RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11837
(192 letters)
>1dar_A EF-G, elongation factor G; ribosomal translocase, translational
GTPase; HET: GDP; 2.40A {Thermus thermophilus} SCOP:
b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 PDB: 1elo_A 1ktv_A
2om7_L* 2wri_Y* 2wrk_Y* 2xsy_Y* 2xuy_Y* 2j7k_A* 2efg_A*
1jqm_B 1efg_A* 1fnm_A* 1pn6_A 2bm1_A* 2bm0_A* 2bv3_A*
3izp_E 1zn0_B 1jqs_C 2bcw_C ...
Length = 691
Score = 107 bits (271), Expect = 1e-27
Identities = 37/107 (34%), Positives = 63/107 (58%), Gaps = 7/107 (6%)
Query: 26 IATGASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSK 81
IA SMA+KE ++LEP M +E+ + E+Y+ ++ DL+ RR I +E RG+++
Sbjct: 584 IA--GSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQ 641
Query: 82 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 128
VI A PL+E+ GY +R+ + GR F M F +++V + + +
Sbjct: 642 VIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEV-PKQVQEKL 687
>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP,
50S subunit, cryo-EM, REAL-space refinement,
ribonucleoprotein; 9.10A {Escherichia coli} PDB: 3j0e_H
Length = 704
Score = 107 bits (270), Expect = 1e-27
Identities = 43/107 (40%), Positives = 65/107 (60%), Gaps = 7/107 (6%)
Query: 26 IATGASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSK 81
+A AS+A KE A +LLEP M +E+ + E+ ++ DLSRRR ++ E +
Sbjct: 595 LA--ASIAFKEGFKKAKPVLLEPIMKVEVETPEENTGDVIGDLSRRRGMLKGQESEVTGV 652
Query: 82 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 128
I AE PLSE+ GY ++R+L+ GR+ ++MEFL + + N AQAV
Sbjct: 653 KIHAEVPLSEMFGYATQLRSLTKGRASYTMEFLKYDEA-PSNVAQAV 698
>2dy1_A Elongation factor G; translocation, GTP complex, structural
genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus}
SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1
PDB: 1wdt_A*
Length = 665
Score = 106 bits (268), Expect = 2e-27
Identities = 36/107 (33%), Positives = 62/107 (57%), Gaps = 7/107 (6%)
Query: 26 IATGASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSK 81
IA AS+A K+ A +LLEP L++++ ++ V +L+DL RR I +E G+
Sbjct: 554 IA--ASLAFKKVMAEAHPVLLEPIYRLKVLAPQERVGDVLSDLQARRGRILGMEQEGALS 611
Query: 82 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 128
V+ AE PL+E+L Y + + L+ G +++EF + +V + AQ +
Sbjct: 612 VVHAEVPLAEVLEYYKALPGLTGGAGAYTLEFSHYAEV-PPHLAQRI 657
>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein;
1.90A {Staphylococcus aureus}
Length = 693
Score = 104 bits (263), Expect = 1e-26
Identities = 37/107 (34%), Positives = 64/107 (59%), Gaps = 7/107 (6%)
Query: 26 IATGASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSK 81
IA AS+ALKE ++LEP M + I E+Y+ I+ D++ RR + +E RG+++
Sbjct: 583 IA--ASLALKEAAKKCDPVILEPMMKVTIEMPEEYMGDIMGDVTSRRGRVDGMEPRGNAQ 640
Query: 82 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 128
V+ A PLSE+ GY +R+ + GR ++M F + +V ++ A+ +
Sbjct: 641 VVNAYVPLSEMFGYATSLRSNTQGRGTYTMYFDHYAEV-PKSIAEDI 686
>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation;
HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP:
b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB:
1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A*
1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T*
2zit_A* 1u2r_A* 3b78_A* 3b8h_A*
Length = 842
Score = 70.8 bits (173), Expect = 9e-15
Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 2/107 (1%)
Query: 15 YSPRTYVILMCIATGASMALKEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSV 74
I+ + A + EP +EI EQ V GI + L+++R + S
Sbjct: 698 IHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSE 757
Query: 75 EDRGSSKV--IIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQV 119
E R + + + A P++E G+ +R + G++ M F + +
Sbjct: 758 EQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTL 804
>3e3x_A BIPA; MCSG,PSI2, structural genomics, protein struct initiative,
midwest center for structural genomics, GTP-BIN
nucleotide-binding; HET: MLZ MLY; 1.95A {Vibrio
parahaemolyticus}
Length = 332
Score = 35.6 bits (82), Expect = 0.005
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 41 LLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKV-IIAEAPLSELLGYCQRV 99
L+EP+ + I E++ GI+ ++ R ++ + G +V + P L+G+
Sbjct: 123 LMEPFETVTIDVMEEHQGGIMENIGLRXGELXDMAPDGKGRVRMDFIMPSRGLIGFQTEF 182
Query: 100 RTLSSGRSHFSMEFLCFK 117
TL+SG F +
Sbjct: 183 MTLTSGSGLLYHTFDHYG 200
>3tow_A Multivesicular BODY subunit 12B; beta prism, membrane binding
domain, negatively charged MEMB protein transport; 1.34A
{Homo sapiens}
Length = 152
Score = 28.5 bits (63), Expect = 0.76
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 113 FLCFKQVSSQNEAQAVRNITGFDPVIIAEA-PLSELLGYCQRVRTLSSGRSHFSMEFLCF 171
+LCF + S+ + + D +I L G+ T+ + F + LC
Sbjct: 47 YLCFTRSFSKENSHLGNVLV--DMKLIDIKDTLPV--GFIPIQETVDTQEVAFRKKRLCI 102
Query: 172 KQVSSQNEAQAVRNI 186
K + + A+ +I
Sbjct: 103 KFIPRDSTEAAICDI 117
Score = 27.7 bits (61), Expect = 1.9
Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 14/115 (12%)
Query: 17 PRTYVILMCIATGASMALKEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVED 76
P Y ++ A G L + G + YL + L ++ D++ ++
Sbjct: 17 PTGYDVVAQTADGVDADLWKDGLFKSKVTRYLCFTRSFSKENSHLGNVL---VDMKLIDI 73
Query: 77 RGSSKVIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNI 131
+ + V G+ T+ + F + LC K + + A+ +I
Sbjct: 74 KDTLPV-----------GFIPIQETVDTQEVAFRKKRLCIKFIPRDSTEAAICDI 117
>2hig_A 6-phospho-1-fructokinase; transferase; 2.40A {Trypanosoma brucei}
PDB: 3f5m_A*
Length = 487
Score = 29.3 bits (66), Expect = 0.78
Identities = 19/131 (14%), Positives = 32/131 (24%), Gaps = 29/131 (22%)
Query: 26 IATGASMALKEAGCILL--EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVI 83
IA A++A +A L+ P +++ L RR S +I
Sbjct: 279 IAAQAAVASAQANICLVPENPI----------SEQEVMSLLERRF------CHSRSCVII 322
Query: 84 IAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNITGFDP-VIIAEA 142
+AE + +SG + + I
Sbjct: 323 VAEGFGQDWGR--GSGGYDASGNKKLIDIGVILTEKVKAFLKANKSRYPDSTVKYID--- 377
Query: 143 PLSELLGYCQR 153
Y R
Sbjct: 378 -----PSYMIR 383
>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like
domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus}
PDB: 2ywf_A* 2ywg_A* 2ywh_A*
Length = 600
Score = 27.8 bits (63), Expect = 2.5
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIA-EAPLSELL 93
EP++ + II+ ++YV I+ +R +++ + V + E PLSE++
Sbjct: 405 EPFVLVTIITPKEYVGPIIQLCQEKRGIQKNMTYLDPNTVYLEYEMPLSEII 456
>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase,
ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET:
ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*
Length = 773
Score = 27.7 bits (62), Expect = 3.1
Identities = 29/109 (26%), Positives = 44/109 (40%), Gaps = 35/109 (32%)
Query: 16 SPRTYVILMCIAT-GASMALKEAGCILLEPYM--YLEIISDEQYVH----------GILA 62
S +T + M T G M L+EA + + + Y II DE H G+L
Sbjct: 183 SNKTILKYM---TDG--MLLREA---MEDHDLSRYSCIILDE--AHERTLATDILMGLLK 232
Query: 63 DLSRRRADIRSVEDRGSSKVIIAEAPL--SELLGYCQRVRTLS-SGRSH 108
+ +RR D+ K+II A L + Y L+ GR++
Sbjct: 233 QVVKRRPDL---------KIIIMSATLDAEKFQRYFNDAPLLAVPGRTY 272
>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane,
nucleotide-binding, translation; 2.80A {Escherichia
coli} PDB: 3deg_C*
Length = 599
Score = 26.7 bits (60), Expect = 5.2
Identities = 8/51 (15%), Positives = 23/51 (45%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELL 93
EP ++ + Y+ ++ +R ++ G+ + E P++E++
Sbjct: 401 EPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVV 451
>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; 2.70A {Haemophilus
influenzae}
Length = 177
Score = 26.0 bits (58), Expect = 6.2
Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 4/47 (8%)
Query: 101 TLSSGRSHFSMEFLCFKQVSSQNEAQAVRNITGFDPVIIAEAPLSEL 147
L + R H + K V + AQ + N+ + + + EL
Sbjct: 48 ELENWRYHNHEIIVKLKGVDDREAAQILANVE----IGVDLSVFPEL 90
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19,
PRC-barrel, STRU genomics, NPPSFA; 2.00A {Thermus
thermophilus} PDB: 3a1p_A 2dog_A
Length = 162
Score = 25.6 bits (57), Expect = 7.4
Identities = 8/51 (15%), Positives = 15/51 (29%), Gaps = 4/51 (7%)
Query: 97 QRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNITGFDPVIIAEAPLSEL 147
R + + V+ + A+A+ + V A L L
Sbjct: 38 HGWRAIEDLYRVGEELVVHLAGVTDRTLAEALVGLR----VYAEVADLPPL 84
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.135 0.392
Gapped
Lambda K H
0.267 0.0529 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,907,768
Number of extensions: 166981
Number of successful extensions: 340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 20
Length of query: 192
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 104
Effective length of database: 4,244,745
Effective search space: 441453480
Effective search space used: 441453480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.0 bits)