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= psy4311
(190 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 = 290 bits (742), Expect = 4e-79, Method: Compositional matrix adjust.
Identities = 135/162 (83%), Positives = 150/162 (92%)
Query: 1 MVLADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVI 60
MVLADLGRKITSALRSLSNAT+INEEVLN+MLKE+C ALLEADVNIKLVK+LRENV+ I
Sbjct: 1 MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAI 60
Query: 61 DFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTK 120
D +EMASGLNKR+MIQ +V+KEL+KLVDPGVKA P KGK NVIMFVGLQGSGKTTTC+K
Sbjct: 61 DLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSK 120
Query: 121 LAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGS 162
LAY+Y +K WK CL+CADTFRAGA+DQLKQNATKARIPFYGS
Sbjct: 121 LAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGS 162
>pdb|1WGW|A Chain A, Solution Structure Of The N-Terminal Domain Of Mouse
Putative Signal Recoginition Particle 54 (Srp54)
Length = 99
Score = 141 bits (355), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 67/83 (80%), Positives = 78/83 (93%)
Query: 4 ADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFD 63
ADLGRKITSALRSLSNAT+INEEVLN+MLKE+C ALLEADVNIKLVK+LRENV+ ID +
Sbjct: 8 ADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDLE 67
Query: 64 EMASGLNKRRMIQSSVYKELIKL 86
EMASGLNKR+MIQ +V+KEL+K+
Sbjct: 68 EMASGLNKRKMIQHAVFKELVKV 90
>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 = 125 bits (314), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 65/165 (39%), Positives = 101/165 (61%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
LG + AL L A ++++++ ++K+I AL++ADVN+KLV K+ + + + ++
Sbjct: 4 LGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKT 63
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
GL+K+ I VY+EL+KL+ K + K NVI+ VG+QGSGKTTT KLA +
Sbjct: 64 PKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYI 123
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
K+ K L+ ADT+R AY+QLKQ A K +P YG ++P+
Sbjct: 124 QKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPV 168
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 125 bits (314), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 65/165 (39%), Positives = 101/165 (61%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
LG + AL L A ++++++ ++K+I AL++ADVN+KLV K+ + + + ++
Sbjct: 4 LGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKT 63
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
GL+K+ I VY+EL+KL+ K + K NVI+ VG+QGSGKTTT KLA +
Sbjct: 64 PKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYI 123
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
K+ K L+ ADT+R AY+QLKQ A K +P YG ++P+
Sbjct: 124 QKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPV 168
>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 = 117 bits (294), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 63/168 (37%), Positives = 113/168 (67%), Gaps = 5/168 (2%)
Query: 1 MVLADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKL-RENVRQV 59
MVL +LG+ + + L+ ++ A+ ++E ++ ++++I AL++ADVN++LV +L RE R+
Sbjct: 1 MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRA 60
Query: 60 IDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQ-KGKPNVIMFVGLQGSGKTTTC 118
++ ++ +G++K+ I VY+EL K + G +A + K KP +++ VG+QGSGKTTT
Sbjct: 61 LE-EKPPAGISKKEHIIKIVYEELTKFL--GTEAKPIEIKEKPTILLMVGIQGSGKTTTV 117
Query: 119 TKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGK 166
KLA ++ K+ +K +VC+DT+R GAY QL+Q + I +G+ + K
Sbjct: 118 AKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEK 165
>pdb|3KL4|A Chain A, Recognition Of A Signal Peptide By The Signal Recognition
Particle
Length = 433
Score = 101 bits (252), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 58/162 (35%), Positives = 89/162 (54%), Gaps = 1/162 (0%)
Query: 10 ITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL 69
I A+R + E+ ++ +K++ +L+ +DVN+KLV L +++ ++ ++ S L
Sbjct: 6 IRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSVL 65
Query: 70 NKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKN 129
++ S VY EL KL + + P +IM VG+QGSGKTTT KLAY Y K+
Sbjct: 66 ERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRG 125
Query: 130 WKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPIH 171
+K LV AD +R AYDQL Q + + YG +NPI
Sbjct: 126 YKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPN-NQNPIE 166
>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 = 101 bits (252), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 58/162 (35%), Positives = 89/162 (54%), Gaps = 1/162 (0%)
Query: 10 ITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL 69
I A+R + E+ ++ +K++ +L+ +DVN+KLV L +++ ++ ++ S L
Sbjct: 13 IRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSVL 72
Query: 70 NKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKN 129
++ S VY EL KL + + P +IM VG+QGSGKTTT KLAY Y K+
Sbjct: 73 ERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRG 132
Query: 130 WKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPIH 171
+K LV AD +R AYDQL Q + + YG +NPI
Sbjct: 133 YKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPN-NQNPIE 173
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/154 (35%), Positives = 82/154 (53%), Gaps = 2/154 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIPF 159
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPV 156
>pdb|1LS1|A Chain A, T. Aquaticus Ffh Ng Domain At 1.1a Resolution
Length = 295
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>pdb|3NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
pdb|3NG1|B Chain B, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
pdb|1OKK|A Chain A, Homo-Heterodimeric Complex Of The Srp Gtpases
pdb|2CNW|A Chain A, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|B Chain B, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|C Chain C, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2J7P|A Chain A, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
pdb|2J7P|B Chain B, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
pdb|1NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
pdb|2XKV|A Chain A, Atomic Model Of The Srp-Ftsy Early Conformation
Length = 294
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>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 = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>pdb|1FFH|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 294
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 4 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQV 63
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 64 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 121
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 122 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 154
>pdb|2C03|A Chain A, Gdp Complex Of Srp Gtpase Ffh Ng Domain
pdb|2C03|B Chain B, Gdp Complex Of Srp Gtpase Ffh Ng Domain
Length = 297
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>pdb|2NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 293
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 4 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQV 63
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 64 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 121
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 122 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 154
>pdb|1JPJ|A Chain A, Gmppnp Complex Of Srp Gtpase Ng Domain
pdb|1JPN|A Chain A, Gmppnp Complex Of Srp Gtpase Ng Domain
pdb|1JPN|B Chain B, Gmppnp Complex Of Srp Gtpase Ng Domain
pdb|1RY1|U Chain U, Structure Of The Signal Recognition Particle Interacting
With The Elongation-Arrested Ribosome
Length = 296
Score = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>pdb|1O87|A Chain A, A New Mggdp Complex Of The Ffh Ng Domain
pdb|1O87|B Chain B, A New Mggdp Complex Of The Ffh Ng Domain
pdb|2C04|A Chain A, Gmppcp Complex Of Srp Gtpase Ffh Ng Domain At Ultra-High
Resolution
pdb|2C04|B Chain B, Gmppcp Complex Of Srp Gtpase Ffh Ng Domain At Ultra-High
Resolution
pdb|2J45|A Chain A, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
pdb|2J45|B Chain B, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
pdb|2J46|A Chain A, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
pdb|2J46|B Chain B, Water Structure Of T. Aquaticus Ffh Ng Domain At 1.1a
Resolution
Length = 297
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>pdb|1RJ9|B Chain B, Structure Of The Heterodimer Of The Conserved Gtpase
Domains Signal Recognition Particle (Ffh) And Its
Receptor (Ftsy)
Length = 300
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 82/153 (53%), Gaps = 2/153 (1%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ A+ L I EE L + L+EI AL++ADVN+++ + E VR+ ++
Sbjct: 5 LSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L +I ++VY+ L + + G +A P N+ VGLQGSGKTTT KLA +Y
Sbjct: 65 LESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYY 122
Query: 126 LKKNWKACLVCADTFRAGAYDQLKQNATKARIP 158
K + LV ADT R A +QL+ K +P
Sbjct: 123 KGKGRRPLLVAADTQRPAAREQLRLLGEKVGVP 155
>pdb|3DMD|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3DMD|A Chain A, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3DMD|C Chain C, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
pdb|3E70|C Chain C, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 49/147 (33%), Positives = 84/147 (57%), Gaps = 4/147 (2%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKE 82
I E+ ++ L E+ LLEADV +++V LRE ++Q + ++ G +K ++I+ +V +
Sbjct: 47 IKEKDVDKALDELEIDLLEADVALEVVDALREKIKQKLVGKKVRIGTDKGKIIEEAVKEA 106
Query: 83 LIKLVDPGVKAHQPQK----GKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCAD 138
+ ++++ + ++ KP VIMFVG GSGKTTT KLA + + +D
Sbjct: 107 VSEILETSRRIDLIEEIRKAEKPYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIAASD 166
Query: 139 TFRAGAYDQLKQNATKARIPFYGSSKG 165
TFRAGA +QL+++A + + S G
Sbjct: 167 TFRAGAIEQLEEHAKRIGVKVIKHSYG 193
>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens
Length = 297
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 51/149 (34%), Positives = 79/149 (53%)
Query: 14 LRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRR 73
+R + ++ + +KE+ +L+ ADVN+KLV L +++ + ++ + + +R
Sbjct: 11 VRKFLTGSSSYDKAVEDFIKELQKSLISADVNVKLVFSLTNKIKERLKNEKPPTYIERRE 70
Query: 74 MIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKAC 133
VY EL L + P VIM VG+QG+GKTTT KLAY Y KK +K
Sbjct: 71 WFIKIVYDELSNLFGGDKEPKVIPDKIPYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVG 130
Query: 134 LVCADTFRAGAYDQLKQNATKARIPFYGS 162
LV AD +R A +QL+Q + +P YG
Sbjct: 131 LVGADVYRPAALEQLQQLGQQIGVPVYGE 159
>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens T112a Mutant
Length = 297
Score = 79.7 bits (195), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 50/149 (33%), Positives = 78/149 (52%)
Query: 14 LRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRR 73
+R + ++ + +KE+ +L+ ADVN+KLV L +++ + ++ + + +R
Sbjct: 11 VRKFLTGSSSYDKAVEDFIKELQKSLISADVNVKLVFSLTNKIKERLKNEKPPTYIERRE 70
Query: 74 MIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKAC 133
VY EL L + P VIM VG+QG+GK TT KLAY Y KK +K
Sbjct: 71 WFIKIVYDELSNLFGGDKEPKVIPDKIPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVG 130
Query: 134 LVCADTFRAGAYDQLKQNATKARIPFYGS 162
LV AD +R A +QL+Q + +P YG
Sbjct: 131 LVGADVYRPAALEQLQQLGQQIGVPVYGE 159
>pdb|3DM9|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 79.7 bits (195), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 48/147 (32%), Positives = 83/147 (56%), Gaps = 4/147 (2%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKE 82
I E+ ++ L E+ LLEADV +++V LRE ++Q + ++ G +K ++I+ +V +
Sbjct: 47 IKEKDVDKALDELEIDLLEADVALEVVDALREKIKQKLVGKKVRIGTDKGKIIEEAVKEA 106
Query: 83 LIKLVDPGVKAHQPQK----GKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCAD 138
+ ++++ + ++ KP VI FVG GSGKTTT KLA + + +D
Sbjct: 107 VSEILETSRRIDLIEEIRKAEKPYVIXFVGFNGSGKTTTIAKLANWLKNHGFSVVIAASD 166
Query: 139 TFRAGAYDQLKQNATKARIPFYGSSKG 165
TFRAGA +QL+++A + + S G
Sbjct: 167 TFRAGAIEQLEEHAKRIGVKVIKHSYG 193
>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 = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 50/168 (29%), Positives = 85/168 (50%), Gaps = 9/168 (5%)
Query: 5 DLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDE 64
+L +++ LR++S + E+ + L+E+ ALLEADV + +V++ V++ E
Sbjct: 4 NLTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFINRVKEKAVGHE 63
Query: 65 MASGLNKRRMIQSSVYKELIKLVDPGVK----AHQPQKGKPNVIMFVGLQGSGKTTTCTK 120
+ L + V EL+ + + A QP P V++ GLQG+GKTT+ K
Sbjct: 64 VNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQP----PAVVLMAGLQGAGKTTSVGK 119
Query: 121 LAYHYLKKNWKACLVC-ADTFRAGAYDQLKQNATKARIPFYGSSKGKR 167
L +K+ K LV AD +R A QL+ A + + F+ S G++
Sbjct: 120 LGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQK 167
>pdb|2J28|9 Chain 9, Model Of E. Coli Srp Bound To 70s Rncs
Length = 430
Score = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 50/168 (29%), Positives = 85/168 (50%), Gaps = 9/168 (5%)
Query: 5 DLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDE 64
+L +++ LR++S + E+ + L+E+ ALLEADV + +V++ V++ E
Sbjct: 3 NLTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFINRVKEKAVGHE 62
Query: 65 MASGLNKRRMIQSSVYKELIKLVDPGVK----AHQPQKGKPNVIMFVGLQGSGKTTTCTK 120
+ L + V EL+ + + A QP P V++ GLQG+GKTT+ K
Sbjct: 63 VNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQP----PAVVLMAGLQGAGKTTSVGK 118
Query: 121 LAYHYLKKNWKACLVC-ADTFRAGAYDQLKQNATKARIPFYGSSKGKR 167
L +K+ K LV AD +R A QL+ A + + F+ S G++
Sbjct: 119 LGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQK 166
>pdb|4AK9|A Chain A, Structure Of Chloroplast Ftsy From Physcomitrella Patens
pdb|4AK9|B Chain B, Structure Of Chloroplast Ftsy From Physcomitrella Patens
Length = 318
Score = 66.2 bits (160), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 43/123 (34%), Positives = 65/123 (52%), Gaps = 6/123 (4%)
Query: 29 NSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVD 88
S+L E+ LL +D K K+ + +R+ D +A L I+ ++ K + KL+
Sbjct: 46 ESILDELEEVLLVSDFGPKTALKIVDTIRK----DILAGRLKSGPQIKEALKKNIFKLLT 101
Query: 89 PGVKAHQPQKG--KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYD 146
V + Q G +P V+M VG+ G GKTTT KLA + K+ K + DTFRA A +
Sbjct: 102 ERVTTTELQLGNSRPAVLMIVGVNGGGKTTTLGKLANRFKKEGVKVLMAAGDTFRAAAGE 161
Query: 147 QLK 149
QL+
Sbjct: 162 QLE 164
>pdb|2OG2|A Chain A, Crystal Structure Of Chloroplast Ftsy From Arabidopsis
Thaliana
Length = 359
Score = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/159 (28%), Positives = 83/159 (52%), Gaps = 21/159 (13%)
Query: 4 ADLGRKITSALRSLSNATVINEEVL-------NSMLKEICAALLEAD----VNIKLVKKL 52
+D+ + + ++ N VI+E +L + +L E+ ALL +D + +++V++L
Sbjct: 55 SDVEKVFSGFSKTRENLAVIDELLLFWNLAETDRVLDELEEALLVSDFGPKITVRIVERL 114
Query: 53 RENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKG--KPNVIMFVGLQ 110
RE++ M+ L I+ ++ + +++++ + Q G KP VIM VG+
Sbjct: 115 REDI--------MSGKLKSGSEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVN 166
Query: 111 GSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLK 149
G GKTT+ KLA+ + K + DTFRA A DQL+
Sbjct: 167 GGGKTTSLGKLAHRLKNEGTKVLMAAGDTFRAAASDQLE 205
>pdb|3B9Q|A Chain A, The Crystal Structure Of Cpftsy From Arabidopsis Thaliana
Length = 302
Score = 63.9 bits (154), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 45/148 (30%), Positives = 78/148 (52%), Gaps = 21/148 (14%)
Query: 15 RSLSNATVINEEVL-------NSMLKEICAALLEAD----VNIKLVKKLRENVRQVIDFD 63
++ N VI+E +L + +L E+ ALL +D + +++V++LRE++
Sbjct: 9 KTRENLAVIDELLLFWNLAETDRVLDELEEALLVSDFGPKITVRIVERLREDI------- 61
Query: 64 EMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKG--KPNVIMFVGLQGSGKTTTCTKL 121
M+ L I+ ++ + +++++ + Q G KP VIM VG+ G GKTT+ KL
Sbjct: 62 -MSGKLKSGSEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKL 120
Query: 122 AYHYLKKNWKACLVCADTFRAGAYDQLK 149
A+ + K + DTFRA A DQL+
Sbjct: 121 AHRLKNEGTKVLMAAGDTFRAAASDQLE 148
>pdb|1ZU4|A Chain A, Crystal Structure Of Ftsy From Mycoplasma Mycoides- Space
Group P21212
pdb|1ZU5|A Chain A, Crystal Structure Of Ftsy From Mycoplasma Mycoides- Space
Group H32
pdb|1ZU5|B Chain B, Crystal Structure Of Ftsy From Mycoplasma Mycoides- Space
Group H32
Length = 320
Score = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 38/124 (30%), Positives = 68/124 (54%), Gaps = 5/124 (4%)
Query: 29 NSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVD 88
+ +E+ L++ D+ +K+V K+ VR+ D S N + + S+Y+ D
Sbjct: 34 DEFFEELEDVLIQTDMGMKMVLKVSNLVRKKTKRD--TSFENIKDALVESLYQAYTD-ND 90
Query: 89 PGVKAHQP--QKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYD 146
K ++ ++ + N+ M VG+ G+GKTT+ K+A +Y + +K + ADTFRAGA
Sbjct: 91 WTNKKYRIDFKENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADTFRAGATQ 150
Query: 147 QLKQ 150
QL++
Sbjct: 151 QLEE 154
>pdb|2YHS|A Chain A, Structure Of The E. Coli Srp Receptor Ftsy
Length = 503
Score = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 42/130 (32%), Positives = 61/130 (46%), Gaps = 16/130 (12%)
Query: 42 ADVNIKLVKKLRENV-----RQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQP 96
ADV ++ +K+ N+ R+ + E GL K M E++ VD +
Sbjct: 238 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEM------GEILAKVDEPLNV--- 288
Query: 97 QKGK-PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKA 155
+GK P VI+ VG+ G GKTTT KLA + ++ L DTFRA A +QL+ +
Sbjct: 289 -EGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRN 347
Query: 156 RIPFYGSSKG 165
IP G
Sbjct: 348 NIPVIAQHTG 357
>pdb|1FTS|A Chain A, Signal Recognition Particle Receptor From E. Coli
Length = 295
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/130 (32%), Positives = 61/130 (46%), Gaps = 16/130 (12%)
Query: 42 ADVNIKLVKKLRENV-----RQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQP 96
ADV ++ +K+ N+ R+ + E GL K M E++ VD +
Sbjct: 38 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEM------GEILAKVDEPLNV--- 88
Query: 97 QKGK-PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKA 155
+GK P VI+ VG+ G GKTTT KLA + ++ L DTFRA A +QL+ +
Sbjct: 89 -EGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRN 147
Query: 156 RIPFYGSSKG 165
IP G
Sbjct: 148 NIPVIAQHTG 157
>pdb|2XXA|B Chain B, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
pdb|2XXA|D Chain D, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
Length = 302
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/130 (32%), Positives = 61/130 (46%), Gaps = 16/130 (12%)
Query: 42 ADVNIKLVKKLRENV-----RQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQP 96
ADV ++ +K+ N+ R+ + E GL K M E++ VD +
Sbjct: 43 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEM------GEILAKVDEPLNV--- 93
Query: 97 QKGK-PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKA 155
+GK P VI+ VG+ G GKTTT KLA + ++ L DTFRA A +QL+ +
Sbjct: 94 -EGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRN 152
Query: 156 RIPFYGSSKG 165
IP G
Sbjct: 153 NIPVIAQHTG 162
>pdb|2QY9|A Chain A, Structure Of The Ng+1 Construct Of The E. Coli Srp
Receptor Ftsy
Length = 309
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/130 (32%), Positives = 61/130 (46%), Gaps = 16/130 (12%)
Query: 42 ADVNIKLVKKLRENV-----RQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQP 96
ADV ++ +K+ N+ R+ + E GL K M E++ VD +
Sbjct: 44 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEM------GEILAKVDEPLNV--- 94
Query: 97 QKGK-PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKA 155
+GK P VI+ VG+ G GKTTT KLA + ++ L DTFRA A +QL+ +
Sbjct: 95 -EGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRN 153
Query: 156 RIPFYGSSKG 165
IP G
Sbjct: 154 NIPVIAQHTG 163
>pdb|2PX0|A Chain A, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|B Chain B, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|C Chain C, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|D Chain D, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|E Chain E, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|F Chain F, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|G Chain G, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX0|H Chain H, Crystal Structure Of Flhf Complexed With GmppnpMG(2+)
pdb|2PX3|A Chain A, Crystal Structure Of Flhf Complexed With GtpMG(2+)
pdb|3SYN|A Chain A, Crystal Structure Of Flhf In Complex With Its Activator
pdb|3SYN|B Chain B, Crystal Structure Of Flhf In Complex With Its Activator
pdb|3SYN|C Chain C, Crystal Structure Of Flhf In Complex With Its Activator
pdb|3SYN|D Chain D, Crystal Structure Of Flhf In Complex With Its Activator
Length = 296
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 4/106 (3%)
Query: 55 NVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGK 114
+++++ F A GL + ++ + + L ++ K +P K I+ G G+GK
Sbjct: 62 TLKKLLRFSVEAGGLTEENVV-GKLQEILCDMLPSADKWQEPIHSK--YIVLFGSTGAGK 118
Query: 115 TTTCTKLA-YHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPF 159
TTT KLA L+K+ K + DT+R A +QLK A + P
Sbjct: 119 TTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQAPL 164
>pdb|1VMA|A Chain A, Crystal Structure Of Cell Division Protein Ftsy (Tm0570)
From Thermotoga Maritima At 1.60 A Resolution
pdb|1VMA|B Chain B, Crystal Structure Of Cell Division Protein Ftsy (Tm0570)
From Thermotoga Maritima At 1.60 A Resolution
Length = 306
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/49 (53%), Positives = 33/49 (67%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLK 149
P VIM VG+ G+GKTT+C KLA ++ + L ADTFRA A +QLK
Sbjct: 104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLK 152
>pdb|2J7P|D Chain D, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
pdb|2J7P|E Chain E, Gmppnp-Stabilized Ng Domain Complex Of The Srp Gtpases Ffh
And Ftsy
Length = 283
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 62/135 (45%), Gaps = 23/135 (17%)
Query: 43 DVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVK-------AHQ 95
DV + +++ + VR ASG R+ ++ +V ++L+ +++P +
Sbjct: 22 DVGLSATEEILQEVR--------ASG---RKDLKEAVKEKLVGMLEPDERRATLRKLGFN 70
Query: 96 PQKGKP-----NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
PQK KP V++ VG+ G GKTTT KL +Y K DTFRA QL +
Sbjct: 71 PQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSE 130
Query: 151 NATKARIPFYGSSKG 165
+ IP +G
Sbjct: 131 WGKRLSIPVIQGPEG 145
>pdb|1RJ9|A Chain A, Structure Of The Heterodimer Of The Conserved Gtpase
Domains Signal Recognition Particle (Ffh) And Its
Receptor (Ftsy)
Length = 304
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 62/135 (45%), Gaps = 23/135 (17%)
Query: 43 DVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVK-------AHQ 95
DV + +++ + VR ASG R+ ++ +V ++L+ +++P +
Sbjct: 43 DVGLSATEEILQEVR--------ASG---RKDLKEAVKEKLVGMLEPDERRATLRKLGFN 91
Query: 96 PQKGKP-----NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
PQK KP V++ VG+ G GKTTT KL +Y K DTFRA QL +
Sbjct: 92 PQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSE 151
Query: 151 NATKARIPFYGSSKG 165
+ IP +G
Sbjct: 152 WGKRLSIPVIQGPEG 166
>pdb|1OKK|D Chain D, Homo-Heterodimeric Complex Of The Srp Gtpases
pdb|2XKV|D Chain D, Atomic Model Of The Srp-Ftsy Early Conformation
Length = 303
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 62/135 (45%), Gaps = 23/135 (17%)
Query: 43 DVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVK-------AHQ 95
DV + +++ + VR ASG R+ ++ +V ++L+ +++P +
Sbjct: 42 DVGLSATEEILQEVR--------ASG---RKDLKEAVKEKLVGMLEPDERRATLRKLGFN 90
Query: 96 PQKGKP-----NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
PQK KP V++ VG+ G GKTTT KL +Y K DTFRA QL +
Sbjct: 91 PQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSE 150
Query: 151 NATKARIPFYGSSKG 165
+ IP +G
Sbjct: 151 WGKRLSIPVIQGPEG 165
>pdb|2CNW|D Chain D, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|E Chain E, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2CNW|F Chain F, Gdpalf4 Complex Of The Srp Gtpases Ffh And Ftsy
pdb|2IYL|D Chain D, Structure Of An Ftsy:gdp Complex
Length = 284
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 62/135 (45%), Gaps = 23/135 (17%)
Query: 43 DVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVK-------AHQ 95
DV + +++ + VR ASG R+ ++ +V ++L+ +++P +
Sbjct: 23 DVGLSATEEILQEVR--------ASG---RKDLKEAVKEKLVGMLEPDERRATLRKLGFN 71
Query: 96 PQKGKP-----NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
PQK KP V++ VG+ G GKTTT KL +Y K DTFRA QL +
Sbjct: 72 PQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSE 131
Query: 151 NATKARIPFYGSSKG 165
+ IP +G
Sbjct: 132 WGKRLSIPVIQGPEG 146
>pdb|2Q9A|A Chain A, Structure Of Apo Ftsy
pdb|2Q9A|B Chain B, Structure Of Apo Ftsy
pdb|2Q9B|A Chain A, Structure Of Ftsy:gmppnp Complex
pdb|2Q9B|B Chain B, Structure Of Ftsy:gmppnp Complex
pdb|2Q9C|A Chain A, Structure Of Ftsy:gmppnp With Mgcl Complex
pdb|2Q9C|B Chain B, Structure Of Ftsy:gmppnp With Mgcl Complex
Length = 304
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 62/135 (45%), Gaps = 23/135 (17%)
Query: 43 DVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGVK-------AHQ 95
DV + +++ + VR ASG R+ ++ +V ++L+ +++P +
Sbjct: 43 DVGLSATEEILQEVR--------ASG---RKDLKEAVKEKLVGMLEPDERRATLRKLGFN 91
Query: 96 PQKGKP-----NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
PQK KP V++ VG+ G GKTTT KL +Y K DTFRA QL +
Sbjct: 92 PQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSE 151
Query: 151 NATKARIPFYGSSKG 165
+ IP +G
Sbjct: 152 WGKRLSIPVIQGPEG 166
>pdb|1YR6|A Chain A, Pab0955 Crystal Structure : A Gtpase In Apo Form From
Pyrococcus Abyssi
pdb|1YR7|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gtp-Gamma-S Bound
Form From Pyrococcus Abyssi
pdb|1YR8|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gtp Bound Form
From Pyrococcus Abyssi
pdb|1YR9|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Po4 Bound
Form From Pyrococcus Abyssi
pdb|1YRA|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp Bound Form
From Pyrococcus Abyssi
pdb|1YRA|B Chain B, Pab0955 Crystal Structure : A Gtpase In Gdp Bound Form
From Pyrococcus Abyssi
pdb|1YRB|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
Form From Pyrococcus Abyssi
pdb|1YRB|B Chain B, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
Form From Pyrococcus Abyssi
pdb|2OXR|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
Form From Pyrococcus Abyssi (After Gtp Hydrolysis)
Length = 262
Score = 33.9 bits (76), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADT 139
+++FVG GSGKTT + YL+ N+K V DT
Sbjct: 16 IVVFVGTAGSGKTTLTGEFG-RYLEDNYKVAYVNLDT 51
>pdb|1QF9|A Chain A, Ph Influences Fluoride Coordination Number Of The Alfx
Phosphoryl Transfer Transition State Analog In UmpCMP
Kinase
pdb|5UKD|A Chain A, Ph Influences Fluoride Coordination Number Of The Alfx
Phosphoryl Transfer Transition State Analog
pdb|1UKE|A Chain A, UmpCMP KINASE FROM SLIME MOLD
pdb|2UKD|A Chain A, UmpCMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP
pdb|3UKD|A Chain A, UmpCMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP, AND
Alf3
pdb|4UKD|A Chain A, UmpCMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP,
Beryllium Fluoride
Length = 194
Score = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 97 QKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
+K KPNV+ +G GSGK T C + +
Sbjct: 2 EKSKPNVVFVLGGPGSGKGTQCANIVRDF 30
>pdb|2PBR|A Chain A, Crystal Structure Of Thymidylate Kinase (Aq_969) From
Aquifex Aeolicus Vf5
pdb|2PBR|B Chain B, Crystal Structure Of Thymidylate Kinase (Aq_969) From
Aquifex Aeolicus Vf5
Length = 195
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/26 (57%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKK 128
+I F G+ GSGKTT KL Y YLK+
Sbjct: 2 LIAFEGIDGSGKTTQAKKL-YEYLKQ 26
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 91 VKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWK 131
+K + +K P+ ++F G G+GKT T LA +NW+
Sbjct: 29 LKGYVERKNIPH-LLFSGPPGTGKTATAIALARDLFGENWR 68
>pdb|3LD6|A Chain A, Crystal Structure Of Human Lanosterol 14alpha-Demethylase
(C Complex With Ketoconazole
pdb|3LD6|B Chain B, Crystal Structure Of Human Lanosterol 14alpha-Demethylase
(C Complex With Ketoconazole
pdb|3JUS|A Chain A, Crystal Structure Of Human Lanosterol 14alpha-Demethylase
(Cyp51) In Complex With Econazole
pdb|3JUS|B Chain B, Crystal Structure Of Human Lanosterol 14alpha-Demethylase
(Cyp51) In Complex With Econazole
pdb|3JUV|A Chain A, Crystal Structure Of Human Lanosterol 14alpha-Demethylase
(C
Length = 461
Score = 30.4 bits (67), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 53/139 (38%), Gaps = 19/139 (13%)
Query: 63 DEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLA 122
D + KRR Q + L L+D K +P M +GL +G+ T+ T A
Sbjct: 214 DIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSA 273
Query: 123 Y--HYLKKN---WKACL-----VCADTFRAGAYDQLK---------QNATKARIPFYGSS 163
+ +L ++ K C VC + YDQLK + + R P
Sbjct: 274 WMGFFLARDKTLQKKCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMM 333
Query: 164 KGKRNPIHNMGLSLIPTYE 182
+ R P G ++ P ++
Sbjct: 334 RMARTPQTVAGYTIPPGHQ 352
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 91 VKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWK 131
+K + +K P+ ++F G G+GKT T LA +NW+
Sbjct: 29 LKGYVERKNIPH-LLFSGPPGTGKTATAIALARDLFGENWR 68
>pdb|2YVU|A Chain A, Crystal Structure Of Ape1195
pdb|2YVU|B Chain B, Crystal Structure Of Ape1195
Length = 186
Score = 30.0 bits (66), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRA 142
V+ GL GSGKTT T+LA K+ ++ ++ D R
Sbjct: 15 VVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWART 54
>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|B Chain B, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|C Chain C, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|D Chain D, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|E Chain E, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
Length = 327
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 94 HQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWK 131
H + G ++F G G GKTT LA +NW+
Sbjct: 39 HYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWR 76
>pdb|1Z83|A Chain A, Crystal Structure Of Human Ak1a In Complex With Ap5a
pdb|1Z83|B Chain B, Crystal Structure Of Human Ak1a In Complex With Ap5a
pdb|1Z83|C Chain C, Crystal Structure Of Human Ak1a In Complex With Ap5a
pdb|2C95|A Chain A, Structure Of Adenylate Kinase 1 In Complex With P1,P4-Di
(Adenosine)tetraphosphate
pdb|2C95|B Chain B, Structure Of Adenylate Kinase 1 In Complex With P1,P4-Di
(Adenosine)tetraphosphate
Length = 196
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHY 125
K N+I VG GSGK T C K+ Y
Sbjct: 8 KTNIIFVVGGPGSGKGTQCEKIVQKY 33
>pdb|1LOH|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase In Complex With
Hexasaccharide Hyaluronan Substrate
pdb|1LXK|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase In Complex With
Tetrasaccharide Hyaluronan Substrate
Length = 721
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|1N7N|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase W292a Mutant
Length = 721
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|1OJN|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex Of The Tyr408phe Mutant With
6-sulphated Chondroitin Disaccharide
Length = 731
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 634 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 692
>pdb|1OJM|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex With Unsulphated Chondroitin
Disaccharide
Length = 729
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|1N7O|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase F343v Mutant
Length = 721
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|1EGU|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase At 1.56 A Resolution
pdb|1F9G|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase Cocrystallized With Ascorbic Acid
pdb|1C82|A Chain A, Mechanism Of Hyaluronan Binding And Degradation: Structure
Of Streptococcus Pneumoniae Hyaluronate Lyase In Complex
With Hyaluronic Acid Disaccharide At 1.7 A Resolution
pdb|1OJP|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex With 6-sulphated Chondroitin
Disaccharide
pdb|1W3Y|A Chain A, Crystal Structure Of S. Pneumoniae Hyaluronate Lyase In
Complex With Palmitoyl-Vitamin C
pdb|2BRP|A Chain A, Crystal Structure Of S.Pneumoniae Hyaluronate Lyase In
Complex With W249b
pdb|2BRV|X Chain X, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase From 70percent Saturated Malonate.
pdb|2BRW|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase From 30percent Pegmme.
pdb|2BRW|B Chain B, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase From 30percent Pegmme
Length = 731
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 634 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 692
>pdb|1OJO|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex Of The Tyr408phe Mutant With
4-sulphated Chondroitin Disaccharide
Length = 731
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 634 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 692
>pdb|1N7Q|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase W291aW292A
DOUBLE MUTANT Complex With Hyaluronan Hexasacchride
Length = 721
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|1N7P|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase W292aF343V
Double Mutant
Length = 721
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 76 QSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNW 130
Q+ V + K VD G H ++F G G+GKT+T LA KN+
Sbjct: 30 QNEVITTVRKFVDEGKLPH---------LLFYGPPGTGKTSTIVALAREIYGKNY 75
>pdb|1N7R|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase
W291a/w292a/f343v Mutant Complex With Hexasaccharide
Hyaluronan
Length = 721
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL-NKRRMIQSSVY 80
++ N M+KE+ ++L+E + ++ V ++ V ++ +D+ S + N+ ++++ VY
Sbjct: 632 VDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVY 690
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 108 GLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
G G+GKT T + YH ++ LVCA + A DQL +
Sbjct: 202 GPPGTGKTVTSATIVYHLARQGNGPVLVCAPS--NIAVDQLTE 242
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 108 GLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
G G+GKT T + YH ++ LVCA + A DQL +
Sbjct: 201 GPPGTGKTVTSATIVYHLARQGNGPVLVCAPS--NIAVDQLTE 241
>pdb|1ODF|A Chain A, Structure Of Ygr205w Protein
Length = 290
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKK---NWKACLVCADTFRAGAYDQLKQN 151
P I F G QGSGK+ T ++ H ++K D F DQLK N
Sbjct: 31 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLN 84
>pdb|1UKY|A Chain A, Substrate Specificity And Assembly Of Catalytic Center
Derived From Two Structures Of Ligated Uridylate Kinase
pdb|1UKZ|A Chain A, Substrate Specificity And Assembly Of Catalytic Center
Derived From Two Structures Of Ligated Uridylate Kinase
Length = 203
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 102 NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKAC-LVCADTFRAGA-YDQLKQNATK 154
+VI +G G+GK T C KL Y + A L+ A+ RAG+ Y +L +N K
Sbjct: 16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAGDLLRAEQGRAGSQYGELIKNCIK 70
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 105 MFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQ 150
+ G G+GKT T + YH ++ LVCA + A DQL +
Sbjct: 375 LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS--NIAVDQLTE 418
>pdb|1T5D|X Chain X, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE BOUND TO
4-Chlorobenzoate
pdb|3CW9|A Chain A, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE IN THE
THIOESTER-Forming Conformation, Bound To
4-Chlorophenacyl-Coa
pdb|3CW9|B Chain B, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE IN THE
THIOESTER-Forming Conformation, Bound To
4-Chlorophenacyl-Coa
Length = 504
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 148 LKQNATKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ Q A ++R+ F + G R+ HN+ L L+P Y
Sbjct: 173 IPQRAAESRVLFMSTQVGLRHGRHNVVLGLMPLY 206
>pdb|3CW8|X Chain X, 4-chlorobenzoyl-coa Ligase/synthetase, Bound To
4cba-adenylate
Length = 504
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 148 LKQNATKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ Q A ++R+ F + G R+ HN+ L L+P Y
Sbjct: 173 IPQRAAESRVLFMSTQVGLRHGRHNVVLGLMPLY 206
>pdb|2QVZ|X Chain X, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE, I303A MUTATION,
BOUND TO 3- Chlorobenzoate
pdb|2QW0|X Chain X, 4-chlorobenzoyl-coa Ligase/synthetase, I303a Mutation,
Bound To 3,4 Dichlorobenzoate
Length = 504
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 148 LKQNATKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ Q A ++R+ F + G R+ HN+ L L+P Y
Sbjct: 173 IPQRAAESRVLFMSTQVGLRHGRHNVVLGLMPLY 206
>pdb|2QVX|X Chain X, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE, I303G MUTATION,
BOUND TO 3- Chlorobenzoate
pdb|2QVY|X Chain X, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE, I303G MUTATION,
BOUND TO 3,4- Dichlorobenzoate
Length = 504
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 148 LKQNATKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ Q A ++R+ F + G R+ HN+ L L+P Y
Sbjct: 173 IPQRAAESRVLFMSTQVGLRHGRHNVVLGLMPLY 206
>pdb|3DLP|X Chain X, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE, MUTANT D402P, BOUND
To 4cb
Length = 504
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 148 LKQNATKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ Q A ++R+ F + G R+ HN+ L L+P Y
Sbjct: 173 IPQRAAESRVLFMSTQVGLRHGRHNVVLGLMPLY 206
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 105 MFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADT 139
+ G G+GKT T + YH K + LVCA +
Sbjct: 379 LIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPS 413
>pdb|3NG0|A Chain A, Crystal Structure Of Glutamine Synthetase From
Synechocystis Sp. Pcc 6803
Length = 473
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 145 YDQLKQNATKARIPFYGSSKGKRNPIHNMGLSLIP 179
YDQL +N+ IPF GSS I+ + ++P
Sbjct: 38 YDQLDENSFTEGIPFDGSSIRGWKAINESDMCMVP 72
>pdb|3ADK|A Chain A, Refined Structure Of Porcine Cytosolic Adenylate Kinase At
2.1 Angstroms Resolution
Length = 195
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHY 125
K +I VG GSGK T C K+ Y
Sbjct: 8 KSKIIFVVGGPGSGKGTQCEKIVQKY 33
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 29 NSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVY-KELIKL 86
N + E C ++ + + L +R++I+ M SG+N++ ++ S+ + KE+ KL
Sbjct: 168 NKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKL 226
>pdb|2BWJ|A Chain A, Structure Of Adenylate Kinase 5
pdb|2BWJ|B Chain B, Structure Of Adenylate Kinase 5
pdb|2BWJ|C Chain C, Structure Of Adenylate Kinase 5
pdb|2BWJ|D Chain D, Structure Of Adenylate Kinase 5
pdb|2BWJ|E Chain E, Structure Of Adenylate Kinase 5
pdb|2BWJ|F Chain F, Structure Of Adenylate Kinase 5
Length = 199
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHY 125
K +I +G GSGK T C KL Y
Sbjct: 11 KCKIIFIIGGPGSGKGTQCEKLVEKY 36
>pdb|1T5H|X Chain X, 4-Chlorobenzoyl-Coa LigaseSYNTHETASE UNLIGANDED,
SELENOMETHIONINE
Length = 504
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 148 LKQNATKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ Q A ++R+ F + G R+ HN+ L L P Y
Sbjct: 173 IPQRAAESRVLFXSTQVGLRHGRHNVVLGLXPLY 206
>pdb|3TQI|A Chain A, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
pdb|3TQI|B Chain B, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
pdb|3TQI|C Chain C, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
pdb|3TQI|D Chain D, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
Length = 527
Score = 26.9 bits (58), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 11/72 (15%)
Query: 25 EEVLNSMLKEICAALLEADVNIKLVKKLR-----ENVRQVID------FDEMASGLNKRR 73
+EVLN K + A ++ D + +K L+ E R++ F+E A LN +
Sbjct: 274 DEVLNVFQKHLGAKVICVDAKDRFMKALKGISDPEEKRKIAGEQFIRVFEEQAKKLNVKW 333
Query: 74 MIQSSVYKELIK 85
+ Q ++Y ++I+
Sbjct: 334 LGQGTIYPDVIE 345
>pdb|3UMF|A Chain A, Schistosoma Mansoni Adenylate Kinase
Length = 217
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 86 LVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLA--YHY 125
LV G + K VI +G GSGK T C KL +H+
Sbjct: 14 LVPRGSHMTDQKLAKAKVIFVLGGPGSGKGTQCEKLVQKFHF 55
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
0.319 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,332,205
Number of Sequences: 62578
Number of extensions: 201918
Number of successful extensions: 795
Number of sequences better than 100.0: 85
Number of HSP's better than 100.0 without gapping: 75
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 690
Number of HSP's gapped (non-prelim): 89
length of query: 190
length of database: 14,973,337
effective HSP length: 93
effective length of query: 97
effective length of database: 9,153,583
effective search space: 887897551
effective search space used: 887897551
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: 48 (23.1 bits)