RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780743|ref|YP_003065156.1| putative uracil-DNA
glycosylase [Candidatus Liberibacter asiaticus str. psy62]
(261 letters)
>1vk2_A Uracil-DNA glycosylase TM0511; structural genomics, JCSG, PSI,
protein structure initiative, joint center for
structural genomics, hydrolase; 1.90A {Thermotoga
maritima} SCOP: c.18.1.2 PDB: 1l9g_A
Length = 204
Score = 85.8 bits (211), Expect = 9e-18
Identities = 35/194 (18%), Positives = 80/194 (41%), Gaps = 5/194 (2%)
Query: 70 IAQKACSLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFS 129
+ + + + ++ C L + + ++ +G P + ++ +G+PF
Sbjct: 13 MYTREELMEIVSERVKKCTACPLHLNRTNVVVGEGNLDTRIVFVGEGPGEEEDKTGRPFV 72
Query: 130 GKTGNMLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKI 189
G+ G +L ++L+ I R ++I + PP NR + E C ++ QIE+I+P +
Sbjct: 73 GRAGMLLTELLRESGIRREDVYICNVVKCRPPNNRTPTPEEQAACGHFLLAQIEIINPDV 132
Query: 190 LLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYP--LIKKNT 247
++ +G +FF + + G + + T HP L++ +++
Sbjct: 133 IVALGATALSFFVDGKKVSITKVRGNPIDW---LGGKKVIPTFHPSYLLRNRSNELRRIV 189
Query: 248 WHALITLKKALKNL 261
+ K +K
Sbjct: 190 LEDIEKAKSFIKKE 203
>1ui0_A Uracil-DNA glycosylase; base excision repair, iron/sulfer cluster,
thermophIle, riken structural genomics/proteomics
initiative, RSGI; 1.50A {Thermus thermophilus} SCOP:
c.18.1.2 PDB: 1ui1_A
Length = 205
Score = 85.6 bits (211), Expect = 1e-17
Identities = 54/192 (28%), Positives = 90/192 (46%), Gaps = 11/192 (5%)
Query: 76 SLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNM 135
+L L++ ++ C L + LMI+G P + ++ +G+PF GK G +
Sbjct: 2 TLELLQAQAQNCTACRLMEGRTRVVFGEGNPDAKLMIVGEGPGEEEDKTGRPFVGKAGQL 61
Query: 136 LDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICR-PIIMRQIELISPKILLFIG 194
L+++L++ I R +++I+ I PP NR E +IC +++QIELI+P+I++ +G
Sbjct: 62 LNRILEAAGIPREEVYITNIVKCRPPQNRAPLPDEAKICTDKWLLKQIELIAPQIIVPLG 121
Query: 195 NKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYP-----LIKKNTWH 249
FF T GKW I HP L++ P K TW
Sbjct: 122 AVAAEFFLGEKVSITKVR-GKWYEWHG----IKVFPMFHPAYLLRNPSRAPGSPKHLTWL 176
Query: 250 ALITLKKALKNL 261
+ +K+AL L
Sbjct: 177 DIQEVKRALDAL 188
>3ikb_A Uncharacterized conserved protein; APC63946, streptococcus mutans
UA159, structural genomics, PSI-2, protein structure
initiative; HET: FLC; 1.67A {Streptococcus mutans}
Length = 198
Score = 83.8 bits (207), Expect = 4e-17
Identities = 21/187 (11%), Positives = 57/187 (30%), Gaps = 12/187 (6%)
Query: 76 SLHELKSLLRSFHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNM 135
SL E+ + + + + + + I+G P S ++ K+G+
Sbjct: 6 SLEEITKAIMADSQNKVFTEKNIEPLFAAPKTARINIVGQAPGIKAQESRLYWNDKSGDR 65
Query: 136 LDKMLQSIEIM---RTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQI--ELISPKIL 190
L + + + + ++P ++ + + I L ++
Sbjct: 66 LREWMGVDYDTFYHSGYFAVIPMDFYYPGKGKSGDLPPRKGFAQKWHQPILDLLPDIQLT 125
Query: 191 LFIGNKTKNFFFNNDAQKT-YQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWH 249
+ IGN + ++ + + + + VHP Q + ++ W
Sbjct: 126 ILIGNYAQKYYLHQKSSVKLTDTVAHYKKYLP-----DYFPLVHPSPRNQ-IWMSRHPWF 179
Query: 250 ALITLKK 256
+
Sbjct: 180 EAQVVPD 186
>1wyw_A TDG, G/T mismatch-specific thymine DNA glycosylase; hydrolase;
2.10A {Homo sapiens} SCOP: c.18.1.2 PDB: 2d07_A 2rba_A*
Length = 230
Score = 72.3 bits (177), Expect = 1e-13
Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 13/111 (11%)
Query: 106 EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMR-------------TQIHI 152
D++IIG P G + G + + S I
Sbjct: 21 FNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGF 80
Query: 153 SMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFN 203
+ + PG+++LS+ E I++++++ P+I +F G F
Sbjct: 81 TNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSK 131
>1mug_A Protein (G:T/U specific DNA glycosylase); hydrolase; 1.80A
{Escherichia coli} SCOP: c.18.1.2 PDB: 1mtl_A 1mwi_A*
1mwj_A
Length = 168
Score = 71.6 bits (175), Expect = 1e-13
Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 23/166 (13%)
Query: 106 EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSI------------EIMRTQIHIS 153
G ++ G P S +G PF+ + Q+ ++ + ++
Sbjct: 8 PGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVT 67
Query: 154 MISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNL 213
+ +S E+ ++ +IE P+ L +G + F+ Q
Sbjct: 68 KLVDRPTVQANEVSKQELHAGGRKLIEKIEDYQPQALAILGKQAYEQGFS-------QRG 120
Query: 214 GKWSNLCTPHSIIPTLATVHPQELIQYPLIKK-NTWHALITLKKAL 258
+W +P L + L K + L +AL
Sbjct: 121 AQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRE---LDQAL 163
>2c2q_A G/U mismatch-specific DNA glycosylase; radiation resistance, DNA
repair enzymes, uracil-DNA glycosylase, MUG, hydrolase;
1.7A {Deinococcus radiodurans} PDB: 2c2p_A
Length = 199
Score = 59.9 bits (144), Expect = 5e-10
Identities = 19/187 (10%), Positives = 46/187 (24%), Gaps = 25/187 (13%)
Query: 95 TSLSTICATQT--------EGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEI- 145
+ + + G L+++G PS + ++ +
Sbjct: 5 HDVPDLTGSGEYLVPDVLQPGLTLVLVGTAPSGISARARAYYANPENKFWRTLHAVGLTP 64
Query: 146 -----------MRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIG 194
+ + ++ ++ H L + R++E P+I+ F
Sbjct: 65 RQLVPQEYATLPQYGLGLTDVAKRHSGVAAALPGEAWRPDE--LRRKVEHYRPRIVAFTS 122
Query: 195 NKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHALITL 254
+ + K G + L + W AL
Sbjct: 123 KRGASETLGVPTGKL--PYGPQPQPLDWPAETELWVLPSTSPLGHNHF-RLEPWQALGDR 179
Query: 255 KKALKNL 261
+ L+
Sbjct: 180 VRELRGA 186
>2d3y_A Uracil-DNA glycosylase; base excision repair, iron/sulfer cluster,
thermophIle, structural genomics, NPPSFA; HET: DU; 1.55A
{Thermus thermophilus HB8} PDB: 2ddg_A* 2dem_A* 2dp6_A*
Length = 219
Score = 54.1 bits (129), Expect = 3e-08
Identities = 17/167 (10%), Positives = 39/167 (23%), Gaps = 16/167 (9%)
Query: 109 DLMIIGYTPSDSDNISGKP--FSGKTGNMLDKMLQSIEIMRTQIHISMIS---------- 156
+++ G P + +G L +L + +
Sbjct: 52 RILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGDDLRLYGVYLTA 111
Query: 157 --PWHPPGNRNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQNLG 214
PP N+ R + L ++ + +G + + +
Sbjct: 112 AVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVALGRIALEALLAHFGLRKSAHPF 171
Query: 215 KWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTWHALITLKKALKNL 261
+ LA+ H + T + + K L
Sbjct: 172 RHGAHYPLPGGRHLLASYHVSRQNTQT--GRLTREMFLEVLMEAKRL 216
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 48.0 bits (114), Expect = 2e-06
Identities = 48/278 (17%), Positives = 89/278 (32%), Gaps = 76/278 (27%)
Query: 2 TSKR--ILSQEQILTIALFYADSGVYWVFDEPNNEATYESQRKEKSIDSAIQPITNIRH- 58
S R LS + V P SQ +E+ +P
Sbjct: 4 YSTRPLTLSHGSLEH------------VLLVPTASFFIASQLQEQFNKILPEPTEGFAAD 51
Query: 59 --IHSP--LVQQ-----ADSIAQKACSLHE--LKSLLRSFHDCHLCSTSLSTICA----- 102
+P LV + + + + L L F +C+L + + A
Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 103 ---TQTEGQDLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQSIEIMRTQIHISMISPWH 159
T + ++L+ T + ++ +PF K+ + L +++ Q+ I +
Sbjct: 112 NDTTLVKTKELIKNYIT---ARIMAKRPFDKKSNSAL---FRAVGEGNAQLV--AI--FG 161
Query: 160 PPGN--------RNLSNIEMEICRPIIMRQIELISPKILLFIGNKTKNFFFNNDAQKTYQ 211
GN R+L ++ I+ + + I DA+K +
Sbjct: 162 GQGNTDDYFEELRDLYQTY----HVLVGDLIKFSAETLSELIRTTL-------DAEKVFT 210
Query: 212 ---NLGKWSNLCTPHSIIPT---LATVHPQELIQYPLI 243
N+ +W L P + P L ++ P I PLI
Sbjct: 211 QGLNILEW--LENPSN-TPDKDYLLSI-P---ISCPLI 241
Score = 39.2 bits (91), Expect = 9e-04
Identities = 32/161 (19%), Positives = 49/161 (30%), Gaps = 86/161 (53%)
Query: 60 HSPLVQ---------QADS------IAQKACSLHELKSL----LRSFHDCHLC--STSLS 98
HS Q + DS +KA ++ L +R C+ +TSL
Sbjct: 273 HS---QGLVTAVAIAETDSWESFFVSVRKAITV-----LFFIGVR----CYEAYPNTSLP 320
Query: 99 TICATQTEGQDLMIIGYTPS---DS-DNISGKPFSGKTGNMLD------KMLQSIEIMRT 148
PS DS +N G P ML + +Q + +T
Sbjct: 321 ------------------PSILEDSLENNEGVP-----SPMLSISNLTQEQVQDY-VNKT 356
Query: 149 --------QIHISMI-SPWH-----PP----G-NRNLSNIE 170
Q+ IS++ + PP G N L +
Sbjct: 357 NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Score = 39.2 bits (91), Expect = 9e-04
Identities = 36/236 (15%), Positives = 58/236 (24%), Gaps = 125/236 (52%)
Query: 1 MTSKRILSQEQILTIALFYADSGVYWVFDEPNNEATYESQRKEKSIDSAIQPITNI---- 56
M S L+QEQ+ + ++ TN
Sbjct: 338 MLSISNLTQEQV------------------------------QDYVNK-----TNSHLPA 362
Query: 57 -RHIHSPLVQQADS--IAQKACSLHELKSLLRS--------------------------- 86
+ + LV A + ++ SL+ L LR
Sbjct: 363 GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP 422
Query: 87 ----FHDCHLCSTSLSTICATQTEGQDLMIIGYTPSDSDNISGK----P-FSGKTGNMLD 137
FH L A+ +DL ++ + + K P + G+ L
Sbjct: 423 VASPFHSHLLVP-------ASDLINKDL------VKNNVSFNAKDIQIPVYDTFDGSDLR 469
Query: 138 KMLQSIEIMRTQIH--ISMI--SP--W---------H----PPG---------NRN 165
+ SI + I P W H PG +RN
Sbjct: 470 VLSGSI------SERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519
Score = 32.2 bits (73), Expect = 0.12
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 27 VFDEPNNEATYESQRKEKSIDSAIQPITNIRHIHSPLVQQADSIAQKACSLHELKS 82
+F E N +T + R EK + SA Q Q A ++ +KA + +LKS
Sbjct: 1706 IFKEINEHSTSYTFRSEKGLLSATQ-----------FTQPALTLMEKA-AFEDLKS 1749
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 28.2 bits (62), Expect = 2.0
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 20/64 (31%)
Query: 123 ISGKPFSGKTGN-MLDKMLQSIEIMRTQIHISMISPWHPPGNRNLSNIEMEICRPIIMRQ 181
++G P G G M++ LQ I+ + I PGNRN N++ I+ Q
Sbjct: 1381 LTGHP-KGAAGAWMMNGALQ---ILNSGI---------IPGNRNADNVDK------ILEQ 1421
Query: 182 IELI 185
E +
Sbjct: 1422 FEYV 1425
>2o9c_A Bacteriophytochrome; phytochrome chromophore, figure-OF-eight knot,
phytochromobilin, biliverdin, PAS, GAF, transferase;
HET: LBV; 1.45A {Deinococcus radiodurans} SCOP:
d.110.2.1 d.110.3.9 PDB: 2o9b_A* 1ztu_A*
Length = 342
Score = 28.1 bits (62), Expect = 2.1
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 2/43 (4%)
Query: 50 IQPITNIRHIHSPLVQQADSIAQKACSLHELKSLLRSFHDCHL 92
++ + R PL + L ++LR+ H+
Sbjct: 236 LRLTADTRAAAVPLDPVLNPQTNAPTPLGG--AVLRATSPMHM 276
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 27.8 bits (61), Expect = 2.7
Identities = 9/61 (14%), Positives = 17/61 (27%), Gaps = 1/61 (1%)
Query: 189 ILLFIGNKTKNFFFNNDAQKTYQNLGKWSNLCTPHSIIPTLATVHPQELIQYPLIKKNTW 248
+ + + TK + K Y L + I+ + Q P +K
Sbjct: 109 LPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKE-FTGRIYQRPPLKAAVK 167
Query: 249 H 249
Sbjct: 168 R 168
>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET:
DNA; 2.30A {Bacteriophage T7} SCOP: c.37.1.11 PDB:
1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*
Length = 296
Score = 27.3 bits (59), Expect = 3.5
Identities = 9/147 (6%), Positives = 36/147 (24%), Gaps = 4/147 (2%)
Query: 109 DLMIIGYTPSDSDNISGKPFSGKTGNMLDKMLQ-SIEIMRTQIHISMISPWHPPGNRNLS 167
+ +G + ++ GK+ + + LQ + + + +
Sbjct: 26 NDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIG 85
Query: 168 NIEMEICRPIIMRQIELISPKILLFIGNK---TKNFFFNNDAQKTYQNLGKWSNLCTPHS 224
R + E+I ++ F + + +
Sbjct: 86 LHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSG 145
Query: 225 IIPTLATVHPQELIQYPLIKKNTWHAL 251
+ + + ++ + + +
Sbjct: 146 LGCDVIILDHISIVVSASGESDERKMI 172
>2ool_A Sensor protein; bacteriophytochrome, photoconversion,
photoreceptor, biliverdin, signaling protein; HET: LBV;
2.20A {Rhodopseudomonas palustris CGA009} SCOP:
d.110.2.1 d.110.3.9
Length = 337
Score = 27.4 bits (60), Expect = 3.6
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 53 ITNIRHIHSPLVQQADSIAQKACSLHELKSLLRSFHDCHL 92
I +I + SPLV + L S+LRS HL
Sbjct: 233 IPDIGYRPSPLVPDINPRLGGPIDLSF--SVLRSVSPTHL 270
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, protein structure initiative;
1.90A {Mycobacterium tuberculosis H37RV} SCOP: b.122.1.1
d.265.1.2
Length = 316
Score = 26.2 bits (57), Expect = 7.2
Identities = 9/73 (12%), Positives = 19/73 (26%), Gaps = 5/73 (6%)
Query: 190 LLFIGNKTKNFFFNNDAQKTYQNLGKW-----SNLCTPHSIIPTLATVHPQELIQYPLIK 244
++ I TK A K+Y + + + A E I + +
Sbjct: 50 VIGIERATKILGLLTAAPKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMER 109
Query: 245 KNTWHALITLKKA 257
+ +
Sbjct: 110 LRGEIRQVPSSVS 122
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.133 0.397
Gapped
Lambda K H
0.267 0.0592 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,154,352
Number of extensions: 92424
Number of successful extensions: 259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 252
Number of HSP's successfully gapped: 21
Length of query: 261
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 170
Effective length of database: 3,487,026
Effective search space: 592794420
Effective search space used: 592794420
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 (21.8 bits)
S2: 56 (25.7 bits)