Citrus Sinensis ID: 045621

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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-----
Protein Sequence
MAVEALTLSPKPAEIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQISS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccEEEEEcccEEEEEEcccHHHHHHHHHHHHcccccccccEEccccccEEEEEEEEEEcccccHHHHHHHcccccEEEEEEEHHHHHHHccccHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHccccccccccccccccccccccccccccEEEEEEcccEEEEEEcccHHHHHHHHHHHcccccccccccccccccccEEEEEEEcccccccHHHHHHHccccEEEEEcccHHHHHHHHcccHHHHcccHHHHHHHHHcccccccccEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEcc
Coil and Loop (DISEMBL)
mavealtlspkpaeikplaynssssieplghniwginfgedYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLfhkdrmpqslvdfldndkftfvgtmdvadmaaakyddeelktFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIialpkpttfdafccfqiss
Flexible Loop (DISEMBL)
mavealtlspkpaeiKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVtsrasdvdrwIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEmekskritlskwdvnnLSKQQIRYAAIDAFVSFKLAIELKKEIialpkpttfdAFCCFQISS
Low Complexity Region (SEG)
MAVEALTLSPKPAEIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQISS
Disordered region (IsUnstruct)
*****************************GHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQI**
Disordered Region (DISOPRED)
**************IKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQISS
Disordered Region (DISEMBL)
MAVEALTLSPKPAEIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQISS
Disordered Region (DISPRO)
********SPK*AEIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQIS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVEALTLSPKPAEIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQISS
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	205	2.2.26 [Sep-21-2011]
Q84LH3	288	Werner Syndrome-like exon	yes	no	0.497	0.354	0.303	2e-06
Q14191	1432	Werner syndrome ATP-depen	yes	no	0.487	0.069	0.310	0.0007

>sp|Q84LH3|WEX_ARATH Werner Syndrome-like exonuclease OS=Arabidopsis thaliana GN=WEX PE=1 SV=1

 Score = 52.8 bits (125), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/135 (30%), Positives = 60/135 (44%), Gaps = 33/135 (24%)

Query: 79  KVAIIQLC----------LFHKDRMPQSLVDFLDNDKFTFVG------------------ 110
           KVA +Q+C          +FH   +PQSL   +++     VG                  
Sbjct: 148 KVATVQICVDSNYCDVMHIFHSG-IPQSLQHLIEDSTLVKVGIGIDGDSVKLFHDYGVSI 206

Query: 111 --TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYA 168
               D++D+A  K   +  K +GL  L    +  E+ K  RI L  W+   LSKQQ++YA
Sbjct: 207 KDVEDLSDLANQKIGGD--KKWGLASLTETLVCKELLKPNRIRLGNWEFYPLSKQQLQYA 264

Query: 169 AIDAFVSFKLAIELK 183
           A DA+ S+ L   LK
Sbjct: 265 ATDAYASWHLYKVLK 279

Exonuclease that digests recessed strands of DNA duplexes in the 3' to 5' direction but hardly single-stranded DNA or blunt-ended duplexes. Also able to digest 3'-protruding strands and 3'-recessed strand termini of duplexes containing mismatched bases.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|Q14191|WRN_HUMAN Werner syndrome ATP-dependent helicase OS=Homo sapiens GN=WRN PE=1 SV=2

 Score = 43.9 bits (102), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 53/132 (40%), Gaps = 32/132 (24%)

Query: 75  NKLQKVAIIQLC-------LFHKDRM---PQSLVDFLDNDKFTFVGT------------- 111
            KL KVA+IQLC       LFH   M   PQ L   L+N      G              
Sbjct: 92  GKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGIEGDQWKLLRDF 151

Query: 112 -------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQ 164
                  +++ D+A  K    E  T+ L  LV   L  ++ K K I  S W    L++ Q
Sbjct: 152 DIKLKNFVELTDVANKKLKCTE--TWSLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQ 209

Query: 165 IRYAAIDAFVSF 176
             YAA DA+  F
Sbjct: 210 KLYAATDAYAGF 221

Multifunctional enzyme that has both magnesium and ATP-dependent DNA-helicase activity and 3'->5' exonuclease activity towards double-stranded DNA with a 5'-overhang. Has no nuclease activity towards single-stranded DNA or blunt-ended double-stranded DNA. Binds preferentially to DNA substrates containing alternate secondary structures, such as replication forks and Holliday junctions. May play an important role in the dissociation of joint DNA molecules that can arise as products of homologous recombination, at stalled replication forks or during DNA repair. Alleviates stalling of DNA polymerases at the site of DNA lesions. Important for genomic integrity. Plays a role in the formation of DNA replication focal centers; stably associates with foci elements generating binding sites for RP-A.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
224117124	199	predicted protein [Populus trichocarpa]	0.731	0.753	0.421	9e-29
242058239	201	hypothetical protein SORBIDRAFT_03g03020	0.736	0.751	0.312	7e-20
147777289	208	hypothetical protein VITISV_011782 [Viti	0.746	0.735	0.331	5e-19
297741701	208	unnamed protein product [Vitis vinifera]	0.726	0.716	0.333	6e-19
242058237	202	hypothetical protein SORBIDRAFT_03g03019	0.702	0.712	0.338	7e-19
125527632	208	hypothetical protein OsI_03659 [Oryza sa	0.785	0.774	0.301	9e-19
297597576	208	Os01g0737600 [Oryza sativa Japonica Grou	0.785	0.774	0.301	9e-19
242054351	210	hypothetical protein SORBIDRAFT_03g03396	0.717	0.7	0.322	4e-18
414881130	200	TPA: 3-5 exonuclease/ nucleic acid bindi	0.702	0.72	0.304	5e-18
226503994	200	LOC100283715 [Zea mays] gi|195636594|gb|	0.702	0.72	0.304	5e-18

>gi|224117124|ref|XP_002317483.1| predicted protein [Populus trichocarpa] gi|222860548|gb|EEE98095.1| predicted protein [Populus trichocarpa]

 Score =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 81/192 (42%), Positives = 107/192 (55%), Gaps = 42/192 (21%)

Query: 36  INFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITN------------KLQKVAII 83
           + +  D+  TTVT  AS VDRWI + + V++ +L +LI                QK+AI+
Sbjct: 8   VEYYGDHIFTTVTKSASAVDRWIDQIMYVYQSKLSKLIIGLDTEWFLPAYPGDYQKIAIL 67

Query: 84  QLC---------LFHKDRMPQSLVDFLDNDKFTFVG--------------------TMDV 114
           QLC         L H D  P+SL+DFL N+K+TFVG                      DV
Sbjct: 68  QLCVGRRCLIFQLCHADYFPRSLIDFLGNEKYTFVGKEVRNDAHKLMNDYGLNVGHCRDV 127

Query: 115 ADMAAAKYD-DEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAF 173
           A  AA+K+  DE+ + FGLKRLVL+FL  E+EK  +ITLS+WD   L  QQI+YA +DAF
Sbjct: 128 AYWAASKHGGDEDFRKFGLKRLVLRFLKKELEKPLKITLSRWDRKKLDYQQIKYACLDAF 187

Query: 174 VSFKLAIELKKE 185
           VSFKL   L K+
Sbjct: 188 VSFKLGELLSKD 199

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242058239|ref|XP_002458265.1| hypothetical protein SORBIDRAFT_03g030200 [Sorghum bicolor] gi|241930240|gb|EES03385.1| hypothetical protein SORBIDRAFT_03g030200 [Sorghum bicolor]

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 96/192 (50%), Gaps = 41/192 (21%)

Query: 32  NIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLI-----------TNKLQKV 80
            ++ + F ED   TTVT+  +DV+ W+   + VHRRRLH+L+           +    K 
Sbjct: 5   RVYKVRFEEDLITTTVTASGADVESWLDEVLAVHRRRLHKLVVGLDVEWRPSFSRAYSKT 64

Query: 81  AIIQLC---------LFHKDRMPQSLVDFLDNDK-FTFVG-------------------- 110
           AI+QLC         +     +P +L +FL +D  +TFVG                    
Sbjct: 65  AILQLCVGRRCLVFQILRAGYVPIALAEFLGDDSGYTFVGVGVEADAQRLCDDYGLEVGH 124

Query: 111 TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAI 170
           T+D+A +AA K +  +L+  GLK +    +   +EK + + +  WD  +LS +Q++YA I
Sbjct: 125 TVDLAYLAAEKMERRDLRNAGLKGIAAAVMDAHVEKPQSVRIGPWDAYDLSDEQVKYATI 184

Query: 171 DAFVSFKLAIEL 182
           DAFVSF++   L
Sbjct: 185 DAFVSFEVGRRL 196

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777289|emb|CAN60287.1| hypothetical protein VITISV_011782 [Vitis vinifera]

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 64/193 (33%), Positives = 92/193 (47%), Gaps = 40/193 (20%)

Query: 31  HNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITN-----------KLQK 79
           H ++ + F +D   T VT     VD WI    ++HR RLH+LI                 
Sbjct: 12  HELFRVAFHDDCIETLVTHVPHMVDSWIGDIEHIHRHRLHKLIVGLDIEWRPNNARYTNP 71

Query: 80  VAIIQLC---------LFHKDRMPQSLVDFLDNDKFTFVGT------------------- 111
           VAI+QLC         L +   +P SL+DFL +  +TFVG                    
Sbjct: 72  VAILQLCVGRRCLIFQLLYAPEIPTSLIDFLGDTDYTFVGVGIQADSQKLLNDHNLRVGN 131

Query: 112 -MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAI 170
            +D+A +AA   +  EL+  G+KRL  + L  E+EK K +  S+WD + LS  Q+ YA +
Sbjct: 132 VVDLAVLAARVLNTRELRNAGIKRLAREVLGREVEKPKHVARSRWDTDWLSDAQVHYACV 191

Query: 171 DAFVSFKLAIELK 183
           DAFVSF++   L 
Sbjct: 192 DAFVSFEVGRSLN 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741701|emb|CBI32833.3| unnamed protein product [Vitis vinifera]

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 63/189 (33%), Positives = 91/189 (48%), Gaps = 40/189 (21%)

Query: 31  HNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITN-----------KLQK 79
           H ++ + F +D   T VT     VD WI    ++HR RLH+LI                 
Sbjct: 12  HELFRVAFHDDCIETLVTHVPHMVDSWIGDIEHIHRHRLHKLIVGLDIEWRPNNARYTNP 71

Query: 80  VAIIQLC---------LFHKDRMPQSLVDFLDNDKFTFVGT------------------- 111
           VAI+QLC         L +   +P SL+DFL +  +TFVG                    
Sbjct: 72  VAILQLCVGRRCLIFQLLYAPEIPTSLIDFLGDTDYTFVGVGIQADSQKLLNDHNLRVGN 131

Query: 112 -MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAI 170
            +D+A +AA   +  EL+  G+KRL  + L  E+EK K +  S+WD + LS  Q+ YA +
Sbjct: 132 VVDLAVLAARVLNTRELRNAGIKRLAREVLGREVEKPKHVARSRWDTDWLSDAQVHYACV 191

Query: 171 DAFVSFKLA 179
           DAFVSF++ 
Sbjct: 192 DAFVSFEVG 200

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242058237|ref|XP_002458264.1| hypothetical protein SORBIDRAFT_03g030190 [Sorghum bicolor] gi|241930239|gb|EES03384.1| hypothetical protein SORBIDRAFT_03g030190 [Sorghum bicolor]

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 65/192 (33%), Positives = 89/192 (46%), Gaps = 48/192 (25%)

Query: 36  INFGEDYFVTTVTSRASDVDRWIARTINVHR----------------RRLHRLITNKLQK 79
           + FG D   TTVTS    VDRWIA  ++VHR                R  +R   N    
Sbjct: 9   VTFGNDVITTTVTSSGQAVDRWIAEILSVHRPGGVGYNITVGLDVEWRPSYRSYQNP--- 65

Query: 80  VAIIQLC---------LFHKDRMPQSLVDFLDNDKFTFVGTMDVADM------------- 117
           VA +QLC         L H D +P +L +FL +    F G    AD              
Sbjct: 66  VATLQLCVGRSCLIFQLLHADYVPGALAEFLGDRGICFFGVGVAADAERLSDDHGLQVAN 125

Query: 118 -------AAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAI 170
                  AA   +  +L+  GL+ LV   + V++ K +R+T+S+WD   LS +QIRYA +
Sbjct: 126 AVDLRGRAAECMNRPDLRQAGLRALVQAVMGVDLAKPQRVTMSRWDAYCLSHEQIRYACV 185

Query: 171 DAFVSFKLAIEL 182
           DAFVSF++A  L
Sbjct: 186 DAFVSFEIARRL 197

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125527632|gb|EAY75746.1| hypothetical protein OsI_03659 [Oryza sativa Indica Group]

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 95/202 (47%), Gaps = 41/202 (20%)

Query: 22  SSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLIT------- 74
           ++S ++  G   + + F EDY  TTVT    DVD W+   + +HRRRL+ L+        
Sbjct: 2   ATSIVDDFGDGTYTVAFDEDYIHTTVTYSGDDVDDWLDEILRIHRRRLNYLVVGLDVEWR 61

Query: 75  -----NKLQKVAIIQLC---------LFHKDRMPQSLVDFLDNDKFTFVG---------- 110
                +    VA++Q+C         + H D +P SL DFL + +FTFVG          
Sbjct: 62  PATYYHGPGPVAVLQICVGRRCLIFQILHADYVPDSLFDFLADGRFTFVGVGIHDDVAKL 121

Query: 111 ----------TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNL 160
                      +D+  +AA       L++ GL+ LV + + V   K   + +S WD  NL
Sbjct: 122 RSHHELEVENAVDLRYLAAQTIGKPALRSAGLQGLVREVMGVWAPKPYHVRVSAWDSWNL 181

Query: 161 SKQQIRYAAIDAFVSFKLAIEL 182
           + +Q+ YA  DAF SF++   L
Sbjct: 182 TPEQVMYACADAFASFEVGRSL 203

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297597576|ref|NP_001044181.2| Os01g0737600 [Oryza sativa Japonica Group] gi|57900569|dbj|BAD87021.1| hypothetical protein [Oryza sativa Japonica Group] gi|125571949|gb|EAZ13464.1| hypothetical protein OsJ_03381 [Oryza sativa Japonica Group] gi|255673665|dbj|BAF06095.2| Os01g0737600 [Oryza sativa Japonica Group]

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 95/202 (47%), Gaps = 41/202 (20%)

Query: 22  SSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLIT------- 74
           ++S ++  G   + + F EDY  TTVT    DVD W+   + +HRRRL+ L+        
Sbjct: 2   ATSIVDDFGDGTYTVAFDEDYIHTTVTYSGDDVDDWLDEILRIHRRRLNYLVVGLDVEWR 61

Query: 75  -----NKLQKVAIIQLC---------LFHKDRMPQSLVDFLDNDKFTFVG---------- 110
                +    VA++Q+C         + H D +P SL DFL + +FTFVG          
Sbjct: 62  PATYYHGPGPVAVLQICVGRRCLIFQILHADYVPDSLFDFLADGRFTFVGVGIHDDVAKL 121

Query: 111 ----------TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNL 160
                      +D+  +AA       L++ GL+ LV + + V   K   + +S WD  NL
Sbjct: 122 RSHHGLEVENVVDLRYLAAQTIGKPALRSAGLQGLVREVMGVWAPKPYHVRVSAWDSWNL 181

Query: 161 SKQQIRYAAIDAFVSFKLAIEL 182
           + +Q+ YA  DAF SF++   L
Sbjct: 182 TPEQVMYACADAFASFEVGRSL 203

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242054351|ref|XP_002456321.1| hypothetical protein SORBIDRAFT_03g033960 [Sorghum bicolor] gi|241928296|gb|EES01441.1| hypothetical protein SORBIDRAFT_03g033960 [Sorghum bicolor]

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 88/186 (47%), Gaps = 39/186 (20%)

Query: 36  INFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLITN----------KLQKVAIIQL 85
           ++F ED F  T+T    +V+ W+  T  +HRR  H LI                VA++Q+
Sbjct: 17  VSFDEDCFEATLTKSGGEVESWLEETYRIHRRCRHMLIVGLDVEWRPAAPVPGPVAVLQI 76

Query: 86  C---------LFHKDRMPQSLVDFLDNDKFTFVG--------------------TMDVAD 116
           C         +   D +P +L DFL + +FTFVG                    T+D+  
Sbjct: 77  CVDRRCLVFQILRADYVPDALSDFLADRRFTFVGVGIRDDAAKLRDGYGLEVPRTVDLRR 136

Query: 117 MAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSF 176
           +AA      +L+  GL+RLV + L V+MEK   + +S WD   LSK Q +YA  DAF S 
Sbjct: 137 LAARTLGKPDLRRAGLQRLVWEVLGVQMEKPHHVRVSAWDKRKLSKAQFKYACADAFASM 196

Query: 177 KLAIEL 182
           ++  EL
Sbjct: 197 EVGQEL 202

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414881130|tpg|DAA58261.1| TPA: 3-5 exonuclease/ nucleic acid binding protein [Zea mays]

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 90/184 (48%), Gaps = 40/184 (21%)

Query: 36  INFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLI-----------TNKLQKVAIIQ 84
           + F  +   TTVT+  + V+ W+   ++VHRRRLH+L+           +    K AI+Q
Sbjct: 9   VRFEGNVITTTVTASGAAVESWLDEILSVHRRRLHKLVVGLDVEWRPSFSRAYSKTAILQ 68

Query: 85  LC---------LFHKDRMPQSLVDFLDNDKFTFVGTM--------------------DVA 115
           LC         L H D +P +L +FL +  +TFVG                      D+A
Sbjct: 69  LCVGRRCLIFQLLHADYVPNTLDEFLSDPDYTFVGVGVAADVERLENDYDLEVANAEDLA 128

Query: 116 DMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVS 175
           ++AA +    +L+  GL+ +    +   +EK + +    WD ++LS +QI YA IDAFVS
Sbjct: 129 ELAAKEMGHPDLRNAGLQGIARVVMDAHVEKPQWVRTGPWDASSLSDEQIEYATIDAFVS 188

Query: 176 FKLA 179
           F++ 
Sbjct: 189 FEVG 192

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226503994|ref|NP_001150086.1| LOC100283715 [Zea mays] gi|195636594|gb|ACG37765.1| 3-5 exonuclease/ nucleic acid binding protein [Zea mays]

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 90/184 (48%), Gaps = 40/184 (21%)

Query: 36  INFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLI-----------TNKLQKVAIIQ 84
           + F  +   TTVT+  + V+ W+   ++VHRRRLH+L+           +    K AI+Q
Sbjct: 9   VRFEGNVITTTVTASGAAVESWLDEILSVHRRRLHKLVVGLDVEWRPSFSRAYSKTAILQ 68

Query: 85  LC---------LFHKDRMPQSLVDFLDNDKFTFVGTM--------------------DVA 115
           LC         L H D +P +L +FL +  +TFVG                      D+A
Sbjct: 69  LCVGRRCLIFQLLHADYVPNTLDEFLSDPDYTFVGVGVAADVERLENDYDLEVANAEDLA 128

Query: 116 DMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVS 175
           ++AA +    +L+  GL+ +    +   +EK + +    WD ++LS +QI YA IDAFVS
Sbjct: 129 ELAAKEMGHPDLRNAGLQGIARVVMDAHVEKPQWVRTGPWDASSLSDEQIEYATIDAFVS 188

Query: 176 FKLA 179
           F++ 
Sbjct: 189 FEVG 192

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
TAIR|locus:2092472	220	AT3G12470 [Arabidopsis thalian	0.156	0.145	0.468	7.7e-05
TAIR|locus:2119525	288	WRNEXO "Werner syndrome-like e	0.336	0.239	0.394	8.1e-05
TAIR|locus:2053519	239	AT2G36110 [Arabidopsis thalian	0.185	0.158	0.368	0.00093

TAIR|locus:2092472 AT3G12470 [Arabidopsis thaliana (taxid:3702)]

 Score = 79 (32.9 bits), Expect = 7.7e-05, Sum P(3) = 7.7e-05
 Identities = 15/32 (46%), Positives = 23/32 (71%)

Query:   150 ITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIE 181
             I +S W V NL+  Q+  A+I+++V FKLA+E
Sbjct:   175 ICMSDWGVYNLNHYQVLQASIESYVCFKLAVE 206

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2119525 WRNEXO "Werner syndrome-like exonuclease" [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 8.1e-05, Sum P(2) = 8.1e-05
 Identities = 28/71 (39%), Positives = 40/71 (56%)

Query:   113 DVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDA 172
             D++D+A  K   +  K +GL  L    +  E+ K  RI L  W+   LSKQQ++YAA DA
Sbjct:   211 DLSDLANQKIGGD--KKWGLASLTETLVCKELLKPNRIRLGNWEFYPLSKQQLQYAATDA 268

Query:   173 FVSFKLAIELK 183
             + S+ L   LK
Sbjct:   269 YASWHLYKVLK 279

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

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2053519 AT2G36110 [Arabidopsis thaliana (taxid:3702)]

 Score = 68 (29.0 bits), Expect = 0.00093, Sum P(3) = 0.00093
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query:   144 MEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIE 181
             + K K I +S W   +LS  QI  A+ D +V  KL ++
Sbjct:   163 VRKDKEICMSNWGARSLSHDQIVQASDDVYVCCKLGVK 200

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

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	205
cd06141	170	cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain o	1e-27
pfam01612	172	pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease	4e-08
cd06142	178	cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domai	1e-05
cd06146	193	cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease d	1e-04
smart00474	172	smart00474, 35EXOc, 3'-5' exonuclease	2e-04
cd09018	150	cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' e	2e-04
COG0349	361	COG0349, Rnd, Ribonuclease D [Translation, ribosom	8e-04

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

 Score =  102 bits (256), Expect = 1e-27
 Identities = 43/178 (24%), Positives = 66/178 (37%), Gaps = 49/178 (27%)

Query: 48  TSRASDVDRWIARTINVHRRRLHRLI------------TNKLQKVAIIQLC--------- 86
           T  A D +  +              +              K  KVA++QL          
Sbjct: 1   TDSAQDAEEAV------KELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQ 54

Query: 87  LFHKDRMPQSLVDFLDNDKFTFVG--------------------TMDVADMAAAKYDDEE 126
           L H D++P SL   L++     VG                     +D++ +A        
Sbjct: 55  LAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRV--GPR 112

Query: 127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK 184
            K   L RLV + L + + K K++  S W+   LSK+QI YAA DA+ S +L  +L  
Sbjct: 113 RKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLLA 170

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|216604 pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 33/141 (23%), Positives = 59/141 (41%), Gaps = 28/141 (19%)

Query: 73  ITNKLQKVAIIQLC----LFHKDRMP-----QSLVDFLDNDKFTFVG---TMDVADMAAA 120
             +      +IQ+      +  D +      + L   L++   T VG     D+  +A  
Sbjct: 34  TYSYTLVGCLIQISTGEGAYIIDPLALGDDLEGLKRLLEDPNITKVGHNAKFDLEVLARD 93

Query: 121 K-------YDDE-------ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIR 166
                   +D           ++  L  L  K+L VE++KS++   + W    LS++Q+R
Sbjct: 94  FGIKLENLFDTMLAAYLLGYPRSHSLDDLAEKYLGVELDKSEQC--ADWRARPLSEEQLR 151

Query: 167 YAAIDAFVSFKLAIELKKEII 187
           YAA DA    +L  +L+KE+ 
Sbjct: 152 YAAEDADYLLRLYDKLRKELE 172

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

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 130 FGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIAL 189
            GL  LV + L VE++K +    S W    L+ +Q+ YAA+D      L  +LK+E+   
Sbjct: 106 VGLAALVEELLGVELDKGE--QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEE 163

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|176655 cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 11/103 (10%)

Query: 76  KLQKVAIIQLCLFHKDRMPQSLVDFLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRL 135
            L        C+F      Q+++D  +  K      +  +DM   K +    KT GL  L
Sbjct: 96  ALSASYPALKCMF---ERVQNVLDLQNLAK-----ELQKSDMGRLKGNLPS-KTKGLADL 146

Query: 136 VLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKL 178
           V + L   ++KS++   S W+   L ++QI YAA+DA+   ++
Sbjct: 147 VQEVLGKPLDKSEQ--CSNWERRPLREEQILYAALDAYCLLEV 187

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. Length = 193

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

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 100 FLDNDKFTFVGTMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNN 159
            L           D   M AA          GL  L+L +L VE++K ++   S W    
Sbjct: 89  VLARFGIELENIFDT--MLAAYLLLGGPSKHGLATLLLGYLGVELDKEEQ--KSDWGARP 144

Query: 160 LSKQQIRYAAIDAFVSFKLAIELKKEII 187
           LS++Q+ YAA DA    +L  +L+KE+ 
Sbjct: 145 LSEEQLEYAAEDADALLRLYEKLEKELE 172

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

>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 = 39.5 bits (92), Expect = 2e-04
 Identities = 29/136 (21%), Positives = 49/136 (36%), Gaps = 28/136 (20%)

Query: 75  NKLQKVAIIQLC-------LFHKDRM---PQSLVDFLDNDKFTFVGTMDVADMAA-AKYD 123
           N    + +IQL        L          + L   L+++K   VG     D      Y 
Sbjct: 13  NISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYF 72

Query: 124 DEELKTF-----------------GLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIR 166
            E                       +  LV ++L  ++ K + I    W    L+++Q R
Sbjct: 73  IELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGR 132

Query: 167 YAAIDAFVSFKLAIEL 182
           YAA DA V+ ++ ++L
Sbjct: 133 YAAEDADVTLQIHLKL 148

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

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

 Score = 39.2 bits (92), Expect = 8e-04
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 131 GLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEII 187
           GL  LV + L VE++KS++   S W    LS+ Q+ YAA D      L  +L +E+ 
Sbjct: 113 GLADLVEELLGVELDKSEQ--RSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167

Length = 361

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
cd06146	193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	99.92
cd06141	170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	99.91
cd06129	161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	99.9
PRK10829	373	ribonuclease D; Provisional	99.87
KOG4373	319	consensus Predicted 3'-5' exonuclease [General fun	99.86
COG0349	361	Rnd Ribonuclease D [Translation, ribosomal structu	99.83
TIGR01388	367	rnd ribonuclease D. This model describes ribonucle	99.75
PF01612	176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	99.74
cd06148	197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	99.73
cd06142	178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	99.34
KOG2207	617	consensus Predicted 3'-5' exonuclease [Replication	99.34
smart00474	172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	99.17
cd09018	150	DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease	99.05
cd00007	155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	98.95
cd06147	192	Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y	98.76
PRK14975	553	bifunctional 3'-5' exonuclease/DNA polymerase; Pro	98.7
KOG2206	687	consensus Exosome 3'-5' exoribonuclease complex, s	98.65
PRK05755	880	DNA polymerase I; Provisional	98.31
cd06140	178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	97.81
cd06139	193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	97.68
TIGR00593	887	pola DNA polymerase I. This family is based on the	95.34
COG0749	593	PolA DNA polymerase I - 3'-5' exonuclease and poly	89.13
cd06137	161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	87.24
cd06128	151	DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam	86.95
cd06145	150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	86.48
cd06143	174	PAN2_exo DEDDh 3'-5' exonuclease domain of the euk	82.43
PRK08517	257	DNA polymerase III subunit epsilon; Provisional	80.98
cd06144	152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	80.23

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

Probab=99.92  E-value=1.7e-24  Score=179.93  Aligned_cols=131  Identities=24%  Similarity=0.391  Sum_probs=103.0

Q ss_pred             EcCCHHHHHHHHHHH-HHhhhccccceee-----------ccCCceeeEEEE------EEeeC--------CCCHHHHHh
Q 045621           47 VTSRASDVDRWIART-INVHRRRLHRLIT-----------NKLQKVAIIQLC------LFHKD--------RMPQSLVDF  100 (205)
Q Consensus        47 vT~~~~~v~~wi~~~-~~~~~~~~~~lvv-----------~~~~~vaLiQLc------L~~~~--------~~p~~L~~f  100 (205)
                      +..+++.+.+++.++ +..     .+.|.           +..+++||||||      ||++.        .+|+.|+++
T Consensus         3 ~i~~~~el~~~~~~~~l~~-----~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~~~~~~~~L~~l   77 (193)
T cd06146           3 IVDSEEELEALLLALSLEA-----GRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLESEDWDRLLKRL   77 (193)
T ss_pred             EecCHHHHHHHHHHHhhcc-----CCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccchHHHHHHHHHH
Confidence            346789999999995 221     22222           236899999999      77753        256789999


Q ss_pred             hcCCCeeEEEe--------------------------eeHHHHHHHhcCCc--------chhcccHHHHHHHHcCccccc
Q 045621          101 LDNDKFTFVGT--------------------------MDVADMAAAKYDDE--------ELKTFGLKRLVLKFLHVEMEK  146 (205)
Q Consensus       101 L~d~~i~kvGv--------------------------~Dl~~la~~~lg~~--------~~~~~gL~~Lv~~~lg~~l~K  146 (205)
                      |+||+|+|||+                          +|++.+|+...+..        ...+.||++|++++||+.++|
T Consensus        78 l~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K  157 (193)
T cd06146          78 FEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDK  157 (193)
T ss_pred             hCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCc
Confidence            99999999999                          55566665332210        024689999999999999999


Q ss_pred             CCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHH
Q 045621          147 SKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK  184 (205)
Q Consensus       147 ~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~  184 (205)
                      ..+  +|||++||||++|++|||.|||+++.||++|.+
T Consensus       158 ~~q--~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~  193 (193)
T cd06146         158 SEQ--CSNWERRPLREEQILYAALDAYCLLEVFDKLLE  193 (193)
T ss_pred             ccc--cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            876  999999999999999999999999999999863

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=99.91  E-value=1.1e-23  Score=169.97  Aligned_cols=127  Identities=33%  Similarity=0.548  Sum_probs=105.3

Q ss_pred             CCHHHHHHHHHHHH-Hhhhccccceee-----------ccCCceeeEEEE------EEee---CCCCHHHHHhhcCCCee
Q 045621           49 SRASDVDRWIARTI-NVHRRRLHRLIT-----------NKLQKVAIIQLC------LFHK---DRMPQSLVDFLDNDKFT  107 (205)
Q Consensus        49 ~~~~~v~~wi~~~~-~~~~~~~~~lvv-----------~~~~~vaLiQLc------L~~~---~~~p~~L~~fL~d~~i~  107 (205)
                      ++++.+++|++.+. .      .+.+.           +..+++|+||||      ||++   +.+|+.|++||++++|+
T Consensus         2 ~~~~~~~~~~~~~~~~------~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~~~l~~ll~~~~i~   75 (170)
T cd06141           2 DSAQDAEEAVKELLGK------EKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSIL   75 (170)
T ss_pred             CCHHHHHHHHHHHhcC------CCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhcccHHHHHHhcCCCee
Confidence            57888999999887 3      22222           145799999999      6764   46799999999999999


Q ss_pred             EEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHH
Q 045621          108 FVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRY  167 (205)
Q Consensus       108 kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~Y  167 (205)
                      |||+                    +|++.++. .++.. ..+.||+.|++.++|..++|++.+++|||..||||++|++|
T Consensus        76 kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~-ll~~~-~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~qi~Y  153 (170)
T cd06141          76 KVGVGIKGDARKLARDFGIEVRGVVDLSHLAK-RVGPR-RKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILY  153 (170)
T ss_pred             EEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHH-HhCCC-cCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHHHHHH
Confidence            9999                    67777665 34422 13469999999999999998888889999999999999999


Q ss_pred             HHhhHHHHHHHHHHHH
Q 045621          168 AAIDAFVSFKLAIELK  183 (205)
Q Consensus       168 AA~DA~~~~~I~~~L~  183 (205)
                      ||.|||++++||++|.
T Consensus       154 Aa~Da~~~~~l~~~l~  169 (170)
T cd06141         154 AATDAYASLELYRKLL  169 (170)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999986

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.

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

Probab=99.90  E-value=3.5e-23  Score=166.88  Aligned_cols=104  Identities=28%  Similarity=0.342  Sum_probs=89.2

Q ss_pred             cCCceeeEEEE-------EEeeC---CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCc
Q 045621           76 KLQKVAIIQLC-------LFHKD---RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDE  125 (205)
Q Consensus        76 ~~~~vaLiQLc-------L~~~~---~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~  125 (205)
                      ..+++||||||       ||++.   ..|+.|+++|+|++|+|||+                    +|++..+. .+|.+
T Consensus        28 ~~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~-ll~~~  106 (161)
T cd06129          28 YYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAAN-LKGLP  106 (161)
T ss_pred             CCCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHH-HhCCC
Confidence            46899999999       77753   36899999999999999999                    67766554 45543


Q ss_pred             chhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHH
Q 045621          126 ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK  184 (205)
Q Consensus       126 ~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~  184 (205)
                        .+.||++|+++++|..++|..+  +|||++||||++|++|||.|||++++||++|.+
T Consensus       107 --~~~~L~~l~~~~lg~~l~K~~~--~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~~  161 (161)
T cd06129         107 --ERWSLASLVEHFLGKTLDKSIS--CADWSYRPLTEDQKLYAAADVYALLIIYTKLRN  161 (161)
T ss_pred             --CCchHHHHHHHHhCCCCCccce--eccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence              3679999999999999988665  999999999999999999999999999999863

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-

>PRK10829 ribonuclease D; Provisional

Probab=99.87  E-value=2e-21  Score=176.44  Aligned_cols=145  Identities=19%  Similarity=0.211  Sum_probs=118.2

Q ss_pred             EEcCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeCCC--CHHHHHhhcCCCeeEE
Q 045621           46 TVTSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKDRM--PQSLVDFLDNDKFTFV  109 (205)
Q Consensus        46 tvT~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~~~--p~~L~~fL~d~~i~kv  109 (205)
                      .+..+++.+.+++......     ..+.+        ++.+++|||||+      ||++-.+  ...|+++|+|++|+||
T Consensus         4 ~~I~t~~~L~~~~~~l~~~-----~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d~~~L~~ll~~~~ivKV   78 (373)
T PRK10829          4 QMITTDDALASVCEAARAF-----PAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKF   78 (373)
T ss_pred             EEeCCHHHHHHHHHHHhcC-----CeEEEecccccCccCCCceeEEEEecCCceEEEecCCccchHHHHHHHcCCCeEEE
Confidence            3557888899999986542     23333        367889999998      6664332  4789999999999999


Q ss_pred             Ee--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHH
Q 045621          110 GT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAA  169 (205)
Q Consensus       110 Gv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA  169 (205)
                      +|                    ||++..|+ .+|.+  .+.||+.|++++||+.++|.++  +|||.+||||++|++|||
T Consensus        79 ~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~-~lg~~--~~~gl~~Lv~~~lgv~ldK~~~--~sDW~~RPLs~~ql~YAa  153 (373)
T PRK10829         79 LHAGSEDLEVFLNAFGELPQPLIDTQILAA-FCGRP--LSCGFASMVEEYTGVTLDKSES--RTDWLARPLSERQCEYAA  153 (373)
T ss_pred             EeChHhHHHHHHHHcCCCcCCeeeHHHHHH-HcCCC--ccccHHHHHHHHhCCccCcccc--cCCCCCCCCCHHHHHHHH
Confidence            98                    78866664 67764  4789999999999999999998  999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHhHHcCCCCCccccccc
Q 045621          170 IDAFVSFKLAIELKKEIIALPKPTTFDAFCC  200 (205)
Q Consensus       170 ~DA~~~~~I~~~L~~~~~~~p~~~~~~~~~~  200 (205)
                      .|+++++.||.+|.+......+-+|...-|+
T Consensus       154 ~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~  184 (373)
T PRK10829        154 ADVFYLLPIAAKLMAETEAAGWLPAALDECR  184 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            9999999999999988666666666655554

>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]

Probab=99.86  E-value=2.7e-21  Score=170.38  Aligned_cols=161  Identities=25%  Similarity=0.385  Sum_probs=134.3

Q ss_pred             CCCCCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHHHhhhc-cccceee--------c--------------------
Q 045621           25 SIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRR-RLHRLIT--------N--------------------   75 (205)
Q Consensus        25 ~~~~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~~~~~-~~~~lvv--------~--------------------   75 (205)
                      ...+-++..|.|.|+|+...+++|.+.+.+.+||.++....+. ..+|++|        .                    
T Consensus         8 ~~~~~t~~~~~vd~~~~~~~Vtvt~~~svi~~~i~d~~~~~~~~~s~p~vvg~~vqw~p~~~~~~~~~~~~~~~~~~~a~   87 (319)
T KOG4373|consen    8 IGSYATVQKYSVDFFGEELIVTVTPDSSVISRWIHDVRFLSRNFSSDPLVVGRGVQWTPPTLTPDQTIYAARDLQISVAR   87 (319)
T ss_pred             ccccccccceeeeecccceEEEEccCcccchhhhhhhhhcccCcccCCcccCcCcccCCCCCCccccccccchhcccccc
Confidence            4567899999999999999999999999999999998865321 1244444        0                    


Q ss_pred             ---------------------------------------------------------cCCceeeEEEE----------EE
Q 045621           76 ---------------------------------------------------------KLQKVAIIQLC----------LF   88 (205)
Q Consensus        76 ---------------------------------------------------------~~~~vaLiQLc----------L~   88 (205)
                                                                               ..++++++|||          |+
T Consensus        88 ~~~~~~~~~~~~~~kl~~~~d~~a~~~~~~~~~~~~~s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~  167 (319)
T KOG4373|consen   88 FLHLLGSSFKHKRQKLGYGSDARASPYIDNSLEIADDSDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLI  167 (319)
T ss_pred             ccccccCcccccccccccccccccccccccccccccccCCcceeecccccccccccccCCCcchhhhhhcccceeeEEee
Confidence                                                                     25678999999          56


Q ss_pred             eeCCCCHHHHHhhcCCCeeEEEe---------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcC---ccc
Q 045621           89 HKDRMPQSLVDFLDNDKFTFVGT---------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLH---VEM  144 (205)
Q Consensus        89 ~~~~~p~~L~~fL~d~~i~kvGv---------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg---~~l  144 (205)
                      |++.+|..|+.||+||+++|||+                     .||+.++...+|. .+.+.|...++.+.+|   ..+
T Consensus       168 ~~~~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~-~~~~~s~e~i~~~~~~~~~~~v  246 (319)
T KOG4373|consen  168 HCKRIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGG-SMPNDSFEEIVSETLGYYGKDV  246 (319)
T ss_pred             ccccchHHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHHhhcchhhcc-CccCccHHHHHHHHhhcccccc
Confidence            77889999999999999999999                     6777777777775 5677888888888887   448


Q ss_pred             ccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          145 EKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       145 ~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                      .|++.|+||||...+|+++|+.||++|||+|..+|..-..+.
T Consensus       247 ~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg~~~~~w~  288 (319)
T KOG4373|consen  247 RLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLGVLERLWE  288 (319)
T ss_pred             ccChhcccccceeeeccHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999996665553

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

Probab=99.83  E-value=4.9e-20  Score=165.45  Aligned_cols=121  Identities=24%  Similarity=0.234  Sum_probs=100.0

Q ss_pred             ccCCceeeEEEE------EEeeC---CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCc
Q 045621           75 NKLQKVAIIQLC------LFHKD---RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDE  125 (205)
Q Consensus        75 ~~~~~vaLiQLc------L~~~~---~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~  125 (205)
                      ++++++||||+|      |++.-   .-.+.|..+|.|++|+||.|                    ||++..+ ..+|.+
T Consensus        31 t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~~l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa-~l~g~~  109 (361)
T COG0349          31 TYYPRLCLIQISDGEGASLIDPLAGILDLPPLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAA-KLAGFG  109 (361)
T ss_pred             ccCCceEEEEEecCCCceEecccccccccchHHHHhcCCceeeeeccccccHHHHHHhcCCCCCchhHHHHHH-HHhCCc
Confidence            488999999999      77742   34689999999999999977                    4444444 356654


Q ss_pred             chhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCCccccccc
Q 045621          126 ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCC  200 (205)
Q Consensus       126 ~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~~~~~~~~  200 (205)
                        .+.||++||++++|+.|+|+++  .|||.+||||++|+.|||.|++|++.||.+|.++...-.+-++...-|+
T Consensus       110 --~~~gl~~Lv~~ll~v~ldK~~q--~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~  180 (361)
T COG0349         110 --TSHGLADLVEELLGVELDKSEQ--RSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFR  180 (361)
T ss_pred             --ccccHHHHHHHHhCCccccccc--ccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHH
Confidence              3999999999999999999999  9999999999999999999999999999999998555445555544444

>TIGR01388 rnd ribonuclease D

Probab=99.75  E-value=2e-17  Score=150.06  Aligned_cols=143  Identities=19%  Similarity=0.213  Sum_probs=113.7

Q ss_pred             cCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeC--CCCHHHHHhhcCCCeeEEEe
Q 045621           48 TSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKD--RMPQSLVDFLDNDKFTFVGT  111 (205)
Q Consensus        48 T~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~--~~p~~L~~fL~d~~i~kvGv  111 (205)
                      ..+++.+..++.++...     ..+.+        ++.+++|||||+      ||++-  .....|.++|+|++|+|||+
T Consensus         2 I~t~~~l~~~~~~l~~~-----~~ia~DtE~~~~~~y~~~l~LiQia~~~~~~liD~~~~~~~~~L~~lL~d~~i~KV~h   76 (367)
T TIGR01388         2 ITTDDELATVCEAVRTF-----PFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLH   76 (367)
T ss_pred             cCCHHHHHHHHHHHhcC-----CEEEEeccccCCCCCCCcceEEEEeeCCeEEEEeCCCcccHHHHHHHHCCCCceEEEe
Confidence            35788899999988753     22222        357889999999      66643  23578999999999999988


Q ss_pred             --------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhh
Q 045621          112 --------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAID  171 (205)
Q Consensus       112 --------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~D  171 (205)
                                          ||++..| ..+|..  .+.||+.|++++||..++|.++  +|||..|||+++|+.|||.|
T Consensus        77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa-~lL~~~--~~~~l~~Lv~~~Lg~~l~K~~~--~sdW~~rPL~~~q~~YAa~D  151 (367)
T TIGR01388        77 AASEDLEVFLNLFGELPQPLFDTQIAA-AFCGFG--MSMGYAKLVQEVLGVELDKSES--RTDWLARPLTDAQLEYAAAD  151 (367)
T ss_pred             ecHHHHHHHHHHhCCCCCCcccHHHHH-HHhCCC--CCccHHHHHHHHcCCCCCcccc--cccCCCCCCCHHHHHHHHHH
Confidence                                7876655 467653  3569999999999999999866  99999999999999999999


Q ss_pred             HHHHHHHHHHHHHhHHcCCCCCccccccc
Q 045621          172 AFVSFKLAIELKKEIIALPKPTTFDAFCC  200 (205)
Q Consensus       172 A~~~~~I~~~L~~~~~~~p~~~~~~~~~~  200 (205)
                      |++++.+|.+|.+......+-+|...-|.
T Consensus       152 v~~L~~L~~~L~~~L~~~g~~~w~~ee~~  180 (367)
T TIGR01388       152 VTYLLPLYAKLMERLEESGRLAWLEEECT  180 (367)
T ss_pred             HHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            99999999999888665556655554444

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.

>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=99.74  E-value=2.9e-17  Score=131.00  Aligned_cols=128  Identities=29%  Similarity=0.481  Sum_probs=98.1

Q ss_pred             cCCHHHHHHHHHHHHHhhhccccceee----------ccCCceeeEEEE------EEeeC---C--CCHHHHHhhcCCCe
Q 045621           48 TSRASDVDRWIARTINVHRRRLHRLIT----------NKLQKVAIIQLC------LFHKD---R--MPQSLVDFLDNDKF  106 (205)
Q Consensus        48 T~~~~~v~~wi~~~~~~~~~~~~~lvv----------~~~~~vaLiQLc------L~~~~---~--~p~~L~~fL~d~~i  106 (205)
                      ..+.+.+++|++.+...     ..+.+          ....++++||+|      +++..   .  ++..|+++|+||+|
T Consensus         4 v~~~~~l~~~~~~l~~~-----~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~~~~~~l~~ll~~~~i   78 (176)
T PF01612_consen    4 VDTEEELEEAIKKLKNA-----KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDNWILDALKELLEDPNI   78 (176)
T ss_dssp             EHSHHHHHHHHHHHTTT-----SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTTTHHHHHHHHHTTTTS
T ss_pred             cCCHHHHHHHHHHHcCC-----CeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeeccccccchHHHHHHHHhCCCc
Confidence            45788899999988764     23332          246789999999      33321   1  35799999999999


Q ss_pred             eEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcC-cccccCCcccccCCC-CCCCCHHH
Q 045621          107 TFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLH-VEMEKSKRITLSKWD-VNNLSKQQ  164 (205)
Q Consensus       107 ~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg-~~l~K~~~v~~SnW~-~rpLs~~Q  164 (205)
                      +|||+                    +|+ .++...++..  .+.||+.|+.+++| ..++|...  +++|. ++||+++|
T Consensus        79 ~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~--~~~~L~~L~~~~l~~~~~~~~~~--~~~~~~~~~l~~~~  153 (176)
T PF01612_consen   79 IKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPT--RSYSLKDLAEEYLGNIDLDKKEQ--MSDWRKARPLSEEQ  153 (176)
T ss_dssp             EEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTS--TTSSHHHHHHHHHSEEE-GHCCT--TSSTTTSSS-HHHH
T ss_pred             cEEEEEEechHHHHHHHhccccCCccch-hhhhhccccc--ccccHHHHHHHHhhhccCcHHHh--hccCCcCCCChHHH
Confidence            99999                    555 4444444433  23899999999999 55555554  99999 89999999


Q ss_pred             HHHHHhhHHHHHHHHHHHHHh
Q 045621          165 IRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       165 i~YAA~DA~~~~~I~~~L~~~  185 (205)
                      ++|||.||+++++||++|..+
T Consensus       154 ~~YAa~D~~~~~~l~~~l~~~  174 (176)
T PF01612_consen  154 IEYAAQDAVVTFRLYEKLKPQ  174 (176)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999875

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 ....

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

Probab=99.73  E-value=1.8e-17  Score=138.00  Aligned_cols=111  Identities=23%  Similarity=0.366  Sum_probs=87.2

Q ss_pred             ccCCceeeEEEE-------EEeeCC-----CCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhc
Q 045621           75 NKLQKVAIIQLC-------LFHKDR-----MPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKY  122 (205)
Q Consensus        75 ~~~~~vaLiQLc-------L~~~~~-----~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~l  122 (205)
                      +..+++||||+|       ||++-.     ++..|+++|+|++|.|||+                    +|++..+. .+
T Consensus        23 ~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~-lL  101 (197)
T cd06148          23 GRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADA-LL  101 (197)
T ss_pred             CCCCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHH-HH
Confidence            356789999999       676532     3578999999999999998                    66654432 33


Q ss_pred             CCc------chhcccHHHHHHHHcCcccccCC------cccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          123 DDE------ELKTFGLKRLVLKFLHVEMEKSK------RITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       123 g~~------~~~~~gL~~Lv~~~lg~~l~K~~------~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                      +..      .....||++++++++|..++|..      +-++|||.+||||++|+.|||.||++++.+|+.|....
T Consensus       102 ~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l  177 (197)
T cd06148         102 QEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDAL  177 (197)
T ss_pred             HHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence            211      01246999999999999987521      23489999999999999999999999999999998873

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.

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

Probab=99.34  E-value=1.1e-11  Score=99.57  Aligned_cols=122  Identities=24%  Similarity=0.306  Sum_probs=93.6

Q ss_pred             CCceeeEEEE------EEeeC--CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchh
Q 045621           77 LQKVAIIQLC------LFHKD--RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELK  128 (205)
Q Consensus        77 ~~~vaLiQLc------L~~~~--~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~  128 (205)
                      ..+++.+|+|      +|++.  ..++.|+.+|+|+++.|||+                    +|+...+ ..++..  .
T Consensus        28 ~~~~~~i~l~~~~~~~~i~~~~~~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laa-yLl~p~--~  104 (178)
T cd06142          28 YPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAA-RLLGLG--D  104 (178)
T ss_pred             CCceEEEEEeeCCCEEEEeCCCcccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHH-HHhCCC--c
Confidence            4678899998      33222  24566999999999999998                    4554333 344432  2


Q ss_pred             cccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCCcccccccccc
Q 045621          129 TFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPTTFDAFCCFQI  203 (205)
Q Consensus       129 ~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~~~~~~~~~~~  203 (205)
                      +.||+.+++.++|..+.|.+  .+++|++++|+.+|+.|||.||++++.++..|.+.......-+.+..-|+++|
T Consensus       105 ~~~l~~l~~~~l~~~~~~~~--~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~~~~~~~~~  177 (178)
T cd06142         105 SVGLAALVEELLGVELDKGE--QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECELLL  177 (178)
T ss_pred             cccHHHHHHHHhCCCCCccc--ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHhh
Confidence            45999999999999877755  48999999999999999999999999999999988655555666666676664

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.

>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]

Probab=99.34  E-value=1.4e-12  Score=122.96  Aligned_cols=133  Identities=20%  Similarity=0.276  Sum_probs=98.7

Q ss_pred             EEcCCHHHHHHHHHHHHHhhhccccceee-----------ccCCceeeEEEE------EEee---CCCC-----HHHHHh
Q 045621           46 TVTSRASDVDRWIARTINVHRRRLHRLIT-----------NKLQKVAIIQLC------LFHK---DRMP-----QSLVDF  100 (205)
Q Consensus        46 tvT~~~~~v~~wi~~~~~~~~~~~~~lvv-----------~~~~~vaLiQLc------L~~~---~~~p-----~~L~~f  100 (205)
                      .+..++..++..+-+-++.     ++.+|           ..+++++++|+.      |+++   ...+     ..+..+
T Consensus       393 ~~V~~e~El~~l~l~~l~~-----e~~yVGiDsEwkps~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~i  467 (617)
T KOG2207|consen  393 GMVGNEKELRDLLLESLSE-----ELRYVGIDSEWKPSKKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQI  467 (617)
T ss_pred             eeeCCHHHHHHHHHHHhhh-----cCEEEEEccccCcccCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHH
Confidence            3446788787777322221     22233           247899999999      5664   2333     468899


Q ss_pred             hcCCCeeEEEe---eeHHHHH-------------------------HHhcCCc------chhcccHHHHHHHHcCccccc
Q 045621          101 LDNDKFTFVGT---MDVADMA-------------------------AAKYDDE------ELKTFGLKRLVLKFLHVEMEK  146 (205)
Q Consensus       101 L~d~~i~kvGv---~Dl~~la-------------------------~~~lg~~------~~~~~gL~~Lv~~~lg~~l~K  146 (205)
                      |+++.|.||||   -|+..+.                         .++.+..      .-...||+.|+..++|+.++|
T Consensus       468 f~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnK  547 (617)
T KOG2207|consen  468 FESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNK  547 (617)
T ss_pred             ccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhccc
Confidence            99999999999   4443333                         2222110      014788999999999999999


Q ss_pred             CCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          147 SKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       147 ~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                      .++  +|||..|||+..||.|||+||.+++.||.++.+.
T Consensus       548 teq--csnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~v  584 (617)
T KOG2207|consen  548 TEQ--CSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSV  584 (617)
T ss_pred             ccc--cchhhcCCchhhHHHHHHhcchhhHHHHHHHHhh
Confidence            999  9999999999999999999999999999999876

>smart00474 35EXOc 3'-5' exonuclease

Probab=99.17  E-value=1.4e-09  Score=85.76  Aligned_cols=129  Identities=25%  Similarity=0.317  Sum_probs=90.0

Q ss_pred             CCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE----EEe---e---CCCCHHHHHhhcCCCeeEEE
Q 045621           49 SRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC----LFH---K---DRMPQSLVDFLDNDKFTFVG  110 (205)
Q Consensus        49 ~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc----L~~---~---~~~p~~L~~fL~d~~i~kvG  110 (205)
                      .+++.+.+|+.++...   . ..+.+        ....+++.+|+|    .+.   .   ...++.|+++|+++++.|||
T Consensus         5 ~~~~~~~~~~~~~~~~---~-~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~kv~   80 (172)
T smart00474        5 TDSETLEELLEKLRAA---G-GEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVG   80 (172)
T ss_pred             cCHHHHHHHHHHHHhc---C-CeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhHHHHHHHhcCCCceEEE
Confidence            3447788988655211   0 12222        125678999999    111   1   12345699999999999999


Q ss_pred             e-------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhh
Q 045621          111 T-------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAID  171 (205)
Q Consensus       111 v-------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~D  171 (205)
                      +                   +|+...+. .+. +.....||+.+++.++|..++|  ....++|..++|.++|+.|||.|
T Consensus        81 ~d~k~~~~~L~~~gi~~~~~~D~~laay-ll~-p~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~l~~~~~~ya~~~  156 (172)
T smart00474       81 HNAKFDLHVLARFGIELENIFDTMLAAY-LLL-GGPSKHGLATLLKEYLGVELDK--EEQKSDWGARPLSEEQLQYAAED  156 (172)
T ss_pred             echHHHHHHHHHCCCcccchhHHHHHHH-HHc-CCCCcCCHHHHHHHHhCCCCCc--ccCccccccCCCCHHHHHHHHHH
Confidence            9                   45544443 222 2113359999999999988755  33467998899999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 045621          172 AFVSFKLAIELKKE  185 (205)
Q Consensus       172 A~~~~~I~~~L~~~  185 (205)
                      |++++.+++.|.+.
T Consensus       157 a~~~~~L~~~l~~~  170 (172)
T smart00474      157 ADALLRLYEKLEKE  170 (172)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999998765

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

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

Probab=99.05  E-value=1.6e-09  Score=84.36  Aligned_cols=105  Identities=26%  Similarity=0.307  Sum_probs=78.1

Q ss_pred             CCceeeEEEE-------EEeeCC---CCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcc
Q 045621           77 LQKVAIIQLC-------LFHKDR---MPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEE  126 (205)
Q Consensus        77 ~~~vaLiQLc-------L~~~~~---~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~  126 (205)
                      ..+++.+|+|       ++++..   .+..|+++|+|+++.|+|+                    +|+...+. .++.. 
T Consensus        15 ~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laay-Ll~p~-   92 (150)
T cd09018          15 SANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAY-ILNSV-   92 (150)
T ss_pred             CceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHH-HhCCC-
Confidence            4567888888       333221   3567999999999999988                    67655553 45432 


Q ss_pred             hhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHH
Q 045621          127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELK  183 (205)
Q Consensus       127 ~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~  183 (205)
                      -.+.+|+.|+++++|..+.|.+++..++|..++|+.+|+.||+.||++++.++..|.
T Consensus        93 ~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~  149 (150)
T cd09018          93 AGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLW  149 (150)
T ss_pred             CCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            113599999999999886552334445696688999999999999999999998874

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=98.95  E-value=8.9e-09  Score=79.64  Aligned_cols=105  Identities=25%  Similarity=0.305  Sum_probs=76.4

Q ss_pred             CCceeeEEEE----EEee--C----CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcc
Q 045621           77 LQKVAIIQLC----LFHK--D----RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEE  126 (205)
Q Consensus        77 ~~~vaLiQLc----L~~~--~----~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~  126 (205)
                      ..+++++|+|    .+.+  .    .+++.|+++|+++++.|||+                    +|+..++. .++...
T Consensus        16 ~~~i~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ay-ll~~~~   94 (155)
T cd00007          16 RGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAY-LLNPGE   94 (155)
T ss_pred             CCeEEEEEEEECCcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHH-HhCCCC
Confidence            4578889988    2221  1    23445999999999999999                    56654443 444321


Q ss_pred             hhcccHHHHHHHHcCcccccCCcccccCCC----CCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWD----VNNLSKQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       127 ~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~----~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                       .+.||+.|+++++|..+.+..+  .++|.    .++|+.+|+.||+.||+++++++..|.+.
T Consensus        95 -~~~~l~~l~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~  154 (155)
T cd00007          95 -GSHSLDDLAKEYLGIELDKDEQ--IYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE  154 (155)
T ss_pred             -CcCCHHHHHHHHcCCCCccHHH--HhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence             1469999999999988655333  44542    57899999999999999999999998764

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).

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

Probab=98.76  E-value=3.2e-07  Score=75.52  Aligned_cols=103  Identities=19%  Similarity=0.295  Sum_probs=77.1

Q ss_pred             CCceeeEEEE----EEee-----CCCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcch
Q 045621           77 LQKVAIIQLC----LFHK-----DRMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEEL  127 (205)
Q Consensus        77 ~~~vaLiQLc----L~~~-----~~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~  127 (205)
                      ..++..+|+|    .+.+     ......|+++|+++++.|+|+                    +|+...| ..++ ++ 
T Consensus        40 ~~~~~~l~l~~~~~~~~i~~l~~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laa-YLL~-p~-  116 (192)
T cd06147          40 LGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAA-RVLN-LP-  116 (192)
T ss_pred             CCceEEEEEecCCCcEEEEecccccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHHHHHH-HHhC-CC-
Confidence            3567888988    2222     223445999999999999988                    3444433 2444 33 


Q ss_pred             hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                      . .+|+.|++++||..++|.  -+++||+.+||+.+|..||+.||++++.++..|...
T Consensus       117 ~-~~l~~l~~~yl~~~~~k~--~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~  171 (192)
T cd06147         117 R-HSLAYLLQKYCNVDADKK--YQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNE  171 (192)
T ss_pred             c-ccHHHHHHHHhCCCcchh--hhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            3 499999999999775452  347889888999999999999999999999988665

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.

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

Probab=98.70  E-value=5.4e-08  Score=92.83  Aligned_cols=129  Identities=16%  Similarity=0.095  Sum_probs=95.1

Q ss_pred             cCCHHHHHHHHHHHHHhhhccccceee------ccCCceeeEEEE------EEeeCCCCHHHHHhhcCCCeeEEEeeeHH
Q 045621           48 TSRASDVDRWIARTINVHRRRLHRLIT------NKLQKVAIIQLC------LFHKDRMPQSLVDFLDNDKFTFVGTMDVA  115 (205)
Q Consensus        48 T~~~~~v~~wi~~~~~~~~~~~~~lvv------~~~~~vaLiQLc------L~~~~~~p~~L~~fL~d~~i~kvGv~Dl~  115 (205)
                      ..+++.+..++.++...      +.+.      +....++++|++      |++.-.   .+..+|...++..-++||++
T Consensus         6 I~~~~~l~~~~~~l~~~------~~~a~DtEf~r~~t~l~liQ~~~~~~~~liDpl~---~l~~~L~~~Gv~~~~~fDT~   76 (553)
T PRK14975          6 ILAPEELGAALERLSPA------GVVAGDTETTGDDAAAAAAQEGEEEPRWVWASTA---ALYPRLLAAGVRVERCHDLM   76 (553)
T ss_pred             EeccchhHHHHHHhccC------CceeCCccccCCcchhheeeecCCCceEEECchH---HhHHHHHHCCCccCCCchHH
Confidence            34566677888877653      2222      223379999998      554211   25555655566655679997


Q ss_pred             HHHHHhcCCcc-hhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621          116 DMAAAKYDDEE-LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIAL  189 (205)
Q Consensus       116 ~la~~~lg~~~-~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~  189 (205)
                      ..+. .++... ..+.||+.+++.++|..++|..+  .|||. +||+++|..|||.|+.++..+|..|.+.....
T Consensus        77 LAa~-lL~~~~~~~~~~l~~la~~~l~~~l~k~~~--~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~  147 (553)
T PRK14975         77 LASQ-LLLGSEGRAGSSLSAAAARALGEGLDKPPQ--TSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRI  147 (553)
T ss_pred             HHHH-HcCCCCCcCCCCHHHHHHHHhCCCCCChhh--hcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence            7764 677531 11679999999999999999887  89997 89999999999999999999999998885544

>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]

Probab=98.65  E-value=7.1e-08  Score=91.38  Aligned_cols=103  Identities=19%  Similarity=0.240  Sum_probs=85.8

Q ss_pred             cCCceeeEEEE------EEee----CCCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCc
Q 045621           76 KLQKVAIIQLC------LFHK----DRMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDE  125 (205)
Q Consensus        76 ~~~~vaLiQLc------L~~~----~~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~  125 (205)
                      +.+=.||+|++      +++-    +.+ ..|++.++||+|.||.+                    ||+...+ .++|. 
T Consensus       227 f~gltclmqISTr~ed~iIDt~~l~~~i-~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~-r~L~~-  303 (687)
T KOG2206|consen  227 FLGLTCLMQISTRTEDFIIDTFKLRDHI-GILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQAS-RLLGL-  303 (687)
T ss_pred             hcCceeEEEeeccchhheehhHHHHHHH-HHhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHH-HHhCC-
Confidence            56678999999      3331    123 38999999999999955                    5544433 46765 


Q ss_pred             chhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          126 ELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       126 ~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                        .+.||+-|.+.+.|+..+|..|  ..||..|||+++.+.||-.|.+|++-||+.|+..
T Consensus       304 --~r~sL~~ll~~~~~v~~nk~yq--ladwR~rpLp~~Mv~yar~dthyllyiyD~lr~e  359 (687)
T KOG2206|consen  304 --PRPSLAYLLECVCGVLTNKKYQ--LADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKE  359 (687)
T ss_pred             --CcccHHHHHHHHHhhhhhhhhh--hchhccccCcHHHHHHHhhcchhHHHHHHHHHHH
Confidence              4899999999999999999888  9999999999999999999999999999999866

>PRK05755 DNA polymerase I; Provisional

Probab=98.31  E-value=1.1e-05  Score=81.03  Aligned_cols=131  Identities=20%  Similarity=0.314  Sum_probs=89.1

Q ss_pred             EcCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE-------EEeeCCCC----HHHHHhhcCCCee
Q 045621           47 VTSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC-------LFHKDRMP----QSLVDFLDNDKFT  107 (205)
Q Consensus        47 vT~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc-------L~~~~~~p----~~L~~fL~d~~i~  107 (205)
                      +..+++.+.+|+..+...     ..+.+        ....+++.+|+|       ++.+..++    +.|+++|+|+.+.
T Consensus       298 ~I~~~~~L~~~l~~l~~~-----~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~l~~~L~d~~v~  372 (880)
T PRK05755        298 TILDEEELEAWLAKLKAA-----GLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPAIK  372 (880)
T ss_pred             EeCCHHHHHHHHHHhhcc-----CeEEEEeccCCCCcccccEEEEEEEeCCCcEEEEecccccHHHHHHHHHHHhCCCCc
Confidence            345788899999877532     12222        246778999998       33333333    5799999999999


Q ss_pred             EEEe---eeHHHHH----------------HHhcCCcchhcccHHHHHHHHcCccccc-----CCcccccCCCCCCCCHH
Q 045621          108 FVGT---MDVADMA----------------AAKYDDEELKTFGLKRLVLKFLHVEMEK-----SKRITLSKWDVNNLSKQ  163 (205)
Q Consensus       108 kvGv---~Dl~~la----------------~~~lg~~~~~~~gL~~Lv~~~lg~~l~K-----~~~v~~SnW~~rpLs~~  163 (205)
                      |||+   +|+..+.                ...++ ++. ..||+.|+++++|..+..     ++..++++|   |+ +.
T Consensus       373 kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~-~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~---pl-e~  446 (880)
T PRK05755        373 KVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLD-PGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQV---DL-EE  446 (880)
T ss_pred             EEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcC-CCC-CCCHHHHHHHHhCCCccchHHhcCCCCCcccc---CH-HH
Confidence            9999   4444332                22333 222 389999999999977421     122234444   66 58


Q ss_pred             HHHHHHhhHHHHHHHHHHHHHhHHc
Q 045621          164 QIRYAAIDAFVSFKLAIELKKEIIA  188 (205)
Q Consensus       164 Qi~YAA~DA~~~~~I~~~L~~~~~~  188 (205)
                      |.+||+.||.+++.||.+|.+.-..
T Consensus       447 ~~~YAa~Dv~~~~~L~~~L~~~L~~  471 (880)
T PRK05755        447 AAEYAAEDADVTLRLHEVLKPKLLE  471 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999987433

>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=97.81  E-value=0.0001  Score=59.28  Aligned_cols=86  Identities=21%  Similarity=0.235  Sum_probs=62.6

Q ss_pred             HHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCC
Q 045621           97 LVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWD  156 (205)
Q Consensus        97 L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~  156 (205)
                      |+++|+|+++.|+|+                    +|+...+ ..++.. -.+.++++++.+++|..+.+..+  .+.|+
T Consensus        48 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laa-YLL~p~-~~~~~l~~l~~~yl~~~~~~~~~--~~~~~  123 (178)
T cd06140          48 LKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAA-YLLDPT-RSSYDLADLAKRYLGRELPSDEE--VYGKG  123 (178)
T ss_pred             HHHHHhCCCCceeccchhHHHHHHHHCCCcCCCcchhHHHHH-HHcCCC-CCCCCHHHHHHHHcCCCCcchHH--hcCCC
Confidence            888899998888877                    5554444 345432 12369999999999988765333  44442


Q ss_pred             ---CCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          157 ---VNNLSKQQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       157 ---~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                         .++..++|..|||.||.+++.++..|.+.-
T Consensus       124 ~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L  156 (178)
T cd06140         124 AKFAVPDEEVLAEHLARKAAAIARLAPKLEEEL  156 (178)
T ss_pred             CCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               245577789999999999999999998763

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=97.68  E-value=0.00039  Score=56.14  Aligned_cols=85  Identities=25%  Similarity=0.319  Sum_probs=58.4

Q ss_pred             HHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCccc-------ccCCc
Q 045621           97 LVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEM-------EKSKR  149 (205)
Q Consensus        97 L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l-------~K~~~  149 (205)
                      |+++|++.++++||+                    +|+..+|. .+. +...+.||+.+++.++|..+       .|.+ 
T Consensus        59 l~~~l~~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~-ll~-p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~-  135 (193)
T cd06139          59 LKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASY-LLN-PGRRRHGLDDLAERYLGHKTISFEDLVGKGK-  135 (193)
T ss_pred             HHHHHhCCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHH-HhC-CCCCCCCHHHHHHHHhCCCCccHHHHcCCCc-
Confidence            666676666666666                    55555553 232 22225699999999998652       1222 


Q ss_pred             ccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          150 ITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       150 v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                       ...+|...++ .++.+||+.||.+++.++..|.+..
T Consensus       136 -~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l  170 (193)
T cd06139         136 -KQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKL  170 (193)
T ss_pred             -CcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             2556765555 7799999999999999999998773

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.

>TIGR00593 pola DNA polymerase I

Probab=95.34  E-value=0.075  Score=53.91  Aligned_cols=90  Identities=21%  Similarity=0.194  Sum_probs=58.6

Q ss_pred             HHHHHhhcCCCeeEEEe---eeHHHHH----------------HHhcCCcchhcccHHHHHHHHcCcccccCCcccccCC
Q 045621           95 QSLVDFLDNDKFTFVGT---MDVADMA----------------AAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKW  155 (205)
Q Consensus        95 ~~L~~fL~d~~i~kvGv---~Dl~~la----------------~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW  155 (205)
                      ..|+.+|+|+.+.|+|+   +|+..+.                ...+...  .+.+|+.++.++++..+.+...+....+
T Consensus       368 ~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~~--~~~~l~~la~~yl~~~~~~~~~~~~~~~  445 (887)
T TIGR00593       368 DKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDPA--QVSTLDTLARRYLVEELILDEKIGGKLA  445 (887)
T ss_pred             HHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCCC--CCCCHHHHHHHHcCcccccHHHhccCCC
Confidence            34899999999999999   4443332                2233321  2359999999999976544222111111


Q ss_pred             CCCCCCH-HHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          156 DVNNLSK-QQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       156 ~~rpLs~-~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                      .-..+.. ....||+.||.+.+.++..|....
T Consensus       446 ~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l  477 (887)
T TIGR00593       446 KFAFPPLEEATEYLARRAAATKRLAEELLKEL  477 (887)
T ss_pred             CcccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            1113433 357899999999999999998763

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

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

Probab=89.13  E-value=1.3  Score=43.20  Aligned_cols=98  Identities=20%  Similarity=0.249  Sum_probs=63.3

Q ss_pred             CHHHHHhhcCCCeeEEEe---eeHHHHHHHh--------------cCCcchhcccHHHHHHHHcCcccccCCcccccCCC
Q 045621           94 PQSLVDFLDNDKFTFVGT---MDVADMAAAK--------------YDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWD  156 (205)
Q Consensus        94 p~~L~~fL~d~~i~kvGv---~Dl~~la~~~--------------lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~  156 (205)
                      -..|+.+|+|+++.|+|.   +|...+++.-              +-.++-...+++.|++.++|......+.+.-..=.
T Consensus        67 ~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~  146 (593)
T COG0749          67 LAALKPLLEDEGIKKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKK  146 (593)
T ss_pred             HHHHHHHhhCcccchhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccc
Confidence            468999999999999999   6665555421              00112235789999999988665433331111111


Q ss_pred             C---CCCC-HHHHHHHHhhHHHHHHHHHHHHHhHHcCCC
Q 045621          157 V---NNLS-KQQIRYAAIDAFVSFKLAIELKKEIIALPK  191 (205)
Q Consensus       157 ~---rpLs-~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~  191 (205)
                      .   .... +.-..|||.||.+.+.++..|.......|.
T Consensus       147 ~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~  185 (593)
T COG0749         147 QLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPV  185 (593)
T ss_pred             cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            1   0111 234899999999999999999876554443

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

Probab=87.24  E-value=2  Score=34.27  Aligned_cols=67  Identities=21%  Similarity=0.318  Sum_probs=41.3

Q ss_pred             HHHHHhhcCCCeeEEEe---e-------------eHHHHHHHhcCCcch---hcccHHHHHHHHcCcccccCCcccccCC
Q 045621           95 QSLVDFLDNDKFTFVGT---M-------------DVADMAAAKYDDEEL---KTFGLKRLVLKFLHVEMEKSKRITLSKW  155 (205)
Q Consensus        95 ~~L~~fL~d~~i~kvGv---~-------------Dl~~la~~~lg~~~~---~~~gL~~Lv~~~lg~~l~K~~~v~~SnW  155 (205)
                      +.|.+|+.+.. +.||+   +             |...+++....  ..   .+.+|+.|++.++|.++.....      
T Consensus        75 ~~~~~~i~~~~-vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~--~~~~~~~~~L~~L~~~~~~~~~~~~~~------  145 (161)
T cd06137          75 AALWKFIDPDT-ILVGHSLQNDLDALRMIHTRVVDTAILTREAVK--GPLAKRQWSLRTLCRDFLGLKIQGGGE------  145 (161)
T ss_pred             HHHHHhcCCCc-EEEeccHHHHHHHHhCcCCCeeEehhhhhhccC--CCcCCCCccHHHHHHHHCCchhcCCCC------
Confidence            45666776533 45777   4             44455543222  12   4789999999999987754111      


Q ss_pred             CCCCCCHHHHHHHHhhHHHHHHHH
Q 045621          156 DVNNLSKQQIRYAAIDAFVSFKLA  179 (205)
Q Consensus       156 ~~rpLs~~Qi~YAA~DA~~~~~I~  179 (205)
                               -+=|..||.++.++|
T Consensus       146 ---------~H~A~~DA~at~~l~  160 (161)
T cd06137         146 ---------GHDSLEDALAAREVV  160 (161)
T ss_pred             ---------CCCcHHHHHHHHHHh
Confidence                     122678888888776

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

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

Probab=86.95  E-value=5.8  Score=30.67  Aligned_cols=67  Identities=21%  Similarity=0.230  Sum_probs=37.1

Q ss_pred             eeHHHHHHHhcCCcchhcccHHHHHHHHcCccccc-CCcccccCCCC--CCC-CHHHHHHHHhhHHHHHHHHHHHH
Q 045621          112 MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEK-SKRITLSKWDV--NNL-SKQQIRYAAIDAFVSFKLAIELK  183 (205)
Q Consensus       112 ~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K-~~~v~~SnW~~--rpL-s~~Qi~YAA~DA~~~~~I~~~L~  183 (205)
                      +|+...+ ..++.. -...+++++++++|+..+-. .. +  ..+++  ..+ -.+.-.|++..|.+.+.++..|.
T Consensus        80 fD~~LAa-YLL~p~-~~~~~l~~la~~yl~~~~~~~~~-~--~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~  150 (151)
T cd06128          80 FDTMLEA-YLLDPV-AGRHDMDSLAERWLKEKTITFEE-I--AGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW  150 (151)
T ss_pred             hhHHHHH-HHcCCC-CCCCCHHHHHHHHcCCCCccHHH-H--cCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            6775444 455532 12139999999998876211 10 1  01110  011 11123488888888888888774

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

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

Probab=86.48  E-value=2.4  Score=33.53  Aligned_cols=67  Identities=18%  Similarity=0.214  Sum_probs=39.7

Q ss_pred             HHHHHhhcCCCeeEEEe---eeHH-------------HHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCC
Q 045621           95 QSLVDFLDNDKFTFVGT---MDVA-------------DMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVN  158 (205)
Q Consensus        95 ~~L~~fL~d~~i~kvGv---~Dl~-------------~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~r  158 (205)
                      +.+.+|+.+ +-+.||+   +|++             .+++...+.  ..+.+|+.|+++++|..+....          
T Consensus        67 ~~~~~fl~~-~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~--~~~~~L~~L~~~~~~~~i~~~~----------  133 (150)
T cd06145          67 KKLLSLISP-DTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGP--PYKPSLKNLAKKYLGRDIQQGE----------  133 (150)
T ss_pred             HHHHHHhCC-CCEEEEcChHHHHHHhhccCCCEEEcHHhccccCCC--CCChhHHHHHHHHCCcceeCCC----------
Confidence            466677752 2345787   5544             444322221  2357999999999886654210          


Q ss_pred             CCCHHHHHHHHhhHHHHHHHH
Q 045621          159 NLSKQQIRYAAIDAFVSFKLA  179 (205)
Q Consensus       159 pLs~~Qi~YAA~DA~~~~~I~  179 (205)
                           +.+=|.-||.++.+||
T Consensus       134 -----~~H~Al~DA~~t~~l~  149 (150)
T cd06145         134 -----GGHDSVEDARAALELV  149 (150)
T ss_pred             -----CCCCcHHHHHHHHHHh
Confidence                 0122678999988876

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

>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2

Probab=82.43  E-value=2.6  Score=34.88  Aligned_cols=63  Identities=19%  Similarity=0.217  Sum_probs=41.4

Q ss_pred             HHHHhhcCCCeeEEEe------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCC
Q 045621           96 SLVDFLDNDKFTFVGT------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDV  157 (205)
Q Consensus        96 ~L~~fL~d~~i~kvGv------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~  157 (205)
                      .|.+++ +++.+.||+                  +|...+..    .+...+.||+.|++++||..|.....        
T Consensus        94 ~l~~li-~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~----~~~~r~~sLk~La~~~L~~~IQ~~~H--------  160 (174)
T cd06143          94 KLRLLV-DLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFH----LPGQRKLSLRFLAWYLLGEKIQSETH--------  160 (174)
T ss_pred             HHHHHc-CCCCEEEeccchhHHHHhcCcCCCcceEEcHHhcc----CCCCCChhHHHHHHHHcCCcccCCCc--------
Confidence            455555 455677999                  44433322    12224789999999999999865321        


Q ss_pred             CCCCHHHHHHHHhhHHHHHHHHH
Q 045621          158 NNLSKQQIRYAAIDAFVSFKLAI  180 (205)
Q Consensus       158 rpLs~~Qi~YAA~DA~~~~~I~~  180 (205)
                               =..-||.+++++|+
T Consensus       161 ---------dSvEDArAam~Ly~  174 (174)
T cd06143         161 ---------DSIEDARTALKLYR  174 (174)
T ss_pred             ---------CcHHHHHHHHHHhC
Confidence                     12679999998873

PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.

>PRK08517 DNA polymerase III subunit epsilon; Provisional

Probab=80.98  E-value=13  Score=32.38  Aligned_cols=72  Identities=19%  Similarity=0.211  Sum_probs=43.9

Q ss_pred             HHHHHhhcCCCeeEEEe---eeHHHHHHHh--cCCcc-----------------hhcccHHHHHHHHcCcccccCCcccc
Q 045621           95 QSLVDFLDNDKFTFVGT---MDVADMAAAK--YDDEE-----------------LKTFGLKRLVLKFLHVEMEKSKRITL  152 (205)
Q Consensus        95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~--lg~~~-----------------~~~~gL~~Lv~~~lg~~l~K~~~v~~  152 (205)
                      ..+.+|+.+.  ++||+   ||...+.+..  .|.+.                 ..+.||+.|++. +|.+.++.     
T Consensus       139 ~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~~-lgi~~~~~-----  210 (257)
T PRK08517        139 EEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKEL-LGIEIEVH-----  210 (257)
T ss_pred             HHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHHH-cCcCCCCC-----
Confidence            4666777653  47888   7766554321  11110                 124556666553 45544433     


Q ss_pred             cCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHH
Q 045621          153 SKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEII  187 (205)
Q Consensus       153 SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~  187 (205)
                                   +=|..||.++.+|+..+..+.+
T Consensus       211 -------------HrAl~DA~ata~ll~~ll~~~~  232 (257)
T PRK08517        211 -------------HRAYADALAAYEIFKICLLNLP  232 (257)
T ss_pred             -------------CChHHHHHHHHHHHHHHHHHhH
Confidence                         3478999999999999987754

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

Probab=80.23  E-value=2.3  Score=33.53  Aligned_cols=66  Identities=18%  Similarity=0.312  Sum_probs=42.9

Q ss_pred             HHHHHhhcCCCeeEEEe---eeHHHHHHHh-------------cCCcc-hhcccHHHHHHHHcCcccc-cCCcccccCCC
Q 045621           95 QSLVDFLDNDKFTFVGT---MDVADMAAAK-------------YDDEE-LKTFGLKRLVLKFLHVEME-KSKRITLSKWD  156 (205)
Q Consensus        95 ~~L~~fL~d~~i~kvGv---~Dl~~la~~~-------------lg~~~-~~~~gL~~Lv~~~lg~~l~-K~~~v~~SnW~  156 (205)
                      +.|.+|+.+ .+ .||+   +|++.+....             ..... ..+.||+.+++.++|..+. ..++       
T Consensus        69 ~~l~~~l~~-~v-lVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~-------  139 (152)
T cd06144          69 KKVAELLKG-RI-LVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHS-------  139 (152)
T ss_pred             HHHHHHhCC-CE-EEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcC-------
Confidence            567788876 44 4888   7776553210             00000 2468999999999998764 3343       


Q ss_pred             CCCCCHHHHHHHHhhHHHHHHHHH
Q 045621          157 VNNLSKQQIRYAAIDAFVSFKLAI  180 (205)
Q Consensus       157 ~rpLs~~Qi~YAA~DA~~~~~I~~  180 (205)
                                 |..||.++.+||+
T Consensus       140 -----------Al~DA~at~~l~~  152 (152)
T cd06144         140 -----------SVEDARAAMRLYR  152 (152)
T ss_pred             -----------cHHHHHHHHHHhC
Confidence                       6789999998873

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	205
2fbt_A	205	Wrn Exonuclease Length = 205		2e-04

>pdb|2FBT|A Chain A, Wrn Exonuclease Length = 205

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 55/132 (41%), Gaps = 32/132 (24%)
Query: 75  NKLQKVAIIQLC-------LFHKDRM---PQSLVDFLDN------------DKFTFVGTM 112
            KL KVA+IQLC       LFH   M   PQ L   L+N            D++  +   
Sbjct: 61  GKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGIEGDQWKLLRDF 120
Query: 113 DV--------ADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQ 164
           D+         D+A  K    E  T+ L  LV   L  ++ K K I  S W    L++ Q
Sbjct: 121 DIKLKNFVELTDVANKKLKCTE--TWSLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQ 178
Query: 165 IRYAAIDAFVSF 176
             YAA DA+  F
Sbjct: 179 KLYAATDAYAGF 190

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	205
1vk0_A	206	Hypothetical protein; homohexamer, AT5G06450, stru	8e-22
2e6m_A	208	Werner syndrome ATP-dependent helicase homolog; AP	7e-20
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-08
1yt3_A	375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	1e-04
3cym_A	440	Uncharacterized protein BAD_0989; structural genom	2e-04
3saf_A	428	Exosome component 10; exoribonuclease, RNA exosome	6e-04
2hbj_A	410	Exosome complex exonuclease RRP6; RNA metabolism,	6e-04

>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 = 87.7 bits (217), Expect = 8e-22
 Identities = 23/149 (15%), Positives = 48/149 (32%), Gaps = 32/149 (21%)

Query: 67  RRLHRLITNKLQKVAIIQLC------LFH----KDRMPQSLVDFLDNDKFTFVG------ 110
                        ++ ++L                   + L  F  +   TFVG      
Sbjct: 60  PETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEED 119

Query: 111 --------------TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWD 156
                          ++V  +AA       L+  G + L  + L  ++ +   I  +KW+
Sbjct: 120 LDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIE-AKWE 178

Query: 157 VNNLSKQQIRYAAIDAFVSFKLAIELKKE 185
                ++Q+  AAI+ ++   +  +L  E
Sbjct: 179 -KAGPEEQLEAAAIEGWLIVNVWDQLSDE 206

>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 = 82.5 bits (204), Expect = 7e-20
 Identities = 34/136 (25%), Positives = 50/136 (36%), Gaps = 32/136 (23%)

Query: 79  KVAIIQLC----------LFHKDRMPQSLVDFLDNDKFTFVG------------------ 110
           +VA+IQLC          +      PQ L   L+N      G                  
Sbjct: 60  RVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFDVKL 119

Query: 111 --TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYA 168
              +++ D+A  K    E  T+ L  LV   L  ++ K K I  S W    L++ Q  YA
Sbjct: 120 ESFVELTDVANEKLKCAE--TWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYA 177

Query: 169 AIDAFVSFKLAIELKK 184
           A DA+    +  +L  
Sbjct: 178 ATDAYAGLIIYQKLGN 193

>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 = 51.8 bits (123), Expect = 4e-08
 Identities = 31/190 (16%), Positives = 63/190 (33%), Gaps = 43/190 (22%)

Query: 1   MAVEALTLSPKPAEIKPLAYNSSSSIEPLGHNI--------WG-INFGEDYFVTTVTSRA 51
            ++  L    +PAE + + ++  S + P   +I        W  +   +   V     + 
Sbjct: 361 SSLNVL----EPAEYRKM-FDRLS-VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 52  SDVDRWIAR-TINVH------------RRRLHRLITNKLQKVAIIQLCLFHKDRMPQSLV 98
           S V++     TI++                LHR I +       I       D +P    
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN----IPKTFDSDDLIP---- 466

Query: 99  DFLDNDKFTFVGT-MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDV 157
            +LD   ++ +G  +   +        E +  F +  L  +FL  ++        +   +
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHP------ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSI 520

Query: 158 NNLSKQQIRY 167
            N  +Q   Y
Sbjct: 521 LNTLQQLKFY 530

>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 = 41.2 bits (97), Expect = 1e-04
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEII 187
            ++G   +V ++  V ++KS+  + + W    L+++Q  YAA D +    +  +L  E  
Sbjct: 114 MSWGFASMVEEYSGVTLDKSE--SRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETE 171

Query: 188 ALPK 191
           A   
Sbjct: 172 ASGW 175

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

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186
           LK FGL  +   FL + + K      + W    L +    YAA+D  +  +L  +++ E+
Sbjct: 130 LKRFGLAAVTEHFLGLTLAKEHS--AADWSYRPLPRDWRNYAALDVELLIELETKMRAEL 187

Query: 187 IALPK 191
               K
Sbjct: 188 KRQGK 192

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

 Score = 39.1 bits (91), Expect = 6e-04
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 130 FGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIAL 189
             L  L+  + +V+  K     L+ W +  L ++ + YA  D      +  +++ E+   
Sbjct: 223 HSLDHLLKLYCNVDSNKQY--QLADWRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWER 280

Query: 190 PKPTTFDAFCCFQIS 204
                      +Q S
Sbjct: 281 GNGQPVQLQVVWQRS 295

>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 = 39.0 bits (91), Expect = 6e-04
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 127 LKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI 186
           L    L  L+  F + +  K  +  L+ W +  LSK     A  D      +  +L+ ++
Sbjct: 197 LPRHSLAYLLENFANFKTSKKYQ--LADWRIRPLSKPMTAAARADTHFLLNIYDQLRNKL 254

Query: 187 IALPK 191
           I   K
Sbjct: 255 IESNK 259

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
1vk0_A	206	Hypothetical protein; homohexamer, AT5G06450, stru	99.94
2e6m_A	208	Werner syndrome ATP-dependent helicase homolog; AP	99.83
3saf_A	428	Exosome component 10; exoribonuclease, RNA exosome	99.74
2hbj_A	410	Exosome complex exonuclease RRP6; RNA metabolism,	99.7
1yt3_A	375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	99.64
3cym_A	440	Uncharacterized protein BAD_0989; structural genom	99.44
2kfn_A	605	Klenow fragment of DNA polymerase I; complex (poly	98.61
3pv8_A	592	DNA polymerase I; DNA polymerase I, protein-DNA co	98.37
1x9m_A	698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	96.95
4dfk_A	540	DNA polymerase I, thermostable; DNA polymerase, tr	91.51
1wlj_A	189	Interferon stimulated gene 20KDA; exoribonuclease,	91.41
2p1j_A	186	POLIII, DNA polymerase III POLC-type; structural g	80.67

>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=99.94  E-value=2.3e-27  Score=198.37  Aligned_cols=105  Identities=20%  Similarity=0.341  Sum_probs=96.3

Q ss_pred             CceeeEEEE------EEee-CCCCHH---HHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcch
Q 045621           78 QKVAIIQLC------LFHK-DRMPQS---LVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEEL  127 (205)
Q Consensus        78 ~~vaLiQLc------L~~~-~~~p~~---L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~  127 (205)
                      +++||||||      |||+ +.+|..   |++||+||+|+||||                    +|++.+|+..+|.+..
T Consensus        71 ~~~~LiQla~~~~~~l~~l~~~~~~~L~~L~~lL~d~~i~Kvg~~~~~D~~~L~~~~g~~~~~~~Dl~~la~~~lg~~~~  150 (206)
T 1vk0_A           71 WSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVL  150 (206)
T ss_dssp             CEEEEEEEECSSEEEEEECCSSCCGGGHHHHHHHTCSSSEEEESSCHHHHHHHHHHHCCCCSSEEEHHHHHHHHHTCGGG
T ss_pred             CceEEEEEecCCCeEEEeccccCCccHHHHHHHhcCCCceEEEeccHHHHHHHHHhcCCCcCCeeeHHHHHHHHcCCCCC
Confidence            489999999      7787 668877   789999999999999                    9999998878887545


Q ss_pred             hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHH
Q 045621          128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK  184 (205)
Q Consensus       128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~  184 (205)
                      .+.||++||+++||+.| |++++++|||++ |||++|++|||.|||++++||++|.+
T Consensus       151 ~~~gL~~Lv~~~lg~~l-K~k~~~~SdW~~-pLs~~Qi~YAA~Da~~l~~l~~~L~~  205 (206)
T 1vk0_A          151 EFLGTRELAHRVLWSDL-GQLDSIEAKWEK-AGPEEQLEAAAIEGWLIVNVWDQLSD  205 (206)
T ss_dssp             GGCCHHHHHHHHHCCCC-HHHHHHHHTGGG-SCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHhCCcC-CCCCcccCCCCC-cCCHHHHHHHHHHHHHHHHHHHHHHc
Confidence            79999999999999999 888888999999 99999999999999999999999975

>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=99.83  E-value=3.7e-20  Score=152.66  Aligned_cols=155  Identities=28%  Similarity=0.322  Sum_probs=117.3

Q ss_pred             CCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHHHhhhccccceee-----c-----cCCceeeEEEE-------EEee
Q 045621           28 PLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLIT-----N-----KLQKVAIIQLC-------LFHK   90 (205)
Q Consensus        28 ~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~~~~~~~~~lvv-----~-----~~~~vaLiQLc-------L~~~   90 (205)
                      +...+.+.+.|.|..+.   ..+++.+...+.++....... ..+.+     +     ..+++++||||       ++++
T Consensus         3 ~~~~~lp~~~f~g~i~~---i~~~~~~~~~~~~~~~~l~~~-~~v~~D~E~~~~~~~~~~~~~~~iqla~~~~~~~~i~~   78 (208)
T 2e6m_A            3 VLEDNLPFLEFPGSIVY---SYEASDCSFLSEDISMRLSDG-DVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHI   78 (208)
T ss_dssp             ----CCCBCCCCSEEEE---ECSHHHHHHHHHHHHHHCCTT-CEEEEEEECCC---CCSCCCCCEEEEECSSSEEEEECG
T ss_pred             chhccCCccccCCcEEE---EeCHHHHHHHHHHHHHHhccC-CEEEEEeecCCCCCCCCCCCeEEEEEecCCCeEEEEEC
Confidence            44566777888887543   357887876555554432222 11222     1     25689999999       4543


Q ss_pred             ---CCCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccC
Q 045621           91 ---DRMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKS  147 (205)
Q Consensus        91 ---~~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~  147 (205)
                         +.+|..|+.+|+|++|+|||+                    +|+..+|...++..  .+.||+.|++++||..+.|+
T Consensus        79 ~~~~~~~~~L~~lL~d~~i~Kv~~~~k~D~~~L~~~~gi~~~~~fDlt~lAayll~~~--~~~~L~~L~~~~l~~~~~K~  156 (208)
T 2e6m_A           79 SSMSVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFDVKLESFVELTDVANEKLKCA--ETWSLNGLVKHVLGKQLLKD  156 (208)
T ss_dssp             GGCSSCCHHHHHHHTCTTSEEEESSHHHHHHHHHHHHCCCCCSEEEHHHHHHHHTTCC--CCCCHHHHHHHHHSCBCCCC
T ss_pred             cccccchHHHHHHhcCCCceEEEEeeHHHHHHHHHHCCCCCCCEEEHHHHHHHHccCC--CChhHHHHHHHHcCCCcCCC
Confidence               457889999999999999998                    89888887777642  58899999999999999887


Q ss_pred             CcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHc
Q 045621          148 KRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIA  188 (205)
Q Consensus       148 ~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~  188 (205)
                      ++.++|||+.+||+++|+.|||.||++++.+|..|.++...
T Consensus       157 k~~~~s~W~~~~L~~~q~~YAa~Da~~~~~L~~~L~~~L~~  197 (208)
T 2e6m_A          157 KSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGNLGDT  197 (208)
T ss_dssp             HHHHTSCTTSSSCCHHHHHHHHHHHHHHHHHHHHHHTCC--
T ss_pred             CCeeeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccch
Confidence            77789999999999999999999999999999999877433

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

Probab=99.74  E-value=5.5e-18  Score=155.17  Aligned_cols=136  Identities=15%  Similarity=0.192  Sum_probs=108.8

Q ss_pred             EeCCcEEEEEEcCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeCC---CCHHHHH
Q 045621           37 NFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKDR---MPQSLVD   99 (205)
Q Consensus        37 ~f~g~~I~vtvT~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~~---~p~~L~~   99 (205)
                      ++++..+.  +..+++.+.+|+..+...     ..+.+        +..+++++||||      +|+.-.   ....|+.
T Consensus       104 p~~~~~y~--~I~t~e~L~~~l~~L~~~-----~~vavDtE~~~~~~~~~~l~lIQLa~~~~~~lidpl~l~~~l~~L~~  176 (428)
T 3saf_A          104 PIEETPCH--FISSLDELVELNEKLLNC-----QEFAVNLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNE  176 (428)
T ss_dssp             CGGGSCEE--EECSHHHHHHHHHHHTTC-----SEEEEEEEEECTTCSSCEEEEEEEECSSCEEEEETTTTGGGGGGGHH
T ss_pred             CCCCCCcE--EECCHHHHHHHHHHHhcC-----CeEEEEEEecCCCCCCCeEEEEEEEeCCcEEEEEeccchhhHHHHHH
Confidence            34444443  446889999999987642     22333        256789999999      566422   3478999


Q ss_pred             hhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCC
Q 045621          100 FLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNN  159 (205)
Q Consensus       100 fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rp  159 (205)
                      +|+|++|.|||+                    ||++..+ ..+|.+   +.||+.|++++||..++|.++  +|||.+||
T Consensus       177 lL~dp~i~KV~H~~k~Dl~~L~~~~Gi~~~~~fDT~lAa-~lL~~~---~~gL~~Lv~~~Lg~~l~K~~~--~sdW~~rp  250 (428)
T 3saf_A          177 SLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQAA-RLLNLG---RHSLDHLLKLYCNVDSNKQYQ--LADWRIRP  250 (428)
T ss_dssp             HHTCTTSEEEESSCHHHHHHHHHHHCCCCSSEEEHHHHH-HHTTCS---CCSHHHHHHHHHCCCCCCTTT--TSCTTCSS
T ss_pred             HHcCCCceEEEeehHHHHHHHHHHcCCCcCceeechhHH-HHhCCC---CCCHHHHHHHHcCCCCCcccc--ccccccCC
Confidence            999999999999                    6776555 356643   579999999999999999887  99999999


Q ss_pred             CCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          160 LSKQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       160 Ls~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                      |+++|+.|||.||++++.||+.|...
T Consensus       251 Ls~~q~~YAA~DA~~ll~L~~~L~~~  276 (428)
T 3saf_A          251 LPEEMLSYARDDTHYLLYIYDKMRLE  276 (428)
T ss_dssp             CCHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999877

>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=99.70  E-value=9.8e-17  Score=145.96  Aligned_cols=161  Identities=16%  Similarity=0.214  Sum_probs=116.4

Q ss_pred             ccccccCCCCCCCCCCCCceeEEEeCCcEEEEEEcCCHHHHHHHHHHHHHhhhccccceee-----c---cCCceeeEEE
Q 045621           14 EIKPLAYNSSSSIEPLGHNIWGINFGEDYFVTTVTSRASDVDRWIARTINVHRRRLHRLIT-----N---KLQKVAIIQL   85 (205)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~y~V~f~g~~I~vtvT~~~~~v~~wi~~~~~~~~~~~~~lvv-----~---~~~~vaLiQL   85 (205)
                      ||....|.++.....  .......|.+..+.+ | .+.+.+..|+..+...     ..+.+     +   ..+++++|||
T Consensus        60 ei~~~~~~~~~~~~~--~~~~~~~~~~~~~~~-I-~t~~~L~~~~~~L~~~-----~~vavDtE~~~~~~~~~~l~liQl  130 (410)
T 2hbj_A           60 EIDHQEYSPEILQIR--EEIPSKSWDDSVPIW-V-DTSTELESMLEDLKNT-----KEIAVDLEHHDYRSYYGIVCLMQI  130 (410)
T ss_dssp             HHHHSCCCGGGSSCC--CCCCCCCGGGCCCEE-E-CSHHHHHHHHHHHTTC-----SEEEEEEEEECSSSSSCEEEEEEE
T ss_pred             HHhhCCCCHHHhccC--CCCCCCCcCCCCcEE-e-CCHHHHHHHHHHHhhC-----CceEEEeeecCCcCCCCcEEEEEE
Confidence            345555544443221  222445566654433 2 3478899999865431     12222     1   3678999999


Q ss_pred             E------EEee---CCCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHH
Q 045621           86 C------LFHK---DRMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLV  136 (205)
Q Consensus        86 c------L~~~---~~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv  136 (205)
                      |      |++.   ......|+.+|+|++|+|||+                    ||++..|. .+|.   .+.||+.|+
T Consensus       131 a~~~~~ylid~l~l~~~l~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~Gi~~~~~fDt~lAa~-LL~~---~~~~L~~L~  206 (410)
T 2hbj_A          131 STRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASK-AIGL---PRHSLAYLL  206 (410)
T ss_dssp             ECSSCEEEEETTTTTTTGGGGHHHHTCTTSEEEESSCHHHHHHHHHHHCCCCSSEEEHHHHHH-HHTC---SCCSHHHHH
T ss_pred             EECCcEEEEechhhhhhHHHHHHHHcCCCceEEEEehHHHHHHHHHHcCCCcCCEEEcHHHHH-HhCC---CccCHHHHH
Confidence            9      5553   123468999999999999998                    77765553 5663   268999999


Q ss_pred             HHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcC
Q 045621          137 LKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIAL  189 (205)
Q Consensus       137 ~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~  189 (205)
                      +++||..++|..+  +|||..|||+++|+.|||.||++++.||..|..+....
T Consensus       207 ~~~lg~~l~K~~~--~sdW~~rpL~~~q~~YAa~Da~~ll~L~~~L~~~L~~~  257 (410)
T 2hbj_A          207 ENFANFKTSKKYQ--LADWRIRPLSKPMTAAARADTHFLLNIYDQLRNKLIES  257 (410)
T ss_dssp             HHHSCCCCCCTTT--TSCTTCSSCCHHHHHHHHHHHHTHHHHHHHHHHHHHHT
T ss_pred             HHHcCCCCCcccc--ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999877  99999999999999999999999999999998874433

>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=99.64  E-value=2.3e-15  Score=134.79  Aligned_cols=130  Identities=19%  Similarity=0.239  Sum_probs=103.6

Q ss_pred             CCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeCC--CCHHHHHhhcCCCeeEEEe-
Q 045621           49 SRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKDR--MPQSLVDFLDNDKFTFVGT-  111 (205)
Q Consensus        49 ~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~~--~p~~L~~fL~d~~i~kvGv-  111 (205)
                      .+.+.+.+|+..+...     ..+.+        ...+++++||||      +++...  ....|+.+|+|++|.|||+ 
T Consensus         7 ~t~~~l~~~~~~l~~~-----~~va~D~E~~~~~~~~~~l~liqla~~~~~~lid~~~l~~~~~L~~ll~d~~i~Kv~h~   81 (375)
T 1yt3_A            7 TTDDALASLCEAVRAF-----PAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHA   81 (375)
T ss_dssp             CSHHHHHHHHHHHTTS-----SEEEEEEEEECCSCSSCEEEEEEEECSSCEEEECGGGCSCCHHHHHHHHCTTSEEEESS
T ss_pred             CCHHHHHHHHHHHcCC-----CeEEEEeeecCCCcCCCceEEEEEecCCcEEEEeCCCCCChHHHHHHHcCCCceEEEee
Confidence            3578899998865431     12222        135789999999      555222  3578999999999999998 


Q ss_pred             -------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhH
Q 045621          112 -------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDA  172 (205)
Q Consensus       112 -------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA  172 (205)
                                         ||++..+ ..+|..  .+.||+.|++++||..++|.++  +|||..+||+++|+.|||.||
T Consensus        82 ~k~Dl~~L~~~~Gi~~~~~fDt~lAa-~lL~~~--~~~~L~~L~~~~l~~~l~K~~~--~sdw~~rpL~~~q~~YAa~Da  156 (375)
T 1yt3_A           82 GSEDLEVFLNVFGELPQPLIDTQILA-AFCGRP--MSWGFASMVEEYSGVTLDKSES--RTDWLARPLTERQCEYAAADV  156 (375)
T ss_dssp             CHHHHHHHHHHHSSCCSSEEEHHHHH-HHTTCC--TTCCHHHHHHHHHCCCCCCTTT--TSCTTSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcEEEcHHHH-HHcCCC--CChhHHHHHHHHcCCCCCCCcc--cCCCCCCCCCHHHHHHHHHHH
Confidence                               7776655 356653  4899999999999999999887  899999999999999999999


Q ss_pred             HHHHHHHHHHHHhHHc
Q 045621          173 FVSFKLAIELKKEIIA  188 (205)
Q Consensus       173 ~~~~~I~~~L~~~~~~  188 (205)
                      ++++.+|..|.+.-..
T Consensus       157 ~~l~~L~~~L~~~L~~  172 (375)
T 1yt3_A          157 WYLLPITAKLMVETEA  172 (375)
T ss_dssp             HTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999877443

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

Probab=99.44  E-value=1.3e-12  Score=119.81  Aligned_cols=124  Identities=18%  Similarity=0.269  Sum_probs=97.0

Q ss_pred             CHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE-------EEee-C-----CCCHHHHHhhcCCCeeE
Q 045621           50 RASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC-------LFHK-D-----RMPQSLVDFLDNDKFTF  108 (205)
Q Consensus        50 ~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc-------L~~~-~-----~~p~~L~~fL~d~~i~k  108 (205)
                      +.+.+.+|+..+....    ..+.+        .+.+++++||||       +|+. .     .....|+.+|+|+  .|
T Consensus        23 t~e~L~~~~~~L~~~~----~~vavDtE~~~~~~~~~~l~liQla~~~~~~~lid~l~~~~~~~~l~~L~~lL~d~--~K   96 (440)
T 3cym_A           23 TLPAFRDYCSELASSH----GSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVGDA--VW   96 (440)
T ss_dssp             SHHHHHHHHHHHHSCE----EEEEEEEEECTTTSSSCCEEEEEEEEETTEEEEECHHHHHHTTCCHHHHHHHHTTC--EE
T ss_pred             CHHHHHHHHHHHHhcC----CeEEEEeeecCCCCCCCCEEEEEEEECCCcEEEEEcCCccccccCHHHHHHHHCCC--CE
Confidence            4688999998754310    11222        136789999999       3332 1     1235899999998  68


Q ss_pred             EEe-------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHH
Q 045621          109 VGT-------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAA  169 (205)
Q Consensus       109 vGv-------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA  169 (205)
                      ||+                   ||+. +|...++.   .+.||+.|++.++|..++|..+  +|||..+||+++|+.|||
T Consensus        97 V~h~~k~Dl~~L~~~gi~~~~~fDt~-lAa~lL~~---~~~gL~~L~~~~lg~~~~K~~~--~sdw~~rpLs~~q~~YAa  170 (440)
T 3cym_A           97 ILHDSLQDLPGFDELGMEPQRLFDTE-IAARLLGL---KRFGLAAVTEHFLGLTLAKEHS--AADWSYRPLPRDWRNYAA  170 (440)
T ss_dssp             EESSHHHHHHHHHHHTCCCCEEEEHH-HHHHHTTC---SSCSHHHHHHHHHCEECCCCCT--TCCTTCSSCCHHHHHHHH
T ss_pred             EEEcCHHHHHHHHHcCCcCCceehHH-HHHHHhCC---CCCCHHHHHHHHhCCCcccccc--cCCCcCCCCCHHHHHHHH
Confidence            887                   8884 55567774   2899999999999999999877  999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHh
Q 045621          170 IDAFVSFKLAIELKKE  185 (205)
Q Consensus       170 ~DA~~~~~I~~~L~~~  185 (205)
                      .||++++.||..|...
T Consensus       171 ~Da~~Ll~L~~~L~~~  186 (440)
T 3cym_A          171 LDVELLIELETKMRAE  186 (440)
T ss_dssp             HHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999665

>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=98.61  E-value=7.7e-07  Score=84.22  Aligned_cols=126  Identities=17%  Similarity=0.234  Sum_probs=90.6

Q ss_pred             CHHHHHHHHHHHHHhhhccccceee-----c---cCCceeeEEEEE-----Eee--C--------CCC-----HHHHHhh
Q 045621           50 RASDVDRWIARTINVHRRRLHRLIT-----N---KLQKVAIIQLCL-----FHK--D--------RMP-----QSLVDFL  101 (205)
Q Consensus        50 ~~~~v~~wi~~~~~~~~~~~~~lvv-----~---~~~~vaLiQLcL-----~~~--~--------~~p-----~~L~~fL  101 (205)
                      +++.+.+|++.+...     ..+++     +   ...++..||+|+     +.+  .        .++     +.|+.||
T Consensus        12 ~~~~l~~~~~~l~~~-----~~va~DtEttgl~~~~~~iv~I~~~~~~g~~~yip~~~~~~~~~~~l~~~~vl~~L~~~L   86 (605)
T 2kfn_A           12 DEETLKAWIAKLEKA-----PVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLL   86 (605)
T ss_dssp             SHHHHHHHHHHHHTS-----SSEEEEEEESCSCTTTCCEEEEEEEEETTEEEEEECCCCSTTCCCCCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhcccC-----CeEEEEEecCCCCcccCceEEEEEEEcCCcEEEEeccccccccccccCHHHHHHHHHHHH
Confidence            468899999875431     12233     2   246788888881     222  1        121     4699999


Q ss_pred             cCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCccc-------ccCCcccccC
Q 045621          102 DNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEM-------EKSKRITLSK  154 (205)
Q Consensus       102 ~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l-------~K~~~v~~Sn  154 (205)
                      +|+++.|||+                    +|+..++. .++ ++..+.||+.|++.+||...       .|.++  .++
T Consensus        87 ~d~~i~kV~hnak~D~~~L~~~Gi~l~~~~~DT~laay-LL~-p~~~~~~L~~La~~~Lg~~~i~~~~~~gKg~~--~~~  162 (605)
T 2kfn_A           87 EDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESY-ILN-SVAGRHDMDSLAERWLKHKTITFEEIAGKGKN--QLT  162 (605)
T ss_dssp             TCTTSCEEESSHHHHHHHHHTTTCCCCCEEEEHHHHHH-HHC-TTSSCCSHHHHHHHHSCCCCCCHHHHHCSSTT--CCC
T ss_pred             cCCCCeEEEECcHHHHHHHHHCCCCCCCccccHHHHHH-HhC-CCCCCCCHHHHHHHhcCCCcccHHHHhCCCcc--cCC
Confidence            9999999998                    55544443 343 22247899999999998764       35555  679


Q ss_pred             CCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          155 WDVNNLSKQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       155 W~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                      |..++| ++|.+||+.||++++.+|.+|...
T Consensus       163 ~~~~~l-e~~~~yAa~Da~~~~~L~~~L~~~  192 (605)
T 2kfn_A          163 FNQIAL-EEAGRYAAEDADVTLQLHLKMWPD  192 (605)
T ss_dssp             GGGSCH-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            998888 789999999999999999999875

>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=98.37  E-value=8.8e-07  Score=83.93  Aligned_cols=108  Identities=9%  Similarity=-0.064  Sum_probs=82.6

Q ss_pred             cCCceeeEEEE----EEeeC----CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcch
Q 045621           76 KLQKVAIIQLC----LFHKD----RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEEL  127 (205)
Q Consensus        76 ~~~~vaLiQLc----L~~~~----~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~  127 (205)
                      ...+++.||+|    .+.++    .....|+.+|+|+++.|||+                    +|+...+ ..++ ++.
T Consensus        44 ~~a~Lvgisla~~~~a~yIp~~~~~~l~~Lk~lLed~~i~KV~hn~K~Dl~vL~~~Gi~l~g~~fDTmLAA-YLL~-p~~  121 (592)
T 3pv8_A           44 HDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAA-YLLD-PAQ  121 (592)
T ss_dssp             TTCCCCEEEEEETTEEEEECHHHHTTCHHHHHHHTCTTSEEEESSHHHHHHHHHHTTCCCCCEEEEHHHHH-HHHC-GGG
T ss_pred             CcccEEEEEEEcCCceEEEccchhhHHHHHHHHHhCCCCeEEEechHHHHHHHHHcCCCCCCccchHHHHH-HHcC-CCC
Confidence            45678889998    33321    34578999999999999998                    5654333 3444 323


Q ss_pred             hcccHHHHHHHHcCcccccCCcccccCCCC---CCCCHHHHHHHHhhHHHHHHHHHHHHHhHH
Q 045621          128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDV---NNLSKQQIRYAAIDAFVSFKLAIELKKEII  187 (205)
Q Consensus       128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~---rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~  187 (205)
                      .+.||+.|++++||..+.+.+.  ..+|++   .+++++|..|||.||.+++.++..|.....
T Consensus       122 ~~~~L~~La~~yLg~~l~~~ee--~~gkg~~~~~~~~e~~~~YAa~DA~~l~~L~~~L~~~L~  182 (592)
T 3pv8_A          122 GVDDVAAAAKMKQYEAVRPDEA--VYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELR  182 (592)
T ss_dssp             CCCSHHHHHGGGTCCSSCCHHH--HHCSGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHcCCCCchHHH--hcCccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999988766  667754   456688999999999999999999987743

>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=96.95  E-value=0.00069  Score=65.08  Aligned_cols=111  Identities=14%  Similarity=0.105  Sum_probs=76.2

Q ss_pred             cCCceeeEEEE--------EEeeCCC---CHHHHHhhcCCCeeEEEe----eeHHHHHHHh-----cCC--c--------
Q 045621           76 KLQKVAIIQLC--------LFHKDRM---PQSLVDFLDNDKFTFVGT----MDVADMAAAK-----YDD--E--------  125 (205)
Q Consensus        76 ~~~~vaLiQLc--------L~~~~~~---p~~L~~fL~d~~i~kvGv----~Dl~~la~~~-----lg~--~--------  125 (205)
                      ...+++++|++        +++...+   .+.|+.||+ +++.|||+    +|+..+.+..     .|.  .        
T Consensus        14 ~~d~i~~iqi~~~~~~~~~~~~p~~i~~~l~~L~~~l~-~~~~kV~HNa~kfD~~~L~~~~~~~~~~Gi~l~~~~~~DTm   92 (698)
T 1x9m_A           14 SVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVA-RGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTL   92 (698)
T ss_dssp             GCCCEEEEEEEETTTTEEEEECGGGHHHHHHHHHHHHH-TTCCEEESSTTTTHHHHHHHHHHHHHCCCCCCCGGGEEEHH
T ss_pred             CCCEEEEEEEEecCCCcEEEEChHHHHHHHHHHHHHHh-cCCeEEEcCChHHHHHHHHHhhhhcccCCccCCCCcchhHH
Confidence            35689999998        3333223   368999999 99999998    6887776531     031  1        


Q ss_pred             --------chhcccHHHHHHHHc-------Cccc-----c-----------cCCccc-ccCCCCCCCCHHHHHHHHhhHH
Q 045621          126 --------ELKTFGLKRLVLKFL-------HVEM-----E-----------KSKRIT-LSKWDVNNLSKQQIRYAAIDAF  173 (205)
Q Consensus       126 --------~~~~~gL~~Lv~~~l-------g~~l-----~-----------K~~~v~-~SnW~~rpLs~~Qi~YAA~DA~  173 (205)
                              +..+.||+.|++.+|       |..+     +           |.++-. .++|..  +++++.+||+.||.
T Consensus        93 laayLL~p~~~~~~L~~La~~~L~~sL~~~g~~lg~~Ki~~~~~~g~~~~~kg~~~~~~~~~~~--~~~~~~~YA~~Da~  170 (698)
T 1x9m_A           93 VLSRLIHSNLKDTDMGLLRSGKLPGALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWN--FNEEMMDYNVQDVV  170 (698)
T ss_dssp             HHHHHHTTTSCCCTTTTSCGGGSCSCCCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCTTGGGTS--CCHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCCCCCHHHHHHHHcccchhhhcccccccccCHHHHhCcccccccccccccCCccc--cCHHHHHHHHHHHH
Confidence                    113677888888877       5333     2           332211 238975  77999999999999


Q ss_pred             HHHHHHHHHHHhHHcC
Q 045621          174 VSFKLAIELKKEIIAL  189 (205)
Q Consensus       174 ~~~~I~~~L~~~~~~~  189 (205)
                      +.+.||.+|.......
T Consensus       171 ~t~~L~~~L~~~L~~~  186 (698)
T 1x9m_A          171 VTKALLEKLLSDKHYF  186 (698)
T ss_dssp             HHHHHHHHHHTCTTTS
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999998874433

>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=91.51  E-value=0.21  Score=46.64  Aligned_cols=84  Identities=13%  Similarity=0.081  Sum_probs=59.9

Q ss_pred             cCCceeeEEEE----EEeeCCCCHHHHHhhcCCCeeEEEe----------------eeHHHHHHHhcCCcchhcccHHHH
Q 045621           76 KLQKVAIIQLC----LFHKDRMPQSLVDFLDNDKFTFVGT----------------MDVADMAAAKYDDEELKTFGLKRL  135 (205)
Q Consensus        76 ~~~~vaLiQLc----L~~~~~~p~~L~~fL~d~~i~kvGv----------------~Dl~~la~~~lg~~~~~~~gL~~L  135 (205)
                      ...+++.+|+|    .+..+...+.|+.||+|  +.|||+                +|+...|. .++ ++  +.||+.|
T Consensus        25 ~~a~Lvgi~la~~~~a~~i~~~l~~l~~~l~d--~~kV~hn~K~Dl~~~Gi~~~~~fDT~laAy-LL~-p~--~~~L~~L   98 (540)
T 4dfk_A           25 MWADLLALAAARGGRVHRAPEPYKALRDLKEA--RGLLAKDLSVLALREGLGLPPGDDPMLLAY-LLD-PS--NTTPEGV   98 (540)
T ss_dssp             TTCCEEEEEEEETTEEEECSSHHHHHTTCSSB--CSTTHHHHHHHHHHTTCCCCBCCCHHHHHH-HHC-TT--CCCHHHH
T ss_pred             CcccEEEEEEEcCCEEEEehhhHHHHHHHHcC--CCEEEeccHHHHHHcCCCCCcceeHHHHHH-HhC-CC--CCCHHHH
Confidence            45677888998    44433344788899988  677765                56554443 444 33  7899999


Q ss_pred             HHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          136 VLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       136 v~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                      +++++|.            |++         +|+.||.+++.+|..|....
T Consensus        99 a~~yl~~------------~gk---------~a~~DA~~t~~L~~~L~~~L  128 (540)
T 4dfk_A           99 ARRYGGE------------WTE---------EAGERAALSERLFANLWGRL  128 (540)
T ss_dssp             HHHHTSC------------CCS---------CHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHhhh------------hcc---------chHHHHHHHHHHHHHHHHHH
Confidence            9999886            221         37799999999999997654

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

Probab=91.41  E-value=0.89  Score=35.83  Aligned_cols=51  Identities=18%  Similarity=0.132  Sum_probs=36.5

Q ss_pred             hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhHHcCCCCC
Q 045621          128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPKPT  193 (205)
Q Consensus       128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~~~~p~~~  193 (205)
                      .+.||+.+++.++|..+....               +-+-|..||.++.+++.++.+..+..-.+.
T Consensus       126 ~~~~L~~l~~~~lgi~~~~~~---------------~~H~Al~Da~ata~l~~~l~~~~~~~~~~~  176 (189)
T 1wlj_A          126 RRVSLRVLSERLLHKSIQNSL---------------LGHSSVEDARATMELYQISQRIRARRGLPR  176 (189)
T ss_dssp             --CCHHHHHHHHTCCCCSCCT---------------TCCCHHHHHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             CCccHHHHHHHHcCCCCCCCC---------------CCcCcHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            578999999998898776521               123488999999999999988854443433

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

Probab=80.67  E-value=4.8  Score=31.31  Aligned_cols=21  Identities=19%  Similarity=0.069  Sum_probs=18.2

Q ss_pred             HHHHHhhHHHHHHHHHHHHHh
Q 045621          165 IRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       165 i~YAA~DA~~~~~I~~~L~~~  185 (205)
                      -+.|..||.++.+|+.++.+.
T Consensus       155 ~H~Al~Da~~t~~l~~~l~~~  175 (186)
T 2p1j_A          155 HHRALDDARVTAQVFLRFVEM  175 (186)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCHHHHHHHHHHHHHHHHHH
Confidence            367999999999999998765

---

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	205
d1vk0a_	206	c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thal	2e-14
d2hbka2	292	c.55.3.5 (A:129-420) Exosome complex exonuclease R	6e-04

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 23/137 (16%), Positives = 49/137 (35%), Gaps = 32/137 (23%)

Query: 79  KVAIIQLC------LFHKDRM----PQSLVDFLDNDKFTFVG------------------ 110
            ++ ++L            +      + L  F  +   TFVG                  
Sbjct: 72  SLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVI 131

Query: 111 --TMDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYA 168
              ++V  +AA       L+  G + L  + L  ++ +   I  +KW+     ++Q+  A
Sbjct: 132 RNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIE-AKWE-KAGPEEQLEAA 189

Query: 169 AIDAFVSFKLAIELKKE 185
           AI+ ++   +  +L  E
Sbjct: 190 AIEGWLIVNVWDQLSDE 206

>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 292

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]

 Score = 37.5 bits (86), Expect = 6e-04
 Identities = 12/51 (23%), Positives = 21/51 (41%)

Query: 141 HVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEIIALPK 191
               + SK+  L+ W +  LSK     A  D      +  +L+ ++I   K
Sbjct: 207 FANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNK 257

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	205
d1vk0a_	206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	99.92
d1yt3a3	193	Ribonuclease D, catalytic domain {Escherichia coli	99.89
d2hbka2	292	Exosome complex exonuclease RRP6 {Baker's yeast (S	99.86
d1kfsa1	195	Exonuclease domain of prokaryotic DNA polymerase {	99.29
d2hhva1	171	Exonuclease domain of prokaryotic DNA polymerase {	98.5
d1wlja_	173	Interferon-stimulated gene 20 kDa protein, ISG20 {	93.15

>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=99.92  E-value=7.2e-26  Score=186.97  Aligned_cols=150  Identities=17%  Similarity=0.231  Sum_probs=118.4

Q ss_pred             eeEEEeCCcEEEEEE--cCCHHHHHHHHHHHHHhhhccccceee-----------------ccCCceeeEEEE------E
Q 045621           33 IWGINFGEDYFVTTV--TSRASDVDRWIARTINVHRRRLHRLIT-----------------NKLQKVAIIQLC------L   87 (205)
Q Consensus        33 ~y~V~f~g~~I~vtv--T~~~~~v~~wi~~~~~~~~~~~~~lvv-----------------~~~~~vaLiQLc------L   87 (205)
                      .....++|+.+.+++  +++...+..|+..++....-.....|.                 ....++|+||||      |
T Consensus         7 ~~~~~~d~~~~~t~~i~~~~~~~~~~~~~~i~~~~~~~~~~~v~~D~Ew~~~~~~~~~~~~~~~~~vallQl~t~~~~~l   86 (206)
T d1vk0a_           7 PKFKMTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLF   86 (206)
T ss_dssp             CEEECTTSCEEEEEEEECCSSCCCHHHHHHHHHHHHHHSTTEEEEEEEEECCC------CGGGGCEEEEEEEECSSEEEE
T ss_pred             ccccccCcchhceeeEecCCHHHHHHHHHHHHHHHhhcCCCEEEEEeecCCCCCcccccccccCceeEEEEEEeCCCEEE
Confidence            344455677776654  566777889999988753211112222                 123469999999      7


Q ss_pred             EeeC----CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcc
Q 045621           88 FHKD----RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVE  143 (205)
Q Consensus        88 ~~~~----~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~  143 (205)
                      ||+.    ..|+.|++||+|++|+||||                    +|++.+|+..++.+...+.||+.|++++||..
T Consensus        87 ~~l~~~~~~~~~~L~~~L~~~~i~kVG~~i~~D~~~L~~~~gi~~~~~~Dl~~la~~~~~~~~~~~~gL~~L~~~~Lg~~  166 (206)
T d1vk0a_          87 LRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSD  166 (206)
T ss_dssp             EECCSSCCGGGHHHHHHHTCSSSEEEESSCHHHHHHHHHHHCCCCSSEEEHHHHHHHHHTCGGGGGCCHHHHHHHHHCCC
T ss_pred             EECCccccccHHHHHHHhcCCCceEEEEeEHHHHHHHHHhcCCcccceEEchHHHHHhhcCCccccchHHHHHHHHhccc
Confidence            8853    35899999999999999999                    99999998777776667899999999999999


Q ss_pred             cccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHH
Q 045621          144 MEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKK  184 (205)
Q Consensus       144 l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~  184 (205)
                      ++|++ .++|||+ +|||++||+|||.|||++++||++|.+
T Consensus       167 l~K~~-~~~SnW~-~pLs~~Qi~YAA~DA~~~~~i~~~L~~  205 (206)
T d1vk0a_         167 LGQLD-SIEAKWE-KAGPEEQLEAAAIEGWLIVNVWDQLSD  205 (206)
T ss_dssp             CHHHH-HHHHTGG-GSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcc-eeecCCC-CcCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99975 3469997 699999999999999999999999976

>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=99.89  E-value=2.3e-23  Score=169.56  Aligned_cols=139  Identities=19%  Similarity=0.209  Sum_probs=112.3

Q ss_pred             EEcCCHHHHHHHHHHHHHhhhccccceee---------ccCCceeeEEEE------EEee--CCCCHHHHHhhcCCCeeE
Q 045621           46 TVTSRASDVDRWIARTINVHRRRLHRLIT---------NKLQKVAIIQLC------LFHK--DRMPQSLVDFLDNDKFTF  108 (205)
Q Consensus        46 tvT~~~~~v~~wi~~~~~~~~~~~~~lvv---------~~~~~vaLiQLc------L~~~--~~~p~~L~~fL~d~~i~k  108 (205)
                      .+..+.+.+++++.++..      .+.+.         ...+++|+||+|      +|+.  ...+..++++|+|++|+|
T Consensus         4 ~~I~t~~~l~~~~~~l~~------~~~i~~DtE~~~~~~~~~~l~liQi~~~~~~~~id~~~~~~~~~l~~ll~~~~i~K   77 (193)
T d1yt3a3           4 QMITTDDALASLCEAVRA------FPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITK   77 (193)
T ss_dssp             EEECSHHHHHHHHHHHTT------SSEEEEEEEEECCSCSSCEEEEEEEECSSCEEEECGGGCSCCHHHHHHHHCTTSEE
T ss_pred             EEECCHHHHHHHHHHHhc------CCeEEEECcccCCCcCCCcEEEEEEecCCcceeehhcchhhhHHHHHHhcCCCceE
Confidence            344677789999988755      23333         257889999999      5553  245789999999999999


Q ss_pred             EEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHH
Q 045621          109 VGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYA  168 (205)
Q Consensus       109 vGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YA  168 (205)
                      |||                    +|++.++. .++.+  .+.||+.|++++||..++|..+  +|||+.||||++|++||
T Consensus        78 v~hn~~~D~~~L~~~~g~~~~~~~Dt~~~~~-~l~~~--~~~~L~~l~~~~lg~~ldK~~q--~sdW~~rPL~~~qi~YA  152 (193)
T d1yt3a3          78 FLHAGSEDLEVFLNVFGELPQPLIDTQILAA-FCGRP--MSWGFASMVEEYSGVTLDKSES--RTDWLARPLTERQCEYA  152 (193)
T ss_dssp             EESSCHHHHHHHHHHHSSCCSSEEEHHHHHH-HTTCC--TTCCHHHHHHHHHCCCCCCTTT--TSCTTSSSCCHHHHHHH
T ss_pred             EEecchhhhhhhhhhcCccccccchhhHHHh-hhccc--cccchhhHHhhhccccccchhh--ccccccccccHHHHHHH
Confidence            999                    77665553 45543  5789999999999999999887  99999999999999999


Q ss_pred             HhhHHHHHHHHHHHHHhHHcCCCCCcc
Q 045621          169 AIDAFVSFKLAIELKKEIIALPKPTTF  195 (205)
Q Consensus       169 A~DA~~~~~I~~~L~~~~~~~p~~~~~  195 (205)
                      |.||+++++||++|..+....+..++.
T Consensus       153 A~Dv~~ll~L~~~L~~~l~~~~~l~~~  179 (193)
T d1yt3a3         153 AADVWYLLPITAKLMVETEASGWLPAA  179 (193)
T ss_dssp             HHHHHTHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHHhCCcHHHH
Confidence            999999999999999886666554443

>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=99.86  E-value=1.8e-21  Score=168.27  Aligned_cols=131  Identities=16%  Similarity=0.222  Sum_probs=108.8

Q ss_pred             EEcCCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EEeeC---CCCHHHHHhhcCCCeeE
Q 045621           46 TVTSRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LFHKD---RMPQSLVDFLDNDKFTF  108 (205)
Q Consensus        46 tvT~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~~~~---~~p~~L~~fL~d~~i~k  108 (205)
                      ++.++.+.+.++++++...     ..+.+        .+.+++|+||||      ++++-   .....|+.+|+|++|+|
T Consensus        86 ~~Vdt~e~L~~li~~L~~~-----~~iavDtE~~~~~s~~g~l~LiQiat~~~~~iiD~~~l~~~l~~L~~ll~d~~I~K  160 (292)
T d2hbka2          86 IWVDTSTELESMLEDLKNT-----KEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVK  160 (292)
T ss_dssp             EEECSHHHHHHHHHHHTTC-----SEEEEEEEEECSSSSSCEEEEEEEECSSCEEEEETTTTTTTGGGGHHHHTCTTSEE
T ss_pred             EEeCCHHHHHHHHHHHhcC-----CcEEEEEEeCcCcccCCeEEEEEEEeCCccEEEEecccccchHHHHHHHhccCeEE
Confidence            4567899999999988653     22333        356789999999      67743   23478999999999999


Q ss_pred             EEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHH
Q 045621          109 VGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYA  168 (205)
Q Consensus       109 vGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YA  168 (205)
                      ||+                    +|++..+. .+|.   .+.||+.|++.+||+.++|..+  +|||..|||+++|+.||
T Consensus       161 V~H~~~~Di~~L~~~~g~~~~n~fDT~~aa~-~l~~---~~~sL~~L~~~yl~~~ldK~~q--~SdW~~RPLs~~qi~YA  234 (292)
T d2hbka2         161 VFHGAFMDIIWLQRDLGLYVVGLFDTYHASK-AIGL---PRHSLAYLLENFANFKTSKKYQ--LADWRIRPLSKPMTAAA  234 (292)
T ss_dssp             EESSCHHHHHHHHHHHCCCCSSEEEHHHHHH-HHTC---SCCSHHHHHHHHHCCCCCCTTT--TSCTTCSSCCHHHHHHH
T ss_pred             EeechHhhhhhhhhcccccccchHHHHHHHH-HhCc---cccchHHHHHHhhhhccccccc--ccccccCcCCHHHHHHH
Confidence            999                    77766554 4553   4789999999999999999887  99999999999999999


Q ss_pred             HhhHHHHHHHHHHHHHhHH
Q 045621          169 AIDAFVSFKLAIELKKEII  187 (205)
Q Consensus       169 A~DA~~~~~I~~~L~~~~~  187 (205)
                      |.||++++.||++|.++-.
T Consensus       235 a~Da~~Ll~ly~~L~~~L~  253 (292)
T d2hbka2         235 RADTHFLLNIYDQLRNKLI  253 (292)
T ss_dssp             HHHHHTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            9999999999999987743

>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=99.29  E-value=2.7e-11  Score=94.92  Aligned_cols=128  Identities=17%  Similarity=0.228  Sum_probs=97.5

Q ss_pred             CCHHHHHHHHHHHHHhhhccccceee--------ccCCceeeEEEE------EE-eeC--------CC-----CHHHHHh
Q 045621           49 SRASDVDRWIARTINVHRRRLHRLIT--------NKLQKVAIIQLC------LF-HKD--------RM-----PQSLVDF  100 (205)
Q Consensus        49 ~~~~~v~~wi~~~~~~~~~~~~~lvv--------~~~~~vaLiQLc------L~-~~~--------~~-----p~~L~~f  100 (205)
                      .+++.+++|++++...     ..+.+        ...+.+..+|+|      .+ ...        ..     ...|+.+
T Consensus        11 ~t~~~l~~~l~~l~~~-----~~~a~DtEt~~l~~~~~~i~~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~   85 (195)
T d1kfsa1          11 LDEETLKAWIAKLEKA-----PVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPL   85 (195)
T ss_dssp             CSHHHHHHHHHHHHHS-----SSEEEEEEESCSCTTTCCEEEEEEEEETTEEEEEECCCCSTTCCCCCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcC-----CeEEEEeeeCCCCccccccccceeeccCCcccccccccccccccccccHHHHHHHHHHH
Confidence            4788899999988663     23333        256789999999      11 111        11     2579999


Q ss_pred             hcCCCeeEEEe--------------------eeHHHHHHHhcCCcchhcccHHHHHHHHcCcccccCCcccccCCCCCCC
Q 045621          101 LDNDKFTFVGT--------------------MDVADMAAAKYDDEELKTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNL  160 (205)
Q Consensus       101 L~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpL  160 (205)
                      |+++++.|+|+                    +|....+ ..+. ++..+.++..+++..+|..+.|..+  .++|.++++
T Consensus        86 le~~~i~ki~hn~~~d~~~l~~~~~~~~~~~~Dt~~a~-~l~~-~~~~~~~l~~~~~~~l~~~~~~~~~--~~~~~~~~~  161 (195)
T d1kfsa1          86 LEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLES-YILN-SVAGRHDMDSLAERWLKHKTITFEE--IAGKGKNQL  161 (195)
T ss_dssp             HTCTTSCEEESSHHHHHHHHHTTTCCCCCEEEEHHHHH-HHHC-TTSSCCSHHHHHHHHSSCCCCCHHH--HHCSGGGCC
T ss_pred             HhcccceeeechHHHHHHHHHHHhccccCccHHHHHHH-HHhc-ccccccchHHHHHHHhhcccchHhh--hcccccCCC
Confidence            99999999999                    4443333 2332 2235889999999999999988776  899999999


Q ss_pred             C------HHHHHHHHhhHHHHHHHHHHHHHh
Q 045621          161 S------KQQIRYAAIDAFVSFKLAIELKKE  185 (205)
Q Consensus       161 s------~~Qi~YAA~DA~~~~~I~~~L~~~  185 (205)
                      +      ++|..|||.||.+++++|+++..+
T Consensus       162 ~~~~i~~~~~~~YAa~D~~~t~~L~~~l~~~  192 (195)
T d1kfsa1         162 TFNQIALEEAGRYAAEDADVTLQLHLKMWPD  192 (195)
T ss_dssp             CGGGSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8      777799999999999999999875

>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=98.50  E-value=4.3e-07  Score=70.90  Aligned_cols=108  Identities=9%  Similarity=-0.056  Sum_probs=80.6

Q ss_pred             CCceeeEEEE----EEeeC----CCCHHHHHhhcCCCeeEEEe--------------------eeHHHHHHHhcCCcchh
Q 045621           77 LQKVAIIQLC----LFHKD----RMPQSLVDFLDNDKFTFVGT--------------------MDVADMAAAKYDDEELK  128 (205)
Q Consensus        77 ~~~vaLiQLc----L~~~~----~~p~~L~~fL~d~~i~kvGv--------------------~Dl~~la~~~lg~~~~~  128 (205)
                      ...+.-+++|    .+..+    .-.+.|+++|+|+++.|||+                    +|+...+. .+. ++..
T Consensus        32 ~~~iiGi~i~~~~~~~~i~~~~~~~~~~l~~~l~~~~~~ki~hn~K~d~~~L~~~gi~~~~~~fDt~laay-ll~-p~~~  109 (171)
T d2hhva1          32 DAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAY-LLD-PAQG  109 (171)
T ss_dssp             TCCCCEEEEEETTEEEEECHHHHTTCHHHHHHHHCTTSEEEESSHHHHHHHHHTTTCCCCCEEEEHHHHHH-HHC-GGGC
T ss_pred             cCeEEEEEEEECCCEEEEechhhhhHHHHHHHHhCccceeeccchHHHHHHHHHCCCCCccccccHHHHHH-Hhc-CCcc
Confidence            3456667777    33332    23578999999999999999                    56655443 442 3335


Q ss_pred             cccHHHHHHHHcCcccccCCcc-cccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHhH
Q 045621          129 TFGLKRLVLKFLHVEMEKSKRI-TLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKEI  186 (205)
Q Consensus       129 ~~gL~~Lv~~~lg~~l~K~~~v-~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~~  186 (205)
                      ..||+.+++++++..+.+.+.+ ..+.+...|..+.+..|||.||++.++++.+|.+.-
T Consensus       110 ~~~L~~la~~yl~~~~~~~e~~~gkg~k~~~~~~~~~~~yaa~da~~~~~L~~~l~~~L  168 (171)
T d2hhva1         110 VDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDEL  168 (171)
T ss_dssp             CCSHHHHHHTTTCCSSCCHHHHHCSGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHcCCCCccceeccCcchhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7799999999999988766553 233455668888899999999999999999998763

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

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

Probab=93.15  E-value=0.14  Score=37.29  Aligned_cols=49  Identities=20%  Similarity=0.217  Sum_probs=34.7

Q ss_pred             hcccHHHHHHHHcCcccccCCcccccCCCCCCCCHHHHHHHHhhHHHHHHHHHHHHHh--HHcCCC
Q 045621          128 KTFGLKRLVLKFLHVEMEKSKRITLSKWDVNNLSKQQIRYAAIDAFVSFKLAIELKKE--IIALPK  191 (205)
Q Consensus       128 ~~~gL~~Lv~~~lg~~l~K~~~v~~SnW~~rpLs~~Qi~YAA~DA~~~~~I~~~L~~~--~~~~p~  191 (205)
                      .+.||+.|++.++|..+....+               -+-|.-||.++.++|+.+.+.  ...+|.
T Consensus       121 ~~~~L~~L~~~~~~~~i~~~~~---------------~H~Al~Da~at~~l~~~~~~~~~~~g~p~  171 (173)
T d1wlja_         121 RRVSLRVLSERLLHKSIQNSLL---------------GHSSVEDARATMELYQISQRIRARRGLPR  171 (173)
T ss_dssp             --CCHHHHHHHHTCCCCSCCTT---------------CCCHHHHHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             CCcCHHHHHHHHhCCcccCCCC---------------CCChHHHHHHHHHHHHHHHHHHhhcCCCC
Confidence            5789999999998887653221               245899999999999877765  445543