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)