Psyllid ID: psy13232

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-
Protein Sequence
MDNIGNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVFSW
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEEEEcccccccEEEEEEccHHHHHHccHHHHHcccccccHHHHHcccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEEEEEEEEEEEcccccEEEEEccHHHHHHHHHHHHHHcccccHHHHHHcccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccEEEEcc
Coil and Loop (DISEMBL)
mdnignrpsntalSSMEQVKAYLQtqgtckcglYYNEEVLQNMNEWCVEhhnasgltdrvraSSVSIEEADKRLHQFVAKyvkpktapmvgeyhtskellkdsdhflvfsw
Flexible Loop (DISEMBL)
mdnignrpsntalSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKyvkpktapmvgeyhtskellkdsdHFLVFSW
Low Complexity Region (SEG)
MDNIGNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVFSW
Disordered region (IsUnstruct)
******************VKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRA**V*I**ADKRLHQFVAKYVKPKTAPMVGEYHT***LL****HFLV***
Disordered Region (DISOPRED)
MDNIGNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVFSW
Disordered Region (DISEMBL)
*********NTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVFSW
Disordered Region (DISPRO)
****GNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVFSW
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDNIGNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVFSW
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	111	2.2.26 [Sep-21-2011]
Q556Y2	190	Probable oligoribonucleas	yes	N/A	0.666	0.389	0.421	2e-11
A4J020	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.416	1e-10
Q2A5M3	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.416	1e-10
A7N9M1	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.416	1e-10
Q5NI61	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.416	1e-10
Q14JL3	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.416	1e-10
Q0BNX6	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.416	1e-10
A1AVF0	180	Oligoribonuclease OS=Ruth	yes	N/A	0.648	0.4	0.397	2e-09
A0Q414	178	Oligoribonuclease OS=Fran	yes	N/A	0.540	0.337	0.366	5e-09
Q47VZ4	181	Oligoribonuclease OS=Colw	yes	N/A	0.495	0.303	0.490	8e-09

>sp|Q556Y2|ORN_DICDI Probable oligoribonuclease OS=Dictyostelium discoideum GN=rexo2-1 PE=3 SV=1

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 50/76 (65%), Gaps = 2/76 (2%)

Query: 33  LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE 92
           ++ ++EVL+NMN+WC+EHH  SGLT+ VR S +S+EEA+K + +FV K+      P+ G 
Sbjct: 59  IHRSDEVLKNMNDWCIEHHGKSGLTEDVRNSKISLEEAEKIMLEFVRKHTDKGICPLAGN 118

Query: 93  --YHTSKELLKDSDHF 106
             +   + LLK+   F
Sbjct: 119 TVHEDRRFLLKEMPTF 134

3'-to-5' exoribonuclease specific for small oligoribonucleotides.
Dictyostelium discoideum (taxid: 44689)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|A4J020|ORN_FRATW Oligoribonuclease OS=Francisella tularensis subsp. tularensis (strain WY96-3418) GN=orn PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. tularensis (strain WY96-3418) (taxid: 418136)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q2A5M3|ORN_FRATH Oligoribonuclease OS=Francisella tularensis subsp. holarctica (strain LVS) GN=orn PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. holarctica (strain LVS) (taxid: 376619)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|A7N9M1|ORN_FRATF Oligoribonuclease OS=Francisella tularensis subsp. holarctica (strain FTNF002-00 / FTA) GN=orn PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. holarctica (strain FTNF002-00 / FTA) (taxid: 458234)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q5NI61|ORN_FRATT Oligoribonuclease OS=Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) GN=orn PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (taxid: 177416)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q14JL3|ORN_FRAT1 Oligoribonuclease OS=Francisella tularensis subsp. tularensis (strain FSC 198) GN=orn PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. tularensis (strain FSC 198) (taxid: 393115)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q0BNX6|ORN_FRATO Oligoribonuclease OS=Francisella tularensis subsp. holarctica (strain OSU18) GN=orn PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. holarctica (strain OSU18) (taxid: 393011)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|A1AVF0|ORN_RUTMC Oligoribonuclease OS=Ruthia magnifica subsp. Calyptogena magnifica GN=orn PE=3 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 19  VKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFV 78
           V+ ++  QG     ++ N+E+L NM++W  EHH +SGL  RVR SS+S ++A+ +  +F+
Sbjct: 34  VQLHIIAQGPSLV-IHQNDEILSNMDQWNTEHHTSSGLLRRVRESSLSCKQAEAQTLEFL 92

Query: 79  AKYVKPKTAPMVG 91
            KYV    +PM G
Sbjct: 93  KKYVHTGASPMCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Ruthia magnifica subsp. Calyptogena magnifica (taxid: 413404)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|A0Q414|ORN_FRATN Oligoribonuclease OS=Francisella tularensis subsp. novicida (strain U112) GN=orn PE=3 SV=1

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 44/60 (73%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            ++ ++E+L +MNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIHQSDEILNSMNEWCIKVHCETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Francisella tularensis subsp. novicida (strain U112) (taxid: 401614)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q47VZ4|ORN_COLP3 Oligoribonuclease OS=Colwellia psychrerythraea (strain 34H / ATCC BAA-681) GN=orn PE=3 SV=1

 Score = 58.9 bits (141), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 34/55 (61%)

Query: 37  EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
           ++VL NMN WC+EHH  SGLT R R S VS+  A K    FV ++V    +PM G
Sbjct: 52  DDVLDNMNPWCIEHHGKSGLTQRCRDSEVSLAHATKESLAFVQEWVPQGKSPMCG 106

3'-to-5' exoribonuclease specific for small oligoribonucleotides.

Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (taxid: 167879)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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	111
66822265	190	RNA exonuclease 2 [Dictyostelium discoid	0.666	0.389	0.421	8e-10
384251560	187	ribonuclease H-like protein, partial [Co	0.648	0.385	0.410	9e-10
330802757	187	hypothetical protein DICPUDRAFT_56059 [D	0.531	0.315	0.457	1e-09
390357728	222	PREDICTED: oligoribonuclease, mitochondr	0.576	0.288	0.430	2e-09
89255617	178	oligoribonuclease [Francisella tularensi	0.540	0.337	0.416	5e-09
56707385	178	oligoribonuclease [Francisella tularensi	0.540	0.337	0.416	6e-09
115314122	178	oligoribonuclease [Francisella tularensi	0.540	0.337	0.416	6e-09
424675325	178	oligoribonuclease [Francisella tularensi	0.540	0.337	0.416	6e-09
62263510	213	unknown protein [synthetic construct]	0.540	0.281	0.416	6e-09
254372051	178	oligoribonuclease [Francisella tularensi	0.540	0.337	0.416	1e-08

>gi|66822265|ref|XP_644487.1| RNA exonuclease 2 [Dictyostelium discoideum AX4] gi|66822817|ref|XP_644763.1| RNA exonuclease 2 [Dictyostelium discoideum AX4] gi|122057700|sp|Q556Y2.1|ORN_DICDI RecName: Full=Probable oligoribonuclease; AltName: Full=RNA exonuclease 2 homolog gi|60472610|gb|EAL70561.1| RNA exonuclease 2 [Dictyostelium discoideum AX4] gi|60472946|gb|EAL70895.1| RNA exonuclease 2 [Dictyostelium discoideum AX4]

 Score = 67.8 bits (164), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 50/76 (65%), Gaps = 2/76 (2%)

Query: 33  LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE 92
           ++ ++EVL+NMN+WC+EHH  SGLT+ VR S +S+EEA+K + +FV K+      P+ G 
Sbjct: 59  IHRSDEVLKNMNDWCIEHHGKSGLTEDVRNSKISLEEAEKIMLEFVRKHTDKGICPLAGN 118

Query: 93  --YHTSKELLKDSDHF 106
             +   + LLK+   F
Sbjct: 119 TVHEDRRFLLKEMPTF 134

Source: Dictyostelium discoideum AX4

Species: Dictyostelium discoideum

Genus: Dictyostelium

Order: Dictyosteliida

Superkingdom: Eukaryota

>gi|384251560|gb|EIE25037.1| ribonuclease H-like protein, partial [Coccomyxa subellipsoidea C-169]

 Score = 67.4 bits (163), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 30  KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPM 89
           +  +  +E VL +MN WC++HH ASGLT R R S+VSIE+A+++L +FV ++ +P  A +
Sbjct: 40  EIAIQQSEAVLASMNPWCIDHHGASGLTQRCRESTVSIEQAEEQLLEFVGRHTEPGEARL 99

Query: 90  VG-EYHTSKELLK 101
            G   H   + L+
Sbjct: 100 AGNSVHVDMQFLR 112

Source: Coccomyxa subellipsoidea C-169

Species: Coccomyxa subellipsoidea

Genus: Coccomyxa

Family: Coccomyxaceae

Class: Trebouxiophyceae

Phylum: Chlorophyta

Superkingdom: Eukaryota

>gi|330802757|ref|XP_003289380.1| hypothetical protein DICPUDRAFT_56059 [Dictyostelium purpureum] gi|325080536|gb|EGC34087.1| hypothetical protein DICPUDRAFT_56059 [Dictyostelium purpureum]

 Score = 67.4 bits (163), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 33  LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
           ++ + EVL++MN WC++HH  SGLTDRV+ S ++IEEA   +  F+ K+V  + AP+ G
Sbjct: 54  IHRSNEVLESMNSWCIDHHGKSGLTDRVKNSKITIEEAQLEMFNFIEKHVGKEQAPLAG 112

Source: Dictyostelium purpureum

Species: Dictyostelium purpureum

Genus: Dictyostelium

Order: Dictyosteliida

Superkingdom: Eukaryota

>gi|390357728|ref|XP_780396.2| PREDICTED: oligoribonuclease, mitochondrial-like [Strongylocentrotus purpuratus]

 Score = 66.2 bits (160), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 42/65 (64%), Gaps = 1/65 (1%)

Query: 37  EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG-EYHT 95
           +E+L  MN+WCV+HH ASGL D V+AS +++++A+  +  FV +Y  PK  P+ G   H 
Sbjct: 93  DEILDKMNDWCVQHHTASGLVDAVKASKITLQQAEYEMLSFVREYTYPKLCPLAGNSIHV 152

Query: 96  SKELL 100
            K  L
Sbjct: 153 DKTFL 157

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

>gi|89255617|ref|YP_512978.1| oligoribonuclease [Francisella tularensis subsp. holarctica LVS] gi|134302673|ref|YP_001122642.1| oligoribonuclease [Francisella tularensis subsp. tularensis WY96-3418] gi|156501565|ref|YP_001427630.1| oligoribonuclease [Francisella tularensis subsp. holarctica FTNF002-00] gi|187932223|ref|YP_001892208.1| oligoribonuclease [Francisella tularensis subsp. mediasiatica FSC147] gi|254367012|ref|ZP_04983048.1| oligoribonuclease [Francisella tularensis subsp. holarctica 257] gi|254368614|ref|ZP_04984630.1| oligoribonuclease [Francisella tularensis subsp. holarctica FSC022] gi|290953723|ref|ZP_06558344.1| oligoribonuclease [Francisella tularensis subsp. holarctica URFT1] gi|421752577|ref|ZP_16189599.1| oligoribonuclease [Francisella tularensis subsp. tularensis AS_713] gi|421754444|ref|ZP_16191416.1| oligoribonuclease [Francisella tularensis subsp. tularensis 831] gi|421758172|ref|ZP_16195029.1| oligoribonuclease [Francisella tularensis subsp. tularensis 80700103] gi|421760000|ref|ZP_16196824.1| oligoribonuclease [Francisella tularensis subsp. tularensis 70102010] gi|422938119|ref|YP_007011266.1| oligoribonuclease [Francisella tularensis subsp. holarctica FSC200] gi|423049929|ref|YP_007008363.1| oligoribonuclease [Francisella tularensis subsp. holarctica F92] gi|122501292|sp|Q2A5M3.1|ORN_FRATH RecName: Full=Oligoribonuclease gi|166216258|sp|A7N9M1.1|ORN_FRATF RecName: Full=Oligoribonuclease gi|166216260|sp|A4J020.1|ORN_FRATW RecName: Full=Oligoribonuclease gi|89143448|emb|CAJ78624.1| Oligoribonuclease [Francisella tularensis subsp. holarctica LVS] gi|134050450|gb|ABO47521.1| exonuclease [Francisella tularensis subsp. tularensis WY96-3418] gi|134252838|gb|EBA51932.1| oligoribonuclease [Francisella tularensis subsp. holarctica 257] gi|156252168|gb|ABU60674.1| oligoribonuclease [Francisella tularensis subsp. holarctica FTNF002-00] gi|157121517|gb|EDO65708.1| oligoribonuclease [Francisella tularensis subsp. holarctica FSC022] gi|187713132|gb|ACD31429.1| oligoribonuclease (3'->5' exoribonuclease) [Francisella tularensis subsp. mediasiatica FSC147] gi|407293270|gb|AFT92176.1| oligoribonuclease [Francisella tularensis subsp. holarctica FSC200] gi|409084616|gb|EKM84786.1| oligoribonuclease [Francisella tularensis subsp. tularensis 831] gi|409084795|gb|EKM84958.1| oligoribonuclease [Francisella tularensis subsp. tularensis AS_713] gi|409089917|gb|EKM89949.1| oligoribonuclease [Francisella tularensis subsp. tularensis 70102010] gi|409090256|gb|EKM90278.1| oligoribonuclease [Francisella tularensis subsp. tularensis 80700103] gi|421950651|gb|AFX69900.1| oligoribonuclease [Francisella tularensis subsp. holarctica F92]

 Score = 65.1 bits (157), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

Source: Francisella tularensis subsp. holarctica LVS

Species: Francisella tularensis

Genus: Francisella

Family: Francisellaceae

Order: Thiotrichales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|56707385|ref|YP_169281.1| oligoribonuclease [Francisella tularensis subsp. tularensis SCHU S4] gi|110669856|ref|YP_666413.1| oligoribonuclease [Francisella tularensis subsp. tularensis FSC198] gi|254370915|ref|ZP_04986920.1| oligoribonuclease [Francisella tularensis subsp. tularensis FSC033] gi|254874223|ref|ZP_05246933.1| oligoribonuclease [Francisella tularensis subsp. tularensis MA00-2987] gi|379716581|ref|YP_005304917.1| 3'-to-5' oligoribonuclease [Francisella tularensis subsp. tularensis TIGB03] gi|379725264|ref|YP_005317450.1| 3'-to-5' oligoribonuclease [Francisella tularensis subsp. tularensis TI0902] gi|385793989|ref|YP_005830395.1| oligoribonuclease [Francisella tularensis subsp. tularensis NE061598] gi|421754846|ref|ZP_16191808.1| oligoribonuclease [Francisella tularensis subsp. tularensis 80700075] gi|81820821|sp|Q5NI61.1|ORN_FRATT RecName: Full=Oligoribonuclease gi|123169637|sp|Q14JL3.1|ORN_FRAT1 RecName: Full=Oligoribonuclease gi|56603877|emb|CAG44861.1| Oligoribonuclease [Francisella tularensis subsp. tularensis SCHU S4] gi|110320189|emb|CAL08244.1| Oligoribonuclease [Francisella tularensis subsp. tularensis FSC198] gi|151569158|gb|EDN34812.1| oligoribonuclease [Francisella tularensis subsp. tularensis FSC033] gi|254840222|gb|EET18658.1| oligoribonuclease [Francisella tularensis subsp. tularensis MA00-2987] gi|282158524|gb|ADA77915.1| oligoribonuclease [Francisella tularensis subsp. tularensis NE061598] gi|377826713|gb|AFB79961.1| 3'-to-5' oligoribonuclease (orn) [Francisella tularensis subsp. tularensis TI0902] gi|377828258|gb|AFB78337.1| 3'-to-5' oligoribonuclease (orn) [Francisella tularensis subsp. tularensis TIGB03] gi|409089971|gb|EKM89999.1| oligoribonuclease [Francisella tularensis subsp. tularensis 80700075]

 Score = 65.1 bits (157), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

Source: Francisella tularensis subsp. tularensis SCHU S4

Species: Francisella tularensis

Genus: Francisella

Family: Francisellaceae

Order: Thiotrichales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|115314122|ref|YP_762845.1| oligoribonuclease [Francisella tularensis subsp. holarctica OSU18] gi|122325833|sp|Q0BNX6.1|ORN_FRATO RecName: Full=Oligoribonuclease gi|115129021|gb|ABI82208.1| oligoribonuclease [Francisella tularensis subsp. holarctica OSU18]

 Score = 65.1 bits (157), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

Source: Francisella tularensis subsp. holarctica OSU18

Species: Francisella tularensis

Genus: Francisella

Family: Francisellaceae

Order: Thiotrichales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|424675325|ref|ZP_18112232.1| oligoribonuclease [Francisella tularensis subsp. tularensis 70001275] gi|417434080|gb|EKT89052.1| oligoribonuclease [Francisella tularensis subsp. tularensis 70001275]

 Score = 65.1 bits (157), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

Source: Francisella tularensis subsp. tularensis 70001275

Species: Francisella tularensis

Genus: Francisella

Family: Francisellaceae

Order: Thiotrichales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi|62263510|gb|AAX78167.1| unknown protein [synthetic construct]

 Score = 64.7 bits (156), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 72  AIYQPDEVLANMNEWCIKTHTETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 131

Source: synthetic construct

Species: synthetic construct

Genus: N/A

Family: N/A

Order: N/A

Class: N/A

Phylum: N/A

>gi|254372051|ref|ZP_04987544.1| oligoribonuclease [Francisella tularensis subsp. novicida GA99-3549] gi|254375197|ref|ZP_04990677.1| oligoribonuclease [Francisella novicida GA99-3548] gi|385791990|ref|YP_005824966.1| hypothetical protein [Francisella cf. novicida Fx1] gi|151569782|gb|EDN35436.1| oligoribonuclease [Francisella novicida GA99-3549] gi|151572915|gb|EDN38569.1| oligoribonuclease [Francisella novicida GA99-3548] gi|328676136|gb|AEB27006.1| Oligoribonuclease [Francisella cf. novicida Fx1]

 Score = 63.9 bits (154), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 43/60 (71%)

Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            +Y  +EVL NMNEWC++ H  +GLT RV+ S +S E A++++ +F+ K+V  +++P+ G
Sbjct: 46  AIYQPDEVLANMNEWCIKTHAETGLTQRVKDSKISTEAAEQQILEFIRKFVPYQSSPLCG 105

Source: Francisella tularensis subsp. novicida GA99-3549

Species: Francisella novicida

Genus: Francisella

Family: Francisellaceae

Order: Thiotrichales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

---

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	111
DICTYBASE|DDB_G0273741	190	rexo2-2 "RNA exonuclease 2" [D	0.666	0.389	0.434	4.4e-13
DICTYBASE|DDB_G0273355	190	rexo2-1 "RNA exonuclease 2" [D	0.666	0.389	0.434	4.4e-13
TIGR_CMR|CPS_4379	181	CPS_4379 "oligoribonuclease" [	0.495	0.303	0.490	8.4e-10
FB|FBgn0039115	211	CG10214 [Drosophila melanogast	0.612	0.322	0.347	2.2e-09
UNIPROTKB|F1NGJ1	236	REXO2 "Uncharacterized protein	0.576	0.271	0.384	3.4e-09
UNIPROTKB|H0YGR4	192	REXO2 "Oligoribonuclease, mito	0.855	0.494	0.3	5.9e-09
MGI|MGI:1888981	237	Rexo2 "REX2, RNA exonuclease 2	0.639	0.299	0.356	7.7e-09
RGD|1304874	237	Rexo2 "REX2, RNA exonuclease 2	0.639	0.299	0.356	7.7e-09
UNIPROTKB|Q5U1X1	237	Rexo2 "Oligoribonuclease, mito	0.639	0.299	0.356	7.7e-09
UNIPROTKB|H0YG54	197	REXO2 "Oligoribonuclease, mito	0.576	0.324	0.353	9.7e-09

DICTYBASE|DDB_G0273741 rexo2-2 "RNA exonuclease 2" [Dictyostelium discoideum (taxid:44689)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 33/76 (43%), Positives = 50/76 (65%)

Query:    33 LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE 92
             ++ ++EVL+NMN+WC+EHH  SGLT+ VR S +S+EEA+K + +FV K+      P+ G 
Sbjct:    59 IHRSDEVLKNMNDWCIEHHGKSGLTEDVRNSKISLEEAEKIMLEFVRKHTDKGICPLAGN 118

Query:    93 -YHTSKE-LLKDSDHF 106
               H  +  LLK+   F
Sbjct:   119 TVHEDRRFLLKEMPTF 134

GO:0005622 "intracellular" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=IC

GO:0008408 "3'-5' exonuclease activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISS

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

DICTYBASE|DDB_G0273355 rexo2-1 "RNA exonuclease 2" [Dictyostelium discoideum (taxid:44689)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 33/76 (43%), Positives = 50/76 (65%)

Query:    33 LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE 92
             ++ ++EVL+NMN+WC+EHH  SGLT+ VR S +S+EEA+K + +FV K+      P+ G 
Sbjct:    59 IHRSDEVLKNMNDWCIEHHGKSGLTEDVRNSKISLEEAEKIMLEFVRKHTDKGICPLAGN 118

Query:    93 -YHTSKE-LLKDSDHF 106
               H  +  LLK+   F
Sbjct:   119 TVHEDRRFLLKEMPTF 134

GO:0005622 "intracellular" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=IC

GO:0008408 "3'-5' exonuclease activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISS

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

TIGR_CMR|CPS_4379 CPS_4379 "oligoribonuclease" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 27/55 (49%), Positives = 34/55 (61%)

Query:    37 EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
             ++VL NMN WC+EHH  SGLT R R S VS+  A K    FV ++V    +PM G
Sbjct:    52 DDVLDNMNPWCIEHHGKSGLTQRCRDSEVSLAHATKESLAFVQEWVPQGKSPMCG 106

GO:0000292 "RNA fragment catabolic process" evidence=ISS

GO:0008946 "oligonucleotidase activity" evidence=ISS

FB|FBgn0039115 CG10214 [Drosophila melanogaster (taxid:7227)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 24/69 (34%), Positives = 44/69 (63%)

Query:    23 LQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYV 82
             ++++G C   + + +EV  +MNEWC++HH  SGL DR ++S V++EEA   +  ++ K +
Sbjct:    69 VKSEGPC-FAINHPQEVYDSMNEWCMKHHYNSGLIDRCKSSDVNLEEASNLVLSYLEKNI 127

Query:    83 KPKTAPMVG 91
               +  P+ G
Sbjct:   128 PKRACPLGG 136

GO:0000175 "3'-5'-exoribonuclease activity" evidence=NAS

GO:0008946 "oligonucleotidase activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0004527 "exonuclease activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NGJ1 REXO2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 137 (53.3 bits), Expect = 3.4e-09, P = 3.4e-09
 Identities = 25/65 (38%), Positives = 38/65 (58%)

Query:    37 EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE-YHT 95
             +E+L +M+EWC EHH  SGLT  V+ S +S+++A+     FV +   P   P+ G   H 
Sbjct:    86 DELLDSMSEWCKEHHGKSGLTKAVKESKISLQQAEYEFLSFVRQQTPPGLCPLAGNSVHA 145

Query:    96 SKELL 100
              K+ L
Sbjct:   146 DKKFL 150

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

UNIPROTKB|H0YGR4 REXO2 "Oligoribonuclease, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 30/100 (30%), Positives = 52/100 (52%)

Query:     5 GNRPSNTALS---SMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVR 61
             G R    A++   SM Q   ++  +G     +   +E+L +M++WC EHH  SGLT  V+
Sbjct:     8 GVREGGAAMAAGESMAQRMVWVDLEGP-NLIIKQPDELLDSMSDWCKEHHGKSGLTKAVK 66

Query:    62 ASSVSIEEADKRLHQFVAKYVKPKTAPMVGE-YHTSKELL 100
              S++++++A+     FV +   P   P+ G   H  K+ L
Sbjct:    67 ESTITLQQAEYEFLSFVRQQTPPGLCPLAGNSVHEDKKFL 106

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

MGI|MGI:1888981 Rexo2 "REX2, RNA exonuclease 2 homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 134 (52.2 bits), Expect = 7.7e-09, P = 7.7e-09
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query:    37 EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE-YHT 95
             +E+L +M++WC EHH  SGLT  V+ S+V++++A+     FV +   P   P+ G   H 
Sbjct:    87 DELLDSMSDWCKEHHGKSGLTKAVKESTVTLQQAEYEFLSFVRQQTPPGLCPLAGNSVHA 146

Query:    96 SKELL-KDSDHFL 107
              K+ L K    F+
Sbjct:   147 DKKFLDKHMPQFM 159

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=ISA

GO:0008408 "3'-5' exonuclease activity" evidence=ISA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA

RGD|1304874 Rexo2 "REX2, RNA exonuclease 2 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 134 (52.2 bits), Expect = 7.7e-09, P = 7.7e-09
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query:    37 EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE-YHT 95
             +E+L +M++WC EHH  SGLT  V+ S+V++++A+     FV +   P   P+ G   H 
Sbjct:    87 DELLDSMSDWCKEHHGKSGLTKAVKESTVTLQQAEYEFLSFVRQQTPPGLCPLAGNSVHA 146

Query:    96 SKELL-KDSDHFL 107
              K+ L K    F+
Sbjct:   147 DKKFLDKHMPQFM 159

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005886 "plasma membrane" evidence=IEA;ISO

GO:0006139 "nucleobase-containing compound metabolic process" evidence=ISO

GO:0008408 "3'-5' exonuclease activity" evidence=IEA;ISO

UNIPROTKB|Q5U1X1 Rexo2 "Oligoribonuclease, mitochondrial" [Rattus norvegicus (taxid:10116)]

 Score = 134 (52.2 bits), Expect = 7.7e-09, P = 7.7e-09
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query:    37 EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE-YHT 95
             +E+L +M++WC EHH  SGLT  V+ S+V++++A+     FV +   P   P+ G   H 
Sbjct:    87 DELLDSMSDWCKEHHGKSGLTKAVKESTVTLQQAEYEFLSFVRQQTPPGLCPLAGNSVHA 146

Query:    96 SKELL-KDSDHFL 107
              K+ L K    F+
Sbjct:   147 DKKFLDKHMPQFM 159

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|H0YG54 REXO2 "Oligoribonuclease, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 23/65 (35%), Positives = 39/65 (60%)

Query:    37 EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE-YHT 95
             +E+L +M++WC EHH  SGLT  V+ S++++++A+     FV +   P   P+ G   H 
Sbjct:    47 DELLDSMSDWCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLAGNSVHE 106

Query:    96 SKELL 100
              K+ L
Sbjct:   107 DKKFL 111

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	111
cd06135	173	cd06135, Orn, DEDDh 3'-5' exonuclease domain of ol	4e-22
PRK05359	181	PRK05359, PRK05359, oligoribonuclease; Provisional	4e-20
COG1949	184	COG1949, Orn, Oligoribonuclease (3'->5' exoribonuc	2e-17

>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins

 Score = 84.9 bits (211), Expect = 4e-22
 Identities = 27/58 (46%), Positives = 40/58 (68%)

Query: 34 YYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
          +  +EVL  M+EWC E H  SGLT+RVRAS+V++ +A+  L +F+ KYV    +P+ G
Sbjct: 42 HQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEAELLEFIKKYVPKGKSPLAG 99

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. Length = 173

>gnl|CDD|235429 PRK05359, PRK05359, oligoribonuclease; Provisional

 Score = 79.8 bits (198), Expect = 4e-20
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 36  NEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
           ++E L  M+EW    H  SGL DRVRAS+VS  EA+ +  +F+ ++V    +P+ G
Sbjct: 48  SDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAEAEAQTLEFLKQWVPAGKSPLCG 103

Length = 181

>gnl|CDD|224860 COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]

 Score = 72.8 bits (179), Expect = 2e-17
 Identities = 23/59 (38%), Positives = 38/59 (64%)

Query: 33  LYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
           ++ ++E L  M+EW  E H  SGLT+RV+AS+V+  EA+ +   F+ K+V    +P+ G
Sbjct: 48  IHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEAEAEAQTLDFLKKWVPKGVSPICG 106

Length = 184

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	111
COG1949	184	Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA	100.0
KOG3242|consensus	208		100.0
PRK05359	181	oligoribonuclease; Provisional	99.87
cd06135	173	Orn DEDDh 3'-5' exonuclease domain of oligoribonuc	99.5
PRK09145	202	DNA polymerase III subunit epsilon; Validated	98.47
smart00479	169	EXOIII exonuclease domain in DNA-polymerase alpha	98.33
cd06131	167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	98.26
cd06127	159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	98.11
cd06138	183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	97.98
TIGR01406	225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	97.59
PRK06309	232	DNA polymerase III subunit epsilon; Validated	97.48
PRK06310	250	DNA polymerase III subunit epsilon; Validated	97.45
PRK05711	240	DNA polymerase III subunit epsilon; Provisional	97.42
cd06133	176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	97.32
PRK07740	244	hypothetical protein; Provisional	97.06
cd06144	152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	96.78
TIGR01298	200	RNaseT ribonuclease T. in gamma-subdivision Proteo	96.72
PRK09146	239	DNA polymerase III subunit epsilon; Validated	96.72
PRK07942	232	DNA polymerase III subunit epsilon; Provisional	96.71
PRK11779	476	sbcB exonuclease I; Provisional	96.69
TIGR00573	217	dnaq exonuclease, DNA polymerase III, epsilon subu	96.67
PRK06807	313	DNA polymerase III subunit epsilon; Validated	96.61
PRK05168	211	ribonuclease T; Provisional	96.59
cd06134	189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	96.56
cd06130	156	DNA_pol_III_epsilon_like an uncharacterized bacter	96.35
PRK08517	257	DNA polymerase III subunit epsilon; Provisional	96.17
PRK06063	313	DNA polymerase III subunit epsilon; Provisional	96.11
cd06145	150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	96.04
PRK07883	557	hypothetical protein; Validated	95.96
cd06137	161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	95.33
TIGR01405	1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	95.31
PF00929	164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	94.81
cd06149	157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	94.49
PRK09182	294	DNA polymerase III subunit epsilon; Validated	94.03
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	93.85
cd06136	177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	93.67
PRK06722	281	exonuclease; Provisional	93.55
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	93.08
PRK05601	377	DNA polymerase III subunit epsilon; Validated	91.97
PRK07748	207	sporulation inhibitor KapD; Provisional	88.93
PRK00448	1437	polC DNA polymerase III PolC; Validated	88.71
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	83.48
PRK07247	195	DNA polymerase III subunit epsilon; Validated	82.85
COG0847	243	DnaQ DNA polymerase III, epsilon subunit and relat	82.72

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

Probab=100.00  E-value=1.1e-43  Score=270.88  Aligned_cols=103  Identities=28%  Similarity=0.409  Sum_probs=99.6

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCC-------ceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQG-------TCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-------G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      .-||++|-++++-+    +|+||||.       ||++|||||+++|+.|||||+++|++|||++||++|.+|+++||.++
T Consensus        14 EMTGLd~~~drIIE----iA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~~~aE~~~   89 (184)
T COG1949          14 EMTGLDPERDRIIE----IATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEAEAEAQT   89 (184)
T ss_pred             eeccCCcCcceEEE----EEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccHHHHHHHH
Confidence            35899999999999    99999974       89999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV  108 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv  108 (111)
                      |+||++|||++.+|||||| +||||||.||||+|.
T Consensus        90 l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le  124 (184)
T COG1949          90 LDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLE  124 (184)
T ss_pred             HHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHH
Confidence            9999999999999999999 999999999999984

>KOG3242|consensus

Probab=100.00  E-value=3.5e-42  Score=265.49  Aligned_cols=102  Identities=28%  Similarity=0.480  Sum_probs=98.9

Q ss_pred             CCCCCCCccccccHhhhhhheeeCC-------ceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQG-------TCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~-------G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      -||++--++++-+    +||||||+       ||++|||||+++|++|+|||++||++|||+++|++|++|++|||+++|
T Consensus        35 MTGLdvekd~i~E----iacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~~aEnevl  110 (208)
T KOG3242|consen   35 MTGLDVEKDRIIE----IACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLADAENEVL  110 (208)
T ss_pred             ccccccccceeEE----EEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccHHHHHHHHH
Confidence            4899999999999    99999975       999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV  108 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv  108 (111)
                      +||++|+|+|.||||||| |+||+||.||||+++
T Consensus       111 ~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~  144 (208)
T KOG3242|consen  111 EYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLI  144 (208)
T ss_pred             HHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHH
Confidence            999999999999999999 999999999999975

>PRK05359 oligoribonuclease; Provisional

Probab=99.87  E-value=4e-22  Score=149.83  Aligned_cols=103  Identities=28%  Similarity=0.412  Sum_probs=96.1

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCC-------ceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQG-------TCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-------G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|.++.+.|    .++|++|+       ++.++|+++.+++..|++||+++|+.|||++++.+++.++++|..++
T Consensus        11 ETTGLdp~~d~Iie----IgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~e~~~~~   86 (181)
T PRK05359         11 EMTGLDPERDRIIE----IATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAEAEAQT   86 (181)
T ss_pred             ecCCCCCCCCeEEE----EEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHHHHHHHH
Confidence            36999999999999    88888864       57889999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV  108 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv  108 (111)
                      ++|++.+++.+.+|||||+ ++|+.||.++||++-
T Consensus        87 l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~  121 (181)
T PRK05359         87 LEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELE  121 (181)
T ss_pred             HHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhc
Confidence            9999999998899999999 999999999998754

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

Probab=99.50  E-value=6.5e-14  Score=103.67  Aligned_cols=102  Identities=34%  Similarity=0.583  Sum_probs=92.2

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|.++++.|    .+++.++++       +...|+++..+...+.+|+.++|..+|++++..++..++++|-.++
T Consensus         7 ETTGl~p~~d~Iie----IgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~~~   82 (173)
T cd06135           7 EMTGLDPEKDRILE----IACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEAEL   82 (173)
T ss_pred             ecCCCCCCCCeeEE----EEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHHHH
Confidence            36999999999999    788888663       5678888888888899999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      ++|+..++..+.++++||+ .+|+.||.++++++
T Consensus        83 ~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~  116 (173)
T cd06135          83 LEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPEL  116 (173)
T ss_pred             HHHHHHhcCCCCCceeecchhhCHHHHHHHHHHH
Confidence            9999999888889999999 99999999988754

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.

>PRK09145 DNA polymerase III subunit epsilon; Validated

Probab=98.47  E-value=3.4e-07  Score=68.88  Aligned_cols=86  Identities=22%  Similarity=0.303  Sum_probs=70.4

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|.++..-|    .+++.+|++       +...|+++    ..++++|++.|   |++++-.+...+.++|-.++
T Consensus        37 ETTGl~~~~d~Iie----IgaV~~~~~~~~~~~~f~~~i~p~----~~i~~~~~~ih---GIt~~~l~~~~~~~~vl~~~  105 (202)
T PRK09145         37 ETTGLDPRRAEIVS----IAAVKIRGNRILTSERLELLVRPP----QSLSAESIKIH---RLRHQDLEDGLSEEEALRQL  105 (202)
T ss_pred             ECCCCCCCCCceEE----EEEEEEECCEEeecCceEEEECCC----CCCCHhHhhhc---CcCHHHHhcCCCHHHHHHHH
Confidence            36899999999888    788887654       34456665    35889999998   68877777889999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      ++|++.      .+++|.. .+|+.||.+++
T Consensus       106 ~~~i~~------~~lv~hn~~fD~~fL~~~~  130 (202)
T PRK09145        106 LAFIGN------RPLVGYYLEFDVAMLNRYV  130 (202)
T ss_pred             HHHHcC------CeEEEeCHHHHHHHHHHHH
Confidence            999953      5799999 99999999875

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

Probab=98.33  E-value=1.1e-06  Score=61.98  Aligned_cols=90  Identities=18%  Similarity=0.261  Sum_probs=72.0

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ   76 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~   76 (111)
                      ..+|++|.+..+-+    .+++.++++     ++..|.+ .   ..+.++|++.|   |++++-.+...+.++|-+++.+
T Consensus         8 Ettg~~~~~~~Iie----ig~v~~~~~~~~~~f~~~v~p-~---~~i~~~~~~~~---Git~~~l~~~~~~~~~~~~~~~   76 (169)
T smart00479        8 ETTGLDPGKDEIIE----IAAVDVDGGRIIVVFDTYVKP-D---RPITDYATEIH---GITPEMLDDAPTFEEVLEELLE   76 (169)
T ss_pred             eCCCCCCCCCeEEE----EEEEEEECCEeEEEEEEEECC-C---CCCCHHHHHHh---CCCHHHHhCCCCHHHHHHHHHH
Confidence            35899998888888    677777775     3334444 2   46788999988   7998888889999999999999


Q ss_pred             HHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         77 FVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        77 fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      |+...     ..++||+ .+|..||.+++++.
T Consensus        77 ~l~~~-----~~v~~n~~~fD~~~L~~~~~~~  103 (169)
T smart00479       77 FLKGK-----ILVAGNALNFDLRFLKLEHPRL  103 (169)
T ss_pred             HhcCC-----EEEEeCCHHHhHHHHHHHHHHh
Confidence            99653     4689999 99999999988764

>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=98.26  E-value=1.1e-06  Score=63.16  Aligned_cols=88  Identities=16%  Similarity=0.204  Sum_probs=67.0

Q ss_pred             CCCCCCC-CccccccHhhhhhheee------CCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRP-SNTALSSMEQVKAYLQT------QGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p-~~~~l~s~~q~~~~lvT------d~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++| .++.+-|    .+++..      ++.+...|+++.    .+++.+++.|   |++++..+...+.++|..++
T Consensus         7 ETTGl~~~~~~~iie----ig~v~v~~~~~~~~~~~~~v~P~~----~i~~~~~~ih---GIt~e~l~~~~~~~~v~~~l   75 (167)
T cd06131           7 ETTGLDPREGHRIIE----IGCVELINRRLTGNTFHVYINPER----DIPEEAFKVH---GITDEFLADKPKFAEIADEF   75 (167)
T ss_pred             eCCCCCCCCCCeEEE----EEEEEEECCcEeccEEEEEECCCC----CCCHHHHHHh---CCCHHHHhcCCCHHHHHHHH
Confidence            4689999 4566666    555543      233455666553    4899999999   79999988889999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      ++|+.+      ++++|.. .+|+.||.+++++
T Consensus        76 ~~~l~~------~~lv~hn~~fD~~~l~~~~~~  102 (167)
T cd06131          76 LDFIRG------AELVIHNASFDVGFLNAELSL  102 (167)
T ss_pred             HHHHCC------CeEEEeChHHhHHHHHHHHHH
Confidence            999855      4577777 9999999988765

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

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

Probab=98.11  E-value=2.1e-06  Score=58.67  Aligned_cols=89  Identities=15%  Similarity=0.174  Sum_probs=68.3

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      ..||++|....+-+    .+++..+++      .+..|+++..    +.+.++..   +|++.+..++..+.++|..+++
T Consensus         6 Ettg~~~~~~~iie----i~~v~~~~~~~~~~~~~~~i~p~~~----~~~~~~~~---~gi~~~~~~~~~~~~~~~~~~~   74 (159)
T cd06127           6 ETTGLDPKKDRIIE----IGAVKVDGGIEIVERFETLVNPGRP----IPPEATAI---HGITDEMLADAPPFEEVLPEFL   74 (159)
T ss_pred             eCCCcCCCCCeEEE----EEEEEEECCcChhhhhheeeCcCCc----CCHhheec---cCCCHHHHhcCCCHHHHHHHHH
Confidence            35899998887777    677777654      3455655543    44445443   7889888889999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      +|+++      .+++|.. .+|+.||.+++++.
T Consensus        75 ~~l~~------~~~v~~n~~fD~~~l~~~~~~~  101 (159)
T cd06127          75 EFLGG------RVLVAHNASFDLRFLNRELRRL  101 (159)
T ss_pred             HHHCC------CEEEEeCcHhhHHHHHHHHHHh
Confidence            99876      5799999 99999999998753

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.

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

Probab=97.98  E-value=1.2e-05  Score=59.73  Aligned_cols=91  Identities=18%  Similarity=0.146  Sum_probs=62.8

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE~~l   74 (111)
                      ..||++|.++..-|    .+++..+++      ++..|+.++.+.  ..+.....   +|++++ +..++.+..+|-.++
T Consensus         6 ETTGl~~~~d~Iie----ig~v~v~~~~~~~~~~~~~v~p~~~~~--~~~~a~~i---hGIt~e~l~~~~~~~~~~l~~~   76 (183)
T cd06138           6 ETFGLNPSFDQILQ----FAAIRTDENFNEIEPFNIFCRLPPDVL--PSPEALIV---TGITPQQLLKEGLSEYEFIAKI   76 (183)
T ss_pred             ecCCCCCCCCceEE----EEEEEECCCCCCccceeEEEeCCCCCC--CCHHHHHH---hCCCHHHHHhcCCCHHHHHHHH
Confidence            36899999998888    788877765      444565554321  22223333   577655 555478999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      ++|+.+   ++..++|.|. .+|+.||.+.+
T Consensus        77 ~~~~~~---~~~~lVahn~~~FD~~fL~~~~  104 (183)
T cd06138          77 HRLFNT---PGTCIVGYNNIRFDDEFLRFAF  104 (183)
T ss_pred             HHHHcc---CCCcEEeeCchhhHHHHHHHHH
Confidence            999875   3334666798 99999998765

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.

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial

Probab=97.59  E-value=7.5e-05  Score=57.95  Aligned_cols=87  Identities=15%  Similarity=0.172  Sum_probs=66.4

Q ss_pred             CCCCCCCCc-cccccHhhhhhhe------eeCCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSN-TALSSMEQVKAYL------QTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~-~~l~s~~q~~~~l------vTd~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|.. ++.-+    .+++      +|.+.+...|++..    .+++.+.+.|   |++++-.+...+.++|-.++
T Consensus         8 ETTGl~p~~~d~IIE----Igav~~~~~~~~~~~f~~~i~P~~----~i~~~a~~vh---GIt~e~l~~~p~f~ev~~~f   76 (225)
T TIGR01406         8 ETTGLDPKGGHRIVE----IGAVELVNRMLTGDNFHVYVNPER----DMPAEAAKVH---GITDEFLADKPKFKEIADEF   76 (225)
T ss_pred             eCCCcCCCCCCeEEE----EEEEEEECCcEecceEEEEECcCC----CCCHHHHhcc---CCCHHHHhCCCCHHHHHHHH
Confidence            368999974 77777    5554      23345677777653    4788999998   99988888889999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDH  105 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP  105 (111)
                      ++|++.      ++|.|-- .+|+.||.+++.
T Consensus        77 ~~fi~~------~~lVaHNa~FD~~fL~~el~  102 (225)
T TIGR01406        77 LDFIGG------SELVIHNAAFDVGFLNYELE  102 (225)
T ss_pred             HHHhCC------CEEEEEecHHHHHHHHHHHH
Confidence            999854      4566655 999999987753

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.

>PRK06309 DNA polymerase III subunit epsilon; Validated

Probab=97.48  E-value=0.00018  Score=55.75  Aligned_cols=90  Identities=13%  Similarity=0.103  Sum_probs=65.1

Q ss_pred             CCCCCCCCccccccHhhhhhhe--eeCCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYL--QTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVA   79 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~l--vTd~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fik   79 (111)
                      ..||++|.+++.-|    .+++  .+.+-....|.+...    ..+-+...|   |++++-.+...+..+|-.++++|+.
T Consensus        10 ETTGl~~~~d~IIe----ig~v~~~~~~~f~~lv~P~~~----I~~~a~~Ih---GIt~e~v~~~p~f~ev~~~~~~fi~   78 (232)
T PRK06309         10 ETTGTQIDKDRIIE----IAAYNGVTSESFQTLVNPEIP----IPAEASKIH---GITTDEVADAPKFPEAYQKFIEFCG   78 (232)
T ss_pred             eCCCCCCCCCEEEE----EEEEcCccccEEEEEeCCCCC----CChhHHhhc---CCCHHHHhCCCCHHHHHHHHHHHHc
Confidence            46899999998888    4444  223334445554332    344566666   9998888888899999999999984


Q ss_pred             hhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         80 KYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        80 k~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .    ....+|-|+ .+|+.||.+.+.+
T Consensus        79 ~----~~~lVaHN~~~FD~~~L~~e~~r  102 (232)
T PRK06309         79 T----DNILVAHNNDAFDFPLLRKECRR  102 (232)
T ss_pred             C----CCEEEEeCCHHHHHHHHHHHHHH
Confidence            2    234678898 9999999988754

>PRK06310 DNA polymerase III subunit epsilon; Validated

Probab=97.45  E-value=0.00032  Score=55.20  Aligned_cols=89  Identities=11%  Similarity=0.079  Sum_probs=66.9

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ   76 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~   76 (111)
                      ..||++|..++.-+    .++|.++.+     .+..|++..    ...+-+...|   |++++..+...+.+++-.++++
T Consensus        15 ETTGl~~~~d~IIE----Ia~v~v~~~~~~~~~~~li~P~~----~I~~~a~~ih---gIt~e~v~~~p~~~ev~~~~~~   83 (250)
T PRK06310         15 ETTGLDVKKDRIIE----FAAIRFTFDEVIDSVEFLINPER----VVSAESQRIH---HISDAMLRDKPKIAEVFPQIKG   83 (250)
T ss_pred             eCCCCCCCCCeEEE----EEEEEEECCeEEEEEEEEECcCC----CCCHhhhhcc---CcCHHHHhCCCCHHHHHHHHHH
Confidence            46899999999888    777777543     333455442    2444555555   5888888888899999999999


Q ss_pred             HHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         77 FVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        77 fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      |+..     ..+|+|.+ .+|+.||.+.+++
T Consensus        84 fl~~-----~~~lvghn~~FD~~~L~~~~~r  109 (250)
T PRK06310         84 FFKE-----GDYIVGHSVGFDLQVLSQESER  109 (250)
T ss_pred             HhCC-----CCEEEEECHHHHHHHHHHHHHH
Confidence            9853     25799999 9999999988754

>PRK05711 DNA polymerase III subunit epsilon; Provisional

Probab=97.42  E-value=0.00023  Score=56.18  Aligned_cols=88  Identities=11%  Similarity=0.131  Sum_probs=67.5

Q ss_pred             CCCCCCCC-ccccccHhhhhhhee------eCCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPS-NTALSSMEQVKAYLQ------TQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~-~~~l~s~~q~~~~lv------Td~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|. +++.-|    .++|.      |.+.+...|++..    .+++.+.+.|   |++++....+.+.+++-.++
T Consensus        12 ETTGldp~~~drIIE----IGaV~v~~~~~~~~~f~~~i~P~~----~i~~~a~~VH---GIT~e~l~~~p~f~ev~~~f   80 (240)
T PRK05711         12 ETTGLNQREGHRIIE----IGAVELINRRLTGRNFHVYIKPDR----LVDPEALAVH---GITDEFLADKPTFAEVADEF   80 (240)
T ss_pred             eCCCcCCCCCCeEEE----EEEEEEECCEEeccEEEEEECcCC----cCCHHHhhhc---CCCHHHHcCCCCHHHHHHHH
Confidence            36899998 788888    55543      3344566676643    5889999998   99999888889999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      ++|++.      ++|+|-- .+|+.||.+++.+
T Consensus        81 ~~fi~~------~~lVaHNa~FD~~fL~~el~r  107 (240)
T PRK05711         81 LDFIRG------AELIIHNAPFDIGFMDYEFAL  107 (240)
T ss_pred             HHHhCC------CEEEEEccHHhHHHHHHHHHH
Confidence            999854      4566766 9999999987533

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

Probab=97.32  E-value=0.00048  Score=49.18  Aligned_cols=90  Identities=12%  Similarity=0.072  Sum_probs=64.3

Q ss_pred             CCCCCCCCc-----cccccHhhhhhheeeCC-c------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHH
Q psy13232          2 DNIGNRPSN-----TALSSMEQVKAYLQTQG-T------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEE   69 (111)
Q Consensus         2 ~~~~~~p~~-----~~l~s~~q~~~~lvTd~-G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~   69 (111)
                      ..+|+.|..     +.+-|    .+++..|+ +      ++..|+++..  ..+++++.+.   +|++.+-.++..+.++
T Consensus         7 Ettg~~~~~~~~~~~~Iie----Igav~v~~~~~~~~~~f~~~i~P~~~--~~i~~~~~~i---~gIt~e~l~~~~~~~~   77 (176)
T cd06133           7 EATCWEGNSKPDYPNEIIE----IGAVLVDVKTKEIIDTFSSYVKPVIN--PKLSDFCTEL---TGITQEDVDNAPSFPE   77 (176)
T ss_pred             eccccCCCCCCCCCcceEE----EEEEEEEcCCCeEEeeeeeeECCCcC--CchhHHHHHh---cCcCHHHHhcCCCHHH
Confidence            357888864     56666    55555443 3      3456665542  4678889888   6799888888899999


Q ss_pred             HHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhc
Q psy13232         70 ADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDS  103 (111)
Q Consensus        70 AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~ky  103 (111)
                      |-.++++|++...   ...+++|..+|.+||.++
T Consensus        78 vl~~~~~~l~~~~---~~~~v~~~~~d~~~l~~~  108 (176)
T cd06133          78 VLKEFLEWLGKNG---KYAFVTWGDWDLKDLLQN  108 (176)
T ss_pred             HHHHHHHHHHhCC---CeEEEeecHhhHHHHHHH
Confidence            9999999998863   357889996666666554

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

>PRK07740 hypothetical protein; Provisional

Probab=97.06  E-value=0.0011  Score=51.95  Aligned_cols=86  Identities=19%  Similarity=0.228  Sum_probs=64.7

Q ss_pred             CCCCCCCCc-cccccHhhhhhheeeCCcee------eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSN-TALSSMEQVKAYLQTQGTCK------CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~-~~l~s~~q~~~~lvTd~G~~------~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|+. +.+.|    .+++.+++|..      ..|+++.    .+.+.+++.   +|++++..+...+.++|-.++
T Consensus        67 ETTGl~p~~~deIIe----IgaV~~~~~~i~~~~f~~lv~P~~----~i~~~~~~l---tGIt~e~l~~ap~~~evl~~f  135 (244)
T PRK07740         67 ETTGFSPQQGDEILS----IGAVKTKGGEVETDTFYSLVKPKR----PIPEHILEL---TGITAEDVAFAPPLAEVLHRF  135 (244)
T ss_pred             eCCCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEEeCcCC----CCChhheec---cCCCHHHHhCCCCHHHHHHHH
Confidence            368999985 77777    78888887643      2444432    567777765   578877777788999999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      ++|+..      .+++|-. .+|+.||.+.+
T Consensus       136 ~~fi~~------~~lVahna~fD~~fL~~~~  160 (244)
T PRK07740        136 YAFIGA------GVLVAHHAGHDKAFLRHAL  160 (244)
T ss_pred             HHHhCC------CEEEEeCHHHHHHHHHHHH
Confidence            998753      4788988 99999998754

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

Probab=96.78  E-value=0.0019  Score=46.65  Aligned_cols=56  Identities=14%  Similarity=0.230  Sum_probs=45.8

Q ss_pred             hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .+.+++++.|   |++++-.+...+.++|-.++++|+..      ++|.|-. .+|+.||....|+
T Consensus        42 ~i~~~~~~ih---GIt~~~v~~a~~~~~~~~~l~~~l~~------~vlVgHn~~fD~~~L~~~~~~   98 (152)
T cd06144          42 PVTDYRTAVS---GIRPEHLKDAPDFEEVQKKVAELLKG------RILVGHALKNDLKVLKLDHPK   98 (152)
T ss_pred             CCCcccccCC---CCCHHHHcCCCCHHHHHHHHHHHhCC------CEEEEcCcHHHHHHhcCcCCC
Confidence            4778999887   88876666788999999999999842      5788877 9999999876664

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

>TIGR01298 RNaseT ribonuclease T

Probab=96.72  E-value=0.002  Score=48.95  Aligned_cols=94  Identities=21%  Similarity=0.150  Sum_probs=64.7

Q ss_pred             CCCCCCCCccccccHhhhhhheee--C--------CceeeeeecCHHHHhhccchhhhccccccchH-HHHhCCCCHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQT--Q--------GTCKCGLYYNEEVLQNMNEWCVEHHNASGLTD-RVRASSVSIEEA   70 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvT--d--------~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~-~vr~S~~s~~~A   70 (111)
                      ..||++|.++.+-|    .+++..  |        +.+...|+++..  ..+.....+.   .|+++ +......+.++|
T Consensus        16 ETTGl~~~~d~Iie----Igav~v~~~~~g~i~~~~~f~~~v~p~p~--~~i~~~a~~i---hGIt~~~~~~~~~~~~~~   86 (200)
T TIGR01298        16 ETGGFNAKTDALLE----IAAITLKMDEQGWLFPDTTLHFHVEPFEG--ANIQPEALEF---TGIDLDHPLRGAVSEYEA   86 (200)
T ss_pred             eCCCCCCCCCeEEE----EEEEEEEEcCCCcEeecceeEEEEcCCCC--CCCCHHHHHc---cCCChhhhhhcCcchHHH
Confidence            36899999998888    555543  2        223445554221  2344555555   47774 445567899999


Q ss_pred             HHHHHHHHHhhCC---CCCCcccCCc-HHhHHHHhhcc
Q psy13232         71 DKRLHQFVAKYVK---PKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        71 E~~ll~fikk~vp---~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      -.++++|+.+++.   .+.++|+|-- -+|.+||.+++
T Consensus        87 ~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~  124 (200)
T TIGR01298        87 LHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAV  124 (200)
T ss_pred             HHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHH
Confidence            9999999988864   2567888877 99999998865

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.

>PRK09146 DNA polymerase III subunit epsilon; Validated

Probab=96.72  E-value=0.0024  Score=50.21  Aligned_cols=87  Identities=15%  Similarity=0.113  Sum_probs=62.2

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCce-------eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGTC-------KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G~-------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      ..||++|.++..-|    .+++..++|-       ...|++..    ...+.+.+.|   |++++-.+...+.+++-.++
T Consensus        55 ETTGl~p~~d~Iie----Ig~v~v~~~~i~~~~~~~~li~P~~----~i~~~~~~Ih---GIt~e~l~~ap~~~evl~~l  123 (239)
T PRK09146         55 ETTGLDAEQDAIVS----IGLVPFTLQRIRCRQARHWVVKPRR----PLEEESVVIH---GITHSELQDAPDLERILDEL  123 (239)
T ss_pred             ECCCCCCCCCcEEE----EEEEEEECCeEeecceEEEEECCCC----CCChhhhhhc---CCCHHHHhCCCCHHHHHHHH
Confidence            36899999999888    7777776652       23344432    3566777776   56666666678999999999


Q ss_pred             HHHHHhhCCCCCCcccCCcHHhHHHHhhcc
Q psy13232         75 HQFVAKYVKPKTAPMVGEYHTSKELLKDSD  104 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS~~DR~FL~kym  104 (111)
                      ++|++.     ..++|.|-.+|+.||.+.+
T Consensus       124 ~~~~~~-----~~lVaHna~FD~~fL~~~l  148 (239)
T PRK09146        124 LEALAG-----KVVVVHYRRIERDFLDQAL  148 (239)
T ss_pred             HHHhCC-----CEEEEECHHHHHHHHHHHH
Confidence            998743     3355666699999998864

>PRK07942 DNA polymerase III subunit epsilon; Provisional

Probab=96.71  E-value=0.0035  Score=48.72  Aligned_cols=93  Identities=14%  Similarity=0.084  Sum_probs=65.1

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCC-c-----eeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQG-T-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEADKRL   74 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE~~l   74 (111)
                      ..||++|..+..-|    .+++..|. |     ....|.+..    .+.+-+.+.|   |++++ ++..+...+++=.++
T Consensus        14 ETTGl~p~~d~Iie----ig~v~v~~~g~~~~~~~~lv~P~~----~i~~~a~~Ih---GIt~e~l~~~g~~~~~vl~e~   82 (232)
T PRK07942         14 ETTGVDPETARIVT----AALVVVDADGEVVESREWLADPGV----EIPEEASAVH---GITTEYARAHGRPAAEVLAEI   82 (232)
T ss_pred             ccCCCCCCCCeeEE----EEEEEEeCCCccccceEEEECCCC----CCCHHHHHHh---CCCHHHHHhhCCCHHHHHHHH
Confidence            36899999988887    66666663 3     223344332    3677778776   56654 454477888999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +++|++++..+. +|+|-- .+|+.||.+.+.+
T Consensus        83 ~~~l~~~~~~~~-~lVahNa~FD~~fL~~~~~r  114 (232)
T PRK07942         83 ADALREAWARGV-PVVVFNAPYDLTVLDRELRR  114 (232)
T ss_pred             HHHHHHHhhcCC-EEEEeCcHhhHHHHHHHHHH
Confidence            999998874454 566655 9999999887643

>PRK11779 sbcB exonuclease I; Provisional

Probab=96.69  E-value=0.0024  Score=55.28  Aligned_cols=93  Identities=15%  Similarity=0.108  Sum_probs=64.0

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCce-------eeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGTC-------KCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEADKR   73 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G~-------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE~~   73 (111)
                      ..||++|..++..+    .++|.+|++.       +..+.++...+-.-.  ...   -+|++++ ++..++++.++-.+
T Consensus        14 ETTGLdP~~DrIIe----iAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~--a~~---IhGIT~e~l~~~g~~e~e~~~~   84 (476)
T PRK11779         14 ETFGANPALDRPAQ----FAGIRTDADLNIIGEPLVFYCKPADDYLPSPE--AVL---ITGITPQEALEKGLPEAEFAAR   84 (476)
T ss_pred             ECCCCCCCCCeeEE----EEEEEEeCCCceecceeEEEEcCCcCcCCCHH--HHH---HhCCCHHHHHhcCCCHHHHHHH
Confidence            36999999999999    8999888763       233444332332111  122   2578865 45678899999999


Q ss_pred             HHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         74 LHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        74 ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +.+|+..   ++.+.++-|+ .+|..||.+.+.+
T Consensus        85 i~~~l~~---~~~~lVGhNni~FD~eflr~~~~r  115 (476)
T PRK11779         85 IHAEFSQ---PGTCILGYNNIRFDDEVTRYIFYR  115 (476)
T ss_pred             HHHHHhc---CCCEEEEeCchhhcHHHHHHHHHh
Confidence            9999862   4556565688 9999999886643

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

Probab=96.67  E-value=0.0041  Score=47.54  Aligned_cols=88  Identities=11%  Similarity=0.140  Sum_probs=63.3

Q ss_pred             CCCCCCCCccccccHhhhhhhee-eCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQ-TQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lv-Td~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      ..||++|.++ .-|    .+++. .+++.     ...|.+.    ..+++-+...|   |++++-.+...+.+++-.++.
T Consensus        15 ETTGl~~~~~-IIe----Igav~v~~~~~~~~~f~~li~P~----~~i~~~a~~ih---GIt~e~l~~~p~~~ev~~~~~   82 (217)
T TIGR00573        15 ETTGLYAGHD-IIE----IGAVEIINRRITGNKFHTYIKPD----RPIDPDAIKIH---GITDDMLKDKPDFKEIAEDFA   82 (217)
T ss_pred             cCCCCCCCCC-EEE----EEEEEEECCCEeeeEEEEEECcC----CCCCHHHHhhc---CCCHHHHcCCCCHHHHHHHHH
Confidence            4689999888 666    56655 44432     2344433    35677777776   688777777889999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      +|++.      .++.|-. .+|+.||.+.+.++
T Consensus        83 ~~~~~------~~lVaHNa~FD~~fL~~~~~r~  109 (217)
T TIGR00573        83 DYIRG------AELVIHNASFDVGFLNYEFSKL  109 (217)
T ss_pred             HHhCC------CEEEEeccHHHHHHHHHHHHHh
Confidence            98853      4677777 99999999987653

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).

>PRK06807 DNA polymerase III subunit epsilon; Validated

Probab=96.61  E-value=0.0046  Score=50.58  Aligned_cols=87  Identities=15%  Similarity=0.153  Sum_probs=64.2

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .||++|..+.+-+    .+++..+.|     ++..|.+..    .+.+.+++.|   |++++..+...+.++|-.++++|
T Consensus        17 TTGl~p~~~eIIE----IgaV~v~~g~i~~~f~~lVkP~~----~I~~~a~~ih---GIT~e~l~~~~~~~evl~~f~~f   85 (313)
T PRK06807         17 TTGFNPYNDKIIQ----VAAVKYRNHELVDQFVSYVNPER----PIPDRITSLT---GITNYRVSDAPTIEEVLPLFLAF   85 (313)
T ss_pred             CCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECcCC----CCCHhhhccC---CCCHHHHhCCCCHHHHHHHHHHH
Confidence            5899998888777    666666665     233455432    4677777664   68888888888999999999999


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +...      +|.|.- .+|++||.+.+.+
T Consensus        86 l~~~------~lVaHNa~FD~~fL~~~~~~  109 (313)
T PRK06807         86 LHTN------VIVAHNASFDMRFLKSNVNM  109 (313)
T ss_pred             HcCC------eEEEEcHHHHHHHHHHHHHH
Confidence            8643      355555 9999999987644

>PRK05168 ribonuclease T; Provisional

Probab=96.59  E-value=0.0021  Score=49.19  Aligned_cols=94  Identities=20%  Similarity=0.185  Sum_probs=66.1

Q ss_pred             CCCCCCCCccccccHhhhhhheee--C--------CceeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQT--Q--------GTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEA   70 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvT--d--------~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~A   70 (111)
                      ..||++|.+++.-|    .+++..  |        +-+...|.+++.  ....+-+++.|   |++++ ..+..++.++|
T Consensus        25 ETTGl~~~~d~Iie----IgaV~v~~d~~g~i~~~~~f~~lv~P~~~--~~i~~~~~~ih---GIt~e~~~~~~~~~~~~   95 (211)
T PRK05168         25 ETAGFNAKTDALLE----IAAVTLKMDEQGWLYPDETLHFHVEPFEG--ANLEPEALAFN---GIDPDNPLRGAVSEKEA   95 (211)
T ss_pred             eCCCCCCCCCEEEE----EeEEEEEecCCCcEeccceEEEEECCCCC--CCCCHHHHhhc---CCCchhhhhcCCChHHH
Confidence            36899999988888    444432  2        223344555322  13566677665   66754 45667899999


Q ss_pred             HHHHHHHHHhhCCC---CCCcccCCc-HHhHHHHhhcc
Q psy13232         71 DKRLHQFVAKYVKP---KTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        71 E~~ll~fikk~vp~---~~~pLaGNS-~~DR~FL~kym  104 (111)
                      -.++++|+.+++..   +.++++|=- .+|..||.+++
T Consensus        96 l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~  133 (211)
T PRK05168         96 LHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAA  133 (211)
T ss_pred             HHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHH
Confidence            99999999988642   346888888 99999998865

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

Probab=96.56  E-value=0.0025  Score=47.86  Aligned_cols=94  Identities=22%  Similarity=0.210  Sum_probs=65.0

Q ss_pred             CCCCCCCCccccccHhhhhhheeeC----------CceeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQ----------GTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEA   70 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd----------~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~A   70 (111)
                      ..||++|.+++.-|    .+++..+          +.+...|.++++  ....+...+.|   |++++ ..+..+..+++
T Consensus        13 ETTGl~~~~d~Iie----igav~v~~~~~~~i~~~~~f~~lv~P~~~--~~i~~~~~~ih---GIt~~~~~~~~~~~~~~   83 (189)
T cd06134          13 ETGGFNPQTDALLE----IAAVTLEMDEQGNLYPDETFHFHILPFEG--ANLDPAALEFN---GIDPFHPFRFAVDEKEA   83 (189)
T ss_pred             cCCCCCCCCCeEEE----EEEEEEEECCCCceeccceEEEEEcCCCC--CCCCHHHHhhc---CCCchhhhccccchHHH
Confidence            46999999999888    5555332          223344554322  24556666665   56654 35567888889


Q ss_pred             HHHHHHHHHhhCCC---CCCcccCCc-HHhHHHHhhcc
Q psy13232         71 DKRLHQFVAKYVKP---KTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        71 E~~ll~fikk~vp~---~~~pLaGNS-~~DR~FL~kym  104 (111)
                      -.++++||.+++..   +.++|+|=- .+|+.||.+++
T Consensus        84 ~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~  121 (189)
T cd06134          84 LKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAV  121 (189)
T ss_pred             HHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHH
Confidence            99999999988742   346888877 99999999875

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.

>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=96.35  E-value=0.0071  Score=42.42  Aligned_cols=56  Identities=13%  Similarity=0.207  Sum_probs=44.5

Q ss_pred             hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .+.+-+++.   +|++.+-.+...+.++|-+++++|+.+      .++.|.. .+|+.||.+++.+
T Consensus        42 ~~~~~~~~i---~GIt~e~l~~~~~~~~v~~~l~~~l~~------~~lv~hn~~fD~~~l~~~~~~   98 (156)
T cd06130          42 RFDPFNIAI---HGITPEDVADAPTFPEVWPEIKPFLGG------SLVVAHNASFDRSVLRAALEA   98 (156)
T ss_pred             CCChhhccc---cCcCHHHHhcCCCHHHHHHHHHHHhCC------CEEEEeChHHhHHHHHHHHHH
Confidence            556666655   578877766777899999999999865      5789999 9999999987755

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

>PRK08517 DNA polymerase III subunit epsilon; Provisional

Probab=96.17  E-value=0.015  Score=46.34  Aligned_cols=86  Identities=13%  Similarity=0.174  Sum_probs=64.0

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .+|++|.++..-|    .+++..++|-     ...|.++     .+.+.+++.   .|++++-.....+.++|-.++++|
T Consensus        77 TTG~~~~~~~IIE----IGAv~v~~g~i~~~f~~~v~p~-----~ip~~~~~i---tGIt~e~l~~ap~~~evl~~f~~f  144 (257)
T PRK08517         77 TNGSKPKKHQIIE----IGAVKVKNGEIIDRFESFVKAK-----EVPEYITEL---TGITYEDLENAPSLKEVLEEFRLF  144 (257)
T ss_pred             CCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECCC-----CCChhhhhh---cCcCHHHHcCCCCHHHHHHHHHHH
Confidence            5899999888777    6777666552     2345543     456677766   578877766788999999999999


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +..      ++++|.. .+|..||.+++.+
T Consensus       145 l~~------~v~VaHNa~FD~~fL~~~l~r  168 (257)
T PRK08517        145 LGD------SVFVAHNVNFDYNFISRSLEE  168 (257)
T ss_pred             HCC------CeEEEECHHHHHHHHHHHHHH
Confidence            854      4678888 9999999876543

>PRK06063 DNA polymerase III subunit epsilon; Provisional

Probab=96.11  E-value=0.0043  Score=50.56  Aligned_cols=86  Identities=15%  Similarity=0.150  Sum_probs=61.2

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCC-c-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQG-T-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      ..||++|..+..-|    .+++..+. |     +...|.+.      .+...+..|   |++++-.+...+.+++-.++.
T Consensus        23 ETTGl~p~~d~IIe----Igav~v~~~g~i~~~~~~lv~P~------~~~~~~~Ih---GIt~e~l~~ap~f~ev~~~l~   89 (313)
T PRK06063         23 ETSGFRPGQARIIS----LAVLGLDADGNVEQSVVTLLNPG------VDPGPTHVH---GLTAEMLEGQPQFADIAGEVA   89 (313)
T ss_pred             ECCCCCCCCCEEEE----EEEEEEECCceeeeEEEEEECcC------CCCCCeecC---CCCHHHHhCCCCHHHHHHHHH
Confidence            36899999888888    77777653 3     11233332      345666666   899888778788999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +|++.      .+|+|-- .+|+.||.+.+.+
T Consensus        90 ~~l~~------~~lVaHNa~FD~~fL~~~~~r  115 (313)
T PRK06063         90 ELLRG------RTLVAHNVAFDYSFLAAEAER  115 (313)
T ss_pred             HHcCC------CEEEEeCHHHHHHHHHHHHHH
Confidence            99842      3455555 9999999987643

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

Probab=96.04  E-value=0.011  Score=42.89  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=46.9

Q ss_pred             eeeecCHHHHhhccchhhhccccccchHHHHhCC-CCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         31 CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASS-VSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        31 ~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~-~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      -.|+++.    ...++.++.   +|++++-.+.. .+.++|..++++|+++     .++|+|.. .+|.+||....|+
T Consensus        32 ~lv~P~~----~i~~~~t~i---tGIt~~~l~~a~~~~~~v~~~~~~fl~~-----~~vlVgHn~~fD~~fL~~~~~~   97 (150)
T cd06145          32 ELVKPDG----EIVDYNTRF---SGITEEMLENVTTTLEDVQKKLLSLISP-----DTILVGHSLENDLKALKLIHPR   97 (150)
T ss_pred             EeECCCC----ccchhccCc---CCCCHHHhccCCCCHHHHHHHHHHHhCC-----CCEEEEcChHHHHHHhhccCCC
Confidence            3455543    355555555   78996554444 6999999999999962     36899999 9999999876654

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.

>PRK07883 hypothetical protein; Validated

Probab=95.96  E-value=0.016  Score=50.80  Aligned_cols=85  Identities=16%  Similarity=0.218  Sum_probs=64.8

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .||++|.++.+-+    .+++..++|-     ...|.+.    ..+.+-++..|   |++++..+...+.++|-.++++|
T Consensus        24 TTGl~p~~~~IIE----IgaV~v~~g~iv~~f~~lV~P~----~~i~~~~~~it---GIt~e~l~~ap~~~evl~~f~~f   92 (557)
T PRK07883         24 TTGGSPAGDAITE----IGAVKVRGGEVLGEFATLVNPG----RPIPPFITVLT---GITTAMVAGAPPIEEVLPAFLEF   92 (557)
T ss_pred             cCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECCC----CCCChhHHhhc---CCCHHHHhCCCCHHHHHHHHHHH
Confidence            6899999888888    7777776652     2344443    24566677664   68888888889999999999999


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      +..      ++++|.. .+|+.||.+.+
T Consensus        93 l~~------~~lVaHNa~FD~~fL~~~~  114 (557)
T PRK07883         93 ARG------AVLVAHNAPFDIGFLRAAA  114 (557)
T ss_pred             hcC------CEEEEeCcHHHHHHHHHHH
Confidence            863      5788977 99999998764

>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=95.33  E-value=0.02  Score=41.77  Aligned_cols=87  Identities=13%  Similarity=0.178  Sum_probs=55.5

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce---eeeeecCHHHHhhccchhhhccccccchHHHHhCCCC-------HHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC---KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVS-------IEEADK   72 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~---~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s-------~~~AE~   72 (111)
                      .||++|.++.+-+    .+++.-.+|-   +..|.++    ..+.++.++.|   |++++-.+...+       .++|..
T Consensus         7 ttGl~~~~d~ii~----Ig~V~v~~g~i~~~~~v~P~----~~i~~~~~~i~---GIt~~~l~~a~~~~~~~~~~~~~~~   75 (161)
T cd06137           7 MVGLADGDSEVVR----ISAVDVLTGEVLIDSLVRPS----VRVTDWRTRFS---GVTPADLEEAAKAGKTIFGWEAARA   75 (161)
T ss_pred             eeeEcCCCCEEEE----EEEEEcCCCeEEEeccccCC----CCCCccceecc---CCCHHHHhhhhhcCCccccHHHHHH
Confidence            5899998888777    5555553332   2223332    34567777664   666554333222       358888


Q ss_pred             HHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccc
Q psy13232         73 RLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDH  105 (111)
Q Consensus        73 ~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP  105 (111)
                      ++++|++.     .++|.|-. .+|.+||....|
T Consensus        76 ~~~~~i~~-----~~vlVgHn~~fD~~fL~~~~~  104 (161)
T cd06137          76 ALWKFIDP-----DTILVGHSLQNDLDALRMIHT  104 (161)
T ss_pred             HHHHhcCC-----CcEEEeccHHHHHHHHhCcCC
Confidence            88888742     36899999 999999986544

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

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

Probab=95.31  E-value=0.033  Score=53.24  Aligned_cols=87  Identities=13%  Similarity=0.180  Sum_probs=65.7

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCcee-----eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTCK-----CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~-----~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .||++|.++.+-+    .+++..+.|-.     ..|. |.   ....+.+++   -+|++++..++..+.++|-.++++|
T Consensus       199 TTGL~~~~d~IIE----IGAVkv~~g~iid~f~~~V~-P~---~~I~~~~~~---ltGIT~e~L~~ap~~~evl~~f~~f  267 (1213)
T TIGR01405       199 TTGLSPQYDEIIE----FGAVKVKNGRIIDKFQFFIK-PH---EPLSAFVTE---LTGITQDMLENAPEIEEVLEKFKEF  267 (1213)
T ss_pred             ecCCCCCCCeEEE----EEEEEEECCeEEEEEEEEEC-CC---CCCCHHHHH---HhCCCHHHHhCCCCHHHHHHHHHHH
Confidence            5899999999888    77777776622     2343 32   234555555   4688988888899999999999999


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      ++.      ++|+|-. .+|..||.+.+.+
T Consensus       268 l~~------~iLVaHNa~FD~~fL~~~~~r  291 (1213)
T TIGR01405       268 FKD------SILVAHNASFDIGFLNTNFEK  291 (1213)
T ss_pred             hCC------CeEEEEChHHHHHHHHHHHHH
Confidence            853      5677777 9999999987654

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

>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=94.81  E-value=0.02  Score=38.86  Aligned_cols=94  Identities=17%  Similarity=0.236  Sum_probs=64.8

Q ss_pred             CCCCCCCccccccHhhhhhheeeCC-c------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQG-T------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~-G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      .+|++|.+...-|    .+++..+. .      ++..|.+..  -..+++|+++.|+   ++.+-.+...+..+|-.++.
T Consensus         7 ttg~~~~~~~iie----ig~v~~~~~~~~~~~~~~~~i~p~~--~~~i~~~~~~~~g---It~~~l~~~~~~~~~~~~~~   77 (164)
T PF00929_consen    7 TTGLDPRQDEIIE----IGAVKVDDDENEEVESFNSLIRPEE--PPKISPWATKVHG---ITQEDLEDAPSFEEALDEFE   77 (164)
T ss_dssp             ESSSTTTTCTEEE----EEEEEEETTTTEEEEEEEEEBEHSS--HCSSEHHHHHHHH---HCHHHHHCHCEHHHHHHHHH
T ss_pred             cCCCCCCCCeEEE----EEEEEeeCCccccceeeeecccccc--cccCCHHHeeecC---CcccccccCCcHHHHHHhhh
Confidence            4788887777776    44444433 2      233343333  2579999999885   66666667778999999999


Q ss_pred             HHHHhh---CCCCCCcccCCc-HHhHHHHhhccc
Q psy13232         76 QFVAKY---VKPKTAPMVGEY-HTSKELLKDSDH  105 (111)
Q Consensus        76 ~fikk~---vp~~~~pLaGNS-~~DR~FL~kymP  105 (111)
                      +|+++.   +..+....+|.. ..+++++.+.+|
T Consensus        78 ~~~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~  111 (164)
T PF00929_consen   78 EFLKKNDILVGHNASFDIGFLRREDKRFLGKPIP  111 (164)
T ss_dssp             HHHHHHTEEEETTCCHEEESSHHHHHHHHHHHHH
T ss_pred             hhhhcccccccccccchhhHHHHhhhhccccccc
Confidence            999853   224456677778 888888777665

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 ....

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

Probab=94.49  E-value=0.091  Score=38.38  Aligned_cols=88  Identities=15%  Similarity=0.151  Sum_probs=58.9

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCcee---eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTCK---CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVA   79 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~---~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fik   79 (111)
                      -||++|.+.. .  +..++.+|...|-.   ..|.++    ..+.+|.++.   +|++++-.+...+.++|..++++|++
T Consensus         7 ttGl~~~~~~-~--~i~~i~~v~~~g~~~~~~lv~P~----~~i~~~~~~i---~GIt~~~l~~a~~~~~v~~~l~~~l~   76 (157)
T cd06149           7 MVGTGPGGRE-S--ELARCSIVNYHGDVLYDKYIRPE----GPVTDYRTRW---SGIRRQHLVNATPFAVAQKEILKILK   76 (157)
T ss_pred             eccccCCCCe-E--EEEEEEEEeCCCCEEEEEeECCC----CccCccceEC---CCCCHHHHhcCCCHHHHHHHHHHHcC
Confidence            5899997511 1  22234444423322   223333    2356777766   58887776778999999999999984


Q ss_pred             hhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         80 KYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        80 k~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .      ++|.|=+ .+|-.||....|.
T Consensus        77 ~------~vlV~Hn~~~D~~~l~~~~~~   98 (157)
T cd06149          77 G------KVVVGHAIHNDFKALKYFHPK   98 (157)
T ss_pred             C------CEEEEeCcHHHHHHhcccCCC
Confidence            3      5799999 9999999987443

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

>PRK09182 DNA polymerase III subunit epsilon; Validated

Probab=94.03  E-value=0.032  Score=45.38  Aligned_cols=88  Identities=9%  Similarity=0.071  Sum_probs=51.3

Q ss_pred             CCCCCCCCccccccHhhhhhheeeC---Cce--------eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQ---GTC--------KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEA   70 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd---~G~--------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~A   70 (111)
                      ..||++|..+...+    .++|..+   .|-        ...+. |.   ..+.+.++..   +|++++-....-...  
T Consensus        45 ETTGLd~~~d~IIE----Ig~V~v~~~~~g~i~~v~~~~~~lv~-P~---~~I~~~~t~I---hGIt~e~v~~~~~~~--  111 (294)
T PRK09182         45 ETTGLDPRKDEIIE----IGMVAFEYDDDGRIGDVLDTFGGLQQ-PS---RPIPPEITRL---TGITDEMVAGQTIDP--  111 (294)
T ss_pred             eCCCCCCCCCeEEE----EEEEEEEecCCCceeeeeeEEEEEeC-CC---CCCCHHHHHh---cCCCHHHHhcCCCcH--
Confidence            36899999998888    6666654   231        11222 22   1244555555   467766544432221  


Q ss_pred             HHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhccccc
Q psy13232         71 DKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFL  107 (111)
Q Consensus        71 E~~ll~fikk~vp~~~~pLaGNS~~DR~FL~kymP~l  107 (111)
                       ..+.+|++.    ....+|=|..+||.||.+++|.+
T Consensus       112 -~~l~~fl~~----~~vlVAHNA~FD~~fL~~~~~~~  143 (294)
T PRK09182        112 -AAVDALIAP----ADLIIAHNAGFDRPFLERFSPVF  143 (294)
T ss_pred             -HHHHHHhcC----CCEEEEeCHHHHHHHHHHHHHhc
Confidence             246666653    22234556699999999987653

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

Probab=93.85  E-value=0.13  Score=46.84  Aligned_cols=86  Identities=12%  Similarity=0.185  Sum_probs=61.8

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ   76 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~   76 (111)
                      ..||++|.++.+-+    .+++..++|     +...|.+..    .+.+-+++.   +|++++-.+...+.+++-.++.+
T Consensus         8 ETTG~~~~~~~IIe----ig~v~v~~~~i~~~f~~~v~P~~----~i~~~~~~l---tGIt~e~l~~ap~~~ev~~~l~~   76 (850)
T TIGR01407         8 ETTGTQLSFDKIIQ----IGIVVVEDGEIVDTFHTDVNPNE----PIPPFIQEL---TGISDNMLQQAPYFSQVAQEIYD   76 (850)
T ss_pred             ECCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEeCCCC----CCChhhhhh---cCcCHHHHhCCCCHHHHHHHHHH
Confidence            36899999888777    666666554     233444432    456666655   57776666667889999999999


Q ss_pred             HHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         77 FVAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        77 fikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      |+.      .++++|-. .+|+.||.+++
T Consensus        77 ~l~------~~~~VahN~~fD~~fL~~~~   99 (850)
T TIGR01407        77 LLE------DGIFVAHNVHFDLNFLAKAL   99 (850)
T ss_pred             HhC------CCEEEEeCcHHHHHHHHHHH
Confidence            984      24688877 99999999864

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.

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

Probab=93.67  E-value=0.16  Score=37.64  Aligned_cols=90  Identities=10%  Similarity=0.159  Sum_probs=55.3

Q ss_pred             CCCCCC-CCccccccHhhhhhheeeCCc------------------eeeeeecCHHHHhhccchhhhccccccchHHHHh
Q psy13232          2 DNIGNR-PSNTALSSMEQVKAYLQTQGT------------------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRA   62 (111)
Q Consensus         2 ~~~~~~-p~~~~l~s~~q~~~~lvTd~G------------------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~   62 (111)
                      ..||++ |.++..-|    .+++..++|                  +...|.+..    .+.+-.++.|   |++++-..
T Consensus         7 ETTGl~~~~~d~Iie----i~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~----~I~~~a~~Ih---GIt~e~l~   75 (177)
T cd06136           7 ETTGLPKHNRPEITE----LCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR----AISPGASEIT---GLSNDLLE   75 (177)
T ss_pred             ecCCCCCCCCCceEE----EEEEEEecccccccccccccccceeeeeeEEeCCCC----cCChhHHHHh---CcCHHHHh
Confidence            369999 68888888    666665543                  233444431    3444445554   66644443


Q ss_pred             CCCCH-HHHHHHHHHHHHhhCCCCCCcccC-Cc-HHhHHHHhhcc
Q psy13232         63 SSVSI-EEADKRLHQFVAKYVKPKTAPMVG-EY-HTSKELLKDSD  104 (111)
Q Consensus        63 S~~s~-~~AE~~ll~fikk~vp~~~~pLaG-NS-~~DR~FL~kym  104 (111)
                      ..-+. +++.+.+.+|+...  .+.++|+| |. .+|.+||.+.+
T Consensus        76 ~~~~~~~~~~~~l~~f~~~~--~~~~~lVaHNa~~FD~~fL~~~~  118 (177)
T cd06136          76 HKAPFDSDTANLIKLFLRRQ--PKPICLVAHNGNRFDFPILRSEL  118 (177)
T ss_pred             cCCCccHHHHHHHHHHHHhc--CCCCEEEEcCCcccCHHHHHHHH
Confidence            33343 35667777887754  33456666 87 89999998765

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

>PRK06722 exonuclease; Provisional

Probab=93.55  E-value=0.21  Score=40.69  Aligned_cols=54  Identities=11%  Similarity=0.155  Sum_probs=44.1

Q ss_pred             hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhc
Q psy13232         42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDS  103 (111)
Q Consensus        42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~ky  103 (111)
                      ...++|++.|   |++++-.....+.++|=.++++|+..     ..++|.|..+|++||.+.
T Consensus        55 ~I~~~i~~LT---GIT~emV~~AP~f~eVl~ef~~fig~-----~~lvahna~FD~~FL~~~  108 (281)
T PRK06722         55 RLTRHTTKLT---GITKKDLIGVEKFPQIIEKFIQFIGE-----DSIFVTWGKEDYRFLSHD  108 (281)
T ss_pred             cCCHhHhhhc---CCCHHHHcCCCCHHHHHHHHHHHHCC-----CcEEEEEeHHHHHHHHHH
Confidence            5678898876   77877777788999999999999853     347888997799999984

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

Probab=93.08  E-value=0.2  Score=46.23  Aligned_cols=86  Identities=13%  Similarity=0.213  Sum_probs=61.8

Q ss_pred             CCCCCCCCc-cccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          2 DNIGNRPSN-TALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         2 ~~~~~~p~~-~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      ..||++|.. +.+-+    .+++..++|     +...|++.    ..+.+.+++.|   |++++-.+...+.++|-.++.
T Consensus        11 ETTG~~p~~~d~IIe----igav~v~~~~i~~~f~~~v~P~----~~i~~~~~~lt---GIt~~~l~~ap~f~ev~~~l~   79 (928)
T PRK08074         11 ETTGNSPKKGDKIIQ----IAAVVVEDGEILERFSSFVNPE----RPIPPFITELT---GISEEMVKQAPLFEDVAPEIV   79 (928)
T ss_pred             eCCCCCCCCCCcEEE----EEEEEEECCEEEEEEEEEECcC----CCCCHHHhhcC---CCCHHHHhcCCCHHHHHHHHH
Confidence            368999875 55666    556555554     33345543    24667777664   688777777889999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      +|++      .++++|-. .+|+.||.+.+
T Consensus        80 ~~l~------~~~~VaHN~~FD~~fL~~~~  103 (928)
T PRK08074         80 ELLE------GAYFVAHNVHFDLNFLNEEL  103 (928)
T ss_pred             HHhC------CCeEEEEChHHHHHHHHHHH
Confidence            9984      35788866 99999998854

>PRK05601 DNA polymerase III subunit epsilon; Validated

Probab=91.97  E-value=0.15  Score=43.47  Aligned_cols=84  Identities=14%  Similarity=0.160  Sum_probs=59.8

Q ss_pred             CCCCCCCCccccccHhhhhhheeeC-Cc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQ-GT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd-~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      ..||++|+.+.+-|    .++|..+ +|     +...|.++...    ..+    | =.||+++-.+...+.+++-.+++
T Consensus        54 ETTGLdp~~drIIe----IgAV~i~~~g~ive~f~tLVnP~~~~----~p~----~-LHGIT~e~La~AP~f~eVl~el~  120 (377)
T PRK05601         54 QTSGIHPSTSRLIT----IDAVTLTADGEEVEHFHAVLNPGEDP----GPF----H-LHGLSAEEFAQGKRFSQILKPLD  120 (377)
T ss_pred             ECCCCCCCCCeEEE----EEEEEEEcCCEEEEEEEEEECcCCCC----CCc----c-ccCCCHHHHhcCCCHHHHHHHHH
Confidence            36899999998888    6566433 33     33445544311    111    2 57999999999999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      +||+..      +|.|-- .+|..||.+.+
T Consensus       121 ~fL~g~------vLVaHNA~FD~~FL~~e~  144 (377)
T PRK05601        121 RLIDGR------TLILHNAPRTWGFIVSEA  144 (377)
T ss_pred             HHhCCC------EEEEECcHHHHHHHHHHH
Confidence            999753      455555 99999998854

>PRK07748 sporulation inhibitor KapD; Provisional

Probab=88.93  E-value=0.46  Score=35.92  Aligned_cols=56  Identities=20%  Similarity=0.299  Sum_probs=43.3

Q ss_pred             hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhcc
Q psy13232         42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSD  104 (111)
Q Consensus        42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~kym  104 (111)
                      ...+.|++.|   |++++-.+...+.++|-.++++|+...    ...+++|+.+|.+||.+..
T Consensus        57 ~i~~~~~~lt---GIt~~~l~~ap~~~evl~~f~~~~~~~----~~~iv~~~~fD~~fL~~~~  112 (207)
T PRK07748         57 SLTERCKSFL---GITQEDVDKGISFEELVEKLAEYDKRC----KPTIVTWGNMDMKVLKHNC  112 (207)
T ss_pred             ccChhhhhhc---CcCHHHHccCCCHHHHHHHHHHHhCcC----CeEEEEECHHHHHHHHHHH
Confidence            4677888776   778776677899999999999988542    3467788888999997654

>PRK00448 polC DNA polymerase III PolC; Validated

Probab=88.71  E-value=0.74  Score=45.06  Aligned_cols=88  Identities=14%  Similarity=0.171  Sum_probs=57.5

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .||++|..+..-+    .+++..+.|.     +..|.+.    ....+.+++.|   |++++......++++|-.++++|
T Consensus       428 TTGL~~~~deIIE----IgAV~V~~G~iie~F~~~V~P~----~~I~~~~~~LT---GIT~e~L~~aps~~EaL~~f~~f  496 (1437)
T PRK00448        428 TTGLSAVYDEIIE----IGAVKIKNGEIIDKFEFFIKPG----HPLSAFTTELT---GITDDMVKDAPSIEEVLPKFKEF  496 (1437)
T ss_pred             hcCCCCchhhhhe----eeeEEEeCCeEeeeEEEEECCC----CCCCHHHHHHh---CCCHHHHcCCCCHHHHHHHHHHH
Confidence            4788888776666    3444445442     2233322    12345555554   88888887889999999999988


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      +.     + +++.|-. .+|..||.+.+.++
T Consensus       497 ig-----g-~vLVAHNa~FD~~fL~~~l~rl  521 (1437)
T PRK00448        497 CG-----D-SILVAHNASFDVGFINTNYEKL  521 (1437)
T ss_pred             hC-----C-CEEEEeCccccHHHHHHHHHHc
Confidence            74     3 3455555 99999998765554

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

Probab=83.48  E-value=2.2  Score=39.22  Aligned_cols=84  Identities=13%  Similarity=0.266  Sum_probs=57.6

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ   76 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~   76 (111)
                      ..||++|. +.+-+    .+++..++|-     ...|.+.    ..+.+-++..   +|++++-.+...+.++|-.++++
T Consensus        15 ETTGl~~~-d~IIe----IgaV~v~~g~i~~~f~~lv~P~----~~i~~~~~~l---tGIt~e~l~~ap~~~ev~~~~~~   82 (820)
T PRK07246         15 EATGAGPN-ASIIQ----VGIVIIEGGEIIDSYTTDVNPH----EPLDEHIKHL---TGITDQQLAQAPDFSQVARHIYD   82 (820)
T ss_pred             ecCCcCCC-CeEEE----EEEEEEECCEEEEEEEEEeCcC----CCCCHhHhhc---CCCCHHHHhcCCCHHHHHHHHHH
Confidence            35899884 55555    4555444442     2224332    2455666655   57887777778899999999999


Q ss_pred             HHHhhCCCCCCcccCCc-HHhHHHHhhc
Q psy13232         77 FVAKYVKPKTAPMVGEY-HTSKELLKDS  103 (111)
Q Consensus        77 fikk~vp~~~~pLaGNS-~~DR~FL~ky  103 (111)
                      |+.      .++++|-. .+|+.||.+.
T Consensus        83 ~l~------~~~lVaHN~~FD~~fL~~~  104 (820)
T PRK07246         83 LIE------DCIFVAHNVKFDANLLAEA  104 (820)
T ss_pred             HhC------CCEEEEECcHHHHHHHHHH
Confidence            975      35788888 9999999875

>PRK07247 DNA polymerase III subunit epsilon; Validated

Probab=82.85  E-value=1.6  Score=33.35  Aligned_cols=85  Identities=11%  Similarity=0.118  Sum_probs=53.6

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .||++|.+. +-+    ..++..++|-     +.-|. |+.   .....+++.   +|++++-.+...++.+|-.++++|
T Consensus        14 tTGl~~~~e-IIe----IgaV~v~~g~~~~~f~~lv~-P~~---~i~~~~~~l---hGIt~~~v~~ap~~~evl~~f~~f   81 (195)
T PRK07247         14 FNTVNGVSH-IIQ----VSAVKYDDHKEVDSFDSYVY-TDV---PLQSFINGL---TGITADKIADAPKVEEVLAAFKEF   81 (195)
T ss_pred             CCCCCCCCe-EEE----EEEEEEECCEEEEEEEEEEC-CCC---CCCccceec---CCCCHHHHhCCCCHHHHHHHHHHH
Confidence            478876433 334    4444444442     22232 332   335556654   689988777888999999999999


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSD  104 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kym  104 (111)
                      ++..     ..++=|. .+|..||.++.
T Consensus        82 ~~~~-----~lVaHNa~~fD~~fL~~~g  104 (195)
T PRK07247         82 VGEL-----PLIGYNAQKSDLPILAENG  104 (195)
T ss_pred             HCCC-----eEEEEeCcHhHHHHHHHcC
Confidence            8544     2444566 68999998863

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

Probab=82.72  E-value=2.3  Score=32.25  Aligned_cols=91  Identities=14%  Similarity=0.149  Sum_probs=60.7

Q ss_pred             CCCCCCCCccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          2 DNIGNRPSNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      ..+|.+|..+++-+    .+++.-..+      +...|++ +..   +.+-..+.|   |++.+-........++-.+++
T Consensus        21 ETtg~~~~~~~iie----Igav~~~~~~i~~~~~~~~v~P-~~~---i~~~~~~i~---git~e~l~~~p~~~~v~~~~~   89 (243)
T COG0847          21 ETTGLNPKKDRIIE----IGAVTLEDGRIVERSFHTLVNP-ERP---IPPEIFKIH---GITDEMLADAPKFAEVLPEFL   89 (243)
T ss_pred             ccCCCCCCCCceEE----EEeEEEECCeeecceeEEEECC-CCC---CChhhhhhc---CCCHHHHhcCCCHHHHHHHHH
Confidence            35888987777777    444443333      2344554 322   444444444   566677677788999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV  108 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv  108 (111)
                      +|+...     +.++|=. .+|..||.+.+.+.-
T Consensus        90 ~~i~~~-----~~~Vahna~fD~~fl~~~~~~~~  118 (243)
T COG0847          90 DFIGGL-----RLLVAHNAAFDVGFLRVESERLG  118 (243)
T ss_pred             HHHCCC-----CeEEEEchhhcHHHHHHHHHHcC
Confidence            998874     4677777 999999988776543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	111
2igi_A	180	Crystal Structure Of E. Coli Oligoribonuclease Leng		2e-05
3tr8_A	186	Structure Of An Oligoribonuclease (Orn) From Coxiel		3e-05
1j9a_A	184	Oligoribonuclease Length = 184		4e-05
1yta_A	180	Crystal Structure Of Oligoribonuclease, The Lone Es		2e-04
2gbz_A	194	The Crystal Structure Of Xc847 From Xanthomonas Cam		5e-04

>pdb|2IGI|A Chain A, Crystal Structure Of E. Coli Oligoribonuclease Length = 180

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 37/61 (60%)
Query: 31  CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMV 90
             ++ ++E L  M++W V  H ASGL +RV+AS++   EA+    +F+ ++V    +P+ 
Sbjct: 45  IAVHQSDEQLALMDDWNVRTHTASGLVERVKASTMGDREAELATLEFLKQWVPAGKSPIC 104
Query: 91  G 91
           G
Sbjct: 105 G 105

>pdb|3TR8|A Chain A, Structure Of An Oligoribonuclease (Orn) From Coxiella Burnetii Length = 186

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 32  GLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVG 91
            ++  +++L   + W   HH ASGL +RV+ SSV   EA+     F+ KYV    +P+ G
Sbjct: 50  AIHQPDKLLTAXDNWNTSHHTASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCG 109

>pdb|1J9A|A Chain A, Oligoribonuclease Length = 184

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 37/61 (60%)
Query: 31  CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMV 90
             ++ ++E+L   N+WC + H+ +GL +R++AS ++   A+ +   F+ K+V    +P+ 
Sbjct: 48  LAVHQSDELLNKXNDWCQKTHSENGLIERIKASKLTERAAELQTLDFLKKWVPKGASPIC 107
Query: 91  G 91
           G
Sbjct: 108 G 108

>pdb|1YTA|A Chain A, Crystal Structure Of Oligoribonuclease, The Lone Essential Exoribonuclease In Escherichia Coli Length = 180

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 31  CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMV 90
             ++ ++E L   ++W V  H ASGL +RV+AS+    EA+    +F+ ++V    +P+ 
Sbjct: 45  IAVHQSDEQLALXDDWNVRTHTASGLVERVKASTXGDREAELATLEFLKQWVPAGKSPIC 104
Query: 91  G 91
           G
Sbjct: 105 G 105

>pdb|2GBZ|A Chain A, The Crystal Structure Of Xc847 From Xanthomonas Campestris: A 3-5 Oligoribonuclease Of Dnaq Fold Family With A Novel Opposingly-Shifted Helix Length = 194

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 34/62 (54%)
Query: 30  KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPM 89
           +  + ++ E L+ M+EW    H  SGL  RV  S V+  +A+ +   F+ ++++   +PM
Sbjct: 48  ELAIAHSLETLEAMDEWNRNQHRRSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPM 107
Query: 90  VG 91
            G
Sbjct: 108 CG 109

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	111
3tr8_A	186	Oligoribonuclease; transcription, hydrolase; 2.50A	1e-07
2igi_A	180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	1e-06
2gbz_A	194	Oligoribonuclease; ORN, deddh, structural genomics	3e-06

>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} Length = 186

 Score = 46.8 bits (110), Expect = 1e-07
 Identities = 22/61 (36%), Positives = 33/61 (54%)

Query: 34  YYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93
           +  +++L  M+ W   HH ASGL +RV+ SSV   EA+     F+ KYV    +P+ G  
Sbjct: 52  HQPDKLLTAMDNWNTSHHTASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNS 111

Query: 94  H 94
            
Sbjct: 112 V 112

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Length = 180

 Score = 44.1 bits (103), Expect = 1e-06
 Identities = 20/57 (35%), Positives = 34/57 (59%)

Query: 37  EEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93
           +E L  M++W V  H ASGL +RV+AS++   EA+    +F+ ++V    +P+ G  
Sbjct: 51  DEQLALMDDWNVRTHTASGLVERVKASTMGDREAELATLEFLKQWVPAGKSPICGNS 107

>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV} Length = 194

 Score = 42.9 bits (100), Expect = 3e-06
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 34  YYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93
            ++ E L+ M+EW    H  SGL  RV  S V+  +A+ +   F+ ++++   +PM G  
Sbjct: 52  AHSLETLEAMDEWNRNQHRRSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPMCGNS 111

Query: 94  H 94
            
Sbjct: 112 I 112

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	111
3tr8_A	186	Oligoribonuclease; transcription, hydrolase; 2.50A	99.88
2gbz_A	194	Oligoribonuclease; ORN, deddh, structural genomics	99.67
2igi_A	180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	99.59
2f96_A	224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	98.33
3u3y_B	314	Three prime repair exonuclease 1; RNAse H fold, 3'	98.28
1w0h_A	204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	98.21
3v9w_A	235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	98.19
1y97_A	238	Three prime repair exonuclease 2; TREX2, hydrolase	98.12
2p1j_A	186	POLIII, DNA polymerase III POLC-type; structural g	98.11
3mxm_B	242	Three prime repair exonuclease 1; RNAse H-like fol	98.1
2xri_A	224	ERI1 exoribonuclease 3; hydrolase, metal binding;	98.03
2gui_A	194	DNA polymerase III epsilon subunit; DNA polymerase	97.97
1wlj_A	189	Interferon stimulated gene 20KDA; exoribonuclease,	97.79
1zbh_A	299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	97.62
2qxf_A	482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	97.33
1zbu_A	349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	97.19
3cg7_A	308	CRN-4, cell death-related nuclease 4; hydrolase, a	96.91

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

Probab=99.88  E-value=3.8e-23  Score=155.05  Aligned_cols=101  Identities=28%  Similarity=0.413  Sum_probs=95.2

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      .||++|.+++.-|    .++|++|++       +.++|++|++.|+.|++||.++|+-+||+++++++..+.++|..+++
T Consensus        18 TTGL~p~~d~IiE----IgaV~~d~~~~i~~~~~~~~i~~p~~~l~~~~~~~~~ih~ltGIt~~~l~~~p~~~ev~~~~l   93 (186)
T 3tr8_A           18 MTGLDPERDRIIE----IATIVTNSHLDILAEGPAFAIHQPDKLLTAMDNWNTSHHTASGLLERVKNSSVDEVEAETLTL   93 (186)
T ss_dssp             ESSSCTTTCCEEE----EEEEEECTTCCEEEECCCEECCCCHHHHTTSCHHHHHHHHHTSHHHHHHTCCCCHHHHHHHHH
T ss_pred             CCCCCCCCCceEE----EEEEEEcCCeEEeeeeEEEEEeCCccccccCCcccHHHHhccCCCHHHHhcCCCHHHHHHHHH
Confidence            5899999999999    889998863       45679999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      +|+++|++++.+||+||+ ++|+.||.++||++
T Consensus        94 ~fl~~~~~~~~~~lvghn~~FD~~FL~~~~~~~  126 (186)
T 3tr8_A           94 AFLEKYVSAGKSPLCGNSVCQDRRFLSRYMPRL  126 (186)
T ss_dssp             HHHTTTSCTTCSCEEESSTHHHHHHHHHHCHHH
T ss_pred             HHHHHhccCCCcEEEEEcHHHhHHHHHHHHHHc
Confidence            999999999999999999 99999999999986

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

Probab=99.67  E-value=6.3e-17  Score=119.33  Aligned_cols=101  Identities=23%  Similarity=0.360  Sum_probs=92.1

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      .||++|..+..-+    .+++.+|+.       +...|+++.++++.|++||.+.|.-+|++++..++..+.++|..+++
T Consensus        18 TTGl~p~~d~Iie----Igav~~~~~~~~~~~~~~~~v~p~~~i~~~~~~~~~~~~~itGIt~~~l~~~p~~~ev~~~~~   93 (194)
T 2gbz_A           18 MTGLDTDRDSIIE----IATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQHRRSGLWQRVLDSQVTHAQAEAQTV   93 (194)
T ss_dssp             ESCSCTTTCCEEE----EEEEEEETTCCEEEECCCEECCCCHHHHHTSCSHHHHHHHHHTHHHHHHHCCCCHHHHHHHHH
T ss_pred             CCCCCCCCCccEE----EEEEEEcCCcceeccCceEEEeCCHHHhhccchHHHHHHHhhCCCHHHHhcCCCHHHHHHHHH
Confidence            5899999999888    777766654       45678999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      +|++.++++++++|+|++ .+|+.||.+++|++
T Consensus        94 ~~l~~~~~~~~~~lvghn~~FD~~fL~~~~~~~  126 (194)
T 2gbz_A           94 AFLGEWIRAGASPMCGNSICQDRRFLHRQMSRL  126 (194)
T ss_dssp             HHHTTTCCTTSSCEEESSHHHHHHHHHHHCHHH
T ss_pred             HHHHHhCCCCCceEEecCHHHhHHHHHHHHHHh
Confidence            999999999999999999 99999999999874

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

Probab=99.59  E-value=2.1e-15  Score=108.63  Aligned_cols=101  Identities=27%  Similarity=0.388  Sum_probs=91.2

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      .||++|.++..-+    .+++++|++       ++..|+++..+.+.|++||++.|.-+|++++..++..+.++|..+++
T Consensus        14 TTGl~~~~~~Iie----Ig~v~~~~~~~~~~~~~~~lv~P~~~i~~~i~~~~~~~~~itGIt~~~l~~~~~~~~v~~~~~   89 (180)
T 2igi_A           14 MTGLDPERDRIIE----IATLVTDANLNILAEGPTIAVHQSDEQLALMDDWNVRTHTASGLVERVKASTMGDREAELATL   89 (180)
T ss_dssp             ESSSCTTTCCEEE----EEEEEECTTCCEEEEEEEEECCCCHHHHTTCCHHHHHHHHHTTHHHHHHHCCCCHHHHHHHHH
T ss_pred             CCCCCCCCCceEE----EEEEEEcCCCcEecCCcceEECCCHHHhhcCCHHHHHHHHHcCCCHHHHhcCCCHHHHHHHHH
Confidence            5899999888888    777777743       66788899999999999999999999999999999999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      +|++++++++.++|+|++ .+|+.||.++++++
T Consensus        90 ~~l~~~~~~~~~~lv~hn~~fD~~fL~~~~~~~  122 (180)
T 2igi_A           90 EFLKQWVPAGKSPICGNSIGQDRRFLFKYMPEL  122 (180)
T ss_dssp             HHHTTTSCTTTSCEEESSHHHHHHHHHHHCHHH
T ss_pred             HHHHHhCCCCCceEEecCHHHHHHHHHHHHHHh
Confidence            999999988889999999 99999999988753

>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=98.33  E-value=1.2e-07  Score=70.45  Aligned_cols=95  Identities=19%  Similarity=0.065  Sum_probs=72.7

Q ss_pred             CCCCCCCccccccHhhhhhheeeC---Cc-------eeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQ---GT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd---~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE   71 (111)
                      .||++|.++..-+    .+++..+   .|       +...|+++..  ..+.++|++.|   |++++ +.+...+.++|-
T Consensus        38 TTGl~~~~~~Iie----Ig~v~~~~~~~g~i~~~~~f~~lV~P~~~--~~i~~~~~~ih---GIt~e~~v~~~~~~~~v~  108 (224)
T 2f96_A           38 TGGFNSATDALLE----IAATTVGMDEKGFLFPEHTYFFRIEPFEG--ANIEPAALEFT---GIKLDHPLRMAVQEEAAL  108 (224)
T ss_dssp             ESSSCTTTBCEEE----EEEEEEEECTTSCEEEEEEEEEEBCCCTT--CBCCHHHHHHH---TCCTTCTTCCCBCHHHHH
T ss_pred             CCCCCCCCCeeEE----EEEEEEEEcCCCcccccceEEEEECCCCC--CCCCHHHHHHh---CCCHHHHHhcCCCHHHHH
Confidence            5899999887777    6666664   33       2344665422  46889999998   88875 566789999999


Q ss_pred             HHHHHHHHhhCC---CCCCcccCCc-HHhHHHHhhcccc
Q psy13232         72 KRLHQFVAKYVK---PKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        72 ~~ll~fikk~vp---~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .++++||+++++   .+.++|+|.. .+|+.||.+++.+
T Consensus       109 ~~~~~~l~~~~~~~~~~~~~lV~hn~~FD~~fL~~~~~~  147 (224)
T 2f96_A          109 TEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVAR  147 (224)
T ss_dssp             HHHHHHHHHHHHHTTCSEEEEEETTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhcccCCCEEEEeChhhhHHHHHHHHHH
Confidence            999999998874   2456899998 9999999987654

>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=98.28  E-value=5.8e-08  Score=78.22  Aligned_cols=99  Identities=12%  Similarity=0.119  Sum_probs=79.6

Q ss_pred             CCCCCCCccccccHhhhhhheeeCC----------ceeeeeecCHHHHhhccchhhhcc--------ccccchHHHHhCC
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQG----------TCKCGLYYNEEVLQNMNEWCVEHH--------NASGLTDRVRASS   64 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~----------G~~~vIhqp~~vL~~MdeWc~~~H--------~~SGL~~~vr~S~   64 (111)
                      .||++|.++..-+    .+++..++          |++.+|+++.++++.+ +||.+-+        .-+|++++..+..
T Consensus        21 TTGL~~~~d~IIE----IgaV~v~~~~l~~~~~~~g~~~~~~~~~~v~~~~-~~lI~P~~~I~~~a~~IhGIT~e~l~~a   95 (314)
T 3u3y_B           21 ATGLPSSRPEVTE----LCLLAVHRRALENTSISQGHPPPVPRPPRVVDKL-SLCIAPGKACSPGASEITGLSKAELEVQ   95 (314)
T ss_dssp             ESSCGGGCCCEEE----EEEEEEEHHHHHC--CCCSSSCCCCCCCSSCEEE-EEECBCSSCCCHHHHHHHSCCHHHHHHT
T ss_pred             CCCCCCCCCeEEE----EEEEEEECCccccccccccccccccccceeeeeE-EEEECCCCCCCHHHHHhcCCCHHHHHhC
Confidence            5899999999999    77777753          4678899999899888 5776664        3579998777665


Q ss_pred             --CCH-HHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         65 --VSI-EEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        65 --~s~-~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                        .+. +++-.++++|++.+ +++.+.+|-|+ .+|+.||.+.+.++
T Consensus        96 G~P~f~~ev~~~l~~fL~~~-~~~~vLVAHNga~FD~~FL~~el~r~  141 (314)
T 3u3y_B           96 GRQRFDDNLAILLRAFLQRQ-PQPCCLVAHNGDRYDFPLLQTELARL  141 (314)
T ss_dssp             TCCBSCHHHHHHHHHHHHTS-CSSEEEEETTTTTTHHHHHHHHHHTS
T ss_pred             CCCCcHHHHHHHHHHHHhcC-CCCcEEEEeCcHHHHHHHHHHHHHHc
Confidence              678 79999999999985 34566889998 99999999877654

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

Probab=98.21  E-value=7.3e-07  Score=64.60  Aligned_cols=95  Identities=5%  Similarity=0.016  Sum_probs=68.8

Q ss_pred             CCCCCC----CccccccHhhhhhheeeC--Cc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHH
Q psy13232          3 NIGNRP----SNTALSSMEQVKAYLQTQ--GT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~p----~~~~l~s~~q~~~~lvTd--~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE   71 (111)
                      .||++|    ..+..-+    .+++..|  .|     +...|++..  ...+.++|++.|   |++++-.++..+.++|-
T Consensus        19 TTGl~~~~~~~~~~Iie----igav~~~~~~g~i~~~f~~lv~P~~--~~~i~~~~~~i~---GIt~~~l~~~~~~~~v~   89 (204)
T 1w0h_A           19 ATCEEGNPPEFVHEIIE----FPVVLLNTHTLEIEDTFQQYVRPEI--NTQLSDFCISLT---GITQDQVDRADTFPQVL   89 (204)
T ss_dssp             ECCCTTCCTTSCCCEEE----EEEEEEETTTCSEEEEEEEEBCCSS--SCSCCHHHHHHH---CCCHHHHHTSBCHHHHH
T ss_pred             cCCcCCCCCCCCCcEEE----EEEEEEECCCCEEeeeeeeEECCCC--CCccCHHHHHHh---CCCHHHHhCCCCHHHHH
Confidence            578887    4455666    5666665  22     334555443  136889999988   89988888899999999


Q ss_pred             HHHHHHHHhhC--CCCCCcccCCcHHhHH-HHhhcccc
Q psy13232         72 KRLHQFVAKYV--KPKTAPMVGEYHTSKE-LLKDSDHF  106 (111)
Q Consensus        72 ~~ll~fikk~v--p~~~~pLaGNS~~DR~-FL~kymP~  106 (111)
                      .++++|+++.+  +++...+|.|..+|++ ||.+++.+
T Consensus        90 ~~~~~~l~~~~~~~~~~~lv~hn~~fD~~~~L~~~~~~  127 (204)
T 1w0h_A           90 KKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQL  127 (204)
T ss_dssp             HHHHHHHHHTTBTTTBCEEEEESSTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCCcEEEEEECcchHHHHHHHHHHH
Confidence            99999999986  2444456666699996 99886543

>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=98.19  E-value=9.3e-07  Score=65.91  Aligned_cols=95  Identities=17%  Similarity=0.114  Sum_probs=72.0

Q ss_pred             CCCCCCCccccccHhhhhhheeeC---Cc-------eeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQ---GT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd---~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE   71 (111)
                      .||++|..+.+-+    .+++..+   .|       +...|.++..  ..+.++|++.|   |++++ ..+...+.++|-
T Consensus        46 TTGl~~~~~~Iie----Igav~~~~~~~g~i~~~~~f~~~v~P~~~--~~i~~~~~~i~---GIt~e~~v~~~~~~~~vl  116 (235)
T 3v9w_A           46 TAGFNAKTDALLE----IAAITLKMDEQGWLMPDTTLHFHVEPFVG--ANLQPEALAFN---GIDPNDPDRGAVSGYEAL  116 (235)
T ss_dssp             ESSSCTTTBCEEE----EEEEEEEECTTSCEEEEEEEEEEBCCCTT--CBCCHHHHHHH---CCCTTCGGGCCBCHHHHH
T ss_pred             CCCCCCCCCeEEE----EEEEEEEEcCCCcccccceEEEEECCCCC--CCCCHHHHHHh---CCCHHHHHhcCCCHHHHH
Confidence            4799998888877    6666554   33       3334555322  35788888876   67776 666789999999


Q ss_pred             HHHHHHHHhhCCC---CCCcccCCc-HHhHHHHhhcccc
Q psy13232         72 KRLHQFVAKYVKP---KTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        72 ~~ll~fikk~vp~---~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .++++|+++|++.   +..+++|.. .+|+.||.+++++
T Consensus       117 ~~~~~~l~~~~~~~~~~~~~lVahN~~fD~~~L~~~~~~  155 (235)
T 3v9w_A          117 HEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAER  155 (235)
T ss_dssp             HHHHHHHHHHHTTTTCCEEEEEETTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhccCCCcEEEEeChHHHHHHHHHHHHH
Confidence            9999999999875   567899998 9999999987654

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

Probab=98.12  E-value=7.1e-07  Score=66.36  Aligned_cols=97  Identities=13%  Similarity=0.108  Sum_probs=66.4

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHh----------hccchhhhccccccchHHHHh--C
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQ----------NMNEWCVEHHNASGLTDRVRA--S   63 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~----------~MdeWc~~~H~~SGL~~~vr~--S   63 (111)
                      .||++|+.+..-+    .+++.++.|       ...+||++.++++          .+.++|++.|   |++++...  .
T Consensus        19 TTGl~~~~~~Iie----Ig~v~~~~~~~~~~~~~~~~~~~~~~i~~~f~~lv~P~~~i~~~~~~i~---GIt~~~l~~~~   91 (238)
T 1y97_A           19 ATGLPSVEPEIAE----LSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERPFTAKASEIT---GLSSEGLARCR   91 (238)
T ss_dssp             ESSCGGGCCCEEE----EEEEEEEHHHHTSCBC---CCCBCCSSCEEEEEECCCSSCCCHHHHHHH---CCCHHHHHHTT
T ss_pred             CCCcCCCCCcEEE----EEEEEecccccccccccccccccccccceeeEEEECCCCcCCHHHHHHh---CCCHHHHhhcC
Confidence            5899998888888    777777754       1222333333332          3566777665   88888763  3


Q ss_pred             CCCH-HHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         64 SVSI-EEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        64 ~~s~-~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      ..+. +++..++.+|++. ++.+...+|.|. .+|+.||.++++++
T Consensus        92 ~p~f~~~v~~~l~~fl~~-~~~~~~lVahN~~~FD~~fL~~~~~~~  136 (238)
T 1y97_A           92 KAGFDGAVVRTLQAFLSR-QAGPICLVAHNGFDYDFPLLCAELRRL  136 (238)
T ss_dssp             CCCSCHHHHHHHHHHHTT-SCSSEEEEETTTTTTHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHHHh-CCCCCEEEecCchhhhHHHHHHHHHHc
Confidence            4555 5899999999986 333355777899 99999999987653

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

Probab=98.11  E-value=2.1e-06  Score=62.15  Aligned_cols=87  Identities=16%  Similarity=0.150  Sum_probs=66.7

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF   77 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f   77 (111)
                      .||++|.++.+-+    .+++..++|     +...|++..    .+.++|++.|   |++++..++..+.++|-.++++|
T Consensus        21 TTGl~~~~~~Iie----Ig~v~~~~g~i~~~f~~lv~P~~----~i~~~~~~i~---GIt~~~l~~~~~~~~v~~~~~~~   89 (186)
T 2p1j_A           21 TTGLDPQVDEIIE----IGAVKIQGGQIVDEYHTLIKPSR----EISRKSSEIT---GITQEMLENKRSIEEVLPEFLGF   89 (186)
T ss_dssp             ESCSCTTTCCEEE----EEEEEEETTEEEEEEEEECBCSS----CCCHHHHHHH---CCCHHHHTTCCBHHHHHHHHHHH
T ss_pred             CCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECcCC----CCCHHHhhhc---CCCHHHHhcCCCHHHHHHHHHHH
Confidence            5899998877777    666665555     344566433    4778888775   78888888889999999999988


Q ss_pred             HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      ++.      .+|+|.. .+|+.||.+.+++
T Consensus        90 l~~------~~lv~hn~~fD~~~L~~~~~~  113 (186)
T 2p1j_A           90 LED------SIIVAHNANFDYRFLRLWIKK  113 (186)
T ss_dssp             SSS------CEEEETTHHHHHHHHHHHHHH
T ss_pred             HCC------CEEEEECcHHHHHHHHHHHHH
Confidence            752      5789988 9999999987654

>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=98.10  E-value=1.9e-07  Score=71.19  Aligned_cols=99  Identities=12%  Similarity=0.121  Sum_probs=76.1

Q ss_pred             CCCCCCCccccccHhhhhhheeeCC----------ceeeeeecCHHHHhhccchhhhcc--------ccccchHHHHhCC
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQG----------TCKCGLYYNEEVLQNMNEWCVEHH--------NASGLTDRVRASS   64 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~----------G~~~vIhqp~~vL~~MdeWc~~~H--------~~SGL~~~vr~S~   64 (111)
                      .||++|.++..-+    .+++..++          |...+++++.++++.++ |+.+-+        .-+|++++..++.
T Consensus        21 TTGl~~~~d~IiE----Igav~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~-~li~P~~~i~~~~~~i~GIt~~~l~~~   95 (242)
T 3mxm_B           21 ATGLPSSRPEVTE----LCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLS-LCIAPGKACSPGASEITGLSKAELEVQ   95 (242)
T ss_dssp             ESSCGGGCCCEEE----EEEEEEEHHHHHTSCCCCSSSCCCCCCCSCCEEEE-EECCCSSCCCHHHHHHHCCCHHHHHHT
T ss_pred             cCCCCCCCCeeEE----EEEEEecCCcccccccccccccccccccchhheeE-EEECCCCCCCHHHHHhcCCCHHHHHhc
Confidence            5899999998888    77777643          45677888877887774 665553        4579998887765


Q ss_pred             --CCHH-HHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         65 --VSIE-EADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        65 --~s~~-~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                        .+.+ +|-.++++|++.. ++....+|-|+ .+|+.||.+.+.+.
T Consensus        96 g~p~~~~ev~~~~~~fl~~~-~~~~~lVaHNav~FD~~fL~~~~~r~  141 (242)
T 3mxm_B           96 GRQRFDDNLAILLRAFLQRQ-PQPCCLVAHNGDRYDFPLLQTELARL  141 (242)
T ss_dssp             TCCCSCHHHHHHHHHHHHTS-CSSEEEEETTTTTTHHHHHHHHHHTS
T ss_pred             CCCchhHHHHHHHHHHHhcC-CCCCEEEEcCChHhhHHHHHHHHHHc
Confidence              6775 9999999999884 34456788999 99999999987554

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

Probab=98.03  E-value=3.6e-06  Score=62.78  Aligned_cols=92  Identities=13%  Similarity=0.152  Sum_probs=66.9

Q ss_pred             CCCCCCCcc--ccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHH
Q psy13232          3 NIGNRPSNT--ALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKR   73 (111)
Q Consensus         3 ~~~~~p~~~--~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~   73 (111)
                      .||++|.++  ..-+    .+++..|++       +...|++..  ...+.++|++.|   |++++..++..+.++|-.+
T Consensus        40 TTGl~~~~d~~~Iie----Igav~v~~~~~~i~~~f~~lV~P~~--~~~i~~~~~~lt---GIt~~~v~~a~~~~~v~~~  110 (224)
T 2xri_A           40 ATCDKPQIHPQEIIE----FPILKLNGRTMEIESTFHMYVQPVV--HPQLTPFCTELT---GIIQAMVDGQPSLQQVLER  110 (224)
T ss_dssp             ECCCC-CCSSCCEEE----EEEEEEETTTCCEEEEEEEECCCSS--SCSCCHHHHHHH---CCCHHHHTTCCCHHHHHHH
T ss_pred             cCCCCCCCCCcceEE----EEEEEEecCCcEEeeeeeeEECCCC--CCcCCHHHHHHh---CcCHHHHcCCCCHHHHHHH
Confidence            589999864  6666    677777665       344555432  236889999986   8998888889999999999


Q ss_pred             HHHHHHhhCCC--C-CCcccCCcHHhHHH-Hhhc
Q psy13232         74 LHQFVAKYVKP--K-TAPMVGEYHTSKEL-LKDS  103 (111)
Q Consensus        74 ll~fikk~vp~--~-~~pLaGNS~~DR~F-L~ky  103 (111)
                      +++|++..+--  + .+++|+.+.+|++| |.+.
T Consensus       111 f~~~l~~~~lv~hn~~~~~~t~g~fD~~fll~~~  144 (224)
T 2xri_A          111 VDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQ  144 (224)
T ss_dssp             HHHHHHHTTTTSTTSCEEEEESSSHHHHTHHHHH
T ss_pred             HHHHHhhcccccCCCceEEEEeChhhHHHHHHHH
Confidence            99999987431  1 35666666999999 5443

>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=97.97  E-value=8.6e-06  Score=58.73  Aligned_cols=87  Identities=9%  Similarity=0.097  Sum_probs=66.2

Q ss_pred             CCCCCC-----CccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHH
Q psy13232          3 NIGNRP-----SNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~p-----~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE   71 (111)
                      .||++|     .++..-+    .+++..++|      ++..|++.    ..++++|++.|   |++++-.+...+.++|-
T Consensus        18 TTGl~~~~~~~~~~~Iie----ig~v~~~~~~~~~~~f~~lv~P~----~~i~~~~~~i~---GIt~~~l~~~~~~~~v~   86 (194)
T 2gui_A           18 TTGMNQIGAHYEGHKIIE----IGAVEVVNRRLTGNNFHVYLKPD----RLVDPEAFGVH---GIADEFLLDKPTFAEVA   86 (194)
T ss_dssp             ESCCCSSSSTTTTCCEEE----EEEEEEETTEECSCCEEEECCCS----SCCCHHHHHHH---CCCHHHHTTSCCHHHHH
T ss_pred             CCCCCCcccCCCCCEEEE----EEEEEEECCeEeccEEEEEECcC----CcCCHHHHHhh---CcCHHHHhCCCCHHHHH
Confidence            589999     4466666    555555443      45556644    26889999998   78888888889999999


Q ss_pred             HHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         72 KRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        72 ~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      .++++|++.      ++|+|.. .+|+.||.+.+.+
T Consensus        87 ~~~~~~l~~------~~lv~hn~~fD~~~L~~~~~~  116 (194)
T 2gui_A           87 DEFMDYIRG------AELVIHNAAFDIGFMDYEFSL  116 (194)
T ss_dssp             HHHHHHHTT------SEEEETTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCC------CeEEEEchHHhHHHHHHHHHH
Confidence            999999864      4688988 9999999987543

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

Probab=97.79  E-value=8.3e-06  Score=59.26  Aligned_cols=87  Identities=15%  Similarity=0.181  Sum_probs=63.4

Q ss_pred             CCCCCCCcc-ccccHhhhhhheeeCCc--eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHH
Q psy13232          3 NIGNRPSNT-ALSSMEQVKAYLQTQGT--CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVA   79 (111)
Q Consensus         3 ~~~~~p~~~-~l~s~~q~~~~lvTd~G--~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fik   79 (111)
                      .||++|.++ .+.+    .+++..++.  ++..|++..    .+.+||++.   +|++++..++..+.++|..++++|++
T Consensus        14 TTGl~~~~~~~iie----i~~v~~~g~~i~~~lV~P~~----~i~~~~~~i---~GIt~~~l~~a~~~~~v~~~~~~~l~   82 (189)
T 1wlj_A           14 MVGLGPHRESGLAR----CSLVNVHGAVLYDKFIRPEG----EITDYRTRV---SGVTPQHMVGATPFAVARLEILQLLK   82 (189)
T ss_dssp             EEEETTTTEEEEEE----EEEECTTCCEEEEEEEECSS----CEEECCHHH---HCCCHHHHTTCEEHHHHHHHHHHHHT
T ss_pred             CcCcCCCCCceEEE----EEEEeCCCCEEEeeEecCCC----CCCccccCC---CCCCHHHHcCCCCHHHHHHHHHHHHC
Confidence            478888763 3333    233322322  223455432    588899987   58998888889999999999999995


Q ss_pred             hhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         80 KYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        80 k~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                            .++|+|.. .+|++||.+++|+
T Consensus        83 ------~~~lV~hn~~fD~~~L~~~~~~  104 (189)
T 1wlj_A           83 ------GKLVVGHDLKHDFQALKEDMSG  104 (189)
T ss_dssp             ------TSEEEESSHHHHHHHTTCCCTT
T ss_pred             ------CCEEEECCcHHHHHHHHHhCCC
Confidence                  25899999 9999999999986

>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=97.62  E-value=3.8e-05  Score=59.91  Aligned_cols=93  Identities=5%  Similarity=0.015  Sum_probs=67.5

Q ss_pred             CCCCC----CCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHH
Q psy13232          3 NIGNR----PSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~----p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE   71 (111)
                      .||++    |.++..-+    .+++..|.+       ++..|++..  -..+.+||++.|   |++++..+...+.++|-
T Consensus        87 TTGl~~~~~~~~~~IIe----IgaV~v~~~~g~i~~~f~~lV~P~~--~~~i~~~~~~ih---GIt~e~v~~ap~~~evl  157 (299)
T 1zbh_A           87 ATCEEGNPPEFVHEIIE----FPVVLLNTHTLEIEDTFQQYVRPEI--NTQLSDFCISLT---GITQDQVDRADTFPQVL  157 (299)
T ss_dssp             ECCCTTCCTTCCCCEEE----EEEEEEETTTCCEEEEEEEEBCCSS--SCSCCHHHHHHH---CCCHHHHHTSBCHHHHH
T ss_pred             cccCCCCCCCCCCceEE----EEEEEEECCCCeEeeeeeeeecCCC--CCCCCHHHHHHh---CCCHHHHhcCCCHHHHH
Confidence            47886    45666666    667766642       344565543  147889999998   78988888889999999


Q ss_pred             HHHHHHHHhh-CC-CCCCcccCCcHHhHH-HHhhcc
Q psy13232         72 KRLHQFVAKY-VK-PKTAPMVGEYHTSKE-LLKDSD  104 (111)
Q Consensus        72 ~~ll~fikk~-vp-~~~~pLaGNS~~DR~-FL~kym  104 (111)
                      .++++|++.+ ++ ++...+|.|..+|+. ||.+.+
T Consensus       158 ~~f~~~l~~~~~~~~~~~lVahn~~fD~~~fL~~~~  193 (299)
T 1zbh_A          158 KKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQC  193 (299)
T ss_dssp             HHHHHHHHHTTBTTTBCEEEEESSSHHHHTHHHHHH
T ss_pred             HHHHHHHhhcccCCCCcEEEEEeCHHHHHHHHHHHH
Confidence            9999999987 32 223455556699999 998753

>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=97.33  E-value=5e-05  Score=63.98  Aligned_cols=93  Identities=16%  Similarity=0.096  Sum_probs=66.1

Q ss_pred             CCCCCCCccccccHhhhhhheeeC-Cc------eeeeeecCHHHHhhccchhhhccccccchHHH-HhCCCCHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQ-GT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRV-RASSVSIEEADKRL   74 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd-~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~v-r~S~~s~~~AE~~l   74 (111)
                      .||++|..+..-+    .++|.+| +|      ++..|+++..++-. .+.+ .   -+|++++- ......+++|-.++
T Consensus        18 TTGl~p~~d~IIE----IgaV~vd~~g~ii~~~f~~lVkP~~~ilp~-p~a~-~---IhGIT~e~l~~ap~~~~evl~~f   88 (482)
T 2qxf_A           18 TFGTHPALDRPAQ----FAAIRTDSEFNVIGEPEVFYCKPADDYLPQ-PGAV-L---ITGITPQEARAKGENEAAFAARI   88 (482)
T ss_dssp             ESSSCTTTSCEEE----EEEEEECTTSCBCSCCEEEEBCCCTTCCCC-HHHH-H---HHCCCHHHHHHHCBCHHHHHHHH
T ss_pred             CCCCCCCCCeEEE----EEEEEEECCCeEEeeeeEEEECCCCCCCCC-HHHH-H---HhCCCHHHHhcCCCCHHHHHHHH
Confidence            5899999888888    7888877 33      44556655443221 1233 3   35788664 44577889999999


Q ss_pred             HHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      ++|+.+   ++.+.+|.|| .+|+.||.+.+.+.
T Consensus        89 ~~~l~~---~~~~lVaHNs~~FD~~fL~~~~~r~  119 (482)
T 2qxf_A           89 HSLFTV---PKTCILGYNNVRFDDEVTRNIFYRN  119 (482)
T ss_dssp             HHHHTS---TTEEEEESSTTTTHHHHHHHHHHHT
T ss_pred             HHHHcC---CCCEEEEECCHHHHHHHHHHHHHHh
Confidence            999975   4566788899 99999999876543

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

Probab=97.19  E-value=0.00018  Score=58.01  Aligned_cols=93  Identities=6%  Similarity=0.051  Sum_probs=65.8

Q ss_pred             CCCCC----CCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHH
Q psy13232          3 NIGNR----PSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~----p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE   71 (111)
                      .||++    |..+..-+    .+++..|.+       +...|.+...  ..+.++|++.|   |++++-.+...+.++|-
T Consensus       137 TTGl~~~~~~~~deIIE----IgaV~vd~~~g~i~~~f~~lVkP~~~--~~I~~~~t~ih---GIT~e~v~~ap~~~eVl  207 (349)
T 1zbu_A          137 ATCEEGNPPEFVHEIIE----FPVVLLNTHTLEIEDTFQQYVRPEIN--TQLSDFCISLT---GITQDQVDRADTFPQVL  207 (349)
T ss_dssp             ECCCTTCCTTCCCCEEE----CCEEEEETTTTEEEEEECCBEECSSS--CSCCHHHHHHH---CCCHHHHHTSEEHHHHH
T ss_pred             cCCCCCcCCCCCCeEEE----EEEEEEECCCceEeEEEEEEECCCCC--CCCCHHHHHHh---CCCHHHHhCCCCHHHHH
Confidence            47885    45566666    666666532       3334554431  36889999998   78888877889999999


Q ss_pred             HHHHHHHHhh-CCCC-CCcccCCcHHhHH-HHhhcc
Q psy13232         72 KRLHQFVAKY-VKPK-TAPMVGEYHTSKE-LLKDSD  104 (111)
Q Consensus        72 ~~ll~fikk~-vp~~-~~pLaGNS~~DR~-FL~kym  104 (111)
                      .++++|++.+ ++.+ ...+|-|..+|+. ||.+.+
T Consensus       208 ~~f~~~l~~~~~~~~~~~lVaHNa~FD~~~fL~~~~  243 (349)
T 1zbu_A          208 KKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQC  243 (349)
T ss_dssp             HHHHHHHHHTTBTTTBCEEEEESSSHHHHTHHHHHH
T ss_pred             HHHHHHHhcccccCCCcEEEEECcHhhHHHHHHHHH
Confidence            9999999887 3322 3445556699999 998853

>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=96.91  E-value=0.0006  Score=53.68  Aligned_cols=93  Identities=8%  Similarity=0.095  Sum_probs=64.0

Q ss_pred             CCCCCCCcc---ccccHhhhhhheeeC--Cc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHH
Q psy13232          3 NIGNRPSNT---ALSSMEQVKAYLQTQ--GT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEA   70 (111)
Q Consensus         3 ~~~~~p~~~---~l~s~~q~~~~lvTd--~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~A   70 (111)
                      .||++|..+   ..-+    .+++..|  .|       ++..|++...  ..+.++|++.|   |++++-.+...+.++|
T Consensus        28 TTGl~~~~d~~~eIIE----IgaV~vd~~~g~i~~~~~f~~lV~P~~~--p~i~~~~~~lt---GIt~e~v~~ap~~~ev   98 (308)
T 3cg7_A           28 TTSDAANQDYPCEVIQ----FAIVAYDVPNDKIREDISFNKYVKPVLN--RTLTKNCVDFT---GIPQRSIDTADTFDVV   98 (308)
T ss_dssp             ECCBTTBCSCCCCEEE----EEEEEEETTTTEEEEEEEEEEECBCSSB--CSCCHHHHHHH---CCCHHHHHTSCBHHHH
T ss_pred             cCCCCCCCCCCCCeEE----EEEEEEEcCCCEEeeccceeeEECCCCC--CCCCHHHHHHc---CCCHHHHhcCCCHHHH
Confidence            478888765   4444    4455543  22       3334444321  23788999876   7888887889999999


Q ss_pred             HHHHHHHHHhhCC-CCCCcccCCcHHhH-HHHhhcc
Q psy13232         71 DKRLHQFVAKYVK-PKTAPMVGEYHTSK-ELLKDSD  104 (111)
Q Consensus        71 E~~ll~fikk~vp-~~~~pLaGNS~~DR-~FL~kym  104 (111)
                      -.++++||+..+. ...+.++.++.+|+ .||.+.+
T Consensus        99 l~~f~~~l~~~~lvahn~~lv~~g~fD~~~fL~~~~  134 (308)
T 3cg7_A           99 YEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQM  134 (308)
T ss_dssp             HHHHHHHHHHHCCCTTSEEEEESSSHHHHTHHHHHH
T ss_pred             HHHHHHHHHhCCcCCcceEEeccCcccHHHHHHHHH
Confidence            9999999999853 33346677777898 6998754

---

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	111
d2igia1	180	Oligoribonuclease {Escherichia coli [TaxId: 562]}	98.74
d1wlja_	173	Interferon-stimulated gene 20 kDa protein, ISG20 {	97.8
d2qxfa1	467	Exonuclease I {Escherichia coli K12 (Escherichia c	97.3
d1y97a1	228	Three prime repair exonuclease 2, TREX2 {Human (Ho	96.93
d2guia1	174	N-terminal exonuclease domain of the epsilon subun	96.91
d3b6oa1	226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	96.46
d2f96a1	202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	95.59
d1w0ha_	200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	88.01
d1fexa_	59	Rap1 {Human (Homo sapiens) [TaxId: 9606]}	85.61

>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=98.74  E-value=9.4e-09  Score=69.22  Aligned_cols=101  Identities=27%  Similarity=0.393  Sum_probs=89.1

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce-------eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC-------KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll   75 (111)
                      .||++|+++..-|    .++|++|.+.       ...+.++.........+....+...+..+.......+.+.+.....
T Consensus        14 TTGLdp~~d~IIe----IaaV~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (180)
T d2igia1          14 MTGLDPERDRIIE----IATLVTDANLNILAEGPTIAVHQSDEQLALMDDWNVRTHTASGLVERVKASTMGDREAELATL   89 (180)
T ss_dssp             ESSSCTTTCCEEE----EEEEEECTTCCEEEEEEEEECCCCHHHHTTCCHHHHHHHHHTTHHHHHHHCCCCHHHHHHHHH
T ss_pred             CCCCCCCCCeEEE----EEEEEEECCceEeeccceeeeeccccccccccccccccccccchhhhhccccccHHHHHHHHH
Confidence            5899999999999    8899887753       3456678888899999999999999999999999999999999999


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      .+.+...-.+..+++||+ ++|+.||.+++++.
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~FD~~~l~~~~~~~  122 (180)
T d2igia1          90 EFLKQWVPAGKSPICGNSIGQDRRFLFKYMPEL  122 (180)
T ss_dssp             HHHTTTSCTTTSCEEESSHHHHHHHHHHHCHHH
T ss_pred             HHHhhhccCCCcEEEechhcchhHHHHHHhhhh
Confidence            999888778888999999 99999999988764

>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=97.80  E-value=4.1e-06  Score=56.61  Aligned_cols=88  Identities=13%  Similarity=0.094  Sum_probs=64.9

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCcee---eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTCK---CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVA   79 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~---~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fik   79 (111)
                      .||++|.++..-+    .++|+...|-.   -.|.++    ..+.+|+++.|   |++++-.....+.+++-.++++|+.
T Consensus         9 ttGl~~~~~~ii~----~~~iv~~~g~~i~~~~v~p~----~~i~~~~~~i~---GIt~e~~~~~~~~~~~~~~~~~~~~   77 (173)
T d1wlja_           9 MVGLGPHRESGLA----RCSLVNVHGAVLYDKFIRPE----GEITDYRTRVS---GVTPQHMVGATPFAVARLEILQLLK   77 (173)
T ss_dssp             EEEETTTTEEEEE----EEEEECTTCCEEEEEEEECS----SCEEECCHHHH---CCCHHHHTTCEEHHHHHHHHHHHHT
T ss_pred             cCCCCCCCCcEEE----EEEEEEecCeEEEEEeeecc----cccCcceeEEe---cCcchhhhcCCcHHHHHHHHHhhcc
Confidence            4799998887555    46666555432   222333    24678888877   7777777778899999999888865


Q ss_pred             hhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         80 KYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        80 k~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      .      ++++|.. .+|++||.+++|+.
T Consensus        78 ~------~~lv~hn~~fD~~~L~~~~~~~  100 (173)
T d1wlja_          78 G------KLVVGHDLKHDFQALKEDMSGY  100 (173)
T ss_dssp             T------SEEEESSHHHHHHHTTCCCTTC
T ss_pred             c------ceEEeechHhHHHHHHHhhccC
Confidence            3      4799999 99999999988864

>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=97.30  E-value=1.7e-05  Score=61.85  Aligned_cols=93  Identities=16%  Similarity=0.080  Sum_probs=64.1

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCceeeeeecCHHHHhhccchh------hhccccccch-HHHHhCCCCHHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWC------VEHHNASGLT-DRVRASSVSIEEADKRLH   75 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~~vIhqp~~vL~~MdeWc------~~~H~~SGL~-~~vr~S~~s~~~AE~~ll   75 (111)
                      .||++|..+...+    .++|.||+..+++ .......-...+++      ...   +|++ +.+.+++.+..++-.++.
T Consensus        11 TtG~~~~~d~ii~----~~ai~~d~~~~~~-~~~~~~~~~~~~~~~p~~~a~~v---~gi~~~~~~~~~~~~~e~~~~i~   82 (467)
T d2qxfa1          11 TFGTHPALDRPAQ----FAAIRTDSEFNVI-GEPEVFYCKPADDYLPQPGAVLI---TGITPQEARAKGENEAAFAARIH   82 (467)
T ss_dssp             ESSSCTTTSCEEE----EEEEEECTTSCBC-SCCEEEEBCCCTTCCCCHHHHHH---HCCCHHHHHHHCBCHHHHHHHHH
T ss_pred             CCCcCCCCCcEEE----EEEEEECCCCcEE-eEEEEEeecCCCCCCCCHHHHHH---hCcCHHHHHcCCCCHHHHHHHHH
Confidence            5899999999998    7888898776643 11111111122332      223   4554 677777889988888888


Q ss_pred             HHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +|+..+   +.+.+++|+ .+|..||.+.+-+
T Consensus        83 ~~~~~~---~~~~v~~n~~~FD~~fl~~~~~r  111 (467)
T d2qxfa1          83 SLFTVP---KTCILGYNNVRFDDEVTRNIFYR  111 (467)
T ss_dssp             HHHTST---TEEEEESSTTTTHHHHHHHHHHH
T ss_pred             HHHhcC---CCcEEEEecchhhHHHHHHHHHH
Confidence            888643   456799999 9999999987644

>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=96.93  E-value=0.0001  Score=51.99  Aligned_cols=97  Identities=12%  Similarity=0.039  Sum_probs=61.2

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce-------eeeeecCHHHHh----------hccchhhhccccccchHHHH--hC
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC-------KCGLYYNEEVLQ----------NMNEWCVEHHNASGLTDRVR--AS   63 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-------~~vIhqp~~vL~----------~MdeWc~~~H~~SGL~~~vr--~S   63 (111)
                      .||++|+++...+    .+++..+.+.       ...+..+..+++          .+++++++.|   |++++..  ++
T Consensus        17 TTGl~~~~~~Iie----ia~i~~~~~~~~~~~~~~~~~~~~~~v~d~~~~~v~P~~~i~~~~~~it---GIt~~~l~~~~   89 (228)
T d1y97a1          17 ATGLPSVEPEIAE----LSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERPFTAKASEIT---GLSSEGLARCR   89 (228)
T ss_dssp             ESSCGGGCCCEEE----EEEEEEEHHHHTSCBC---CCCBCCSSCEEEEEECCCSSCCCHHHHHHH---CCCHHHHHHTT
T ss_pred             cCCcCCCCCCeEE----EEEEEEECCccccccccccccccccceecceeeEECCCCCCCHHHHHhc---CCCHHHHHhcc
Confidence            4899999888777    5666654321       111111111222          4667777777   5665544  33


Q ss_pred             CCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232         64 SVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        64 ~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      ..+..+...++++++.++...+...+++|+ .+|+.||.+.+.+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~n~~~fD~~~l~~~l~r  133 (228)
T d1y97a1          90 KAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAELRR  133 (228)
T ss_dssp             CCCSCHHHHHHHHHHHTTSCSSEEEEETTTTTTHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHhhhccCCceEEeechHHHhHHHHHHHHHH
Confidence            455566666777777777656666788999 9999999987654

>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=96.91  E-value=0.00067  Score=44.61  Aligned_cols=86  Identities=8%  Similarity=0.067  Sum_probs=58.5

Q ss_pred             CCCCCCC-----ccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHH
Q psy13232          3 NIGNRPS-----NTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEAD   71 (111)
Q Consensus         3 ~~~~~p~-----~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE   71 (111)
                      .||++|.     ++..-+    .+++.++++      ++..|++.    .....-+.+   -+|++++......+..++-
T Consensus         9 TTGl~~~~~~~~~d~IIe----Ig~v~~~~~~~~~~~~~~~v~P~----~~i~~~~~~---i~gIt~e~~~~~~~~~~~~   77 (174)
T d2guia1           9 TTGMNQIGAHYEGHKIIE----IGAVEVVNRRLTGNNFHVYLKPD----RLVDPEAFG---VHGIADEFLLDKPTFAEVA   77 (174)
T ss_dssp             ESCCCSSSSTTTTCCEEE----EEEEEEETTEECSCCEEEECCCS----SCCCHHHHH---HHCCCHHHHTTSCCHHHHH
T ss_pred             CCCCCcccccCCCCEEEE----EEEEEEECCEEeeeEEEEEeccC----ccchhhhhh---ccccchhhhhcchhHHHHH
Confidence            5899885     344555    566656554      23344432    123444444   4588888888888999999


Q ss_pred             HHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccc
Q psy13232         72 KRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDH  105 (111)
Q Consensus        72 ~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP  105 (111)
                      .++++|++.      +++.|+. .+|..|+...+.
T Consensus        78 ~~~~~~~~~------~~~v~~~~~~d~~~~~~~~~  106 (174)
T d2guia1          78 DEFMDYIRG------AELVIHNAAFDIGFMDYEFS  106 (174)
T ss_dssp             HHHHHHHTT------SEEEETTHHHHHHHHHHHHH
T ss_pred             HHHHHhcCC------CeEEEeecchhhHHHHHHHH
Confidence            999999964      4677887 999999887643

>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=96.46  E-value=0.00051  Score=48.30  Aligned_cols=94  Identities=11%  Similarity=0.018  Sum_probs=57.5

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce------------------------eeeeecCHHHHhhccchhhhccccccchH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC------------------------KCGLYYNEEVLQNMNEWCVEHHNASGLTD   58 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~------------------------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~   58 (111)
                      .||++|.++...+    .+++.++.+.                        +..|. |.   ....+++++.||=+-  +
T Consensus        13 TTGl~~~~~~Iie----ia~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~-P~---~~I~~~~~~i~GIt~--~   82 (226)
T d3b6oa1          13 ATGLPSSRPEVTE----LCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIA-PG---KACSPGASEITGLSK--A   82 (226)
T ss_dssp             ESSCGGGCCCEEE----EEEEEEEHHHHHTSCCCCSSSCCCCCCCSSCEEEEEECC-CS---SCCCHHHHHHHCCCH--H
T ss_pred             CCCCCCCCCceEE----EEEEEEeCCcccccccccccccccccccceeceeeeeEC-CC---CCCCHHHHHhcCCCH--H
Confidence            5899999998888    5666655321                        12222 22   235678887775552  2


Q ss_pred             HHHhC-C-CCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232         59 RVRAS-S-VSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL  107 (111)
Q Consensus        59 ~vr~S-~-~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l  107 (111)
                      .++.. . -..+.+.+.+.+|++. .+.+...+|-|+ .+|+.||.+.+.+.
T Consensus        83 ~l~~~~~~~~~~~~~~~~~~f~~~-~~~~~~lVahN~~~FD~~~l~~~~~r~  133 (226)
T d3b6oa1          83 ELEVQGRQRFDDNLAILLRAFLQR-QPQPCCLVAHNGDRYDFPLLQTELARL  133 (226)
T ss_dssp             HHHHTTCCCSCHHHHHHHHHHHHT-SCSSEEEEETTTTTTHHHHHHHHHHTS
T ss_pred             HHHhcccchhHHHHHHHHHHHHHh-ccCCceEEEechhHHHHHHHHHHHHHc
Confidence            33322 1 2345555666666654 445555677799 99999999876654

>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=95.59  E-value=0.0014  Score=43.60  Aligned_cols=98  Identities=17%  Similarity=0.020  Sum_probs=62.2

Q ss_pred             CCCCCCCccccccHhhhhhheeeCCce--------eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232          3 NIGNRPSNTALSSMEQVKAYLQTQGTC--------KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL   74 (111)
Q Consensus         3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~--------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l   74 (111)
                      .||++|.++..-|    .+++..|.+.        ...+...........+++++.|+-+  .+.+....+..+.+-.+.
T Consensus        20 TTGl~~~~~~IIe----igav~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~git--~~~~~~~~~~~~~~~~~~   93 (202)
T d2f96a1          20 TGGFNSATDALLE----IAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEPAALEFTGIK--LDHPLRMAVQEEAALTEI   93 (202)
T ss_dssp             ESSSCTTTBCEEE----EEEEEEEECTTSCEEEEEEEEEEBCCCTTCBCCHHHHHHHTCC--TTCTTCCCBCHHHHHHHH
T ss_pred             CCCCCCCCCceEE----EEEEEEEecccCceecceeEEEeeccCccccCCHHHHHhcCCc--HHHHHhcccchhHHHHHH
Confidence            5899999998877    6666554221        1122222223456777888888765  445555666666666666


Q ss_pred             HHHHHhhCC---CCCCcccCCc-HHhHHHHhhcccc
Q psy13232         75 HQFVAKYVK---PKTAPMVGEY-HTSKELLKDSDHF  106 (111)
Q Consensus        75 l~fikk~vp---~~~~pLaGNS-~~DR~FL~kymP~  106 (111)
                      +..+.+++.   ...+.++++. ..|+.|+....++
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~  129 (202)
T d2f96a1          94 FRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVAR  129 (202)
T ss_dssp             HHHHHHHHHHTTCSEEEEEETTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccccceeeeehhhhHHHHHHHHHH
Confidence            665555442   4445678888 9999999887554

>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=88.01  E-value=0.18  Score=33.38  Aligned_cols=60  Identities=8%  Similarity=0.185  Sum_probs=45.3

Q ss_pred             hhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCC--CCCCcccCCc-HHhHHHHhhc
Q psy13232         41 QNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVK--PKTAPMVGEY-HTSKELLKDS  103 (111)
Q Consensus        41 ~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp--~~~~pLaGNS-~~DR~FL~ky  103 (111)
                      ..+++.+++.|   |++++-..+..+.++|-.++++|+..+..  ......+.|. ..|++||...
T Consensus        58 ~~i~~~~~~it---git~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~L~~~  120 (200)
T d1w0ha_          58 TQLSDFCISLT---GITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQ  120 (200)
T ss_dssp             CSCCHHHHHHH---CCCHHHHHTSBCHHHHHHHHHHHHHHTTBTTTBCEEEEESSTTTTHHHHHHH
T ss_pred             ccCCHHHHHHH---CCCHHHhhhhhhhHhHHHHHHHHhcCCcEEeeeeeeeccchhhhHHHHHHHH
Confidence            35677777666   67766666789999999999999988743  3334567788 8899999764

>d1fexa_ a.4.1.3 (A:) Rap1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Rap1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.61  E-value=0.37  Score=28.63  Aligned_cols=32  Identities=9%  Similarity=0.247  Sum_probs=23.7

Q ss_pred             CCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhH
Q psy13232         64 SVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSK   97 (111)
Q Consensus        64 ~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR   97 (111)
                      ..|.+| ++.|++||+++.+. .++++||. +++-
T Consensus         4 ~fT~ee-D~~l~~yv~~~~~~-~~~~~Gn~iwk~l   36 (59)
T d1fexa_           4 AFTDAD-DVAILTYVKENARS-PSSVTGNALWKAM   36 (59)
T ss_dssp             CCCHHH-HHHHHHHHHHTCCS-TTTTTSSHHHHHH
T ss_pred             CCCHHH-HHHHHHHHHHhccC-cCCccHHHHHHHH
Confidence            345544 56789999999754 47899999 9764