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= psy5830
(503 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WWB|A Chain A, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
Length = 476
Score = 807 bits (2084), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 404/520 (77%), Positives = 435/520 (83%), Gaps = 61/520 (11%)
Query: 1 MGIKFLEVIKPFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSA 60
M IKFLEVIKPFC ILPEI KPE RKIQF+EKVLWTAITLFIFLVCCQIPLFGIMSSDSA
Sbjct: 1 MAIKFLEVIKPFCVILPEIQKPE-RKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSA 59
Query: 61 DPFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVGDTPKDRALFNGAQKLF 120
DPFYW+RVILASNRGTLMELGISPIVTSGLIMQLLAGAK+IEVGDTPKDRALFNGAQKLF
Sbjct: 60 DPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLF 119
Query: 121 GMVITVGQAIVYVMTGMYGDPSEIGA------------AGVPDDE-----QKGYGLGSGI 163
GM+IT+GQ+IVYVMTGMYGDPSE+GA AG+ QKGYGLGSGI
Sbjct: 120 GMIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGI 179
Query: 164 SLFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNL 223
SLFIATNICETIVWKAFSP TVNTGRG EFEGA+IALFHLLATR DKVRALREAFYRQNL
Sbjct: 180 SLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNL 239
Query: 224 PNLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVS 283
PNLMNL+AT+ VFA+VIYFQGFRVDLPIKSARYRGQY++YPIKLFYTSNIPIILQSALVS
Sbjct: 240 PNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVS 299
Query: 284 NXXXXXXXXXXXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNI 343
N L V++Q ML+ +F GN+
Sbjct: 300 N---------------------LYVISQ----------------------MLSARFSGNL 316
Query: 344 FVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFS 403
V+LLG W+D GGPARAYP+GGLC+YLSPPE+ G +LEDP+HA++YIVFMLGSCAFFS
Sbjct: 317 LVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFS 376
Query: 404 KTWIEVSGSSAKDVAKQLKEQQMVMRGHREQSMIHELNRYIPTAAAFGGLCIGALSVLAD 463
KTWIEVSGSSAKDVAKQLKEQQMVMRGHRE SM+HELNRYIPTAAAFGGLCIGALSVLAD
Sbjct: 377 KTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLAD 436
Query: 464 FMGAIGSGTGILLAVTIIYQYFEIFVKEQSEMGGMGTLLF 503
F+GAIGSGTGILLAVTIIYQYFEIFVKEQSE+G MG LLF
Sbjct: 437 FLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF 476
>pdb|3MP7|A Chain A, Lateral Opening Of A Translocon Upon Entry Of Protein
Suggests The Mechanism Of Insertion Into Membranes
Length = 482
Score = 219 bits (559), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 150/518 (28%), Positives = 265/518 (51%), Gaps = 93/518 (17%)
Query: 7 EVIKPFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWI 66
++I PE+ +P+ R++ RE+ +WT + L ++ V +IP++GI D F ++
Sbjct: 5 DIIYALERWFPEVERPK-RRVPLRERFMWTGVALILYYVLAEIPVYGI-PERIQDYFQFL 62
Query: 67 RVILASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVIT 125
RV+LA G+++ LGI PIVT+G+I+QLL G+++I++ P+DR + Q++F + +
Sbjct: 63 RVVLAGRNGSILTLGIGPIVTAGIILQLLVGSEIIKLDLANPEDRRFYQALQRVFSVFMC 122
Query: 126 VGQAIVYVMTGMYGDPS-------------EIGAAGVP----DDEQKGYGLGSGISLFIA 168
+A V+++ G +G ++ G+ D+ +G+GSGISLFIA
Sbjct: 123 FFEAAVWILGGAFGRVGVDVTYAIAVLMILQLAMGGIVLIILDELVSKWGIGSGISLFIA 182
Query: 169 TNICETIVWKAFSPAT----VNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQ-NL 223
+ +TI+ ++ +P T ++ G I F + D L A YR +
Sbjct: 183 AGVSQTILTRSLNPLTDPNIIDPLTGQPAIVGAIPYFIQHILKGD----LWGAIYRGGSA 238
Query: 224 PNLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQ--YSSYPIKLFYTSNIPIILQSAL 281
P++++++AT++VF IV+YF+ RV++P+ YRG SYPI+ Y
Sbjct: 239 PDMLSVVATIVVFFIVVYFESMRVEIPLG---YRGVTVRGSYPIRFLY------------ 283
Query: 282 VSNXXXXXXXXXXXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHG 341
VSN I ++++ + + + W +++
Sbjct: 284 VSN------------------------------IPIILTFALYANIQLWARVL------- 306
Query: 342 NIFVNLLGE-WADVGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCA 400
+ LG W +G P PI G Y+ PP N+ ++++P+ AI+Y++ +
Sbjct: 307 ----DRLGHPW--LGRFDPTTGSPISGFVLYVIPPRNIFSVIDNPVRAIVYLILTVIFSL 360
Query: 401 FFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHREQSMIHE--LNRYIPTAAAFGGLCIGAL 458
F W+E++G A+ +A+QL+ + + G R E L RYIP +G L + +
Sbjct: 361 LFGYLWVELTGLDARSIARQLQRAGLQIPGFRRDPRTLEKVLQRYIPYVTFWGSLTVALI 420
Query: 459 SVLADFMGAIGSGTGILLAVTIIYQYFEIFVKEQ-SEM 495
+VLADF+GA+G+GTGILL V I+Y+++E +EQ +EM
Sbjct: 421 AVLADFLGALGTGTGILLTVGILYRFYEEIAREQITEM 458
>pdb|3DKN|A Chain A, Sec61 In The Canine Ribosome-Channel Complex From The
Endoplasmic Reticulum
Length = 430
Score = 217 bits (552), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 150/499 (30%), Positives = 247/499 (49%), Gaps = 101/499 (20%)
Query: 11 PFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWIRVIL 70
P +PE+ P ++I F+EK+ WT I L ++ + I ++ + A +W + I
Sbjct: 5 PILEKIPEVELPV-KEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFW-QTIT 62
Query: 71 ASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVITVGQA 129
AS GTL+ LGI PIVT+G+IMQLL G+ +I++ P++RALF G QKL +++ +A
Sbjct: 63 ASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEA 122
Query: 130 IVYVMTGMYGDPSEIGAAGVP-------------DDEQKGYGLGSGISLFIATNICETIV 176
+++V G +G + + A V D+ YG+GSGI LFIA + +TI
Sbjct: 123 VLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIF 182
Query: 177 WKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNLPNL---MNLLATV 233
A P G +F ++I Q +PN+ ++ T+
Sbjct: 183 VGALGP----EGYLWKFLNSLI----------------------QGVPNIEYIAPIIGTI 216
Query: 234 LVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNXXXXXXXXX 293
+VF +V+Y + RV++P+ R +G YPIK Y SNIP+
Sbjct: 217 IVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPV------------------ 258
Query: 294 XXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNIFVNLLGEWAD 353
+++A + + + W LA+ G + +LG +
Sbjct: 259 ------------------------ILAAALFANIQLW---GLALYRMG---IPILGHYE- 287
Query: 354 VGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFSKTWIEVSGSS 413
GG A + G+ YYLS P L ++ DPIHAI+Y++ M+ +C F W+E +G
Sbjct: 288 ---GGRA----VDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLD 340
Query: 414 AKDVAKQLKEQQMVMRGHREQSMIHELNRYIPTAAAFGGLCIGALSVLADFMGAIGSGTG 473
K +AK++ M ++G R+ ++ H L RYIP +G L+ +A+F+GA+G GTG
Sbjct: 341 PKSMAKRIGSLGMAIKGFRKSAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTG 400
Query: 474 ILLAVTIIYQYFEIFVKEQ 492
+LL V+I+Y+ +E ++E+
Sbjct: 401 VLLTVSIVYRMYEQLLREK 419
>pdb|1RH5|A Chain A, The Structure Of A Protein Conducting Channel
Length = 436
Score = 215 bits (547), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 151/503 (30%), Positives = 249/503 (49%), Gaps = 103/503 (20%)
Query: 11 PFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWIRVIL 70
P +PE+ P ++I F+EK+ WT I L ++ + I ++ + A +W + I
Sbjct: 6 PILEKIPEVELPV-KEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFW-QTIT 63
Query: 71 ASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVITVGQA 129
AS GTL+ LGI PIVT+G+IMQLL G+ +I++ P++RALF G QKL +++ +A
Sbjct: 64 ASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEA 123
Query: 130 IVYVMTGMYGDPSEIGAAGVP-------------DDEQKGYGLGSGISLFIATNICETIV 176
+++V G +G + + A V D+ YG+GSGI LFIA + +TI
Sbjct: 124 VLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIF 183
Query: 177 WKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNLPNL---MNLLATV 233
A P G +F ++I Q +PN+ ++ T+
Sbjct: 184 VGALGP----EGYLWKFLNSLI----------------------QGVPNIEYIAPIIGTI 217
Query: 234 LVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNXXXXXXXXX 293
+VF +V+Y + RV++P+ R +G YPIK Y SNIP+
Sbjct: 218 IVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPV------------------ 259
Query: 294 XXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNIFVNLLGEWAD 353
+++A + + + W LA+ G + +LG +
Sbjct: 260 ------------------------ILAAALFANIQLW---GLALYRMG---IPILGHYE- 288
Query: 354 VGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFSKTWIEVSGSS 413
GG A + G+ YYLS P L ++ DPIHAI+Y++ M+ +C F W+E +G
Sbjct: 289 ---GGRA----VDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLD 341
Query: 414 AKDVAKQLKEQQMVMRGHR--EQSMIHELNRYIPTAAAFGGLCIGALSVLADFMGAIGSG 471
K +AK++ M ++G R E+++ H L RYIP +G L+ +A+F+GA+G G
Sbjct: 342 PKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGG 401
Query: 472 TGILLAVTIIYQYFEIFVKEQSE 494
TG+LL V+I+Y+ +E ++E++
Sbjct: 402 TGVLLTVSIVYRMYEQLLRERTS 424
>pdb|1RHZ|A Chain A, The Structure Of A Protein Conducting Channel
Length = 436
Score = 214 bits (546), Expect = 7e-56, Method: Compositional matrix adjust.
Identities = 151/501 (30%), Positives = 248/501 (49%), Gaps = 103/501 (20%)
Query: 11 PFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWIRVIL 70
P +PE+ P ++I F+EK+ WT I L ++ + I ++ + A +W + I
Sbjct: 6 PILEKIPEVELPV-KEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFW-QTIT 63
Query: 71 ASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVITVGQA 129
AS GTL+ LGI PIVT+G+IMQLL G+ +I++ P++RALF G QKL +++ +A
Sbjct: 64 ASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEA 123
Query: 130 IVYVMTGMYGDPSEIGAAGVP-------------DDEQKGYGLGSGISLFIATNICETIV 176
+++V G +G + + A V D+ YG+GSGI LFIA + +TI
Sbjct: 124 VLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIF 183
Query: 177 WKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNLPNL---MNLLATV 233
A P G +F ++I Q +PN+ ++ T+
Sbjct: 184 VGALGP----EGYLWKFLNSLI----------------------QGVPNIEYIAPIIGTI 217
Query: 234 LVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNXXXXXXXXX 293
+VF +V+Y + RV++P+ R +G YPIK Y SNIP+
Sbjct: 218 IVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPV------------------ 259
Query: 294 XXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNIFVNLLGEWAD 353
+++A + + + W LA+ G + +LG +
Sbjct: 260 ------------------------ILAAALFANIQLW---GLALYRMG---IPILGHYE- 288
Query: 354 VGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFSKTWIEVSGSS 413
GG A + G+ YYLS P L ++ DPIHAI+Y++ M+ +C F W+E +G
Sbjct: 289 ---GGRA----VDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLD 341
Query: 414 AKDVAKQLKEQQMVMRGHR--EQSMIHELNRYIPTAAAFGGLCIGALSVLADFMGAIGSG 471
K +AK++ M ++G R E+++ H L RYIP +G L+ +A+F+GA+G G
Sbjct: 342 PKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGG 401
Query: 472 TGILLAVTIIYQYFEIFVKEQ 492
TG+LL V+I+Y+ +E ++E+
Sbjct: 402 TGVLLTVSIVYRMYEQLLREK 422
>pdb|2YXQ|A Chain A, The Plug Domain Of The Secy Protein Stablizes The Closed
State Of The Translocation Channel And Maintains A
Membrane Seal
Length = 431
Score = 210 bits (535), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 149/501 (29%), Positives = 246/501 (49%), Gaps = 108/501 (21%)
Query: 11 PFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWIRVIL 70
P +PE+ P ++I F+EK+ WT I L ++ + I ++ + A +W R+
Sbjct: 6 PILEKIPEVELPV-KEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWGRI-- 62
Query: 71 ASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVITVGQA 129
GTL+ LGI PIVT+G+IMQLL G+ +I++ P++RALF G QKL +++ +A
Sbjct: 63 ----GTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEA 118
Query: 130 IVYVMTGMYGDPSEIGAAGVP-------------DDEQKGYGLGSGISLFIATNICETIV 176
+++V G +G + + A V D+ YG+GSGI LFIA + +TI
Sbjct: 119 VLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIF 178
Query: 177 WKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNLPNL---MNLLATV 233
A P G +F ++I Q +PN+ ++ T+
Sbjct: 179 VGALGP----EGYLWKFLNSLI----------------------QGVPNIEYIAPIIGTI 212
Query: 234 LVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNXXXXXXXXX 293
+VF +V+Y + RV++P+ R +G YPIK Y SNIP+
Sbjct: 213 IVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPV------------------ 254
Query: 294 XXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNIFVNLLGEWAD 353
+++A + + + W LA+ G + +LG +
Sbjct: 255 ------------------------ILAAALFANIQLW---GLALYRMG---IPILGHYE- 283
Query: 354 VGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFSKTWIEVSGSS 413
GG A + G+ YYLS P L ++ DPIHAI+Y++ M+ +C F W+E +G
Sbjct: 284 ---GGRA----VDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLD 336
Query: 414 AKDVAKQLKEQQMVMRGHR--EQSMIHELNRYIPTAAAFGGLCIGALSVLADFMGAIGSG 471
K +AK++ M ++G R E+++ H L RYIP +G L+ +A+F+GA+G G
Sbjct: 337 PKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGG 396
Query: 472 TGILLAVTIIYQYFEIFVKEQ 492
TG+LL V+I+Y+ +E ++E+
Sbjct: 397 TGVLLTVSIVYRMYEQLLREK 417
>pdb|2YXR|A Chain A, The Plug Domain Of The Secy Protein Stablizes The Closed
State Of The Translocation Channel And Maintains A
Membrane Seal
Length = 426
Score = 205 bits (522), Expect = 4e-53, Method: Compositional matrix adjust.
Identities = 148/501 (29%), Positives = 245/501 (48%), Gaps = 113/501 (22%)
Query: 11 PFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWIRVIL 70
P +PE+ P ++I F+EK+ WT I L ++ + I ++ ++ + P
Sbjct: 6 PILEKIPEVELPV-KEITFKEKLKWTGIVLVLYFIMGCIDVY---TAGAQIP-------- 53
Query: 71 ASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVITVGQA 129
A GTL+ LGI PIVT+G+IMQLL G+ +I++ P++RALF G QKL +++ +A
Sbjct: 54 AIFGGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEA 113
Query: 130 IVYVMTGMYGDPSEIGAAGVP-------------DDEQKGYGLGSGISLFIATNICETIV 176
+++V G +G + + A V D+ YG+GSGI LFIA + +TI
Sbjct: 114 VLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIF 173
Query: 177 WKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNLPNL---MNLLATV 233
A P G +F ++I Q +PN+ ++ T+
Sbjct: 174 VGALGP----EGYLWKFLNSLI----------------------QGVPNIEYIAPIIGTI 207
Query: 234 LVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNXXXXXXXXX 293
+VF +V+Y + RV++P+ R +G YPIK Y SNIP+
Sbjct: 208 IVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPV------------------ 249
Query: 294 XXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNIFVNLLGEWAD 353
+++A + + + W LA+ G + +LG +
Sbjct: 250 ------------------------ILAAALFANIQLW---GLALYRMG---IPILGHYE- 278
Query: 354 VGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFSKTWIEVSGSS 413
GG A + G+ YYLS P L ++ DPIHAI+Y++ M+ +C F W+E +G
Sbjct: 279 ---GGRA----VDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLD 331
Query: 414 AKDVAKQLKEQQMVMRGHR--EQSMIHELNRYIPTAAAFGGLCIGALSVLADFMGAIGSG 471
K +AK++ M ++G R E+++ H L RYIP +G L+ +A+F+GA+G G
Sbjct: 332 PKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGG 391
Query: 472 TGILLAVTIIYQYFEIFVKEQ 492
TG+LL V+I+Y+ +E ++E+
Sbjct: 392 TGVLLTVSIVYRMYEQLLREK 412
>pdb|2WW9|A Chain A, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|A Chain A, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
Length = 490
Score = 196 bits (498), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 146/523 (27%), Positives = 241/523 (46%), Gaps = 68/523 (13%)
Query: 2 GIKFLEVIKPFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGI---MSSD 58
G + ++++KP ILPE+ P K+ F +K+++T I+L Q PL G+ + +
Sbjct: 3 GFRLIDIVKPILPILPEVELPF-EKLPFDDKIVYTIFAGLIYLFA-QFPLVGLPKATTPN 60
Query: 59 SADPFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQ 117
DP Y++R + TL+E G+ P ++SGLI+QLLAG K+I+V DR LF
Sbjct: 61 VNDPIYFLRGVFGCEPRTLLEFGLFPNISSGLILQLLAGLKVIKVNFKIQSDRELFQSLT 120
Query: 118 KLFGMVITVGQAIVYVMTGMYGDPSEIGAAGVPDDE---------------QKGYGLGSG 162
K+F +V V +++ G +GD + G+ + + KG+G SG
Sbjct: 121 KVFAIVQYVILTNIFIFAGYFGDDLSVVQIGLINFQLVGAGIFTTLLAEVIDKGFGFSSG 180
Query: 163 ISLFIATNICETIVWKAFSPATVNTGRG--TEFEGAVIALFHLLATRQDK-VRALREAFY 219
+ I +V F + + G TE +GA+I L L ++ + + AF
Sbjct: 181 AMIINTVVIATNLVADTFGVSQIKVGEDDQTEAQGALINLIQGLRSKHKTFIGGIISAFN 240
Query: 220 RQNLPNLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQS 279
R LPNL + + + IV Y Q RV+LPI+S R RG + YPIKL YT + ++
Sbjct: 241 RDYLPNLTTTIIVLAIAIIVCYLQSVRVELPIRSTRARGTNNVYPIKLLYTGCLSVLFSY 300
Query: 280 ALVSNXXXXXXXXXXXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKF 339
+ L + + VLI LV A
Sbjct: 301 TI----------------------LFYIHIFAFVLIQLV-----------------AKNE 321
Query: 340 HGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPEN-LGHILEDPIHAILYIVFMLGS 398
+I ++G + + +P+ L+PP + + + P+ I Y F+L +
Sbjct: 322 PTHIICKIMGHYENANNLLAVPTFPLS----LLAPPTSFFKGVTQQPLTFITYSAFILVT 377
Query: 399 CAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHREQSMIHELNRYIPTAAAFGGLCIGAL 458
+F+ W +SGSSA+DVA + K+Q + + G REQ++ ELN+ IP AA G + +
Sbjct: 378 GIWFADKWQAISGSSARDVALEFKDQGITLMGRREQNVAKELNKVIPIAAVTGASVLSLI 437
Query: 459 SVLADFMGAIGSGTGILLAVTIIYQYFEIFVKEQSEMGGMGTL 501
+V+ + +G G GI++ + + E+ E + GG L
Sbjct: 438 TVIGESLGLKGKAAGIVVGIAGGFSLLEVITIEYQQSGGQSAL 480
>pdb|3BO0|A Chain A, Ribosome-Secy Complex
pdb|3BO1|A Chain A, Ribosome-Secy Complex
pdb|3KCR|A Chain A, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found
In Pdb Entry 3kc4
Length = 442
Score = 193 bits (491), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 149/511 (29%), Positives = 246/511 (48%), Gaps = 113/511 (22%)
Query: 11 PFCSILPEIAKPEGRKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWIRVIL 70
P +PE+ P ++I F+EK+ WT I L ++ + I ++ + A +W + I
Sbjct: 5 PILEKIPEVELPV-KEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFW-QTIT 62
Query: 71 ASNRGTLMELGISPIVTSGLIMQLLAGAKLIEVG-DTPKDRALFNGAQKLFGMVITVGQA 129
AS GTL+ LGI PIVT+G+IMQLL G+ +I++ P++RALF G QKL +++ +A
Sbjct: 63 ASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEA 122
Query: 130 IVYVMTGMYGDPSEIGAAGVP-------------DDEQKGYGLGSGISLFIATNICETIV 176
+++V G +G + + A V D+ YG+GSGI LFIA + +TI
Sbjct: 123 VLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIF 182
Query: 177 WKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRALREAFYRQNLPNL---MNLLATV 233
A P EG + + L Q +PN+ ++ T+
Sbjct: 183 VGALGP-----------EGYLWKFLNSLI---------------QGVPNIEYIAPIIGTI 216
Query: 234 LVFAIVIYFQGFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPIILQSALVSNXX 286
+VF +V+Y + R + + A+ Y Q + P+K+ Y SNIP+
Sbjct: 217 IVFLMVVYAECMRRRIVVNYAKRQQGRRVYAAQSTHLPLKVVYVSNIPV----------- 265
Query: 287 XXXXXXXXXXXXXXENGLMLVVVAQHVLILLVVSATICPHPRTWLQLMLAVKFHGNIFVN 346
+++A + + + W LA+ G +
Sbjct: 266 -------------------------------ILAAALFANIQLW---GLALYRMG---IP 288
Query: 347 LLGEWADVGGGGPARAYPIGGLCYYLSPPENLGHILEDPIHAILYIVFMLGSCAFFSKTW 406
+LG + GG A + G+ YYLS P L ++ DPIHAI+Y++ M+ +C F W
Sbjct: 289 ILGHYE----GGRA----VDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFW 340
Query: 407 IEVSGSSAKDVAKQLKEQQMVMRGHR--EQS---MIHELNRYIPTAAAFGGLCIGALSVL 461
+E +G K +AK++K+ + G R EQ+ + H L RYIP +G L+ +
Sbjct: 341 VETTGLDPKSMAKRIKKSGAFVPGIRPGEQTAKYIEHRLKRYIPPLTVMSSAFVGFLATI 400
Query: 462 ADFMGAIGSGTGILLAVTIIYQYFEIFVKEQ 492
A+F+GA+G GTG+LL V+I+Y+ +E ++E+
Sbjct: 401 ANFIGALGGGTGVLLTVSIVYRMYEQLLREK 431
>pdb|2ZJS|Y Chain Y, Crystal Structure Of Secye Translocon From Thermus
Thermophilus With A Fab Fragment
pdb|2ZQP|Y Chain Y, Crystal Structure Of Secye Translocon From Thermus
Thermophilus
Length = 434
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 69/287 (24%), Positives = 115/287 (40%), Gaps = 48/287 (16%)
Query: 28 QFREKVLWTAITLFIFLVCCQIPLFGI--------MSSDSADPFYWIRVILASN--RGTL 77
+ R++VL+T + L + + IP G+ + + F I + N R ++
Sbjct: 13 ELRQRVLFTLLVLAAYRLGAFIPTPGVDLDKIQEFLRTAQGGVFGIINLFSGGNFERFSI 72
Query: 78 MELGISPIVTSGLIMQLL-----AGAKLIEVGDTPKDRALFNGAQKLFGMVITVGQAIVY 132
LGI P +T+ +IMQ+L A KL + G+ + R + N ++ G+ + Q +
Sbjct: 73 FALGIMPYITAAIIMQILVTVVPALEKLSKEGE--EGRRIINQYTRIGGIALGAFQGF-F 129
Query: 133 VMTGMYGDPSEIGAAGVPDDEQKGYGLGSGISLFIATNICET-----IVWKAFSPATVNT 187
+ T G +E G +P G G + + + ++W A
Sbjct: 130 LATAFLG--AEGGRFLLP-------GWSPGPFFWFVVVVTQVAGIALLLWMAERITEYGI 180
Query: 188 GRGTE---FEGAVIALFHLLATRQDKVRALREAFYRQNLPNLMNLLA-TVLVFAIVIYFQ 243
G GT F G V+ + +R NL + LA VL FA + Q
Sbjct: 181 GNGTSLIIFAGIVVEWLPQILRTIGLIRT-----GEVNLVAFLFFLAFIVLAFAGMAAVQ 235
Query: 244 GFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPIILQSALVS 283
+P++ AR Y GQ + PIKL IPII +A++
Sbjct: 236 QAERRIPVQYARKVVGGRVYGGQATYIPIKLNAAGVIPIIFAAAILQ 282
>pdb|3FOA|A Chain A, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOA|B Chain B, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOA|C Chain C, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOA|D Chain D, Crystal Structure Of The Bacteriophage T4 Tail Sheath
Protein, Deletion Mutant Gp18m
pdb|3FOH|A Chain A, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|B Chain B, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|C Chain C, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|D Chain D, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|E Chain E, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOH|F Chain F, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Extended Tail
pdb|3FOI|A Chain A, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|B Chain B, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|C Chain C, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|D Chain D, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|E Chain E, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
pdb|3FOI|F Chain F, Fitting Of Gp18m Crystal Structure Into 3d Cryo-Em
Reconstruction Of Bacteriophage T4 Contracted Tail
Length = 510
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 438 HELNRYIPTAAAFGGLCIGALSVLADFMGAIGSGTGILLAV 478
+++NR++P AA GLC +V +M G G +L V
Sbjct: 462 NDVNRWVPLAADIAGLCARTDNVSQTWMSPAGYNRGQILNV 502
>pdb|3ELI|A Chain A, Crystal Structure Of The Ahsa1 (Spo3351) Protein From
Silicibacter Pomeroyi, Northeast Structural Genomics
Consortium Target Sir160
Length = 152
Score = 29.6 bits (65), Expect = 4.6, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 348 LGEWADVGGGGPARAYPIGGLCYYLSPPENLG-----HILEDPIHAILYIVFMLGSCA 400
LG W V G + Y + G ++ PP+++G H +D A ++ F++ CA
Sbjct: 50 LGPWFSVXVNGEGQRYKVSGQVTHVKPPQSVGFTWGWHDDDDRRGAESHVXFIVEPCA 107
>pdb|3DL8|G Chain G, Structure Of The Complex Of Aquifex Aeolicus Secyeg And
Bacillus Subtilis Seca
pdb|3DL8|H Chain H, Structure Of The Complex Of Aquifex Aeolicus Secyeg And
Bacillus Subtilis Seca
Length = 429
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 28 QFREKVLWTAITLFIFLVCCQIPLFGI--------MSSDSADPFYWIRVILASNRG--TL 77
+ R+K ++T + I+ + IP+ GI + + F + N G T+
Sbjct: 13 ELRQKFIFTLLMFVIYRLGSHIPIPGINPEALRDFLKAFEGSVFALYDIFSGGNLGRLTV 72
Query: 78 MELGISPIVTSGLIMQLLAGA 98
LG+ P +++ ++MQLL A
Sbjct: 73 FALGVMPYISASIMMQLLTVA 93
>pdb|3DIN|C Chain C, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
pdb|3DIN|F Chain F, Crystal Structure Of The Protein-Translocation Complex
Formed By The Secy Channel And The Seca Atpase
Length = 431
Score = 28.5 bits (62), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 63/286 (22%), Positives = 120/286 (41%), Gaps = 47/286 (16%)
Query: 28 QFREKVLWTAITLFIFLVCCQIPLFGI----------MSSDSAD-----PFYWIRVILAS 72
+ R+++++T + L +F + IP+ G+ +++A FY + A
Sbjct: 13 ELRDRIIFTFLALIVFRMGIYIPVPGLNLEAWGEIFRRIAETAGVAGILSFYDVFTGGAL 72
Query: 73 NRGTLMELGISPIVTSGLIMQLLAGA-----KLIEVGDTPKDRALFNGAQKLFGMVITVG 127
+R ++ + ++P +T+ +I+QLLA +++ G+ + R F + ++I
Sbjct: 73 SRFSVFTMSVTPYITASIILQLLASVMPSLKEMLREGE--EGRKKFAKYTRRLTLLIGGF 130
Query: 128 QAIVYVMTGMYGDPSEIGAAGVPDDEQKGYGLGSGISLFIATNICETIVWKAFSPATVNT 187
QA + +P + P + + S +S+ T ++W
Sbjct: 131 QAFFVSFSLARSNPDMVA----PGVNVLQFTVLSTMSMLAGTMF---LLWLGERITEKGI 183
Query: 188 GRGTEFEGAVIALFHLLATRQDKVRALREAFYRQ-NLPNLMNLLATVL--VFAIVIYFQG 244
G G I +F + R +R+A+ NL + L+A L +F I++ Q
Sbjct: 184 GNGIS-----ILIFAGIVARYPSY--IRQAYLGGLNLLEWIFLIAVALITIFGIILVQQA 236
Query: 245 FRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPIILQSALVS 283
R + I+ AR Y G + PIK+ IPII SA+VS
Sbjct: 237 ER-RITIQYARRVTGRRVYGGASTYLPIKVNQGGVIPIIFASAIVS 281
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
0.326 0.142 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,992,000
Number of Sequences: 62578
Number of extensions: 561197
Number of successful extensions: 1317
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1252
Number of HSP's gapped (non-prelim): 29
length of query: 503
length of database: 14,973,337
effective HSP length: 103
effective length of query: 400
effective length of database: 8,527,803
effective search space: 3411121200
effective search space used: 3411121200
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)