RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780995|ref|YP_003065408.1|
Endonuclease/exonuclease/phosphatase [Candidatus Liberibacter
asiaticus str. psy62]
(125 letters)
>2f1n_A CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I,
microbatch; 1.73A {Escherichia coli} SCOP: d.151.1.1
Length = 262
Score = 32.4 bits (72), Expect = 0.027
Identities = 17/115 (14%), Positives = 30/115 (26%), Gaps = 14/115 (12%)
Query: 4 QQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQEKESTC 63
++ + + + + ++I GDFN D P +T
Sbjct: 161 EEVYNFFRDSRDPVHQALNWMILGDFN-----REPADLEMNLTVPVRRASEIISPAAATQ 215
Query: 64 NVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEY 118
+ LDY V S + R S H P+ +
Sbjct: 216 TSQRT----LDYAVAGNSVA-----FRPSPLQAGIVYGARRTQISSDHFPVGVSR 261
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A
{Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A
Length = 317
Score = 30.7 bits (68), Expect = 0.082
Identities = 20/125 (16%), Positives = 35/125 (28%), Gaps = 14/125 (11%)
Query: 3 SQQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQEKEST 62
Q E + I I GD N + + D + ++ + +L
Sbjct: 189 EQMKEISDFVKKKNIPKDETVYIGGDLNVNKGT-PEFKDMLKNLNVNDVLYAGHNSTWDP 247
Query: 63 C-------NVIKRNKSSLDYFVIDRDNK------NFLIDNSFSIVSYDQSDLDTRRSKLS 109
N LDY D+D+K N ++ + + S
Sbjct: 248 QSNSIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAAAYYYVYNDFS 307
Query: 110 THCPL 114
H P+
Sbjct: 308 DHYPI 312
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein;
alpha-beta protein, structural genomics, PSI-2; 2.50A
{Bacteroides vulgatus atcc 8482}
Length = 267
Score = 29.6 bits (65), Expect = 0.19
Identities = 20/119 (16%), Positives = 35/119 (29%), Gaps = 7/119 (5%)
Query: 4 QQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIG-DTDDFWQKMDPDGLLIRFPQEKEST 62
Q + + + I P V+ GDFN S +T + + D
Sbjct: 149 QSALLIIRKIKE-IVGERPAVVTGDFNVTDASDAYETITTNEFVMKDAYKTAARVTGVDY 207
Query: 63 CNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYDFE 121
+ D ID + + S + + + LS H P + + E
Sbjct: 208 TFHDFARIPAEDCEKIDF----IFVTPQVLVKSC-EIPAEVPEALLSDHNPQLADLELE 261
>2fim_A Tubby related protein 1; tubby filled-barrel, beta-barrel,
filled-beta-roll, 12- stranded-beta-barrel,
helix-filled-barrel, retinitis pigmentosa; HET: 3DP;
1.90A {Homo sapiens} PDB: 1s31_A*
Length = 276
Score = 29.5 bits (66), Expect = 0.21
Identities = 18/101 (17%), Positives = 41/101 (40%), Gaps = 21/101 (20%)
Query: 36 IGDTDDFWQKMDPDGLLIRFPQEKESTCN-VIKRNKSSLDY-------FVIDRDNKNFLI 87
+G + ++Q M+P ++R P + T + R+K +D +D + K FL+
Sbjct: 13 LGTENLYFQSMEPREFVLR-PAPQGRTVRCRLTRDKKGMDRGMYPSYFLHLDTEKKVFLL 71
Query: 88 --------DNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYDF 120
+ ++S D ++L S+ + + +
Sbjct: 72 AGRKRKRSKTANYLISIDPTNL----SRGGENFIGKLRSNL 108
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: 1PE; 1.90A
{Neisseria meningitidis}
Length = 256
Score = 28.6 bits (62), Expect = 0.42
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 73 LDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYDF 120
+D+ ++ L D V + L+ + S H P+T E+D+
Sbjct: 216 IDHILVSPAMAAALKD---VRVDLETRALE----RPSDHAPVTAEFDW 256
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 28.4 bits (61), Expect = 0.53
Identities = 20/127 (15%), Positives = 34/127 (26%), Gaps = 13/127 (10%)
Query: 1 MLSQQGEWLKKWADQKIKTGIPFVIAGDFNRKINS--IGDTDDFWQKMDPDGLLIRFPQE 58
Q E A + I I GD N + D P +
Sbjct: 168 RAEQMQEIQTFIAKKNIPKDEIIFIGGDLNVNYGTDEYHDMLKLLNVSSPANFNGQMATW 227
Query: 59 KESTCNVIKRNKSS-----LDYFVIDRDNK------NFLIDNSFSIVSYDQSDLDTRRSK 107
+T +++K + LDY ++ + N ++ S
Sbjct: 228 DPTTNSMLKESYPKAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQD 287
Query: 108 LSTHCPL 114
S H P+
Sbjct: 288 FSDHYPV 294
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken
structural genomics/proteomics initiative, RSGI,
structural genomics, hydrolase; 1.40A {Bacillus cereus}
SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X
Length = 306
Score = 27.6 bits (59), Expect = 0.89
Identities = 16/139 (11%), Positives = 32/139 (23%), Gaps = 18/139 (12%)
Query: 1 MLSQQGEWLKKWADQKIKTGIPFVIAGDFNRKINS------------IGDTDDFWQKMDP 48
+Q E ++ I +I GD N + +
Sbjct: 168 RTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTG 227
Query: 49 DGLLIRFPQEKESTCNVIKRNKSSLDYFVIDRDNK------NFLIDNSFSIVSYDQSDLD 102
+ N LDY + +D+ N ++ +
Sbjct: 228 HTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQK 287
Query: 103 TRRSKLSTHCPLTIEYDFE 121
+ S H P+ +
Sbjct: 288 YTYNDYSDHYPVEATISMK 306
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 27.5 bits (61), Expect = 0.94
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 19 TGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQ 57
T + AGD R + ++ + PD +L R P+
Sbjct: 178 TDLSPAPAGDVRRGLETVRA-AELTVTGTPDDVLARLPE 215
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein,
enterococcus faecalis V583, PSI-2, MCSG, structural
genomics; 1.60A {Enterococcus faecalis}
Length = 257
Score = 27.1 bits (58), Expect = 1.0
Identities = 19/119 (15%), Positives = 30/119 (25%), Gaps = 7/119 (5%)
Query: 4 QQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQEKESTC 63
G + P ++ GDFN + + QK D + T
Sbjct: 142 LAGMTVILEELHDKIAQYPTLLMGDFNAESGE--EVHQLVQKKFQDSKNLATHYGPRGTF 199
Query: 64 NVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYDFEK 122
K + ID ++ + + S H PL E E
Sbjct: 200 QNFTYTKPWAELEEID-----YIYVKGWQVQQTASLTDSIDGRFPSDHFPLEAEVAGEN 253
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.5 bits (57), Expect = 1.5
Identities = 6/22 (27%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 58 EKESTCNVIKRNKSSLDYFVID 79
EK++ +K+ ++SL + D
Sbjct: 18 EKQA----LKKLQASLKLYADD 35
>1sr4_B CDT B, cytolethal distending toxin protein B; bacterial, virulence,
DNA damage, genotoxin, cytotoxins, cell cycle,
apoptosis, lectin; 2.00A {Haemophilus ducreyi} SCOP:
d.151.1.1 PDB: 2f2f_B
Length = 261
Score = 26.3 bits (56), Expect = 2.0
Identities = 15/113 (13%), Positives = 31/113 (27%), Gaps = 14/113 (12%)
Query: 4 QQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQEKESTC 63
+ + +++ GDFNR + Q+ I + +
Sbjct: 153 NIFTTFNSSSSPPERRVYSWMVVGDFNRAPAN--LEVALRQEPAVSENTIIIAPTEPTH- 209
Query: 64 NVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRR---SKLSTHCP 113
R+ + LDY ++ + + L + S H P
Sbjct: 210 ----RSGNILDYAILHDA----HLPRREQARERIGASLMLNQLRSQITSDHFP 254
>2nyk_A M157; LY49, NK cells, viral protein; HET: NAG FUC; 2.10A {Murid
herpesvirus 1}
Length = 285
Score = 26.0 bits (57), Expect = 2.4
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 7/38 (18%)
Query: 87 IDNSFSIVSYDQSDLDTRRSKLSTHCP----LTIEYDF 120
+DN +V +D D D + K+ CP IEY F
Sbjct: 41 VDNGRPVVVWDVGDRDPKICKI---CPDVSSTDIEYVF 75
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 25.8 bits (55), Expect = 2.5
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 73 LDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYDF 120
+DY ++ + + + V D+ K S H PL +EYD+
Sbjct: 220 IDYQMVTPELAAKAVS---AHVYKDE--------KFSDHAPLVVEYDY 256
>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix,
tumour suppressor, DNA damage, DNA recombination, DNA
repair, hydrolase, magnesium; NMR {Mus musculus}
Length = 87
Score = 25.9 bits (57), Expect = 2.9
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 7 EWLKKWADQKIKTGIPFVIAGDFNRKINSI 36
WL +W D+ G F + + S+
Sbjct: 20 RWLTEWRDEAASRGRHTRFV--FQKALRSL 47
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5'
exonuclease, AP endonuclease; HET: PG4; 1.23A
{Methanothermobacter thermautotrophicusorganism_taxid}
PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A*
3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A
Length = 265
Score = 25.4 bits (55), Expect = 3.3
Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 20/95 (21%)
Query: 28 DFNRKINSIGDTDDFWQKMDPDGLLIRFP-QEKESTCNVIKRNKSSLDYFVIDRDNKNFL 86
+ K G D F G + + + NV R LDYF ++ + K +
Sbjct: 179 AWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWR----LDYFFVNEEFKGKV 234
Query: 87 IDNSFSIVSYDQ--SDLDTRRSKLSTHCPLTIEYD 119
S + D SD HCP+ +E +
Sbjct: 235 KR---SWILSDVMGSD----------HCPIGLEIE 256
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.7 bits (55), Expect = 3.5
Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 30/102 (29%)
Query: 2 LSQQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFW-QKMDPDGLLIRFPQEKE 60
L+Q+ E ++KW +++ K + D K+ + W +K D L + Q +
Sbjct: 80 LTQEPESIRKWREEQRKR----LQELDAASKV-----MEQEWREKAKKD--LEEWNQRQS 128
Query: 61 STCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLD 102
+++NK + N + D +F Y Q D D
Sbjct: 129 EQ---VEKNKIN-----------NRIADKAF----YQQPDAD 152
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 25.4 bits (54), Expect = 3.6
Identities = 17/124 (13%), Positives = 32/124 (25%), Gaps = 21/124 (16%)
Query: 7 EWLKKWADQKIKTGIPFVIAGDFN--------RKINSIGDTDDFWQKMDPDGLLIRFPQE 58
E +K+ + + GD N ++ ++ GD +L
Sbjct: 135 EQIKRVERKM--GPKRLIFGGDANAKSTWWGSKEDDARGDQLMGTLGELGLHILNEGDVP 192
Query: 59 KESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEY 118
T KR +S +D D + + S H +
Sbjct: 193 TFDTIRGGKRYQSRVDVTFCTEDMLDLIDGWRVD-----------EDLVSSDHNGMVFNI 241
Query: 119 DFEK 122
+K
Sbjct: 242 RLQK 245
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease,
lyase; 1.7A {Archaeoglobus fulgidus}
Length = 257
Score = 25.0 bits (53), Expect = 4.9
Identities = 8/47 (17%), Positives = 12/47 (25%), Gaps = 7/47 (14%)
Query: 73 LDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYD 119
D + +D + K S H PL +D
Sbjct: 217 GDAILATPPLAERCVD---CYADIKPRLAE----KPSDHLPLVAVFD 256
>2rk9_A Glyoxalase/bleomycin resistance protein/dioxygenase; NYSGXRC,
structural genomics, protein structure initiative II;
1.60A {Vibrio splendidus 12B01}
Length = 145
Score = 25.0 bits (53), Expect = 5.2
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 47 DPDGLLIRFPQEKE 60
PDG L RF Q+
Sbjct: 124 TPDGYLFRFCQDIH 137
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 24.8 bits (53), Expect = 5.6
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 11/48 (22%)
Query: 73 LDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYDF 120
LDYFV+ ++++D S HCP +
Sbjct: 430 LDYFVVSSRLASYVVD---CFPMPTV--------MGSDHCPFQMWMRH 466
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia
coli} SCOP: d.151.1.1
Length = 268
Score = 24.7 bits (52), Expect = 5.8
Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 13/93 (13%)
Query: 28 DFNRKINSIGDTDDFWQ--KMDPDGLLIRFPQEKESTCNVIKRNKSSLDYFVIDRDNKNF 85
++ ++ S G D F D + K N R +D + +
Sbjct: 185 EWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLR----IDLLLASQPLAEC 240
Query: 86 LIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEY 118
++ + + Y+ ++ K S H P+ +
Sbjct: 241 CVE---TGIDYEIRSME----KPSDHAPVWATF 266
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A
{Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A*
2o3c_A
Length = 285
Score = 24.6 bits (52), Expect = 6.4
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 11/47 (23%)
Query: 73 LDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYD 119
LDYF++ L D+ ++ S HCP+T+
Sbjct: 249 LDYFLLSHSLLPALCDSKIR-----------SKALGSDHCPITLYLA 284
>1xrk_A Bleomycin resistance protein; arm exchange, ligand binding protein,
thermostable mutant, antibiotic inhibitor; HET: BLM;
1.50A {Streptoalloteichus hindustanus} SCOP: d.32.1.2
PDB: 2zhp_A* 1byl_A
Length = 124
Score = 24.6 bits (52), Expect = 7.0
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 47 DPDGLLIRFPQEKE 60
DP G + F E++
Sbjct: 110 DPAGNCVHFVAEEQ 123
>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 = 24.5 bits (53), Expect = 7.4
Identities = 6/25 (24%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 16 KIK--TGIPFVIAGDFNRKINS-IG 37
+ K TG+ ++AG + + G
Sbjct: 518 RNKDGTGVRVIVAGTLDINPDDDYG 542
>3g7p_A Nitrogen fixation protein; YP_002425942.1, NIFX-associated
protein of unknown function, DUF269, structural
genomics; HET: SO4 PG6; 2.00A {Acidithiobacillus
ferrooxidans ATCC23270}
Length = 156
Score = 24.2 bits (53), Expect = 9.3
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 6 GEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDD 41
G W +K +D ++ P+V+ + R I IGD D
Sbjct: 33 GTW-EKKSDMELLA--PYVLDKEQRRAIPIIGDPDP 65
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 0.137 0.416
Gapped
Lambda K H
0.267 0.0450 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,127,725
Number of extensions: 46940
Number of successful extensions: 156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 34
Length of query: 125
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 44
Effective length of database: 3,729,466
Effective search space: 164096504
Effective search space used: 164096504
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 (21.7 bits)
S2: 51 (24.1 bits)