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= 032740
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1UEB|A Chain A, Crystal Structure Of Translation Elongation Factor P From
Thermus Thermophilus Hb8
pdb|1UEB|B Chain B, Crystal Structure Of Translation Elongation Factor P From
Thermus Thermophilus Hb8
pdb|3HUW|V Chain V, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P For
Molecule I.
pdb|3HUY|V Chain V, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P For
Molecule Ii
Length = 184
Score = 62.0 bits (149), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 36/123 (29%), Positives = 62/123 (50%), Gaps = 1/123 (0%)
Query: 12 VFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALS 71
++VE + LY E + ++ ET+EQ VP A + +EGM +Y+G+ +
Sbjct: 63 IYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGA-EFFKEGMTALGDMYEGQPIK 121
Query: 72 GSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYI 131
+ P V + + +G TV+ + A L+ G V VP ++E GE I ++ + Y+
Sbjct: 122 VTPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYV 181
Query: 132 GRA 134
GRA
Sbjct: 182 GRA 184
>pdb|3A5Z|B Chain B, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
pdb|3A5Z|D Chain D, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
pdb|3A5Z|F Chain F, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
pdb|3A5Z|H Chain H, Crystal Structure Of Escherichia Coli Genx In Complex With
Elongation Factor P
Length = 191
Score = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 37/127 (29%), Positives = 60/127 (47%)
Query: 9 AAGVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 68
A G V D + T LY + + + +ETFEQL G +L + + + L++G+
Sbjct: 65 AEGADVVDMNLTYLYNDGEFWHFMNNETFEQLSADAKAIGDNAKWLLDQAECIVTLWNGQ 124
Query: 69 ALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDD 128
+S + P V I + KG T + A L G V VP +++IGE I ++ +
Sbjct: 125 PISVTPPNFVELEIVDTDPGLKGDTAGTGGKPATLSTGAVVKVPLFVQIGEVIKVDTRSG 184
Query: 129 SYIGRAK 135
Y+ R K
Sbjct: 185 EYVSRVK 191
>pdb|3TRE|A Chain A, Structure Of A Translation Elongation Factor P (Efp) From
Coxiella Burnetii
Length = 191
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 52/114 (45%)
Query: 22 LYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACT 81
LY + + SE +EQ + +A +L+E + ++G LS P V
Sbjct: 78 LYNDGEFWHFXTSENYEQHAASKEAVAEAKQWLKEEALCXVTXWNGVPLSVEPPNFVELK 137
Query: 82 IKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 135
I E +G T T +RA L+ G V VP +L GE I ++ + Y+ RAK
Sbjct: 138 ITETEPGVRGDTATGGTKRAKLETGAVVRVPLFLNEGEIIKVDTRRGEYVSRAK 191
>pdb|1YBY|A Chain A, Conserved Hypothetical Protein Cth-95 From Clostridium
Thermocellum
pdb|1YBY|B Chain B, Conserved Hypothetical Protein Cth-95 From Clostridium
Thermocellum
Length = 215
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 56/120 (46%)
Query: 14 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 73
+E K LY + D + ++ETFEQL + D G A +++E V + + G
Sbjct: 95 IERKDXQYLYNDGDLYYFXDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIE 154
Query: 74 IPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 133
P V + + KG T T + A+++ G ++ VP ++ G+ I I+ + Y R
Sbjct: 155 PPNFVELEVTDTEPGFKGDTATGATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYXER 214
>pdb|3OYY|A Chain A, Structure Of Pseudomonas Aeruginosa Elongation Factor P
pdb|3OYY|B Chain B, Structure Of Pseudomonas Aeruginosa Elongation Factor P
Length = 191
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 49/111 (44%), Gaps = 2/111 (1%)
Query: 27 DTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQ--LYDGRALSGSIPKRVACTIKE 84
D +V F Q E+ D ++++GM + Y+ + +S +P + I
Sbjct: 80 DPLYVFMDSEFNQYEIEKDDLEGVLTFIEDGMTDICEAVFYNDKVISVELPTTIVRQIAY 139
Query: 85 IHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 135
+ +G T + A L+NG + V ++ EIG+ I I+ + Y R K
Sbjct: 140 TEPAVRGDTSGKVMKTARLNNGAELQVSAFCEIGDSIEIDTRTGEYKSRVK 190
>pdb|2A5Y|B Chain B, Structure Of A Ced-4CED-9 Complex
pdb|2A5Y|C Chain C, Structure Of A Ced-4CED-9 Complex
pdb|3LQQ|A Chain A, Structure Of The Ced-4 Apoptosome
pdb|3LQQ|B Chain B, Structure Of The Ced-4 Apoptosome
pdb|3LQR|A Chain A, Structure Of Ced-4:ced-3 Complex
pdb|3LQR|B Chain B, Structure Of Ced-4:ced-3 Complex
Length = 549
Score = 29.6 bits (65), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 63 QLYDGRALSGSIPKRVACTIKEIH 86
Q+ D + L G++PK++ C I+E H
Sbjct: 113 QMLDRKLLLGNVPKQMTCYIREYH 136
>pdb|1XDI|A Chain A, Crystal Structure Of Lpda (Rv3303c) From Mycobacterium
Tuberculosis
pdb|1XDI|B Chain B, Crystal Structure Of Lpda (Rv3303c) From Mycobacterium
Tuberculosis
Length = 499
Score = 28.9 bits (63), Expect = 0.92, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 23 YTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 73
Y + D A V+E E+F + V L +A + + G V + + DGR + GS
Sbjct: 220 YEDADAALVLE-ESFAERGVRLFKNARAASVTRTGAGVLVTMTDGRTVEGS 269
>pdb|2IV0|A Chain A, Thermal Stability Of Isocitrate Dehydrogenase From
Archaeoglobus Fulgidus Studied By Crystal Structure
Analysis And Engineering Of Chimers
pdb|2IV0|B Chain B, Thermal Stability Of Isocitrate Dehydrogenase From
Archaeoglobus Fulgidus Studied By Crystal Structure
Analysis And Engineering Of Chimers
Length = 412
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 60 VWLQLY---DGRALSGS-IPKRVACTIKEIHASTKGPTVTP 96
VW Q+Y D L G+ +P IKE + KGP TP
Sbjct: 62 VWFQVYAGEDAYKLYGNYLPDDTLNAIKEFRVALKGPLTTP 102
>pdb|1IZ6|A Chain A, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
pdb|1IZ6|B Chain B, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
pdb|1IZ6|C Chain C, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
Length = 138
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 13 FVEDKSFTCLYTENDTAFVIESETFEQLEVPLD--VFGKAGAYLQEGMKV--WLQL 64
++ K+ + DT +++ ET+E EVP+D V + L+EG+ V W L
Sbjct: 70 IIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETL 125
>pdb|2CWO|A Chain A, Crystal Structure Of Rna Silencing Suppressor P21 From
Beet Yellows Virus
pdb|2CWO|B Chain B, Crystal Structure Of Rna Silencing Suppressor P21 From
Beet Yellows Virus
pdb|2CWO|C Chain C, Crystal Structure Of Rna Silencing Suppressor P21 From
Beet Yellows Virus
pdb|2CWO|D Chain D, Crystal Structure Of Rna Silencing Suppressor P21 From
Beet Yellows Virus
Length = 197
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 61 WLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLD 104
W++ + ++ +P R+ +KEI A K VTP ++ D
Sbjct: 81 WMEQHPNQSSKLRVPSRIGEMLKEIRAFLKVRVVTPMHKETASD 124
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
0.321 0.138 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,065,366
Number of Sequences: 62578
Number of extensions: 161782
Number of successful extensions: 628
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 617
Number of HSP's gapped (non-prelim): 13
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
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: 46 (22.3 bits)