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= 042996
(261 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JTH|A Chain A, Crystal Structure And Biophysical Properties Of A Complex
Between The N-Terminal Region Of Snap25 And The Snare
Region Of Syntaxin 1a
pdb|1JTH|C Chain C, Crystal Structure And Biophysical Properties Of A Complex
Between The N-Terminal Region Of Snap25 And The Snare
Region Of Syntaxin 1a
Length = 82
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 38/65 (58%)
Query: 141 GNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNELDSIHFSIKKASQL 200
+++ DE+ ++ R Q+V E+ + G T +L Q EQ+ RI +D I+ +K+A +
Sbjct: 18 ADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLERIEEGMDQINKDMKEAEKN 77
Query: 201 VKEIG 205
+ ++G
Sbjct: 78 LTDLG 82
>pdb|1N7S|C Chain C, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 79
Score = 35.4 bits (80), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 130 SSMTNQ--QLMDSGNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNEL 187
SM N+ ++ +++ DE+ ++ R Q+V E+ + G T +L Q EQ+ R+ +
Sbjct: 1 GSMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGM 60
Query: 188 DSIHFSIKKASQLVKEIGR 206
+ I+ +K+A + +K++G+
Sbjct: 61 NHINQDMKEAEKNLKDLGK 79
>pdb|1SFC|C Chain C, Neuronal Synaptic Fusion Complex
pdb|1SFC|G Chain G, Neuronal Synaptic Fusion Complex
pdb|1SFC|K Chain K, Neuronal Synaptic Fusion Complex
Length = 83
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 40/66 (60%)
Query: 141 GNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNELDSIHFSIKKASQL 200
+++ DE+ ++ R Q+V E+ + G T +L Q EQ+ R+ ++ I+ +K+A +
Sbjct: 18 ADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKN 77
Query: 201 VKEIGR 206
+K++G+
Sbjct: 78 LKDLGK 83
>pdb|1URQ|C Chain C, Crystal Structure Of Neuronal Q-Snares In Complex With
R-Snare Motif Of Tomosyn
pdb|3HD7|C Chain C, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3HD7|G Chain G, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3IPD|C Chain C, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
pdb|3IPD|G Chain G, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
Length = 80
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 129 ASSMTNQ--QLMDSGNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNE 186
S M N+ ++ +++ DE+ ++ R Q+V E+ + G T +L Q EQ+ R+
Sbjct: 1 GSHMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEG 60
Query: 187 LDSIHFSIKKASQLVKEIGR 206
++ I+ +K+A + +K++G+
Sbjct: 61 MNHINQDMKEAEKNLKDLGK 80
>pdb|3RK2|C Chain C, Truncated Snare Complex
pdb|3RK2|G Chain G, Truncated Snare Complex
pdb|3RK3|C Chain C, Truncated Snare Complex With Complexin
pdb|3RL0|C Chain C, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|G Chain G, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|K Chain K, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|O Chain O, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|S Chain S, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|W Chain W, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|AA Chain a, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|EE Chain e, Truncated Snare Complex With Complexin (P1)
Length = 81
Score = 34.7 bits (78), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 39/64 (60%)
Query: 142 NRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNELDSIHFSIKKASQLV 201
+++ DE+ ++ R Q+V E+ + G T +L Q EQ+ R+ ++ I+ +K+A + +
Sbjct: 17 DQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNL 76
Query: 202 KEIG 205
K++G
Sbjct: 77 KDLG 80
>pdb|1GL2|C Chain C, Crystal Structure Of An Endosomal Snare Core Complex
Length = 65
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 36/62 (58%)
Query: 145 MDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNELDSIHFSIKKASQLVKEI 204
M+ Q+IERS ++ ET +GTE L Q +Q+ R + L + + ++ K+ ++++ +
Sbjct: 4 MNRATQSIERSHRIATETDQIGTEIIEELGEQRDQLERTKSRLVNTNENLSKSRKILRSM 63
Query: 205 GR 206
R
Sbjct: 64 SR 65
>pdb|1KIL|C Chain C, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 74
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%)
Query: 141 GNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRIVNELDSIHFSIKKASQL 200
+++ DE+ ++ R Q+V E+ + G T +L Q EQ+ R+ ++ I+ +K+A +
Sbjct: 10 ADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKN 69
Query: 201 VKEI 204
+K++
Sbjct: 70 LKDL 73
>pdb|1X3L|A Chain A, Crystal Structure Of The Ph0495 Protein From Pyrococccus
Horikoshii Ot3
Length = 440
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 34/79 (43%), Gaps = 17/79 (21%)
Query: 48 TDKMRECKRLIKEFDREVKD-----IEGRNDPETNKMLSEKK---QSMVKELNSYVALKK 99
T K+ + + LI FD + D G D T K L EK + ++KE NSY ALKK
Sbjct: 352 TRKISDLEALIVAFDTDGTDGPTDAAGGIVDGTTYKKLREKGIDVEKVLKEHNSYEALKK 411
Query: 100 QHQTNLENNKRVDLFDGPN 118
LF GP
Sbjct: 412 VGGL---------LFTGPT 421
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 42/211 (19%), Positives = 93/211 (44%), Gaps = 28/211 (13%)
Query: 19 DIFRALSNGFQKLEKIKDVNRQSRQLEELTDKMRECKRLIKEFDREVKDIEGRNDPETNK 78
D+ R + G +E IK ++ + +EL ++ K L +++ ++ + DP+T +
Sbjct: 116 DLARKVEEG---MEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE 172
Query: 79 MLSEKKQSMVKELNSYVALKKQHQTNLENNKRVDLFDGPNEGFAEDNVLLASSMTNQQ-- 136
+ K +S+ KEL Y+ + ++ + ++ E N+ L S+ +
Sbjct: 173 EVDGKLKSLPKELKRYLHIAREGEAARQH-------------LIEANLRLVVSIAKKYTG 219
Query: 137 -------LMDSGNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRI---VNE 186
L+ GN+ + + E ++ T A+ +A +Q I V+
Sbjct: 220 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 279
Query: 187 LDSIHFSIKKASQLVKEIGRQVATDKCIMAM 217
+++I+ + A QL +E+GR+ + ++ AM
Sbjct: 280 VETINKLSRTARQLQQELGREPSYEEIAEAM 310
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 27.7 bits (60), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 42/211 (19%), Positives = 93/211 (44%), Gaps = 28/211 (13%)
Query: 19 DIFRALSNGFQKLEKIKDVNRQSRQLEELTDKMRECKRLIKEFDREVKDIEGRNDPETNK 78
D+ R + G +E IK ++ + +EL ++ K L +++ ++ + DP+T +
Sbjct: 29 DLARKVEEG---MEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE 85
Query: 79 MLSEKKQSMVKELNSYVALKKQHQTNLENNKRVDLFDGPNEGFAEDNVLLASSMTNQQ-- 136
+ K +S+ KEL Y+ + ++ + ++ E N+ L S+ +
Sbjct: 86 EVDGKLKSLPKELKRYLHIAREGEAARQH-------------LIEANLRLVVSIAKKYTG 132
Query: 137 -------LMDSGNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRI---VNE 186
L+ GN+ + + E ++ T A+ +A +Q I V+
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 192
Query: 187 LDSIHFSIKKASQLVKEIGRQVATDKCIMAM 217
+++I+ + A QL +E+GR+ + ++ AM
Sbjct: 193 VETINKLSRTARQLQQELGREPSYEEIAEAM 223
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 42/211 (19%), Positives = 93/211 (44%), Gaps = 28/211 (13%)
Query: 19 DIFRALSNGFQKLEKIKDVNRQSRQLEELTDKMRECKRLIKEFDREVKDIEGRNDPETNK 78
D+ R + G +E IK ++ + +EL ++ K L +++ ++ + DP+T +
Sbjct: 25 DLARKVEEG---MEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE 81
Query: 79 MLSEKKQSMVKELNSYVALKKQHQTNLENNKRVDLFDGPNEGFAEDNVLLASSMTNQQ-- 136
+ K +S+ KEL Y+ + ++ + ++ E N+ L S+ +
Sbjct: 82 EVDGKLKSLPKELKRYLHIAREGEAARQH-------------LIEANLRLVVSIAKKYTG 128
Query: 137 -------LMDSGNRMMDETDQAIERSKQVVHETINVGTETAAVLKAQTEQMSRI---VNE 186
L+ GN+ + + E ++ T A+ +A +Q I V+
Sbjct: 129 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 188
Query: 187 LDSIHFSIKKASQLVKEIGRQVATDKCIMAM 217
+++I+ + A QL +E+GR+ + ++ AM
Sbjct: 189 VETINKLSRTARQLQQELGREPSYEEIAEAM 219
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400
Length = 365
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 36 DVNRQSRQLEELTDKM----RECKRLIKEFDREVKDIEGRNDPETNKMLSEKKQSMVKEL 91
D+ R +++LE L + +E + +KE +R ++D NDPE + +S++ + + +
Sbjct: 2 DLERLAQRLEGLRGYLDIPQKETR--LKELERRLEDPSLWNDPEAARKVSQEAARLRRTV 59
Query: 92 NSYVALKKQHQTNLE 106
+++ +L+ Q LE
Sbjct: 60 DTFRSLESDLQGLLE 74
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
0.313 0.129 0.344
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,326,693
Number of Sequences: 62578
Number of extensions: 221846
Number of successful extensions: 616
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 581
Number of HSP's gapped (non-prelim): 56
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)