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= 010158
(516 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 = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 101/331 (30%), Positives = 168/331 (50%), Gaps = 30/331 (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 VACYSL----PYSIYAASH-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 KEILNPETSVGA--RPWVYYTIYAFFVFLFN 469
++ P GA ++Y T FF + +
Sbjct: 301 ADMFQP----GAIFYNFLYVTFIVFFTYFYT 327
>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 = 106 bits (265), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 81/335 (24%), Positives = 162/335 (48%), Gaps = 33/335 (9%)
Query: 149 ESFFKSEIRRRLFVTAVLIVISRIGYFIPLPGFD--------RRLIPQDYLSFVSGSVDE 200
+F E+R R+ T + +++ R+G +IP+PG + RR+ ++ + D
Sbjct: 7 NAFKIPELRDRIIFTFLALIVFRMGIYIPVPGLNLEAWGEIFRRIAETAGVAGILSFYDV 66
Query: 201 LGDFGAELKLSFFQLGISPQIVASILMQVLCHIVPSLVQLRKEGLDGHEKIKSYIWWISL 260
GA + S F + ++P I ASI++Q+L ++PSL ++ +EG +G +K Y ++L
Sbjct: 67 FTG-GALSRFSVFTMSVTPYITASIILQLLASVMPSLKEMLREGEEGRKKFAKYTRRLTL 125
Query: 261 GFAILEAVIVA---CYSLPYSIYAASHSVKHVMVTAFLLVCGAMTMSWICDTISESGFGQ 317
+A V+ S P + + ++ +++ ++ G M + W+ + I+E G G
Sbjct: 126 LIGGFQAFFVSFSLARSNPDMVAPGVNVLQFTVLSTMSMLAGTMFLLWLGERITEKGIGN 185
Query: 318 GSSLIICVGILTGYTETLYKMLSQLLGSSVRWWPFMLGLLGVFTIVTMWAVV-VTEGCRK 376
G S++I GI+ Y Y + L G ++ W F++ + ++T++ ++ V + R+
Sbjct: 186 GISILIFAGIVARYPS--YIRQAYLGGLNLLEWIFLIAV----ALITIFGIILVQQAERR 239
Query: 377 VKLQYYGFKLASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASILGSPF 436
+ +QY A Y+P +N G+ P++ + +++ PS +ASI +
Sbjct: 240 ITIQY-----ARRVTGRRVYGGASTYLPIKVNQGGVIPIIFASAIVSIPSAIASITNN-- 292
Query: 437 WQHVKEILNPETSVGARPWVYYTIYAFFVFLFNIF 471
+ +K + A ++Y IY VF F F
Sbjct: 293 -ETLKNLFR------AGGFLYLLIYGLLVFFFTYF 320
>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 = 99.0 bits (245), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 85/306 (27%), Positives = 135/306 (44%), Gaps = 16/306 (5%)
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 PETSVG 451
P G
Sbjct: 306 PTRPSG 311
>pdb|3J01|A Chain A, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
Length = 435
Score = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 85/289 (29%), Positives = 140/289 (48%), Gaps = 17/289 (5%)
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 LASAAREDSPITEVEPYIPFNINPSGMQPVLTTTYLLAFPSILASILGS 434
A + ++P +N +G+ P + + ++ FP+ +AS G
Sbjct: 242 -AKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGG 289
>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 = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 71/259 (27%), Positives = 119/259 (45%), Gaps = 24/259 (9%)
Query: 182 DRRLIPQDYLSFVSGS--VDELGDFGAELKLSFFQLGISPQIVASILMQVLCHIVPSLVQ 239
RRL+ FV G+ V +G F +S F LGI P I ASI++Q+L + P+L +
Sbjct: 20 KRRLL------FVIGALIVFRIGSF-----ISIFALGIMPYISASIIIQLLTVVHPTLAE 68
Query: 240 LRKEGLDGHEKIKSYIWWISLGFAILEAVIVACYSLP----YSIYAASHSVKHVMVTAFL 295
++KEG G KI Y + +L AI +++ +A LP +
Sbjct: 69 IKKEGESGRRKISQYTRYGTLVLAIFQSIGIAT-GLPNMPGMQGLVINPGFAFYFTAVVS 127
Query: 296 LVCGAMTMSWICDTISESGFGQGSSLIICVGILTGYTETLYKMLSQLLGSSVRWWPFMLG 355
LV G M + W+ + I+E G G G S+II GI+ G + + Q + + +L
Sbjct: 128 LVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLL- 186
Query: 356 LLGVFTIVTMWAVVVTEGCRKVKLQYYGFKLASAAREDSPITEVEPYIPFNINPSGMQPV 415
+ + VT + V V G R++ + Y A + ++P +N +G+ P
Sbjct: 187 VAVLVFAVTFFVVFVERGQRRIVVNY-----AKRQQGRRVYAAQSTHLPLKVNMAGVIPA 241
Query: 416 LTTTYLLAFPSILASILGS 434
+ + ++ FP+ +AS G
Sbjct: 242 IFASSIILFPATIASWFGG 260
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
0.327 0.140 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,380,144
Number of Sequences: 62578
Number of extensions: 560702
Number of successful extensions: 1280
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1259
Number of HSP's gapped (non-prelim): 15
length of query: 516
length of database: 14,973,337
effective HSP length: 103
effective length of query: 413
effective length of database: 8,527,803
effective search space: 3521982639
effective search space used: 3521982639
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)