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= 039839
(825 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2B8W|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GmpALF4
pdb|2B8W|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GmpALF4
pdb|2B92|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GdpALF3
pdb|2B92|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GdpALF3
pdb|2BC9|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Non-Hydrolysable Gtp Analogue Gppnhp
pdb|2D4H|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Gmp
pdb|2D4H|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Gmp
Length = 328
Score = 33.5 bits (75), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 46/90 (51%), Gaps = 14/90 (15%)
Query: 41 AVVAIMGPQSSGKSTLMNHLFHTNFREMDAFRGRSQT-TKGIWIAKCVGIEP-----FTI 94
VVAI+G +GKS LMN L ++ + Q+ TKGIW+ CV P +
Sbjct: 50 VVVAIVGLYRTGKSYLMNKL--AGKKKGFSLGSTVQSHTKGIWMW-CVP-HPKKPGHILV 105
Query: 95 AMDLEGSDSRERGEDDTTFEKQSALFALAI 124
+D EG E+G++ + S +FALA+
Sbjct: 106 LLDTEGLGDVEKGDN----QNDSWIFALAV 131
>pdb|1DG3|A Chain A, Structure Of Human Guanylate Binding Protein-1 In
Nucleotide Free Form
pdb|1F5N|A Chain A, Human Guanylate Binding Protein-1 In Complex With The Gtp
Analogue, Gmppnp
Length = 592
Score = 32.3 bits (72), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 46/90 (51%), Gaps = 14/90 (15%)
Query: 41 AVVAIMGPQSSGKSTLMNHLFHTNFREMDAFRGRSQT-TKGIWIAKCVGIEP-----FTI 94
VVAI+G +GKS LMN L ++ + Q+ TKGIW+ CV P +
Sbjct: 39 VVVAIVGLYRTGKSYLMNKL--AGKKKGFSLGSTVQSHTKGIWMW-CVP-HPKKPGHILV 94
Query: 95 AMDLEGSDSRERGEDDTTFEKQSALFALAI 124
+D EG E+G++ + S +FALA+
Sbjct: 95 LLDTEGLGDVEKGDN----QNDSWIFALAV 120
>pdb|1J2Z|A Chain A, Crystal Structure Of Udp-n-acetylglucosamine
Acyltransferase
Length = 270
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 351 RNAKRKQLESKALDFVYPTYSTLLGHLRSKAFESFKIQLEQ 391
R+ R+ LESK +DF+Y Y L + S ES K++LE+
Sbjct: 195 RHRMRQLLESKDIDFIYALYKRLFRPIPSLR-ESAKLELEE 234
>pdb|2CCG|A Chain A, Crystal Structure Of His-Tagged S. Aureus Thymidylate
Kinase Complexed With Thymidine Monophosphate (Tmp)
pdb|2CCG|B Chain B, Crystal Structure Of His-Tagged S. Aureus Thymidylate
Kinase Complexed With Thymidine Monophosphate (Tmp)
Length = 225
Score = 30.4 bits (67), Expect = 4.5, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 41 AVVAIMGPQSSGKSTLMNHLFHTNFREMDAFRGR 74
A + GP+ SGK+T++N ++H ++ D R
Sbjct: 23 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTR 56
>pdb|2IX8|A Chain A, Model For Eef3 Bound To An 80s Ribosome
Length = 976
Score = 30.4 bits (67), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 16 NGEFNVDGLENFVRTTKLN-HCGLSYAVVAIMGPQSSGKSTLMNHL 60
N EF G + T +N C LS + +A++GP +GKSTL+N L
Sbjct: 670 NXEFQYPGTSK-PQITDINFQCSLS-SRIAVIGPNGAGKSTLINVL 713
>pdb|2IW3|A Chain A, Elongation Factor 3 In Complex With Adp
pdb|2IW3|B Chain B, Elongation Factor 3 In Complex With Adp
Length = 986
Score = 30.4 bits (67), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 16 NGEFNVDGLENFVRTTKLN-HCGLSYAVVAIMGPQSSGKSTLMNHL 60
N EF G + T +N C LS + +A++GP +GKSTL+N L
Sbjct: 676 NXEFQYPGTSK-PQITDINFQCSLS-SRIAVIGPNGAGKSTLINVL 719
>pdb|4DWJ|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|C Chain C, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|D Chain D, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|E Chain E, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|F Chain F, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|G Chain G, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|H Chain H, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4EAQ|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With
3'-Azido-3'-Deoxythymidine-5'-Monophosphate
pdb|4EAQ|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With
3'-Azido-3'-Deoxythymidine-5'-Monophosphate
pdb|4F4I|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Apo-Form
pdb|4F4I|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Apo-Form
Length = 229
Score = 30.4 bits (67), Expect = 4.7, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 41 AVVAIMGPQSSGKSTLMNHLFHTNFREMDAFRGR 74
A + GP+ SGK+T++N ++H ++ D R
Sbjct: 27 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTR 60
>pdb|2CCJ|A Chain A, Crystal Structure Of S. Aureus Thymidylate Kinase
Complexed With Thymidine Monophosphate
pdb|2CCJ|B Chain B, Crystal Structure Of S. Aureus Thymidylate Kinase
Complexed With Thymidine Monophosphate
pdb|2CCK|A Chain A, Crystal Structure Of Unliganded S. Aureus Thymidylate
Kinase
pdb|2CCK|B Chain B, Crystal Structure Of Unliganded S. Aureus Thymidylate
Kinase
pdb|4GFD|A Chain A, Thymidylate Kinase (Tmk) From S. Aureus In Complex With
Tk-666
pdb|4GFD|B Chain B, Thymidylate Kinase (Tmk) From S. Aureus In Complex With
Tk-666
pdb|4GSY|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus Bound To Inhibitor.
pdb|4GSY|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus Bound To Inhibitor.
pdb|4HDC|A Chain A, Discovery Of Selective And Potent Inhibitors Of
Gram-Positive Bacterial Thymidylate Kinase (Tmk:
Compound 41)
pdb|4HDC|B Chain B, Discovery Of Selective And Potent Inhibitors Of
Gram-Positive Bacterial Thymidylate Kinase (Tmk:
Compound 41)
pdb|4HEJ|A Chain A, Discovery Of Selective And Potent Inhibitors Of
Gram-Positive Bacterial Thymidylate Kinase (Tmk):
Compund 16
pdb|4HEJ|B Chain B, Discovery Of Selective And Potent Inhibitors Of
Gram-Positive Bacterial Thymidylate Kinase (Tmk):
Compund 16
pdb|4HLC|A Chain A, Sulfonylpiperidines As Novel, Antibacterial Inhibitors
Of Gram- Positive Thymidylate Kinase (Tmk): Compound 5
pdb|4HLC|B Chain B, Sulfonylpiperidines As Novel, Antibacterial Inhibitors
Of Gram- Positive Thymidylate Kinase (Tmk): Compound 5
pdb|4HLD|A Chain A, Sulfonylpiperidines As Novel, Antibacterial Inhibitors
Of Gram- Positive Thymidylate Kinase (Tmk): Compound 11
pdb|4HLD|B Chain B, Sulfonylpiperidines As Novel, Antibacterial Inhibitors
Of Gram- Positive Thymidylate Kinase (Tmk): Compound 11
Length = 205
Score = 30.0 bits (66), Expect = 4.8, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 41 AVVAIMGPQSSGKSTLMNHLFHTNFREMDAFRGR 74
A + GP+ SGK+T++N ++H ++ D R
Sbjct: 3 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTR 36
>pdb|3CNL|A Chain A, Crystal Structure Of Gnp-Bound Ylqf From T. Maritima
pdb|3CNN|A Chain A, Gtp-Bound Structure Of Tm Ylqf
pdb|3CNO|A Chain A, Gdp-Bound Structue Of Tm Ylqf
Length = 262
Score = 30.0 bits (66), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 49/118 (41%), Gaps = 19/118 (16%)
Query: 41 AVVAIMGPQSSGKSTLMNHLFHTNFREMDAFRGRSQTTKGI-WIAKCVGI---------- 89
A V I+G ++GKST++N L + A G TKGI W + G+
Sbjct: 100 ARVLIVGVPNTGKSTIINKLKGKRASSVGAQPG---ITKGIQWFSLENGVKILDTPGILY 156
Query: 90 -----EPFTIAMDLEGSDSRERGEDDTTFEKQSALFALAIADIVLINMWCHDIGREQA 142
E + L GS ER ED FE+ +FA +I + + D R++
Sbjct: 157 KNIFSEDLAAKLLLVGSLPVERIEDQRIFERAFEIFARSIGIESSFSEFFEDFARKRG 214
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
0.319 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,390,063
Number of Sequences: 62578
Number of extensions: 805867
Number of successful extensions: 2431
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2426
Number of HSP's gapped (non-prelim): 12
length of query: 825
length of database: 14,973,337
effective HSP length: 107
effective length of query: 718
effective length of database: 8,277,491
effective search space: 5943238538
effective search space used: 5943238538
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)