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= psy5829
(147 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WWB|A Chain A, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
Length = 476
Score = 189 bits (479), Expect = 7e-49, Method: Compositional matrix adjust.
Identities = 87/116 (75%), Positives = 102/116 (87%)
Query: 16 QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSA 75
QN + ++AT+ VFA+VIYFQGFRVDLPIKSARYRGQY++YPIKLFYTSNIPIILQSA
Sbjct: 237 QNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSA 296
Query: 76 LVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENLG 131
LVSNLYVISQML+ +F GN+ V+LLG W+D GGPARAYP+GGLC+YLSPPE+ G
Sbjct: 297 LVSNLYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFG 352
>pdb|2YXQ|A Chain A, The Plug Domain Of The Secy Protein Stablizes The Closed
State Of The Translocation Channel And Maintains A
Membrane Seal
Length = 431
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/125 (34%), Positives = 69/125 (55%), Gaps = 17/125 (13%)
Query: 10 KFLSSL----QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYT 65
KFL+SL N + ++ T++VF +V+Y + RV++P+ R +G YPIK Y
Sbjct: 190 KFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYV 249
Query: 66 SNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLS 125
SNIP+IL +AL +N+ Q+ + + + + +LG + GG A + G+ YYLS
Sbjct: 250 SNIPVILAAALFANI----QLWGLALY-RMGIPILGHYE----GGRA----VDGIAYYLS 296
Query: 126 PPENL 130
P L
Sbjct: 297 TPYGL 301
>pdb|3DKN|A Chain A, Sec61 In The Canine Ribosome-Channel Complex From The
Endoplasmic Reticulum
Length = 430
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/125 (34%), Positives = 69/125 (55%), Gaps = 17/125 (13%)
Query: 10 KFLSSL----QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYT 65
KFL+SL N + ++ T++VF +V+Y + RV++P+ R +G YPIK Y
Sbjct: 194 KFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYV 253
Query: 66 SNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLS 125
SNIP+IL +AL +N+ Q+ + + + + +LG + GG A + G+ YYLS
Sbjct: 254 SNIPVILAAALFANI----QLWGLALY-RMGIPILGHYE----GGRA----VDGIAYYLS 300
Query: 126 PPENL 130
P L
Sbjct: 301 TPYGL 305
>pdb|2YXR|A Chain A, The Plug Domain Of The Secy Protein Stablizes The Closed
State Of The Translocation Channel And Maintains A
Membrane Seal
Length = 426
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/125 (34%), Positives = 69/125 (55%), Gaps = 17/125 (13%)
Query: 10 KFLSSL----QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYT 65
KFL+SL N + ++ T++VF +V+Y + RV++P+ R +G YPIK Y
Sbjct: 185 KFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYV 244
Query: 66 SNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLS 125
SNIP+IL +AL +N+ Q+ + + + + +LG + GG A + G+ YYLS
Sbjct: 245 SNIPVILAAALFANI----QLWGLALY-RMGIPILGHYE----GGRA----VDGIAYYLS 291
Query: 126 PPENL 130
P L
Sbjct: 292 TPYGL 296
>pdb|1RH5|A Chain A, The Structure Of A Protein Conducting Channel
Length = 436
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/125 (34%), Positives = 69/125 (55%), Gaps = 17/125 (13%)
Query: 10 KFLSSL----QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYT 65
KFL+SL N + ++ T++VF +V+Y + RV++P+ R +G YPIK Y
Sbjct: 195 KFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYV 254
Query: 66 SNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLS 125
SNIP+IL +AL +N+ Q+ + + + + +LG + GG A + G+ YYLS
Sbjct: 255 SNIPVILAAALFANI----QLWGLALY-RMGIPILGHYE----GGRA----VDGIAYYLS 301
Query: 126 PPENL 130
P L
Sbjct: 302 TPYGL 306
>pdb|1RHZ|A Chain A, The Structure Of A Protein Conducting Channel
Length = 436
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 43/125 (34%), Positives = 69/125 (55%), Gaps = 17/125 (13%)
Query: 10 KFLSSL----QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYT 65
KFL+SL N + ++ T++VF +V+Y + RV++P+ R +G YPIK Y
Sbjct: 195 KFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYV 254
Query: 66 SNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLS 125
SNIP+IL +AL +N+ Q+ + + + + +LG + GG A + G+ YYLS
Sbjct: 255 SNIPVILAAALFANI----QLWGLALY-RMGIPILGHYE----GGRA----VDGIAYYLS 301
Query: 126 PPENL 130
P L
Sbjct: 302 TPYGL 306
>pdb|3MP7|A Chain A, Lateral Opening Of A Translocon Upon Entry Of Protein
Suggests The Mechanism Of Insertion Into Membranes
Length = 482
Score = 63.5 bits (153), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 41/109 (37%), Positives = 60/109 (55%), Gaps = 16/109 (14%)
Query: 24 MLATVLVFAIVIYFQGFRVDLPIKSARYRGQY--SSYPIKLFYTSNIPIILQSALVSNLY 81
++AT++VF IV+YF+ RV++P+ YRG SYPI+ Y SNIPIIL AL +N+
Sbjct: 244 VVATIVVFFIVVYFESMRVEIPLG---YRGVTVRGSYPIRFLYVSNIPIILTFALYANIQ 300
Query: 82 VISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPENL 130
+ +++L H W +G P PI G Y+ PP N+
Sbjct: 301 LWARVLDRLGH---------PW--LGRFDPTTGSPISGFVLYVIPPRNI 338
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 40/132 (30%), Positives = 68/132 (51%), Gaps = 24/132 (18%)
Query: 10 KFLSSL----QNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSAR-------YRGQYSSY 58
KFL+SL N + ++ T++VF +V+Y + R + + A+ Y Q +
Sbjct: 194 KFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRRRIVVNYAKRQQGRRVYAAQSTHL 253
Query: 59 PIKLFYTSNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIG 118
P+K+ Y SNIP+IL +AL +N+ Q+ + + + + +LG + GG A +
Sbjct: 254 PLKVVYVSNIPVILAAALFANI----QLWGLALY-RMGIPILGHYE----GGRA----VD 300
Query: 119 GLCYYLSPPENL 130
G+ YYLS P L
Sbjct: 301 GIAYYLSTPYGL 312
>pdb|2WW9|A Chain A, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|A Chain A, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
Length = 490
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 8/98 (8%)
Query: 36 YFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNL----YVISQMLAVKF 91
Y Q RV+LPI+S R RG + YPIKL YT + ++ ++ + +V+ Q++A
Sbjct: 262 YLQSVRVELPIRSTRARGTNNVYPIKLLYTGCLSVLFSYTILFYIHIFAFVLIQLVAKNE 321
Query: 92 HGNIFVNLLGEWADVGGGGPARAYPIGGLCYYLSPPEN 129
+I ++G + + +P+ L+PP +
Sbjct: 322 PTHIICKIMGHYENANNLLAVPTFPLS----LLAPPTS 355
>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 = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 11/74 (14%)
Query: 28 VLVFAIVIYFQGFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPIILQSALVSNL 80
VL FA + Q +P++ AR Y GQ + PIKL IPII +A++
Sbjct: 225 VLAFAGMAAVQQAERRIPVQYARKVVGGRVYGGQATYIPIKLNAAGVIPIIFAAAILQ-- 282
Query: 81 YVISQMLAVKFHGN 94
I LA F N
Sbjct: 283 --IPIFLAAPFQDN 294
>pdb|3A3U|A Chain A, Crystal Structure Of Mqnd (Ttha1568), A Menaquinone
Biosynthetic Enzyme From Thermus Thermophilus Hb8
Length = 272
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 44/109 (40%), Gaps = 20/109 (18%)
Query: 12 LSSLQNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPII 71
L +L+ ++AV T F + +Y QGF P+++ Y +P++
Sbjct: 91 LQALEGLRVAVPGRHTTAYFLLSLYAQGF-----------------VPVEVRYDRILPMV 133
Query: 72 LQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGL 120
Q + + L + +G + V LG W + G P P+G +
Sbjct: 134 AQGEVEAGLIIHESRFTYPRYGLVQVVDLGAWWEERTGLP---LPLGAI 179
>pdb|2CZL|A Chain A, Crystal Structure Of Mqnd (Ttha1568), A Menaquinone
Biosynthetic Enzyme From Thermus Thermophilus Hb8 (Cys11
Modified With Beta- Mercaptoethanol)
Length = 272
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/109 (22%), Positives = 44/109 (40%), Gaps = 20/109 (18%)
Query: 12 LSSLQNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPII 71
L +L+ ++AV T F + +Y QGF P+++ Y +P++
Sbjct: 91 LQALEGLRVAVPGRHTTAYFLLSLYAQGF-----------------VPVEVRYDRILPMV 133
Query: 72 LQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGGGGPARAYPIGGL 120
Q + + L + +G + V LG W + G P P+G +
Sbjct: 134 AQGEVEAGLIIHESRFTYPRYGLVQVVDLGAWWEERTGLP---LPLGAI 179
>pdb|3ELI|A Chain A, Crystal Structure Of The Ahsa1 (Spo3351) Protein From
Silicibacter Pomeroyi, Northeast Structural Genomics
Consortium Target Sir160
Length = 152
Score = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 7/83 (8%)
Query: 50 RYRGQYSSYPIKLF-YTSNIPIILQSALVSNLYVISQMLAVKFHGNIFVNLLGEWADVGG 108
R +++ P LF + S+ +LQ L+V + + F LG W V
Sbjct: 5 RLEREFAVAPEALFAWVSDGAKLLQWWGPEGLHVPADQHDLDF------TRLGPWFSVXV 58
Query: 109 GGPARAYPIGGLCYYLSPPENLG 131
G + Y + G ++ PP+++G
Sbjct: 59 NGEGQRYKVSGQVTHVKPPQSVG 81
>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 = 26.2 bits (56), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 22 VMMLATVLVFAIVIYFQGFRVDLPIKSAR-------YRGQYSSYPIKLFYTSNIPIILQS 74
++ +A + +F I++ Q R + I+ AR Y G + PIK+ IPII S
Sbjct: 219 LIAVALITIFGIILVQQAER-RITIQYARRVTGRRVYGGASTYLPIKVNQGGVIPIIFAS 277
Query: 75 ALVS 78
A+VS
Sbjct: 278 AIVS 281
>pdb|4FX5|A Chain A, Von Willebrand Factor Type A From Catenulispora Acidiphila
Length = 464
Score = 26.2 bits (56), Expect = 7.1, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 8 RSKFLSSLQNSKMAVMMLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSS 57
R+K ++ + +K+A+ L FA+V +G RV P R Y S
Sbjct: 94 RTKXXAAKEATKVAIDTLTDGAFFAVVAGTEGARVVYPTGGQLLRADYQS 143
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
0.328 0.142 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,814,936
Number of Sequences: 62578
Number of extensions: 130215
Number of successful extensions: 255
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 19
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
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: 47 (22.7 bits)