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= 011010
(495 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 = 572 bits (1474), Expect = e-163, Method: Compositional matrix adjust.
Identities = 284/502 (56%), Positives = 380/502 (75%), Gaps = 12/502 (2%)
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 KENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXS 240
EN ++IIVDTSGRHKQE +LFEEM QV+ A + PD +++VMD+SIG
Sbjct: 181 NENFEIIIVDTSGRHKQEDSLFEEMLQVANA-IQPDNIVYVMDASIGQACEAQAKAFKDK 239
Query: 241 VSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 300
V V +VIVTK+DGHAKGGGALSAVAATKSP+IFIGTGEH+D+FE F +PF+S+LLGMGD
Sbjct: 240 VDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLGMGD 299
Query: 301 WSGFMDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSE 360
G +DK++E + +D L++KL G FTLR MYEQFQNI+KMGP Q+ M+PGF ++
Sbjct: 300 IEGLIDKVNE-LKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTD 358
Query: 361 LMPKGREKESQAKIKRYMTMMDSMTNEELDSSN-PKLMNDS--RIMRIARGSGRQVREVM 417
M KG E+ES A++K+ MT+MDSM ++ELDS++ K+ + RI R+ARGSG R+V
Sbjct: 359 FMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQ 418
Query: 418 EMLEEYKRLAKIWSKMKGLK-IPKKGEMSA-LSRNMNA---QHMSKVLPQGMLKQIGGVG 472
E+L +Y + A++ KM G+K + K G+MS +S++ A Q M+K++ +L +GG+
Sbjct: 419 ELLTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMA 478
Query: 473 GLQNLMKQM--GSTKDMMGMFG 492
GLQ++M+Q G+ +M GM G
Sbjct: 479 GLQSMMRQFQQGAAGNMKGMMG 500
>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 = 352 bits (903), Expect = 3e-97, Method: Compositional matrix adjust.
Identities = 187/453 (41%), Positives = 290/453 (64%), Gaps = 14/453 (3%)
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 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXX 239
K + D+IIVDT+GRHK++ AL EEM+Q+S ++P VI V+D +IG
Sbjct: 179 KSKGVDIIIVDTAGRHKEDKALIEEMKQISN-VIHPHEVILVIDGTIGQQAYNQALAFKE 237
Query: 240 SVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 299
+ +G++IVTK+DG AKGGGALSAVAAT +P+ FIGTGE +D+ E FD FVSRLLG+G
Sbjct: 238 ATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLG 297
Query: 300 DWSGFMDKIHEV-VPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFS 358
D G ++K E+ ++ + E +++ G FTL+ MY Q + + KMGP+ Q+ M+PG
Sbjct: 298 DIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRMIPGLG 357
Query: 359 SELMPKGREKESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVME 418
L P + ++K++ +MDSMT EEL NP+++N SRI RIARGSG ++V E
Sbjct: 358 YSL-PDDVISIGEERLKKFKVIMDSMTEEEL--LNPEIINYSRIKRIARGSGTSTKDVKE 414
Query: 419 MLEEYKRLAKIWSKMKGLKIPKKGEMSALSRNM 451
+L++Y+++ K++ M K ++S L+R
Sbjct: 415 LLDQYRQMKKLFKSM------NKRQLSRLARRF 441
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 345 bits (884), Expect = 5e-95, Method: Compositional matrix adjust.
Identities = 189/434 (43%), Positives = 272/434 (62%), Gaps = 13/434 (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 ENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSV 241
D++I+DT+GRHK+E L EEM+Q+ E T NPD +I V+D +IG +V
Sbjct: 181 --ADVLIIDTAGRHKEEKGLLEEMKQIKEIT-NPDEIILVIDGTIGQQAGIQAKAFKEAV 237
Query: 242 -SVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 300
+G++IVTK+DG AKGGGALSAVA TK+P+ FIG GE +D+ E FD K F+SRLLGMGD
Sbjct: 238 GEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGD 297
Query: 301 WSGFMDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSE 360
++K ++V ++ E + + G FTL + Q + I MG + ++ SM+PGF
Sbjct: 298 LESLLEKAEDMVD-EKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGG- 355
Query: 361 LMPKGREKESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVMEML 420
MPK ++AKIK+Y ++ SMT EE NPK++ SRI RIARGSG +V E+L
Sbjct: 356 AMPKELSHLTEAKIKKYKVIISSMTKEE--RENPKIIKASRIRRIARGSGTTENDVREVL 413
Query: 421 EEYKRLAKIWSKMK 434
Y+ K++
Sbjct: 414 RYYETTKNAIDKLR 427
>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 = 344 bits (882), Expect = 7e-95, Method: Compositional matrix adjust.
Identities = 188/423 (44%), Positives = 268/423 (63%), Gaps = 13/423 (3%)
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 ENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSV 241
D++I+DT+GRHK+E L EEM+Q+ E T NPD +I V+D +IG +V
Sbjct: 181 --ADVLIIDTAGRHKEEKGLLEEMKQIKEIT-NPDEIILVIDGTIGQQAGIQAKAFKEAV 237
Query: 242 -SVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 300
+G++IVTK+DG AKGGGALSAVA TK+P+ FIG GE +D+ E FD K F+SRLLGMGD
Sbjct: 238 GEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGD 297
Query: 301 WSGFMDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSE 360
++K ++V ++ E + + G FTL + Q + I MG + ++ SM+PGF
Sbjct: 298 LESLLEKAEDMVD-EKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGG- 355
Query: 361 LMPKGREKESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVMEML 420
MPK ++AKIK+Y ++ SMT EE NPK++ SRI RIARGSG +V E+L
Sbjct: 356 AMPKELSHLTEAKIKKYKVIISSMTKEE--RENPKIIKASRIRRIARGSGTTENDVREVL 413
Query: 421 EEY 423
Y
Sbjct: 414 RYY 416
>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 = 282 bits (722), Expect = 2e-76, Method: Compositional matrix adjust.
Identities = 159/410 (38%), Positives = 247/410 (60%), Gaps = 13/410 (3%)
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--KQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 245
IVDT+GRH +E L EEM+++ + + PD VI V+D+SIG + +G+
Sbjct: 191 IVDTAGRHGYGEETKLLEEMKEMYD-VLKPDDVILVIDASIGQKAYDLASRFHQASPIGS 249
Query: 246 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFM 305
VI+TKMDG AKGGGALSAV AT + + FIGTGE +DE E F+ K FVSR+LGMGD +
Sbjct: 250 VIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESIL 309
Query: 306 DKIHEVVPMDQQPELLQKLSE--GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMP 363
+K+ + D+ + ++ + E G TLR +Y Q + KMGP+ +V +PG ++P
Sbjct: 310 EKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGI-MLP 368
Query: 364 KGRE---KESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSG 410
E K + KI+R++ ++SMT +EL+ NP +++ SR+ RIA GSG
Sbjct: 369 TPSEDQLKIGEEKIRRWLAALNSMTYKELE--NPNIIDKSRMRRIAEGSG 416
>pdb|3KL4|A Chain A, Recognition Of A Signal Peptide By The Signal Recognition
Particle
Length = 433
Score = 282 bits (722), Expect = 3e-76, Method: Compositional matrix adjust.
Identities = 159/410 (38%), Positives = 247/410 (60%), Gaps = 13/410 (3%)
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--KQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGA 245
IVDT+GRH +E L EEM+++ + + PD VI V+D+SIG + +G+
Sbjct: 184 IVDTAGRHGYGEETKLLEEMKEMYD-VLKPDDVILVIDASIGQKAYDLASRFHQASPIGS 242
Query: 246 VIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFM 305
VI+TKMDG AKGGGALSAV AT + + FIGTGE +DE E F+ K FVSR+LGMGD +
Sbjct: 243 VIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESIL 302
Query: 306 DKIHEVVPMDQQPELLQKLSE--GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMP 363
+K+ + D+ + ++ + E G TLR +Y Q + KMGP+ +V +PG ++P
Sbjct: 303 EKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGI-MLP 361
Query: 364 KGRE---KESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSG 410
E K + KI+R++ ++SMT +EL+ NP +++ SR+ RIA GSG
Sbjct: 362 TPSEDQLKIGEEKIRRWLAALNSMTYKELE--NPNIIDKSRMRRIAEGSG 409
>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 = 206 bits (525), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 142/434 (32%), Positives = 218/434 (50%), Gaps = 19/434 (4%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGF 304
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD +
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDVASL 300
Query: 305 MDKIHEVVPMDQQPELLQKLSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPK 364
+K+ + P+ ++LS +F +Q QN+ ++GP ++ +LPG +P+
Sbjct: 301 AEKVRAAGLEAEAPKSAKELSLEDF-----LKQMQNLKRLGPFSEILGLLPG-----VPQ 350
Query: 365 GREKESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREV---MEMLE 421
G + + +A IKR ++ SMT EE +P+++N SR RIA+GSG V+EV ++ E
Sbjct: 351 GLKVDEKA-IKRLEAIVLSMTPEE--RKDPRILNGSRRKRIAKGSGTSVQEVNRFIKAFE 407
Query: 422 EYKRLAKIWSKMKG 435
E K L K K KG
Sbjct: 408 EMKALMKSLEKKKG 421
>pdb|2IY3|A Chain A, Structure Of The E. Coli Signal Recognition Particle Bound
To A Translating Ribosome
Length = 432
Score = 205 bits (521), Expect = 5e-53, Method: Compositional matrix adjust.
Identities = 134/411 (32%), Positives = 208/411 (50%), Gaps = 11/411 (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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGF 304
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDIESI 300
Query: 305 MDKIHEVVPMDQQPELLQKLSE--GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELM 362
++K+ + D+ + ++ + E G TLR +Y Q + KMGP+ +V +PG ++
Sbjct: 301 LEKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGI-ML 359
Query: 363 PKGRE---KESQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSG 410
P E K + KI+R++ ++SMT +EL+ NP +++ SR+ RIA GSG
Sbjct: 360 PTPSEDQLKIGEEKIRRWLAALNSMTYKELE--NPNIIDKSRMRRIAEGSG 408
>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens
Length = 297
Score = 205 bits (521), Expect = 5e-53, Method: Compositional matrix adjust.
Identities = 120/274 (43%), Positives = 168/274 (61%), Gaps = 5/274 (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 FEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGAL 261
EEM+ + EA + PD V V+D+SIG + +G +I+TKMDG AKGGGAL
Sbjct: 201 LEEMKNIYEA-IKPDEVTLVIDASIGQKAYDLASKFNQASKIGTIIITKMDGTAKGGGAL 259
Query: 262 SAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRL 295
SAVAAT + + FIGTGE +DE EVF+ + FV+RL
Sbjct: 260 SAVAATGATIKFIGTGEKIDELEVFNPRRFVARL 293
>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens T112a Mutant
Length = 297
Score = 203 bits (516), Expect = 2e-52, Method: Compositional matrix adjust.
Identities = 119/274 (43%), Positives = 167/274 (60%), Gaps = 5/274 (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 FEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGAL 261
EEM+ + EA + PD V V+D+SIG + +G +I+TKMDG AKGGGAL
Sbjct: 201 LEEMKNIYEA-IKPDEVTLVIDASIGQKAYDLASKFNQASKIGTIIITKMDGTAKGGGAL 259
Query: 262 SAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRL 295
SAVAAT + + FIGTGE +DE EVF+ + FV+RL
Sbjct: 260 SAVAATGATIKFIGTGEKIDELEVFNPRRFVARL 293
>pdb|2J28|9 Chain 9, Model Of E. Coli Srp Bound To 70s Rncs
Length = 430
Score = 193 bits (491), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 132/438 (30%), Positives = 221/438 (50%), Gaps = 20/438 (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 FKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXX 238
K + D+++VDT+GR + A+ +E++QV A++NP +FV+D+ G
Sbjct: 178 AKLKFYDVLLVDTAGRLHVDEAMMDEIKQV-HASINPVETLFVVDAMTGQDAANTAKAFN 236
Query: 239 XSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGM 298
++ + V++TK+DG A+GG ALS T P+ F+G GE + E F SR+LGM
Sbjct: 237 EALPLTGVVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGM 296
Query: 299 GDWSGFMDKIHEVVPMDQQPELLQKLSEGN-FTLRIMYEQFQNILKMGPIGQVFSMLPGF 357
GD ++ I V Q +L KL +G+ F L EQ + + MG + + LPG
Sbjct: 297 GDVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMASLMGKLPGM 356
Query: 358 SSELMPKGREKESQAKI-KRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREV 416
+P + + K+ R +++SMT +E + P+++ SR RIA G G QV++V
Sbjct: 357 GQ--IPDNVKSQMDDKVLVRMEAIINSMTMKE--RAKPEIIKGSRKRRIAAGCGMQVQDV 412
Query: 417 MEMLEEYKRLAKIWSKMK 434
+L+++ + ++ KMK
Sbjct: 413 NRLLKQFDDMQRMMKKMK 430
>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 = 189 bits (481), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 130/427 (30%), Positives = 216/427 (50%), Gaps = 20/427 (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 FKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXX 238
K + D+++VDT+GR + A+ +E++QV A++NP +FV+D+ G
Sbjct: 179 AKLKFYDVLLVDTAGRLHVDEAMMDEIKQV-HASINPVETLFVVDAMTGQDAANTAKAFN 237
Query: 239 XSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGM 298
++ + V++TK+DG A+GG ALS T P+ F+G GE + E F SR+LGM
Sbjct: 238 EALPLTGVVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGM 297
Query: 299 GDWSGFMDKIHEVVPMDQQPELLQKLSEGN-FTLRIMYEQFQNILKMGPIGQVFSMLPGF 357
GD ++ I V Q +L KL +G+ F L EQ + + MG + + LPG
Sbjct: 298 GDVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMASLMGKLPGM 357
Query: 358 SSELMPKGREKESQAKI-KRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREV 416
+P + + K+ R +++SMT +E + P+++ SR RIA GSG QV++V
Sbjct: 358 GQ--IPDNVKSQMDDKVLVRMEAIINSMTMKE--RAKPEIIKGSRKRRIAAGSGMQVQDV 413
Query: 417 MEMLEEY 423
+L+++
Sbjct: 414 NRLLKQF 420
>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 = 165 bits (417), Expect = 7e-41, Method: Compositional matrix adjust.
Identities = 89/279 (31%), Positives = 157/279 (56%), Gaps = 5/279 (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 AALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGG 258
L +EM++++ T P+LVIFV D+ G +V + +I+TK+D A+GG
Sbjct: 227 RNLMDEMKKIARVT-KPNLVIFVGDALAGNAIVEQARQFNEAVKIDGIILTKLDADARGG 285
Query: 259 GALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLG 297
ALS +P++F+G G+ D+ F+ + F+ R+ G
Sbjct: 286 AALSISYVIDAPILFVGVGQGYDDLRPFEKEWFLERIFG 324
>pdb|3DM9|B Chain B, Structures And Conformations In Solution Of The Signal
Recognition Particle Receptor From The Archaeon
Pyrococcus Furiosus
Length = 328
Score = 158 bits (400), Expect = 5e-39, Method: Compositional matrix adjust.
Identities = 87/279 (31%), Positives = 155/279 (55%), Gaps = 5/279 (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 AALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGG 258
L +E ++++ T P+LVIFV D+ G +V + +I+TK+D A+GG
Sbjct: 227 RNLXDEXKKIARVT-KPNLVIFVGDALAGNAIVEQARQFNEAVKIDGIILTKLDADARGG 285
Query: 259 GALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLG 297
ALS +P++F+G G+ D+ F+ + F+ R+ G
Sbjct: 286 AALSISYVIDAPILFVGVGQGYDDLRPFEKEWFLERIFG 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 = 150 bits (378), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 97/300 (32%), Positives = 144/300 (48%), Gaps = 3/300 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGF 304
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD +
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDVASL 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 = 149 bits (377), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 97/296 (32%), Positives = 143/296 (48%), Gaps = 3/296 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 300
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 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 = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 97/296 (32%), Positives = 143/296 (48%), Gaps = 3/296 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 300
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 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 = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 97/296 (32%), Positives = 143/296 (48%), Gaps = 3/296 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGD 300
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMGD
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
>pdb|1LS1|A Chain A, T. Aquaticus Ffh Ng Domain At 1.1a Resolution
Length = 295
Score = 147 bits (371), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 96/295 (32%), Positives = 142/295 (48%), Gaps = 3/295 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 299
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMG
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
>pdb|1FFH|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 294
Score = 147 bits (370), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 96/295 (32%), Positives = 142/295 (48%), Gaps = 3/295 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 181 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 239
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMG 299
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGMG
Sbjct: 240 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 294
>pdb|2NG1|A Chain A, N And Gtpase Domains Of The Signal Sequence Recognition
Protein Ffh From Thermus Aquaticus
Length = 293
Score = 144 bits (364), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 95/294 (32%), Positives = 141/294 (47%), Gaps = 3/294 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 181 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 239
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGM 298
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGM
Sbjct: 240 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 293
>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 = 144 bits (364), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 95/294 (32%), Positives = 141/294 (47%), Gaps = 3/294 (1%)
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 DLIIVDTSGRHKQEAALFEEMRQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DLI+VDT+GR + + L E+ ++ E + PD V+ V+D+ G V V
Sbjct: 182 DLILVDTAGRLQIDEPLMGELARLKE-VLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT 240
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGM 298
+++TK+DG A+GG ALSA T P+ F G E + E F + R+LGM
Sbjct: 241 GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
>pdb|1MFQ|C Chain C, Crystal Structure Analysis Of A Ternary S-Domain Complex
Of Human Signal Recognition Particle
Length = 129
Score = 122 bits (307), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 59/114 (51%), Positives = 83/114 (72%), Gaps = 3/114 (2%)
Query: 327 GNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKIKRYMTMMDSMTN 386
G FTLR MYEQFQNI+KMGP Q+ M+PGF ++ M KG E+ES A++K+ MT+MDSM +
Sbjct: 13 GQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMND 72
Query: 387 EELDSSN-PKLMND--SRIMRIARGSGRQVREVMEMLEEYKRLAKIWSKMKGLK 437
+ELDS++ K+ + RI R+ARGSG R+V E+L +Y + A++ KM G+K
Sbjct: 73 QELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKMGGIK 126
>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 = 117 bits (293), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 89/292 (30%), Positives = 144/292 (49%), Gaps = 17/292 (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 PALVCADTFRAGAFDQLKQNA--TKAKIPFYGSYTESDPVRIAVEGVETFKKENCDLIIV 189
+ DTFRA A +QL+ A T ++I + P + + V +E+ D+++
Sbjct: 147 VLMAAGDTFRAAAGEQLEVWAQRTGSEI-VMAEGPKPRPAAVLSQAVRRAVEEDFDVVLC 205
Query: 190 DTSGRHKQEAALFEEMR----QVSEA-TVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVG 244
DTSGR L EE+R VS+A + P+ V+ V+D + G + V
Sbjct: 206 DTSGRLHTNYNLMEELRGCKRAVSKALSSAPNEVLLVLDGTTGLNMLAQAREFNQVIGVT 265
Query: 245 AVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLL 296
I+TK+DG A+GG +S V PV F+G GE +D+ + FD + FV L
Sbjct: 266 GFILTKLDGTARGGCVVSVVDELSIPVKFVGVGEGIDDLQPFDAQSFVDALF 317
>pdb|3B9Q|A Chain A, The Crystal Structure Of Cpftsy From Arabidopsis Thaliana
Length = 302
Score = 117 bits (292), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 85/293 (29%), Positives = 142/293 (48%), Gaps = 19/293 (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 VDTSGRHKQEAALFEEMRQVSEA-----TVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSV 243
DTSGR +L EE+ +A + P+ ++ V+D + G V +
Sbjct: 189 CDTSGRLHTNYSLMEELIACKKAVGKIVSGAPNEILLVLDGNTGLNMLPQAREFNEVVGI 248
Query: 244 GAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLL 296
+I+TK+DG A+GG +S V PV FIG GE +++ + FD + FV+ +
Sbjct: 249 TGLILTKLDGSARGGCVVSVVEELGIPVKFIGVGEAVEDLQPFDPEAFVNAIF 301
>pdb|2OG2|A Chain A, Crystal Structure Of Chloroplast Ftsy From Arabidopsis
Thaliana
Length = 359
Score = 117 bits (292), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 85/293 (29%), Positives = 142/293 (48%), Gaps = 19/293 (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 VDTSGRHKQEAALFEEMRQVSEA-----TVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSV 243
DTSGR +L EE+ +A + P+ ++ V+D + G V +
Sbjct: 246 CDTSGRLHTNYSLMEELIACKKAVGKIVSGAPNEILLVLDGNTGLNMLPQAREFNEVVGI 305
Query: 244 GAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLL 296
+I+TK+DG A+GG +S V PV FIG GE +++ + FD + FV+ +
Sbjct: 306 TGLILTKLDGSARGGCVVSVVEELGIPVKFIGVGEAVEDLQPFDPEAFVNAIF 358
>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 = 116 bits (291), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 56/108 (51%), Positives = 79/108 (73%), Gaps = 3/108 (2%)
Query: 329 FTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKIKRYMTMMDSMTNEE 388
FTLR MYEQFQNI+KMGP Q+ M+PGF ++ M KG E+ES A++K+ MT+MDSM ++E
Sbjct: 2 FTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQE 61
Query: 389 LDSSN-PKLMNDS--RIMRIARGSGRQVREVMEMLEEYKRLAKIWSKM 433
LDS++ K+ + RI R+ARGSG R+V E+L +Y + A++ KM
Sbjct: 62 LDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKM 109
>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 = 116 bits (290), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 17/242 (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 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATV-----NPDLVIFVMDSSIGXXXXXXX 234
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 181 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 240
Query: 235 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 294
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 241 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 300
Query: 295 LL 296
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 (289), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 17/242 (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 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATV-----NPDLVIFVMDSSIGXXXXXXX 234
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 180 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 239
Query: 235 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 294
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 240 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 299
Query: 295 LL 296
LL
Sbjct: 300 LL 301
>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 (289), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 17/242 (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 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATV-----NPDLVIFVMDSSIGXXXXXXX 234
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 160 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 219
Query: 235 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 294
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 220 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 279
Query: 295 LL 296
LL
Sbjct: 280 LL 281
>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 (289), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 83/242 (34%), Positives = 118/242 (48%), Gaps = 17/242 (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 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATV-----NPDLVIFVMDSSIGXXXXXXX 234
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 161 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 220
Query: 235 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 294
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 221 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 280
Query: 295 LL 296
LL
Sbjct: 281 LL 282
>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 = 114 bits (286), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 21/289 (7%)
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 EM-------RQVSEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAK 256
E+ +QV ++ P V+ V+D++ G V +I+TKMD +K
Sbjct: 212 ELEKMNKIIQQVEKSA--PHEVLLVIDATTGQNGVIQAEEFSKVADVSGIILTKMDSTSK 269
Query: 257 GGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSRLLGMGDWSGFM 305
GG L+ P+ IG GE +D+ FD+ ++ L SGFM
Sbjct: 270 GGIGLAIKELLNIPIKMIGVGEKVDDLLAFDIDQYIVHL-----SSGFM 313
>pdb|2QY9|A Chain A, Structure Of The Ng+1 Construct Of The E. Coli Srp
Receptor Ftsy
Length = 309
Score = 114 bits (285), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 72/264 (27%), Positives = 125/264 (47%), Gaps = 9/264 (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 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDL---- 217
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ D+
Sbjct: 160 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 219
Query: 218 -VIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 276
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 220 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 279
Query: 277 GEHMDEFEVFDVKPFVSRLLGMGD 300
GE +++ F F+ L D
Sbjct: 280 GERIEDLRPFKADDFIEALFARED 303
>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 = 114 bits (285), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 72/264 (27%), Positives = 125/264 (47%), Gaps = 9/264 (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 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDL---- 217
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ D+
Sbjct: 159 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 218
Query: 218 -VIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 276
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 219 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 278
Query: 277 GEHMDEFEVFDVKPFVSRLLGMGD 300
GE +++ F F+ L D
Sbjct: 279 GERIEDLRPFKADDFIEALFARED 302
>pdb|1FTS|A Chain A, Signal Recognition Particle Receptor From E. Coli
Length = 295
Score = 113 bits (283), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 71/260 (27%), Positives = 124/260 (47%), Gaps = 9/260 (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 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVNPDL---- 217
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ D+
Sbjct: 154 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 213
Query: 218 -VIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 276
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 214 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 273
Query: 277 GEHMDEFEVFDVKPFVSRLL 296
GE +++ F F+ L
Sbjct: 274 GERIEDLRPFKADDFIEALF 293
>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 (281), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 82/242 (33%), Positives = 117/242 (48%), Gaps = 17/242 (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 KKENCDLIIVDTSGRHKQEAALFEEMRQVSEATV-----NPDLVIFVMDSSIGXXXXXXX 234
K DL+ VDT+GR + L EE+++V A P V V+D+ G
Sbjct: 181 KARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA 240
Query: 235 XXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHMDEFEVFDVKPFVSR 294
+V + VIVTK+DG AKGG + V K P+ F+G GE D+ + FD + FV
Sbjct: 241 KKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEA 300
Query: 295 LL 296
LL
Sbjct: 301 LL 302
>pdb|2YHS|A Chain A, Structure Of The E. Coli Srp Receptor Ftsy
Length = 503
Score = 112 bits (280), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 72/264 (27%), Positives = 124/264 (46%), Gaps = 9/264 (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 SYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVSEA-----TVNPD 216
+T +D + + ++ K N D++I DT+GR + ++ L EE++++ P
Sbjct: 354 QHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPH 413
Query: 217 LVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGT 276
V+ +D+S G +V + + +TK+DG AKGG S P+ +IG
Sbjct: 414 EVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFSVADQFGIPIRYIGV 473
Query: 277 GEHMDEFEVFDVKPFVSRLLGMGD 300
GE +++ F F+ L D
Sbjct: 474 GERIEDLRPFKADDFIEALFARED 497
>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 = 99.4 bits (246), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 70/201 (34%), Positives = 100/201 (49%), Gaps = 5/201 (2%)
Query: 101 PSVIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADTFRAGAFDQLKQNATKAKIPFY 160
P VIM VG+ G+GKTT+C K A +G L ADTFRA A +QLK +
Sbjct: 104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVI 163
Query: 161 GSYTESDPVRIAVEGVETFKKENCDLIIVDTSGRHKQEAALFEEMRQVSEATVN-----P 215
+DP +A + V N D++I+DT+GR + L EE+R+V P
Sbjct: 164 SHSEGADPAAVAFDAVAHALARNKDVVIIDTAGRLHTKKNLMEELRKVHRVVKKKIPDAP 223
Query: 216 DLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIG 275
+ V+D++ G +V+V +I+TK+DG AKGG L+ P+ FIG
Sbjct: 224 HETLLVIDATTGQNGLVQAKIFKEAVNVTGIILTKLDGTAKGGITLAIARELGIPIKFIG 283
Query: 276 TGEHMDEFEVFDVKPFVSRLL 296
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 = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
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|2JQE|A Chain A, Soution Structure Of Af54 M-Domain
Length = 119
Score = 76.3 bits (186), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 46/102 (45%), Positives = 66/102 (64%), Gaps = 4/102 (3%)
Query: 324 LSEGNFTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKE-SQAKIKRYMTMMD 382
+ +G FTL+ +Y+Q + + KMGP+ ++F MLP F L E +Q K+K++ +MD
Sbjct: 5 MEKGTFTLKDIYKQIEAMNKMGPVRKIFEMLP-FGLGLKVDNDVMEMTQEKMKKFRVIMD 63
Query: 383 SMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEYK 424
SMT EEL NPK+++ SRI RIA GSG +EV E+L YK
Sbjct: 64 SMTEEEL--LNPKIIDSSRIRRIAIGSGTSPQEVKELLNYYK 103
>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 = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 67/262 (25%), Positives = 116/262 (44%), Gaps = 20/262 (7%)
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 EEMRQV--SEATVNPDLVIFVMDSSIGXXXXXXXXXXXXSVSVGAVIVTKMDGHAKGGGA 260
+E+++ E+++ L V+ ++ SV V I TK+D G
Sbjct: 202 DELKETIPFESSIQSFL---VLSATAKYEDMKHIVKRFSSVPVNQYIFTKIDETTSLGSV 258
Query: 261 LSAVAATKSPVIFIGTGEHMDE 282
+ +A +K V F+ G+++ E
Sbjct: 259 FNILAESKIGVGFMTNGQNVPE 280
>pdb|1HQ1|A Chain A, Structural And Energetic Analysis Of Rna Recognition By A
Universally Conserved Protein From The Signal
Recognition Particle
Length = 105
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 51/96 (53%), Gaps = 5/96 (5%)
Query: 329 FTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKI-KRYMTMMDSMTNE 387
F L EQ + + MG + + LPG +P + + K+ R +++SMT +
Sbjct: 2 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQ--IPDNVKSQMDDKVLVRMEAIINSMTMK 59
Query: 388 ELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEY 423
E + P+++ SR RIA GSG QV++V +L+++
Sbjct: 60 E--RAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQF 93
>pdb|3LQX|A Chain A, Srp Ribonucleoprotein Core Complexed With Cobalt Hexammine
Length = 105
Score = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 50/107 (46%), Gaps = 5/107 (4%)
Query: 329 FTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKI-KRYMTMMDSMTNE 387
F L EQ + G + LPG +P + + K+ R +++S T +
Sbjct: 2 FDLNDFLEQLRQXKNXGGXASLXGKLPGXGQ--IPDNVKSQXDDKVLVRXEAIINSXTXK 59
Query: 388 ELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEYKRLAKIWSKMK 434
E + P+++ SR RIA GSG QV++V +L+++ + K K
Sbjct: 60 E--RAKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQFDDXQRXXKKXK 104
>pdb|2PXB|A Chain A, Variant 2 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXD|A Chain A, Variant 1 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXE|A Chain A, Variant 4 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXF|A Chain A, Variant 5 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXK|A Chain A, Variant 8 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXL|A Chain A, Variant 9 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXP|A Chain A, Variant 13 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXQ|A Chain A, Variant 14 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXT|A Chain A, Variant 15 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXU|A Chain A, Variant 16 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
pdb|2PXV|A Chain A, Variant 6 Of Ribonucleoprotein Core Of The E. Coli Signal
Recognition Particle
Length = 102
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 48/96 (50%), Gaps = 5/96 (5%)
Query: 329 FTLRIMYEQFQNILKMGPIGQVFSMLPGFSSELMPKGREKESQAKI-KRYMTMMDSMTNE 387
F L EQ + + G + LPG +P + + K+ R +++S T +
Sbjct: 1 FDLNDFLEQLRQMKNXGGXASLXGKLPGXGQ--IPDNVKSQXDDKVLVRXEAIINSXTXK 58
Query: 388 ELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEY 423
E + P+++ SR RIA GSG QV++V +L+++
Sbjct: 59 E--RAKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQF 92
>pdb|2XKV|C Chain C, Atomic Model Of The Srp-Ftsy Early Conformation
Length = 69
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 37/58 (63%), Gaps = 2/58 (3%)
Query: 376 RYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEYKRLAKIWSKM 433
R +++SMT +E + P+++ SR RIA GSG QV++V +L+++ + ++ KM
Sbjct: 14 RMEAIINSMTMKE--RAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFDDMQRMMKKM 69
>pdb|1DUL|A Chain A, Structure Of The Ribonucleoprotein Core Of The E. Coli
Signal Recognition Particle
Length = 69
Score = 32.7 bits (73), Expect = 0.47, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 371 QAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEY 423
Q + R +++S T +E + P+++ SR RIA GSG QV++V +L+++
Sbjct: 9 QKVLVRXEAIINSXTXKE--RAKPEIIKGSRKRRIAAGSGXQVQDVNRLLKQF 59
>pdb|2YVU|A Chain A, Crystal Structure Of Ape1195
pdb|2YVU|B Chain B, Crystal Structure Of Ape1195
Length = 186
Score = 32.3 bits (72), Expect = 0.65, 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 = 32.3 bits (72), Expect = 0.70, 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 QPAFSP--DQVSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG---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 = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 103 VIMFVGLQGSGKTTTCTKYAYYHQKKGWKPAL 134
+I F G+ GSGKTT K Y ++KG+ +L
Sbjct: 2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSL 33
>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 = 2.3, 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 = 2.4, 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|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 = 30.0 bits (66), Expect = 2.7, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 291 FVSRLLGMGDWSGFMDKIHEVVPMDQQPELLQKLSE 326
F+ G FMDK+HEV+ D +P +KL +
Sbjct: 33 FLPLFFHFGSTRQFMDKLHEVISGDYEPSQAEKLVQ 68
>pdb|3B02|A Chain A, Crystal Structure Of Tthb099, A Transcriptional Regulator
Crp Family From Thermus Thermophilus Hb8
Length = 195
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 15/92 (16%)
Query: 330 TLRIMYEQFQNILKMGPIGQVFSM---LPG--FSSELMPKGREKESQAKIKRYMTMMDSM 384
TL + E ++++ P G++ ++ LPG F E + + K RY ++M
Sbjct: 19 TLYRLEEGLVRVVELLPDGRLITLRHVLPGDYFGEEAL--------EGKAYRYTA--EAM 68
Query: 385 TNEELDSSNPKLMNDSRIMRIARGSGRQVREV 416
T + P+ M+ + R+AR RQ+R V
Sbjct: 69 TEAVVQGLEPRAMDHEALHRVARNLARQMRRV 100
>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
(Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
2.80 A Resolution
Length = 876
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 370 SQAKIKRYMTMMDSMTNEELDSSNPKLMNDSRIMRIARGSGRQVREVMEMLEEYKRLAKI 429
SQ+ IKR S+ E + KL D+ + Q++E E +++YK L I
Sbjct: 225 SQSGIKRSELETQSVRGESFTVIDNKLTKDANV-------PIQLKETAEYIKDYKALKAI 277
Query: 430 WSKMKG 435
W + G
Sbjct: 278 WEALDG 283
>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 = 29.6 bits (65), Expect = 3.8, 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: 378 GPPGTGKTVTSATIVYHLARQGNGPVLVCAPS--NIAVDQLTE 418
>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 = 28.9 bits (63), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 103 VIMFVGLQGSGKTTTCTKYAYYHQKKGWKPALVCADT 139
+++FVG GSGKTT ++ Y + +K A V DT
Sbjct: 16 IVVFVGTAGSGKTTLTGEFGRYLE-DNYKVAYVNLDT 51
>pdb|1WF3|A Chain A, Crystal Structure Of Gtp-Binding Protein Tt1341 From
Thermus Thermophilus Hb8
Length = 301
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 186 LIIVDTSGRHKQEAALFEEMRQ-VSEATVNPDLVIFVMD 223
++ VDT G HK AL E M Q V EA + + V++V+D
Sbjct: 57 IVFVDTPGLHKPMDALGEFMDQEVYEALADVNAVVWVVD 95
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,325,520
Number of Sequences: 62578
Number of extensions: 530804
Number of successful extensions: 1936
Number of sequences better than 100.0: 59
Number of HSP's better than 100.0 without gapping: 54
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1772
Number of HSP's gapped (non-prelim): 62
length of query: 495
length of database: 14,973,337
effective HSP length: 103
effective length of query: 392
effective length of database: 8,527,803
effective search space: 3342898776
effective search space used: 3342898776
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)