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= 026400
(239 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W6J|A Chain A, Structure Of Human Osc In Complex With Ro 48-8071
Length = 732
Score = 189 bits (481), Expect = 8e-49, Method: Compositional matrix adjust.
Identities = 91/238 (38%), Positives = 140/238 (58%), Gaps = 5/238 (2%)
Query: 5 LMKAHDFLKNSQVTDNPQGDFRSMFRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLST 64
L KAH+FL+ SQV DNP D++ +R + KGG++FS D G VSDC++E+ L L
Sbjct: 411 LQKAHEFLRLSQVPDNPP-DYQKYYRQMRKGGFSFSTLDCGWIVSDCTAEALKAVLLLQE 469
Query: 65 MPPEIVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPIEFLDEVIIEH 124
P + E + ER DA +L +++ GG +E +ELLNP E +++I++
Sbjct: 470 KCPHVT-EHIPRERLCDAVAVLLNMRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDY 528
Query: 125 DYVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYS 184
YVECT++ ++A+ F K +P+H+ E+ +T G++F Q+ DGSW G+WGVCF Y
Sbjct: 529 TYVECTSAVMQALKYFHKRFPEHRAAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYG 588
Query: 185 TWWAISGLVAAEKTYSN---CLAIRKATDFLLNIQCDDGGWGESYLSCPNKLHMNRIQ 239
TW+ + +TY + C + +A DFLL+ Q DGGWGE + SC + ++ Q
Sbjct: 589 TWFGLEAFACMGQTYRDGTACAEVSRACDFLLSRQMADGGWGEDFESCEERRYLQSAQ 646
>pdb|1W6K|A Chain A, Structure Of Human Osc In Complex With Lanosterol
Length = 732
Score = 189 bits (480), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 91/238 (38%), Positives = 140/238 (58%), Gaps = 5/238 (2%)
Query: 5 LMKAHDFLKNSQVTDNPQGDFRSMFRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLST 64
L KAH+FL+ SQV DNP D++ +R + KGG++FS D G VSDC++E+ L L
Sbjct: 411 LQKAHEFLRLSQVPDNPP-DYQKYYRQMRKGGFSFSTLDCGWIVSDCTAEALKAVLLLQE 469
Query: 65 MPPEIVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPIEFLDEVIIEH 124
P + E + ER DA +L +++ GG +E +ELLNP E +++I++
Sbjct: 470 KCPHVT-EHIPRERLCDAVAVLLNMRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDY 528
Query: 125 DYVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYS 184
YVECT++ ++A+ F K +P+H+ E+ +T G++F Q+ DGSW G+WGVCF Y
Sbjct: 529 TYVECTSAVMQALKYFHKRFPEHRAAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYG 588
Query: 185 TWWAISGLVAAEKTYSN---CLAIRKATDFLLNIQCDDGGWGESYLSCPNKLHMNRIQ 239
TW+ + +TY + C + +A DFLL+ Q DGGWGE + SC + ++ Q
Sbjct: 589 TWFGLEAFACMGQTYRDGTACAEVSRACDFLLSRQMADGGWGEDFESCEERRYVQSAQ 646
>pdb|3SQC|A Chain A, Squalene-Hopene Cyclase
pdb|3SQC|B Chain B, Squalene-Hopene Cyclase
pdb|3SQC|C Chain C, Squalene-Hopene Cyclase
Length = 631
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 59/221 (26%), Positives = 96/221 (43%), Gaps = 19/221 (8%)
Query: 5 LMKAHDFLKNSQVTDNPQGDFRSMFRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLST 64
L+KA ++L + Q+T GD+ ++ GG+ F + P C + V L+
Sbjct: 333 LVKAGEWLLDRQIT--VPGDWAVKRPNLKPGGFAFQFDNVYYP-DVCDTAVVVWALNTLR 389
Query: 65 MPPEIVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPIEFLD-EVIIE 123
+P E+ + +++ +QS GG W + +L N I F D + +
Sbjct: 390 LP----DERRRRDAMTKGFRWIVGMQSSNGG---WGAYDVDNTSDLPNHIPFCDFGEVTD 442
Query: 124 HDYVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIY 183
+ TA L+ F ++ I V++ + QK DGSW+G WGV ++Y
Sbjct: 443 PPSEDVTAHVLECFGSF-------GYDDAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLY 495
Query: 184 STWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGE 224
T +S L A I+KA D++ Q DGGWGE
Sbjct: 496 GTGAVVSALKAVGIDTREPY-IQKALDWVEQHQNPDGGWGE 535
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 42/111 (37%), Gaps = 23/111 (20%)
Query: 129 CTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSW-----------YGTW 177
SALKA+ + + +I + + E Q DG W Y
Sbjct: 499 AVVSALKAVGI----------DTREPYIQKALDWVEQHQNPDGGWGEDCRSYEDPAYAGK 548
Query: 178 GVCFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGESYLS 228
G T WA+ L+A + S A R+ +L+ Q DGGW E Y +
Sbjct: 549 GASTPSQTAWALMALIAGGRAESE--AARRGVQYLVETQRPDGGWDEPYYT 597
>pdb|2SQC|A Chain A, Squalene-Hopene Cyclase From Alicyclobacillus
Acidocaldarius
pdb|2SQC|B Chain B, Squalene-Hopene Cyclase From Alicyclobacillus
Acidocaldarius
Length = 631
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 59/221 (26%), Positives = 96/221 (43%), Gaps = 19/221 (8%)
Query: 5 LMKAHDFLKNSQVTDNPQGDFRSMFRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLST 64
L+KA ++L + Q+T GD+ ++ GG+ F + P C + V L+
Sbjct: 333 LVKAGEWLLDRQIT--VPGDWAVKRPNLKPGGFAFQFDNVYYP-DVCDTAVVVWALNTLR 389
Query: 65 MPPEIVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPIEFLD-EVIIE 123
+P E+ + +++ +QS GG W + +L N I F D + +
Sbjct: 390 LP----DERRRRDAMTKGFRWIVGMQSSNGG---WGAYDVDNTSDLPNHIPFSDFGEVTD 442
Query: 124 HDYVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIY 183
+ TA L+ F ++ I V++ + QK DGSW+G WGV ++Y
Sbjct: 443 PPSEDVTAHVLECFGSF-------GYDDAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLY 495
Query: 184 STWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGE 224
T +S L A I+KA D++ Q DGGWGE
Sbjct: 496 GTGAVVSALKAVGIDTREPY-IQKALDWVEQHQNPDGGWGE 535
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 42/111 (37%), Gaps = 23/111 (20%)
Query: 129 CTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSW-----------YGTW 177
SALKA+ + + +I + + E Q DG W Y
Sbjct: 499 AVVSALKAVGI----------DTREPYIQKALDWVEQHQNPDGGWGEDCRSYEDPAYAGK 548
Query: 178 GVCFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGESYLS 228
G T WA+ L+A + S A R+ +L+ Q DGGW E Y +
Sbjct: 549 GASTPSQTAWALMALIAGGRAESE--AARRGVQYLVETQRPDGGWDEPYYT 597
>pdb|1GSZ|A Chain A, Crystal Structure Of A Squalene Cyclase In Complex With
The Potential Anticholesteremic Drug Ro48-8071
pdb|1GSZ|B Chain B, Crystal Structure Of A Squalene Cyclase In Complex With
The Potential Anticholesteremic Drug Ro48-8071
pdb|1GSZ|C Chain C, Crystal Structure Of A Squalene Cyclase In Complex With
The Potential Anticholesteremic Drug Ro48-8071
pdb|1H35|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H35|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H35|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H36|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H36|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H36|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H37|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H37|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H37|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H39|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H39|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H39|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3A|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3A|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3A|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3B|A Chain A, Squalene-Hopene Cyclase
pdb|1H3B|B Chain B, Squalene-Hopene Cyclase
pdb|1H3B|C Chain C, Squalene-Hopene Cyclase
pdb|1H3C|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3C|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1H3C|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6H|A Chain A, Squalene-Hopene Cyclase
pdb|1O6H|B Chain B, Squalene-Hopene Cyclase
pdb|1O6H|C Chain C, Squalene-Hopene Cyclase
pdb|1O6Q|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6Q|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6Q|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6R|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6R|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O6R|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O79|A Chain A, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O79|B Chain B, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1O79|C Chain C, Structures Of Human Oxidosqualene Cyclase Inhibitors Bound
To A Homolgous Enzyme
pdb|1UMP|A Chain A, Geometry Of Triterpene Conversion To Pentacarbocyclic
Hopene
pdb|1UMP|B Chain B, Geometry Of Triterpene Conversion To Pentacarbocyclic
Hopene
pdb|1UMP|C Chain C, Geometry Of Triterpene Conversion To Pentacarbocyclic
Hopene
pdb|1SQC|A Chain A, Squalene-Hopene-Cyclase From Alicyclobacillus
Acidocaldarius
Length = 631
Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 59/221 (26%), Positives = 98/221 (44%), Gaps = 19/221 (8%)
Query: 5 LMKAHDFLKNSQVTDNPQGDFRSMFRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLST 64
L+KA ++L + Q+T GD+ ++ GG+ F + P D ++ V L+T
Sbjct: 333 LVKAGEWLLDRQIT--VPGDWAVKRPNLKPGGFAFQFDNVYYPDVD---DTAVVVWALNT 387
Query: 65 MPPEIVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPIEFLD-EVIIE 123
+ + E+ + +++ +QS GG W + +L N I F D + +
Sbjct: 388 L--RLPDERRRRDAMTKGFRWIVGMQSSNGG---WGAYDVDNTSDLPNHIPFCDFGEVTD 442
Query: 124 HDYVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIY 183
+ TA L+ F ++ I V++ + QK DGSW+G WGV ++Y
Sbjct: 443 PPSEDVTAHVLECFGSF-------GYDDAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLY 495
Query: 184 STWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGE 224
T +S L A I+KA D++ Q DGGWGE
Sbjct: 496 GTGAVVSALKAVGIDTREPY-IQKALDWVEQHQNPDGGWGE 535
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 42/111 (37%), Gaps = 23/111 (20%)
Query: 129 CTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSW-----------YGTW 177
SALKA+ + + +I + + E Q DG W Y
Sbjct: 499 AVVSALKAVGI----------DTREPYIQKALDWVEQHQNPDGGWGEDCRSYEDPAYAGK 548
Query: 178 GVCFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGESYLS 228
G T WA+ L+A + S A R+ +L+ Q DGGW E Y +
Sbjct: 549 GASTPSQTAWALMALIAGGRAESE--AARRGVQYLVETQRPDGGWDEPYYT 597
>pdb|1DCE|B Chain B, Crystal Structure Of Rab Geranylgeranyltransferase From
Rat Brain
pdb|1DCE|D Chain D, Crystal Structure Of Rab Geranylgeranyltransferase From
Rat Brain
pdb|1LTX|B Chain B, Structure Of Rab Escort Protein-1 In Complex With Rab
Geranylgeranyl Transferase And Isoprenoid
pdb|3C72|B Chain B, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor
pdb|3DSS|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)
pdb|3DST|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Geranylgeranyl Pyrophosphate
pdb|3DSU|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Farnesyl Pyrophosphate
pdb|3DSV|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Mono-Prenylated Peptide Ser-Cys-Ser-Cys(Gg)
Derivated From Rab7
pdb|3DSW|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Mono-Prenylated Peptide Ser-Cys(Gg)-Ser-Cys
Derivated From Rab7
pdb|3DSX|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Di-Prenylated Peptide
Ser-Cys(Gg)-Ser-Cys(Gg) Derivated From Rab7
pdb|3HXB|B Chain B, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (Compound 6)
pdb|3HXC|B Chain B, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (compound 8)
pdb|3HXD|B Chain B, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (Compound 9)
pdb|3HXE|B Chain B, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (compound 37)
pdb|3HXF|B Chain B, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (compound 32)
Length = 331
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 52/104 (50%), Gaps = 12/104 (11%)
Query: 122 IEHD-YVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYG-TWGV 179
I HD ++ T SA++ +TL+ + H N + V + + QK DGS+ G WG
Sbjct: 89 IGHDPHLLYTLSAVQILTLYDSI---HVIN-----VDKVVAYVQSLQKEDGSFAGDIWGE 140
Query: 180 CFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWG 223
++ A++ L K + + + KA +F+L+ DGG+G
Sbjct: 141 IDTRFSFCAVATLALLGKL--DAINVEKAIEFVLSCMNFDGGFG 182
>pdb|3PZ1|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig) In
Complex With Bms3
pdb|3PZ2|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig) In
Complex With Bms3 And Lipid Substrate Ggpp
pdb|3PZ3|B Chain B, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig) In
Complex With Bms-Analogue 14
pdb|4EHM|B Chain B, Rabggtase In Complex With Covalently Bound Psoromic Acid
pdb|4GTS|B Chain B, Engineered Rabggtase In Complex With Bms Analogue 16
pdb|4GTT|B Chain B, Engineered Rabggtase In Complex With Bms Analogue 12
pdb|4GTV|B Chain B, Engineered Rabggtase In Complex With Bms Analogue 13
Length = 330
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 52/104 (50%), Gaps = 12/104 (11%)
Query: 122 IEHD-YVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYG-TWGV 179
I HD ++ T SA++ +TL+ + H N + V + + QK DGS+ G WG
Sbjct: 88 IGHDPHLLYTLSAVQILTLYDSI---HVIN-----VDKVVAYVQSLQKEDGSFAGDIWGE 139
Query: 180 CFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWG 223
++ A++ L K + + + KA +F+L+ DGG+G
Sbjct: 140 IDTRFSFCAVATLALLGKL--DAINVEKAIEFVLSCMNFDGGFG 181
>pdb|3DRA|B Chain B, Candida Albicans Protein Geranylgeranyltransferase-I
Complexed With Ggpp
Length = 390
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 185 TWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDD--GGWGESYLSCPNKLH 234
+WW L + + + + KA D+LLN + GG+G S P+ +H
Sbjct: 298 SWWCTGSLYNIDVNFIKLVDLNKAEDYLLNKTQNQLFGGFGRDPDSTPDPMH 349
>pdb|2YBV|A Chain A, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|C Chain C, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|E Chain E, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|G Chain G, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|I Chain I, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|K Chain K, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|M Chain M, Structure Of Rubisco From Thermosynechococcus Elongatus
pdb|2YBV|O Chain O, Structure Of Rubisco From Thermosynechococcus Elongatus
Length = 475
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 26/138 (18%), Positives = 53/138 (38%), Gaps = 12/138 (8%)
Query: 58 CCLHLSTMPPE---IVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPI 114
CC + +P E + P ++ + + S G + G++ A +L P+
Sbjct: 83 CCYDIEPLPGEDNQFIAYIAYPLDLFEEGSVTNMLTSIVGNVFGFKALKALRLEDLRIPV 142
Query: 115 EFLDE-------VIIEHDYVECTASALKAMTLFQKL--YPKHKKNEVNNFITNGVKFTED 165
+L + +E D + L T+ KL K+ V + G+ FT+D
Sbjct: 143 AYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKD 202
Query: 166 SQKLDGSWYGTWGVCFIY 183
+ ++ + W F++
Sbjct: 203 DENINSQPFQRWRDRFLF 220
>pdb|2FGW|L Chain L, X-Ray Structures Of Fragments From Binding And Nonbinding
Versions Of A Humanized Anti-Cd18 Antibody: Structural
Indications Of The Key Role Of Vh Residues 59 To 65
Length = 214
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFVC--CLHLSTMPPEI-VGEKMEPERFYDAANFMLY------IQ 90
S D+ L +S E F C +T+PP G K+E +R A + ++ ++
Sbjct: 67 SGTDYTLTISSLQPEDFATYYCQQGNTLPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 145 PKHK 148
KHK
Sbjct: 187 EKHK 190
>pdb|3KDM|L Chain L, Crystal Structure Of Human Anti-Steroid Fab 5f2 In Complex
With Testosterone
pdb|3KDM|A Chain A, Crystal Structure Of Human Anti-Steroid Fab 5f2 In Complex
With Testosterone
Length = 218
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 61/146 (41%), Gaps = 18/146 (12%)
Query: 17 VTDNPQGDFRSMFRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEI--VGEKM 74
VT+ P G + F SK G T S GL D + C + ST P + G K+
Sbjct: 53 VTNRPSG-VSNRFSG-SKSGNTASLTISGLQAGD--EADYYCSSYTSTRTPYVFGTGTKV 108
Query: 75 EPERFYDAANFMLY------IQSKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVII 122
E +R A + ++ ++S T + + P A ++ N ++ + E +
Sbjct: 109 EIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVT 168
Query: 123 EHDYVECTASALKAMTLFQKLYPKHK 148
E D + T S +TL + Y KHK
Sbjct: 169 EQDSKDSTYSLSSTLTLSKADYEKHK 194
>pdb|1C5B|L Chain L, Decarboxylase Catalytic Antibody 21d8 Unliganded Form
pdb|1C5C|L Chain L, Decarboxylase Catalytic Antibody 21d8-Hapten Complex
Length = 214
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASFPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLK 126
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 145 PKHK 148
KHK
Sbjct: 187 EKHK 190
>pdb|2HH0|L Chain L, Structure Of An Anti-Prp Fab, P-Clone, In Complex With Its
Cognate Bovine Peptide Epitope
Length = 210
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 52/124 (41%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL T P G K+E +R A + ++ ++
Sbjct: 66 SGSDYSLTISSLESEDFADYYCLQHDTFPLTFGGGTKLEIKRTVAAPSVFIFPPSDEQLK 125
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 126 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 185
Query: 145 PKHK 148
KHK
Sbjct: 186 EKHK 189
>pdb|1B6R|A Chain A, N5-Carboxyaminoimidazole Ribonucleotide Synthetase From E.
Coli
pdb|3ETH|A Chain A, Crystal Structure Of E. Coli Purk In Complex With Mgatp
pdb|3ETH|B Chain B, Crystal Structure Of E. Coli Purk In Complex With Mgatp
pdb|3ETJ|A Chain A, Crystal Structure E. Coli Purk In Complex With Mg, Adp,
And Pi
pdb|3ETJ|B Chain B, Crystal Structure E. Coli Purk In Complex With Mg, Adp,
And Pi
Length = 355
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 26 RSMFRHISKGGWTFSDKDHGLPVSD-CSSESFVCCLHLSTMPPEIVGEKMEPERFYDAAN 84
R + RH + F ++D ++D + + LHL T P +++ E+ E +D
Sbjct: 60 RQLARHPA-----FVNRDVFPIIADRLTQKQLFDKLHLPTAPWQLLAERSEWPAVFDRLG 114
Query: 85 FMLYIQSKTGGITG 98
+ ++ +TGG G
Sbjct: 115 ELAIVKRRTGGYDG 128
>pdb|1B6S|A Chain A, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
pdb|1B6S|B Chain B, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
pdb|1B6S|C Chain C, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
pdb|1B6S|D Chain D, Structure Of N5-Carboxyaminoimidazole Ribonucleotide
Synthetase
Length = 355
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 26 RSMFRHISKGGWTFSDKDHGLPVSD-CSSESFVCCLHLSTMPPEIVGEKMEPERFYDAAN 84
R + RH + F ++D ++D + + LHL T P +++ E+ E +D
Sbjct: 60 RELARHPA-----FVNRDVFPIIADRLTQKQLFDKLHLPTAPWQLLAERSEWPAVFDRLG 114
Query: 85 FMLYIQSKTGGITG 98
+ ++ +TGG G
Sbjct: 115 ELAIVKRRTGGYDG 128
>pdb|1HKL|L Chain L, Free And Liganded Form Of An Esterolytic Catalytic
Antibody
Length = 214
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 145 PKHK 148
KHK
Sbjct: 187 EKHK 190
>pdb|1UM4|L Chain L, Catalytic Antibody 21h3 With Hapten
pdb|1UM5|L Chain L, Catalytic Antibody 21h3 With Alcohol Substrate
pdb|1UM6|L Chain L, Catalytic Antibody 21h3
Length = 219
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 68 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 127
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 128 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 187
Query: 145 PKHK 148
KHK
Sbjct: 188 EKHK 191
>pdb|1GAF|L Chain L, 48g7 Hybridoma Line Fab Complexed With Hapten 5-(Para-
Nitrophenyl Phosphonate)-Pentanoic Acid
Length = 214
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 145 PKHK 148
KHK
Sbjct: 187 EKHK 190
>pdb|2RCS|L Chain L, Immunoglobulin 48g7 Germline Fab-Affinity Maturation Of An
Esterolytic Antibody
Length = 214
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 145 PKHK 148
KHK
Sbjct: 187 EKHK 190
>pdb|1AJ7|L Chain L, Immunoglobulin 48g7 Germline Fab Antibody Complexed With
Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid.
Affinity Maturation Of An Esterolytic Antibody
Length = 214
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 40 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 90
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 91 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 144
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 145 PKHK 148
KHK
Sbjct: 187 EKHK 190
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
0.320 0.136 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,790,230
Number of Sequences: 62578
Number of extensions: 328908
Number of successful extensions: 946
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 905
Number of HSP's gapped (non-prelim): 38
length of query: 239
length of database: 14,973,337
effective HSP length: 96
effective length of query: 143
effective length of database: 8,965,849
effective search space: 1282116407
effective search space used: 1282116407
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)