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= 005508
(693 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 = 94.4 bits (233), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 78/279 (27%), Positives = 128/279 (45%), Gaps = 19/279 (6%)
Query: 341 KLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLL-QGQASEWALLRRHSSEDLFGV 399
K+ LAP + FR + GAD E L Q +E L + H E V
Sbjct: 6 KVGLAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEELLPQPH--ERNVAV 63
Query: 400 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 459
QI G+ P+ L+ ++ ++ +ID+N GCP+ VV +GAG LL + I+
Sbjct: 64 QIFGSEPNELSEAARILSEKY--KWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVREL 121
Query: 460 SGTVDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQ 519
+V ++K R G+ KN ++ + + G V +H RT Q ++ A+W +
Sbjct: 122 RKSVSGKFSVKTRLGW--EKNEVEEIYRILVEEGVDEVFIHTRTVVQSFTGRAEWKALSV 179
Query: 520 CARKASDDLQVLGNGDIYSYLDWNK--HKSDCPELASCMIARGALIKPWIFTEIKE-QRH 576
++ + +GDI++ D + +S C L ++ARGA+ +PWIF +IK+ R
Sbjct: 180 LEKR----IPTFVSGDIFTPEDAKRALEESGCDGL---LVARGAIGRPWIFKQIKDFLRS 232
Query: 577 WDITSGERLNIMKDFARF--GLEHWGSDKKGVETTRHFL 613
+ 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 = 63.2 bits (152), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 60/241 (24%), Positives = 101/241 (41%), Gaps = 19/241 (7%)
Query: 341 KLYLAPLTTVGNLPFRRVCKVLGADVTC-GEMAMCTNLLQGQASEWALLRRHSSEDLFGV 399
+L +AP+ + FR + + + V EM + +L+G LL E +
Sbjct: 5 RLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRER--LLAFRPEEHPIAL 62
Query: 400 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 459
Q+ G+ P +LA I + D I++N+GCP + G G+CLL R++ I++A
Sbjct: 63 QLAGSDPKSLAEAAR-IGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAM 121
Query: 460 SGTVDKPITIKVRTGYFEGKNRIDSL---IADIGTWGASAVTVHGR-------TRQQRYS 509
V P+T+K+R G EGK L + + G VH R T+ R
Sbjct: 122 GEAVRVPVTVKMRLG-LEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREI 180
Query: 510 KLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFT 569
D++++ + L + NG I S + H + M+ R P++
Sbjct: 181 PPLRHDWVHRL-KGDFPQLTFVTNGGIRSLEEALFH---LKRVDGVMLGRAVYEDPFVLE 236
Query: 570 E 570
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 = 2e-08, Method: Compositional matrix adjust.
Identities = 46/167 (27%), Positives = 73/167 (43%), Gaps = 8/167 (4%)
Query: 341 KLYLAPLTTVGNLPFRRVCKVLGADVTC-GEMAMCTNLLQGQASEWALLRRHSSEDLFGV 399
+L +AP + FR + + + V E + +L+G LL E +
Sbjct: 26 RLSVAPXVDRTDRHFRFLVRQVSLGVRLYTEXTVDQAVLRGNRER--LLAFRPEEHPIAL 83
Query: 400 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 459
Q+ G+ P +LA I + D I++N+GCP + G G+CLL R++ I++A
Sbjct: 84 QLAGSDPKSLAEAAR-IGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAX 142
Query: 460 SGTVDKPITIKVRTGYFEGKNRIDSLIADI---GTWGASAVTVHGRT 503
V P+T+K R G EGK L + G VH R+
Sbjct: 143 GEAVRVPVTVKXRLG-LEGKETYRGLAQSVEAXAEAGVKVFVVHARS 188
>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii Au-
Rich Element By The Tandem Zinc Finger Domain Of Tis11d
Length = 70
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 101 SHLCPEVAKSGDVSSCPYKDKCRFSHDLDGFKA--QKPDDLEGECPFLSSEGPCPYGLAC 158
+ LC +SG +C Y +KC+F+H ++ + P C + G CPYG C
Sbjct: 6 TELCRPFEESG---TCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRC 62
Query: 159 RF 160
F
Sbjct: 63 HF 64
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 101 SHLCPEVAKSGDVSSCPYKDKCRFSHDLDGFKA--QKPDDLEGECPFLSSEGPCPYGLAC 158
+ LC ++SG C Y KC+F+H L + + P C +G CPYG C
Sbjct: 12 TELCRTYSESG---RCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRC 68
Query: 159 RF 160
F
Sbjct: 69 HF 70
>pdb|3V33|A Chain A, Crystal Structure Of Mcpip1 Conserved Domain With
Zinc-Finger Motif
pdb|3V33|B Chain B, Crystal Structure Of Mcpip1 Conserved Domain With
Zinc-Finger Motif
Length = 223
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 36/93 (38%), Gaps = 6/93 (6%)
Query: 76 SSTLVKEKKSKRQLKRERQQEKKSASHLCPEVAKSGDVSSCPYKDKCRFSHDLDGFKAQK 135
S +V + R L+ ERQ+ K+ + D P R LD F +K
Sbjct: 125 SDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKK 184
Query: 136 PDDLEGE---CPFLSSEGPCPYGLACRFSGTHR 165
P LE CP+ C YG+ CRF R
Sbjct: 185 PLTLEHRKQPCPYGRK---CTYGIKCRFFHPER 214
>pdb|3OOS|A Chain A, The Structure Of An AlphaBETA FOLD FAMILY HYDROLASE FROM
BACILLUS Anthracis Str. Sterne
Length = 278
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 515 DYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFTEIKEQ 574
+Y Q K D Q L I S++ KH CP + SC IA LI T+ +E
Sbjct: 201 NYFRQVEYKDYDVRQKLKFVKIPSFIYCGKHDVQCPYIFSCEIAN--LIPNATLTKFEES 258
Query: 575 RH 576
H
Sbjct: 259 NH 260
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
0.315 0.132 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,664,492
Number of Sequences: 62578
Number of extensions: 945319
Number of successful extensions: 1908
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1896
Number of HSP's gapped (non-prelim): 14
length of query: 693
length of database: 14,973,337
effective HSP length: 106
effective length of query: 587
effective length of database: 8,340,069
effective search space: 4895620503
effective search space used: 4895620503
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: 55 (25.8 bits)