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= 005707
(681 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 36/78 (46%), Positives = 49/78 (62%)
Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
+DL PG G V ++ FGAF+D G DGLVH+S LS+ FVKD +V G VKV++
Sbjct: 651 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 710
Query: 203 IEANAETGRISLTMRESD 220
+E + R+ L+MR SD
Sbjct: 711 MEVDIPRNRVGLSMRMSD 728
Score = 37.4 bits (85), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 15/113 (13%)
Query: 247 KPGQK-RDEMKTTKFVKGQD----------LEGTVKNLTRSGAFISLPEGEEGFLPTSEE 295
KPG+ R E KT +F +G + LEG V N+T GAF+ + ++G + S
Sbjct: 629 KPGRDPRPEFKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISAL 688
Query: 296 SDDGFANMMGGSSLQVGQEVSVRVLR--ISRGQVTLTMKKEDDVGSNLQLTQG 346
S+ + ++ G V V+V+ I R +V L+M+ D G ++ +G
Sbjct: 689 SEKFVKDPY--EVVKAGDIVKVKVMEVDIPRNRVGLSMRMSDTPGEKVEGQRG 739
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 76.6 bits (187), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 36/78 (46%), Positives = 49/78 (62%)
Query: 143 EDLIPGATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRL 202
+DL PG G V ++ FGAF+D G DGLVH+S LS+ FVKD +V G VKV++
Sbjct: 650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 709
Query: 203 IEANAETGRISLTMRESD 220
+E + R+ L+MR SD
Sbjct: 710 MEVDIPRNRVGLSMRMSD 727
Score = 37.4 bits (85), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 15/113 (13%)
Query: 247 KPGQK-RDEMKTTKFVKGQD----------LEGTVKNLTRSGAFISLPEGEEGFLPTSEE 295
KPG+ R E KT +F +G + LEG V N+T GAF+ + ++G + S
Sbjct: 628 KPGRDPRPEFKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISAL 687
Query: 296 SDDGFANMMGGSSLQVGQEVSVRVLR--ISRGQVTLTMKKEDDVGSNLQLTQG 346
S+ + ++ G V V+V+ I R +V L+M+ D G ++ +G
Sbjct: 688 SEKFVKDPY--EVVKAGDIVKVKVMEVDIPRNRVGLSMRMSDTPGEKVEGQRG 738
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 73.2 bits (178), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 31/70 (44%), Positives = 49/70 (70%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
G+ +TGKV +Q +GAF+ T GLVH+S ++ FVKD+ +SVG EV+V+++ +
Sbjct: 8 GSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDE 67
Query: 208 ETGRISLTMR 217
E G+ISL++R
Sbjct: 68 EKGKISLSIR 77
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVR 318
KF G G V L GAF++L E +G + SE + GF + L VG EV V+
Sbjct: 4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVT-HGFVKDI-NEHLSVGDEVQVK 61
Query: 319 VLRI--SRGQVTLTMK 332
VL + +G+++L+++
Sbjct: 62 VLAVDEEKGKISLSIR 77
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 62.4 bits (150), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
G +TGKV I FGAF+ G +GLVH+S+++D V+ V + +GQEV V+++E +
Sbjct: 628 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR 687
Query: 208 ETGRISLTMRES 219
+ GRI L+++E+
Sbjct: 688 Q-GRIRLSIKEA 698
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 52/98 (53%), Gaps = 3/98 (3%)
Query: 237 KVRTTRRSTSKPGQKRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEES 296
K+ T +K +R E T + G+ G V + GAF+++ G+EG + S+ +
Sbjct: 602 KIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIA 661
Query: 297 DDGFANMMGGSSLQVGQEVSVRVLRISR-GQVTLTMKK 333
D + LQ+GQEV V+VL + R G++ L++K+
Sbjct: 662 DKRVEKVT--DYLQMGQEVPVKVLEVDRQGRIRLSIKE 697
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 59.3 bits (142), Expect = 7e-09, Method: Composition-based stats.
Identities = 30/72 (41%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
G +TGKV I FGAF+ G +GLVH+S+++D V+ V + +GQEV V+++E +
Sbjct: 6 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR 65
Query: 208 ETGRISLTMRES 219
+ GRI L+++E+
Sbjct: 66 Q-GRIRLSIKEA 76
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVLRI 322
G+ G V + GAF+++ G+EG + S+ +D + LQ+GQEV V+VL +
Sbjct: 6 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVT--DYLQMGQEVPVKVLEV 63
Query: 323 SR-GQVTLTMKK 333
R G++ L++K+
Sbjct: 64 DRQGRIRLSIKE 75
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 6/82 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
G + GKV + FGAF++F DGLVHVS++S+ V ++ GQ VKV+L+ +
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 696
Query: 208 ETGRISLTMRESD-----DISK 224
+ G+ L+M+ D D+SK
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSK 718
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 6/82 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
G + GKV + FGAF++F DGLVHVS++S+ V ++ GQ VKV+L+ +
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 696
Query: 208 ETGRISLTMRESD-----DISK 224
+ G+ L+M+ D D+SK
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSK 718
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 6/82 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
G + GKV + FGAF++F DGLVHVS++S+ V ++ GQ VKV+L+ +
Sbjct: 629 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 687
Query: 208 ETGRISLTMRESD-----DISK 224
+ G+ L+M+ D D+SK
Sbjct: 688 DRGKTKLSMKVVDQETGEDLSK 709
>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2
Length = 308
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 155 VRSIQPFGAFIDFGAFTD--GLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
VRSIQ GA++ + + G++H+S LS ++ + ++ +G+ V++I + E G I
Sbjct: 21 VRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYI 80
Query: 213 SLTMR 217
L+ R
Sbjct: 81 DLSKR 85
>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Atp-Dependent Rna Helicase Dhx8
Length = 103
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAF---TDGLVHVSRL-SDNFVKDVGSIVSVGQEVKVRLI 203
G + GKV SI FG F+ +GLVH+S L + V +V +VS GQ VKV+++
Sbjct: 13 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVL 72
Query: 204 EANAETGRISLTMRESD 220
+ SL+M++ D
Sbjct: 73 SFTGT--KTSLSMKDVD 87
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 50/97 (51%), Gaps = 5/97 (5%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA 205
G V+ I +GAF++ + + +H+S ++ +V+++ + GQ+V ++I
Sbjct: 12 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV 71
Query: 206 NAETGRISLTMR---ESDDISKLQQQKDATASGDKVR 239
+ G I L++R + +KLQ+ K A + + +R
Sbjct: 72 DPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLR 108
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
G+ + TVK + GAF+ L E G+E F+ SE + N+ L+ GQ+V +V+
Sbjct: 12 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIR--DYLKEGQKVVAKVI 69
Query: 321 RI--SRGQVTLTMKK 333
R+ +G + L++++
Sbjct: 70 RVDPRKGHIDLSLRR 84
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 5/89 (5%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEA 205
G V+ I +GAF++ + + +H+S ++ +V+++ + GQ+V ++I
Sbjct: 11 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV 70
Query: 206 NAETGRISLTMR---ESDDISKLQQQKDA 231
+ G I L++R + +KLQ+ K A
Sbjct: 71 DPRKGHIDLSLRRVTQQQRKAKLQEFKRA 99
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 263 GQDLEGTVKNLTRSGAFISLPE--GEEGFLPTSEESDDGFANMMGGSSLQVGQEVSVRVL 320
G+ + TVK + GAF+ L E G+E F+ SE + N+ L+ GQ+V +V+
Sbjct: 11 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIR--DYLKEGQKVVAKVI 68
Query: 321 RI--SRGQVTLTMKK 333
R+ +G + L++++
Sbjct: 69 RVDPRKGHIDLSLRR 83
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
Length = 187
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 17/82 (20%)
Query: 153 GKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFV-----------KDVGSIVSVGQEVKVR 201
G+V + FG+F+ G DGL+HVS++ D++V K+ G ++ +G V+ R
Sbjct: 87 GEVVDVVEFGSFVRLGPL-DGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRAR 145
Query: 202 LIEANAETGR-----ISLTMRE 218
++ + + R I+LTMR+
Sbjct: 146 IVAISLKAERKRGSKIALTMRQ 167
>pdb|2KHJ|A Chain A, Nmr Structure Of The Domain 6 Of The E. Coli Ribosomal
Protein S1
Length = 109
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 40/74 (54%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANA 207
GA TGKV ++ GA ++ +G + S S + V+D ++SVG EV+ + +
Sbjct: 32 GAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDR 91
Query: 208 ETGRISLTMRESDD 221
+ ISL++R D+
Sbjct: 92 KNRAISLSVRAKDE 105
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL----SDNFVKDVGSIVSVGQEVKVRLI 203
G G V FGAF+ DGL+H+S++ V++V ++ VGQ+V+V +
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 204 EANAETGRISL 214
E ++ G++SL
Sbjct: 728 EIDSR-GKLSL 737
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 13/75 (17%)
Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSS-------LQVGQEV 315
G+ + G+V T GAF+SL G++G L S+ + GG L VGQ+V
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQ-----IRKLAGGKRVENVEDVLGVGQKV 722
Query: 316 SVRVLRI-SRGQVTL 329
V + I SRG+++L
Sbjct: 723 QVEIAEIDSRGKLSL 737
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 37.4 bits (85), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL----SDNFVKDVGSIVSVGQEVKVRLI 203
G G V FGAF+ DGL+H+S++ V++V ++ VGQ+V+V +
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 204 EANAETGRISL 214
E ++ G++SL
Sbjct: 728 EIDSR-GKLSL 737
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 13/75 (17%)
Query: 263 GQDLEGTVKNLTRSGAFISLPEGEEGFLPTSEESDDGFANMMGGSS-------LQVGQEV 315
G+ + G+V T GAF+SL G++G L S+ + GG L VGQ+V
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQ-----IRKLAGGKRVENVEDVLGVGQKV 722
Query: 316 SVRVLRI-SRGQVTL 329
V + I SRG+++L
Sbjct: 723 QVEIAEIDSRGKLSL 737
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|T Chain T, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|E Chain E, Rnap At 3.2ang
pdb|4B1O|E Chain E, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|T Chain T, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 180
Score = 36.6 bits (83), Expect = 0.047, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 16/76 (21%)
Query: 158 IQPFGAFIDFGAFTDGLVHVSRLSDN-----------FVKDVGSIVSVGQEVKVRLIE-A 205
+ +G F++ G DGLVH+S+++D+ F + ++ G +V+ R+I A
Sbjct: 92 VDNYGVFVNLGPM-DGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVA 150
Query: 206 NAETG---RISLTMRE 218
+ TG RI+LTMR+
Sbjct: 151 STVTGRLPRIALTMRQ 166
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|T Chain T, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 180
Score = 36.2 bits (82), Expect = 0.063, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 16/76 (21%)
Query: 158 IQPFGAFIDFGAFTDGLVHVSRLSDN-----------FVKDVGSIVSVGQEVKVRLIE-A 205
+ +G F++ G DGLVH+S+++D+ F + ++ G +V+ R+I A
Sbjct: 92 VDNYGIFVNLGPM-DGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVA 150
Query: 206 NAETG---RISLTMRE 218
+ TG RI+LTMR+
Sbjct: 151 STVTGRLPRIALTMRQ 166
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|T Chain T, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|E Chain E, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|Q Chain Q, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 180
Score = 36.2 bits (82), Expect = 0.067, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 16/76 (21%)
Query: 158 IQPFGAFIDFGAFTDGLVHVSRLSDN-----------FVKDVGSIVSVGQEVKVRLIE-A 205
+ +G F++ G DGLVH+S+++D+ F + ++ G +V+ R+I A
Sbjct: 92 VDNYGIFVNLGPM-DGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVA 150
Query: 206 NAETG---RISLTMRE 218
+ TG RI+LTMR+
Sbjct: 151 STVTGRLPRIALTMRQ 166
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 33.5 bits (75), Expect = 0.43, Method: Composition-based stats.
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRLS 181
G GK++SI FG FI DGLVH+S +S
Sbjct: 62 GDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDIS 95
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 33.1 bits (74), Expect = 0.55, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 259 KFVKGQDLEGTVKNLTRSGAFISLPEGEEGFLPTSE 294
++ +G L G V NLT G F+ + EG EG + SE
Sbjct: 27 RYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSE 62
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 148 GATFTGKVRSIQPFGAFIDFGAFTDGLVHVSRL 180
G TG+V ++ +G F++ +GLVHVS +
Sbjct: 31 GTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEM 63
>pdb|1KY2|A Chain A, Gppnhp-Bound Ypt7p At 1.6 A Resolution
pdb|1KY3|A Chain A, Gdp-Bound Ypt7p At 1.35 A Resolution
Length = 182
Score = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 14/100 (14%)
Query: 202 LIEANAETGRISLTMRESDDISKLQQQ-----------KDATASGDKVRTTRRSTSKPGQ 250
+I ++ G+ SL R +D K QQ K+ T GDKV T + GQ
Sbjct: 12 IILGDSGVGKTSLMHRYVND--KYSQQYKATIGADFLTKEVTVDGDKV-ATMQVWDTAGQ 68
Query: 251 KRDEMKTTKFVKGQDLEGTVKNLTRSGAFISLPEGEEGFL 290
+R + F +G D V ++T + +F ++ + FL
Sbjct: 69 ERFQSLGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFL 108
>pdb|2A19|A Chain A, Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex.
pdb|2A1A|A Chain A, Pkr Kinase Domain-Eif2alpha Complex
Length = 175
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 155 VRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
V+ I GA++ + +G++ +S LS ++ + ++ VG+ ++ + E G I
Sbjct: 23 VQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYI 82
Query: 213 SLTMRE--SDDISKLQQQ 228
L+ R S+DI K +++
Sbjct: 83 DLSKRRVSSEDIIKCEEK 100
>pdb|1Q46|A Chain A, Crystal Structure Of The Eif2 Alpha Subunit From
Saccharomyces Cerevisia
Length = 175
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 155 VRSIQPFGAFIDFGAF--TDGLVHVSRLSDNFVKDVGSIVSVGQEVKVRLIEANAETGRI 212
V+ I GA++ + +G++ +S LS ++ + ++ VG+ ++ + E G I
Sbjct: 23 VQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYI 82
Query: 213 SLTMRE--SDDISKLQQQ 228
L+ R S+DI K +++
Sbjct: 83 DLSKRRVSSEDIIKCEEK 100
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
0.306 0.124 0.328
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,272,143
Number of Sequences: 62578
Number of extensions: 624416
Number of successful extensions: 1254
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1222
Number of HSP's gapped (non-prelim): 41
length of query: 681
length of database: 14,973,337
effective HSP length: 105
effective length of query: 576
effective length of database: 8,402,647
effective search space: 4839924672
effective search space used: 4839924672
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 55 (25.8 bits)