RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10067
(124 letters)
>2zkq_g 40S ribosomal protein S5E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protei complex; 8.70A {Canis
familiaris}
Length = 204
Score = 168 bits (427), Expect = 2e-54
Identities = 84/101 (83%), Positives = 93/101 (92%)
Query: 23 SSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQ 82
++ A AE P+IKLFG+WS DDVQ++D+SLQDYIAVKEK AK+LPHSAGRYAAKRFRKAQ
Sbjct: 6 TAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQ 65
Query: 83 CPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
CPIVERLTNS+MMHGRNN KKLM VRIVKHAFEIIHLLTGE
Sbjct: 66 CPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGE 106
>2xzm_G Ribosomal protein S7 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_G 3j0o_T
3j0l_T
Length = 200
Score = 158 bits (402), Expect = 1e-50
Identities = 51/98 (52%), Positives = 69/98 (70%), Gaps = 1/98 (1%)
Query: 27 APAELPEIKLFGRWSCDDVQVSDMSLQDYIAV-KEKNAKFLPHSAGRYAAKRFRKAQCPI 85
+ KLFG+W+ D+V++ D Q+YIA K+ F+PH+AGRY K+FRK QCPI
Sbjct: 4 EKGFATQPKLFGKWNYDEVKIQDPCFQNYIACTTTKSQVFVPHTAGRYQVKKFRKTQCPI 63
Query: 86 VERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
VERL +LM HGRN KK + +++VK+AFEIIHL+TG
Sbjct: 64 VERLIGTLMFHGRNAGKKALCIKVVKNAFEIIHLVTGR 101
>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G*
2noq_F 1s1h_G 3iz6_F
Length = 225
Score = 159 bits (404), Expect = 1e-50
Identities = 58/98 (59%), Positives = 74/98 (75%), Gaps = 2/98 (2%)
Query: 26 AAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPI 85
EIKLF +WS ++V+V D SL DY+ V++ F+ H+AGRYA KRFRKAQCPI
Sbjct: 32 EVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQP--IFVAHTAGRYANKRFRKAQCPI 89
Query: 86 VERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
+ERLTNSLMM+GRNN KKL AVRI+KH +II++LT +
Sbjct: 90 IERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQ 127
>1iqv_A Ribosomal protein S7; RNA-binding, decoding center, helix-turn-
helix, ribosome; 2.10A {Pyrococcus horikoshii} SCOP:
a.75.1.1
Length = 218
Score = 144 bits (364), Expect = 7e-45
Identities = 45/107 (42%), Positives = 61/107 (57%), Gaps = 19/107 (17%)
Query: 33 EIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNS 92
EIK+ GRWS +DV+V D SL+ YI ++ + LPH+ GR+A K F KA IVERL N
Sbjct: 17 EIKVMGRWSTEDVEVKDPSLKPYINLE---PRLLPHTHGRHAKKHFGKANVHIVERLINK 73
Query: 93 LMMHGRN----------------NAKKLMAVRIVKHAFEIIHLLTGE 123
+M G + N+KK+ A +VK AF+II TG+
Sbjct: 74 VMRSGGSHYKVAGHFMRREHRSLNSKKVRAYEVVKEAFKIIEKRTGK 120
>3gty_S TF, 30S ribosomal protein S7; chaperone-client complex, cell cycle,
cell division, chapero isomerase, rotamase,
ribonucleoprotein, binding; 3.40A {Thermotoga maritima}
Length = 149
Score = 32.9 bits (76), Expect = 0.012
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 84 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
+V +L N +M G KK +A +IV AF+II T +
Sbjct: 14 VLVAKLINRVMWDG----KKTIAQKIVYGAFDIIREKTKK 49
>3r8n_G 30S ribosomal protein S7; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_G 3oaq_G 3ofa_G 3ofx_G 3ofo_G 3r8o_G
3sfs_G* 3ofp_G 3fih_G* 2wwl_G 3oar_G 3ofb_G 3ofy_G
4a2i_G 2gy9_G 2gyb_G
Length = 151
Score = 32.9 bits (76), Expect = 0.012
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 84 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
++ + N LM+ G KK A IV A E + +G+
Sbjct: 20 ELLAKFVNILMVDG----KKSTAESIVYSALETLAQRSGK 55
>3bbn_G Ribosomal protein S7; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 155
Score = 32.5 bits (75), Expect = 0.013
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 85 IVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
+V L N ++ HG KK +A +I+ A + I T
Sbjct: 22 LVNMLVNRILKHG----KKSLAYQILYRAVKKIQQKTET 56
>1hus_A Ribosomal protein S7; RNA-binding protein, decoding center,; 2.50A
{Geobacillus stearothermophilus} SCOP: a.75.1.1
Length = 155
Score = 32.5 bits (75), Expect = 0.014
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 84 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
+V RL N +M+ G KK A +I+ AF+II TG+
Sbjct: 20 KLVTRLINKIMIDG----KKSKAQKILYTAFDIIRERTGK 55
>3i1m_G 30S ribosomal protein S7; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_G* 3e1a_U 3e1c_U 1vs5_G 3i1o_G
3i1q_G 3i1s_G 3i1z_G 3i21_G 3izv_K* 3izw_K* 3kc4_G
3or9_G 3ora_G 3uoq_G* 2qal_G* 1p6g_G 1p87_G 2aw7_G
2avy_G ...
Length = 179
Score = 32.6 bits (75), Expect = 0.014
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 84 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
++ + N LM+ G KK A IV A E + +G+
Sbjct: 21 ELLAKFVNILMVDG----KKSTAESIVYSALETLAQRSGK 56
>1rss_A Ribosomal protein S7; RNA-binding, translation; 1.90A {Thermus
thermophilus} SCOP: a.75.1.1 PDB: 1n32_G* 1i95_G*
1i96_G* 1i97_G* 1i94_G 1j5e_G* 1n33_G* 1n34_G 1n36_G
1pns_G 1pnx_G 1voq_G 1vos_G 1vov_G 1vox_G 1voz_G 2e5l_G
2zm6_G 3fic_G* 3mr8_G ...
Length = 151
Score = 32.5 bits (75), Expect = 0.015
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 84 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
+V N +M G KK +A RI A +II TG+
Sbjct: 16 VLVTAFINKIMRDG----KKNLAARIFYDACKIIQEKTGQ 51
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 0.61
Identities = 6/23 (26%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 86 VERLTNSLMMHGRNNAKKLMAVR 108
+++L SL ++ ++A L A++
Sbjct: 22 LKKLQASLKLYADDSAPAL-AIK 43
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 27.1 bits (61), Expect = 1.4
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 17 GGPVGLSSIAA 27
P+GL+SIAA
Sbjct: 277 QKPIGLASIAA 287
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase,
winged-helix domain, ATP hydrolysis, walker A, walker B,
sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga
maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A*
1in8_A* 1in7_A* 1j7k_A*
Length = 334
Score = 27.1 bits (61), Expect = 1.5
Identities = 8/11 (72%), Positives = 11/11 (100%)
Query: 17 GGPVGLSSIAA 27
GGPVGL+++AA
Sbjct: 274 GGPVGLNALAA 284
>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide,
hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP:
a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*
Length = 324
Score = 27.1 bits (61), Expect = 1.7
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 17 GGPVGLSSIAA 27
GGPVGL+++A
Sbjct: 262 GGPVGLATLAT 272
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.1 bits (59), Expect = 1.9
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 20/73 (27%)
Query: 12 PSE-STGGPVGLSSIAAPAELPE-IKLFGRW---SCDDV-QVSDMSLQ-----------D 54
P E T P LS IA + + + + W +CD + + + SL D
Sbjct: 319 PREVLTTNPRRLSIIA--ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 55 YIAVKEKNAKFLP 67
++V +A +P
Sbjct: 377 RLSVFPPSAH-IP 388
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 25.8 bits (56), Expect = 5.5
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 50 MSLQDYIAVKEK-----NAKFLPHSAGRYAA 75
M + +K K +A F HS G YAA
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFAGHSLGEYAA 1769
>1fui_A L-fucose isomerase; ketol isomerase, fucose metabolism, L-fucose to
L conversion; HET: FOC; 2.50A {Escherichia coli} SCOP:
b.43.2.1 c.85.1.1
Length = 591
Score = 24.8 bits (53), Expect = 9.7
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 10 AYPSESTGGPVGLSSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFL 66
+ G V L++ A I F + D D S+ V+EK +F
Sbjct: 109 GFNGTERPGAVYLAAALAAHSQKGIPAFSIYGHDVQDADDTSIPA--DVEEKLLRFA 163
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
0.319 0.133 0.397
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,933,528
Number of extensions: 102581
Number of successful extensions: 166
Number of sequences better than 10.0: 1
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 21
Length of query: 124
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,412,271
Effective search space: 185315382
Effective search space used: 185315382
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 (21.8 bits)
S2: 51 (23.5 bits)