RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781003|ref|YP_003065416.1| hypothetical protein
CLIBASIA_04520 [Candidatus Liberibacter asiaticus str. psy62]
(304 letters)
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A
{Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A
Length = 317
Score = 78.9 bits (193), Expect = 1e-15
Identities = 58/313 (18%), Positives = 91/313 (29%), Gaps = 39/313 (12%)
Query: 13 LVPCTASVAQK-----VRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDAD 67
LVP + + K ++LVS N+ LS + + L+ Q + + D
Sbjct: 14 LVPRGSHMESKKDDTDLKLVSHNVYMLSTVLYPNWGQYKRAD------LIGQSSYIKNND 67
Query: 68 IVFLQEMGSYNAVAKVFPKNTWCIFYSTERLINHSKRDSN----------NDIHTAIAVR 117
+V E A K+ Y T L D AI +
Sbjct: 68 VVIFNEAFDNGASDKLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSK 127
Query: 118 KKNVRVLQQSYPLLGAKDSFSRAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTY 177
+Q + D+ S N+ V +E NGK + V+ H +S +
Sbjct: 128 YPIKEKIQHVFKSGCGFDNDS---NKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDR 184
Query: 178 SPSCSLLSQQAQWLKDWITQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRF 237
Q + + I GD N D K ++ ND L
Sbjct: 185 KIRA---EQMKEISDFVKKKNIPKDETVYIGGDLNVNKGTPE-FKDMLKNLNVNDVLYAG 240
Query: 238 PKEKDSRCN---ANKNLRNKIP--IDYFVMDQNAYK------FLIQESFSEILYNEDDIK 286
+ A N N P +DY D++ + ++ E
Sbjct: 241 HNSTWDPQSNSIAKYNYPNGKPEHLDYIFTDKDHKQPKQLVNEVVTEKPKPWDVYAAAYY 300
Query: 287 SRGKRLSDHCPIS 299
SDH PI
Sbjct: 301 YVYNDFSDHYPIK 313
>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 = 65.9 bits (159), Expect = 1e-11
Identities = 43/284 (15%), Positives = 79/284 (27%), Gaps = 37/284 (13%)
Query: 21 AQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAV 80
R+ +WN+ ++ + + + + + DI+ +QE GS +
Sbjct: 13 LTDFRVATWNLQ----------GASATTESKWNINVRQLISGENAVDILAVQEAGSPPST 62
Query: 81 AKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAI--AVRKKNVRVLQQSYPLLGAKDSFS 138
A + LI + +S AV RV A + F
Sbjct: 63 AVDTGRVIPSPGIPVRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSNRRADEVFV 122
Query: 139 RAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQK 198
+ R+ L+ I H + D+ L ++
Sbjct: 123 LSPVRQGGRPLLGIRIGNDAFFTAHAIAMRNNDAPA---------LVEEVYNFFRDSRDP 173
Query: 199 KESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPID 258
+ ++I GDFNR+ L N + R +D
Sbjct: 174 VHQALNWMILGDFNREPADLEMNLTVPVRRASEIISPAAATQTSQRT-----------LD 222
Query: 259 YFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDY 302
Y V + + S + R + SDH P+ +
Sbjct: 223 YAVAGNS-----VAFRPSPLQAGIVYGARRTQISSDHFPVGVSR 261
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein;
alpha-beta protein, structural genomics, PSI-2; 2.50A
{Bacteroides vulgatus atcc 8482}
Length = 267
Score = 65.0 bits (157), Expect = 2e-11
Identities = 46/294 (15%), Positives = 79/294 (26%), Gaps = 52/294 (17%)
Query: 24 VRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEM--GSYNAVA 81
VR ++NI + Q+ ++ W+ R + Q+ K+ + DIV +QE+ + +
Sbjct: 4 VRWATFNIRYDNPQDSLNNWQYRKDR-------VCQFIKDHELDIVGMQEVLHNQFQDLR 56
Query: 82 KVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQS------YPLLGAKD 135
P+ + + RK VL + P
Sbjct: 57 AGLPEYDGIGVGRD--------DGKTAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGMM 108
Query: 136 SFSRAGNRRAVELLVEI--NGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKD 193
+ R A + GK ++ H Q A +
Sbjct: 109 GWDAVCVRIATWAKFKDKATGKIFMAVNTHFDHVGEEARR------------QSALLIIR 156
Query: 194 WITQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCN----ANK 249
I + P V+ GDFN D+ + A
Sbjct: 157 KIKEIVGER-PAVVTGDFNVTDASDAYETITTNEFVMKDAYKTAARVTGVDYTFHDFARI 215
Query: 250 NLRNKIPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
+ ID+ + + EI LSDH P D +
Sbjct: 216 PAEDCEKIDFIFVTPQ-----VLVKSCEIPAEVP-----EALLSDHNPQLADLE 259
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 59.9 bits (143), Expect = 7e-10
Identities = 33/300 (11%), Positives = 84/300 (28%), Gaps = 27/300 (9%)
Query: 17 TASVAQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGS 76
+ ++ S N+ S + + L+ Q + D+V L E
Sbjct: 4 SDEYPGNFKITSHNVYLFSRNIYPNWGQMHRAD------LIAQADYMKNNDVVILNEAFD 57
Query: 77 YNAVAKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLL----- 131
+A ++ + T + + + + + + +P++
Sbjct: 58 TSASHRLLNNLREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQH 117
Query: 132 --GAKDSFSRAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQ 189
R N+ + + NGK ++ H ++ L S + + Q +
Sbjct: 118 IFQRGGGADRLSNKGFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSR---AIRAEQMQE 174
Query: 190 WLKDWITQKKESLVPFVIAGDFN-----RKINYLGNNDDFWKTIDPNDSLIRFPKEKDSR 244
+ I GD N + + + + + N + + +S
Sbjct: 175 IQTFIAKKNIPKDEIIFIGGDLNVNYGTDEYHDMLKLLNVSSPANFNGQMATWDPTTNSM 234
Query: 245 CNANKNLRNKIPIDYFVMDQNAYK------FLIQESFSEILYNEDDIKSRGKRLSDHCPI 298
+ +DY ++ + ++ + + SDH P+
Sbjct: 235 LKESYPKAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQDFSDHYPV 294
>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 = 59.0 bits (142), Expect = 1e-09
Identities = 46/307 (14%), Positives = 91/307 (29%), Gaps = 41/307 (13%)
Query: 23 KVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAK 82
+ ++N+N S +E + LW L + D V QE+ +
Sbjct: 9 RFFAGTYNVNGQSPKECLRLW-------------LSNGIQAPDVYCVGFQELDL--SKEA 53
Query: 83 VFPKNTWCIFYSTERLINHSKRDSN---------NDIHTAIAVRKKNVRVLQQSYPLLGA 133
F +T + + D+ I + V++++ + +
Sbjct: 54 FFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVG 113
Query: 134 KDSFSRAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKD 193
R GN+ V + + + I V++ HL + N Q Q
Sbjct: 114 TGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPS 173
Query: 194 WITQKKESLVPFVIAGDFNRKINYLGNND-------DFWKTIDPNDSLIRFPKEK---DS 243
+ + GD N +I L ++ + D L K +
Sbjct: 174 LPPLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEG 233
Query: 244 RCNANKNLRNKIPIDYFVMDQNAYKFLIQESFSE-ILYNEDDIKSR------GKRLSDHC 296
+ D D + + ++ + IL+ +I + SDH
Sbjct: 234 FTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHK 293
Query: 297 PISIDYD 303
P+S +D
Sbjct: 294 PVSSVFD 300
>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 = 56.7 bits (135), Expect = 6e-09
Identities = 35/288 (12%), Positives = 85/288 (29%), Gaps = 34/288 (11%)
Query: 21 AQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAV 80
++ +WN+ ++V + + + + + ADI+ +QE GS +
Sbjct: 2 LSDFKVATWNLQ----------GSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSS 51
Query: 81 AKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLL---GAKDSF 137
A + E + + I + +V + + ++ A ++F
Sbjct: 52 AVRTSRVIQHGGTPIEEYTWN-LGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAF 110
Query: 138 SRAGNRRAVEL--LVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWI 195
+ ++ V I +H + D++
Sbjct: 111 IVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIR--------NIFTTFNSSS 162
Query: 196 TQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKI 255
+ + + +++ GDFNR + +
Sbjct: 163 SPPERRVYSWMVVGDFNR-----APANLEVALRQEPAVSENTIIIAPTEPTHRSGNI--- 214
Query: 256 PIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
+DY ++ +++ I + + R + SDH P+S D
Sbjct: 215 -LDYAILHDAHLPR-REQARERIGASLMLNQLRSQITSDHFPVSFVRD 260
>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 = 55.8 bits (132), Expect = 1e-08
Identities = 39/315 (12%), Positives = 92/315 (29%), Gaps = 39/315 (12%)
Query: 17 TASVAQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGS 76
+ + +++++ N+ LS + + L+ + D+V L E+
Sbjct: 3 STTQNDTLKVMTHNVYMLSTNLYPNWGQTERAD------LIGAADYIKNQDVVILNEVFD 56
Query: 77 YNAVAKVFPKNTWCIFYSTERLINHSKRDSNN-----------DIHTAIAVRKKNVRVLQ 125
+A ++ T L S + + D AI + +Q
Sbjct: 57 NSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQ 116
Query: 126 QSYPLLGAKDSFSRAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLS 185
+ D+ S + V ++ N + + V+ HL++ + + +
Sbjct: 117 YVFAKGCGPDNLSN---KGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPA---SVRTN 170
Query: 186 QQAQWLKDWITQKKESLVPFVIAGDFN--------RKINYLGNNDDFWKTIDPNDSLIRF 237
Q + + + +I GD N + + P+ +
Sbjct: 171 QLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTA 230
Query: 238 PKEKDSRCNANKNLRNKIP--IDYFVMDQNAYK------FLIQESFSEILYNEDDIKSRG 289
+ + A N + +DY + ++ ++Q + K
Sbjct: 231 TWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTY 290
Query: 290 KRLSDHCPISIDYDF 304
SDH P+
Sbjct: 291 NDYSDHYPVEATISM 305
>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 = 54.0 bits (128), Expect = 4e-08
Identities = 35/312 (11%), Positives = 83/312 (26%), Gaps = 54/312 (17%)
Query: 21 AQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEM--GSYN 78
+ + S+N+ + + + ++ Q + D DI QE
Sbjct: 4 PTSLTVASYNLRNANGSDSARGDGWGQRYP-----VIAQMVQYHDFDIFGTQECFLHQLK 58
Query: 79 AVAKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSY---------P 129
+ + P + + H+AI R ++++ P
Sbjct: 59 DMKEALPGYDYIGV--------GRDDGKDKGEHSAIFYRTDKFDIVEKGDFWLSETPDVP 110
Query: 130 LLGAKDSFSRAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQ 189
G R + G + ++H+ + + +
Sbjct: 111 SKGWDAVLPR--ICSWGHFKCKDTGFEFLFFNLHMD-----------HIGKKARVESAFL 157
Query: 190 WLKDWITQKKESLVPFVIAGDFNRKINY--LGNNDDFWKTIDPNDSLIRFPKEKDSRCNA 247
+ + +P ++ GDFN + D + + N
Sbjct: 158 VQEKMKELGRGKNLPAILTGDFNVDQTHQSYDAFVSKGVLCDSYEKCDYRYALNGTFNNF 217
Query: 248 NKNLRNKIPIDYF------------VMDQNAYKFLIQESFSEILYNEDDIKSR---GKRL 292
+ N + ID+ V+ ++ ++I + +
Sbjct: 218 DPNSFTESRIDHIFVSPSFHVKRYGVLTDTYRSVRENSKKEDVRDCPEEITIKAYEARTP 277
Query: 293 SDHCPISIDYDF 304
SDH P+ ++ F
Sbjct: 278 SDHFPVKVELVF 289
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 53.1 bits (126), Expect = 8e-08
Identities = 32/286 (11%), Positives = 66/286 (23%), Gaps = 69/286 (24%)
Query: 24 VRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAKV 83
R++ N+ R L A A I +QE A +
Sbjct: 20 YRVLQANLQ----------------RKKLATAELAIEAATRKAAIALIQEPYVGGAKSMK 63
Query: 84 FPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNR 143
+ S + + AIAV ++ V+Q
Sbjct: 64 GFRGVRV---------FQSTAQGDGTVKAAIAVFDHDLDVIQYPQL-----------TTN 103
Query: 144 RAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKESLV 203
V + + +I ++ + Y + + +K +
Sbjct: 104 NIVVVGIRTRAWEITLV--------------SYYFEPDKPIESYLEQIKRVERKMGPK-- 147
Query: 204 PFVIAGDFN------RKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPI 257
+ GD N D T+ I + + R + +
Sbjct: 148 RLIFGGDANAKSTWWGSKEDDARGDQLMGTLGELGLHILNEGDVPTFDTIRGGKRYQSRV 207
Query: 258 DYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
D ++ + + + SDH + +
Sbjct: 208 DVTFCTEDMLDLIDG---WRVDEDL--------VSSDHNGMVFNIR 242
>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 = 52.2 bits (123), Expect = 1e-07
Identities = 36/286 (12%), Positives = 84/286 (29%), Gaps = 38/286 (13%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNL-DADIVFLQEM--GSYNAVA 81
++ ++NI T E S+ TL + + DIV +QE+ AV
Sbjct: 2 KIAAFNIRTFGE------------TKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVG 49
Query: 82 KVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAG 141
K+ + +++ ++ R V VL G + + +
Sbjct: 50 KLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSF 109
Query: 142 NRRAVELLVEI---NGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQK 198
+R + K+ ++ +H + + D +
Sbjct: 110 SREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEIN-----------SLYDVYLDVQQKW 158
Query: 199 KESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPID 258
++ GDFN +Y+ ++ + + + + + N D
Sbjct: 159 HL--NDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCA----YD 212
Query: 259 YFVMDQNAYKFLIQESFSEILYNEDDIK---SRGKRLSDHCPISID 301
V+ + + + + + +SDH P+ +
Sbjct: 213 RIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVT 258
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: 1PE; 1.90A
{Neisseria meningitidis}
Length = 256
Score = 51.3 bits (121), Expect = 3e-07
Identities = 34/282 (12%), Positives = 73/282 (25%), Gaps = 29/282 (10%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQE--MGSYNAVAK 82
++ +WN+N +++ V+ + DI+ LQE + A
Sbjct: 2 KITTWNVN------SLNVRLPQVQ----------NLLADNPPDILVLQELKLDQDKFPAA 45
Query: 83 VFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGN 142
W +S ++ N S + Q+
Sbjct: 46 ALQMMGWHCVWSGQKTYNGVAIVSRSVPQDVHFGLPALPDDPQRRVIAATVSGVRVINVY 105
Query: 143 RRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKESL 202
E L K L F + + + + +K
Sbjct: 106 CVNGEALDSPKFKYKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEK 165
Query: 203 VPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPIDYFVM 262
+ + D + + P + + + + LR ID+ ++
Sbjct: 166 IHCSSVERQWFQNLLDLGLTDSLRQVHPEGAFYTWFDYRGAMFQRKLGLR----IDHILV 221
Query: 263 DQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYDF 304
L + +R SDH P++ ++D+
Sbjct: 222 SPAMAAALKD---VRVDLETRA----LERPSDHAPVTAEFDW 256
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein,
enterococcus faecalis V583, PSI-2, MCSG, structural
genomics; 1.60A {Enterococcus faecalis}
Length = 257
Score = 47.1 bits (110), Expect = 5e-06
Identities = 33/282 (11%), Positives = 73/282 (25%), Gaps = 32/282 (11%)
Query: 24 VRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAKV 83
+++ ++N+ +E + W + + Q D + +QE+
Sbjct: 1 MKIATYNVRVDTEYDQDWQWSFRKEA-------VCQLINFHDWSLCCIQEVRPNQV---- 49
Query: 84 FPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNR 143
Y+T ++ + AI ++ V+ + Y S +
Sbjct: 50 ----RDLKAYTTFTCLSAEREGDGQGEGLAILYNEQKVQAIDTGYF------WLSETPQQ 99
Query: 144 RAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKESLV 203
++ +W L + + + K +
Sbjct: 100 PSIHPEAGCPRIALWGLFKETTQNTPFLVINVHLDHISAHARLAGMTVILEELHDKIAQY 159
Query: 204 PFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKD-SRCNANKNLRNKIPIDYFVM 262
P ++ GDFN + + K D + + K IDY +
Sbjct: 160 PTLLMGDFNAESGEEVHQLVQKKFQDSKNLATHYGPRGTFQNFTYTKPWAELEEIDYIYV 219
Query: 263 DQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYDF 304
+ G+ SDH P+ +
Sbjct: 220 K----------GWQVQQTASLTDSIDGRFPSDHFPLEAEVAG 251
>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 = 46.5 bits (110), Expect = 7e-06
Identities = 38/246 (15%), Positives = 71/246 (28%), Gaps = 108/246 (43%)
Query: 12 FLVPCTAS--VAQKVRLVSWN--INTLSEQ-EGVSLWKNSVKRTTSDYTLLRQYAKNLD- 65
LVP TAS +A +++ L E EG + T+ L+ ++ L
Sbjct: 20 LLVP-TASFFIASQLQ----EQFNKILPEPTEG--FAADD--EPTTPAELVGKF---LGY 67
Query: 66 -ADIVFLQEMGSYNAVAKVFPKNTWCIFYSTERLINHSKRD--SNNDIHTAIA------- 115
+ +V ++G ++ V + + + NDIH A
Sbjct: 68 VSSLVEPSKVGQFDQVLNL--------------CLTEFENCYLEGNDIHALAAKLLQEND 113
Query: 116 ---VRKKNV--------RVLQQSYPLLGAKDS--FSRAGNRRAVELLVEINGKKIWVLDI 162
V+ K + + ++ + +S F G A ++ +
Sbjct: 114 TTLVKTKELIKNYITARIMAKRPFD--KKSNSALFRAVGEGNA----------QLVAI-- 159
Query: 163 HLKSF--------CF--LDSLENTYSP-------SCS--L--LSQQA------------- 188
F F L L TY + L L +
Sbjct: 160 ----FGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215
Query: 189 -QWLKD 193
+WL++
Sbjct: 216 LEWLEN 221
Score = 35.3 bits (81), Expect = 0.017
Identities = 24/150 (16%), Positives = 42/150 (28%), Gaps = 64/150 (42%)
Query: 209 GDFNRKINYLGNND----------DFWKTIDPNDSLIR------------FPKEKDSRC- 245
+F YL ND + T+ LI+ F K+ +S
Sbjct: 89 TEFEN--CYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF 146
Query: 246 -NANKNLRNKIPI-----------DYFVMDQ-----NAYKFLIQE---SFSEILY----N 281
+ + DYF ++ Y L+ + +E L
Sbjct: 147 RAVGE---GNAQLVAIFGGQGNTDDYF--EELRDLYQTYHVLVGDLIKFSAETLSELIRT 201
Query: 282 EDDIK---SRG----KRLS--DHCPISIDY 302
D + ++G + L + P DY
Sbjct: 202 TLDAEKVFTQGLNILEWLENPSNTP-DKDY 230
Score = 33.8 bits (77), Expect = 0.053
Identities = 18/100 (18%), Positives = 32/100 (32%), Gaps = 31/100 (31%)
Query: 3 RKYVLALVF---FLVPCTA--------SVAQKV--RLVSWNINTLSEQEGVSLWKNSVKR 49
RK L F FL P + + + LV N++ ++ + ++
Sbjct: 412 RK----LKFSNRFL-PVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT---F 463
Query: 50 TTSDYTLLRQYAKNLDADIVFLQEMGSYNAV----AKVFP 85
SD LR + ++ IV + V F
Sbjct: 464 DGSD---LRVLSGSISERIV---DCIIRLPVKWETTTQFK 497
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA
repair, exonuclease, endonuclease; HET: BCN DIO GOL;
1.50A {Neisseria meningitidis}
Length = 259
Score = 46.3 bits (108), Expect = 9e-06
Identities = 29/283 (10%), Positives = 69/283 (24%), Gaps = 32/283 (11%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAKVF 84
+++S N+N + +++ K+ +Y ADIV +QE+ A
Sbjct: 3 KIISANVNGI---------RSAYKKG------FYEYIAASGADIVCVQEL---KAQEADL 44
Query: 85 PKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNRR 144
+ KR + + + + G
Sbjct: 45 SADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLS 104
Query: 145 AVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKESLVP 204
+ L + + + + + W ++
Sbjct: 105 VISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKG 164
Query: 205 FVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIP---IDYFV 261
F + + + + K IDY +
Sbjct: 165 NQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQM 224
Query: 262 MDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYDF 304
+ + + + +E + SDH P+ ++YD+
Sbjct: 225 VTPELAAKAVS---AHVYKDE--------KFSDHAPLVVEYDY 256
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease,
lyase; 1.7A {Archaeoglobus fulgidus}
Length = 257
Score = 45.4 bits (106), Expect = 1e-05
Identities = 32/295 (10%), Positives = 71/295 (24%), Gaps = 57/295 (19%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQE----------- 73
++ ++N+N + + V + K DI+ +QE
Sbjct: 3 KIATFNVN------SIRSRLHIVI----------PWLKENKPDILCMQETKVENRKFPEA 46
Query: 74 ----MGSYNAVAKVFPKNTWCIFYSTERL-INHSKRDSNNDIHTAIAVRKKNVRVLQQSY 128
+G + + +N I E ++ D I + + V+
Sbjct: 47 DFHRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYV 106
Query: 129 PLLGAKDSFSRAGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQA 188
P D + + L + ++ + + +P +
Sbjct: 107 PQGFKID------SEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPD 160
Query: 189 QWLKDWITQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNAN 248
+ + +KI LG D K +
Sbjct: 161 KLKNHVCFHEDAR--------RAYKKILELGFVDVLRKIHPNERIYTFYDYRVKGAIERG 212
Query: 249 KNLRNKIPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
R D + + + ++ SDH P+ +D
Sbjct: 213 LGWR----GDAILATPPLAERCVD---CYADIKPRL----AEKPSDHLPLVAVFD 256
>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 = 44.6 bits (104), Expect = 3e-05
Identities = 41/353 (11%), Positives = 89/353 (25%), Gaps = 69/353 (19%)
Query: 21 AQKVRLVSWNI--NTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGS-- 76
+ ++ +N+ + + ++ + + + N DADI+ LQE+ +
Sbjct: 29 SASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQ 88
Query: 77 -YNAVAKVFPK-NTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQS------- 127
+ + F R S+++ + AI + + ++Q+
Sbjct: 89 YFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQV 148
Query: 128 --YPLLGAKDSFSRAGNRRAVELLVEINGKKIWVLDIHL---KSFCFLDSLENTYSPSCS 182
G++ +R + + + V + K + L + N +
Sbjct: 149 AMANSDGSEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDP 208
Query: 183 LLS----QQAQWLKDWITQKKESL-------------VPFVIAGDFN--------RKINY 217
S Q + E +P V+ D N ++
Sbjct: 209 EYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSN 268
Query: 218 LGNNDDF-----------WKTIDPNDSLIRFPKEKDSRCNANKNLRNKIP---------- 256
G D+ N N +
Sbjct: 269 GGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGFQLKSAYENNLMPYTNYTFDFK 328
Query: 257 --IDY-FVMDQNAY--KFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYDF 304
IDY F + L ++ N SDH + +
Sbjct: 329 GVIDYIFYSKTHMNVEGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQLEL 381
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 42.9 bits (100), Expect = 1e-04
Identities = 45/350 (12%), Positives = 90/350 (25%), Gaps = 96/350 (27%)
Query: 21 AQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAV 80
++ + ++WN+ L + +K+ S LR + + D++ LQE
Sbjct: 147 SRMYKFITWNVAGL---------RGLLKKNASA---LRAFMEAEKPDVLCLQE---TKLN 191
Query: 81 AKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRV-----LQQSYPLLGAKD 135
N ++H T ++ + + L
Sbjct: 192 VDEADANATLGVVDGYSFVDHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQ 251
Query: 136 SFSRAGNR-----------RAVELLVEING------KKIWVLDIHLKSFC-FLDSLENTY 177
+ + AG+R R + + + +I +++ ++ + L L
Sbjct: 252 ADAAAGSRVLVEGAGDEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRV 311
Query: 178 SPSCSLLSQQAQWLKDWITQKKESLV-----------PFVIAGDFNRKINYLGNNDDFWK 226
+ + L W T+ F+ AGD N
Sbjct: 312 QSFDPSMREYLHRLDTWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTF 371
Query: 227 TIDPNDSLIR-----------------------FPKEK------DSRCNA---NKNLRNK 254
S +P+ R N N R
Sbjct: 372 KSMQECSGFAPEERMSFRETMQRTNSVDIFRQLYPQAGPVYSFWSQRINGRPRNLGWR-- 429
Query: 255 IPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYDF 304
+DYFV+ +++ + SDHCP +
Sbjct: 430 --LDYFVVSSRLASYVVD---CFPMPTV--------MGSDHCPFQMWMRH 466
>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 = 42.3 bits (98), Expect = 1e-04
Identities = 33/288 (11%), Positives = 69/288 (23%), Gaps = 42/288 (14%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAKVF 84
++ SWN++ L + +K+ + K DI+ LQE
Sbjct: 30 KIASWNVDGL---------RAWIKK------KGLDWVKEEAPDILCLQET---KCSENKL 71
Query: 85 PKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNRR 144
P + + + + ++ + + A
Sbjct: 72 PAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDS 131
Query: 145 AVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKESLVP 204
V + + ++ + + + + L +
Sbjct: 132 FVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPK 191
Query: 205 FVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEK------DSRCNA---NKNLRNKI 255
G + + +P NA N R
Sbjct: 192 GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWR--- 248
Query: 256 PIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
+DYF++ + L S+I SDHCPI++
Sbjct: 249 -LDYFLLSHSLLPALCD---SKIRSKA--------LGSDHCPITLYLA 284
>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 = 42.1 bits (98), Expect = 2e-04
Identities = 46/312 (14%), Positives = 92/312 (29%), Gaps = 41/312 (13%)
Query: 23 KVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVF--LQEMGSYNAV 80
V + +WN+ ++ + V+ W S + L + + DI QE +
Sbjct: 9 SVFIGTWNMGSVPPPKNVTSWFTSKGLGKT----LDEVTVTIPHDIYVFGTQEN---SVG 61
Query: 81 AKVFPKN-TWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSR 139
+ + + T+ S +I A+ V+ ++ + +
Sbjct: 62 DREWLDLLRGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANT 121
Query: 140 AGNRRAVELLVEINGKKIWVLDIHLKSF-CFLDSLENTYSPSCSLLSQQAQWLKDWITQK 198
GN+ AV + NG ++ HL S Y LLS + L
Sbjct: 122 LGNKGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRLLSLGDRQL--NAFDI 179
Query: 199 KESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPID 258
GD N +++ + + + L+R + R LR
Sbjct: 180 SLRFTHLFWFGDLNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEI 239
Query: 259 YFVMDQNAYKFLIQESFSE------------------ILY--------NEDDIKSRGK-R 291
F Y+ +++++ IL+ +
Sbjct: 240 SFP-PTYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGCTDDIV 298
Query: 292 LSDHCPISIDYD 303
SDH P+ ++
Sbjct: 299 TSDHSPVFGTFE 310
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia
coli} SCOP: d.151.1.1
Length = 268
Score = 41.3 bits (95), Expect = 3e-04
Identities = 39/294 (13%), Positives = 87/294 (29%), Gaps = 45/294 (15%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQE----------- 73
+ VS+NIN G+ + ++ + D++ LQE
Sbjct: 2 KFVSFNIN------GLRARPHQLE----------AIVEKHQPDVIGLQETKVHDDMFPLE 45
Query: 74 ---MGSYNAVAKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPL 130
YN + + E I + +D + + L + +
Sbjct: 46 EVAKLGYNVFYHGQKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTV 105
Query: 131 LGAKDSFSRAGNRRAVELLVEINGKKI--WVLDIHLKSFCFLDSLENTYSPSCSLLSQQA 188
+ + + + + ++ + L + SP+ +
Sbjct: 106 INGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGE 165
Query: 189 QWLKDWITQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNAN 248
+ K W+ K S +P ++ ++ G D F + + + N
Sbjct: 166 ENRKRWLRTGKCSFLPEER--EWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDN 223
Query: 249 KNLRNKIPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDY 302
+ LR ID + Q + ++ + I Y ++ SDH P+ +
Sbjct: 224 RGLR----IDLLLASQPLAECCVE---TGIDYEIRS----MEKPSDHAPVWATF 266
>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 = 7e-04
Identities = 43/286 (15%), Positives = 79/286 (27%), Gaps = 41/286 (14%)
Query: 25 RLVSWNINTLSEQEGV-SLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQE--MGSYNAVA 81
+++SWN+N G+ ++ + + + DI+ LQE
Sbjct: 5 KIISWNVN------GLRAVHRKGFLK----------WFMEEKPDILCLQEIKAAPEQLPR 48
Query: 82 KVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAG 141
K+ + F++ +S + + V + A
Sbjct: 49 KLRHVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLY 108
Query: 142 N---RRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQK 198
N + K + DS N + + L
Sbjct: 109 NIYFPNGAMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENS 168
Query: 199 KESLV-PFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPI 257
S P A + K G D F + +R N R +
Sbjct: 169 NVSGFLPVERA--WIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARER-NVGWR----L 221
Query: 258 DYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
DYF +++ + + S IL + SDHCPI ++ +
Sbjct: 222 DYFFVNEEFKGKVKR---SWILSDV--------MGSDHCPIGLEIE 256
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha
beta sandwich, gene regulation; 2.00A {Bombyx mori}
Length = 240
Score = 38.4 bits (88), Expect = 0.002
Identities = 27/280 (9%), Positives = 61/280 (21%), Gaps = 69/280 (24%)
Query: 22 QKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVA 81
++R+ N+ L A++L DIV +QE
Sbjct: 6 PRLRIGQINLGGAE----------------DATRELPSIARDLGLDIVLVQE-------- 41
Query: 82 KVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAG 141
+ + + H K + +R + +
Sbjct: 42 ------QYSMVGFLAQCGAHPK--------AGVYIRNRVLPCAVL-----------HHLS 76
Query: 142 NRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKES 201
+ +V I G ++++ + + +D + L +
Sbjct: 77 STHIT--VVHIGGWDLYMVSAYFQYSDPIDPYLHRLGNILDRLRGARVVICADTNAHSPL 134
Query: 202 LVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPIDYFV 261
+ D K D + D + +D +
Sbjct: 135 WHSL----PRHYVGRGQEVADRRAKMEDFIGARRLVVHNADGHLPTFSTANGESYVDVTL 190
Query: 262 MDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISID 301
+ + + + SDH I
Sbjct: 191 STRGV--------------RVSEWRVTNESSSDHRLIVFG 216
>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 = 37.4 bits (85), Expect = 0.004
Identities = 31/283 (10%), Positives = 67/283 (23%), Gaps = 57/283 (20%)
Query: 23 KVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAK 82
+ +++ NIN L + L + K+ D + +QE
Sbjct: 7 HITILTLNINGL--------------NSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTH 52
Query: 83 VFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGN 142
W Y + AI V K R
Sbjct: 53 RLKIKGWRKIYQANGKQKKA--------GVAILVSDKTDFKP----------TKIKRDKE 94
Query: 143 RRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKESL 202
+ + I +++ +L+I+ + +++K ++ + L
Sbjct: 95 GHYIMVKGSIQQEELTILNIYAPNTGAP------------------RFIKQVLSDLQRDL 136
Query: 203 VPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLRNKIPIDYFVM 262
+ + K L + D +F
Sbjct: 137 DSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSA 196
Query: 263 DQNAYK----FLIQESFSEILYNEDDIKSRGKRLSDHCPISID 301
+ Y + ++ + LSDH I ++
Sbjct: 197 PHHTYSKIDHIVGSKALLSKC---KRTEIITNYLSDHSAIKLE 236
>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 = 36.4 bits (83), Expect = 0.008
Identities = 41/291 (14%), Positives = 83/291 (28%), Gaps = 48/291 (16%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAKVF 84
++ SWN++ L + +K+ + K DI+ LQE
Sbjct: 63 KICSWNVDGL---------RAWIKK------KGLDWVKEEAPDILCLQET---KCSENKL 104
Query: 85 PKNT-WCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNR 143
P S + S ++ + + R+ ++V ++
Sbjct: 105 PAELQELPGLSHQYWSAPSDKEGYS--GVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEF 162
Query: 144 RAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSL-----------LSQQAQWLK 192
+ +LV + L+ D + + ++ + L+
Sbjct: 163 DSF-VLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 221
Query: 193 DWITQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLR 252
+ KK + F + + D F F + + N R
Sbjct: 222 NPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWR 281
Query: 253 NKIPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
+DYF++ + L S+I SDHCPI++
Sbjct: 282 ----LDYFLLSHSLLPALCD---SKIRSKA--------LGSDHCPITLYLA 317
>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 = 35.3 bits (80), Expect = 0.016
Identities = 36/298 (12%), Positives = 73/298 (24%), Gaps = 43/298 (14%)
Query: 23 KVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAK 82
V VSWN + L + D V +Q G
Sbjct: 8 SVHTVSWNSGHERAPTNLEEL------------LGLNSGETPDVIAVAVQGFGFQTD--- 52
Query: 83 VFPKNTWCIFYSTERL--INHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRA 140
+ C+ L ++K + + V + Q + +
Sbjct: 53 KPQQGPACVKNFQSLLTSKGYTKLKNTITETMGLTVYCLEKHLDQNTLKNETIIVTVDDQ 112
Query: 141 GNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKE 200
+ I K+ + + A + ++K +
Sbjct: 113 KKSGGIVTSFTIYNKRFSFTTSRMSDEDVTSTNTK-----------YAYDTRLDYSKKDD 161
Query: 201 SLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRF-----PKEKDSRCNANKNLRNKI 255
GD N ++ + + D L+ F KE+ +
Sbjct: 162 PSDFLFWIGDLNVRVETNATHAKSLVDQNNIDGLMAFDQLKKAKEQKLFDGWTEPQVTFK 221
Query: 256 PIDYFVMDQNAYKFLIQESFSE-ILYNEDD--------IKSRGK-RLSDHCPISIDYD 303
P F + + Y S+++ LY S + ++H P+ +
Sbjct: 222 PTYKFKPNTDEYDLSATPSWTDRALYKSGTGKTIQPLSYNSLTNYKQTEHRPVLAKFR 279
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling,
SGC stockholm, structural genomics CONS hydrolase; 1.90A
{Homo sapiens}
Length = 357
Score = 30.0 bits (67), Expect = 0.75
Identities = 38/320 (11%), Positives = 82/320 (25%), Gaps = 66/320 (20%)
Query: 23 KVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVF--LQEMGSYN-- 78
+ + +WN+ G S+ L + D+ +QE S
Sbjct: 27 ALFVATWNMQ------GQKELPPSLDE------FLLPAEADYAQDLYVIGVQEGCSDRRE 74
Query: 79 ---AVAKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKD 135
+ + + + S+ ++ ++ +R+ + +
Sbjct: 75 WETRLQETLGPH--YVLLSSAAH---------GVLYMSLFIRRDLIWFCSEVECSTVTTR 123
Query: 136 SFSRAGNRRAVELLVEINGKKIWVLDIHLKSF------CFLDSLENTYSPSCSLLSQQAQ 189
S+ + A+ + G + H S LD +
Sbjct: 124 IVSQIKTKGALGISFTFFGTSFLFITSHFTSGDGKVAERLLDYTRTVQALVLPRNVPDTN 183
Query: 190 WLKDWITQKKESLVPFVIAGDFNRKINYLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANK 249
+ GDFN +++ D L+ +
Sbjct: 184 PYRSSAADVTTRFDEVFWFGDFNFRLSGGRTVVDALL----CQGLVVDVPALLQHDQLIR 239
Query: 250 NLRNKIPIDYF----VMDQNAYKFLIQESFSE-------------ILY---NEDDIKSRG 289
+R F + +YKF I + + +LY ++ DI
Sbjct: 240 EMRKGSIFKGFQEPDIHFLPSYKFDIGKDTYDSTSKQRTPSYTDRVLYRSRHKGDICPVS 299
Query: 290 K------RLSDHCPISIDYD 303
+ SDH P+ +
Sbjct: 300 YSSCPGIKTSDHRPVYGLFR 319
>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 = 28.0 bits (61), Expect = 2.9
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 118 KKNVRVLQQSYPLLGAKDS 136
K+ ++ LQ S L A DS
Sbjct: 19 KQALKKLQASLKLY-ADDS 36
>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial;
mitochondrion, DNA binding protein, transcription
factor, transcription termination; 1.60A {Homo sapiens}
PDB: 3opg_A 3my3_A
Length = 270
Score = 27.7 bits (61), Expect = 3.1
Identities = 24/105 (22%), Positives = 40/105 (38%), Gaps = 9/105 (8%)
Query: 39 GVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMG-SYNAVAKVFPKNTWCIFYSTER 97
GV L K ++ L + K++ ++FL+++G N + KN E
Sbjct: 16 GVDLSKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN 75
Query: 98 LIN-----HSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSF 137
L HSK S D+ + +K +L S L + F
Sbjct: 76 LKTRVAYLHSKNFSKADVAQMV---RKAPFLLNFSVERLDNRLGF 117
>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 = 27.5 bits (60), Expect = 4.1
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 26/76 (34%)
Query: 183 LLSQQAQWLKDWITQKKESL------VPFVIAGDF----NRKIN------------YLGN 220
L++++AQ +KDW+ + E+L +P +F R+I+ GN
Sbjct: 1253 LVTREAQ-IKDWVENELEALKLEAEEIPSEDQNEFLLERTREIHNEAESQLRAAQQQWGN 1311
Query: 221 NDDFWKTIDPNDSLIR 236
DF+K DP + +R
Sbjct: 1312 --DFYKR-DPRIAPLR 1324
>2gdt_A Leader protein; P65 homolog; NSP1 (EC 3.4.22.-); beta-barrel,
alpha-beta, replicase, structural genomics, PSI-2,
protein structure initiative; NMR {Sars coronavirus}
SCOP: d.346.1.1 PDB: 2hsx_A
Length = 116
Score = 27.3 bits (60), Expect = 4.5
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 94 STERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNRRAVELLVEIN 153
S E ++ ++ N + + K + L+Q Y + D+ S + VEL+ E++
Sbjct: 23 SVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEMD 82
Query: 154 G 154
G
Sbjct: 83 G 83
>3ice_A Transcription termination factor RHO; transcription, ATPase,
hexamer, helicase, RNA, RECA, OB fold, motor,
ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A
{Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A*
1xpr_A* 1xpu_A* 2ht1_A
Length = 422
Score = 27.3 bits (60), Expect = 5.1
Identities = 20/118 (16%), Positives = 39/118 (33%), Gaps = 21/118 (17%)
Query: 159 VLDIHLKSFCFLDSLENTYSP-------SCSLLSQQ----AQWLKDWITQKKESLVPFVI 207
VL+I F FL S +++Y S S + + + I KE F +
Sbjct: 57 VLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFAL 116
Query: 208 AGDFNRKINYLGNND-DFWKTIDPNDSL-IRFPKEKDSRCNANKNLRNKIPIDYFVMD 263
K+N + + + + ++L R + + + V+D
Sbjct: 117 -----LKVNEVNFDKPENARNKILFENLTPLHANS---RLRMERGNGSTEDLTARVLD 166
>1xv5_A AGT, DNA alpha-glucosyltransferase; HET: DNA CME UDP; 1.73A
{Enterobacteria phage T4} PDB: 1y6f_A* 1y6g_A* 1ya6_A*
1y8z_A*
Length = 401
Score = 26.8 bits (59), Expect = 5.6
Identities = 7/52 (13%), Positives = 16/52 (30%), Gaps = 4/52 (7%)
Query: 188 AQWLKD-WITQKKESLVPFVIAG---DFNRKINYLGNNDDFWKTIDPNDSLI 235
+ L W + A +F ++ + +WK + + I
Sbjct: 148 NKVLMKEWYPETVSLFDDIEEAPTVYNFQPPMDIVKVRSTYWKDVSEINMNI 199
>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA
capture mechanism, ATP-binding, hydrolase,
nucleotide-binding, RN binding; 2.35A {Thermotoga
maritima}
Length = 427
Score = 26.5 bits (58), Expect = 6.7
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 159 VLDIHLKSFCFLDSLENTYSPS 180
VL+IH + F FL +E+ PS
Sbjct: 61 VLEIHPEGFGFLRRIEDNLLPS 82
>2fqx_A Membrane lipoprotein TMPC; ABC transport system, ligand-binding
protein, guanosine, TP0319, transport protein; HET:
GMP; 1.70A {Treponema pallidum} PDB: 2fqw_A* 2fqy_A*
Length = 318
Score = 26.6 bits (58), Expect = 7.2
Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 50 TTSDY-TLLRQYAKNLDADIVFL---QEMGSYNAVAKVFPKNTWCIFYST 95
T ++Y L +A + +V + + + FPK + + +
Sbjct: 47 TDAEYVPSLSAFADE-NMGLVVACGSFLVEAVIETSARFPKQKFLVIDAV 95
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 0.135 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: 2,577,672
Number of extensions: 114224
Number of successful extensions: 395
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 47
Length of query: 304
Length of database: 5,693,230
Length adjustment: 92
Effective length of query: 212
Effective length of database: 3,462,782
Effective search space: 734109784
Effective search space used: 734109784
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: 56 (25.9 bits)