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= 026237
(241 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 = 99.0 bits (245), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 52/184 (28%), Positives = 100/184 (54%), Gaps = 3/184 (1%)
Query: 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVE 118
++ + +RPG ++ G +++ ++ +H++ GRGGA + + ++++TG V F + E +E
Sbjct: 2 ISVTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLE 61
Query: 119 RVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLD-VFGKAGAYLQEGMKVWLQLYDGRA 177
++VE + LY E + ++ ET+EQ VP V G + +EGM +Y+G+
Sbjct: 62 DIYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVG--AEFFKEGMTALGDMYEGQP 119
Query: 178 LSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDS 237
+ + P V + + +G TV+ + A L+ G V VP ++E GE I ++ +
Sbjct: 120 IKVTPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGE 179
Query: 238 YIGR 241
Y+GR
Sbjct: 180 YVGR 183
>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 = 84.0 bits (206), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 49/192 (25%), Positives = 94/192 (48%)
Query: 50 SATQQRAVKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSL 109
S ++ + ++A + G E G+++QVI+ +H + G+G A ++ +L++I TG +
Sbjct: 23 SLYKKAGLXISAGDFKNGVTFELDGQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEK 82
Query: 110 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVW 169
F + + +E K LY + D + ++ETFEQL + D G A +++E V
Sbjct: 83 TFNPTDKXPKAHIERKDXQYLYNDGDLYYFXDTETFEQLPLGKDKIGDALKFVKENEIVK 142
Query: 170 LQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEI 229
+ + G P V + + KG T T + A+++ G ++ VP ++ G+ I
Sbjct: 143 VLSHKGNVFGIEPPNFVELEVTDTEPGFKGDTATGATKPAIVETGASIKVPLFVNKGDII 202
Query: 230 FINPQDDSYIGR 241
I+ + Y R
Sbjct: 203 RIDTRTGEYXER 214
>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 = 79.0 bits (193), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 51/181 (28%), Positives = 88/181 (48%)
Query: 61 ASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERV 120
++ R G I G+ Y V +E + G+G A +++LR + TG +V F + ++ E
Sbjct: 9 SNDFRAGLKIMLDGEPYAVEASEFVKPGKGQAFARVKLRRLLTGTRVEKTFKSTDSAEGA 68
Query: 121 FVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSG 180
V D + T LY + + + +ETFEQL G +L + + + L++G+ +S
Sbjct: 69 DVVDMNLTYLYNDGEFWHFMNNETFEQLSADAKAIGDNAKWLLDQAECIVTLWNGQPISV 128
Query: 181 SIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIG 240
+ P V I + KG T + A L G V VP +++IGE I ++ + Y+
Sbjct: 129 TPPNFVELEIVDTDPGLKGDTAGTGGKPATLSTGAVVKVPLFVQIGEVIKVDTRSGEYVS 188
Query: 241 R 241
R
Sbjct: 189 R 189
>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 = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 86/183 (46%), Gaps = 3/183 (1%)
Query: 61 ASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERV 120
A R G V +G + + AE + GR A+++M+L+++ TG F ++ +E +
Sbjct: 7 AQEFRAGQVANINGAPWVIQKAEFNKSGRNAAVVKMKLKNLLTGAGTETVFKADDKLEPI 66
Query: 121 FVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQ--LYDGRAL 178
++ K T Y + ++SE F Q E+ D ++++GM + Y+ + +
Sbjct: 67 ILDRKEVTYSYFADPLYVFMDSE-FNQYEIEKDDLEGVLTFIEDGMTDICEAVFYNDKVI 125
Query: 179 SGSIPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSY 238
S +P + I + +G T + A L+NG + V ++ EIG+ I I+ + Y
Sbjct: 126 SVELPTTIVRQIAYTEPAVRGDTSGKVMKTARLNNGAELQVSAFCEIGDSIEIDTRTGEY 185
Query: 239 IGR 241
R
Sbjct: 186 KSR 188
>pdb|3TRE|A Chain A, Structure Of A Translation Elongation Factor P (Efp) From
Coxiella Burnetii
Length = 191
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 79/180 (43%)
Query: 62 SHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVF 121
+ R G + G +ID E + G+G A +++ R++ TG + F + E +
Sbjct: 10 NEFRGGLKVXVDGDPCSIIDNEFVKPGKGQAFNRVKFRNLKTGRVLERTFKSGETLPAAD 69
Query: 122 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 181
V + LY + + SE +EQ + +A +L+E + ++G LS
Sbjct: 70 VVEVEXQYLYNDGEFWHFXTSENYEQHAASKEAVAEAKQWLKEEALCXVTXWNGVPLSVE 129
Query: 182 IPKRVACTIKEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 241
P V I E +G T T +RA L+ G V VP +L GE I ++ + Y+ R
Sbjct: 130 PPNFVELKITETEPGVRGDTATGGTKRAKLETGAVVRVPLFLNEGEIIKVDTRRGEYVSR 189
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 56/120 (46%), Gaps = 5/120 (4%)
Query: 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEA 116
KV S ++PG I + ++++ G+ G A ++E I G S+ T
Sbjct: 6 KVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAE 65
Query: 117 VERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLD--VFGKAGAYLQEGMKV--WLQL 172
V+ ++ K+ + DT +++ ET+E EVP+D V + L+EG+ V W L
Sbjct: 66 VDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETL 125
>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 = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 113 TEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQL 172
TE V V + Y + D A V+E E+F + V L +A + + G V + +
Sbjct: 202 TELGVPVTVVASQDHVLPYEDADAALVLE-ESFAERGVRLFKNARAASVTRTGAGVLVTM 260
Query: 173 YDGRALSGS 181
DGR + GS
Sbjct: 261 TDGRTVEGS 269
>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 = 1.7, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 171 QLYDGRALSGSIPKRVACTIKEIHA 195
Q+ D + L G++PK++ C I+E H
Sbjct: 113 QMLDRKLLLGNVPKQMTCYIREYHV 137
>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 = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 168 VWLQLY---DGRALSGS-IPKRVACTIKEIHASTKGPTVTP 204
VW Q+Y D L G+ +P IKE + KGP TP
Sbjct: 62 VWFQVYAGEDAYKLYGNYLPDDTLNAIKEFRVALKGPLTTP 102
>pdb|3E2Q|A Chain A, Crystal Structure Reduced Puta86-630 Mutant Y540s
Complexed With Trans-4-Hydroxy-L-Proline
pdb|3E2R|A Chain A, Crystal Structure Puta86-630 Mutant Y540s Complexed With
L-Tetrahydro- 2-Furoic Acid
pdb|3E2S|A Chain A, Crystal Structure Reduced Puta86-630 Mutant Y540s
Complexed With L- Proline
Length = 551
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 114 EEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 157
+ +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 258 DRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEK 301
>pdb|1K87|A Chain A, Crystal Structure Of E.coli Puta (residues 1-669)
Length = 669
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 110 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 157
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 339 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEEADRLEISLDLLEK 386
>pdb|1TJ2|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With Acetate
Length = 584
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 110 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 157
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 254 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEK 301
>pdb|1TIW|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With
L-Tetrahydro-2-Furoic Acid
pdb|1TJ0|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Co-Crystallized With L-Lactate
pdb|1TJ1|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With L-Lactate
pdb|2FZN|A Chain A, Structure Of The E. Coli Puta Proline Dehydrogenase Domain
Reduced By Dithionite And Complexed With Proline
pdb|2FZM|A Chain A, Structure Of The E. Coli Puta Proline Dehydrogenase Domain
Reduced By Dithionite And Complexed With So2
Length = 602
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 110 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 157
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 254 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEK 301
>pdb|3ITG|A Chain A, Structure The Proline Utilization A Proline Dehydrogenase
Domain (Puta86-630) Inactivated With N-Propargylglycine
pdb|3ITG|B Chain B, Structure The Proline Utilization A Proline Dehydrogenase
Domain (Puta86-630) Inactivated With N-Propargylglycine
Length = 602
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 110 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 157
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 254 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEK 301
>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 = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 169 WLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLD 212
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
0.319 0.134 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,106,435
Number of Sequences: 62578
Number of extensions: 292649
Number of successful extensions: 916
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 902
Number of HSP's gapped (non-prelim): 20
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
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: 50 (23.9 bits)