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= psy2326
(181 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B54|A Chain A, Crystal Structure Of A Yeast Hypothetical Protein-A
Structure From Bnl's Human Proteome Project
Length = 257
Score = 87.0 bits (214), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 62/176 (35%), Positives = 87/176 (49%), Gaps = 36/176 (20%)
Query: 7 DIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFC--QI 64
DI+WHFIG LQ+NK + KVPNL +ETI + A ++N + AK QPD + C QI
Sbjct: 85 DIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCN-PILCNVQI 143
Query: 65 NTSGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFT 124
NTS E+ K G + E E E + + C ++
Sbjct: 144 NTSHEDQKSGLNNE-------------------------AEIFEVIDFFLSEECKYIKLN 178
Query: 125 GLMTIGKYGY---DTKHGPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRE 177
GLMTIG + D+K N DF L + +K + K ++++LSMGMS+D RE
Sbjct: 179 GLMTIGSWNVSHEDSKE--NRDFATLVEWKKKIDAKFG---TSLKLSMGMSADFRE 229
>pdb|1CT5|A Chain A, Crystal Structure Of Yeast Hypothetical Protein
Ybl036c-Selenomet Crystal
Length = 256
Score = 79.0 bits (193), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 59/176 (33%), Positives = 84/176 (47%), Gaps = 36/176 (20%)
Query: 7 DIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFC--QI 64
DI+WHFIG LQ+NK + KVPNL +ETI + A ++N + AK QPD + C QI
Sbjct: 84 DIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCN-PILCNVQI 142
Query: 65 NTSGEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFT 124
NTS E+ K G + E E E + + C ++
Sbjct: 143 NTSHEDQKSGLNNE-------------------------AEIFEVIDFFLSEECKYIKLN 177
Query: 125 GLMTIGKYGY---DTKHGPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRE 177
GL TIG + D+K N DF L + +K + K ++++LS G S+D RE
Sbjct: 178 GLXTIGSWNVSHEDSKE--NRDFATLVEWKKKIDAKFG---TSLKLSXGXSADFRE 228
>pdb|3CPG|A Chain A, Crystal Structure Of An Unknown Protein From
Bifidobacterium Adolescentis
Length = 282
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 55/128 (42%), Gaps = 32/128 (25%)
Query: 8 IRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQINTS 67
I +H IG LQSNK+ KV+ P ++ IE++ LA +++ + V ++N S
Sbjct: 115 IPFHLIGQLQSNKIGKVL--PVVDTIESVDSIDLAEKISRRAVARGI--TVGVLLEVNES 170
Query: 68 GEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGLM 127
GEE+K G P HA ++ I + +E GL
Sbjct: 171 GEESKSGCDPAHA----------------------------IRIAQKIGTLDGIELQGLX 202
Query: 128 TIGKYGYD 135
TIG + +D
Sbjct: 203 TIGAHVHD 210
>pdb|1W8G|A Chain A, Crystal Structure Of E. Coli K-12 Yggs
Length = 234
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 36/121 (29%), Positives = 52/121 (42%), Gaps = 5/121 (4%)
Query: 8 IRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQINTS 67
+ WHFIG LQSNK V + + ++ TI R+AT++N+ P L V QIN S
Sbjct: 77 LEWHFIGPLQSNKSRLVAE--HFDWCHTIDRLRIATRLNDQRPAELP--PLNVLIQINIS 132
Query: 68 GEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGLM 127
E +K G + L + V P L +E + + + F GL
Sbjct: 133 DENSKSGIQLAELDELAAAVAE-LPRLRLRGLMAIPAPESEYVRQFEVARQMAVAFAGLK 191
Query: 128 T 128
T
Sbjct: 192 T 192
>pdb|3R79|A Chain A, Crystal Structure Of An Uncharactertized Protein From
Agrobacterium Tumefaciens
pdb|3R79|B Chain B, Crystal Structure Of An Uncharactertized Protein From
Agrobacterium Tumefaciens
Length = 244
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 1 ITSKCKDIRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKV 60
+ K DI H IG LQSNK + + + +E+I ++A ++ A+ + L+
Sbjct: 71 LKEKTSDIELHLIGPLQSNKAADAVAL--FDVVESIDREKIARALSEECARQ--GRSLRF 126
Query: 61 FCQINTSGEENKHGAHPEHAEALVSH 86
+ Q+NT E K G P A V+
Sbjct: 127 YVQVNTGLEPQKAGIDPRETVAFVAF 152
>pdb|3SY1|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or70
Length = 245
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 51/121 (42%), Gaps = 5/121 (4%)
Query: 8 IRWHFIGHLQSNKVPKVIKVPNLEYIETIHDTRLATQVNNAWAKHQPDKKLKVFCQINTS 67
+ W+F G LQSNK V + + ++ TI R+AT++N+ P L V QIN S
Sbjct: 78 LEWNFAGPLQSNKSRLVAE--HFDWCITIDRLRIATRLNDQRPAELP--PLNVLIQINIS 133
Query: 68 GEENKHGAHPEHAEALVSHVINSCPNLEFTDKHGAHPEHAEALVSHVINSCPNLEFTGLM 127
E +K G + L + V P L +E + + + F GL
Sbjct: 134 DENSKSGIQLAELDELAAAVAE-LPRLRLRGLSAIPAPESEYVRQFEVARQMAVAFAGLK 192
Query: 128 T 128
T
Sbjct: 193 T 193
>pdb|4I1M|A Chain A, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb
pdb|4I1M|B Chain B, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb
pdb|4I1M|C Chain C, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb
pdb|4I1O|B Chain B, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb In Complex With Rab1b Bound To Gdp And Bef3
pdb|4I1O|D Chain D, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb In Complex With Rab1b Bound To Gdp And Bef3
pdb|4I1O|F Chain F, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb In Complex With Rab1b Bound To Gdp And Bef3
pdb|4I1O|H Chain H, Crystal Structure Of The Legionella Pneumophila Gap Domain
Of Lepb In Complex With Rab1b Bound To Gdp And Bef3
Length = 302
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 36 IHDTRLATQVNNAWAKHQPDKKLKVFCQINTSGEENKHG--AHPEHAEALV 84
+ + + + NN WAK + D +F + SG E HG P + E++V
Sbjct: 62 VDELAITCEANNVWAKERIDSTPNLFALYDNSGGEAIHGHAFVPYYKESIV 112
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 143 DFLELAKCRKDVCKKLNLNESNVELSMGMSSDLR 176
D +E K D CK L L+E++ L MG +R
Sbjct: 164 DMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIR 197
>pdb|1LTX|A Chain A, Structure Of Rab Escort Protein-1 In Complex With Rab
Geranylgeranyl Transferase And Isoprenoid
Length = 567
Score = 28.1 bits (61), Expect = 2.5, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 139 GPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRERES 180
G NPDF L CR++V + L +S E + + ++L ES
Sbjct: 57 GANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLES 98
>pdb|1DCE|A Chain A, Crystal Structure Of Rab Geranylgeranyltransferase From
Rat Brain
pdb|1DCE|C Chain C, Crystal Structure Of Rab Geranylgeranyltransferase From
Rat Brain
Length = 567
Score = 28.1 bits (61), Expect = 2.6, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 139 GPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRERES 180
G NPDF L CR++V + L +S E + + ++L ES
Sbjct: 57 GANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLES 98
>pdb|2H1P|H Chain H, The Three-Dimensional Structures Of A Polysaccharide
Binding Antibody To Cryptococcus Neoformans And Its
Complex With A Peptide From A Phage Display Library:
Implications For The Identification Of Peptide
Mimotopes
Length = 220
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 48 AWAKHQPDKKLKVFCQINTSGEENKH 73
+W + P+K+L++ IN++G++ H
Sbjct: 35 SWVRQTPEKRLELVATINSNGDKTYH 60
>pdb|3A3J|A Chain A, Crystal Structures Of Penicillin Binding Protein 5 From
Haemophilus Influenzae
Length = 344
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 36 IHDTRLATQVNNAWAKHQPDKKLKVFCQINT--SGEENKHG----AHPEHAEALVSHVIN 89
IH+T + T +AW ++ PD K+F +NT S + G + + AL H+
Sbjct: 55 IHNTDMVTIGESAWGRNFPDSS-KMFLDLNTQVSVADLNRGVIVVSGNDATVALAEHISG 113
Query: 90 SCPNL 94
+ PN
Sbjct: 114 NVPNF 118
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 143 DFLELAKCRKDVCKKLNLNESNVELSMGMSSDLRE 177
DF+E K + CK + L+E++ L MG +R+
Sbjct: 163 DFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRK 197
>pdb|3C72|A Chain A, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor
Length = 334
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 139 GPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDL 175
G NPDF L CR++V + L +S E + + ++L
Sbjct: 61 GANPDFATLWNCRREVLQHLETEKSPEESAALVKAEL 97
>pdb|3DSS|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)
pdb|3DST|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Geranylgeranyl Pyrophosphate
pdb|3DSU|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Farnesyl Pyrophosphate
pdb|3DSV|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Mono-Prenylated Peptide Ser-Cys-Ser-Cys(Gg)
Derivated From Rab7
pdb|3DSW|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Mono-Prenylated Peptide Ser-Cys(Gg)-Ser-Cys
Derivated From Rab7
pdb|3DSX|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig)in
Complex With Di-Prenylated Peptide
Ser-Cys(Gg)-Ser-Cys(Gg) Derivated From Rab7
pdb|3HXB|A Chain A, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (Compound 6)
pdb|3HXC|A Chain A, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (compound 8)
pdb|3HXD|A Chain A, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (Compound 9)
pdb|3HXE|A Chain A, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (compound 37)
pdb|3HXF|A Chain A, Engineered Rabggtase In Complex With A Peptidomimetic
Inhibitor (compound 32)
Length = 331
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 139 GPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDL 175
G NPDF L CR++V + L +S E + + ++L
Sbjct: 58 GANPDFATLWNCRREVLQHLETEKSPEESAALVKAEL 94
>pdb|3PZ1|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig) In
Complex With Bms3
pdb|3PZ2|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig) In
Complex With Bms3 And Lipid Substrate Ggpp
pdb|3PZ3|A Chain A, Crystal Structure Of Rabggtase(Delta Lrr; Delta Ig) In
Complex With Bms-Analogue 14
Length = 332
Score = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 139 GPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDL 175
G NPDF L CR++V + L +S E + + ++L
Sbjct: 59 GANPDFATLWNCRREVLQHLETEKSPEESAALVKAEL 95
>pdb|4EHM|A Chain A, Rabggtase In Complex With Covalently Bound Psoromic Acid
pdb|4GTS|A Chain A, Engineered Rabggtase In Complex With Bms Analogue 16
pdb|4GTT|A Chain A, Engineered Rabggtase In Complex With Bms Analogue 12
pdb|4GTV|A Chain A, Engineered Rabggtase In Complex With Bms Analogue 13
Length = 330
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 139 GPNPDFLELAKCRKDVCKKLNLNESNVELSMGMSSDL 175
G NPDF L CR++V + L +S E + + ++L
Sbjct: 57 GANPDFATLWNCRREVLQHLETEKSPEESAALVKAEL 93
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
0.315 0.131 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,664,984
Number of Sequences: 62578
Number of extensions: 226660
Number of successful extensions: 534
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 517
Number of HSP's gapped (non-prelim): 17
length of query: 181
length of database: 14,973,337
effective HSP length: 93
effective length of query: 88
effective length of database: 9,153,583
effective search space: 805515304
effective search space used: 805515304
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: 48 (23.1 bits)