RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10000
(193 letters)
>2zkq_q 40S ribosomal protein S11E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 3jyv_Q* 1s1h_Q
Length = 158
Score = 205 bits (523), Expect = 1e-68
Identities = 121/153 (79%), Positives = 135/153 (88%), Gaps = 5/153 (3%)
Query: 46 TERAFQKQPTIFLARKP-----TYKKKSLRYHKTVGLGFKTPREAIDGTYIDKKCPFTGN 100
TERA+QKQPTIF +K T K+K RY+K +GLGFKTP+EAI+GTYIDKKCPFTGN
Sbjct: 6 TERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGN 65
Query: 101 VSIRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDV 160
VSIRGRIL G+V KMKMQRTIVIRRDYLHYI+KYNRFEKRH+NMSVHLSP FRDV+IGD+
Sbjct: 66 VSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDI 125
Query: 161 VTVGECRPLSKTVRFNVLKVTKGTGSKKAFKKF 193
VTVGECRPLSKTVRFNVLKVTK G+KK F+KF
Sbjct: 126 VTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF 158
>3u5c_L RP41, S18, YS12, 40S ribosomal protein S11-A; translation,
ribosome, ribosomal, ribosomal R ribosomal protein,
eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_P 3o30_F 3o2z_F 3u5g_L 3jyv_Q*
1s1h_Q
Length = 156
Score = 190 bits (483), Expect = 2e-62
Identities = 97/149 (65%), Positives = 118/149 (79%), Gaps = 2/149 (1%)
Query: 46 TERAFQKQPTIFLARKPTYKKKSLRYHKTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRG 105
+ERAFQKQP IF K K++ R++K GLGFKTP+ AI+G+YIDKKCPFTG VSIRG
Sbjct: 9 SERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFTGLVSIRG 68
Query: 106 RILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGE 165
+IL G V KM RTIVIRR YLHYI KYNR+EKRH+N+ VH+SPAF V++GD+VTVG+
Sbjct: 69 KILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAF-RVQVGDIVTVGQ 127
Query: 166 CRPLSKTVRFNVLKVTKGTG-SKKAFKKF 193
CRP+SKTVRFNV+KV+ G + K F KF
Sbjct: 128 CRPISKTVRFNVVKVSAAAGKANKQFAKF 156
>3iz6_P 40S ribosomal protein S11 (S17P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 161
Score = 186 bits (474), Expect = 4e-61
Identities = 93/193 (48%), Positives = 115/193 (59%), Gaps = 37/193 (19%)
Query: 1 MAEQNERSFQKQPTVFLNRKKGLSKKRKELRYFRDVGLGFKSPRETERAFQKQPTIFLAR 60
MAEQ E++F KQP VFL+ KK K+
Sbjct: 1 MAEQTEKAFLKQPKVFLSSKKSGKGKKP-------------------------------- 28
Query: 61 KPTYKKKSLRYHKTVGLGFKTPREAIDGTYIDKKCPFTGNVSIRGRILIGIVRKMKMQRT 120
K R+ K++GLGFKTPREAI+GTYIDKKCPFTG VSIRGRI+ G KM RT
Sbjct: 29 ----GKGGNRFWKSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRIIAGTCHSAKMNRT 84
Query: 121 IVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVRFNVLKV 180
I++RR+YLH++KKY R+EKRH N+ H+SP F V+ GD V +G+CRPLSKTVRFNVLKV
Sbjct: 85 IIVRRNYLHFVKKYQRYEKRHSNIPAHVSPCF-RVKEGDHVIIGQCRPLSKTVRFNVLKV 143
Query: 181 TKGTGSKKAFKKF 193
+ + K
Sbjct: 144 IPAGSTGGSGGKK 156
>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_Q
Length = 157
Score = 185 bits (472), Expect = 7e-61
Identities = 87/154 (56%), Positives = 115/154 (74%), Gaps = 7/154 (4%)
Query: 46 TERAFQKQPTIFLARKPTYKKKS---LRYHKTVGLGFKTPREAIDGTYIDKKCPFTGNVS 102
+RA+QKQ +FL K KK+ +RY+K +GLGFKTP+EAI+GTY+DKKCPFT N+S
Sbjct: 5 IQRAYQKQDGVFLNSKKLLAKKTSAGVRYYKNIGLGFKTPKEAIEGTYVDKKCPFTSNLS 64
Query: 103 IRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVT 162
IRG+I+ G+V KM RT++IRRDYLHY++KYNR+EKRHRN+ VH+SP F V+ GD++
Sbjct: 65 IRGKIIKGLVISTKMNRTVIIRRDYLHYVRKYNRYEKRHRNIPVHISPCF-SVKEGDILV 123
Query: 163 VGECRPLSKTVRFNVLKVTKGT---GSKKAFKKF 193
G+CRP+SKTVRFN L+V +K F F
Sbjct: 124 AGQCRPISKTVRFNALQVVPNEIIGSVRKQFLLF 157
>3r8n_Q 30S ribosomal protein S17; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_Q 3fih_Q* 3iy8_Q 2wwl_Q
3oar_Q 3oaq_Q 3ofb_Q 3ofa_Q 3ofp_Q 3ofx_Q 3ofy_Q 3ofo_Q
3r8o_Q 4a2i_Q 3i1m_Q 1vs7_Q* 3e1a_J 3e1c_J 1vs5_Q 3i1o_Q
...
Length = 80
Score = 47.5 bits (114), Expect = 5e-08
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 104 RGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTV 163
+ R L G V KM+++IV+ + Y +F KR + VH + IGDVV +
Sbjct: 1 KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVH--DENNECGIGDVVEI 58
Query: 164 GECRPLSKTVRFNVLKV 180
ECRPLSKT + +++V
Sbjct: 59 RECRPLSKTKSWTLVRV 75
>1qd7_I S17 ribosomal protein; 30S ribosomal subunit, low resolution model,
ribosome; 5.50A {Thermus thermophilus} SCOP: i.1.1.3
PDB: 1eg0_G 1rip_A
Length = 89
Score = 47.2 bits (113), Expect = 7e-08
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 104 RGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTV 163
+ ++ +G V KM +TI + + Y + K + H + ++GD+V +
Sbjct: 1 QRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAH--DEHNEAKVGDIVKI 58
Query: 164 GECRPLSKTVRFNVLKV 180
E RPLS T RF ++++
Sbjct: 59 METRPLSATKRFRLVEI 75
>3bbn_Q Ribosomal protein S17; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 142
Score = 47.9 bits (114), Expect = 1e-07
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 106 RILIGIVRKMKMQRTIVIR--RDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTV 163
+ + G V +T+ + R H KY R + + H ++GDVV +
Sbjct: 61 KTMQGRVVCATSDKTVAVEVVRLAPH--PKYKRRVRMKKKYQAH--DPDNQFKVGDVVRL 116
Query: 164 GECRPLSKTVRFNVLKV 180
+ RP+SKT F L V
Sbjct: 117 EKSRPISKTKSFVALPV 133
>2vqe_Q 30S ribosomal protein S17; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: b.40.4.5 PDB: 1gix_T*
1hnw_Q* 1hnx_Q* 1hnz_Q* 1hr0_Q 1ibk_Q* 1ibl_Q* 1ibm_Q
1jgo_T* 1jgp_T* 1jgq_T* 1ml5_T* 1xmo_Q* 1xmq_Q* 1xnq_Q*
1xnr_Q* 1yl4_T 2b64_Q* 2b9m_Q* 2b9o_Q* ...
Length = 105
Score = 45.8 bits (109), Expect = 4e-07
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 106 RILIGIVRKMKMQRTIV--IRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTV 163
++L G+V KMQ+T+ + R + H Y + KR + H ++GDVV +
Sbjct: 4 KVLTGVVVSDKMQKTVTVLVERQFPH--PLYGKVIKRSKKYLAH--DPEEKYKLGDVVEI 59
Query: 164 GECRPLSKTVRFNVLKV 180
E RP+SK RF VL++
Sbjct: 60 IESRPISKRKRFRVLRL 76
>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 = 33.5 bits (76), Expect = 0.040
Identities = 38/213 (17%), Positives = 64/213 (30%), Gaps = 68/213 (31%)
Query: 17 LNRKKGLSKKRKELRYFRDVG-----LGFKSPRE----TERAFQKQPTIFLARKPTY--- 64
+ + + K K + F+++ F+S + T+ QP + L K +
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFT---QPALTLMEKAAFEDL 1747
Query: 65 KKKSLRYHKTV--G--LG-------------FKTPREAID-----GTYIDKKCPFTGNVS 102
K K L G LG + ++ G + P
Sbjct: 1748 KSKGLIPADATFAGHSLGEYAALASLADVMSIE---SLVEVVFYRGMTMQVAVP----RD 1800
Query: 103 IRGRILIGIVRKMKMQRTIVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEI----- 157
GR G++ + ++ L Y+ + R KR + VEI
Sbjct: 1801 ELGRSNYGMIAINPGRVAASFSQEALQYVVE--RVGKRTGWL----------VEIVNYNV 1848
Query: 158 -GD-VVTVGECRPLSKTVRFNVLKVTKGTGSKK 188
V G+ R L NVL K +K
Sbjct: 1849 ENQQYVAAGDLRALDTVT--NVLNFIK---LQK 1876
>1ixd_A Cylindromatosis tumour-suppressor CYLD; structural genomics, riken
structural genomics/proteomics initiative, RSGI,
antitumor protein; NMR {Homo sapiens} SCOP: b.34.10.1
Length = 104
Score = 26.6 bits (59), Expect = 2.5
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 153 RDVEIGDVVTVGECRPLSKTVRF 175
+E+G + V E P +R+
Sbjct: 16 HGLEVGSLAEVKENPPFYGVIRW 38
>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial;
mitochondrion, DNA binding protein, transcription
factor, transcription termination; 1.60A {Homo sapiens}
PDB: 3opg_A 3my3_A
Length = 270
Score = 27.1 bits (60), Expect = 3.6
Identities = 11/80 (13%), Positives = 23/80 (28%), Gaps = 6/80 (7%)
Query: 7 RSFQKQPTVFLNRKKGLSKKRKELRYFRDVGLGFKSPRETERAFQKQPTIFLARKPTYKK 66
K +F L + + Y S + + +K P +
Sbjct: 60 AFLTKNHAIFSED---LENLKTRVAYLHSKNF---SKADVAQMVRKAPFLLNFSVERLDN 113
Query: 67 KSLRYHKTVGLGFKTPREAI 86
+ + K + L K R+ +
Sbjct: 114 RLGFFQKELELSVKKTRDLV 133
>3ddj_A CBS domain-containing protein; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2; HET: AMP; 1.80A {Sulfolobus solfataricus} SCOP:
d.37.1.1 d.37.1.1
Length = 296
Score = 26.3 bits (58), Expect = 6.0
Identities = 8/54 (14%), Positives = 18/54 (33%)
Query: 121 IVIRRDYLHYIKKYNRFEKRHRNMSVHLSPAFRDVEIGDVVTVGECRPLSKTVR 174
++ RD L ++ Y + ++ + D + VTV +
Sbjct: 64 LLTTRDLLSTVESYCKDSCSQGDLYHISTTPIIDYMTPNPVTVYNTSDEFTAIN 117
>3ixc_A Hexapeptide transferase family protein; niaid, ssgcid, seattle
structural genomics center for infect disease,
GRAM-negative bacteria; 1.61A {Anaplasma
phagocytophilum}
Length = 191
Score = 26.1 bits (58), Expect = 6.5
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 146 VHLSPAFRDVEIGDVVTVG 164
VH D IG VT+G
Sbjct: 87 VHTDSMHGDTVIGKFVTIG 105
>2ky8_A Methyl-CPG-binding domain protein 2; DNA binding domain,
transcription-DNA complex; HET: DNA 5CM TED; NMR
{Gallus gallus}
Length = 72
Score = 24.5 bits (53), Expect = 8.7
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 19 RKKGLSKKRKELRYFRDVGLGFKSPRETERAFQKQPTI 56
RK GLS + ++ YF G F+S + R +
Sbjct: 24 RKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVDL 61
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 0.139 0.403
Gapped
Lambda K H
0.267 0.0633 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,957,049
Number of extensions: 175644
Number of successful extensions: 381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 19
Length of query: 193
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 105
Effective length of database: 4,244,745
Effective search space: 445698225
Effective search space used: 445698225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.2 bits)