RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780797|ref|YP_003065210.1| hypothetical protein
CLIBASIA_03440 [Candidatus Liberibacter asiaticus str. psy62]
(231 letters)
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A
{Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A
Length = 317
Score = 61.9 bits (149), Expect = 1e-10
Identities = 28/223 (12%), Positives = 65/223 (29%), Gaps = 28/223 (12%)
Query: 5 QRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIK 64
+++ S N+ LS + L+ + + + D+V E A
Sbjct: 28 TDLKLVSHNVYMLSTVLYPN------WGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASD 81
Query: 65 RVFPNDKWDILYSGSNTDKHAMHTAIVIRKGA--------------IHLLQKSYLPMDTE 110
++ N K + Y + + + +K +
Sbjct: 82 KLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSG 141
Query: 111 GLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQW 170
+ V E +G+ + ++ H +S + Q + +
Sbjct: 142 CGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDR----KIRAEQMKEISDF 197
Query: 171 VDQKNNLN-MPFIIAGDFNRKINHSHSGIKDELWQKINQDNTL 212
V +KN I GD N + + ++ + +N ++ L
Sbjct: 198 VKKKNIPKDETVYIGGDLN---VNKGTPEFKDMLKNLNVNDVL 237
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas;
INPP5BA,phosphoinositide 5-phosphatase, inositol
signalling, phosphatase, magnesium; HET: PIF; 2.40A
{Homo sapiens}
Length = 313
Score = 59.4 bits (143), Expect = 7e-10
Identities = 29/223 (13%), Positives = 61/223 (27%), Gaps = 27/223 (12%)
Query: 6 RIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI-------- 57
R ++N+N S K + L+ L + D V QE+
Sbjct: 9 RFFAGTYNVNGQSPKECLRLW-------------LSNGIQAPDVYCVGFQELDLSKEAFF 55
Query: 58 -----GSYEAIKRVFPNDKWDILYSGSNT-DKHAMHTAIVIRKGAIHLLQKSYLPMDTEG 111
E K V D Y+ + + +++ + + G
Sbjct: 56 FHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTG 115
Query: 112 LDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWV 171
+ + G + V I F+ I +++ HL + +
Sbjct: 116 IMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLP 175
Query: 172 DQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMR 214
+ + + GD N +I +L ++ +
Sbjct: 176 PLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAY 218
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 52.2 bits (123), Expect = 9e-08
Identities = 26/234 (11%), Positives = 63/234 (26%), Gaps = 26/234 (11%)
Query: 3 LAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEA 62
+I S N+ S + + L+ + + D+V L E A
Sbjct: 7 YPGNFKITSHNVYLFSRNI------YPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSA 60
Query: 63 IKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKS--------------YLPMD 108
R+ N + + + + L+
Sbjct: 61 SHRLLNNLREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQ 120
Query: 109 TEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLK 168
G + + + +G+ ++ H ++ L S + S + T++
Sbjct: 121 RGGGADRLSNKGFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSRAIRAEQMQEIQTFIA 180
Query: 169 QWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHN 222
+ K+ I GD N + + ++ + +N + +
Sbjct: 181 KKNIPKDE---IIFIGGDLN---VNYGTDEYHDMLKLLNVSSPANFNGQMATWD 228
>3nr8_B Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; structural
genomics consortium, SGC, trisphosphate 5-phosphatase 2,
SHIP2, INPPL1, SHIP-2; 2.80A {Homo sapiens}
Length = 316
Score = 52.1 bits (124), Expect = 1e-07
Identities = 26/204 (12%), Positives = 60/204 (29%), Gaps = 12/204 (5%)
Query: 6 RIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADI--VCLQEIGS---- 59
+ I +WN+ ++ V S L + + DI QE
Sbjct: 9 SVFIGTWNMGSVPPPKNV----TSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDRE 64
Query: 60 -YEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGK 118
+ ++ + + A++++ + + G+ + G
Sbjct: 65 WLDLLRGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGN 124
Query: 119 RRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLN 178
+ AV + F +G ++ HL S + + L L + +
Sbjct: 125 KGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRL-LSLGDRQLNAFDISLRF 183
Query: 179 MPFIIAGDFNRKINHSHSGIKDEL 202
GD N +++ I + +
Sbjct: 184 THLFWFGDLNYRLDMDIQEILNYI 207
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein;
structural genomics, PSI-2, protein structure
initiative; HET: MSE PEG; 1.90A {Bacteroides
thetaiotaomicron}
Length = 298
Score = 52.0 bits (123), Expect = 1e-07
Identities = 27/187 (14%), Positives = 57/187 (30%), Gaps = 12/187 (6%)
Query: 4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI--GSYE 61
+ +AS+N+ N + + Y ++ + + D DI QE +
Sbjct: 4 PTSLTVASYNLRNANGSDSA--RGDGW---GQRYPVIAQMVQYHDFDIFGTQECFLHQLK 58
Query: 62 AIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRA 121
+K P + I + H+AI R +++K + G
Sbjct: 59 DMKEALPGYDY-IGVGRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVPSKGWDAV 117
Query: 122 VEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPF 181
+ + ++ +I + ++ + N+P
Sbjct: 118 LPRICSW----GHFKCKDTGFEFLFFNLHMDHIGKKARVESAFLVQEKMKELGRGKNLPA 173
Query: 182 IIAGDFN 188
I+ GDFN
Sbjct: 174 ILTGDFN 180
>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 = 51.7 bits (122), Expect = 1e-07
Identities = 31/203 (15%), Positives = 62/203 (30%), Gaps = 32/203 (15%)
Query: 4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEA- 62
R+A+WN+ ++ + + Q + + DI+ +QE GS +
Sbjct: 13 LTDFRVATWNLQGA----------SATTESKWNINVRQLISGENAVDILAVQEAGSPPST 62
Query: 63 ---IKRVFPNDKWDILYSGSNTDK-------HAMHTAIVIRKGAIHLLQKSYLPMDTEGL 112
RV P+ + N + +A+ G ++L S D +
Sbjct: 63 AVDTGRVIPSPGIPVRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSNRRADEVFV 122
Query: 113 DSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVD 172
S + L + H + D+ L + +
Sbjct: 123 LSPVRQGG--RPLLGIRIGNDAFFTAHAIAMRNNDA---------PALVEEVYNFFRDSR 171
Query: 173 QKNNLNMPFIIAGDFNRKINHSH 195
+ + ++I GDFNR+
Sbjct: 172 DPVHQALNWMILGDFNREPADLE 194
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein;
alpha-beta protein, structural genomics, PSI-2; 2.50A
{Bacteroides vulgatus atcc 8482}
Length = 267
Score = 51.6 bits (122), Expect = 1e-07
Identities = 24/192 (12%), Positives = 61/192 (31%), Gaps = 31/192 (16%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI--GSYEAIK 64
+R A++NI + + + ++ + ++ + + DIV +QE+ ++ ++
Sbjct: 4 VRWATFNIRYDNPQDSLNNWQYR-------KDRVCQFIKDHELDIVGMQEVLHNQFQDLR 56
Query: 65 RVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDS------KAGK 118
P + + + + RK +L + +
Sbjct: 57 AGLPEYDGIGVGR-DDGKTAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGMMGWDAVCV 115
Query: 119 RRAVEILFEV--DGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNN 176
R A F+ G+ ++ H + A + + + +
Sbjct: 116 RIATWAKFKDKATGKIFMAVNTHFDHVGEEARRQ------------SALLIIRKIKEIVG 163
Query: 177 LNMPFIIAGDFN 188
P ++ GDFN
Sbjct: 164 -ERPAVVTGDFN 174
>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 = 50.9 bits (120), Expect = 2e-07
Identities = 25/212 (11%), Positives = 58/212 (27%), Gaps = 29/212 (13%)
Query: 4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGS---- 59
++A+WN+ S + + + Q + + ADI+ +QE GS
Sbjct: 2 LSDFKVATWNLQGSSAVNESKW----------NINVRQLLSGEQGADILMVQEAGSLPSS 51
Query: 60 -------YEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGL 112
+ W++ + ++ + + ++L S D +
Sbjct: 52 AVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFI 111
Query: 113 DSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVD 172
+ +H + D++ T
Sbjct: 112 VHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIR--------NIFTTFNSSSS 163
Query: 173 QKNNLNMPFIIAGDFNRKINHSHSGIKDELWQ 204
+++ GDFNR + ++ E
Sbjct: 164 PPERRVYSWMVVGDFNRAPANLEVALRQEPAV 195
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling,
SGC stockholm, structural genomics CONS hydrolase; 1.90A
{Homo sapiens}
Length = 357
Score = 46.2 bits (109), Expect = 7e-06
Identities = 32/217 (14%), Positives = 65/217 (29%), Gaps = 29/217 (13%)
Query: 6 RIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADI--VCLQEIGSYE-- 61
+ +A+WN+ E + L D+ + +QE S
Sbjct: 27 ALFVATWNMQGQKE------------LPPSLDEFLLPAEADYAQDLYVIGVQEGCSDRRE 74
Query: 62 ---AIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGK 118
++ + +L S + ++ ++ IR+ I + T + S+
Sbjct: 75 WETRLQETL-GPHYVLLSSAA---HGVLYMSLFIRRDLIWFCSEVECSTVTTRIVSQIKT 130
Query: 119 RRAVEILFEVDGRKIWLLDIHLKS-FCFLDSIEDSYISSCYMLNLQA-----TWLKQWVD 172
+ A+ I F G + H S + Y + L L +
Sbjct: 131 KGALGISFTFFGTSFLFITSHFTSGDGKVAERLLDYTRTVQALVLPRNVPDTNPYRSSAA 190
Query: 173 QKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQD 209
GDFN +++ + + L Q + D
Sbjct: 191 DVTTRFDEVFWFGDFNFRLSGGRTVVDALLCQGLVVD 227
>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 = 45.7 bits (108), Expect = 8e-06
Identities = 40/259 (15%), Positives = 75/259 (28%), Gaps = 119/259 (45%)
Query: 32 REDNDY-----------ALLQ--KYAEQLDADIVCLQEIGSYEAIKRVF---PNDKWDIL 75
D DY ++Q Y + ++ P + L
Sbjct: 225 TPDKDYLLSIPISCPLIGVIQLAHYV------VTA-----------KLLGFTPGELRSYL 267
Query: 76 YSGSNTDKHAMH-----TAIVIRKGAIHLLQKSYLPMDT-EGLDSKAGKRRAVEILFEVD 129
G+ H TA+ I A D+ E R+A+ +LF
Sbjct: 268 -KGA-----TGHSQGLVTAVAI---AE---------TDSWESFFVSV--RKAITVLF--- 304
Query: 130 GRKIWLLDIHLKSF-CF----L------DSIEDSYISSCYML---NLQATWLKQWVDQKN 175
+ I ++ + + L DS+E++ ML NL ++ +V++ N
Sbjct: 305 ----F---IGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN 357
Query: 176 N-----------L-NMP--FIIAGD------FN---RKINHSHSGIKDELWQKINQDNTL 212
+ L N +++G N RK ++Q
Sbjct: 358 SHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP---------SGLDQS--- 405
Query: 213 MRLPHKKNHNAIRTKILKI 231
R+P + + L +
Sbjct: 406 -RIPFSERKLKFSNRFLPV 423
>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3,
structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus}
SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B*
2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D*
Length = 260
Score = 44.1 bits (102), Expect = 2e-05
Identities = 26/208 (12%), Positives = 57/208 (27%), Gaps = 18/208 (8%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQL-DADIVCLQEI--GSYEAI 63
++IA++NI E + ++ L + DIV +QE+ A+
Sbjct: 1 LKIAAFNIRTFGE------------TKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAV 48
Query: 64 KRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVE 123
++ D + + + +DT D
Sbjct: 49 GKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDS 108
Query: 124 ILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFII 183
E K +K F + + + + + Q+ ++
Sbjct: 109 FSREPAVVKFSSHSTKVKEFAIVALHSAPS---DAVAEINSLYDVYLDVQQKWHLNDVML 165
Query: 184 AGDFNRKINHSHSGIKDELWQKINQDNT 211
GDFN ++ S + + +
Sbjct: 166 MGDFNADCSYVTSSQWSSIRLRTSSTFQ 193
>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 = 43.8 bits (101), Expect = 4e-05
Identities = 21/201 (10%), Positives = 50/201 (24%), Gaps = 24/201 (11%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRV 66
+++ + N+ LS + L+ + D+V L E+ A R+
Sbjct: 10 LKVMTHNVYMLSTN------LYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRL 63
Query: 67 FPN--DKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKS-------------YLPMDTEG 111
N ++ + + + +
Sbjct: 64 LGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGC 123
Query: 112 LDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWV 171
+ V + + R + ++ HL++ + N
Sbjct: 124 GPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPA---SVRTNQLKEIQDFIK 180
Query: 172 DQKNNLNMPFIIAGDFNRKIN 192
++ N +I GD N
Sbjct: 181 NKNIPNNEYVLIGGDMNVNKI 201
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein,
enterococcus faecalis V583, PSI-2, MCSG, structural
genomics; 1.60A {Enterococcus faecalis}
Length = 257
Score = 43.3 bits (100), Expect = 5e-05
Identities = 22/182 (12%), Positives = 56/182 (30%), Gaps = 14/182 (7%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRV 66
++IA++N+ +E + + + D + C+QE+ ++ +
Sbjct: 1 MKIATYNVRVDTEYDQDWQW-------SFRKEAVCQLINFHDWSLCCIQEV-RPNQVRDL 52
Query: 67 FPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILF 126
+ L + D AI+ + + + Y + +
Sbjct: 53 KAYTTFTCLSAEREGDGQGEGLAILYNEQKVQAIDTGYFWLSETPQQPSIHPEAGCPRIA 112
Query: 127 EVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGD 186
+ + + ++ +IS+ L L++ P ++ GD
Sbjct: 113 LW----GLFKETTQNTPFLVINVHLDHISAHARLAGMTVILEEL--HDKIAQYPTLLMGD 166
Query: 187 FN 188
FN
Sbjct: 167 FN 168
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 42.2 bits (98), Expect = 1e-04
Identities = 13/96 (13%), Positives = 34/96 (35%), Gaps = 16/96 (16%)
Query: 4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI----GS 59
++ + +WN+ L +++ + + L+ + E D++CLQE
Sbjct: 147 SRMYKFITWNVAGL----------RGLLK--KNASALRAFMEAEKPDVLCLQETKLNVDE 194
Query: 60 YEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKG 95
+A + D + + + T ++
Sbjct: 195 ADANATLGVVDGYSFVDHPCAFKRGYSGTRTYMKNS 230
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 41.9 bits (97), Expect = 1e-04
Identities = 25/223 (11%), Positives = 54/223 (24%), Gaps = 49/223 (21%)
Query: 4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAI 63
R+ N+ A L A A I +QE A
Sbjct: 17 GPPYRVLQANLQRKKL----------------ATAELAIEAATRKAAIALIQEPYVGGA- 59
Query: 64 KRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVE 123
+ + ++ + + AI + + ++Q L V
Sbjct: 60 -KSMKGFRGVRVFQSTAQGDGTVKAAIAVFDHDLDVIQYPQLTT-----------NNIVV 107
Query: 124 ILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFII 183
+ +I L+ + + ++S + +K+ + I
Sbjct: 108 VGIRTRAWEITLVSYYFEPDKPIESYLE--------------QIKRVERKMG--PKRLIF 151
Query: 184 AGDFN----RKINHSHSGIKDELWQKINQDNTLMRLPHKKNHN 222
GD N + D+L + + +
Sbjct: 152 GGDANAKSTWWGSKEDDARGDQLMGTLGELGLHILNEGDVPTF 194
>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 = 40.0 bits (93), Expect = 4e-04
Identities = 31/181 (17%), Positives = 55/181 (30%), Gaps = 32/181 (17%)
Query: 8 RIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVF 67
+I SWN+N L +V R+ K+ + DI+CLQEI +
Sbjct: 5 KIISWNVNGL----------RAVHRKG-----FLKWFMEEKPDILCLQEIKAAPE---QL 46
Query: 68 PNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFE 127
P + + RKG + + +P + + +
Sbjct: 47 PRKLRHVEG-------YRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQI 99
Query: 128 VDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDF 187
D L +I+ + + V+++ + II GDF
Sbjct: 100 ADFDDFLLYNIYFPNGA-------MSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDF 152
Query: 188 N 188
N
Sbjct: 153 N 153
>2imq_X Salivary nitrophorin; ferrous heme, beta-sandwich, transport
protein; HET: HEM; 1.30A {Cimex lectularius} SCOP:
d.151.1.2 PDB: 1ntf_A* 1y21_A* 1yjh_A* 1si6_X*
Length = 282
Score = 39.5 bits (91), Expect = 6e-04
Identities = 27/221 (12%), Positives = 51/221 (23%), Gaps = 18/221 (8%)
Query: 6 RIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKR 65
+ SWN + + + L E D V +Q G
Sbjct: 8 SVHTVSWNSGHERA------------PTNLEELLGLNSGETPDVIAVAVQGFGFQTD--- 52
Query: 66 VFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEIL 125
+ S + L + V+
Sbjct: 53 KPQQGPACVKNFQSLLTSKGYTKLKNTITETMGLTVYCLEKHLDQNTLKNETIIVTVDDQ 112
Query: 126 FEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAG 185
+ G I+ K F F S + A + +K++ + G
Sbjct: 113 KKSGGIVTSFT-IYNKRFSFTTSRMSDEDVTSTNTK-YAYDTRLDYSKKDDPSDFLFWIG 170
Query: 186 DFNRKINHSHSGIKDEL-WQKINQDNTLMRLPHKKNHNAIR 225
D N ++ + + K + I+ +L K
Sbjct: 171 DLNVRVETNATHAKSLVDQNNIDGLMAFDQLKKAKEQKLFD 211
>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich
fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB:
3ngo_A 3ngn_A
Length = 398
Score = 38.9 bits (89), Expect = 0.001
Identities = 23/231 (9%), Positives = 63/231 (27%), Gaps = 42/231 (18%)
Query: 4 AQRIRIASWNI--NNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGS-- 59
+ + +N+ + + + + + + + + DADI+ LQE+ +
Sbjct: 29 SASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQ 88
Query: 60 -YEAIKRVFPNDKWDILY--------SGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTE 110
+ +D + KH AI + L+QK + +
Sbjct: 89 YFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQV 148
Query: 111 GLDSKAGKRRAVEILFEVDGRKIWLL----------------DIHLKSFCFLDSIEDSYI 154
+ + G + + D + ++ + ++
Sbjct: 149 AMANSDGSEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDP 208
Query: 155 SSCYMLNLQATWLKQWV-------------DQKNNLNMPFIIAGDFNRKIN 192
+ +Q V + ++P ++ D N +
Sbjct: 209 EYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLPD 259
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair,
endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens}
SCOP: d.151.1.1 PDB: 1e9n_A 2isi_A
Length = 318
Score = 37.2 bits (85), Expect = 0.003
Identities = 20/185 (10%), Positives = 49/185 (26%), Gaps = 35/185 (18%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAI--K 64
++I SWN++ L + I++ + ++ DI+CLQE E
Sbjct: 62 LKICSWNVDGL----------RAWIKKK-----GLDWVKEEAPDILCLQETKCSENKLPA 106
Query: 65 RVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEI 124
+ Y + +DK ++ + + + +
Sbjct: 107 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHD-------------- 152
Query: 125 LFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIA 184
++ + + + + + P ++
Sbjct: 153 ----QEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 208
Query: 185 GDFNR 189
GD N
Sbjct: 209 GDLNV 213
>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 = 36.2 bits (82), Expect = 0.007
Identities = 30/217 (13%), Positives = 66/217 (30%), Gaps = 25/217 (11%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAI--K 64
++IASWN++ L + I++ + ++ DI+CLQE E
Sbjct: 29 LKIASWNVDGL----------RAWIKK-----KGLDWVKEEAPDILCLQETKCSENKLPA 73
Query: 65 RVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEI 124
+ Y + +DK ++ + + + + I
Sbjct: 74 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEE--------HDQEGRVI 125
Query: 125 LFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIA 184
+ E D + + + + L+ ++ + +LN+
Sbjct: 126 VAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEI 185
Query: 185 GDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNH 221
N K N ++G + Q + + L H
Sbjct: 186 DLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRH 222
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 35.1 bits (79), Expect = 0.014
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 15/50 (30%)
Query: 8 RIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI 57
+I S N+N + S ++ +Y ADIVC+QE+
Sbjct: 3 KIISANVNGI----------RSAYKKG-----FYEYIAASGADIVCVQEL 37
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha
beta sandwich, gene regulation; 2.00A {Bombyx mori}
Length = 240
Score = 34.9 bits (79), Expect = 0.016
Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 16/56 (28%)
Query: 1 MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQE 56
M + R+RI N+ + + L A L DIV +QE
Sbjct: 2 MDIRPRLRIGQINLGGAEDAT----------------RELPSIARDLGLDIVLVQE 41
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1
type, retrotransposition, retrotransposon, transferase;
1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A
Length = 238
Score = 34.7 bits (78), Expect = 0.016
Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 14/79 (17%)
Query: 7 IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRV 66
I I + NIN L NS I+ L + + D + C+QE
Sbjct: 8 ITILTLNINGL----------NSAIKRHR----LASWIKSQDPSVCCIQETHLTCRDTHR 53
Query: 67 FPNDKWDILYSGSNTDKHA 85
W +Y + K A
Sbjct: 54 LKIKGWRKIYQANGKQKKA 72
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease,
lyase; 1.7A {Archaeoglobus fulgidus}
Length = 257
Score = 33.5 bits (75), Expect = 0.047
Identities = 10/50 (20%), Positives = 24/50 (48%), Gaps = 16/50 (32%)
Query: 8 RIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI 57
+IA++N+N++ S + ++ + ++ DI+C+QE
Sbjct: 3 KIATFNVNSI----------RSRLH------IVIPWLKENKPDILCMQET 36
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase,
DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A
{Neisseria meningitidis}
Length = 256
Score = 33.2 bits (74), Expect = 0.048
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 16/50 (32%)
Query: 8 RIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI 57
+I +WN+N+L N + +Q DI+ LQE+
Sbjct: 2 KITTWNVNSL----------NVRLP------QVQNLLADNPPDILVLQEL 35
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia
coli} SCOP: d.151.1.1
Length = 268
Score = 33.2 bits (74), Expect = 0.049
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 16/50 (32%)
Query: 8 RIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEI 57
+ S+NIN L + L+ E+ D++ LQE
Sbjct: 2 KFVSFNINGL----------RARPH------QLEAIVEKHQPDVIGLQET 35
>3l0z_A Putative nicotinate-nucleotide- dimethylbenzimidazole
phosphoribosyltransferase; COBT, MCSG, PSI, structural
genomics; 2.65A {Methanocaldococcus jannaschii}
Length = 350
Score = 30.2 bits (68), Expect = 0.38
Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 10/87 (11%)
Query: 32 REDNDYALLQKYAEQLDADIVCLQEIG-----SYEAIKRVFPNDKWDILYSGSNTDKHAM 86
Y + LDA+++ + E + + D + SGS + H +
Sbjct: 126 NSKELYMKGYLLGKNLDAELLIVGESVPGGTTTALGVLLGLGYDAEGKVSSGSINNPHEL 185
Query: 87 HTAIVIRKGAIHLLQKSYLPMDTEGLD 113
+V L+K+ + + D
Sbjct: 186 KIKVVREG-----LKKAGINEKSSVFD 207
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
0.321 0.136 0.408
Gapped
Lambda K H
0.267 0.0490 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,024,734
Number of extensions: 92310
Number of successful extensions: 237
Number of sequences better than 10.0: 1
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 33
Length of query: 231
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 142
Effective length of database: 3,535,514
Effective search space: 502042988
Effective search space used: 502042988
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: 55 (25.5 bits)