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= psy7343
(487 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 = 104 bits (259), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 67/221 (30%), Positives = 113/221 (51%), Gaps = 7/221 (3%)
Query: 153 LAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQFCG 212
LAP ++ +R L+ +G+ ++ VSA F+ + + +E L+ P +R + +Q G
Sbjct: 9 LAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEE-LLPQPHERNVAVQIFG 67
Query: 213 NDSKNLTEAAKLAEPHCDGIDINIGCP-QMVAKRGHYGAYLQDDWPLLTNLVSSLRQAVQ 271
++ L+EAA++ ID+N GCP + V K G GA L+ D +V LR++V
Sbjct: 68 SEPNELSEAARILSEKYKWIDLNAGCPVRKVVKEGAGGALLK-DLRHFRYIVRELRKSVS 126
Query: 272 VPVSCKIRIYQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKAL 331
S K R+ + N+ E R+L G + +H RTV Q TG A W+ ++ + K
Sbjct: 127 GKFSVKTRLGWEKNEVEEIYRILVEEGVDEVFIHTRTVVQ--SFTGRAEWKALSVLEK-- 182
Query: 332 TIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPALF 372
IP +G+I D + L ++G G++ A G + P +F
Sbjct: 183 RIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAIGRPWIF 223
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 83 LAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQ 139
LAP ++ +R L+ +G+ ++ VSA F+ + + +E L+ P +R + +Q
Sbjct: 9 LAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEE-LLPQPHERNVAVQ 64
>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 = 93.2 bits (230), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 79/271 (29%), Positives = 125/271 (46%), Gaps = 34/271 (12%)
Query: 148 SPRFILAPMVDASELPWRLLSRRYGSHL-CYTPMVSAHQFIADKKLRQEILMSTPEDRPL 206
PR +APMVD ++ +R L R+ + YT M + R+ +L PE+ P+
Sbjct: 3 DPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGN--RERLLAFRPEEHPI 60
Query: 207 IIQFCGNDSKNLTEAAKLAEPHC-DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSS 265
+Q G+D K+L EAA++ E D I++N+GCP A+ G YGA L D + ++ +
Sbjct: 61 ALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKA 120
Query: 266 LRQAVQVPVSCKIRI-------YQDVNKTVEYARMLERAGCQLLAVHGR-------TVDQ 311
+ +AV+VPV+ K+R+ Y+ + ++VE + AG ++ VH R T
Sbjct: 121 MGEAVRVPVTVKMRLGLEGKETYRGLAQSVE---AMAEAGVKVFVVHARSALLALSTKAN 177
Query: 312 RGMNTGLASWEH-ITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPA 370
R + W H + LT + NG I+ L EA V GVM +P
Sbjct: 178 REIPPLRHDWVHRLKGDFPQLTF--VTNGGIRSLE--EALFHLKRVDGVMLGRAVYEDPF 233
Query: 371 LFTGQTRPAWELASEYLDLVAQYPVRLQYAR 401
+ R + L + P RL+ AR
Sbjct: 234 VLEEADRRVFGL--------PRRPSRLEVAR 256
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 78 SPRFILAPMVDASELPWRLLSRRYGSHL-CYTPMVSAHQFIADKKLRQEILMSTPEDRPL 136
PR +APMVD ++ +R L R+ + YT M + R+ +L PE+ P+
Sbjct: 3 DPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGN--RERLLAFRPEEHPI 60
Query: 137 IIQ 139
+Q
Sbjct: 61 ALQ 63
>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 = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 52/169 (30%), Positives = 89/169 (52%), Gaps = 12/169 (7%)
Query: 148 SPRFILAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDRPLI 207
PR +AP VD ++ +R L R+ + + Q + + R+ +L PE+ P+
Sbjct: 24 DPRLSVAPXVDRTDRHFRFLVRQVSLGVRLYTEXTVDQAVL-RGNRERLLAFRPEEHPIA 82
Query: 208 IQFCGNDSKNLTEAAKLAEPHC-DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSSL 266
+Q G+D K+L EAA++ E D I++N+GCP A+ G YGA L D + ++ +
Sbjct: 83 LQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAX 142
Query: 267 RQAVQVPVSCKIRI-------YQDVNKTVEYARMLERAGCQLLAVHGRT 308
+AV+VPV+ K R+ Y+ + ++VE AG ++ VH R+
Sbjct: 143 GEAVRVPVTVKXRLGLEGKETYRGLAQSVE---AXAEAGVKVFVVHARS 188
>pdb|1H7W|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1GT8|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GTE|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTH|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
Length = 1025
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 31/136 (22%), Positives = 57/136 (41%), Gaps = 4/136 (2%)
Query: 195 EILMSTPEDRPLIIQFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQ 253
E+ P++ + C + + E ++ AE D +++N+ CP + +RG G
Sbjct: 627 ELKADFPDNIVIASIMCSYNKNDWMELSRKAEASGADALELNLSCPHGMGERG-MGLACG 685
Query: 254 DDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQLLAVHGRTVDQRG 313
D L+ N+ +RQAVQ+P K+ +V V AR + G + G
Sbjct: 686 QDPELVRNICRWVRQAVQIPFFAKLT--PNVTDIVSIARAAKEGGADGVTATNTVSGLMG 743
Query: 314 MNTGLASWEHITAVRK 329
+ W + A ++
Sbjct: 744 LKADGTPWPAVGAGKR 759
>pdb|1H7X|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
Length = 1025
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 4/136 (2%)
Query: 195 EILMSTPEDRPLIIQFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQ 253
E+ P++ + C + + E ++ AE D +++N+ P + +RG G
Sbjct: 627 ELKADFPDNIVIASIMCSYNKNDWMELSRKAEASGADALELNLSAPHGMGERG-MGLACG 685
Query: 254 DDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQLLAVHGRTVDQRG 313
D L+ N+ +RQAVQ+P K+ +V V AR + G + G
Sbjct: 686 QDPELVRNICRWVRQAVQIPFFAKLT--PNVTDIVSIARAAKEGGADGVTATNTVSGLMG 743
Query: 314 MNTGLASWEHITAVRK 329
+ W + A ++
Sbjct: 744 LKADGTPWPAVGAGKR 759
>pdb|3IZ6|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 195
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 387 LDLVAQYPVR-------LQYARGHVFNMCHHLLTLPENSDVRLLVGKT 427
L LV +Y +R +QYA + N HLLTL E + R+ G+
Sbjct: 30 LKLVGEYGLRCKRELWRVQYALSRIRNNARHLLTLDEKNPRRIFEGEA 77
>pdb|2QR6|A Chain A, Crystal Structure Of Imp DehydrogenaseGMP REDUCTASE-Like
Protein (Np_599840.1) From Corynebacterium Glutamicum
Atcc 13032 Kitasato At 1.50 A Resolution
Length = 393
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 44/86 (51%), Gaps = 8/86 (9%)
Query: 255 DWPLLTNLVSSLRQAVQVPVSCKIRIY-QDVNKTVEYARMLERAGCQLLAVHGRTVDQRG 313
D LL+ ++ +R + ++ +R+ Q+V E A ++ +AG LL + G +
Sbjct: 140 DTELLSERIAQVRDSGEI---VAVRVSPQNVR---EIAPIVIKAGADLLVIQGTLISAEH 193
Query: 314 MNTGLASWEHITAVRKALTIPVIANG 339
+NTG + ++ +L +PVIA G
Sbjct: 194 VNTGGEAL-NLKEFIGSLDVPVIAGG 218
>pdb|3IVT|A Chain A, Homocitrate Synthase Lys4 Bound To 2-Og
pdb|3IVT|B Chain B, Homocitrate Synthase Lys4 Bound To 2-Og
pdb|3IVU|A Chain A, Homocitrate Synthase Lys4 Bound To 2-Og
pdb|3IVU|B Chain B, Homocitrate Synthase Lys4 Bound To 2-Og
pdb|3MI3|A Chain A, Homocitrate Synthase Lys4 Bound To Lysine
pdb|3MI3|B Chain B, Homocitrate Synthase Lys4 Bound To Lysine
Length = 423
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 31/158 (19%), Positives = 60/158 (37%), Gaps = 17/158 (10%)
Query: 218 LTEAAKLAEPHCDGIDINIGCPQMVAKRGHYG--AYLQDDWPLLTNLVSSLRQAVQVPVS 275
+ +A E DG+D+ IG Q + K H Y+ D + N V S + ++V S
Sbjct: 113 MDDARVAVETGVDGVDVVIGTSQYLRKYSHGKDMTYIIDSATEVINFVKS--KGIEVRFS 170
Query: 276 CKIRIYQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPV 335
+ D+ + + +++ G + + D G T ++ I +R ++ +
Sbjct: 171 SEDSFRSDLVDLLSLYKAVDKIGVNRVGI----ADTVGCATPRQVYDLIRTLRGVVSCDI 226
Query: 336 ---------IANGNIQCLADVEACLAQTGVAGVMTAEG 364
+A N C + A T + G+ G
Sbjct: 227 ECHFHNDTGMAIANAYCALEAGATHIDTSILGIGERNG 264
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 0.136 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,036,396
Number of Sequences: 62578
Number of extensions: 614271
Number of successful extensions: 1345
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1331
Number of HSP's gapped (non-prelim): 19
length of query: 487
length of database: 14,973,337
effective HSP length: 103
effective length of query: 384
effective length of database: 8,527,803
effective search space: 3274676352
effective search space used: 3274676352
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)