RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8196
(230 letters)
>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading
domain, transferase; HET: DNA U5P; 1.60A {Escherichia
coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A*
2xy8_A*
Length = 194
Score = 275 bits (707), Expect = 2e-95
Identities = 95/184 (51%), Positives = 130/184 (70%), Gaps = 5/184 (2%)
Query: 1 MHRHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALA 56
+ R IVLD ETTG+N I +GH+IIEIG VE+ NR++TGNN H Y+ P R + A
Sbjct: 8 ITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFG 67
Query: 57 IHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIY 116
+HG+ +FL +K F+E+ D F++Y+ +E++IHNAAFD+GF+D E SLL +
Sbjct: 68 VHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTF 127
Query: 117 -RITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSN 175
++TD+L +ARK+ GKRNSLDALC RY I RTLHG LLDA++LAEVYLAMT GQ++
Sbjct: 128 CKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTS 187
Query: 176 LNFK 179
+ +
Sbjct: 188 MATR 191
>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA
complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A
3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A*
3v9s_A* 3v9x_A* 3va0_A* 2is3_A
Length = 235
Score = 144 bits (365), Expect = 3e-43
Identities = 35/181 (19%), Positives = 66/181 (36%), Gaps = 19/181 (10%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIK----NRQITGNNLHYYINP--GRDSEKSALAIH 58
+V+D+ET G N ++EI + +K + LH+++ P G + + ALA +
Sbjct: 40 VVIDVETAGFNA-KTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFN 98
Query: 59 GLT-TKFLKNKLKFSEIVDNFLNYV---------SNSEIIIHNAAFDVGFLDMELSLLGY 108
G+ + + E + V + + ++ HNA FD F+
Sbjct: 99 GIDPNDPDRGAVSGYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASL 158
Query: 109 SNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLA 168
+ + DT +A + L C + H L D E A ++
Sbjct: 159 KRNPFHPFATFDTAALAGLAL--GQTVLSKACQTAGMDFDSTQAHSALYDTERTAVLFCE 216
Query: 169 M 169
+
Sbjct: 217 I 217
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS
protein structure initiative, midwest center for
structural genomics; 2.09A {Pseudomonas aeruginosa}
SCOP: c.55.3.5
Length = 224
Score = 141 bits (358), Expect = 3e-42
Identities = 36/181 (19%), Positives = 72/181 (39%), Gaps = 19/181 (10%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQ----ITGNNLHYYINP--GRDSEKSALAIH 58
+V+D+ET G N ++EI + + + + I P G + E +AL
Sbjct: 32 VVVDVETGGFNSA-TDALLEIAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEPAALEFT 90
Query: 59 GLTTKF-----LKNKLKFSEIVDNFLNYV-----SNSEIIIHNAAFDVGFLDMELSLLGY 108
G+ ++ + +EI + + ++ HN++FD+GFL+ ++ G
Sbjct: 91 GIKLDHPLRMAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAAVARTGI 150
Query: 109 SNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLA 168
+ + DT +A + + L C + +R H D E AE++
Sbjct: 151 KRNPFHPFSSFDTATLAGLAY--GQTVLAKACQAAGMEFDNREAHSARYDTEKTAELFCG 208
Query: 169 M 169
+
Sbjct: 209 I 209
>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 = 136 bits (344), Expect = 2e-40
Identities = 53/165 (32%), Positives = 86/165 (52%), Gaps = 7/165 (4%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+VLD ETTGL+ IIEIG V+I+ QI H I P R+ + + I G+T +
Sbjct: 15 VVLDFETTGLDP-QVDEIIEIGAVKIQGGQIVDE-YHTLIKPSREISRKSSEITGITQEM 72
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLM 124
L+NK E++ FL ++ +S I+ HNA FD FL + + + ++ DTL +
Sbjct: 73 LENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWE---RPYIDTLAL 129
Query: 125 ARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAM 169
A+ + + SLD++ ++ + H L DA + A+V+L
Sbjct: 130 AKSLLKLRSYSLDSVVEKLGLGPFRH--HRALDDARVTAQVFLRF 172
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 117 bits (295), Expect = 1e-32
Identities = 42/200 (21%), Positives = 62/200 (31%), Gaps = 37/200 (18%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNN---------------LHYYINPGRD 49
+ LD+E TGL I E+ + + L + P R
Sbjct: 13 VFLDLEATGLPS-VEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERP 71
Query: 50 SEKSALAIHGLTTKFLKN--KLKFSEIVDN----FLNYVSNSEIII-HNA-AFDVGFLDM 101
A I GL+++ L K F V FL+ + ++ HN +D L
Sbjct: 72 FTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCA 131
Query: 102 ELSLLGYSNFTKYIYRITDTLLMARKIHT----------GKRNSLDALCDRYNISKIHRT 151
EL LG + DTL R + + SL +L RY
Sbjct: 132 ELRRLGARLPRDTVC--LDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFR-AEPSA 188
Query: 152 LHGGLLDAELLAEVYLAMTR 171
H D L ++L
Sbjct: 189 AHSAEGDVHTLLLIFLHRAA 208
>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 = 105 bits (262), Expect = 7e-28
Identities = 36/202 (17%), Positives = 66/202 (32%), Gaps = 38/202 (18%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNN------------------LHYYINP 46
I LD+E TGL + E+ + + R + + L I P
Sbjct: 15 IFLDLEATGLP-SSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAP 73
Query: 47 GRDSEKSALAIHGLTTKFLKN--KLKFSEIV----DNFLNYVSNSEIII-HNA-AFDVGF 98
G+ A I GL+ L+ + +F + + FL ++ HN +D
Sbjct: 74 GKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPL 133
Query: 99 LDMELSLLGYSNFTKYIYRITDTLLMARKIHTG---------KRNSLDALCDRYNISKIH 149
L EL+ L + + + D++ + + K SL ++ R
Sbjct: 134 LQTELARLSTPSPLDGTFCV-DSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT 192
Query: 150 RTLHGGLLDAELLAEVYLAMTR 171
+ H D L + +
Sbjct: 193 DS-HTAEGDDLTLLSICQWKPQ 213
>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 = 106 bits (265), Expect = 1e-27
Identities = 34/201 (16%), Positives = 66/201 (32%), Gaps = 36/201 (17%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNN------------------LHYYINP 46
I LD+E TGL + E+ + + R + + L I P
Sbjct: 15 IFLDLEATGLP-SSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAP 73
Query: 47 GRDSEKSALAIHGLTTKFLKN--KLKFSEIV----DNFLNYVSNSEIII-HNA-AFDVGF 98
G+ A I GL+ L+ + +F + + FL ++ HN +D
Sbjct: 74 GKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPL 133
Query: 99 LDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGG--- 155
L EL+ L + + + D++ + + S + Y++ I+ L+
Sbjct: 134 LQTELARLSTPSPLDGTFCV-DSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPT 192
Query: 156 -----LLDAELLAEVYLAMTR 171
L + +
Sbjct: 193 DSHTAEGHVLTLLSICQWKPQ 213
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo
sapiens}
Length = 224
Score = 79.1 bits (195), Expect = 3e-18
Identities = 27/180 (15%), Positives = 61/180 (33%), Gaps = 18/180 (10%)
Query: 5 IVLDIETTGLNI-IDGHRIIEIGCVEI--KNRQITGNNLHYYINPGRDSEKSAL--AIHG 59
+VLD E T I IIE +++ + +I H Y+ P + + + G
Sbjct: 34 LVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTF-HMYVQPVVHPQLTPFCTELTG 92
Query: 60 LTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDV---------GFLDMELSLLGYSN 110
+ + + ++++ +++ ++ N L + LG
Sbjct: 93 IIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLP- 151
Query: 111 FTKYIYRITDTLLMARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAM 169
Y + + +N L + ++ I R H G+ D + +A + +
Sbjct: 152 VADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGR-PHSGIDDCKNIANIMKTL 210
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A
{Homo sapiens}
Length = 349
Score = 80.5 bits (198), Expect = 4e-18
Identities = 33/218 (15%), Positives = 80/218 (36%), Gaps = 24/218 (11%)
Query: 1 MHRHIVLDIETT---GLNIIDGHRIIEIGCVEI--KNRQITGNNLHYYINPGRDSEKSAL 55
++D E T G H IIE V + +I Y+ P +++ S
Sbjct: 127 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDT-FQQYVRPEINTQLSDF 185
Query: 56 A--IHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDV--------GFLDMELSL 105
+ G+T + F +++ ++ + E+ + FL+++ L
Sbjct: 186 CISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQL 245
Query: 106 LGYSNFTKYIYRITDTLLMARKIHTGKRN--SLDALCDRYNISKIHRTLHGGLLDAELLA 163
+ + + + + R+ L + ++ + R H GL D++ +A
Sbjct: 246 SRL-KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PHCGLDDSKNIA 303
Query: 164 EVYLAMTRGQSNLNFKPKINNSNNIETKIKIPNNIPIK 201
+ + M + + +IN + + + +++PI+
Sbjct: 304 RIAVRMLQ----DGCELRINEKMHAGQLMSVSSSLPIE 337
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A
{Homo sapiens} SCOP: c.55.3.5
Length = 204
Score = 78.3 bits (193), Expect = 5e-18
Identities = 28/186 (15%), Positives = 66/186 (35%), Gaps = 20/186 (10%)
Query: 1 MHRHIVLDIETT---GLNIIDGHRIIEIGCVEI--KNRQITGNNLHYYINPGRDSEKSAL 55
++D E T G H IIE V + +I Y+ P +++ S
Sbjct: 9 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDT-FQQYVRPEINTQLSDF 67
Query: 56 A--IHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVG--------FLDMELSL 105
+ G+T + F +++ ++++ E+ + FL+++ L
Sbjct: 68 CISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQL 127
Query: 106 LGYSNFTKYIYRITDTLLMARKIHTGKRN--SLDALCDRYNISKIHRTLHGGLLDAELLA 163
+ + + + + R+ L + ++ + H GL D++ +A
Sbjct: 128 SRL-KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMD-YDGRPHCGLDDSKNIA 185
Query: 164 EVYLAM 169
+ + M
Sbjct: 186 RIAVRM 191
>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 = 76.2 bits (187), Expect = 1e-16
Identities = 34/236 (14%), Positives = 67/236 (28%), Gaps = 33/236 (13%)
Query: 5 IVLDIETTGL--NIIDGHRIIEIGCVEIKNRQITGNNLHY---YINPGRDSEKSALA--I 57
++LD ETT N +I+ V Y+ P + +
Sbjct: 22 LILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCVDF 81
Query: 58 HGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAF------DVG-FLDMELSLLGYSN 110
G+ + + F + + F ++ + AF D+ ++ L
Sbjct: 82 TGIPQRSIDTADTFDVVYEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMKLSNIQM 141
Query: 111 ---FTKYI-YRITDTLLMARKIHTG--KRNSLDALCDRYNISKIHRTLHGGLLDAELLAE 164
F +YI T M R ++ + + Y++ I R H + D +A
Sbjct: 142 PAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEYYDLPTIGR-AHDAMDDCLNIAT 200
Query: 165 VYLAMTRGQSNLNFKPKINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDK 220
+ M N+ K +N + + + K
Sbjct: 201 ILQRM----INMGAKVTVNE--------LLTCCASWRRQPLVYNKEWRSSFMDAGK 244
>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 = 72.7 bits (178), Expect = 2e-15
Identities = 32/218 (14%), Positives = 80/218 (36%), Gaps = 24/218 (11%)
Query: 1 MHRHIVLDIETT---GLNIIDGHRIIEIGCVEI--KNRQITGNNLHYYINPGRDSEKSAL 55
++D E T G H IIE V + +I Y+ P +++ S
Sbjct: 77 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDT-FQQYVRPEINTQLSDF 135
Query: 56 --AIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDV--------GFLDMELSL 105
++ G+T + F +++ ++ + E+ + FL+++ L
Sbjct: 136 CISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQL 195
Query: 106 LGYSNFTKYIYRITDTLLMARKIHTGKRN--SLDALCDRYNISKIHRTLHGGLLDAELLA 163
+ + + + + R+ L + ++ + + GL D++ +A
Sbjct: 196 SRL-KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMD-YDGRPNCGLDDSKNIA 253
Query: 164 EVYLAMTRGQSNLNFKPKINNSNNIETKIKIPNNIPIK 201
+ + M + L +IN + + + +++PI+
Sbjct: 254 RIAVRMLQDGCEL----RINEKMHAGQLMSVSSSLPIE 287
>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 = 38.3 bits (88), Expect = 0.002
Identities = 35/263 (13%), Positives = 76/263 (28%), Gaps = 89/263 (33%)
Query: 23 IEIGCVEIKNRQITG-NNLHYYINPGRDSEKSALAIHGLTTKFLKNKLK--FSE------ 73
+ + + L Y I+P S + L ++ +L+
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 74 --IVDNFLNYVSNSEIIIHNAAFDVG--------------FLD--------MELSLLGYS 109
++ N V N++ AF++ FL ++ + +
Sbjct: 247 LLVLLN----VQNAKAW---NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT 299
Query: 110 N------FTKYIYRITDTL-------------LMARKIHTGKRNSLDALCDRYNISKIHR 150
KY+ L ++A I G + D N K+
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL-ATWDNW-KHVNCDKLTT 357
Query: 151 TLHGGL--LDAELLAEVY--LAMTRGQSNLNFKPKINNSNNIETKI------KIPNNIPI 200
+ L L+ +++ L++ F P S +I T + + + +
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSV--------F-PP---SAHIPTILLSLIWFDVIKSDVM 405
Query: 201 KLANSNELVQHNMILSKIDKHSN 223
+ N+L + S ++K
Sbjct: 406 VVV--NKLHK----YSLVEKQPK 422
Score = 32.9 bits (74), Expect = 0.086
Identities = 44/263 (16%), Positives = 80/263 (30%), Gaps = 88/263 (33%)
Query: 3 RHIVLDIETTGLNIIDGHRIIEIGCVEIKN----RQITGNNLHYYINPGRDSEKSALAIH 58
HI LD + L + ++ + ++ + R++ NP R S +
Sbjct: 287 THISLDHHSMTLTPDEVKSLL-LKYLDCRPQDLPREVLT------TNPRRLSIIAESIRD 339
Query: 59 GLTT-KFLK--NKLKFSEIVDNFLNYVSNSE-----------------------IIIHNA 92
GL T K N K + I+++ LN + +E +I +
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV 399
Query: 93 AFDVGFLDMELSLLGYS----NFTKYIYRITDTLLMARKIHTGKRNSL-DALCDRYNISK 147
+ + L YS + I + + K+ +L ++ D YNI K
Sbjct: 400 IKSDVMVVVN-KLHKYSLVEKQPKESTISIPS-IYLELKVKLENEYALHRSIVDHYNIPK 457
Query: 148 ---------------IHRTL--HGGLLDAE------LLAEVYLAMTRGQSNLNFKPKINN 184
+ + H L + E L V+L + F
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHH--LKNIEHPERMTLFRMVFL-------DFRF------ 502
Query: 185 SNNIETKIK---IPNNIPIKLAN 204
+E KI+ N + N
Sbjct: 503 ---LEQKIRHDSTAWNASGSILN 522
Score = 31.4 bits (70), Expect = 0.29
Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 65/194 (33%)
Query: 48 RDSEKSALAIHGLTTKFLKNKLKFSE-------IVDNF---LNYVSNSEIIIHNAAFDVG 97
+ ++S ++I + +L+ K+K IVD++ + S+ I +
Sbjct: 419 KQPKESTISIPSI---YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPY------- 468
Query: 98 FLDMEL-SLLGY-----------SNFTKYIYRITDTLLMARKI-HTG-----KRNSLDAL 139
LD S +G+ + F ++ D + +KI H + L+ L
Sbjct: 469 -LDQYFYSHIGHHLKNIEHPERMTLFRM-VF--LDFRFLEQKIRHDSTAWNASGSILNTL 524
Query: 140 CD--RYN--ISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKINNSNNIETKIKIP 195
Y I L+ + L+F PKI N I +K
Sbjct: 525 QQLKFYKPYICDNDPKYE------RLVNAI----------LDFLPKI-EENLICSKYT-- 565
Query: 196 NNIPIKLANSNELV 209
+ + I L +E +
Sbjct: 566 DLLRIALMAEDEAI 579
Score = 29.8 bits (66), Expect = 0.86
Identities = 27/184 (14%), Positives = 58/184 (31%), Gaps = 49/184 (26%)
Query: 1 MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNL-----------H--YYINPG 47
+ I L+++ N HR I + I + ++L H +++
Sbjct: 428 IP-SIYLELKVKLENEYALHRSI-VDHYNIP-KTFDSDDLIPPYLDQYFYSHIGHHLKNI 484
Query: 48 RDSEKSAL--AIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSL 105
E+ L + L +FL+ K++ N + N+ ++
Sbjct: 485 EHPERMTLFRMVF-LDFRFLEQKIRHDSTAWNASGSILNT------------LQQLKF-- 529
Query: 106 LGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAE- 164
Y YI R + N++ + + + + LL L+AE
Sbjct: 530 --YK---PYICDNDPKY--ERLV-----NAILDFLPKIE-ENLICSKYTDLLRIALMAED 576
Query: 165 --VY 166
++
Sbjct: 577 EAIF 580
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA
polymerase III; HET: DGT; 2.39A {Geobacillus
kaustophilus} PDB: 3f2c_A* 3f2d_A*
Length = 1041
Score = 38.1 bits (89), Expect = 0.002
Identities = 20/180 (11%), Positives = 48/180 (26%), Gaps = 17/180 (9%)
Query: 6 VLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFL 65
V D E + L G ++ + + N + + D+E + + +
Sbjct: 26 VFDAEVSELK--SGRTLLTMKITDYTN----SILVKMFSRDKEDAELMS-GVKKGMWVKV 78
Query: 66 KNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMA 125
+ ++ V + + ++ I N D + L T D +
Sbjct: 79 RGSVQNDTFVRDLVIIANDLNEIAANERQDTAPEGEKRVELHLH--TPMSQ--MDAVTSV 134
Query: 126 RKIH-TGKRNSLDALCDRYNIS-----KIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFK 179
K+ K+ A+ + + + + E + N
Sbjct: 135 TKLIEQAKKWGHPAIAVTDHAVVQSFPEAYSAAKKHGMKVIYGLEANIVDDGVPIAYNET 194
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene,
replication block, mutagenesis, transferase/electron
transport/DNA complex; HET: DNA 2DT 8FG; 2.10A
{Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB:
1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A*
1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A*
1zyq_A* 2ajq_A*
Length = 698
Score = 35.6 bits (82), Expect = 0.010
Identities = 26/132 (19%), Positives = 41/132 (31%), Gaps = 31/132 (23%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
IV DIE L + + C I + + P
Sbjct: 2 IVSDIEANALL----ESVTKFHCGVIYD---YSTAEYVSYRPS----------------- 37
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIII-HNAA-FDVGFLDMELSLLGYSNFTKYIYRITDTL 122
F +D V+ +I+ HN +DV L L F DTL
Sbjct: 38 -----DFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTL 92
Query: 123 LMARKIHTGKRN 134
+++R IH+ ++
Sbjct: 93 VLSRLIHSNLKD 104
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase;
2.30A {Xanthomonas campestris PV}
Length = 194
Score = 32.9 bits (74), Expect = 0.045
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 7/39 (17%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYY 43
I +D+E TGL+ D IIEI + +T L+
Sbjct: 12 IWIDLEMTGLD-TDRDSIIEIATI------VTDAQLNVL 43
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella
burnetii}
Length = 186
Score = 32.9 bits (74), Expect = 0.048
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 9/88 (10%)
Query: 3 RHIVLDIETTGLNIIDGHRIIEIGCVEIK---NRQITGNNLH-----YYINPGRDSEKSA 54
I LD+E TGL+ + RIIEI + + G + + S
Sbjct: 10 NLIWLDLEMTGLD-PERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAMDNWNTSH 68
Query: 55 LAIHGLTTKFLKNKLKFSEIVDNFLNYV 82
GL + + + E L ++
Sbjct: 69 HTASGLLERVKNSSVDEVEAETLTLAFL 96
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease,
hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP:
c.55.3.5 PDB: 1yta_A 1j9a_A
Length = 180
Score = 31.0 bits (69), Expect = 0.19
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 9/85 (10%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIK---NRQITGNNLHYY-----INPGRDSEKSALA 56
I +D+E TGL+ + RIIEI + N G + + + D
Sbjct: 8 IWIDLEMTGLD-PERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALMDDWNVRTHT 66
Query: 57 IHGLTTKFLKNKLKFSEIVDNFLNY 81
GL + + + E L +
Sbjct: 67 ASGLVERVKASTMGDREAELATLEF 91
>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 = 31.6 bits (71), Expect = 0.23
Identities = 14/83 (16%), Positives = 23/83 (27%), Gaps = 36/83 (43%)
Query: 101 MELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRY-------NISKIHR--- 150
M+L Y A+ + + D + +I I
Sbjct: 1633 MDL----YKTSKA-----------AQDV-------WNR-ADNHFKDTYGFSILDIVINNP 1669
Query: 151 ---TLHGGLLDAELLAEVYLAMT 170
T+H G + + E Y AM
Sbjct: 1670 VNLTIHFGGEKGKRIRENYSAMI 1692
Score = 31.6 bits (71), Expect = 0.25
Identities = 34/232 (14%), Positives = 64/232 (27%), Gaps = 104/232 (44%)
Query: 40 LHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFL 99
L + L+I LT + ++ + V+ +++ + +
Sbjct: 324 LEDSLENNEGVPSPMLSISNLTQEQVQ------DYVNKTNSHLPAGKQV----------- 366
Query: 100 DMELSLL-GYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRY---------NISKI- 148
E+SL+ G N + +G SL L + S+I
Sbjct: 367 --EISLVNGAKNL----------------VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIP 408
Query: 149 ---------HRTL------HGGLL-DAELLAEVYLAMTRGQSNLNFKPKINNSNNIETKI 192
+R L H LL A L L ++N++F K I
Sbjct: 409 FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLV----KNNVSFNAK---------DI 455
Query: 193 KIP--------------NNIPIKLANSNELVQHNMILSKIDKHSNGRCIWKK 230
+IP +I ++ + I+ W+
Sbjct: 456 QIPVYDTFDGSDLRVLSGSISERIV--------DCIIRL-------PVKWET 492
Score = 28.9 bits (64), Expect = 1.6
Identities = 26/131 (19%), Positives = 38/131 (29%), Gaps = 42/131 (32%)
Query: 73 EIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHT-- 130
E+V FL YVS+ FD ++ L + F + L IH
Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFD------QVLNLCLTEF-------ENCYLEGNDIHALA 105
Query: 131 -----------GKRNSL-------DALCDRYNISKIHRTLHGGLLDA--ELLAEVYLAMT 170
K L + R K + L A E A++
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITARIMAKR-PFDKKSNSA---LFRAVGEGNAQLVAIFG 161
Query: 171 RGQSNLN--FK 179
GQ N + F+
Sbjct: 162 -GQGNTDDYFE 171
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily,
SH3-like domain, produc structure, DNA damage, DNA
repair, exonuclease; HET: TMP; 1.50A {Escherichia coli}
SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A*
3hp9_A*
Length = 482
Score = 29.6 bits (65), Expect = 1.0
Identities = 28/222 (12%), Positives = 62/222 (27%), Gaps = 24/222 (10%)
Query: 1 MHRHIVLDIETTGLNIIDGHRIIEIGCVEI-KNRQITGNNLHYY--INPGRDSEKSALAI 57
+ D ET G + R + + + G +Y + A+ I
Sbjct: 8 QSTFLFHDYETFGTH-PALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLI 66
Query: 58 HGLT-TKFLKNKLKFSEIVDNF--LNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKY 114
G+T + + L V + I+ +N + + + + +
Sbjct: 67 TGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAW 126
Query: 115 IY----RITDTLLMARKIHTGKRNSLDALCDRYNISKI------------HRTLHGGLLD 158
+ D L + R + + ++ + + H H + D
Sbjct: 127 SWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNAHDAMAD 186
Query: 159 AELLAEVY-LAMTRGQSNLNFKPKINNSNNIETKIKIPNNIP 199
+ L TR ++ N + + I +P P
Sbjct: 187 VYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKP 228
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA
complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP:
c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A*
2pyj_A* 2pyl_A* 2pzs_A*
Length = 575
Score = 27.2 bits (59), Expect = 5.1
Identities = 13/83 (15%), Positives = 28/83 (33%), Gaps = 2/83 (2%)
Query: 49 DSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSE--IIIHNAAFDVGFLDMELSLL 106
E + +G ++ K +D F+ +V + + HN F F+ L
Sbjct: 18 KVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERN 77
Query: 107 GYSNFTKYIYRITDTLLMARKIH 129
G+ + +T++
Sbjct: 78 GFKWSADGLPNTYNTIISRMGQW 100
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA),
exonuclease, transferase, transferase/DNA complex; HET:
US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1
PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A*
2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*
Length = 605
Score = 27.1 bits (61), Expect = 5.2
Identities = 21/146 (14%), Positives = 49/146 (33%), Gaps = 37/146 (25%)
Query: 4 HIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTK 63
D ET L+ I ++ + + YI D +
Sbjct: 28 VFAFDTETDSLDNISA-NLVGLSFA-------IEPGVAAYIPVAHDYLDA---------- 69
Query: 64 FLKNKLKFSEIVDNFLNYVSNSEI--IIHNAAFDVGFL---DMELSLLGYSNFTKYIYRI 118
+++ ++ + + + + N +D G L +EL + +
Sbjct: 70 --PDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAF---------- 117
Query: 119 TDTLLMARKIH-TGKRNSLDALCDRY 143
DT+L + ++ R+ +D+L +R+
Sbjct: 118 -DTMLESYILNSVAGRHDMDSLAERW 142
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
0.321 0.138 0.399
Gapped
Lambda K H
0.267 0.0631 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,481,596
Number of extensions: 201460
Number of successful extensions: 489
Number of sequences better than 10.0: 1
Number of HSP's gapped: 445
Number of HSP's successfully gapped: 37
Length of query: 230
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 140
Effective length of database: 4,188,903
Effective search space: 586446420
Effective search space used: 586446420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.6 bits)