RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6806
(89 letters)
>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding
protein, retroviral integration, preintegration
complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB:
1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A
Length = 89
Score = 155 bits (394), Expect = 1e-51
Identities = 62/89 (69%), Positives = 80/89 (89%)
Query: 1 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFV 60
M+TSQKH++FV+EPMGEKPV LAG+G+VLGK+LE +GFDKAYVVLGQFL+LK++E+LF
Sbjct: 1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFR 60
Query: 61 DWMKETCQANAKQSGDCYNCLKDWCGEFL 89
+W+K+TC ANAKQS DC+ CL++WC FL
Sbjct: 61 EWLKDTCGANAKQSRDCFGCLREWCDAFL 89
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 308
Score = 27.1 bits (60), Expect = 0.58
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 20 VTELAGVGDVLGKRLESK 37
V E+AGV + LGK+L S
Sbjct: 256 VLEMAGVENALGKQLGSN 273
>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA
repair, DNA synthesis, binding, magnesium,
metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens}
Length = 504
Score = 26.7 bits (59), Expect = 1.1
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 15 MGEKPVTELAGVGDVLGKRLESKG 38
+ + VT L GVG + +L S G
Sbjct: 312 IRGQLVTNLPGVGHSMESKLASLG 335
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP:
d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D
Length = 150
Score = 25.9 bits (58), Expect = 1.6
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 20 VTELAGVGDVLGKRLES 36
V ELAG+ D+L K + S
Sbjct: 114 VLELAGISDILSKSIGS 130
>3oaa_G ATP synthase gamma chain; rossmann fold, hydrolase,
hydrolase-transport PROT complex; HET: ANP ADP; 3.26A
{Escherichia coli DH1}
Length = 286
Score = 25.9 bits (58), Expect = 1.7
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 15 MGEKP-VTELAGVGDVLGKRLESKGFDKAYVVLGQF 49
MG+ P ++EL G V+ + + DK Y+V +F
Sbjct: 139 MGDNPSLSELIGPVKVMLQAYDEGRLDKLYIVSNKF 174
>1fs0_G ATP synthase gamma subunit; coiled coil, epsilon, hydrolase; 2.10A
{Escherichia coli} SCOP: c.49.2.1
Length = 230
Score = 26.0 bits (58), Expect = 1.9
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 15 MGEKP-VTELAGVGDVLGKRLESKGFDKAYVVLGQF 49
MG+ P ++EL G V+ + + DK Y+V +F
Sbjct: 122 MGDNPSLSELIGPVKVMLQAYDEGRLDKLYIVSNKF 157
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E
1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E*
1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E*
1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ...
Length = 162
Score = 25.6 bits (57), Expect = 2.0
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 19 PVTELAGVGDVLGKRLES 36
+ ELAGV D+L K L S
Sbjct: 108 AILELAGVTDILTKELGS 125
>3r8n_E 30S ribosomal protein S5; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_E 3fih_E* 3iy8_E 2wwl_E 3oar_E 3oaq_E
3ofb_E 3ofa_E 3ofp_E 3ofx_E 3ofy_E 3ofo_E 3r8o_E 4a2i_E
2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E ...
Length = 150
Score = 25.5 bits (57), Expect = 2.4
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 20 VTELAGVGDVLGKRLES 36
V E+AGV +VL K S
Sbjct: 105 VLEVAGVHNVLAKAYGS 121
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E
3i1z_E 3i21_E 3izv_I* 3izw_I* 3kc4_E 3or9_E 3ora_E
3sfs_E* 3uoq_E*
Length = 167
Score = 25.2 bits (56), Expect = 2.5
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 20 VTELAGVGDVLGKRLES 36
V E+AGV +VL K S
Sbjct: 114 VLEVAGVHNVLAKAYGS 130
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 25.3 bits (56), Expect = 3.6
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 17 EKPVTELAGVGDVLGKRLESKG 38
+ GVG K+L+ G
Sbjct: 114 STDIQYAKGVGPNRKKKLKKLG 135
>2qe7_G ATP synthase subunit gamma; blockage of ATP hydrolysis, F1-ATPase,
single analysis, thermoalkaliphilic, hydrolase; 3.06A
{Bacillus SP}
Length = 286
Score = 24.8 bits (55), Expect = 3.9
Identities = 7/36 (19%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 15 MGEKP-VTELAGVGDVLGKRLESKGFDKAYVVLGQF 49
+ + P +TE+ + + FDK + +F
Sbjct: 140 ISDTPSLTEIQDIAQSAIGMFADETFDKLTIFYNEF 175
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex,
Y-family DNA polym translesion synthesis, nucleoside
triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens}
PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A*
2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A*
3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 3h4d_A* 3h4b_A*
...
Length = 420
Score = 25.0 bits (55), Expect = 3.9
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 18 KPVTELAGVGDVLGKRLESKG 38
+ E+ G+G K LE+ G
Sbjct: 234 NHIKEIPGIGYKTAKCLEALG 254
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family,
transferase-D complex; HET: DNA MSE ADI; 1.70A
{Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB:
1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A*
1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A*
2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Length = 352
Score = 24.8 bits (55), Expect = 4.6
Identities = 4/21 (19%), Positives = 13/21 (61%)
Query: 19 PVTELAGVGDVLGKRLESKGF 39
+ ++ G+G++ ++L+ G
Sbjct: 179 DIADVPGIGNITAEKLKKLGI 199
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 24.4 bits (53), Expect = 6.0
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 19 PVTELAGVGDVLGKRLESKGFD 40
P+ +L VG + L + GF
Sbjct: 647 PLMQLPLVGRRRARALYNSGFR 668
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop,
transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces
cerevisiae} PDB: 3bjy_A* 3osp_A*
Length = 434
Score = 24.2 bits (53), Expect = 6.4
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 15 MGEKPVTELAGVGDVLGKRLES 36
+ +L GVG RLES
Sbjct: 238 WSSFKLDDLPGVGHSTLSRLES 259
>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding
nucleotide binding M binding, nucleus; HET: DNA TTD DTP;
3.34A {Homo sapiens}
Length = 517
Score = 24.6 bits (53), Expect = 6.5
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 15 MGEKPVTELAGVGDVLGKRLESKGF 39
+ + P+ +++G+G V K L++ G
Sbjct: 335 IKDLPIRKVSGIGKVTEKMLKALGI 359
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family
DNA polymerase, translesion DNA synthesis, lesion
bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7
PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*
Length = 459
Score = 24.1 bits (52), Expect = 7.5
Identities = 8/33 (24%), Positives = 20/33 (60%)
Query: 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGF 39
++ V + + + P+ +++G+G V K L++ G
Sbjct: 271 NRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGI 303
>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA
binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A
{Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A*
2zuc_A* 2zud_A*
Length = 324
Score = 23.9 bits (52), Expect = 9.4
Identities = 6/30 (20%), Positives = 13/30 (43%)
Query: 11 VSEPMGEKPVTELAGVGDVLGKRLESKGFD 40
V + K + +L G+ + +L G+
Sbjct: 5 VEQKKNIKTINDLPGISQTVINKLIEAGYS 34
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
0.318 0.135 0.418
Gapped
Lambda K H
0.267 0.0835 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,312,022
Number of extensions: 64657
Number of successful extensions: 224
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 23
Length of query: 89
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 32
Effective length of database: 5,110,296
Effective search space: 163529472
Effective search space used: 163529472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.2 bits)