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= 008044
(579 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 165 bits (418), Expect = 5e-41, Method: Compositional matrix adjust.
Identities = 134/439 (30%), Positives = 218/439 (49%), Gaps = 37/439 (8%)
Query: 154 SEIRRRLFVTAVLIVISRIGYFIPLPGFDRRLIPQDYLSFVSGSVDELGDF--GAEL-KL 210
E+R++ T ++ VI R+G IP+PG + + +D+L GSV L D G L +L
Sbjct: 12 KELRQKFIFTLLMFVIYRLGSHIPIPGINPEAL-RDFLKAFEGSVFALYDIFSGGNLGRL 70
Query: 211 SFFQLGISPQIVASILMQVLCHIVPSLVQLRKEGLD-GHEKIKSYIWWISLGFAILEAVI 269
+ F LG+ P I ASI+MQ+L +PSL +L KE D G KI Y +++L A ++++
Sbjct: 71 TVFALGVMPYISASIMMQLLTVAIPSLQRLAKEEGDYGRYKINEYTKYLTLFVATVQSLG 130
Query: 270 VACY----SLPYSIYAASH-SVKHVMVTAFLLVCGAMTMSWICDTISESGFGQGSSLIIC 324
+A + P I + + +++T LV G M + WI D I+E G G G+SLII
Sbjct: 131 IAFWIRGQVSPKGIPVVENPGISFILITVLTLVAGTMFLVWIADRITEKGIGNGASLIIF 190
Query: 325 VGILTGYTETLYKMLSQLLGSSVRWWPFMLGLLGVFTIVTMWAVV-VTEGCRKVKLQYYG 383
GI+ + + + ++ + P L L+ I + +V V E R++ +QY G
Sbjct: 191 AGIVANFPNAVIQFYEKVKTGDI--GPLTLLLIIALIIAIIVGIVYVQEAERRIPIQYPG 248
Query: 384 FKLAS---AAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASILGSPFWQHV 440
++ A R+ Y+P INP+G+ P++ LL PS L + + +PF + +
Sbjct: 249 RQVGRQLYAGRKT--------YLPIKINPAGVIPIIFAQALLLIPSTLLNFVQNPFIKVI 300
Query: 441 KEILNPETSVGARPWVYYT-IYAFFVFLFNIFDIANL--PKEIADYLNKMGARIPNVKPG 497
++ P GA ++Y +Y F+ F F A L P E+A+ L+K GA IP V+PG
Sbjct: 301 ADMFQP----GA---IFYNFLYVTFIVFFTYFYTAVLINPVELAENLHKAGAFIPGVRPG 353
Query: 498 KATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLRRINEGFSIGFTSVLIIVGSIIEL 557
+ T++YL +I F+G + N F G T+ LI+VG ++
Sbjct: 354 QDTVKYLERIINRLIFFGALFLSVIALIPILISVWF---NIPFYFGGTTALIVVGVALDT 410
Query: 558 RRSYQAYNVMPSLSKALRR 576
R + Y + +RR
Sbjct: 411 FRQIETYLIQKKYKSYVRR 429
>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 = 134 bits (336), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 107/431 (24%), Positives = 204/431 (47%), Gaps = 46/431 (10%)
Query: 155 EIRRRLFVTAVLIVISRIGYFIPLPGFD--------RRLIPQDYLSFVSGSVDELGDFGA 206
E+R R+ T + +++ R+G +IP+PG + RR+ ++ + D GA
Sbjct: 13 ELRDRIIFTFLALIVFRMGIYIPVPGLNLEAWGEIFRRIAETAGVAGILSFYDVFTG-GA 71
Query: 207 ELKLSFFQLGISPQIVASILMQVLCHIVPSLVQLRKEGLDGHEKIKSYIWWISLGFAILE 266
+ S F + ++P I ASI++Q+L ++PSL ++ +EG +G +K Y ++L +
Sbjct: 72 LSRFSVFTMSVTPYITASIILQLLASVMPSLKEMLREGEEGRKKFAKYTRRLTLLIGGFQ 131
Query: 267 AVIVA---CYSLPYSIYAASHSVKHVMVTAFLLVCGAMTMSWICDTISESGFGQGSSLII 323
A V+ S P + + ++ +++ ++ G M + W+ + I+E G G G S++I
Sbjct: 132 AFFVSFSLARSNPDMVAPGVNVLQFTVLSTMSMLAGTMFLLWLGERITEKGIGNGISILI 191
Query: 324 CVGILTGYTETLYKMLSQLLGSSVRWWPFMLGLLGVFTIVTMWAVV-VTEGCRKVKLQYY 382
GI+ Y Y + L G ++ W F++ + ++T++ ++ V + R++ +QY
Sbjct: 192 FAGIVARYPS--YIRQAYLGGLNLLEWIFLIAV----ALITIFGIILVQQAERRITIQY- 244
Query: 383 GFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASILGSPFWQHVKE 442
A Y+P +N G+ P++ + +++ PS +ASI + + +K
Sbjct: 245 ----ARRVTGRRVYGGASTYLPIKVNQGGVIPIIFASAIVSIPSAIASITNN---ETLKN 297
Query: 443 ILNPETSVGARPWVYYTIYAFFVFLFN------IFDIANLPKEIADYLNKMGARIPNVKP 496
+ A ++Y IY VF F IFD P+EI++ + K G IP ++P
Sbjct: 298 LFR------AGGFLYLLIYGLLVFFFTYFYSVVIFD----PREISENIRKYGGYIPGLRP 347
Query: 497 GKATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLRRINEGFSIGFTSVLIIVGSIIE 556
G++T +YL ++ F G I IG TS LI VG ++
Sbjct: 348 GRSTEQYLHRVLNRVTFIGAVFLVVIALLPYLVQG---AIKVNVWIGGTSALIAVGVALD 404
Query: 557 LRRSYQAYNVM 567
+ + + + VM
Sbjct: 405 IIQQMETHMVM 415
>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 = 127 bits (319), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 116/433 (26%), Positives = 189/433 (43%), Gaps = 26/433 (6%)
Query: 155 EIRRRLFVTAVLIVISRIGYFIPLPGFDRRLIPQDYLSFVSGSVDELGDF---GAELKLS 211
E+R+R+ T +++ R+G FIP PG D I Q++L G V + + G + S
Sbjct: 13 ELRQRVLFTLLVLAAYRLGAFIPTPGVDLDKI-QEFLRTAQGGVFGIINLFSGGNFERFS 71
Query: 212 FFQLGISPQIVASILMQVLCHIVPSLVQLRKEGLDGHEKIKSY--IWWISLGF---AILE 266
F LGI P I A+I+MQ+L +VP+L +L KEG +G I Y I I+LG L
Sbjct: 72 IFALGIMPYITAAIIMQILVTVVPALEKLSKEGEEGRRIINQYTRIGGIALGAFQGFFLA 131
Query: 267 AVIVACYSLPYSIYAASHSVKHVMVTAFLLVCGAMTMSWICDTISESGFGQGSSLIICVG 326
+ + + S V V G + W+ + I+E G G G+SLII G
Sbjct: 132 TAFLGAEGGRFLLPGWSPGPFFWFVVVVTQVAGIALLLWMAERITEYGIGNGTSLIIFAG 191
Query: 327 ILTGYTETLYKMLSQLLGSSVRWWPFMLGLLGVFTIVTMWAVVVTEGCRKVKLQYYGFKL 386
I+ + + + + + V F+ L + V + R++ +Q Y K+
Sbjct: 192 IVVEWLPQILRTIGLIRTGEVNLVAFLF-FLAFIVLAFAGMAAVQQAERRIPVQ-YARKV 249
Query: 387 ASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILAS-ILGSPFWQHVKEILN 445
T YIP +N +G+ P++ +L P LA+ +P Q + N
Sbjct: 250 VGGRVYGGQAT----YIPIKLNAAGVIPIIFAAAILQIPIFLAAPFQDNPVLQGIANFFN 305
Query: 446 PETSVGARPWVYYTIYAFFVFLFNIFDIANLPKEIADYLNKMGARIPNVKPGKATIEYLT 505
P G V I +V+ FD PK IA+ L + G IP ++PG+ T+++L
Sbjct: 306 PTRPSGLFIEVLLVILFTYVYTAVQFD----PKRIAESLREYGGFIPGIRPGEPTVKFLE 361
Query: 506 KIQASTRFWGGXXXXXXXXXXXXXDHYLRRINEGFSIGFTSV--LIIVGSIIELRRSYQA 563
I + WG ++ + SI F+ + LI+VG ++ R ++
Sbjct: 362 HIVSRLTLWGA----LFLGLVTLLPQIIQNLTGIHSIAFSGIGLLIVVGVALDTLRQVES 417
Query: 564 YNVMPSLSKALRR 576
++ S L R
Sbjct: 418 QLMLRSYEGFLSR 430
>pdb|3J01|A Chain A, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
Length = 435
Score = 108 bits (270), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 123/438 (28%), Positives = 202/438 (46%), Gaps = 34/438 (7%)
Query: 154 SEIRRRL-FVTAVLIVISRIGYFIPLPGFDRRLIPQDYLSFVSGSVDELGDF---GAELK 209
E++RRL FV LIV RIG FIP+PG D ++ + L G++ E+ + GA +
Sbjct: 10 GELKRRLLFVIGALIVF-RIGSFIPIPGIDAAVLAK-LLEQQRGTIIEMFNMFSGGALSR 67
Query: 210 LSFFQLGISPQIVASILMQVLCHIVPSLVQLRKEGLDGHEKIKSYIWWISLGFAILEAVI 269
S F LGI P I ASI++Q+L + P+L +++KEG G KI Y + +L AI +++
Sbjct: 68 ASIFALGIMPYISASIIIQLLTVVHPTLAEIKKEGESGRRKISQYTRYGTLVLAIFQSIG 127
Query: 270 VACYSLP----YSIYAASHSVKHVMVTAFLLVCGAMTMSWICDTISESGFGQGSSLIICV 325
+A LP + LV G M + W+ + I+E G G G S+II
Sbjct: 128 IAT-GLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFA 186
Query: 326 GILTGYTETLYKMLSQLLGSSVRWWPFMLGLLGVFTIVTMWAVVVTEGCRKVKLQYYGFK 385
GI+ G + + Q + + +L + + VT + V V G R++ + Y
Sbjct: 187 GIVAGLPPAIAHTIEQARQGDLHFLVLLL-VAVLVFAVTFFVVFVERGQRRIVVNY---- 241
Query: 386 LASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASIL-GSPFWQHVKEI- 443
A + ++P +N +G+ P + + ++ FP+ +AS G W + I
Sbjct: 242 -AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTIS 300
Query: 444 --LNPETSVGARPWVYYTIYAFFVFLFNIFDIANL--PKEIADYLNKMGARIPNVKPGKA 499
L P +P +Y +YA + F F A + P+E AD L K GA +P ++PG+
Sbjct: 301 LYLQP-----GQP-LYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQ 354
Query: 500 TIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLR-RINEGFSIGFTSVLIIVGSIIELR 558
T +Y+ K+ G ++R + F G TS+LI+V I++
Sbjct: 355 TAKYIDKVMTRLTLVGA----LYITFICLIPEFMRDAMKVPFYFGGTSLLIVVVVIMDFM 410
Query: 559 RSYQAYNVMPSLSKALRR 576
Q + AL++
Sbjct: 411 AQVQTLMMSSQYESALKK 428
>pdb|2AKH|Y Chain Y, Normal Mode-Based Flexible Fitted Coordinates Of A Non-
Translocating Secyeg Protein-Conducting Channel Into The
Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
Complex From E. Coli
pdb|2AKH|B Chain B, Normal Mode-Based Flexible Fitted Coordinates Of A Non-
Translocating Secyeg Protein-Conducting Channel Into The
Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
Complex From E. Coli
pdb|2AKI|Y Chain Y, Normal Mode-Based Flexible Fitted Coordinates Of A
Translocating Secyeg Protein-Conducting Channel Into The
Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
Complex From E. Coli
pdb|2AKI|B Chain B, Normal Mode-Based Flexible Fitted Coordinates Of A
Translocating Secyeg Protein-Conducting Channel Into The
Cryo-Em Map Of A Secyeg-Nascent Chain-70s Ribosome
Complex From E. Coli
Length = 400
Score = 85.9 bits (211), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 107/399 (26%), Positives = 178/399 (44%), Gaps = 35/399 (8%)
Query: 191 LSFVSGS--VDELGDFGAELKLSFFQLGISPQIVASILMQVLCHIVPSLVQLRKEGLDGH 248
L FV G+ V +G F +S F LGI P I ASI++Q+L + P+L +++KEG G
Sbjct: 23 LLFVIGALIVFRIGSF-----ISIFALGIMPYISASIIIQLLTVVHPTLAEIKKEGESGR 77
Query: 249 EKIKSYIWWISLGFAILEAVIVACYSLP----YSIYAASHSVKHVMVTAFLLVCGAMTMS 304
KI Y + +L AI +++ +A LP + LV G M +
Sbjct: 78 RKISQYTRYGTLVLAIFQSIGIAT-GLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLM 136
Query: 305 WICDTISESGFGQGSSLIICVGILTGYTETLYKMLSQLLGSSVRWWPFMLGLLGVFTIVT 364
W+ + I+E G G G S+II GI+ G + + Q + + +L + + VT
Sbjct: 137 WLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLL-VAVLVFAVT 195
Query: 365 MWAVVVTEGCRKVKLQYYGFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAF 424
+ V V G R++ + Y A + ++P +N +G+ P + + ++ F
Sbjct: 196 FFVVFVERGQRRIVVNY-----AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILF 250
Query: 425 PSILASIL-GSPFWQHVKEI---LNPETSVGARPWVYYTIYAFFVFLFNIFDIANL--PK 478
P+ +AS G W + I L P +P +Y +YA + F F A + P+
Sbjct: 251 PATIASWFGGGTGWNWLTTISLYLQP-----GQP-LYVLLYASAIIFFCFFYTALVFNPR 304
Query: 479 EIADYLNKMGARIPNVKPGKATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLR-RIN 537
E AD L K GA +P ++PG+ T +Y+ K+ G ++R +
Sbjct: 305 ETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGA----LYITFICLIPEFMRDAMK 360
Query: 538 EGFSIGFTSVLIIVGSIIELRRSYQAYNVMPSLSKALRR 576
F G TS+LI+V I++ Q + AL++
Sbjct: 361 VPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKK 399
>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 = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 73/337 (21%), Positives = 132/337 (39%), Gaps = 72/337 (21%)
Query: 211 SFFQLGISPQIVASILMQVLCHIVPSLVQL------RKEGLDGHEKIKSYIWWISLGFAI 264
+ LGI P + A I+MQ+L ++Q+ + G +K+ S I
Sbjct: 68 TLITLGIGPIVTAGIIMQLLVG--SGIIQMDLSIPENRALFQGCQKLLSII------MCF 119
Query: 265 LEAVIVACYSLPYSIYAASHSVKHVMVTAFLLVCGAMTMSWICDTISESGFGQGSSLIIC 324
+EAV+ + I + ++ AF G++ + ++ + +S+ G G G L I
Sbjct: 120 VEAVLFVGAG-AFGILTPLLAFLVIIQIAF----GSIILIYLDEIVSKYGIGSGIGLFIA 174
Query: 325 VGI-------LTGYTETLYKMLSQLLGS--SVRWWPFMLGLLGVFTIVTMWA-----VVV 370
G+ G L+K L+ L+ ++ + ++G + VF +V +VV
Sbjct: 175 AGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRRRIVV 234
Query: 371 TEGCRKVKLQYYGFK-----------------LASAAREDSPITEVEPY---IPFNINPS 410
R+ + Y + LA+A + + + Y IP +
Sbjct: 235 NYAKRQQGRRVYAAQSTHLPLKVVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYE 294
Query: 411 GMQPVLTTTYLLAFPSILASILGSPFWQHVKEILNPETSVGARPWVYYTIYAFFVFLFNI 470
G + V Y L+ P L+S++ P V I T V +F I
Sbjct: 295 GGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCV----------------MFGI 338
Query: 471 FDIANL---PKEIADYLNKMGARIPNVKPGKATIEYL 504
F + PK +A + K GA +P ++PG+ T +Y+
Sbjct: 339 FWVETTGLDPKSMAKRIKKSGAFVPGIRPGEQTAKYI 375
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
0.324 0.139 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,942,675
Number of Sequences: 62578
Number of extensions: 617813
Number of successful extensions: 1492
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1462
Number of HSP's gapped (non-prelim): 16
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)