Psyllid ID: psy5654

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220----
Protein Sequence
MHSNVFNIQSNTVKLVDNITHTNSSSPEQANGKVLKNNAINLTQIPLSPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Secondary Structure (PSIPRED)
cccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHcccEEEEEEccccccccccEEEEEEEEccccEEEEEccccccccccHHHHHHHccccEEEEEEcHHHHHHHHHHHHccEEccEEccccccc
Secondary Structure Prediction (SSPRO)
cccccEHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHcHHHHHHHHHHHHHHHHHcHHHcccccccccccccccccHHHHHHccEEEEccHHHHHHHHHHHHcccEEEEEEcccEcccccEEEEEEEEEccccEEEEEEccccHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHcccccccEEcEEEEcc
Coil and Loop (DISEMBL)
mhsnvfniqsNTVKLVDNithtnssspeqangkvlknnainltqiplsppeskanlthssppaslaqnqTFKQRFNSLVLKTIAQntekdqrypssnggyvannsdnfktkVLQNTKVITNIKECSSVVEELMRNElvtfdceginpgikgQITLFSLGLLSGQVYIFdlvtcpevvgtgglskllESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Flexible Loop (DISEMBL)
MHSNVFNIQSNTVKLVDNITHTnssspeqangkVLKNNAINLTQIPLSPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAqntekdqrypssngGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Low Complexity Region (SEG)
MHSNVFNIQSNTVKLVDNITHTNSSSPEQANGKVLKNNAINLTQIPLSPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Disordered region (IsUnstruct)
****************************************************************************SLVLKT***********************DNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLF*
Disordered Region (DISOPRED)
*******IQSNTVK***************************************************************LVL******************************KVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Disordered Region (DISEMBL)
MHSNVFNIQSNTVKLVDNITHTNSSSPEQANGKVLKNNAINLTQIPLSPP************ASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Disordered Region (DISPRO)
*HSNVFNIQSNTVKLVDNIT******************************************ASLAQNQTFKQRFNSLVLKTIAQNTEKDQR************SDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHSNVFNIQSNTVKLVDNITHTNSSSPEQANGKVLKNNAINLTQIPLSPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL
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	224	2.2.26 [Sep-21-2011]
Q6NRD5	444	Exonuclease 3'-5' domain-	N/A	N/A	0.415	0.209	0.340	1e-08
Q8CDF7	570	Exonuclease 3'-5' domain-	yes	N/A	0.397	0.156	0.355	3e-08
Q8NHP7	514	Exonuclease 3'-5' domain-	yes	N/A	0.419	0.182	0.326	6e-08
Q0P3U3	378	Exonuclease 3'-5' domain-	yes	N/A	0.330	0.195	0.386	5e-06
Q6AJF4	374	Ribonuclease D OS=Desulfo	yes	N/A	0.473	0.283	0.245	0.0004

>sp|Q6NRD5|EXD1_XENLA Exonuclease 3'-5' domain-containing protein 1 OS=Xenopus laevis GN=exd1 PE=2 SV=1

 Score = 60.1 bits (144), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 51/94 (54%), Gaps = 1/94 (1%)

Query: 128 VVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLE 187
            +  L   ++++    G N    G+++       S +VY+FD++     V   GL  +LE
Sbjct: 113 AIRHLQNQKVISIGAVGQNICRHGKLSWLQFATRS-RVYLFDVLVLGSKVFKNGLQMVLE 171

Query: 188 SENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
            + ++KVIHDCR    +L  Q+GI L NVFDTQ+
Sbjct: 172 DKGILKVIHDCRWLGDILSHQYGIILNNVFDTQV 205

Xenopus laevis (taxid: 8355)

>sp|Q8CDF7|EXD1_MOUSE Exonuclease 3'-5' domain-containing protein 1 OS=Mus musculus GN=Exd1 PE=2 SV=1

 Score = 58.5 bits (140), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 132 LMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENV 191
           + +  +++   EG N    G++    +   S +VY+FD+          GL  +LE + +
Sbjct: 152 IKKQSVLSVAAEGANVCRHGKLCWLQVATNS-RVYLFDIFLLGSRAFNNGLQMILEDKRI 210

Query: 192 IKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
           +KVIHDCR  S  L  Q+GI L NVFDTQ+
Sbjct: 211 LKVIHDCRWLSDCLSHQYGIMLNNVFDTQV 240

Mus musculus (taxid: 10090)

>sp|Q8NHP7|EXD1_HUMAN Exonuclease 3'-5' domain-containing protein 1 OS=Homo sapiens GN=EXD1 PE=2 SV=4

 Score = 57.8 bits (138), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 51/95 (53%), Gaps = 1/95 (1%)

Query: 127 SVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLL 186
           + +  + +  +++   EG N    G++    +   + +VY+FD+          GL  +L
Sbjct: 90  AAILHIKKQNVLSVAAEGANVCRHGKLCWLQVAT-NCRVYLFDIFLLGSRAFHNGLQMIL 148

Query: 187 ESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
           E + ++KVIHDCR  S  L  Q+GI L NVFDTQ+
Sbjct: 149 EDKRILKVIHDCRWLSDCLSHQYGILLNNVFDTQV 183

Homo sapiens (taxid: 9606)

>sp|Q0P3U3|EXD1_DANRE Exonuclease 3'-5' domain-containing protein 1 OS=Danio rerio GN=exd1 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 148 GIKGQITLFSLGLLSGQV-YIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLY 206
           G  GQ  L  L + + +V Y+FD++         GLS +LE+ +++KV+HDCR  +  L 
Sbjct: 145 GQSGQERLCWLQVATKKVVYLFDILLLGGPAFKNGLSMILENTHILKVLHDCRCITRCLR 204

Query: 207 EQFGITLRNVFDTQL 221
            +F + L NVFDTQ+
Sbjct: 205 TEFRVQLTNVFDTQV 219

Danio rerio (taxid: 7955)

>sp|Q6AJF4|RND_DESPS Ribonuclease D OS=Desulfotalea psychrophila (strain LSv54 / DSM 12343) GN=rnd PE=3 SV=1

 Score = 45.1 bits (105), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/110 (24%), Positives = 55/110 (50%), Gaps = 4/110 (3%)

Query: 113 LQNTKVITNIKECSSVVEELMRNELVTFDCEGI-NPGIKGQITLFSLGLLSGQVYIFDLV 171
           ++   +I+  ++   +V + ++ + V  D E +       Q+ L  + L   + Y  D +
Sbjct: 1   MKQENIISTTEDLKKIVNKALKLDAVGLDTEFVWERTYYPQLGLIQIALSDEECYAIDPL 60

Query: 172 TCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
           +  ++     L +LL   N IK++HD   D I++ +  G T +N+FDT+L
Sbjct: 61  SIKDL---SPLGELLADRNTIKILHDAPQDLIIMSQATGATPQNIFDTRL 107

Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.

Desulfotalea psychrophila (strain LSv54 / DSM 12343) (taxid: 177439)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 5

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	224
332021038	832	Exonuclease 3'-5' domain-containing prot	0.852	0.229	0.450	5e-44
307198047	831	Exonuclease 3'-5' domain-like-containing	0.933	0.251	0.399	2e-43
307172596	651	Exonuclease 3'-5' domain-like-containing	0.727	0.250	0.524	2e-43
383858820	823	PREDICTED: uncharacterized protein LOC10	0.799	0.217	0.492	2e-43
350401760	826	PREDICTED: hypothetical protein LOC10074	0.691	0.187	0.535	1e-42
218749845	829	egalitarian [Nasonia vitripennis]	0.799	0.215	0.455	1e-41
328780055	664	PREDICTED: hypothetical protein LOC55082	0.700	0.236	0.523	1e-41
380014058	825	PREDICTED: uncharacterized protein LOC10	0.700	0.190	0.523	2e-41
242008039	843	conserved hypothetical protein [Pediculu	0.950	0.252	0.416	3e-41
322788034	880	hypothetical protein SINV_15885 [Solenop	0.723	0.184	0.431	3e-38

>gi|332021038|gb|EGI61427.1| Exonuclease 3'-5' domain-containing protein 1 [Acromyrmex echinatior]

 Score =  183 bits (464), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 104/231 (45%), Positives = 138/231 (59%), Gaps = 40/231 (17%)

Query: 17  DNITHTNSSSPEQANGKVLKNNAINLTQIPLSPPESKANLTHS----------------- 59
           +N+ HTN+  P      ++  + I L+Q PL   ES  N   S                 
Sbjct: 283 NNVAHTNNVVP------IIPPSKIQLSQPPLDQLESVCNNATSQSNSLQNACTSPAVESN 336

Query: 60  --SPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTK 117
             SPP SL Q Q+ KQRFN++V++T+A NTE+D+   ++  G      D +K KVLQ TK
Sbjct: 337 NNSPPVSL-QQQSLKQRFNTIVMRTLADNTERDRSLQAAQMG------DAWKLKVLQQTK 389

Query: 118 VITNIKECSSVVEELMRNE--------LVTFDCEGINPGIKGQITLFSLGLLSGQVYIFD 169
           VI  ++E   V E+++           +V+FDCEGIN G++GQ+TL  +G +SGQ Y+FD
Sbjct: 390 VIATLRESLQVTEDIINPRKPPSDGKVVVSFDCEGINLGVRGQLTLVQIGTMSGQAYVFD 449

Query: 170 LVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           LVTCP +V  GGL KLLE  +V KVIHDCRNDS+ LY QF ITL NVFDTQ
Sbjct: 450 LVTCPGLVQAGGLQKLLEHPHVTKVIHDCRNDSVNLYNQFNITLTNVFDTQ 500

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307198047|gb|EFN79100.1| Exonuclease 3'-5' domain-like-containing protein 1 [Harpegnathos saltator]

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 109/273 (39%), Positives = 149/273 (54%), Gaps = 64/273 (23%)

Query: 1   MHSNVFNIQSNTVKLVDNITHTNSS-SPEQANGKVLKNNAIN---------------LTQ 44
           M  + F++QSN V L   I+ + SS +PE A G   K   +N               +  
Sbjct: 242 MFPDTFHVQSNLVTL---ISRSKSSIAPESATGLAAKTKTLNNGSGRSQSNNSSTPHMNA 298

Query: 45  IPLSPPESKANLTH-----------------------------SSPPASLAQNQTFKQRF 75
           +P+ PP SK   +                              +SPP SL Q QT KQR 
Sbjct: 299 LPIIPP-SKIQFSQPENVCNNATAQPNSLQNAYTPPPVVESNNNSPPVSL-QQQTLKQRI 356

Query: 76  NSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRN 135
           N+LV+KT+A NTE+D+   ++  G      D +K KVLQ T+VI   ++   ++E+++  
Sbjct: 357 NTLVMKTLADNTERDRSLQTAQMG------DAWKLKVLQQTRVIATPRDSLQIIEDIINP 410

Query: 136 E--------LVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLE 187
                    +++FDCEGIN G+KGQ+TL  +G +SGQ Y+FDL TCP +V  GGL KLLE
Sbjct: 411 RKPPLDGKVVISFDCEGINLGVKGQLTLVQIGTMSGQAYVFDLFTCPSLVQAGGLQKLLE 470

Query: 188 SENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
            +NV+KVIHDCRNDS+ LY QF I L NVFDTQ
Sbjct: 471 HKNVVKVIHDCRNDSVNLYNQFKIMLTNVFDTQ 503

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307172596|gb|EFN63955.1| Exonuclease 3'-5' domain-like-containing protein 1 [Camponotus floridanus]

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 95/181 (52%), Positives = 123/181 (67%), Gaps = 18/181 (9%)

Query: 48  SPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDN 107
           SP ES  N   +SPP SL Q Q+ KQRFN++V++T+A NTE+D+   ++  G      D 
Sbjct: 157 SPVESNNN---NSPPVSL-QQQSLKQRFNTIVMRTLADNTERDRSLQTAQMG------DA 206

Query: 108 FKTKVLQNTKVITNIKECSSVVEELMRNE--------LVTFDCEGINPGIKGQITLFSLG 159
           +K KVLQ T+VI   +E   V+E+++           +V+FDCEGIN G+KGQ+TL  +G
Sbjct: 207 WKLKVLQQTRVIATTRESLQVIEDIINPRKPPPDGKVVVSFDCEGINLGVKGQLTLVQIG 266

Query: 160 LLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDT 219
            +SGQ Y+FDL TCP +V  GGL KLLE  +VIKVIHDCRNDS+ LY QF ITL NVFDT
Sbjct: 267 TMSGQAYMFDLFTCPRLVQDGGLQKLLEHPHVIKVIHDCRNDSVNLYNQFTITLMNVFDT 326

Query: 220 Q 220
           Q
Sbjct: 327 Q 327

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858820|ref|XP_003704897.1| PREDICTED: uncharacterized protein LOC100875978 [Megachile rotundata]

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 103/209 (49%), Positives = 129/209 (61%), Gaps = 30/209 (14%)

Query: 20  THTNSSSPEQANGKVLKNNAINLTQIPLSPPESKANLTHSSPPASLAQNQTFKQRFNSLV 79
           THTN++            N IN  Q   SP     N   SSPP SL Q QT KQR N+LV
Sbjct: 310 THTNAT------------NQINSVQNSHSPIIETNN---SSPPVSL-QQQTLKQRINTLV 353

Query: 80  LKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNE--- 136
           +KT+A NTEKD+   ++  G      D +K KVLQ T+VI N +E   ++E+++      
Sbjct: 354 MKTLADNTEKDRTLQTAQMG------DAWKLKVLQQTRVIVNPRESLQIIEDIINPRKPP 407

Query: 137 -----LVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENV 191
                ++ FDCEGIN G+KGQ+TL  +G +SGQ Y+FDL TCP +V  GGL KLLE  +V
Sbjct: 408 PDGKIVIAFDCEGINLGVKGQLTLVQIGTMSGQAYVFDLFTCPNLVQAGGLQKLLEHNDV 467

Query: 192 IKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           IKVIHDCRNDS+ LY QF I L NVFDTQ
Sbjct: 468 IKVIHDCRNDSVNLYRQFKIMLNNVFDTQ 496

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350401760|ref|XP_003486252.1| PREDICTED: hypothetical protein LOC100742773 [Bombus impatiens]

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/170 (53%), Positives = 115/170 (67%), Gaps = 15/170 (8%)

Query: 59  SSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKV 118
           SSPP SL Q QT KQR N LV+KT+A NTEKD+   +   G      D +K K+LQ TK+
Sbjct: 334 SSPPVSL-QQQTLKQRINMLVMKTLADNTEKDRSLQTMQMG------DAWKLKILQQTKI 386

Query: 119 ITNIKECSSVVEELMRNE--------LVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDL 170
           I N +E   ++E+++           +V+FDCEGIN G+KGQ+TL  +G +SGQ Y+FDL
Sbjct: 387 IVNPRESLQIIEDIINPRKPPPNGKIVVSFDCEGINLGVKGQLTLVQIGTMSGQAYVFDL 446

Query: 171 VTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
             CP +V  GGL KLLE ++VIKVIHDCRNDS+ LY QF I L NVFDTQ
Sbjct: 447 FACPNLVQAGGLQKLLEHKDVIKVIHDCRNDSVNLYRQFKIMLNNVFDTQ 496

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|218749845|ref|NP_001136335.1| egalitarian [Nasonia vitripennis]

 Score =  175 bits (444), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 97/213 (45%), Positives = 135/213 (63%), Gaps = 34/213 (15%)

Query: 36  KNNAINL-TQIPLSP---PESKANLTHSSPPASLA----------------QNQTFKQRF 75
           +NN I+   Q+P+ P   P+S  +   S+ P SL                 Q QT KQR 
Sbjct: 288 QNNHISFNRQVPVQPSSQPDSLTSNNSSTQPNSLTSNSVEVNNSVSPTVSIQQQTLKQRI 347

Query: 76  NSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMR- 134
           NSL++KT+A+NTE+D+   ++  G      +  K+KV Q TKVI ++++C  +V+E++  
Sbjct: 348 NSLLMKTLAENTERDRSLQNAVIG------EALKSKVSQQTKVIVSVRDCLQIVDEIIYP 401

Query: 135 -------NELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLE 187
                    +V+FDCEGIN G KG++TL  +G +SG +YIFDL+TCP ++  GGL KLLE
Sbjct: 402 RKSAADGKSVVSFDCEGINVGPKGRLTLLQIGTMSGLIYIFDLITCPNILQAGGLQKLLE 461

Query: 188 SENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           SENVIKVIHDC+NDS  L+ QFGITL N+FDTQ
Sbjct: 462 SENVIKVIHDCKNDSANLFHQFGITLVNIFDTQ 494

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328780055|ref|XP_623215.2| PREDICTED: hypothetical protein LOC550822 isoform 1 [Apis mellifera]

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 90/172 (52%), Positives = 117/172 (68%), Gaps = 15/172 (8%)

Query: 57  THSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNT 116
           ++S+ P SL Q QT KQR N+LV+KT+A NTEKD+   +   G      D +K KVLQ T
Sbjct: 170 SNSTSPISL-QQQTLKQRINTLVMKTLADNTEKDRSLQTMQMG------DAWKLKVLQQT 222

Query: 117 KVITNIKECSSVVEELMRNE--------LVTFDCEGINPGIKGQITLFSLGLLSGQVYIF 168
           +VI N +E   ++E+++           +V+FDCEGIN G+KGQ+TL  +G +SGQ Y+F
Sbjct: 223 RVIVNPRESLQIIEDIINPRKPPSDGKIVVSFDCEGINLGVKGQLTLVQIGTMSGQAYVF 282

Query: 169 DLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           DL  CP +V  GGL KLLE ++VIKVIHDCRNDS+ LY QF I L NVFDTQ
Sbjct: 283 DLFACPNLVQAGGLQKLLEHKDVIKVIHDCRNDSVNLYRQFKIMLNNVFDTQ 334

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380014058|ref|XP_003691060.1| PREDICTED: uncharacterized protein LOC100862929 [Apis florea]

 Score =  174 bits (442), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 90/172 (52%), Positives = 117/172 (68%), Gaps = 15/172 (8%)

Query: 57  THSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNT 116
           ++S+ P SL Q QT KQR N+LV+KT+A NTEKD+   +   G      D +K KVLQ T
Sbjct: 331 SNSTSPISL-QQQTLKQRINTLVMKTLADNTEKDRSLQTMQMG------DAWKLKVLQQT 383

Query: 117 KVITNIKECSSVVEELMRNE--------LVTFDCEGINPGIKGQITLFSLGLLSGQVYIF 168
           +VI N +E   ++E+++           +V+FDCEGIN G+KGQ+TL  +G +SGQ Y+F
Sbjct: 384 RVIVNPRESLQIIEDIINPRKPSPDGKIVVSFDCEGINLGVKGQLTLVQIGTMSGQAYVF 443

Query: 169 DLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           DL  CP +V  GGL KLLE ++VIKVIHDCRNDS+ LY QF I L NVFDTQ
Sbjct: 444 DLFACPNLVQAGGLQKLLEHKDVIKVIHDCRNDSVNLYRQFKIMLNNVFDTQ 495

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242008039|ref|XP_002424820.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212508370|gb|EEB12082.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  174 bits (440), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 104/250 (41%), Positives = 153/250 (61%), Gaps = 37/250 (14%)

Query: 1   MHSNVFNIQSNTVKLVD-------------NITHTNSSSPEQANGK----------VLKN 37
           M+S+ F++QSN V LV+             N+ + N++     N K          +  N
Sbjct: 241 MYSDSFHVQSNLVTLVNPLKKPLQNIALKNNLNYQNNTDEANNNLKPKFLPSELPQLTDN 300

Query: 38  NAINLTQIPLSPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSN 97
           N  N T+IP SP ++  +LT   PP+   QNQT KQR NSLV+KT+A N+EKD+    + 
Sbjct: 301 N--NQTEIPYSPQKTTGSLT---PPS--IQNQTLKQRINSLVMKTLADNSEKDKNLVQNL 353

Query: 98  GGYVANN-SDNFKTKVLQNTKVITNIKECSSVVEELMRNE------LVTFDCEGINPGIK 150
             Y ++  ++ +K K++  TKVI  IKE + ++++++         +V+ DCEGIN G K
Sbjct: 354 NNYNSSGVTEQWKIKIMSVTKVINTIKESNQIIDDILSKAKEGSEVVVSVDCEGINLGSK 413

Query: 151 GQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFG 210
           G++TL  +G ++G VY+FDLVTC  +   GGL++LL S+ VIKVIHDCRNDS  +Y QFG
Sbjct: 414 GKLTLIQIGTMNGNVYVFDLVTCSNLFEAGGLARLLTSDQVIKVIHDCRNDSSTIYFQFG 473

Query: 211 ITLRNVFDTQ 220
           + LRNVFDT+
Sbjct: 474 VILRNVFDTK 483

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322788034|gb|EFZ13875.1| hypothetical protein SINV_15885 [Solenopsis invicta]

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 123/218 (56%), Gaps = 56/218 (25%)

Query: 48  SPPESKANLTHSSPPASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDN 107
           SP ES  N    SPP SL Q Q+ KQRFN++V++T+A NTE+D+   ++  G      D 
Sbjct: 330 SPAESNNN----SPPVSL-QQQSLKQRFNTIVMRTLADNTERDRSLQTAQMG------DA 378

Query: 108 FKTKVLQNTKVITNIKECSSVVEELMRNE--------LVTFDCEGINPGIKGQITLFSLG 159
           +K KVLQ T+VI   +E   V+E+++           +++FDCEGIN G+KGQ+TL  +G
Sbjct: 379 WKLKVLQQTRVIATSRESLQVIEDIINPRKPPPDGKVIISFDCEGINLGVKGQLTLVQIG 438

Query: 160 LLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIK-------------------------- 193
            +SGQ Y+FDLVTCP ++  GGL KLLE  +VIK                          
Sbjct: 439 TMSGQAYVFDLVTCPNLIQAGGLQKLLEHPHVIKVKMFYIVYNKQKYIRYIIISQRYANT 498

Query: 194 -----------VIHDCRNDSILLYEQFGITLRNVFDTQ 220
                      VIHDCRNDS+ LY QF ITL NVFDTQ
Sbjct: 499 STYVKSCLFLQVIHDCRNDSVNLYNQFKITLTNVFDTQ 536

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	224
FB|FBgn0000562	1004	egl "egalitarian" [Drosophila	0.875	0.195	0.392	3.3e-30
GENEDB_PFALCIPARUM|MAL8P1.35	406	MAL8P1.35 "exonuclease, putati	0.517	0.285	0.369	6.8e-15
UNIPROTKB|Q8IB75	406	MAL8P1.35 "Exonuclease, putati	0.517	0.285	0.369	6.8e-15
DICTYBASE|DDB_G0282387	390	DDB_G0282387 "3'-5' exonucleas	0.477	0.274	0.311	1.6e-13
WB|WBGene00015680	574	egal-1 [Caenorhabditis elegans	0.647	0.252	0.303	3.5e-12
UNIPROTKB|Q17902	574	egal-1 "Protein EGAL-1, isofor	0.647	0.252	0.303	3.5e-12
GENEDB_PFALCIPARUM|PFB0215c	416	PFB0215c "3'-5' exonuclease, p	0.508	0.274	0.317	4e-12
UNIPROTKB|O96144	416	PFB0215c "3'-5' exonuclease, p	0.508	0.274	0.317	4e-12
TAIR|locus:2043555	342	AT2G25910 [Arabidopsis thalian	0.379	0.248	0.390	1.1e-11
MGI|MGI:3045306	570	Exd1 "exonuclease 3'-5' domain	0.397	0.156	0.355	1.5e-07

FB|FBgn0000562 egl "egalitarian" [Drosophila melanogaster (taxid:7227)]

 Score = 345 (126.5 bits), Expect = 3.3e-30, P = 3.3e-30
 Identities = 84/214 (39%), Positives = 121/214 (56%)

Query:    19 ITHTNSSSPEQANGKVLKNNAINLTQIPLSPPESKAN--LTHSSPPASLAQNQTFKQRFN 76
             +   N +  ++ N  V++  A NL +   S    +      H+SP  S+A N +  Q   
Sbjct:   433 LNSVNQTLKQRINTLVIRTLAENLEKDKQSLANQQGGPISPHASPVHSIA-NSSSNQNAG 491

Query:    77 SLVLKTIAQNTEKDQRYPSSNGGYVANNS----DNFKTKVLQNTKVITNIKECSSVVEEL 132
             S      A N   +     +N  +  ++S    D +K KVLQNT VI N+K+   V + +
Sbjct:   492 SA-----ANNANSNSNANPNNANHSPSHSYFVGDTWKIKVLQNTTVIANVKQSVFVTDII 546

Query:   133 MR----NE--LVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLL 186
             ++    NE  +V+ DCEGIN G+KG+ITL  +G   G+ ++FD+ +CP +V  GGL  +L
Sbjct:   547 LKYAAKNESIVVSLDCEGINLGLKGEITLIEIGTTRGEAFLFDVQSCPAMVTDGGLKTVL 606

Query:   187 ESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
             E + VIKVIHDCRND+  LY QFGI LRNVFDTQ
Sbjct:   607 EHDQVIKVIHDCRNDAANLYLQFGILLRNVFDTQ 640

GO:0048477 "oogenesis" evidence=IDA;NAS;IMP;TAS

GO:0007312 "oocyte nucleus migration involved in oocyte dorsal/ventral axis specification" evidence=TAS

GO:0007294 "germarium-derived oocyte fate determination" evidence=IMP;NAS;TAS

GO:0007310 "oocyte dorsal/ventral axis specification" evidence=TAS

GO:0016325 "oocyte microtubule cytoskeleton organization" evidence=TAS

GO:0008298 "intracellular mRNA localization" evidence=IMP;TAS

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

GO:0005622 "intracellular" evidence=IEA

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

GO:0051028 "mRNA transport" evidence=IMP;IDA

GO:0003729 "mRNA binding" evidence=IDA

GENEDB_PFALCIPARUM|MAL8P1.35 MAL8P1.35 "exonuclease, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 195 (73.7 bits), Expect = 6.8e-15, P = 6.8e-15
 Identities = 51/138 (36%), Positives = 76/138 (55%)

Query:   100 YVANNSDNFKTKVLQNT-------KVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQ 152
             Y  NN+D  K  +L+NT       K+I N KEC    EE+ R+E++  D EG N G  G+
Sbjct:    57 YDRNNNDK-KCIILRNTESVSKDIKIIENEKECEEAAEEINRSEIIAIDFEGTNLGRYGK 115

Query:   153 ITLFSLGL----LSGQ-------VYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRND 201
             + L  + +    ++ Q        YIFDL+    V+ +    K++E++  +K+IHDCR D
Sbjct:   116 VCLMQVYVEKKNMNEQSDNILQKYYIFDLLKT-SVIKSA--QKIIENKKTLKLIHDCRED 172

Query:   202 SILLYEQFGITLRNVFDT 219
             S  LY Q G+ L NV+DT
Sbjct:   173 SSALYNQLGMKLENVYDT 190

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8IB75 MAL8P1.35 "Exonuclease, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 195 (73.7 bits), Expect = 6.8e-15, P = 6.8e-15
 Identities = 51/138 (36%), Positives = 76/138 (55%)

Query:   100 YVANNSDNFKTKVLQNT-------KVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQ 152
             Y  NN+D  K  +L+NT       K+I N KEC    EE+ R+E++  D EG N G  G+
Sbjct:    57 YDRNNNDK-KCIILRNTESVSKDIKIIENEKECEEAAEEINRSEIIAIDFEGTNLGRYGK 115

Query:   153 ITLFSLGL----LSGQ-------VYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRND 201
             + L  + +    ++ Q        YIFDL+    V+ +    K++E++  +K+IHDCR D
Sbjct:   116 VCLMQVYVEKKNMNEQSDNILQKYYIFDLLKT-SVIKSA--QKIIENKKTLKLIHDCRED 172

Query:   202 SILLYEQFGITLRNVFDT 219
             S  LY Q G+ L NV+DT
Sbjct:   173 SSALYNQLGMKLENVYDT 190

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0282387 DDB_G0282387 "3'-5' exonuclease domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 182 (69.1 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 34/109 (31%), Positives = 65/109 (59%)

Query:   115 NTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCP 174
             N  ++  + + +  + E+ + +L+  D E I  G KG I+L  +   +G++Y+FD++   
Sbjct:   164 NIYMVDCLSKMNYAIHEIKKEKLIGLDIEAIEMGKKGDISLVQISTPNGRIYLFDIIKMG 223

Query:   175 EVVGTG--GLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
               V     GL ++LES  ++KV+HDCR DS +L+ ++ + L +V+D Q+
Sbjct:   224 ANVTPFKYGLKEVLESVKILKVVHDCRRDSEILFHRYQVALAHVYDVQI 272

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

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

GO:0005622 "intracellular" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0004527 "exonuclease activity" evidence=IEA

WB|WBGene00015680 egal-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 173 (66.0 bits), Expect = 3.5e-12, P = 3.5e-12
 Identities = 48/158 (30%), Positives = 80/158 (50%)

Query:    74 RFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKV--ITNIKECSSVVEE 131
             R N + L  +     +D     S+ G   NN+  F       T++  +  +K    ++  
Sbjct:   248 RSNKVSL--VKNRLNEDGSENGSDEGEETNNNGMFPLDQSALTRIHFVKALKPAQDLISR 305

Query:   132 L------MRNELVTFDCEGINPGIKGQITLFSLGLLS--GQVYIFDLVTCPEVVGTGGLS 183
             L      M  ++V  D + +  G+ G+I L SLG+++   Q+ IFDL +   ++   G  
Sbjct:   306 LWQDINNMEKKVVGLDLKTVTVGVDGEIFL-SLGVIATTSQIGIFDLASSDVIILESGFK 364

Query:   184 KLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
              +LESE V+KVIHD R  + LL  ++ + +RNVFDTQ+
Sbjct:   365 GILESEKVVKVIHDARRVASLLAHKYAVHMRNVFDTQV 402

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

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

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

UNIPROTKB|Q17902 egal-1 "Protein EGAL-1, isoform a" [Caenorhabditis elegans (taxid:6239)]

 Score = 173 (66.0 bits), Expect = 3.5e-12, P = 3.5e-12
 Identities = 48/158 (30%), Positives = 80/158 (50%)

Query:    74 RFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKV--ITNIKECSSVVEE 131
             R N + L  +     +D     S+ G   NN+  F       T++  +  +K    ++  
Sbjct:   248 RSNKVSL--VKNRLNEDGSENGSDEGEETNNNGMFPLDQSALTRIHFVKALKPAQDLISR 305

Query:   132 L------MRNELVTFDCEGINPGIKGQITLFSLGLLS--GQVYIFDLVTCPEVVGTGGLS 183
             L      M  ++V  D + +  G+ G+I L SLG+++   Q+ IFDL +   ++   G  
Sbjct:   306 LWQDINNMEKKVVGLDLKTVTVGVDGEIFL-SLGVIATTSQIGIFDLASSDVIILESGFK 364

Query:   184 KLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
              +LESE V+KVIHD R  + LL  ++ + +RNVFDTQ+
Sbjct:   365 GILESEKVVKVIHDARRVASLLAHKYAVHMRNVFDTQV 402

GO:0005515 "protein binding" evidence=IPI

GENEDB_PFALCIPARUM|PFB0215c PFB0215c "3'-5' exonuclease, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 170 (64.9 bits), Expect = 4.0e-12, P = 4.0e-12
 Identities = 41/129 (31%), Positives = 69/129 (53%)

Query:   106 DNFKTKVLQNTKVITNIKECSSVVEE-------LMRN---ELVTFDCEGINPGIKGQITL 155
             DN   K  +N K I++ K C   V+E       L+++   +++  D EG   G  G +++
Sbjct:    37 DNIDKK--RNIKYISDCKSCKECVDEIKNGNYNLLKDFNMKMIGLDIEGYKIGKYGIVSI 94

Query:   156 FSLGLLSGQVYIFDLVTCPEV-VGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLR 214
               +      +YIFD+  C  V +    +  +LE +++IKV HDCR D  +LY Q+ I L+
Sbjct:    95 IQI--CYEDIYIFDIYKCDNVYLFINYIKDILECDDIIKVTHDCREDCSILYNQYNIHLK 152

Query:   215 NVFDTQLLF 223
             N+ DTQ+ +
Sbjct:   153 NILDTQVAY 161

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|O96144 PFB0215c "3'-5' exonuclease, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 170 (64.9 bits), Expect = 4.0e-12, P = 4.0e-12
 Identities = 41/129 (31%), Positives = 69/129 (53%)

Query:   106 DNFKTKVLQNTKVITNIKECSSVVEE-------LMRN---ELVTFDCEGINPGIKGQITL 155
             DN   K  +N K I++ K C   V+E       L+++   +++  D EG   G  G +++
Sbjct:    37 DNIDKK--RNIKYISDCKSCKECVDEIKNGNYNLLKDFNMKMIGLDIEGYKIGKYGIVSI 94

Query:   156 FSLGLLSGQVYIFDLVTCPEV-VGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLR 214
               +      +YIFD+  C  V +    +  +LE +++IKV HDCR D  +LY Q+ I L+
Sbjct:    95 IQI--CYEDIYIFDIYKCDNVYLFINYIKDILECDDIIKVTHDCREDCSILYNQYNIHLK 152

Query:   215 NVFDTQLLF 223
             N+ DTQ+ +
Sbjct:   153 NILDTQVAY 161

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2043555 AT2G25910 [Arabidopsis thaliana (taxid:3702)]

 Score = 164 (62.8 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 34/87 (39%), Positives = 51/87 (58%)

Query:   137 LVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIH 196
             ++ FDCEG++    G++ +  +   S  +Y+ D++   EV+        LES  + KVIH
Sbjct:    57 VIGFDCEGVDLCRHGKLCIMQIAF-SNAIYLVDVIEGGEVI-MKACKPALESNYITKVIH 114

Query:   197 DCRNDSILLYEQFGITLRNVFDTQLLF 223
             DC+ DS  LY QFGI L NV DTQ+ +
Sbjct:   115 DCKRDSEALYFQFGIRLHNVVDTQIAY 141

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

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

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

GO:0006623 "protein targeting to vacuole" evidence=RCA

GO:0016192 "vesicle-mediated transport" evidence=RCA

MGI|MGI:3045306 Exd1 "exonuclease 3'-5' domain containing 1" [Mus musculus (taxid:10090)]

 Score = 140 (54.3 bits), Expect = 1.5e-07, Sum P(2) = 1.5e-07
 Identities = 32/90 (35%), Positives = 49/90 (54%)

Query:   132 LMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENV 191
             + +  +++   EG N    G++    +   S +VY+FD+          GL  +LE + +
Sbjct:   152 IKKQSVLSVAAEGANVCRHGKLCWLQVATNS-RVYLFDIFLLGSRAFNNGLQMILEDKRI 210

Query:   192 IKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
             +KVIHDCR  S  L  Q+GI L NVFDTQ+
Sbjct:   211 LKVIHDCRWLSDCLSHQYGIMLNNVFDTQV 240

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005622 "intracellular" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

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

GO:0016787 "hydrolase activity" evidence=IEA

---

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	224
cd06148	197	cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease dom	1e-36
smart00474	172	smart00474, 35EXOc, 3'-5' exonuclease	1e-16
cd06142	178	cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domai	1e-14
pfam01612	172	pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease	2e-13
cd06141	170	cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain o	2e-08
PRK05755	880	PRK05755, PRK05755, DNA polymerase I; Provisional	2e-08
COG0349	361	COG0349, Rnd, Ribonuclease D [Translation, ribosom	8e-07
TIGR01388	367	TIGR01388, rnd, ribonuclease D	2e-05
cd06140	178	cd06140, DNA_polA_I_Bacillus_like_exo, inactive DE	3e-05
cd06139	193	cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' ex	4e-04
cd06129	161	cd06129, RNaseD_like, DEDDy 3'-5' exonuclease doma	0.003
cd09018	150	cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' e	0.003

>gnl|CDD|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

 Score =  127 bits (320), Expect = 1e-36
 Identities = 42/92 (45%), Positives = 62/92 (67%)

Query: 129 VEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLES 188
           +  L + +++  DCEG+N G KG++ L  +   +GQ+Y+FD++    +V   GL  +LES
Sbjct: 4   IIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILES 63

Query: 189 ENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
           + ++KVIHDCR DS  LY Q+GI L NVFDTQ
Sbjct: 64  KKILKVIHDCRRDSDALYHQYGIKLNNVFDTQ 95

The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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 conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif. Length = 197

>gnl|CDD|214681 smart00474, 35EXOc, 3'-5' exonuclease

 Score = 74.3 bits (183), Expect = 1e-16
 Identities = 30/107 (28%), Positives = 50/107 (46%), Gaps = 5/107 (4%)

Query: 118 VITNIKECSSVVEELMRNEL-VTFDCEGINPGIK-GQITLFSLGLLSGQVYIFDLVTCPE 175
           V+T+ +    ++E+L      V  D E        G++ L  + +     +I D +   +
Sbjct: 3   VVTDSETLEELLEKLRAAGGEVALDTETTGLDSYSGKLVLIQISVTGEGAFIIDPLALGD 62

Query: 176 VVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLL 222
            +    L  LLE E + KV H+ + D  +L  +FGI L N+FDT L 
Sbjct: 63  DLE--ILKDLLEDETITKVGHNAKFDLHVLA-RFGIELENIFDTMLA 106

3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes. Length = 172

>gnl|CDD|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins

 Score = 69.1 bits (170), Expect = 1e-14
 Identities = 30/99 (30%), Positives = 46/99 (46%), Gaps = 13/99 (13%)

Query: 128 VVEELMRNELVTFDCEGINPGIKGQITLFS-LGLL----SGQVYIFDLVTCPEVVGTGGL 182
           + E L    ++  D E +        T +  L L+     G+VY+ D +   +      L
Sbjct: 5   LCERLASAGVIAVDTEFM-----RLNTYYPRLCLIQISTGGEVYLIDPLAIGD---LSPL 56

Query: 183 SKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
            +LL   N++KV H  R D  LL   FGI  +N+FDTQ+
Sbjct: 57  KELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQI 95

Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein. Length = 178

>gnl|CDD|216604 pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 33/106 (31%), Positives = 50/106 (47%), Gaps = 6/106 (5%)

Query: 119 ITNIKECSSVVEELMRNELVTFDCEGIN---PGIKGQITLFSLGLLSGQVYIFDLVTCPE 175
           +T   E   ++EEL+  ++V  D E  +           L  +    G  YI D +   +
Sbjct: 4   VTTEDELEDLIEELLNAKVVAVDTETTSLDTYSYTLVGCLIQISTGEG-AYIIDPLALGD 62

Query: 176 VVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
            +   GL +LLE  N+ KV H+ + D  +L   FGI L N+FDT L
Sbjct: 63  DLE--GLKRLLEDPNITKVGHNAKFDLEVLARDFGIKLENLFDTML 106

This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome. Length = 172

>gnl|CDD|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar proteins

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 5/108 (4%)

Query: 119 ITNIKECSSVVEELMRNELVT-FDCEGINPGIKGQITLFSLGLLS--GQVYIFDLVTCPE 175
             + ++    V+EL+  E V  FD E      KG+    +L  L+   +  +F L    +
Sbjct: 1   TDSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDK 60

Query: 176 VVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLF 223
           +     L +LLE  +++KV    + D+  L   FGI +R V D   L 
Sbjct: 61  L--PPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLA 106

WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability. Length = 170

>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional

 Score = 53.6 bits (130), Expect = 2e-08
 Identities = 28/109 (25%), Positives = 49/109 (44%), Gaps = 6/109 (5%)

Query: 117 KVITNIKECSSVVEELMRNELVTFDCE--GINPGIKGQITLFSLGLLSGQVYIFDLVTCP 174
           + I + +E  + + +L    L  FD E   ++P ++ ++   S  +  G+     L    
Sbjct: 297 ETILDEEELEAWLAKLKAAGLFAFDTETTSLDP-MQAELVGLSFAVEPGEAAYIPLDQLD 355

Query: 175 EVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNV-FDTQLL 222
             V    L  LLE   + KV  + + D  +L  ++GI LR + FDT L 
Sbjct: 356 REV-LAALKPLLEDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDTMLA 402

Length = 880

>gnl|CDD|223426 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis]

 Score = 48.4 bits (116), Expect = 8e-07
 Identities = 16/40 (40%), Positives = 22/40 (55%)

Query: 182 LSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
           L  LL   NV+K+ H  R D  +L   FG+    +FDTQ+
Sbjct: 62  LVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQI 101

Length = 361

>gnl|CDD|130455 TIGR01388, rnd, ribonuclease D

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 31/110 (28%), Positives = 48/110 (43%), Gaps = 13/110 (11%)

Query: 118 VITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLF--SLGLLSGQVYIFD--LVTC 173
            IT   E ++V E +     V  D E +      +   F   LGL+  QV   +   +  
Sbjct: 1   WITTDDELATVCEAVRTFPFVALDTEFV------RERTFWPQLGLI--QVADGEQLALID 52

Query: 174 PEVVG-TGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLL 222
           P V+     L +LL  E+V+KV+H    D  +    FG   + +FDTQ+ 
Sbjct: 53  PLVIIDWSPLKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIA 102

This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown [Transcription, RNA processing]. Length = 367

>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases

 Score = 43.0 bits (102), Expect = 3e-05
 Identities = 24/85 (28%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 138 VTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHD 197
           +  +  G N      I   +L    G  Y   L           L + LE E + KV HD
Sbjct: 8   LYVELLGENYH-TADIIGLALAN-GGGAYYIPLELALLD--LAALKEWLEDEKIPKVGHD 63

Query: 198 CRNDSILLYEQFGITLRNV-FDTQL 221
            +   + L  + GI L  V FDT L
Sbjct: 64  AKRAYVALK-RHGIELAGVAFDTML 87

Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases. Length = 178

>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases

 Score = 39.8 bits (94), Expect = 4e-04
 Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 17/104 (16%)

Query: 131 ELMRNELVTFDCE--GINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSK---- 184
           EL + ++  FD E   ++P  + ++   S  +  G+ Y   L       G   L +    
Sbjct: 1   ELEKAKVFAFDTETTSLDPM-QAELVGISFAVEPGEAYYIPL---GHDYGGEQLPREEVL 56

Query: 185 -----LLESENVIKVIHDCRNDSILLYEQFGITLRNV-FDTQLL 222
                LLE  ++ KV  + + D  +L    GI LR   FDT L 
Sbjct: 57  AALKPLLEDPSIKKVGQNLKFDLHVLANH-GIELRGPAFDTMLA 99

Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. Length = 193

>gnl|CDD|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 32/102 (31%), Positives = 51/102 (50%), Gaps = 6/102 (5%)

Query: 124 ECSSVVEEL-MRNELVTFDCEGINPGIK--GQITLFSLGLLSGQVYIFDLVTCPEVVGTG 180
             SS+ E+L M  +++ FD E   PG +  G++ L  L +   + Y+FD       V   
Sbjct: 1   ALSSLCEDLSMDGDVIAFDMEWP-PGRRYYGEVALIQLCVSEEKCYLFD--PLSLSVDWQ 57

Query: 181 GLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLL 222
           GL  LLE+ +++K +H    D   L   FG  L+ +FDT + 
Sbjct: 58  GLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIA 99

The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif. Length = 161

>gnl|CDD|176656 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 149 IKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQ 208
           I   + L  L +  G   +  +    + +    L  LLE E  +KV  + + D  +L   
Sbjct: 14  ISANLVLIQLAIEPGVAALIPVAH--DYLALELLKPLLEDEKALKVGQNLKYDRGILLNY 71

Query: 209 FGITLRNVFDTQLL 222
           F       FDT L 
Sbjct: 72  FIELRGIAFDTMLE 85

DEDDy 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. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity. Length = 150

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	224
PRK10829	373	ribonuclease D; Provisional	99.64
cd06129	161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	99.59
TIGR01388	367	rnd ribonuclease D. This model describes ribonucle	99.58
cd06148	197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	99.58
PF01612	176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	99.58
cd06146	193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	99.55
cd06141	170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	99.51
COG0349	361	Rnd Ribonuclease D [Translation, ribosomal structu	99.44
smart00474	172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	99.23
cd06147	192	Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y	99.17
cd06142	178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	99.16
PRK05755	880	DNA polymerase I; Provisional	99.03
KOG2206|consensus	687		98.96
cd09018	150	DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease	98.88
cd00007	155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	98.75
cd06140	178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	98.72
cd06139	193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	98.52
COG0749	593	PolA DNA polymerase I - 3'-5' exonuclease and poly	98.36
cd06128	151	DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam	98.25
TIGR00593	887	pola DNA polymerase I. This family is based on the	98.15
cd06125	96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	97.3
KOG2405|consensus	458		97.2
KOG2207|consensus	617		97.03
PRK14975	553	bifunctional 3'-5' exonuclease/DNA polymerase; Pro	96.49
KOG2405|consensus	458		88.5

>PRK10829 ribonuclease D; Provisional

Probab=99.64  E-value=1e-15  Score=142.28  Aligned_cols=104  Identities=23%  Similarity=0.236  Sum_probs=95.6

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      |.+|+++++++.+++.+...+++++|+|+... .+++++|++||++. +.+|+||+.+..+.   +.|+++|+++.+.||
T Consensus         3 ~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~-~~~~LiD~l~~~d~---~~L~~ll~~~~ivKV   78 (373)
T PRK10829          3 YQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDG-EQLSLIDPLGITDW---SPFKALLRDPQVTKF   78 (373)
T ss_pred             cEEeCCHHHHHHHHHHHhcCCeEEEecccccCccCCCceeEEEEecC-CceEEEecCCccch---HHHHHHHcCCCeEEE
Confidence            78999999999999999999999999999877 78899999999975 57999999877554   689999999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +|++++|+..|++.+|+.+.++||||+|+
T Consensus        79 ~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa  107 (373)
T PRK10829         79 LHAGSEDLEVFLNAFGELPQPLIDTQILA  107 (373)
T ss_pred             EeChHhHHHHHHHHcCCCcCCeeeHHHHH
Confidence            99999999999888999999999999986

>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins

Probab=99.59  E-value=5.9e-15  Score=121.21  Aligned_cols=97  Identities=29%  Similarity=0.459  Sum_probs=84.9

Q ss_pred             HHHHHHHHc-cCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHH
Q psy5654         125 CSSVVEELM-RNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDS  202 (224)
Q Consensus       125 La~lie~L~-~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl  202 (224)
                      ++++++.+. ...++|||+|+.+. .+.++++++||++..+.+|+||+.......  ..|+++|+++.+.||+|++|.|+
T Consensus         2 l~~~~~~l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~~~--~~L~~lL~d~~i~Kvg~~~k~D~   79 (161)
T cd06129           2 LSSLCEDLSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDW--QGLKMLLENPSIVKALHGIEGDL   79 (161)
T ss_pred             HHHHHHHHhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCccCH--HHHHHHhCCCCEEEEEeccHHHH
Confidence            567788888 89999999999877 566899999999964789999998765333  57899999999999999999999


Q ss_pred             HHHHHhcCCccCCccchhhcc
Q psy5654         203 ILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       203 ~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      ..|.+.+|+.+.++|||++|+
T Consensus        80 ~~L~~~~gi~~~~~~D~~~aa  100 (161)
T cd06129          80 WKLLRDFGEKLQRLFDTTIAA  100 (161)
T ss_pred             HHHHHHcCCCcccHhHHHHHH
Confidence            999777999999999999975

The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-

>TIGR01388 rnd ribonuclease D

Probab=99.58  E-value=7.3e-15  Score=136.14  Aligned_cols=102  Identities=26%  Similarity=0.315  Sum_probs=90.7

Q ss_pred             EecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEE
Q psy5654         118 VITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIH  196 (224)
Q Consensus       118 vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~H  196 (224)
                      +|++.++++.+++.+..+++++||+|+... .+++++|++|+++. +.+|+||+....+.   ..|+++|+++.+.||+|
T Consensus         1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~-~~~~liD~~~~~~~---~~L~~lL~d~~i~KV~h   76 (367)
T TIGR01388         1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADG-EQLALIDPLVIIDW---SPLKELLRDESVVKVLH   76 (367)
T ss_pred             CcCCHHHHHHHHHHHhcCCEEEEeccccCCCCCCCcceEEEEeeC-CeEEEEeCCCcccH---HHHHHHHCCCCceEEEe
Confidence            367899999999999999999999999877 78899999999985 57899999876443   68999999999999999


Q ss_pred             ecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         197 DCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       197 d~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      ++|+|+..|++.+|+.+.++||||+|+
T Consensus        77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa  103 (367)
T TIGR01388        77 AASEDLEVFLNLFGELPQPLFDTQIAA  103 (367)
T ss_pred             ecHHHHHHHHHHhCCCCCCcccHHHHH
Confidence            999999999876777778899999986

This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.

>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

Probab=99.58  E-value=5.9e-15  Score=125.39  Aligned_cols=94  Identities=44%  Similarity=0.833  Sum_probs=82.3

Q ss_pred             HHHHHccCCeEEEEEeeeCCCccceEEEEEEEeeCCeEEEEeCCCCcc--ccccchhHhhhcCCCceEEEEecHHHHHHH
Q psy5654         128 VVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPE--VVGTGGLSKLLESENVIKVIHDCRNDSILL  205 (224)
Q Consensus       128 lie~L~~~~~Ia~D~E~~~l~~~g~L~lIQIat~~g~a~lIDi~al~~--l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL  205 (224)
                      .++.+..+..+|||+|+...+.+|+++++|+++..+.+|+||+.+++.  ..  ..|+++|+++.+.||+||+|.|+..|
T Consensus         3 ~~~~l~~~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~--~~L~~iLe~~~i~Kv~h~~k~D~~~L   80 (197)
T cd06148           3 AIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFI--NGLKDILESKKILKVIHDCRRDSDAL   80 (197)
T ss_pred             hhhhhhhCCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHH--HHHHHHhcCCCccEEEEechhHHHHH
Confidence            456677789999999998776689999999998647999999998752  22  57899999999999999999999999


Q ss_pred             HHhcCCccCCccchhhcc
Q psy5654         206 YEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       206 ~~~~GI~L~nvFDTqLAa  223 (224)
                      ++.+|+.+.++|||++|+
T Consensus        81 ~~~~gi~~~~~fDt~iA~   98 (197)
T cd06148          81 YHQYGIKLNNVFDTQVAD   98 (197)
T ss_pred             HHhcCccccceeeHHHHH
Confidence            778999999999999985

The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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 conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.

>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides

Probab=99.58  E-value=2.1e-14  Score=116.37  Aligned_cols=105  Identities=31%  Similarity=0.480  Sum_probs=89.8

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-C--ccceEEEEEEEeeCCeEEEEeCCCCccc--cccchhHhhhcCCC
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-G--IKGQITLFSLGLLSGQVYIFDLVTCPEV--VGTGGLSKLLESEN  190 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~--~~g~L~lIQIat~~g~a~lIDi~al~~l--~~~~~Lr~lLed~~  190 (224)
                      |++|++.+++.++++.+.....++||+|+.+. .  ..+.++++|+++. ..+|+++.......  .  ..|+++|+++.
T Consensus         1 y~~v~~~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~-~~~~i~~~~~~~~~~~~--~~l~~ll~~~~   77 (176)
T PF01612_consen    1 YQIVDTEEELEEAIKKLKNAKVLAFDTETTGLDPYSYNPKIALIQLATG-EGCYIIDPIDLGDNWIL--DALKELLEDPN   77 (176)
T ss_dssp             SEEEHSHHHHHHHHHHHTTTSEEEEEEEEETSTSTTSSEEEEEEEEEES-CEEEEECGTTSTTTTHH--HHHHHHHTTTT
T ss_pred             CEecCCHHHHHHHHHHHcCCCeEEEEEEECCCCccccCCeEEEEEEecC-CCceeeeeccccccchH--HHHHHHHhCCC
Confidence            57899999999999999999999999999877 4  4677999999986 57788887765542  3  57999999999


Q ss_pred             ceEEEEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         191 VIKVIHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       191 I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +.||+||+|+|..+|++.+|+.+.+++|||+|+
T Consensus        78 i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~  110 (176)
T PF01612_consen   78 IIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAA  110 (176)
T ss_dssp             SEEEESSHHHHHHHHHHHHTS--SSEEEHHHHH
T ss_pred             ccEEEEEEechHHHHHHHhccccCCccchhhhh
Confidence            999999999999999877999999999999875

This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....

>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins

Probab=99.55  E-value=2.3e-14  Score=121.63  Aligned_cols=106  Identities=20%  Similarity=0.282  Sum_probs=89.4

Q ss_pred             cEEecCHHHHHHHHHH--HccCCeEEEEEeeeCC---CccceEEEEEEEeeCCeEEEEeCCCCcc----ccccchhHhhh
Q psy5654         116 TKVITNIKECSSVVEE--LMRNELVTFDCEGINP---GIKGQITLFSLGLLSGQVYIFDLVTCPE----VVGTGGLSKLL  186 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~--L~~~~~Ia~D~E~~~l---~~~g~L~lIQIat~~g~a~lIDi~al~~----l~~~~~Lr~lL  186 (224)
                      +.+|++++++.+++++  +....++|||+|+...   +..++++++||++. +.+|+||+..++.    .+. ..|+++|
T Consensus         1 ~~~i~~~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~-~~~~lid~~~~~~~~~~~~~-~~L~~ll   78 (193)
T cd06146           1 IHIVDSEEELEALLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATE-DEVFLLDLLALENLESEDWD-RLLKRLF   78 (193)
T ss_pred             CeEecCHHHHHHHHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecC-CCEEEEEchhccccchHHHH-HHHHHHh
Confidence            4688999999999999  8889999999999755   23688999999985 6899999987641    111 4689999


Q ss_pred             cCCCceEEEEecHHHHHHHHHhcCCc------cCCccchhhcc
Q psy5654         187 ESENVIKVIHDCRNDSILLYEQFGIT------LRNVFDTQLLF  223 (224)
Q Consensus       187 ed~~I~KV~Hd~K~Dl~lL~~~~GI~------L~nvFDTqLAa  223 (224)
                      +++.+.||||+++.|+..|++.+|+.      +.++|||+.++
T Consensus        79 ~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a  121 (193)
T cd06146          79 EDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLA  121 (193)
T ss_pred             CCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHH
Confidence            99999999999999999999889974      57899998653

The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.

>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins

Probab=99.51  E-value=9.8e-14  Score=113.91  Aligned_cols=101  Identities=26%  Similarity=0.416  Sum_probs=88.4

Q ss_pred             cCHHHHHHHHHHHc-cCCeEEEEEeeeCC-C--ccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEE
Q psy5654         120 TNIKECSSVVEELM-RNELVTFDCEGINP-G--IKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVI  195 (224)
Q Consensus       120 dt~eeLa~lie~L~-~~~~Ia~D~E~~~l-~--~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~  195 (224)
                      +++.++..+++.+. ....+|||+|+.+. .  ..+.++++|+|+. +.+|+||+.......  ..|+++|+++.+.||+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~-~~~~l~~~~~~~~~~--~~l~~ll~~~~i~kv~   78 (170)
T cd06141           2 DSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATE-SRCLLFQLAHMDKLP--PSLKQLLEDPSILKVG   78 (170)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEEeCccCCccCCCCCCCceEEEEecC-CcEEEEEhhhhhccc--HHHHHHhcCCCeeEEE
Confidence            46778999999998 89999999999876 3  6788999999974 689999998764443  5799999999999999


Q ss_pred             EecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         196 HDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       196 Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      |++|.|+..|.+.+|+.+.++|||++|+
T Consensus        79 ~~~k~D~~~L~~~~g~~~~~~~Dl~~aa  106 (170)
T cd06141          79 VGIKGDARKLARDFGIEVRGVVDLSHLA  106 (170)
T ss_pred             eeeHHHHHHHHhHcCCCCCCeeeHHHHH
Confidence            9999999999878999999999999985

WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.

>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]

Probab=99.44  E-value=2.2e-13  Score=125.55  Aligned_cols=101  Identities=23%  Similarity=0.270  Sum_probs=90.2

Q ss_pred             cCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCc-cccccchhHhhhcCCCceEEEEe
Q psy5654         120 TNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCP-EVVGTGGLSKLLESENVIKVIHD  197 (224)
Q Consensus       120 dt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~-~l~~~~~Lr~lLed~~I~KV~Hd  197 (224)
                      ++.+.++.++..+..++.+++|+|+... ++++++|+||++..++ +++||+.... +.   ..|..+|.|++|.||+|.
T Consensus         2 ~~~~~l~~~~~~~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~-~~lIdpl~~~~d~---~~l~~Ll~d~~v~KIfHa   77 (361)
T COG0349           2 TTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEG-ASLIDPLAGILDL---PPLVALLADPNVVKIFHA   77 (361)
T ss_pred             CchhHHHHHHHHhcCCCceEEecccccccccCCceEEEEEecCCC-ceEeccccccccc---chHHHHhcCCceeeeecc
Confidence            4566788899998889999999999988 9999999999998766 9999998743 33   578999999999999999


Q ss_pred             cHHHHHHHHHhcCCccCCccchhhccC
Q psy5654         198 CRNDSILLYEQFGITLRNVFDTQLLFL  224 (224)
Q Consensus       198 ~K~Dl~lL~~~~GI~L~nvFDTqLAa~  224 (224)
                      +++|+.+|++.||+.+.++|||++|++
T Consensus        78 a~~DL~~l~~~~g~~p~plfdTqiAa~  104 (361)
T COG0349          78 ARFDLEVLLNLFGLLPTPLFDTQIAAK  104 (361)
T ss_pred             ccccHHHHHHhcCCCCCchhHHHHHHH
Confidence            999999999999999999999999973

>smart00474 35EXOc 3'-5' exonuclease

Probab=99.23  E-value=8.9e-11  Score=94.17  Aligned_cols=104  Identities=29%  Similarity=0.438  Sum_probs=78.5

Q ss_pred             EEecCHHHHHHHHHHHc-cCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         117 KVITNIKECSSVVEELM-RNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       117 ~vIdt~eeLa~lie~L~-~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      .+|++.+++..+++.+. ....+++|+|+... .+.+++++++++...+.+|+++........  ..|+++|+++.+.||
T Consensus         2 ~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~--~~l~~~l~~~~~~kv   79 (172)
T smart00474        2 RVVTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDL--EILKDLLEDETITKV   79 (172)
T ss_pred             EEecCHHHHHHHHHHHHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhH--HHHHHHhcCCCceEE
Confidence            46777787888776665 45689999987655 456889999999642244544332222212  358899999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +||+|.|.+.|.+ +|+.+.++||||+|+
T Consensus        80 ~~d~k~~~~~L~~-~gi~~~~~~D~~laa  107 (172)
T smart00474       80 GHNAKFDLHVLAR-FGIELENIFDTMLAA  107 (172)
T ss_pred             EechHHHHHHHHH-CCCcccchhHHHHHH
Confidence            9999999999974 999998889999986

3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes

>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins

Probab=99.17  E-value=3e-10  Score=95.41  Aligned_cols=105  Identities=23%  Similarity=0.320  Sum_probs=80.7

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      |.++++++++..+++.+...+.+++++|+... ++.+++++++++..++ +|+||+.......  ..|+++|+++.+.|+
T Consensus         5 ~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~-~~~i~~l~~~~~~--~~L~~~L~~~~i~kv   81 (192)
T cd06147           5 LTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREE-DYIVDTLKLRDDM--HILNEVFTDPNILKV   81 (192)
T ss_pred             cEEECCHHHHHHHHHHHhcCCeEEEEeEecCCccCCCceEEEEEecCCC-cEEEEecccccch--HHHHHHhcCCCceEE
Confidence            66786667778877666555689999976554 5578899999997554 7888742221111  358899999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +||+|.+++.|.+.+|+.+.++||||+|+
T Consensus        82 ~~d~K~~~~~L~~~~gi~~~~~fD~~laa  110 (192)
T cd06147          82 FHGADSDIIWLQRDFGLYVVNLFDTGQAA  110 (192)
T ss_pred             EechHHHHHHHHHHhCCCcCchHHHHHHH
Confidence            99999999999647999997779999986

Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.

>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins

Probab=99.16  E-value=2.3e-10  Score=93.43  Aligned_cols=95  Identities=29%  Similarity=0.449  Sum_probs=73.5

Q ss_pred             HHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHH
Q psy5654         125 CSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSI  203 (224)
Q Consensus       125 La~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~  203 (224)
                      +.++++.+...+.+++|+|+... +..++++++++++. +.+|+||+... ...  ..|+++|+++.+.||+||+|.|.+
T Consensus         2 ~~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~-~~~~~i~~~~~-~~~--~~l~~ll~~~~i~kv~~d~K~~~~   77 (178)
T cd06142           2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTG-GEVYLIDPLAI-GDL--SPLKELLADPNIVKVFHAAREDLE   77 (178)
T ss_pred             HHHHHHHHhcCCeEEEECCccCCCcCCCceEEEEEeeC-CCEEEEeCCCc-ccH--HHHHHHHcCCCceEEEeccHHHHH
Confidence            34455555445689999987554 44688999999986 56899986533 222  468899999999999999999999


Q ss_pred             HHHHhcCCccCCccchhhcc
Q psy5654         204 LLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       204 lL~~~~GI~L~nvFDTqLAa  223 (224)
                      .|.+.+|+..+++|||++|+
T Consensus        78 ~L~~~~gi~~~~~~D~~laa   97 (178)
T cd06142          78 LLKRDFGILPQNLFDTQIAA   97 (178)
T ss_pred             HHHHHcCCCCCCcccHHHHH
Confidence            99766699955679999985

Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.

>PRK05755 DNA polymerase I; Provisional

Probab=99.03  E-value=1.2e-09  Score=111.21  Aligned_cols=137  Identities=22%  Similarity=0.290  Sum_probs=105.3

Q ss_pred             cchHHHHHHHHHHHHHHhhcccCCCCCCCCCCccccCCCCccccCCCCcEEecCHHHHHHHHHHHccCCeEEEEEeeeCC
Q psy5654          68 NQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINP  147 (224)
Q Consensus        68 ~~~~~q~~~~~~~~~l~~n~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l  147 (224)
                      ...|..=+..+.++.|....+-..        .+       ..+.+ .|.+|++++++..+++.+.....+++|+|+...
T Consensus       264 ~~~l~~~~~~~~~~~~~~~~~~~~--------~~-------~~~~~-~~~~I~~~~~L~~~l~~l~~~~~~a~DtEt~~l  327 (880)
T PRK05755        264 REKLIALFKELEFKSLLRRAAAAE--------AA-------PLDEE-DYETILDEEELEAWLAKLKAAGLFAFDTETTSL  327 (880)
T ss_pred             HHHHHHHHHHhCcHHHHHHhhccc--------cc-------cCCCC-ceEEeCCHHHHHHHHHHhhccCeEEEEeccCCC
Confidence            356777777788888776421000        00       01112 267888999999999998888899999999877


Q ss_pred             -CccceEEEEEEEeeCCeEEEEeCCCCc-cccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc-CCccchhhcc
Q psy5654         148 -GIKGQITLFSLGLLSGQVYIFDLVTCP-EVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL-RNVFDTQLLF  223 (224)
Q Consensus       148 -~~~g~L~lIQIat~~g~a~lIDi~al~-~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L-~nvFDTqLAa  223 (224)
                       ++.+++++++++..++.++++|+...+ ...  ..|+++|+++.+.||+||+|+|+.+|. .+|+.+ ..+||||+|+
T Consensus       328 ~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l--~~l~~~L~d~~v~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa  403 (880)
T PRK05755        328 DPMQAELVGLSFAVEPGEAAYIPLDQLDREVL--AALKPLLEDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDTMLAS  403 (880)
T ss_pred             CcccccEEEEEEEeCCCcEEEEecccccHHHH--HHHHHHHhCCCCcEEEeccHhHHHHHH-hCCCCcCCCcccHHHHH
Confidence             788999999999877778999885433 222  578899999999999999999999997 489987 5689999985

>KOG2206|consensus

Probab=98.96  E-value=2.2e-10  Score=110.71  Aligned_cols=104  Identities=24%  Similarity=0.317  Sum_probs=94.9

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      +.+|++..++.++.+.+....++++|.|.... .+.|-.|++||+|.+ +.|+||...+.+.+  +.|++.|.+|.+.||
T Consensus       193 ~~~I~t~~el~~l~~~l~~~~Efavdlehhsyrsf~gltclmqISTr~-ed~iIDt~~l~~~i--~~l~e~fsdp~ivkv  269 (687)
T KOG2206|consen  193 KVWICTLGELEALPEILDSVIEFAVDLEHHSYRSFLGLTCLMQISTRT-EDFIIDTFKLRDHI--GILNEVFSDPGIVKV  269 (687)
T ss_pred             ceeeechHHHHHHHHHHhhhhhhhhhccccchhhhcCceeEEEeeccc-hhheehhHHHHHHH--HHhhhhccCCCeEEE
Confidence            57789999999999999889999999999888 888999999999964 77999998887666  789999999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLL  222 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLA  222 (224)
                      +|++..|+.||++.|||.+.++|||.-|
T Consensus       270 fhgaD~diiwlqrdfgiyvvnLfdt~~a  297 (687)
T KOG2206|consen  270 FHGADTDIIWLQRDFGIYVVNLFDTIQA  297 (687)
T ss_pred             EecCccchhhhhccceEEEEechhhHHH
Confidence            9999999999999999999999999766

>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins

Probab=98.88  E-value=8.6e-09  Score=81.61  Aligned_cols=83  Identities=28%  Similarity=0.325  Sum_probs=64.2

Q ss_pred             EEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccC-C
Q psy5654         138 VTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLR-N  215 (224)
Q Consensus       138 Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~-n  215 (224)
                      +++|+|+.+. ++.++++++|++..++.+|++++.......  ..|+++|+++.+.|++||+|.|++.|. ..|+.+. +
T Consensus         2 ~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~--~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~   78 (150)
T cd09018           2 FAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLAL--ELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGI   78 (150)
T ss_pred             EEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCcccCH--HHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCc
Confidence            6788876554 457889999999754558888865321012  468899999999999999999999996 5787774 5


Q ss_pred             ccchhhcc
Q psy5654         216 VFDTQLLF  223 (224)
Q Consensus       216 vFDTqLAa  223 (224)
                      +||||+|+
T Consensus        79 ~~D~~laa   86 (150)
T cd09018          79 AFDTMLEA   86 (150)
T ss_pred             chhHHHHH
Confidence            69999986

DEDDy 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. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle

>cd00007 35EXOc 3'-5' exonuclease

Probab=98.75  E-value=3.7e-08  Score=77.41  Aligned_cols=83  Identities=31%  Similarity=0.373  Sum_probs=61.5

Q ss_pred             eEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCC-ccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc-
Q psy5654         137 LVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTC-PEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL-  213 (224)
Q Consensus       137 ~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al-~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L-  213 (224)
                      .+++|+|+.+. ++.++++++++++. +.+++++.... ....  ..++++|+++.+.||+||+|+|...|.+ .|+.. 
T Consensus         2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~i~~~~~~~~~~--~~l~~~l~~~~~~~v~~~~k~d~~~L~~-~~~~~~   77 (155)
T cd00007           2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAYIPDELELEEDL--EALKELLEDEDITKVGHDAKFDLVVLAR-DGIELP   77 (155)
T ss_pred             ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEEEEcCCCHHHHH--HHHHHHHcCCCCcEEeccHHHHHHHHHH-CCCCCC
Confidence            47889987654 45788999999975 44666654322 1122  3588899999999999999999999965 55544 


Q ss_pred             CCccchhhcc
Q psy5654         214 RNVFDTQLLF  223 (224)
Q Consensus       214 ~nvFDTqLAa  223 (224)
                      ..+|||++|+
T Consensus        78 ~~~~D~~~~a   87 (155)
T cd00007          78 GNIFDTMLAA   87 (155)
T ss_pred             CCcccHHHHH
Confidence            5679999985

The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).

>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases

Probab=98.72  E-value=3.8e-08  Score=80.87  Aligned_cols=85  Identities=26%  Similarity=0.265  Sum_probs=66.7

Q ss_pred             CCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc
Q psy5654         135 NELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL  213 (224)
Q Consensus       135 ~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L  213 (224)
                      .+.+++++|.... ++.+++++++++..+ ++|++++.......  ..++++|+++.+.|++||+|++++.|. .+|+.+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~~i~~~~~~~~~--~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~   78 (178)
T cd06140           3 ADEVALYVELLGENYHTADIIGLALANGG-GAYYIPLELALLDL--AALKEWLEDEKIPKVGHDAKRAYVALK-RHGIEL   78 (178)
T ss_pred             CCceEEEEEEcCCCcceeeEEEEEEEeCC-cEEEEeccchHHHH--HHHHHHHhCCCCceeccchhHHHHHHH-HCCCcC
Confidence            3567889888766 678899999999754 68888753210111  458889999999999999999999996 599998


Q ss_pred             CC-ccchhhcc
Q psy5654         214 RN-VFDTQLLF  223 (224)
Q Consensus       214 ~n-vFDTqLAa  223 (224)
                      .+ +||||+|+
T Consensus        79 ~~~~fDt~laa   89 (178)
T cd06140          79 AGVAFDTMLAA   89 (178)
T ss_pred             CCcchhHHHHH
Confidence            54 69999986

Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.

>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases

Probab=98.52  E-value=3.6e-07  Score=75.31  Aligned_cols=87  Identities=30%  Similarity=0.434  Sum_probs=66.6

Q ss_pred             cCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCC------c--cccccchhHhhhcCCCceEEEEecHHHHHH
Q psy5654         134 RNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTC------P--EVVGTGGLSKLLESENVIKVIHDCRNDSIL  204 (224)
Q Consensus       134 ~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al------~--~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~l  204 (224)
                      +.+.+++|+|..+. ++.+++++++++..++..+++++...      .  ...  ..|+++|++..+.+|+||+|+|+.+
T Consensus         4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~~~~~~v~hn~k~d~~~   81 (193)
T cd06139           4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVL--AALKPLLEDPSIKKVGQNLKFDLHV   81 (193)
T ss_pred             cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHH--HHHHHHHhCCCCcEEeeccHHHHHH
Confidence            45679999987665 56788999999976555788875431      1  111  3488899998889999999999999


Q ss_pred             HHHhcCCccC-Cccchhhcc
Q psy5654         205 LYEQFGITLR-NVFDTQLLF  223 (224)
Q Consensus       205 L~~~~GI~L~-nvFDTqLAa  223 (224)
                      |. .+|+.+. .+|||++++
T Consensus        82 l~-~~gi~~~~~~~Dt~l~a  100 (193)
T cd06139          82 LA-NHGIELRGPAFDTMLAS  100 (193)
T ss_pred             HH-HCCCCCCCCcccHHHHH
Confidence            96 5898874 469999985

Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.

>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]

Probab=98.36  E-value=5.7e-07  Score=88.06  Aligned_cols=101  Identities=25%  Similarity=0.282  Sum_probs=79.7

Q ss_pred             ecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCc---cccccchhHhhhcCCCceEE
Q psy5654         119 ITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCP---EVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       119 Idt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~---~l~~~~~Lr~lLed~~I~KV  194 (224)
                      +.+...+..|.........+++|+|...+ +..++++++.++..+ +++|++....+   ...  +.|++||+++...|+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~-~~~yi~~~~~~~~~~~~--~~l~~~l~~~~~~kv   82 (593)
T COG0749           6 ITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVASEE-EAAYIPLLHGPEQLNVL--AALKPLLEDEGIKKV   82 (593)
T ss_pred             hhHHHHHHHHHHHHhhcccceeeccccccCcccCCeeEEEeeccc-cceeEeeccchhhhhhH--HHHHHHhhCcccchh
Confidence            44555677777776666669999998877 777889999999866 77888776522   222  689999999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +||.|+|.++|. .+|+..+..||||+|+
T Consensus        83 ~~~~K~d~~~l~-~~Gi~~~~~~Dtmlas  110 (593)
T COG0749          83 GQNLKYDYKVLA-NLGIEPGVAFDTMLAS  110 (593)
T ss_pred             ccccchhHHHHH-HcCCcccchHHHHHHH
Confidence            999999999996 5996645569999985

>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases

Probab=98.25  E-value=4.9e-06  Score=66.75  Aligned_cols=69  Identities=25%  Similarity=0.350  Sum_probs=53.4

Q ss_pred             cceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccCC-ccchhhcc
Q psy5654         150 KGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRN-VFDTQLLF  223 (224)
Q Consensus       150 ~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~n-vFDTqLAa  223 (224)
                      .+++.++.++..+ ++|++++... ...  +.|+++|+++.+.|++||.|.++++|. .+|+.+.+ +||||||+
T Consensus        17 ~~~~~glal~~~~-~~~yi~~~~~-~~~--~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~l~~~~fD~~LAa   86 (151)
T cd06128          17 SANLVGLAFAIEG-VAAYIPVAHD-YAL--ELLKPLLEDEKALKVGQNLKYDRVILA-NYGIELRGIAFDTMLEA   86 (151)
T ss_pred             cCcEEEEEEEcCC-CeEEEeCCCC-cCH--HHHHHHHcCCCCCEEeeehHHHHHHHH-HCCCCCCCcchhHHHHH
Confidence            5678888888754 4777763211 012  468899999999999999999999995 69999866 59999986

The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po

>TIGR00593 pola DNA polymerase I

Probab=98.15  E-value=1e-05  Score=82.98  Aligned_cols=100  Identities=17%  Similarity=0.085  Sum_probs=72.0

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeC-CeEEEEeCCC-----CccccccchhHhhhcC
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLS-GQVYIFDLVT-----CPEVVGTGGLSKLLES  188 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~-g~a~lIDi~a-----l~~l~~~~~Lr~lLed  188 (224)
                      +..+.+.+++..+++. ...+.+++    ... ++.+++.++++++.+ +.+||++...     .....  ..|+++|++
T Consensus       304 ~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~  376 (887)
T TIGR00593       304 AKESEEAAPLANPAEK-AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTD--DKFARWLLN  376 (887)
T ss_pred             ceEeCCHHHHHHHHHh-CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHH--HHHHHHHhC
Confidence            4456566777777755 33445666    222 456778899999865 5578887531     00111  458899999


Q ss_pred             CCceEEEEecHHHHHHHHHhcCCccCC-ccchhhcc
Q psy5654         189 ENVIKVIHDCRNDSILLYEQFGITLRN-VFDTQLLF  223 (224)
Q Consensus       189 ~~I~KV~Hd~K~Dl~lL~~~~GI~L~n-vFDTqLAa  223 (224)
                      +.+.||+||+|+|+++|. .+|+.+.+ +||||+|+
T Consensus       377 ~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~  411 (887)
T TIGR00593       377 EQIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAA  411 (887)
T ss_pred             CCCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHH
Confidence            999999999999999996 69999854 69999986

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=97.30  E-value=0.00092  Score=50.57  Aligned_cols=73  Identities=23%  Similarity=0.309  Sum_probs=53.0

Q ss_pred             EEEEEeeeCC-CccceEEEEEEEee-CCeEEEEeCCCCccccccchhHhhhcCCC-ceEEEEecHHHHHHHHHh---cCC
Q psy5654         138 VTFDCEGINP-GIKGQITLFSLGLL-SGQVYIFDLVTCPEVVGTGGLSKLLESEN-VIKVIHDCRNDSILLYEQ---FGI  211 (224)
Q Consensus       138 Ia~D~E~~~l-~~~g~L~lIQIat~-~g~a~lIDi~al~~l~~~~~Lr~lLed~~-I~KV~Hd~K~Dl~lL~~~---~GI  211 (224)
                      +++|+|..+. +...++++++++.. ++..|++|            +.+++++.. ...|+|++++|...|.+.   +|+
T Consensus         1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~------------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~   68 (96)
T cd06125           1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID------------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGL   68 (96)
T ss_pred             CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh------------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCC
Confidence            4789998877 77788999999875 35667654            445777766 678999999998777643   343


Q ss_pred             cc----CCccchhhc
Q psy5654         212 TL----RNVFDTQLL  222 (224)
Q Consensus       212 ~L----~nvFDTqLA  222 (224)
                      ..    ...+||+.+
T Consensus        69 ~~p~~~~~~lDT~~l   83 (96)
T cd06125          69 KYPLLAGSWIDTIKL   83 (96)
T ss_pred             CCCCcCCcEEEehHH
Confidence            32    446899865

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

>KOG2405|consensus

Probab=97.20  E-value=5.9e-06  Score=77.06  Aligned_cols=90  Identities=34%  Similarity=0.529  Sum_probs=70.3

Q ss_pred             HccCCeEEEEEeeeCCCccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCC
Q psy5654         132 LMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGI  211 (224)
Q Consensus       132 L~~~~~Ia~D~E~~~l~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI  211 (224)
                      ++.+... ...|+.....+|++|++|.++. -..|++|+..+........++-++++.+|.|+.|+|+.-++.+.++|||
T Consensus        56 ik~qn~~-~~~e~a~~~~~~~l~~~q~~~~-~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i  133 (458)
T KOG2405|consen   56 IKKQNVL-VAAEGANVCRHGKLCWLQVATN-CRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGI  133 (458)
T ss_pred             hHhhcCc-ccccCccccccCcchhHHHHHH-HHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhccccee
Confidence            4444443 4566766667889999999974 3678888876542111156788999999999999999999999999999


Q ss_pred             ccCCccchhhcc
Q psy5654         212 TLRNVFDTQLLF  223 (224)
Q Consensus       212 ~L~nvFDTqLAa  223 (224)
                      .+.++|||++|.
T Consensus       134 ~~n~v~~~q~~d  145 (458)
T KOG2405|consen  134 LLNNVFDTQVAD  145 (458)
T ss_pred             eecchhhhhhhh
Confidence            999999999874

>KOG2207|consensus

Probab=97.03  E-value=0.00038  Score=68.21  Aligned_cols=91  Identities=23%  Similarity=0.283  Sum_probs=71.5

Q ss_pred             cEEecCHHHHHHHH-HHHccC-CeEEEEEeeeCC--CccceEEEEEEEeeCCeEEEEeCCCCcccccc---chhHhhhcC
Q psy5654         116 TKVITNIKECSSVV-EELMRN-ELVTFDCEGINP--GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGT---GGLSKLLES  188 (224)
Q Consensus       116 ~~vIdt~eeLa~li-e~L~~~-~~Ia~D~E~~~l--~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~---~~Lr~lLed  188 (224)
                      +.++.++.++..++ +.+... .++|+|+||.+.  ....+++.+|++.. ..+|++|+.++.....+   -.+..+|++
T Consensus       392 i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~-~~v~Lidc~~l~~~~se~w~~~~s~if~s  470 (617)
T KOG2207|consen  392 IGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFK-DCVYLIDCVKLENLASEIWHLLLSQIFES  470 (617)
T ss_pred             eeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhc-CeEEEeehHHhhhchHHHHHHHHHHHccC
Confidence            67789999998887 455555 779999999765  33577999999985 58999999876422110   245569999


Q ss_pred             CCceEEEEecHHHHHHHHH
Q psy5654         189 ENVIKVIHDCRNDSILLYE  207 (224)
Q Consensus       189 ~~I~KV~Hd~K~Dl~lL~~  207 (224)
                      +.+.|||++.+.|+..+.+
T Consensus       471 ~~i~kvGf~~~eDL~~l~~  489 (617)
T KOG2207|consen  471 KSILKVGFSMREDLEVLEA  489 (617)
T ss_pred             CceeeeecchhhhHHHHHh
Confidence            9999999999999999974

>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional

Probab=96.49  E-value=0.0025  Score=62.35  Aligned_cols=76  Identities=20%  Similarity=0.178  Sum_probs=60.0

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      +.+|++.+++..+++.+...+.+++|+|+... .   .++++|++.. +.+|++|....        +.++         
T Consensus         3 ~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~t---~l~liQ~~~~-~~~~liDpl~~--------l~~~---------   61 (553)
T PRK14975          3 MKVILAPEELGAALERLSPAGVVAGDTETTGDDA---AAAAAQEGEE-EPRWVWASTAA--------LYPR---------   61 (553)
T ss_pred             ceEEeccchhHHHHHHhccCCceeCCccccCCcc---hhheeeecCC-CceEEECchHH--------hHHH---------
Confidence            56888999999999999999999999999865 3   7889999864 57898876321        1111         


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                                |. .+|+.+.++||||+|+
T Consensus        62 ----------L~-~~Gv~~~~~fDT~LAa   79 (553)
T PRK14975         62 ----------LL-AAGVRVERCHDLMLAS   79 (553)
T ss_pred             ----------HH-HCCCccCCCchHHHHH
Confidence                      43 4799988899999986

>KOG2405|consensus

Probab=88.50  E-value=0.069  Score=50.46  Aligned_cols=72  Identities=24%  Similarity=0.211  Sum_probs=52.2

Q ss_pred             CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         148 GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       148 ~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      ...++.+..++|+. .++|++|...-+.....+..+..|+...+  +. |++.+...+...|++.+.+++|||+|+
T Consensus       208 ~~~~e~~~m~ia~~-n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~  279 (458)
T KOG2405|consen  208 ILALEATYMNIADG-NEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIAS  279 (458)
T ss_pred             hhhhhhhhhhhccc-chhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHH
Confidence            34455666777764 47888888654311111446667877655  55 999999999999999999999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	224
2e6m_A	208	Werner syndrome ATP-dependent helicase homolog; AP	9e-13
1yt3_A	375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	4e-11
3saf_A	428	Exosome component 10; exoribonuclease, RNA exosome	1e-09
2hbj_A	410	Exosome complex exonuclease RRP6; RNA metabolism,	6e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08
3cym_A	440	Uncharacterized protein BAD_0989; structural genom	8e-07
1vk0_A	206	Hypothetical protein; homohexamer, AT5G06450, stru	4e-06
2kfn_A	605	Klenow fragment of DNA polymerase I; complex (poly	4e-05

>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* Length = 208

 Score = 63.7 bits (155), Expect = 9e-13
 Identities = 22/112 (19%), Positives = 45/112 (40%), Gaps = 9/112 (8%)

Query: 118 VITNIKECSSVVEELMRN----ELVTFDCE---GINPGIKGQITLFSLGLLSGQVYIFDL 170
                 +CS + E++       ++V FD E      PG + ++ +  L +   + Y+F +
Sbjct: 19  YSYEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHI 78

Query: 171 VTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLL 222
            +        GL  LLE++++ K       D   L   F + L +  +   +
Sbjct: 79  SSMSVF--PQGLKMLLENKSIKKAGVGIEGDQWKLLRDFDVKLESFVELTDV 128

>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Length = 375

 Score = 60.5 bits (147), Expect = 4e-11
 Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 13/112 (11%)

Query: 115 NTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFS-LGLL----SGQVYIFD 169
           N ++IT     +S+ E +     +  D E +        T +  LGL+       + + D
Sbjct: 2   NYQMITTDDALASLCEAVRAFPAIALDTEFVR-----TRTYYPQLGLIQLFDGEHLALID 56

Query: 170 LVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
            +   +      L  +L   ++ K +H    D  +    FG   + + DTQ+
Sbjct: 57  PLGITD---WSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQI 105

>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A Length = 428

 Score = 56.4 bits (136), Expect = 1e-09
 Identities = 21/110 (19%), Positives = 44/110 (40%), Gaps = 12/110 (10%)

Query: 117 KVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFS-LGLL----SGQVYIFDLV 171
             I+++ E   + E+L+  +    + E  +       +      L+      + +I D +
Sbjct: 111 HFISSLDELVELNEKLLNCQEFAVNLEHHS-----YRSFLGLTCLMQISTRTEDFIIDTL 165

Query: 172 TCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
                     L++ L    ++KV H   +D   L + FG+ + N+FDT  
Sbjct: 166 ELRS--DMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQ 213

>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* Length = 410

 Score = 54.1 bits (130), Expect = 6e-09
 Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 20/113 (17%)

Query: 118 VITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFS----LGLL----SGQVYIFD 169
            +    E  S++E+L   + +  D E             S    + L+      + Y+ D
Sbjct: 89  WVDTSTELESMLEDLKNTKEIAVDLE--------HHDYRSYYGIVCLMQISTRERDYLVD 140

Query: 170 -LVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
            L     +     L+++  + +++KV H    D I L    G+ +  +FDT  
Sbjct: 141 TLKLRENL---HILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYH 190

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

 Score = 53.7 bits (128), Expect = 1e-08
 Identities = 33/230 (14%), Positives = 67/230 (29%), Gaps = 62/230 (26%)

Query: 4   NVFNIQSNTVKLVDNITHTNSSSPEQANGKVLKNNAINLTQIPLSPPESK---ANLTHSS 60
           N FN+    +     +T       +  +     + +++   + L+P E K          
Sbjct: 260 NAFNLSCKIL-----LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314

Query: 61  P---PASLAQNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTK 117
           P   P  +          N   L  IA   E  +              DN+K   +   K
Sbjct: 315 PQDLPREVLTT-------NPRRLSIIA---ESIRDGL--------ATWDNWKH--VNCDK 354

Query: 118 VITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVV 177
           + T I+     +  L   E               +     L +     +I      P ++
Sbjct: 355 LTTIIESS---LNVLEPAEY--------------RKMFDRLSVFPPSAHI------PTIL 391

Query: 178 GTGGLSKL---LESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLFL 224
               LS +   +   +V+ V++     S++  +    T+  +    L   
Sbjct: 392 ----LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS-IPSIYLELK 436

>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID} Length = 440

 Score = 48.0 bits (114), Expect = 8e-07
 Identities = 18/114 (15%), Positives = 38/114 (33%), Gaps = 20/114 (17%)

Query: 118 VITNIKECSSVVEELMRNE-LVTFDCEGINPGIKGQITLFS-LGLL-----SGQVYIFDL 170
           VI  +        EL  +   +  D E  +              L+        + + D 
Sbjct: 20  VIDTLPAFRDYCSELASSHGSLAADAERAS-----GFRYGHEDWLVQFKRDGAGIGLLD- 73

Query: 171 VTCPEVVGTGG--LSKLLES-ENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
              P+ +   G   +    +  + + ++HD   D     E  G+  + +FDT++
Sbjct: 74  ---PQALAAAGADWNDFNRAVGDAVWILHDSLQDLPGFDE-LGMEPQRLFDTEI 123

>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics, protein structure initiative, center for eukaryot structural genomics, CESG; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Length = 206

 Score = 45.4 bits (107), Expect = 4e-06
 Identities = 23/130 (17%), Positives = 39/130 (30%), Gaps = 11/130 (8%)

Query: 99  GYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRN--ELVTFDCE----GINPGIKGQ 152
            +   +    +TK +            S + E+ + N    V FD            K +
Sbjct: 8   KFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTK 67

Query: 153 ITLFSLGLL----SGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQ 208
            + +SL  +            L           L +   S+ V  V      D  LL E 
Sbjct: 68  TSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKD-LYRFFASKFVTFVGVQIEEDLDLLREN 126

Query: 209 FGITLRNVFD 218
            G+ +RN  +
Sbjct: 127 HGLVIRNAIN 136

>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Length = 605

 Score = 42.9 bits (102), Expect = 4e-05
 Identities = 29/116 (25%), Positives = 49/116 (42%), Gaps = 13/116 (11%)

Query: 117 KVITNIKECSSVVEELMRNELVTFDCE--GINPGIKGQITLFSLGLLSGQ-VYI---FDL 170
             I + +   + + +L +  +  FD E   ++  I   +   S  +  G   YI    D 
Sbjct: 8   VTILDEETLKAWIAKLEKAPVFAFDTETDSLDN-ISANLVGLSFAIEPGVAAYIPVAHDY 66

Query: 171 VTCPEVVGT----GGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNV-FDTQL 221
           +  P+ +        L  LLE E  +KV  + + D  +L   +GI LR + FDT L
Sbjct: 67  LDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILA-NYGIELRGIAFDTML 121

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	224
3saf_A	428	Exosome component 10; exoribonuclease, RNA exosome	99.63
2e6m_A	208	Werner syndrome ATP-dependent helicase homolog; AP	99.56
2hbj_A	410	Exosome complex exonuclease RRP6; RNA metabolism,	99.54
1yt3_A	375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	99.48
1vk0_A	206	Hypothetical protein; homohexamer, AT5G06450, stru	99.29
3cym_A	440	Uncharacterized protein BAD_0989; structural genom	99.2
2kfn_A	605	Klenow fragment of DNA polymerase I; complex (poly	99.13
3pv8_A	592	DNA polymerase I; DNA polymerase I, protein-DNA co	98.7
1x9m_A	698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	98.33
4dfk_A	540	DNA polymerase I, thermostable; DNA polymerase, tr	98.2
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	96.64
3v9w_A	235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	95.2

>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A

Probab=99.63  E-value=1.7e-15  Score=141.58  Aligned_cols=105  Identities=21%  Similarity=0.291  Sum_probs=95.4

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      |.+|++.++++.+++.+...+.++||+|+... .+.++++++||++. +.+|+||+..+....  ..|+++|+++.+.||
T Consensus       110 y~~I~t~e~L~~~l~~L~~~~~vavDtE~~~~~~~~~~l~lIQLa~~-~~~~lidpl~l~~~l--~~L~~lL~dp~i~KV  186 (428)
T 3saf_A          110 CHFISSLDELVELNEKLLNCQEFAVNLEHHSYRSFLGLTCLMQISTR-TEDFIIDTLELRSDM--YILNESLTDPAIVKV  186 (428)
T ss_dssp             EEEECSHHHHHHHHHHHTTCSEEEEEEEEECTTCSSCEEEEEEEECS-SCEEEEETTTTGGGG--GGGHHHHTCTTSEEE
T ss_pred             cEEECCHHHHHHHHHHHhcCCeEEEEEEecCCCCCCCeEEEEEEEeC-CcEEEEEeccchhhH--HHHHHHHcCCCceEE
Confidence            77899999999999999999999999999877 78899999999985 478999998875333  689999999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +|++|+|+.+|++.+|+.+.++||||+|+
T Consensus       187 ~H~~k~Dl~~L~~~~Gi~~~~~fDT~lAa  215 (428)
T 3saf_A          187 FHGADSDIEWLQKDFGLYVVNMFDTHQAA  215 (428)
T ss_dssp             ESSCHHHHHHHHHHHCCCCSSEEEHHHHH
T ss_pred             EeehHHHHHHHHHHcCCCcCceeechhHH
Confidence            99999999999778999999999999986

>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A*

Probab=99.56  E-value=1.1e-14  Score=121.88  Aligned_cols=106  Identities=21%  Similarity=0.339  Sum_probs=88.5

Q ss_pred             cEEecCHHHHH----HHHHHHccCCeEEEEEeeeCC---CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcC
Q psy5654         116 TKVITNIKECS----SVVEELMRNELVTFDCEGINP---GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLES  188 (224)
Q Consensus       116 ~~vIdt~eeLa----~lie~L~~~~~Ia~D~E~~~l---~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed  188 (224)
                      +.+|++.+++.    .+++.+.....+++|+|+.+.   ++.+.++++|+++.++.+|++|+.......  ..|+++|++
T Consensus        17 i~~i~~~~~~~~~~~~~~~~l~~~~~v~~D~E~~~~~~~~~~~~~~~iqla~~~~~~~~i~~~~~~~~~--~~L~~lL~d   94 (208)
T 2e6m_A           17 IVYSYEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHISSMSVFP--QGLKMLLEN   94 (208)
T ss_dssp             EEEECSHHHHHHHHHHHHHHCCTTCEEEEEEECCC---CCSCCCCCEEEEECSSSEEEEECGGGCSSCC--HHHHHHHTC
T ss_pred             EEEEeCHHHHHHHHHHHHHHhccCCEEEEEeecCCCCCCCCCCCeEEEEEecCCCeEEEEECcccccch--HHHHHHhcC
Confidence            67899999998    555666677889999998764   456889999999866789999886554333  579999999


Q ss_pred             CCceEEEEecHHHHHHHHHhcCCccCCccc-hhhcc
Q psy5654         189 ENVIKVIHDCRNDSILLYEQFGITLRNVFD-TQLLF  223 (224)
Q Consensus       189 ~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFD-TqLAa  223 (224)
                      +.+.||+||+|+|+..|.+.+|+.+.++|| ||+|+
T Consensus        95 ~~i~Kv~~~~k~D~~~L~~~~gi~~~~~fDlt~lAa  130 (208)
T 2e6m_A           95 KSIKKAGVGIEGDQWKLLRDFDVKLESFVELTDVAN  130 (208)
T ss_dssp             TTSEEEESSHHHHHHHHHHHHCCCCCSEEEHHHHHH
T ss_pred             CCceEEEEeeHHHHHHHHHHCCCCCCCEEEHHHHHH
Confidence            999999999999999998679999988999 89985

>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A*

Probab=99.54  E-value=4.8e-14  Score=130.83  Aligned_cols=106  Identities=21%  Similarity=0.285  Sum_probs=92.2

Q ss_pred             CcEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceE
Q psy5654         115 NTKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIK  193 (224)
Q Consensus       115 ~~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~K  193 (224)
                      .+.+|++.++++.+++.+.....+++|+|+.+. .+.++++++|+++. +.+|++|...+....  ..|+++|+++.+.|
T Consensus        86 ~~~~I~t~~~L~~~~~~L~~~~~vavDtE~~~~~~~~~~l~liQla~~-~~~ylid~l~l~~~l--~~L~~lL~d~~i~K  162 (410)
T 2hbj_A           86 VPIWVDTSTELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTR-ERDYLVDTLKLRENL--HILNEVFTNPSIVK  162 (410)
T ss_dssp             CCEEECSHHHHHHHHHHHTTCSEEEEEEEEECSSSSSCEEEEEEEECS-SCEEEEETTTTTTTG--GGGHHHHTCTTSEE
T ss_pred             CcEEeCCHHHHHHHHHHHhhCCceEEEeeecCCcCCCCcEEEEEEEEC-CcEEEEechhhhhhH--HHHHHHHcCCCceE
Confidence            367898999999999998888899999999877 67899999999984 578999975543222  57999999999999


Q ss_pred             EEEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         194 VIHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       194 V~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      |+||+|+|+.+|++.+|+.+.++||||+|+
T Consensus       163 V~h~~k~Dl~~L~~~~Gi~~~~~fDt~lAa  192 (410)
T 2hbj_A          163 VFHGAFMDIIWLQRDLGLYVVGLFDTYHAS  192 (410)
T ss_dssp             EESSCHHHHHHHHHHHCCCCSSEEEHHHHH
T ss_pred             EEEehHHHHHHHHHHcCCCcCCEEEcHHHH
Confidence            999999999999877999998899999986

>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5

Probab=99.48  E-value=1.4e-13  Score=125.66  Aligned_cols=104  Identities=20%  Similarity=0.211  Sum_probs=90.1

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      |.+|++.++++.+++.+...+.+++|+|+... .+.+.++++|+++. +.+|++|...+. ..  ..|+++|+++.+.||
T Consensus         3 ~~~I~t~~~l~~~~~~l~~~~~va~D~E~~~~~~~~~~l~liqla~~-~~~~lid~~~l~-~~--~~L~~ll~d~~i~Kv   78 (375)
T 1yt3_A            3 YQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDG-EHLALIDPLGIT-DW--SPLKAILRDPSITKF   78 (375)
T ss_dssp             CEEECSHHHHHHHHHHHTTSSEEEEEEEEECCSCSSCEEEEEEEECS-SCEEEECGGGCS-CC--HHHHHHHHCTTSEEE
T ss_pred             eEEeCCHHHHHHHHHHHcCCCeEEEEeeecCCCcCCCceEEEEEecC-CcEEEEeCCCCC-Ch--HHHHHHHcCCCceEE
Confidence            67888889999999998888889999999877 66789999999984 478999864332 22  579999999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +||+|+|+..|++.+|+.+.++||||+|+
T Consensus        79 ~h~~k~Dl~~L~~~~Gi~~~~~fDt~lAa  107 (375)
T 1yt3_A           79 LHAGSEDLEVFLNVFGELPQPLIDTQILA  107 (375)
T ss_dssp             ESSCHHHHHHHHHHHSSCCSSEEEHHHHH
T ss_pred             EeeHHHHHHHHHHHcCCCCCcEEEcHHHH
Confidence            99999999999867999999999999986

>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics, protein structure initiative, center for eukaryot structural genomics, CESG; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A

Probab=99.29  E-value=7.1e-12  Score=106.57  Aligned_cols=102  Identities=19%  Similarity=0.149  Sum_probs=77.1

Q ss_pred             EecCHHHHHHHHHHH------ccCCeEEEEEeeeCC-------Ccc--ceEEEEEEEeeCCeEEEEeCC-CCccccccch
Q psy5654         118 VITNIKECSSVVEEL------MRNELVTFDCEGINP-------GIK--GQITLFSLGLLSGQVYIFDLV-TCPEVVGTGG  181 (224)
Q Consensus       118 vIdt~eeLa~lie~L------~~~~~Ia~D~E~~~l-------~~~--g~L~lIQIat~~g~a~lIDi~-al~~l~~~~~  181 (224)
                      .|.+.+++..+++.+      ....++|||+|+.+.       ...  ++++++|+|+.+ .+++|++. ..+...  ..
T Consensus        23 ~v~~~~~l~~~~~~~~~~~~~~~~~vvg~DtEw~p~~~~~~~~~~~~~~~~~LiQla~~~-~~~l~~l~~~~~~~L--~~   99 (206)
T 1vk0_A           23 DVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRN-LCLFLRLPKPFHDNL--KD   99 (206)
T ss_dssp             ECCSSCCCHHHHHHHHHHHHHHSTTEEEEEEEEECCC------CGGGGCEEEEEEEECSS-EEEEEECCSSCCGGG--HH
T ss_pred             EEecHHHHHHHHHHHHHhhhhcCCCEEEEEeeccCCCcccccccCCCCCceEEEEEecCC-CeEEEeccccCCccH--HH
Confidence            344555555555544      446789999999742       133  489999999864 69999982 111111  23


Q ss_pred             hHhhhcCCCceEEEEecHHHHHHHHHhcCCccCCccchh-hc
Q psy5654         182 LSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ-LL  222 (224)
Q Consensus       182 Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTq-LA  222 (224)
                      |+.+|+|+++.||||+++.|+..|++.+|+.+.++|||+ +|
T Consensus       100 L~~lL~d~~i~Kvg~~~~~D~~~L~~~~g~~~~~~~Dl~~la  141 (206)
T 1vk0_A          100 LYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLA  141 (206)
T ss_dssp             HHHHHTCSSSEEEESSCHHHHHHHHHHHCCCCSSEEEHHHHH
T ss_pred             HHHHhcCCCceEEEeccHHHHHHHHHhcCCCcCCeeeHHHHH
Confidence            789999999999999999999999989999999999986 65

>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID}

Probab=99.20  E-value=2.1e-11  Score=114.02  Aligned_cols=102  Identities=15%  Similarity=0.177  Sum_probs=85.1

Q ss_pred             EEecCHHHHHHHHHHHccC-CeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCc---cccccchhHhhhcCCCc
Q psy5654         117 KVITNIKECSSVVEELMRN-ELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCP---EVVGTGGLSKLLESENV  191 (224)
Q Consensus       117 ~vIdt~eeLa~lie~L~~~-~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~---~l~~~~~Lr~lLed~~I  191 (224)
                      .+|++.++++.+++.+... +.++||+|+... .+.++++++||++.++.+||||.....   ...  ..|+++|+++  
T Consensus        19 ~~I~t~e~L~~~~~~L~~~~~~vavDtE~~~~~~~~~~l~liQla~~~~~~~lid~l~~~~~~~~l--~~L~~lL~d~--   94 (440)
T 3cym_A           19 NVIDTLPAFRDYCSELASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADW--NDFNRAVGDA--   94 (440)
T ss_dssp             CEECSHHHHHHHHHHHHSCEEEEEEEEEECTTTSSSCCEEEEEEEEETTEEEEECHHHHHHTTCCH--HHHHHHHTTC--
T ss_pred             EeeCCHHHHHHHHHHHHhcCCeEEEEeeecCCCCCCCCEEEEEEEECCCcEEEEEcCCccccccCH--HHHHHHHCCC--
Confidence            4678889999999988776 789999999876 668899999999877778999873211   112  5799999997  


Q ss_pred             eEEEEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         192 IKVIHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       192 ~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      .||+|++|+|+.+|. .+|+.+.++|||++|+
T Consensus        95 ~KV~h~~k~Dl~~L~-~~gi~~~~~fDt~lAa  125 (440)
T 3cym_A           95 VWILHDSLQDLPGFD-ELGMEPQRLFDTEIAA  125 (440)
T ss_dssp             EEEESSHHHHHHHHH-HHTCCCCEEEEHHHHH
T ss_pred             CEEEEcCHHHHHHHH-HcCCcCCceehHHHHH
Confidence            699999999999996 7999999899999985

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

Probab=99.13  E-value=1.8e-10  Score=111.27  Aligned_cols=106  Identities=25%  Similarity=0.311  Sum_probs=88.1

Q ss_pred             CcEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCC-----c-----cccccchhH
Q psy5654         115 NTKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTC-----P-----EVVGTGGLS  183 (224)
Q Consensus       115 ~~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al-----~-----~l~~~~~Lr  183 (224)
                      .|.+|++.++++.|++.+...+.++||+|+.+. ++.+++++++++..+++++|+++...     .     ...  ..|+
T Consensus         6 ~y~~I~~~~~l~~~~~~l~~~~~va~DtEttgl~~~~~~iv~I~~~~~~g~~~yip~~~~~~~~~~~l~~~~vl--~~L~   83 (605)
T 2kfn_A            6 NYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERAL--ELLK   83 (605)
T ss_dssp             SSEECCSHHHHHHHHHHHHTSSSEEEEEEESCSCTTTCCEEEEEEEEETTEEEEEECCCCSTTCCCCCCHHHHH--HHHH
T ss_pred             heEEecCHHHHHHHHHhcccCCeEEEEEecCCCCcccCceEEEEEEEcCCcEEEEeccccccccccccCHHHHH--HHHH
Confidence            367788888999999988777889999999887 77889999999976788888866431     0     111  4689


Q ss_pred             hhhcCCCceEEEEecHHHHHHHHHhcCCccCC-ccchhhcc
Q psy5654         184 KLLESENVIKVIHDCRNDSILLYEQFGITLRN-VFDTQLLF  223 (224)
Q Consensus       184 ~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~n-vFDTqLAa  223 (224)
                      ++|+++.+.||+||+|+|+..|. ++|+.+.+ +||||+|+
T Consensus        84 ~~L~d~~i~kV~hnak~D~~~L~-~~Gi~l~~~~~DT~laa  123 (605)
T 2kfn_A           84 PLLEDEKALKVGQNLKYDRGILA-NYGIELRGIAFDTMLES  123 (605)
T ss_dssp             HHHTCTTSCEEESSHHHHHHHHH-TTTCCCCCEEEEHHHHH
T ss_pred             HHHcCCCCeEEEECcHHHHHHHH-HCCCCCCCccccHHHHH
Confidence            99999999999999999999996 58999976 79999986

>3pv8_A DNA polymerase I; DNA polymerase I, protein-DNA complex, thymine-adenine, CLOS conformation; HET: DNA 2DT D3T; 1.52A {Geobacillus kaustophilus} PDB: 3px0_A* 3px4_A* 3px6_A* 3thv_A* 3ti0_A* 4dse_A* 4dsf_A* 4ds4_A* 4dqp_A* 4dqi_A* 4ds5_A* 4e0d_A* 4dqr_A* 4dqq_A* 3tan_A* 3tap_A* 3taq_A* 3tar_A* 4dqs_A* 3hp6_A* ...

Probab=98.70  E-value=9.1e-09  Score=99.62  Aligned_cols=84  Identities=17%  Similarity=0.097  Sum_probs=69.0

Q ss_pred             CCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc
Q psy5654         135 NELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL  213 (224)
Q Consensus       135 ~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L  213 (224)
                      ....++|+|.... ++.+++++++++..+ ++||+++... ...  ..|+++|+++.+.||+||+|+|+++|. .+|+.+
T Consensus        29 ~~~~aldtE~~~~~~~~a~Lvgisla~~~-~a~yIp~~~~-~~l--~~Lk~lLed~~i~KV~hn~K~Dl~vL~-~~Gi~l  103 (592)
T 3pv8_A           29 ADKAALVVEVVEENYHDAPIVGIAVVNEH-GRFFLRPETA-LAD--PQFVAWLGDETKKKSMFDSKRAAVALK-WKGIEL  103 (592)
T ss_dssp             CSEEEEEEECCSSSCTTCCCCEEEEEETT-EEEEECHHHH-TTC--HHHHHHHTCTTSEEEESSHHHHHHHHH-HTTCCC
T ss_pred             ccCcEEEEEEcCCccCcccEEEEEEEcCC-ceEEEccchh-hHH--HHHHHHHhCCCCeEEEechHHHHHHHH-HcCCCC
Confidence            3457899998877 788999999999854 6899876321 122  579999999999999999999999996 599999


Q ss_pred             CC-ccchhhcc
Q psy5654         214 RN-VFDTQLLF  223 (224)
Q Consensus       214 ~n-vFDTqLAa  223 (224)
                      .+ +||||+|+
T Consensus       104 ~g~~fDTmLAA  114 (592)
T 3pv8_A          104 CGVSFDLLLAA  114 (592)
T ss_dssp             CCEEEEHHHHH
T ss_pred             CCccchHHHHH
Confidence            54 79999986

>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A*

Probab=98.33  E-value=3.7e-07  Score=89.66  Aligned_cols=83  Identities=16%  Similarity=0.066  Sum_probs=66.7

Q ss_pred             EEEEEeeeCC-CccceEEEEEEEeeC-CeEEEEeCCCCccccccchhHhhhcCCCceEEEEec-HHHHHHHHHhc-----
Q psy5654         138 VTFDCEGINP-GIKGQITLFSLGLLS-GQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDC-RNDSILLYEQF-----  209 (224)
Q Consensus       138 Ia~D~E~~~l-~~~g~L~lIQIat~~-g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~-K~Dl~lL~~~~-----  209 (224)
                      ++||+|+.++ ...++++++|+.... +..+++|....+...  ..|+++|+ +.+.||+||+ |+|+.+|.+.+     
T Consensus         2 vv~D~ETtGl~~~~d~i~~iqi~~~~~~~~~~~~p~~i~~~l--~~L~~~l~-~~~~kV~HNa~kfD~~~L~~~~~~~~~   78 (698)
T 1x9m_A            2 IVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYL--DALEAEVA-RGGLIVFHNGHKYDVPALTKLAKLQLN   78 (698)
T ss_dssp             EEEEEEESSCGGGCCCEEEEEEEETTTTEEEEECGGGHHHHH--HHHHHHHH-TTCCEEESSTTTTHHHHHHHHHHHHHC
T ss_pred             EEEEcCCCCcCCCCCEEEEEEEEecCCCcEEEEChHHHHHHH--HHHHHHHh-cCCeEEEcCChHHHHHHHHHhhhhccc
Confidence            7899999988 667889999999633 578888765333233  67999999 9999999999 99999997543     


Q ss_pred             -CCccC--Cccchhhcc
Q psy5654         210 -GITLR--NVFDTQLLF  223 (224)
Q Consensus       210 -GI~L~--nvFDTqLAa  223 (224)
                       |+.+.  .+||||+|+
T Consensus        79 ~Gi~l~~~~~~DTmlaa   95 (698)
T 1x9m_A           79 REFHLPRENCIDTLVLS   95 (698)
T ss_dssp             CCCCCCGGGEEEHHHHH
T ss_pred             CCccCCCCcchhHHHHH
Confidence             98876  479999986

>4dfk_A DNA polymerase I, thermostable; DNA polymerase, transferase-DNA complex; HET: DNA DOC 0L5; 1.65A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 3m8r_A* 3oju_A* 3rr7_A* 3rr8_A* 3rrg_A* 3ojs_A* 3rtv_A* 3sv3_A* 3sv4_A* 3syz_A* 3sz2_A* 3t3f_A* 4df4_A* 4df8_A* 4dfj_A* ...

Probab=98.20  E-value=3.5e-07  Score=87.68  Aligned_cols=74  Identities=18%  Similarity=0.030  Sum_probs=62.2

Q ss_pred             CeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccC
Q psy5654         136 ELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLR  214 (224)
Q Consensus       136 ~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~  214 (224)
                      +++++|+|.... .+.+++++++++. ++++|+++     ...  ..|+++|++  +.||+||+|+|+.    ++|+.+.
T Consensus        11 ~~valDtE~~~~~~~~a~Lvgi~la~-~~~a~~i~-----~~l--~~l~~~l~d--~~kV~hn~K~Dl~----~~Gi~~~   76 (540)
T 4dfk_A           11 EGAFVGFVLSRKEPMWADLLALAAAR-GGRVHRAP-----EPY--KALRDLKEA--RGLLAKDLSVLAL----REGLGLP   76 (540)
T ss_dssp             TTCEEEEEESSSCTTTCCEEEEEEEE-TTEEEECS-----SHH--HHHTTCSSB--CSTTHHHHHHHHH----HTTCCCC
T ss_pred             CceEEEEEecCCccCcccEEEEEEEc-CCEEEEeh-----hhH--HHHHHHHcC--CCEEEeccHHHHH----HcCCCCC
Confidence            458999999877 7889999999996 57888775     122  578899998  8899999999999    4899887


Q ss_pred             Cccchhhcc
Q psy5654         215 NVFDTQLLF  223 (224)
Q Consensus       215 nvFDTqLAa  223 (224)
                      .+||||+|+
T Consensus        77 ~~fDT~laA   85 (540)
T 4dfk_A           77 PGDDPMLLA   85 (540)
T ss_dssp             BCCCHHHHH
T ss_pred             cceeHHHHH
Confidence            779999986

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*

Probab=96.64  E-value=0.00054  Score=68.71  Aligned_cols=74  Identities=19%  Similarity=0.111  Sum_probs=57.7

Q ss_pred             CCeEEEEEeeeCCCccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccC
Q psy5654         135 NELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLR  214 (224)
Q Consensus       135 ~~~Ia~D~E~~~l~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~  214 (224)
                      .+.+++|+|+.+ ++.+++| ++++..+++++|+++ .  +    ..|++||+++.+     |+|+|+++|. .+||.+.
T Consensus       304 ~~~va~d~et~~-~~~~~l~-vg~a~~~g~a~yvp~-~--~----~~Lk~lLed~~i-----n~K~d~~~L~-~~Gi~~~  368 (832)
T 1bgx_T          304 GAFVGFVLSRKE-PMWADLL-ALAAARGGRVHRAPE-P--Y----KALRDLKEARGL-----LAKDLSVLAL-REGLGLP  368 (832)
T ss_dssp             TCCBEEECSSSC-TTTCCCC-EEECBSSSEEECCSC-H--H----HHHHHCSSBCBT-----THHHHHHHHH-HHTCCCC
T ss_pred             CceEEEEEecCC-cccCcee-EEEEEcCCCEEEEEC-C--H----HHHHHHHhCCCC-----ChHHHHHHHH-HcCCccC
Confidence            456899998766 4556773 336666788888866 2  1    369999999987     9999999996 5999998


Q ss_pred             Cccchhhcc
Q psy5654         215 NVFDTQLLF  223 (224)
Q Consensus       215 nvFDTqLAa  223 (224)
                      .+||||+|+
T Consensus       369 ~~~Dt~laa  377 (832)
T 1bgx_T          369 PGDDPMLLA  377 (832)
T ss_dssp             BCCCHHHHH
T ss_pred             cccCHHHHH
Confidence            569999986

>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=95.20  E-value=0.012  Score=49.25  Aligned_cols=105  Identities=13%  Similarity=0.121  Sum_probs=58.7

Q ss_pred             ecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEee----CCeE-----E--EEeCC---CCc---------
Q psy5654         119 ITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLL----SGQV-----Y--IFDLV---TCP---------  174 (224)
Q Consensus       119 Idt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~----~g~a-----~--lIDi~---al~---------  174 (224)
                      +++.+.+..+...+.....+.+|+|+.++ +...+++.+++...    +|..     |  ++.+.   ..+         
T Consensus        21 ~~~~~~~~~l~~~l~~~~~vviD~ETTGl~~~~~~IieIgav~~~~~~~g~i~~~~~f~~~v~P~~~~~i~~~~~~i~GI  100 (235)
T 3v9w_A           21 MSDNAQLTGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGI  100 (235)
T ss_dssp             --------CHHHHTTTEEEEEEEEEESSSCTTTBCEEEEEEEEEEECTTSCEEEEEEEEEEBCCCTTCBCCHHHHHHHCC
T ss_pred             ccccccccCchhcccCCcEEEEEEeCCCCCCCCCeEEEEEEEEEEEcCCCcccccceEEEEECCCCCCCCCHHHHHHhCC
Confidence            44555666777778777889999999876 55566665555531    3332     2  23321   000         


Q ss_pred             --c-ccc-----c---chhHhhhcC-------CCceEEEEecHHHHHHHHH---hcCCcc-----CCccchhhcc
Q psy5654         175 --E-VVG-----T---GGLSKLLES-------ENVIKVIHDCRNDSILLYE---QFGITL-----RNVFDTQLLF  223 (224)
Q Consensus       175 --~-l~~-----~---~~Lr~lLed-------~~I~KV~Hd~K~Dl~lL~~---~~GI~L-----~nvFDTqLAa  223 (224)
                        + .+.     .   ..|.+++++       +....|+||+++|+.+|.+   ++|+..     ...+||+.++
T Consensus       101 t~e~~v~~~~~~~~vl~~~~~~l~~~~~~~~~~~~~lVahN~~fD~~~L~~~~~~~g~~~~p~~~~~~~Dt~~la  175 (235)
T 3v9w_A          101 DPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALA  175 (235)
T ss_dssp             CTTCGGGCCBCHHHHHHHHHHHHHHHHTTTTCCEEEEEETTTHHHHHHHHHHHHHTTCCCCCEEEEEEEEHHHHH
T ss_pred             CHHHHHhcCCCHHHHHHHHHHHHHHHhhhccCCCcEEEEeChHHHHHHHHHHHHHcCCCCCCCCCCcEEEhHHHH
Confidence              0 100     0   234555542       4678899999999998854   358753     2368998753

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	224
d1vk0a_	206	c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thal	1e-09
d1yt3a3	193	c.55.3.5 (A:1-193) Ribonuclease D, catalytic domai	5e-05
d1kfsa1	195	c.55.3.5 (A:324-518) Exonuclease domain of prokary	0.004

>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 206

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Hypothetical protein AT5G06450
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 54.2 bits (130), Expect = 1e-09
 Identities = 21/135 (15%), Positives = 39/135 (28%), Gaps = 19/135 (14%)

Query: 100 YVANNSDNFKTKVLQNTKVITNIKECSSVVEELMR------NELVTFDCEGINPGIKGQI 153
           +   +    +TK +     + +  + S  +  +        N  V FD        + + 
Sbjct: 9   FKMTDGSYVQTKTID----VGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETET 64

Query: 154 T----LFSLGLL----SGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILL 205
                 +SL  +            L           L +   S+ V  V      D  LL
Sbjct: 65  KTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDN-LKDLYRFFASKFVTFVGVQIEEDLDLL 123

Query: 206 YEQFGITLRNVFDTQ 220
            E  G+ +RN  +  
Sbjct: 124 RENHGLVIRNAINVG 138

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Length = 193

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

 Score = 40.3 bits (93), Expect = 5e-05
 Identities = 22/109 (20%), Positives = 41/109 (37%), Gaps = 7/109 (6%)

Query: 115 NTKVITNIKECSSVVEELMRNELVTFDCEGINPGIKGQITLFS-LGLLSGQV-YIFDLVT 172
           N ++IT     +S+ E +     +  D E +        T +  LGL+         L+ 
Sbjct: 2   NYQMITTDDALASLCEAVRAFPAIALDTEFV-----RTRTYYPQLGLIQLFDGEHLALID 56

Query: 173 CPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221
              +     L  +L   ++ K +H    D  +    FG   + + DTQ+
Sbjct: 57  PLGITDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQI 105

>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]} Length = 195

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

 Score = 34.6 bits (78), Expect = 0.004
 Identities = 21/117 (17%), Positives = 37/117 (31%), Gaps = 11/117 (9%)

Query: 114 QNTKVITNIKECSSVVEELMRNELVTFDCE--GINPGIKGQITLFSLGLLSGQVYIFDLV 171
            N   I + +   + + +L +  +  FD E   ++  I   +   S  +  G      + 
Sbjct: 5   DNYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDN-ISANLVGLSFAIEPGVAAYIPVA 63

Query: 172 TCPEVVGTGG--------LSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220
                             L  LLE E  +KV  + + D  +L           FDT 
Sbjct: 64  HDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTM 120

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	224
d2hbka2	292	Exosome complex exonuclease RRP6 {Baker's yeast (S	99.72
d1yt3a3	193	Ribonuclease D, catalytic domain {Escherichia coli	99.7
d1kfsa1	195	Exonuclease domain of prokaryotic DNA polymerase {	99.5
d1vk0a_	206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	99.2
d2hhva1	171	Exonuclease domain of prokaryotic DNA polymerase {	99.16
d1x9ma1	204	Exonuclease domain of T7 DNA polymerase {Bacteriop	88.14

>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exosome complex exonuclease RRP6
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.72  E-value=2.4e-17  Score=145.26  Aligned_cols=105  Identities=21%  Similarity=0.295  Sum_probs=96.9

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      +.+|++.+++.++++.+..+..+|||+|+... .+.|.+|++|||+. +.+|+||+.++....  ..|+++|+|+.|.||
T Consensus        85 ~~~Vdt~e~L~~li~~L~~~~~iavDtE~~~~~s~~g~l~LiQiat~-~~~~iiD~~~l~~~l--~~L~~ll~d~~I~KV  161 (292)
T d2hbka2          85 PIWVDTSTELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTR-ERDYLVDTLKLRENL--HILNEVFTNPSIVKV  161 (292)
T ss_dssp             CEEECSHHHHHHHHHHHTTCSEEEEEEEEECSSSSSCEEEEEEEECS-SCEEEEETTTTTTTG--GGGHHHHTCTTSEEE
T ss_pred             cEEeCCHHHHHHHHHHHhcCCcEEEEEEeCcCcccCCeEEEEEEEeC-CccEEEEecccccch--HHHHHHHhccCeEEE
Confidence            57899999999999999999999999999887 88899999999986 478999998876444  679999999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +|++++|+.+|++.+|+.+.++||||+|+
T Consensus       162 ~H~~~~Di~~L~~~~g~~~~n~fDT~~aa  190 (292)
T d2hbka2         162 FHGAFMDIIWLQRDLGLYVVGLFDTYHAS  190 (292)
T ss_dssp             ESSCHHHHHHHHHHHCCCCSSEEEHHHHH
T ss_pred             eechHhhhhhhhhcccccccchHHHHHHH
Confidence            99999999999999999999999999985

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {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: Ribonuclease D, catalytic domain
species: Escherichia coli [TaxId: 562]

Probab=99.70  E-value=3e-17  Score=135.54  Aligned_cols=104  Identities=20%  Similarity=0.232  Sum_probs=94.8

Q ss_pred             cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654         116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV  194 (224)
Q Consensus       116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV  194 (224)
                      |.+|++.+++..+++.+..++.+|||+|+.+. ++.++++++|+++.+ .+|+||+......   ..++++|+++.+.||
T Consensus         3 y~~I~t~~~l~~~~~~l~~~~~i~~DtE~~~~~~~~~~l~liQi~~~~-~~~~id~~~~~~~---~~l~~ll~~~~i~Kv   78 (193)
T d1yt3a3           3 YQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGE-HLALIDPLGITDW---SPLKAILRDPSITKF   78 (193)
T ss_dssp             CEEECSHHHHHHHHHHHTTSSEEEEEEEEECCSCSSCEEEEEEEECSS-CEEEECGGGCSCC---HHHHHHHHCTTSEEE
T ss_pred             EEEECCHHHHHHHHHHHhcCCeEEEECcccCCCcCCCcEEEEEEecCC-cceeehhcchhhh---HHHHHHhcCCCceEE
Confidence            88999999999999999999999999999888 888999999999864 7899998765443   468899999999999


Q ss_pred             EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654         195 IHDCRNDSILLYEQFGITLRNVFDTQLLF  223 (224)
Q Consensus       195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa  223 (224)
                      +||+++|..+|.+.+|+.+.++||||+|+
T Consensus        79 ~hn~~~D~~~L~~~~g~~~~~~~Dt~~~~  107 (193)
T d1yt3a3          79 LHAGSEDLEVFLNVFGELPQPLIDTQILA  107 (193)
T ss_dssp             ESSCHHHHHHHHHHHSSCCSSEEEHHHHH
T ss_pred             EecchhhhhhhhhhcCccccccchhhHHH
Confidence            99999999999889999999999999975

>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {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: Exonuclease domain of prokaryotic DNA polymerase
species: Escherichia coli [TaxId: 562]

Probab=99.50  E-value=6.8e-14  Score=112.01  Aligned_cols=107  Identities=24%  Similarity=0.303  Sum_probs=92.6

Q ss_pred             CCcEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCc----------cccccchh
Q psy5654         114 QNTKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCP----------EVVGTGGL  182 (224)
Q Consensus       114 ~~~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~----------~l~~~~~L  182 (224)
                      .+|.+|++++++.++++.+...+.+++|+|+.++ ++.+.++++++++..+..+++++....          ...  ..+
T Consensus         5 ~~y~~I~t~~~l~~~l~~l~~~~~~a~DtEt~~l~~~~~~i~~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l--~~l   82 (195)
T d1kfsa1           5 DNYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERAL--ELL   82 (195)
T ss_dssp             TTSEECCSHHHHHHHHHHHHHSSSEEEEEEESCSCTTTCCEEEEEEEEETTEEEEEECCCCSTTCCCCCCHHHHH--HHH
T ss_pred             ccceEECCHHHHHHHHHHHhcCCeEEEEeeeCCCCccccccccceeeccCCcccccccccccccccccccHHHHH--HHH
Confidence            4589999999999999999999999999999988 899999999999988888888775432          111  568


Q ss_pred             HhhhcCCCceEEEEecHHHHHHHHHhcCCccCC-ccchhhcc
Q psy5654         183 SKLLESENVIKVIHDCRNDSILLYEQFGITLRN-VFDTQLLF  223 (224)
Q Consensus       183 r~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~n-vFDTqLAa  223 (224)
                      +++|+++.+.|++|++++|+.+|. .+|+.+.+ +||||+|+
T Consensus        83 ~~~le~~~i~ki~hn~~~d~~~l~-~~~~~~~~~~~Dt~~a~  123 (195)
T d1kfsa1          83 KPLLEDEKALKVGQNLKYDRGILA-NYGIELRGIAFDTMLES  123 (195)
T ss_dssp             HHHHTCTTSCEEESSHHHHHHHHH-TTTCCCCCEEEEHHHHH
T ss_pred             HHHHhcccceeeechHHHHHHHHH-HHhccccCccHHHHHHH
Confidence            999999999999999999999997 58888755 69999986

>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Hypothetical protein AT5G06450
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.20  E-value=1.3e-11  Score=102.69  Aligned_cols=86  Identities=21%  Similarity=0.155  Sum_probs=70.3

Q ss_pred             cCCeEEEEEeeeCC-C--------ccceEEEEEEEeeCCeEEEEeCCCCc-cccccchhHhhhcCCCceEEEEecHHHHH
Q psy5654         134 RNELVTFDCEGINP-G--------IKGQITLFSLGLLSGQVYIFDLVTCP-EVVGTGGLSKLLESENVIKVIHDCRNDSI  203 (224)
Q Consensus       134 ~~~~Ia~D~E~~~l-~--------~~g~L~lIQIat~~g~a~lIDi~al~-~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~  203 (224)
                      ....+|||+|+... .        ..++++++|||+. ..+|+|++.... ...  ..|+++|+++.+.||||++++|+.
T Consensus        45 ~~~~v~~D~Ew~~~~~~~~~~~~~~~~~vallQl~t~-~~~~l~~l~~~~~~~~--~~L~~~L~~~~i~kVG~~i~~D~~  121 (206)
T d1vk0a_          45 GNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTR-NLCLFLRLPKPFHDNL--KDLYRFFASKFVTFVGVQIEEDLD  121 (206)
T ss_dssp             STTEEEEEEEEECCC------CGGGGCEEEEEEEECS-SEEEEEECCSSCCGGG--HHHHHHHTCSSSEEEESSCHHHHH
T ss_pred             CCCEEEEEeecCCCCCcccccccccCceeEEEEEEeC-CCEEEEECCccccccH--HHHHHHhcCCCceEEEEeEHHHHH
Confidence            45789999998654 1        2256999999985 589999987643 233  579999999999999999999999


Q ss_pred             HHHHhcCCccCCccch-hhc
Q psy5654         204 LLYEQFGITLRNVFDT-QLL  222 (224)
Q Consensus       204 lL~~~~GI~L~nvFDT-qLA  222 (224)
                      .|++.||+.+.+++|+ ++|
T Consensus       122 ~L~~~~gi~~~~~~Dl~~la  141 (206)
T d1vk0a_         122 LLRENHGLVIRNAINVGKLA  141 (206)
T ss_dssp             HHHHHHCCCCSSEEEHHHHH
T ss_pred             HHHHhcCCcccceEEchHHH
Confidence            9988899999998885 454

>d2hhva1 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic DNA polymerase {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of prokaryotic DNA polymerase
species: Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]

Probab=99.16  E-value=1.1e-11  Score=100.08  Aligned_cols=84  Identities=18%  Similarity=0.112  Sum_probs=69.1

Q ss_pred             CCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc
Q psy5654         135 NELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL  213 (224)
Q Consensus       135 ~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L  213 (224)
                      ...+++|+|.... .++++++++++++. .++|+++.......   ..|+++|+++++.||+||+|+|+++|. ++|+.+
T Consensus        16 ~~~~a~~~E~~~~n~~~~~iiGi~i~~~-~~~~~i~~~~~~~~---~~l~~~l~~~~~~ki~hn~K~d~~~L~-~~gi~~   90 (171)
T d2hhva1          16 ADKAALVVEVVEENYHDAPIVGIAVVNE-HGRFFLRPETALAD---PQFVAWLGDETKKKSMFDSKRAAVALK-WKGIEL   90 (171)
T ss_dssp             CSEEEEEEECCSSSCTTCCCCEEEEEET-TEEEEECHHHHTTC---HHHHHHHHCTTSEEEESSHHHHHHHHH-TTTCCC
T ss_pred             cCCeEEEEEcCCCccccCeEEEEEEEEC-CCEEEEechhhhhH---HHHHHHHhCccceeeccchHHHHHHHH-HCCCCC
Confidence            3568999998777 77899999999975 46788865322112   579999999999999999999999996 599999


Q ss_pred             CCc-cchhhcc
Q psy5654         214 RNV-FDTQLLF  223 (224)
Q Consensus       214 ~nv-FDTqLAa  223 (224)
                      .+. ||||+|+
T Consensus        91 ~~~~fDt~laa  101 (171)
T d2hhva1          91 CGVSFDLLLAA  101 (171)
T ss_dssp             CCEEEEHHHHH
T ss_pred             ccccccHHHHH
Confidence            775 9999986

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

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

Probab=88.14  E-value=0.26  Score=37.50  Aligned_cols=71  Identities=10%  Similarity=0.003  Sum_probs=43.6

Q ss_pred             EEEEEeeeCC-CccceEEEEEEEe-eCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEe-cHHHHHHHHHhcCC
Q psy5654         138 VTFDCEGINP-GIKGQITLFSLGL-LSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHD-CRNDSILLYEQFGI  211 (224)
Q Consensus       138 Ia~D~E~~~l-~~~g~L~lIQIat-~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd-~K~Dl~lL~~~~GI  211 (224)
                      +.||+|+.++ .-..++..+++-. .+++++.++........  ..+..++.++.+ .|+|| ..+|+..|.+.++.
T Consensus         2 l~~DIET~gl~~~~~~I~ci~~~d~~~~~~~~~~~~~~~~~l--~~~~~~l~~~D~-ivghN~~~FD~P~L~~~~~~   75 (204)
T d1x9ma1           2 IVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYL--DALEAEVARGGL-IVFHNGHKYDVPALTKLAKL   75 (204)
T ss_dssp             EEEEEEESSCGGGCCCEEEEEEEETTTTEEEEECGGGHHHHH--HHHHHHHHTTCC-EEESSTTTTHHHHHHHHHHH
T ss_pred             EEEEecCCCCCCCCCEEEEEEEEECCCCeEEEEeCCCchhHH--HHHHHHHhcCCE-EEEEccccccHHHHHHHHHH
Confidence            6899999876 4334554444332 34566655432222222  456667778775 59999 66999888655443