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= 018538
(354 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
Length = 231
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 220 IIAVTESHV-VLDKPAGTSVGGTTD---NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
+I + H+ VL+KP+GT+V G + + E A L H++D T G
Sbjct: 6 VILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA----RFLELVHRLDRDTSG 61
Query: 276 CVVLARTQEYCSIFHRKIREKKVKKLYLAL 305
+++A+ + H ++REK ++K YLAL
Sbjct: 62 VLLVAKKRSALRSLHEQLREKGMQKDYLAL 91
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
Length = 228
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 8/90 (8%)
Query: 220 IIAVTESHV-VLDKPAGTSVGGTTD---NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
+I + H+ VL+KP+GT+V G + + E A L H++D T G
Sbjct: 3 VIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA----RFLELVHRLDRDTSG 58
Query: 276 CVVLARTQEYCSIFHRKIREKKVKKLYLAL 305
+++A+ + H ++REK +K YLAL
Sbjct: 59 VLLVAKKRSALRSLHEQLREKGXQKDYLAL 88
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
Length = 217
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 220 IIAVTESHV-VLDKPAGT-SVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCV 277
+I + H+ V++KP+G SV G + ++S T R + H++D T G +
Sbjct: 13 VILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQA---ESVHRLDXATSGVI 69
Query: 278 VLARTQEYCSIFHRKIREKKVKKLYLA 304
V+A T+ R+ RE++ KK Y+A
Sbjct: 70 VVALTKAAERELKRQFREREPKKQYVA 96
>pdb|3AQO|A Chain A, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
pdb|3AQO|B Chain B, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
pdb|3AQO|C Chain C, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
pdb|3AQO|D Chain D, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
Length = 229
Score = 31.2 bits (69), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 123 PPLFV-ADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSI 172
PPL ADL AV+ P+ LT TPE + F+EVT ++ KR +I
Sbjct: 123 PPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNI-GKRLAI 172
>pdb|3AQP|A Chain A, Crystal Structure Of Secdf, A Translocon-Associated
Membrane Protein, From Thermus Thrmophilus
pdb|3AQP|B Chain B, Crystal Structure Of Secdf, A Translocon-Associated
Membrane Protein, From Thermus Thrmophilus
Length = 741
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 123 PPLFV-ADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSI 172
PPL ADL AV+ P+ LT TPE + F+EVT ++ KR +I
Sbjct: 157 PPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNI-GKRLAI 206
>pdb|3ASI|A Chain A, Alpha-Neurexin-1 Ectodomain Fragment; Lns5-Egf3-Lns6
Length = 410
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 246 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 300
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 301 IEESNAIIND 310
>pdb|3QCW|A Chain A, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), No Splice
Inserts
pdb|3QCW|B Chain B, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), No Splice
Inserts
Length = 1245
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 1078 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNV--GTDDIA 1132
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 1133 IEESNAIIND 1142
>pdb|3POY|A Chain A, Crystal Structure Of The Alpha-Neurexin-1 Ectodomain, Lns
2-6
Length = 1019
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 862 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 916
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 917 IEESNAIIND 926
>pdb|3R05|A Chain A, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), With
Splice Insert Ss3
pdb|3R05|B Chain B, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), With
Splice Insert Ss3
Length = 1254
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 1087 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNV--GTDDIA 1141
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 1142 IEESNAIIND 1151
>pdb|3BOD|A Chain A, Structure Of Mouse Beta-Neurexin 1
Length = 178
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 26 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 80
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 81 IEESNAIIND 90
>pdb|3VKF|C Chain C, Crystal Structure Of Neurexin 1betaNEUROLIGIN 1 COMPLEX
pdb|3VKF|D Chain D, Crystal Structure Of Neurexin 1betaNEUROLIGIN 1 COMPLEX
Length = 181
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 25 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 79
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 80 IEESNAIIND 89
>pdb|1C4R|A Chain A, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|B Chain B, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|C Chain C, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|D Chain D, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|E Chain E, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|F Chain F, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|G Chain G, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
pdb|1C4R|H Chain H, The Structure Of The Ligand-Binding Domain Of Neurexin
1beta: Regulation Of Lns Domain Function By Alternative
Splicing
Length = 182
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 26 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 80
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 81 IEESNAIIND 90
>pdb|2WQZ|C Chain C, Crystal Structure Of Synaptic Protein Neuroligin-4 In
Complex With Neurexin-beta 1: Alternative Refinement
pdb|2WQZ|D Chain D, Crystal Structure Of Synaptic Protein Neuroligin-4 In
Complex With Neurexin-beta 1: Alternative Refinement
pdb|2XB6|C Chain C, Revisited Crystal Structure Of Neurexin1beta-neuroligin4
Complex
pdb|2XB6|D Chain D, Revisited Crystal Structure Of Neurexin1beta-neuroligin4
Complex
Length = 179
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 27 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 81
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 82 IEESNAIIND 91
>pdb|3B3Q|E Chain E, Crystal Structure Of A Synaptic Adhesion Complex
pdb|3B3Q|F Chain F, Crystal Structure Of A Synaptic Adhesion Complex
Length = 197
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 34 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 88
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 89 IEESNAIIND 98
>pdb|2R1B|A Chain A, Crystal Structure Of Rat Neurexin 1beta With A Splice
Insert At Ss#4
pdb|2R1B|B Chain B, Crystal Structure Of Rat Neurexin 1beta With A Splice
Insert At Ss#4
Length = 220
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 32 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 86
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 87 IEESNAIIND 96
>pdb|3BIW|E Chain E, Crystal Structure Of The Neuroligin-1NEUREXIN-1beta
Synaptic Adhesion Complex
pdb|3BIW|F Chain F, Crystal Structure Of The Neuroligin-1NEUREXIN-1beta
Synaptic Adhesion Complex
pdb|3BIW|G Chain G, Crystal Structure Of The Neuroligin-1NEUREXIN-1beta
Synaptic Adhesion Complex
pdb|3BIW|H Chain H, Crystal Structure Of The Neuroligin-1NEUREXIN-1beta
Synaptic Adhesion Complex
Length = 243
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 74 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 128
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 129 IEESNAIIND 138
>pdb|3MW2|A Chain A, Crystal Structure Of Beta-Neurexin 1 With The Splice
Insert 4
pdb|3MW2|B Chain B, Crystal Structure Of Beta-Neurexin 1 With The Splice
Insert 4
Length = 207
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 25 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 79
Query: 223 VTESHVVLD 231
+ ES+ +++
Sbjct: 80 IEESNAIIN 88
>pdb|2R1D|A Chain A, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|B Chain B, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|C Chain C, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|D Chain D, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|E Chain E, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|F Chain F, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|G Chain G, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|H Chain H, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|I Chain I, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
pdb|2R1D|W Chain W, Crystal Structure Of Rat Neurexin 1beta In The Ca2+
Containing Form
Length = 226
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 163 PSVLSKRSSIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIA 222
PS + R +I TV QK + VD G YL +H+H + +++ + IA
Sbjct: 60 PSTRADRLAIGFSTV---QKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDD--IA 114
Query: 223 VTESHVVLDK 232
+ ES+ +++
Sbjct: 115 IEESNAIIND 124
>pdb|2PA4|A Chain A, Crystal Structure Of Udp-Glucose Pyrophosphorylase From
Corynebacteria Glutamicum In Complex With Magnesium And
Udp-Glucose
pdb|2PA4|B Chain B, Crystal Structure Of Udp-Glucose Pyrophosphorylase From
Corynebacteria Glutamicum In Complex With Magnesium And
Udp-Glucose
pdb|2PA4|C Chain C, Crystal Structure Of Udp-Glucose Pyrophosphorylase From
Corynebacteria Glutamicum In Complex With Magnesium And
Udp-Glucose
pdb|2PA4|D Chain D, Crystal Structure Of Udp-Glucose Pyrophosphorylase From
Corynebacteria Glutamicum In Complex With Magnesium And
Udp-Glucose
Length = 323
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 303 LALTTAPLPVGIMTHYMRPINIAPRLVSEGKT 334
LA+ TAP G++ H+ R + L+ GKT
Sbjct: 61 LAIITAPNKAGVLAHFERSSELEETLMERGKT 92
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 0.136 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,166,667
Number of Sequences: 62578
Number of extensions: 396451
Number of successful extensions: 824
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 816
Number of HSP's gapped (non-prelim): 19
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)