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)