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= 028222
(212 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 = 166 bits (420), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 78/214 (36%), Positives = 123/214 (57%), Gaps = 4/214 (1%)
Query: 2 FRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEIVGEKMEPERFYDAANFMLY 61
+R + KGG++FS D G VSDC++E+ L L P + E + ER DA +L
Sbjct: 434 YRQMRKGGFSFSTLDCGWIVSDCTAEALKAVLLLQEKCPHVT-EHIPRERLCDAVAVLLN 492
Query: 62 IQSKTGGITGWEPAGAPSWIELLNPIEFLDEVIIEHDYVECTASALKAMTLFQKLYPKHK 121
+++ GG +E +ELLNP E +++I++ YVECT++ ++A+ F K +P+H+
Sbjct: 493 MRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTSAVMQALKYFHKRFPEHR 552
Query: 122 KNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYSTWWAISGLVAAEKTYSN---CLAI 178
E+ +T G++F Q+ DGSW G+WGVCF Y TW+ + +TY + C +
Sbjct: 553 AAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTACAEV 612
Query: 179 RKATDFLLNIQCDDGGWGESYLSCPNKLHMNRIQ 212
+A DFLL+ Q DGGWGE + SC + ++ Q
Sbjct: 613 SRACDFLLSRQMADGGWGEDFESCEERRYLQSAQ 646
>pdb|1W6K|A Chain A, Structure Of Human Osc In Complex With Lanosterol
Length = 732
Score = 165 bits (418), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 78/214 (36%), Positives = 123/214 (57%), Gaps = 4/214 (1%)
Query: 2 FRHISKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEIVGEKMEPERFYDAANFMLY 61
+R + KGG++FS D G VSDC++E+ L L P + E + ER DA +L
Sbjct: 434 YRQMRKGGFSFSTLDCGWIVSDCTAEALKAVLLLQEKCPHVT-EHIPRERLCDAVAVLLN 492
Query: 62 IQSKTGGITGWEPAGAPSWIELLNPIEFLDEVIIEHDYVECTASALKAMTLFQKLYPKHK 121
+++ GG +E +ELLNP E +++I++ YVECT++ ++A+ F K +P+H+
Sbjct: 493 MRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTSAVMQALKYFHKRFPEHR 552
Query: 122 KNEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYSTWWAISGLVAAEKTYSN---CLAI 178
E+ +T G++F Q+ DGSW G+WGVCF Y TW+ + +TY + C +
Sbjct: 553 AAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTACAEV 612
Query: 179 RKATDFLLNIQCDDGGWGESYLSCPNKLHMNRIQ 212
+A DFLL+ Q DGGWGE + SC + ++ Q
Sbjct: 613 SRACDFLLSRQMADGGWGEDFESCEERRYVQSAQ 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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 51/195 (26%), Positives = 82/195 (42%), Gaps = 17/195 (8%)
Query: 4 HISKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEIVGEKMEPERFYDAANFMLYIQ 63
++ GG+ F + P C + V L+ +P E+ + +++ +Q
Sbjct: 357 NLKPGGFAFQFDNVYYP-DVCDTAVVVWALNTLRLP----DERRRRDAMTKGFRWIVGMQ 411
Query: 64 SKTGGITGWEPAGAPSWIELLNPIEFLD-EVIIEHDYVECTASALKAMTLFQKLYPKHKK 122
S GG W + +L N I F D + + + TA L+ F
Sbjct: 412 SSNGG---WGAYDVDNTSDLPNHIPFCDFGEVTDPPSEDVTAHVLECFGSF-------GY 461
Query: 123 NEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYSTWWAISGLVAAEKTYSNCLAIRKAT 182
++ I V++ + QK DGSW+G WGV ++Y T +S L A I+KA
Sbjct: 462 DDAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLYGTGAVVSALKAVGIDTREPY-IQKAL 520
Query: 183 DFLLNIQCDDGGWGE 197
D++ Q DGGWGE
Sbjct: 521 DWVEQHQNPDGGWGE 535
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 42/111 (37%), Gaps = 23/111 (20%)
Query: 102 CTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSW-----------YGTW 150
SALKA+ + + +I + + E Q DG W Y
Sbjct: 499 AVVSALKAVGI----------DTREPYIQKALDWVEQHQNPDGGWGEDCRSYEDPAYAGK 548
Query: 151 GVCFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGESYLS 201
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 = 53.5 bits (127), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 51/195 (26%), Positives = 82/195 (42%), Gaps = 17/195 (8%)
Query: 4 HISKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEIVGEKMEPERFYDAANFMLYIQ 63
++ GG+ F + P C + V L+ +P E+ + +++ +Q
Sbjct: 357 NLKPGGFAFQFDNVYYP-DVCDTAVVVWALNTLRLP----DERRRRDAMTKGFRWIVGMQ 411
Query: 64 SKTGGITGWEPAGAPSWIELLNPIEFLD-EVIIEHDYVECTASALKAMTLFQKLYPKHKK 122
S GG W + +L N I F D + + + TA L+ F
Sbjct: 412 SSNGG---WGAYDVDNTSDLPNHIPFSDFGEVTDPPSEDVTAHVLECFGSF-------GY 461
Query: 123 NEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYSTWWAISGLVAAEKTYSNCLAIRKAT 182
++ I V++ + QK DGSW+G WGV ++Y T +S L A I+KA
Sbjct: 462 DDAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLYGTGAVVSALKAVGIDTREPY-IQKAL 520
Query: 183 DFLLNIQCDDGGWGE 197
D++ Q DGGWGE
Sbjct: 521 DWVEQHQNPDGGWGE 535
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 42/111 (37%), Gaps = 23/111 (20%)
Query: 102 CTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSW-----------YGTW 150
SALKA+ + + +I + + E Q DG W Y
Sbjct: 499 AVVSALKAVGI----------DTREPYIQKALDWVEQHQNPDGGWGEDCRSYEDPAYAGK 548
Query: 151 GVCFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGESYLS 201
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 = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 51/195 (26%), Positives = 84/195 (43%), Gaps = 17/195 (8%)
Query: 4 HISKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEIVGEKMEPERFYDAANFMLYIQ 63
++ GG+ F + P D ++ V L+T+ + E+ + +++ +Q
Sbjct: 357 NLKPGGFAFQFDNVYYPDVD---DTAVVVWALNTL--RLPDERRRRDAMTKGFRWIVGMQ 411
Query: 64 SKTGGITGWEPAGAPSWIELLNPIEFLD-EVIIEHDYVECTASALKAMTLFQKLYPKHKK 122
S GG W + +L N I F D + + + TA L+ F
Sbjct: 412 SSNGG---WGAYDVDNTSDLPNHIPFCDFGEVTDPPSEDVTAHVLECFGSF-------GY 461
Query: 123 NEVNNFITNGVKFTEDSQKLDGSWYGTWGVCFIYSTWWAISGLVAAEKTYSNCLAIRKAT 182
++ I V++ + QK DGSW+G WGV ++Y T +S L A I+KA
Sbjct: 462 DDAWKVIRRAVEYLKREQKPDGSWFGRWGVNYLYGTGAVVSALKAVGIDTREPY-IQKAL 520
Query: 183 DFLLNIQCDDGGWGE 197
D++ Q DGGWGE
Sbjct: 521 DWVEQHQNPDGGWGE 535
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 42/111 (37%), Gaps = 23/111 (20%)
Query: 102 CTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSW-----------YGTW 150
SALKA+ + + +I + + E Q DG W Y
Sbjct: 499 AVVSALKAVGI----------DTREPYIQKALDWVEQHQNPDGGWGEDCRSYEDPAYAGK 548
Query: 151 GVCFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWGESYLS 201
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 = 0.11, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 52/104 (50%), Gaps = 12/104 (11%)
Query: 95 IEHD-YVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYG-TWGV 152
I HD ++ T SA++ +TL+ + H N + V + + QK DGS+ G WG
Sbjct: 89 IGHDPHLLYTLSAVQILTLYDSI---HVIN-----VDKVVAYVQSLQKEDGSFAGDIWGE 140
Query: 153 CFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWG 196
++ 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 = 0.12, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 52/104 (50%), Gaps = 12/104 (11%)
Query: 95 IEHD-YVECTASALKAMTLFQKLYPKHKKNEVNNFITNGVKFTEDSQKLDGSWYG-TWGV 152
I HD ++ T SA++ +TL+ + H N + V + + QK DGS+ G WG
Sbjct: 88 IGHDPHLLYTLSAVQILTLYDSI---HVIN-----VDKVVAYVQSLQKEDGSFAGDIWGE 139
Query: 153 CFIYSTWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDDGGWG 196
++ 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 = 1.1, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 158 TWWAISGLVAAEKTYSNCLAIRKATDFLLNIQCDD--GGWGESYLSCPNKLH 207
+WW L + + + + KA D+LLN + GG+G S P+ +H
Sbjct: 298 SWWCTGSLYNIDVNFIKLVDLNKAEDYLLNKTQNQLFGGFGRDPDSTPDPMH 349
>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 = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFVC--CLHLSTMPPEI-VGEKMEPERFYDAANFMLY------IQ 63
S D+ L +S E F C +T+PP G K+E +R A + ++ ++
Sbjct: 67 SGTDYTLTISSLQPEDFATYYCQQGNTLPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 118 PKHK 121
KHK
Sbjct: 187 EKHK 190
>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 = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 26/138 (18%), Positives = 53/138 (38%), Gaps = 12/138 (8%)
Query: 31 CCLHLSTMPPE---IVGEKMEPERFYDAANFMLYIQSKTGGITGWEPAGAPSWIELLNPI 87
CC + +P E + P ++ + + S G + G++ A +L P+
Sbjct: 83 CCYDIEPLPGEDNQFIAYIAYPLDLFEEGSVTNMLTSIVGNVFGFKALKALRLEDLRIPV 142
Query: 88 EFLDE-------VIIEHDYVECTASALKAMTLFQKL--YPKHKKNEVNNFITNGVKFTED 138
+L + +E D + L T+ KL K+ V + G+ FT+D
Sbjct: 143 AYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKD 202
Query: 139 SQKLDGSWYGTWGVCFIY 156
+ ++ + W F++
Sbjct: 203 DENINSQPFQRWRDRFLF 220
>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 = 4.1, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASFPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLK 126
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 118 PKHK 121
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 = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 52/124 (41%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL T P G K+E +R A + ++ ++
Sbjct: 66 SGSDYSLTISSLESEDFADYYCLQHDTFPLTFGGGTKLEIKRTVAAPSVFIFPPSDEQLK 125
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 126 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 185
Query: 118 PKHK 121
KHK
Sbjct: 186 EKHK 189
>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 = 5.9, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 68 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 127
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 128 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 187
Query: 118 PKHK 121
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 = 6.8, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 118 PKHK 121
KHK
Sbjct: 187 EKHK 190
>pdb|1HKL|L Chain L, Free And Liganded Form Of An Esterolytic Catalytic
Antibody
Length = 214
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 118 PKHK 121
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 = 7.1, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 118 PKHK 121
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 = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV--CCLHLSTMPPEIVG-EKMEPERFYDAANFMLY------IQ 63
S D+ L +S SE F CL ++ P G K+E +R A + ++ ++
Sbjct: 67 SGSDYSLTISSLESEDFADYYCLQYASYPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLK 126
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 127 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 186
Query: 118 PKHK 121
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 = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 33/130 (25%), Positives = 54/130 (41%), Gaps = 16/130 (12%)
Query: 6 SKGGWTFSDKDHGLPVSDCSSESFVCCLHLSTMPPEI--VGEKMEPERFYDAANFMLY-- 61
SK G T S GL D + C + ST P + G K+E +R A + ++
Sbjct: 67 SKSGNTASLTISGLQAGD--EADYYCSSYTSTRTPYVFGTGTKVEIKRTVAAPSVFIFPP 124
Query: 62 ----IQSKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMT 111
++S T + + P A ++ N ++ + E + E D + T S +T
Sbjct: 125 SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT 184
Query: 112 LFQKLYPKHK 121
L + Y KHK
Sbjct: 185 LSKADYEKHK 194
>pdb|3BDY|L Chain L, Dual Specific Bh1 Fab In Complex With Vegf
pdb|3BE1|L Chain L, Dual Specific Bh1 Fab In Complex With The Extracellular
Domain Of Her2ERBB-2
Length = 218
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 15/124 (12%)
Query: 13 SDKDHGLPVSDCSSESFV---CCLHLSTMPPEIVGEKMEPERFYDAANFMLY------IQ 63
S D L +S E F C H +T P G K+E +R A + ++ ++
Sbjct: 71 SGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLK 130
Query: 64 SKTGGIT----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLY 117
S T + + P A ++ N ++ + E + E D + T S +TL + Y
Sbjct: 131 SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY 190
Query: 118 PKHK 121
KHK
Sbjct: 191 EKHK 194
>pdb|2JIX|A Chain A, Crystal Structure Of Abt-007 Fab Fragment With The Soluble
Domain Of Epo Receptor
pdb|2JIX|G Chain G, Crystal Structure Of Abt-007 Fab Fragment With The Soluble
Domain Of Epo Receptor
pdb|2JIX|L Chain L, Crystal Structure Of Abt-007 Fab Fragment With The Soluble
Domain Of Epo Receptor
Length = 214
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 30/118 (25%), Positives = 50/118 (42%), Gaps = 15/118 (12%)
Query: 19 LPVSDCSSESFVC--CLHLSTMPPEI-VGEKMEPERFYDAANFMLY------IQSKTGGI 69
L +S E F CL +T PP G K+E +R A + ++ ++S T +
Sbjct: 73 LTISSLQPEDFATYYCLQHNTYPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASV 132
Query: 70 T----GWEPAGAPSWIELLNPIEFLD--EVIIEHDYVECTASALKAMTLFQKLYPKHK 121
+ P A ++ N ++ + E + E D + T S +TL + Y KHK
Sbjct: 133 VCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHK 190
>pdb|1FVD|A Chain A, X-Ray Structures Of The Antigen-Binding Domains From Three
Variants Of Humanized Anti-P185-Her2 Antibody 4d5 And
Comparison With Molecular Modeling
pdb|1FVD|C Chain C, X-Ray Structures Of The Antigen-Binding Domains From Three
Variants Of Humanized Anti-P185-Her2 Antibody 4d5 And
Comparison With Molecular Modeling
pdb|1FVE|A Chain A, X-Ray Structures Of The Antigen-Binding Domains From Three
Variants Of Humanized Anti-P185-Her2 Antibody 4d5 And
Comparison With Molecular Modeling
pdb|1FVE|C Chain C, X-Ray Structures Of The Antigen-Binding Domains From Three
Variants Of Humanized Anti-P185-Her2 Antibody 4d5 And
Comparison With Molecular Modeling
Length = 214
Score = 26.6 bits (57), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 15/131 (11%)
Query: 6 SKGGWTFSDKDHGLPVSDCSSESFV---CCLHLSTMPPEIVGEKMEPERFYDAANFMLY- 61
S+ + S D L +S E F C H +T P G K+E +R A + ++
Sbjct: 60 SRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFP 119
Query: 62 -----IQSKTGGIT----GWEPAGAPSWIELLNPIEF--LDEVIIEHDYVECTASALKAM 110
++S T + + P A ++ N ++ E + E D + T S +
Sbjct: 120 PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL 179
Query: 111 TLFQKLYPKHK 121
TL + Y KHK
Sbjct: 180 TLSKADYEKHK 190
>pdb|1N8Z|A Chain A, Crystal Structure Of Extracellular Domain Of Human Her2
Complexed With Herceptin Fab
Length = 214
Score = 26.6 bits (57), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 15/131 (11%)
Query: 6 SKGGWTFSDKDHGLPVSDCSSESFV---CCLHLSTMPPEIVGEKMEPERFYDAANFMLY- 61
S+ + S D L +S E F C H +T P G K+E +R A + ++
Sbjct: 60 SRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFP 119
Query: 62 -----IQSKTGGIT----GWEPAGAPSWIELLNPIEF--LDEVIIEHDYVECTASALKAM 110
++S T + + P A ++ N ++ E + E D + T S +
Sbjct: 120 PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL 179
Query: 111 TLFQKLYPKHK 121
TL + Y KHK
Sbjct: 180 TLSKADYEKHK 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 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,959,025
Number of Sequences: 62578
Number of extensions: 289164
Number of successful extensions: 863
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: 824
Number of HSP's gapped (non-prelim): 38
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
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: 49 (23.5 bits)