Psyllid ID: psy8633

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------

MIIESCPDVYFTGNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYATPVFNPRTTLSNNENKYVNHSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVEDLTEER

ccccccHHHHHHHHHHcccHHHHHHHccccccEEEEEccccccccEEEEEEEEEEccccccccHHHHHHccccccccccccccccccEEEEEcccccEEEEEccccccEEEEEEEEEEccccccccEEEEEEccccccccccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccEEcccccEEEEccEEEEEEccccHHHHHHccccccHHHHHHHHHHHcccccccccccccccccccccEEEcccccEEEEcccccccEEEEEEccccEEEEEEccccccccEEEEEEcccccEEEEEEccccccc

ccccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEcccccEEEEEEEEEccccccccHHHHHHHHcccccccccccccccccEEEEEccccEEEEEEccccccEEEEEEEEEEccEcccccEEEEEEccccccccccccHHHHHHHHHHHcccccEEccccccccccccccccccHHHcccHccccccccccccEEEEEccEEEEEcccccHHHHHHHcccccHHHHHHHHHHHHccccccccccccccccccccEEEccccEEEEEEccccccEEEEEcccccEEEEEEEcccccccEEEEEEccccEEEEEEEccccccc

miiescpdvyftgnqskfetktieiekgksvsvlklsdlnetdteeCVIIGTlfkhqqlkpNILKEISEelklvpqpqhthfvsdsdeliledelqriplhgnidihnQVTGVVVAIkgtpvgngkfkvsdvcyatpvfnprttlsnnenkyvnhssievdlmpgefdpanttlpqqplhpclfpeaskystfhpvtnpyifemegkllmgtsgqpvsdiakfsnlsnpldILEYTlrcghvaptapdtlacypfydndpmiiescpdvyftgnqskfetktieiekdknvrlisvpdffssRTVAILNLSTLECHSLVVEDLTEER

miiescpdvyftgnqskfetktieiekgksvsvlklsdlnetdTEECVIIGtlfkhqqlkpNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYATPvfnprttlsnnenKYVNHSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQSKFEtktieiekdknvrlisvpDFFSSRTVAILNLstlechslvvedlteer

*****CPDVYFTGNQSKFETKTIEIEKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYATPVFNPRTTLSNN*NKYVNHSSIEVDL***************PLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVE******

**IESCPDVYFTGNQSKFETKTI*IEKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEEL***********VSDSDELILEDELQRIPLHGNIDIHNQVTGVVVA*********KFKVSDVCYATPVFNPRTTLSNNENKYVNHSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVEDL****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		327	2.2.26 [Sep-21-2011]
O35654		469	DNA polymerase delta subu	yes	N/A	0.519	0.362	0.523	1e-49
P49005		469	DNA polymerase delta subu	yes	N/A	0.516	0.360	0.520	2e-49
Q6AXY4		469	DNA polymerase delta subu	yes	N/A	0.519	0.362	0.517	2e-49
P49004		469	DNA polymerase delta subu	yes	N/A	0.516	0.360	0.514	4e-49
O93610		463	DNA polymerase delta subu	N/A	N/A	0.477	0.336	0.521	7e-49
Q9LRE5		429	DNA polymerase delta smal	yes	N/A	0.489	0.372	0.496	4e-45
O48520		440	DNA polymerase delta smal	yes	N/A	0.446	0.331	0.496	5e-45
Q9W088		431	DNA polymerase delta smal	yes	N/A	0.489	0.371	0.5	1e-44
P87324		462	DNA polymerase subunit de	yes	N/A	0.574	0.406	0.397	4e-34
P46957		487	DNA polymerase delta smal	yes	N/A	0.501	0.336	0.358	3e-30

>sp\|O35654\|DPOD2_MOUSE DNA polymerase delta subunit 2 OS=Mus musculus GN=Pold2 PE=2 SV=2	Back alignment and function desciption

 Score =  197 bits (500), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 90/172 (52%), Positives = 119/172 (69%)

Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215
           +S+ VD+MPGEFDP N TLPQQPLHPC+FP A+ YST   VTNPY   ++G   +GTSGQ
Sbjct: 288 ASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQ 347

Query: 216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275
            VSDI ++S++ + L+ILE+TLR  H++PTAPDTL CYPFY  DP I   CP VYF GN 
Sbjct: 348 NVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNT 407

Query: 276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVEDLTEER 327
             F +K I   +D+ V L++VPDF S++T  ++NL +L C  +       E+
Sbjct: 408 PSFGSKIIRGPEDQVVLLVAVPDFSSTQTACLVNLRSLACQPISFAGFGAEQ 459

The function of the small subunit is not yet clear.
Mus musculus (taxid: 10090)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7

>sp\|P49005\|DPOD2_HUMAN DNA polymerase delta subunit 2 OS=Homo sapiens GN=POLD2 PE=1 SV=1	Back alignment and function description

>sp\|Q6AXY4\|DPOD2_RAT DNA polymerase delta subunit 2 OS=Rattus norvegicus GN=Pold2 PE=1 SV=1	Back alignment and function description

>sp\|P49004\|DPOD2_BOVIN DNA polymerase delta subunit 2 OS=Bos taurus GN=POLD2 PE=1 SV=2	Back alignment and function description

>sp\|O93610\|DPOD2_XENLA DNA polymerase delta subunit 2 OS=Xenopus laevis GN=pold2 PE=2 SV=1	Back alignment and function description

>sp\|Q9LRE5\|DPOD2_ORYSJ DNA polymerase delta small subunit OS=Oryza sativa subsp. japonica GN=POLD2 PE=2 SV=1	Back alignment and function description

>sp\|O48520\|DPOD2_ARATH DNA polymerase delta small subunit OS=Arabidopsis thaliana GN=POLD2 PE=2 SV=2	Back alignment and function description

>sp\|Q9W088\|DPOD2_DROME DNA polymerase delta small subunit OS=Drosophila melanogaster GN=CG12018 PE=2 SV=1	Back alignment and function description

>sp\|P87324\|DPOD2_SCHPO DNA polymerase subunit delta-2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cdc1 PE=1 SV=1	Back alignment and function description

>sp\|P46957\|DPOD2_YEAST DNA polymerase delta small subunit OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=POL31 PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		327
242023263		328	DNA polymerase delta small subunit, puta	0.825	0.823	0.432	3e-65
23306120		404	Putataive DNA polymerase delta small sub	0.837	0.678	0.363	4e-52
405975321		462	DNA polymerase delta subunit 2 [Crassost	0.477	0.337	0.6	2e-51
346471337		444	hypothetical protein [Amblyomma maculatu	0.498	0.367	0.551	7e-50
149557343		471	PREDICTED: DNA polymerase delta subunit	0.516	0.358	0.532	2e-49
395850111		543	PREDICTED: DNA polymerase delta subunit	0.486	0.292	0.552	3e-49
390343504		445	PREDICTED: DNA polymerase delta subunit	0.495	0.364	0.536	3e-49
260824487		449	hypothetical protein BRAFLDRAFT_68004 [B	0.516	0.376	0.520	1e-48
395506992		537	PREDICTED: DNA polymerase delta subunit	0.516	0.314	0.526	1e-48
444517803		469	DNA polymerase delta subunit 2 [Tupaia c	0.516	0.360	0.526	3e-48

>gi\|242023263\|ref\|XP_002432055.1\| DNA polymerase delta small subunit, putative [Pediculus humanus corporis] gi\|212517413\|gb\|EEB19317.1\| DNA polymerase delta small subunit, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

 Score =  254 bits (649), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 135/312 (43%), Positives = 188/312 (60%), Gaps = 42/312 (13%)

Query: 11  FTGNQSKFETKTIEI---EKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEI 67
           + G     + +TI+    + G  + + KLS+L +   E+C++IGTLFKHQ+LKP++LKEI
Sbjct: 53  YAGRLKIMKQRTIQACSAKWGSQIPIRKLSELADESKEKCIVIGTLFKHQELKPSVLKEI 112

Query: 68  SEELKLVPQPQHTHFVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKF 127
           SEE ++ PQP  + F+S++D+LILEDE+QRI L   ++   Q+  ++  +  T       
Sbjct: 113 SEEHQITPQPVLSKFISENDQLILEDEMQRISL-DTLNAVKQLDEILSELAKT------- 164

Query: 128 KVSDVCYATPVFNPRTTLSNNENKYVNHSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEA 187
                                         + VD+MPG FDP+N  +PQQP + CLFP A
Sbjct: 165 ------------------------------VHVDVMPGGFDPSNYLMPQQPFYKCLFPNA 194

Query: 188 SKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDILEYTLRCGHVAPTAP 247
           SKY++F  VTNPY   +EG  ++GTSGQP+ DI   S+ +N +DILE TL+ GH+AP+AP
Sbjct: 195 SKYNSFQCVTNPYECTIEGIRILGTSGQPIDDIKSLSDFNNSIDILENTLKWGHLAPSAP 254

Query: 248 DTLACYPFYDNDPMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAI 307
           DT ACYP+YD DP II   P VYF GNQ K+ TK I +      RLIS+P F  ++T  +
Sbjct: 255 DTQACYPYYDEDPFIITEQPHVYFVGNQDKYSTKVINLN-GHFTRLISLPTFHDTQTCIL 313

Query: 308 LNLSTLECHSLV 319
           LNL TLE   LV
Sbjct: 314 LNLKTLESVPLV 325

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|23306120\|gb\|AAN17387.1\| Putataive DNA polymerase delta small subunit [Oryza sativa Japonica Group]	Back alignment and taxonomy information

>gi\|405975321\|gb\|EKC39895.1\| DNA polymerase delta subunit 2 [Crassostrea gigas]	Back alignment and taxonomy information

>gi\|346471337\|gb\|AEO35513.1\| hypothetical protein [Amblyomma maculatum]	Back alignment and taxonomy information

>gi\|149557343\|ref\|XP_001520117.1\| PREDICTED: DNA polymerase delta subunit 2-like [Ornithorhynchus anatinus]	Back alignment and taxonomy information

>gi\|395850111\|ref\|XP_003797642.1\| PREDICTED: DNA polymerase delta subunit 2 [Otolemur garnettii]	Back alignment and taxonomy information

>gi\|390343504\|ref\|XP_782368.2\| PREDICTED: DNA polymerase delta subunit 2-like [Strongylocentrotus purpuratus]	Back alignment and taxonomy information

>gi\|260824487\|ref\|XP_002607199.1\| hypothetical protein BRAFLDRAFT_68004 [Branchiostoma floridae] gi\|229292545\|gb\|EEN63209.1\| hypothetical protein BRAFLDRAFT_68004 [Branchiostoma floridae]	Back alignment and taxonomy information

>gi\|395506992\|ref\|XP_003757812.1\| PREDICTED: DNA polymerase delta subunit 2 [Sarcophilus harrisii]	Back alignment and taxonomy information

>gi\|444517803\|gb\|ELV11799.1\| DNA polymerase delta subunit 2 [Tupaia chinensis]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		327
ZFIN\|ZDB-GENE-030616-157		467	pold2 "polymerase (DNA directe	0.522	0.366	0.479	7.5e-76
MGI\|MGI:1097163		469	Pold2 "polymerase (DNA directe	0.498	0.347	0.546	2e-73
RGD\|1304954		469	Pold2 "polymerase (DNA directe	0.498	0.347	0.539	5.3e-73
UNIPROTKB\|P49005		469	POLD2 "DNA polymerase delta su	0.498	0.347	0.539	6.7e-73
UNIPROTKB\|P49004		469	POLD2 "DNA polymerase delta su	0.498	0.347	0.533	1.4e-72
UNIPROTKB\|H9GW60		511	POLD2 "Uncharacterized protein	0.498	0.318	0.539	2.9e-72
UNIPROTKB\|F1SSF8		469	POLD2 "Uncharacterized protein	0.498	0.347	0.533	4.7e-72
FB\|FBgn0027903		431	CG12018 [Drosophila melanogast	0.486	0.368	0.503	2.9e-64
UNIPROTKB\|F8W8R3		455	POLD2 "DNA polymerase delta su	0.455	0.327	0.490	7.7e-64
TAIR\|locus:2060010		441	POLD2 "DNA polymerase delta sm	0.498	0.369	0.496	2.6e-61

ZFIN\|ZDB-GENE-030616-157 pold2 "polymerase (DNA directed), delta 2, regulatory subunit" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

 Score = 465 (168.7 bits), Expect = 7.5e-76, Sum P(2) = 7.5e-76
 Identities = 82/171 (47%), Positives = 119/171 (69%)

Query:   156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215
             +S+ VD+MPG++DP N TLPQQPLH C+FP +  + T   V NPY   ++G   +GT+GQ
Sbjct:   286 ASVSVDVMPGQYDPTNYTLPQQPLHRCMFPLSIPFPTLQLVINPYQAIVDGVRFLGTAGQ 345

Query:   216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275
              VSDI K+S++ + L+ILE TLR  H+APTAPDTL CYPFY  DP I+E CP VYF+GN 
Sbjct:   346 NVSDIGKYSSVDDHLEILESTLRLRHLAPTAPDTLGCYPFYQKDPFILEECPHVYFSGNA 405

Query:   276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVEDLTEE 326
               +++K +   + ++V L+++P+F S++T  ++NL TLEC  +     + E
Sbjct:   406 PSYQSKRVTGPEGQDVLLVAIPEFSSTQTACLVNLRTLECEPISFSSFSTE 456

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

MGI\|MGI:1097163 Pold2 "polymerase (DNA directed), delta 2, regulatory subunit" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1304954 Pold2 "polymerase (DNA directed), delta 2, accessory subunit" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|P49005 POLD2 "DNA polymerase delta subunit 2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|P49004 POLD2 "DNA polymerase delta subunit 2" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|H9GW60 POLD2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SSF8 POLD2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

FB\|FBgn0027903 CG12018 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

UNIPROTKB\|F8W8R3 POLD2 "DNA polymerase delta subunit 2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

TAIR\|locus:2060010 POLD2 "DNA polymerase delta small subunit" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P49005	DPOD2_HUMAN	2, ., 7, ., 7, ., 7	0.5204	0.5168	0.3603	yes	N/A
P49004	DPOD2_BOVIN	2, ., 7, ., 7, ., 7	0.5146	0.5168	0.3603	yes	N/A
O35654	DPOD2_MOUSE	2, ., 7, ., 7, ., 7	0.5232	0.5198	0.3624	yes	N/A
Q6AXY4	DPOD2_RAT	2, ., 7, ., 7, ., 7	0.5174	0.5198	0.3624	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.766
4th Layer	2.7.7.7	0.824

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		327
cd07387		257	cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta,	5e-94
pfam04042		189	pfam04042, DNA_pol_E_B, DNA polymerase alpha/epsil	6e-38
COG1311		481	COG1311, HYS2, Archaeal DNA polymerase II, small s	8e-23
cd07387		257	cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta,	2e-07
cd07386		243	cd07386, MPP_DNA_pol_II_small_archeal_C, archeal D	5e-06
PRK04036		504	PRK04036, PRK04036, DNA polymerase II small subuni	0.001

>gnl\|CDD\|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2), C-terminal domain	Back alignment and domain information

 Score =  279 bits (716), Expect = 5e-94
 Identities = 98/161 (60%), Positives = 120/161 (74%)

Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215
           SS+ VDLMPGEFDPAN +LPQQPLH CLFP++S YST + VTNPY F ++G  ++GTSGQ
Sbjct: 93  SSVPVDLMPGEFDPANHSLPQQPLHRCLFPKSSNYSTLNLVTNPYEFSIDGVRVLGTSGQ 152

Query: 216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275
            V DI K+S+L + LDILE TL+  H+APTAPDTL CYPF D DP I+E CP VYF GNQ
Sbjct: 153 NVDDILKYSSLESRLDILERTLKWRHIAPTAPDTLWCYPFTDRDPFILEECPHVYFAGNQ 212

Query: 276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECH 316
            KF TK +E E+ + V L+ VP F  + T  ++NL TLEC 
Sbjct: 213 PKFGTKLVEGEEGQRVLLVCVPSFSKTGTAVLVNLRTLECE 253

PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 257

>gnl\|CDD\|217857 pfam04042, DNA_pol_E_B, DNA polymerase alpha/epsilon subunit B	Back alignment and domain information

>gnl\|CDD\|224230 COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2), C-terminal domain	Back alignment and domain information

>gnl\|CDD\|163629 cd07386, MPP_DNA_pol_II_small_archeal_C, archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain	Back alignment and domain information

>gnl\|CDD\|235208 PRK04036, PRK04036, DNA polymerase II small subunit; Validated	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		327
KOG2732\|consensus		435		100.0
cd07387		257	MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2	100.0
PRK04036		504	DNA polymerase II small subunit; Validated	100.0
COG1311		481	HYS2 Archaeal DNA polymerase II, small subunit/DNA	100.0
cd07386		243	MPP_DNA_pol_II_small_archeal_C archeal DNA polymer	99.96
PF04042		209	DNA_pol_E_B: DNA polymerase alpha/epsilon subunit	99.96
KOG3818\|consensus		525		99.12
PTZ00235		291	DNA polymerase epsilon subunit B; Provisional	98.83
KOG1625\|consensus		600		98.8
cd07387		257	MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2	98.78
KOG2732\|consensus		435		98.74
COG5214		581	POL12 DNA polymerase alpha-primase complex, polyme	98.07
PRK05340		241	UDP-2,3-diacylglucosamine hydrolase; Provisional	96.6
PHA02546		340	47 endonuclease subunit; Provisional	95.74
cd04490		79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	95.68
TIGR01854		231	lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase.	95.67
cd08163		257	MPP_Cdc1 Saccharomyces cerevisiae CDC1 and related	95.25
cd00841		155	MPP_YfcE Escherichia coli YfcE and related protein	93.43
cd07402		240	MPP_GpdQ Enterobacter aerogenes GpdQ and related p	92.58
TIGR00040		158	yfcE phosphoesterase, MJ0936 family. Members of th	91.82
PRK09453		182	phosphodiesterase; Provisional	91.78
cd07394		178	MPP_Vps29 Homo sapiens Vps29 and related proteins,	90.74
PRK04036		504	DNA polymerase II small subunit; Validated	90.6
PF12850		156	Metallophos_2: Calcineurin-like phosphoesterase su	89.79
COG0622		172	Predicted phosphoesterase [General function predic	85.42
cd07388		224	MPP_Tt1561 Thermus thermophilus Tt1561 and related	84.51
cd07401		256	MPP_TMEM62_N Homo sapiens TMEM62, N-terminal metal	83.47
cd07398		217	MPP_YbbF-LpxH Escherichia coli YbbF/LpxH and relat	82.16

>KOG2732\|consensus	Back alignment and domain information

Probab=100.00  E-value=6.2e-101  Score=739.47  Aligned_cols=315  Identities=44%  Similarity=0.740  Sum_probs=293.7

Q ss_pred             cCCcEEEeCCC--CchhhhhhhhhcCCceeEEeecccccCCce-EEEEEceeeecCCCCcchHHHHHhhccCCCCCCCCC
Q psy8633           5 SCPDVYFTGNQ--SKFETKTIEIEKGKSVSVLKLSDLNETDTE-ECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTH   81 (327)
Q Consensus         5 ~~phvYf~gnq--~~~~~~~a~~kwg~~v~i~~l~~~~~~~~~-~~viiGTL~k~m~lkPsiL~e~~~e~~~~~~~~~~~   81 (327)
                      ..-|+||+|++  +.+.++.|++|||++.++.+++++  ++++ .||++|||||+|+||||||+|+++|+++++++++++
T Consensus        28 Qy~~iY~aRL~elRp~i~~~A~k~wg~~~~l~~~l~l--~~~~~~C~vVGTlfk~~~lKPsIl~~v~~e~~~~p~~~~~~  105 (435)
T KOG2732|consen   28 QYFHIYFARLKELRPRILELAQKKWGSGPPLKKQLDL--EKGKGECWVVGTLFKAMALKPSILDEVSNEHKVAPDPEESN  105 (435)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHhhcCCCCchhhheee--ccCCccEEEEEehhhhcccCcHHHHHHhhhhccCCCCcccc
Confidence            35689999994  479999999999999999999999  4555 999999999999999999999999999999999999


Q ss_pred             ccCCCCeEEEecCCceEEEEec-ccccccccceEEEEEeeEecCCcEEEEEEEecC-CCC-CCCCCCCCC----------
Q psy8633          82 FVSDSDELILEDELQRIPLHGN-IDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYAT-PVF-NPRTTLSNN----------  148 (327)
Q Consensus        82 y~~~~D~l~LED~sgRi~L~g~-~~~~~lvTG~Vvav~G~~~~~G~F~V~di~~p~-~~~-~~~~~~~~d----------  148 (327)
                      |.+.+|+|+||||+|||+|.|. +....++||+||||+|+++++|.|.|+|+|||+ .|| .|.+...++          
T Consensus       106 y~~ped~i~LEDe~grV~L~G~~i~~~~~vTGvvvavlG~~~e~G~F~VeDv~fp~~~pq~~P~~~~~~~~~i~lVSGL~  185 (435)
T KOG2732|consen  106 YHSPEDEIVLEDESGRVRLEGSFISHAVLVTGVVVAVLGKEAEAGRFLVEDVLFPGSSPQGKPRATLPSQRKIALVSGLD  185 (435)
T ss_pred             cCCccceEEEecCCceEEEEeecccccceeeeEEEEEecccccCceEEEEEEeccCCCccCCCCCcCCCCCEEEEEeccc
Confidence            9999999999999999999995 999999999999999999999999999999999 888 554433221          


Q ss_pred             -----------------------------------------------C-------Cc--c-----------e--------
Q psy8633         149 -----------------------------------------------E-------NK--Y-----------V--------  153 (327)
Q Consensus       149 -----------------------------------------------k-------~~--~-----------v--------  153 (327)
                                                                     +       +.  +           +        
T Consensus       186 l~~~~~~~~~l~~l~D~l~g~lg~e~~~~~~~i~rliv~Gn~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ld~~L~  265 (435)
T KOG2732|consen  186 LGGGSKNLLRLELLVDWLRGQLGNEYEQSASSIGRLIVAGNSLSFSIKILDSQSTSISRLTKKDSAASVIPVKELDNFLA  265 (435)
T ss_pred             cCCCcchhHHHHHHHHHHhcccCccccccccccceEEEeccccchhhhccccceeeeeeccccccccccccHHHHHHHHH
Confidence                                                           0       00  0           0        


Q ss_pred             e-cCceeEEEcCCCCCCCCCCCCCCCCCcCCcCCccC-CCCeeeecCCcEEEECCEEEEEEcCCchhhhhccCCCCChHH
Q psy8633         154 N-HSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASK-YSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLD  231 (327)
Q Consensus       154 ~-~~~i~V~lmPG~~Dp~~~~lPQqplh~~lf~~~~~-~~~~~~vtNP~~~~i~g~~vlgtsGq~i~di~k~~~~~~~l~  231 (327)
                      + +.+++||+|||..||+|.+|||||||+||||++.. +++++++||||+|++||.+|||||||||+|+.||++.++.||
T Consensus       266 ~~~~s~~VdimPG~~Dp~~~~lPqqPlh~~lfp~s~~~~~~~q~vTNPy~~~ld~~~vl~tSGqNvsDl~ry~~~~s~ld  345 (435)
T KOG2732|consen  266 QIPASISVDIMPGVNDPSNFMLPQQPLHRCLFPKSPQSLSTLQLVTNPYEFSLDGARVLGTSGQNVSDLLRYSSKKSGLD  345 (435)
T ss_pred             hccccCCccCCCCCCChhhccCCcCCcchhhhccCccccchhhcccCceEEEEcCEEEEecCCccHHHHhhhcchhhHHH
Confidence            1 78999999999999999999999999999999988 799999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccCCCCCCCceecCcCCCCCCeeecCCCcEEEcCCccccceeEEeecCCceEEEEecCCCCCCCeEEEEeCC
Q psy8633         232 ILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLS  311 (327)
Q Consensus       232 ~m~~~L~~rHlaPtaPdtl~~~P~~~~Dpfvi~~~Phv~f~Gn~~~f~~~~~~~~~~~~v~lv~vP~F~~t~~~vlvnl~  311 (327)
                      +||.||+|||+|||||||||||||.++|||||++|||||+|||||+|+++.++++ |++++|||||+||+||.+|+|||+
T Consensus       346 ~le~tlkw~HvaPTaPDTL~cyPftekDPFv~~~~Phvy~~GNqp~f~~r~i~~~-g~~~~Lv~VP~FskT~~~vllnL~  424 (435)
T KOG2732|consen  346 ALENTLKWGHVAPTAPDTLWCYPFTEKDPFVMDECPHVYIVGNQPKFGTRLIEGG-GKNTLLVCVPKFSKTGVAVLLNLE  424 (435)
T ss_pred             HHhhhheeccccCCCCCcccccccccCCCeeecCCCeEEEecCCCcccceeeecC-CceEEEEEcccccccceEEEEEcc
Confidence            9999999999999999999999999999999999999999999999999999986 999999999999999999999999


Q ss_pred             CCcEEEEEEcc
Q psy8633         312 TLECHSLVVED  322 (327)
Q Consensus       312 tl~~~~v~F~~  322 (327)
                      ||+|++++|+.
T Consensus       425 tL~~~~v~Fd~  435 (435)
T KOG2732|consen  425 TLACETVNFDM  435 (435)
T ss_pred             cccceeEeccC
Confidence            99999999973

>cd07387 MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2), C-terminal domain	Back alignment and domain information

>PRK04036 DNA polymerase II small subunit; Validated	Back alignment and domain information

>COG1311 HYS2 Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [DNA replication, recombination, and repair]	Back alignment and domain information

>cd07386 MPP_DNA_pol_II_small_archeal_C archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain	Back alignment and domain information

>PF04042 DNA_pol_E_B: DNA polymerase alpha/epsilon subunit B; InterPro: IPR007185 DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast	Back alignment and domain information

>KOG3818\|consensus	Back alignment and domain information

>PTZ00235 DNA polymerase epsilon subunit B; Provisional	Back alignment and domain information

>KOG1625\|consensus	Back alignment and domain information

>cd07387 MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2), C-terminal domain	Back alignment and domain information

>KOG2732\|consensus	Back alignment and domain information

>COG5214 POL12 DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK05340 UDP-2,3-diacylglucosamine hydrolase; Provisional	Back alignment and domain information

>PHA02546 47 endonuclease subunit; Provisional	Back alignment and domain information

>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit	Back alignment and domain information

>TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase	Back alignment and domain information

>cd08163 MPP_Cdc1 Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain	Back alignment and domain information

>cd00841 MPP_YfcE Escherichia coli YfcE and related proteins, metallophosphatase domain	Back alignment and domain information

>cd07402 MPP_GpdQ Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain	Back alignment and domain information

>TIGR00040 yfcE phosphoesterase, MJ0936 family	Back alignment and domain information

>PRK09453 phosphodiesterase; Provisional	Back alignment and domain information

>cd07394 MPP_Vps29 Homo sapiens Vps29 and related proteins, metallophosphatase domain	Back alignment and domain information

>PRK04036 DNA polymerase II small subunit; Validated	Back alignment and domain information

>PF12850 Metallophos_2: Calcineurin-like phosphoesterase superfamily domain; InterPro: IPR024654 Domains in this entry are members of the calcineurin-like phosphoesterase domain superfamily []	Back alignment and domain information

>COG0622 Predicted phosphoesterase [General function prediction only]	Back alignment and domain information

>cd07388 MPP_Tt1561 Thermus thermophilus Tt1561 and related proteins, metallophosphatase domain	Back alignment and domain information

>cd07401 MPP_TMEM62_N Homo sapiens TMEM62, N-terminal metallophosphatase domain	Back alignment and domain information

>cd07398 MPP_YbbF-LpxH Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		327
3e0j_A		476	X-Ray Structure Of The Complex Of Regulatory Subuni		1e-50

>pdb|3E0J|A Chain A, X-Ray Structure Of The Complex Of Regulatory Subunits Of Human Dna Polymerase Delta Length = 476

Back alignment and structure

Iteration: 1

Score = 196 bits (499), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 89/171 (52%), Positives = 118/171 (69%) Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215 +S+ VD+MPGEFDP N TLPQQPLHPC+FP A+ YST VTNPY ++G +GTSGQ Sbjct: 295 ASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQ 354 Query: 216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275 VSDI ++S++ + L+ILE+TLR H++PTAPDTL CYPFY DP I CP VYF GN Sbjct: 355 NVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNT 414 Query: 276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVEDLTEE 326 F +K I +D+ V L++VPDF +++T ++NL +L C + E Sbjct: 415 PSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAE 465

PyMOL of 3e0j

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		327
3e0j_A		476	DNA polymerase subunit delta-2; DNA polymerase del	5e-68
3e0j_A		476	DNA polymerase subunit delta-2; DNA polymerase del	2e-29
3e0j_A		476	DNA polymerase subunit delta-2; DNA polymerase del	7e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08

>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit, P50 subunit, human, DNA replication, DNA-directed DNA polymerase; HET: DNA; 3.00A {Homo sapiens} Length = 476	Back alignment and structure

 Score =  219 bits (558), Expect = 5e-68
 Identities = 88/163 (53%), Positives = 117/163 (71%)

Query: 156 SSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQ 215
           +S+ VD+MPGEFDP N TLPQQPLHPC+FP A+ YST   VTNPY   ++G   +GTSGQ
Sbjct: 295 ASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQ 354

Query: 216 PVSDIAKFSNLSNPLDILEYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQ 275
            VSDI ++S++ + L+ILE+TLR  H++PTAPDTL CYPFY  DP I   CP VYF GN 
Sbjct: 355 NVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNT 414

Query: 276 SKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSL 318
             F +K I   +D+ V L++VPDF +++T  ++NL +L C  +
Sbjct: 415 PSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPI 457

PyMOL of 3e0j

>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit, P50 subunit, human, DNA replication, DNA-directed DNA polymerase; HET: DNA; 3.00A {Homo sapiens} Length = 476	Back alignment and structure

>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit, P50 subunit, human, DNA replication, DNA-directed DNA polymerase; HET: DNA; 3.00A {Homo sapiens} Length = 476	Back alignment and structure

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		327
3e0j_A		476	DNA polymerase subunit delta-2; DNA polymerase del	100.0
3flo_A		460	DNA polymerase alpha subunit B; protein-protein co	99.54
3e0j_A		476	DNA polymerase subunit delta-2; DNA polymerase del	98.61
2yvt_A		260	Hypothetical protein AQ_1956; structural genomics,	94.34
1z2w_A		192	Vacuolar protein sorting 29; VPS29, retromer, phos	93.94
3ib7_A		330	ICC protein; metallophosphoesterase, alpha-beta fo	93.2
1s3l_A		190	Hypothetical protein MJ0936; phosphodiesterase, nu	93.07
3ck2_A		176	Conserved uncharacterized protein (predicted phosp	92.24
2a22_A		215	Vacuolar protein sorting 29; alpha-beta-BETA-alpha	91.95
2kkn_A		178	Uncharacterized protein; protein phosphatase 2A ho	90.83
1o7i_A		119	SSB, SSO2364, single stranded DNA binding protein;	81.4
3d03_A		274	Phosphohydrolase; glycerophosphodiesterase, metall	81.05
1su1_A		208	Hypothetical protein YFCE; structural genomics, ph	80.84
1nnw_A		252	Hypothetical protein; structural genomics, PSI, pr	80.66

>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit, P50 subunit, human, DNA replication, DNA-directed DNA polymerase; HET: DNA; 3.00A {Homo sapiens}	Back alignment and structure

Probab=100.00  E-value=1.3e-104  Score=795.10  Aligned_cols=321  Identities=46%  Similarity=0.846  Sum_probs=269.5

Q ss_pred             ccCCcEEEeCCCC--chhhhhhhhhcCCceeEEeecccccCCceEEEEEceeeecCCCCcchHHHHHhhccCCCCCCCCC
Q psy8633           4 ESCPDVYFTGNQS--KFETKTIEIEKGKSVSVLKLSDLNETDTEECVIIGTLFKHQQLKPNILKEISEELKLVPQPQHTH   81 (327)
Q Consensus         4 ~~~phvYf~gnq~--~~~~~~a~~kwg~~v~i~~l~~~~~~~~~~~viiGTL~k~m~lkPsiL~e~~~e~~~~~~~~~~~   81 (327)
                      +...||||.|+..  +...++|++|||+.+++.+|+++  ++++.||+||||||+|+||||||+||++|+++.+++++.+
T Consensus        55 ~QY~~iY~~RL~~Lr~~l~~~a~~kw~~~~~i~klldl--~~ge~c~viGTvyk~m~lKPsIL~eis~e~~~~~~~~~~~  132 (476)
T 3e0j_A           55 RQYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCEL--QPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSK  132 (476)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHSCSCCCBCCSSSC--CTTCCEEEEEEEEEEC----------------------CC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHhhcc--cCCCEEEEEEEEEecccCCCcHHHHHhhhhccCCCCcccc
Confidence            3567999999954  68899999999988999999999  7899999999999999999999999999999999999999


Q ss_pred             ccCCCCeEEEecCCceEEEEecccccccccceEEEEEeeEecCCcEEEEEEEecC-CCCCCCCCCCCC------------
Q psy8633          82 FVSDSDELILEDELQRIPLHGNIDIHNQVTGVVVAIKGTPVGNGKFKVSDVCYAT-PVFNPRTTLSNN------------  148 (327)
Q Consensus        82 y~~~~D~l~LED~sgRi~L~g~~~~~~lvTG~Vvav~G~~~~~G~F~V~di~~p~-~~~~~~~~~~~d------------  148 (327)
                      |++++|+++|||+||||+|+|.++++.||||+||||+|++.++|.|+|+|||||+ ++|++++...++            
T Consensus       133 y~~~~D~l~LEDesGRv~L~g~~~~~~lVTG~VvaV~G~~~~~G~F~V~di~~Pd~ppq~~~~~~~~~~~ialVSGL~ig  212 (476)
T 3e0j_A          133 YIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFADLAPQKPAPPLDTDRFVLLVSGLGLG  212 (476)
T ss_dssp             CCCSSCEEEEECSSCEEEEEESCCTTTCCTTCEEEEEEEECTTSSEEEEEEEECBCCCCCCCCCCSSCCEEEEECCCCBT
T ss_pred             ccCCCceEEEECCCCEEEEEEEcccccccCCcEEEEEEEEcCCCeEEEEEEEcCCCCCCCCCCcCCCCCEEEEECCcccC
Confidence            9999999999999999999998899999999999999999999999999999999 999887643322            


Q ss_pred             ------------------------------------------------------CCcc---------------ee-----
Q psy8633         149 ------------------------------------------------------ENKY---------------VN-----  154 (327)
Q Consensus       149 ------------------------------------------------------k~~~---------------v~-----  154 (327)
                                                                            +++|               ++     
T Consensus       213 s~~~~~~~~~~ll~d~L~G~~g~~~~~~~as~I~rlIIAGn~v~~~~~~~e~~~~~~y~~~~~~~~~~~~~~~ld~~L~~  292 (476)
T 3e0j_A          213 GGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQ  292 (476)
T ss_dssp             SSCHHHHHHHHHHHHHHHTCSSCHHHHHHHTTEEEEEEESCSBCC-------------CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccchHHHHHHHHHHcCCCCCccccchhhceeEEEEECCccccccccchhhhhhhccccccchhhHHHHHHHHHHHHh
Confidence                                                                  1112               00     


Q ss_pred             -cCceeEEEcCCCCCCCCCCCCCCCCCcCCcCCccCCCCeeeecCCcEEEECCEEEEEEcCCchhhhhccCCCCChHHHH
Q psy8633         155 -HSSIEVDLMPGEFDPANTTLPQQPLHPCLFPEASKYSTFHPVTNPYIFEMEGKLLMGTSGQPVSDIAKFSNLSNPLDIL  233 (327)
Q Consensus       155 -~~~i~V~lmPG~~Dp~~~~lPQqplh~~lf~~~~~~~~~~~vtNP~~~~i~g~~vlgtsGq~i~di~k~~~~~~~l~~m  233 (327)
                       +++|+|+||||+|||+|.+|||||||+||||++++|.+++++||||+++|+|++|||||||||+||+||+++++++++|
T Consensus       293 l~~~i~V~lmPG~~DP~~~~lPQqplh~~lfp~s~~~~~~~~vtNP~~~~i~G~~~LgtsGqnidDi~ky~~~~~~l~~m  372 (476)
T 3e0j_A          293 LSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEIL  372 (476)
T ss_dssp             HHTTSCEEEECCTTSSSCSSSSCCCCCTTSCHHHHTSTTEEECCSSEEEEETTEEEEECSSHHHHHHHHHSCCCCHHHHH
T ss_pred             cccCceEEecCCCCCcccccCCCCCcCHHHhhhhhhcCccEEeCCCeEEEECCEEEEEECCCCHHHHHhcCCCCCHHHHH
Confidence             7899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcccCCCCCCCceecCcCCCCCCeeecCCCcEEEcCCccccceeEEeecCCceEEEEecCCCCCCCeEEEEeCCCC
Q psy8633         234 EYTLRCGHVAPTAPDTLACYPFYDNDPMIIESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTL  313 (327)
Q Consensus       234 ~~~L~~rHlaPtaPdtl~~~P~~~~Dpfvi~~~Phv~f~Gn~~~f~~~~~~~~~~~~v~lv~vP~F~~t~~~vlvnl~tl  313 (327)
                      ++||+|||+|||||||||||||.++|||||+++||||||||||+|+++++.++++++|||||||+|++||++|||||+||
T Consensus       373 e~~LkwrHlAPTaPdTl~~yP~~~~DpfVi~~~PhVyf~Gnq~~f~t~~~~~~~~~~vrLv~VP~Fs~T~~~vLvdl~tL  452 (476)
T 3e0j_A          373 EWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSL  452 (476)
T ss_dssp             HHHHHBTCSCTTSCCC------CCSCTTSCSSCCSEEEEEEESSCEEEEEECSSCCEEEEEEEECHHHHCEEEEEETTTT
T ss_pred             HHHHHHhccCCCCCCceeeccCCCCCceeecCCCcEEEeCCCCccceeEEecCCCCeEEEEEcCCcCCCCeEEEEECccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEEcccccc
Q psy8633         314 ECHSLVVEDLTEE  326 (327)
Q Consensus       314 ~~~~v~F~~~~~~  326 (327)
                      +|++|+|+.++++
T Consensus       453 e~~~v~f~~~~~~  465 (476)
T 3e0j_A          453 ACQPISFSGFGAE  465 (476)
T ss_dssp             BCCEEEEEECCSC
T ss_pred             cEEEEEEecccCC
Confidence            9999999987764

PyMOL of 3e0j

>3flo_A DNA polymerase alpha subunit B; protein-protein complex, phosphoesterase fold, OB fold, zinc motif, DNA replication, nucleus; HET: DNA; 2.50A {Saccharomyces cerevisiae}	Back alignment and structure

>3e0j_A DNA polymerase subunit delta-2; DNA polymerase delta, P66 subunit, P50 subunit, human, DNA replication, DNA-directed DNA polymerase; HET: DNA; 3.00A {Homo sapiens}	Back alignment and structure

>2yvt_A Hypothetical protein AQ_1956; structural genomics, unknown function, NPPSFA, national PROJ protein structural and functional analyses; 1.60A {Aquifex aeolicus} SCOP: d.159.1.6	Back alignment and structure

>1z2w_A Vacuolar protein sorting 29; VPS29, retromer, phosphatase, manganese, protein transport; 2.00A {Mus musculus} SCOP: d.159.1.7 PDB: 1z2x_A 3lh6_A 3lh7_A 3psn_A 3pso_A 1w24_A 2r17_A	Back alignment and structure

>3ib7_A ICC protein; metallophosphoesterase, alpha-beta fold, swapped-dimer, HYDR; HET: BTB; 1.60A {Mycobacterium tuberculosis} PDB: 3ib8_A* 2hy1_A 2hyp_A 2hyo_A	Back alignment and structure

>1s3l_A Hypothetical protein MJ0936; phosphodiesterase, nuclease, structural genomics, BSGC struc funded by NIH; 2.40A {Methanocaldococcus jannaschii} SCOP: d.159.1.7 PDB: 1s3m_A 1s3n_A 2ahd_A	Back alignment and structure

>3ck2_A Conserved uncharacterized protein (predicted phosphoesterase COG0622); structural genomics, predicted phosphodiesterase, PSI-2; HET: SRT; 2.30A {Streptococcus pneumoniae} SCOP: d.159.1.7	Back alignment and structure

>2a22_A Vacuolar protein sorting 29; alpha-beta-BETA-alpha sandwich, structural genomics, structural genomics consortium, SGC, protein transport; 2.20A {Cryptosporidium parvum} SCOP: d.159.1.7	Back alignment and structure

>2kkn_A Uncharacterized protein; protein phosphatase 2A homologue, structural genomics, PSI- 2, protein structure initiative; NMR {Thermotoga maritima}	Back alignment and structure

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3	Back alignment and structure

>3d03_A Phosphohydrolase; glycerophosphodiesterase, metallohydrolase, phosphatase, metal ION; 1.90A {Enterobacter aerogenes} SCOP: d.159.1.11 PDB: 2zoa_A 2zo9_B 2dxn_A 2dxl_A	Back alignment and structure

>1su1_A Hypothetical protein YFCE; structural genomics, phosphoesterase, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.25A {Escherichia coli} SCOP: d.159.1.7	Back alignment and structure

>1nnw_A Hypothetical protein; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics, secsg; 1.90A {Pyrococcus furiosus} SCOP: d.159.1.5 PDB: 2gju_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		327
d2yvta1		257	Uncharacterized protein Aq_1956 {Aquifex aeolicus	94.5
d2a22a1		193	Vacuolar protein sorting 29, VPS29 {Cryptosporidiu	93.74
d3d03a1		271	Glycerophosphodiesterase GpdQ {Enterobacter aeroge	92.87
d1s3la_		165	Putative phosphodiesterase MJ0936 {Methanococcus j	90.82
d1z2wa1		182	Vacuolar protein sorting 29, VPS29 {Mouse (Mus mus	89.8
d1uf3a_		228	Hypothetical protein TT1561 {Thermus thermophilus	82.08
d2hy1a1		256	Rv0805 cyclic nucleotide phosphodiesterase {Mycoba	81.9
d3ck2a1		173	Uncharacterized protein SP1879 {Streptococcus pneu	81.34

>d2yvta1 d.159.1.6 (A:4-260) Uncharacterized protein Aq_1956 {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Metallo-dependent phosphatases
superfamily: Metallo-dependent phosphatases
family: TT1561-like
domain: Uncharacterized protein Aq 1956
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.50  E-value=0.033  Score=46.11  Aligned_cols=51  Identities=18%  Similarity=0.205  Sum_probs=35.0

Q ss_pred             cCCCcEEEcCCccccceeEEeecCCceEEEEecCCCCCCCeEEEEeCCCCcEEEEEEc
Q psy8633         264 ESCPDVYFTGNQSKFETKTIEIEKDKNVRLISVPDFFSSRTVAILNLSTLECHSLVVE  321 (327)
Q Consensus       264 ~~~Phv~f~Gn~~~f~~~~~~~~~~~~v~lv~vP~F~~t~~~vlvnl~tl~~~~v~F~  321 (327)
                      +.-|+++++||.|+-. ...     .+..++.-.++.+ |.-+++|+++-+.+.-.|+
T Consensus       207 ~~~~~~~~~GHiH~~~-~~~-----g~~~~~~pGs~~~-g~y~~id~~~~~i~~~~~~  257 (257)
T d2yvta1         207 SLNPEVAIVGHVGKGH-ELV-----GNTIVVNPGEFEE-GRYAFLDLTQHKIKLEQFS  257 (257)
T ss_dssp             HHCCSEEEECSSCCEE-EEE-----TTEEEEECCBGGG-TEEEEEETTTTEEEEEECC
T ss_pred             hcCCcEEEEEeecCCe-Eec-----CCeEEEECCcccc-CEEEEEEEeCCEEEEEECC
Confidence            3469999999999732 221     2345666556644 5678999999877777664

PyMOL of d2yvta1

>d2a22a1 d.159.1.7 (A:4-196) Vacuolar protein sorting 29, VPS29 {Cryptosporidium parvum [TaxId: 5807]}	Back information, alignment and structure

>d3d03a1 d.159.1.11 (A:1-271) Glycerophosphodiesterase GpdQ {Enterobacter aerogenes [TaxId: 548]}	Back information, alignment and structure

>d1s3la_ d.159.1.7 (A:) Putative phosphodiesterase MJ0936 {Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1z2wa1 d.159.1.7 (A:1-182) Vacuolar protein sorting 29, VPS29 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1uf3a_ d.159.1.6 (A:) Hypothetical protein TT1561 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d2hy1a1 d.159.1.11 (A:10-265) Rv0805 cyclic nucleotide phosphodiesterase {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d3ck2a1 d.159.1.7 (A:1-173) Uncharacterized protein SP1879 {Streptococcus pneumoniae [TaxId: 1313]}	Back information, alignment and structure