RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 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} (D:1-144) Length = 144 Score = 59.2 bits (143), Expect = 7e-10 Identities = 16/150 (10%), Positives = 56/150 (37%), Gaps = 9/150 (6%) Query: 1 MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60 M + + + + L ++ G+D L+ E + ++ + F + Sbjct: 1 MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54 Query: 61 LEIQKNISTFWNEINSTSLFSKKKIILIENLS--TEKKVLDCLEEIIIKNICNHIIIIKS 118 ++ + + ++ + SLF+ ++ +L+ + + L + + ++I++ Sbjct: 55 IDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114 Query: 119 NEIKKNNTLRKIAEKFTSV-LAISCYPDNK 147 N++ K + + ++C + Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTCQTPEQ 144 >1jql_B DNA polymerase III, delta subunit; processivity clamp, clamp loader, DNA replication, AAA+ ATPase, transferase; HET: DNA; 2.50A {Escherichia coli} (B:) Length = 140 Score = 53.4 bits (128), Expect = 4e-08 Identities = 16/145 (11%), Positives = 55/145 (37%), Gaps = 9/145 (6%) Query: 1 MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60 M + + + + L ++ G+D L+ E + ++ + F + Sbjct: 1 MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54 Query: 61 LEIQKNISTFWNEINSTSLFSKKKIILIENLS--TEKKVLDCLEEIIIKNICNHIIIIKS 118 ++ + + ++ + SLF+ ++ +L+ + + L + + ++I++ Sbjct: 55 IDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114 Query: 119 NEIKKNNTLRKIAEKFTSV-LAISC 142 N++ K + + ++C Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTC 139 >1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} (D:145-211) Length = 67 Score = 48.9 bits (117), Expect = 9e-07 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 1/65 (1%) Query: 149 HLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKD 208 L + + A Q+L G+ +A L++LS + +T V+ Sbjct: 2 QLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGK-LTLPRVEQ 60 Query: 209 IICDT 213 + D Sbjct: 61 AVNDA 65 >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} (A:81-353,A:947-1009) Length = 336 Score = 29.5 bits (66), Expect = 0.68 Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 3/47 (6%) Query: 158 LLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQ 204 L +G + KE +++ + G R Q L YC +D+ T + Sbjct: 215 LYVGGPPLEKEPRELFVK---GTMKDIRENFQDLMQYCAQDVWATHE 258 >2iee_A ORF2, probable ABC transporter extracellular-binding protein YCKB; SR574, NESG, X-RAY, structural genomics, PSI-2; 2.20A {Bacillus subtilis} (A:1-94,A:217-271) Length = 149 Score = 28.2 bits (63), Expect = 1.7 Identities = 10/37 (27%), Positives = 21/37 (56%) Query: 119 NEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIE 155 E K+ +L K++++F + +S D + +DL+E Sbjct: 107 KEXSKDGSLTKLSKQFFNKADVSKKIDADVQDVDLLE 143 >3jwd_A HIV-1 GP120 envelope glycoprotein; HIV-1 viral spike, molecular motion, protein architecture, receptor-triggered entry, type 1 fusion protein, cell membrane; HET: YCM NAG; 2.61A {Human immunodeficiency virus 1} PDB: 3jwo_A* 1meq_A (A:153-342) Length = 190 Score = 26.6 bits (59), Expect = 5.0 Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 20/52 (38%) Query: 102 EEIII--KNICN--HIIII---KSNEI-------------KKNNTLRKIAEK 133 EE++I N + II+ S EI K NNTL++IA K Sbjct: 13 EEVVIRSVNFTDNAKTIIVQLNTSVEINCTGAGHCNIARAKWNNTLKQIASK 64 >2z1d_A Hydrogenase expression/formation protein HYPD; [NIFE] hydrogenase maturation, [4Fe-4S] cluster, thiol redox; HET: CSW; 2.07A {Thermococcus kodakarensis KOD1} (A:69-192,A:261-346) Length = 210 Score = 25.8 bits (57), Expect = 8.2 Identities = 6/22 (27%), Positives = 9/22 (40%) Query: 313 IDHRIHLARKKKYLEKNIIFQT 334 I + RK + + II T Sbjct: 8 IVAMQLIMRKAREEGEEIILTT 29 >1l5w_A Maltodextrin phosphorylase; enzymatic catalysis, substrate complex, transferase; HET: GLC PLP; 1.80A {Escherichia coli} (A:54-455,A:778-796) Length = 421 Score = 25.8 bits (56), Expect = 8.4 Identities = 11/62 (17%), Positives = 26/62 (41%) Query: 258 FQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRI 317 + E + ++ + +S++ T K ++ E+L W+ LV+ L + I Sbjct: 259 IAIPELLRVLIDEHQMSWDDAWAITSKTFAYTNHTLMPEALERWDVKLVKGLLPRHMQII 318 Query: 318 HL 319 + Sbjct: 319 NE 320 >1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (C:1-40,C:169-318) Length = 190 Score = 25.6 bits (56), Expect = 9.5 Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 2/34 (5%) Query: 125 NTLRK--IAEKFTSVLAISCYPDNKIHLMDLIEE 156 N+LR+ IAEK+ AI D L Sbjct: 31 NSLRRVMIAEKWGPAAAIEFEYDPWNKLKHTDYW 64 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.323 0.137 0.386 Gapped Lambda K H 0.267 0.0666 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 2,502,346 Number of extensions: 111037 Number of successful extensions: 290 Number of sequences better than 10.0: 1 Number of HSP's gapped: 286 Number of HSP's successfully gapped: 17 Length of query: 352 Length of database: 4,956,049 Length adjustment: 89 Effective length of query: 263 Effective length of database: 1,947,404 Effective search space: 512167252 Effective search space used: 512167252 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: 55 (25.1 bits)