YRC Public Data Repository - Protein Structure Prediction

Protein:	NEIL1
Organism:	Homo sapiens
Length:	390 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for NEIL1.

Description	E-value	Query Range	Subject Range
NEIL1_MOUSE - Endonuclease 8-like 1 OS=Mus musculus GN=Neil1 PE=2 SV=3	0.0	[1..390]	[1..389]
gi\|123995859, gi... - gi\|123995859\|gb\|ABM85531.1\| nei endonuclease VIII-like 1 (E. coli) [synthetic construct], gi\|1239810... gi\|22004053, gi\|... - gi\|22004053\|dbj\|BAC06476.1\| endonuclease VIII [Homo sapiens], gi\|14790078\|gb\|AAH10876.1\| NEIL1 prote...	0.0	[1..390]	[1..390]
gi\|71043710, gi\|... - gi\|71043710\|ref\|NP_001020925.1\| nei endonuclease VIII-like 1 [Rattus norvegicus], gi\|68533825\|gb\|AAH...	8.0E-99	[1..390]	[1..387]
gi\|114658208, gi... - gi\|114658214\|ref\|XP_001144235.1\| PREDICTED: nei endonuclease VIII-like 1 isoform 10 [Pan troglodytes...	4.0E-98	[1..390]	[1..390]
FPG_ECODH - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli (strain K12 / DH10B) GN=mutM PE=3 SV=1 EG10329 - formamidopyrimidine /5-formyluracil / 5-hydroxymethyluracil DNA glycosylase / Formamidopyrimidine-DNA ... FPG_ECOBW - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=mutM PE=3 ... gi\|242379159, gi... - gi\|251786886\|ref\|YP_003001190.1\| hypothetical protein B21_03444 [Escherichia coli BL21], gi\|24237915... gi\|253771524, gi... - gi\|254290313\|ref\|YP_003056061.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli BL21(DE3)], g... gi\|254163563, gi... - gi\|254163563\|ref\|YP_003046671.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli B str. REL606... gi\|83588518, gi\|... - gi\|83588518\|ref\|ZP_00927142.1\| COG0266: Formamidopyrimidine-DNA glycosylase [Escherichia coli 101-1]... FPG_ECOLI - Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23) (Fapy-DNA glycosylase) (DNA-(apurinic or apyrimidi... FPG_ECOHS - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O9:H4 (strain HS) GN=mutM PE=3 SV=1 EG10329 - formamidopyrimidine /5-formyluracil / 5-hydroxymethyluracil DNA glycosylase / Formamidopyrimidine-DNA ... gi\|85676407, gi\|... - gi\|89110376\|ref\|AP_004156.1\| formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosyla...	9.0E-86	[1..297]	[1..269]
FPG_SHISS - Formamidopyrimidine-DNA glycosylase OS=Shigella sonnei (strain Ss046) GN=mutM PE=3 SV=3 gi\|124530495, gi... - gi\|124530495\|ref\|ZP_01701122.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli B], gi\|1244991... FPG_ECOLC - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=mu... FPG_ECO45 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=mutM PE=3 SV=... FPG_SHIBS - Formamidopyrimidine-DNA glycosylase OS=Shigella boydii serotype 4 (strain Sb227) GN=mutM PE=3 SV=3 FPG_ECO81 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O81 (strain ED1a) GN=mutM PE=3 SV=1 gi\|75242586, gi\|... - gi\|75242586\|ref\|ZP_00726330.1\| COG0266: Formamidopyrimidine-DNA glycosylase [Escherichia coli F11], ... FPG_ECOLU - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=mutM ... gi\|188487129, gi... - gi\|75514303\|ref\|ZP_00736611.1\| COG0266: Formamidopyrimidine-DNA glycosylase [Escherichia coli 53638]... gi\|15833764, gi\|... - gi\|15833764\|ref\|NP_312537.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. Saka... FPG_SHIF8 - Formamidopyrimidine-DNA glycosylase OS=Shigella flexneri serotype 5b (strain 8401) GN=mutM PE=3 SV=1 gi\|56480390, gi\|... - gi\|56480390\|ref\|NP_709414.2\| formamidopyrimidine-DNA glycosylase [Shigella flexneri 2a str. 301], gi... gi\|208814029, gi... - gi\|208814029\|ref\|ZP_03255358.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. E... gi\|208820753, gi... - gi\|208820753\|ref\|ZP_03261073.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. E... FPG_ECO5E - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=mutM PE=3 ... FPG_ECOSE - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli (strain SE11) GN=mutM PE=3 SV=1 FPG_ECO24 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=mutM PE=... FPG_ECO27 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=mutM PE=... gi\|191167823, gi... - gi\|75229026\|ref\|ZP_00715610.1\| COG0266: Formamidopyrimidine-DNA glycosylase [Escherichia coli B7A], ... gi\|217324519, gi... - gi\|217324519\|ref\|ZP_03440603.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. T... gi\|194430989, gi... - gi\|83571421\|ref\|ZP_00922861.1\| COG0266: Formamidopyrimidine-DNA glycosylase [Shigella dysenteriae 10... FPG_ESCF3 - Formamidopyrimidine-DNA glycosylase OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0... FPG_SHIB3 - Formamidopyrimidine-DNA glycosylase OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=m... FPG_ECO8A - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O8 (strain IAI1) GN=mutM PE=3 SV=1 FPG_SHIFL - Formamidopyrimidine-DNA glycosylase OS=Shigella flexneri GN=mutM PE=3 SV=3 gi\|254795590, gi... - gi\|254795590\|ref\|YP_003080427.1\| formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glyco... gi\|254038834, gi... - gi\|254038834\|ref\|ZP_04872886.1\| formamidopyrimidine-DNA glycosylase [Escherichia sp. 1_1_43], gi\|226... gi\|226902669, gi... - gi\|237703405\|ref\|ZP_04533886.1\| formamidopyrimidine-DNA glycosylase [Escherichia sp. 3_2_53FAA], gi\|... FPG_ECO57 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O157:H7 GN=mutM PE=3 SV=3 sp\|B7ULJ0\|FPG_ECO27 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=mutM PE=... gi\|168753459, gi... - gi\|189358964\|gb\|EDU77383.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC440... gi\|189369599, gi... - gi\|189369599\|gb\|EDU88015.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC450... gi\|189364460, gi... - gi\|189364460\|gb\|EDU82879.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC448... gi\|168772399, gi... - gi\|187771367\|gb\|EDU35211.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC419... gi\|189002553, gi... - gi\|189002553\|gb\|EDU71539.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC407... gi\|189374639, gi... - gi\|189374639\|gb\|EDU93055.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC869... FPG_ECOSM - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=mutM PE=3 SV=1 gi\|195936196 - gi\|195936196\|ref\|ZP_03081578.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. E... FPG_ECOUT - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli (strain UTI89 / UPEC) GN=mutM PE=3 SV=1 gi\|30065089, gi\|... - gi\|30065089\|ref\|NP_839260.1\| formamidopyrimidine-DNA glycosylase [Shigella flexneri 2a str. 2457T], ... gi\|209754676, gi... - pir\|\|G86039 formamidopyrimidine DNA glycosylase [imported] - Escherichia coli (strain O157:H7, subst... gi\|15804176, gi\|... - gi\|15804176\|ref\|NP_290215.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 EDL933], ... FPG_ECOK1 - Formamidopyrimidine-DNA glycosylase OS=Escherichia coli O1:K1 / APEC GN=mutM PE=3 SV=1 gi\|188016969, gi... - gi\|188016969\|gb\|EDU55091.1\| formamidopyrimidine-DNA glycosylase [Escherichia coli O157:H7 str. EC411...	1.0E-85	[1..297]	[1..269]

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Predicted Domain #1

Region A:
Residues: [1-390]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPEGPELHLA SQFVNEACRA LVFGGCVEKS SVSRNPEVPF ESSAYRISAS ARGKELRLIL  60
   61 SPLPGAQPQQ EPLALVFRFG MSGSFQLVPR EELPRHAHLR FYTAPPGPRL ALCFVDIRRF 120
  121 GRWDLGGKWQ PGRGPCVLQE YQQFRENVLR NLADKAFDRP ICEALLDQRF FNGIGNYLRA 180
  181 EILYRLKIPP FEKARSVLEA LQQHRPSPEL TLSQKIRTKL QNPDLLELCH SVPKEVVQLG 240
  241 GKGYGSESGE EDFAAFRAWL RCYGMPGMSS LQDRHGRTIW FQGDPGPLAP KGRKSRKKKS 300
  301 KATQLSPEDR VEDALPPSKA PSRTRRAKRD LPKRTATQRP EGTSLQQDPE APTVPKKGRR 360
  361 KGRQAASGHC RPRKVKADIP SLEPEGTSAS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	88.30103
Match:	1tdhA
Description:	Crystal structure of human endonuclease VIII-like 1 (NEIL1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA N-glycosylase activity	4.96603037464775	bayes_pls_golite062009
hydrolase activity, hydrolyzing N-glycosyl compounds	4.42310295950282	bayes_pls_golite062009
oxidized base lesion DNA N-glycosylase activity	4.07532318409219	bayes_pls_golite062009
DNA-(apurinic or apyrimidinic site) lyase activity	4.07268074802746	bayes_pls_golite062009
oxidized purine base lesion DNA N-glycosylase activity	3.59184355710115	bayes_pls_golite062009
binding	2.76561765026195	bayes_pls_golite062009
hydrolase activity, acting on glycosyl bonds	2.40884427300274	bayes_pls_golite062009
transcription regulator activity	2.20400142735918	bayes_pls_golite062009
DNA binding	2.18702281581791	bayes_pls_golite062009
nucleic acid binding	2.04270847321412	bayes_pls_golite062009
hydrolase activity	1.74627738237592	bayes_pls_golite062009
transcription factor activity	1.44182975349714	bayes_pls_golite062009
protein binding	1.29473277650963	bayes_pls_golite062009
sequence-specific DNA binding	0.71242082351425	bayes_pls_golite062009
transcription activator activity	0.612819891085	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.51536225088963	bayes_pls_golite062009
transcription factor binding	0.40850395411512	bayes_pls_golite062009
ligand-dependent nuclear receptor activity	0.39641256766754	bayes_pls_golite062009
catalytic activity	0.101795606736461	bayes_pls_golite062009
lyase activity	0.0836281676510939	bayes_pls_golite062009
structure-specific DNA binding	0.0775494030801263	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: