RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780383|ref|YP_003064796.1| endonuclease III [Candidatus
Liberibacter asiaticus str. psy62]
(227 letters)
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster,
iron-sulfur cluster, hydrolase/DNA complex; HET: PED;
1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1
PDB: 1orp_A* 1p59_A*
Length = 226
Score = 181 bits (460), Expect = 1e-46
Identities = 84/204 (41%), Positives = 133/204 (65%), Gaps = 1/204 (0%)
Query: 21 TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTP 80
T +++ + +P EL + N F L++AV+LSAQ TD VNK TK LFE TP
Sbjct: 6 TKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTP 65
Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKG 140
+A+ ++L+ IR+IG+YR K+ NI L +LI++++ ++P+ + L +LPG+GRK
Sbjct: 66 HDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKT 125
Query: 141 ANVILSMAFGIPTIGVDTHIFRISNRIGLAPG-KTPNKVEQSLLRIIPPKHQYNAHYWLV 199
ANV++S+AFG+P I VDTH+ R+S R+G + +VE++L++IIP + H+ ++
Sbjct: 126 ANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMI 185
Query: 200 LHGRYVCKARKPQCQSCIISNLCK 223
GRY CKA+ PQC SC + +LC+
Sbjct: 186 FFGRYHCKAQSPQCPSCPLLHLCR 209
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase,
DNA mismatch, methylation, base twisting, hydrolase;
2.00A {Methanothermobacterthermautotrophicus} SCOP:
a.96.1.2
Length = 221
Score = 164 bits (417), Expect = 1e-41
Identities = 41/211 (19%), Positives = 98/211 (46%), Gaps = 8/211 (3%)
Query: 21 TPKELEEIFYLFSLKW-PSPKGELYYVNH---FTLIVAVLLSAQSTDVNVNKATKHLFEI 76
+ ++F L + + + + + + + +++ +L ++T +V K F
Sbjct: 4 ATNKKRKVFVSTILTFWNTDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVK 63
Query: 77 ADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGI 136
+ +L + ++ I+ IG+ +++E + L+ ++IN++ ++P+ + + LPG+
Sbjct: 64 YKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGV 123
Query: 137 GRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLR----IIPPKHQY 192
G+ ++ +AFG VD + R+ NR + N ++L ++P
Sbjct: 124 GKYTCAAVMCLAFGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCR 183
Query: 193 NAHYWLVLHGRYVCKARKPQCQSCIISNLCK 223
+ + L+ +C RKP+C+ C +S LC
Sbjct: 184 DFNLGLMDFSAIICAPRKPKCEKCGMSKLCS 214
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
{Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
1wef_A* 1kg7_A 1kqj_A
Length = 225
Score = 153 bits (387), Expect = 4e-38
Identities = 35/182 (19%), Positives = 70/182 (38%), Gaps = 6/182 (3%)
Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSE 106
+ + ++ ++ Q+ V + T + ++ + +G Y +
Sbjct: 29 TPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARAR- 87
Query: 107 NIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNR 166
N+ + + K P+T E + LPG+GR A ILS++ G +D ++ R+ R
Sbjct: 88 NLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLAR 147
Query: 167 IGLAPGKTPNKVEQSLLR-----IIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNL 221
G K ++ L + P + ++ G +C KP+C C + N
Sbjct: 148 CYAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNG 207
Query: 222 CK 223
C
Sbjct: 208 CI 209
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
glycosylase, transition state analog, DNA repair; HET:
NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Length = 369
Score = 149 bits (377), Expect = 4e-37
Identities = 37/182 (20%), Positives = 79/182 (43%), Gaps = 6/182 (3%)
Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSE 106
+ + + V+ ++ Q+ V + + T + + E ++ +G Y +
Sbjct: 38 DPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVR- 96
Query: 107 NIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNR 166
N+ + + + K+P + +RL G+G +LS+A+G+P VD ++ R+ +R
Sbjct: 97 NLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSR 156
Query: 167 IGLAPGK-----TPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNL 221
+ L T + EQ + I+ ++ + L+ G VC R+P C C +
Sbjct: 157 LFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAY 216
Query: 222 CK 223
C+
Sbjct: 217 CQ 218
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision
repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori}
SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*
Length = 218
Score = 142 bits (359), Expect = 6e-35
Identities = 33/190 (17%), Positives = 72/190 (37%), Gaps = 28/190 (14%)
Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEI-------ADTPQKMLAIGEKKLQNYIRTIG 99
F ++ +L+ + V K+ ++L +K+ I KL +R G
Sbjct: 29 LKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSG 88
Query: 100 IYRKKSENIISLSHILINEFDN----KIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIG 155
Y +K++ +I LS ++ +F + K T E L GIG++ A+ IL A +
Sbjct: 89 FYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMV 148
Query: 156 VDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNA----------------HYWLV 199
VD + + ++G+ + ++++ + + H +V
Sbjct: 149 VDKYSYLFLKKLGIEI-EDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIV 207
Query: 200 LHGRYVCKAR 209
+ + +
Sbjct: 208 EFSKQKLELK 217
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia
coli} SCOP: a.96.1.1
Length = 211
Score = 133 bits (334), Expect = 4e-32
Identities = 99/203 (48%), Positives = 139/203 (68%)
Query: 21 TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTP 80
+ EI P P EL + + F L++AVLLSAQ+TDV+VNKAT L+ +A+TP
Sbjct: 2 NKAKRLEILTRLRENNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTP 61
Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKG 140
ML +G + ++ YI+TIG+Y K+ENII IL+ + + ++P+ L LPG+GRK
Sbjct: 62 AAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKT 121
Query: 141 ANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVL 200
ANV+L+ AFG PTI VDTHIFR+ NR APGK +VE+ LL+++P + + + H+WL+L
Sbjct: 122 ANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLIL 181
Query: 201 HGRYVCKARKPQCQSCIISNLCK 223
HGRY C ARKP+C SCII +LC+
Sbjct: 182 HGRYTCIARKPRCGSCIIEDLCE 204
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
2.30A {Homo sapiens}
Length = 287
Score = 132 bits (333), Expect = 7e-32
Identities = 34/198 (17%), Positives = 71/198 (35%), Gaps = 7/198 (3%)
Query: 33 SLKW--PSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKK 90
L W + + + V+ ++ Q+ V + T Q + + ++
Sbjct: 32 DLPWRRRAEDEMDLDRRAYAVWVSEVMLQQTQVATVINYYTGWMQKWPTLQDLASASLEE 91
Query: 91 LQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFG 150
+ +G Y + ++ + LPG+GR A I S+AFG
Sbjct: 92 VNQLWAGLGYYSRGRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIAFG 151
Query: 151 IPTIGVDTHIFRISNRIGLAPGKTPNKVEQS-----LLRIIPPKHQYNAHYWLVLHGRYV 205
T VD ++ R+ R+ + + +++ P + + + G V
Sbjct: 152 QATGVVDGNVARVLCRVRAIGADPSSTLVSQQLWGLAQQLVDPARPGDFNQAAMELGATV 211
Query: 206 CKARKPQCQSCIISNLCK 223
C ++P C C + +LC+
Sbjct: 212 CTPQRPLCSQCPVESLCR 229
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase, hydrolase; 2.00A {Methanocaldococcus
jannaschii}
Length = 214
Score = 112 bits (280), Expect = 9e-26
Identities = 27/159 (16%), Positives = 53/159 (33%), Gaps = 13/159 (8%)
Query: 34 LKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQN 93
++ F + +L+A T + K + + L + ++L+
Sbjct: 30 IQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGD------GFLTLPREELEE 83
Query: 94 YIRTIGI--YRKKSENIISLSHIL-----INEFDNKIPQTLEGLTRLPGIGRKGANVILS 146
++ +G YRK++E I+ + F+N+ + + GIG K A+ L
Sbjct: 84 KLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLR 143
Query: 147 MAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRI 185
+D HI R + L I
Sbjct: 144 NVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEI 182
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair,
glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}
Length = 207
Score = 93.2 bits (231), Expect = 4e-20
Identities = 30/150 (20%), Positives = 56/150 (37%), Gaps = 16/150 (10%)
Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGI--YRKK 104
F + LL+A S+ ++ +A L + K+ E++++N +++ Y K
Sbjct: 32 VWFRELTLCLLTANSSFISAYQALNCLGQ------KIYYANEEEIRNILKSCKYRFYNLK 85
Query: 105 SENIISLSHILINEFDNKI--------PQTLEGLTRLPGIGRKGANVILSMAFGIPTIGV 156
++ II + +I E L + GIG + A+ L +
Sbjct: 86 AKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFLRNVGYFDLAII 145
Query: 157 DTHIFRISNRIGLAPGKTPNKVEQSLLRII 186
D HI RIG ++ +SL
Sbjct: 146 DRHIIDFMRRIGAIGETNVKQLSKSLYISF 175
>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA,
DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2
PDB: 3iho_A
Length = 155
Score = 92.3 bits (229), Expect = 9e-20
Identities = 19/141 (13%), Positives = 49/141 (34%), Gaps = 15/141 (10%)
Query: 35 KWPSPKG------ELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGE 88
KW P+ E+ + + + L++A + +++ E + + A
Sbjct: 12 KWTPPRSPFNLVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADW 71
Query: 89 KKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148
+ + ++ +G+Y +++ II S + + L GIG+ G +
Sbjct: 72 RDVSELLKPLGLYDLRAKTIIKFSDEYLTKQ-------WRYPIELHGIGKYGNDSYRIFC 124
Query: 149 FG--IPTIGVDTHIFRISNRI 167
D + + + +
Sbjct: 125 VNEWKQVHPEDHKLNKYHDWL 145
>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG,
8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET:
DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2
PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A*
1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A*
2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A*
...
Length = 317
Score = 74.0 bits (181), Expect = 3e-14
Identities = 27/192 (14%), Positives = 62/192 (32%), Gaps = 35/192 (18%)
Query: 39 PKGELYYVNHFTLIVAVLLSAQSTDVNVNKATK---------------HLFEIADTPQKM 83
L + + + + S+ + + + + + Q +
Sbjct: 120 QGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQAL 179
Query: 84 LAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKI----------PQTLEGLTRL 133
+ +R +G+ + + + + ++ E + + L L
Sbjct: 180 AGPEVEAH---LRKLGLGYRA-RYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCIL 235
Query: 134 PGIGRKGANVILSMAFGIP-TIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQY 192
PG+G K A+ I MA P + V+ H++ I+ R T S P ++
Sbjct: 236 PGVGTKVADCICLMALDKPQAVPVEVHMWHIAQRDYSWHPTTSQAKGPS-----PQTNKE 290
Query: 193 NAHYWLVLHGRY 204
+++ L G Y
Sbjct: 291 LGNFFRSLWGPY 302
>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG,
glycosylase, cytosine, hydrolase,lyase/DNA complex; HET:
8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A*
3f10_A* 3f0z_A
Length = 290
Score = 69.7 bits (170), Expect = 4e-13
Identities = 25/179 (13%), Positives = 59/179 (32%), Gaps = 28/179 (15%)
Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHL--------------FEIADTPQKMLAIGEKKLQ 92
+ F ++++ ++SA + + K ++ + T K+ EK
Sbjct: 114 DPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEK--- 170
Query: 93 NYIRTIGIYRKKSENIISLS-HILINEFD------NKIPQTLEGLTRLPGIGRKGANVIL 145
+++ + I E + + E L + G+G + A+ I+
Sbjct: 171 --DFEECTAGFRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIM 228
Query: 146 SMAFGIP-TIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGR 203
+ VDT + + + +AP + K+ + A +L + R
Sbjct: 229 LFSMQKYSAFPVDTWVKKAMMSLYVAPDVSLKKIRDFGREKFGSLSGF-AQQYLFYYAR 286
>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 = 65.0 bits (158), Expect = 1e-11
Identities = 55/275 (20%), Positives = 91/275 (33%), Gaps = 112/275 (40%)
Query: 16 LGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFT-LIVAVLLSAQST----DVNVNKAT 70
LG TP EL LK + G H L+ AV ++ + V+V KA
Sbjct: 256 LGF--TPGELRS-----YLKGAT--G------HSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 71 KHLFEI------------------AD-------TPQKMLAI---GEKKLQNYIRTIGIYR 102
LF I D P ML+I ++++Q+Y+ +
Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHL 360
Query: 103 KKSENIISLSHILINEFDNKI----PQTLEGL-TRLPGIGRKGANVILSMAFGIPTIGVD 157
+ + +S L+N N + PQ+L GL L RK P+ G+D
Sbjct: 361 PAGKQ-VEIS--LVNGAKNLVVSGPPQSLYGLNLTL----RK---------AKAPS-GLD 403
Query: 158 -THI-F-----RISNR---IGLAPGKTP------NKVEQSL-----------LRIIPPKH 190
+ I F + SNR + +P + + + + L ++ IP
Sbjct: 404 QSRIPFSERKLKFSNRFLPVA-SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ-IPVYD 461
Query: 191 QYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRI 225
++ G + R I + I
Sbjct: 462 TFD--------GSDL---R--VLSGSISERIVDCI 483
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair,
N1-methyladenine, N3-methylcytosine, hyperthermophiles,
hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus}
PDB: 2jhj_A
Length = 295
Score = 60.5 bits (146), Expect = 3e-10
Identities = 37/185 (20%), Positives = 70/185 (37%), Gaps = 21/185 (11%)
Query: 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIA--------------DTPQKMLAIGE 88
L ++ F I ++ Q + V K + T + +L G
Sbjct: 113 LMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGV 172
Query: 89 KKLQNYIRTIGIYRKKSENIISLSHILINEFDNKI--PQTLEGLTRLPGIGRKGANVILS 146
+ L R G+ R+K+E I+ ++ E + + E LT GIGR A ++LS
Sbjct: 173 EGL----RECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLS 228
Query: 147 MAFGIPTIGV-DTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYV 205
+A G D + R +R+ + + + R + + ++L L+ R+
Sbjct: 229 IALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFF 288
Query: 206 CKARK 210
K +
Sbjct: 289 SKKTE 293
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base
excision, methylation, hydrolase; 1.80A {Escherichia
coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A*
3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A*
3d4v_A*
Length = 282
Score = 36.1 bits (83), Expect = 0.006
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 9/81 (11%)
Query: 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISL-----SHILINEFDNKIPQTLEGLTRL 133
TPQ++ A + L + +G+ K++E +I L L + Q ++ L
Sbjct: 157 TPQRLAAADPQAL----KALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTF 212
Query: 134 PGIGRKGANVILSMAFGIPTI 154
PGIGR AN + +
Sbjct: 213 PGIGRWTANYFALRGWQAKDV 233
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication;
2.46A {Deinococcus radiodurans}
Length = 578
Score = 32.5 bits (74), Expect = 0.071
Identities = 10/79 (12%), Positives = 30/79 (37%), Gaps = 12/79 (15%)
Query: 67 NKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQT 126
+ ++H + ++ + + ++ YR + ++ L+ + P+
Sbjct: 6 DAPSRH--RLVHALERTADLLDILGGEDFKSRA-YRSAARSLEELNE--------ETPEL 54
Query: 127 L-EGLTRLPGIGRKGANVI 144
L T +P +G+ A +
Sbjct: 55 LAREFTGIPKVGKGIAAEL 73
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA
complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A*
1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A*
1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A*
1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ...
Length = 335
Score = 32.4 bits (73), Expect = 0.087
Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 10/70 (14%)
Query: 75 EIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLP 134
I D ++ + Q + YRK + I H + ++ +LP
Sbjct: 14 GITDMLTELANFEKNVSQAIHKYNA-YRKAASVIAKYPHKI---------KSGAEAKKLP 63
Query: 135 GIGRKGANVI 144
G+G K A I
Sbjct: 64 GVGTKIAEKI 73
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis,
mutation, deletion, streisinger, slippage, transferase,
lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A*
2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A*
1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A*
1rzt_A* 3hx0_A* 1nzp_A*
Length = 335
Score = 32.1 bits (72), Expect = 0.10
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 13/78 (16%)
Query: 68 KATKHLFEIADTPQKMLAIGEKKLQNY-IRTIGIYRKKSENIISLSHILINEFDNKIPQT 126
KAT H I + + + + + Y K + S + +
Sbjct: 8 KATNHNLHITEKLEVLAKAYSVQGDKWRALG---YAKAINALKSFHKPV---------TS 55
Query: 127 LEGLTRLPGIGRKGANVI 144
+ +PGIG++ A I
Sbjct: 56 YQEACSIPGIGKRMAEKI 73
>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold,
ligase; 2.80A {Shigella flexneri 2A}
Length = 571
Score = 29.2 bits (65), Expect = 0.79
Identities = 20/105 (19%), Positives = 33/105 (31%), Gaps = 8/105 (7%)
Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQ-NYIRTI--GIYRK 103
N T + + S ++ DV+ N + + N I I I
Sbjct: 170 NQLTFLPELPESLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRENRITHIPENILSL 229
Query: 104 KSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148
I L N ++I ++L T P G + SM+
Sbjct: 230 DPTCTIILED---NPLSSRIRESLSQQTAQP--DYHGPRIYFSMS 269
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus
musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB:
1kdh_A* 1kej_A*
Length = 381
Score = 28.5 bits (63), Expect = 1.4
Identities = 13/84 (15%), Positives = 30/84 (35%), Gaps = 17/84 (20%)
Query: 61 STDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFD 120
+T N N+ D + E + +N + + + S + SL +
Sbjct: 30 TTLNNYNQ------LFTDALDILAENDELR-ENEGSCLA-FMRASSVLKSLPFPI----- 76
Query: 121 NKIPQTLEGLTRLPGIGRKGANVI 144
+++ +P +G K ++I
Sbjct: 77 ----TSMKDTEGIPCLGDKVKSII 96
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
toprim, walker B ATP binding motif; 2.50A {Deinococcus
radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Length = 228
Score = 27.5 bits (61), Expect = 2.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 118 EFDNKIPQTLEGLTRLPGIGRKGA 141
++ + + L+RLPGIG K A
Sbjct: 2 KYPPSLVSLIRELSRLPGIGPKSA 25
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA
complex; HET: DNA D3T; 2.40A {Mus musculus}
Length = 360
Score = 27.4 bits (60), Expect = 2.5
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 11/70 (15%)
Query: 75 EIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLP 134
+++ + + + N R + + + + + SL + +L L LP
Sbjct: 19 LLSEALETLAEAAGFE-ANEGRLLS-FSRAASVLKSLPCPV---------ASLSQLHGLP 67
Query: 135 GIGRKGANVI 144
G VI
Sbjct: 68 YFGEHSTRVI 77
>3klk_A Glucansucrase; native form, open conformation, multidomain protein,
glycosyltransferase, transferase; 1.65A {Lactobacillus
reuteri} PDB: 3kll_A* 3hz3_A*
Length = 1039
Score = 27.3 bits (60), Expect = 2.6
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 11/82 (13%)
Query: 36 WPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKML--AIGEKK--- 90
WP+ + YY+N+ LL A + + + L ++ Q+ + I E
Sbjct: 113 WPNTVTQAYYLNYMKQ-YGNLLPASLPSFSTDADSAELNHYSELVQQNIEKRISETGSTD 171
Query: 91 -----LQNYIRTIGIYRKKSEN 107
+ ++ ++ K SEN
Sbjct: 172 WLRTLMHEFVTKNSMWNKDSEN 193
>2qh9_A UPF0215 protein AF_1433; structural genomics, PSI-2, MCSG, protein
structure initiative, midwest center for structural
genomics; 1.80A {Archaeoglobus fulgidus}
Length = 184
Score = 27.1 bits (60), Expect = 3.2
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 133 LPGIGRKGANVI----LSMAFGIPTIGV 156
LPGI G N++ + IP + V
Sbjct: 70 LPGITLGGFNLVDIQRVYRETKIPVVVV 97
>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 = 27.3 bits (59), Expect = 3.4
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 18/48 (37%)
Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLE 128
+K A+ KKLQ ++ +Y S +L+ I T+E
Sbjct: 18 EKQ-AL--KKLQASLK---LYADDSAP--ALA----------IKATME 47
>3g5c_A ADAM 22; alpha/beta fold, cross-linked domain, alternative
splicing, cell adhesion, cleavage on PAIR of basic
residues, EGF-like domain; HET: NAG; 2.36A {Homo
sapiens}
Length = 510
Score = 26.5 bits (57), Expect = 4.7
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 8/77 (10%)
Query: 65 NVNKATKH--LFEIAD-TPQKMLAIGEKKLQNYIRTI-----GIYRKKSENIISLSHILI 116
NV + TK+ L + D K + Y +++ IY+ + + I L +
Sbjct: 1 NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMET 60
Query: 117 NEFDNKIPQTLEGLTRL 133
DNK + L L
Sbjct: 61 WATDNKFAISENPLITL 77
>1ybe_A Naprtase, nicotinate phosphoribosyltransferase; structural
genomics, protein structure initiative, NYSGXRC, PSI;
2.50A {Agrobacterium tumefaciens} SCOP: c.1.17.2
d.41.2.2
Length = 449
Score = 26.5 bits (58), Expect = 4.8
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 141 ANVILSMAFGIPTIGVDTHIF 161
+NV+L+M + +G + H
Sbjct: 231 SNVLLAMDSDLEAVGTNAHEL 251
>2c36_A Glycoprotein D HSV-1; viral protein, immunoglobulin-like,
transmembrane; HET: NAG MAN BMA NDG; 2.11A {Human
herpesvirus 1} PDB: 2c3a_A* 1l2g_A* 1jma_A*
Length = 285
Score = 26.5 bits (58), Expect = 5.9
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 184 RIIPPKHQYNAHYWLVLHGRYVCKA 208
R IP + A Y L + G + KA
Sbjct: 200 RFIPENQRTVAVYSLKIAGWHGPKA 224
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
recombination, helicase; 1.90A {Escherichia coli} SCOP:
a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A
1d8l_A
Length = 203
Score = 25.9 bits (57), Expect = 7.1
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 130 LTRLPGIGRKGA 141
L +LPGIG+K A
Sbjct: 110 LVKLPGIGKKTA 121
>2l4j_A YES-associated protein 2 (YAP2); WW domain, medaka,
transcription; NMR {Oryzias latipes}
Length = 46
Score = 25.7 bits (57), Expect = 8.6
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 38 SPKGELYYVNHFT 50
+P+GE+YY+NH
Sbjct: 21 TPEGEIYYINHKN 33
>2kpz_A E3 ubiquitin-protein ligase NEDD4; WW domain, HTLV1, NEDD4, human
modular domain, complex, HOST interaction, ligase; NMR
{Homo sapiens} PDB: 2kq0_A
Length = 49
Score = 25.8 bits (57), Expect = 9.6
Identities = 4/13 (30%), Positives = 9/13 (69%)
Query: 38 SPKGELYYVNHFT 50
+P G ++++H T
Sbjct: 22 APNGRPFFIDHNT 34
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 0.138 0.411
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,908,043
Number of extensions: 85674
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 37
Length of query: 227
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 138
Effective length of database: 3,535,514
Effective search space: 487900932
Effective search space used: 487900932
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 (25.0 bits)