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= 009196
(540 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
Flavin
Length = 318
Score = 96.3 bits (238), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 78/279 (27%), Positives = 128/279 (45%), Gaps = 19/279 (6%)
Query: 188 KLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLL-QGQASEWALLRRHSSEDLFGV 246
K+ LAP + FR + GAD E L Q +E L + H E V
Sbjct: 6 KVGLAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEELLPQPH--ERNVAV 63
Query: 247 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 306
QI G+ P+ L+ ++ ++ +ID+N GCP+ VV +GAG LL + I+
Sbjct: 64 QIFGSEPNELSEAARILSEKY--KWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVREL 121
Query: 307 SGTVDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQ 366
+V ++K R G+ KN ++ + + G V +H RT Q ++ A+W +
Sbjct: 122 RKSVSGKFSVKTRLGW--EKNEVEEIYRILVEEGVDEVFIHTRTVVQSFTGRAEWKALSV 179
Query: 367 CARKASDDLQVLGNGDIYSYLDWNK--HKSDCPELASCMIARGALIKPWIFTEIKE-QRH 423
++ + +GDI++ D + +S C L ++ARGA+ +PWIF +IK+ R
Sbjct: 180 LEKR----IPTFVSGDIFTPEDAKRALEESGCDGL---LVARGAIGRPWIFKQIKDFLRS 232
Query: 424 WDITSGERLNIMKDFARF--GLEHWGSDKKGVETTRHFL 460
+ R I++ F R L ++K V R FL
Sbjct: 233 GKYSEPSREEILRTFERHLELLIKTKGERKAVVEXRKFL 271
>pdb|3B0P|A Chain A, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0P|B Chain B, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0U|X Chain X, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
pdb|3B0U|Y Chain Y, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
Length = 350
Score = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 60/241 (24%), Positives = 101/241 (41%), Gaps = 19/241 (7%)
Query: 188 KLYLAPLTTVGNLPFRRVCKVLGADVTC-GEMAMCTNLLQGQASEWALLRRHSSEDLFGV 246
+L +AP+ + FR + + + V EM + +L+G LL E +
Sbjct: 5 RLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRER--LLAFRPEEHPIAL 62
Query: 247 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 306
Q+ G+ P +LA I + D I++N+GCP + G G+CLL R++ I++A
Sbjct: 63 QLAGSDPKSLAEAAR-IGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAM 121
Query: 307 SGTVDKPITIKVRTGYFEGKNRIDSL---IADIGTWGASAVTVHGR-------TRQQRYS 356
V P+T+K+R G EGK L + + G VH R T+ R
Sbjct: 122 GEAVRVPVTVKMRLG-LEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREI 180
Query: 357 KLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFT 416
D++++ + L + NG I S + H + M+ R P++
Sbjct: 181 PPLRHDWVHRL-KGDFPQLTFVTNGGIRSLEEALFH---LKRVDGVMLGRAVYEDPFVLE 236
Query: 417 E 417
E
Sbjct: 237 E 237
>pdb|3B0V|C Chain C, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
pdb|3B0V|D Chain D, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
Length = 363
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 37/120 (30%), Positives = 55/120 (45%), Gaps = 5/120 (4%)
Query: 234 LLRRHSSEDLFGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLL 293
LL E +Q+ G+ P +LA I + D I++N+GCP + G G+CLL
Sbjct: 71 LLAFRPEEHPIALQLAGSDPKSLAEAAR-IGEAFGYDEINLNLGCPSEKAQEGGYGACLL 129
Query: 294 TKPMRMKGIIEATSGTVDKPITIKVRTGYFEGKNRIDSLIADI---GTWGASAVTVHGRT 350
R++ I++A V P+T+K R G EGK L + G VH R+
Sbjct: 130 LDLARVREILKAXGEAVRVPVTVKXRLG-LEGKETYRGLAQSVEAXAEAGVKVFVVHARS 188
>pdb|3OOS|A Chain A, The Structure Of An AlphaBETA FOLD FAMILY HYDROLASE FROM
BACILLUS Anthracis Str. Sterne
Length = 278
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 362 DYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFTEIKEQ 421
+Y Q K D Q L I S++ KH CP + SC IA LI T+ +E
Sbjct: 201 NYFRQVEYKDYDVRQKLKFVKIPSFIYCGKHDVQCPYIFSCEIAN--LIPNATLTKFEES 258
Query: 422 RH 423
H
Sbjct: 259 NH 260
>pdb|2IPI|A Chain A, Crystal Structure Of Aclacinomycin Oxidoreductase
pdb|2IPI|B Chain B, Crystal Structure Of Aclacinomycin Oxidoreductase
pdb|2IPI|C Chain C, Crystal Structure Of Aclacinomycin Oxidoreductase
pdb|2IPI|D Chain D, Crystal Structure Of Aclacinomycin Oxidoreductase
Length = 521
Score = 28.5 bits (62), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 369 RKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFTEIKEQRH 423
R S D QV G +YSY + PE A+ R ++IK W+ + H
Sbjct: 382 RHLSADSQVWGEVSLYSY---GGKVNSVPETATATAQRDSIIKVWMSATWMDPAH 433
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
0.317 0.134 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,929,669
Number of Sequences: 62578
Number of extensions: 738723
Number of successful extensions: 1431
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1426
Number of HSP's gapped (non-prelim): 5
length of query: 540
length of database: 14,973,337
effective HSP length: 104
effective length of query: 436
effective length of database: 8,465,225
effective search space: 3690838100
effective search space used: 3690838100
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)