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= 030538
(175 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 = 91.3 bits (225), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 50/170 (29%), Positives = 92/170 (54%), Gaps = 3/170 (1%)
Query: 6 GKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTE 65
G +++ ++ +H++ GRGGA + + ++++TG V F + E +E ++VE + LY E
Sbjct: 17 GGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDIYVETRELQYLYPE 76
Query: 66 NDTAFVIESETFEQLEVPLD-VFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKE 124
+ ++ ET+EQ VP V G + +EGM +Y+G+ + + P V + +
Sbjct: 77 GEEMVFMDLETYEQFAVPRSRVVG--AEFFKEGMTALGDMYEGQPIKVTPPTVVELKVVD 134
Query: 125 IHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRA 174
+G TV+ + A L+ G V VP ++E GE I ++ + Y+GRA
Sbjct: 135 TPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGRA 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 = 79.3 bits (194), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 49/170 (28%), Positives = 84/170 (49%)
Query: 6 GKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTE 65
G+ Y V +E + G+G A +++LR + TG +V F + ++ E V D + T LY +
Sbjct: 22 GEPYAVEASEFVKPGKGQAFARVKLRRLLTGTRVEKTFKSTDSAEGADVVDMNLTYLYND 81
Query: 66 NDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEI 125
+ + +ETFEQL G +L + + + L++G+ +S + P V I +
Sbjct: 82 GEFWHFMNNETFEQLSADAKAIGDNAKWLLDQAECIVTLWNGQPISVTPPNFVELEIVDT 141
Query: 126 HASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 175
KG T + A L G V VP +++IGE I ++ + Y+ R K
Sbjct: 142 DPGLKGDTAGTGGKPATLSTGAVVKVPLFVQIGEVIKVDTRSGEYVSRVK 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 = 79.0 bits (193), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 45/168 (26%), Positives = 84/168 (50%)
Query: 6 GKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTE 65
G+++QVI+ +H + G+G A ++ +L++I TG + F + + +E K LY +
Sbjct: 47 GQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEKTFNPTDKXPKAHIERKDXQYLYND 106
Query: 66 NDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEI 125
D + ++ETFEQL + D G A +++E V + + G P V + +
Sbjct: 107 GDLYYFXDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIEPPNFVELEVTDT 166
Query: 126 HASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGR 173
KG T T + A+++ G ++ VP ++ G+ I I+ + Y R
Sbjct: 167 EPGFKGDTATGATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYXER 214
>pdb|3TRE|A Chain A, Structure Of A Translation Elongation Factor P (Efp) From
Coxiella Burnetii
Length = 191
Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 47/170 (27%), Positives = 77/170 (45%)
Query: 6 GKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTE 65
G +ID E + G+G A +++ R++ TG + F + E + V + LY +
Sbjct: 22 GDPCSIIDNEFVKPGKGQAFNRVKFRNLKTGRVLERTFKSGETLPAADVVEVEXQYLYND 81
Query: 66 NDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEI 125
+ SE +EQ + +A +L+E + ++G LS P V I E
Sbjct: 82 GEFWHFXTSENYEQHAASKEAVAEAKQWLKEEALCXVTXWNGVPLSVEPPNFVELKITET 141
Query: 126 HASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 175
+G T T +RA L+ G V VP +L GE I ++ + Y+ RAK
Sbjct: 142 EPGVRGDTATGGTKRAKLETGAVVRVPLFLNEGEIIKVDTRRGEYVSRAK 191
>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 = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 42/173 (24%), Positives = 82/173 (47%), Gaps = 3/173 (1%)
Query: 5 TGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYT 64
G + + AE + GR A+++M+L+++ TG F ++ +E + ++ K T Y
Sbjct: 19 NGAPWVIQKAEFNKSGRNAAVVKMKLKNLLTGAGTETVFKADDKLEPIILDRKEVTYSYF 78
Query: 65 ENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQ--LYDGRALSGSIPKRVACTI 122
+ ++SE F Q E+ D ++++GM + Y+ + +S +P + I
Sbjct: 79 ADPLYVFMDSE-FNQYEIEKDDLEGVLTFIEDGMTDICEAVFYNDKVISVELPTTIVRQI 137
Query: 123 KEIHASTKGPTVTPRYRRALLDNGVTVMVPSYLEIGEEIFINPQDDSYIGRAK 175
+ +G T + A L+NG + V ++ EIG+ I I+ + Y R K
Sbjct: 138 AYTEPAVRGDTSGKVMKTARLNNGAELQVSAFCEIGDSIEIDTRTGEYKSRVK 190
>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 = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 4/87 (4%)
Query: 22 GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLE 81
G A ++E I G S+ T V+ ++ K+ + DT +++ ET+E E
Sbjct: 39 GSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFE 98
Query: 82 VPLD--VFGKAGAYLQEGMKV--WLQL 104
VP+D V + L+EG+ V W L
Sbjct: 99 VPIDTGVADEIRDQLKEGINVEYWETL 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 = 0.27, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 45 TEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQL 104
TE V V + Y + D A V+E E+F + V L +A + + G V + +
Sbjct: 202 TELGVPVTVVASQDHVLPYEDADAALVLE-ESFAERGVRLFKNARAASVTRTGAGVLVTM 260
Query: 105 YDGRALSGS 113
DGR + GS
Sbjct: 261 TDGRTVEGS 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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 100 VWLQLY---DGRALSGS-IPKRVACTIKEIHASTKGPTVTP 136
VW Q+Y D L G+ +P IKE + KGP TP
Sbjct: 62 VWFQVYAGEDAYKLYGNYLPDDTLNAIKEFRVALKGPLTTP 102
>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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 103 QLYDGRALSGSIPKRVACTIKEIHA 127
Q+ D + L G++PK++ C I+E H
Sbjct: 113 QMLDRKLLLGNVPKQMTCYIREYHV 137
>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 = 2.8, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 101 WLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYRRALLD 144
W++ + ++ +P R+ +KEI A K VTP ++ D
Sbjct: 81 WMEQHPNQSSKLRVPSRIGEMLKEIRAFLKVRVVTPMHKETASD 124
>pdb|1TJ2|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With Acetate
Length = 584
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 42 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 89
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 254 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEK 301
>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 = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 42 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 89
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 = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 42 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 89
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 = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 42 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 89
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 254 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEK 301
>pdb|1K87|A Chain A, Crystal Structure Of E.coli Puta (residues 1-669)
Length = 669
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 42 RFGTEEAVERVFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGK 89
R + +E ++ KS T L + D I++E ++LE+ LD+ K
Sbjct: 339 RAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEEADRLEISLDLLEK 386
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
0.318 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,301,227
Number of Sequences: 62578
Number of extensions: 216253
Number of successful extensions: 829
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 815
Number of HSP's gapped (non-prelim): 16
length of query: 175
length of database: 14,973,337
effective HSP length: 92
effective length of query: 83
effective length of database: 9,216,161
effective search space: 764941363
effective search space used: 764941363
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)