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= 013813
(436 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 = 1e-19, Method: Compositional matrix adjust.
Identities = 59/223 (26%), Positives = 113/223 (50%), Gaps = 5/223 (2%)
Query: 104 KLIVAPMVDNSELPFRMLCRRYGAEAAYTPMLHSRIFTESEKYRNEEFATCKEDRPLFVQ 163
K+ +AP ++ FR L +GA+ A++ + ++ F + + + EE +R + VQ
Sbjct: 6 KVGLAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQ-KTEELLPQPHERNVAVQ 64
Query: 164 FCANDPEILLNAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALN 223
++P L AAR + ++D+N GCP R + G L+ +L + +V +L +
Sbjct: 65 IFGSEPNELSEAARILSEKYKWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVRELRKS 124
Query: 224 LNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKN 283
++ S K R+ + + ++L + G + +H RT + RA+W A+ ++
Sbjct: 125 VSGKFSVKTRLGWEKNEVEEIYRILVEEGVDEVFIHTRTVVQSFTG--RAEWKALSVLEK 182
Query: 284 ALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALF 326
RIP +G++ ED ++ LEE+GC+G+L A + P +F
Sbjct: 183 --RIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAIGRPWIF 223
>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 = 91.7 bits (226), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 66/235 (28%), Positives = 117/235 (49%), Gaps = 20/235 (8%)
Query: 103 PKLIVAPMVDNSELPFRMLCRRYGAEA-AYTPMLHSRIFTESEKYRNEEFATCKEDRPLF 161
P+L VAPMVD ++ FR L R+ YT M + + R F E+ P+
Sbjct: 4 PRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRP--EEHPIA 61
Query: 162 VQFCANDPEILLNAARRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKL 220
+Q +DP+ L AAR E + D +++NLGCP A+ G YGA L+ +L V+ +++ +
Sbjct: 62 LQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAM 121
Query: 221 ALNLNVPVSCKIRVFPNLQDTIK----YAKMLEDAGCSLLAVHGR-------TRDEKDGK 269
+ VPV+ K+R+ ++T + + + +AG + VH R T+ ++
Sbjct: 122 GEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIP 181
Query: 270 KFRADWNAIKAVKNAL-RIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENP 323
R DW + +K ++ + NG +R +E+ L+ +GV+ ++ E+P
Sbjct: 182 PLRHDW--VHRLKGDFPQLTFVTNGGIRSLEEALFHLKR--VDGVMLGRAVYEDP 232
>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 = 85.5 bits (210), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 68/241 (28%), Positives = 116/241 (48%), Gaps = 32/241 (13%)
Query: 103 PKLIVAPMVDNSELPFRMLCRRYGAEAAYTPMLHSRIFTES-------EKYRNEEFATCK 155
P+L VAP VD ++ FR L R+ L R++TE R A
Sbjct: 25 PRLSVAPXVDRTDRHFRFLVRQVS--------LGVRLYTEXTVDQAVLRGNRERLLAFRP 76
Query: 156 EDRPLFVQFCANDPEILLNAARRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVK 214
E+ P+ +Q +DP+ L AAR E + D +++NLGCP A+ G YGA L+ +L V+
Sbjct: 77 EEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVR 136
Query: 215 SLVEKLALNLNVPVSCKIRVFPNLQDTIK-YAKMLE---DAGCSLLAVHGR-------TR 263
+++ + VPV+ K R+ ++T + A+ +E +AG + VH R T+
Sbjct: 137 EILKAXGEAVRVPVTVKXRLGLEGKETYRGLAQSVEAXAEAGVKVFVVHARSALLALSTK 196
Query: 264 DEKDGKKFRADWNAIKAVKNAL-RIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLEN 322
++ R DW + +K ++ + NG +R +E+ L+ +GV ++ E+
Sbjct: 197 ANREIPPLRHDW--VHRLKGDFPQLTFVTNGGIRSLEEALFHLKR--VDGVXLGRAVYED 252
Query: 323 P 323
P
Sbjct: 253 P 253
>pdb|1H5Y|A Chain A, Hisf Protein From Pyrobaculum Aerophilum
pdb|1H5Y|B Chain B, Hisf Protein From Pyrobaculum Aerophilum
Length = 253
Score = 36.2 bits (82), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 240 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 299
D +K+AK +E+ G + + T ++DG D I+ V +++RIPV+A+G +E
Sbjct: 155 DAVKWAKEVEELGAGEILL---TSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVE 211
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 276 NAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFA 327
+++K V A+ IPVL G VR +ED L G + V + + NP L A
Sbjct: 67 DSVKRVAEAVSIPVLVGGGVRSLED-ATTLFRAGADKVSVNTAAVRNPQLVA 117
>pdb|3C5W|P Chain P, Complex Between Pp2a-Specific Methylesterase Pme-1 And
Pp2a Core Enzyme
Length = 310
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 305 LEETGCEGVLSAESLLEN-PALFAGFRTA-EWIVGSEEISKDGNLDQADL-LVEYLKLCE 361
+E T + + S ++ L P F A EW V S +I NL+ A + +V +K CE
Sbjct: 149 VEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSVKSGQIR---NLESARVSMVGQVKQCE 205
Query: 362 KYPVPWRMIRSHVHKLLGEWFR 383
P WR+ + K WFR
Sbjct: 206 GKPYTWRIELAKTEKYWDGWFR 227
>pdb|1ULZ|A Chain A, Crystal Structure Of The Biotin Carboxylase Subunit Of
Pyruvate Carboxylase
Length = 451
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 71/159 (44%), Gaps = 14/159 (8%)
Query: 204 AFLMDNLPLVKSLVEKLALNLNVPVSCKIRVFPN---LQDTIKYAKMLEDAGCSLLAVHG 260
A+++ PL L ++ +NL + V + P L + ++AKM E+AG + + H
Sbjct: 48 AYMIGTDPLDTYLNKQRIINLALEVGAD-AIHPGYGFLAENAEFAKMCEEAGITFIGPHW 106
Query: 261 RTRDEKDGKKFRADWNAIKAVKNALRIPVL--ANGNVRHMEDVQKCLEETGCEGVLSAES 318
+ E G K R+ K V +PV+ ++G ++ +E+ + E G +L A +
Sbjct: 107 KVI-ELMGDKARS-----KEVMKKAGVPVVPGSDGVLKSLEEAKALAREIGYPVLLKATA 160
Query: 319 LLENPALFAGFRTAEWIVGSEEISKDGN--LDQADLLVE 355
+ E + E+ S++ + DLL+E
Sbjct: 161 GGGGRGIRICRNEEELVKNYEQASREAEKAFGRGDLLLE 199
>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 = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/120 (20%), Positives = 49/120 (40%), Gaps = 4/120 (3%)
Query: 164 FCANDPEILLNAARRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLAL 222
C+ + + +R+ E D +++NL CP + RG G + LV+++ +
Sbjct: 642 MCSYNKNDWMELSRKAEASGADALELNLSCPHGMGERG-MGLACGQDPELVRNICRWVRQ 700
Query: 223 NLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVK 282
+ +P K+ PN+ D + A+ ++ G + K W A+ A K
Sbjct: 701 AVQIPFFAKLT--PNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGK 758
>pdb|2WFD|A Chain A, Structure Of The Human Cytosolic Leucyl-Trna Synthetase
Editing Domain
pdb|2WFD|B Chain B, Structure Of The Human Cytosolic Leucyl-Trna Synthetase
Editing Domain
Length = 252
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 13/72 (18%)
Query: 192 CPQRIARRGNYGAFLMDN--LPLVKSLV--EKLALNLNVPVSCK--IRVFPNLQDTIKYA 245
C Q+ AR +Y F DN +P+VK L E L +L+ P++ I V P L TIK
Sbjct: 69 CTQKAARNXSYQGFTKDNGVVPVVKELXGEEILGASLSAPLTSYKVIYVLPXL--TIK-- 124
Query: 246 KMLEDAGCSLLA 257
ED G ++
Sbjct: 125 ---EDKGTGVVT 133
>pdb|1OX4|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX6|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 265 EKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSA 316
+KDG D I+ VK+A++IPV+A+ E ++ +T + L A
Sbjct: 475 DKDGSNSGYDLELIEHVKDAVKIPVIASSGAGVPEHFEEAFLKTRADACLGA 526
>pdb|1JVN|A Chain A, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1JVN|B Chain B, Crystal Structure Of Imidazole Glycerol Phosphate
Synthase: A Tunnel Through A (BetaALPHA)8 BARREL JOINS
TWO ACTIVE SITES
pdb|1OX4|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|A Chain A, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
pdb|1OX5|B Chain B, Towards Understanding The Mechanism Of The Complex
Cyclization Reaction Catalyzed By Imidazole
Glycerophosphate Synthase
Length = 555
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 265 EKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSA 316
+KDG D I+ VK+A++IPV+A+ E ++ +T + L A
Sbjct: 475 DKDGSNSGYDLELIEHVKDAVKIPVIASSGAGVPEHFEEAFLKTRADACLGA 526
>pdb|3F4W|A Chain A, The 1.65a Crystal Structure Of 3-Hexulose-6-Phosphate
Synthase From Salmonella Typhimurium
pdb|3F4W|B Chain B, The 1.65a Crystal Structure Of 3-Hexulose-6-Phosphate
Synthase From Salmonella Typhimurium
Length = 211
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 246 KMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMED 300
++LE+AG +LAVH T + G+K D + V+ RI V + + ++D
Sbjct: 121 RLLEEAGADMLAVHTGTDQQAAGRKPIDDLITMLKVRRKARIAVAGGISSQTVKD 175
>pdb|2Y88|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase (Variant D11n) With Bound Prfar
pdb|2Y89|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase A (Variant D11n)
Length = 244
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 248 LEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQ--KCL 305
L+ GCS V T KDG + + + V + PV+A+G V ++D++ L
Sbjct: 158 LDSEGCSRFVV---TDITKDGTLGGPNLDLLAGVADRTDAPVIASGGVSSLDDLRAIATL 214
Query: 306 EETGCEGVLSAESL 319
G EG + ++L
Sbjct: 215 THRGVEGAIVGKAL 228
>pdb|2Y85|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase With Bound Rcdrp
pdb|2Y85|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase With Bound Rcdrp
pdb|2Y85|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase With Bound Rcdrp
pdb|2Y85|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase With Bound Rcdrp
pdb|3ZS4|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Phosphoribosyl Isomerase With Bound Prfar
Length = 244
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 248 LEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQ--KCL 305
L+ GCS V T KDG + + + V + PV+A+G V ++D++ L
Sbjct: 158 LDSEGCSRFVV---TDITKDGTLGGPNLDLLAGVADRTDAPVIASGGVSSLDDLRAIATL 214
Query: 306 EETGCEGVLSAESL 319
G EG + ++L
Sbjct: 215 THRGVEGAIVGKAL 228
>pdb|3IZR|EE Chain e, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 244
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 21/45 (46%)
Query: 173 LNAARRVEPYCDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLV 217
+N RRVEPY Y NL + + + YG +PL + V
Sbjct: 126 INMLRRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIPLANNKV 170
>pdb|2NV1|A Chain A, Structure Of The Synthase Subunit Pdx1 (Yaad) Of Plp
Synthase From Bacillus Subtilis
pdb|2NV1|B Chain B, Structure Of The Synthase Subunit Pdx1 (Yaad) Of Plp
Synthase From Bacillus Subtilis
pdb|2NV1|C Chain C, Structure Of The Synthase Subunit Pdx1 (Yaad) Of Plp
Synthase From Bacillus Subtilis
pdb|2NV1|D Chain D, Structure Of The Synthase Subunit Pdx1 (Yaad) Of Plp
Synthase From Bacillus Subtilis
pdb|2NV1|E Chain E, Structure Of The Synthase Subunit Pdx1 (Yaad) Of Plp
Synthase From Bacillus Subtilis
pdb|2NV1|F Chain F, Structure Of The Synthase Subunit Pdx1 (Yaad) Of Plp
Synthase From Bacillus Subtilis
Length = 305
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 243 KYAKMLEDAGCSLLAVHGRTRDEKD-----GKKFRADWNAIKAVKNALRIPVLANGNVRH 297
+ AK+ E+AG +AV R D G AD ++ V NA+ IPV+A + H
Sbjct: 32 EQAKIAEEAGA--VAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGH 89
Query: 298 MEDVQKCLEETGCEGVLSAESL 319
+ + + LE G + + +E L
Sbjct: 90 IVEA-RVLEAMGVDYIDESEVL 110
>pdb|3TDM|A Chain A, Computationally Designed Tim-Barrel Protein, Halfflr
pdb|3TDM|B Chain B, Computationally Designed Tim-Barrel Protein, Halfflr
pdb|3TDM|C Chain C, Computationally Designed Tim-Barrel Protein, Halfflr
pdb|3TDM|D Chain D, Computationally Designed Tim-Barrel Protein, Halfflr
Length = 126
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 262 TRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 321
T ++DG K D I+ V+ +P++A+G ME + G + V + +E
Sbjct: 55 TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLR-GADKVSINTAAVE 113
Query: 322 NPAL 325
NP+L
Sbjct: 114 NPSL 117
>pdb|2NV2|A Chain A, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|C Chain C, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|E Chain E, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|G Chain G, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|I Chain I, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|K Chain K, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|M Chain M, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|O Chain O, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|Q Chain Q, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|S Chain S, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|U Chain U, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
pdb|2NV2|W Chain W, Structure Of The Plp Synthase Complex Pdx12 (YAADE) FROM
BACILLUS Subtilis
Length = 294
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 243 KYAKMLEDAGCSLLAVHGRTRDEKD-----GKKFRADWNAIKAVKNALRIPVLANGNVRH 297
+ AK+ E+AG +AV R D G AD ++ V NA+ IPV+A + H
Sbjct: 29 EQAKIAEEAGA--VAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGH 86
Query: 298 MEDVQKCLEETGCEGVLSAESL 319
+ + + LE G + + +E L
Sbjct: 87 IVEA-RVLEAMGVDYIDESEVL 107
>pdb|1JF9|A Chain A, Crystal Structure Of Selenocysteine Lyase
Length = 408
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 81 RGYLSGEARAERAWAHWTKLGRPKLIVAPMVDNSEL-PFRMLCRRYGAEAAYTPM 134
RG G +W + +I++ M ++ + P++MLC R GAE P+
Sbjct: 94 RGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPL 148
>pdb|1I29|A Chain A, Crystal Structure Of Csdb Complexed With
L-Propargylglycine
Length = 406
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 81 RGYLSGEARAERAWAHWTKLGRPKLIVAPMVDNSEL-PFRMLCRRYGAEAAYTPM 134
RG G +W + +I++ M ++ + P++MLC R GAE P+
Sbjct: 92 RGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPL 146
>pdb|3TDN|A Chain A, Computationally Designed Two-Fold Symmetric Tim-Barrel
Protein, Flr
pdb|3TDN|B Chain B, Computationally Designed Two-Fold Symmetric Tim-Barrel
Protein, Flr
Length = 247
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 262 TRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 321
T ++DG K D I+ V+ +P++A+G ME + G + V + +E
Sbjct: 55 TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLR-GADKVSINTAAVE 113
Query: 322 NPALF 326
NP+L
Sbjct: 114 NPSLI 118
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 262 TRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 321
T ++DG K D I+ V+ +P++A+G ME + G + V + +E
Sbjct: 176 TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLR-GADKVSINTAAVE 234
Query: 322 NPALF 326
NP+L
Sbjct: 235 NPSLI 239
>pdb|3OG3|A Chain A, Crystal Structure Of An Artificial Thermostable
(Ba)8-Barrel Protein From Identical Half Barrels
Length = 251
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 262 TRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 321
T ++DG K D I+ V+ +P++A+G ME + G + V + +E
Sbjct: 50 TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAF-LAGADKVSINTAAVE 108
Query: 322 NPALF 326
NP+L
Sbjct: 109 NPSLI 113
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 262 TRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 321
T ++DG K D I+ V+ +P++A+G ME + G + V + +E
Sbjct: 171 TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAF-LAGADKVSINTAAVE 229
Query: 322 NPALF 326
NP+L
Sbjct: 230 NPSLI 234
>pdb|1KMJ|A Chain A, E. Coli NifsCSDB PROTEIN AT 2.0A WITH THE CYSTEINE
PERSULFIDE Intermediate (Residue Css).
pdb|1KMK|A Chain A, E. Coli NifsCSDB PROTEIN AT 2.20A WITH THE CYSTEINE
PERSELENIDE Intermediate (Residue Csz)
Length = 406
Score = 28.1 bits (61), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 81 RGYLSGEARAERAWAHWTKLGRPKLIVAPMVDNSEL-PFRMLCRRYGAEAAYTPM 134
RG G +W + +I++ M ++ + P++MLC R GAE P+
Sbjct: 92 RGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPL 146
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
0.321 0.137 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,543,309
Number of Sequences: 62578
Number of extensions: 458353
Number of successful extensions: 1139
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1120
Number of HSP's gapped (non-prelim): 29
length of query: 436
length of database: 14,973,337
effective HSP length: 102
effective length of query: 334
effective length of database: 8,590,381
effective search space: 2869187254
effective search space used: 2869187254
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)