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= 014159
(429 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 = 249 bits (636), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 148/405 (36%), Positives = 234/405 (57%), Gaps = 17/405 (4%)
Query: 27 LALSRLGIYIPLGGVNREAFVGNLD--QNSLLSTLDSFSGGGIGRLGICSLGIVPFINAQ 84
+ RLG +IP+ G+N EA L + S+ + D FSGG +GRL + +LG++P+I+A
Sbjct: 25 FVIYRLGSHIPIPGINPEALRDFLKAFEGSVFALYDIFSGGNLGRLTVFALGVMPYISAS 84
Query: 85 IVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAIGQVLYLR-------- 136
I+ QLL P LQ L K EG+ GR K+ +YT+Y ++ A VQ++G ++R
Sbjct: 85 IMMQLLTVAIPSLQRLAKEEGDYGRYKINEYTKYLTLFVATVQSLGIAFWIRGQVSPKGI 144
Query: 137 PYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSIISYLPASFGRT 196
P V + G+ F +I +RI++ +GNG SL+IF I++ P + +
Sbjct: 145 PVVENPGISFILITVLTLVAGTMFLVWIADRITEKGIGNGASLIIFAGIVANFPNAVIQ- 203
Query: 197 VAEAFQDGNYIGLATIIISFILLV---LGIVYVQEAERKIPINYASRYTSRSGGLQRSAY 253
E + G+ IG T+++ L++ +GIVYVQEAER+IPI Y R R R Y
Sbjct: 204 FYEKVKTGD-IGPLTLLLIIALIIAIIVGIVYVQEAERRIPIQYPGRQVGRQLYAGRKTY 262
Query: 254 LPFKVNSSGVMPIIFSTSSLALPGTLARFTGIAALKKAAVALNPGGSFYLPTNILLIAFF 313
LP K+N +GV+PIIF+ + L +P TL F +K A PG FY + I FF
Sbjct: 263 LPIKINPAGVIPIIFAQALLLIPSTLLNFVQNPFIKVIADMFQPGAIFYNFLYVTFIVFF 322
Query: 314 NYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAILAAGP 373
Y+YT + ++P +++E L + GA IP VRPG+ T +L+ +++R+ G++FL+++A P
Sbjct: 323 TYFYTAVLINPVELAENLHKAGAFIPGVRPGQDTVKYLERIINRLIFFGALFLSVIALIP 382
Query: 374 AVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYKN 418
+I ++ + F GT+ LI+VG A DT R+++ +I +KYK+
Sbjct: 383 ILISVWFNIPFY--FGGTTALIVVGVALDTFRQIETYLIQKKYKS 425
>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 = 224 bits (571), Expect = 7e-59, Method: Compositional matrix adjust.
Identities = 139/410 (33%), Positives = 228/410 (55%), Gaps = 34/410 (8%)
Query: 27 LALSRLGIYIPLGGVNREAFVGNLDQN--------SLLSTLDSFSGGGIGRLGICSLGIV 78
L + R+GIYIP+ G+N EA+ G + + +LS D F+GG + R + ++ +
Sbjct: 25 LIVFRMGIYIPVPGLNLEAW-GEIFRRIAETAGVAGILSFYDVFTGGALSRFSVFTMSVT 83
Query: 79 PFINAQIVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYAS----------VGFAIVQA 128
P+I A I+ QLLA + P L+++ REGE GRKK +YTR + V F++ ++
Sbjct: 84 PYITASIILQLLASVMPSLKEML-REGEEGRKKFAKYTRRLTLLIGGFQAFFVSFSLARS 142
Query: 129 IGQVLYLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSIISY 188
++ P VN G+ F ++GERI++ +GNG S+LIF I++
Sbjct: 143 NPDMV--APGVN--VLQFTVLSTMSMLAGTMFLLWLGERITEKGIGNGISILIFAGIVAR 198
Query: 189 LPASFGRTVAEAFQDG-NYIGLATIIISFILLVLGIVYVQEAERKIPINYASRYTSRSGG 247
P+ + +A+ G N + +I ++ + GI+ VQ+AER+I I YA R T R
Sbjct: 199 YPSY----IRQAYLGGLNLLEWIFLIAVALITIFGIILVQQAERRITIQYARRVTGRRVY 254
Query: 248 LQRSAYLPFKVNSSGVMPIIFSTSSLALPGTLARFTGIAALKKAAVALNPGGSFYLPTNI 307
S YLP KVN GV+PIIF+++ +++P +A T LK GG YL
Sbjct: 255 GGASTYLPIKVNQGGVIPIIFASAIVSIPSAIASITNNETLKNL---FRAGGFLYLLIYG 311
Query: 308 LLIAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLA 367
LL+ FF Y+Y+ + DP ++SE +++ G IP +RPG+ST +L VL+R++ +G+VFL
Sbjct: 312 LLVFFFTYFYSVVIFDPREISENIRKYGGYIPGLRPGRSTEQYLHRVLNRVTFIGAVFLV 371
Query: 368 ILAAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYK 417
++A P +++ + + G GTS LI VG A D ++++ ++ + Y+
Sbjct: 372 VIALLPYLVQGAIKVNVWIG--GTSALIAVGVALDIIQQMETHMVMRHYE 419
>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 = 197 bits (500), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 136/409 (33%), Positives = 216/409 (52%), Gaps = 24/409 (5%)
Query: 27 LALSRLGIYIPLGGVNREAFVGNLD--QNSLLSTLDSFSGGGIGRLGICSLGIVPFINAQ 84
LA RLG +IP GV+ + L Q + ++ FSGG R I +LGI+P+I A
Sbjct: 25 LAAYRLGAFIPTPGVDLDKIQEFLRTAQGGVFGIINLFSGGNFERFSIFALGIMPYITAA 84
Query: 85 IVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASV------GFAIVQAI-----GQVL 133
I+ Q+L + P L+ L K EGE GR+ + QYTR + GF + A G+ L
Sbjct: 85 IIMQILVTVVPALEKLSK-EGEEGRRIINQYTRIGGIALGAFQGFFLATAFLGAEGGRFL 143
Query: 134 YLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSII-SYLPAS 192
F G A ++ ERI++ +GNGTSL+IF I+ +LP
Sbjct: 144 LPGWSPGPFFWFVVVVTQVA---GIALLLWMAERITEYGIGNGTSLIIFAGIVVEWLPQI 200
Query: 193 FGRTVAEAFQDG--NYIGLATIIISFILLVLGIVYVQEAERKIPINYASRYTSRSGGLQR 250
RT+ + G N + + +L G+ VQ+AER+IP+ YA + +
Sbjct: 201 L-RTIG-LIRTGEVNLVAFLFFLAFIVLAFAGMAAVQQAERRIPVQYARKVVGGRVYGGQ 258
Query: 251 SAYLPFKVNSSGVMPIIFSTSSLALPGTLAR-FTGIAALKKAAVALNPGGSFYLPTNILL 309
+ Y+P K+N++GV+PIIF+ + L +P LA F L+ A NP L +LL
Sbjct: 259 ATYIPIKLNAAGVIPIIFAAAILQIPIFLAAPFQDNPVLQGIANFFNPTRPSGLFIEVLL 318
Query: 310 IAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAIL 369
+ F Y YT +Q DP ++E L+ G IP +RPG+ T FL+ ++SR+++ G++FL ++
Sbjct: 319 VILFTYVYTAVQFDPKRIAESLREYGGFIPGIRPGEPTVKFLEHIVSRLTLWGALFLGLV 378
Query: 370 AAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYKN 418
P +I+ T + + F+G +LI+VG A DT R+V+++++ + Y+
Sbjct: 379 TLLPQIIQNLTGIHSI-AFSGIGLLIVVGVALDTLRQVESQLMLRSYEG 426
>pdb|3J01|A Chain A, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
Length = 435
Score = 195 bits (496), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 131/421 (31%), Positives = 237/421 (56%), Gaps = 27/421 (6%)
Query: 27 LALSRLGIYIPLGGVNREAFVGNLDQN--SLLSTLDSFSGGGIGRLGICSLGIVPFINAQ 84
L + R+G +IP+ G++ L+Q +++ + FSGG + R I +LGI+P+I+A
Sbjct: 23 LIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISAS 82
Query: 85 IVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAIG-----------QVL 133
I+ QLL ++P L ++ K+EGE+GR+K+ QYTRY ++ AI Q+IG Q L
Sbjct: 83 IIIQLLTVVHPTLAEI-KKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGL 141
Query: 134 YLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSIISYLPASF 193
+ P + G+ F ++GE+I++ +GNG S++IF I++ LP +
Sbjct: 142 VINPGFAFYFTAVVSLVT-----GTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAI 196
Query: 194 GRTVAEAFQ-DGNYIGLATIIISFILLVLGIVYVQEAERKIPINYASRYTSRSGGLQRSA 252
T+ +A Q D +++ L + + + +V+V+ +R+I +NYA R R +S
Sbjct: 197 AHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQST 256
Query: 253 YLPFKVNSSGVMPIIFSTSSLALPGTLARF----TGIAALKKAAVALNPGGSFYLPTNIL 308
+LP KVN +GV+P IF++S + P T+A + TG L ++ L PG Y+
Sbjct: 257 HLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISLYLQPGQPLYVLLYAS 316
Query: 309 LIAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAI 368
I FF ++YT L +P + ++ LK+ GA +P +RPG+ TA ++ V++R++++G++++
Sbjct: 317 AIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITF 376
Query: 369 LAAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYKN-IEFYDIDSY 427
+ P + + + F GTS+LI+V D +VQ ++S +Y++ ++ ++ Y
Sbjct: 377 ICLIPEFMRDAMKVPFY--FGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGY 434
Query: 428 G 428
G
Sbjct: 435 G 435
>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 = 174 bits (440), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 116/365 (31%), Positives = 207/365 (56%), Gaps = 24/365 (6%)
Query: 70 LGICSLGIVPFINAQIVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAI 129
+ I +LGI+P+I+A I+ QLL ++P L ++ K+EGE+GR+K+ QYTRY ++ AI Q+I
Sbjct: 39 ISIFALGIMPYISASIIIQLLTVVHPTLAEI-KKEGESGRRKISQYTRYGTLVLAIFQSI 97
Query: 130 G-----------QVLYLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTS 178
G Q L + P + G+ F ++GE+I++ +GNG S
Sbjct: 98 GIATGLPNMPGMQGLVINPGFAFYFTAVVSLVT-----GTMFLMWLGEQITERGIGNGIS 152
Query: 179 LLIFTSIISYLPASFGRTVAEAFQ-DGNYIGLATIIISFILLVLGIVYVQEAERKIPINY 237
++IF I++ LP + T+ +A Q D +++ L + + + +V+V+ +R+I +NY
Sbjct: 153 IIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNY 212
Query: 238 ASRYTSRSGGLQRSAYLPFKVNSSGVMPIIFSTSSLALPGTLARF----TGIAALKKAAV 293
A R R +S +LP KVN +GV+P IF++S + P T+A + TG L ++
Sbjct: 213 AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISL 272
Query: 294 ALNPGGSFYLPTNILLIAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKT 353
L PG Y+ I FF ++YT L +P + ++ LK+ GA +P +RPG+ TA ++
Sbjct: 273 YLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDK 332
Query: 354 VLSRISVLGSVFLAILAAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIIS 413
V++R++++G++++ + P + + + F GTS+LI+V D +VQ ++S
Sbjct: 333 VMTRLTLVGALYITFICLIPEFMRDAMKVPFY--FGGTSLLIVVVVIMDFMAQVQTLMMS 390
Query: 414 QKYKN 418
+Y++
Sbjct: 391 SQYES 395
>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 = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 90/352 (25%), Positives = 146/352 (41%), Gaps = 68/352 (19%)
Query: 69 RLG-ICSLGIVPFINAQIVFQLLAQINPKLQDLQKREGEA---GRKKVLQYTRYASVGFA 124
R+G + +LGI P + A I+ QLL DL E A G +K+L S+
Sbjct: 65 RIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLL------SIIMC 118
Query: 125 IVQAI-----GQVLYLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSL 179
V+A+ G L P + GS Y+ E +S +G+G L
Sbjct: 119 FVEAVLFVGAGAFGILTPLL-------AFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGL 171
Query: 180 LIFTSIIS-----------YLPASFGRTVAEAFQDGNYIGLATIIISFILLVLGIVYVQE 228
I + YL F ++ + + YI II I++ L +VY +
Sbjct: 172 FIAAGVSQTIFVGALGPEGYL-WKFLNSLIQGVPNIEYIAP---IIGTIIVFLMVVYAEC 227
Query: 229 AERKIPINYASRYTSRSGGLQRSAYLPFKVNSSGVMPIIFSTSSLA---LPGTLARFTGI 285
R+I +NYA R R +S +LP KV +P+I + + A L G GI
Sbjct: 228 MRRRIVVNYAKRQQGRRVYAAQSTHLPLKVVYVSNIPVILAAALFANIQLWGLALYRMGI 287
Query: 286 AALK--KAAVALNPGGSFYLPTN---------------------ILLIAFFNYYYTFLQL 322
L + A++ G ++YL T I + F ++ L
Sbjct: 288 PILGHYEGGRAVD-GIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGL 346
Query: 323 DPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSR----ISVLGSVFLAILA 370
DP +++++K+ GA +P +RPG+ TA +++ L R ++V+ S F+ LA
Sbjct: 347 DPKSMAKRIKKSGAFVPGIRPGEQTAKYIEHRLKRYIPPLTVMSSAFVGFLA 398
>pdb|3OXN|A Chain A, The Crystal Structure Of A Putative Transcriptional
Regulator From Vibrio Parahaemolyticus
pdb|3OXN|B Chain B, The Crystal Structure Of A Putative Transcriptional
Regulator From Vibrio Parahaemolyticus
pdb|3OXN|C Chain C, The Crystal Structure Of A Putative Transcriptional
Regulator From Vibrio Parahaemolyticus
pdb|3OXN|D Chain D, The Crystal Structure Of A Putative Transcriptional
Regulator From Vibrio Parahaemolyticus
Length = 241
Score = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 314 NYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVL 361
N + FL L D +S+QL +GA + + RP +L R+ VL
Sbjct: 47 NVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVEPLRSEILGRVGVL 94
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
0.322 0.140 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,740,083
Number of Sequences: 62578
Number of extensions: 401485
Number of successful extensions: 804
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 768
Number of HSP's gapped (non-prelim): 11
length of query: 429
length of database: 14,973,337
effective HSP length: 102
effective length of query: 327
effective length of database: 8,590,381
effective search space: 2809054587
effective search space used: 2809054587
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)