RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254781074|ref|YP_003065487.1| uracil-DNA glycosylase
[Candidatus Liberibacter asiaticus str. psy62]
(227 letters)
>3fci_A UDG, uracil-DNA glycosylase; DNA repair, alternative
splicing, disease mutation, DNA damage, glycosidase,
HOST- virus interaction, hydrolase; HET: 3FI; 1.27A
{Homo sapiens} PDB: 1emh_A* 1emj_A* 1q3f_A* 1ssp_E*
1ugh_E 1akz_A* 2oxm_A* 2oyt_A* 3fcf_A* 2hxm_A* 3fck_B*
3fcl_A* 2ssp_E* 1yuo_A 4skn_E* 1okb_A (A:)
Length = 223
Score = 296 bits (759), Expect = 2e-81
Identities = 112/220 (50%), Positives = 137/220 (62%), Gaps = 2/220 (0%)
Query: 6 IHESWKSLLENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVKVVILG 65
ESWK L F + L F+ E RK ++P F + VKVVILG
Sbjct: 4 FGESWKKHLSGEFGKPYFIKLMGFVAEE-RKHYTVYPPPHQVFTWTQMCDIKDVKVVILG 62
Query: 66 QDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDVN-FIPPTHGFLEHWGHEGVLLL 124
QDPYH QAHGLCFSV + PPSL N+YKEL D+ F+ P HG L W +GVLLL
Sbjct: 63 QDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLL 122
Query: 125 NAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQKKQDVLDHKRHLV 184
NAVLTV +A SH+ RGWEQFTD+V+ ++ N +VF+LWG+ AQKK +D KRH V
Sbjct: 123 NAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHV 182
Query: 185 LKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQI 224
L+ AHPSPLS GFFGCRHFSK N LQ+ GK ++W+
Sbjct: 183 LQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKE 222
>2boo_A UDG, uracil-DNA glycosylase; UNG, base excision repair,
radiation resistance, DNA damage, DNA repair,
glycosidase, hydrolase; 1.8A {Deinococcus radiodurans}
(A:)
Length = 247
Score = 295 bits (756), Expect = 4e-81
Identities = 109/226 (48%), Positives = 147/226 (65%), Gaps = 3/226 (1%)
Query: 1 MEGVKIHESWKSLLENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVK 60
+ + E W+ L F + + L +FL E RK I+P F A TP +VK
Sbjct: 18 IIPANLPEDWQEALLPEFSAPYFHELTDFLRQE-RKEYTIYPPAPDVFNALRYTPLGEVK 76
Query: 61 VVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDV-NFIPPTHGFLEHWGHE 119
V+ILGQDPYH QAHGL FSV G+R+PPSL N+YKEL ED+ F+ P HG+L W +
Sbjct: 77 VLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQ 136
Query: 120 GVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQKKQDVLDH 179
GVLLLNAVLTV G+A SH+G+GWE FTD+VI ++ + +VF+LWG+ A+KK+ ++
Sbjct: 137 GVLLLNAVLTVRAGQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITG 196
Query: 180 KRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQIP 225
K H+V+++ HPSPLS FFG R FSK N L++ G+ V WQ+P
Sbjct: 197 KNHVVIESGHPSPLSE-QYFFGTRPFSKTNEALEKAGRGPVEWQLP 241
>2zhx_A UDG, uracil-DNA glycosylase; DNA repair, UNG-UGI complex,
UNG-DNA interactions, cytoplasm, DNA damage; 3.10A
{Mycobacterium tuberculosis} (A:)
Length = 238
Score = 292 bits (749), Expect = 3e-80
Identities = 89/223 (39%), Positives = 128/223 (57%), Gaps = 4/223 (1%)
Query: 4 VKIHESWKSLLENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVKVVI 63
+ W + LE ++ + ++ +FL +E G+R P GS+ RAF PF+ V+V+I
Sbjct: 19 ELVERGWAAALE--PVADQVAHMGQFLRAEIAAGRRYLPAGSNVLRAFT-FPFDNVRVLI 75
Query: 64 LGQDPYHNYGQAHGLCFSVPLGIR-IPPSLVNVYKELQEDVNFIPPTHGFLEHWGHEGVL 122
+GQDPY G A GL FSV +R P SL N++ E D+ + P++G L W GVL
Sbjct: 76 VGQDPYPTPGHAVGLSFSVAPDVRPWPRSLANIFDEYTADLGYPLPSNGDLTPWAQRGVL 135
Query: 123 LLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQKKQDVLDHKRH 182
LLN VLTV ASHRG+GWE T+ I ++ +V +LWG A + +L
Sbjct: 136 LLNRVLTVRPSNPASHRGKGWEAVTECAIRALAARAAPLVAILWGRDASTLKPMLAAGNC 195
Query: 183 LVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQIP 225
+ +++ HPSPLSAS GFFG R FS+AN L G ++W++P
Sbjct: 196 VAIESPHPSPLSASRGFFGSRPFSRANELLVGMGAEPIDWRLP 238
>4eug_A UDG, UNG, protein (glycosylase); 1.40A {Escherichia coli}
(A:45-229)
Length = 185
Score = 265 bits (679), Expect = 4e-72
Identities = 105/180 (58%), Positives = 128/180 (71%), Gaps = 1/180 (0%)
Query: 48 FRAFDITPFNKVKVVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDV-NFI 106
F AF T VKVVILGQDPYH GQAHGL FSV GI IPPSL+N+YKEL+ + F
Sbjct: 1 FNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFT 60
Query: 107 PPTHGFLEHWGHEGVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLW 166
P HG+LE W +GVLLLN VLTV G+A SH GWE FTD VI LI+ + + +VF+LW
Sbjct: 61 RPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLW 120
Query: 167 GASAQKKQDVLDHKRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQIPL 226
G+ AQKK ++D +RH VLKA PSPLSA GFFGC HF AN++L++HG+T ++W L
Sbjct: 121 GSHAQKKGAIIDKQRHHVLKAPQPSPLSAHRGFFGCNHFVLANQWLEQHGETPIDWMPVL 180
>1udg_A Uracil-DNA glycosylase; hydrolase; 1.75A {Herpes simplex
virus} (A:70-244)
Length = 175
Score = 249 bits (638), Expect = 2e-67
Identities = 78/176 (44%), Positives = 101/176 (57%), Gaps = 3/176 (1%)
Query: 50 AFDITPFNKVKVVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDV-NFIPP 108
++V+VVI+GQDPYH+ GQAHGL FSV + PPSL NV ++
Sbjct: 2 WTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNCYPEARMS 61
Query: 109 THGFLEHWGHEGVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGA 168
HG LE W +GVLLLN LTV+ G AASH GW++F VI ++ +VFMLWG
Sbjct: 62 GHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGLVFMLWGT 121
Query: 169 SAQKKQDVLDHKRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQI 224
AQ D + H VLK +HPSPLS F C+HF ANRYL+ + ++W +
Sbjct: 122 HAQNAIR-PDPRVHCVLKFSHPSPLSK-VPFGTCQHFLVANRYLETRSISPIDWSV 175
>3cxm_A Uracil-DNA glycosylase; base excision repair, BER, DNA
damage repair, MSGPP, SGPP, hydrolase, 5-bromouracil,
structural genomics; 1.50A {Leishmania naiffi}
(A:83-268)
Length = 186
Score = 248 bits (635), Expect = 4e-67
Identities = 92/180 (51%), Positives = 124/180 (68%), Gaps = 3/180 (1%)
Query: 49 RAFDITPFNKVKVVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDV-NFIP 107
AF+ PF +KVV+LGQDPYH+ QAHGLCFSV + +PPSL N+YKEL D+ F
Sbjct: 1 NAFNSCPFRGLKVVLLGQDPYHDLHQAHGLCFSVLPEVPLPPSLRNIYKELTTDIAGFQA 60
Query: 108 PTHGFLEHWGHEGVLLLNAVLTVEEGRAASH-RGRGWEQFTDSVIDLIS-NNHQNIVFML 165
P HG+L+ W +G+L+LNA LTVE +A SH + GW FTD+VI +S ++ +VF+L
Sbjct: 61 PKHGYLQSWSEQGMLMLNATLTVEAHKANSHSKTSGWAAFTDAVIQHLSQHHPNRLVFLL 120
Query: 166 WGASAQKKQDVLDHKRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQIP 225
WG AQ+K+ ++D RH+VL+ HPSPLSA+ G+FGCR FS N LQ ++WQ+P
Sbjct: 121 WGGYAQQKKRLIDANRHVVLENVHPSPLSANRGWFGCRCFSACNEALQRMSHLPMHWQLP 180
>2j8x_A Uracil-DNA glycosylase; hydrolase/inhibitor,
hydrolase/inhibitor complex, EBV, DNA repair, lytic
protein, epstein-BARR virus; 2.3A {Epstein-barr virus}
(A:48-231)
Length = 184
Score = 247 bits (631), Expect = 1e-66
Identities = 87/185 (47%), Positives = 112/185 (60%), Gaps = 9/185 (4%)
Query: 48 FRAFDITPFNKVKVVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDV-NFI 106
+ +KVVILGQDPYH GQA+GL FSV G +PPSL N+Y EL + F
Sbjct: 1 MAWARFCDPSDIKVVILGQDPYHG-GQANGLAFSVAYGFPVPPSLRNIYAELHRSLPEFS 59
Query: 107 PPTHGFLEHWGHEGVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLW 166
PP HG L+ W +GVLLLN +LTV++G+ SH GW FTD VI L+S + VFMLW
Sbjct: 60 PPDHGCLDAWASQGVLLLNTILTVQKGKPGSHADIGWAWFTDHVISLLSERLKACVFMLW 119
Query: 167 GASAQKKQDVLDHKRHLVLKAAHPSPL-------SASHGFFGCRHFSKANRYLQEHGKTT 219
GA A K +++ K+HLVL + HPSPL SA F G HF AN +L+E G
Sbjct: 120 GAKAGDKASLINSKKHLVLTSQHPSPLAQNSTRKSAQQKFLGNNHFVLANNFLREKGLGE 179
Query: 220 VNWQI 224
++W++
Sbjct: 180 IDWRL 184
>2owr_A UDG, uracil-DNA glycosylase; uracil-DNA glycosylase fold in
the core: 3 layers (A/B/A); HET: EPE; 2.30A {Vaccinia
virus} PDB: 2owq_A (A:48-218)
Length = 171
Score = 207 bits (528), Expect = 1e-54
Identities = 33/180 (18%), Positives = 60/180 (33%), Gaps = 12/180 (6%)
Query: 48 FRAFDITPFNKVKVVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDVNFIP 107
F P +V + G DPY G+ F P S+ + + +
Sbjct: 3 FIQLK-QPLRNKRVCVCGIDPYPK--DGTGVPFESPNFT--KKSIKEIASSISRLT-GVI 56
Query: 108 PTHGFLEHWGHEGVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWG 167
G+ + GV+ N L+ + G SH W++ + ++ I H ++++ L
Sbjct: 57 DYKGYNLNIID-GVIPWNYYLSCKLGETKSHA-IYWDKISKLLLQHI-TKHVSVLYCLGK 113
Query: 168 ASAQKKQDVLDHKRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQIPLS 227
+ L+ + P + F R F N L+ K +NW
Sbjct: 114 TDFSNIRAKLESPVTTI---VGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFI 170
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
translation termination, ATP-binding, cytoplasm,
hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
(A:1-326)
Length = 326
Score = 41.7 bits (97), Expect = 9e-05
Identities = 15/109 (13%), Positives = 31/109 (28%), Gaps = 12/109 (11%)
Query: 80 FSVPLGIRIPPSLVNV-YKELQEDVNFIPPTHGFLEHWGHEGVLLLNAVLTV---EEGRA 135
++ + + K + D + T G + L + E
Sbjct: 212 MGKYTEVKTAFGIKDSVPKGAKIDAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNM 271
Query: 136 ASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQKKQDVLD-HKRHL 183
+G + + L+ N Q ++F SA + V +R
Sbjct: 272 LDQQG--LGDQSMRIKHLLPRNTQIVLF-----SATFSERVEKYAERFA 313
>2hp0_A IDS-epimerase; MMGE/PRPD fold, 6 helix bundle, chorismate
mutase like, isomerase; HET: MSE CSO; 1.50A
{Agrobacterium tumefaciens} PDB: 2hp3_A*
(A:1-266,A:421-466)
Length = 312
Score = 26.4 bits (58), Expect = 3.0
Identities = 9/41 (21%), Positives = 12/41 (29%), Gaps = 5/41 (12%)
Query: 111 GFLEHWGHEGVLLLNAVLTVEEGRAASHRGRGWEQFTDSVI 151
F GH L+ A+ V H G S +
Sbjct: 112 SFPVXRGHPSSSLVPAIFAV-----GEHVGANGHNCLKSYV 147
>3f44_A Putative monooxygenase; YP_193413.1, structural genomics,
joint center for structural genomics, JCSG; HET: MSE;
1.55A {Lactobacillus acidophilus ncfm} (A:97-206)
Length = 110
Score = 26.3 bits (58), Expect = 3.9
Identities = 4/25 (16%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 6 IHESWKSL--LENHFQSEHMRNLKE 28
E + + + H ++ H + E
Sbjct: 72 FIEVYANDEAYDIHVKTPHYKEYIE 96
>2z3y_A Lysine-specific histone demethylase 1; chromatin,
nucleosome, transcription, LSD1, alternative splicing,
chromatin regulator, coiled coil; HET: F2N; 2.25A {Homo
sapiens} (A:1-98)
Length = 98
Score = 25.5 bits (56), Expect = 6.0
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 101 EDVNFIPPTHGFLEHWG 117
D + H +LE G
Sbjct: 73 SDTVLVHRVHSYLERHG 89
>1q8b_A Protein YJCS; structural genomics, PSI, protein structure
initiative, midwest center for structural genomics,
MCSG, unknown function; 1.90A {Bacillus subtilis} (A:)
Length = 105
Score = 25.5 bits (56), Expect = 6.3
Identities = 5/25 (20%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 6 IHESWKSL--LENHFQSEHMRNLKE 28
+ E W++ ++ HF +H ++++
Sbjct: 65 LWEIWENEEAVKIHFTKKHTIDVQK 89
>1tuv_A Protein YGIN; menadione oxidase, monooxygenase, CO-crystal
with natural product, ferredoxin fold, unknown function;
HET: VK3; 1.70A {Escherichia coli} (A:)
Length = 114
Score = 25.3 bits (55), Expect = 7.5
Identities = 12/67 (17%), Positives = 19/67 (28%), Gaps = 16/67 (23%)
Query: 6 IHESWKSL--LENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVKVVI 63
+ E W+S+ LE H Q+ HM K +I
Sbjct: 62 MIEQWESIAHLEAHLQTPHM--------------KAYSEAVKGDVLEMNIRILQPGISGR 107
Query: 64 LGQDPYH 70
+ +H
Sbjct: 108 VHHHHHH 114
>2omo_A DUF176; structural genomics, APC6266, PSI-2, protein
structure initiative, midwest center for structural
genomics, MCSG, oxidoreductase; HET: MSE; 1.83A
{Nitrosomonas europaea} (A:)
Length = 124
Score = 25.2 bits (55), Expect = 8.6
Identities = 4/25 (16%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 6 IHESWKSL--LENHFQSEHMRNLKE 28
++E++K+ H ++ H ++
Sbjct: 74 LYEAYKTRKDAAAHKETAHYLTWRD 98
>2dce_A KIAA1915 protein; swirm domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} (A:)
Length = 111
Score = 25.2 bits (55), Expect = 8.6
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 102 DVNFIPPTHGFLEHWG 117
DVN I H +LE G
Sbjct: 83 DVNCIGRIHTYLELIG 98
>1miu_A BRCA2, breast cancer type 2 susceptibility protein; tumor
suppressor, breast cancer susceptibility, DNA-binding;
3.10A {Mus musculus} (A:349-387,A:507-596)
Length = 129
Score = 25.2 bits (55), Expect = 8.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 42 PRGSHYFRAFDITPFNKVKVV 62
G + FR+ D+T K++V
Sbjct: 31 VSGLYIFRSRDVTTVWKLRVT 51
>3bm7_A Protein of unknown function with ferredoxin-like fold;
NP_420935.1, antibiotic biosynthesis monooxygenase,
structural genomics; HET: MSE; 1.35A {Caulobacter
crescentus CB15} (A:)
Length = 115
Score = 25.2 bits (55), Expect = 8.8
Identities = 4/25 (16%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 6 IHESWKSL--LENHFQSEHMRNLKE 28
+ E + S L++H +++ +
Sbjct: 72 VLELYASXDALKHHGGTDYFKAAGA 96
>2com_A Lysine-specific histone demethylase 1; swirm domain, LSD1,
AOF2, KIAA0601, histone modulation, structural genomics,
NPPSFA; NMR {Homo sapiens} (A:40-124)
Length = 85
Score = 25.2 bits (55), Expect = 9.0
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 101 EDVNFIPPTHGFLEHWG 117
D + H +LE G
Sbjct: 44 SDTVLVHRVHSYLERHG 60
>3kkf_A Putative antibiotic biosynthesis monooxygenase; structural
genomics, joint center for structural genomics, JCSG;
HET: MSE P6G; 1.30A {Bacteroides thetaiotaomicron} (A:)
Length = 105
Score = 24.8 bits (54), Expect = 10.0
Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 10/57 (17%)
Query: 6 IHESWKSL--LENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVK 60
I E + ++H + H + KE + A + P K K
Sbjct: 57 ILEIYADEAAYKSHIATPHFKKYKEGT----LDXVQXLEL----IDATPLIPGLKXK 105
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.322 0.138 0.436
Gapped
Lambda K H
0.267 0.0621 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,878,432
Number of extensions: 85600
Number of successful extensions: 263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 238
Number of HSP's successfully gapped: 36
Length of query: 227
Length of database: 4,956,049
Length adjustment: 85
Effective length of query: 142
Effective length of database: 2,082,624
Effective search space: 295732608
Effective search space used: 295732608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.4 bits)