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= 015221
(411 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 = 513 bits (1322), Expect = e-146, Method: Compositional matrix adjust.
Identities = 239/386 (61%), Positives = 306/386 (79%), Gaps = 1/386 (0%)
Query: 1 MVLAQLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIV 60
MVLA LG I+ A++ +SNATII+E+VLN L E+ ALL+ADV KLV++++ N+K +
Sbjct: 1 MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAI 60
Query: 61 NLDDLAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTK 120
+L+++A+G NKR++IQ A+F EL K++DPG ++TP KGK +VIMFVGLQGSGKTTTC+K
Sbjct: 61 DLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGKTTTCSK 120
Query: 121 YAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFK 180
AYY+Q+KGWK L+CADTFRAGAFDQLKQNATKA+IPFYGSYTE DPV IA EGVE FK
Sbjct: 121 LAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFK 180
Query: 181 KENCDLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSV 240
EN ++IIVDTSGRHKQE +LFEEM QV+ A PD +++VMD+SIG V
Sbjct: 181 NENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQAKAFKDKV 240
Query: 241 SVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDW 300
V +VIVTK+DGHAKGGGALSAVAATKSP+IFIGTGEH+D+FE F +PF+S+LLGMGD
Sbjct: 241 DVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLGMGDI 300
Query: 301 SGFMDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSEL 360
G +DK++E + +D L++KL G FTLR MYEQFQNI+KMGP Q+ M+PGF ++
Sbjct: 301 EGLIDKVNE-LKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDF 359
Query: 361 MPKGREKESQAKIKRYMTMMDSMTNE 386
M KG E+ES A++K+ MT+MDSM ++
Sbjct: 360 MSKGNEQESMARLKKLMTIMDSMNDQ 385
>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 = 322 bits (824), Expect = 3e-88, Method: Compositional matrix adjust.
Identities = 170/389 (43%), Positives = 248/389 (63%), Gaps = 10/389 (2%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
+LG ++++A+ ++ A +D+K++ E + +I RAL+QADV KLV +M I++ +
Sbjct: 3 KLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEK 62
Query: 65 LAAGHNKRRIIQQAIFNELCKML--DPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYA 122
G +K+ I + ++ EL K+L + K PKK +VI+ VG+QGSGKTTT K A
Sbjct: 63 TPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKK--QNVILLVGIQGSGKTTTAAKLA 120
Query: 123 YYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTES-DPVRIAVEGVETFKK 181
Y QK+G KPAL+ ADT+R A++QLKQ A K +P YG T + PV I EG+E FKK
Sbjct: 121 RYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKK 180
Query: 182 ENCDLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSV- 240
D++I+DT+GRHK+E L EEM+Q+ E TNPD +I V+D +IG +V
Sbjct: 181 --ADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVG 238
Query: 241 SVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDW 300
+G++IVTK+DG AKGGGALSAVA TK+P+ FIG GE +D+ E FD K F+SRLLGMGD
Sbjct: 239 EIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDL 298
Query: 301 SGFMDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSEL 360
++K ++V ++ E + + G FTL + Q + I MG + ++ SM+PGF
Sbjct: 299 ESLLEKAEDMVD-EKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGG-A 356
Query: 361 MPKGREKESQAKIKRYMTMMDSMTNEGKQ 389
MPK ++AKIK+Y ++ SMT E ++
Sbjct: 357 MPKELSHLTEAKIKKYKVIISSMTKEERE 385
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 322 bits (824), Expect = 3e-88, Method: Compositional matrix adjust.
Identities = 170/389 (43%), Positives = 248/389 (63%), Gaps = 10/389 (2%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
+LG ++++A+ ++ A +D+K++ E + +I RAL+QADV KLV +M I++ +
Sbjct: 3 KLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEK 62
Query: 65 LAAGHNKRRIIQQAIFNELCKML--DPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYA 122
G +K+ I + ++ EL K+L + K PKK +VI+ VG+QGSGKTTT K A
Sbjct: 63 TPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKK--QNVILLVGIQGSGKTTTAAKLA 120
Query: 123 YYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTES-DPVRIAVEGVETFKK 181
Y QK+G KPAL+ ADT+R A++QLKQ A K +P YG T + PV I EG+E FKK
Sbjct: 121 RYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKK 180
Query: 182 ENCDLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSV- 240
D++I+DT+GRHK+E L EEM+Q+ E TNPD +I V+D +IG +V
Sbjct: 181 --ADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVG 238
Query: 241 SVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDW 300
+G++IVTK+DG AKGGGALSAVA TK+P+ FIG GE +D+ E FD K F+SRLLGMGD
Sbjct: 239 EIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDL 298
Query: 301 SGFMDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSEL 360
++K ++V ++ E + + G FTL + Q + I MG + ++ SM+PGF
Sbjct: 299 ESLLEKAEDMVD-EKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGG-A 356
Query: 361 MPKGREKESQAKIKRYMTMMDSMTNEGKQ 389
MPK ++AKIK+Y ++ SMT E ++
Sbjct: 357 MPKELSHLTEAKIKKYKVIISSMTKEERE 385
>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 = 314 bits (804), Expect = 6e-86, Method: Compositional matrix adjust.
Identities = 162/388 (41%), Positives = 248/388 (63%), Gaps = 5/388 (1%)
Query: 1 MVLAQLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIV 60
MVL LG +++ +++++ A+ +DE ++ E + +I RAL+QADV +LV ++ I++
Sbjct: 1 MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRA 60
Query: 61 NLDDLAAGHNKRRIIQQAIFNELCKML-DPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCT 119
+ AG +K+ I + ++ EL K L KP K KP++++ VG+QGSGKTTT
Sbjct: 61 LEEKPPAGISKKEHIIKIVYEELTKFLGTEAKP--IEIKEKPTILLMVGIQGSGKTTTVA 118
Query: 120 KYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETF 179
K A Y QK+G+K +VC+DT+R GA+ QL+Q + I +G+ E D +++A EGV+ F
Sbjct: 119 KLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYF 178
Query: 180 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXS 239
K + D+IIVDT+GRHK++ AL EEM+Q+S +P VI V+D +IG +
Sbjct: 179 KSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEA 238
Query: 240 VSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 299
+G++IVTK+DG AKGGGALSAVAAT +P+ FIGTGE +D+ E FD FVSRLLG+GD
Sbjct: 239 TPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGD 298
Query: 300 WSGFMDKIHEV-VPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSS 358
G ++K E+ ++ + E +++ G FTL+ MY Q + + KMGP+ Q+ M+PG
Sbjct: 299 IQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRMIPGLGY 358
Query: 359 ELMPKGREKESQAKIKRYMTMMDSMTNE 386
L P + ++K++ +MDSMT E
Sbjct: 359 SL-PDDVISIGEERLKKFKVIMDSMTEE 385
>pdb|3KL4|A Chain A, Recognition Of A Signal Peptide By The Signal Recognition
Particle
Length = 433
Score = 266 bits (679), Expect = 2e-71, Method: Compositional matrix adjust.
Identities = 147/384 (38%), Positives = 228/384 (59%), Gaps = 10/384 (2%)
Query: 9 SISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAG 68
+I A+++ + EK ++E + ++ ++L+ +DV KLV + IK+ +N + +
Sbjct: 5 NIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSV 64
Query: 69 HNKRRIIQQAIFNELCKMLDPGK-PSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQK 127
++ +++EL K+ K P+ P K P +IM VG+QGSGKTTT K AY+++K
Sbjct: 65 LERKEWFISIVYDELSKLFGGDKEPNVNPTK-LPFIIMLVGVQGSGKTTTAGKLAYFYKK 123
Query: 128 KGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLI 187
+G+K LV AD +R A+DQL Q + + YG +P+ IA +GV+ F K D+I
Sbjct: 124 RGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDII 183
Query: 188 IVDTSGRH--KQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAV 245
IVDT+GRH +E L EEM+++ + PD VI V+D+SIG + +G+V
Sbjct: 184 IVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQASPIGSV 243
Query: 246 IVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFMD 305
I+TKMDG AKGGGALSAV AT + + FIGTGE +DE E F+ K FVSR+LGMGD ++
Sbjct: 244 IITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESILE 303
Query: 306 KIHEVVPMDQQPELLQKLSE--GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPK 363
K+ + D+ + ++ + E G TLR +Y Q + KMGP+ +V +PG ++P
Sbjct: 304 KVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGI-MLPT 362
Query: 364 GRE---KESQAKIKRYMTMMDSMT 384
E K + KI+R++ ++SMT
Sbjct: 363 PSEDQLKIGEEKIRRWLAALNSMT 386
>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 = 266 bits (679), Expect = 2e-71, Method: Compositional matrix adjust.
Identities = 147/384 (38%), Positives = 228/384 (59%), Gaps = 10/384 (2%)
Query: 9 SISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAG 68
+I A+++ + EK ++E + ++ ++L+ +DV KLV + IK+ +N + +
Sbjct: 12 NIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSV 71
Query: 69 HNKRRIIQQAIFNELCKMLDPGK-PSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQK 127
++ +++EL K+ K P+ P K P +IM VG+QGSGKTTT K AY+++K
Sbjct: 72 LERKEWFISIVYDELSKLFGGDKEPNVNPTK-LPFIIMLVGVQGSGKTTTAGKLAYFYKK 130
Query: 128 KGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLI 187
+G+K LV AD +R A+DQL Q + + YG +P+ IA +GV+ F K D+I
Sbjct: 131 RGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDII 190
Query: 188 IVDTSGRH--KQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAV 245
IVDT+GRH +E L EEM+++ + PD VI V+D+SIG + +G+V
Sbjct: 191 IVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQASPIGSV 250
Query: 246 IVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFMD 305
I+TKMDG AKGGGALSAV AT + + FIGTGE +DE E F+ K FVSR+LGMGD ++
Sbjct: 251 IITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESILE 310
Query: 306 KIHEVVPMDQQPELLQKLSE--GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPK 363
K+ + D+ + ++ + E G TLR +Y Q + KMGP+ +V +PG ++P
Sbjct: 311 KVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGI-MLPT 369
Query: 364 GRE---KESQAKIKRYMTMMDSMT 384
E K + KI+R++ ++SMT
Sbjct: 370 PSEDQLKIGEEKIRRWLAALNSMT 393
>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens
Length = 297
Score = 209 bits (531), Expect = 3e-54, Method: Compositional matrix adjust.
Identities = 120/273 (43%), Positives = 167/273 (61%), Gaps = 4/273 (1%)
Query: 25 EKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELC 84
+K + + + E+ ++L+ ADV KLV + IK+ + + +R + +++EL
Sbjct: 22 DKAVEDFIKELQKSLISADVNVKLVFSLTNKIKERLKNEKPPTYIERREWFIKIVYDELS 81
Query: 85 KMLDPGK-PSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAG 143
+ K P P K P VIM VG+QG+GKTTT K AY+++KKG+K LV AD +R
Sbjct: 82 NLFGGDKEPKVIPDK-IPYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADVYRPA 140
Query: 144 AFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRH--KQEAAL 201
A +QL+Q + +P YG E D V IA GVE F E ++IIVDT+GRH +EAAL
Sbjct: 141 ALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEKFLSEKMEIIIVDTAGRHGYGEEAAL 200
Query: 202 FEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALS 261
EEM+ + EA PD V V+D+SIG + +G +I+TKMDG AKGGGALS
Sbjct: 201 LEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKFNQASKIGTIIITKMDGTAKGGGALS 260
Query: 262 AVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRL 294
AVAAT + + FIGTGE +DE EVF+ + FV+RL
Sbjct: 261 AVAATGATIKFIGTGEKIDELEVFNPRRFVARL 293
>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens T112a Mutant
Length = 297
Score = 206 bits (525), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 119/273 (43%), Positives = 166/273 (60%), Gaps = 4/273 (1%)
Query: 25 EKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELC 84
+K + + + E+ ++L+ ADV KLV + IK+ + + +R + +++EL
Sbjct: 22 DKAVEDFIKELQKSLISADVNVKLVFSLTNKIKERLKNEKPPTYIERREWFIKIVYDELS 81
Query: 85 KMLDPGK-PSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAG 143
+ K P P K P VIM VG+QG+GK TT K AY+++KKG+K LV AD +R
Sbjct: 82 NLFGGDKEPKVIPDK-IPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADVYRPA 140
Query: 144 AFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRH--KQEAAL 201
A +QL+Q + +P YG E D V IA GVE F E ++IIVDT+GRH +EAAL
Sbjct: 141 ALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEKFLSEKMEIIIVDTAGRHGYGEEAAL 200
Query: 202 FEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALS 261
EEM+ + EA PD V V+D+SIG + +G +I+TKMDG AKGGGALS
Sbjct: 201 LEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKFNQASKIGTIIITKMDGTAKGGGALS 260
Query: 262 AVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRL 294
AVAAT + + FIGTGE +DE EVF+ + FV+RL
Sbjct: 261 AVAATGATIKFIGTGEKIDELEVFNPRRFVARL 293
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 189 bits (480), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 122/385 (31%), Positives = 189/385 (49%), Gaps = 8/385 (2%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFM 304
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD +
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDIESIL 301
Query: 305 DKIHEVVPMDQQPELLQKLSE--GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMP 362
+K+ + D+ + ++ + E G TLR +Y Q + KMGP+ +V +PG ++P
Sbjct: 302 EKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGI-MLP 360
Query: 363 KGRE---KESQAKIKRYMTMMDSMT 384
E K + KI+R++ ++SMT
Sbjct: 361 TPSEDQLKIGEEKIRRWLAALNSMT 385
>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 = 182 bits (462), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 120/385 (31%), Positives = 189/385 (49%), Gaps = 13/385 (3%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFM 304
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD +
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDVASLA 301
Query: 305 DKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKG 364
+K+ + P+ ++LS +F +Q QN+ ++GP ++ +LPG +P+G
Sbjct: 302 EKVRAAGLEAEAPKSAKELSLEDF-----LKQMQNLKRLGPFSEILGLLPG-----VPQG 351
Query: 365 REKESQAKIKRYMTMMDSMTNEGKQ 389
+ + +A IKR ++ SMT E ++
Sbjct: 352 LKVDEKA-IKRLEAIVLSMTPEERK 375
>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 = 169 bits (428), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 89/278 (32%), Positives = 157/278 (56%), Gaps = 4/278 (1%)
Query: 23 IDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNE 82
I EK +++ L+E+ LL+ADV ++V ++ IK+ + + G +K +II++A+
Sbjct: 47 IKEKDVDKALDELEIDLLEADVALEVVDALREKIKQKLVGKKVRIGTDKGKIIEEAVKEA 106
Query: 83 LCKMLDPGKP----SFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCAD 138
+ ++L+ + K KP VIMFVG GSGKTTT K A + + G+ + +D
Sbjct: 107 VSEILETSRRIDLIEEIRKAEKPYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIAASD 166
Query: 139 TFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQE 198
TFRAGA +QL+++A + + +DP +A + ++ K D++++DT+GR +
Sbjct: 167 TFRAGAIEQLEEHAKRIGVKVIKHSYGADPAAVAYDAIQHAKARGIDVVLIDTAGRSETN 226
Query: 199 AALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGG 258
L +EM++++ T P+LVIFV D+ G +V + +I+TK+D A+GG
Sbjct: 227 RNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQFNEAVKIDGIILTKLDADARGGA 286
Query: 259 ALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLG 296
ALS +P++F+G G+ D+ F+ + F+ R+ G
Sbjct: 287 ALSISYVIDAPILFVGVGQGYDDLRPFEKEWFLERIFG 324
>pdb|2J28|9 Chain 9, Model Of E. Coli Srp Bound To 70s Rncs
Length = 430
Score = 169 bits (428), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 115/388 (29%), Positives = 189/388 (48%), Gaps = 17/388 (4%)
Query: 6 LGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDL 65
L +SR ++ +S + E + + L E+ ALL+ADV +VRE +K +
Sbjct: 4 LTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFINRVK------EK 57
Query: 66 AAGHNKRRIIQ------QAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCT 119
A GH + + + + NEL + + P+V++ GLQG+GKTT+
Sbjct: 58 AVGHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVG 117
Query: 120 KYAYYHQKKGWKPALVC-ADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVET 178
K + ++K K LV AD +R A QL+ A + + F+ S PV I ++
Sbjct: 118 KLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALKE 177
Query: 179 FKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXX 238
K + D+++VDT+GR + A+ +E++QV + NP +FV+D+ G
Sbjct: 178 AKLKFYDVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTGQDAANTAKAFNE 237
Query: 239 SVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 298
++ + V++TK+DG A+GG ALS T P+ F+G GE + E F SR+LGMG
Sbjct: 238 ALPLTGVVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGMG 297
Query: 299 DWSGFMDKIHEVVPMDQQPELLQKLSEGN-FTLRIMYEQFQNILKMGPIGQVFSMLPGFS 357
D ++ I V Q +L KL +G+ F L EQ + + MG + + LPG
Sbjct: 298 DVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMASLMGKLPGMG 357
Query: 358 SELMPKGREKESQAKI-KRYMTMMDSMT 384
+P + + K+ R +++SMT
Sbjct: 358 Q--IPDNVKSQMDDKVLVRMEAIINSMT 383
>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 = 169 bits (427), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 115/388 (29%), Positives = 189/388 (48%), Gaps = 17/388 (4%)
Query: 6 LGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDL 65
L +SR ++ +S + E + + L E+ ALL+ADV +VRE +K +
Sbjct: 5 LTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFINRVK------EK 58
Query: 66 AAGHNKRRIIQ------QAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCT 119
A GH + + + + NEL + + P+V++ GLQG+GKTT+
Sbjct: 59 AVGHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVG 118
Query: 120 KYAYYHQKKGWKPALVC-ADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVET 178
K + ++K K LV AD +R A QL+ A + + F+ S PV I ++
Sbjct: 119 KLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALKE 178
Query: 179 FKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXX 238
K + D+++VDT+GR + A+ +E++QV + NP +FV+D+ G
Sbjct: 179 AKLKFYDVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTGQDAANTAKAFNE 238
Query: 239 SVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 298
++ + V++TK+DG A+GG ALS T P+ F+G GE + E F SR+LGMG
Sbjct: 239 ALPLTGVVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGMG 298
Query: 299 DWSGFMDKIHEVVPMDQQPELLQKLSEGN-FTLRIMYEQFQNILKMGPIGQVFSMLPGFS 357
D ++ I V Q +L KL +G+ F L EQ + + MG + + LPG
Sbjct: 299 DVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMASLMGKLPGMG 358
Query: 358 SELMPKGREKESQAKI-KRYMTMMDSMT 384
+P + + K+ R +++SMT
Sbjct: 359 Q--IPDNVKSQMDDKVLVRMEAIINSMT 384
>pdb|3DM9|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 163 bits (413), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 87/278 (31%), Positives = 155/278 (55%), Gaps = 4/278 (1%)
Query: 23 IDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNE 82
I EK +++ L+E+ LL+ADV ++V ++ IK+ + + G +K +II++A+
Sbjct: 47 IKEKDVDKALDELEIDLLEADVALEVVDALREKIKQKLVGKKVRIGTDKGKIIEEAVKEA 106
Query: 83 LCKMLDPGKP----SFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCAD 138
+ ++L+ + K KP VI FVG GSGKTTT K A + + G+ + +D
Sbjct: 107 VSEILETSRRIDLIEEIRKAEKPYVIXFVGFNGSGKTTTIAKLANWLKNHGFSVVIAASD 166
Query: 139 TFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQE 198
TFRAGA +QL+++A + + +DP +A + ++ K D++++DT+GR +
Sbjct: 167 TFRAGAIEQLEEHAKRIGVKVIKHSYGADPAAVAYDAIQHAKARGIDVVLIDTAGRSETN 226
Query: 199 AALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGG 258
L +E ++++ T P+LVIFV D+ G +V + +I+TK+D A+GG
Sbjct: 227 RNLXDEXKKIARVTKPNLVIFVGDALAGNAIVEQARQFNEAVKIDGIILTKLDADARGGA 286
Query: 259 ALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLG 296
ALS +P++F+G G+ D+ F+ + F+ R+ G
Sbjct: 287 ALSISYVIDAPILFVGVGQGYDDLRPFEKEWFLERIFG 324
>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 = 154 bits (389), Expect = 8e-38, Method: Compositional matrix adjust.
Identities = 97/299 (32%), Positives = 143/299 (47%), Gaps = 2/299 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGF 303
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD +
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDVASL 300
>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 = 154 bits (389), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 97/295 (32%), Positives = 142/295 (48%), Gaps = 2/295 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 299
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
>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 = 154 bits (388), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 97/295 (32%), Positives = 142/295 (48%), Gaps = 2/295 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 299
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
>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 = 154 bits (388), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 97/295 (32%), Positives = 142/295 (48%), Gaps = 2/295 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 299
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
>pdb|1LS1|A Chain A, T. Aquaticus Ffh Ng Domain At 1.1a Resolution
Length = 295
Score = 152 bits (383), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 96/294 (32%), Positives = 141/294 (47%), Gaps = 2/294 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 298
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMG
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
>pdb|1FFH|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 294
Score = 151 bits (382), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 96/294 (32%), Positives = 141/294 (47%), Gaps = 2/294 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 3 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQ 62
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 63 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 120
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 121 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 180
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 181 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 240
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 298
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMG
Sbjct: 241 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 294
>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 = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 95/293 (32%), Positives = 140/293 (47%), Gaps = 2/293 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQ 63
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 64 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 121
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 122 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 181
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 241
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGM 297
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGM
Sbjct: 242 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
>pdb|2NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 293
Score = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 95/293 (32%), Positives = 140/293 (47%), Gaps = 2/293 (0%)
Query: 5 QLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLDD 64
QL + AI ++ I E+ L L EI RAL+ ADV ++ R+ +++
Sbjct: 3 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQ 62
Query: 65 LAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYY 124
+ +I ++ L + L G + P ++ VGLQGSGKTTT K A Y
Sbjct: 63 VLESLTPAEVILATVYEALKEAL--GGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALY 120
Query: 125 HQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENC 184
++ KG +P LV ADT R A +QL+ K +P P I E + E
Sbjct: 121 YKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEAR 180
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
DLI+VDT+GR + + L E+ ++ E PD V+ V+D+ G V V
Sbjct: 181 DLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTG 240
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGM 297
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGM
Sbjct: 241 LVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 293
>pdb|3B9Q|A Chain A, The Crystal Structure Of Cpftsy From Arabidopsis Thaliana
Length = 302
Score = 119 bits (297), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 85/292 (29%), Positives = 141/292 (48%), Gaps = 20/292 (6%)
Query: 19 NATIIDEKVL-------NECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNK 71
N +IDE +L + L+E+ ALL +D K+ + +++ + L +G
Sbjct: 13 NLAVIDELLLFWNLAETDRVLDELEEALLVSDFGPKITVRIVERLREDIMSGKLKSGSEI 72
Query: 72 RRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWK 131
+ +++++ L K K KP+VIM VG+ G GKTT+ K A+ + +G K
Sbjct: 73 KDALKESVLEMLAK--KNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTK 130
Query: 132 PALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAV---EGVETFKKENCDLII 188
+ DTFRA A DQL+ A + E D + A + V+ K+E D+++
Sbjct: 131 VLMAAGDTFRAAASDQLEIWAERTGCEIV--VAEGDKAKAATVLSKAVKRGKEEGYDVVL 188
Query: 189 VDTSGRHKQEAALFEEMRQVSEATN------PDLVIFVMDSSIGXXXXXXXXXXXXSVSV 242
DTSGR +L EE+ +A P+ ++ V+D + G V +
Sbjct: 189 CDTSGRLHTNYSLMEELIACKKAVGKIVSGAPNEILLVLDGNTGLNMLPQAREFNEVVGI 248
Query: 243 GAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRL 294
+I+TK+DG A+GG +S V PV FIG GE +++ + FD + FV+ +
Sbjct: 249 TGLILTKLDGSARGGCVVSVVEELGIPVKFIGVGEAVEDLQPFDPEAFVNAI 300
>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 = 118 bits (296), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 85/290 (29%), Positives = 138/290 (47%), Gaps = 16/290 (5%)
Query: 19 NATIIDEKV----LNEC---LNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNK 71
N ++DE + L+E L+E+ LL +D K ++ I+K + L +G
Sbjct: 29 NLAVVDELLTYWNLDESESILDELEEVLLVSDFGPKTALKIVDTIRKDILAGRLKSGPQI 88
Query: 72 RRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWK 131
+ +++ IF L + + + +P+V+M VG+ G GKTTT K A +K+G K
Sbjct: 89 KEALKKNIFKLLTERVTTTELQL--GNSRPAVLMIVGVNGGGKTTTLGKLANRFKKEGVK 146
Query: 132 PALVCADTFRAGAFDQLKQNATKAKIPFY-GSYTESDPVRIAVEGVETFKKENCDLIIVD 190
+ DTFRA A +QL+ A + + P + + V +E+ D+++ D
Sbjct: 147 VLMAAGDTFRAAAGEQLEVWAQRTGSEIVMAEGPKPRPAAVLSQAVRRAVEEDFDVVLCD 206
Query: 191 TSGRHKQEAALFEEMRQVSEATN------PDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 244
TSGR L EE+R A + P+ V+ V+D + G + V
Sbjct: 207 TSGRLHTNYNLMEELRGCKRAVSKALSSAPNEVLLVLDGTTGLNMLAQAREFNQVIGVTG 266
Query: 245 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRL 294
I+TK+DG A+GG +S V PV F+G GE +D+ + FD + FV L
Sbjct: 267 FILTKLDGTARGGCVVSVVDELSIPVKFVGVGEGIDDLQPFDAQSFVDAL 316
>pdb|2OG2|A Chain A, Crystal Structure Of Chloroplast Ftsy From Arabidopsis
Thaliana
Length = 359
Score = 118 bits (295), Expect = 7e-27, Method: Compositional matrix adjust.
Identities = 85/293 (29%), Positives = 141/293 (48%), Gaps = 20/293 (6%)
Query: 19 NATIIDEKVL-------NECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNK 71
N +IDE +L + L+E+ ALL +D K+ + +++ + L +G
Sbjct: 70 NLAVIDELLLFWNLAETDRVLDELEEALLVSDFGPKITVRIVERLREDIMSGKLKSGSEI 129
Query: 72 RRIIQQAIFNELCKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWK 131
+ +++++ L K K KP+VIM VG+ G GKTT+ K A+ + +G K
Sbjct: 130 KDALKESVLEMLAK--KNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTK 187
Query: 132 PALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAV---EGVETFKKENCDLII 188
+ DTFRA A DQL+ A + E D + A + V+ K+E D+++
Sbjct: 188 VLMAAGDTFRAAASDQLEIWAERTGCEIV--VAEGDKAKAATVLSKAVKRGKEEGYDVVL 245
Query: 189 VDTSGRHKQEAALFEEMRQVSEATN------PDLVIFVMDSSIGXXXXXXXXXXXXSVSV 242
DTSGR +L EE+ +A P+ ++ V+D + G V +
Sbjct: 246 CDTSGRLHTNYSLMEELIACKKAVGKIVSGAPNEILLVLDGNTGLNMLPQAREFNEVVGI 305
Query: 243 GAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLL 295
+I+TK+DG A+GG +S V PV FIG GE +++ + FD + FV+ +
Sbjct: 306 TGLILTKLDGSARGGCVVSVVEELGIPVKFIGVGEAVEDLQPFDPEAFVNAIF 358
>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 = 117 bits (294), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 77/287 (26%), Positives = 140/287 (48%), Gaps = 18/287 (6%)
Query: 29 NECLNEITRALLQADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELCKM-L 87
+E E+ L+Q D+ K+V ++ ++K D + N + + ++++
Sbjct: 34 DEFFEELEDVLIQTDMGMKMVLKVSNLVRKKTKRD--TSFENIKDALVESLYQAYTDNDW 91
Query: 88 DPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQ 147
K K+ + ++ M VG+ G+GKTT+ K A Y+ + G+K + ADTFRAGA Q
Sbjct: 92 TNKKYRIDFKENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADTFRAGATQQ 151
Query: 148 LKQ---NATKAKIPFY-GSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFE 203
L++ K+ + +DP + + ++ K++N DL+++DT+GR + + L
Sbjct: 152 LEEWIKTRLNNKVDLVKANKLNADPASVVFDAIKKAKEQNYDLLLIDTAGRLQNKTNLMA 211
Query: 204 EMRQVS------EATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGG 257
E+ +++ E + P V+ V+D++ G V +I+TKMD +KGG
Sbjct: 212 ELEKMNKIIQQVEKSAPHEVLLVIDATTGQNGVIQAEEFSKVADVSGIILTKMDSTSKGG 271
Query: 258 GALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFM 304
L+ P+ IG GE +D+ FD+ ++ L SGFM
Sbjct: 272 IGLAIKELLNIPIKMIGVGEKVDDLLAFDIDQYIVHL-----SSGFM 313
>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 = 115 bits (289), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 18/242 (7%)
Query: 72 RRIIQQAIFNELCKMLDPG-------KPSFTPKKGKP-----SVIMFVGLQGSGKTTTCT 119
R+ +++A+ +L ML+P K F P+K KP V++ VG+ G GKTTT
Sbjct: 61 RKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIA 120
Query: 120 KYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETF 179
K Y+Q G K DTFRA QL + + IP +DP +A + V+
Sbjct: 121 KLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAM 180
Query: 180 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEA------TNPDLVIFVMDSSIGXXXXXXX 233
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 181 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 240
Query: 234 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 293
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 241 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 300
Query: 294 LL 295
LL
Sbjct: 301 LL 302
>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 = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 18/242 (7%)
Query: 72 RRIIQQAIFNELCKMLDPG-------KPSFTPKKGKP-----SVIMFVGLQGSGKTTTCT 119
R+ +++A+ +L ML+P K F P+K KP V++ VG+ G GKTTT
Sbjct: 60 RKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIA 119
Query: 120 KYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETF 179
K Y+Q G K DTFRA QL + + IP +DP +A + V+
Sbjct: 120 KLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAM 179
Query: 180 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEA------TNPDLVIFVMDSSIGXXXXXXX 233
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 180 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 239
Query: 234 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 293
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 240 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 299
Query: 294 LL 295
LL
Sbjct: 300 LL 301
>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 = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 18/242 (7%)
Query: 72 RRIIQQAIFNELCKMLDPG-------KPSFTPKKGKP-----SVIMFVGLQGSGKTTTCT 119
R+ +++A+ +L ML+P K F P+K KP V++ VG+ G GKTTT
Sbjct: 41 RKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIA 100
Query: 120 KYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETF 179
K Y+Q G K DTFRA QL + + IP +DP +A + V+
Sbjct: 101 KLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAM 160
Query: 180 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEA------TNPDLVIFVMDSSIGXXXXXXX 233
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 161 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 220
Query: 234 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 293
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 221 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 280
Query: 294 LL 295
LL
Sbjct: 281 LL 282
>pdb|2QY9|A Chain A, Structure Of The Ng+1 Construct Of The E. Coli Srp
Receptor Ftsy
Length = 309
Score = 115 bits (288), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 72/264 (27%), Positives = 125/264 (47%), Gaps = 10/264 (3%)
Query: 42 ADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKP 101
ADV + R++ TN+ + + L ++++ + L K+ +P + P
Sbjct: 44 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEMGEILAKVDEP----LNVEGKAP 99
Query: 102 SVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYG 161
VI+ VG+ G GKTTT K A +++G L DTFRA A +QL+ + IP
Sbjct: 100 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIA 159
Query: 162 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVS------EATNPD 215
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ + P
Sbjct: 160 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 219
Query: 216 LVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 275
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 220 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 279
Query: 276 GEHMDEFEVFDVKPFVSRLLGMGD 299
GE +++ F F+ L D
Sbjct: 280 GERIEDLRPFKADDFIEALFARED 303
>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 = 115 bits (288), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 18/242 (7%)
Query: 72 RRIIQQAIFNELCKMLDPG-------KPSFTPKKGKP-----SVIMFVGLQGSGKTTTCT 119
R+ +++A+ +L ML+P K F P+K KP V++ VG+ G GKTTT
Sbjct: 40 RKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIA 99
Query: 120 KYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETF 179
K Y+Q G K DTFRA QL + + IP +DP +A + V+
Sbjct: 100 KLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAM 159
Query: 180 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEA------TNPDLVIFVMDSSIGXXXXXXX 233
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 160 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 219
Query: 234 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 293
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 220 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 279
Query: 294 LL 295
LL
Sbjct: 280 LL 281
>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 = 115 bits (287), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 72/264 (27%), Positives = 125/264 (47%), Gaps = 10/264 (3%)
Query: 42 ADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKP 101
ADV + R++ TN+ + + L ++++ + L K+ +P + P
Sbjct: 43 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEMGEILAKVDEP----LNVEGKAP 98
Query: 102 SVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYG 161
VI+ VG+ G GKTTT K A +++G L DTFRA A +QL+ + IP
Sbjct: 99 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIA 158
Query: 162 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVS------EATNPD 215
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ + P
Sbjct: 159 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 218
Query: 216 LVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 275
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 219 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 278
Query: 276 GEHMDEFEVFDVKPFVSRLLGMGD 299
GE +++ F F+ L D
Sbjct: 279 GERIEDLRPFKADDFIEALFARED 302
>pdb|1FTS|A Chain A, Signal Recognition Particle Receptor From E. Coli
Length = 295
Score = 114 bits (286), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 71/260 (27%), Positives = 124/260 (47%), Gaps = 10/260 (3%)
Query: 42 ADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKP 101
ADV + R++ TN+ + + L ++++ + L K+ +P + P
Sbjct: 38 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEMGEILAKVDEP----LNVEGKAP 93
Query: 102 SVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYG 161
VI+ VG+ G GKTTT K A +++G L DTFRA A +QL+ + IP
Sbjct: 94 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIA 153
Query: 162 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVS------EATNPD 215
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ + P
Sbjct: 154 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 213
Query: 216 LVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 275
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 214 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 273
Query: 276 GEHMDEFEVFDVKPFVSRLL 295
GE +++ F F+ L
Sbjct: 274 GERIEDLRPFKADDFIEALF 293
>pdb|2YHS|A Chain A, Structure Of The E. Coli Srp Receptor Ftsy
Length = 503
Score = 113 bits (282), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 72/264 (27%), Positives = 125/264 (47%), Gaps = 10/264 (3%)
Query: 42 ADVQFKLVREMQTNIKKIVNLDDLAAGHNKRRIIQQAIFNELCKMLDPGKPSFTPKKGKP 101
ADV + R++ TN+ + + L ++++ + L K+ +P + P
Sbjct: 238 ADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEMGEILAKVDEP----LNVEGKAP 293
Query: 102 SVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYG 161
VI+ VG+ G GKTTT K A +++G L DTFRA A +QL+ + IP
Sbjct: 294 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIA 353
Query: 162 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVS------EATNPD 215
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ + P
Sbjct: 354 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 413
Query: 216 LVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 275
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 414 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 473
Query: 276 GEHMDEFEVFDVKPFVSRLLGMGD 299
GE +++ F F+ L D
Sbjct: 474 GERIEDLRPFKADDFIEALFARED 497
>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 = 112 bits (280), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 82/242 (33%), Positives = 117/242 (48%), Gaps = 18/242 (7%)
Query: 72 RRIIQQAIFNELCKMLDPG-------KPSFTPKKGKP-----SVIMFVGLQGSGKTTTCT 119
R+ +++A+ +L ML+P K F P+K KP V++ VG+ G GKTTT
Sbjct: 61 RKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIA 120
Query: 120 KYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETF 179
K Y+Q G K DTFRA QL + + IP +D +A + V+
Sbjct: 121 KLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDSAALAYDAVQAM 180
Query: 180 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEA------TNPDLVIFVMDSSIGXXXXXXX 233
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 181 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 240
Query: 234 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 293
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 241 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 300
Query: 294 LL 295
LL
Sbjct: 301 LL 302
>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 = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 70/201 (34%), Positives = 100/201 (49%), Gaps = 6/201 (2%)
Query: 101 PSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFY 160
P VIM VG+ G+GKTT+C K A +G L ADTFRA A +QLK +
Sbjct: 104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVI 163
Query: 161 GSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATN------P 214
+DP +A + V N D++I+DT+GR + L EE+R+V P
Sbjct: 164 SHSEGADPAAVAFDAVAHALARNKDVVIIDTAGRLHTKKNLMEELRKVHRVVKKKIPDAP 223
Query: 215 DLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIG 274
+ V+D++ G +V+V +I+TK+DG AKGG L+ P+ FIG
Sbjct: 224 HETLLVIDATTGQNGLVQAKIFKEAVNVTGIILTKLDGTAKGGITLAIARELGIPIKFIG 283
Query: 275 TGEHMDEFEVFDVKPFVSRLL 295
GE ++ FD + FV LL
Sbjct: 284 VGEKAEDLRPFDPEAFVEVLL 304
>pdb|1WGW|A Chain A, Solution Structure Of The N-Terminal Domain Of Mouse
Putative Signal Recoginition Particle 54 (Srp54)
Length = 99
Score = 88.2 bits (217), Expect = 8e-18, Method: Composition-based stats.
Identities = 43/90 (47%), Positives = 66/90 (73%)
Query: 4 AQLGGSISRAIQQMSNATIIDEKVLNECLNEITRALLQADVQFKLVREMQTNIKKIVNLD 63
A LG I+ A++ +SNATII+E+VLN L E+ ALL+ADV KLV++++ N+K ++L+
Sbjct: 8 ADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDLE 67
Query: 64 DLAAGHNKRRIIQQAIFNELCKMLDPGKPS 93
++A+G NKR++IQ A+F EL K+ PS
Sbjct: 68 EMASGLNKRKMIQHAVFKELVKVKVYSGPS 97
>pdb|1MFQ|C Chain C, Crystal Structure Analysis Of A Ternary S-Domain Complex
Of Human Signal Recognition Particle
Length = 129
Score = 85.1 bits (209), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 326 GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKIKRYMTMMDSMTN 385
G FTLR MYEQFQNI+KMGP Q+ M+PGF ++ M KG E+ES A++K+ MT+MDSM +
Sbjct: 13 GQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMND 72
Query: 386 E 386
+
Sbjct: 73 Q 73
>pdb|1QB2|A Chain A, Crystal Structure Of The Conserved Subdomain Of Human
Protein Srp54m At 2.1a Resolution: Evidence For The
Mechanism Of Signal Peptide Binding
pdb|1QB2|B Chain B, Crystal Structure Of The Conserved Subdomain Of Human
Protein Srp54m At 2.1a Resolution: Evidence For The
Mechanism Of Signal Peptide Binding
pdb|1RY1|W Chain W, Structure Of The Signal Recognition Particle Interacting
With The Elongation-Arrested Ribosome
pdb|2GO5|W Chain W, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
Length = 109
Score = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 35/59 (59%), Positives = 47/59 (79%)
Query: 328 FTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKIKRYMTMMDSMTNE 386
FTLR MYEQFQNI+KMGP Q+ M+PGF ++ M KG E+ES A++K+ MT+MDSM ++
Sbjct: 2 FTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQ 60
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 65/259 (25%), Positives = 112/259 (43%), Gaps = 15/259 (5%)
Query: 25 EKVLNECLNEITRALLQADVQFKLVREMQTN-IKKIVNLDDLAAGHNKRRIIQQAIFNEL 83
+ VL E L + + L + ++ +TN +KK++ A G + ++ + + L
Sbjct: 35 QSVLPEPLRKAEKLLQETGIK----ESTKTNTLKKLLRFSVEAGGLTEENVVGK-LQEIL 89
Query: 84 CKMLDPGKPSFTPKKGKPSVIMFVGLQGSGKTTTCTKYAYYHQ-KKGWKPALVCADTFRA 142
C ML P K I+ G G+GKTTT K A +K K A + DT+R
Sbjct: 90 CDMLPSADKWQEPIHSK--YIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRI 147
Query: 143 GAFDQLKQNATKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALF 202
A +QLK A + P YT+ + + E F + D + VDT+GR+ ++
Sbjct: 148 AAVEQLKTYAELLQAPLEVCYTKEE----FQQAKELFSE--YDHVFVDTAGRNFKDPQYI 201
Query: 203 EEMRQVSEATNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSA 262
+E+++ + V+ ++ SV V I TK+D G +
Sbjct: 202 DELKETIPFESSIQSFLVLSATAKYEDMKHIVKRFSSVPVNQYIFTKIDETTSLGSVFNI 261
Query: 263 VAATKSPVIFIGTGEHMDE 281
+A +K V F+ G+++ E
Sbjct: 262 LAESKIGVGFMTNGQNVPE 280
>pdb|2JQE|A Chain A, Soution Structure Of Af54 M-Domain
Length = 119
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 323 LSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKE-SQAKIKRYMTMMD 381
+ +G FTL+ +Y+Q + + KMGP+ ++F MLP F L E +Q K+K++ +MD
Sbjct: 5 MEKGTFTLKDIYKQIEAMNKMGPVRKIFEMLP-FGLGLKVDNDVMEMTQEKMKKFRVIMD 63
Query: 382 SMTNE 386
SMT E
Sbjct: 64 SMTEE 68
>pdb|2YVU|A Chain A, Crystal Structure Of Ape1195
pdb|2YVU|B Chain B, Crystal Structure Of Ape1195
Length = 186
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 103 VIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRA 142
V+ GL GSGKTT T+ A QK+G++ ++ D R
Sbjct: 15 VVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWART 54
>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 = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 10/69 (14%)
Query: 91 KPSFTPKKGKPSVIMFVGLQGSGKTTTCTK----YAYYHQKKGWKPALVCADTFRAGA-F 145
+P+F+P + SVI +G G+GK T C K Y++ H G L+ A+ RAG+ +
Sbjct: 7 QPAFSPDQ--VSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG---DLLRAEQGRAGSQY 61
Query: 146 DQLKQNATK 154
+L +N K
Sbjct: 62 GELIKNCIK 70
>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 = 1.1, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 103 VIMFVGLQGSGKTTTCTKYAYYHQKKGW 130
+I F G+ GSGKTT K Y ++KG+
Sbjct: 2 LIAFEGIDGSGKTTQAKKLYEYLKQKGY 29
>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 = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 108 GLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQ 150
G G+GKT T Y+ ++G P 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 = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 108 GLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQ 150
G G+GKT T Y+ ++G P LVCA + A DQL +
Sbjct: 201 GPPGTGKTVTSATIVYHLARQGNGPVLVCAPS--NIAVDQLTE 241
>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 = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 105 MFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQ 150
+ G G+GKT T Y+ ++G P LVCA + A DQL +
Sbjct: 375 LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS--NIAVDQLTE 418
>pdb|3OWT|A Chain A, Crystal Structure Of S. Cerevisiae Rap1-Sir3 Complex
pdb|3OWT|B Chain B, Crystal Structure Of S. Cerevisiae Rap1-Sir3 Complex
Length = 157
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 290 FVSRLLGMGDWSGFMDKIHEVVPMDQQPELLQKL 323
F+ G FMDK+HEV+ D +P +KL
Sbjct: 33 FLPLFFHFGSTRQFMDKLHEVISGDYEPSQAEKL 66
>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 = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 62/140 (44%), Gaps = 23/140 (16%)
Query: 103 VIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADT----------FRAGAFDQLKQNA 152
+++FVG GSGKTT ++ Y + +K A V DT F +++
Sbjct: 16 IVVFVGTAGSGKTTLTGEFGRYLE-DNYKVAYVNLDTGVKELPYEPSIDVREFVTVEEIM 74
Query: 153 TKAKIPFYGSYTES-----DPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEE--M 205
+ P G+ ES + + + +KEN D +++DT G + E LF E +
Sbjct: 75 REGYGP-NGAIVESYDRLMEKFNEYLNKILRLEKEN-DYVLIDTPG--QMETFLFHEFGV 130
Query: 206 RQVSEATNPDLVIFVMDSSI 225
R + P LV+++ D I
Sbjct: 131 RLMENLPYP-LVVYISDPEI 149
>pdb|3TOV|A Chain A, The Crystal Structure Of The Glycosyl Transferase Family 9
From Veillonella Parvula Dsm 2008
pdb|3TOV|B Chain B, The Crystal Structure Of The Glycosyl Transferase Family 9
From Veillonella Parvula Dsm 2008
Length = 349
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 185 DLIIVDTSGRHKQEAALFEEMRQVSEATNPDLVI 218
+LI+VD GRH + L E R+++ D+VI
Sbjct: 61 ELIVVDKKGRHNSISGLNEVAREINAKGKTDIVI 94
>pdb|3HJN|A Chain A, Crystal Structure Of Thymidylate Kinase In Complex With
Dtdp And Adp From Thermotoga Maritima
pdb|3HJN|B Chain B, Crystal Structure Of Thymidylate Kinase In Complex With
Dtdp And Adp From Thermotoga Maritima
Length = 197
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 104 IMFVGLQGSGKTTTCTKYAYYHQKKGWKPAL 134
I F G+ GSGK+T A Y +K+G K L
Sbjct: 3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVIL 33
>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 = 28.1 bits (61), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 93 SFTPKKGKPSVIMFVGLQGSGKTTTCT----KYAYYHQKKG 129
S K K ++I VG GSGK T C KY Y H G
Sbjct: 1 SMEEKLKKTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTG 41
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.135 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,013,459
Number of Sequences: 62578
Number of extensions: 439476
Number of successful extensions: 1609
Number of sequences better than 100.0: 55
Number of HSP's better than 100.0 without gapping: 51
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1487
Number of HSP's gapped (non-prelim): 56
length of query: 411
length of database: 14,973,337
effective HSP length: 101
effective length of query: 310
effective length of database: 8,652,959
effective search space: 2682417290
effective search space used: 2682417290
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: 53 (25.0 bits)