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= 009193
(540 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 = 3e-66, Method: Compositional matrix adjust.
Identities = 148/405 (36%), Positives = 234/405 (57%), Gaps = 17/405 (4%)
Query: 138 LALSRLGIYIPLGGVNREAFVGNLD--QNSLLSTLDSFSGGGIGRLGICSLGIVPFINAQ 195
+ RLG +IP+ G+N EA L + S+ + D FSGG +GRL + +LG++P+I+A
Sbjct: 25 FVIYRLGSHIPIPGINPEALRDFLKAFEGSVFALYDIFSGGNLGRLTVFALGVMPYISAS 84
Query: 196 IVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAIGQVLYLR-------- 247
I+ QLL P LQ L K EG+ GR K+ +YT+Y ++ A VQ++G ++R
Sbjct: 85 IMMQLLTVAIPSLQRLAKEEGDYGRYKINEYTKYLTLFVATVQSLGIAFWIRGQVSPKGI 144
Query: 248 PYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSIISYLPASFGRT 307
P V + G+ F +I +RI++ +GNG SL+IF I++ P + +
Sbjct: 145 PVVENPGISFILITVLTLVAGTMFLVWIADRITEKGIGNGASLIIFAGIVANFPNAVIQ- 203
Query: 308 VAEAFQDGNYIGLATIIISFILLV---LGIVYVQEAERKIPINYASRYTSRSGGLQRSAY 364
E + G+ IG T+++ L++ +GIVYVQEAER+IPI Y R R R Y
Sbjct: 204 FYEKVKTGD-IGPLTLLLIIALIIAIIVGIVYVQEAERRIPIQYPGRQVGRQLYAGRKTY 262
Query: 365 LPFKVNSSGVMPIIFSTSSLALPGTLARFTGIAALKKAAVALNPGGSFYLPTNILLIAFF 424
LP K+N +GV+PIIF+ + L +P TL F +K A PG FY + I FF
Sbjct: 263 LPIKINPAGVIPIIFAQALLLIPSTLLNFVQNPFIKVIADMFQPGAIFYNFLYVTFIVFF 322
Query: 425 NYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAILAAGP 484
Y+YT + ++P +++E L + GA IP VRPG+ T +L+ +++R+ G++FL+++A P
Sbjct: 323 TYFYTAVLINPVELAENLHKAGAFIPGVRPGQDTVKYLERIINRLIFFGALFLSVIALIP 382
Query: 485 AVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYKN 529
+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 = 225 bits (573), Expect = 6e-59, Method: Compositional matrix adjust.
Identities = 140/408 (34%), Positives = 224/408 (54%), Gaps = 30/408 (7%)
Query: 138 LALSRLGIYIPLGGVNREAFVGNLDQN--------SLLSTLDSFSGGGIGRLGICSLGIV 189
L + R+GIYIP+ G+N EA+ G + + +LS D F+GG + R + ++ +
Sbjct: 25 LIVFRMGIYIPVPGLNLEAW-GEIFRRIAETAGVAGILSFYDVFTGGALSRFSVFTMSVT 83
Query: 190 PFINAQIVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAIGQVLYLR-- 247
P+I A I+ QLLA + P L+++ REGE GRKK +YTR ++ QA L
Sbjct: 84 PYITASIILQLLASVMPSLKEML-REGEEGRKKFAKYTRRLTLLIGGFQAFFVSFSLARS 142
Query: 248 ------PYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSIISYLP 301
P VN G+ F ++GERI++ +GNG S+LIF I++ P
Sbjct: 143 NPDMVAPGVN--VLQFTVLSTMSMLAGTMFLLWLGERITEKGIGNGISILIFAGIVARYP 200
Query: 302 ASFGRTVAEAFQDG-NYIGLATIIISFILLVLGIVYVQEAERKIPINYASRYTSRSGGLQ 360
+ + +A+ G N + +I ++ + GI+ VQ+AER+I I YA R T R
Sbjct: 201 SY----IRQAYLGGLNLLEWIFLIAVALITIFGIILVQQAERRITIQYARRVTGRRVYGG 256
Query: 361 RSAYLPFKVNSSGVMPIIFSTSSLALPGTLARFTGIAALKKAAVALNPGGSFYLPTNILL 420
S YLP KVN GV+PIIF+++ +++P +A T LK GG YL LL
Sbjct: 257 ASTYLPIKVNQGGVIPIIFASAIVSIPSAIASITNNETLKNL---FRAGGFLYLLIYGLL 313
Query: 421 IAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAIL 480
+ FF Y+Y+ + DP ++SE +++ G IP +RPG+ST +L VL+R++ +G+VFL ++
Sbjct: 314 VFFFTYFYSVVIFDPREISENIRKYGGYIPGLRPGRSTEQYLHRVLNRVTFIGAVFLVVI 373
Query: 481 AAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYK 528
A P +++ + + G GTS LI VG A D ++++ ++ + Y+
Sbjct: 374 ALLPYLVQGAIKVNVWIG--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 (501), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 134/409 (32%), Positives = 213/409 (52%), Gaps = 24/409 (5%)
Query: 138 LALSRLGIYIPLGGVNREAFVGNLD--QNSLLSTLDSFSGGGIGRLGICSLGIVPFINAQ 195
LA RLG +IP GV+ + L Q + ++ FSGG R I +LGI+P+I A
Sbjct: 25 LAAYRLGAFIPTPGVDLDKIQEFLRTAQGGVFGIINLFSGGNFERFSIFALGIMPYITAA 84
Query: 196 IVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAI-----------GQVL 244
I+ Q+L + P L+ L K EGE GR+ + QYTR + Q G+ L
Sbjct: 85 IIMQILVTVVPALEKLSK-EGEEGRRIINQYTRIGGIALGAFQGFFLATAFLGAEGGRFL 143
Query: 245 YLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSII-SYLPAS 303
F G A ++ ERI++ +GNGTSL+IF I+ +LP
Sbjct: 144 LPGWSPGPFFWFVVVVTQVA---GIALLLWMAERITEYGIGNGTSLIIFAGIVVEWLPQI 200
Query: 304 FGRTVAEAFQDG--NYIGLATIIISFILLVLGIVYVQEAERKIPINYASRYTSRSGGLQR 361
RT+ + G N + + +L G+ VQ+AER+IP+ YA + +
Sbjct: 201 L-RTIG-LIRTGEVNLVAFLFFLAFIVLAFAGMAAVQQAERRIPVQYARKVVGGRVYGGQ 258
Query: 362 SAYLPFKVNSSGVMPIIFSTSSLALPGTLAR-FTGIAALKKAAVALNPGGSFYLPTNILL 420
+ Y+P K+N++GV+PIIF+ + L +P LA F L+ A NP L +LL
Sbjct: 259 ATYIPIKLNAAGVIPIIFAAAILQIPIFLAAPFQDNPVLQGIANFFNPTRPSGLFIEVLL 318
Query: 421 IAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAIL 480
+ F Y YT +Q DP ++E L+ G IP +RPG+ T FL+ ++SR+++ G++FL ++
Sbjct: 319 VILFTYVYTAVQFDPKRIAESLREYGGFIPGIRPGEPTVKFLEHIVSRLTLWGALFLGLV 378
Query: 481 AAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYKN 529
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 = 194 bits (494), Expect = 9e-50, Method: Compositional matrix adjust.
Identities = 131/421 (31%), Positives = 237/421 (56%), Gaps = 27/421 (6%)
Query: 138 LALSRLGIYIPLGGVNREAFVGNLDQN--SLLSTLDSFSGGGIGRLGICSLGIVPFINAQ 195
L + R+G +IP+ G++ L+Q +++ + FSGG + R I +LGI+P+I+A
Sbjct: 23 LIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISAS 82
Query: 196 IVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAIG-----------QVL 244
I+ QLL ++P L ++ K+EGE+GR+K+ QYTRY ++ AI Q+IG Q L
Sbjct: 83 IIIQLLTVVHPTLAEI-KKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGL 141
Query: 245 YLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSLLIFTSIISYLPASF 304
+ P + G+ F ++GE+I++ +GNG S++IF I++ LP +
Sbjct: 142 VINPGFAFYFTAVVSLVT-----GTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAI 196
Query: 305 GRTVAEAFQ-DGNYIGLATIIISFILLVLGIVYVQEAERKIPINYASRYTSRSGGLQRSA 363
T+ +A Q D +++ L + + + +V+V+ +R+I +NYA R R +S
Sbjct: 197 AHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQST 256
Query: 364 YLPFKVNSSGVMPIIFSTSSLALPGTLARF----TGIAALKKAAVALNPGGSFYLPTNIL 419
+LP KVN +GV+P IF++S + P T+A + TG L ++ L PG Y+
Sbjct: 257 HLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISLYLQPGQPLYVLLYAS 316
Query: 420 LIAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVLGSVFLAI 479
I FF ++YT L +P + ++ LK+ GA +P +RPG+ TA ++ V++R++++G++++
Sbjct: 317 AIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITF 376
Query: 480 LAAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIISQKYKN-IEFYDIDSY 538
+ P + + + F GTS+LI+V D +VQ ++S +Y++ ++ ++ Y
Sbjct: 377 ICLIPEFMRDAMKVPFY--FGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGY 434
Query: 539 G 539
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 = 173 bits (438), Expect = 3e-43, Method: Compositional matrix adjust.
Identities = 116/365 (31%), Positives = 207/365 (56%), Gaps = 24/365 (6%)
Query: 181 LGICSLGIVPFINAQIVFQLLAQINPKLQDLQKREGEAGRKKVLQYTRYASVGFAIVQAI 240
+ I +LGI+P+I+A I+ QLL ++P L ++ K+EGE+GR+K+ QYTRY ++ AI Q+I
Sbjct: 39 ISIFALGIMPYISASIIIQLLTVVHPTLAEI-KKEGESGRRKISQYTRYGTLVLAIFQSI 97
Query: 241 G-----------QVLYLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTS 289
G Q L + P + G+ F ++GE+I++ +GNG S
Sbjct: 98 GIATGLPNMPGMQGLVINPGFAFYFTAVVSLVT-----GTMFLMWLGEQITERGIGNGIS 152
Query: 290 LLIFTSIISYLPASFGRTVAEAFQ-DGNYIGLATIIISFILLVLGIVYVQEAERKIPINY 348
++IF I++ LP + T+ +A Q D +++ L + + + +V+V+ +R+I +NY
Sbjct: 153 IIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNY 212
Query: 349 ASRYTSRSGGLQRSAYLPFKVNSSGVMPIIFSTSSLALPGTLARF----TGIAALKKAAV 404
A R R +S +LP KVN +GV+P IF++S + P T+A + TG L ++
Sbjct: 213 AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISL 272
Query: 405 ALNPGGSFYLPTNILLIAFFNYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKT 464
L PG Y+ I FF ++YT L +P + ++ LK+ GA +P +RPG+ TA ++
Sbjct: 273 YLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDK 332
Query: 465 VLSRISVLGSVFLAILAAGPAVIEQTTHLTAFRGFAGTSVLILVGCATDTARKVQAEIIS 524
V++R++++G++++ + P + + + F GTS+LI+V D +VQ ++S
Sbjct: 333 VMTRLTLVGALYITFICLIPEFMRDAMKVPFY--FGGTSLLIVVVVIMDFMAQVQTLMMS 390
Query: 525 QKYKN 529
+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 = 63.2 bits (152), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 89/352 (25%), Positives = 145/352 (41%), Gaps = 68/352 (19%)
Query: 180 RLG-ICSLGIVPFINAQIVFQLLAQINPKLQDLQKREGEA---GRKKVLQYTRYASVGFA 235
R+G + +LGI P + A I+ QLL DL E A G +K+L S+
Sbjct: 65 RIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLL------SIIMC 118
Query: 236 IVQAI-----GQVLYLRPYVNDFXXXXXXXXXXXXXXGSAFTTYIGERISDLKLGNGTSL 290
V+A+ G L P + GS Y+ E +S +G+G L
Sbjct: 119 FVEAVLFVGAGAFGILTPLLAFLVIIQIAF-------GSIILIYLDEIVSKYGIGSGIGL 171
Query: 291 LIFTSIIS-----------YLPASFGRTVAEAFQDGNYIGLATIIISFILLVLGIVYVQE 339
I + YL F ++ + + YI II I++ L +VY +
Sbjct: 172 FIAAGVSQTIFVGALGPEGYL-WKFLNSLIQGVPNIEYIAP---IIGTIIVFLMVVYAEC 227
Query: 340 AERKIPINYASRYTSRSGGLQRSAYLPFKVNSSGVMPIIFSTSSLA-------------L 386
R+I +NYA R R +S +LP KV +P+I + + A +
Sbjct: 228 MRRRIVVNYAKRQQGRRVYAAQSTHLPLKVVYVSNIPVILAAALFANIQLWGLALYRMGI 287
Query: 387 PGTLARFTGIAALKKAAVALN-PGG-----------SFYLPTNILLIAFFNYYYTFLQ-L 433
P L + G A+ A L+ P G Y+ I+ F ++ L
Sbjct: 288 P-ILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGL 346
Query: 434 DPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSR----ISVLGSVFLAILA 481
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 = 32.3 bits (72), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 425 NYYYTFLQLDPDDVSEQLKRQGASIPLVRPGKSTAAFLKTVLSRISVL 472
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
0.320 0.136 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,678,946
Number of Sequences: 62578
Number of extensions: 507841
Number of successful extensions: 1042
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1007
Number of HSP's gapped (non-prelim): 10
length of query: 540
length of database: 14,973,337
effective HSP length: 104
effective length of query: 436
effective length of database: 8,465,225
effective search space: 3690838100
effective search space used: 3690838100
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)