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= psy5985
(153 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O8L|A Chain A, Structure Of Phosphofructokinase From Rabbit Skeletal
Muscle
pdb|3O8L|B Chain B, Structure Of Phosphofructokinase From Rabbit Skeletal
Muscle
pdb|3O8N|A Chain A, Structure Of Phosphofructokinase From Rabbit Skeletal
Muscle
pdb|3O8N|B Chain B, Structure Of Phosphofructokinase From Rabbit Skeletal
Muscle
Length = 762
Score = 127 bits (318), Expect = 3e-30, Method: Composition-based stats.
Identities = 64/100 (64%), Positives = 81/100 (81%)
Query: 32 GGFEVSFFALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGV 91
G + F ++TMGGYCGYLAT+AGLA GADAAYI+EE F+I+DLQ ++ H+ KM V
Sbjct: 561 AGTKRRVFIIETMGGYCGYLATMAGLAAGADAAYIFEEPFTIRDLQANVEHLVQKMKTTV 620
Query: 92 QRGLILRNEKCNDNYNTDFIYRLYSEEGKGLFSARQNVLA 131
+RGL+LRNEKCN+NY TDFI+ LYSEEGKG+F +R+NVL
Sbjct: 621 KRGLVLRNEKCNENYTTDFIFNLYSEEGKGIFDSRKNVLG 660
Score = 49.3 bits (116), Expect = 9e-07, Method: Composition-based stats.
Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 2 LGTKRTLPEKKLPQIAAKLKELKIQALLIIGGFEVSFFALKTMGG 46
LG+KRTLP+K QI+A + + IQ L+IIGGFE L+ M G
Sbjct: 467 LGSKRTLPKKSFEQISANITKFNIQGLVIIGGFEAYTGGLELMEG 511
Score = 37.4 bits (85), Expect = 0.004, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGVQRG 94
F L+ MG +CGYLA V L+ GAD +I E D +D H+ +++E RG
Sbjct: 203 FVLEVMGRHCGYLALVTSLSCGADWVFIPE--CPPDDNWED--HLCRRLSETRTRG 254
>pdb|3OPY|A Chain A, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|C Chain C, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|E Chain E, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|G Chain G, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
Length = 989
Score = 60.5 bits (145), Expect = 3e-10, Method: Composition-based stats.
Identities = 35/95 (36%), Positives = 50/95 (52%), Gaps = 4/95 (4%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAE--GVQRG-- 94
F ++ GGY GYLA+ AGL GA A Y E +++ +Q+D+ + E G R
Sbjct: 767 FVVEVQGGYSGYLASYAGLITGALAVYTPENPINLQTVQEDIELLTRTYEEDDGKNRSGK 826
Query: 95 LILRNEKCNDNYNTDFIYRLYSEEGKGLFSARQNV 129
+ + NEK + Y TD I + E GKG F +R V
Sbjct: 827 IFIHNEKASKVYTTDLIAAIIGEAGKGRFESRTAV 861
Score = 36.2 bits (82), Expect = 0.007, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGVQR 93
F ++ MG +CG+L ++G+A GAD +I E S + + DL + + E +R
Sbjct: 398 FVVEVMGRHCGWLGLMSGIATGADYIFIPERPPSESNWKDDLKKVCLRHREKGRR 452
>pdb|3O8O|A Chain A, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|C Chain C, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|E Chain E, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|G Chain G, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
Length = 787
Score = 50.8 bits (120), Expect = 3e-07, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKM----AEGVQRG 94
F + GG+ GY+A+ GL GA + Y E+K + +++D+ + E
Sbjct: 562 FVCEVQGGHSGYIASFTGLITGAVSVYTPEKKIDLASIREDITLLKENFRHDKGENRNGK 621
Query: 95 LILRNEKCNDNYNTDFIYRLYSEEGKGLFSARQNV 129
L++RNE+ + Y+T + + SE KG F R +
Sbjct: 622 LLVRNEQASSVYSTQLLADIISEASKGKFGVRTAI 656
Score = 36.6 bits (83), Expect = 0.006, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASK 86
F ++ MG +CG+LA +AG+A GAD +I E Q +L + +
Sbjct: 193 FVVEVMGRHCGWLALMAGIATGADYIFIPERAVPHGKWQDELKEVCQR 240
Score = 31.2 bits (69), Expect = 0.24, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 2 LGTKRTLPEKKLPQIAAKLKELKIQALLIIGGFEVSFFALKTM 44
+GT R++ + L IA ++ K+ L+I+GGFE F +LK +
Sbjct: 461 IGTNRSVASEDLGTIAYYFQKNKLDGLIILGGFE-GFRSLKQL 502
>pdb|3O8O|B Chain B, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|D Chain D, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|F Chain F, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|H Chain H, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
Length = 766
Score = 50.8 bits (120), Expect = 3e-07, Method: Composition-based stats.
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 4/92 (4%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGVQRG---- 94
F + GG GYLAT A LA GA +Y+ EE S++ L +D+ ++A + RG
Sbjct: 563 FVVDCQGGNSGYLATYASLAVGAQVSYVPEEGISLEQLSEDIEYLAQSFEKAEGRGRFGK 622
Query: 95 LILRNEKCNDNYNTDFIYRLYSEEGKGLFSAR 126
LIL++ + + + + + E G F A+
Sbjct: 623 LILKSTNASKALSATKLAEVITAEADGRFDAK 654
Score = 35.8 bits (81), Expect = 0.011, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGVQRGLIL 97
F ++ MG CG+LA +AG+A AD +I E+ + + Q + + SK +R I+
Sbjct: 192 FVVEVMGRNCGWLALLAGIATSADYIFIPEKPATSSEWQDQMCDIVSKHRSRGKRTTIV 250
Score = 28.9 bits (63), Expect = 1.4, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 2 LGTKRTLPEK-KLPQIAAKLKELKIQALLIIGGFE 35
+GT R PE+ L IA ++ + L+I+GGFE
Sbjct: 461 IGTNRVTPEEADLGMIAYYFQKYEFDGLIIVGGFE 495
>pdb|3OPY|B Chain B, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|D Chain D, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|F Chain F, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
pdb|3OPY|H Chain H, Crystal Structure Of Pichia Pastoris Phosphofructokinase
In The T- State
Length = 941
Score = 49.3 bits (116), Expect = 9e-07, Method: Composition-based stats.
Identities = 29/95 (30%), Positives = 49/95 (51%), Gaps = 4/95 (4%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMA--EGVQRG-- 94
F ++ GG GY+AT A LA GA +Y+ EE S+ L+ D+ + A +G +
Sbjct: 741 FVVEVQGGNSGYIATHAQLACGAQISYVPEEGISLAQLEMDINSLKESFANDQGKTKSGR 800
Query: 95 LILRNEKCNDNYNTDFIYRLYSEEGKGLFSARQNV 129
LIL++E + T+ I + +E G F ++ +
Sbjct: 801 LILKSENASKVLTTEVISTIIDDEASGRFDSKTAI 835
Score = 36.6 bits (83), Expect = 0.006, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASK-MAEGVQRGLIL 97
F ++ MG +CG+L +AGLA AD I E+ S ++ Q + + K A G ++ +++
Sbjct: 370 FIVEVMGRHCGWLGLLAGLATSADYILIPEKPASSREWQDQMCDIVGKHRARGKRKTIVI 429
Query: 98 RNEKCNDN 105
E N
Sbjct: 430 VAEGAISN 437
>pdb|4A3S|A Chain A, Crystal Structure Of Pfk From Bacillus Subtilis
pdb|4A3S|B Chain B, Crystal Structure Of Pfk From Bacillus Subtilis
Length = 319
Score = 33.1 bits (74), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 7/56 (12%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGVQRG 94
+ ++ MG + G +A AGLAGGA++ I E + D++ + +++ G +RG
Sbjct: 164 YVIEVMGRHAGDIALWAGLAGGAESILIPEADY-------DMHEIIARLKRGHERG 212
>pdb|1PFK|A Chain A, Crystal Structure Of The Complex Of Phosphofructokinase
From Escherichia Coli With Its Reaction Products
pdb|1PFK|B Chain B, Crystal Structure Of The Complex Of Phosphofructokinase
From Escherichia Coli With Its Reaction Products
pdb|2PFK|A Chain A, The Crystal Structure Of Unliganded Phosphofructokinase
From Escherichia Coli
pdb|2PFK|B Chain B, The Crystal Structure Of Unliganded Phosphofructokinase
From Escherichia Coli
pdb|2PFK|C Chain C, The Crystal Structure Of Unliganded Phosphofructokinase
From Escherichia Coli
pdb|2PFK|D Chain D, The Crystal Structure Of Unliganded Phosphofructokinase
From Escherichia Coli
Length = 320
Score = 32.7 bits (73), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 41 LKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDLYHMASKMAEGVQRGLILRNE 100
++ MG YCG L A +AGG + + E +FS +DL ++ + +A+G + ++ E
Sbjct: 167 VEVMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEI---KAGIAKGKKHAIVAITE 223
Query: 101 KCND 104
D
Sbjct: 224 HMCD 227
>pdb|1ZXX|A Chain A, The Crystal Structure Of Phosphofructokinase From
Lactobacillus Delbrueckii
Length = 319
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDLQQDL 80
F + MG CG +A G+A GADA I E + ++++ L
Sbjct: 164 FIVNVMGRNCGDIAMRVGVACGADAIVIPERPYDVEEIANRL 205
>pdb|6PFK|A Chain A, Phosphofructokinase, Inhibited T-State
pdb|6PFK|B Chain B, Phosphofructokinase, Inhibited T-State
pdb|6PFK|C Chain C, Phosphofructokinase, Inhibited T-State
pdb|6PFK|D Chain D, Phosphofructokinase, Inhibited T-State
pdb|3U39|A Chain A, Crystal Stucture Of The Apo Bacillus Stearothermophilus
Phosphofructokinase
pdb|3U39|B Chain B, Crystal Stucture Of The Apo Bacillus Stearothermophilus
Phosphofructokinase
pdb|3U39|C Chain C, Crystal Stucture Of The Apo Bacillus Stearothermophilus
Phosphofructokinase
pdb|3U39|D Chain D, Crystal Stucture Of The Apo Bacillus Stearothermophilus
Phosphofructokinase
Length = 319
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDL--------QQDLYHMASKMAEG 90
+ ++ MG + G +A +GLAGGA+ I E + + D+ ++ H +AEG
Sbjct: 164 YVIEVMGRHAGDIALWSGLAGGAETILIPEADYDMNDVIARLKRGHERGKKHSIIIVAEG 223
Query: 91 VQRGL 95
V G+
Sbjct: 224 VGSGV 228
>pdb|3PFK|A Chain A, Phosphofructokinase. Structure And Control
pdb|4PFK|A Chain A, Phosphofructokinase. Structure And Control
Length = 319
Score = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDL--------QQDLYHMASKMAEG 90
+ ++ MG + G +A +GLAGGA+ I E + + D+ ++ H +AEG
Sbjct: 164 YVIEVMGRHAGDIALWSGLAGGAETILIPEADYDMNDVIARLKRGHERGKKHSIIIVAEG 223
Query: 91 VQRGL 95
V G+
Sbjct: 224 VGSGV 228
>pdb|1MTO|A Chain A, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|B Chain B, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|C Chain C, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|D Chain D, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|E Chain E, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|F Chain F, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|G Chain G, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
pdb|1MTO|H Chain H, Crystal Structure Of A Phosphofructokinase Mutant From
Bacillus Stearothermophilus Bound With
Fructose-6-Phosphate
Length = 319
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 39 FALKTMGGYCGYLATVAGLAGGADAAYIYEEKFSIKDL--------QQDLYHMASKMAEG 90
+ ++ MG + G +A +GLAGGA+ I E + + D+ ++ H +AEG
Sbjct: 164 WVIEVMGRHAGDIALYSGLAGGAETILIPEADYDMNDVIARLKRGHERGKKHSIIIVAEG 223
Query: 91 VQRGL 95
V G+
Sbjct: 224 VGSGV 228
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 30.0 bits (66), Expect = 0.51, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 6 RTLPEKKLPQIAAKLKELKIQALLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGADAAY 65
+ L + +PQ LK+L QA L +G E + L + Y L+T +G+ G D A
Sbjct: 637 QELIQMDVPQEKNSLKDLVYQAFLRLG-MEKTARLLDALKYYGFTLSTTSGITIGIDDAV 695
Query: 66 IYEEK 70
I EEK
Sbjct: 696 IPEEK 700
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 30.0 bits (66), Expect = 0.53, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 6 RTLPEKKLPQIAAKLKELKIQALLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGADAAY 65
+ L + +PQ LK+L QA L +G E + L + Y L+T +G+ G D A
Sbjct: 606 QELIQMDVPQEKNSLKDLVYQAFLRLG-MEKTARLLDALKYYGFTLSTTSGITIGIDDAV 664
Query: 66 IYEEK 70
I EEK
Sbjct: 665 IPEEK 669
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 30.0 bits (66), Expect = 0.57, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 6 RTLPEKKLPQIAAKLKELKIQALLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGADAAY 65
+ L + +PQ LK+L QA L +G E + L + Y L+T +G+ G D A
Sbjct: 897 QELIQMDVPQEKNSLKDLVYQAFLRLG-MEKTARLLDALKYYGFTLSTTSGITIGIDDAV 955
Query: 66 IYEEK 70
I EEK
Sbjct: 956 IPEEK 960
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 28.1 bits (61), Expect = 2.1, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 13 LPQIAAKLKELKIQALLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGADAAYIYEEK 70
+PQ LK+L QA L +G E + L + Y +T +G+ G D A I EEK
Sbjct: 904 VPQEKNSLKDLVYQAFLRLG-MEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEK 960
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 28.1 bits (61), Expect = 2.1, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 13 LPQIAAKLKELKIQALLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGADAAYIYEEK 70
+PQ LK+L QA L +G E + L + Y +T +G+ G D A I EEK
Sbjct: 904 VPQEKNSLKDLVYQAFLRLG-MEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEK 960
>pdb|3DH4|A Chain A, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
pdb|3DH4|B Chain B, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
pdb|3DH4|C Chain C, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
pdb|3DH4|D Chain D, Crystal Structure Of SodiumSUGAR SYMPORTER WITH BOUND
GALACTOSE FROM Vibrio Parahaemolyticus
Length = 530
Score = 28.1 bits (61), Expect = 2.2, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 28 LLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGA 61
L++GGF ++ A+ +GG G+ A V+ + A
Sbjct: 166 FLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAA 199
>pdb|2XQ2|B Chain B, Structure Of The K294a Mutant Of Vsglt
Length = 593
Score = 28.1 bits (61), Expect = 2.2, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 28 LLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGA 61
L++GGF ++ A+ +GG G+ A V+ + A
Sbjct: 195 FLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAA 228
>pdb|2XQ2|A Chain A, Structure Of The K294a Mutant Of Vsglt
Length = 593
Score = 27.7 bits (60), Expect = 2.3, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 28 LLIIGGFEVSFFALKTMGGYCGYLATVAGLAGGADAAY 65
L++GGF ++ A+ +GG G+ A V+ + A +
Sbjct: 195 FLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHF 232
>pdb|3QI9|D Chain D, Crystal Structure Of Mouse Cd1d-Alpha-Phosphotidylinositol
With Mouse Valpha14-Vbeta6 2a3-D Nkt Tcr
Length = 243
Score = 26.9 bits (58), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 101 KCNDNYNTDFIYRLYSEEGKGL 122
KC N+N D +Y + GKGL
Sbjct: 22 KCQQNFNHDTMYWYRQDSGKGL 43
>pdb|3SCM|D Chain D, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Isoglobotrihexosylceramide
pdb|3SDA|D Chain D, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Beta-Galactosylceramide
pdb|3SDC|D Chain D, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Globotrihexosylceramide
pdb|3SDD|D Chain D, Crystal Structure Of Autoreactive-Valpha14-Vbeta6 Nkt Tcr
In Complex With Cd1d-Beta-Lactosylceramide
Length = 245
Score = 26.6 bits (57), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 101 KCNDNYNTDFIYRLYSEEGKGL 122
KC N+N D +Y + GKGL
Sbjct: 24 KCQQNFNHDTMYWYRQDSGKGL 45
>pdb|3LWS|A Chain A, Crystal Structure Of Putative Aromatic Amino Acid Beta-
Eliminating LyaseTHREONINE ALDOLASE. (YP_001813866.1)
FROM Exiguobacterium Sp. 255-15 At 2.00 A Resolution
pdb|3LWS|B Chain B, Crystal Structure Of Putative Aromatic Amino Acid Beta-
Eliminating LyaseTHREONINE ALDOLASE. (YP_001813866.1)
FROM Exiguobacterium Sp. 255-15 At 2.00 A Resolution
pdb|3LWS|C Chain C, Crystal Structure Of Putative Aromatic Amino Acid Beta-
Eliminating LyaseTHREONINE ALDOLASE. (YP_001813866.1)
FROM Exiguobacterium Sp. 255-15 At 2.00 A Resolution
pdb|3LWS|D Chain D, Crystal Structure Of Putative Aromatic Amino Acid Beta-
Eliminating LyaseTHREONINE ALDOLASE. (YP_001813866.1)
FROM Exiguobacterium Sp. 255-15 At 2.00 A Resolution
pdb|3LWS|E Chain E, Crystal Structure Of Putative Aromatic Amino Acid Beta-
Eliminating LyaseTHREONINE ALDOLASE. (YP_001813866.1)
FROM Exiguobacterium Sp. 255-15 At 2.00 A Resolution
pdb|3LWS|F Chain F, Crystal Structure Of Putative Aromatic Amino Acid Beta-
Eliminating LyaseTHREONINE ALDOLASE. (YP_001813866.1)
FROM Exiguobacterium Sp. 255-15 At 2.00 A Resolution
Length = 357
Score = 26.6 bits (57), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 11 KKLPQIAAKLKELKIQALLIIGGFEVSFFALKTMGGYC 48
K LP IA L EL + IGG +F L+T+ YC
Sbjct: 131 KALPDIACLLLELPQRE---IGGVAPAFSELETISRYC 165
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
0.318 0.136 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,463,281
Number of Sequences: 62578
Number of extensions: 174735
Number of successful extensions: 496
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 468
Number of HSP's gapped (non-prelim): 32
length of query: 153
length of database: 14,973,337
effective HSP length: 90
effective length of query: 63
effective length of database: 9,341,317
effective search space: 588502971
effective search space used: 588502971
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)