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= 007921
(585 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 = 162 bits (409), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 135/445 (30%), Positives = 217/445 (48%), Gaps = 43/445 (9%)
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 VGILTGYTETLYKMLSQLLVFKYTAGSSVRWWPFMLGLLGVFTIVTMWAVV-VTEGCRKV 383
GI+ + + + Y + P L L+ I + +V V E R++
Sbjct: 191 AGIVANFPNAVIQF--------YEKVKTGDIGPLTLLLIIALIIAIIVGIVYVQEAERRI 242
Query: 384 KLQYYGFKLAS---AAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASILGS 440
+QY G ++ A R+ Y+P INP+G+ P++ LL PS L + + +
Sbjct: 243 PIQYPGRQVGRQLYAGRKT--------YLPIKINPAGVIPIIFAQALLLIPSTLLNFVQN 294
Query: 441 PFWQHVKEILNPETSVGARPWVYYT-IYAFFVFLFNIFDIANL--PKEIADYLNKMGARI 497
PF + + ++ P GA ++Y +Y F+ F F A L P E+A+ L+K GA I
Sbjct: 295 PFIKVIADMFQP----GA---IFYNFLYVTFIVFFTYFYTAVLINPVELAENLHKAGAFI 347
Query: 498 PNVKPGKATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLRRINEGFSIGFTSVLIIV 557
P V+PG+ T++YL +I F+G + N F G T+ LI+V
Sbjct: 348 PGVRPGQDTVKYLERIINRLIFFGALFLSVIALIPILISVWF---NIPFYFGGTTALIVV 404
Query: 558 GSIIELRRSYQAYNVMPSLSKALRR 582
G ++ R + Y + +RR
Sbjct: 405 GVALDTFRQIETYLIQKKYKSYVRR 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 = 133 bits (335), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 106/437 (24%), Positives = 204/437 (46%), Gaps = 52/437 (11%)
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 CVGILTGYTETLYKMLSQLLVFKYTAGSSVRWWPFMLGLLGVFTIVTMWAVV-VTEGCRK 382
GI+ Y + + Y G ++ W F++ + ++T++ ++ V + R+
Sbjct: 192 FAGIVARYPSYIRQ--------AYLGGLNLLEWIFLIAV----ALITIFGIILVQQAERR 239
Query: 383 VKLQYYGFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASILGSPF 442
+ +QY A Y+P +N G+ P++ + +++ PS +ASI +
Sbjct: 240 ITIQY-----ARRVTGRRVYGGASTYLPIKVNQGGVIPIIFASAIVSIPSAIASITNN-- 292
Query: 443 WQHVKEILNPETSVGARPWVYYTIYAFFVFLFN------IFDIANLPKEIADYLNKMGAR 496
+ +K + A ++Y IY VF F IFD P+EI++ + K G
Sbjct: 293 -ETLKNLFR------AGGFLYLLIYGLLVFFFTYFYSVVIFD----PREISENIRKYGGY 341
Query: 497 IPNVKPGKATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLRRINEGFSIGFTSVLII 556
IP ++PG++T +YL ++ F G I IG TS LI
Sbjct: 342 IPGLRPGRSTEQYLHRVLNRVTFIGAVFLVVIALLPYLVQG---AIKVNVWIGGTSALIA 398
Query: 557 VGSIIELRRSYQAYNVM 573
VG +++ + + + VM
Sbjct: 399 VGVALDIIQQMETHMVM 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 = 123 bits (309), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 123/439 (28%), Positives = 197/439 (44%), Gaps = 32/439 (7%)
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 ILTGYTETLYKMLSQLLVFKYTAGSSVRWWPFMLGLLGVFTIVTMWAVVVTEGCRKVKLQ 386
I+ E L ++L + + + T ++ + F L + V M AV E R++ +Q
Sbjct: 192 IV---VEWLPQILRTIGLIR-TGEVNLVAFLFFLAFI-VLAFAGMAAVQQAE--RRIPVQ 244
Query: 387 YYGFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILAS-ILGSPFWQH 445
Y K+ T YIP +N +G+ P++ +L P LA+ +P Q
Sbjct: 245 -YARKVVGGRVYGGQAT----YIPIKLNAAGVIPIIFAAAILQIPIFLAAPFQDNPVLQG 299
Query: 446 VKEILNPETSVGARPWVYYTIYAFFVFLFNIFDIANLPKEIADYLNKMGARIPNVKPGKA 505
+ NP G V I +V+ FD PK IA+ L + G IP ++PG+
Sbjct: 300 IANFFNPTRPSGLFIEVLLVILFTYVYTAVQFD----PKRIAESLREYGGFIPGIRPGEP 355
Query: 506 TIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLRRINEGFSIGFTSV--LIIVGSIIEL 563
T+++L I + WG ++ + SI F+ + LI+VG ++
Sbjct: 356 TVKFLEHIVSRLTLWGA----LFLGLVTLLPQIIQNLTGIHSIAFSGIGLLIVVGVALDT 411
Query: 564 RRSYQAYNVMPSLSKALRR 582
R ++ ++ S L R
Sbjct: 412 LRQVESQLMLRSYEGFLSR 430
>pdb|3J01|A Chain A, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
Length = 435
Score = 105 bits (263), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 124/444 (27%), Positives = 202/444 (45%), Gaps = 40/444 (9%)
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 GILTGYTETLYKMLSQLLVFKYTAGSSVRWWPFMLGLLGVFTIVTMWAVVVTEGCRKVKL 385
GI+ G + + Q A + +L + + VT + V V G R++ +
Sbjct: 187 GIVAGLPPAIAHTIEQ-------ARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVV 239
Query: 386 QYYGFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASIL-GSPFWQ 444
Y A + ++P +N +G+ P + + ++ FP+ +AS G W
Sbjct: 240 NY-----AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWN 294
Query: 445 HVKEI---LNPETSVGARPWVYYTIYAFFVFLFNIFDIANL--PKEIADYLNKMGARIPN 499
+ I L P +P +Y +YA + F F A + P+E AD L K GA +P
Sbjct: 295 WLTTISLYLQP-----GQP-LYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPG 348
Query: 500 VKPGKATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHYLR-RINEGFSIGFTSVLIIVG 558
++PG+ T +Y+ K+ G ++R + F G TS+LI+V
Sbjct: 349 IRPGEQTAKYIDKVMTRLTLVGA----LYITFICLIPEFMRDAMKVPFYFGGTSLLIVVV 404
Query: 559 SIIELRRSYQAYNVMPSLSKALRR 582
I++ Q + AL++
Sbjct: 405 VIMDFMAQVQTLMMSSQYESALKK 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 = 82.8 bits (203), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 108/405 (26%), Positives = 178/405 (43%), Gaps = 41/405 (10%)
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 WICDTISESGFGQGSSLIICVGILTGYTETLYKMLSQLLVFKYTAGSSVRWWPFMLGLLG 364
W+ + I+E G G G S+II GI+ G + + Q A + +L +
Sbjct: 137 WLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQ-------ARQGDLHFLVLLLVAV 189
Query: 365 VFTIVTMWAVVVTEGCRKVKLQYYGFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTT 424
+ VT + V V G R++ + Y A + ++P +N +G+ P +
Sbjct: 190 LVFAVTFFVVFVERGQRRIVVNY-----AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFA 244
Query: 425 TYLLAFPSILASIL-GSPFWQHVKEI---LNPETSVGARPWVYYTIYAFFVFLFNIFDIA 480
+ ++ FP+ +AS G W + I L P +P +Y +YA + F F A
Sbjct: 245 SSIILFPATIASWFGGGTGWNWLTTISLYLQP-----GQP-LYVLLYASAIIFFCFFYTA 298
Query: 481 NL--PKEIADYLNKMGARIPNVKPGKATIEYLTKIQASTRFWGGXXXXXXXXXXXXXDHY 538
+ P+E AD L K GA +P ++PG+ T +Y+ K+ G +
Sbjct: 299 LVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGA----LYITFICLIPEF 354
Query: 539 LR-RINEGFSIGFTSVLIIVGSIIELRRSYQAYNVMPSLSKALRR 582
+R + F G TS+LI+V I++ Q + AL++
Sbjct: 355 MRDAMKVPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKK 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 = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 73/341 (21%), Positives = 132/341 (38%), Gaps = 74/341 (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-------LTGYTETLYKMLSQLLVFKYTAGSSVRWWPFMLGLLGVFTIVTMWA---- 373
G+ G L+K L+ L+ ++ + ++G + VF +V
Sbjct: 175 AGVSQTIFVGALGPEGYLWKFLNSLI----QGVPNIEYIAPIIGTIIVFLMVVYAECMRR 230
Query: 374 -VVVTEGCRKVKLQYYGFK-----------------LASAAREDSPITEVEPY---IPFN 412
+VV R+ + Y + LA+A + + + Y IP
Sbjct: 231 RIVVNYAKRQQGRRVYAAQSTHLPLKVVYVSNIPVILAAALFANIQLWGLALYRMGIPIL 290
Query: 413 INPSGMQPVLTTTYLLAFPSILASILGSPFWQHVKEILNPETSVGARPWVYYTIYAFFVF 472
+ G + V Y L+ P L+S++ P V I T V
Sbjct: 291 GHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCV---------------- 334
Query: 473 LFNIFDIANL---PKEIADYLNKMGARIPNVKPGKATIEYL 510
+F IF + PK +A + K GA +P ++PG+ T +Y+
Sbjct: 335 MFGIFWVETTGLDPKSMAKRIKKSGAFVPGIRPGEQTAKYI 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
0.325 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: 16,097,658
Number of Sequences: 62578
Number of extensions: 625836
Number of successful extensions: 1520
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: 1490
Number of HSP's gapped (non-prelim): 16
length of query: 585
length of database: 14,973,337
effective HSP length: 104
effective length of query: 481
effective length of database: 8,465,225
effective search space: 4071773225
effective search space used: 4071773225
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)