Citrus Sinensis ID: 023627

---

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-------28
Protein Sequence
MDPRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHccccccccccccHHEEEcccEEcccccccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHEEEEEcccccccccccEEEcccccEEccccccccccccccccEEcccEEEEccccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHHHcccccccccccEEEcccccccEEEEccccccccccEEEEEEEEccccccccEEEEccccHHHHHHHcccccEEEEEEEcccccHHHHccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEEEcccccccccccEEEEEEEEEEEcccccEEEccHHHHHccHHHHcccccccccccccccccHHHHHccHcHHHHHHHcHHHccccEEEEcccEEEEccccccccccccccEcccccEEEEEEcccccccccccEEEEEEcccHHHHHHHHHHHHHHHHccccccccccccEEEEEccccccEEEEEEEEEEcccccEEEEEEEEEcccccEEEEEEccccHHHHHHHcccccEEEEEEEEccccHHHHHHccHHEEEEEEEEEcc
Coil and Loop (DISEMBL)
MDPRQDRFEIAFfdvetafpnppgqriaILEFGAILvcpktleelQPYSTLLASLATYFglgqqthrsLDDVRMNLEVLKYCATVLFlesglpdiftvnrWEMCSAasvsegssgyarfmepdelYCSRLKIRygistrfvdqagrprlsFVVDASQSLCTVLDACEVVAKKLFEdsrsnsewnpvvtrqsgndpaarlriptvvFGDVAQYATEMyrkepsgdiqkleFVRFDAAEldsllkpgtfvdaflsldpydyvyeQSAGIRLVAKKLIIHSE
Flexible Loop (DISEMBL)
MDPRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLfedsrsnsewnpvvtrqsgndpaarlriptvvFGDVAQYATEMyrkepsgdiQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE
Low Complexity Region (SEG)
MDPRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE
Disordered region (IsUnstruct)
*******FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFE*********************ARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLII***
Disordered Region (DISOPRED)
******R***AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIF***********************MEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVA***********EW*PVVTRQSGNDPAARLRIPTVVFGDVAQYATEMYRKEPS**I**LEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHS*
Disordered Region (DISEMBL)
MDPRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE
Disordered Region (DISPRO)
******RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFE*SRSNSEWNPVVTRQSGNDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDPRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	279
255547337	448	exonuclease, putative [Ricinus communis]	0.810	0.504	0.461	8e-61
224124082	470	predicted protein [Populus trichocarpa]	0.551	0.327	0.658	4e-53
297733948	447	unnamed protein product [Vitis vinifera]	0.659	0.411	0.572	2e-52
225457353	497	PREDICTED: uncharacterized protein LOC10	0.630	0.354	0.528	6e-52
449477209	359	PREDICTED: uncharacterized LOC101223607	0.548	0.426	0.649	9e-51
449440810	471	PREDICTED: uncharacterized protein LOC10	0.548	0.324	0.649	2e-50
356562862	501	PREDICTED: uncharacterized protein LOC10	0.548	0.305	0.643	6e-50
356512002	501	PREDICTED: uncharacterized protein LOC10	0.551	0.307	0.632	7e-50
147817752	535	hypothetical protein VITISV_031720 [Viti	0.630	0.328	0.451	7e-47
255547339	501	exonuclease, putative [Ricinus communis]	0.630	0.351	0.490	1e-45

>gi|255547337|ref|XP_002514726.1| exonuclease, putative [Ricinus communis] gi|223546330|gb|EEF47832.1| exonuclease, putative [Ricinus communis]

 Score =  239 bits (611), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 136/295 (46%), Positives = 174/295 (58%), Gaps = 69/295 (23%)

Query: 52  LASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRW---------- 101
           +ASLATYFGLG+QTHRSLDDVRMN++VLK CATVL L + LP  F V             
Sbjct: 152 MASLATYFGLGKQTHRSLDDVRMNVDVLKCCATVLLLVTILPYAFVVTNVGSTTFQPAPF 211

Query: 102 ---------------------------EMCSAASVSEGSSGYARFMEPDE---------- 124
                                      E+ S+ +V EG SG+  F+EPDE          
Sbjct: 212 SRGTLGNEMNIDSLQQDAAIEPKKESSEIPSSLTVPEGGSGHGGFLEPDEVSVSFIRASF 271

Query: 125 --------------------LYCSRLKIRY-GISTRFVDQAGRPRLSFVVDASQSLCTVL 163
                               L+CS L++RY G+ST+F D AGRPRLSFVVDA  +L ++L
Sbjct: 272 CPHSWGVQRMVLLYKDVPLQLHCSHLRVRYNGLSTKFADYAGRPRLSFVVDAPPNLYSIL 331

Query: 164 DACEVVAKKLFEDSRSNSEWNPVVTRQS-GNDPAARLRIPTVVFGDVAQYATEMYRKEPS 222
           DAC+ +A+K+  +S S+S+W  VVT+    N P  RL IPT V GDVAQYATE++ K+ S
Sbjct: 332 DACDKIAQKVSAESGSSSKWKHVVTKHDFDNSPTVRLHIPTEVTGDVAQYATEIFHKDSS 391

Query: 223 GDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIH 277
             ++K EF R  AAEL++  + GTFV A+ SLDPYDY+ E+ AGIRLVAKKLI+H
Sbjct: 392 ETMKKHEFSRLGAAELNTWFRQGTFVAAYFSLDPYDYLQEKKAGIRLVAKKLIMH 446

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124082|ref|XP_002330100.1| predicted protein [Populus trichocarpa] gi|222871234|gb|EEF08365.1| predicted protein [Populus trichocarpa]

 Score =  214 bits (545), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 104/158 (65%), Positives = 125/158 (79%), Gaps = 4/158 (2%)

Query: 124 ELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEW 183
           +L C RL+IR+G+ST+F D AGRPRLSFVVDAS SLC VLD CE + +K+  DS  +S+W
Sbjct: 315 QLRCPRLRIRFGLSTKFSDHAGRPRLSFVVDASPSLCDVLDTCESIVRKVCADSDCSSDW 374

Query: 184 NPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSL 241
             VVTR+ G  N+P  RL IPT V GDVAQYAT+MY KEPSG  QKL F +FDAAELD+ 
Sbjct: 375 RSVVTRKQGFVNNPTVRLNIPTAVNGDVAQYATDMYLKEPSGTTQKLIFSKFDAAELDTW 434

Query: 242 LKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE 279
            +PGTFVDA+LSLDPYD  Y+Q++GIRLVA KLIIH+E
Sbjct: 435 FRPGTFVDAYLSLDPYD--YQQTSGIRLVANKLIIHNE 470

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297733948|emb|CBI15195.3| unnamed protein product [Vitis vinifera]

 Score =  212 bits (539), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 111/194 (57%), Positives = 139/194 (71%), Gaps = 10/194 (5%)

Query: 93  PDIFTVNR-----WEMCSAASVSEGSSGYARFMEPDELYCSRLKIRYGISTRFVDQAGRP 147
           PD F + +      EM S  + S+    YA F++P E+  + + +R+GISTRFVD AGRP
Sbjct: 257 PDPFNLEKPVTESLEMLSTTTASQDCCDYAGFLDPAEVSVASI-MRFGISTRFVDPAGRP 315

Query: 148 RLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSG--NDPAARLRIPTVV 205
           RLSFVVD S SLC VLDAC+ +A KL  DS S+SEW PVV R++G  N P  RL IPTV 
Sbjct: 316 RLSFVVDGSPSLCQVLDACDQLAYKLSVDSGSSSEWRPVVIRKTGFLNTPTIRLSIPTVT 375

Query: 206 FGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSA 265
            GD+A YATE+Y+K+PSG  Q+L F RFDAAELD+L  PGT VD + +LDPYD  Y+Q+A
Sbjct: 376 NGDIAIYATEIYQKDPSGTTQRLIFSRFDAAELDTLFVPGTLVDTYFALDPYD--YQQNA 433

Query: 266 GIRLVAKKLIIHSE 279
           GI+LVAKKLIIH +
Sbjct: 434 GIKLVAKKLIIHGK 447

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457353|ref|XP_002281793.1| PREDICTED: uncharacterized protein LOC100265514 [Vitis vinifera]

 Score =  210 bits (534), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 111/210 (52%), Positives = 138/210 (65%), Gaps = 34/210 (16%)

Query: 102 EMCSAASVSEGSSGYARFMEPDE------------------------------LYCSRLK 131
           EM S  + S+    YA F++P E                              L+C++L+
Sbjct: 290 EMLSTTTASQDCCDYAGFLDPAEVSVASISASFVPLYRGTRRMQILHNDVKLLLHCTQLR 349

Query: 132 IRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQS 191
           +R+GISTRFVD AGRPRLSFVVD S SLC VLDAC+ +A KL  DS S+SEW PVV R++
Sbjct: 350 VRFGISTRFVDPAGRPRLSFVVDGSPSLCQVLDACDQLAYKLSVDSGSSSEWRPVVIRKT 409

Query: 192 G--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVD 249
           G  N P  RL IPTV  GD+A YATE+Y+K+PSG  Q+L F RFDAAELD+L  PGT VD
Sbjct: 410 GFLNTPTIRLSIPTVTNGDIAIYATEIYQKDPSGTTQRLIFSRFDAAELDTLFVPGTLVD 469

Query: 250 AFLSLDPYDYVYEQSAGIRLVAKKLIIHSE 279
            + +LDPYD  Y+Q+AGI+LVAKKLIIH +
Sbjct: 470 TYFALDPYD--YQQNAGIKLVAKKLIIHGK 497

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449477209|ref|XP_004154961.1| PREDICTED: uncharacterized LOC101223607 [Cucumis sativus]

 Score =  206 bits (524), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 102/157 (64%), Positives = 124/157 (78%), Gaps = 4/157 (2%)

Query: 124 ELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEW 183
           +L C+ L++R+GIST+F D AGRPRLSFVVD   +LCTVL+A + VA++LF DS S SEW
Sbjct: 205 QLLCNNLRVRFGISTKFTDYAGRPRLSFVVDVPPNLCTVLEASDGVAQRLFSDSGSGSEW 264

Query: 184 NPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSL 241
            P VTR++G  N P  RL IPT V GDVA YATEM++KE SG +Q+L F +FDAAELDSL
Sbjct: 265 RPAVTRKNGYFNYPTMRLHIPTAVSGDVANYATEMHQKEASGAVQRLIFSKFDAAELDSL 324

Query: 242 LKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHS 278
           +KPG  +DAF+SLD YD  Y+QSAGIRLVAKKLII S
Sbjct: 325 IKPGAILDAFISLDTYD--YQQSAGIRLVAKKLIIRS 359

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440810|ref|XP_004138177.1| PREDICTED: uncharacterized protein LOC101203629 [Cucumis sativus]

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 102/157 (64%), Positives = 124/157 (78%), Gaps = 4/157 (2%)

Query: 124 ELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEW 183
           +L C+ L++R+GIST+F D AGRPRLSFVVD   +LCTVL+A + VA++LF DS S SEW
Sbjct: 317 QLLCNNLRVRFGISTKFTDYAGRPRLSFVVDVPPNLCTVLEASDGVAQRLFSDSGSGSEW 376

Query: 184 NPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSL 241
            P VTR++G  N P  RL IPT V GDVA YATEM++KE SG +Q+L F +FDAAELDSL
Sbjct: 377 RPAVTRKNGYFNYPTMRLHIPTAVSGDVANYATEMHQKEASGAVQRLIFSKFDAAELDSL 436

Query: 242 LKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHS 278
           +KPG  +DAF+SLD YD  Y+QSAGIRLVAKKLII S
Sbjct: 437 IKPGAILDAFISLDTYD--YQQSAGIRLVAKKLIIRS 471

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562862|ref|XP_003549687.1| PREDICTED: uncharacterized protein LOC100818863 [Glycine max]

 Score =  203 bits (517), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 101/157 (64%), Positives = 124/157 (78%), Gaps = 4/157 (2%)

Query: 125 LYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWN 184
           L+C+ LK+R+GI++RF D+AGRPRLSFVVD S SLC VLDAC+ VA+KL  DS S+S+W 
Sbjct: 347 LHCTDLKVRFGINSRFFDRAGRPRLSFVVDPSPSLCNVLDACDRVAQKLNMDSGSSSDWR 406

Query: 185 PVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLL 242
           PVV R+ G  N P  RL IPT V  DV  YATE+Y++E SG +Q+L F +FDAAEL SL 
Sbjct: 407 PVVIRKEGFFNYPTIRLHIPTAVVADVDIYATEIYQRESSGTVQRLLFSKFDAAELGSLF 466

Query: 243 KPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE 279
            PGTFVDAFLSLDPYD  Y+Q+AGI+LV+KKLIIH +
Sbjct: 467 MPGTFVDAFLSLDPYD--YQQNAGIKLVSKKLIIHGK 501

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512002|ref|XP_003524710.1| PREDICTED: uncharacterized protein LOC100788659 [Glycine max]

 Score =  203 bits (516), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 100/158 (63%), Positives = 124/158 (78%), Gaps = 4/158 (2%)

Query: 124 ELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEW 183
           +L+C+ LK+R+GI+++F D AGRPRLSFVVD S SLC VLDAC+ VA+KL  DS S+S+W
Sbjct: 346 QLHCTDLKVRFGINSKFFDSAGRPRLSFVVDPSPSLCNVLDACDRVAQKLTVDSGSSSDW 405

Query: 184 NPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSL 241
            PVV R+ G  N P  RL IPT V  D+A YATE+Y++E SG +Q+L F +FDAAEL SL
Sbjct: 406 RPVVIRKEGFFNYPTVRLHIPTAVVADIAIYATEIYQRESSGTVQRLLFSKFDAAELGSL 465

Query: 242 LKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHSE 279
             PGTFVDA  SLDPYD  Y+Q+AGI+LVAKKLIIHS+
Sbjct: 466 FMPGTFVDAVFSLDPYD--YQQNAGIKLVAKKLIIHSK 501

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147817752|emb|CAN66660.1| hypothetical protein VITISV_031720 [Vitis vinifera]

 Score =  193 bits (491), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 112/248 (45%), Positives = 139/248 (56%), Gaps = 72/248 (29%)

Query: 102 EMCSAASVSEGSSGYARFMEPDE------------------------------LYCSRLK 131
           EM S  + S+    YA F++P E                              L+C++L+
Sbjct: 290 EMLSTTTASQDCCDYAGFLDPAEVSVASISASFVPLYRGTRRMQILHNDVKLLLHCTQLR 349

Query: 132 IRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQS 191
           +R+GISTRFVD AGRPRLSFVVD S SLC VLDAC+ +A KL  DS S+SEW PVV R++
Sbjct: 350 VRFGISTRFVDPAGRPRLSFVVDGSPSLCQVLDACDQLAYKLSVDSGSSSEWRPVVIRKT 409

Query: 192 G--NDPAARLR--------------------------------------IPTVVFGDVAQ 211
           G  N P  RLR                                      IPTV  GD+A 
Sbjct: 410 GFLNTPTIRLRQVLILFAFYENKQYAVGVWLLLSLLVLMCKNCKMQRKIIPTVTNGDIAI 469

Query: 212 YATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVA 271
           YATE+Y+K+PSG  Q+L F RFDAAELD+L  PGT VD + +LDPYD  Y+Q+AGI+LVA
Sbjct: 470 YATEIYQKDPSGTTQRLIFSRFDAAELDTLFVPGTLVDTYFALDPYD--YQQNAGIKLVA 527

Query: 272 KKLIIHSE 279
           KKLIIH +
Sbjct: 528 KKLIIHGK 535

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547339|ref|XP_002514727.1| exonuclease, putative [Ricinus communis] gi|223546331|gb|EEF47833.1| exonuclease, putative [Ricinus communis]

 Score =  189 bits (480), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 103/210 (49%), Positives = 135/210 (64%), Gaps = 34/210 (16%)

Query: 102 EMCSAASVSEGSSGYARFMEPD------------------------------ELYCSRLK 131
           EM S  +V +G S YA F+E +                              +L C RL+
Sbjct: 294 EMPSLVTVRDGGSAYAGFLETEKVSISSIRASFVPLFRGAQRMVLLHEDVILQLCCPRLR 353

Query: 132 IRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQS 191
           +R+G+ST+FVD AGRPRLSFVVDA  +LC++LD C+  A+KL  +S S S+W  VV+R+ 
Sbjct: 354 VRFGLSTKFVDSAGRPRLSFVVDAPPNLCSILDTCDGSAQKLSVESGSTSDWRQVVSRKP 413

Query: 192 G--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELDSLLKPGTFVD 249
           G  N P  RL IPT V GDVAQYATE+Y+++ SG ++KL F +F+AAEL++    GTF+D
Sbjct: 414 GFVNYPIVRLHIPTAVNGDVAQYATEIYQRDSSGAMEKLVFSKFEAAELETWFISGTFLD 473

Query: 250 AFLSLDPYDYVYEQSAGIRLVAKKLIIHSE 279
           A+ SL PYD  Y+QSAGIRLVAKKLII  E
Sbjct: 474 AYFSLHPYD--YQQSAGIRLVAKKLIIDKE 501

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

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	279
TAIR|locus:2160359	468	AT5G07710 [Arabidopsis thalian	0.555	0.331	0.559	3e-77
TAIR|locus:2163208	487	AT5G61390 [Arabidopsis thalian	0.551	0.316	0.518	1.9e-74
TAIR|locus:2019100	506	AT1G74390 [Arabidopsis thalian	0.548	0.302	0.487	1.4e-67
TAIR|locus:2135302	255	AT4G39810 [Arabidopsis thalian	0.326	0.356	0.494	6.2e-14

TAIR|locus:2160359 AT5G07710 [Arabidopsis thaliana (taxid:3702)]

 Score = 418 (152.2 bits), Expect = 3.0e-77, Sum P(4) = 3.0e-77
 Identities = 89/159 (55%), Positives = 115/159 (72%)

Query:   122 PDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNS 181
             P +LYCS LKIR+G++ +F+D  GR RL+FVVD + SL ++L+AC+  A+KL  DS S S
Sbjct:   312 PLQLYCSYLKIRFGVNGKFLDNTGRRRLNFVVDLNPSLYSILEACDSNAQKLSVDSGSTS 371

Query:   182 EWNPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDIQKLEFVRFDAAELD 239
             EWNPVV    G  N P AR+ I T + GD A+YATE++++E SG  QKL F   +  EL+
Sbjct:   372 EWNPVVNPMKGFVNYPNARIHIATEINGDEARYATEIHQRESSGATQKLIFSNPNNEELE 431

Query:   240 SLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIHS 278
             SLL  G+ VDAFLSL+PYDY  +Q AGIRLVAKKL+I S
Sbjct:   432 SLLTTGSVVDAFLSLEPYDY--QQKAGIRLVAKKLVIQS 468

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2163208 AT5G61390 [Arabidopsis thaliana (taxid:3702)]

 Score = 395 (144.1 bits), Expect = 1.9e-74, Sum P(4) = 1.9e-74
 Identities = 83/160 (51%), Positives = 112/160 (70%)

Query:   122 PDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNS 181
             P +L+C RLK+R+GI+ +F+D+AGR RL+FV+D   SLC VL  C+  A+ +  DS S S
Sbjct:   330 PLQLHCPRLKVRFGINGKFMDKAGRRRLNFVIDLYPSLCNVLQECDSAAQTISVDSGSGS 389

Query:   182 EWNPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKEPSGDI--QKLEFVRFDAAE 237
             +WNP+V    G  N P AR+ IPT + GD+ +YA E+++KE SG    QKL      A E
Sbjct:   390 DWNPLVIPMKGFLNCPTARIHIPTELNGDIDRYAAEIHQKEFSGATATQKLISSNPKAEE 449

Query:   238 LDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLIIH 277
             ++SLL P T +DAFLSL+PYDY  +Q AGIRLVA+KL+IH
Sbjct:   450 IESLLNPRTVLDAFLSLEPYDY--QQRAGIRLVARKLVIH 487

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2019100 AT1G74390 [Arabidopsis thaliana (taxid:3702)]

 Score = 348 (127.6 bits), Expect = 1.4e-67, Sum P(3) = 1.4e-67
 Identities = 77/158 (48%), Positives = 99/158 (62%)

Query:   122 PDELYCSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNS 181
             P  L    LK+R+GIS +FVD AGRP+L+ +VDA   LC +LDA +  A  L  DS +NS
Sbjct:   347 PLHLCWHSLKVRFGISRKFVDHAGRPKLNIIVDAPLDLCKILDAVDAAAHNLPTDSSTNS 406

Query:   182 EWNPVVTRQSG--NDPAARLRIPTVVFGDVAQYATEMYRKE-PSGDIQKLEFVRFDAAEL 238
             +W P V R+ G  N P ARL I +   GD     T++Y+KE P G  QKL+    +  +L
Sbjct:   407 DWRPTVIRKEGFANYPTARLHISSESNGDDTLCGTQVYQKEEPLGTNQKLDVSSDNLEKL 466

Query:   239 DSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLII 276
             +S L PGT VDAF SL+PY Y  +Q AGIRL  KKL+I
Sbjct:   467 ESALLPGTLVDAFFSLEPYSY--QQMAGIRLAVKKLVI 502

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2135302 AT4G39810 [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 6.2e-14, P = 6.2e-14
 Identities = 49/99 (49%), Positives = 59/99 (59%)

Query:     7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLGQQTH 66
             R + AF ++  A P P G    I   G  L+  K  +     +  +ASLA YFGLG Q H
Sbjct:   109 RIKEAFAEIGKAAPEPSG---IIDSLG--LLSDKFGKRAG--NMKMASLAAYFGLGVQKH 161

Query:    67 RSLDDVRMNLEVLKYCATVLFLESGLPDIFTVNRWEMCS 105
             RSLDDVRMNLEVLK+CATVLFLES LP+     +W   S
Sbjct:   162 RSLDDVRMNLEVLKHCATVLFLESTLPNHLE-GKWHTSS 199

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=ISM

---

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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	279
PRK07883	557	hypothetical protein; Validated	99.88
PRK07740	244	hypothetical protein; Provisional	99.39
cd06133	176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	99.39
PRK08517	257	DNA polymerase III subunit epsilon; Provisional	99.35
PRK07247	195	DNA polymerase III subunit epsilon; Validated	99.34
PF00929	164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	99.34
smart00479	169	EXOIII exonuclease domain in DNA-polymerase alpha	99.34
PRK09145	202	DNA polymerase III subunit epsilon; Validated	99.32
PRK07748	207	sporulation inhibitor KapD; Provisional	99.32
PRK09146	239	DNA polymerase III subunit epsilon; Validated	99.31
PRK06807	313	DNA polymerase III subunit epsilon; Validated	99.31
PRK07942	232	DNA polymerase III subunit epsilon; Provisional	99.3
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	99.29
cd06131	167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	99.29
cd06136	177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	99.28
TIGR00573	217	dnaq exonuclease, DNA polymerase III, epsilon subu	99.27
cd06130	156	DNA_pol_III_epsilon_like an uncharacterized bacter	99.26
PRK06310	250	DNA polymerase III subunit epsilon; Validated	99.26
TIGR01298	200	RNaseT ribonuclease T. in gamma-subdivision Proteo	99.19
PRK05168	211	ribonuclease T; Provisional	99.18
PRK06722	281	exonuclease; Provisional	99.17
cd06134	189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	99.17
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.16
cd06127	159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	99.15
PRK06195	309	DNA polymerase III subunit epsilon; Validated	99.14
TIGR01406	225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	99.13
PRK09182	294	DNA polymerase III subunit epsilon; Validated	99.13
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.13
cd06135	173	Orn DEDDh 3'-5' exonuclease domain of oligoribonuc	99.13
PRK06309	232	DNA polymerase III subunit epsilon; Validated	99.1
TIGR01405	1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	99.09
COG2176	1444	PolC DNA polymerase III, alpha subunit (gram-posit	99.09
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.09
PRK05711	240	DNA polymerase III subunit epsilon; Provisional	99.07
PRK07983	219	exodeoxyribonuclease X; Provisional	99.04
cd06138	183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	99.03
PRK05359	181	oligoribonuclease; Provisional	98.94
PRK11779	476	sbcB exonuclease I; Provisional	98.86
COG0847	243	DnaQ DNA polymerase III, epsilon subunit and relat	98.83
cd06149	157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	98.77
PRK00448	1437	polC DNA polymerase III PolC; Validated	98.68
PRK05601	377	DNA polymerase III subunit epsilon; Validated	98.68
PTZ00315	582	2'-phosphotransferase; Provisional	98.68
cd06137	161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	98.67
cd06144	152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	98.56
cd06145	150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	98.08
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	97.97
COG5018	210	KapD Inhibitor of the KinA pathway to sporulation,	97.96
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	97.9
PRK12306	519	uvrC excinuclease ABC subunit C; Reviewed	97.89
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	97.86
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	97.86
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	97.85
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	97.75
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	97.7
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	97.65
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	97.56
PRK10545	286	nucleotide excision repair endonuclease; Provision	97.55
COG1949	184	Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA	96.76
KOG0542	280	consensus Predicted exonuclease [Replication, reco	92.99
cd05160	199	DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain	92.89
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	92.54
smart00465	84	GIYc GIY-YIG type nucleases (URI domain).	92.24
COG3359	278	Predicted exonuclease [DNA replication, recombinat	90.73
PHA02598	138	denA endonuclease II; Provisional	88.93
PHA02570	220	dexA exonuclease; Provisional	86.34
PF13482	164	RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A	82.31
cd06125	96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	81.16

>PRK07883 hypothetical protein; Validated

Probab=99.88  E-value=1.2e-23  Score=206.65  Aligned_cols=176  Identities=26%  Similarity=0.325  Sum_probs=136.3

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------   51 (279)
                      .+..||+||+||||.++..  ++|+|||||+|..+.+  ++.|++|                                  
T Consensus        13 ~~~~~Vv~D~ETTGl~p~~--~~IIEIgaV~v~~g~i--v~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~   88 (557)
T PRK07883         13 RDVTFVVVDLETTGGSPAG--DAITEIGAVKVRGGEV--LGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA   88 (557)
T ss_pred             cCCCEEEEEEecCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence            4578999999999998865  8999999999998877  4456555                                  


Q ss_pred             ----------------------------------------------------------HHHHHHhhCCC-CCccccchhh
Q 023627           52 ----------------------------------------------------------LASLATYFGLG-QQTHRSLDDV   72 (279)
Q Consensus        52 ----------------------------------------------------------LatLA~~Fg~~-~~~HRALdDa   72 (279)
                                                                                |++|+.+||++ .+.||||+||
T Consensus        89 f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~~~H~Al~DA  168 (557)
T PRK07883         89 FLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTTPTHRALDDA  168 (557)
T ss_pred             HHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccCCCCCHHHHH
Confidence                                                                      89999999999 8999999999


Q ss_pred             hccHHHHHhhhHHHHhhhccC------cccccC-cccCcc-------ccCCCCCCCCeeeecCCCc--cc-ccCcceeee
Q 023627           73 RMNLEVLKYCATVLFLESGLP------DIFTVN-RWEMCS-------AASVSEGSSGYARFMEPDE--LY-CSRLKIRYG  135 (279)
Q Consensus        73 r~t~dVl~~catvlllE~~~~------~~l~~~-~~~~p~-------a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~r  135 (279)
                      ++|++||..     ++++...      ++|..+ +..+|.       ...+| ..||||.|.+.++  || |.+.|||.|
T Consensus       169 ~ata~l~~~-----l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~lP-~~PGVY~~~d~~g~viYVGKAknLr~R  242 (557)
T PRK07883        169 RATVDVLHG-----LIERLGNLGVHTLEELLTYLPRVTPAQRRKRHLADGLP-HAPGVYLFRGPSGEVLYVGTAVNLRRR  242 (557)
T ss_pred             HHHHHHHHH-----HHHHHHhcCCCCHHHHHHhhhhcChhhhcchHHHhhCC-CCceEEEEECCCCcEEEeehhhhHHHH
Confidence            999999999     7776643      344444 444442       46799 9999999999988  99 999999999


Q ss_pred             ccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHhhhccCCCCCCcccceeeccCCCcceEE
Q 023627          136 ISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARL  199 (279)
Q Consensus       136 VrsyFt~se~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~~~~~sgs~S~W~p~v~~~~gn~ptvRl  199 (279)
                      |++||..+..++|...||.-..+         +++.|-.|.-|-|-...       +|-.+ |..-.+|.|+|
T Consensus       243 v~sYF~~~~~~~k~~~lv~~i~~ie~i~t~sE~eAllLE~~lIk~~~P~-------yN~~l-kd~k~ypyi~i  307 (557)
T PRK07883        243 VRSYFTAAETRGRMREMVALAERVDHVECAHALEAEVRELRLIAAHKPP-------YNRRS-KFPERRWWVRL  307 (557)
T ss_pred             HHHHcCCCCCCchHHHHHhhhceEEEEEeCCHHHHHHHHHHHHHHhCCc-------chhhc-cCCCCceEEEE
Confidence            99999987788898888776555         55666666655443221       33332 33335666666

>PRK07740 hypothetical protein; Provisional

Probab=99.39  E-value=5.3e-13  Score=119.05  Aligned_cols=78  Identities=24%  Similarity=0.393  Sum_probs=68.3

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-----------------------------------   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-----------------------------------   51 (279)
                      +..|||||+||||.+|..+ .+|||||||++..+.+ |.++|+++                                   
T Consensus        58 ~~~~vv~D~ETTGl~p~~~-deIIeIgaV~~~~~~i-~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~f  135 (244)
T PRK07740         58 DLPFVVFDLETTGFSPQQG-DEILSIGAVKTKGGEV-ETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRF  135 (244)
T ss_pred             CCCEEEEEEeCCCCCCCCC-CeEEEEEEEEEECCEE-EEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHHH
Confidence            4479999999999988753 7999999999998876 66788777                                   


Q ss_pred             -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627           52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN   75 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t   75 (279)
                                                                             |.+|+.+||++ ...|+||+||++|
T Consensus       136 ~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~~~~H~Al~Da~at  215 (244)
T PRK07740        136 YAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMT  215 (244)
T ss_pred             HHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCCCCCCcHHHHHHH
Confidence                                                                   89999999999 7889999999999


Q ss_pred             HHHHHhhhHHHHhhhc
Q 023627           76 LEVLKYCATVLFLESG   91 (279)
Q Consensus        76 ~dVl~~catvlllE~~   91 (279)
                      ++||++     ++++.
T Consensus       216 a~l~~~-----ll~~~  226 (244)
T PRK07740        216 AKLWAI-----LLVEA  226 (244)
T ss_pred             HHHHHH-----HHHHH
Confidence            999999     66553

>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins

Probab=99.39  E-value=6.6e-13  Score=107.60  Aligned_cols=73  Identities=33%  Similarity=0.435  Sum_probs=62.1

Q ss_pred             EEEEEeecCCCCCCC---CceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627           10 IAFFDVETAFPNPPG---QRIAILEFGAILVCPKTLEELQPYSTL-----------------------------------   51 (279)
Q Consensus        10 ~vffDvETT~p~~~~---~~~~ilEfgAI~Vcp~~l~e~~sf~TL-----------------------------------   51 (279)
                      +|+||+||||+.+..   ...+|||||||+|.++...++++|+++                                   
T Consensus         1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~   80 (176)
T cd06133           1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK   80 (176)
T ss_pred             CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence            689999999998852   248999999999999875445666555                                   


Q ss_pred             --------------------------------------------------------------HHHHHHhhCCC-C-Cccc
Q 023627           52 --------------------------------------------------------------LASLATYFGLG-Q-QTHR   67 (279)
Q Consensus        52 --------------------------------------------------------------LatLA~~Fg~~-~-~~HR   67 (279)
                                                                                    |.+|+.+||++ . +.||
T Consensus        81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~  160 (176)
T cd06133          81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHR  160 (176)
T ss_pred             HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCCCCCcC
Confidence                                                                          89999999999 4 7999


Q ss_pred             cchhhhccHHHHHhh
Q 023627           68 SLDDVRMNLEVLKYC   82 (279)
Q Consensus        68 ALdDar~t~dVl~~c   82 (279)
                      ||+||++|++||+++
T Consensus       161 Al~DA~~~a~l~~~~  175 (176)
T cd06133         161 GLDDARNIARILKRL  175 (176)
T ss_pred             cHHHHHHHHHHHHHh
Confidence            999999999999983

This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho

>PRK08517 DNA polymerase III subunit epsilon; Provisional

Probab=99.35  E-value=1.2e-12  Score=118.56  Aligned_cols=74  Identities=26%  Similarity=0.463  Sum_probs=64.0

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------   51 (279)
                      .+..||+||+||||+++..  .+|||||||+|..|.+  +++|+++                                  
T Consensus        66 ~~~~~vv~DiETTG~~~~~--~~IIEIGAv~v~~g~i--~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f  141 (257)
T PRK08517         66 KDQVFCFVDIETNGSKPKK--HQIIEIGAVKVKNGEI--IDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF  141 (257)
T ss_pred             CCCCEEEEEEeCCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence            4568999999999998876  6999999999998877  3455433                                  


Q ss_pred             ------------------------------------------------------HHHHHHhhCCC-CCccccchhhhccH
Q 023627           52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL   76 (279)
Q Consensus        52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t~   76 (279)
                                                                            |++|+++||+. .+.||||+||.+|+
T Consensus       142 ~~fl~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~~~HrAl~DA~ata  221 (257)
T PRK08517        142 RLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAY  221 (257)
T ss_pred             HHHHCCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCCCCCChHHHHHHHH
Confidence                                                                  88999999999 79999999999999


Q ss_pred             HHHHhhh
Q 023627           77 EVLKYCA   83 (279)
Q Consensus        77 dVl~~ca   83 (279)
                      +||..|.
T Consensus       222 ~ll~~ll  228 (257)
T PRK08517        222 EIFKICL  228 (257)
T ss_pred             HHHHHHH
Confidence            9999943

>PRK07247 DNA polymerase III subunit epsilon; Validated

Probab=99.34  E-value=1.5e-12  Score=113.46  Aligned_cols=76  Identities=26%  Similarity=0.378  Sum_probs=66.0

Q ss_pred             ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH------------------------------------
Q 023627            8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------   51 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------   51 (279)
                      ..||+||+||||.++   +.+|||||||+|..+.+  +++|++|                                    
T Consensus         5 ~~~vvlD~EtTGl~~---~~eIIeIgaV~v~~g~~--~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~   79 (195)
T PRK07247          5 ETYIAFDLEFNTVNG---VSHIIQVSAVKYDDHKE--VDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK   79 (195)
T ss_pred             CeEEEEEeeCCCCCC---CCeEEEEEEEEEECCEE--EEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHH
Confidence            479999999999874   36899999999999876  5677777                                    


Q ss_pred             -------------------------------------------------------HHHHHHhhCCCCCccccchhhhccH
Q 023627           52 -------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNL   76 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~   76 (279)
                                                                             |.+||++||++...||||+||++|.
T Consensus        80 ~f~~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~~HrAl~DA~~ta  159 (195)
T PRK07247         80 EFVGELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGRGHNSLEDARMTA  159 (195)
T ss_pred             HHHCCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCCCcCCHHHHHHHH
Confidence                                                                   7899999999977899999999999


Q ss_pred             HHHHhhhHHHHhhhccC
Q 023627           77 EVLKYCATVLFLESGLP   93 (279)
Q Consensus        77 dVl~~catvlllE~~~~   93 (279)
                      .||.+     +++.--+
T Consensus       160 ~v~~~-----ll~~~~~  171 (195)
T PRK07247        160 RVYES-----FLESDQN  171 (195)
T ss_pred             HHHHH-----HHhhccc
Confidence            99999     7776554

>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III

Probab=99.34  E-value=1.3e-12  Score=100.73  Aligned_cols=39  Identities=33%  Similarity=0.480  Sum_probs=32.6

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      ||||+||||+++..  ..|+|||||++.++...+.++|+++
T Consensus         1 v~~D~Ettg~~~~~--~~iieig~v~~~~~~~~~~~~~~~~   39 (164)
T PF00929_consen    1 VVFDTETTGLDPRQ--DEIIEIGAVKVDDDENEEVESFNSL   39 (164)
T ss_dssp             EEEEEEESSSTTTT--CTEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             cEEEeEcCCCCCCC--CeEEEEEEEEeeCCccccceeeeec
Confidence            79999999999844  8999999999999985445566665

Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....

>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases

Probab=99.34  E-value=2.5e-12  Score=102.73  Aligned_cols=71  Identities=30%  Similarity=0.388  Sum_probs=60.9

Q ss_pred             eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------------
Q 023627            9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------   51 (279)
Q Consensus         9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------------   51 (279)
                      .+|+||+||||+++..  .+|+|||||++.++.+  .++|+++                                     
T Consensus         1 ~~v~~D~Ettg~~~~~--~~Iieig~v~~~~~~~--~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~   76 (169)
T smart00479        1 TLVVIDCETTGLDPGK--DEIIEIAAVDVDGGRI--IVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLE   76 (169)
T ss_pred             CEEEEEeeCCCCCCCC--CeEEEEEEEEEECCEe--EEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHH
Confidence            4899999999998864  8999999999999873  4556555                                     


Q ss_pred             ------------------------------------------------------HHHHHHhhCCC-CCc-cccchhhhcc
Q 023627           52 ------------------------------------------------------LASLATYFGLG-QQT-HRSLDDVRMN   75 (279)
Q Consensus        52 ------------------------------------------------------LatLA~~Fg~~-~~~-HRALdDar~t   75 (279)
                                                                            |.+|+.+||+. .++ ||||+||++|
T Consensus        77 ~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t  156 (169)
T smart00479       77 FLKGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGRAHRALDDARAT  156 (169)
T ss_pred             HhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHH
Confidence                                                                  89999999999 555 9999999999


Q ss_pred             HHHHHhhh
Q 023627           76 LEVLKYCA   83 (279)
Q Consensus        76 ~dVl~~ca   83 (279)
                      ++|++.+.
T Consensus       157 ~~l~~~~~  164 (169)
T smart00479      157 AKLFKKLV  164 (169)
T ss_pred             HHHHHHHH
Confidence            99999943

>PRK09145 DNA polymerase III subunit epsilon; Validated

Probab=99.32  E-value=2.8e-12  Score=109.76  Aligned_cols=74  Identities=18%  Similarity=0.179  Sum_probs=62.6

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------   51 (279)
                      .+..+|+||+||||+++..  .+|||||||++.++.++..++|+++                                  
T Consensus        27 ~~~~~vviD~ETTGl~~~~--d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~  104 (202)
T PRK09145         27 PPDEWVALDCETTGLDPRR--AEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ  104 (202)
T ss_pred             CCCCEEEEEeECCCCCCCC--CceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence            4468999999999998865  7999999999998876533455443                                  


Q ss_pred             -------------------------------------------------------------HHHHHHhhCCC-CCccccc
Q 023627           52 -------------------------------------------------------------LASLATYFGLG-QQTHRSL   69 (279)
Q Consensus        52 -------------------------------------------------------------LatLA~~Fg~~-~~~HRAL   69 (279)
                                                                                   |++|+++||++ ...||||
T Consensus       105 ~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~H~Al  184 (202)
T PRK09145        105 LLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLGRHDAL  184 (202)
T ss_pred             HHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCCCCCcH
Confidence                                                                         77889999999 7899999


Q ss_pred             hhhhccHHHHHh
Q 023627           70 DDVRMNLEVLKY   81 (279)
Q Consensus        70 dDar~t~dVl~~   81 (279)
                      +||++|++||.+
T Consensus       185 ~DA~ata~l~~~  196 (202)
T PRK09145        185 NDAIMAALIFLR  196 (202)
T ss_pred             HHHHHHHHHHHH
Confidence            999999999988

>PRK07748 sporulation inhibitor KapD; Provisional

Probab=99.32  E-value=4.1e-12  Score=109.50  Aligned_cols=73  Identities=22%  Similarity=0.316  Sum_probs=62.6

Q ss_pred             CceEEEEEeecCCCCCCC----CceeEEEEeeEEEecCceeeccchHHH-------------------------------
Q 023627            7 RFEIAFFDVETAFPNPPG----QRIAILEFGAILVCPKTLEELQPYSTL-------------------------------   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~----~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------   51 (279)
                      +-.||+||+||||+++..    ...+|||||||+|..+.+  +++|++|                               
T Consensus         3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i--~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~   80 (207)
T PRK07748          3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEV--EDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE   80 (207)
T ss_pred             cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcC--hhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence            457999999999976432    136899999999999976  5788888                               


Q ss_pred             ---------------------------------------------------------------HHHHHHhhCCC--CCcc
Q 023627           52 ---------------------------------------------------------------LASLATYFGLG--QQTH   66 (279)
Q Consensus        52 ---------------------------------------------------------------LatLA~~Fg~~--~~~H   66 (279)
                                                                                     |++++++||++  ..+|
T Consensus        81 evl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~~~~~H  160 (207)
T PRK07748         81 ELVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHH  160 (207)
T ss_pred             HHHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHHcCCCCCCCCc
Confidence                                                                           88899999999  4589


Q ss_pred             ccchhhhccHHHHHh
Q 023627           67 RSLDDVRMNLEVLKY   81 (279)
Q Consensus        67 RALdDar~t~dVl~~   81 (279)
                      |||+||++|.++|..
T Consensus       161 ~Al~DA~~ta~l~~~  175 (207)
T PRK07748        161 CALDDAMTTYNIFKL  175 (207)
T ss_pred             ChHHHHHHHHHHHHH
Confidence            999999999999999

>PRK09146 DNA polymerase III subunit epsilon; Validated

Probab=99.31  E-value=3.4e-12  Score=114.13  Aligned_cols=44  Identities=16%  Similarity=0.108  Sum_probs=36.2

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      .+..||+||+||||.++..  .+|||+|||++.++.++..++|++|
T Consensus        45 ~~~~~vviD~ETTGl~p~~--d~IieIg~v~v~~~~i~~~~~~~~l   88 (239)
T PRK09146         45 SEVPFVALDFETTGLDAEQ--DAIVSIGLVPFTLQRIRCRQARHWV   88 (239)
T ss_pred             ccCCEEEEEeECCCCCCCC--CcEEEEEEEEEECCeEeecceEEEE
Confidence            3568999999999999865  8999999999999877544555555

>PRK06807 DNA polymerase III subunit epsilon; Validated

Probab=99.31  E-value=3.7e-12  Score=118.29  Aligned_cols=76  Identities=22%  Similarity=0.364  Sum_probs=65.6

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-----------------------------------   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-----------------------------------   51 (279)
                      ...+|+||+||||.++..  ++|||||||+|+.|.+  +++|++|                                   
T Consensus         7 ~~~~Vv~DlETTGl~p~~--~eIIEIgaV~v~~g~i--~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f   82 (313)
T PRK06807          7 PLDYVVIDFETTGFNPYN--DKIIQVAAVKYRNHEL--VDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF   82 (313)
T ss_pred             CCCEEEEEEECCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHH
Confidence            357999999999998865  7999999999999877  4555444                                   


Q ss_pred             -------------------------------------------------------HHHHHHhhCCCCCccccchhhhccH
Q 023627           52 -------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNL   76 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~   76 (279)
                                                                             |.+|+.+||++.+.||||+||++|.
T Consensus        83 ~~fl~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~~~H~Al~DA~~ta  162 (313)
T PRK06807         83 LAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCA  162 (313)
T ss_pred             HHHHcCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcChHHHHHHHH
Confidence                                                                   8999999999988999999999999


Q ss_pred             HHHHhhhHHH
Q 023627           77 EVLKYCATVL   86 (279)
Q Consensus        77 dVl~~catvl   86 (279)
                      +|+.+|..-.
T Consensus       163 ~l~~~l~~~~  172 (313)
T PRK06807        163 AVYQKCASIE  172 (313)
T ss_pred             HHHHHHHHhh
Confidence            9999965533

>PRK07942 DNA polymerase III subunit epsilon; Provisional

Probab=99.30  E-value=3e-12  Score=113.13  Aligned_cols=92  Identities=20%  Similarity=0.176  Sum_probs=71.5

Q ss_pred             CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeeccchHHH-------------------------------
Q 023627            4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL-------------------------------   51 (279)
Q Consensus         4 ~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp-~~l~e~~sf~TL-------------------------------   51 (279)
                      .=.+..||+||+||||.++..  .+|||+|+|+|.+ |.+  +++|++|                               
T Consensus         2 ~~~~~~~vv~D~ETTGl~p~~--d~Iieig~v~v~~~g~~--~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~   77 (232)
T PRK07942          2 SWHPGPLAAFDLETTGVDPET--ARIVTAALVVVDADGEV--VESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAE   77 (232)
T ss_pred             CcccCcEEEEEeccCCCCCCC--CeeEEEEEEEEeCCCcc--ccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHH
Confidence            345678999999999999865  7999999999985 655  4556555                               


Q ss_pred             -------------------------------------------------------------------HHHHHHhhCCC-C
Q 023627           52 -------------------------------------------------------------------LASLATYFGLG-Q   63 (279)
Q Consensus        52 -------------------------------------------------------------------LatLA~~Fg~~-~   63 (279)
                                                                                         |++|+.+||+. .
T Consensus        78 vl~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~  157 (232)
T PRK07942         78 VLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLD  157 (232)
T ss_pred             HHHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCC
Confidence                                                                               88899999999 8


Q ss_pred             CccccchhhhccHHHHHhhhHHHH-hhhccCcccccC
Q 023627           64 QTHRSLDDVRMNLEVLKYCATVLF-LESGLPDIFTVN   99 (279)
Q Consensus        64 ~~HRALdDar~t~dVl~~catvll-lE~~~~~~l~~~   99 (279)
                      +.||||+||+||++||..++.-.- |..+..++|...
T Consensus       158 ~aH~Al~Da~ata~l~~~l~~~~~~l~~~~~~~l~~~  194 (232)
T PRK07942        158 NAHEATADALAAARVAWALARRFPELAALSPAELHEL  194 (232)
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHH
Confidence            899999999999999999554432 333333444433

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=99.29  E-value=4.9e-12  Score=117.01  Aligned_cols=77  Identities=30%  Similarity=0.324  Sum_probs=66.1

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeeccchHHH---------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL---------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp-~~l~e~~sf~TL---------------------------------   51 (279)
                      ....||+||+||||+++..  .+|||||||+|.. |.+  +++|++|                                 
T Consensus        13 ~~~~fvvlD~ETTGl~p~~--d~IIeIgav~v~~~g~i--~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l   88 (313)
T PRK06063         13 YPRGWAVVDVETSGFRPGQ--ARIISLAVLGLDADGNV--EQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEV   88 (313)
T ss_pred             CCCCEEEEEEECCCCCCCC--CEEEEEEEEEEECCcee--eeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence            3467999999999998865  8999999999975 555  4667666                                 


Q ss_pred             -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627           52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN   75 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t   75 (279)
                                                                             |.+|+.+||+. .+.||||+||++|
T Consensus        89 ~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~~~H~Al~DA~at  168 (313)
T PRK06063         89 AELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVL  168 (313)
T ss_pred             HHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHH
Confidence                                                                   99999999999 8899999999999


Q ss_pred             HHHHHhhhHHHHhhhc
Q 023627           76 LEVLKYCATVLFLESG   91 (279)
Q Consensus        76 ~dVl~~catvlllE~~   91 (279)
                      .+||.+     ++++.
T Consensus       169 a~l~~~-----ll~~~  179 (313)
T PRK06063        169 AGILRP-----SLERA  179 (313)
T ss_pred             HHHHHH-----HHHHH
Confidence            999998     66664

>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins

Probab=99.29  E-value=5e-12  Score=103.08  Aligned_cols=71  Identities=24%  Similarity=0.324  Sum_probs=58.3

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------------
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL--------------------------------------   51 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL--------------------------------------   51 (279)
                      .|+||+||||+++.. +++|||||||+|..+.+ ..++|+++                                      
T Consensus         1 ~v~~D~ETTGl~~~~-~~~iieig~v~v~~~~~-~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~   78 (167)
T cd06131           1 QIVLDTETTGLDPRE-GHRIIEIGCVELINRRL-TGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDF   78 (167)
T ss_pred             CEEEEeeCCCCCCCC-CCeEEEEEEEEEECCcE-eccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHH
Confidence            389999999999844 38999999999988765 22355444                                      


Q ss_pred             ------------------------------------------------------HHHHHHhhCCC---CCccccchhhhc
Q 023627           52 ------------------------------------------------------LASLATYFGLG---QQTHRSLDDVRM   74 (279)
Q Consensus        52 ------------------------------------------------------LatLA~~Fg~~---~~~HRALdDar~   74 (279)
                                                                            |++|++++|++   .+.||||+||++
T Consensus        79 l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~~~~H~Al~Da~~  158 (167)
T cd06131          79 IRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAEL  158 (167)
T ss_pred             HCCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCChHHHHHH
Confidence                                                                  89999999998   256999999999


Q ss_pred             cHHHHHhh
Q 023627           75 NLEVLKYC   82 (279)
Q Consensus        75 t~dVl~~c   82 (279)
                      |.+||..+
T Consensus       159 ~a~l~~~l  166 (167)
T cd06131         159 LAEVYLEL  166 (167)
T ss_pred             HHHHHHHh
Confidence            99999874

This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon

>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins

Probab=99.28  E-value=4.1e-12  Score=107.40  Aligned_cols=32  Identities=25%  Similarity=0.261  Sum_probs=27.6

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      ||+||+||||+++..+ .+|||+|||+|.++.+
T Consensus         1 ~vv~D~ETTGl~~~~~-d~Iiei~av~v~~~~~   32 (177)
T cd06136           1 FVFLDLETTGLPKHNR-PEITELCLVAVHRDHL   32 (177)
T ss_pred             CeEEeeecCCCCCCCC-CceEEEEEEEEecccc
Confidence            6999999999995443 8999999999998764

Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE

>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family

Probab=99.27  E-value=6.2e-12  Score=109.32  Aligned_cols=76  Identities=17%  Similarity=0.117  Sum_probs=63.0

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------   51 (279)
                      .+.+||+||+||||+++..  . |||||||+|.++... .++|++|                                  
T Consensus         5 ~~~~fvv~D~ETTGl~~~~--~-IIeIgav~v~~~~~~-~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~   80 (217)
T TIGR00573         5 VLDTETTGDNETTGLYAGH--D-IIEIGAVEIINRRIT-GNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED   80 (217)
T ss_pred             EecCEEEEEecCCCCCCCC--C-EEEEEEEEEECCCEe-eeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence            3568999999999998754  5 999999998877542 3566655                                  


Q ss_pred             -----------------------------------------------------------HHHHHHhhCCC-C--Cccccc
Q 023627           52 -----------------------------------------------------------LASLATYFGLG-Q--QTHRSL   69 (279)
Q Consensus        52 -----------------------------------------------------------LatLA~~Fg~~-~--~~HRAL   69 (279)
                                                                                 |.+|+.+||++ .  ..||||
T Consensus        81 ~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al  160 (217)
T TIGR00573        81 FADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL  160 (217)
T ss_pred             HHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHH
Confidence                                                                       88999999998 3  679999


Q ss_pred             hhhhccHHHHHhhhHHHHhhh
Q 023627           70 DDVRMNLEVLKYCATVLFLES   90 (279)
Q Consensus        70 dDar~t~dVl~~catvlllE~   90 (279)
                      +||++|.+||.+     ++++
T Consensus       161 ~DA~~ta~l~~~-----l~~~  176 (217)
T TIGR00573       161 ADAFILAKLYLV-----MTGK  176 (217)
T ss_pred             HHHHHHHHHHHH-----HHhc
Confidence            999999999999     6555

All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III

Probab=99.26  E-value=5.9e-12  Score=100.56  Aligned_cols=28  Identities=32%  Similarity=0.554  Sum_probs=25.8

Q ss_pred             HHHHHHhhCCCCCccccchhhhccHHHH
Q 023627           52 LASLATYFGLGQQTHRSLDDVRMNLEVL   79 (279)
Q Consensus        52 LatLA~~Fg~~~~~HRALdDar~t~dVl   79 (279)
                      |.+|+++||+....||||+||++|.++|
T Consensus       127 L~~l~~~~g~~~~~H~Al~Da~~ta~l~  154 (156)
T cd06130         127 LNTVAEHLGIELNHHDALEDARACAEIL  154 (156)
T ss_pred             HHHHHHHcCCCccCcCchHHHHHHHHHH
Confidence            8999999999933999999999999987

This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser

>PRK06310 DNA polymerase III subunit epsilon; Validated

Probab=99.26  E-value=8.6e-12  Score=111.70  Aligned_cols=78  Identities=27%  Similarity=0.337  Sum_probs=66.3

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-----------------------------------   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-----------------------------------   51 (279)
                      +..+|+||+||||.++..  .+|||||||+|.++.+  +++|++|                                   
T Consensus         6 ~~~~v~~D~ETTGl~~~~--d~IIEIa~v~v~~~~~--~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~   81 (250)
T PRK06310          6 DTEFVCLDCETTGLDVKK--DRIIEFAAIRFTFDEV--IDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI   81 (250)
T ss_pred             CCcEEEEEEeCCCCCCCC--CeEEEEEEEEEECCeE--EEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence            367999999999998866  8999999999998866  3456555                                   


Q ss_pred             ---------------------------------------------------------HHHHHHhhCCC-CCccccchhhh
Q 023627           52 ---------------------------------------------------------LASLATYFGLG-QQTHRSLDDVR   73 (279)
Q Consensus        52 ---------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar   73 (279)
                                                                               |++|+.+||+. ...|||++||.
T Consensus        82 ~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~~aH~Al~Da~  161 (250)
T PRK06310         82 KGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGNHRAMKDVE  161 (250)
T ss_pred             HHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCCCCcChHHHHH
Confidence                                                                     78899999999 88999999999


Q ss_pred             ccHHHHHhhhHHHHhhhccC
Q 023627           74 MNLEVLKYCATVLFLESGLP   93 (279)
Q Consensus        74 ~t~dVl~~catvlllE~~~~   93 (279)
                      +|.+||.+     ++++..+
T Consensus       162 at~~vl~~-----l~~~~~~  176 (250)
T PRK06310        162 INIKVFKH-----LCKRFRT  176 (250)
T ss_pred             HHHHHHHH-----HHHhccc
Confidence            99999999     6666543

>TIGR01298 RNaseT ribonuclease T

Probab=99.19  E-value=3.5e-11  Score=104.12  Aligned_cols=30  Identities=27%  Similarity=0.267  Sum_probs=27.3

Q ss_pred             HHHHHHhhCCC---CCccccchhhhccHHHHHh
Q 023627           52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKY   81 (279)
Q Consensus        52 LatLA~~Fg~~---~~~HRALdDar~t~dVl~~   81 (279)
                      |..|++++|++   .+.||||+||.+|.+||..
T Consensus       155 L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~  187 (200)
T TIGR01298       155 LAKACQAAGXDFDSTQAHSALYDTEKTAELFCE  187 (200)
T ss_pred             HHHHHHHcCCCccccchhhhHHhHHHHHHHHHH
Confidence            77888899997   4899999999999999999

in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.

>PRK05168 ribonuclease T; Provisional

Probab=99.18  E-value=3.8e-11  Score=104.61  Aligned_cols=31  Identities=35%  Similarity=0.273  Sum_probs=27.3

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEe
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVC   38 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vc   38 (279)
                      .+..+|+||+||||+++.+  .+|||||||+|.
T Consensus        15 ~~~~~vv~D~ETTGl~~~~--d~IieIgaV~v~   45 (211)
T PRK05168         15 RGFLPVVIDVETAGFNAKT--DALLEIAAVTLK   45 (211)
T ss_pred             cCCceEEEEeeCCCCCCCC--CEEEEEeEEEEE
Confidence            3567899999999999865  899999999987

>PRK06722 exonuclease; Provisional

Probab=99.17  E-value=4.5e-11  Score=110.49  Aligned_cols=45  Identities=24%  Similarity=0.477  Sum_probs=35.0

Q ss_pred             CCceEEEEEeecCCCCCC--CCceeEEEEeeEEEecCceeeccchHHH
Q 023627            6 DRFEIAFFDVETAFPNPP--GQRIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~--~~~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      ....||+||+|||+ +|.  ..+.+|||||||+|..|.+..++.|++|
T Consensus         3 ~~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sL   49 (281)
T PRK06722          3 NATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSEL   49 (281)
T ss_pred             CCCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEE
Confidence            34789999999995 442  2358999999999999843336789888

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T

Probab=99.17  E-value=4.8e-11  Score=102.08  Aligned_cols=34  Identities=21%  Similarity=0.314  Sum_probs=29.6

Q ss_pred             HHHHHHhhCCC---CCccccchhhhccHHHHHhhhHHHHhhh
Q 023627           52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLFLES   90 (279)
Q Consensus        52 LatLA~~Fg~~---~~~HRALdDar~t~dVl~~catvlllE~   90 (279)
                      |++|+++||++   ...||||+||.+|.++|.+     ++++
T Consensus       152 L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~-----l~~~  188 (189)
T cd06134         152 LAKACQAAGIEFDNKEAHSALYDTQKTAELFCK-----IVNR  188 (189)
T ss_pred             HHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHH-----HHHh
Confidence            78888999997   3689999999999999999     6654

RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.16  E-value=3.6e-11  Score=123.64  Aligned_cols=127  Identities=18%  Similarity=0.205  Sum_probs=91.2

Q ss_pred             CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------
Q 023627            4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL--------------------------------   51 (279)
Q Consensus         4 ~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL--------------------------------   51 (279)
                      ......||+||+||||.++ .  ++|||||||+|..+++  +++|++|                                
T Consensus         3 ~~~~~~~vvvD~ETTGl~~-~--d~IIeIgaV~v~~g~i--~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~   77 (820)
T PRK07246          3 QKKLRKYAVVDLEATGAGP-N--ASIIQVGIVIIEGGEI--IDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVA   77 (820)
T ss_pred             cccCCCEEEEEEecCCcCC-C--CeEEEEEEEEEECCEE--EEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHH
Confidence            3445789999999999985 2  7999999999999988  5788877                                


Q ss_pred             ---------------------------------------------------------HHHHHHhhCCC-CCccccchhhh
Q 023627           52 ---------------------------------------------------------LASLATYFGLG-QQTHRSLDDVR   73 (279)
Q Consensus        52 ---------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar   73 (279)
                                                                               |.+|+++||++ .+.||||+||+
T Consensus        78 ~~~~~~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~~~H~Al~DA~  157 (820)
T PRK07246         78 RHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADAR  157 (820)
T ss_pred             HHHHHHhCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCCCCHHHHHH
Confidence                                                                     99999999999 78899999999


Q ss_pred             ccHHHHHhhhHHHHhhhc--cC----cccccCc-ccC-c------c--ccCCCCCCCCeeeecCCCccc-ccCcceeeec
Q 023627           74 MNLEVLKYCATVLFLESG--LP----DIFTVNR-WEM-C------S--AASVSEGSSGYARFMEPDELY-CSRLKIRYGI  136 (279)
Q Consensus        74 ~t~dVl~~catvlllE~~--~~----~~l~~~~-~~~-p------~--a~~lp~~~pGvy~F~~p~dLy-gt~~~vR~rV  136 (279)
                      +|.++|..     ++++.  +|    ++|.... ... +      .  ....+ ..|+.|.|.+.-.|+ +.....+.++
T Consensus       158 ata~L~~~-----l~~~l~~l~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~l  231 (820)
T PRK07246        158 ATAELFLK-----LLQKIESLPKECLERLLEYADSLLFESYLVIEEALANAKP-YSSPDYIKVQGIVLKKTAASLKPRKL  231 (820)
T ss_pred             HHHHHHHH-----HHHHHhhcCchhHHHHHHHHhhccccHHHHHHHHHHhcCC-CCCCceEEecCeeeecccccccccch
Confidence            99999999     56554  23    3222221 110 1      0  11222 467778877755566 6555555566


Q ss_pred             ccccc
Q 023627          137 STRFV  141 (279)
Q Consensus       137 rsyFt  141 (279)
                      +++|.
T Consensus       232 ~~~F~  236 (820)
T PRK07246        232 SQDFS  236 (820)
T ss_pred             hhcCc
Confidence            66553

>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family

Probab=99.15  E-value=5.4e-11  Score=91.87  Aligned_cols=38  Identities=34%  Similarity=0.455  Sum_probs=30.8

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      ||||+||||+++..  .+|+|+|||++.++ +.++++|+.+
T Consensus         1 v~~D~Ettg~~~~~--~~iiei~~v~~~~~-~~~~~~~~~~   38 (159)
T cd06127           1 VVFDTETTGLDPKK--DRIIEIGAVKVDGG-IEIVERFETL   38 (159)
T ss_pred             CeEEeeCCCcCCCC--CeEEEEEEEEEECC-cChhhhhhee
Confidence            68999999998744  89999999999987 3345666655

DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.

>PRK06195 DNA polymerase III subunit epsilon; Validated

Probab=99.14  E-value=5.7e-11  Score=108.98  Aligned_cols=74  Identities=19%  Similarity=0.239  Sum_probs=62.9

Q ss_pred             eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------------
Q 023627            9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------   51 (279)
Q Consensus         9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------------   51 (279)
                      +||+||+|||++.    +.+|+|+|||+|..+.+  +++|++|                                     
T Consensus         2 ~~vviD~ETTg~~----~d~IieIgav~v~~g~i--~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~   75 (309)
T PRK06195          2 NFVAIDFETANEK----RNSPCSIGIVVVKDGEI--VEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIK   75 (309)
T ss_pred             cEEEEEEeCCCCC----CCceEEEEEEEEECCEE--EEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHH
Confidence            6999999999763    37899999999999887  4556666                                     


Q ss_pred             ------------------------------------------------------HHHHHHhhCCCCCccccchhhhccHH
Q 023627           52 ------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNLE   77 (279)
Q Consensus        52 ------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~d   77 (279)
                                                                            |.+|+.+||+...+||||+||++|.+
T Consensus        76 ~fl~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~~~H~Al~DA~ata~  155 (309)
T PRK06195         76 HYFNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSN  155 (309)
T ss_pred             HHhCCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCCcccCCHHHHHHHHH
Confidence                                                                  89999999999679999999999999


Q ss_pred             HHHhhhHHHHhhhccC
Q 023627           78 VLKYCATVLFLESGLP   93 (279)
Q Consensus        78 Vl~~catvlllE~~~~   93 (279)
                      ||..     ++++...
T Consensus       156 l~~~-----l~~~~~~  166 (309)
T PRK06195        156 ILLN-----ISKELNS  166 (309)
T ss_pred             HHHH-----HHHHhcc
Confidence            9998     6666544

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial

Probab=99.13  E-value=6.9e-11  Score=104.45  Aligned_cols=70  Identities=26%  Similarity=0.339  Sum_probs=60.1

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------------
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL--------------------------------------   51 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL--------------------------------------   51 (279)
                      +|+||+||||+++..+ .+|||||||++..+.+. .++|+++                                      
T Consensus         2 ~vvlD~ETTGl~p~~~-d~IIEIgav~~~~~~~~-~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~f   79 (225)
T TIGR01406         2 QIILDTETTGLDPKGG-HRIVEIGAVELVNRMLT-GDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDF   79 (225)
T ss_pred             EEEEEeeCCCcCCCCC-CeEEEEEEEEEECCcEe-cceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHH
Confidence            7999999999998753 89999999999877652 3567666                                      


Q ss_pred             -------------------------------------------------------HHHHHHhhCCCC---Cccccchhhh
Q 023627           52 -------------------------------------------------------LASLATYFGLGQ---QTHRSLDDVR   73 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~~---~~HRALdDar   73 (279)
                                                                             |.+|+.+||++.   +.||||+||+
T Consensus        80 i~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~  159 (225)
T TIGR01406        80 IGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH  159 (225)
T ss_pred             hCCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCCCcCHHHHHH
Confidence                                                                   899999999982   4699999999


Q ss_pred             ccHHHHHh
Q 023627           74 MNLEVLKY   81 (279)
Q Consensus        74 ~t~dVl~~   81 (279)
                      ++.+|+..
T Consensus       160 ~~a~v~~~  167 (225)
T TIGR01406       160 LLAEVYLA  167 (225)
T ss_pred             HHHHHHHH
Confidence            99999998

This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.

>PRK09182 DNA polymerase III subunit epsilon; Validated

Probab=99.13  E-value=9.8e-11  Score=108.19  Aligned_cols=74  Identities=27%  Similarity=0.280  Sum_probs=62.3

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEec---Ccee-eccchHHH-------------------------------
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCP---KTLE-ELQPYSTL-------------------------------   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp---~~l~-e~~sf~TL-------------------------------   51 (279)
                      ...+|+||+||||.++..  ++|||||||+|..   |.+. .+++|++|                               
T Consensus        36 ~~~~vvlD~ETTGLd~~~--d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~~~  113 (294)
T PRK09182         36 VRLGVILDTETTGLDPRK--DEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAA  113 (294)
T ss_pred             CCeEEEEEeeCCCCCCCC--CeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcHHH
Confidence            356899999999999876  8999999999983   4442 34567666                               


Q ss_pred             -----------------------------------------------------HHHHHHhhCCCCCccccchhhhccHHH
Q 023627           52 -----------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNLEV   78 (279)
Q Consensus        52 -----------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~dV   78 (279)
                                                                           |.+|+.+||.....||||+||++|++|
T Consensus       114 l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~g~~~~aHrAl~Da~Ata~l  193 (294)
T PRK09182        114 VDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQAGFFHEGHRAVDDCQALLEL  193 (294)
T ss_pred             HHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHcCCCCCCcChHHHHHHHHHH
Confidence                                                                 899999999668899999999999999


Q ss_pred             HHhh
Q 023627           79 LKYC   82 (279)
Q Consensus        79 l~~c   82 (279)
                      |..|
T Consensus       194 l~~~  197 (294)
T PRK09182        194 LARP  197 (294)
T ss_pred             HHHH
Confidence            9983

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.13  E-value=6.1e-11  Score=122.93  Aligned_cols=76  Identities=25%  Similarity=0.368  Sum_probs=67.8

Q ss_pred             ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH------------------------------------
Q 023627            8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------   51 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------   51 (279)
                      ..||+||+||||.++..+ .+|||||||+|..|++  +++|+++                                    
T Consensus         3 ~~~vvvD~ETTG~~p~~~-d~IIeigav~v~~~~i--~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~   79 (928)
T PRK08074          3 KRFVVVDLETTGNSPKKG-DKIIQIAAVVVEDGEI--LERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIV   79 (928)
T ss_pred             CCEEEEEEeCCCCCCCCC-CcEEEEEEEEEECCEE--EEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence            469999999999987753 8999999999999988  5688888                                    


Q ss_pred             ------------------------------------------------------HHHHHHhhCCC-CCccccchhhhccH
Q 023627           52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL   76 (279)
Q Consensus        52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t~   76 (279)
                                                                            |++||++||++ ...||||+||++|+
T Consensus        80 ~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~~~~H~Al~DA~ata  159 (928)
T PRK08074         80 ELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTA  159 (928)
T ss_pred             HHhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCCCCCCChHHHHHHHH
Confidence                                                                  89999999999 88899999999999


Q ss_pred             HHHHhhhHHHHhhhc
Q 023627           77 EVLKYCATVLFLESG   91 (279)
Q Consensus        77 dVl~~catvlllE~~   91 (279)
                      ++|.+     ++++.
T Consensus       160 ~l~~~-----l~~~~  169 (928)
T PRK08074        160 ELFLQ-----LLNKL  169 (928)
T ss_pred             HHHHH-----HHHHH
Confidence            99999     55554

>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins

Probab=99.13  E-value=9.7e-11  Score=98.75  Aligned_cols=37  Identities=19%  Similarity=0.147  Sum_probs=29.5

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccch
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPY   48 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf   48 (279)
                      +++||+||||.+|.+  .+|||+|||++.++.....++|
T Consensus         1 lv~iD~ETTGl~p~~--d~IieIgaV~~~~~~~~i~~~f   37 (173)
T cd06135           1 LVWIDLEMTGLDPEK--DRILEIACIITDGDLNIIAEGP   37 (173)
T ss_pred             CEEEEEecCCCCCCC--CeeEEEEEEEEeCCCceecCce
Confidence            589999999999865  8999999999998643323333

Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.

>PRK06309 DNA polymerase III subunit epsilon; Validated

Probab=99.10  E-value=2.2e-10  Score=101.04  Aligned_cols=40  Identities=30%  Similarity=0.411  Sum_probs=34.4

Q ss_pred             HHHHHHhhCCC-CCccccchhhhccHHHHHhhhHHHHhhhccCccc
Q 023627           52 LASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIF   96 (279)
Q Consensus        52 LatLA~~Fg~~-~~~HRALdDar~t~dVl~~catvlllE~~~~~~l   96 (279)
                      |.+|+.+||+. ...|||++||.+|.+||.+     ++++...+++
T Consensus       131 L~~l~~~~~~~~~~aH~Al~Da~~t~~vl~~-----l~~~~~~~~l  171 (232)
T PRK06309        131 LQYLRQVYGFEENQAHRALDDVITLHRVFSA-----LVGDLSPQQV  171 (232)
T ss_pred             HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHH-----HHHHHHHhhH
Confidence            88899999999 8899999999999999999     6776655433

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type

Probab=99.09  E-value=1.1e-10  Score=125.13  Aligned_cols=73  Identities=26%  Similarity=0.378  Sum_probs=63.5

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------   51 (279)
                      ++.+||+||+||||+++..  .+|||||||++..+.++  ++|++|                                  
T Consensus       188 ~~~~~VVfDiETTGL~~~~--d~IIEIGAVkv~~g~ii--d~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~  263 (1213)
T TIGR01405       188 DDATYVVFDIETTGLSPQY--DEIIEFGAVKVKNGRII--DKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEK  263 (1213)
T ss_pred             cCCcEEEEEeEecCCCCCC--CeEEEEEEEEEECCeEE--EEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence            3568999999999998865  89999999999998773  444443                                  


Q ss_pred             --------------------------------------------------------HHHHHHhhCCC-CCccccchhhhc
Q 023627           52 --------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRM   74 (279)
Q Consensus        52 --------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~   74 (279)
                                                                              |++||.+||+. .+.|||++||++
T Consensus       264 f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~~HrAl~DA~a  343 (1213)
T TIGR01405       264 FKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDDHHRADYDAEA  343 (1213)
T ss_pred             HHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCCCcCHHHHHHH
Confidence                                                                    89999999999 889999999999


Q ss_pred             cHHHHHhh
Q 023627           75 NLEVLKYC   82 (279)
Q Consensus        75 t~dVl~~c   82 (279)
                      |++||..+
T Consensus       344 Ta~I~~~l  351 (1213)
T TIGR01405       344 TAKVFKVM  351 (1213)
T ss_pred             HHHHHHHH
Confidence            99999993

The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.

>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]

Probab=99.09  E-value=7e-11  Score=126.08  Aligned_cols=81  Identities=22%  Similarity=0.322  Sum_probs=74.7

Q ss_pred             CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------
Q 023627            3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------   51 (279)
Q Consensus         3 ~~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------   51 (279)
                      +.-+++++|+||+||||+++.-  ..||||||+++..|++  ++.|+.+                               
T Consensus       416 ~~l~datyVVfDiETTGLs~~~--d~iIE~aAvKikng~i--Id~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~v  491 (1444)
T COG2176         416 QKLDDATYVVFDIETTGLSPVY--DEIIEIAAVKIKNGRI--IDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEV  491 (1444)
T ss_pred             cccccccEEEEEeecCCcCccc--chhhhheeeeeeCCcc--hHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHH
Confidence            4456789999999999999988  8999999999999999  7899998                               


Q ss_pred             -----------------------------------------------------------HHHHHHhhCCC-CCccccchh
Q 023627           52 -----------------------------------------------------------LASLATYFGLG-QQTHRSLDD   71 (279)
Q Consensus        52 -----------------------------------------------------------LatLA~~Fg~~-~~~HRALdD   71 (279)
                                                                                 |++|+.-||+. .++|||.+|
T Consensus       492 L~kf~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~le~hHRA~yD  571 (1444)
T COG2176         492 LEKFREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKLGVELERHHRADYD  571 (1444)
T ss_pred             HHHHHHHhcCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHhCccHHHhhhhhhh
Confidence                                                                       99999999999 999999999


Q ss_pred             hhccHHHHHhhhHHHHhhhcc
Q 023627           72 VRMNLEVLKYCATVLFLESGL   92 (279)
Q Consensus        72 ar~t~dVl~~catvlllE~~~   92 (279)
                      +.+|..||..     |++.+-
T Consensus       572 aeat~~vf~~-----f~~~~k  587 (1444)
T COG2176         572 AEATAKVFFV-----FLKDLK  587 (1444)
T ss_pred             HHHHHHHHHH-----HHHHHH
Confidence            9999999999     777653

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.09  E-value=1.2e-10  Score=119.21  Aligned_cols=70  Identities=24%  Similarity=0.328  Sum_probs=63.3

Q ss_pred             eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------------
Q 023627            9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------   51 (279)
Q Consensus         9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------------   51 (279)
                      +||+||+||||+++..  ++|||||||+|..|++  ++.|+++                                     
T Consensus         1 ~~vvvD~ETTG~~~~~--~~IIeig~v~v~~~~i--~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~   76 (850)
T TIGR01407         1 RYAVVDLETTGTQLSF--DKIIQIGIVVVEDGEI--VDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYD   76 (850)
T ss_pred             CEEEEEEECCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHH
Confidence            4899999999998765  8999999999999887  4677776                                     


Q ss_pred             -----------------------------------------------------HHHHHHhhCCC-CCccccchhhhccHH
Q 023627           52 -----------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNLE   77 (279)
Q Consensus        52 -----------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t~d   77 (279)
                                                                           |.+|+++||+. ...||||+||++|++
T Consensus        77 ~l~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~~~H~Al~DA~ata~  156 (850)
T TIGR01407        77 LLEDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAE  156 (850)
T ss_pred             HhCCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCCCCCChHHHHHHHHH
Confidence                                                                 99999999999 788999999999999


Q ss_pred             HHHhh
Q 023627           78 VLKYC   82 (279)
Q Consensus        78 Vl~~c   82 (279)
                      +|.++
T Consensus       157 l~~~l  161 (850)
T TIGR01407       157 LLLLL  161 (850)
T ss_pred             HHHHH
Confidence            99994

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>PRK05711 DNA polymerase III subunit epsilon; Provisional

Probab=99.07  E-value=2.5e-10  Score=102.67  Aligned_cols=43  Identities=21%  Similarity=0.227  Sum_probs=34.6

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      +-.+|+||+||||+++.. +.+|||||||++..+++. .++|+++
T Consensus         3 ~~r~vvlDtETTGldp~~-~drIIEIGaV~v~~~~~~-~~~f~~~   45 (240)
T PRK05711          3 IMRQIVLDTETTGLNQRE-GHRIIEIGAVELINRRLT-GRNFHVY   45 (240)
T ss_pred             CCeEEEEEeeCCCcCCCC-CCeEEEEEEEEEECCEEe-ccEEEEE
Confidence            346899999999999873 389999999999988763 2466655

>PRK07983 exodeoxyribonuclease X; Provisional

Probab=99.04  E-value=2.7e-10  Score=100.95  Aligned_cols=70  Identities=23%  Similarity=0.282  Sum_probs=59.3

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------------
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL--------------------------------------   51 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL--------------------------------------   51 (279)
                      +++||+||||.++     .|||+||++|..+++  +++|++|                                      
T Consensus         2 ~~vlD~ETTGl~~-----~IieIg~v~v~~~~i--~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~~~~   74 (219)
T PRK07983          2 LRVIDTETCGLQG-----GIVEIASVDVIDGKI--VNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYGS   74 (219)
T ss_pred             eEEEEEECCCCCC-----CCEEEEEEEEECCEE--EEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHHHcCC
Confidence            7899999999964     299999999998877  4567666                                      


Q ss_pred             ---------------------------------------HHHHHHhhCCC------CCccccchhhhccHHHHHhhhHHH
Q 023627           52 ---------------------------------------LASLATYFGLG------QQTHRSLDDVRMNLEVLKYCATVL   86 (279)
Q Consensus        52 ---------------------------------------LatLA~~Fg~~------~~~HRALdDar~t~dVl~~catvl   86 (279)
                                                             +.+|+.+||++      ...||||+||.+|.+||.+     
T Consensus        75 ~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~-----  149 (219)
T PRK07983         75 EWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLID-----  149 (219)
T ss_pred             CEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHH-----
Confidence                                                   88899999986      3599999999999999999     


Q ss_pred             Hhhhc
Q 023627           87 FLESG   91 (279)
Q Consensus        87 llE~~   91 (279)
                      +++..
T Consensus       150 l~~~~  154 (219)
T PRK07983        150 IMNTS  154 (219)
T ss_pred             HHHHc
Confidence            66544

>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins

Probab=99.03  E-value=1.9e-10  Score=97.37  Aligned_cols=37  Identities=32%  Similarity=0.443  Sum_probs=29.0

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecC-ceeeccchHHH
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPK-TLEELQPYSTL   51 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~-~l~e~~sf~TL   51 (279)
                      +|||+||||+++..  .+|||+|||+|.++ ..  +++|+++
T Consensus         1 ~~~D~ETTGl~~~~--d~Iieig~v~v~~~~~~--~~~~~~~   38 (183)
T cd06138           1 LFYDYETFGLNPSF--DQILQFAAIRTDENFNE--IEPFNIF   38 (183)
T ss_pred             CEEEeecCCCCCCC--CceEEEEEEEECCCCCC--ccceeEE
Confidence            58999999999865  79999999999876 33  2455544

This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.

>PRK05359 oligoribonuclease; Provisional

Probab=98.94  E-value=2e-09  Score=92.48  Aligned_cols=32  Identities=19%  Similarity=0.270  Sum_probs=28.4

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      +..||+||+||||++|..  .+|||+|||++..+
T Consensus         2 ~~~~vvlD~ETTGLdp~~--d~IieIgaV~~~~~   33 (181)
T PRK05359          2 EDNLIWIDLEMTGLDPER--DRIIEIATIVTDAD   33 (181)
T ss_pred             CCcEEEEEeecCCCCCCC--CeEEEEEEEEEcCC
Confidence            457999999999999976  79999999998665

>PRK11779 sbcB exonuclease I; Provisional

Probab=98.86  E-value=4.6e-09  Score=103.32  Aligned_cols=35  Identities=20%  Similarity=0.086  Sum_probs=30.5

Q ss_pred             CCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 023627            5 QDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKT   41 (279)
Q Consensus         5 ~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~   41 (279)
                      ..+.+|||||+||||.+|..  .+|||||||+|..+.
T Consensus         3 ~~~~~fvv~D~ETTGLdP~~--DrIIeiAaVrvd~~~   37 (476)
T PRK11779          3 KMQPTFLWHDYETFGANPAL--DRPAQFAGIRTDADL   37 (476)
T ss_pred             CCCCcEEEEEEECCCCCCCC--CeeEEEEEEEEeCCC
Confidence            34678999999999999976  899999999998763

>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]

Probab=98.83  E-value=5.2e-09  Score=90.55  Aligned_cols=71  Identities=30%  Similarity=0.386  Sum_probs=63.2

Q ss_pred             ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH------------------------------------
Q 023627            8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------   51 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------   51 (279)
                      ..+|+||+||||.++.+  .+|||+|||.+..+.+++ .+|+++                                    
T Consensus        13 ~~~vv~D~ETtg~~~~~--~~iieIgav~~~~~~i~~-~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~   89 (243)
T COG0847          13 TRFVVIDLETTGLNPKK--DRIIEIGAVTLEDGRIVE-RSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFL   89 (243)
T ss_pred             CcEEEEecccCCCCCCC--CceEEEEeEEEECCeeec-ceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHH
Confidence            47899999999999844  899999999999999854 346666                                    


Q ss_pred             -------------------------------------------------------HHHHHHhhCCC---CCccccchhhh
Q 023627           52 -------------------------------------------------------LASLATYFGLG---QQTHRSLDDVR   73 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~---~~~HRALdDar   73 (279)
                                                                             |..|+.++|+.   ...||||.||.
T Consensus        90 ~~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~  169 (243)
T COG0847          90 DFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDAL  169 (243)
T ss_pred             HHHCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHH
Confidence                                                                   99999999999   57799999999


Q ss_pred             ccHHHHHh
Q 023627           74 MNLEVLKY   81 (279)
Q Consensus        74 ~t~dVl~~   81 (279)
                      ++.+++..
T Consensus       170 ~~a~~~~~  177 (243)
T COG0847         170 ALAELFLL  177 (243)
T ss_pred             HHHHHHHH
Confidence            99999988

>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins

Probab=98.77  E-value=6.4e-09  Score=86.89  Aligned_cols=30  Identities=13%  Similarity=0.135  Sum_probs=25.1

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      |+||+||||.+|.++...|+++++|.+..+
T Consensus         1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~   30 (157)
T cd06149           1 VAIDCEMVGTGPGGRESELARCSIVNYHGD   30 (157)
T ss_pred             CEEEeEeccccCCCCeEEEEEEEEEeCCCC
Confidence            689999999998765689999999986444

Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli

>PRK00448 polC DNA polymerase III PolC; Validated

Probab=98.68  E-value=1.1e-08  Score=111.51  Aligned_cols=71  Identities=25%  Similarity=0.294  Sum_probs=60.5

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-----------------------------------   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-----------------------------------   51 (279)
                      +.++|+||+||||+++..  ..||||||+++..|.++  +.|+++                                   
T Consensus       418 ~~~~VVfDLETTGL~~~~--deIIEIgAV~V~~G~ii--e~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f  493 (1437)
T PRK00448        418 DATYVVFDVETTGLSAVY--DEIIEIGAVKIKNGEII--DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKF  493 (1437)
T ss_pred             cCcEEEEEhhhcCCCCch--hhhheeeeEEEeCCeEe--eeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHH
Confidence            457999999999999876  79999999999877653  222211                                   


Q ss_pred             -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627           52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN   75 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t   75 (279)
                                                                             |.+||.+||+. .++||||+||++|
T Consensus       494 ~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~~~HrAl~DA~aT  573 (1437)
T PRK00448        494 KEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEAT  573 (1437)
T ss_pred             HHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHHcCCCCCCCcChHHHHHHH
Confidence                                                                   88999999999 8899999999999


Q ss_pred             HHHHHh
Q 023627           76 LEVLKY   81 (279)
Q Consensus        76 ~dVl~~   81 (279)
                      .+||..
T Consensus       574 a~lf~~  579 (1437)
T PRK00448        574 AYLLIK  579 (1437)
T ss_pred             HHHHHH
Confidence            999999

>PRK05601 DNA polymerase III subunit epsilon; Validated

Probab=98.68  E-value=2.5e-08  Score=96.41  Aligned_cols=42  Identities=7%  Similarity=0.185  Sum_probs=34.7

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeeccchHHH
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp-~~l~e~~sf~TL   51 (279)
                      .+..||+||+||||+++..  .+|||||||++.+ |.+  +++|++|
T Consensus        44 ~~~~fVvlDiETTGLdp~~--drIIeIgAV~i~~~g~i--ve~f~tL   86 (377)
T PRK05601         44 EAAPFVAVSIQTSGIHPST--SRLITIDAVTLTADGEE--VEHFHAV   86 (377)
T ss_pred             CCCCEEEEEEECCCCCCCC--CeEEEEEEEEEEcCCEE--EEEEEEE
Confidence            3467999999999999866  8999999999985 544  4677777

>PTZ00315 2'-phosphotransferase; Provisional

Probab=98.68  E-value=3e-08  Score=100.14  Aligned_cols=42  Identities=17%  Similarity=0.244  Sum_probs=32.3

Q ss_pred             ceEEEEEeecCCCCCCC-CceeEEEEeeEEEe--cCceeeccchHHH
Q 023627            8 FEIAFFDVETAFPNPPG-QRIAILEFGAILVC--PKTLEELQPYSTL   51 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~-~~~~ilEfgAI~Vc--p~~l~e~~sf~TL   51 (279)
                      ..|++||+|||++++.. ...+|||||||+|.  .+++  ++.|++|
T Consensus        56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~I--i~~F~~y  100 (582)
T PTZ00315         56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATP--VAEFQRY  100 (582)
T ss_pred             CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEE--EEEEEEE
Confidence            56999999999987643 24799999999996  4444  4566666

>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins

Probab=98.67  E-value=2.3e-08  Score=83.33  Aligned_cols=30  Identities=13%  Similarity=0.076  Sum_probs=26.1

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      |+||+||||.++.+  .+|+|+|||++..|++
T Consensus         1 v~lD~EttGl~~~~--d~ii~Ig~V~v~~g~i   30 (161)
T cd06137           1 VALDCEMVGLADGD--SEVVRISAVDVLTGEV   30 (161)
T ss_pred             CEEEeeeeeEcCCC--CEEEEEEEEEcCCCeE
Confidence            68999999999865  8999999999976654

This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere

>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins

Probab=98.56  E-value=6.7e-08  Score=79.74  Aligned_cols=29  Identities=31%  Similarity=0.581  Sum_probs=25.0

Q ss_pred             HHHHHHh-hCCC--CCccccchhhhccHHHHH
Q 023627           52 LASLATY-FGLG--QQTHRSLDDVRMNLEVLK   80 (279)
Q Consensus        52 LatLA~~-Fg~~--~~~HRALdDar~t~dVl~   80 (279)
                      |++||.+ +|++  ...||||+||++|.++|+
T Consensus       121 L~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~  152 (152)
T cd06144         121 LKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR  152 (152)
T ss_pred             HHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence            7889986 6998  368999999999999874

This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus

>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins

Probab=98.08  E-value=3.2e-06  Score=70.11  Aligned_cols=29  Identities=38%  Similarity=0.614  Sum_probs=23.9

Q ss_pred             HHHHHHhh-CCC----CCccccchhhhccHHHHH
Q 023627           52 LASLATYF-GLG----QQTHRSLDDVRMNLEVLK   80 (279)
Q Consensus        52 LatLA~~F-g~~----~~~HRALdDar~t~dVl~   80 (279)
                      |.+|+.+| |..    ..+||||+||++|.+|++
T Consensus       117 L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~  150 (150)
T cd06145         117 LKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK  150 (150)
T ss_pred             HHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence            88999776 543    378999999999999874

This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=97.97  E-value=3.5e-06  Score=84.87  Aligned_cols=66  Identities=8%  Similarity=0.169  Sum_probs=54.2

Q ss_pred             ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecc---------ccchHHHHHHHHHHHHhh
Q 023627          106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDA---------SQSLCTVLDACEVVAKKL  173 (279)
Q Consensus       106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdl---------a~~v~~Vl~~Cd~~aq~~  173 (279)
                      ...+| ..||||.|. +++  || |.+.|||.||++||+++..++|+..||.-         +..+++.|-.|.-|-+-.
T Consensus        10 l~~lP-~~PGVYl~~-~~g~viYVGKAknLr~RV~sYF~~~~~~~K~~~lv~~i~~ie~i~t~sE~EALlLE~~LIK~~~   87 (567)
T PRK14667         10 IEKAP-EEPGVYLFK-KKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLIQQYK   87 (567)
T ss_pred             HHhCC-CCCeEEEEe-cCCeEEEeeCcHhHHHHHHHHcCCCCCChHHHHHHHhhCeEEEEEeCCHHHHHHHHHHHHHHhC
Confidence            35688 999999999 777  99 99999999999999987788999989854         455667777777776543

>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]

Probab=97.96  E-value=6.2e-06  Score=74.25  Aligned_cols=45  Identities=22%  Similarity=0.270  Sum_probs=36.4

Q ss_pred             CceEEEEEeecCCCCCCCC--ceeEEEEeeEEEecCceeeccchHHH
Q 023627            7 RFEIAFFDVETAFPNPPGQ--RIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~--~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      .+...++|+|.|.+...+.  .+.|||++|.+|..---.+++.||..
T Consensus         3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~sy   49 (210)
T COG5018           3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSY   49 (210)
T ss_pred             CceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHh
Confidence            3567899999999988765  78999999999876554567888876

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=97.90  E-value=1.5e-06  Score=88.15  Aligned_cols=66  Identities=14%  Similarity=0.193  Sum_probs=53.3

Q ss_pred             ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCC-CCccceeeeccccc---------hHHHHHHHHHHHHh
Q 023627          106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA-GRPRLSFVVDASQS---------LCTVLDACEVVAKK  172 (279)
Q Consensus       106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se-~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~  172 (279)
                      ...+| ..||||.|.+.++  || |.+.|||.||++||+++. .++|+..||.-..+         +++.|-.|.-|-+-
T Consensus        16 l~~lP-~~PGVYl~~d~~g~viYVGKAknLr~RV~sYF~~~~~~~~K~~~lv~~i~~ie~i~t~sE~EALlLE~~LIk~~   94 (621)
T PRK14671         16 LASLP-TSPGVYQFKNAAGRVIYVGKAKNLRNRVRSYFRNSRQLSGKTLVLVGHIADLEVIITSSEVEALILENNLIKEL   94 (621)
T ss_pred             HHhCC-CCCeEEEEECCCCCEEEeecchhHHHHHHHHcCCCCCCChHHHHHHHhhceEEEEEeCCHHHHHHHHHHHHHHh
Confidence            45688 9999999999988  99 999999999999999765 48898888776554         55666666666553

>PRK12306 uvrC excinuclease ABC subunit C; Reviewed

Probab=97.89  E-value=1.6e-06  Score=86.49  Aligned_cols=65  Identities=14%  Similarity=0.296  Sum_probs=53.3

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecccc---------chHHHHHHHHHHHHh
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQ---------SLCTVLDACEVVAKK  172 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~---------~v~~Vl~~Cd~~aq~  172 (279)
                      ..+| ..||||.|.+.++  || |.+.|||.||++||+++..++|...||.-..         .+++.|-.|.-|-+-
T Consensus         5 ~~lP-~~PGVYl~~d~~g~vIYVGKAknLr~RV~sYF~~~~~~~K~~~lv~~i~~ie~ivt~sE~eALlLE~~LIK~~   81 (519)
T PRK12306          5 STIP-TNPGCYLYKDEEGTIIYVGKAKNLKKRVSSYFQKKDHDPKTQSLVKAIRDIEFIVTDNEVEALLLENTLIKKH   81 (519)
T ss_pred             hHCC-CCCeEEEEECCCCCEEEeccchhHHHHHHHhCCCCCCChHHHHHHHHhcEEEEEEeCCHHHHHHHHHHHHHHh
Confidence            4578 8999999999988  99 9999999999999998777889888876554         456667677666554

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=97.86  E-value=1.9e-06  Score=88.84  Aligned_cols=65  Identities=12%  Similarity=0.231  Sum_probs=53.9

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCC-CCccceeeeccccc---------hHHHHHHHHHHHHh
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA-GRPRLSFVVDASQS---------LCTVLDACEVVAKK  172 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se-~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~  172 (279)
                      ..+| ..||||.|.+.++  || |.+.|||.||++||+++. .++|+..||.-..+         +++.|-.|.-|-+-
T Consensus         7 ~~LP-~~PGVYlfkD~~G~VIYVGKAKNLR~RV~SYF~~~~~~~~K~~~Lv~~i~~Ie~ivT~sE~EALLLE~~LIK~~   84 (694)
T PRK14666          7 STIP-LTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSALTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKH   84 (694)
T ss_pred             hhCC-CCCeEEEEECCCCCEEEeeCcHhHHHHHHHHcCCCCCCChHHHHHHHhcCeeEEEEeCCHHHHHHHHHHHHHHh
Confidence            4688 8999999999988  99 999999999999999866 68999888876554         55667777766654

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=97.86  E-value=1.8e-06  Score=87.89  Aligned_cols=55  Identities=11%  Similarity=0.251  Sum_probs=47.0

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCC-CCCccceeeeccccchHHH
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQ-AGRPRLSFVVDASQSLCTV  162 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~s-e~RpR~~~mVdla~~v~~V  162 (279)
                      ..+| ..||||.|.+.++  || |.+.|||.||++||+++ ..++|+..||.-..+++-|
T Consensus         8 ~~lP-~~PGVYl~~d~~g~viYVGKAknLr~RV~sYF~~~~~~~~K~~~lv~~i~~ie~i   66 (624)
T PRK14669          8 RTLP-TSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFSEDKLGNIKTGSLIREAVDIDYI   66 (624)
T ss_pred             HhCC-CCCeEEEEECCCCCEEEeeCchhHHHHHHHHhccCccCChHHHHHHHhhceEEEE
Confidence            4578 8999999999988  99 99999999999999964 5789999998876665443

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=97.85  E-value=2.5e-06  Score=85.98  Aligned_cols=67  Identities=13%  Similarity=0.218  Sum_probs=54.4

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccc---------cchHHHHHHHHHHHHhhh
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDAS---------QSLCTVLDACEVVAKKLF  174 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla---------~~v~~Vl~~Cd~~aq~~~  174 (279)
                      ..+| ..||||.|.+.++  || |.+.|||.||++||+.+..++|...||.-.         ..+++.|-.|.-|-+-..
T Consensus         9 ~~lP-~~PGVY~~~d~~g~viYVGKAknLr~Rv~sYF~~~~~~~k~~~lv~~i~~ie~i~t~sE~eALlLE~~LIK~~~P   87 (598)
T PRK00558          9 KTLP-DSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKKYKP   87 (598)
T ss_pred             hhCC-CCCeEEEEECCCCCEEEecCchhHHHHHHhhCCCCCcChHHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHhCC
Confidence            4578 8999999999988  99 999999999999999877778887777544         455677777777766543

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=97.75  E-value=2.2e-06  Score=86.70  Aligned_cols=55  Identities=16%  Similarity=0.295  Sum_probs=50.0

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccchHHHH
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVL  163 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~v~~Vl  163 (279)
                      ..+| +.||||.|.+.++  || |.+.+||.||++||.++.. +|+..||.-+..++.|+
T Consensus        10 ~~lP-~~PGvY~~~d~~g~VlYVGKAknLr~Rv~sYF~~~~~-~kt~~lv~~i~~iE~iv   67 (581)
T COG0322          10 KNLP-HSPGVYLMKDENGTVLYVGKAKNLRKRVSSYFRGRLD-PKTAALVENIADIEYIV   67 (581)
T ss_pred             HhCC-CCCeeEEEECCCCCEEEEeehhhHHHHHHHhhcCCCc-HHHHHHHHhhcceeEEE
Confidence            4578 9999999999998  99 9999999999999998888 99999999888877665

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=97.70  E-value=5.1e-06  Score=83.75  Aligned_cols=64  Identities=9%  Similarity=0.192  Sum_probs=51.3

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHh
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKK  172 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~  172 (279)
                      ..+| ..||||.|.+..+  || |.+.|||.||++||+.+ .++|+..||.-..+         +++.|-.|.-|-+-
T Consensus         6 ~~lP-~~PGVYl~~d~~g~viYVGKAknLr~Rv~sYF~~~-~~~K~~~mv~~i~~ie~ivt~sE~eALlLE~~lIK~~   81 (574)
T TIGR00194         6 KNLP-DKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQY   81 (574)
T ss_pred             hhCC-CCCeEEEEECCCCCEEEEecHHHHHHHHHHhcCCC-CCchHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHh
Confidence            4578 8999999999988  99 99999999999999976 48888888776554         45556666666554

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=97.65  E-value=2e-05  Score=79.57  Aligned_cols=64  Identities=16%  Similarity=0.255  Sum_probs=50.2

Q ss_pred             ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccc---------cchHHHHHHHHHHHHhh
Q 023627          106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDAS---------QSLCTVLDACEVVAKKL  173 (279)
Q Consensus       106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla---------~~v~~Vl~~Cd~~aq~~  173 (279)
                      ...+| ..||||.|.+ ++  || |.+.|||.||++||+.  ..+|...||.-.         ..+++.|-.|.-|-+-.
T Consensus        10 ~~~LP-~~PGVYl~~d-~g~viYVGKAknLr~RV~sYF~~--~~~k~~~lv~~i~~ie~i~t~sE~eALlLE~~LIK~~~   85 (577)
T PRK14668         10 AAELP-REPGVYQFVA-GGTVLYVGKAVDLRDRVRSYADP--RSERIRRMVERADDIDFAVTDTETQALLLEANLIKRHQ   85 (577)
T ss_pred             HHhCC-CCCEEEEEcC-CCeEEEeeCcHhHHHHHHHHcCC--CChHHHHHHHhhCeEEEEEeCCHHHHHHHHHHHHHHhC
Confidence            45688 9999999998 66  99 9999999999999975  356787777644         45667777777776543

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=97.56  E-value=1.1e-05  Score=83.33  Aligned_cols=65  Identities=15%  Similarity=0.244  Sum_probs=51.0

Q ss_pred             ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecccc---------chHHHHHHHHHHHHh
Q 023627          106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQ---------SLCTVLDACEVVAKK  172 (279)
Q Consensus       106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~---------~v~~Vl~~Cd~~aq~  172 (279)
                      ...+| ..||||.|.+.++  || |.+.|||.||++||+.. .++|...||.-..         .+++.|-.|.-|-+-
T Consensus        15 ~~~LP-~~PGVYlfkd~~G~VLYVGKAKNLR~RV~SYF~~~-~~~K~~~Lv~~i~~Ie~ivT~sE~EALLLE~~LIK~~   91 (691)
T PRK14672         15 ALSAP-STSGVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCR-HDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKH   91 (691)
T ss_pred             HHhCC-CCCeEEEEECCCCCEEEeeCcHHHHHHHHHHcCCC-CCchHHHHHHhhCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            45688 9999999999988  99 99999999999999864 5667666766544         456666667666553

>PRK10545 nucleotide excision repair endonuclease; Provisional

Probab=97.55  E-value=8.2e-06  Score=76.31  Aligned_cols=82  Identities=13%  Similarity=0.209  Sum_probs=57.7

Q ss_pred             ccCCCCCCCCeeeecCCCc---cc-ccCcceeeeccccccCCCCCccceeeec---------cccchHHHHHHHHHHHHh
Q 023627          106 AASVSEGSSGYARFMEPDE---LY-CSRLKIRYGISTRFVDQAGRPRLSFVVD---------ASQSLCTVLDACEVVAKK  172 (279)
Q Consensus       106 a~~lp~~~pGvy~F~~p~d---Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVd---------la~~v~~Vl~~Cd~~aq~  172 (279)
                      .+++| +.||||.|.+.++   || |++.|||.||++||++    +|...|+.         -+..+.+.|-.++-|-+-
T Consensus        28 l~~LP-~~PGVYlf~d~~g~~~LYVGKAknLR~RV~syF~~----~k~~~m~~~i~~Ie~i~T~sEleALLLE~~LIK~~  102 (286)
T PRK10545         28 LEDLP-KLPGVYLFHGESDTMPLYIGKSVNIRSRVLSHLRT----PDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQ  102 (286)
T ss_pred             HHhCC-CCCeEEEEEcCCCCEEEEEechHhHHHHHHHHcCc----HHHHHHHHhcceEEEEEeCCHHHHHHHHHHHHHHh
Confidence            56799 9999999998776   89 9999999999999975    22233332         345677888888888776


Q ss_pred             hhccCCCCCCcccceeeccCCCcceEEe
Q 023627          173 LFEDSRSNSEWNPVVTRQSGNDPAARLR  200 (279)
Q Consensus       173 ~~~~sgs~S~W~p~v~~~~gn~ptvRl~  200 (279)
                      ...       .|-.. |+...+|.+|+.
T Consensus       103 ~P~-------yN~~l-k~~k~~~~i~l~  122 (286)
T PRK10545        103 QPL-------FNKRL-RRNRQLCSLQLN  122 (286)
T ss_pred             CCc-------chhhc-cCCCCCeEEEEE
Confidence            431       22221 333467777764

>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]

Probab=96.76  E-value=0.004  Score=55.92  Aligned_cols=34  Identities=18%  Similarity=0.277  Sum_probs=29.1

Q ss_pred             CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEe
Q 023627            3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVC   38 (279)
Q Consensus         3 ~~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vc   38 (279)
                      |...+...|-+|+|-||+++..  .+|||+++|+--
T Consensus         1 m~~~~~nLiWIDlEMTGLd~~~--drIIEiA~iVTD   34 (184)
T COG1949           1 MSANKNNLIWIDLEMTGLDPER--DRIIEIATIVTD   34 (184)
T ss_pred             CCCcCCceEEEeeeeccCCcCc--ceEEEEEEEEec
Confidence            3566788999999999999988  899999998643

>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]

Probab=92.99  E-value=0.24  Score=47.22  Aligned_cols=30  Identities=20%  Similarity=0.419  Sum_probs=26.3

Q ss_pred             HHHHHHhhCCC--CCccccchhhhccHHHHHh
Q 023627           52 LASLATYFGLG--QQTHRSLDDVRMNLEVLKY   81 (279)
Q Consensus        52 LatLA~~Fg~~--~~~HRALdDar~t~dVl~~   81 (279)
                      +..+-++.|+.  +..|++||||+-...+...
T Consensus       206 it~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~k  237 (280)
T KOG0542|consen  206 ITGMLEHYGLQFEGRAHSGIDDARNIARIAQK  237 (280)
T ss_pred             HHHHHHHhCCcccCCcccCchhHHHHHHHHHH
Confidence            67777888999  8899999999998888877

>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases

Probab=92.89  E-value=0.12  Score=43.75  Aligned_cols=31  Identities=23%  Similarity=0.203  Sum_probs=24.9

Q ss_pred             EEEEEeecCCC----CCCCCceeEEEEeeEEEecCce
Q 023627           10 IAFFDVETAFP----NPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus        10 ~vffDvETT~p----~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      +++||+|||++    ++..  ..|+++|++....|..
T Consensus         1 v~~~DIEt~~~~~~p~~~~--d~Ii~I~~~~~~~g~~   35 (199)
T cd05160           1 VLSFDIETTPPVGGPEPDR--DPIICITYADSFDGVK   35 (199)
T ss_pred             CccEEEeecCCCCCcCCCC--CCEEEEEEEEeeCCce
Confidence            37899999998    5544  8999999998855654

The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=92.54  E-value=0.016  Score=59.11  Aligned_cols=52  Identities=12%  Similarity=0.321  Sum_probs=39.6

Q ss_pred             ecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHH
Q 023627          119 FMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAK  171 (279)
Q Consensus       119 F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq  171 (279)
                      |.+.++  || |.+.|||.||++||+.+ .++|...||.-..+         +++.|-.|.-|-|
T Consensus         1 ~~d~~g~vIYVGKAknLr~RV~sYF~~~-~~~K~~~lv~~i~~ie~ivt~sE~EALlLE~~LIK~   64 (574)
T PRK14670          1 MYSENNKILYIGKAKNLRSRVKNYFLEK-ISHKTKILMKNVKNIEVITTNSEYEALLLECNLIKT   64 (574)
T ss_pred             CCCCCCCEEEeeCcHhHHHHHHHHcCCC-CCchHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHH
Confidence            445666  99 99999999999999975 57888888776554         5566666666655

>smart00465 GIYc GIY-YIG type nucleases (URI domain)

Probab=92.24  E-value=0.021  Score=40.93  Aligned_cols=31  Identities=16%  Similarity=0.282  Sum_probs=28.0

Q ss_pred             CCeeeecCCCc--cc-ccCcceeeeccccccCCC
Q 023627          114 SGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA  144 (279)
Q Consensus       114 pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se  144 (279)
                      ||+|.|..+++  +| |++.+++.|++++|.+..
T Consensus         2 ~gvY~i~~~~~~~~YVG~t~nl~~R~~~h~~~~~   35 (84)
T smart00465        2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSR   35 (84)
T ss_pred             CEEEEEEECCCCEEEEEEccCHHHHHHHHHhCCC
Confidence            79999999666  99 999999999999998766

>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]

Probab=90.73  E-value=0.37  Score=45.96  Aligned_cols=33  Identities=27%  Similarity=0.345  Sum_probs=24.1

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      +..+++|||+||||+++.+  ..|+=.|--.+..+
T Consensus        96 ~~e~~~FFDiETTGL~~ag--~~I~~~g~a~~~~~  128 (278)
T COG3359          96 EAEDVAFFDIETTGLDRAG--NTITLVGGARGVDD  128 (278)
T ss_pred             cccceEEEeeeccccCCCC--CeEEEEEEEEccCc
Confidence            4678999999999999955  66666665444433

>PHA02598 denA endonuclease II; Provisional

Probab=88.93  E-value=0.11  Score=45.26  Aligned_cols=37  Identities=14%  Similarity=0.072  Sum_probs=29.9

Q ss_pred             cCCCCCCCCeeeecCCCc-cc-ccCcceeeeccccccCC
Q 023627          107 ASVSEGSSGYARFMEPDE-LY-CSRLKIRYGISTRFVDQ  143 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d-Ly-gt~~~vR~rVrsyFt~s  143 (279)
                      ...|+-.-|||.|...++ || |.+.+||.||++||++.
T Consensus        27 ~~~~~~~n~VY~~~~~~~viYVGKAknLkkRv~sYf~~~   65 (138)
T PHA02598         27 IKCPNKKNVIYAIAVDDELVYIGKTKNLRKRIDYYRNSK   65 (138)
T ss_pred             cCCcccceEEEEEEeCCeEEEEeehhhHHHHHHHHhCcc
Confidence            345666779999994444 99 99999999999999853

>PHA02570 dexA exonuclease; Provisional

Probab=86.34  E-value=1.5  Score=40.67  Aligned_cols=47  Identities=17%  Similarity=0.188  Sum_probs=34.7

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHHHHHHHHhhCCC
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLG   62 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TLLatLA~~Fg~~   62 (279)
                      +.+|+||-|..|.   ..||++|||.+-|..- ....|..|. +++.++.+.
T Consensus         4 lMIDlETmG~~p~---AaIisIgAV~Fdp~~~-~g~tF~elV-~~~~~~k~d   50 (220)
T PHA02570          4 FIIDFETFGNTPD---GAVIDLAVIAFEHDPH-NPPTFEELV-SRGRRIKFD   50 (220)
T ss_pred             EEEEeeccCCCCC---ceEEEEEEEEecCCCC-ccccHHHHh-hcccccccc
Confidence            5799999999764   5899999999997543 468898885 344444443

>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A

Probab=82.31  E-value=1.1  Score=36.57  Aligned_cols=30  Identities=27%  Similarity=0.368  Sum_probs=17.4

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      +|||+||||.++..+  .|.=||...+-.+..
T Consensus         1 l~~DIET~Gl~~~~~--~i~liG~~~~~~~~~   30 (164)
T PF13482_consen    1 LFFDIETTGLSPDND--TIYLIGVADFDDDEI   30 (164)
T ss_dssp             --EEEEESS-GG-G-----EEEEEEE-ETTTT
T ss_pred             CcEEecCCCCCCCCC--CEEEEEEEEeCCCce
Confidence            589999999988663  466678777666554

...

>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily

Probab=81.16  E-value=2.1  Score=33.27  Aligned_cols=29  Identities=21%  Similarity=0.135  Sum_probs=22.6

Q ss_pred             EEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 023627           11 AFFDVETAFPNPPGQRIAILEFGAILVCPKT   41 (279)
Q Consensus        11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~   41 (279)
                      ++||+|||++++..  ..|++++.....+++
T Consensus         1 ~~~DiEt~~~~~~~--~~i~~i~~~~~~~~~   29 (96)
T cd06125           1 IAIDTEATGLDGAV--HEIIEIALADVNPED   29 (96)
T ss_pred             CEEEEECCCCCCCC--CcEEEEEEEEccCCC
Confidence            47999999988755  789999977653344

The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy

---

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	279
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-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 = 42.5 bits (99), Expect = 1e-04
 Identities = 49/266 (18%), Positives = 81/266 (30%), Gaps = 79/266 (29%)

Query: 35  IL--VC-PKTLEELQPYSTLL-----ASLATYFGLGQQTHRSLDDVRMNL---EVLKYCA 83
           +L  V   K          +L       +  +      TH SLD   M L   EV     
Sbjct: 249 VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308

Query: 84  TVLFLE-SGLPDIFTVNRWEMCSAASVSEGSSGYARFMEPDELYCSRL--KIRYGIST-R 139
             L      LP        E+ +                P     S +   IR G++T  
Sbjct: 309 KYLDCRPQDLPR-------EVLTTN--------------P--RRLSIIAESIRDGLATWD 345

Query: 140 FVDQAGRPRLSFVVDASQSLCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARL 199
                   +L+ ++++S     VL+  E   +K+F+           V   S + P   L
Sbjct: 346 NWKHVNCDKLTTIIESS---LNVLEPAEY--RKMFDRL--------SVFPPSAHIPTILL 392

Query: 200 RI--PTVVFGDVAQYATEMYR-----KEPSG------DIQKLEFVRFDAAELDSLLKPGT 246
            +    V+  DV     ++++     K+P         I  LE  +       +L +  +
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY-LEL-KVKLENEYALHR--S 448

Query: 247 FVDAF----------LSLDPYD-YVY 261
            VD +          L     D Y Y
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFY 474

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	279
2p1j_A	186	POLIII, DNA polymerase III POLC-type; structural g	99.33
2xri_A	224	ERI1 exoribonuclease 3; hydrolase, metal binding;	99.22
2gui_A	194	DNA polymerase III epsilon subunit; DNA polymerase	99.18
2gbz_A	194	Oligoribonuclease; ORN, deddh, structural genomics	99.16
1w0h_A	204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	99.15
3tr8_A	186	Oligoribonuclease; transcription, hydrolase; 2.50A	99.14
2f96_A	224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	99.13
3mxm_B	242	Three prime repair exonuclease 1; RNAse H-like fol	99.11
2igi_A	180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	99.1
1y97_A	238	Three prime repair exonuclease 2; TREX2, hydrolase	99.08
3v9w_A	235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	99.06
3cg7_A	308	CRN-4, cell death-related nuclease 4; hydrolase, a	99.02
1zbh_A	299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	98.99
3u3y_B	314	Three prime repair exonuclease 1; RNAse H fold, 3'	98.95
1wlj_A	189	Interferon stimulated gene 20KDA; exoribonuclease,	98.92
1zbu_A	349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	98.87
2qxf_A	482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	98.82
1yd6_A	99	UVRC; DNA binding protein; 2.00A {Bacillus caldote	98.47
1yd0_A	96	Uvrabc system protein C; DNA binding protein; 1.50	98.31
2wsh_A	143	Endonuclease II; GIY-YIG, hydrolase; 1.90A {Entero	96.52
4hec_A	190	Putative uncharacterized protein; ssgcid, structur	95.51
2kfn_A	605	Klenow fragment of DNA polymerase I; complex (poly	88.84

>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8}

Probab=99.33  E-value=1e-12  Score=108.73  Aligned_cols=72  Identities=32%  Similarity=0.461  Sum_probs=59.3

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------   51 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------   51 (279)
                      .+..+|+||+||||.++..  .+|+|||||++..|+++  ++|++|                                  
T Consensus        10 ~~~~~v~iD~ETTGl~~~~--~~IieIg~v~~~~g~i~--~~f~~lv~P~~~i~~~~~~i~GIt~~~l~~~~~~~~v~~~   85 (186)
T 2p1j_A           10 GDATFVVLDFETTGLDPQV--DEIIEIGAVKIQGGQIV--DEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVLPE   85 (186)
T ss_dssp             ---CEEEEEEEESCSCTTT--CCEEEEEEEEEETTEEE--EEEEEECBCSSCCCHHHHHHHCCCHHHHTTCCBHHHHHHH
T ss_pred             cCCCEEEEEEECCCCCCCC--CeEEEEEEEEEECCEEE--EEEEEEECcCCCCCHHHhhhcCCCHHHHhcCCCHHHHHHH
Confidence            4568999999999998765  68999999999988764  333322                                  


Q ss_pred             -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627           52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN   75 (279)
Q Consensus        52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t   75 (279)
                                                                             |.+|+.+||+. .+.||||+||++|
T Consensus        86 ~~~~l~~~~lv~hn~~fD~~~L~~~~~~~g~~~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~~gi~~~~~H~Al~Da~~t  165 (186)
T 2p1j_A           86 FLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLKLRSYSLDSVVEKLGLGPFRHHRALDDARVT  165 (186)
T ss_dssp             HHHHSSSCEEEETTHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHTCCSCCSHHHHHHHTTCCSTTCCHHHHHHHHH
T ss_pred             HHHHHCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCCEEeHHHHHHHHhhcCCCCHHHHHHHcCCCCCCCcCHHHHHHHH
Confidence                                                                   67799999998 7899999999999


Q ss_pred             HHHHHh
Q 023627           76 LEVLKY   81 (279)
Q Consensus        76 ~dVl~~   81 (279)
                      ++++..
T Consensus       166 ~~l~~~  171 (186)
T 2p1j_A          166 AQVFLR  171 (186)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999998

>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens}

Probab=99.22  E-value=1e-11  Score=105.94  Aligned_cols=33  Identities=18%  Similarity=0.265  Sum_probs=28.1

Q ss_pred             ceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      ..+|+||+||||+++...+.+|||||||++.++
T Consensus        31 ~~~vviD~ETTGl~~~~d~~~IieIgav~v~~~   63 (224)
T 2xri_A           31 HYFLVLDFEATCDKPQIHPQEIIEFPILKLNGR   63 (224)
T ss_dssp             SEEEEECCEECCCC-CCSSCCEEEEEEEEEETT
T ss_pred             CeEEEEEEEcCCCCCCCCCcceEEEEEEEEecC
Confidence            579999999999998764469999999999987

>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A*

Probab=99.18  E-value=2.2e-11  Score=100.35  Aligned_cols=36  Identities=28%  Similarity=0.243  Sum_probs=29.5

Q ss_pred             ceEEEEEeecCCCCCC---CCceeEEEEeeEEEecCcee
Q 023627            8 FEIAFFDVETAFPNPP---GQRIAILEFGAILVCPKTLE   43 (279)
Q Consensus         8 ~e~vffDvETT~p~~~---~~~~~ilEfgAI~Vcp~~l~   43 (279)
                      ..+|+||+||||+++.   +.+.+|||||||++..|.++
T Consensus         9 ~~~vviD~ETTGl~~~~~~~~~~~Iieig~v~~~~~~~~   47 (194)
T 2gui_A            9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLT   47 (194)
T ss_dssp             CEEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEEC
T ss_pred             CCEEEEEeeCCCCCCcccCCCCCEEEEEEEEEEECCeEe
Confidence            4689999999999872   12389999999999887663

>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV}

Probab=99.16  E-value=4.1e-11  Score=100.12  Aligned_cols=33  Identities=15%  Similarity=0.207  Sum_probs=27.5

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      .+..+|+||+||||+++..  .+|||||||+.-++
T Consensus         7 ~~~~~vviD~ETTGl~p~~--d~IieIgav~~~~~   39 (194)
T 2gbz_A            7 GNDRLIWIDLEMTGLDTDR--DSIIEIATIVTDAQ   39 (194)
T ss_dssp             -CCEEEEEEEEESCSCTTT--CCEEEEEEEEEETT
T ss_pred             CCCCEEEEEeECCCCCCCC--CccEEEEEEEEcCC
Confidence            4568999999999999865  89999999985544

>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5

Probab=99.15  E-value=3.5e-11  Score=99.32  Aligned_cols=35  Identities=23%  Similarity=0.406  Sum_probs=30.2

Q ss_pred             HHHHHHhhCCC-C-CccccchhhhccHHHHHhhhHHHHhhhc
Q 023627           52 LASLATYFGLG-Q-QTHRSLDDVRMNLEVLKYCATVLFLESG   91 (279)
Q Consensus        52 LatLA~~Fg~~-~-~~HRALdDar~t~dVl~~catvlllE~~   91 (279)
                      |.+|+.+||+. . ..||||+||++|++||..     ++++.
T Consensus       159 L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~-----l~~~~  195 (204)
T 1w0h_A          159 LTIMLEKLGMDYDGRPHCGLDDSKNIARIAVR-----MLQDG  195 (204)
T ss_dssp             HHHHHHHTTCCCCSCTTCHHHHHHHHHHHHHH-----HHHTT
T ss_pred             HHHHHHHcCCCCCCCccCcHHHHHHHHHHHHH-----HHHCC
Confidence            77789999998 4 479999999999999999     67654

>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii}

Probab=99.14  E-value=6.4e-11  Score=100.93  Aligned_cols=35  Identities=17%  Similarity=0.214  Sum_probs=29.7

Q ss_pred             CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEec
Q 023627            3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP   39 (279)
Q Consensus         3 ~~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp   39 (279)
                      |...+..+|+||+||||++|.+  .+|||||||++.+
T Consensus         4 ~~~~~~~~v~~D~ETTGL~p~~--d~IiEIgaV~~d~   38 (186)
T 3tr8_A            4 MDFSDDNLIWLDLEMTGLDPER--DRIIEIATIVTNS   38 (186)
T ss_dssp             CCCCTTCEEEEEEEESSSCTTT--CCEEEEEEEEECT
T ss_pred             CcCCCCcEEEEEEECCCCCCCC--CceEEEEEEEEcC
Confidence            4557789999999999999975  9999999995544

>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5

Probab=99.13  E-value=6.2e-11  Score=100.34  Aligned_cols=30  Identities=20%  Similarity=0.215  Sum_probs=27.2

Q ss_pred             HHHHHHhhCCC---CCccccchhhhccHHHHHh
Q 023627           52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKY   81 (279)
Q Consensus        52 LatLA~~Fg~~---~~~HRALdDar~t~dVl~~   81 (279)
                      |.+|+.+||+.   .+.||||+||++|++||..
T Consensus       176 L~~l~~~~gi~~~~~~~H~Al~Da~~ta~l~~~  208 (224)
T 2f96_A          176 LAKACQAAGMEFDNREAHSARYDTEKTAELFCG  208 (224)
T ss_dssp             HHHHHHHTTCCCCTTSCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcCCCCCCChHHHHHHHHHHHHH
Confidence            67888999997   3799999999999999999

>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A

Probab=99.11  E-value=4e-11  Score=104.39  Aligned_cols=32  Identities=16%  Similarity=0.173  Sum_probs=28.5

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      -.+||+||+||||+++..  .+|||||||+|..+
T Consensus        11 ~~~~vv~D~ETTGl~~~~--d~IiEIgav~v~~~   42 (242)
T 3mxm_B           11 MQTLIFLDLEATGLPSSR--PEVTELCLLAVHRR   42 (242)
T ss_dssp             CSEEEEEEEEESSCGGGC--CCEEEEEEEEEEHH
T ss_pred             cceEEEEEeecCCCCCCC--CeeEEEEEEEecCC
Confidence            467999999999998865  89999999999876

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A

Probab=99.10  E-value=1e-10  Score=95.30  Aligned_cols=33  Identities=15%  Similarity=0.289  Sum_probs=28.2

Q ss_pred             CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      .+..+|+||+||||+++..  .+|||+|||++.++
T Consensus         3 ~~~~~v~iD~ETTGl~~~~--~~IieIg~v~~~~~   35 (180)
T 2igi_A            3 NENNLIWIDLEMTGLDPER--DRIIEIATLVTDAN   35 (180)
T ss_dssp             GGGCEEEEEEEESSSCTTT--CCEEEEEEEEECTT
T ss_pred             CCCcEEEEEeeCCCCCCCC--CceEEEEEEEEcCC
Confidence            3567999999999998865  78999999988754

>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5

Probab=99.08  E-value=9.3e-11  Score=99.39  Aligned_cols=35  Identities=17%  Similarity=0.109  Sum_probs=29.2

Q ss_pred             CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627            4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK   40 (279)
Q Consensus         4 ~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~   40 (279)
                      ......+|+||+||||+++..  .+|||||||++.++
T Consensus         6 ~~~~~~~v~iD~ETTGl~~~~--~~IieIg~v~~~~~   40 (238)
T 1y97_A            6 APRAETFVFLDLEATGLPSVE--PEIAELSLFAVHRS   40 (238)
T ss_dssp             SCCCSEEEEEEEEESSCGGGC--CCEEEEEEEEEEHH
T ss_pred             CCccCeEEEEEeeCCCcCCCC--CcEEEEEEEEeccc
Confidence            344568999999999998654  79999999999865

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A

Probab=99.06  E-value=1.8e-10  Score=97.96  Aligned_cols=35  Identities=17%  Similarity=0.199  Sum_probs=30.3

Q ss_pred             HHHHHHhhCCC-C--CccccchhhhccHHHHHhhhHHHHhhhc
Q 023627           52 LASLATYFGLG-Q--QTHRSLDDVRMNLEVLKYCATVLFLESG   91 (279)
Q Consensus        52 LatLA~~Fg~~-~--~~HRALdDar~t~dVl~~catvlllE~~   91 (279)
                      |.+|+.+||+. .  +.||||+||++|++++..     ++++.
T Consensus       184 L~~l~~~~gi~~~~~~~H~Al~DA~~ta~l~~~-----l~~~l  221 (235)
T 3v9w_A          184 LSKACQTAGMDFDSTQAHSALYDTERTAVLFCE-----IVNRW  221 (235)
T ss_dssp             HHHHHHHHTCCCCTTTTTCHHHHHHHHHHHHHH-----HHHHH
T ss_pred             HHHHHHHcCCCCCCCCCcChHHHHHHHHHHHHH-----HHHHH
Confidence            77899999998 2  699999999999999999     55554

>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A

Probab=99.02  E-value=3.1e-10  Score=102.54  Aligned_cols=44  Identities=11%  Similarity=0.184  Sum_probs=32.0

Q ss_pred             ceEEEEEeecCCCCCCCC-ceeEEEEeeEEE--ecCceeeccchHHH
Q 023627            8 FEIAFFDVETAFPNPPGQ-RIAILEFGAILV--CPKTLEELQPYSTL   51 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~~-~~~ilEfgAI~V--cp~~l~e~~sf~TL   51 (279)
                      ..+|+||+||||.++... ..+|||||||+|  ..|++++.++|++|
T Consensus        19 ~~~vviD~ETTGl~~~~d~~~eIIEIgaV~vd~~~g~i~~~~~f~~l   65 (308)
T 3cg7_A           19 DTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKY   65 (308)
T ss_dssp             SEEEEEEEEECCBTTBCSCCCCEEEEEEEEEETTTTEEEEEEEEEEE
T ss_pred             CeEEEEEeecCCCCCCCCCCCCeEEEEEEEEEcCCCEEeeccceeeE
Confidence            579999999999987641 248999999999  45666432244444

>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens}

Probab=98.99  E-value=4.5e-10  Score=100.34  Aligned_cols=36  Identities=19%  Similarity=0.337  Sum_probs=30.4

Q ss_pred             HHHHHHhhCCC-C-CccccchhhhccHHHHHhhhHHHHhhhcc
Q 023627           52 LASLATYFGLG-Q-QTHRSLDDVRMNLEVLKYCATVLFLESGL   92 (279)
Q Consensus        52 LatLA~~Fg~~-~-~~HRALdDar~t~dVl~~catvlllE~~~   92 (279)
                      |.+|+.+||+. . ..||||+||++|++||..     ++++..
T Consensus       227 L~~l~~~~gi~~~g~~H~Al~DA~ata~l~~~-----l~~~~~  264 (299)
T 1zbh_A          227 LTIMLEKLGMDYDGRPNCGLDDSKNIARIAVR-----MLQDGC  264 (299)
T ss_dssp             HHHHHHHTTCCCCSCTTCHHHHHHHHHHHHHH-----HHHTTC
T ss_pred             HHHHHHHcCCCCCCCCCChHHHHHHHHHHHHH-----HHHhCC
Confidence            66788899998 4 479999999999999999     777653

>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B*

Probab=98.95  E-value=4.6e-10  Score=103.55  Aligned_cols=33  Identities=15%  Similarity=0.174  Sum_probs=29.0

Q ss_pred             CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 023627            7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKT   41 (279)
Q Consensus         7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~   41 (279)
                      -.+|||||+||||.++..  .+|||||||+|..+.
T Consensus        11 ~~tfVv~DlETTGL~~~~--d~IIEIgaV~v~~~~   43 (314)
T 3u3y_B           11 MQTLIFLDLEATGLPSSR--PEVTELCLLAVHRRA   43 (314)
T ss_dssp             CSEEEEEEEEESSCGGGC--CCEEEEEEEEEEHHH
T ss_pred             cCCEEEEEEECCCCCCCC--CeEEEEEEEEEECCc
Confidence            467999999999999865  899999999998763

>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5

Probab=98.92  E-value=1.5e-09  Score=90.15  Aligned_cols=30  Identities=27%  Similarity=0.419  Sum_probs=26.7

Q ss_pred             HHHHHHh-hCCC-CC---ccccchhhhccHHHHHh
Q 023627           52 LASLATY-FGLG-QQ---THRSLDDVRMNLEVLKY   81 (279)
Q Consensus        52 LatLA~~-Fg~~-~~---~HRALdDar~t~dVl~~   81 (279)
                      |.+|+.+ ||+. ..   .||||+||++|+++|..
T Consensus       130 L~~l~~~~lgi~~~~~~~~H~Al~Da~ata~l~~~  164 (189)
T 1wlj_A          130 LRVLSERLLHKSIQNSLLGHSSVEDARATMELYQI  164 (189)
T ss_dssp             HHHHHHHHTCCCCSCCTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCCCCCcCcHHHHHHHHHHHHH
Confidence            6778887 7998 44   89999999999999998

>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens}

Probab=98.87  E-value=1.4e-09  Score=100.52  Aligned_cols=36  Identities=22%  Similarity=0.381  Sum_probs=30.3

Q ss_pred             HHHHHHhhCCC-C-CccccchhhhccHHHHHhhhHHHHhhhcc
Q 023627           52 LASLATYFGLG-Q-QTHRSLDDVRMNLEVLKYCATVLFLESGL   92 (279)
Q Consensus        52 LatLA~~Fg~~-~-~~HRALdDar~t~dVl~~catvlllE~~~   92 (279)
                      |.+|+.+||+. . ..||||+||++|++||..     ++++..
T Consensus       277 L~~l~~~~gi~~~g~~HrAl~DA~ata~ll~~-----ll~~~~  314 (349)
T 1zbu_A          277 LTIMLEKLGMDYDGRPHCGLDDSKNIARIAVR-----MLQDGC  314 (349)
T ss_dssp             HHHHHHHTTCCCCSCTTCHHHHHHHHHHHHHH-----HHHTTC
T ss_pred             HHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHH-----HHHhcc
Confidence            66788899998 4 479999999999999999     776653

>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A*

Probab=98.82  E-value=4.1e-09  Score=101.64  Aligned_cols=36  Identities=22%  Similarity=0.143  Sum_probs=30.1

Q ss_pred             CCCceEEEEEeecCCCCCCCCceeEEEEeeEEEe-cCce
Q 023627            5 QDRFEIAFFDVETAFPNPPGQRIAILEFGAILVC-PKTL   42 (279)
Q Consensus         5 ~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vc-p~~l   42 (279)
                      ..+..||+||+||||.++..  .+|||||||++. .|.+
T Consensus         6 ~~~~~~vv~DlETTGl~p~~--d~IIEIgaV~vd~~g~i   42 (482)
T 2qxf_A            6 KQQSTFLFHDYETFGTHPAL--DRPAQFAAIRTDSEFNV   42 (482)
T ss_dssp             -CCCEEEEEEEEESSSCTTT--SCEEEEEEEEECTTSCB
T ss_pred             CCCCCEEEEEEECCCCCCCC--CeEEEEEEEEEECCCeE
Confidence            45678999999999999876  799999999998 4444

>1yd6_A UVRC; DNA binding protein; 2.00A {Bacillus caldotenax}

Probab=98.47  E-value=8e-09  Score=81.57  Aligned_cols=50  Identities=10%  Similarity=0.176  Sum_probs=43.0

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccc
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS  158 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~  158 (279)
                      ..+| ..||||.|.+.++  || |.+.|||.||++||+++ .++|+..||.-..+
T Consensus        10 ~~lP-~~pGVY~~~d~~g~vlYVGKAknLr~Rv~syf~~~-~~~k~~~m~~~~~~   62 (99)
T 1yd6_A           10 AVLP-EQPGCYLMKDKHGTVIYVGKAKSLKERVRSYFTGT-HDGKTQRLVEEIAD   62 (99)
T ss_dssp             HTCC-SSCEEEEEECSSCCEEEEEEESCHHHHHHGGGSSC-CCHHHHHHHHHCSE
T ss_pred             HhCC-CCCeEEEEEcCCCCEEEEecCcCHHHHHHHHcccC-CChHHHHHHHheeE
Confidence            4578 8999999999888  99 99999999999999998 78888877654433

>1yd0_A Uvrabc system protein C; DNA binding protein; 1.50A {Thermotoga maritima} PDB: 1ycz_A 1yd1_A 1yd4_A 1yd3_A 1yd2_A 1yd5_A

Probab=98.31  E-value=3e-08  Score=78.03  Aligned_cols=61  Identities=8%  Similarity=0.128  Sum_probs=46.9

Q ss_pred             cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecccc---------chHHHHHHHHHHHH
Q 023627          107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQ---------SLCTVLDACEVVAK  171 (279)
Q Consensus       107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~---------~v~~Vl~~Cd~~aq  171 (279)
                      ..+| ..||||.|.+ ++  || |.+.|||.||++||+++  .+|...|+.-..         .+++.|-.|.-|-+
T Consensus        10 ~~lP-~~pGVY~~~d-~g~vlYVGKAknLr~Rv~syf~~~--~~k~~~~~~~~~~i~~~~t~sE~eAlllE~~lIk~   82 (96)
T 1yd0_A           10 LLAP-EEPGVYIFKN-KGVPIYIGKAKRLSNRLRSYLNPQ--TEKVFRIGEEADELETIVVMNEREAFILEANLIKK   82 (96)
T ss_dssp             HHCC-SSCEEEEEEE-TTEEEEEEEESSHHHHHHGGGSCS--SHHHHHHHHHCSEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             HhCC-CCCeEEEEEC-CCeEEEEecCcCHHHHHHHHccCC--CHHHHHHHHhccEEEEEEECCHHHHHHHHHHHHHH
Confidence            4578 8999999999 77  99 99999999999999987  788877765443         34555555554443

>2wsh_A Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacteria phage T4}

Probab=96.52  E-value=0.00013  Score=61.85  Aligned_cols=41  Identities=10%  Similarity=0.087  Sum_probs=31.9

Q ss_pred             CCeeeecCCCc--cc-ccCcceeeeccccccCCC------CCccceeeecc
Q 023627          114 SGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA------GRPRLSFVVDA  155 (279)
Q Consensus       114 pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se------~RpR~~~mVdl  155 (279)
                      ||||.|.+ ++  || |.+.+||.||++||+.+.      ..||...||..
T Consensus        41 ~GVY~~~~-~g~ViYVGKAknLkkRv~sYf~~~~~~~~~~~~~Kt~~mv~~   90 (143)
T 2wsh_A           41 NVIYAIAI-NDELVYIGKTKNLRKRINYYRTAINRKDKTSDSTKSALIHSA   90 (143)
T ss_dssp             SEEEEEEE-TTEEEEEEEESCHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             ceEEEEEc-CCeEEEEEecccHhHHHHHhcCCCCcccccCCCHHHHHHHHH
Confidence            44999997 55  99 999999999999998652      46666656543

>4hec_A Putative uncharacterized protein; ssgcid, structural genomics, SEA structural genomics center for infectious disease, unknown; 1.80A {Mycobacterium tuberculosis}

Probab=95.51  E-value=0.022  Score=49.46  Aligned_cols=30  Identities=17%  Similarity=0.231  Sum_probs=22.1

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      -+|+|.|+|+- ..  ...||.+|+|--.++-.
T Consensus        24 r~FlDTEFt~d-~~--~~eLISIGlV~EdGrEF   53 (190)
T 4hec_A           24 RYFYDTEFIED-GH--TIELISIGVVAEDGREY   53 (190)
T ss_dssp             EEEEEEEEEEC-SS--CEEEEEEEEEETTSCEE
T ss_pred             EEEEeeeecCC-CC--CCCEEEEEEEcCCCCEE
Confidence            58999999982 22  37899999986554433

>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*

Probab=88.84  E-value=0.92  Score=44.29  Aligned_cols=26  Identities=15%  Similarity=0.120  Sum_probs=21.3

Q ss_pred             ceEEEEEeecCCCCCCCCceeEEEEeeE
Q 023627            8 FEIAFFDVETAFPNPPGQRIAILEFGAI   35 (279)
Q Consensus         8 ~e~vffDvETT~p~~~~~~~~ilEfgAI   35 (279)
                      .++++||+|||+.++..  ..|+++|+.
T Consensus        26 ~~~va~DtEttgl~~~~--~~iv~I~~~   51 (605)
T 2kfn_A           26 APVFAFDTETDSLDNIS--ANLVGLSFA   51 (605)
T ss_dssp             SSSEEEEEEESCSCTTT--CCEEEEEEE
T ss_pred             CCeEEEEEecCCCCccc--CceEEEEEE
Confidence            36799999999998754  579998866

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	279
d2igia1	180	Oligoribonuclease {Escherichia coli [TaxId: 562]}	99.43
d2guia1	174	N-terminal exonuclease domain of the epsilon subun	99.43
d1w0ha_	200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	99.4
d2f96a1	202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	99.38
d1y97a1	228	Three prime repair exonuclease 2, TREX2 {Human (Ho	99.23
d3b6oa1	226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	99.22
d2qxfa1	467	Exonuclease I {Escherichia coli K12 (Escherichia c	99.16
d1wlja_	173	Interferon-stimulated gene 20 kDa protein, ISG20 {	99.01
d1x9ma1	204	Exonuclease domain of T7 DNA polymerase {Bacteriop	87.8

>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Oligoribonuclease
species: Escherichia coli [TaxId: 562]

Probab=99.43  E-value=2.5e-14  Score=109.81  Aligned_cols=36  Identities=14%  Similarity=0.224  Sum_probs=31.2

Q ss_pred             CCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627            5 QDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus         5 ~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      .++..+||+|+||||++|..  ..|||||||++..+..
T Consensus         2 ~~~~~lv~lD~ETTGLdp~~--d~IIeIaaV~~d~~~~   37 (180)
T d2igia1           2 ANENNLIWIDLEMTGLDPER--DRIIEIATLVTDANLN   37 (180)
T ss_dssp             CGGGCEEEEEEEESSSCTTT--CCEEEEEEEEECTTCC
T ss_pred             CCCCCEEEEEEECCCCCCCC--CeEEEEEEEEEECCce
Confidence            45788999999999999977  8999999999877643

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III
species: Escherichia coli [TaxId: 562]

Probab=99.43  E-value=6.1e-14  Score=107.82  Aligned_cols=41  Identities=27%  Similarity=0.331  Sum_probs=33.5

Q ss_pred             EEEEEeecCCCCCCCC---ceeEEEEeeEEEecCceeeccchHHH
Q 023627           10 IAFFDVETAFPNPPGQ---RIAILEFGAILVCPKTLEELQPYSTL   51 (279)
Q Consensus        10 ~vffDvETT~p~~~~~---~~~ilEfgAI~Vcp~~l~e~~sf~TL   51 (279)
                      .||||+||||+++.+.   +.+|||||||++..+.+++ ++|+++
T Consensus         2 ~vv~D~ETTGl~~~~~~~~~d~IIeIg~v~~~~~~~~~-~~~~~~   45 (174)
T d2guia1           2 QIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTG-NNFHVY   45 (174)
T ss_dssp             EEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECS-CCEEEE
T ss_pred             EEEEEeeCCCCCcccccCCCCEEEEEEEEEEECCEEee-eEEEEE
Confidence            6899999999988642   3689999999999887643 577777

>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease ERI1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=8.6e-14  Score=110.49  Aligned_cols=35  Identities=23%  Similarity=0.406  Sum_probs=30.8

Q ss_pred             HHHHHHhhCCC-C-CccccchhhhccHHHHHhhhHHHHhhhc
Q 023627           52 LASLATYFGLG-Q-QTHRSLDDVRMNLEVLKYCATVLFLESG   91 (279)
Q Consensus        52 LatLA~~Fg~~-~-~~HRALdDar~t~dVl~~catvlllE~~   91 (279)
                      |.+|+.+||++ . +.||||+||++|++||++     ++.+-
T Consensus       155 L~~l~~~~gi~~~~~aH~Al~Da~~~a~v~~~-----ll~~g  191 (200)
T d1w0ha_         155 LTIMLEKLGMDYDGRPHCGLDDSKNIARIAVR-----MLQDG  191 (200)
T ss_dssp             HHHHHHHTTCCCCSCTTCHHHHHHHHHHHHHH-----HHHTT
T ss_pred             HHHHHHHcCCCCCCCCcChHHHHHHHHHHHHH-----HHHcC
Confidence            99999999998 3 569999999999999999     66543

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Ribonuclease T
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.38  E-value=5.2e-13  Score=103.80  Aligned_cols=35  Identities=17%  Similarity=0.180  Sum_probs=30.8

Q ss_pred             HHHHHHhhCCC---CCccccchhhhccHHHHHhhhHHHHhhhc
Q 023627           52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLFLESG   91 (279)
Q Consensus        52 LatLA~~Fg~~---~~~HRALdDar~t~dVl~~catvlllE~~   91 (279)
                      |..++.++|+.   .+.||||+||++|++||.+     ++++.
T Consensus       158 L~~~~~~~gi~~~~~~aH~Al~Da~~ta~i~~~-----l~~~~  195 (202)
T d2f96a1         158 LAKACQAAGMEFDNREAHSARYDTEKTAELFCG-----IVNRW  195 (202)
T ss_dssp             HHHHHHHTTCCCCTTSCCCHHHHHHHHHHHHHH-----HHHHH
T ss_pred             HHHHHHHcCCCCCCCCCCChHHHHHHHHHHHHH-----HHHHH
Confidence            99999999996   4569999999999999998     77664

>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Three prime repair exonuclease 2, TREX2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=2.8e-12  Score=105.00  Aligned_cols=37  Identities=19%  Similarity=0.141  Sum_probs=31.0

Q ss_pred             CCCCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEec
Q 023627            1 MDPRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP   39 (279)
Q Consensus         1 ~~~~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp   39 (279)
                      |-.+....+|||||+||||+++..  ..|||+|||.|..
T Consensus         1 ~~~~~~~~~~v~~D~ETTGl~~~~--~~Iieia~i~~~~   37 (228)
T d1y97a1           1 MSEAPRAETFVFLDLEATGLPSVE--PEIAELSLFAVHR   37 (228)
T ss_dssp             CCSSCCCSEEEEEEEEESSCGGGC--CCEEEEEEEEEEH
T ss_pred             CCCCCCCCEEEEEEEecCCcCCCC--CCeEEEEEEEEEC
Confidence            455666678999999999998765  7899999999864

>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Three prime repair exonuclease 1, TREX1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.22  E-value=2e-12  Score=106.00  Aligned_cols=32  Identities=22%  Similarity=0.289  Sum_probs=27.1

Q ss_pred             HHHHHH-hhCCC-CCccccchhhhccHHHHHhhh
Q 023627           52 LASLAT-YFGLG-QQTHRSLDDVRMNLEVLKYCA   83 (279)
Q Consensus        52 LatLA~-~Fg~~-~~~HRALdDar~t~dVl~~ca   83 (279)
                      |++|+. +||.. .+.||||+||++|++||++++
T Consensus       171 L~~l~~~~~g~~~~~aH~Al~D~~~~~~l~~~~~  204 (226)
T d3b6oa1         171 LGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKP  204 (226)
T ss_dssp             HHHHHHHHHSSCCSSTTSHHHHHHHHHHHHTSSH
T ss_pred             hHHHHHHHcCCCCCCCcChHHHHHHHHHHHHHHH
Confidence            666644 58998 889999999999999999944

>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease I
species: Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]

Probab=99.16  E-value=1.5e-11  Score=110.74  Aligned_cols=30  Identities=23%  Similarity=0.391  Sum_probs=26.0

Q ss_pred             HHHHHHhhCCC-CCccccchhhhccHHHHHh
Q 023627           52 LASLATYFGLG-QQTHRSLDDVRMNLEVLKY   81 (279)
Q Consensus        52 LatLA~~Fg~~-~~~HRALdDar~t~dVl~~   81 (279)
                      |..||..||+. ...|+||+||.+|++|++.
T Consensus       159 L~~la~~~gi~~~~aH~Al~D~~~t~~l~~~  189 (467)
T d2qxfa1         159 LEHLTKANGIEHSNAHDAMADVYATIAMAKL  189 (467)
T ss_dssp             HHHHHHHTTCCCC---CTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCccccccccCCHHHHHHHHHH
Confidence            89999999999 7899999999999999987

>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Interferon-stimulated gene 20 kDa protein, ISG20
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=9.2e-11  Score=91.02  Aligned_cols=32  Identities=16%  Similarity=0.093  Sum_probs=26.7

Q ss_pred             eEEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627            9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus         9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      ++|+||+||||+++..  ..+|+.+||....|..
T Consensus         1 ~~v~iD~EttGl~~~~--~~ii~~~~iv~~~g~~   32 (173)
T d1wlja_           1 EVVAMDCEMVGLGPHR--ESGLARCSLVNVHGAV   32 (173)
T ss_dssp             CEEEEEEEEEEETTTT--EEEEEEEEEECTTCCE
T ss_pred             CEEEEEEEcCCCCCCC--CcEEEEEEEEEecCeE
Confidence            5899999999998855  8899989987666654

>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of T7 DNA polymerase
species: Bacteriophage T7 [TaxId: 10760]

Probab=87.80  E-value=0.14  Score=39.25  Aligned_cols=31  Identities=6%  Similarity=-0.218  Sum_probs=23.1

Q ss_pred             EEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627           10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTL   42 (279)
Q Consensus        10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l   42 (279)
                      |++||+||+|+.+..  ..|.-+|+.-..-+..
T Consensus         1 il~~DIET~gl~~~~--~~I~ci~~~d~~~~~~   31 (204)
T d1x9ma1           1 MIVSDIEANALLESV--TKFHCGVIYDYSTAEY   31 (204)
T ss_dssp             CEEEEEEESSCGGGC--CCEEEEEEEETTTTEE
T ss_pred             CEEEEecCCCCCCCC--CEEEEEEEEECCCCeE
Confidence            689999999998876  4677787665444443