RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780818|ref|YP_003065231.1| DNA polymerase III subunit
epsilon [Candidatus Liberibacter asiaticus str. psy62]
(245 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*
Length = 194
Score = 126 bits (316), Expect = 6e-30
Identities = 77/190 (40%), Positives = 115/190 (60%), Gaps = 13/190 (6%)
Query: 7 MRKIVFDIETTGLD-----SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALK 61
R+IV D ETTG++ + +IIEIGAVE+++ T F V+L P R PEA
Sbjct: 9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKP-DRLVDPEAFG 67
Query: 62 LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP- 120
+HGI DEFL DKP+F+ + EF D+ + AE + HNA FD+GF++ E + +D
Sbjct: 68 VHGIADEFLLDKPTFAEVADEFMDYI--RGAELVIHNAAFDIGFMDYEFSLLKRDIPKTN 125
Query: 121 --SRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGG 178
++ D+L++AR+ P RN L++LC RY I S R+ HGALLD+ +L++VY+ M G
Sbjct: 126 TFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMT--G 183
Query: 179 SQINFGFKTN 188
Q + + +
Sbjct: 184 GQTSMATRES 193
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo
sapiens}
Length = 224
Score = 108 bits (271), Expect = 1e-24
Identities = 26/181 (14%), Positives = 57/181 (31%), Gaps = 18/181 (9%)
Query: 10 IVFDIETTGLDSKND--RIIEIGAVELLDYS-KTNRTFQVFLCP-NGRKNSPEALKLHGI 65
+V D E T + IIE ++L + + TF +++ P + +P +L GI
Sbjct: 34 LVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGI 93
Query: 66 TDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGF---------INAELQRINKD 116
+ +PS + ++ + N K + + Q +
Sbjct: 94 IQAMVDGQPSLQQVLERVDEWM--AKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLP 151
Query: 117 -PLDPSRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174
+ I+ L + K + R H + D ++++ +
Sbjct: 152 VADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGR-PHSGIDDCKNIANIMKTL 210
Query: 175 M 175
Sbjct: 211 A 211
>2is3_A Ribonuclease T; RNAse, exoribonuclease, exonuclease, hydrolase,
stable RNA maturation, tRNA END-turnover; 3.10A
{Escherichia coli K12}
Length = 215
Score = 105 bits (263), Expect = 8e-24
Identities = 38/188 (20%), Positives = 70/188 (37%), Gaps = 16/188 (8%)
Query: 4 KNKMRK---IVFDIETTGLDSKNDRIIEIGAVELLDYSKTN-----RTFQVFLCPNGRKN 55
++ R +V D+ET G ++K D ++EI A+ L + G
Sbjct: 11 CDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANL 70
Query: 56 SPEALKLHG-ITDEFLKDKPSFSSIFSEFWDFFNE-------QNAEWIAHNAKFDVGFIN 107
PEAL +G ++ + S E + + A +AHNA FD F+
Sbjct: 71 QPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMM 130
Query: 108 AELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL 167
A +R + + A + L+ C+ G+ H AL D+
Sbjct: 131 AAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERT 190
Query: 168 SDVYIKMM 175
+ ++ +++
Sbjct: 191 AVLFCEIV 198
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A
{Homo sapiens}
Length = 349
Score = 103 bits (259), Expect = 3e-23
Identities = 35/199 (17%), Positives = 69/199 (34%), Gaps = 20/199 (10%)
Query: 10 IVFDIETTGLDSKN----DRIIEIGAVEL-LDYSKTNRTFQVFLCPNGRKN-SPEALKLH 63
+ D E T + IIE V L + TFQ ++ P S + L
Sbjct: 131 CIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLT 190
Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKD------- 116
GIT + + +F + + D + E + + ++ +
Sbjct: 191 GITQDQVDRADTFPQVLKKVIDLM--KLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRL 248
Query: 117 --PLDPSRIIDTLSIARR--KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172
P + I+ K P S+ L + ++ G+ R H L DS ++ + +
Sbjct: 249 KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PHCGLDDSKNIARIAV 307
Query: 173 KMMVGGSQINFGFKTNEDR 191
+M+ G ++ K + +
Sbjct: 308 RMLQDGCELRINEKMHAGQ 326
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PSI,
MCSG, protein structure initiative; 2.09A {Pseudomonas
aeruginosa PAO1} SCOP: c.55.3.5
Length = 224
Score = 102 bits (253), Expect = 1e-22
Identities = 44/188 (23%), Positives = 75/188 (39%), Gaps = 17/188 (9%)
Query: 3 RKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSK----TNRTFQVFLCPN-GRKNSP 57
R +V D+ET G +S D ++EI A + K T+ + P G P
Sbjct: 25 RFRGYLPVVVDVETGGFNSATDALLEIAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEP 84
Query: 58 EALKLHGITDEFLKDK-----PSFSSIFSEFWDFFNEQ---NAEWIAHNAKFDVGFINAE 109
AL+ GI + + + IF A + HN+ FD+GF+NA
Sbjct: 85 AALEFTGIKLDHPLRMAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAA 144
Query: 110 LQRINKD--PLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL 167
+ R P P DT ++A + + L C+ G+ +R H A D+
Sbjct: 145 VARTGIKRNPFHPFSSFDTATLAGLAYG--QTVLAKACQAAGMEFDNREAHSARYDTEKT 202
Query: 168 SDVYIKMM 175
++++ ++
Sbjct: 203 AELFCGIV 210
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo
sapiens} SCOP: c.55.3.5
Length = 238
Score = 99.7 bits (247), Expect = 5e-22
Identities = 35/195 (17%), Positives = 61/195 (31%), Gaps = 31/195 (15%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPN--------------GRKN 55
+ D+E TGL S I E+ + S N R
Sbjct: 13 VFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERPF 72
Query: 56 SPEALKLHGITDEFLKDKPSF---SSIFSEFWDFFNEQNAEWI---AHNAKFDVGFINAE 109
+ +A ++ G++ E L ++ F + Q + +D + AE
Sbjct: 73 TAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAE 132
Query: 110 LQRINKDPLDPSRIIDTLSIARRKHPSSRNDLN----------SLCKRYGITISHRSKHG 159
L+R+ + +DTL R + + SL RY + H
Sbjct: 133 LRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFR-AEPSAAHS 191
Query: 160 ALLDSHLLSDVYIKM 174
A D H L +++
Sbjct: 192 AEGDVHTLLLIFLHR 206
>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 = 99.0 bits (246), Expect = 7e-22
Identities = 27/195 (13%), Positives = 66/195 (33%), Gaps = 25/195 (12%)
Query: 10 IVFDIETTGLDSKNDR---IIEIGAVELLDYSK---TNRTFQVFLCPN-GRKNSPEALKL 62
++ D ETT + D +I+ V + + +F ++ P R + +
Sbjct: 22 LILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCVDF 81
Query: 63 HGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDV-------GFINAELQRINK 115
GI + +F ++ +F + F +++ N
Sbjct: 82 TGIPQRSIDTADTFDVVYEQFQQWL--ITLGLEEGKFAFVCDSRQDLWRIAQYQMKLSNI 139
Query: 116 D-PLDPSRIIDT-------LSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL 167
P + I+ + K S+ ++ + + Y + R H A+ D +
Sbjct: 140 QMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEYYDLPTIGR-AHDAMDDCLNI 198
Query: 168 SDVYIKMMVGGSQIN 182
+ + +M+ G+++
Sbjct: 199 ATILQRMINMGAKVT 213
>2ioc_B Three prime repair exonuclease 1; proline helix, nucleotide
complex, DNAQ family, hydrolase; HET: D5M; 2.10A {Mus
musculus} SCOP: c.55.3.5 PDB: 3b6o_A* 2o4g_A* 3b6p_A*
2o4i_A 2oa8_A
Length = 242
Score = 97.7 bits (242), Expect = 2e-21
Identities = 37/197 (18%), Positives = 66/197 (33%), Gaps = 32/197 (16%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPN-----------------G 52
I D+E TGL S + E+ + + + N + P G
Sbjct: 15 IFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPG 74
Query: 53 RKNSPEALKLHGITDEFLKDKP--SFSSIFSEFWDFFN---EQNAEWIAHNAKFDV-GFI 106
+ SP A ++ G++ L+ + F + F Q +AHN +
Sbjct: 75 KACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLL 134
Query: 107 NAELQRINKD-PLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGIT--------ISHRSK 157
EL R++ PLD + +D+++ + +S N K Y + +
Sbjct: 135 QTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDS 194
Query: 158 HGALLDSHLLSDVYIKM 174
H A D L +
Sbjct: 195 HTAEGDVLTLLSICQWK 211
>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 = 94.8 bits (235), Expect = 2e-20
Identities = 35/189 (18%), Positives = 66/189 (34%), Gaps = 16/189 (8%)
Query: 10 IVFDIETT----GLDSKNDRIIEIGAVEL-LDYSKTNRTFQVFLCPNGRKN-SPEALKLH 63
+ D E T IIE V L + TFQ ++ P S + L
Sbjct: 81 CIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLT 140
Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQ------NAEWIAHNAKFDVGFINAELQRINKD- 116
GIT + + +F + + D + + + F+N + Q
Sbjct: 141 GITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKY 200
Query: 117 PLDPSRIIDTLSIARR--KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174
P + I+ K P S+ L + ++ G+ R + L DS ++ + ++M
Sbjct: 201 PPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PNCGLDDSKNIARIAVRM 259
Query: 175 MVGGSQINF 183
+ G ++
Sbjct: 260 LQDGCELRI 268
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A
{Homo sapiens} SCOP: c.55.3.5
Length = 204
Score = 84.2 bits (207), Expect = 2e-17
Identities = 35/191 (18%), Positives = 66/191 (34%), Gaps = 20/191 (10%)
Query: 10 IVFDIETT----GLDSKNDRIIEIGAVEL-LDYSKTNRTFQVFLCPNGRKN-SPEALKLH 63
+ D E T IIE V L + TFQ ++ P S + L
Sbjct: 13 CIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLT 72
Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRI 123
GIT + + +F + + D+ + E + + ++ + SR+
Sbjct: 73 GITQDQVDRADTFPQVLKKVIDWM--KLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRL 130
Query: 124 -----------IDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172
I K P S+ L + ++ G+ R H L DS ++ + +
Sbjct: 131 KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PHCGLDDSKNIARIAV 189
Query: 173 KMMVGGSQINF 183
+M+ G ++
Sbjct: 190 RMLQDGCELRI 200
>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 = 81.7 bits (200), Expect = 1e-16
Identities = 49/166 (29%), Positives = 84/166 (50%), Gaps = 7/166 (4%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+V D ETTGLD + D IIEIGAV++ + L R+ S ++ ++ GIT E
Sbjct: 15 VVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDE--YHTLIKPSREISRKSSEITGITQEM 72
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129
L++K S + EF F + +AHNA FD F+ ++++ IDTL++
Sbjct: 73 LENKRSIEEVLPEFLGFLEDS--IIVAHNANFDYRFLRLWIKKVMGLD-WERPYIDTLAL 129
Query: 130 ARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
A+ L+S+ ++ G+ H AL D+ + + V+++ +
Sbjct: 130 AKSLLKLRSYSLDSVVEKLGLGPFRH--HRALDDARVTAQVFLRFV 173
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily,
SH3-like domain, product bound structure, DNA damage,
DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia
coli K12} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A
Length = 482
Score = 78.5 bits (192), Expect = 1e-15
Identities = 24/120 (20%), Positives = 41/120 (34%), Gaps = 4/120 (3%)
Query: 3 RKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLC--PNGRKNSPEAL 60
K + + D ET G DR + A+ +VF C + P A+
Sbjct: 5 GKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAV 64
Query: 61 KLHGITDEFLKDKP-SFSSIFSEFWDFFNEQNAEWIAHN-AKFDVGFINAELQRINKDPL 118
+ GIT + + K + ++ + F + +N +FD R DP
Sbjct: 65 LITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPY 124
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET:
U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5
Length = 189
Score = 66.5 bits (161), Expect = 5e-12
Identities = 24/169 (14%), Positives = 54/169 (31%), Gaps = 13/169 (7%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+ D E GL + + ++ + + F+ P + + ++ G+T +
Sbjct: 8 VAMDCEMVGLGPHRESGLARCSLVNVH---GAVLYDKFIRPE-GEITDYRTRVSGVTPQH 63
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129
+ F+ E + + H+ K D + ++ D L
Sbjct: 64 MVGATPFAVARLEILQLLKGKL--VVGHDLKHDFQALKEDMSGYTIYD----TSTDRLLW 117
Query: 130 ARRK-HPSSRNDLNSLCKRY-GITI-SHRSKHGALLDSHLLSDVYIKMM 175
K R L L +R +I + H ++ D+ ++Y
Sbjct: 118 REAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQ 166
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase,
mRNA decay; 1.70A {Escherichia coli K12} SCOP: c.55.3.5
PDB: 1yta_A 1j9a_A
Length = 180
Score = 63.5 bits (153), Expect = 4e-11
Identities = 25/169 (14%), Positives = 46/169 (27%), Gaps = 17/169 (10%)
Query: 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAV-------ELLDYSKTNRTFQVFLCPNGRKNS 56
N+ I D+E TGLD + DRIIEI + L + +
Sbjct: 2 ANENNLIWIDLEMTGLDPERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALMDDWN 61
Query: 57 PEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKD 116
G+ + +F + + +G L + +
Sbjct: 62 VRTHTASGLVERVKASTMGDREAELATLEFLKQWVPAGKSPICGNSIGQDRRFLFKYMPE 121
Query: 117 PLDPS--RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163
R +D ++ L+ + + H A+ D
Sbjct: 122 LEAYFHYRYLDVSTLKELARRWKPEILDG--------FTKQGTHQAMDD 162
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, X-RAY
diffraction, hydrolase; 2.30A {Xanthomonas campestris
PV}
Length = 194
Score = 57.7 bits (138), Expect = 2e-09
Identities = 28/165 (16%), Positives = 50/165 (30%), Gaps = 17/165 (10%)
Query: 8 RKIVFDIETTGLDSKNDRIIEIGAV-------ELLDYSKTNRTFQVFLCPNGRKNSPEAL 60
R I D+E TGLD+ D IIEI + L + + + + +
Sbjct: 10 RLIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQH 69
Query: 61 KLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP 120
+ G+ L + + + ++ F E + + L R
Sbjct: 70 RRSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPMCGNSICQDRRFLHRQMSRLERY 129
Query: 121 S--RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163
R +D +I + + + S H AL D
Sbjct: 130 FHYRNLDVSTIKELARRWAPAVASG--------FAKSSAHTALSD 166
>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 = 44.5 bits (105), Expect = 2e-05
Identities = 40/234 (17%), Positives = 75/234 (32%), Gaps = 70/234 (29%)
Query: 57 PEALKLHG--ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN 114
P A + ++F K P + F+ + AE + KF +G++++ ++
Sbjct: 23 PTASFFIASQLQEQFNKILPEPTEGFAADDEP--TTPAELVG---KF-LGYVSSLVE--- 73
Query: 115 KDPLDPSRIIDTL------------------SIARRKHPSSRNDL---NSLCKRY----- 148
P + L ++A + + L L K Y
Sbjct: 74 --PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARI 131
Query: 149 ----GITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKE--EKKTV-- 200
S AL + + + + GG Q G N D +F+E +
Sbjct: 132 MAKRPFDKKSNS---ALFRAVGEGNAQLVAIFGG-Q---G---NTDDYFEELRDLYQTYH 181
Query: 201 PNI-SLLKRDKPLFTRITKEELDEHDKTIQTLGKNAI-W--------DR-YISS 243
+ L+K + + + LD + T G N + W D+ Y+ S
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEK--VFTQGLNILEWLENPSNTPDKDYLLS 233
Score = 31.8 bits (72), Expect = 0.15
Identities = 20/88 (22%), Positives = 31/88 (35%), Gaps = 31/88 (35%)
Query: 25 RIIEIGAVE-LLDYSKTNRTF----QVFLC-PNGRKN-----SPEAL-----KLHGI--- 65
+ V+ ++ KTN QV + NG KN P++L L
Sbjct: 342 SNLTQEQVQDYVN--KTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP 399
Query: 66 --TDE----FLKDKPSFSS----IFSEF 83
D+ F + K FS+ + S F
Sbjct: 400 SGLDQSRIPFSERKLKFSNRFLPVASPF 427
>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 = 40.1 bits (92), Expect = 5e-04
Identities = 25/133 (18%), Positives = 41/133 (30%), Gaps = 33/133 (24%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
IV DIE L + + T P+ +AL+
Sbjct: 2 IVSDIEANALLESVTKFHCGVIYDY----STAEYV--SYRPSDFGAYLDALEA------- 48
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFIN--AELQRINKDPLDPSRIIDT 126
+ + HN K+DV + A+LQ + L IDT
Sbjct: 49 -----------------EVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDT 91
Query: 127 LSIARRKHPSSRN 139
L ++R H + ++
Sbjct: 92 LVLSRLIHSNLKD 104
>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 = 39.4 bits (91), Expect = 8e-04
Identities = 24/174 (13%), Positives = 46/174 (26%), Gaps = 29/174 (16%)
Query: 5 NKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHG 64
K FD ET LD+ + ++ + S P H
Sbjct: 24 EKAPVFAFDTETDSLDNISANLVGL--------SFAIEPGVAAYIPVA----------HD 65
Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRII 124
D D+ S ++ A + N K+D G L +
Sbjct: 66 YLDA--PDQISRERALELLKPLLEDEKALKVGQNLKYDRGI----LANYGIEL--RGIAF 117
Query: 125 DTLSIARRKHPSSRNDLNSLCKRYGI---TISHRSKHGALLDSHLLSDVYIKMM 175
DT+ + + + + TI+ G + + + ++
Sbjct: 118 DTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEA 171
>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA
complex, O6-methyl-guanine, transferase/DNA complex;
HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus}
SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A*
2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A*
1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A*
1nk5_A* 1nk6_A* 1nk7_A* ...
Length = 580
Score = 35.4 bits (80), Expect = 0.012
Identities = 17/142 (11%), Positives = 37/142 (26%), Gaps = 39/142 (27%)
Query: 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDE 68
K +E + + I+ I + N + FL P P+
Sbjct: 19 KAALVVEVVEENYHDAPIVGI--------AVVNEHGRFFLRPETALADPQ---------- 60
Query: 69 FLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLS 128
F + ++ + ++K + + + D L
Sbjct: 61 --------------FVAWLGDETKKKSMFDSKRAAVALKWKGIELC------GVSFDLLL 100
Query: 129 IARRKHPS-SRNDLNSLCKRYG 149
A P+ +D+ + K
Sbjct: 101 AAYLLDPAQGVDDVAAAAKMKQ 122
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown
function, ribonuclease D, exonuclease; 2.10A
{Bifidobacterium adolescentis ATCC15703}
Length = 440
Score = 35.4 bits (81), Expect = 0.012
Identities = 24/112 (21%), Positives = 42/112 (37%), Gaps = 25/112 (22%)
Query: 81 SEFWDFFNE--QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSR 138
W+ FN +A WI H++ D+ + ++P R+ DT AR
Sbjct: 81 GADWNDFNRAVGDAVWILHDSLQDLPG----FDELG---MEPQRLFDTEIAARLLGLKRF 133
Query: 139 NDLNSLCKRY-GITISHRSKHG--------------ALLDSHLLSDVYIKMM 175
L ++ + + G+T++ A LD LL ++ KM
Sbjct: 134 G-LAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMR 184
>3pbh_A Procathepsin B; thiol protease, cysteine protease, proenzyme,
papain; 2.50A {Homo sapiens} SCOP: d.3.1.1 PDB: 2pbh_A
1pbh_A 1mir_A
Length = 317
Score = 28.0 bits (61), Expect = 1.8
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGF 105
++ +PSF + E ++ N++N W A + ++V
Sbjct: 1 MRSRPSFHPLSDELVNYVNKRNTTWQAGHNFYNVDM 36
>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 = 27.0 bits (59), Expect = 3.5
Identities = 20/137 (14%), Positives = 39/137 (28%), Gaps = 3/137 (2%)
Query: 62 LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPS 121
+G + + + EF + + A+ HN KF FI L+R N
Sbjct: 26 AYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLER-NGFKWSAD 84
Query: 122 RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDV--YIKMMVGGS 179
+ +T + + L + I + + K+ V
Sbjct: 85 GLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKG 144
Query: 180 QINFGFKTNEDRFFKEE 196
I++ + E
Sbjct: 145 DIDYHKERPVGYKITPE 161
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene
biosynthesis, multifunctional enzyme, carotenoid
biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A
Length = 293
Score = 26.5 bits (57), Expect = 5.6
Identities = 9/80 (11%), Positives = 27/80 (33%), Gaps = 1/80 (1%)
Query: 145 CKRYGITISHRSKHGALLDSHLLSDV-YIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNI 203
+ + + G ++ ++ ++ + F + K K T P +
Sbjct: 190 LHKTAALLEASAVLGGIIGGGSDEEIERLRKFARCIGLLFQVVDDILDVTKSSKLTYPKL 249
Query: 204 SLLKRDKPLFTRITKEELDE 223
L++ + ++ E D+
Sbjct: 250 MGLEKSREFAEKLNTEARDQ 269
>3lji_A Geranyltranstransferase; structural genomics, protein structure
initiative, NEW YORK structural genomix research
consortium, nysgxrc; HET: MSE; 1.39A {Pseudomonas
fluorescens}
Length = 304
Score = 26.4 bits (57), Expect = 6.0
Identities = 10/57 (17%), Positives = 16/57 (28%), Gaps = 5/57 (8%)
Query: 178 GSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKE---ELDEHDKTIQTL 231
G + D +K T P + L K + + L D + L
Sbjct: 230 SDTATLGKRQGAD--IARDKPTYPALLGLAAAKEYALELRDQALHALRPFDAAAEPL 284
>3lsn_A Geranyltranstransferase; structural genomics, protein structure
initiative, NEW YORK structural genomix research
consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas
fluorescens} PDB: 3lji_A*
Length = 304
Score = 26.2 bits (57), Expect = 6.4
Identities = 10/57 (17%), Positives = 16/57 (28%), Gaps = 5/57 (8%)
Query: 178 GSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKE---ELDEHDKTIQTL 231
G + D +K T P + L K + + L D + L
Sbjct: 230 SDTATLGKRQGAD--IARDKPTYPALLGLAAAKEYALELRDQALHALRPFDAAAEPL 284
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 26.4 bits (58), Expect = 6.9
Identities = 7/36 (19%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 96 AHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIAR 131
AH + + + K L P+ ++++L A
Sbjct: 517 AHVPG-GLRDARYGVMQARKAGLTPAHVVNSLGRAE 551
>3nae_A DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 DOC DTP;
2.00A {Enterobacteria phage RB69} PDB: 3lzi_A* 3lzj_A*
1ig9_A* 1q9x_A* 2atq_A* 2dy4_A* 2oyq_A* 2ozm_A* 2ozs_A*
2p5g_A* 2p5o_A* 1q9y_A* 3l8b_A* 3lds_A* 3cq8_A* 1ih7_A*
1clq_A* 1waf_A* 1waj_A* 3cfr_A* ...
Length = 903
Score = 26.1 bits (56), Expect = 7.8
Identities = 19/111 (17%), Positives = 31/111 (27%), Gaps = 10/111 (9%)
Query: 4 KNKMRKIVFDIETTGLD------SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSP 57
K+R FDIE T D I I F + P G
Sbjct: 105 HTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHY--DSIDDRFYVFDLLNSPYGNVEEW 162
Query: 58 EALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQN--AEWIAHNAKFDVGFI 106
+ ++ + PS + F NE+ E++ + +
Sbjct: 163 SIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVIL 213
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation;
1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A
Length = 333
Score = 26.0 bits (57), Expect = 8.3
Identities = 24/140 (17%), Positives = 52/140 (37%), Gaps = 27/140 (19%)
Query: 55 NSPEALKLHGITDEFLKDKPSFSSIFSEF---WDFFNEQNAEWIAHNAKFDVGFINAELQ 111
S E L GI + ++ + F+E ++ WI ++ +D ++ L+
Sbjct: 122 ESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYL---LK 178
Query: 112 RINKDPLDPS--------------RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHR-- 155
+ + PL P+ + D I + ++ L + I HR
Sbjct: 179 AMTQIPL-PAEYEEFYKILCIYFPKNYDIKYIMKSVL-NNSKGLQDIADDLQI---HRIG 233
Query: 156 SKHGALLDSHLLSDVYIKMM 175
+H A D+ L + ++ ++
Sbjct: 234 PQHQAGSDALLTARIFFEIR 253
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.136 0.398
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,150,030
Number of extensions: 98733
Number of successful extensions: 388
Number of sequences better than 10.0: 1
Number of HSP's gapped: 361
Number of HSP's successfully gapped: 49
Length of query: 245
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 155
Effective length of database: 3,511,270
Effective search space: 544246850
Effective search space used: 544246850
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: 55 (25.7 bits)