Citrus Sinensis ID: 042232

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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----
Protein Sequence
MAYQQSLNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccEEEEcccccccEEEEEEccHHHHHHHHHHHHHccccccccccccEEHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHccccEEEEcccccccccccccccccEEEEEcccccccEEEEEccHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mayqqslnLHIHSFWRSLNcfrkdfskpqrtgntlfnikrfdlarlsssqftkgscslsnnlitnvhgvghanfHSIVTckkapsngrvmliDGTSIIYRAYYKILLHhghlshadgngdWVLTIFSALSLIIDVLEFIPSHVV
Flexible Loop (DISEMBL)
mayqqslnLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV
Low Complexity Region (SEG)
MAYQQSLNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV
Disordered region (IsUnstruct)
******LNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIP****
Disordered Region (DISOPRED)
*******NLHIHSFWRSLNCFRKD****************FDLAR********************VHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSH**
Disordered Region (DISEMBL)
MAYQQSLNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV
Disordered Region (DISPRO)
MAYQQSLNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPS***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAYQQSLNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSNNLITNVHGVGHANFHSIVTCKKAPSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV
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

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	144
359478321	441	PREDICTED: DNA polymerase I-like [Vitis	1.0	0.326	0.5	2e-33
255579460	180	hypothetical protein RCOM_0547690 [Ricin	1.0	0.8	0.480	1e-28
357475547	491	DNA polymerase I [Medicago truncatula] g	0.465	0.136	0.826	2e-24
356502746	444	PREDICTED: DNA polymerase I, thermostabl	0.972	0.315	0.457	5e-24
356519672	436	PREDICTED: DNA polymerase I, thermostabl	0.75	0.247	0.511	2e-23
297816476	454	hypothetical protein ARALYDRAFT_485561 [	0.923	0.292	0.447	3e-23
449453197	461	PREDICTED: DNA polymerase I-like [Cucumi	0.416	0.130	0.822	1e-22
42565846	425	5'-3' exonuclease-like protein [Arabidop	0.465	0.157	0.768	2e-22
145332811	413	5'-3' exonuclease-like protein [Arabidop	0.465	0.162	0.768	2e-22
145332809	448	5'-3' exonuclease-like protein [Arabidop	0.465	0.149	0.768	2e-22

>gi|359478321|ref|XP_002275974.2| PREDICTED: DNA polymerase I-like [Vitis vinifera] gi|296084279|emb|CBI24667.3| unnamed protein product [Vitis vinifera]

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/170 (50%), Positives = 106/170 (62%), Gaps = 26/170 (15%)

Query: 1   MAYQQSLNLHIHSFWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSLSN 60
           MA  +S + HI   W +LNC+R  FS+ Q+ GN    ++R +L    S    KG C+LSN
Sbjct: 1   MACYRSSHHHIRFLWGNLNCWRSSFSRTQKIGNNSCCLQRRNLIHSPSILSRKGCCTLSN 60

Query: 61  NLITNVHGVGHANFHSIVT---------CKKA---------------PSNGRVMLIDGTS 96
           +L +++H V H   +   T         C+ A                SNGRVMLIDGTS
Sbjct: 61  SLDSSIHEVAHTISYGNTTISSKSERKLCQGAFVDSVDHKERKMDISSSNGRVMLIDGTS 120

Query: 97  IIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV 144
           IIYRAYYK+L  LHHG+LSHADGNGDWVLTIF+ALSLI+DVL+FIPSHV 
Sbjct: 121 IIYRAYYKLLAKLHHGYLSHADGNGDWVLTIFAALSLIVDVLDFIPSHVA 170

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579460|ref|XP_002530573.1| hypothetical protein RCOM_0547690 [Ricinus communis] gi|223529872|gb|EEF31803.1| hypothetical protein RCOM_0547690 [Ricinus communis]

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 86/179 (48%), Positives = 101/179 (56%), Gaps = 35/179 (19%)

Query: 1   MAYQQSLNLHIHS-FWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKG----- 54
           MAY QSLNL + S  WR+ N   +   + +R G+ L N+K       SS+   KG     
Sbjct: 1   MAYCQSLNLRVQSSLWRNFNYLGEKLKRARRVGSFLSNLKTLVQIHPSSTLSKKGFYGIS 60

Query: 55  ---------SCSLSNNLITNVHGVGH-----ANFHSIVTCKK-------------APSNG 87
                    +C  S +         H     A F SI   ++             +PSNG
Sbjct: 61  STSSALPQDACVTSRSSTFTSSEELHMPHQGAIFDSIKYEERLVNTTSQSDVANSSPSNG 120

Query: 88  RVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV 144
           R+MLIDGTSIIYRAYYK+L  LHHGHLS ADGNGDWVLTIFSALSLIIDVLEFIPSHVV
Sbjct: 121 RLMLIDGTSIIYRAYYKLLAKLHHGHLSQADGNGDWVLTIFSALSLIIDVLEFIPSHVV 179

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357475547|ref|XP_003608059.1| DNA polymerase I [Medicago truncatula] gi|355509114|gb|AES90256.1| DNA polymerase I [Medicago truncatula]

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 62/69 (89%), Gaps = 2/69 (2%)

Query: 78  VTCKKAPSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDV 135
           VT   A +NGRVMLIDGTS+I+RAYYK+L  LHHGHL+HADGNGDWVLTIFSALS IIDV
Sbjct: 100 VTNADAAANGRVMLIDGTSVIHRAYYKLLAKLHHGHLAHADGNGDWVLTIFSALSFIIDV 159

Query: 136 LEFIPSHVV 144
           LEFIPSHVV
Sbjct: 160 LEFIPSHVV 168

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356502746|ref|XP_003520177.1| PREDICTED: DNA polymerase I, thermostable-like [Glycine max]

 Score =  115 bits (288), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 76/166 (45%), Positives = 94/166 (56%), Gaps = 26/166 (15%)

Query: 5   QSLNLHIHSFWRSLNCFR----KDFSKPQRTGNTLFNIKRFDL-----ARLSSS-----Q 50
           Q L LH HSFWR L   R      F+   +T + L + +   L      R +S       
Sbjct: 8   QFLFLHSHSFWRKLPFPRHVTASGFTCNLQTPSLLLSSRSRALLSKGYCRATSESPGAVP 67

Query: 51  FTKGSCSLSNNLITNVH-GVGHANFHSI---------VTCKKAPSNGRVMLIDGTSIIYR 100
            T  S + S  LI     G+G     ++         +     P NGRVM+IDGTSII+R
Sbjct: 68  ATPRSAAASGTLIPEAGIGIGTGTAQALQSGSAGNAELVTNAEPLNGRVMIIDGTSIIHR 127

Query: 101 AYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV 144
           AYYK+L  LHHGHL+HADGNGDWVL +F+ALSLIIDVL+FIPSHVV
Sbjct: 128 AYYKLLAKLHHGHLTHADGNGDWVLMMFTALSLIIDVLKFIPSHVV 173

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519672|ref|XP_003528494.1| PREDICTED: DNA polymerase I, thermostable-like [Glycine max]

 Score =  113 bits (283), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 67/131 (51%), Positives = 82/131 (62%), Gaps = 23/131 (17%)

Query: 37  NIKRFDLARLSSSQFTKGSCSLSNNLITNVH--------------GVGHA---NFHSIVT 79
           N++   L R S +  +KG CS ++     V               G+G A      S V 
Sbjct: 35  NLRTPWLLRSSRAPLSKGYCSATSESPGAVPATPPTAAATLVPGAGIGTARAMQLGSAVN 94

Query: 80  CKKA----PSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLII 133
            ++     P NGRVM+IDGTSII+RAYYK+L  LHHGHL+HADGNGDWVL +F+ALSLII
Sbjct: 95  AERVTNSDPLNGRVMIIDGTSIIHRAYYKLLAKLHHGHLTHADGNGDWVLMMFTALSLII 154

Query: 134 DVLEFIPSHVV 144
           DVLEFIPSHVV
Sbjct: 155 DVLEFIPSHVV 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297816476|ref|XP_002876121.1| hypothetical protein ARALYDRAFT_485561 [Arabidopsis lyrata subsp. lyrata] gi|297321959|gb|EFH52380.1| hypothetical protein ARALYDRAFT_485561 [Arabidopsis lyrata subsp. lyrata]

 Score =  113 bits (282), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 73/163 (44%), Positives = 96/163 (58%), Gaps = 30/163 (18%)

Query: 6   SLNLHIHS--FWRSLNCFRKDFSKPQRTGNTLFNIKRFDLARLSSSQFTKGSCSL----- 58
           +L+L+ HS   WR+L CF +         ++L +     LAR S+  +   +C+L     
Sbjct: 24  TLHLYHHSRFLWRNL-CFTRRIGNLCNRNSSLISPS---LAR-SAKYYCSSTCNLDAAVS 78

Query: 59  -------SNNLITNVHGVGHANFHSI---------VTCKKAPSNGRVMLIDGTSIIYRAY 102
                  S N++T+          +I         V    A SNGRVMLIDGTSIIYRAY
Sbjct: 79  EISNDAASGNMLTSYKSEDVVAPETIKYPFKSEERVASTAASSNGRVMLIDGTSIIYRAY 138

Query: 103 YKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV 143
           YK+L  L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHV
Sbjct: 139 YKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHV 181

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453197|ref|XP_004144345.1| PREDICTED: DNA polymerase I-like [Cucumis sativus]

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/62 (82%), Positives = 58/62 (93%), Gaps = 2/62 (3%)

Query: 84  PSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPS 141
           P++ RVMLIDGTSII+RAYYK+L  LHHGHLSHADGNGDWVLTIF+ALSLI+DVLE +PS
Sbjct: 128 PADARVMLIDGTSIIFRAYYKLLAKLHHGHLSHADGNGDWVLTIFTALSLIVDVLEIMPS 187

Query: 142 HV 143
           HV
Sbjct: 188 HV 189

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42565846|ref|NP_190773.2| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|145362483|ref|NP_974414.2| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|109946597|gb|ABG48477.1| At3g52050 [Arabidopsis thaliana] gi|332645358|gb|AEE78879.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645359|gb|AEE78880.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/69 (76%), Positives = 60/69 (86%), Gaps = 2/69 (2%)

Query: 78  VTCKKAPSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDV 135
           V    A SNGRVMLIDGTSIIYRAYYK+L  L+HGHL+HADGN DWVLTIFS+LSL+IDV
Sbjct: 85  VASTAASSNGRVMLIDGTSIIYRAYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDV 144

Query: 136 LEFIPSHVV 144
           L+F+PSHV 
Sbjct: 145 LKFLPSHVA 153

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145332811|ref|NP_001078271.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645361|gb|AEE78882.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/69 (76%), Positives = 60/69 (86%), Gaps = 2/69 (2%)

Query: 78  VTCKKAPSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDV 135
           V    A SNGRVMLIDGTSIIYRAYYK+L  L+HGHL+HADGN DWVLTIFS+LSL+IDV
Sbjct: 85  VASTAASSNGRVMLIDGTSIIYRAYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDV 144

Query: 136 LEFIPSHVV 144
           L+F+PSHV 
Sbjct: 145 LKFLPSHVA 153

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145332809|ref|NP_001078270.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645360|gb|AEE78881.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/69 (76%), Positives = 60/69 (86%), Gaps = 2/69 (2%)

Query: 78  VTCKKAPSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDV 135
           V    A SNGRVMLIDGTSIIYRAYYK+L  L+HGHL+HADGN DWVLTIFS+LSL+IDV
Sbjct: 108 VASTAASSNGRVMLIDGTSIIYRAYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDV 167

Query: 136 LEFIPSHVV 144
           L+F+PSHV 
Sbjct: 168 LKFLPSHVA 176

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	144
TAIR|locus:2083775	448	AT3G52050 [Arabidopsis thalian	0.458	0.147	0.779	2.6e-23

TAIR|locus:2083775 AT3G52050 [Arabidopsis thaliana (taxid:3702)]

 Score = 272 (100.8 bits), Expect = 2.6e-23, P = 2.6e-23
 Identities = 53/68 (77%), Positives = 60/68 (88%)

Query:    78 VTCKKAPSNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDV 135
             V    A SNGRVMLIDGTSIIYRAYYK+L  L+HGHL+HADGN DWVLTIFS+LSL+IDV
Sbjct:   108 VASTAASSNGRVMLIDGTSIIYRAYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDV 167

Query:   136 LEFIPSHV 143
             L+F+PSHV
Sbjct:   168 LKFLPSHV 175


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.325   0.137   0.426    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      144       144   0.00091  102 3  11 22  0.38    31
                                                     30  0.48    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  594 (63 KB)
  Total size of DFA:  151 KB (2091 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  13.57u 0.14s 13.71t   Elapsed:  00:00:01
  Total cpu time:  13.57u 0.14s 13.71t   Elapsed:  00:00:01
  Start:  Thu May  9 22:27:39 2013   End:  Thu May  9 22:27:40 2013

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008409 "5'-3' exonuclease activity" evidence=IEA

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	144
cd09859	174	cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuc	4e-06
smart00475	259	smart00475, 53EXOc, 5'-3' exonuclease	6e-06

>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs

 Score = 44.0 bits (105), Expect = 4e-06
 Identities = 18/57 (31%), Positives = 38/57 (66%), Gaps = 6/57 (10%)

Query: 89  VMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVL-EFIPSHVV 144
           ++LIDG+S+++RAYY +      L+++D +G+    ++  L++++ +L E  P+HV 
Sbjct: 1   LLLIDGSSLLFRAYYALP----PLTNSD-DGEPTNAVYGFLNMLLKLLKEEKPTHVA 52

The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 residues in 53EXO PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA/RNA binding. The active site includes a set of conserved acidic residues that are essential for binding divalent metal ions required for nuclease activity. Length = 174

>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease

 Score = 43.7 bits (104), Expect = 6e-06
 Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 13/62 (20%)

Query: 87  GRVMLIDGTSIIYRAYYK---ILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLEFIPSH 142
            +++L+DG+S+ +RAY+    +    G   +   G    +L +           E  P++
Sbjct: 1   KKLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIK---------EEKPTY 51

Query: 143 VV 144
           V 
Sbjct: 52  VA 53

Length = 259

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	144
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	97.51
PRK14976	281	5'-3' exonuclease; Provisional	97.49
smart00475	259	53EXOc 5'-3' exonuclease.	97.43
PRK09482	256	flap endonuclease-like protein; Provisional	97.31
PF02739	169	5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv	97.2
PRK05755	880	DNA polymerase I; Provisional	97.08
PHA00439	286	exonuclease	96.92
TIGR00593	887	pola DNA polymerase I. This family is based on the	96.45
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	95.57
PHA02567	304	rnh RnaseH; Provisional	92.65
PTZ00217	393	flap endonuclease-1; Provisional	90.29
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	88.09
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	81.74

>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes

Probab=97.51  E-value=9.5e-05  Score=58.67  Aligned_cols=51  Identities=27%  Similarity=0.593  Sum_probs=40.8

Q ss_pred             eEEEEeCchHHHHHHHHHHHhcCCccCCCC-CCCeehhHHHHHHHHHHHhhcc-CCCCC
Q 042232           88 RVMLIDGTSIIYRAYYKILLHHGHLSHADG-NGDWVLTIFSALSLIIDVLEFI-PSHVV  144 (144)
Q Consensus        88 rimLiDGtsiiyRaYyKlllhhg~l~hadg-n~DWVLTiF~Als~iid~L~~~-PSH~~  144 (144)
                      ++|||||++++||+||-..      ...+. +|.++-.++..+..++.+++-. |+|++
T Consensus         2 ~~llIDg~~l~yr~~~a~~------~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~   54 (240)
T cd00008           2 RLLLIDGSSLAYRAYFALP------PLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVA   54 (240)
T ss_pred             cEEEEEChHHHHHHHHCCC------CcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEE
Confidence            6999999999999999752      11222 7888889999999999999754 98864

They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.

>PRK14976 5'-3' exonuclease; Provisional

Probab=97.49  E-value=0.0001  Score=60.48  Aligned_cols=56  Identities=32%  Similarity=0.601  Sum_probs=38.8

Q ss_pred             CeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232           87 GRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV  144 (144)
Q Consensus        87 grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~  144 (144)
                      .+++||||++++|||||..+-+-..+...+|+-..  .++.-+..++.+++ +.|+|++
T Consensus         3 ~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~--a~~gf~~~l~~ll~~~~p~~~~   59 (281)
T PRK14976          3 KKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTN--AIHTFLTMIFKILKKLNPSYIL   59 (281)
T ss_pred             CcEEEEeCcHHHHHHHHccCccCCCccCCCCCCch--HHHHHHHHHHHHHHhcCCCEEE
Confidence            47999999999999999975111224444555444  45666777888885 5798864

>smart00475 53EXOc 5'-3' exonuclease

Probab=97.43  E-value=0.00017  Score=58.59  Aligned_cols=51  Identities=24%  Similarity=0.611  Sum_probs=37.5

Q ss_pred             eEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232           88 RVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV  144 (144)
Q Consensus        88 rimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~  144 (144)
                      +++||||++++|||||-.-    .+...+  |..+=.++.-+..++.+++ +.|+|++
T Consensus         2 ~lllIDg~~~i~R~~~a~~----~l~~~~--G~~t~a~~g~~~~l~~l~~~~~p~~~~   53 (259)
T smart00475        2 KLLLVDGSSLAFRAYFALP----PLKNSK--GEPTNAVYGFLRMLLKLIKEEKPTYVA   53 (259)
T ss_pred             cEEEEeCcHHHHHHHHCCC----cccCCC--CCcccHHHHHHHHHHHHHHHcCCCeEE
Confidence            5899999999999999751    244344  4455566777778888886 5699874

>PRK09482 flap endonuclease-like protein; Provisional

Probab=97.31  E-value=0.00029  Score=58.07  Aligned_cols=47  Identities=15%  Similarity=0.217  Sum_probs=35.2

Q ss_pred             eEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHh-hccCCCCC
Q 042232           88 RVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVL-EFIPSHVV  144 (144)
Q Consensus        88 rimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L-~~~PSH~~  144 (144)
                      +++||||++++||+||-.       +..+|.   +=.|+.-+..++.++ ++.|+|++
T Consensus         4 ~llLiDg~~l~~R~~~a~-------~~~~g~---t~av~gf~~~l~~ll~~~~p~~i~   51 (256)
T PRK09482          4 HLLIIDALNLIRRIHAVQ-------PSPNDI---NACVETCQHALDKLIRHSQPTHAV   51 (256)
T ss_pred             eEEEEeCcHHHHHHHhCC-------CCCCCc---chHHHHHHHHHHHHHHHcCCCEEE
Confidence            599999999999999862       223343   555777778888888 56699974

>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities

Probab=97.20  E-value=0.00014  Score=55.54  Aligned_cols=52  Identities=31%  Similarity=0.683  Sum_probs=36.5

Q ss_pred             eEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCC
Q 042232           88 RVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHV  143 (144)
Q Consensus        88 rimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~  143 (144)
                      +++||||++++|||||-.-.  .  .-...+|.++=.|+..+..+..+++ +.|+|+
T Consensus         2 ~llLIDg~~l~~Ra~~a~~~--~--~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~   54 (169)
T PF02739_consen    2 KLLLIDGNSLLFRAYYALPK--D--PLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYV   54 (169)
T ss_dssp             EEEEEEHHHHHHHCCCCCTT--S--T-BETTSEB-HHHHHHHHHHHHHHHHTTEEEE
T ss_pred             eEEEEechHHHHHHHHhhcc--C--CCcCCCCCChHHHHHHHHHHHHHHHHcCCceE
Confidence            79999999999999974321  1  3345567787788887777777665 446775

The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....

>PRK05755 DNA polymerase I; Provisional

Probab=97.08  E-value=0.00069  Score=62.47  Aligned_cols=53  Identities=30%  Similarity=0.624  Sum_probs=38.5

Q ss_pred             CeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHh-hccCCCCC
Q 042232           87 GRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVL-EFIPSHVV  144 (144)
Q Consensus        87 grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L-~~~PSH~~  144 (144)
                      .++|||||++++|||||-.  . -.+..  .+|..+=.|+..+..++.++ ++.|+|++
T Consensus         2 ~~~~liDg~~~~~r~~~a~--~-~~~~~--~~g~~~~a~~g~~~~l~~~~~~~~p~~~~   55 (880)
T PRK05755          2 KTLLLIDGSSLLFRAFYAL--L-PTLRN--SDGLPTGAVYGFLNMLLKLLKEEKPTHVA   55 (880)
T ss_pred             CeEEEEeCcHHHHHHHHCC--C-CcccC--CCCCcccHHHHHHHHHHHHHHhcCCCEEE
Confidence            3699999999999999975  1 12233  34555666777778888888 46699964

>PHA00439 exonuclease

Probab=96.92  E-value=0.0013  Score=55.76  Aligned_cols=59  Identities=15%  Similarity=0.125  Sum_probs=44.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHH--HhcCCccCCCCCCCeehhHHHHHHHHHHHhh----ccCCCCC
Q 042232           85 SNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLE----FIPSHVV  144 (144)
Q Consensus        85 s~grimLiDGtsiiyRaYyKll--lhhg~l~hadgn~DWVLTiF~Als~iid~L~----~~PSH~~  144 (144)
                      ++-.++||||.+++|||||-+-  ..-+. .-...+|+.+=.++.-+..++.+++    +.|+|++
T Consensus         4 ~~~~llLIDG~~l~fRA~~A~~~~~~~~~-~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~   68 (286)
T PHA00439          4 SDKGVLVMDGDYLVFQAMAAAEVETDWGE-DIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIV   68 (286)
T ss_pred             CCCcEEEEeCcHHHHHHHHccCcccccCC-CCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEE
Confidence            3678999999999999999863  11111 1125788888888888888888885    4899874

>TIGR00593 pola DNA polymerase I

Probab=96.45  E-value=0.003  Score=59.62  Aligned_cols=52  Identities=25%  Similarity=0.578  Sum_probs=39.7

Q ss_pred             EEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232           89 VMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV  144 (144)
Q Consensus        89 imLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~  144 (144)
                      ++||||++++|||||-+- .. .+.  .++|..+=.|+.-+..++.+++ +.|+|++
T Consensus         1 l~lIDg~~l~~Ra~~a~~-~~-~l~--~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~   53 (887)
T TIGR00593         1 LLLIDGHSLAFRAYFALK-NK-PLT--NSKGEPTNAVYGFTKMLLKLLKEEKPTYVA   53 (887)
T ss_pred             CEEEeCcHHHHHHHHCCC-cc-cCc--CCCCCEecHHHHHHHHHHHHHHhcCCCEEE
Confidence            589999999999999751 00 132  4567778888888999999995 6799964

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

>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

Probab=95.57  E-value=0.026  Score=45.98  Aligned_cols=54  Identities=24%  Similarity=0.505  Sum_probs=36.6

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhhccC-CCC
Q 042232           85 SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIP-SHV  143 (144)
Q Consensus        85 s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~~~P-SH~  143 (144)
                      ..|++++|||.+.+||+||-+-..   +..-+|.-.|  +++.-...+..++...+ .|.
T Consensus         9 ~~~~l~~IDg~~~lyr~~~a~~~~---~~~~~g~~~~--~~~~~~~~l~~~~~~~~~~~~   63 (310)
T COG0258           9 KSGKLLLIDGSSLLYRALHALPQP---LGNPLGDPTG--AVSGFLGMLYRLIRLLEPTHP   63 (310)
T ss_pred             ccCcEEEEechHHHHHHHHhcchh---cCCCCCCCcc--HHHHHHHHHHHHHHhcCCCcE
Confidence            457999999999999999988644   4445555555  55555555555554433 554

>PHA02567 rnh RnaseH; Provisional

Probab=92.65  E-value=0.058  Score=46.40  Aligned_cols=52  Identities=17%  Similarity=0.160  Sum_probs=30.8

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcCCccCCCC-CCCeeh-hHHHHHHHHHHHhhccCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADG-NGDWVL-TIFSALSLIIDVLEFIPSHV  143 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadg-n~DWVL-TiF~Als~iid~L~~~PSH~  143 (144)
                      +--++||||++++|||||.-      ++..+| +..=+. .|+..|--+++...-.|.|+
T Consensus        13 ~~~~~LiDgs~i~~~~~~a~------l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i   66 (304)
T PHA02567         13 KEGVNLIDFSQIIIATIMAN------FKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEI   66 (304)
T ss_pred             CCCEEEEehHHHHHHHHHhh------CCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeE
Confidence            56799999999999999984      333332 222221 25555555555433345554

>PTZ00217 flap endonuclease-1; Provisional

Probab=90.29  E-value=0.46  Score=41.25  Aligned_cols=54  Identities=28%  Similarity=0.363  Sum_probs=37.3

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHH--hcCCccCCCCCCCeehhHHHHHHHHHHHhhc--cC
Q 042232           85 SNGRVMLIDGTSIIYRAYYKILL--HHGHLSHADGNGDWVLTIFSALSLIIDVLEF--IP  140 (144)
Q Consensus        85 s~grimLiDGtsiiyRaYyKlll--hhg~l~hadgn~DWVLTiF~Als~iid~L~~--~P  140 (144)
                      -.|+.++|||.+.|||+||.+-.  +++.|...+|+-  .-.++..+..++.+|+.  .|
T Consensus        26 l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~--t~~l~g~~~r~~~Ll~~gikP   83 (393)
T PTZ00217         26 YFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEV--TSHISGLFNRTIRLLEAGIKP   83 (393)
T ss_pred             hCCcEEEEeHHHHHHHHHHHcccccccccchhccCCc--cHHHHHHHHHHHHHHHCCCCE
Confidence            35899999999999999998642  334455444443  34566667777777763  55

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=88.09  E-value=0.65  Score=39.13  Aligned_cols=50  Identities=24%  Similarity=0.350  Sum_probs=32.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCe-ehhHHHHHHHHHHHhhc
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDW-VLTIFSALSLIIDVLEF  138 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DW-VLTiF~Als~iid~L~~  138 (144)
                      .|++++|||.+.+||+||.+-..+| .+..++|+-.. +..+|   .-++.+++.
T Consensus        20 ~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~---~~~~~ll~~   71 (338)
T TIGR03674        20 SGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLF---YRTINLLEN   71 (338)
T ss_pred             CCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHH---HHHHHHHHC
Confidence            5889999999999999998643333 55556666543 33333   455555554

Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA

>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases

Probab=81.74  E-value=3.2  Score=33.81  Aligned_cols=21  Identities=19%  Similarity=0.309  Sum_probs=18.8

Q ss_pred             CCeEEEEeCchHHHHHHHHHH
Q 042232           86 NGRVMLIDGTSIIYRAYYKIL  106 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKll  106 (144)
                      +|+.++|||.+.+||+||..-
T Consensus        23 ~gk~laID~~~~l~r~~~a~~   43 (316)
T cd00128          23 RGKKVAIDASIWLYQFLKACR   43 (316)
T ss_pred             CCcEEEecHHHHHHHHHHHhh
Confidence            688999999999999999863

XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	144
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	4e-04
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	6e-04

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Length = 832

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 12/63 (19%)

Query: 85  SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADG---NGDWVLTIFSALSLIIDVLEFIPS 141
             GRV+L+DG  + YR ++ +      L+ + G          ++     ++  L+    
Sbjct: 10  PKGRVLLVDGHHLAYRTFHAL----KGLTTSRGEPVQA-----VYGFAKSLLKALKEDGD 60

Query: 142 HVV 144
            V+
Sbjct: 61  AVI 63

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Length = 290

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 6/23 (26%), Positives = 14/23 (60%)

Query: 81  KKAPSNGRVMLIDGTSIIYRAYY 103
            +  S   +M++DGT++ +R  +
Sbjct: 13  AEMASRRNLMIVDGTNLGFRFKH 35

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	144
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	97.3
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	96.2
3h7i_A	305	Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu	95.47
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	95.23
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	94.47
1rxw_A	336	Flap structure-specific endonuclease; helical clam	94.18
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	93.26
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	92.42
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	91.47
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	89.42

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A

Probab=97.30  E-value=9.9e-05  Score=60.16  Aligned_cols=45  Identities=18%  Similarity=0.259  Sum_probs=32.1

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV  144 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~  144 (144)
                      ++|++||||.+++|||||          ..+|.-    .++.-+..++.+++ +.|+|++
T Consensus        18 ~~~lllIDg~~llyRa~~----------~~~G~p----av~Gf~~~l~~ll~~~~p~~~v   63 (290)
T 1exn_A           18 RRNLMIVDGTNLGFRFKH----------NNSKKP----FASSYVSTIQSLAKSYSARTTI   63 (290)
T ss_dssp             -CEEEEEEHHHHHHHHHH----------HCSSSC----CHHHHHHHHHHHHHHTTEEEEE
T ss_pred             CCCEEEEECcHHHHHHHh----------CCCCch----HHHHHHHHHHHHHHHcCCCeEE
Confidence            789999999999999998          234443    55666666666665 4588863

>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A*

Probab=96.20  E-value=0.0017  Score=53.05  Aligned_cols=57  Identities=21%  Similarity=0.274  Sum_probs=38.5

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh--ccCCCC
Q 042232           85 SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHV  143 (144)
Q Consensus        85 s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~--~~PSH~  143 (144)
                      -.|++++|||++.+||+||.+-.....|...  +|--.-.++.-+..++.+|+  ..|.||
T Consensus        25 l~gk~l~IDgs~~lyr~~~a~~~~~~~l~~~--~G~~T~al~g~~~~~~~ll~~~i~P~~V   83 (341)
T 3q8k_A           25 YFGRKVAIDASMSIYQFLIAVRQGGDVLQNE--EGETTSHLMGMFYRTIRMMENGIKPVYV   83 (341)
T ss_dssp             GTTCEEEEEHHHHHHHHHHHCEETTEECBCT--TSCBCHHHHHHHHHHHHHHTTTCEEEEE
T ss_pred             hCCCEEEEecHHHHHHHHHccccccCCCCCC--CCCCchHHHHHHHHHHHHHHCCCCceEE
Confidence            3589999999999999999743111234433  44455566666667777776  677764

>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A

Probab=95.47  E-value=0.0091  Score=49.93  Aligned_cols=51  Identities=14%  Similarity=0.006  Sum_probs=31.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHH-HHHHHHHHhhc----cCCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFS-ALSLIIDVLEF----IPSHVV  144 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~-Als~iid~L~~----~PSH~~  144 (144)
                      +-++|||||+|++||||+.-      ++-.+|  -=+=.|+. -+.++..+++-    .|+|++
T Consensus        12 ~~~llLIDgssl~~ra~~~~------f~~~~g--~~tnav~ggf~~~L~~ll~~~k~~~P~~ia   67 (305)
T 3h7i_A           12 KEGICLIDFSQIALSTALVN------FPDKEK--INLSMVRHLILNSIKFNVKKAKTLGYTKIV   67 (305)
T ss_dssp             SCCEEEEEHHHHHHHHHHHH------SCSSSC--CCHHHHHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCCEEEEeccHHHHHHHHHh------cCCCCC--cchHHHHHHHHHHHHHHHHhhhccCCCEEE
Confidence            44899999999999998532      333332  22333433 44555555544    899874

>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2

Probab=95.23  E-value=0.0045  Score=50.76  Aligned_cols=56  Identities=21%  Similarity=0.290  Sum_probs=33.0

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh--ccCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHV  143 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~--~~PSH~  143 (144)
                      .|++++|||++.+||+||.+--....|...  .|...-.++.-+..++.+|+  ..|.||
T Consensus        26 ~g~~l~IDg~~~lyr~~~a~~~~~~~l~~~--~G~~t~~l~g~~~~~~~ll~~~i~P~~V   83 (379)
T 1ul1_X           26 FGRKVAIDASMSIYQFLIAVRQGGDVLQNE--EGETTSHLMGMFYRTIRMMENGIKPVYV   83 (379)
T ss_dssp             TTCCEEEEHHHHHHHHHSCC---------------CCHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCEEEEEchHHHHHHHHhCCCcccccCcC--CCCCchHHHHHHHHHHHHHHCCCCeEEE
Confidence            578999999999999999652111123333  34444456666677777776  467664

>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A

Probab=94.47  E-value=0.031  Score=44.74  Aligned_cols=55  Identities=20%  Similarity=0.269  Sum_probs=34.3

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHHhhccCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV  143 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~L~~~PSH~  143 (144)
                      +|++++|||.+.+||+||.+=...| .|...+|.  -.-.++.-+..++.+++ .|.|.
T Consensus        20 ~g~~l~ID~~~~l~r~~~a~~~~~~~~l~~~~G~--~t~~l~g~~~~l~~ll~-~~i~p   75 (340)
T 1b43_A           20 YGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGR--ITSHLSGLFYRTINLME-AGIKP   75 (340)
T ss_dssp             TTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSC--BCHHHHHHHHHHHHHHH-TTCEE
T ss_pred             CCCEEEEEhHHHHHHHHHHhccccCCccccccCC--chHHHHHHHHHHHHHHh-CCCEE
Confidence            4789999999999999996511122 23333333  33455555556667776 56553

>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A

Probab=94.18  E-value=0.049  Score=43.51  Aligned_cols=50  Identities=18%  Similarity=0.295  Sum_probs=32.7

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHHhh
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLE  137 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~L~  137 (144)
                      +|++++|||.+.+||+||.+=...| .+..  ..|...-.++.-+..++.+++
T Consensus        20 ~~~~l~IDg~~~l~r~~~a~~~~~~~~l~~--~~G~~t~a~~g~~~~l~~ll~   70 (336)
T 1rxw_A           20 SGKKIAVDAFNTLYQFISIIRQPDGTPLKD--SQGRITSHLSGILYRVSNMVE   70 (336)
T ss_dssp             TTCEEEEEHHHHHHHHHHHSBCTTSCBCBC--TTSCBCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEhHHHHHHHHHhhccccCCcccc--cCCCccHHHHHHHHHHHHHHH
Confidence            4689999999999999996411112 2333  344455566666666666665

>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}

Probab=93.26  E-value=0.12  Score=41.65  Aligned_cols=50  Identities=26%  Similarity=0.377  Sum_probs=31.8

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHHhh
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDVLE  137 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~L~  137 (144)
                      +|++++|||.+.+||+||-+=...| .|.  +..|...-.++.-+..++.+++
T Consensus        17 ~~~~l~IDg~~~l~r~~~a~~~~~g~~l~--~~~G~~t~al~g~~~~~~~ll~   67 (346)
T 2izo_A           17 KGKRVSIDGYNALYQFLAAIRQPDGTPLM--DSQGRVTSHLSGLFYRTINILE   67 (346)
T ss_dssp             TTEEEEEEHHHHHHHHHHSCCCC---CCB--CSSSCBCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEhHHHHHHHHHhcccccccccc--ccCCCccHHHHHHHHHHHHHHH
Confidence            4789999999999999984310011 132  3345555566666666666765

>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A

Probab=92.42  E-value=0.14  Score=40.73  Aligned_cols=48  Identities=23%  Similarity=0.384  Sum_probs=28.5

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCeehhHHHHHHHHHHH
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDWVLTIFSALSLIIDV  135 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DWVLTiF~Als~iid~  135 (144)
                      +|++++|||.+.+||+||.+-...| .+...+|  .-.-.++.-+..++.+
T Consensus        20 ~~~~l~IDg~~~l~r~~~a~~~~~~~~l~~~~G--~~t~~l~g~~~~l~~l   68 (326)
T 1a76_A           20 KGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKG--EITSAYNGVFYKTIHL   68 (326)
T ss_dssp             TTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTS--CBCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEhHHHHHHHHHhhccccccccccccC--CccHHHHHHHHHHHHH
Confidence            5789999999999999996511112 2333333  3333444444444444

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

Probab=91.47  E-value=0.029  Score=51.03  Aligned_cols=53  Identities=25%  Similarity=0.473  Sum_probs=34.9

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCCCC
Q 042232           85 SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV  143 (144)
Q Consensus        85 s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PSH~  143 (144)
                      -+|+++||||++++|||||-+-    .|...  +|..+=.|+.-+..++.+|+-...|+
T Consensus        10 ~~~~~llIDg~~~l~ra~~a~~----~l~~~--~G~~t~av~gf~~~l~~ll~~~~~~~   62 (832)
T 1bgx_T           10 PKGRVLLVDGHHLAYRTFHALK----GLTTS--RGEPVQAVYGFAKSLLKALKEDGDAV   62 (832)
T ss_dssp             CCTTSCCCCCSTHHHHTTSSCT----TCBCS--SSCBCSSSTTHHHHHHHGGGTCCSCC
T ss_pred             hCCCEEEEEChHHHHHHHhcCC----ccccC--CCcEehHHHHHHHHHHHHHHHcCCeE
Confidence            3568999999999999998651    23333  34444345555667777776644554

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}

Probab=89.42  E-value=0.25  Score=40.75  Aligned_cols=54  Identities=20%  Similarity=0.421  Sum_probs=32.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHHh-cC-CccCCCCCCCeehhHHHHHHHHHHHhh--ccCC
Q 042232           85 SNGRVMLIDGTSIIYRAYYKILLH-HG-HLSHADGNGDWVLTIFSALSLIIDVLE--FIPS  141 (144)
Q Consensus        85 s~grimLiDGtsiiyRaYyKlllh-hg-~l~hadgn~DWVLTiF~Als~iid~L~--~~PS  141 (144)
                      -+|++++|||.+.+||+|+ .+-+ .| .|...+|.  =.-.++.-+..++.+|+  ..|.
T Consensus        33 l~gk~l~IDg~~~l~r~~~-~~~~~~g~~l~~~~G~--~T~al~gf~~r~~~ll~~~i~Pv   90 (363)
T 3ory_A           33 LHGKIIVIDGYNALYQFLA-AIRQPDGTPLMDNNGR--ITSHLSGLFYRTINIVEAGIKPV   90 (363)
T ss_dssp             GTTCEEEEEHHHHHHHHHH-HCBCTTSCBCBCTTSC--BCHHHHHHHHHHHHHHHTTCEEE
T ss_pred             hCCCEEEEehHHHHHHHHH-hhhccCCCccCCCCCC--CccHHHHHHHHHHHHHHcCCCcE
Confidence            3589999999999999554 3321 22 45444443  33345555555555554  4554

---

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	144
d1cmwa2	164	c.120.1.2 (A:10-173) 5' to 3' exonuclease domain o	1e-04

>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Length = 164

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

 Score = 37.5 bits (86), Expect = 1e-04
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 6/59 (10%)

Query: 86  NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVV 144
            GRV+L+DG  + YR +      H         G+ V  ++     ++  L+     V+
Sbjct: 2   KGRVLLVDGHHLAYRTF------HALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVI 54

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	144
d1cmwa2	164	5' to 3' exonuclease domain of DNA polymerase Taq	98.36
d1tfra2	169	T4 RNase H {Bacteriophage T4 [TaxId: 10665]}	96.78
d1xo1a2	167	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	94.4

>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=98.36  E-value=1.7e-07  Score=66.75  Aligned_cols=52  Identities=23%  Similarity=0.445  Sum_probs=45.2

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV  143 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PSH~  143 (144)
                      |+|+|||||++++||+||..      -+.-..+|+++-+|+..+..+..++++.|+|+
T Consensus         2 ~~~~lLIDg~~l~~R~~~a~------~~~~~~~g~~~~~i~gf~~~l~~~~~~~~~~~   53 (164)
T d1cmwa2           2 KGRVLLVDGHHLAYRTFHAL------KGLTTSRGEPVQAVYGFAKSLLKALKEDGDAV   53 (164)
T ss_dssp             CEEEEEEETTHHHHHHHTSS------TTCBCTTSCBCHHHHHHHHHHHHHHHHCCSEE
T ss_pred             CCeEEEEeChHHHHHHHHcC------CcccCCCCCeeHHHHHHHHHHHHHHhcCCceE
Confidence            78999999999999999843      23446889999999999999999999999875

>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T4 RNase H
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.78  E-value=0.0002  Score=51.86  Aligned_cols=54  Identities=15%  Similarity=0.113  Sum_probs=34.5

Q ss_pred             CCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCee-hhHHHHHHHHHHHhh-ccCCCCC
Q 042232           86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWV-LTIFSALSLIIDVLE-FIPSHVV  144 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWV-LTiF~Als~iid~L~-~~PSH~~  144 (144)
                      |+++|||||++++||+||-.   ++.-...  +.+=+ -.++.+|..++..++ +.|+|++
T Consensus         1 k~~~~liD~s~~~~~~~~~~---~~~~~~~--~~~~~~h~~lnsi~~~~k~~~~~~p~~vi   56 (169)
T d1tfra2           1 KEGICLIDFSQIALSTALVN---FPDKEKI--NLSMVRHLILNSIKFNVKKAKTLGYTKIV   56 (169)
T ss_dssp             CCEEEEEEHHHHHHHHHHHH---SCTTSCC--CHHHHHHHHHHHHHHHHHHHHHTTEEEEE
T ss_pred             CCCEEEEechHHHHHHHHHh---ccCCCCC--ChhHHHHHHHHHHHHHHHHhhhcCCCeEE
Confidence            67999999999999999743   3332222  11112 125567777777665 6687763

>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=94.40  E-value=0.0032  Score=44.51  Aligned_cols=19  Identities=26%  Similarity=0.503  Sum_probs=14.5

Q ss_pred             CCeEEEEeCchHHHHHHHH
Q 042232           86 NGRVMLIDGTSIIYRAYYK  104 (144)
Q Consensus        86 ~grimLiDGtsiiyRaYyK  104 (144)
                      +-++|||||++++||+||.
T Consensus         1 k~~~lliDg~~l~~R~~~~   19 (167)
T d1xo1a2           1 RRNLMIVDGTNLGFRFKHN   19 (167)
T ss_dssp             CCEEEEEEHHHHHTTC---
T ss_pred             CCeEEEEcChHHHHHHHHc
Confidence            3579999999999999984