RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6037
(286 letters)
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation;
1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A
Length = 333
Score = 352 bits (904), Expect = e-122
Identities = 140/279 (50%), Positives = 191/279 (68%), Gaps = 4/279 (1%)
Query: 9 NEKYGIREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLK 68
++ IR+VW+ N+Q+E I SLI Y + +DTEFPGVVA+PLG F+S+ +Y Y L+
Sbjct: 18 SQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDDYHYQTLR 77
Query: 69 INVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQR 128
NVD LKIIQIGL D + P T WQFNF F+LQ+DMYA +SI+LL SGI F++
Sbjct: 78 ANVDSLKIIQIGLALSDEEGNAPVEACT-WQFNFTFNLQDDMYAPESIELLTKSGIDFKK 136
Query: 129 HKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFEL 188
H+E GIEPADFAELL SG+VL ++V W++FHSGYDF YLLK + LP+E EF+++
Sbjct: 137 HQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQ-IPLPAEYEEFYKI 195
Query: 189 QRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248
++F YD+KY+MKS N GLQ++A+ L + RIGPQHQAGSD+LLT R+FF++R
Sbjct: 196 LCIYFPKNYDIKYIMKSVLNNSKGLQDIADDLQIHRIGPQHQAGSDALLTARIFFEIRSR 255
Query: 249 FFEDAIDDDKYCGHIYGLG-PAGWNGHTNGNAENIEVTN 286
+F+ +I D + +YGLG H N + I+ +
Sbjct: 256 YFDGSI-DSRMLNQLYGLGSTGSVLWHNNSSTPQIQFRD 293
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail,
transcription regulation, repressor, phosphorylation.;
2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9
Length = 289
Score = 347 bits (891), Expect = e-121
Identities = 93/277 (33%), Positives = 155/277 (55%), Gaps = 19/277 (6%)
Query: 9 NEKYGIREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLK 68
+R+VW N+ EF IR L++ YN++ I TEF G +A+P+G FRS +Y Y ++
Sbjct: 11 PNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMR 70
Query: 69 INVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQR 128
NVD L IQ+GL+ D+ P +TWQFNF+FD ++++ + +S++LL+ SGI F++
Sbjct: 71 ANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIMSTESLELLRKSGINFEK 130
Query: 129 HKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFEL 188
H+ GI+ +F++LL SG++++D V W+++H+ YD G+L+ +LM S+P+ + +F
Sbjct: 131 HENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMN-DSMPNNKEDFEWW 189
Query: 189 QRLFFKSIYDVKYLMKSCKNLKG---------------GLQEVAEQLDLSRIGPQHQAGS 233
+ + YD+ + K + K L +A++L L R G
Sbjct: 190 VHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGG 249
Query: 234 DSLLTGRVFFKMRELF---FEDAIDDDKYCGHIYGLG 267
SLL F ++ +L F + D KY G IYG+
Sbjct: 250 QSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGID 286
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase,
antiproliferative protein, transcription; 2.50A {Homo
sapiens} SCOP: c.55.3.9
Length = 252
Score = 339 bits (870), Expect = e-118
Identities = 181/253 (71%), Positives = 209/253 (82%), Gaps = 2/253 (0%)
Query: 14 IREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDL 73
I EVWA N+ EE IR +I YNY+ +DTEFPGVVA+P+G+FRS ++YQY L+ NVDL
Sbjct: 2 ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDL 61
Query: 74 LKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEG 133
LKIIQ+GLTF + + PPG +TWQFNFKF+L EDMYAQDSI+LL SGIQF++H+EEG
Sbjct: 62 LKIIQLGLTFMNEQGEYPPGT-STWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEG 120
Query: 134 IEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFF 193
IE FAELL TSGVVL + VKWLSFHSGYDFGYL+K+L +LP EE +FFE+ RLFF
Sbjct: 121 IETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTN-SNLPEEELDFFEILRLFF 179
Query: 194 KSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDA 253
IYDVKYLMKSCKNLKGGLQEVAEQL+L RIGPQHQAGSDSLLTG FFKMRE+FFED
Sbjct: 180 PVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDH 239
Query: 254 IDDDKYCGHIYGL 266
IDD KYCGH+YGL
Sbjct: 240 IDDAKYCGHLYGL 252
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain,
hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A
Length = 430
Score = 105 bits (262), Expect = 4e-26
Identities = 31/137 (22%), Positives = 48/137 (35%), Gaps = 11/137 (8%)
Query: 16 EVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFR----STSEYQYHFLKINV 71
E+ N + + I ++ ID EF G+ P T E +Y LK +
Sbjct: 2 EIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHS 61
Query: 72 DLLKIIQIGLTFFD---SKSCTPPGPFTTWQFNFKFDL----QEDMYAQDSIDLLQNSGI 124
+ Q GL F + S F + F F+ + + SID L + G
Sbjct: 62 MDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGF 121
Query: 125 QFQRHKEEGIEPADFAE 141
F + GI + E
Sbjct: 122 DFNKVFRNGIPYLNQEE 138
Score = 81.1 bits (199), Expect = 2e-17
Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 50/250 (20%)
Query: 24 EEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTF 83
++ I ++ + E + +P F+ + Y L ++ T
Sbjct: 176 DQKKFIDQVVEKIEDLLQSEENKNLDLEPCTGFQR--KLIYQTLSWKYPKGIHVETLETE 233
Query: 84 FDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELL 143
+ + + ++ +A++ +L G F+ ++
Sbjct: 234 KKERYIV----ISKVDEEERKRREQQKHAKEQEELNDAVG---------------FSRVI 274
Query: 144 TTSGVVLNDKVKWLSFHSG-YDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYL 202
+ + K + H+ D + + LP++ +EF E+ F + D K +
Sbjct: 275 H----AIANSGKLVIGHNMLLDVMHTVHQFYCP--LPADLSEFKEMTTCVFPRLLDTKLM 328
Query: 203 MKSC----KNLKGGLQEVAEQLDLSRIGPQ------------------HQAGSDSLLTGR 240
+ L E+ ++L + P H+AG D+ +TG
Sbjct: 329 ASTQPFKDIINNTSLAELEKRLKETPFNPPKVESAEGFPSYDTASEQLHEAGYDAYITGL 388
Query: 241 VFFKMRELFF 250
F M
Sbjct: 389 CFISMANYLG 398
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease,
hydrolase, magnesium, metal nonsense-mediated mRNA
decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}
Length = 507
Score = 105 bits (261), Expect = 1e-25
Identities = 30/137 (21%), Positives = 46/137 (33%), Gaps = 11/137 (8%)
Query: 16 EVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRS----TSEYQYHFLKINV 71
E+ N + + I ++ ID EF G+ P + T E +Y LK +
Sbjct: 4 EIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHS 63
Query: 72 DLLKIIQIGLTFFDSKSCTP---PGPFTTWQFNFKFDL----QEDMYAQDSIDLLQNSGI 124
+ Q GL F F + F F + + SID L + G
Sbjct: 64 MDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPKPFSRSSPDVKFVCQSSSIDFLASQGF 123
Query: 125 QFQRHKEEGIEPADFAE 141
F + GI + E
Sbjct: 124 DFNKVFCSGIPYLNQEE 140
Score = 64.3 bits (155), Expect = 9e-12
Identities = 33/239 (13%), Positives = 70/239 (29%), Gaps = 35/239 (14%)
Query: 42 DTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLLK--IIQIGLTFFDSKSCTPPGPFTTWQ 99
+F V + + DF + E + L + I Q + +
Sbjct: 172 QKKFIDQVIEKIEDFLQSEEKRSLELDPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKE 231
Query: 100 FNFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSF 159
+ + + ++ Q + Q + + + + SG ++ +
Sbjct: 232 ---RHIVISKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLV------VGH 282
Query: 160 HSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLK----GGLQE 215
+ D + + LP++ EF E+ F + D K + + L E
Sbjct: 283 NMLLDVMHTIHQFYCP--LPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAE 340
Query: 216 VAEQLDLSRIGPQ------------------HQAGSDSLLTGRVFFKMRELFFEDAIDD 256
+ ++L + P H+AG D+ +TG F M
Sbjct: 341 LEKRLKETPFDPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSLLSPP 399
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 46.2 bits (109), Expect = 8e-06
Identities = 42/251 (16%), Positives = 84/251 (33%), Gaps = 63/251 (25%)
Query: 13 GIREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDF-RSTSEYQYHFLKINV 71
G + + +E +R L TY+ + + A+ L + R+T + + F + +
Sbjct: 164 GNTDDY---FEE----LRDLYQTYH--VLVGDLIKFSAETLSELIRTTLDAEKVFTQ-GL 213
Query: 72 DLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDS---IDLLQNSGIQFQR 128
++L+ + ++ S TP + S I ++Q + +
Sbjct: 214 NILE-------WLENPSNTPDKDYLL-------------SIPISCPLIGVIQLA--HYVV 251
Query: 129 -HKEEGIEPADFAELLTTSGVVLNDKV---------KWLSFHSGYDFGYLLKLL--MGTR 176
K G P + L + V W SF + +L +G R
Sbjct: 252 TAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKA--ITVLFFIGVR 309
Query: 177 SL---PSEEAEFFELQRLFFKSIYD---VKYLMKSCKNLKGGLQEVAEQLD-LSRIGPQH 229
P+ L+ S+ + V M S NL ++V + ++ + P
Sbjct: 310 CYEAYPNTSLPPSILE----DSLENNEGVPSPMLSISNLT--QEQVQDYVNKTNSHLPAG 363
Query: 230 QAGSDSLLTGR 240
+ SL+ G
Sbjct: 364 KQVEISLVNGA 374
Score = 40.8 bits (95), Expect = 4e-04
Identities = 44/236 (18%), Positives = 75/236 (31%), Gaps = 74/236 (31%)
Query: 10 EKYG--IREVWARNVQEEFVH--------IRSLINTYNYIGIDTEFPGVVAKPLGDFRST 59
+ YG I ++ N +H IR NY + E + D +
Sbjct: 1655 DTYGFSILDIVINNPVNLTIHFGGEKGKRIRE-----NYSAMIFE-------TIVDGKLK 1702
Query: 60 SEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLL 119
+E F +IN TF K L + Q ++ L+
Sbjct: 1703 TEKI--FKEINEHSTSY-----TFRSEKG----------------LLSATQFTQPALTLM 1739
Query: 120 QNSGIQFQRHKEEGIEPAD--FA-----E---LLTTSGVV-LNDKVKWLSFHSGYDFGYL 168
F+ K +G+ PAD FA E L + + V+ + V+ + F+ G
Sbjct: 1740 --EKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVE-VVFYRGMTMQVA 1796
Query: 169 LKLLMGTRS-------LPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVA 217
+ RS P A F + ++Y+++ G L E+
Sbjct: 1797 VPRDELGRSNYGMIAINPGRVAASFSQE--------ALQYVVERVGKRTGWLVEIV 1844
Score = 38.9 bits (90), Expect = 0.002
Identities = 31/211 (14%), Positives = 57/211 (27%), Gaps = 70/211 (33%)
Query: 102 FKFDLQE--DMYAQD-----SIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKV 154
F L E + +A D +L+ + + E + F ++L L +
Sbjct: 37 FNKILPEPTEGFAADDEPTTPAELVG-KFLGYVSSLVEPSKVGQFDQVLNL---CLTE-- 90
Query: 155 KWLSFHSGYDFGYLLKLLMG------TRSLPSEEAEFFELQRLFFKSIYDVKYLMKS--C 206
F + Y L G L E + K+ + + K
Sbjct: 91 ----FENCY--------LEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFD 138
Query: 207 KNLKGGLQEVAEQLDLSRI----GPQHQAGSDSLLTGRVFFK-MRELF------------ 249
K L + +++ G Q G +F+ +R+L+
Sbjct: 139 KKSNSALFRAVGE-GNAQLVAIFGGQ---G-----NTDDYFEELRDLYQTYHVLVGDLIK 189
Query: 250 ---------FEDAIDDDKYCGHIYGLGPAGW 271
+D +K GL W
Sbjct: 190 FSAETLSELIRTTLDAEKVFTQ--GLNILEW 218
Score = 28.1 bits (62), Expect = 5.0
Identities = 20/127 (15%), Positives = 40/127 (31%), Gaps = 37/127 (29%)
Query: 159 FHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGG--LQEV 216
FHS LL+ L +++ + ++ K + + G L+ +
Sbjct: 427 FHS--------HLLVPASDLINKDLVKNNVS-------FNAKDIQIPVYDTFDGSDLRVL 471
Query: 217 AEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDAIDDDKYCGHIYGLGPAGWNGH-- 274
+ + + D ++ V + E HI GP G +G
Sbjct: 472 SGSISERIV--------DCIIRLPVKW-------ETTTQFK--ATHILDFGPGGASGLGV 514
Query: 275 -TNGNAE 280
T+ N +
Sbjct: 515 LTHRNKD 521
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A
{Homo sapiens}
Length = 349
Score = 42.3 bits (99), Expect = 9e-05
Identities = 17/112 (15%), Positives = 36/112 (32%), Gaps = 15/112 (13%)
Query: 138 DFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRL-FFKSI 196
+L+ + K L+ +D L + + L+ F K
Sbjct: 209 KVIDLMKLKELGTKYKYSLLT-DGSWDMSKFLN----------IQCQLSRLKYPPFAKKW 257
Query: 197 YDVKYLMKSCKNL---KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245
+++ + + + L + E+L + G H DS R+ +M
Sbjct: 258 INIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRM 309
>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition,
structures of 3'- exonuclease and ITS RNA complex,
hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens}
Length = 299
Score = 41.9 bits (98), Expect = 1e-04
Identities = 16/112 (14%), Positives = 36/112 (32%), Gaps = 15/112 (13%)
Query: 138 DFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRL-FFKSI 196
+L+ + K L+ +D L + + L+ F K
Sbjct: 159 KVIDLMKLKELGTKYKYSLLT-DGSWDMSKFLN----------IQCQLSRLKYPPFAKKW 207
Query: 197 YDVKYLMKSCKNL---KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245
+++ + + + L + E+L + G + DS R+ +M
Sbjct: 208 INIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPNCGLDDSKNIARIAVRM 259
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A
{Homo sapiens} SCOP: c.55.3.5
Length = 204
Score = 39.8 bits (93), Expect = 4e-04
Identities = 16/112 (14%), Positives = 35/112 (31%), Gaps = 15/112 (13%)
Query: 138 DFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRL-FFKSI 196
+ + + K L+ +D L + + L+ F K
Sbjct: 91 KVIDWMKLKELGTKYKYSLLT-DGSWDMSKFLN----------IQCQLSRLKYPPFAKKW 139
Query: 197 YDVKYLMKSCKNL---KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245
+++ + + + L + E+L + G H DS R+ +M
Sbjct: 140 INIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRM 191
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 39.5 bits (91), Expect = 0.001
Identities = 28/174 (16%), Positives = 50/174 (28%), Gaps = 38/174 (21%)
Query: 9 NEKYGI----REVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGD--FRSTSEY 62
I E+ + E +H RS+++ YN T + P D F Y
Sbjct: 423 ESTISIPSIYLELKVKLENEYALH-RSIVDHYNI--PKTFDSDDLIPPYLDQYF-----Y 474
Query: 63 Q---YHFLKIN----VDLLKIIQIGLTFFDSK------SCTPPGPFTTWQFNFKF----- 104
+H I + L +++ + F + K + G KF
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYI 534
Query: 105 ---DLQEDMYAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVK 155
D + + +D L K + A L+ + + K
Sbjct: 535 CDNDPKYERLVNAILDFLPKIEENLICSKYTDL--LRIA-LMAEDEAIFEEAHK 585
Score = 36.4 bits (83), Expect = 0.012
Identities = 39/312 (12%), Positives = 81/312 (25%), Gaps = 119/312 (38%)
Query: 14 IREVWARNVQEEF-VHIRSLINTYN----------------------------------- 37
+ V F + + L+ T
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309
Query: 38 YIGIDTE---------FP---GVVAKPLGDFRSTSEYQYHFLKINVD-LLKIIQIGLTFF 84
Y+ + P ++A+ + D +T + + +N D L II+ L
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN---WKHVNCDKLTTIIESSLNVL 366
Query: 85 DS-------KSCT--PPG---PFTT----WQFNFKFDLQEDMYAQDSIDLLQNS------ 122
+ + PP P W F+ + ++ L
Sbjct: 367 EPAEYRKMFDRLSVFPPSAHIPTILLSLIW-FDVIKSDVMVV-----VNKLHKYSLVEKQ 420
Query: 123 ---------GIQFQRHKEEGIEPADFAELLT----TSGVVLNDKVKWLSFHSGYDFGYL- 168
I + + E A ++ +D + + Y + ++
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP--PYLDQYFYSHIG 478
Query: 169 --LKLLMGTRSLPSEEAEFFELQRLFFKSIY-DVKYLMK------SCKNLKGGLQEVAEQ 219
LK + E E L F+ ++ D ++L + + N G + +Q
Sbjct: 479 HHLKNI--------EHPERMTL----FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQ 526
Query: 220 LDLSR--IGPQH 229
L + I
Sbjct: 527 LKFYKPYICDND 538
Score = 32.5 bits (73), Expect = 0.20
Identities = 40/242 (16%), Positives = 69/242 (28%), Gaps = 45/242 (18%)
Query: 33 INTYNYIGIDTEFPGVVA-KPLGDFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTP 91
++ + + + L + S L++ LL I T S
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPET----VLEMLQKLLYQIDPNWTSRSDHSSNI 223
Query: 92 PGPFTTWQFNFKFDLQEDMYAQDSIDL--LQNSGI--QFQ---------RHKEEGIEPAD 138
+ Q + L+ Y + L +QN+ F R K+ D
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQV----TD 279
Query: 139 FAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLL-MGTRSLPSEEAEFFELQ-RLFFKSI 196
F TT+ + L+ + LLK L + LP E + + +SI
Sbjct: 280 FLSAATTTHISLDHHSM--TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337
Query: 197 YDVK-----YLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFE 251
D + +C L ++ L+ P R F +F
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLE-----PAEY---------RKMFDRLSVFPP 383
Query: 252 DA 253
A
Sbjct: 384 SA 385
Score = 32.1 bits (72), Expect = 0.24
Identities = 36/239 (15%), Positives = 75/239 (31%), Gaps = 48/239 (20%)
Query: 55 DFRSTSEYQYHFLKINVDLLKIIQIGLTFFDSKSCTPPGPFTTWQFN------------- 101
DF T E+QY + I D + P + + +
Sbjct: 8 DF-ETGEHQYQYKDILSVFEDAFVDNFDCKDVQD-MPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 102 FKFDL----QEDMYAQDSIDLLQ-NSGIQFQRHKEEGIEPADFAEL-LTTSGVVLNDKVK 155
F QE+M + ++L+ N K E +P+ + + + ND
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 156 WLSFH--SGYDFGYLLKLL-------------M---GTRSLPSEEAEFFELQRLFFKSIY 197
+ ++ + L + L + G + + +++Q I+
Sbjct: 126 FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF 185
Query: 198 DVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFF-----KMRELFFE 251
+L N + E+ ++L L +I P + SD ++ ++R L
Sbjct: 186 ---WLNLKNCNSPETVLEMLQKL-LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5'
exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB:
3cm5_A 3cm6_A
Length = 308
Score = 36.9 bits (85), Expect = 0.004
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 178 LPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLL 237
+P+ ++ L ++F + + S + ++ E DL IG H A D L
Sbjct: 141 MPAFFRQYINLYKIFTNEMDRMGPKELSATT---NIGKMNEYYDLPTIGRAHDAMDDCLN 197
Query: 238 TGRVFFKM 245
+ +M
Sbjct: 198 IATILQRM 205
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo
sapiens}
Length = 224
Score = 36.0 bits (83), Expect = 0.007
Identities = 16/111 (14%), Positives = 33/111 (29%), Gaps = 13/111 (11%)
Query: 138 DFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRL-FFKSI 196
E + G++ + +D +L + ++ L +FK
Sbjct: 110 RVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLP----------GQCQYLGLPVADYFKQW 159
Query: 197 YDVKYLMKSCKNLKG--GLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245
++K GL ++ + L L IG H D + +
Sbjct: 160 INLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL 210
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics,
exonuclease, PSI-2, protein structure initiative; HET:
DNA; 2.50A {Thermotoga maritima MSB8}
Length = 186
Score = 32.1 bits (74), Expect = 0.11
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 212 GLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDAI 254
L V E+L L H+A D+ +T +VF + E+ ++
Sbjct: 140 SLDSVVEKLGLG-PFRHHRALDDARVTAQVFLRFVEMMKKEGH 181
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 29.1 bits (65), Expect = 1.4
Identities = 7/62 (11%), Positives = 15/62 (24%), Gaps = 1/62 (1%)
Query: 193 FKSIYDVKYLMKSCKNLKG-GLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFE 251
+ + + +G L + + + H A D +F
Sbjct: 153 LRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLLLIFLHRAAELLA 212
Query: 252 DA 253
A
Sbjct: 213 WA 214
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline
type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus
musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A*
3b6p_A* 2o4i_A 2oa8_A
Length = 242
Score = 28.4 bits (63), Expect = 2.5
Identities = 10/65 (15%), Positives = 16/65 (24%), Gaps = 5/65 (7%)
Query: 189 QRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMREL 248
+ L S KS L + +L H A D L + +
Sbjct: 160 KALEQASSPSGNGSRKSYS-----LGSIYTRLYWQAPTDSHTAEGDDLTLLSICQWKPQA 214
Query: 249 FFEDA 253
+
Sbjct: 215 LLQWV 219
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease,
homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus
musculus} PDB: 3u6f_B*
Length = 314
Score = 27.8 bits (61), Expect = 4.2
Identities = 6/61 (9%), Positives = 14/61 (22%)
Query: 193 FKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFED 252
K++ + L + +L H A L + + +
Sbjct: 159 LKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGHVLTLLSICQWKPQALLQW 218
Query: 253 A 253
Sbjct: 219 V 219
>1mus_A TN5 transposase; hairpin, DNA binding, transcription/DNA complex;
HET: DNA; 1.90A {Escherichia coli} SCOP: c.55.3.4 PDB:
1mur_A* 4dm0_A* 1mm8_A 1muh_A* 3ecp_A* 1b7e_A*
Length = 477
Score = 27.8 bits (60), Expect = 4.3
Identities = 9/44 (20%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 83 FFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQF 126
F DSK W+ + D + + L GI+
Sbjct: 435 FMDSKRTGIASWGALWEGWEALQSKLDGFL--AAKDLMAQGIKI 476
>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic
hypermutat protein-DNA complex, DNA mispair, cancer;
HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B*
2o8e_B* 2o8f_B*
Length = 1022
Score = 27.3 bits (61), Expect = 6.5
Identities = 6/24 (25%), Positives = 12/24 (50%), Gaps = 7/24 (29%)
Query: 234 DSLLTGRVFFKM---RELFFEDAI 254
D ++ +K+ EL+ DA+
Sbjct: 84 DLVI----CYKVGKFYELYHMDAL 103
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.139 0.420
Gapped
Lambda K H
0.267 0.0498 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,538,347
Number of extensions: 268643
Number of successful extensions: 568
Number of sequences better than 10.0: 1
Number of HSP's gapped: 546
Number of HSP's successfully gapped: 32
Length of query: 286
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 193
Effective length of database: 4,105,140
Effective search space: 792292020
Effective search space used: 792292020
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: 57 (26.3 bits)