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= psy9514
(611 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 = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 54/224 (24%), Positives = 97/224 (43%), Gaps = 57/224 (25%)
Query: 372 GVQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVIT 431
VQ+ G+ P L++ ++L E+ ++D+N GCP+ + K+G+G LL+ + ++
Sbjct: 62 AVQIFGSEPNELSEAARILSEKY--KWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVR 119
Query: 432 CMNEVSSLPITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYI 491
+ + S +VKTR G K N + + G + +H RT Q +T +A+W
Sbjct: 120 ELRKSVSGKFSVKTRLGWEK--NEVEEIYRILVEEGVDEVFIHTRTVVQSFTGRAEWK-- 175
Query: 492 EKCAQLCSRDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSPAP 551
+L L R P
Sbjct: 176 --------------------------ALSVLEKRI------------------------P 185
Query: 552 LYGNGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKE 595
+ +GDI + ED +L++S G+++ RGA+ +PWIF++IK+
Sbjct: 186 TFVSGDIFTPEDAKRALEES-GCDGLLVARGAIGRPWIFKQIKD 228
Score = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/107 (30%), Positives = 58/107 (54%), Gaps = 3/107 (2%)
Query: 260 KLYLSPLTTVGNLPFRRLCKKWGADITCSEMAVATELLKSSPQEWALIKRHESEDLFGVQ 319
K+ L+P + FR L +WGAD SE A L +S + L+ + ++ VQ
Sbjct: 6 KVGLAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEELLPQPHERNV-AVQ 64
Query: 320 LCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQ 366
+ G+ P L++ ++L E+ ++D+N GCP+ + K+G+G LL+
Sbjct: 65 IFGSEPNELSEAARILSEKY--KWIDLNAGCPVRKVVKEGAGGALLK 109
>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 = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 52/234 (22%), Positives = 93/234 (39%), Gaps = 51/234 (21%)
Query: 371 FGVQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVI 430
+QL G++P L + ++ E D +++NLGCP E + G G+ LL ++ ++
Sbjct: 60 IALQLAGSDPKSLAEAARI-GEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREIL 118
Query: 431 TCMNEVSSLPITVKTRTGIHKDNNI--IHNFMPKFRDWGASLITLHGRTREQRYTKQADW 488
M E +P+TVK R G+ + + + G + +H R+
Sbjct: 119 KAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARS----------- 167
Query: 489 DYIEKCAQLCSRDNNIIHNFMPKFR-DWGASLITLHGRTREQRYTKQADWDYIEKCAQLC 547
L ++ N I P R DW L + D+ +
Sbjct: 168 ----ALLALSTKANREI----PPLRHDWVHRL--------------KGDFPQLT------ 199
Query: 548 SPAPLYGNGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKEKKLFDI 601
NG I S E+ LK+ + GVM+GR P++ +E ++++F +
Sbjct: 200 ----FVTNGGIRSLEEALFHLKR---VDGVMLGRAVYEDPFVLEE-ADRRVFGL 245
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 4/107 (3%)
Query: 260 KLYLSPLTTVGNLPFRRLCKKWGADITC-SEMAVATELLKSSPQEWALIKRHESEDLFGV 318
+L ++P+ + FR L ++ + +EM V +L+ + +E L R E E +
Sbjct: 5 RLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGN-RERLLAFRPE-EHPIAL 62
Query: 319 QLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLL 365
QL G++P L + ++ E D +++NLGCP E + G G+ LL
Sbjct: 63 QLAGSDPKSLAEAARI-GEAFGYDEINLNLGCPSEKAQEGGYGACLL 108
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 50/234 (21%), Positives = 91/234 (38%), Gaps = 51/234 (21%)
Query: 371 FGVQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVI 430
+QL G++P L + ++ E D +++NLGCP E + G G+ LL ++ ++
Sbjct: 81 IALQLAGSDPKSLAEAARI-GEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREIL 139
Query: 431 TCMNEVSSLPITVKTRTGIHKDNNI--IHNFMPKFRDWGASLITLHGRTREQRYTKQADW 488
E +P+TVK R G+ + + + G + +H R+
Sbjct: 140 KAXGEAVRVPVTVKXRLGLEGKETYRGLAQSVEAXAEAGVKVFVVHARS----------- 188
Query: 489 DYIEKCAQLCSRDNNIIHNFMPKFR-DWGASLITLHGRTREQRYTKQADWDYIEKCAQLC 547
L ++ N I P R DW L + D+ +
Sbjct: 189 ----ALLALSTKANREI----PPLRHDWVHRL--------------KGDFPQLT------ 220
Query: 548 SPAPLYGNGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKEKKLFDI 601
NG I S E+ LK+ + GV +GR P++ +E ++++F +
Sbjct: 221 ----FVTNGGIRSLEEALFHLKR---VDGVXLGRAVYEDPFVLEE-ADRRVFGL 266
Score = 35.4 bits (80), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 53/107 (49%), Gaps = 4/107 (3%)
Query: 260 KLYLSPLTTVGNLPFRRLCKKWGADITC-SEMAVATELLKSSPQEWALIKRHESEDLFGV 318
+L ++P + FR L ++ + +E V +L+ + +E L R E E +
Sbjct: 26 RLSVAPXVDRTDRHFRFLVRQVSLGVRLYTEXTVDQAVLRGN-RERLLAFRPE-EHPIAL 83
Query: 319 QLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLL 365
QL G++P L + ++ E D +++NLGCP E + G G+ LL
Sbjct: 84 QLAGSDPKSLAEAARI-GEAFGYDEINLNLGCPSEKAQEGGYGACLL 129
>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 = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 88 TCKYGEKCKFVHDKNVF--MKSKPEDISEQCYVFLQHGYCPMGIACRF 133
TCKYGEKC+F H + + P+ +E C F G+CP G C F
Sbjct: 17 TCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCHF 64
>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
Nup475TTPTIS11
Length = 77
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 89 CKYGEKCKFVHDKNVFMKSK--PEDISEQCYVFLQHGYCPMGIACRF 133
C+YG KC+F H ++ P+ +E C+ F G CP G C F
Sbjct: 24 CRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHF 70
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
0.318 0.135 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,457,089
Number of Sequences: 62578
Number of extensions: 778288
Number of successful extensions: 1852
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1833
Number of HSP's gapped (non-prelim): 17
length of query: 611
length of database: 14,973,337
effective HSP length: 105
effective length of query: 506
effective length of database: 8,402,647
effective search space: 4251739382
effective search space used: 4251739382
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)