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= 028094
(214 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
Structures
Length = 70
Score = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 33/57 (57%), Positives = 41/57 (71%), Gaps = 1/57 (1%)
Query: 47 YRGVRRRDSGKWVCEVREPNKK-SRIWLGTFPTAEMAARAHDVAAIALRGRLACLNF 102
YRGVR+R GK+ E+R+P K +R+WLGTF TAE AA A+D AA +RG A LNF
Sbjct: 6 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/57 (57%), Positives = 41/57 (71%), Gaps = 1/57 (1%)
Query: 47 YRGVRRRDSGKWVCEVREPNKK-SRIWLGTFPTAEMAARAHDVAAIALRGRLACLNF 102
YRGVR+R GK+ E+R+P K +R+WLGTF TAE AA A+D AA +RG A LNF
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59
>pdb|1BET|A Chain A, New Protein Fold Revealed By A 2.3 Angstrom Resolution
Crystal Structure Of Nerve Growth Factor
Length = 107
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 1 MDSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSG 56
DS+S W ++ + ++V +LA N R+ F ET+ +PV G R DS
Sbjct: 6 CDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSK 65
Query: 57 KW 58
W
Sbjct: 66 HW 67
>pdb|1BTG|A Chain A, Crystal Structure Of Beta Nerve Growth Factor At 2.5 A
Resolution In C2 Space Group With Zn Ions Bound
pdb|1BTG|B Chain B, Crystal Structure Of Beta Nerve Growth Factor At 2.5 A
Resolution In C2 Space Group With Zn Ions Bound
pdb|1BTG|C Chain C, Crystal Structure Of Beta Nerve Growth Factor At 2.5 A
Resolution In C2 Space Group With Zn Ions Bound
Length = 110
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 1 MDSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSG 56
DS+S W ++ + ++V +LA N R+ F ET+ +PV G R DS
Sbjct: 7 CDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSK 66
Query: 57 KW 58
W
Sbjct: 67 HW 68
>pdb|1SGF|B Chain B, Crystal Structure Of 7s Ngf: A Complex Of Nerve Growth
Factor With Four Binding Proteins (serine Proteinases)
pdb|1SGF|Y Chain Y, Crystal Structure Of 7s Ngf: A Complex Of Nerve Growth
Factor With Four Binding Proteins (serine Proteinases)
Length = 118
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 1 MDSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSG 56
DS+S W ++ + ++V +LA N R+ F ET+ +PV G R DS
Sbjct: 15 CDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSK 74
Query: 57 KW 58
W
Sbjct: 75 HW 76
>pdb|4EAX|A Chain A, Mouse Ngf In Complex With Lyso-Ps
pdb|4EAX|B Chain B, Mouse Ngf In Complex With Lyso-Ps
pdb|4EAX|C Chain C, Mouse Ngf In Complex With Lyso-Ps
pdb|4EAX|D Chain D, Mouse Ngf In Complex With Lyso-Ps
Length = 120
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 1 MDSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSG 56
DS+S W ++ + ++V +LA N R+ F ET+ +PV G R DS
Sbjct: 15 CDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSK 74
Query: 57 KW 58
W
Sbjct: 75 HW 76
>pdb|3IJ2|A Chain A, Ligand-Receptor Structure
pdb|3IJ2|B Chain B, Ligand-Receptor Structure
Length = 230
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 2 DSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSGK 57
DS+S W ++ + ++V +LA N R+ F ET+ +PV G R DS
Sbjct: 119 DSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSKH 178
Query: 58 W 58
W
Sbjct: 179 W 179
>pdb|4EFV|A Chain A, Crystal Structure Of Oif From Llama Seminal Plasma
pdb|4EFV|B Chain B, Crystal Structure Of Oif From Llama Seminal Plasma
Length = 117
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 2 DSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSGK 57
DS+S W + ++ + ++V++L N ++ F ET+ +PV G R DS
Sbjct: 16 DSVSVWVADKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVASGCRGIDSKH 75
Query: 58 W 58
W
Sbjct: 76 W 76
>pdb|1WWW|V Chain V, Ngf In Complex With Domain 5 Of The Trka Receptor
pdb|1WWW|W Chain W, Ngf In Complex With Domain 5 Of The Trka Receptor
pdb|1SG1|A Chain A, Crystal Structure Of The Receptor-Ligand Complex Between
Nerve Growth Factor And The Common Neurotrophin
Receptor P75
pdb|1SG1|B Chain B, Crystal Structure Of The Receptor-Ligand Complex Between
Nerve Growth Factor And The Common Neurotrophin
Receptor P75
pdb|2IFG|E Chain E, Structure Of The Extracellular Segment Of Human Trka In
Complex With Nerve Growth Factor
pdb|2IFG|F Chain F, Structure Of The Extracellular Segment Of Human Trka In
Complex With Nerve Growth Factor
Length = 120
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 2 DSLSSWSSPESRVGNFSDEDVVLLASSNPKKRAGRKKFRETR----HPVYRGVRRRDSGK 57
DS+S W ++ + ++V++L N ++ F ET+ +PV G R DS
Sbjct: 16 DSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKH 75
Query: 58 W 58
W
Sbjct: 76 W 76
>pdb|4G29|A Chain A, Structure Of The Catalytic Domain Of The Salmonella
Virulence Factor Ssei
Length = 186
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 57 KWVCEVREPNKKSRIWLGTFPTAEMAARAHD 87
+WVC+ R ++ I+ F + +AA A+D
Sbjct: 119 EWVCKYRXATRRKLIYYTDFSNSSIAANAYD 149
>pdb|4G2B|A Chain A, Structure Of The Catalytic Domain Of The Salmonella
Virulence Factor Ssei
pdb|4G2B|B Chain B, Structure Of The Catalytic Domain Of The Salmonella
Virulence Factor Ssei
Length = 186
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 57 KWVCEVREPNKKSRIWLGTFPTAEMAARAHD 87
+WVC+ R ++ I+ F + +AA A+D
Sbjct: 119 EWVCKYRMATRRKLIYYTDFSNSSIAANAYD 149
>pdb|3BZJ|A Chain A, Uvde K229l
Length = 301
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 22 VVLLASSNPKKRAGRKKFRETR 43
+V LAS +PKKR G FR TR
Sbjct: 250 LVHLASQDPKKRPGAHAFRVTR 271
>pdb|4FS0|A Chain A, Crystal Structure Of Mutant F136d Of Mouse Nectin-2
Extracellular Fragment D1-D2
Length = 225
Score = 27.3 bits (59), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 47 YRGVRRRDSGKWVCE-VREPNKKSR--IWLGTFPTAEMAARAHDV 88
+RG+R D G + CE +PN R WL E A A +V
Sbjct: 87 FRGLRVEDEGNYTCEFATDPNGTRRGVTWLRVIAQPENHAEAQEV 131
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
0.316 0.131 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,110,249
Number of Sequences: 62578
Number of extensions: 217646
Number of successful extensions: 436
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: 429
Number of HSP's gapped (non-prelim): 13
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)