RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780804|ref|YP_003065217.1| DNA polymerase III subunit delta [Candidatus Liberibacter asiaticus str. psy62] (352 letters) >1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A* Length = 343 Score = 77.6 bits (190), Expect = 4e-15 Identities = 41/316 (12%), Positives = 110/316 (34%), Gaps = 14/316 (4%) Query: 1 MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60 M + + + + L ++ G+D L+ E + ++ + F + Sbjct: 1 MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54 Query: 61 LEIQKNISTFWNEINSTSLFSKKKIILIENLSTEK--KVLDCLEEIIIKNICNHIIIIKS 118 ++ + + ++ + SLF+ ++ + + L + + ++I++ Sbjct: 55 IDPNTDWNAIFSLCQAMSLFASRQTXXXXXPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114 Query: 119 NEIKKNNTLRKIAEKFTSV-LAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANL 177 N++ K + + ++C + L + + A Q+L Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCY 174 Query: 178 GGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLA 237 G+ +A L++LS D +T V+ + D ++A + GK A+ + Sbjct: 175 EGNLLALAQALERLSLLW-PDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHIL 233 Query: 238 DFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQES 297 LL ++ LL + + + K + +R ++ E+ Sbjct: 234 QQLRLEGSEPVILLRTLQRELLLLVNLKRQSA--HTPLRALFDKH--RVWQNRRGMMGEA 289 Query: 298 LRIWNKNLVRETLHKI 313 L ++ +R+ + + Sbjct: 290 LNRLSQTQLRQAVQLL 305 >1jql_B DNA polymerase III, delta subunit; processivity clamp, clamp loader, DNA replication, AAA+ ATPase, transferase; HET: DNA; 2.50A {Escherichia coli} SCOP: c.37.1.20 Length = 140 Score = 36.1 bits (83), Expect = 0.011 Identities = 15/145 (10%), Positives = 52/145 (35%), Gaps = 9/145 (6%) Query: 1 MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60 M + + + + L ++ G+D L+ E + ++ + F + Sbjct: 1 MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54 Query: 61 LEIQKNISTFWNEINSTSLFSKKKIILIENLSTEK--KVLDCLEEIIIKNICNHIIIIKS 118 ++ + + ++ + SLF+ ++ + + L + + ++I++ Sbjct: 55 IDPNTDWNAIFSLCQAMSLFASRQTXXXXXPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114 Query: 119 NEIKKNNTLRKIAEKFTSV-LAISC 142 N++ K + + ++C Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTC 139 >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 = 33.4 bits (76), Expect = 0.089 Identities = 23/157 (14%), Positives = 50/157 (31%), Gaps = 43/157 (27%) Query: 112 HIIIIKSNEIKKNNTLRKIAEKFTSVL-------AISCYPDNKIHL----MDLIEESLLI 160 H++++ + + L+ E+F +L A P L + + + Sbjct: 18 HVLLVPTASFFIASQLQ---EQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP 74 Query: 161 GQKSISKEAKQILL-----ANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHV 215 + + + L L G N++ L++ L++ T K++I + Sbjct: 75 SKVGQFDQVLNLCLTEFENCYLEG------NDIHALAAKLLQENDTTLVKTKELIKN--- 125 Query: 216 LYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLH 252 Y A ++A K + AL Sbjct: 126 -Y-------------ITARIMAKRPF-DKKSNSALFR 147 >1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B* Length = 373 Score = 33.2 bits (75), Expect = 0.10 Identities = 24/215 (11%), Positives = 68/215 (31%), Gaps = 10/215 (4%) Query: 72 NEINSTSLFSKKKIILIENL-STEKKVLDCLEEIIIKNICNHIIIIKSNEIKK-NNTLRK 129 + + + K+ LI+ + + + L + + + + ++ + + +K T+ Sbjct: 109 DNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILS 168 Query: 130 IAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQ 189 +F + + +E L + A Q+L G + + Sbjct: 169 RCLQFH------LKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD 222 Query: 190 KLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHA 249 + + D ++ Q V ++ ++ A ++ + L + A + A Sbjct: 223 QAIASG--DGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEA 280 Query: 250 LLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEK 284 LL L + + + I + + Sbjct: 281 LLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRE 315 >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 = 32.7 bits (73), Expect = 0.13 Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 9/33 (27%) Query: 283 EKNIIPMKRNILQESLRIWNKN----L-VRETL 310 EK +K+ LQ SL+++ + L ++ T+ Sbjct: 18 EKQ--ALKK--LQASLKLYADDSAPALAIKATM 46 >1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A* Length = 250 Score = 30.8 bits (69), Expect = 0.43 Identities = 16/141 (11%), Positives = 48/141 (34%), Gaps = 10/141 (7%) Query: 72 NEINSTSLFSKKKIILIENL-STEKKVLDCLEEIIIKNICNHIIIIKSNEIKK-NNTLRK 129 + + + K+ LI+ + + + L + + + + ++ + + +K T+ Sbjct: 116 DNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILS 175 Query: 130 IAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQ 189 +F + + +E L + A Q+L G + + Sbjct: 176 RCLQFH------LKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD 229 Query: 190 KLSSYCLEDILITEQHVKDII 210 + + D ++ Q V ++ Sbjct: 230 QAIASG--DGQVSTQAVSAML 248 >3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase, disease mutation, DNA replication, DNA-binding, DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo sapiens} Length = 1172 Score = 30.3 bits (68), Expect = 0.76 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 3/45 (6%) Query: 158 LLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILIT 202 L +G + KE +++ + G R Q L YC +D+ T Sbjct: 295 LYVGGPPLEKEPRELFVK---GTMKDIRENFQDLMQYCAQDVWAT 336 >1lox_A 15-lipoxygenase, 15LOX; oxidoreductase, 15LO_depot2; HET: RS7; 2.40A {Oryctolagus cuniculus} SCOP: a.119.1.2 b.12.1.1 PDB: 2p0m_A* Length = 662 Score = 29.2 bits (65), Expect = 1.3 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 7/88 (7%) Query: 26 FYGSDKGLIFELINQF-KKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKK 84 FY D ++E+I+++ + + + Y V + LE+Q ++ EI L +K Sbjct: 459 FYAQDALRLWEIISRYVQGIMGLYYKTD--EAVRDDLELQ----SWCREITEIGLQGAQK 512 Query: 85 IILIENLSTEKKVLDCLEEIIIKNICNH 112 +L + + + I H Sbjct: 513 QGFPTSLQSVAQACHFVTMCIFTCTGQH 540 >3ckj_A Putative uncharacterized protein; mycobacteria, unknown function; HET: CIT; 1.80A {Mycobacterium paratuberculosis} PDB: 3ckn_A* 3cko_A* 3ckq_A* 3ckv_A* 3e26_A 3e25_A Length = 329 Score = 29.1 bits (64), Expect = 1.4 Identities = 13/103 (12%), Positives = 33/103 (32%) Query: 56 VVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIII 115 VVL AL+ + I + + I+ ++I++++ ST+ + + + Sbjct: 52 VVLPALDEEDTIGSVIDSISPLVDGLVDELIVLDSGSTDDTEIRAVAAGARVVSREQALP 111 Query: 116 IKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESL 158 K L + + + D + + Sbjct: 112 EVPIRPGKGEALWRSLAASRGDIVVFVDSDLINPHPMFVPWLV 154 >3k7l_A Atragin; SVMP, metalloprotease, hydrolase; HET: NAG; 2.50A {Naja atra} Length = 422 Score = 28.7 bits (63), Expect = 1.9 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 4/58 (6%) Query: 21 HFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTS 78 + ++ Y D+ +I + + +++ Y + L LEI NI NEIN S Sbjct: 24 NIMYRHYKRDQPVIKRKVYEMINTMNMIYRRLNFHIALIGLEIWSNI----NEINVQS 77 >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 = 27.7 bits (60), Expect = 4.3 Identities = 9/59 (15%), Positives = 16/59 (27%), Gaps = 5/59 (8%) Query: 21 HFVFIFYGSDKGLIFELINQFKKNISITYHDPFSL-VVLNALEIQKNISTFWNEINSTS 78 H +F + + Y D +VL A+E N+ + Sbjct: 17 HLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATD----NKFAISE 71 >2pt0_A MYO-inositol hexaphosphate phosphohydrolase; PTP, protein tyrosine phosphatase, phytase, P-loop, cysteine-sulfonic acid, oxidized thiol.; 1.70A {Selenomonas ruminantium} SCOP: c.45.1.4 PDB: 2psz_A 3d1h_A 3d1o_A 3d1q_A 1u24_A 1u25_A* 1u26_A* 2b4o_A 2b4p_A 2b4u_A Length = 340 Score = 27.2 bits (60), Expect = 5.2 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 6/92 (6%) Query: 137 VLAISCYPDNKIHLMDLIEESLL-IGQKSISKEAKQILLANLGGDRIASRNELQKLSSYC 195 + I+ +DL +ES + +S ++ ANLG S++E + Sbjct: 111 AAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGER-DWANLGK----SQHEALADERHR 165 Query: 196 LEDILITEQHVKDIICDTHVLYIEEIINATIQ 227 L L ++ + E +Q Sbjct: 166 LHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQ 197 >1l5w_A Maltodextrin phosphorylase; enzymatic catalysis, substrate complex, transferase; HET: GLC PLP; 1.80A {Escherichia coli} SCOP: c.87.1.4 PDB: 1l5v_A* 1l6i_A* 2asv_A* 2av6_A* 2aw3_A* 2azd_A* 1qm5_A* 1e4o_A* 2ecp_A* 1ahp_A* Length = 796 Score = 26.9 bits (59), Expect = 6.9 Identities = 23/136 (16%), Positives = 47/136 (34%), Gaps = 24/136 (17%) Query: 213 THVLYIEEIINA-----TIQGKIYNAIMLADFFLASKMPSHALLHGFLQK---------- 257 T VLY + +Q A +AD L + LH Sbjct: 252 TKVLYPNDNAFEGKKLRLMQQYFQCACSVADI-LRRHHLAGRKLHELADYEVIQLNDTHP 310 Query: 258 -FQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVR-------ET 309 + E + ++ + +S++ T K ++ E+L W+ LV+ + Sbjct: 311 TIAIPELLRVLIDEHQMSWDDAWAITSKTFAYTNHTLMPEALERWDVKLVKGLLPRHMQI 370 Query: 310 LHKIDHRIHLARKKKY 325 +++I+ R +K + Sbjct: 371 INEINTRFKTLVEKTW 386 >2gj4_A Glycogen phosphorylase, muscle form; transferase; HET: PLR 2TH; 1.60A {Oryctolagus cuniculus} SCOP: c.87.1.4 PDB: 2gm9_A* 1abb_A* 2pyi_A* 2pyd_A* 2qnb_A* 1c8l_A* 1axr_A* 1gpy_A* 1e1y_A* 1lwo_A* 1pyg_A* 1uzu_A* 1lwn_A* 1xkx_A* 1xl0_A* 1xl1_A* 1z62_A* 2amv_A* 2f3p_A* 2f3q_A* ... Length = 824 Score = 26.5 bits (58), Expect = 8.1 Identities = 11/62 (17%), Positives = 26/62 (41%) Query: 258 FQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRI 317 + E + ++ + + ++K + T K +L E+L W +L+ L + I Sbjct: 333 LAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQII 392 Query: 318 HL 319 + Sbjct: 393 YE 394 >2wl2_A GYRA, DNA gyrase subunit A; isomerase, aminocoumarin antibiotic, drug target, protein-ligand complex; HET: DNA SM8; 2.62A {Escherichia coli} PDB: 1ab4_A 1x75_A* Length = 522 Score = 26.4 bits (58), Expect = 9.8 Identities = 19/124 (15%), Positives = 42/124 (33%), Gaps = 13/124 (10%) Query: 101 LEEIIIKNICNHIIIIKSNEIKKN--NTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESL 158 + + NI I +I+ L + +V A+ + + +E Sbjct: 381 ALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEF 440 Query: 159 LIGQKSIS---KEAKQIL------LANLGGDRI-ASRNELQKLSSYCLEDILITEQHVKD 208 + ++A+ IL L L +++ EL + L IL + + + Sbjct: 441 GVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAE-LLRILGSADRLME 499 Query: 209 IICD 212 +I + Sbjct: 500 VIRE 503 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 0.323 0.137 0.386 Gapped Lambda K H 0.267 0.0686 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,972,961 Number of extensions: 141657 Number of successful extensions: 460 Number of sequences better than 10.0: 1 Number of HSP's gapped: 458 Number of HSP's successfully gapped: 42 Length of query: 352 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 259 Effective length of database: 3,438,538 Effective search space: 890581342 Effective search space used: 890581342 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 57 (25.8 bits)