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= psy4310
(203 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J37|W Chain W, Model Of Mammalian Srp Bound To 80s Rncs
Length = 504
Score = 311 bits (797), Expect = 2e-85, Method: Compositional matrix adjust.
Identities = 148/187 (79%), Positives = 170/187 (90%)
Query: 16 PLYCGICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQI 75
P + MGDIEGLIDKVNELKLDDNE LIEK+KHGQFTLRDMYEQFQNIMKMGPFSQI
Sbjct: 289 PFISKLLGMGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQI 348
Query: 76 MGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQ 135
+GMIPGF DF+SKG+EQESMARLK+LMTIMDSMND ELD+ DGAK+FSKQ GRI RVA+
Sbjct: 349 LGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVAR 408
Query: 136 GAGVTEKEVKDLISQYTKFAAVVKKMGGIKGLFKGGDITKNVNQTQMMKLNQQMAKMMDP 195
G+GV+ ++V++L++QYTKFA +VKKMGGIKGLFKGGD++KNV+Q+QM KLNQQMAKMMDP
Sbjct: 409 GSGVSTRDVQELLTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDP 468
Query: 196 RVLHQMG 202
RVLH MG
Sbjct: 469 RVLHHMG 475
>pdb|1MFQ|C Chain C, Crystal Structure Analysis Of A Ternary S-Domain Complex
Of Human Signal Recognition Particle
Length = 129
Score = 196 bits (498), Expect = 7e-51, Method: Compositional matrix adjust.
Identities = 93/117 (79%), Positives = 109/117 (93%)
Query: 52 GQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMND 111
GQFTLRDMYEQFQNIMKMGPFSQI+GMIPGF DF+SKG+EQESMARLK+LMTIMDSMND
Sbjct: 13 GQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMND 72
Query: 112 GELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMGGIKGLF 168
ELD+ DGAK+FSKQ GRI RVA+G+GV+ ++V++L++QYTKFA +VKKMGGIKGLF
Sbjct: 73 QELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKMGGIKGLF 129
>pdb|1QB2|A Chain A, Crystal Structure Of The Conserved Subdomain Of Human
Protein Srp54m At 2.1a Resolution: Evidence For The
Mechanism Of Signal Peptide Binding
pdb|1QB2|B Chain B, Crystal Structure Of The Conserved Subdomain Of Human
Protein Srp54m At 2.1a Resolution: Evidence For The
Mechanism Of Signal Peptide Binding
pdb|1RY1|W Chain W, Structure Of The Signal Recognition Particle Interacting
With The Elongation-Arrested Ribosome
pdb|2GO5|W Chain W, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
Length = 109
Score = 181 bits (458), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 85/109 (77%), Positives = 101/109 (92%)
Query: 53 QFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDG 112
QFTLRDMYEQFQNIMKMGPFSQI+GMIPGF DF+SKG+EQESMARLK+LMTIMDSMND
Sbjct: 1 QFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQ 60
Query: 113 ELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKM 161
ELD+ DGAK+FSKQ GRI RVA+G+GV+ ++V++L++QYTKFA +VKKM
Sbjct: 61 ELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKM 109
>pdb|3DM5|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins Assembling
The Ribonucleic Core Of The Signal Recognition Particle
From The Archaeon Pyrococcus Furiosus.
pdb|3DM5|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins Assembling
The Ribonucleic Core Of The Signal Recognition Particle
From The Archaeon Pyrococcus Furiosus
Length = 443
Score = 97.4 bits (241), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 59/147 (40%), Positives = 86/147 (58%), Gaps = 16/147 (10%)
Query: 21 ICCMGDIEGLIDKVNELK--LDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGM 78
+ +GDI+GL++K EL+ ++ EE IE+ G+FTL+DMY Q + + KMGP QI+ M
Sbjct: 293 LLGLGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRM 352
Query: 79 IPG----FSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVA 134
IPG D +S G E RLK+ IMDSM + EL N + RI R+A
Sbjct: 353 IPGLGYSLPDDVISIGEE-----RLKKFKVIMDSMTEEELLNPEII-----NYSRIKRIA 402
Query: 135 QGAGVTEKEVKDLISQYTKFAAVVKKM 161
+G+G + K+VK+L+ QY + + K M
Sbjct: 403 RGSGTSTKDVKELLDQYRQMKKLFKSM 429
>pdb|2V3C|C Chain C, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
pdb|2V3C|D Chain D, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
Length = 432
Score = 74.7 bits (182), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 44/141 (31%), Positives = 77/141 (54%), Gaps = 6/141 (4%)
Query: 21 ICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIP 80
+ MGD+E L++K ++ + EE I+ I G+FTL ++ Q + I MG +I+ MIP
Sbjct: 292 LLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIP 351
Query: 81 GFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVT 140
GF + K + A++K+ I+ SM E R+ K+ + RI R+A+G+G T
Sbjct: 352 GFG-GAMPKELSHLTEAKIKKYKVIISSMTKEE---RENPKII--KASRIRRIARGSGTT 405
Query: 141 EKEVKDLISQYTKFAAVVKKM 161
E +V++++ Y + K+
Sbjct: 406 ENDVREVLRYYETTKNAIDKL 426
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 74.7 bits (182), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 44/141 (31%), Positives = 77/141 (54%), Gaps = 6/141 (4%)
Query: 21 ICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIP 80
+ MGD+E L++K ++ + EE I+ I G+FTL ++ Q + I MG +I+ MIP
Sbjct: 292 LLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIP 351
Query: 81 GFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVT 140
GF + K + A++K+ I+ SM E R+ K+ + RI R+A+G+G T
Sbjct: 352 GFG-GAMPKELSHLTEAKIKKYKVIISSMTKEE---RENPKII--KASRIRRIARGSGTT 405
Query: 141 EKEVKDLISQYTKFAAVVKKM 161
E +V++++ Y + K+
Sbjct: 406 ENDVREVLRYYETTKNAIDKL 426
>pdb|2FFH|A Chain A, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
pdb|2FFH|B Chain B, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
pdb|2FFH|C Chain C, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
Length = 425
Score = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 44/146 (30%), Positives = 74/146 (50%), Gaps = 15/146 (10%)
Query: 21 ICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIP 80
I MGD+ L +KV L+ K + +L D +Q QN+ ++GPFS+I+G++P
Sbjct: 291 ILGMGDVASLAEKVRAAGLEAEAPKSAK----ELSLEDFLKQMQNLKRLGPFSEILGLLP 346
Query: 81 GFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVT 140
G Q K E+ +KRL I+ SM + R ++ + R R+A+G+G +
Sbjct: 347 GVPQGL--KVDEKA----IKRLEAIVLSMTP---EERKDPRILN--GSRRKRIAKGSGTS 395
Query: 141 EKEVKDLISQYTKFAAVVKKMGGIKG 166
+EV I + + A++K + KG
Sbjct: 396 VQEVNRFIKAFEEMKALMKSLEKKKG 421
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 44/130 (33%), Positives = 71/130 (54%), Gaps = 24/130 (18%)
Query: 21 ICCMGDIEGLIDKVNELKLDDN-----EELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQI 75
I MGDIE +++KV L+ D E+++E G+ TLRD+Y Q + KMGP S++
Sbjct: 291 ILGMGDIESILEKVKGLEEYDKIQKKMEDVMEG--KGKLTLRDVYAQIIALRKMGPLSKV 348
Query: 76 MGMIPGF-------SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTG 128
+ IPG S+D L G E +++R + ++SM EL+N + + K
Sbjct: 349 LQHIPGLGIMLPTPSEDQLKIGEE-----KIRRWLAALNSMTYKELENPN---IIDKS-- 398
Query: 129 RITRVAQGAG 138
R+ R+A+G+G
Sbjct: 399 RMRRIAEGSG 408
>pdb|1QZW|A Chain A, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZW|C Chain C, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZW|E Chain E, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZW|G Chain G, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZX|A Chain A, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
pdb|1QZX|B Chain B, Crystal Structure Of The Complete Core Of Archaeal Srp And
Implications For Inter-Domain Communication
Length = 440
Score = 61.2 bits (147), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 44/130 (33%), Positives = 71/130 (54%), Gaps = 24/130 (18%)
Query: 21 ICCMGDIEGLIDKVNELKLDDN-----EELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQI 75
I MGDIE +++KV L+ D E+++E G+ TLRD+Y Q + KMGP S++
Sbjct: 299 ILGMGDIESILEKVKGLEEYDKIQKKMEDVMEG--KGKLTLRDVYAQIIALRKMGPLSKV 356
Query: 76 MGMIPGF-------SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTG 128
+ IPG S+D L G E +++R + ++SM EL+N + + K
Sbjct: 357 LQHIPGLGIMLPTPSEDQLKIGEE-----KIRRWLAALNSMTYKELENPN---IIDKS-- 406
Query: 129 RITRVAQGAG 138
R+ R+A+G+G
Sbjct: 407 RMRRIAEGSG 416
>pdb|3KL4|A Chain A, Recognition Of A Signal Peptide By The Signal Recognition
Particle
Length = 433
Score = 61.2 bits (147), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 44/130 (33%), Positives = 71/130 (54%), Gaps = 24/130 (18%)
Query: 21 ICCMGDIEGLIDKVNELKLDDN-----EELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQI 75
I MGDIE +++KV L+ D E+++E G+ TLRD+Y Q + KMGP S++
Sbjct: 292 ILGMGDIESILEKVKGLEEYDKIQKKMEDVMEG--KGKLTLRDVYAQIIALRKMGPLSKV 349
Query: 76 MGMIPGF-------SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTG 128
+ IPG S+D L G E +++R + ++SM EL+N + + K
Sbjct: 350 LQHIPGLGIMLPTPSEDQLKIGEE-----KIRRWLAALNSMTYKELENPN---IIDKS-- 399
Query: 129 RITRVAQGAG 138
R+ R+A+G+G
Sbjct: 400 RMRRIAEGSG 409
>pdb|2JQE|A Chain A, Soution Structure Of Af54 M-Domain
Length = 119
Score = 60.1 bits (144), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 40/106 (37%), Positives = 60/106 (56%), Gaps = 11/106 (10%)
Query: 49 IKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIP---GFSQDFLSKGSEQESMARLKRLMTI 105
++ G FTL+D+Y+Q + + KMGP +I M+P G D QE M K+ I
Sbjct: 5 MEKGTFTLKDIYKQIEAMNKMGPVRKIFEMLPFGLGLKVDNDVMEMTQEKM---KKFRVI 61
Query: 106 MDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQY 151
MDSM + EL N K+ + RI R+A G+G + +EVK+L++ Y
Sbjct: 62 MDSMTEEELLN---PKIID--SSRIRRIAIGSGTSPQEVKELLNYY 102
>pdb|2J28|9 Chain 9, Model Of E. Coli Srp Bound To 70s Rncs
Length = 430
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 45/148 (30%), Positives = 74/148 (50%), Gaps = 10/148 (6%)
Query: 17 LYCGICCMGDIEGLIDKVNELKLD--DNEELIEKIKHGQ-FTLRDMYEQFQNIMKMGPFS 73
+ I MGD+ LI+ + E K+D E+L K+K G F L D EQ + + MG +
Sbjct: 289 IASRILGMGDVLSLIEDI-ESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMA 347
Query: 74 QIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRV 133
+MG +PG Q + S+ + L R+ I++SM ++ AK + R R+
Sbjct: 348 SLMGKLPGMGQIPDNVKSQMDDKV-LVRMEAIINSMT-----MKERAKPEIIKGSRKRRI 401
Query: 134 AQGAGVTEKEVKDLISQYTKFAAVVKKM 161
A G G+ ++V L+ Q+ ++KKM
Sbjct: 402 AAGCGMQVQDVNRLLKQFDDMQRMMKKM 429
>pdb|2XXA|A Chain A, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
pdb|2XXA|C Chain C, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
Length = 433
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 42/138 (30%), Positives = 70/138 (50%), Gaps = 10/138 (7%)
Query: 17 LYCGICCMGDIEGLIDKVNELKLD--DNEELIEKIKHGQ-FTLRDMYEQFQNIMKMGPFS 73
+ I MGD+ LI+ + E K+D E+L K+K G F L D EQ + + MG +
Sbjct: 290 IASRILGMGDVLSLIEDI-ESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMA 348
Query: 74 QIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRV 133
+MG +PG Q + S+ + L R+ I++SM ++ AK + R R+
Sbjct: 349 SLMGKLPGMGQIPDNVKSQMDDKV-LVRMEAIINSMT-----MKERAKPEIIKGSRKRRI 402
Query: 134 AQGAGVTEKEVKDLISQY 151
A G+G+ ++V L+ Q+
Sbjct: 403 AAGSGMQVQDVNRLLKQF 420
>pdb|1HQ1|A Chain A, Structural And Energetic Analysis Of Rna Recognition By A
Universally Conserved Protein From The Signal
Recognition Particle
Length = 105
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 49/98 (50%), Gaps = 6/98 (6%)
Query: 54 FTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGE 113
F L D EQ + + MG + +MG +PG Q + S+ + L R+ I++SM
Sbjct: 2 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKV-LVRMEAIINSMT--- 57
Query: 114 LDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQY 151
++ AK + R R+A G+G+ ++V L+ Q+
Sbjct: 58 --MKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQF 93
>pdb|1WIK|A Chain A, Solution Structure Of The Picot Homology 2 Domain Of The
Mouse Pkc-Interacting Cousin Of Thioredoxin Protein
Length = 109
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 9 LCHYLNFPLYCGICCMGDIEGLIDKVNELKLDDNEELIEKIK 50
L + N+P Y + GD+ G +D V ELK DN EL+ +K
Sbjct: 62 LKTFSNWPTYPQLYVRGDLVGGLDIVKELK--DNGELLPILK 101
>pdb|3MW9|A Chain A, Bovine Glutamate Dehydrogenase Complexed With Nadh, Gtp,
Glu
pdb|3MW9|B Chain B, Bovine Glutamate Dehydrogenase Complexed With Nadh, Gtp,
Glu
pdb|3MW9|C Chain C, Bovine Glutamate Dehydrogenase Complexed With Nadh, Gtp,
Glu
pdb|3MW9|D Chain D, Bovine Glutamate Dehydrogenase Complexed With Nadh, Gtp,
Glu
pdb|3MW9|E Chain E, Bovine Glutamate Dehydrogenase Complexed With Nadh, Gtp,
Glu
pdb|3MW9|F Chain F, Bovine Glutamate Dehydrogenase Complexed With Nadh, Gtp,
Glu
pdb|3MVO|A Chain A, Crystal Structure Of Bovine Glutamate Dehydrogenase
Complexed With Eu3+
pdb|3MVO|B Chain B, Crystal Structure Of Bovine Glutamate Dehydrogenase
Complexed With Eu3+
pdb|3MVO|C Chain C, Crystal Structure Of Bovine Glutamate Dehydrogenase
Complexed With Eu3+
pdb|3MVO|D Chain D, Crystal Structure Of Bovine Glutamate Dehydrogenase
Complexed With Eu3+
pdb|3MVO|E Chain E, Crystal Structure Of Bovine Glutamate Dehydrogenase
Complexed With Eu3+
pdb|3MVO|F Chain F, Crystal Structure Of Bovine Glutamate Dehydrogenase
Complexed With Eu3+
pdb|3MVQ|A Chain A, Bovine Glutamate Dehydrogenase Complexed With Zinc
pdb|3MVQ|B Chain B, Bovine Glutamate Dehydrogenase Complexed With Zinc
pdb|3MVQ|C Chain C, Bovine Glutamate Dehydrogenase Complexed With Zinc
pdb|3MVQ|D Chain D, Bovine Glutamate Dehydrogenase Complexed With Zinc
pdb|3MVQ|E Chain E, Bovine Glutamate Dehydrogenase Complexed With Zinc
pdb|3MVQ|F Chain F, Bovine Glutamate Dehydrogenase Complexed With Zinc
pdb|3QMU|A Chain A, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|B Chain B, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|C Chain C, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|D Chain D, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|E Chain E, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|F Chain F, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|G Chain G, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|H Chain H, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|I Chain I, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|J Chain J, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|K Chain K, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
pdb|3QMU|L Chain L, Bovine Glutamate Dehydrogenase Complexed With
Epicatechin-3-Gallate (Ecg)
Length = 501
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 12/79 (15%)
Query: 51 HGQF--TLRDMYEQFQNIMKMGPFSQIMGMIPGF-SQDFLSKGSEQ---ESMARLKRL-- 102
HG+ T R ++ +N + + I+GM PGF + F+ +G SM L R
Sbjct: 209 HGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGA 268
Query: 103 --MTIMDSMNDGELDNRDG 119
+T+ +S DG + N DG
Sbjct: 269 KCITVGES--DGSIWNPDG 285
>pdb|1EZJ|A Chain A, Crystal Structure Of The Multimerization Domain Of The
Phosphoprotein From Sendai Virus
Length = 115
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 28/43 (65%), Gaps = 3/43 (6%)
Query: 29 GLI---DKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMK 68
GLI +K + K+D+N++L+++I+ + RD+Y++F K
Sbjct: 55 GLILSAEKSSARKVDENKQLLKQIQESVESFRDIYKRFSEYQK 97
>pdb|3VGP|A Chain A, Crystal Structure Of The C-Terminal Globular Domain Of
Oligosaccharyltransferase (Af_0329) From Archaeoglobus
Fulgidus
Length = 164
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 6/92 (6%)
Query: 118 DGAKLFS-KQTGRITRVAQGAGV----TEKEVKDLISQYTKFAAVVKKMGGIKGLFKGGD 172
D AK F+ K ++A+ GV T E+ + TKF A+ + G L G+
Sbjct: 64 DAAKFFTAKSEDEAIKIAKKRGVRYVVTADEITXKDANNTKFPAIXRIAGYNVDLXTEGE 123
Query: 173 ITKNVNQTQMMKLNQQMAK-MMDPRVLHQMGE 203
I N T + +L+ + A+ + R++ + G+
Sbjct: 124 ILNFFNHTVLYRLHXENAENLTHFRLVKEFGD 155
>pdb|2BYK|A Chain A, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYK|C Chain C, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYM|A Chain A, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYM|C Chain C, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
Length = 140
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 47/108 (43%), Gaps = 3/108 (2%)
Query: 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEK 142
SQ + + E+ L R+ TIM S D L + L +K T R GA TE+
Sbjct: 6 SQPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEE 65
Query: 143 --EVKDLISQYTKFAAVVKKMGGIKGLFKGGDITKNVNQTQ-MMKLNQ 187
+ +Y + VV K ++ L + V+Q Q M++LN+
Sbjct: 66 FGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKIRVHQFQEMLRLNR 113
>pdb|1NR1|A Chain A, Crystal Structure Of The R463a Mutant Of Human Glutamate
Dehydrogenase
pdb|1NR1|B Chain B, Crystal Structure Of The R463a Mutant Of Human Glutamate
Dehydrogenase
pdb|1NR1|C Chain C, Crystal Structure Of The R463a Mutant Of Human Glutamate
Dehydrogenase
pdb|1NR1|D Chain D, Crystal Structure Of The R463a Mutant Of Human Glutamate
Dehydrogenase
pdb|1NR1|E Chain E, Crystal Structure Of The R463a Mutant Of Human Glutamate
Dehydrogenase
pdb|1NR1|F Chain F, Crystal Structure Of The R463a Mutant Of Human Glutamate
Dehydrogenase
Length = 496
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 51 HGQF--TLRDMYEQFQNIMKMGPFSQIMGMIPGFS-QDFLSKGSEQ---ESMARLKRLMT 104
HG+ T R ++ +N + + I+GM PGF + F+ +G SM L R
Sbjct: 204 HGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGA 263
Query: 105 --IMDSMNDGELDNRDG 119
I +DG + N DG
Sbjct: 264 KCIAVGESDGSIWNPDG 280
>pdb|1NQT|A Chain A, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|B Chain B, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|C Chain C, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|D Chain D, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|E Chain E, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|F Chain F, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|G Chain G, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|H Chain H, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|I Chain I, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|J Chain J, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|K Chain K, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NQT|L Chain L, Crystal Structure Of Bovine Glutamate Dehydrogenase-adp
Complex
pdb|1NR7|A Chain A, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|B Chain B, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|C Chain C, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|D Chain D, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|E Chain E, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|F Chain F, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|G Chain G, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|H Chain H, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|I Chain I, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|J Chain J, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|K Chain K, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
pdb|1NR7|L Chain L, Crystal Structure Of Apo Bovine Glutamate Dehydrogenase
Length = 496
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 51 HGQF--TLRDMYEQFQNIMKMGPFSQIMGMIPGFS-QDFLSKGSEQ---ESMARLKRLMT 104
HG+ T R ++ +N + + I+GM PGF + F+ +G SM L R
Sbjct: 204 HGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGA 263
Query: 105 --IMDSMNDGELDNRDG 119
I +DG + N DG
Sbjct: 264 KCIAVGESDGSIWNPDG 280
>pdb|1SQJ|A Chain A, Crystal Structure Analysis Of Oligoxyloglucan
Reducing-End- Specific Cellobiohydrolase (Oxg-Rcbh)
pdb|1SQJ|B Chain B, Crystal Structure Analysis Of Oligoxyloglucan
Reducing-End- Specific Cellobiohydrolase (Oxg-Rcbh)
Length = 789
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 25/60 (41%)
Query: 80 PGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGV 139
P +S D+ S + + + D + DG DG K F G + A+GAG+
Sbjct: 571 PWYSHDYGKTWSVPAGDLKAQTANVLSDKVQDGTFYATDGGKFFVSTDGGKSYAAKGAGL 630
>pdb|2EBS|A Chain A, Crystal Structure Anaalysis Of Oligoxyloglucan
Reducing-End- Specific Cellobiohydrolase (Oxg-Rcbh)
D465n Mutant Complexed With A Xyloglucan Heptasaccharide
pdb|2EBS|B Chain B, Crystal Structure Anaalysis Of Oligoxyloglucan
Reducing-End- Specific Cellobiohydrolase (Oxg-Rcbh)
D465n Mutant Complexed With A Xyloglucan Heptasaccharide
Length = 789
Score = 28.5 bits (62), Expect = 2.5, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 25/60 (41%)
Query: 80 PGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGV 139
P +S D+ S + + + D + DG DG K F G + A+GAG+
Sbjct: 571 PWYSHDYGKTWSVPAGDLKAQTANVLSDKVQDGTFYATDGGKFFVSTDGGKSYAAKGAGL 630
>pdb|1L1F|A Chain A, Structure Of Human Glutamate Dehydrogenase-Apo Form
pdb|1L1F|B Chain B, Structure Of Human Glutamate Dehydrogenase-Apo Form
pdb|1L1F|C Chain C, Structure Of Human Glutamate Dehydrogenase-Apo Form
pdb|1L1F|D Chain D, Structure Of Human Glutamate Dehydrogenase-Apo Form
pdb|1L1F|E Chain E, Structure Of Human Glutamate Dehydrogenase-Apo Form
pdb|1L1F|F Chain F, Structure Of Human Glutamate Dehydrogenase-Apo Form
Length = 505
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 51 HGQF--TLRDMYEQFQNIMKMGPFSQIMGMIPGF-SQDFLSKGSEQ---ESMARLKRLMT 104
HG+ T R ++ +N + + I+GM PGF + F+ +G SM L R
Sbjct: 213 HGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGA 272
Query: 105 --IMDSMNDGELDNRDG 119
I +DG + N DG
Sbjct: 273 KCIAVGESDGSIWNPDG 289
>pdb|2PXB|A Chain A, Variant 2 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXD|A Chain A, Variant 1 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXE|A Chain A, Variant 4 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXF|A Chain A, Variant 5 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXK|A Chain A, Variant 8 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXL|A Chain A, Variant 9 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXP|A Chain A, Variant 13 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXQ|A Chain A, Variant 14 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXT|A Chain A, Variant 15 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXU|A Chain A, Variant 16 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXV|A Chain A, Variant 6 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
Length = 102
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 45/107 (42%), Gaps = 6/107 (5%)
Query: 54 FTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGE 113
F L D EQ + + G + + G +PG Q + S+ + L R I++S E
Sbjct: 1 FDLNDFLEQLRQMKNXGGXASLXGKLPGXGQIPDNVKSQXDDKV-LVRXEAIINSXTXKE 59
Query: 114 LDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKK 160
AK + R R+A G+G ++V L+ Q+ KK
Sbjct: 60 R-----AKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQFDDXQRXXKK 101
>pdb|1CGT|A Chain A, Structure Of Cyclodextrin Glycosyltransferase Refined At
2.0 Angstroms Resolution
Length = 684
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 14 NFPLYCGICCMGDIEGLIDKVNELKLDD 41
N LYCG GD +GLI+K+N+ D
Sbjct: 45 NLKLYCG----GDWQGLINKINDNYFSD 68
>pdb|6CGT|A Chain A, Hoxa Complex Of Cyclodextrin Glycosyltransferase Mutant
Length = 684
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 14 NFPLYCGICCMGDIEGLIDKVNELKLDD 41
N LYCG GD +GLI+K+N+ D
Sbjct: 45 NLKLYCG----GDWQGLINKINDNYFSD 68
>pdb|1CGU|A Chain A, Catalytic Center Of Cyclodextrin Glycosyltransferase
Derived From X-Ray Structure Analysis Combined With
Site- Directed Mutagenesis
pdb|5CGT|A Chain A, Maltotriose Complex Of Preconditioned Cyclodextrin
Glycosyltransferase Mutant
pdb|7CGT|A Chain A, Rameb Complex Of Cyclodextrin Glycosyltransferase Mutant
Length = 684
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 14 NFPLYCGICCMGDIEGLIDKVNELKLDD 41
N LYCG GD +GLI+K+N+ D
Sbjct: 45 NLKLYCG----GDWQGLINKINDNYFSD 68
>pdb|8CGT|A Chain A, Structure Of Cyclodextrin Glycosyltransferase Complexed
With A Thio-Maltohexaose
pdb|9CGT|A Chain A, Structure Of Cyclodextrin Glycosyltransferase Complexed
With A Thio-Maltopentaose
pdb|3CGT|A Chain A, Structure Of Cyclodextrin Glycosyltransferase Complexed
With Its Main Product Beta-Cyclodextrin
Length = 684
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 14 NFPLYCGICCMGDIEGLIDKVNELKLDD 41
N LYCG GD +GLI+K+N+ D
Sbjct: 45 NLKLYCG----GDWQGLINKINDNYFSD 68
>pdb|4CGT|A Chain A, Deletion Mutant Delta(145-150), F151d Of Cyclodextrin
Glycosyltransferase
Length = 678
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 14 NFPLYCGICCMGDIEGLIDKVNELKLDD 41
N LYCG GD +GLI+K+N+ D
Sbjct: 45 NLKLYCG----GDWQGLINKINDNYFSD 68
>pdb|3LQX|A Chain A, Srp Ribonucleoprotein Core Complexed With Cobalt Hexammine
Length = 105
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 44/107 (41%), Gaps = 6/107 (5%)
Query: 54 FTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGE 113
F L D EQ + G + + G +PG Q + S+ + L R I++S E
Sbjct: 2 FDLNDFLEQLRQXKNXGGXASLXGKLPGXGQIPDNVKSQXDDKV-LVRXEAIINSXTXKE 60
Query: 114 LDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKK 160
AK + R R+A G+G ++V L+ Q+ KK
Sbjct: 61 R-----AKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQFDDXQRXXKK 102
>pdb|2X42|A Chain A, Structure Of Beta-Glucosidase 3b From Thermotoga
Neapolitana In Complex With Alpha-D-Glucose
Length = 721
Score = 27.3 bits (59), Expect = 6.4, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 33 KVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKM 69
+VN + D+ EE++E +K G+ + + E +NI+K+
Sbjct: 267 QVNTERRDEIEEIMEALKEGKLSEEVLDECVRNILKV 303
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered Orthorhombic
Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 27.3 bits (59), Expect = 6.6, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 23/32 (71%), Gaps = 4/32 (12%)
Query: 43 EELIEKIKHG----QFTLRDMYEQFQNIMKMG 70
EE+++K++ G Q TLR +YE+ +++M+ G
Sbjct: 1073 EEIMDKVERGEEDYQATLRLLYEEIKSLMEEG 1104
>pdb|2QZA|A Chain A, Crystal Structure Of Salmonella Effector Protein Sopa
pdb|2QZA|B Chain B, Crystal Structure Of Salmonella Effector Protein Sopa
Length = 618
Score = 26.9 bits (58), Expect = 6.7, Method: Composition-based stats.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 12 YLNFPLYCGICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFT---LRDMYEQFQNIMK 68
+LN G + I+ L DK ++ K+ E+L++ ++ G+ T +R + +++
Sbjct: 181 FLNHEHNNGKSILXTIDSLPDKYSQEKVQAXEDLVKSLRGGRLTEACIRPVESSLVSVLA 240
Query: 69 MGPFSQ 74
P++Q
Sbjct: 241 HPPYTQ 246
>pdb|2X40|A Chain A, Structure Of Beta-Glucosidase 3b From Thermotoga
Neapolitana In Complex With Glycerol
pdb|2X41|A Chain A, Structure Of Beta-Glucosidase 3b From Thermotoga
Neapolitana In Complex With Glucose
Length = 721
Score = 26.9 bits (58), Expect = 6.8, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 33 KVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKM 69
+VN + D+ EE++E +K G+ + + E +NI+K+
Sbjct: 267 QVNTERRDEIEEIMEALKEGKLSEEVLDECVRNILKV 303
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 0.138 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,642,747
Number of Sequences: 62578
Number of extensions: 223795
Number of successful extensions: 837
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 796
Number of HSP's gapped (non-prelim): 45
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
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: 49 (23.5 bits)