BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy15222
(444 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core
pdb|1DDE|A Chain A, Structure Of The Dnag Catalytic Core
Length = 338
Score = 209 bits (532), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 104/271 (38%), Positives = 163/271 (60%), Gaps = 15/271 (5%)
Query: 7 FYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEW-NALNKVFLDYNNINTLASS 63
FY+ L+ + A +L+KRGL+ E+I RF +G+AP W N L + + N +L +
Sbjct: 31 FYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDA 90
Query: 64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
G++V ++ + YDRFR R+MFPI++ G++IGFGGR++ + + KY+NS
Sbjct: 91 GMLVTN-----------DQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYLNS 138
Query: 124 PETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH 183
PET +FHK +LYGL+EA+ + +L+ EGYMDV+ L+Q+G VA LGT+ T+ H
Sbjct: 139 PETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADH 198
Query: 184 IKKILFYTNSIIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243
I+ + TN++I +DGD+ LE L Y TD + ++F+FLPD DPD+ +RK
Sbjct: 199 IQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKE 258
Query: 244 GYKIFSKKVLEAMSLLQFFLEEIILNYNLKT 274
G + F ++ +AM L F ++ +L T
Sbjct: 259 GKEAFEARMEQAMPLSAFLFNSLMPQVDLST 289
>pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To
Ssdna
pdb|3B39|B Chain B, Structure Of The Dnag Primase Catalytic Domain Bound To
Ssdna
Length = 322
Score = 209 bits (531), Expect = 3e-54, Method: Compositional matrix adjust.
Identities = 104/271 (38%), Positives = 163/271 (60%), Gaps = 15/271 (5%)
Query: 7 FYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEW-NALNKVFLDYNNINTLASS 63
FY+ L+ + A +L+KRGL+ E+I RF +G+AP W N L + + N +L +
Sbjct: 19 FYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDA 78
Query: 64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
G++V ++ + YDRFR R+MFPI++ G++IGFGGR++ + + KY+NS
Sbjct: 79 GMLVTN-----------DQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYLNS 126
Query: 124 PETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH 183
PET +FHK +LYGL+EA+ + +L+ EGYMDV+ L+Q+G VA LGT+ T+ H
Sbjct: 127 PETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADH 186
Query: 184 IKKILFYTNSIIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243
I+ + TN++I +DGD+ LE L Y TD + ++F+FLPD DPD+ +RK
Sbjct: 187 IQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLRFMFLPDGEDPDTLVRKE 246
Query: 244 GYKIFSKKVLEAMSLLQFFLEEIILNYNLKT 274
G + F ++ +AM L F ++ +L T
Sbjct: 247 GKEAFEARMEQAMPLSAFLFNSLMPQVDLST 277
>pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core
pdb|1EQN|B Chain B, E.Coli Primase Catalytic Core
pdb|1EQN|C Chain C, E.Coli Primase Catalytic Core
pdb|1EQN|D Chain D, E.Coli Primase Catalytic Core
pdb|1EQN|E Chain E, E.Coli Primase Catalytic Core
Length = 321
Score = 197 bits (500), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 101/271 (37%), Positives = 156/271 (57%), Gaps = 15/271 (5%)
Query: 7 FYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEW-NALNKVFLDYNNINTLASS 63
FY+ L+ + A +L+KRGL+ E+I RF +G+AP W N L + + N +L +
Sbjct: 18 FYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDA 77
Query: 64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
G +V ++ + YDRFR R+ FPI++ G++IGFGGR++ + + KY+NS
Sbjct: 78 GXLVTN-----------DQGRSYDRFRERVXFPIRDKRGRVIGFGGRVLGN-DTPKYLNS 125
Query: 124 PETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH 183
PET +FHK +LYGL+EA+ + +L+ EGY DV+ L+Q+G VA LGT+ T+ H
Sbjct: 126 PETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYXDVVALAQYGINYAVASLGTSTTADH 185
Query: 184 IKKILFYTNSIIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243
I+ + TN++I +DGD+ LE L Y TD + ++F FLPD DPD+ +RK
Sbjct: 186 IQLLFRATNNVICCYDGDRAGRDAAWRALETALPYXTDGRQLRFXFLPDGEDPDTLVRKE 245
Query: 244 GYKIFSKKVLEAMSLLQFFLEEIILNYNLKT 274
G + F + +A L F + +L T
Sbjct: 246 GKEAFEARXEQAXPLSAFLFNSLXPQVDLST 276
>pdb|2AU3|A Chain A, Crystal Structure Of The Aquifex Aeolicus Primase (Zinc
Binding And Rna Polymerase Domains)
Length = 407
Score = 140 bits (353), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 83/243 (34%), Positives = 133/243 (54%), Gaps = 17/243 (6%)
Query: 2 ICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLA 61
+C DFY+ L ++EA ++K RG++ ++ +F+LGYAP+ AL KV + N L
Sbjct: 112 VC--DFYRESLLKNREASEYVKSRGIDPKVARKFDLGYAPSS-EALVKVLKE----NDLL 164
Query: 62 SSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYI 121
+ L ++ SP Y+ D F R++ PIK+ G++IGFGGR I + KYI
Sbjct: 165 EAYLETKNLL-----SPTKGVYR--DLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYI 217
Query: 122 NSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTS 181
NSP++ +F K L+GL+EAK I++ G+ ++ EGY D++ L G VA LGTA T
Sbjct: 218 NSPDSRVFKKGENLFGLYEAKEYIKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQ 277
Query: 182 THIKKILFYTNSIIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIR 241
+ +T + +DGD + + L + + ++LP+ YDPD +I+
Sbjct: 278 NQANLLSKFTKKVYILYDGDDAGRKAMKSAIPLLLSAGVE---VYPVYLPEGYDPDEFIK 334
Query: 242 KFG 244
+FG
Sbjct: 335 EFG 337
>pdb|4E2K|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
pdb|4EDG|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Atp And Manganese
pdb|4EDK|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Gtp And Manganese
pdb|4EDR|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Utp And Manganese
pdb|4EDT|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ppgpp And Manganese
pdb|4EDV|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Pppgpp And Manganese
pdb|4EE1|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ctp And Manganese
Length = 329
Score = 128 bits (322), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 79/236 (33%), Positives = 119/236 (50%), Gaps = 15/236 (6%)
Query: 15 SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NINTLASSGLVVDKIINK 73
++A+ +L++RG + +I +G+AP+ + + +I +GL+
Sbjct: 29 GEQALTYLQERGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDIELAYEAGLL------- 81
Query: 74 VNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSN 133
S E + YDRFR RIMFP+KN G+I+G+ GR E KY+NSPETP+F K
Sbjct: 82 ---SRNEENFSYYDRFRNRIMFPLKNAQGRIVGYSGRTYT-GQEPKYLNSPETPIFQKRK 137
Query: 134 ELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNS 193
LY L +A+ +I K +++ EG+MDVI G VA +GT + HI I T++
Sbjct: 138 LLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNVVATMGTQLSDEHITFIRKLTSN 197
Query: 194 IIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFS 249
I FDGD + L + +I+ LP DPD YI K+G F+
Sbjct: 198 ITLMFDGDFAGSEATLKTGQHLLQQGLNVFVIQ---LPSGMDPDEYIGKYGNDAFT 250
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.141 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,875,000
Number of Sequences: 62578
Number of extensions: 475656
Number of successful extensions: 1248
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1231
Number of HSP's gapped (non-prelim): 9
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)