAAAAL 168

This family is made up of members from various Burkholderia spp. The function is unknown. Length = 245

>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF; Provisional

 Score = 43.1 bits (101), Expect = 5e-04
 Identities = 32/201 (15%), Positives = 56/201 (27%), Gaps = 12/201 (5%)

Query: 254 SPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSA 313
             V++   T     P  A  PAP P      +               S   + A++    
Sbjct: 49  ELVQRALETARSDTPATAAAPAPAPQAPTKPAAPVHAPLKLSANANMSQRQRVASAAEDM 108

Query: 314 APKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTS 373
               +  +P +  +   A AP    +  +PA + L +    R       A       + +
Sbjct: 109 IAAMALRQPVSVPRQAPAAAPVRAASIPSPAAQALAHAAAVRTAPRQEHALSAVPEQLFA 168

Query: 374 ASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTT 433
                   PR P+             A    +    P  A+  A     A    +     
Sbjct: 169 DFLTTAPVPRAPV------------QAPVVAAPAPVPAIAAALAAHAAYAQDDDEQLDDD 216

Query: 434 STDIEDEMNQPFTPEELEAAI 454
             D++D + Q   P  L   +
Sbjct: 217 GFDLDDALPQILPPAALPPIV 237

Length = 559

>gnl|CDD|235571 PRK05704, PRK05704, dihydrolipoamide succinyltransferase; Validated

 Score = 42.9 bits (102), Expect = 5e-04
 Identities = 40/154 (25%), Positives = 48/154 (31%), Gaps = 20/154 (12%)

Query: 208 AGAAVAVKKATAAKKTDK-----PGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATT 262
            G AV   +     +TDK     P PAA   S+ LA+   T T       I         
Sbjct: 26  PGDAVKRDEVLVEIETDKVVLEVPAPAAGVLSEILAEEGDTVTVGQVLGRIDEGAAAGAA 85

Query: 263 TAKPAPKPATKPAPKPTTAAPKSTTTAPKPAP-VRKPVASTITKTATSTVSAAPK----- 316
            A  A   A   AP    AA  +  +    +P  RK  A        S V    K     
Sbjct: 86  AAAAAAAAAAAAAPAQAQAAAAAEQSNDALSPAARKLAAE--NGLDASAVKGTGKGGRVT 143

Query: 317 -------PSAPKPAAPKKPVAAPAPKPRPATAAP 343
                   +A   A      AAPA  P P  A P
Sbjct: 144 KEDVLAALAAAAAAPAAPAAAAPAAAPAPLGARP 177

Length = 407

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 2/105 (1%)

Query: 216 KATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPA 275
           K        +P  A +P++   A  + ++++ AA+P+          T            
Sbjct: 376 KQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAV 435

Query: 276 P-KPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSA 319
           P  P + AP++   A      +K   S ++    ST+    + + 
Sbjct: 436 PVNPPSTAPQAVRPAQFKEE-KKIPVSKVSSLGPSTLRPIQEKAE 479

Length = 614

>gnl|CDD|183756 PRK12799, motB, flagellar motor protein MotB; Reviewed

 Score = 43.2 bits (101), Expect = 5e-04
 Identities = 33/136 (24%), Positives = 56/136 (41%), Gaps = 15/136 (11%)

Query: 302 TITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATT 361
           T+   A +  SA  + SA  P++   P  +PA  P   T   A              A+ 
Sbjct: 298 TVPVAAVTPSSAVTQSSAITPSSAAIP--SPAVIPSSVTTQSAT----------TTQASA 345

Query: 362 TASRTSSSSVTSASAAKPAAPRVPLSQRTSA-AKPATKPATAKPSTTSKPTTASKPATAT 420
            A   SS+ V  +    P    +P ++  +   +P +   T + ST +  +TA+ P T+ 
Sbjct: 346 VA--LSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQSSTGNITSTANGPTTSL 403

Query: 421 RPATTTSKPATTTSTD 436
             A  ++ P + TS D
Sbjct: 404 PAAPASNIPVSPTSRD 419

Length = 421

>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase

 Score = 43.5 bits (102), Expect = 5e-04
 Identities = 72/344 (20%), Positives = 95/344 (27%), Gaps = 44/344 (12%)

Query: 98  TPEVSEPKEEVLDDLV--SVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTD 155
           T E  EP  EV  D V   +P+    V+    A E+       +   I E  EA   P  
Sbjct: 29  TVEADEPLLEVSTDKVDTEIPSPAAGVLLEIRAPEDDTVEVGGVLAIIGEPGEAGSEPAP 88

Query: 156 ETNSETAEKETPLSEVPVIPQEAQTVESAEESTASS--------DLAAKVA-GALVVGAA 206
                 A  E         P       +A ++  S         +L   V  G +     
Sbjct: 89  AAPEPEAAPEPEAPAPAPTPAAEAPAPAAPQAGGSGEATEVKMPELGESVTEGTVTSWLK 148

Query: 207 AAGAAVAVKKATAAKKTDK-----PGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTAT 261
           A G  V V +      TDK     P P A    +  A    T         I        
Sbjct: 149 AVGDTVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAPEDDTVEVGTVLAIIGDANAAPA 208

Query: 262 TTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPK 321
             A+      ++   +P          A    P   P              A  K +AP 
Sbjct: 209 EPAEEEAPAPSEAGSEPAPDPAARAPHAAPDPPAPAP--------------APAKTAAPA 254

Query: 322 PAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAA 381
            AAP        P   P     A      GV    V  T    R     V +A+ A   A
Sbjct: 255 AAAPVSS-GDSGPYVTPLVRKLAKD---KGVDLSTVKGTGVGGRIRKQDVLAAAKAAEEA 310

Query: 382 PRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATT 425
                      A  A   A A P+  +     ++P TA    TT
Sbjct: 311 ----------RAAAAAPAAAAAPAAPAAAAKPAEPDTAKLRGTT 344

This model represents an Actinobacterial clade of E2 enzyme, a component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (pfam00198), one or two biotin domains (pfam00364) and an E3-component binding domain (pfam02817). Length = 579

>gnl|CDD|219392 pfam07382, HC2, Histone H1-like nucleoprotein HC2

 Score = 41.7 bits (97), Expect = 5e-04
 Identities = 37/158 (23%), Positives = 54/158 (34%), Gaps = 4/158 (2%)

Query: 183 SAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTT 242
           +A+++      A K A    V    A    A +K  A K      PAAK A+K       
Sbjct: 14  AAKKAAVRKPAAKKAAAKKTVVRKVAAKKPAARKTVAKKTVAAKKPAAKKAAKKAVAKKV 73

Query: 243 TKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVAST 302
                 AK A++  K TA   A          A K     P +     K A  RKP A  
Sbjct: 74  VAKKPVAKKAVAK-KATAKKVAAKKVVAKKTVAKKAAAKKPAAKKAVAKKAVARKPAAK- 131

Query: 303 ITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPAT 340
             K      ++    +    AA K+  ++ A +    +
Sbjct: 132 --KAVAKKAASTCHKNHKHTAACKRVASSSATRAACGS 167

This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles. Length = 187

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 43.2 bits (102), Expect = 6e-04
 Identities = 25/104 (24%), Positives = 34/104 (32%), Gaps = 7/104 (6%)

Query: 218 TAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKP-APKPATKPAP 276
           T        G   K   KP+          +A  A SP    ++  A+P AP+ AT+PA 
Sbjct: 363 TQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAG 422

Query: 277 KPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAP 320
            P T       +   PA V     ST  +          K    
Sbjct: 423 TPPTV------SVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIPV 460

Length = 614

>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413)

 Score = 42.9 bits (101), Expect = 6e-04
 Identities = 31/156 (19%), Positives = 56/156 (35%), Gaps = 17/156 (10%)

Query: 228 PAAKPASKPLAKTTTTKTTTAAKPAI-----SPVKKTATTTAKPAPKPATKPAPKPTTAA 282
           P  K  +K   K   +K +T     I        +       K   + +    P+    +
Sbjct: 9   PDEKAPTKKPKKGDASKDSTEDDEDILEFLDELEQSEKAKPPKKPKEASRPGTPRNPKKS 68

Query: 283 PKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAA 342
            K T ++   +  +        K+A ST S+ PK  AP   + ++      P P  +   
Sbjct: 69  SKPTESSAASSEEKPAKPR---KSAESTRSSHPKSKAPSTESEEEEEPEETPDPIAS--- 122

Query: 343 PAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAK 378
                +    +    S T+TA+ T+S++V  A  A 
Sbjct: 123 -----IGGWWSLWG-SITSTATSTASAAVKQAEQAV 152

This is a family of proteins conserved in fungi. The function is not known. Length = 436

>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.8 bits (101), Expect = 7e-04
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 355 RPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTAS 414
           +P +A   A+     +     AA PAA   P++Q  +A  PA  PA A  +  + P  A+
Sbjct: 365 KPAAAAEAAAPAEKKTPARPEAAAPAA--APVAQAAAAPAPAAAPAAAASAPAA-PPAAA 421

Query: 415 KPATATRPATTTSKPA 430
            PA    PA      A
Sbjct: 422 PPAPVAAPAAAAPAAA 437

Length = 618

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 25/107 (23%), Positives = 35/107 (32%), Gaps = 13/107 (12%)

Query: 294 PVRKPVASTITKT------------ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATA 341
            +R P +  ITK               S +     P A  PAA     A      +P  A
Sbjct: 89  DIRAPASGVITKIFAEEGDTVEVGAPLSEIDTGGAPPAAAPAAAAAAKAEKTTPEKPKAA 148

Query: 342 AP-APKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLS 387
           AP    P  +  T    +     +  +    T  + A P   RVP+S
Sbjct: 149 APTPEPPAASKPTPPAAAKPPEPAPAAKPPPTPVARADPRETRVPMS 195

Length = 418

>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI

 Score = 40.2 bits (95), Expect = 7e-04
 Identities = 26/130 (20%), Positives = 43/130 (33%), Gaps = 11/130 (8%)

Query: 676 ICIYTD-ASKKNEK---VGAAWFCPTYKS-KACFKLHPATSTYTAEVIGIWEALKYSASL 730
             +Y D AS+ N      G     P  +  +    L    +   AE   +   L+ +  L
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALEL 60

Query: 731 KNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIK 790
              ++ I  DS+    ++                L   + L    + V++ WI   E   
Sbjct: 61  GIKKLEIYGDSQLVVNQIQGEYEVKNERLAPY--LEEARELLKKFEEVEIKWIPREE--- 115

Query: 791 GNVEVDRLAK 800
            N E D LA 
Sbjct: 116 -NKEADALAN 124

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 35/201 (17%), Positives = 50/201 (24%), Gaps = 9/201 (4%)

Query: 276  PKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPK 335
            P P T A  S   A     +R PV             A      P  A      A     
Sbjct: 824  PMPLTVACASPEMASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVV 883

Query: 336  PRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKP 395
              P   A A       V   P         T+   V +A       P+V      + A+ 
Sbjct: 884  SAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVT--EQPQVITESDVAVAQE 941

Query: 396  ATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEE---LEA 452
                  A+P    +  TA     A       ++P                  E    +E 
Sbjct: 942  VA--EHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEP 999

Query: 453  AIKSGLITTPGRDNIH--YPM 471
             +    +     ++ H   PM
Sbjct: 1000 EVAPAQVPEATVEHNHATAPM 1020

Length = 1068

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 42.8 bits (100), Expect = 8e-04
 Identities = 40/205 (19%), Positives = 68/205 (33%), Gaps = 3/205 (1%)

Query: 227 GPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKST 286
           GP +       A   +    T +  A+ P  + +   A+PAP+P         +A     
Sbjct: 177 GPPSIQVPPGAALAPSAPPPTPSAQAVPP--QGSPIAAQPAPQPQQPSPLSLISAPSLHP 234

Query: 287 TTAPKPAPVRKPV-ASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAP 345
              P P P  +P  AS  +    +  S  P+ S   P  P        P      ++  P
Sbjct: 235 QRLPSPHPPLQPQTASQQSPQPPAPSSRHPQSSHHGPGPPMPHALQQGPVFLQHPSSNPP 294

Query: 346 KPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPS 405
           +P     ++ P     + ++  S +  S SA +P  P        + + P  KP    P 
Sbjct: 295 QPFGLAQSQVPPLPLPSQAQPHSHTPPSQSALQPQQPPREQPLPPAPSMPHIKPPPTTPI 354

Query: 406 TTSKPTTASKPATATRPATTTSKPA 430
                 +   P     P+     P+
Sbjct: 355 PQLPNQSHKHPPHLQGPSPFPQMPS 379

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|223066 PHA03379, PHA03379, EBNA-3A; Provisional

 Score = 42.7 bits (100), Expect = 8e-04
 Identities = 48/244 (19%), Positives = 75/244 (30%), Gaps = 43/244 (17%)

Query: 242 TTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVAS 301
             K T  A+ A+    +    T +P       P  KP    P+S  TA      + P   
Sbjct: 394 AGKLTERAREALEKASEPTYGTPRP-------PVEKPRPEVPQSLETATSHGSAQVPEPP 446

Query: 302 TITKTATSTV----SAAPKPSAPKPAAPKKPVAA------------PAPKPRPATAAPAP 345
            +       +    S AP P A  P  P + +              PA  P PA A P  
Sbjct: 447 PVHDLEPGPLHDQHSMAPCPVAQLPPGPLQDLEPGDQLPGVVQDGRPACAPVPAPAGPIV 506

Query: 346 KPLTNGVTKRPVSATTTAS----RTSSSSVTSASAAKPAAPRVPLSQRTSAAKPAT---- 397
           +P    +++ P  A               V + +  +P  P  PL       + +     
Sbjct: 507 RPWEASLSQVPGVAFAPVMPQPMPVEPVPVPTVALERPVCPAPPLIAMQGPGETSGIVRV 566

Query: 398 ----KPATAKPSTTSKPTTAS--------KPATATRPATTTSKPATTTSTDIEDEMNQPF 445
               +PA   P+    P+  S        +       A+   +P   T    +  M  P 
Sbjct: 567 RERWRPAPWTPNPPRSPSQMSVRDRLARLRAEAQPYQASVEVQPPQLTQVSPQQPMEYPL 626

Query: 446 TPEE 449
            PE+
Sbjct: 627 EPEQ 630

Length = 935

>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane glycoprotein G

 Score = 42.3 bits (99), Expect = 9e-04
 Identities = 40/179 (22%), Positives = 55/179 (30%), Gaps = 20/179 (11%)

Query: 256 VKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAP 315
             KTA TT+K    P     P      P   T   +PA          T TA   +S+  
Sbjct: 167 EPKTAVTTSKTTSWPTEVSHP----TYPSQVTPQSQPATQ-----GHQTATANQRLSSTE 217

Query: 316 KPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSAS 375
                       P   P  +P P+   P+  P     T     +TT   +  +    +  
Sbjct: 218 PVGTQGTTTSSNP--EPQTEPPPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQRRKTPP 275

Query: 376 AAKPAAPRVPLSQRTSAAKP---ATKPATAKPSTT----SKPTTASKPATATRPATTTS 427
           A   +  R P S  T         T   T +P+ T    S P  +S P     P T   
Sbjct: 276 A--TSNRRSPHSTATPPPTTKRQETGRPTPRPTATTQSGSSPPHSSPPGVQANPTTQNL 332

Length = 408

>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown]

 Score = 42.5 bits (100), Expect = 9e-04
 Identities = 30/90 (33%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 247 TAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVAST-ITK 305
             A+ A  PV K A      AP+ A    P P  A   ++   P P P   P  +     
Sbjct: 38  LVAEGAAGPVAKAAEQM--AAPEAAEAA-PLPAAAESIASPEVPPPVP---PAPAQEGEA 91

Query: 306 TATSTVSAAPKPS-APKPAAPKKPVAAPAP 334
            A    SA P PS AP PA P +P  A  P
Sbjct: 92  PAAEQPSAVPAPSAAPAPAEPVEPSLAANP 121

Length = 931

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 42.2 bits (100), Expect = 0.001
 Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 358 SATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPA 417
           +A   A+  ++S+  +A AAK  A   P     +AA PA  P  A  +  +    A   A
Sbjct: 45  TAAAAAAAAAASAPAAAPAAKAPAAPAP--APPAAAAPAAPPKPAAAAAAAAAPAAPPAA 102

Query: 418 TATRPATTTSKPATTT 433
            A       +     T
Sbjct: 103 AAAAAPAAAAVEDEVT 118

Length = 1228

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 42.2 bits (99), Expect = 0.001
 Identities = 34/208 (16%), Positives = 55/208 (26%), Gaps = 24/208 (11%)

Query: 265  KPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAA 324
            + A +  +  A K +  APK     P P    K  + + T   T   SA    +  +   
Sbjct: 1184 RAAARGESGAAKKVSRQAPK----KPAPKKTTKKASESETTEETYGSSAMETENVAEVVK 1239

Query: 325  PK----KPVAAPAPKP------RPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSA 374
            PK        APA                              +      +   +   +A
Sbjct: 1240 PKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEETVKAVPARRAAA 1299

Query: 375  SAAKPAAPRVPLSQ---------RTSAAKPATKPATAKPSTTSKPTTASKPATATRPATT 425
                 A+  V               S A+   K    KP+  +K   A  PA A +    
Sbjct: 1300 RKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKA-AKPPAAAKKRGPA 1358

Query: 426  TSKPATTTSTDIEDEMNQPFTPEELEAA 453
            T +      T++           E +  
Sbjct: 1359 TVQSGQKLLTEMLKPAEAIGISPEKKVR 1386

Length = 1465

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 27/116 (23%), Positives = 40/116 (34%), Gaps = 8/116 (6%)

Query: 287 TTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPK 346
           TT+    P+   V   +     +   A P  +AP P  P      PAP  RP  AA A  
Sbjct: 343 TTSYGQLPLELAVIEALLVPVPAPQPAKPTAAAPSPVRPT-----PAPSTRPKAAAAANI 397

Query: 347 PLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPR--VPLSQRTSAAKPATKPA 400
           P    V +   +      R  +  V     + P   R  +P+ ++     PA    
Sbjct: 398 PPKEPVRETA-TPPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPKE 452

Length = 585

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 42.3 bits (100), Expect = 0.001
 Identities = 21/104 (20%), Positives = 34/104 (32%), Gaps = 9/104 (8%)

Query: 299 VASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPR---PATAAPAPKPLTNGVTKR 355
           +A+     A +  +A P P+A   A  +    A  P P     A    A +         
Sbjct: 48  LAALAPPAAAAPAAAQPPPAAAPAAVSRPAAPAAEPAPWLVEHAKRLTAQREQLVARAAA 107

Query: 356 PVSATTTASRTSSS------SVTSASAAKPAAPRVPLSQRTSAA 393
           P +    A    +       +    + A  AAPR  +    +AA
Sbjct: 108 PAAPEAQAPAAPAERAAAENAARRLARAAAAAPRPRVPADAAAA 151

Length = 484

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 23/117 (19%), Positives = 34/117 (29%), Gaps = 7/117 (5%)

Query: 252 AISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTV 311
           A++P        A  A +P    AP    + P +    P P  V      T  +      
Sbjct: 50  ALAP----PAAAAPAAAQPPPAAAP-AAVSRPAAPAAEPAPWLVEHAKRLTAQREQLVAR 104

Query: 312 SAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSS 368
           +AAP     +  A     AA     R    A A  P          +A    +  + 
Sbjct: 105 AAAPAAPEAQAPAAPAERAAAENAARRLARAAAAAPRPR--VPADAAAAVADAVKAR 159

Length = 484

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 30/113 (26%), Positives = 36/113 (31%), Gaps = 9/113 (7%)

Query: 178 AQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPL 237
           A   + AE +T    +        V   A A A  A     AA          K  +KP 
Sbjct: 106 ATENKPAEVTTPVEPMGLPETPPAVPVPAPAPAVAAAAAQAAAA--------PKAPAKPR 157

Query: 238 AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAP 290
           AK+       A KP  +   K A  TA  APKP       P     K   T  
Sbjct: 158 AKSPRPAAKAAPKPTETITAKKAKKTA-AAPKPTADKTATPAKKTTKKKKTKA 209

Length = 209

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 42.5 bits (100), Expect = 0.001
 Identities = 19/110 (17%), Positives = 30/110 (27%), Gaps = 8/110 (7%)

Query: 326 KKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVP 385
                 P    +P    PA  P          +A  + S + SS+    SA + A     
Sbjct: 369 ASGGRGPKQHIKPVFTQPAAAPQP------SAAAAASPSPSQSSAAAQPSAPQSATQPAG 422

Query: 386 LSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTST 435
                S   PA       P +T+            +    +   +   ST
Sbjct: 423 TPPTVSVDPPA--AVPVNPPSTAPQAVRPAQFKEEKKIPVSKVSSLGPST 470

Length = 614

>gnl|CDD|219392 pfam07382, HC2, Histone H1-like nucleoprotein HC2

 Score = 40.5 bits (94), Expect = 0.001
 Identities = 41/170 (24%), Positives = 54/170 (31%), Gaps = 1/170 (0%)

Query: 211 AVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKP 270
             A KK ++ K   K     KPA+K  A   T     AAK   +       T A   P  
Sbjct: 2   LGAQKKRSSKKTAAKKAAVRKPAAKKAAAKKTVVRKVAAKKPAARKTVAKKTVAAKKPAA 61

Query: 271 ATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVA 330
                             A K    +        K   +  + A K +A KPAA KK VA
Sbjct: 62  KKAAKKAVAKKVVAKKPVAKKAVAKKATAKKVAAKKVVAKKTVAKKAAAKKPAA-KKAVA 120

Query: 331 APAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPA 380
             A   +PA      K   +   K            SSS+  +A  +K  
Sbjct: 121 KKAVARKPAAKKAVAKKAASTCHKNHKHTAACKRVASSSATRAACGSKSR 170

This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles. Length = 187

>gnl|CDD|219392 pfam07382, HC2, Histone H1-like nucleoprotein HC2

 Score = 40.1 bits (93), Expect = 0.001
 Identities = 49/184 (26%), Positives = 65/184 (35%), Gaps = 11/184 (5%)

Query: 214 VKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATK 273
            +K  ++KKT     A +   KP AK    K T   K A    K  A  T       A K
Sbjct: 4   AQKKRSSKKTAAKKAAVR---KPAAKKAAAKKTVVRKVAAK--KPAARKTVAKKTVAAKK 58

Query: 274 PAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPA 333
           PA K       +     K    +K VA    K AT+   AA K  A K  A K     PA
Sbjct: 59  PAAKKAAKKAVAKKVVAKKPVAKKAVA----KKATAKKVAAKKVVAKKTVAKKAAAKKPA 114

Query: 334 PKPRPATAAPAPKPLTNGVTKRPVSAT--TTASRTSSSSVTSASAAKPAAPRVPLSQRTS 391
            K   A  A A KP       +  ++T       T++    ++S+A  AA         +
Sbjct: 115 AKKAVAKKAVARKPAAKKAVAKKAASTCHKNHKHTAACKRVASSSATRAACGSKSRVNPA 174

Query: 392 AAKP 395
               
Sbjct: 175 HGWR 178

This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles. Length = 187

>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown]

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 2/81 (2%)

Query: 267 APKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPK 326
               +          A  +   A   A    P+ +     A+  V     P+  +     
Sbjct: 33  RELRSLVAEGAAGPVAKAAEQMAAPEAAEAAPLPAAAESIASPEVPPPVPPAPAQE-GEA 91

Query: 327 KPVAAPAPKPRPATAAPAPKP 347
                P+  P P+ AAPAP  
Sbjct: 92  PAAEQPSAVPAPS-AAPAPAE 111

Length = 931

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

 Score = 39.4 bits (93), Expect = 0.001
 Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 2/38 (5%)

Query: 768 YKHLQNTCKTVKLAWIK--GHEGIKGNVEVDRLAKYAT 803
            + +    K +K++++K   H G K N   D+LAK A 
Sbjct: 96  KEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.8 bits (98), Expect = 0.001
 Identities = 33/223 (14%), Positives = 55/223 (24%), Gaps = 8/223 (3%)

Query: 213 AVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKT-----ATTTAKPA 267
           AVK+    +K    GPAAK       K  + K     K  +   KK              
Sbjct: 76  AVKRV---EKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRK 132

Query: 268 PKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKK 327
           PK   K    P     +      +P    +       +  +       K    K   P +
Sbjct: 133 PKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPE 192

Query: 328 PVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLS 387
                          P    +     K         + TS      +  +   + R   S
Sbjct: 193 EEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSS 252

Query: 388 QRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPA 430
            +     P+      + S+    T              +++PA
Sbjct: 253 LKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPASARPA 295

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 33/151 (21%), Positives = 47/151 (31%), Gaps = 25/151 (16%)

Query: 281  AAPKSTTTAPKPAP-VRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPA 339
              P     A +  P     V  +  K A + VS A + +A   A+  + VA    K    
Sbjct: 922  QKPTQDGPAAEAQPAQENTVVESAEK-AVAAVSEAAQQAATAVASGIEKVAEAVRKTVRR 980

Query: 340  TAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKP 399
            +   A         K                V   + AK AA +   +++ +A K   K 
Sbjct: 981  SVKKAAATRAAMKKK----------------VAKKAPAKKAAAKKAAAKKAAAKKKVAKK 1024

Query: 400  ATAKPSTTSKPTTASKPATATRPATTTSKPA 430
            A AK         A KPA          K A
Sbjct: 1025 APAK-------KVARKPAAKKAAKKPARKAA 1048

Length = 1052

>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated

 Score = 41.5 bits (98), Expect = 0.002
 Identities = 33/125 (26%), Positives = 41/125 (32%), Gaps = 11/125 (8%)

Query: 189 ASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPG-PAAKPASKPLAKTTTTKTTT 247
           A SDLAA     L   AAAA AA     A A     +P  PAA+PA   +          
Sbjct: 44  ADSDLAA-----LAPPAAAAPAAAQPPPAAAPAAVSRPAAPAAEPAPWLVEHAKR----- 93

Query: 248 AAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTA 307
                   V + A   A  A  PA          A +    A   AP  +  A      A
Sbjct: 94  LTAQREQLVARAAAPAAPEAQAPAAPAERAAAENAARRLARAAAAAPRPRVPADAAAAVA 153

Query: 308 TSTVS 312
            +  +
Sbjct: 154 DAVKA 158

Length = 484

>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated

 Score = 41.6 bits (97), Expect = 0.002
 Identities = 35/167 (20%), Positives = 49/167 (29%), Gaps = 8/167 (4%)

Query: 278 PTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPR 337
           P+    +  T A KP P      +   +T   T SAA  PS  K A P          P 
Sbjct: 380 PSAQTAEKETAAKKPQPR---PEAETAQTPVQTASAAAMPSEGKTAGPVSNQENNDVPPW 436

Query: 338 PATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPAT 397
                 A        T      T + + T   +  S + A       PLS+      P+ 
Sbjct: 437 EDAPDEAQTAAGTAQTSAKSIQTASEAETPPENQVSKNKAADNETDAPLSE-----VPSE 491

Query: 398 KPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQP 444
            P  A P+  +  T          P      P      +   E+  P
Sbjct: 492 NPIQATPNDEAVETETFAHEAPAEPFYGYGFPDNDCPPEDGAEIPPP 538

Length = 709

>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 14/73 (19%), Positives = 26/73 (35%)

Query: 241 TTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVA 300
             T T   A PA +P      T + PA   +   A   +    KS +     A   +  +
Sbjct: 77  PKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPS 136

Query: 301 STITKTATSTVSA 313
           +++  + +   S 
Sbjct: 137 TSVPSSGSDAAST 149

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 378

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 24/94 (25%), Positives = 34/94 (36%)

Query: 255 PVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAA 314
            V    +TT  PA  PA       T    ++   A  PAP   P  + +   + + V  A
Sbjct: 161 SVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTA 220

Query: 315 PKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPL 348
             P+   PA P      P  +   +T A  P  L
Sbjct: 221 ATPAPAAPATPDGAAPLPTDQAGVSTPAADPNAL 254

Length = 331

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 35/176 (19%), Positives = 51/176 (28%), Gaps = 25/176 (14%)

Query: 173 VIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVA-VKKATAAKKTDKPGPAAK 231
            +  EA   E AE + A+   AA   G +  G       VA   KA  A+ TD+    + 
Sbjct: 290 YVVDEALEREPAELAAAAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAESV 349

Query: 232 PASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPK 291
                    +T      ++  I   +        PA       A +    A  +    P 
Sbjct: 350 VQVADRDGESTPAVEETSEADIEREQPGDLAGQAPA-------AHQVDAEAASAAPEEPA 402

Query: 292 PAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKP 347
                    +              +P  P+ AAP      PA     A A P   P
Sbjct: 403 ALASEAHDET--------------EPEVPEKAAPI---PDPAKPDELAVAGPGDDP 441

Length = 460

>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 14/79 (17%), Positives = 21/79 (26%)

Query: 229 AAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTT 288
           A++ A    +   T   T A            T    P      KPA      A  +   
Sbjct: 163 ASQNAQGNTSTLPTAPATVAPSKGAKVPATAETHPTPPQKPATKKPAVNHHKTATVAVPP 222

Query: 289 APKPAPVRKPVASTITKTA 307
           A    P     ++    +A
Sbjct: 223 ATSGKPKSGAASARALSSA 241

Length = 327

>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 44/198 (22%), Positives = 65/198 (32%), Gaps = 17/198 (8%)

Query: 217 ATAAKKTDKPGPAAKPA-SKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPA 275
           A A K  D  G ++  + ++         +       +         +A P     T+ A
Sbjct: 73  AGAEKNIDLSGSSSLSSGNQSSPSAANNTSDGHDASGVKNTAPPQDISAPPISPTPTQAA 132

Query: 276 PKPTTAA------PKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPV 329
           P  T         P + + A      +   AS   +  TST+  AP   AP      K  
Sbjct: 133 PPQTPNGQQRIELPGNISDALSQQQGQVNAASQNAQGNTSTLPTAPATVAPS--KGAKVP 190

Query: 330 AAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLS-- 387
           A     P P       KP  N       +AT      +S    S +A+  A    P S  
Sbjct: 191 ATAETHPTPPQKPATKKPAVN----HHKTATVAVPPATSGKPKSGAASARALSSAPASHY 246

Query: 388 --QRTSAAKPATKPATAK 403
             Q +SA++  T  A AK
Sbjct: 247 TLQLSSASRSDTLNAYAK 264

Length = 327

>gnl|CDD|223033 PHA03291, PHA03291, envelope glycoprotein I; Provisional

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 27/110 (24%), Positives = 40/110 (36%)

Query: 228 PAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTT 287
                A+ PL + +   +   A P  +P    A       P+P  +    P T    STT
Sbjct: 168 AEGTLAAPPLGEGSADGSCDPALPLSAPRLGPADVFVPATPRPTPRTTASPETTPTPSTT 227

Query: 288 TAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPR 337
           T+P    +  P  +     A +T  A   P+ P P   + P A   P P 
Sbjct: 228 TSPPSTTIPAPSTTIAAPQAGTTPEAEGTPAPPTPGGGEAPPANATPAPE 277

Length = 401

>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional

 Score = 41.6 bits (97), Expect = 0.002
 Identities = 51/249 (20%), Positives = 75/249 (30%), Gaps = 17/249 (6%)

Query: 220 AKKTDKPGPAAKPAS-KPLAKTTTTKTTTAAKPAISPVKKTATTTAKPA-PKPATKPAPK 277
           +K++D+P    KP   K              KP+     K  T + KP  PK    P   
Sbjct: 537 SKESDEPKEGGKPGETKEGEVGKKPGPAKEHKPS-----KIPTLSKKPEFPKDPKHPKDP 591

Query: 278 PTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPR 337
                PK   +A +P   + P    +     S        S  +P  P++P +     P 
Sbjct: 592 EEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPKRPPPPQRPSS-----PE 646

Query: 338 PATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPAT 397
                   K      + +P        +     + +A+ +K     V L +   +    T
Sbjct: 647 RPEGPKIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKETKTTVVLDESFESILKET 706

Query: 398 KPAT-AKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKS 456
            P T   P TT +P     P     P      P      DIE        PEE       
Sbjct: 707 LPETPGTPFTTPRPLPPKLPRDEEFPFEPIGDPDAEQPDDIEFFT----PPEEERTFFHE 762

Query: 457 GLITTPGRD 465
               TP  D
Sbjct: 763 TPADTPLPD 771

Length = 943

>gnl|CDD|191251 pfam05283, MGC-24, Multi-glycosylated core protein 24 (MGC-24)

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 240 TTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPK-STTTAPKPAPVRKP 298
                 TT +    +       +TAKP   P+   +    T+ PK +TT  P   P RK 
Sbjct: 98  GCQIYNTTDSCSVATTTPVPTNSTAKPTITPSPTTSHHHVTSEPKTNTTVTPTSQPDRKS 157

This family consists of several MGC-24 (or Cd164 antigen) proteins from eukaryotic organisms. MGC-24/CD164 is a sialomucin expressed in many normal and cancerous tissues. In humans, soluble and transmembrane forms of MGC-24 are produced by alternative splicing. Length = 187

>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional

 Score = 41.1 bits (97), Expect = 0.002
 Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 3/95 (3%)

Query: 257 KKTATTTAKPAPKPA-TKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAP 315
             +A+ TAK  P P  + P P PT   P+ T TAP P P   P   T T+ +++  +  P
Sbjct: 514 SGSASNTAKTPPPPQKSPPPPAPTPPLPQPTATAPPPTPP--PPPPTATQASSNAPAQIP 571

Query: 316 KPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTN 350
             S+P P  P++P  +P     P     A K L +
Sbjct: 572 ADSSPPPPIPEEPTPSPTKDSSPEEIDKAAKNLAD 606

Length = 620

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 23/94 (24%), Positives = 30/94 (31%), Gaps = 4/94 (4%)

Query: 235 KPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPA- 293
               K TT K TT  K    P  K ATT+ + A    T        A   +     K   
Sbjct: 1   MAETKKTTKKKTTEEK---KPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVK 57

Query: 294 PVRKPVASTITKTATSTVSAAPKPSAPKPAAPKK 327
              K V     KT +    +  K +  K A   +
Sbjct: 58  TTTKKVTVKFEKTESVKKESVAKKTVKKEAVSAE 91

Length = 295

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 33/143 (23%), Positives = 47/143 (32%), Gaps = 10/143 (6%)

Query: 144 VEEKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVV 203
              K+A  TP  ++ ++ A  +           +  + + A ++  S+  AAK A     
Sbjct: 197 ANAKKAAKTPAAKSGAKKASAKAK------SAAKKVSKKKAAKTAVSAKKAAKTAAKAAK 250

Query: 204 GAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTT 263
            A         K A A KK  K   AAK A+K  A     K T     A     K A   
Sbjct: 251 KAKKTAKKALKKAAKAVKKAAK--KAAKAAAK--AAKGAAKATKGKAKAKKKAGKKAAAG 306

Query: 264 AKPAPKPATKPAPKPTTAAPKST 286
           +K                A K T
Sbjct: 307 SKAKATAKAPKRGAKGKKAKKVT 329

Length = 333

>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 28/123 (22%), Positives = 38/123 (30%), Gaps = 6/123 (4%)

Query: 238  AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRK 297
             K T       A+PA         T  + A K     +     AA    +   K A   +
Sbjct: 922  QKPTQDGPAAEAQPAQE------NTVVESAEKAVAAVSEAAQQAATAVASGIEKVAEAVR 975

Query: 298  PVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPV 357
                   K A +T +A  K  A K  A K      A K   A    A K     V ++P 
Sbjct: 976  KTVRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPA 1035

Query: 358  SAT 360
            +  
Sbjct: 1036 AKK 1038

Length = 1052

>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 26/101 (25%), Positives = 38/101 (37%), Gaps = 9/101 (8%)

Query: 356 PVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASK 415
           PV A   A  T+++   S     PA    P ++  +AA     P      T + P    +
Sbjct: 362 PVPAPQPAKPTAAA--PSPVRPTPA----PSTRPKAAAAANIPPKEPVRETATPPPVPPR 415

Query: 416 PATATRPATTTSKPATTTS---TDIEDEMNQPFTPEELEAA 453
           P     P T  S P  T +    D + +   P  P+E E A
Sbjct: 416 PVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPKEEEKA 456

Length = 585

>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase; Provisional

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 20/74 (27%), Positives = 28/74 (37%), Gaps = 1/74 (1%)

Query: 374 ASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTT 433
             AA PAA     +++T+  KP     T +P   SKPT  +       PA     P T  
Sbjct: 124 PPAAAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPE-PAPAAKPPPTPV 182

Query: 434 STDIEDEMNQPFTP 447
           +     E   P + 
Sbjct: 183 ARADPRETRVPMSR 196

Length = 418

>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed

 Score = 40.6 bits (96), Expect = 0.003
 Identities = 19/61 (31%), Positives = 22/61 (36%)

Query: 293 APVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGV 352
             V   +       A    +AAP  +AP  AA   P  APA    PA AAPA        
Sbjct: 183 VSVGSLLVVIEVAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAPGKA 242

Query: 353 T 353
            
Sbjct: 243 P 243

Length = 547

>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional

 Score = 40.9 bits (95), Expect = 0.003
 Identities = 34/139 (24%), Positives = 48/139 (34%), Gaps = 10/139 (7%)

Query: 229 AAKPASKPLAKTTTTKTTTAAKPAISPVKKTATT-TAKPAPKPATKPAPKPTTAAPKSTT 287
           A    + P+ +  T+  T    PA +P +  +       AP  A    P    A   + +
Sbjct: 20  ANLNTNIPIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAAS 79

Query: 288 TAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPA-----TAA 342
               PAP     AS     A +   AA    APKP A +   +A      PA      A+
Sbjct: 80  EKFDPAPAPHQAASRAPDPAVAPQLAA----APKPDAAEAFTSAAQAHEAPADAGTSAAS 135

Query: 343 PAPKPLTNGVTKRPVSATT 361
             P P  +     P  A T
Sbjct: 136 KKPDPAAHTQHSPPPFAYT 154

Length = 566

>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional

 Score = 40.9 bits (95), Expect = 0.003
 Identities = 31/133 (23%), Positives = 51/133 (38%), Gaps = 8/133 (6%)

Query: 315 PKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRP---VSATTTASRTSSSSV 371
           P P     AA +KP  APAP    + A       T+  +++P    + T  AS     + 
Sbjct: 27  PIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAP 86

Query: 372 --TSASAAKP---AAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTT 426
               A++  P    AP++  + +  AA+  T  A A  +     T+A+         T  
Sbjct: 87  APHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQAHEAPADAGTSAASKKPDPAAHTQH 146

Query: 427 SKPATTTSTDIED 439
           S P    +  +E 
Sbjct: 147 SPPPFAYTRSMEH 159

Length = 566

>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 22/129 (17%), Positives = 37/129 (28%), Gaps = 7/129 (5%)

Query: 249 AKPAISPVK--KTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKT 306
           A     P +  K   T    AP+P+   A  P+ +   +      P    +P  +     
Sbjct: 369 ASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTP---P 425

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRT 366
             S    A  P  P   AP+     PA          +        T RP+      +  
Sbjct: 426 TVSVDPPAAVPVNPPSTAPQA--VRPAQFKEEKKIPVSKVSSLGPSTLRPIQEKAEQATG 483

Query: 367 SSSSVTSAS 375
           +     + +
Sbjct: 484 NIKEAPTGT 492

Length = 614

>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase

 Score = 40.8 bits (95), Expect = 0.003
 Identities = 59/296 (19%), Positives = 90/296 (30%), Gaps = 27/296 (9%)

Query: 101 VSEPKEEVLDDLVSVPTSVPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSE 160
           + EP E   +   +     P+  P  +A   +P+PA +       +       T+    E
Sbjct: 76  IGEPGEAGSEP--APAAPEPEAAPEPEAPAPAPTPAAEAPAPAAPQAGGSGEATEVKMPE 133

Query: 161 TAEKETPLSEVPVIPQEAQTVESAE------ESTASSDLAAKVAGALVVGAAAAGAAVAV 214
             E  T  +    +     TVE  E           +++ + VAG L+   A     V V
Sbjct: 134 LGESVTEGTVTSWLKAVGDTVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAPEDDTVEV 193

Query: 215 KKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKP 274
               A        PA     +  A +   +  +   P  +     A            K 
Sbjct: 194 GTVLAIIGDANAAPAEPAEEEAPAPS---EAGSEPAPDPAARAPHAAPDPPAPAPAPAKT 250

Query: 275 APKPTTAAPKSTTTAPKPAPVRKPVA-------STITKTAT-------STVSAAPKPSAP 320
           A     A   S  + P   P+ + +A       ST+  T           ++AA      
Sbjct: 251 AAPAAAAPVSSGDSGPYVTPLVRKLAKDKGVDLSTVKGTGVGGRIRKQDVLAAAKAAEEA 310

Query: 321 K--PAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSA 374
           +   AAP    A  AP      A P    L     K       TA +T  S  TSA
Sbjct: 311 RAAAAAPAAAAAPAAPAAAAKPAEPDTAKLRGTTQKMNRIRQITADKTIESLQTSA 366

This model represents an Actinobacterial clade of E2 enzyme, a component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (pfam00198), one or two biotin domains (pfam00364) and an E3-component binding domain (pfam02817). Length = 579

>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 21/96 (21%)

Query: 714 TAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQN 773
            AE   + E L+ +  L    +++ +DS+   Q++              E  S    L  
Sbjct: 4   EAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEY----------EARSRLAALLR 53

Query: 774 TCKTVKLAWIKGHEGI-------KGNVEVDRLAKYA 802
             +      +K  + +       + N   D LAK A
Sbjct: 54  EIR----KLLKKFDSVSVSHVPRECNRVADALAKLA 85

This domain is found in plants and appears to be part of a retrotransposon. Length = 88

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 20/116 (17%), Positives = 33/116 (28%), Gaps = 1/116 (0%)

Query: 228 PAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTT 287
               P   P A      T    +P+  P K   +   K      T+   K TT       
Sbjct: 140 GVGLPPVAPAASPALKPTANGKRPSSKPPKSIMSPEVKVKSAKKTQDTSKETTTEKTEGK 199

Query: 288 TAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAP 343
           T+ K A +++      +   +S      K    K  A +  V   + +        
Sbjct: 200 TSVKAASLKRNPPKK-SNIMSSFFKKKTKEKKEKKEASESTVKEESEEESGKRDVI 254

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 40.8 bits (95), Expect = 0.003
 Identities = 36/198 (18%), Positives = 62/198 (31%), Gaps = 24/198 (12%)

Query: 293 APVRKPVASTITKTATSTVSAAP----KPSAPKPAA---PKKPVAAPAPKPRPATAAPAP 345
           AP+ +PVA     T  +   AAP      + P  +    P +P  A  P P P T  P  
Sbjct: 314 APITEPVAVAAAATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPVI 373

Query: 346 KPLTNGVTKRPVSATTTAS--------------RTSSSSVTSASAAKPAAPRVPLSQRTS 391
            P   G  ++   A                     + ++   A     A      +Q+  
Sbjct: 374 APAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPY 433

Query: 392 AAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELE 451
            A    +P         +  +   P +  +   T  +PA       + +  +     E E
Sbjct: 434 YAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPE 493

Query: 452 AAIKSGLITTPGRDNIHY 469
             ++    T P R  ++Y
Sbjct: 494 PVVEE---TKPARPPLYY 508

Length = 1355

>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 22/68 (32%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 204 GAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTT 263
            AAA   A +               AAKPA K  AK    KT  A  P  +  KK A   
Sbjct: 859 TAAAKAGAASAAFGGTVA-----VKAAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPA 913

Query: 264 AKPAPKPA 271
           A   P  A
Sbjct: 914 AGLKPSAA 921

Length = 987

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 58/277 (20%), Positives = 88/277 (31%), Gaps = 30/277 (10%)

Query: 145 EEKEAVVTPTDETNSETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVG 204
           E ++ +V       S+  E+     E  +   +  T+E A+   A++  A   A AL   
Sbjct: 21  EARKRLVAKHGAEISKLEEENRE-KEKALPKNDDMTIEEAKRRAAAAAKAK--AAALAKQ 77

Query: 205 AAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTA 264
                  V  ++   AK   K   AAK  +  LAK     T    +   +  K  A   A
Sbjct: 78  KREGTEEVTEEEKAKAKA--KAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAA 135

Query: 265 KPAPKPATKPAPKPTTAAPKSTTTAP------KPAPVRKPVASTITKTATSTVSAAPKPS 318
           K       K   + T    +            K A   K  A+ + K   +      +  
Sbjct: 136 KAKAAALAKQKREGTEEVTEEEEETDKEKAKAKAAAAAKAKAAALAKQKAAEAGEGTEEV 195

Query: 319 APKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAK 378
             +  A  K  AA A K + A  A       NG          +    + +   +A+ AK
Sbjct: 196 TEEEKAKAKAKAAAAAKAKAAALAKQKASQGNG---------DSGDEDAKAKAIAAAKAK 246

Query: 379 PAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASK 415
            AA          AA+  TK A  K     K    S 
Sbjct: 247 AAA----------AARAKTKGAEGKKEEEPKQEEPSV 273

Length = 430

>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 33/119 (27%), Positives = 47/119 (39%), Gaps = 13/119 (10%)

Query: 217 ATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAP 276
           A+A   +   GPA+  A+     T  T+      PA      T ++ A   P P+  P+P
Sbjct: 378 ASAPSGSAAEGPASGGAAT--IPTPGTQGPQGTAPAAG---MTPSSAAPATPAPSAAPSP 432

Query: 277 K----PTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKP---SAPKPAAPKKP 328
           +        AP  +   P+PAP R P AS +     S  SA+  P     P   A   P
Sbjct: 433 RVPWDDAPPAPPRSGIPPRPAP-RMPEASPVPGAPDSVASASDAPPTLGDPSDTAEHTP 490

Length = 624

>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional

 Score = 40.7 bits (95), Expect = 0.004
 Identities = 43/238 (18%), Positives = 65/238 (27%), Gaps = 28/238 (11%)

Query: 198 AGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKP-------LAKTTTTKTTTAAK 250
           A   VVG  A  A    + AT      +       A+ P       LA            
Sbjct: 256 APPPVVGEGADRAPETARGATGPPPPPEAAAPNGAAAPPDGVWGAALAGAPLALPAPPDP 315

Query: 251 PAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATST 310
           P  +P         +        P P+P    P      PK    R+P  +  +     +
Sbjct: 316 PPPAPAGDAEEEDDEDGAMEVVSPLPRPRQHYP---LGFPKR---RRPTWTPPSSLEDLS 369

Query: 311 VSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSS 370
                   A  P   ++             A P  +        RP +    +  T + +
Sbjct: 370 AGRHHPKRASLPTRKRRSA--------RHAATPFARGPGGDDQTRPAAPVPASVPTPAPT 421

Query: 371 VTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSK 428
              ASA  P A  +P ++  S   PA  P         +P   +       P   T K
Sbjct: 422 PVPASAPPPPATPLPSAEPGSDDGPAPPPE-------RQPPAPATEPAPDDPDDATRK 472

Length = 3151

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 32/136 (23%), Positives = 42/136 (30%), Gaps = 11/136 (8%)

Query: 296 RKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKR 355
           +K   +   K+     SA  K +A K +  K    A + K    TAA A K       K 
Sbjct: 200 KKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKA 259

Query: 356 PVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASK 415
              A     +       +  AAK AA          AAK     A AK     K    SK
Sbjct: 260 LKKAAKAVKK------AAKKAAKAAAKAA-----KGAAKATKGKAKAKKKAGKKAAAGSK 308

Query: 416 PATATRPATTTSKPAT 431
                +     +K   
Sbjct: 309 AKATAKAPKRGAKGKK 324

Length = 333

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 39.9 bits (92), Expect = 0.004
 Identities = 34/133 (25%), Positives = 47/133 (35%), Gaps = 5/133 (3%)

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRT 366
           A +  +A  K +A K AAP    +A A  P  A AAPA             +    A   
Sbjct: 193 AAAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAK 252

Query: 367 SSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPAT-----AKPSTTSKPTTASKPATATR 421
           +++    A+A    A   P       AK A  PA      AK +       A+    A  
Sbjct: 253 AAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAA 312

Query: 422 PATTTSKPATTTS 434
           PA   + PA   +
Sbjct: 313 PAKAAAPPAKAAA 325

Length = 357

>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 25/121 (20%), Positives = 34/121 (28%), Gaps = 8/121 (6%)

Query: 301 STITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSAT 360
           S + K  + +  A     A     P +P+  P   P     APAP               
Sbjct: 94  SDLQKATSMSEPATENKPAE-VTTPVEPMGLPETPPAVPVPAPAPAVAAAAAQAAAAPKA 152

Query: 361 TTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATAT 420
               R  S    + +A KP            A K     A  KP+     T A K     
Sbjct: 153 PAKPRAKSPRPAAKAAPKPTETIT-------AKKAKKTAAAPKPTADKTATPAKKTTKKK 205

Query: 421 R 421
           +
Sbjct: 206 K 206

Length = 209

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 40.3 bits (95), Expect = 0.004
 Identities = 39/209 (18%), Positives = 60/209 (28%), Gaps = 4/209 (1%)

Query: 215 KKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKP 274
           KKA  A+        A   ++  AK          K    P   +A   A+ A K   + 
Sbjct: 474 KKAAEARAAKDKDAVAAALARVKAKKAAATQPIVIKAGARP-DNSAVIAAREARKAQARA 532

Query: 275 APKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAP 334
                     +    PK A V   +A    K A    + A       P       A    
Sbjct: 533 RQA---EKQAAAAADPKKAAVAAAIARAKAKKAAQQAANAEAEEEVDPKKAAVAAAIARA 589

Query: 335 KPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAK 394
           K + A    A       V +        A+  + +    A     A P  P+  R +A  
Sbjct: 590 KAKKAAQQAASAEPEEQVAEVDPKKAAVAAAIARAKAKKAEQQANAEPEEPVDPRKAAVA 649

Query: 395 PATKPATAKPSTTSKPTTASKPATATRPA 423
            A   A A+ +   +     + A   + A
Sbjct: 650 AAIARAKARKAAQQQANAEPEEAEDPKKA 678

Length = 695

>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope glycoprotein (BLLF1)

 Score = 40.2 bits (93), Expect = 0.004
 Identities = 62/362 (17%), Positives = 107/362 (29%), Gaps = 22/362 (6%)

Query: 59  ETKVESSFQETHVALETNLDDFTSQETKLDDFISAHTEKTPEVSEPKEEVLDDLVSVPTS 118
           +T     F  T V +E +          L    +  T  T + +               +
Sbjct: 427 DTTKSVIFVYTLVHVEPHKTTAVPTTPSLPPASTGPTVSTADPTSGTPTGTTSSTLPEDT 486

Query: 119 VPDVVPNQDANEESPSPAVDLTQDIVEEKEAVVTPTDETNSETAEKETPLSEVPVIPQEA 178
            P           +       T +         + T    S T       +     P   
Sbjct: 487 SPTSRTTSATPNATSPTPAVTTPNATSPTTQKTSDTPNATSPTPIVIGVTTTATSPPTGT 546

Query: 179 QTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASK-PL 237
            +V +A     + +       + V          A    T+A  T + G  + P S+ P 
Sbjct: 547 TSVPNATSPQVTEE-------SPVNNTNTPVVTSAPSVLTSAVTTGQHGTGSSPTSQQPG 599

Query: 238 AKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRK 297
             +++  T  +   + +P+  +A  T        T   P  T      +T +P P P   
Sbjct: 600 IPSSSHSTPRSNSTSTTPLLTSAHPTGGENITEETPSVPSTTHV----STLSPGPGPGTT 655

Query: 298 PVASTITKTATSTVSAA-------PKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTN 350
              S    ++TS            P P+A  P+AP     A          A +    T+
Sbjct: 656 SQVSGPGNSSTSRYPGEVHVTEGMPNPNATSPSAPSGQKTAVPTVTSTGGKANSTTKETS 715

Query: 351 GVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKP 410
           G T    ++  T      ++  +A+   P +    L  R +   P   P T K +T   P
Sbjct: 716 GSTLMASTSPHTNEGAFRTTPYNATTYLPPSTSSKLRPRWTFTSP---PVTTKQATVPVP 772

Query: 411 TT 412
            T
Sbjct: 773 PT 774

This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Length = 830

>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 22/103 (21%), Positives = 31/103 (30%), Gaps = 7/103 (6%)

Query: 275 APKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAP 334
           +     + P  T+T   PA    P A   T    S   A     AP     +  V AP+ 
Sbjct: 155 SQNSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQ 214

Query: 335 KPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAA 377
                 A PAP                    T  + V++ +A 
Sbjct: 215 ANVDTAATPAPAAPAT-------PDGAAPLPTDQAGVSTPAAD 250

Length = 331

>gnl|CDD|183756 PRK12799, motB, flagellar motor protein MotB; Reviewed

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 32/138 (23%), Positives = 49/138 (35%), Gaps = 8/138 (5%)

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPV-ASTITKTATSTV 311
            + +K+  T    P        A   ++A   S+   P PA +   V   + T T  S V
Sbjct: 287 ATGLKQIDTHGTVPVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSATTTQASAV 346

Query: 312 SAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSV 371
           + +     P        VA PA +P      P     T        S+T   + T++   
Sbjct: 347 ALSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQ------SSTGNITSTANGPT 400

Query: 372 TSASAAKPA-APRVPLSQ 388
           TS  AA  +  P  P S+
Sbjct: 401 TSLPAAPASNIPVSPTSR 418

Length = 421

>gnl|CDD|218881 pfam06070, Herpes_UL32, Herpesvirus large structural phosphoprotein UL32

 Score = 40.7 bits (95), Expect = 0.004
 Identities = 39/249 (15%), Positives = 73/249 (29%), Gaps = 19/249 (7%)

Query: 199 GALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTT-----------TTKTTT 247
           G L  G    G AV  +++ A   +            PL   +           + +  +
Sbjct: 420 GILAWGLKTPGLAVNDERSIAV--SSDGITDVLDPPSPLRLHSSDKVIDSVSPPSKRRVS 477

Query: 248 AAKPAISPVKKTA-TTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKT 306
           A    +   K+   T T + +   +   A            +      +R P    I K+
Sbjct: 478 APASRLDDAKRPEVTATPESSGSDSEGGASGREDETSSDAESVVSIKELR-PRIGFINKS 536

Query: 307 ATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRT 366
                    + +     +   P  A +P+P+P+        +         +   T +  
Sbjct: 537 PPPKSPPKSRRTLIVALSLASPSTAGSPRPKPSLG---KFVIGTDPFAFANTVRLTDNMR 593

Query: 367 SSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPA-TAKPSTTSKPTTASKPATATRPATT 425
             + V S+   K +A   PL+   S  KPAT    T   S       A   +    P+  
Sbjct: 594 GGNGVGSSVKPKGSASSKPLTGPGSDLKPATLNGKTPSSSLVGAARNAGASSKVKIPSGL 653

Query: 426 TSKPATTTS 434
               +  + 
Sbjct: 654 GGFTSPISL 662

The large phosphorylated protein (UL32-like) of herpes viruses is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins. Length = 777

>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein; Reviewed

 Score = 40.6 bits (95), Expect = 0.004
 Identities = 25/99 (25%), Positives = 38/99 (38%), Gaps = 1/99 (1%)

Query: 339 ATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATK 398
             + P        VT  P ++T     T   S  +  A     P V  +    A   +  
Sbjct: 19  TASNPKLAQAEEIVTTTPATSTEAEQTTPVESDATEEADNTETP-VAATTAAEAPSSSET 77

Query: 399 PATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDI 437
             T+ P++ +  TT S+  T T  AT TSKP    + D+
Sbjct: 78  AETSDPTSEATDTTTSEARTVTPAATETSKPVEGQTVDV 116

Length = 814

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	821
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.84
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.83
PRK06548	161	ribonuclease H; Provisional	99.83
PRK08719	147	ribonuclease H; Reviewed	99.82
PRK00203	150	rnhA ribonuclease H; Reviewed	99.82
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.7
KOG3752|consensus	371		99.69
PRK13907	128	rnhA ribonuclease H; Provisional	99.61
PRK07708	219	hypothetical protein; Validated	99.51
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.35
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.01
PF09004	42	DUF1891: Domain of unknown function (DUF1891); Int	89.53
PHA03378	991	EBNA-3B; Provisional	88.15
PHA03378	991	EBNA-3B; Provisional	87.9
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	81.37

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

Probab=99.84  E-value=1.3e-20  Score=184.92  Aligned_cols=130  Identities=22%  Similarity=0.163  Sum_probs=104.2

Q ss_pred             cEEEeccccccC--CCcceEEecCCCc--cceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhh
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTYK--SKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSK  750 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~~--~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~  750 (821)
                      .+.||+||+|..  |-.|+|+|+..++  ...+..+. .+||+++||+|++.||+++.+.+...|.|+|||++|+++|..
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~   81 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR   81 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence            578999999994  5566777665333  23444444 889999999999999999999888999999999999999998


Q ss_pred             cccC----CCC------CCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcC
Q psy16749        751 NCLN----TTP------THLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHG  806 (821)
Q Consensus       751 ~~~~----~~p------~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~  806 (821)
                      |..+    +|.      ..+..+++++..++ .....|.+.||+||.|.++||+||+||+.|+...
T Consensus        82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~-~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          82 WIVKWKKNGWKTADKKPVKNKDLWEELDELL-KRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHhhccccCccccccCccccHHHHHHHHHHH-hhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            7553    333      23445677777666 4556999999999999999999999999998765

>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=99.83  E-value=6.1e-21  Score=180.03  Aligned_cols=125  Identities=32%  Similarity=0.365  Sum_probs=95.8

Q ss_pred             CcEEEecccccc--CCCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        674 NAICIYTDASKK--NEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       674 ~~i~IYTDGS~~--~g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      +.+.||||||+.  .+..|+|++++.+ ....+.++ ..+++.+||.||++||+.+ .  ...+.|||||+++++.|..|
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~   76 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKW   76 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHh
Confidence            578999999987  3445666655434 34445555 7899999999999999944 2  38999999999999988886


Q ss_pred             ccC-CCCCCc-h-HHHHHHHHHHHhcCCcEEEEEecCCCCC-cccHHHHHHHHHHhh
Q psy16749        752 CLN-TTPTHL-E-LEILSSYKHLQNTCKTVKLAWIKGHEGI-KGNVEVDRLAKYATV  804 (821)
Q Consensus       752 ~~~-~~p~~~-s-~~i~~i~~~L~~~~~~V~~~WVPGHsGI-~GNE~AD~LAK~A~~  804 (821)
                      ..+ +|+... . .++.++++++ ..+..|+|+|||||+|+ .||+.||+|||.|+.
T Consensus        77 ~~~~~~~~~~~~~~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   77 LHGNGWKKTSNGRPIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             HHHTTSBSCTSSSBHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccchhheeecc-ccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            543 333222 2 4666777777 45899999999999999 799999999999873

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=99.83  E-value=2.7e-20  Score=184.85  Aligned_cols=129  Identities=24%  Similarity=0.271  Sum_probs=99.1

Q ss_pred             CcEEEeccccccC--CCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        674 NAICIYTDASKKN--EKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       674 ~~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      ..++|||||++..  |..|+|+|+.+.. ..... ....||++|||.||+.||+.+.. ....|.|||||++++++|..|
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~-~~~g~-~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENT-WDSGG-WDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCc-EEccC-CCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHH
Confidence            3589999999994  5678888875322 11222 24579999999999999986643 345799999999999999965


Q ss_pred             cc----CCCCC------CchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCC
Q psy16749        752 CL----NTTPT------HLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGE  807 (821)
Q Consensus       752 ~~----~~~p~------~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~  807 (821)
                      ..    ++|..      .+.++|++|..++.+  ..|+|.||+||+|+.|||.||+||++|+....
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~  144 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNIRMSWVNAHTGHPLNEAADSLARQAANNFS  144 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhc--CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence            44    44432      345678888777743  47999999999999999999999999986544

>PRK08719 ribonuclease H; Reviewed

Probab=99.82  E-value=3.7e-20  Score=181.45  Aligned_cols=126  Identities=20%  Similarity=0.188  Sum_probs=93.6

Q ss_pred             CCcEEEeccccccCC-----CcceEEecCC--Ccc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHH
Q psy16749        673 PNAICIYTDASKKNE-----KVGAAWFCPT--YKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKS  743 (821)
Q Consensus       673 ~~~i~IYTDGS~~~g-----~vGagvv~~~--~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqs  743 (821)
                      +..++||||||+..+     ..|+|+++..  +..  ...+.+....+|++|||.||+.||+.+.+.    ..|++||++
T Consensus         2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y   77 (147)
T PRK08719          2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY   77 (147)
T ss_pred             CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence            356899999999853     2478877543  222  234445556799999999999999998753    489999999


Q ss_pred             HHHHHhhcc----cCCCCCC------chHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhh
Q psy16749        744 ACQKLSKNC----LNTTPTH------LELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATV  804 (821)
Q Consensus       744 AL~~L~~~~----~~~~p~~------~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~  804 (821)
                      |+++|+.|.    .++|...      +.++++.+..++.  ...|+|.|||||+|++||+.||+||++|..
T Consensus        78 vi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         78 CVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            999986543    3445333      2345555554443  467999999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.82  E-value=5.4e-20  Score=180.30  Aligned_cols=130  Identities=22%  Similarity=0.158  Sum_probs=98.7

Q ss_pred             cEEEeccccccC--CCcceEEecCCCccce-eeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTYKSKA-CFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~~~~~-~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      .+.||||||+..  +..|+|+|+...+... ........++++|||+||+.||+++.+  ...+.|||||++++++|..|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            488999999983  5667777764333221 112234678999999999999998865  36799999999999999875


Q ss_pred             cc----CCCCC------CchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCCC
Q psy16749        752 CL----NTTPT------HLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEA  808 (821)
Q Consensus       752 ~~----~~~p~------~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~~  808 (821)
                      ..    ++|..      .+.++++++..++.  ...|.|.|||||+|++||+.||+|||+|+.....
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~--~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~  145 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK--RHQIKWHWVKGHAGHPENERCDELARAGAEEATL  145 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhc--cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhhh
Confidence            43    34432      23456777776663  3789999999999999999999999999876543

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

Probab=99.70  E-value=1.8e-16  Score=143.89  Aligned_cols=125  Identities=28%  Similarity=0.314  Sum_probs=97.5

Q ss_pred             EEeccccccC--CCcceEEecCCCcc--ce-eeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        677 CIYTDASKKN--EKVGAAWFCPTYKS--KA-CFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       677 ~IYTDGS~~~--g~vGagvv~~~~~~--~~-~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      .+|+|||...  ++.|+|+++.+.+.  .. ........+++.+|+.||+.||+++...+...+.|++||+.+++.++++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            4899999985  48888888754432  11 1122256799999999999999999988889999999999999999984


Q ss_pred             ccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHh
Q psy16749        752 CLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYAT  803 (821)
Q Consensus       752 ~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~  803 (821)
                      ... .......++.++.+.+ +.+..+.|.|||+|+|+.+|+.||.|||.++
T Consensus        81 ~~~-~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEG-KPVKNVDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccC-CChhhHHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            321 1123344566666655 5678999999999999999999999999874

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

>KOG3752|consensus

Probab=99.69  E-value=1.5e-16  Score=173.03  Aligned_cols=131  Identities=25%  Similarity=0.223  Sum_probs=106.4

Q ss_pred             cEEEeccccccC-----CCcceEEecCCCc-cceeeccC-CCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHH
Q psy16749        675 AICIYTDASKKN-----EKVGAAWFCPTYK-SKACFKLH-PATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQK  747 (821)
Q Consensus       675 ~i~IYTDGS~~~-----g~vGagvv~~~~~-~~~~~~l~-~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~  747 (821)
                      ..++|||||+..     ..+|+|||++++. ....+.+. +..++|+|||.||.+||+.+.+..+.+|+|.|||.++++.
T Consensus       212 ~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~  291 (371)
T KOG3752|consen  212 IQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINS  291 (371)
T ss_pred             ceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHH
Confidence            489999999995     2689999997664 46667775 7899999999999999999999888899999999999999


Q ss_pred             HhhcccC----CCCC-----------CchHHHHHHHHHHHh-cCCcEEEEEecCCCCCcccHHHHHHHHHHhhc
Q psy16749        748 LSKNCLN----TTPT-----------HLELEILSSYKHLQN-TCKTVKLAWIKGHEGIKGNVEVDRLAKYATVH  805 (821)
Q Consensus       748 L~~~~~~----~~p~-----------~~s~~i~~i~~~L~~-~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~  805 (821)
                      |+.|..+    +|-.           .....+.++.++++. .+.+|.+.||+||.||.||++||.||+++..+
T Consensus       292 l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  292 LTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            9988763    1211           112235555565554 57899999999999999999999999998543

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.61  E-value=4.6e-15  Score=141.02  Aligned_cols=122  Identities=21%  Similarity=0.264  Sum_probs=95.9

Q ss_pred             EEEeccccccC--CCcceEEecCCCcc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        676 ICIYTDASKKN--EKVGAAWFCPTYKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       676 i~IYTDGS~~~--g~vGagvv~~~~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      +.||+|||+..  |..|+|+|+.+.+.  ...+. ....+++.||+.|++.||+++.+.+...+.|++||+++++.|+++
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            68999999994  67888988854322  22222 245799999999999999999998889999999999999999882


Q ss_pred             ccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhc
Q psy16749        752 CLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVH  805 (821)
Q Consensus       752 ~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~  805 (821)
                      ...  ......++.++..++ ..+..+.|.|||+    .+|+.||.||+.|+..
T Consensus        81 ~~~--~~~~~~l~~~~~~l~-~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         81 YAK--NKMFAPLLEEALQYI-KSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             Hhc--ChhHHHHHHHHHHHH-hcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            221  123456777777766 4677888999996    5899999999999864

>PRK07708 hypothetical protein; Validated

Probab=99.51  E-value=1.4e-13  Score=143.50  Aligned_cols=130  Identities=18%  Similarity=0.090  Sum_probs=96.1

Q ss_pred             hhCCCcEEEecccccc--CCCcceEEecCC--Cccce----eeccCCCCCcchhHHHHHHHHHHHHHhcCCCc--EEEEc
Q psy16749        670 EKCPNAICIYTDASKK--NEKVGAAWFCPT--YKSKA----CFKLHPATSTYTAEVIGIWEALKYSASLKNNE--ILILT  739 (821)
Q Consensus       670 ~~~~~~i~IYTDGS~~--~g~vGagvv~~~--~~~~~----~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~--I~I~S  739 (821)
                      ...++.+++|+|||+.  .++.|+|+++..  ++...    ...+....+|+.||+.|++.||+++.+.+.+.  |.|++
T Consensus        68 ~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~  147 (219)
T PRK07708         68 EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRG  147 (219)
T ss_pred             ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEe
Confidence            4456789999999997  467788887642  32221    22455568999999999999999999987655  89999


Q ss_pred             chHHHHHHHhhcccCCCCCCc---hHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCC
Q psy16749        740 DSKSACQKLSKNCLNTTPTHL---ELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGE  807 (821)
Q Consensus       740 DSqsAL~~L~~~~~~~~p~~~---s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~  807 (821)
                      ||+.+++.|++    .|....   ..+..++..++.+....+.|.|||    +..|+.||+||+.|++...
T Consensus       148 DSqlVi~qi~g----~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        148 DSQVVLNQLAG----EWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV  210 (219)
T ss_pred             ccHHHHHHhCC----CceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence            99999999987    222222   234455555565555567888987    5779999999999998543

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.35  E-value=4.9e-12  Score=141.05  Aligned_cols=123  Identities=18%  Similarity=0.172  Sum_probs=94.8

Q ss_pred             cEEEeccccccC--CCcceEEecCCC--c-c--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHH
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTY--K-S--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQK  747 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~--~-~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~  747 (821)
                      .+.||+|||+..  |..|+|+++.+.  + .  .....+ ...+|+.||+.|++.||+++.+.+...|.|++||+++++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            368999999995  567888887543  2 1  122333 3678999999999999999999988999999999999999


Q ss_pred             HhhcccCCCCCCc---hHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCC
Q psy16749        748 LSKNCLNTTPTHL---ELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGE  807 (821)
Q Consensus       748 L~~~~~~~~p~~~---s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~  807 (821)
                      |++    +|...+   ..++.++..++ +++..|.|.|||+    .+|+.||.||+.|+....
T Consensus        81 i~~----~~~~~~~~l~~~~~~i~~l~-~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238         81 MSG----RWKVKHPDMKPLAAQARELA-SQFGRVTYTWIPR----ARNAHADRLANEAMDAAA  134 (372)
T ss_pred             hCC----CCccCChHHHHHHHHHHHHH-hcCCceEEEECCc----hhhhHHHHHHHHHHHhhc
Confidence            976    222222   23455555554 5678899999995    789999999999987654

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

Probab=99.01  E-value=2.2e-09  Score=93.81  Aligned_cols=85  Identities=24%  Similarity=0.256  Sum_probs=67.6

Q ss_pred             chhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCccc
Q psy16749        713 YTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGN  792 (821)
Q Consensus       713 ~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GN  792 (821)
                      ..||+.|++.||+++.+.+.++|.|++||+.+++.|++...  .......++.++...+. ....+.|.||+    +++|
T Consensus         2 ~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~--~~~~~~~~~~~i~~~~~-~~~~~~~~~i~----r~~N   74 (87)
T PF13456_consen    2 LEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSS--SRSELRPLIQDIRSLLD-RFWNVSVSHIP----REQN   74 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS-----SCCHHHHHHHHHHHC-CCSCEEEEE------GGGS
T ss_pred             cHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccc--ccccccccchhhhhhhc-cccceEEEEEC----hHHh
Confidence            57999999999999999999999999999999999988211  12344567778777774 58899999998    7999


Q ss_pred             HHHHHHHHHHhh
Q psy16749        793 VEVDRLAKYATV  804 (821)
Q Consensus       793 E~AD~LAK~A~~  804 (821)
                      ..||.|||.|..
T Consensus        75 ~~A~~LA~~a~~   86 (87)
T PF13456_consen   75 KVADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh
Confidence            999999999874

>PF09004 DUF1891: Domain of unknown function (DUF1891); InterPro: IPR015095 This domain is found at the extreme N terminus of eukaryotic alkylated DNA repair protein homologs

Probab=89.53  E-value=0.051  Score=42.99  Aligned_cols=41  Identities=7%  Similarity=0.184  Sum_probs=7.7

Q ss_pred             chHHHHHHHHHHHHHHHHHHhhccCCCCCChHHHHHHHHHHhH
Q psy16749        467 IHYPMIENLPDCNKYLNIMKMICNKHWGMNPTIGLNYYKATIR  509 (821)
Q Consensus       467 f~~HI~~i~~KA~k~ln~Lr~L~~~~wGls~~~lr~LYkAvVr  509 (821)
                      |+.|+..+.+|+..++..||+|..  .+++...+..+|+++|.
T Consensus         1 W~~n~~~~~KKa~qRlyFLRkl~k--~~~~~~~l~lfY~s~Ie   41 (42)
T PF09004_consen    1 WTSNTTSLYKKAQQRLYFLRKLRK--FNVDSKLLTLFYHSVIE   41 (42)
T ss_dssp             ---------------------------SS-----SHTTTTT--
T ss_pred             CCcchHHHHHHHHhHHHHHHHHHH--ccchhHHHHHHHHHHhc
Confidence            889999999999999999999997  46788888999988875

; GO: 0008168 methyltransferase activity, 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process; PDB: 2CQ2_A 3THT_C 3THP_A.

>PHA03378 EBNA-3B; Provisional

Probab=88.15  E-value=6.1  Score=47.62  Aligned_cols=24  Identities=21%  Similarity=0.371  Sum_probs=11.9

Q ss_pred             cCcchhhhccCCcccccCCCCcch
Q psy16749        156 ETNSETAEKETPLSEVPVIPQEAQ  179 (821)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~  179 (821)
                      |+.-|-.+|.--+--+|-+|.++-
T Consensus       510 e~d~e~~eq~vmat~l~~~p~~p~  533 (991)
T PHA03378        510 EKDDEDMEQRVMATLLPPSPPQPR  533 (991)
T ss_pred             hhchHHHHHHHHHhhCCCCCCCCc
Confidence            344445555544444555555553

>PHA03378 EBNA-3B; Provisional

Probab=87.90  E-value=6.4  Score=47.50  Aligned_cols=15  Identities=13%  Similarity=-0.132  Sum_probs=6.3

Q ss_pred             CCCcCCcchhhhhcc
Q psy16749         36 KPQEHDDLTFETKES   50 (821)
Q Consensus        36 ~~~~~~~~~~~~~~~   50 (821)
                      .|.++-++-|++--+
T Consensus       476 ~p~~pl~~~~~~~vi  490 (991)
T PHA03378        476 EPWQPLPHPQVTPVI  490 (991)
T ss_pred             CCCCCCCCcceeeeE
Confidence            344444444444433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.37  E-value=7.5  Score=46.86  Aligned_cols=8  Identities=0%  Similarity=0.127  Sum_probs=3.5

Q ss_pred             hhhhhhhH
Q psy16749        525 SKLKTLDK  532 (821)
Q Consensus       525 ~~ikkLe~  532 (821)
                      .+.++|+.
T Consensus       511 ~~~~~~~~  518 (585)
T PRK14950        511 FHKDKIEE  518 (585)
T ss_pred             HHHHHhhc
Confidence            34444444

---

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	821
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-10
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	4e-11
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	9e-11
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-07
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	3e-06
3v1v_A	433	2-MIB synthase, 2-methylisoborneol synthase; class	8e-05
2xag_A	852	Lysine-specific histone demethylase 1; amine oxida	2e-06
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	2e-06
2wvr_C	546	DNA replication factor CDT1; DNA replication licen	6e-06
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	9e-06
3dva_I	428	Dihydrolipoyllysine-residue acetyltransferase comp	1e-05
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	2e-05
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	2e-05
3gdb_A	937	Endo-D, putative uncharacterized protein SPR0440;	1e-04
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	4e-05
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	6e-05
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	8e-05
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	4e-04
2grx_C	229	Protein TONB; beta barrel, outer membrane, heteroc	5e-04
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	1e-04
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	4e-04
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	8e-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 = 75.7 bits (185), Expect = 5e-14
 Identities = 59/375 (15%), Positives = 104/375 (27%), Gaps = 125/375 (33%)

Query: 420 TRPATTTSKPATTTSTDIE-DEMNQPFTPEELEA----------------AIKS-----G 457
           TR    T   +  T+T I  D  +   TP+E+++                 + +      
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 458 LITTPGRDNIHYPMIENLP--DCNKYLNIMKMICNKHWGMNPTIGLNYYKATIRATLDFG 515
           +I    RD +     +N    +C+K   I++   N    + P      +           
Sbjct: 332 IIAESIRDGLA--TWDNWKHVNCDKLTTIIESSLNV---LEPAEYRKMFD-------RL- 378

Query: 516 SVFYSESCSSKLKTL-----DKVQNQALRLAMGYLNSTPIDNILVECRENPMSKRTPQLV 570
           SVF   S       L     D +++  + +       +     LVE +    +   P + 
Sbjct: 379 SVF-PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS-----LVEKQPKESTISIPSIY 432

Query: 571 DRFVLKVISSQTALAAKLNTLTVTH--MTSKYCKTKPTPPIVNSYCNISHQYGRELITYE 628
               +K + ++ AL   +    V H  +   +      PP ++ Y               
Sbjct: 433 LELKVK-LENEYALHRSI----VDHYNIPKTFDSDDLIPPYLDQY--------------- 472

Query: 629 KPIIYNYDYDIG---KVSLQSETFNEYRKHPDSLQDAALSSEIQEKCPNAICIYTD---A 682
               Y++   IG   K     E    +R                        ++ D    
Sbjct: 473 ---FYSH---IGHHLKNIEHPERMTLFRM-----------------------VFLDFRFL 503

Query: 683 SKKNEKVGAAWFCP-----------TYKSKACFKLHPATSTYTAEVIGIWEALKYSASLK 731
            +K      AW               YK   C    P    Y   V  I + L      K
Sbjct: 504 EQKIRHDSTAWNASGSILNTLQQLKFYKPYIC-DNDP---KYERLVNAILDFLP-----K 554

Query: 732 NNEILILTDSKSACQ 746
             E LI +      +
Sbjct: 555 IEENLICSKYTDLLR 569

>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 = 64.1 bits (155), Expect = 1e-10
 Identities = 66/449 (14%), Positives = 127/449 (28%), Gaps = 128/449 (28%)

Query: 436 DIEDEMNQPFTPEELEAAIKSGLITTPGRDNIHYPMIENLPDCNKYLNIMKMICNKHWGM 495
           D++D      + EE++  I S         +    +   L   +K   +++        +
Sbjct: 37  DVQDMPKSILSKEEIDHIIMS-----KDAVSGTLRLFWTL--LSKQEEMVQKF------V 83

Query: 496 NPTIGLNYYKATIRATLDFGSVFYSESCSSKLKTLDKVQNQALRLAMGYLNSTPIDNILV 555
              + +NY          F          S +KT  +  +   R+ +   +    DN + 
Sbjct: 84  EEVLRINY---------KF--------LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126

Query: 556 E----CRENPMSK-RTPQLVDRFVLKVI------SSQTALAAK-LNTLTVTH-------- 595
                 R  P  K R   L  R    V+      S +T +A     +  V          
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 596 MTSKYCKTKPTPPIVNSYCNISHQYGRELITYEKPIIYNYDYDIGKVSLQSETFNEYRKH 655
           +  K C +  T  ++     + +Q      +       N    I  +  +     + + +
Sbjct: 187 LNLKNCNSPET--VLEMLQKLLYQIDPNWTSRSDH-SSNIKLRIHSIQAELRRLLKSKPY 243

Query: 656 PDSL------QDAALSSEIQE----KCPNAICIYT-DAS--------------------- 683
            + L      Q+A    +        C   I + T                         
Sbjct: 244 ENCLLVLLNVQNA----KAWNAFNLSCK--ILLTTRFKQVTDFLSAATTTHISLDHHSMT 297

Query: 684 ---KKNEKVGAAWF-CPTYK--SKACFKLHP-ATSTYTAEV---IGIWEALKYSASLKNN 733
               + + +   +  C       +     +P   S     +   +  W+  K+    K  
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVL-TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLT 356

Query: 734 EILILTDSKSACQKLSKNCLNTTPTHL-----ELEILSSYKHLQNTCKTVKLAWIKGHEG 788
            I+          + S N L   P         L +             + L W    + 
Sbjct: 357 TII----------ESSLNVLE--PAEYRKMFDRLSVFP--PSAHIPTILLSLIW---FDV 399

Query: 789 IKGNVE--VDRLAKYATV--HGEASTIVI 813
           IK +V   V++L KY+ V    + STI I
Sbjct: 400 IKSDVMVVVNKLHKYSLVEKQPKESTISI 428

>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 = 60.8 bits (148), Expect = 4e-11
 Identities = 26/138 (18%), Positives = 42/138 (30%), Gaps = 17/138 (12%)

Query: 674 NAICIYTDASKKNEKVGAAW-FCPTYKSKACFKLHPATSTYT------AEVIGIWEALKY 726
               +YTD S  N +   A+ F    K                      E+     A+K 
Sbjct: 5   TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKK 64

Query: 727 SASLKNNEILILTDSKSACQKLSKNC--LNTTPTHLELEILSSYKHLQNTCKTVKLAWIK 784
           ++     +I IL D        +          T    ++++ Y+             +K
Sbjct: 65  ASQ-LGVKIRILHDYAGIA-FWATGEWKAKNEFTQAYAKLMNQYRG------IYSFEKVK 116

Query: 785 GHEGIKGNVEVDRLAKYA 802
            H G + N  VD  AK A
Sbjct: 117 AHSGNEFNDYVDMKAKSA 134

>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 = 60.2 bits (146), Expect = 9e-11
 Identities = 31/133 (23%), Positives = 50/133 (37%), Gaps = 13/133 (9%)

Query: 678 IYTD-ASKKNEKVG--AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNE 734
            YTD +S   E      A      +      L   TS   AE+I + +ALK +   +  +
Sbjct: 26  WYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKK 82

Query: 735 ILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGH-----EGI 789
           + + TDS+ A      +       +    IL+  K L    K + +    GH        
Sbjct: 83  LNVYTDSRYAFATAHVHSEGREIKNKNE-ILALLKALFLP-KRLSIIHCPGHQKGNSAEA 140

Query: 790 KGNVEVDRLAKYA 802
           +GN   D+ A+ A
Sbjct: 141 RGNRMADQAAREA 153

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 53.6 bits (128), Expect = 2e-07
 Identities = 22/104 (21%), Positives = 36/104 (34%)

Query: 283 PKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAA 342
             S+   P+ + +  P AS  +  +    +  P  + P PA P  P  A    P   T  
Sbjct: 9   HHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGD 68

Query: 343 PAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPL 386
              + +  G T    ++   A R        A A+ P A    +
Sbjct: 69  SVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAV 112

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 49.4 bits (117), Expect = 3e-06
 Identities = 18/145 (12%), Positives = 31/145 (21%), Gaps = 15/145 (10%)

Query: 223 TDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAA 282
                 +            +         +++           P         P P   A
Sbjct: 6   HHHHHSSGLVPRGSHMVIPS--------ASVTSAASDFLAALHPPVTVPDPAPPPPPAPA 57

Query: 283 PKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAA 342
             +         V + +    T   T+    +  P+      P     A AP   PA   
Sbjct: 58  AGNPPDTVTGDSVLQRILRGPTGPGTT----SLAPAVRYGRQPGPEAPASAP---PAAGR 110

Query: 343 PAPKPLTNGVTKRPVSATTTASRTS 367
             P    + V +         SR  
Sbjct: 111 AVPGLYHHPVPEPDPVRVEEVSRRI 135

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433

 Score = 44.7 bits (105), Expect = 8e-05
 Identities = 16/116 (13%), Positives = 24/116 (20%), Gaps = 19/116 (16%)

Query: 232 PASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPK 291
                 +     + +    P+ S      T+ A         P   P  A P     A  
Sbjct: 5   HHHHHHSSGLVPRGSHMVIPSASV-----TSAASDFLAALHPPVTVPDPAPPPPPAPAAG 59

Query: 292 PAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKP 347
             P                  +  +     P  P     + AP  R         P
Sbjct: 60  NPPDTVTGD------------SVLQRILRGPTGP--GTTSLAPAVRYGRQPGPEAP 101

>2xag_A Lysine-specific histone demethylase 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_A* 2xah_A* 2xaj_A* 2xaq_A* 2xas_A* 2com_A Length = 852

 Score = 50.7 bits (120), Expect = 2e-06
 Identities = 38/230 (16%), Positives = 59/230 (25%), Gaps = 18/230 (7%)

Query: 283 PKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKP---SAPKPAAPKKPVAAPAPKPRPA 339
             +   A   A             + +    A +P   S P    P         K  P 
Sbjct: 7   AAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPRKKEPP 66

Query: 340 TAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKP 399
            A+P         +  P +  T    +++   T  +   P   R    +R          
Sbjct: 67  RASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAET-PEGRRTSRRKRAKVEYREMDE 125

Query: 400 ATAKPSTTSKPTTASKPATATRPATTTSKPATTTSTDIEDEMNQPFTPEELEAAIKSGLI 459
           + A  S     +   + A A +       P      + E+E           AA +S L 
Sbjct: 126 SLANLSEDEYYSEEERNAKAEKEKKL-PPPPPQAPPEEENESEPEEPSGVEGAAFQSRL- 183

Query: 460 TTPGRDNIHYPMIENLPDCNK--------YLNIMKMICNKHWGMNPTIGL 501
                D +        PD           +L I        W  NP I L
Sbjct: 184 ---PHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL-WLDNPKIQL 229

>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 = 47.2 bits (113), Expect = 2e-06
 Identities = 39/160 (24%), Positives = 61/160 (38%), Gaps = 47/160 (29%)

Query: 669 QEKCPNAICIYTD-ASKKNEKVG--AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALK 725
           +E    A   Y D A+ +  K+G        T + +        T+    E+  I+ AL+
Sbjct: 6   KEPIVGAETFYVDGAANRETKLGKAGYV---TNRGRQKVVTLTDTTNQKTELQAIYLALQ 62

Query: 726 YSASLKNNEILILTDS-------------------KSACQKLSKNCLNTTPTHLEL--EI 764
            S      E+ I+TDS                   K+A +K  KN        ++L  +I
Sbjct: 63  DSGL----EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKN--------VDLVNQI 110

Query: 765 LSSY--KHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYA 802
           +     K        V LAW+  H+GI GN +VD+L    
Sbjct: 111 IEQLIKKE------KVYLAWVPAHKGIGGNEQVDKLVSAG 144

>2wvr_C DNA replication factor CDT1; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens} PDB: 2klo_A* Length = 546

 Score = 48.6 bits (114), Expect = 6e-06
 Identities = 25/193 (12%), Positives = 41/193 (21%), Gaps = 6/193 (3%)

Query: 237 LAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVR 296
           + +   T      +P    +         P+P      AP   T+  +      K A   
Sbjct: 1   MEQRRVTDFFARRRPGPPRIAPPKLACRTPSPARPALRAPASATSGSR------KRARPP 54

Query: 297 KPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRP 356
                   +                P+ P+ P     P P        P           
Sbjct: 55  AAPGRDQARPPARRRLRLSVDEVSSPSTPEAPDIPACPSPGQKIKKSTPAAGQPPHLTSA 114

Query: 357 VSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKP 416
               T +   S         A+  A +        +  P  +    +P     P      
Sbjct: 115 QDQDTISELASCLQRARELGARVRALKASAQDAGESCTPEAEGRPEEPCGEKAPAYQRFH 174

Query: 417 ATATRPATTTSKP 429
           A A         P
Sbjct: 175 ALAQPGLPGLVLP 187

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

 Score = 45.6 bits (109), Expect = 9e-06
 Identities = 27/155 (17%), Positives = 55/155 (35%), Gaps = 38/155 (24%)

Query: 674 NAICIYTD-ASKKNEKVGA-----AWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYS 727
           + + +YTD     N +         ++ P +      +L    +   AE+    +A++ +
Sbjct: 6   DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQA 65

Query: 728 ASLKNNEILILTDSKSACQKLSKNCLNT-----------TPTH---------LELEILSS 767
            +   N++++ T+S       + N +             T            + LE L+ 
Sbjct: 66  KTQNINKLVLYTNSM-----FTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ 120

Query: 768 YKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYA 802
                     ++   + GH G  GN E DRLA+  
Sbjct: 121 -GM------DIQWMHVPGHSGFIGNEEADRLAREG 148

>3dva_I Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase...; oxidoreductase, multienzyme complex; HET: TPW; 2.35A {Bacillus stearothermophilus} PDB: 3dv0_I* 3duf_I* 1b5s_A 1lab_A 1lac_A 1w3d_A Length = 428

 Score = 47.2 bits (113), Expect = 1e-05
 Identities = 33/203 (16%), Positives = 51/203 (25%), Gaps = 41/203 (20%)

Query: 189 ASSDLAAKVAGALVVGAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTA 248
           A  ++ + V G ++      G    V +                                
Sbjct: 44  AVVEIPSPVKGKVLEILVPEGTVATVGQTLITLDAPGYENMTFKG--------------Q 89

Query: 249 AKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRK----------P 298
            +      +KT T + +         AP     A  +      P+ VRK           
Sbjct: 90  EQEEAKKEEKTETVSKEEKVDAVAPNAPAAEAEAGPNRRVIAMPS-VRKYAREKGVDIRL 148

Query: 299 VAST-----ITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVT 353
           V  T     + K     + A     A    A  +  AAPA       A PA        T
Sbjct: 149 VQGTGKNGRVLK---EDIDAFLAGGAKPAPAAAEEKAAPAA------AKPATTEGEFPET 199

Query: 354 KRPVSAT--TTASRTSSSSVTSA 374
           +  +S      A     S  T+ 
Sbjct: 200 REKMSGIRRAIAKAMVHSKHTAP 222

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 47.3 bits (111), Expect = 2e-05
 Identities = 17/187 (9%), Positives = 31/187 (16%), Gaps = 3/187 (1%)

Query: 230 AKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTA 289
            +  + P      T+  +            A    +       K       A    T + 
Sbjct: 21  GEETAVPENSGANTELVSGESE---HSTNEADKQNEGEHARENKLEKAEGVATASETASP 77

Query: 290 PKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLT 349
                     A   +       ++      P   A  K       KP         KP  
Sbjct: 78  ASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKPEATNQGDESKPAA 137

Query: 350 NGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSK 409
                           T  +              +             + +    S  + 
Sbjct: 138 EANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGAREDDAINRGSVVLASRRTG 197

Query: 410 PTTASKP 416
                K 
Sbjct: 198 HLVNEKA 204

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 47.3 bits (111), Expect = 2e-05
 Identities = 24/195 (12%), Positives = 46/195 (23%), Gaps = 18/195 (9%)

Query: 253 ISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVS 312
           +  +      TA P    A        +    +                           
Sbjct: 14  LENLYFQGEETAVPENSGANTELVSGESEHSTNEADKQNEGE---------HARENKLEK 64

Query: 313 AAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVT 372
           A    +A + A+P    AA       A+AA   +  +  V + P +     S   + +  
Sbjct: 65  AEGVATASETASPASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKP 124

Query: 373 SASAAKPAAPRVPLSQRTSAAKPATKPATAKPSTTSKPTTASKPATATRPATTTSKPATT 432
            A+              +  A  A K          K T  +      +  +        
Sbjct: 125 EATNQGDE---------SKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWE 175

Query: 433 TSTDIEDEMNQPFTP 447
                +D +N+    
Sbjct: 176 PGAREDDAINRGSVV 190

>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels, cell WALL, peptidoglycan-anchor, secreted, hydrolase; HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A Length = 937

 Score = 45.0 bits (105), Expect = 1e-04
 Identities = 28/189 (14%), Positives = 47/189 (24%), Gaps = 2/189 (1%)

Query: 160 ETAEKETPLSEVPVIPQEAQTVESAEESTASSDLAAKVAGALVVGAAAAGAAVAVKKATA 219
                   L  +    +E    E++  +T      ++ +          G      K   
Sbjct: 6   HHHGHHHQLENLYFQGEETAVPENSGANTELVSGESEHSTN-EADKQNEGEHARENKLEK 64

Query: 220 AKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTA-TTTAKPAPKPATKPAPKP 278
           A+        A PAS   A T T +  +AAKP     +  A T +A+  PK   +   KP
Sbjct: 65  AEGVATASETASPASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKP 124

Query: 279 TTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRP 338
                   +     A   +          T       +          K           
Sbjct: 125 EATNQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGAREDDAI 184

Query: 339 ATAAPAPKP 347
              +     
Sbjct: 185 NRGSVVLAS 193

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 45.1 bits (106), Expect = 4e-05
 Identities = 21/145 (14%), Positives = 39/145 (26%)

Query: 241 TTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVA 300
                ++   P  S +            +P +     P    P      P    V     
Sbjct: 5   HHHHHSSGLVPRGSHMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPE 64

Query: 301 STITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSAT 360
                          +   PKP    KPV     +P+        +P +      P   T
Sbjct: 65  PEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLT 124

Query: 361 TTASRTSSSSVTSASAAKPAAPRVP 385
           ++ +  ++S   ++ A+ P A    
Sbjct: 125 SSTATAATSKPVTSVASGPRALSRN 149

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 44.3 bits (104), Expect = 6e-05
 Identities = 21/123 (17%), Positives = 31/123 (25%)

Query: 228 PAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPKSTT 287
                 ++P++ T  T        A+ P  +               P   P         
Sbjct: 26  IELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPK 85

Query: 288 TAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAAPAPKP 347
             PKP PV+K                A       PA      A  A      + A  P+ 
Sbjct: 86  PKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRA 145

Query: 348 LTN 350
           L+ 
Sbjct: 146 LSR 148

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 43.9 bits (103), Expect = 8e-05
 Identities = 30/144 (20%), Positives = 41/144 (28%), Gaps = 1/144 (0%)

Query: 204 GAAAAGAAVAVKKATAAKKTDKPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTT 263
           G    G+ ++V +        +P          L      +          P  +     
Sbjct: 12  GLVPRGSHMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEP 71

Query: 264 AKPAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPA 323
            K AP    KP PKP            +P    KPV S       +T  A    S    A
Sbjct: 72  PKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAA 131

Query: 324 APKKPVAAPAPKPRPATAAPAPKP 347
              KPV + A  PR  +      P
Sbjct: 132 TS-KPVTSVASGPRALSRNQPQYP 154

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 41.6 bits (97), Expect = 4e-04
 Identities = 21/135 (15%), Positives = 40/135 (29%)

Query: 266 PAPKPATKPAPKPTTAAPKSTTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAP 325
                +     +    A   + T   PA +  P A              P+P    P   
Sbjct: 16  RGSHMSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEA 75

Query: 326 KKPVAAPAPKPRPATAAPAPKPLTNGVTKRPVSATTTASRTSSSSVTSASAAKPAAPRVP 385
              +  P PKP+P                +PV +   +   +++     S+   AA   P
Sbjct: 76  PVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKP 135

Query: 386 LSQRTSAAKPATKPA 400
           ++   S  +  ++  
Sbjct: 136 VTSVASGPRALSRNQ 150

>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229

 Score = 41.6 bits (97), Expect = 5e-04
 Identities = 18/118 (15%), Positives = 28/118 (23%)

Query: 225 KPGPAAKPASKPLAKTTTTKTTTAAKPAISPVKKTATTTAKPAPKPATKPAPKPTTAAPK 284
                 +    P       +      P             KP PKP  KP  K      +
Sbjct: 43  ADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKR 102

Query: 285 STTTAPKPAPVRKPVASTITKTATSTVSAAPKPSAPKPAAPKKPVAAPAPKPRPATAA 342
                           +    T+++  +A  KP     + P+         P  A A 
Sbjct: 103 DVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQAL 160

>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 = 44.3 bits (105), Expect = 1e-04
 Identities = 36/132 (27%), Positives = 56/132 (42%), Gaps = 11/132 (8%)

Query: 668 IQEKCPNAICIYTD-ASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKY 726
           + +  P A   YTD +  +  K G A +  T + K   K    T+   AE+     AL  
Sbjct: 429 VGDPIPGAETFYTDGSCNRQSKEGKAGYV-TDRGKDKVKKLEQTTNQQAELEAFAMALTD 487

Query: 727 SASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGH 786
           S    N    I+ DS+          + + PT  E +I++         + + +AW+  H
Sbjct: 488 SGPKVN----IIVDSQYVM-----GIVASQPTESESKIVNQIIEEMIKKEAIYVAWVPAH 538

Query: 787 EGIKGNVEVDRL 798
           +GI GN EVD L
Sbjct: 539 KGIGGNQEVDHL 550

>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 = 42.8 bits (101), Expect = 4e-04
 Identities = 37/131 (28%), Positives = 58/131 (44%), Gaps = 11/131 (8%)

Query: 669 QEKCPNAICIYTD-ASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYS 727
           +E    A   Y D A+ +  K+G A +  T K +        T+    E+  I+ AL+ S
Sbjct: 433 KEPIVGAETFYVDGAANRETKLGKAGYV-TNKGRQKVVPLTNTTNQKTELQAIYLALQDS 491

Query: 728 ASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHE 787
               N    I+TDS+ A        +   P   E E+++         + V LAW+  H+
Sbjct: 492 GLEVN----IVTDSQYAL-----GIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHK 542

Query: 788 GIKGNVEVDRL 798
           GI GN +VD+L
Sbjct: 543 GIGGNEQVDKL 553

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	821
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.89
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.86
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.85
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.83
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.83
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.83
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.83
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.81
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.8
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.73
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.72
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.7
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.7
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.68
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.22
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.08

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

Probab=99.89  E-value=5.7e-23  Score=199.84  Aligned_cols=132  Identities=17%  Similarity=0.248  Sum_probs=107.5

Q ss_pred             CCcEEEeccccccCC-----CcceEEecCCCcc-ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHH
Q psy16749        673 PNAICIYTDASKKNE-----KVGAAWFCPTYKS-KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQ  746 (821)
Q Consensus       673 ~~~i~IYTDGS~~~g-----~vGagvv~~~~~~-~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~  746 (821)
                      .+.++||||||+..+     ..|+|+|+.+++. .....+...++++.|||.||+.||+++.+.+...|.||+||+++++
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~   84 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTIN   84 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHh
Confidence            467899999999843     2799999865432 3445565578999999999999999999888899999999999999


Q ss_pred             HHhhccc----CCCC------CCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcC
Q psy16749        747 KLSKNCL----NTTP------THLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHG  806 (821)
Q Consensus       747 ~L~~~~~----~~~p------~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~  806 (821)
                      +|..|..    ++|.      ..+..++.++..++.  +..|.|.|||||+|++||++||+|||+|+..+
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~--~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ--GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT--TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc--CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            9998642    3333      334567888877764  46799999999999999999999999999865

>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=99.86  E-value=9.2e-22  Score=191.63  Aligned_cols=128  Identities=24%  Similarity=0.257  Sum_probs=99.4

Q ss_pred             hCCCcEEEeccccccC--CCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHH
Q psy16749        671 KCPNAICIYTDASKKN--EKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL  748 (821)
Q Consensus       671 ~~~~~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L  748 (821)
                      ...+.+.|||||||..  |..|+|+++.+++. ..+.+ ..++|++|||.|++.||+.+    ...|.|||||++++++|
T Consensus         8 P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~-~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i   81 (150)
T 3qio_A            8 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGII   81 (150)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHH
T ss_pred             CCCCCEEEEEccCCCCCCCCeEEEEEEEcCCE-EEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHH
Confidence            4567899999999984  45678887765432 22233 56899999999999999985    47899999999999999


Q ss_pred             hhccc----CCCCC------CchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhc
Q psy16749        749 SKNCL----NTTPT------HLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVH  805 (821)
Q Consensus       749 ~~~~~----~~~p~------~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~  805 (821)
                      ..|..    ++|..      .+.+++.++++++. .+..|.|.|||||+|+.|||+||+||++|+..
T Consensus        82 ~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           82 TQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI-KKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHCC------------CHHHHHHHHHHHT-TCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHh-hcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            88742    33332      34567777776663 57899999999999999999999999999875

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

Probab=99.85  E-value=5.4e-22  Score=191.00  Aligned_cols=128  Identities=20%  Similarity=0.120  Sum_probs=100.0

Q ss_pred             CcEEEeccccccC--CCcceEEecCCCcc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHh
Q psy16749        674 NAICIYTDASKKN--EKVGAAWFCPTYKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLS  749 (821)
Q Consensus       674 ~~i~IYTDGS~~~--g~vGagvv~~~~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~  749 (821)
                      ..++||||||+..  +..|+|+|+..++.  ..+..+ ...+++.|||.||+.||+++.+  ...|.||+||++++++|.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            4689999999985  45788888754432  222333 3578999999999999999876  579999999999999998


Q ss_pred             h-cc----cCCCC------CCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcC
Q psy16749        750 K-NC----LNTTP------THLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHG  806 (821)
Q Consensus       750 ~-~~----~~~~p------~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~  806 (821)
                      + |.    .++|.      ..+..++.++..++..  ..|.|.|||||+|+.||++||+|||+|+...
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~--~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~~  145 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL--HRVTFHKVKGHSDNPYNSRADELARLAIKEN  145 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH--SEEEEEECCC-CCSHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh--CceEEEEcCCcCCcHhHHHHHHHHHHHHHhC
Confidence            7 53    34443      2345678888777753  4799999999999999999999999998754

>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=99.83  E-value=3e-21  Score=188.39  Aligned_cols=129  Identities=20%  Similarity=0.174  Sum_probs=101.1

Q ss_pred             cEEEeccccccC--CCcceEEecCCCcc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhh
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTYKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSK  750 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~  750 (821)
                      .+.||||||+..  +..|+|+|+...+.  .....+ ...+++.|||.||+.||+++.+  ...|.|+|||++++++|..
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            588999999984  45788888754322  222333 4578999999999999999876  3799999999999999998


Q ss_pred             ccc----CCC------CCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCCC
Q psy16749        751 NCL----NTT------PTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEA  808 (821)
Q Consensus       751 ~~~----~~~------p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~~  808 (821)
                      |..    ++|      +..+..++.++..++.  ...|.|.|||||+|+.||+.||+|||+|+.....
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT--TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHc--cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            643    233      2334567777777664  4689999999999999999999999999987644

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

Probab=99.83  E-value=3.1e-21  Score=188.98  Aligned_cols=126  Identities=21%  Similarity=0.163  Sum_probs=99.4

Q ss_pred             cEEEeccccccC--CCcceEEecCCCcc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhh
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTYKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSK  750 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~  750 (821)
                      .+.||||||+..  +..|+|+|+..++.  .....+ ...+++.|||.||+.||+++.+  ...|.||+||++++++|..
T Consensus         6 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~   82 (158)
T 2e4l_A            6 LIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIMT   82 (158)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHHH
Confidence            589999999984  46788888753332  222333 3578999999999999999865  3899999999999999988


Q ss_pred             ccc----CCC------CCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhc
Q psy16749        751 NCL----NTT------PTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVH  805 (821)
Q Consensus       751 ~~~----~~~------p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~  805 (821)
                      |..    ++|      +..+..++.++..++.  +..|.|.|||||+|+.||+.||+|||+|+..
T Consensus        83 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           83 WIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ--LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT--TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHccccccCCCcccCHHHHHHHHHHHc--cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            543    233      2334567777777764  4699999999999999999999999999987

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

Probab=99.83  E-value=8.4e-21  Score=187.85  Aligned_cols=128  Identities=25%  Similarity=0.222  Sum_probs=100.6

Q ss_pred             cEEEecccccc--CCCcceEEecCCCc-cceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        675 AICIYTDASKK--NEKVGAAWFCPTYK-SKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       675 ~i~IYTDGS~~--~g~vGagvv~~~~~-~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      .+.||||||+.  +|..|+|+++..++ ......+...++|++|||.|++.||+++   ....|.||+||++++++|  |
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~i--w   97 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATA--H   97 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHH--H
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhh--h
Confidence            58999999998  45566776553333 2222244567899999999999999998   368999999999999999  4


Q ss_pred             ccC-CCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCC-----CcccHHHHHHHHHHhhcCCC
Q psy16749        752 CLN-TTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEG-----IKGNVEVDRLAKYATVHGEA  808 (821)
Q Consensus       752 ~~~-~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsG-----I~GNE~AD~LAK~A~~~~~~  808 (821)
                      ... +.+..+.++|+++++.+. .+..|+|+|||||+|     +.|||+||+|||+|+.....
T Consensus        98 ~~~~g~~v~n~dl~~~l~~~l~-~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~~  159 (165)
T 3p1g_A           98 VHSEGREIKNKNEILALLKALF-LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVL  159 (165)
T ss_dssp             SCCCSCCCSSHHHHHHHHHHTT-SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccCCCcccCHHHHHHHHHHHh-cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCCC
Confidence            332 234556677888877664 578999999999999     99999999999999986643

>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=99.83  E-value=2.8e-21  Score=187.21  Aligned_cols=130  Identities=19%  Similarity=0.055  Sum_probs=95.2

Q ss_pred             CCcEEEeccccccCCCcceEEecCCCcc--ceee-cc--CC--CCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHH
Q psy16749        673 PNAICIYTDASKKNEKVGAAWFCPTYKS--KACF-KL--HP--ATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSAC  745 (821)
Q Consensus       673 ~~~i~IYTDGS~~~g~vGagvv~~~~~~--~~~~-~l--~~--~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL  745 (821)
                      .+.+.||||||+..|..|+|+|+...+.  ...+ .+  ..  .++|+.|||.|++.||+++.+.+. .|.||+||+.+.
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~   82 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIA   82 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHH
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHH
Confidence            4578999999999988899998853332  2222 22  22  368999999999999999888777 999999997555


Q ss_pred             HHHhhcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCCC
Q psy16749        746 QKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEA  808 (821)
Q Consensus       746 ~~L~~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~~  808 (821)
                      +    |..++|...... .....+++++....|.|.|||||+|++||++||+|||+|+.....
T Consensus        83 ~----w~~~~w~~~~~~-~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           83 F----WATGEWKAKNEF-TQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             H----HTTSSSSCCHHH-HHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             H----HHhCCCccCCcc-hHHHHHHHHHhcCCeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            4    444455544322 222222332222389999999999999999999999999987644

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

Probab=99.81  E-value=6.3e-21  Score=188.44  Aligned_cols=131  Identities=18%  Similarity=0.090  Sum_probs=101.7

Q ss_pred             CcEEEeccccccC--CCcceEEecCCCcc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHh
Q psy16749        674 NAICIYTDASKKN--EKVGAAWFCPTYKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLS  749 (821)
Q Consensus       674 ~~i~IYTDGS~~~--g~vGagvv~~~~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~  749 (821)
                      ..+.||||||+..  +..|+|+|+...+.  .....+ ...+|+.|||.||+.||+++.+.  ..|.||+||++++++|.
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~   83 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFT   83 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHh
Confidence            4688999999984  46788888754322  222222 35789999999999999988653  58999999999999998


Q ss_pred             h-ccc----CCCC------CCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCCCC
Q psy16749        750 K-NCL----NTTP------THLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEAS  809 (821)
Q Consensus       750 ~-~~~----~~~p------~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~~~  809 (821)
                      . |..    ++|.      ..+..++.++..++.  ...|.|.|||||+|+.||+.||+|||+|+......
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~--~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~~~  152 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA--PHRVRFHFVKGHTGHPENERVDREARRQAQSQAKT  152 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT--TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSCCC
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHh--cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhhcC
Confidence            8 543    2332      234567888777764  36999999999999999999999999999877543

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

Probab=99.80  E-value=9.9e-20  Score=180.23  Aligned_cols=130  Identities=22%  Similarity=0.204  Sum_probs=96.3

Q ss_pred             CcEEEeccccccC--CC-----cceEEecCCCc----cceeecc-CCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcch
Q psy16749        674 NAICIYTDASKKN--EK-----VGAAWFCPTYK----SKACFKL-HPATSTYTAEVIGIWEALKYSASLKNNEILILTDS  741 (821)
Q Consensus       674 ~~i~IYTDGS~~~--g~-----vGagvv~~~~~----~~~~~~l-~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDS  741 (821)
                      ..++|||||||+.  |.     .|+|+|+..++    ....+.. .+..+++.||+.||..+|+.+.... ..|.|+|||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS   84 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDS   84 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESC
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeCh
Confidence            3589999999994  22     78998864322    2222322 3456777788888888887776643 579999999


Q ss_pred             HHHHHHHhhccc----CCCC------CCchHHHHHHHHHHHhcCCcEEEEEecCCCCC------cccHHHHHHHHHHhhc
Q psy16749        742 KSACQKLSKNCL----NTTP------THLELEILSSYKHLQNTCKTVKLAWIKGHEGI------KGNVEVDRLAKYATVH  805 (821)
Q Consensus       742 qsAL~~L~~~~~----~~~p------~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI------~GNE~AD~LAK~A~~~  805 (821)
                      +|++++|..|..    ++|.      ..+.++|+++.+++. ....|.|.||+||+|+      +|||+||+||++|+..
T Consensus        85 ~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~-~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~~  163 (165)
T 2lsn_A           85 FYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLS-MKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSYV  163 (165)
T ss_dssp             HHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHH-HCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHh-CCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhhh
Confidence            999999987543    4443      345678888887775 3468999999999995      5899999999999864

>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=99.73  E-value=8.4e-18  Score=159.26  Aligned_cols=122  Identities=18%  Similarity=0.179  Sum_probs=93.8

Q ss_pred             cEEEeccccccC--CCcceEEecCCC--c-c--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHH
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTY--K-S--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQK  747 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~--~-~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~  747 (821)
                      .++||||||+..  |..|+|+++.+.  + .  .....+ ..++++.||+.|++.||+++.+.+..+|.|++||+++++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            478999999994  467888877432  2 2  122233 4679999999999999999999888999999999999999


Q ss_pred             HhhcccCCCCCCchH---HHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcC
Q psy16749        748 LSKNCLNTTPTHLEL---EILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHG  806 (821)
Q Consensus       748 L~~~~~~~~p~~~s~---~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~  806 (821)
                      |.+    +|...+..   ++.++..++ +.+..|.|.|||+    .+|+.||+|||+|+...
T Consensus        82 i~~----~~~~~~~~l~~~~~~i~~l~-~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           82 MSG----RWKVKHPDLLKLYVQAQALA-SQFRRINYEWVPR----ARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HTT----SSCCCSHHHHHHHHHHHHHH-TTSSEEEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HhC----CcccCCHHHHHHHHHHHHHH-hcCCeEEEEEcCC----cccHHHHHHHHHHHHHh
Confidence            987    23333333   344444444 4578999999994    89999999999999764

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

Probab=99.72  E-value=1.2e-17  Score=157.28  Aligned_cols=122  Identities=16%  Similarity=0.171  Sum_probs=94.0

Q ss_pred             cEEEeccccccC--CCcceEEecCC--Ccc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCC----cEEEEcchHHH
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPT--YKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNN----EILILTDSKSA  744 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~--~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~----~I~I~SDSqsA  744 (821)
                      .++||||||+..  |..|+|+++.+  +..  .....+ ..++++.||+.||+.||+++.+.+..    +|.|++||+++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            589999999984  46788888754  222  222233 34799999999999999999987777    99999999999


Q ss_pred             HHHHhhcccCCCCCC---chHHHHHHHHH-HHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcC
Q psy16749        745 CQKLSKNCLNTTPTH---LELEILSSYKH-LQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHG  806 (821)
Q Consensus       745 L~~L~~~~~~~~p~~---~s~~i~~i~~~-L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~  806 (821)
                      ++.|.++    |+..   ...++.++..+ + +.+..|.|.|||    +.||+.||+|||+|+...
T Consensus        82 i~~i~~~----~~~~~~~l~~~~~~i~~l~~-~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~~  138 (140)
T 3u3g_D           82 VRQMQGV----YKVKEPTLKEKFAKIAHIKM-ERVPNLVFVHIP----REKNARADELVNEAIDKA  138 (140)
T ss_dssp             HHHHTTS----SCCCCGGGHHHHHHHHHHHH-HHCTTCEEEECC----GGGGHHHHHHHHHHHHHH
T ss_pred             HHHhCCC----cccCCHHHHHHHHHHHHHhh-cCCCcEEEEEcC----chhhHHHHHHHHHHHHhc
Confidence            9999882    2222   23456666665 4 455699999999    489999999999998753

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

Probab=99.70  E-value=2.9e-17  Score=158.15  Aligned_cols=125  Identities=14%  Similarity=0.123  Sum_probs=95.1

Q ss_pred             EEEecccccc-C--CCcce-EEecCCCc-cceee--ccC---CCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHH
Q psy16749        676 ICIYTDASKK-N--EKVGA-AWFCPTYK-SKACF--KLH---PATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSAC  745 (821)
Q Consensus       676 i~IYTDGS~~-~--g~vGa-gvv~~~~~-~~~~~--~l~---~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL  745 (821)
                      +.||||||+. .  |..|+ |+++.+.+ ....+  .++   ...+|+.||+.|++.||+++.+.+..+|.|++||++++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            6899999998 2  56775 87765433 22222  222   37899999999999999999998889999999999999


Q ss_pred             HHHhhcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCC
Q psy16749        746 QKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGE  807 (821)
Q Consensus       746 ~~L~~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~  807 (821)
                      +.|.+|-.... .....++.++..++.+.  .|.|.||||    .+|+.||+|||+|+....
T Consensus        82 ~~i~~~w~~~~-~~~~~l~~~i~~l~~~~--~v~~~~V~~----~~N~~AD~LA~~a~~~~~  136 (149)
T 2ehg_A           82 KQMNGEYKVKA-KRIIPLYEKAIELKKKL--NATLIWVPR----EENKEADRLSRVAYELVR  136 (149)
T ss_dssp             HHHTTSSCCCC-TTHHHHHHHHHHHHHHH--TCEEEECCG----GGCHHHHHHHHHHHHHHH
T ss_pred             HHHhCccccCC-HHHHHHHHHHHHHHhcC--CEEEEEcCC----cccHHHHHHHHHHHHhhc
Confidence            99998522111 23446777777776544  599999998    589999999999997653

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

Probab=99.70  E-value=2e-17  Score=191.23  Aligned_cols=122  Identities=25%  Similarity=0.285  Sum_probs=97.4

Q ss_pred             hCCCcEEEeccccccC--CCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHH
Q psy16749        671 KCPNAICIYTDASKKN--EKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL  748 (821)
Q Consensus       671 ~~~~~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L  748 (821)
                      ...+.+.||||||+..  |..|+|+++..++.. ...+ ...+|+.||+.|++.||+.    +...+.|++||++|+++|
T Consensus       432 p~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i  505 (555)
T 1mu2_A          432 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIV  505 (555)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHH
T ss_pred             CCCCceEEEEcccccCCCCCceEEEEEEeCCEe-eccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHH
Confidence            3466799999999984  346788877654322 2333 4679999999999999998    568999999999999999


Q ss_pred             hhcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHh
Q psy16749        749 SKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYAT  803 (821)
Q Consensus       749 ~~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~  803 (821)
                      ++|..    ..+..++.++++++. .+..|.|.|||||+|+.|||+||+|||+|+
T Consensus       506 ~~~~~----~~~~~l~~~~~~~~~-~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          506 ASQPT----ESESKIVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HTCCS----EESCHHHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             hcccc----cccHHHHHHHHHHhc-cCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            98543    234567777777664 367899999999999999999999999874

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

Probab=99.68  E-value=1.9e-17  Score=191.47  Aligned_cols=121  Identities=25%  Similarity=0.284  Sum_probs=93.9

Q ss_pred             hCCCcEEEeccccccC--CCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHH
Q psy16749        671 KCPNAICIYTDASKKN--EKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL  748 (821)
Q Consensus       671 ~~~~~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L  748 (821)
                      ...+.+.||||||+..  |..|+|+++..++. ..+.+ ..++|+.||+.||+.||+++    ...+.|++||++|+++|
T Consensus       435 p~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~-~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i  508 (557)
T 2zd1_A          435 PIVGAETFYVDGAANRETKLGKAGYVTNKGRQ-KVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGII  508 (557)
T ss_dssp             CCTTSCEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHH
T ss_pred             CCCCCEEEEEccCCCCCCCceEEEEEEECCcE-EEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHH
Confidence            3456799999999984  44678887764432 22233 46799999999999999998    57899999999999999


Q ss_pred             hhcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHH
Q psy16749        749 SKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYA  802 (821)
Q Consensus       749 ~~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A  802 (821)
                      ++|..    ..+..++.++++.+.+ ...|.|.|||||+|+.|||+||+|||+|
T Consensus       509 ~~~~~----~~~~~l~~~~~~~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          509 QAQPD----KSESELVNQIIEQLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             TTCCS----EESSHHHHHHHHHHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             hcCCc----cCCHHHHHHHHHHHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            98432    1245677777766654 4689999999999999999999999986

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

Probab=99.22  E-value=2.4e-12  Score=124.45  Aligned_cols=121  Identities=13%  Similarity=0.062  Sum_probs=86.8

Q ss_pred             CCCcEEEeccccccC--CCcceEEecCCCccc--eeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHH
Q psy16749        672 CPNAICIYTDASKKN--EKVGAAWFCPTYKSK--ACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQK  747 (821)
Q Consensus       672 ~~~~i~IYTDGS~~~--g~vGagvv~~~~~~~--~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~  747 (821)
                      ..+.+.||+||||..  |..|+|+|+...+..  ....+ ...+|+.|||+|++.||+++.+.+. .|.|++||++|++.
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~-~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w   85 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKW   85 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEeccc-CCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHH
Confidence            346788999999984  567888887633222  22223 2578999999999999999998776 99999999999999


Q ss_pred             HhhcccCC---CCCCchHHHHHHHH---HHHhcCCcEEEEEecCCCCCcccHHHH
Q psy16749        748 LSKNCLNT---TPTHLELEILSSYK---HLQNTCKTVKLAWIKGHEGIKGNVEVD  796 (821)
Q Consensus       748 L~~~~~~~---~p~~~s~~i~~i~~---~L~~~~~~V~~~WVPGHsGI~GNE~AD  796 (821)
                      +.++..+.   .+..+.++++.+.+   .++.  ..+...+|+.|.+.-||.-||
T Consensus        86 ~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           86 VKDKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTC
T ss_pred             HHcCCccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCccc
Confidence            98843221   12344556555443   4544  355566677799888998888

>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=99.08  E-value=1.4e-10  Score=110.94  Aligned_cols=102  Identities=13%  Similarity=0.017  Sum_probs=69.8

Q ss_pred             CCcEEEeccccccC--CCcceEE-ecCCCcc-ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHH
Q psy16749        673 PNAICIYTDASKKN--EKVGAAW-FCPTYKS-KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKL  748 (821)
Q Consensus       673 ~~~i~IYTDGS~~~--g~vGagv-v~~~~~~-~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L  748 (821)
                      .+...|||||||+.  |..|+|+ ++.++.. .....+ ...||++|||+|++.||+.+.+.+.. +.|+|||++|++.|
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi   80 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWV   80 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHH
Confidence            34567999999994  4567744 4443332 222333 36899999999999999999886544 89999999999999


Q ss_pred             hhcccCC---CCCCchHHHHHHH---HHHHhcCC
Q psy16749        749 SKNCLNT---TPTHLELEILSSY---KHLQNTCK  776 (821)
Q Consensus       749 ~~~~~~~---~p~~~s~~i~~i~---~~L~~~~~  776 (821)
                      .+|..+.   .+..+.++++++.   ..|+....
T Consensus        81 ~~~~~kt~~~~~vkN~dLw~~ld~~~~~l~~~~~  114 (134)
T 4htu_A           81 KDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTY  114 (134)
T ss_dssp             HHTCCCCCCCCSSTTHHHHHHHHHHHHHHHHCCC
T ss_pred             HcCCcccCCCCCccCHHHHHHHHHHHHHHHhCCC
Confidence            9865432   2334556666555   34544433

---

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	821
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	4e-13
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	4e-09
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	2e-08
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	3e-07

>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 = 64.5 bits (156), Expect = 4e-13
 Identities = 32/130 (24%), Positives = 47/130 (36%), Gaps = 9/130 (6%)

Query: 673 PNAICIYTDASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKN 732
           P A   YTD S   +         T + K   K    T+   AE+     AL  S    N
Sbjct: 5   PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSGPKVN 64

Query: 733 NEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGN 792
               I+ DS+     ++     +    +   I    K      + + +AW+  H+GI GN
Sbjct: 65  ----IIVDSQYVMGIVASQPTESESKIVNQIIEEMIKK-----EAIYVAWVPAHKGIGGN 115

Query: 793 VEVDRLAKYA 802
            EVD L    
Sbjct: 116 QEVDHLVSQG 125

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

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]

 Score = 52.7 bits (126), Expect = 4e-09
 Identities = 28/119 (23%), Positives = 48/119 (40%), Gaps = 11/119 (9%)

Query: 669 QEKCPNAICIYTD-ASKKNEKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYS 727
           +E    A   Y D A+ +  K+G A +      +    L   T+    E+  I+ AL+ S
Sbjct: 2   KEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTD-TTNQKTELQAIYLALQDS 60

Query: 728 ASLKNNEILILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGH 786
                 E+ I+TDS     + +   +   P   E E+++         + V LAW+  H
Sbjct: 61  GL----EVNIVTDS-----QYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH 110

>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 = 52.3 bits (124), Expect = 2e-08
 Identities = 22/136 (16%), Positives = 41/136 (30%), Gaps = 9/136 (6%)

Query: 676 ICIYTD-ASKKNEKVG--AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKN 732
           + I+T  ++  N   G   A      + K     +  T+    E++    AL+       
Sbjct: 3   VEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAE 62

Query: 733 NEIL------ILTDSKSACQKLSKNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGH 786
             +           ++       +         ++   L            +K  W+KGH
Sbjct: 63  VILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGH 122

Query: 787 EGIKGNVEVDRLAKYA 802
            G   N   D LA+ A
Sbjct: 123 AGHPENERADELARAA 138

>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 = 48.4 bits (114), Expect = 3e-07
 Identities = 28/139 (20%), Positives = 45/139 (32%), Gaps = 14/139 (10%)

Query: 676 ICIYTD-ASKKNEKVG--AAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKN 732
           + ++TD A   N   G  AA        K        T+    E+    E     A  + 
Sbjct: 4   VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIE--GLKALKEP 61

Query: 733 NEILILTDSKSACQKLS---------KNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWI 783
            E+ + TDS    +  +         +         ++   L     L      V+  ++
Sbjct: 62  CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFV 121

Query: 784 KGHEGIKGNVEVDRLAKYA 802
           KGH G   N  VDR A+  
Sbjct: 122 KGHTGHPENERVDREARRQ 140

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	821
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.85
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.84
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.84
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.62
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.4

>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=99.85  E-value=5.6e-22  Score=184.63  Aligned_cols=121  Identities=24%  Similarity=0.279  Sum_probs=89.5

Q ss_pred             CCCcEEEeccccccC--CCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHh
Q psy16749        672 CPNAICIYTDASKKN--EKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLS  749 (821)
Q Consensus       672 ~~~~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~  749 (821)
                      ..+...||||||+..  +..|+|+++..++. ....+ ...+|+.|||.||++||++    ....+.||+||+++++.|.
T Consensus         4 ~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~-~~~~~-~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~   77 (126)
T d1mu2a1           4 IPGAETFYTDGSCNRQSKEGKAGYVTDRGKD-KVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVA   77 (126)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHH
T ss_pred             CCCCcEEEEcCCCCCCCCcEEEEEEecCCCE-EEEec-CCCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHh
Confidence            356689999999884  34566666654432 22333 3579999999999999975    4578999999999999999


Q ss_pred             hcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHh
Q psy16749        750 KNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYAT  803 (821)
Q Consensus       750 ~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~  803 (821)
                      +|..    ......+.+++..+. +...|+|.|||||+|+.|||+||+||++|+
T Consensus        78 ~~~~----~~~~~~~~~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          78 SQPT----ESESKIVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             TCCS----EESCHHHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cCCc----cccchHHHHHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            8432    122233444344333 346999999999999999999999999874

>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=99.84  E-value=3.4e-22  Score=190.10  Aligned_cols=129  Identities=20%  Similarity=0.168  Sum_probs=97.4

Q ss_pred             cEEEeccccccC--CCcceEEecCCCc-cceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTYK-SKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~~-~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      .++|||||||..  |..|+|+|+...+ ....+......++++|||.||+.||+++.  ....+.|++||++++++|..+
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhcccccc
Confidence            578999999995  3467777764333 22222222446899999999999998754  356899999999999988764


Q ss_pred             cc-----CC------CCCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCC
Q psy16749        752 CL-----NT------TPTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGE  807 (821)
Q Consensus       752 ~~-----~~------~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~  807 (821)
                      ..     ++      .+..+.++|++++.++  ....|+|+|||||+|++|||+||+|||+|+.+..
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~--~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~~  145 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAM--APHRVRFHFVKGHTGHPENERVDREARRQAQSQA  145 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH--TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHh--hhcccceEEccCCCCCcchHHHHHHHHHHHHHhc
Confidence            22     11      2334456788887766  3578999999999999999999999999998764

>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=99.84  E-value=9.5e-22  Score=186.71  Aligned_cols=136  Identities=20%  Similarity=0.175  Sum_probs=100.3

Q ss_pred             cEEEeccccccC--CCcceEEecCCCccceee-ccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhc
Q psy16749        675 AICIYTDASKKN--EKVGAAWFCPTYKSKACF-KLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKN  751 (821)
Q Consensus       675 ~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~-~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~  751 (821)
                      .|.||||||+..  |..|+|+|+..++....+ ......+++.||++||+.||+++.  ....+.|++||++++..+..|
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcccch
Confidence            478999999985  457888887544322222 222456899999999999998764  356899999999999999775


Q ss_pred             cc----CCC------CCCchHHHHHHHHHHHhcCCcEEEEEecCCCCCcccHHHHHHHHHHhhcCCCCccccCCCC
Q psy16749        752 CL----NTT------PTHLELEILSSYKHLQNTCKTVKLAWIKGHEGIKGNVEVDRLAKYATVHGEASTIVISPTN  817 (821)
Q Consensus       752 ~~----~~~------p~~~s~~i~~i~~~L~~~~~~V~~~WVPGHsGI~GNE~AD~LAK~A~~~~~~~~i~~~~~~  817 (821)
                      ..    ++|      +..+..++.++..++  ....|+|+|||||+|++||++||+|||+|+....   +.+.+|.
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~--~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~---~~d~~~~  150 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAAL--GQHQIKWEWVKGHAGHPENERADELARAAAMNPT---LEDTGYQ  150 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHT--TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC---BCCTTCC
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHh--hcceeEEEEecccCCCccHHHHHHHHHHHHhCCC---CCccCCC
Confidence            43    222      222345666666655  3568999999999999999999999999998763   4455664

>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=99.62  E-value=3.7e-16  Score=142.62  Aligned_cols=104  Identities=21%  Similarity=0.217  Sum_probs=78.0

Q ss_pred             CCCcEEEeccccccC--CCcceEEecCCCccceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHh
Q psy16749        672 CPNAICIYTDASKKN--EKVGAAWFCPTYKSKACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLS  749 (821)
Q Consensus       672 ~~~~i~IYTDGS~~~--g~vGagvv~~~~~~~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~  749 (821)
                      ..+...+|||||++.  +..|+|++..++.. ....+ ...||++|||.||+.||+.    ....|.|||||+|++++|+
T Consensus         5 i~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~-~~~~~-~~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~   78 (110)
T d1s1ta1           5 IVGAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTL-TDTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQ   78 (110)
T ss_dssp             CTTSEEEEEEEEEETTTTEEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCcEEEEEEecCCe-EEEec-ccCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHh
Confidence            456778999999884  34456666554432 23333 4569999999999999975    4568999999999999999


Q ss_pred             hcccCCCCCCchHHHHHHHHHHHhcCCcEEEEEecCC
Q psy16749        750 KNCLNTTPTHLELEILSSYKHLQNTCKTVKLAWIKGH  786 (821)
Q Consensus       750 ~~~~~~~p~~~s~~i~~i~~~L~~~~~~V~~~WVPGH  786 (821)
                      +|..    .....++.++++++.+ ...|+|.|||||
T Consensus        79 ~~~~----~~~~~l~~~il~~l~~-~~~v~i~WVpgH  110 (110)
T d1s1ta1          79 AQPD----QSESELVNQIIEQLIK-KEKVYLAWVPAH  110 (110)
T ss_dssp             HCCS----EESCHHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred             cCcc----ccchHHHHHHHHHHhc-CCceEEEEeCCC
Confidence            9543    3345677888777754 578999999999

>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=99.40  E-value=2.7e-14  Score=133.95  Aligned_cols=116  Identities=15%  Similarity=0.108  Sum_probs=85.3

Q ss_pred             EEeccccccC--CCcceEEecCCCcc--ceeeccCCCCCcchhHHHHHHHHHHHHHhcCCCcEEEEcchHHHHHHHhhcc
Q psy16749        677 CIYTDASKKN--EKVGAAWFCPTYKS--KACFKLHPATSTYTAEVIGIWEALKYSASLKNNEILILTDSKSACQKLSKNC  752 (821)
Q Consensus       677 ~IYTDGS~~~--g~vGagvv~~~~~~--~~~~~l~~~~T~~~AEL~AI~~ALe~a~~~~~~~I~I~SDSqsAL~~L~~~~  752 (821)
                      -||+||||..  |-.|+|+|+...+.  ..+..+ ...||++|||+||+.||+++.+.+ .++.|||||+++++.|.+|.
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~   83 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKK   83 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCc
Confidence            3899999994  66777777654432  222233 457999999999999999998754 67999999999999999876


Q ss_pred             cCCC---CCCchHHHHHH---HHHHHhcCCcEEEEEecCCCCCcccHHHH
Q psy16749        753 LNTT---PTHLELEILSS---YKHLQNTCKTVKLAWIKGHEGIKGNVEVD  796 (821)
Q Consensus       753 ~~~~---p~~~s~~i~~i---~~~L~~~~~~V~~~WVPGHsGI~GNE~AD  796 (821)
                      .+++   +..+.+++..+   .+.|+  .+.+.+.||++|...-||..||
T Consensus        84 ~kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          84 AKSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             eecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence            5432   23344554433   34454  4567799999999999998887