RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 034020
(106 letters)
>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 = 121 bits (307), Expect = 4e-38
Identities = 37/77 (48%), Positives = 56/77 (72%)
Query: 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSR 61
+++ G VVS+KM+KS+VVA++R H +Y +++KRT+K HDENN+C IGD V + R
Sbjct: 3 RTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECR 62
Query: 62 PLSKHKHWAVAEILKKA 78
PLSK K W + +++KA
Sbjct: 63 PLSKTKSWTLVRVVEKA 79
>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 = 120 bits (303), Expect = 2e-37
Identities = 36/91 (39%), Positives = 55/91 (60%), Gaps = 4/91 (4%)
Query: 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSR 61
K VG VVS+KM K++ V V+ H +Y + VK + K+ AHDE+N+ +GD V++ +R
Sbjct: 3 KVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETR 62
Query: 62 PLSKHKHWAVAEILKKARIYVPPSADNAAAA 92
PLS K + + EI++KA + A AA
Sbjct: 63 PLSATKRFRLVEIVEKA----VRAGAGAGAA 89
>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 = 119 bits (301), Expect = 6e-37
Identities = 35/100 (35%), Positives = 57/100 (57%), Gaps = 4/100 (4%)
Query: 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSR 61
K + G+VVS+KMQK+V V V+R F H +Y + +KR+ K++AHD + +GD V + SR
Sbjct: 4 KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 63
Query: 62 PLSKHKHWAVAEILKKARIYVPPSADNAAAAAVSNTQTEA 101
P+SK K + V +++ R+ N Q+ +
Sbjct: 64 PISKRKRFRVLRLVESGRM----DLVEKYLIRRQNYQSLS 99
>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 = 119 bits (301), Expect = 1e-36
Identities = 32/77 (41%), Positives = 45/77 (58%)
Query: 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSR 61
K++ G VV K+V V V RL H Y R V+ K+ AHD +NQ +GD VRL+ SR
Sbjct: 61 KTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKSR 120
Query: 62 PLSKHKHWAVAEILKKA 78
P+SK K + ++ +A
Sbjct: 121 PISKTKSFVALPVIARA 137
>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 = 105 bits (264), Expect = 1e-30
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 2 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH-DENNQCNIGDRVRLDPS 60
K + G VVS KM +++V+ L + YNRY KR H + +GD V +
Sbjct: 69 KILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQC 128
Query: 61 RPLSKHKHWAVAEILKKA 78
RP+SK + V ++ A
Sbjct: 129 RPISKTVRFNVVKVSAAA 146
>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_Q
Length = 157
Score = 104 bits (261), Expect = 3e-30
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 1 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH-DENNQCNIGDRVRLDP 59
K + GLV+S KM ++V++ D L + + YNRY KR H GD +
Sbjct: 67 GKIIKGLVISTKMNRTVIIRRDYLHYVRKYNRYEKRHRNIPVHISPCFSVKEGDILVAGQ 126
Query: 60 SRPLSKHKHWAVAEILKKARI 80
RP+SK + +++ I
Sbjct: 127 CRPISKTVRFNALQVVPNEII 147
>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 = 103 bits (258), Expect = 8e-30
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 6 GLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN--NQCNIGDRVRLDPSRPL 63
G+V KMQ+++V+ D L + + YNR+ KR H IGD V + RPL
Sbjct: 75 GVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPL 134
Query: 64 SKHKHWAVAEILKKA 78
SK + V ++ K A
Sbjct: 135 SKTVRFNVLKVTKAA 149
>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 = 102 bits (256), Expect = 2e-29
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 1 MKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH-DENNQCNIGDRVRLDP 59
+ + G S KM ++++V + L K Y RY KR S AH + GD V +
Sbjct: 69 GRIIAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQ 128
Query: 60 SRPLSKHKHWAVAEILKKA 78
RPLSK + V +++
Sbjct: 129 CRPLSKTVRFNVLKVIPAG 147
>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 = 36.5 bits (83), Expect = 4e-04
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 8/30 (26%)
Query: 75 LKKA----RIYVPPSADNAAAAAVSNTQTE 100
LKK ++Y D+A A A+ E
Sbjct: 22 LKKLQASLKLYAD---DSAPALAI-KATME 47
>1pc3_A Phosphate-binding protein 1; phosphate transport receptor,
immonodominant antigen, mycoba tuberculosis, ION-dipole
interactions; 2.16A {Mycobacterium tuberculosis} SCOP:
c.94.1.1
Length = 350
Score = 27.1 bits (60), Expect = 1.0
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 64 SKHKHWAVAEILKKARIYVPPSADNAAAAA 93
+ + A++ + ++ P A + AAA
Sbjct: 232 ASQRGLGEAQLGNSSGNFLLPDAQSIQAAA 261
>1ixh_A Phosphate-binding protein; phosphate transport, ultra high
resolution, phosphate bindin protein; 0.98A {Escherichia
coli} SCOP: c.94.1.1 PDB: 2abh_A 1a54_A* 1a55_A 1ixi_A
1quk_A 1ixg_A 1oib_A 1pbp_A 1qul_A 1qui_A 1quj_A 1a40_A
2z22_X
Length = 321
Score = 27.1 bits (60), Expect = 1.1
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 65 KHKHWAVAEILKKARIYVPPSADNAAAAA 93
K + A +++ V P+ +N A AA
Sbjct: 200 KQNNLAYTKLISADGKPVSPTEENFANAA 228
>3nfk_A Tyrosine-protein phosphatase non-receptor type 4; PDZ-PDZ-binding
site complex, protein binding; 1.43A {Homo sapiens}
PDB: 3nfl_A 2vph_A
Length = 107
Score = 24.4 bits (53), Expect = 7.2
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 42 AHDENNQCNIGDRVRLDPSRPLSKHKHWAVAEILKKAR 79
A + N GD+V L R +++H H V +K +
Sbjct: 56 ADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASC 93
>3lqc_A DNA repair protein XRCC1; allosteric disulfide, scaffolding
protein, DNA repair, DNA D nucleus, phosphoprotein,
polymorphism, DNA replication; HET: DNA; 2.35A {Homo
sapiens} PDB: 3k75_B* 1xna_A 1xnt_A 3k77_A*
Length = 189
Score = 24.6 bits (53), Expect = 7.2
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 53 DRVRLDPSRPLSKHKHWAVAEILKKARIYVPPSADNAAAAAVSNTQTE 100
DRV++ S+P SK + ++ + R + PP D A A + T T+
Sbjct: 126 DRVKIVCSQPYSKDSPFGLSFV----RFHSPPDKDEAEAPSQKVTVTK 169
>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ehrlich chaffeensis; 2.15A
{Ehrlichia chaffeensis}
Length = 223
Score = 24.1 bits (53), Expect = 9.6
Identities = 6/64 (9%), Positives = 19/64 (29%), Gaps = 18/64 (28%)
Query: 22 DRL------FHHKVYNRYVKRTSKFMAHDENNQCNIGDRVRLDPSRPLSK--HKHWAVAE 73
+ F+++V + + A ++C + ++ E
Sbjct: 166 NGYEFADMEFYYRVRDGFYDI-----AKKNPHRC-----HVITDKSETYDIDDINFVHLE 215
Query: 74 ILKK 77
++K
Sbjct: 216 VIKV 219
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
0.316 0.126 0.355
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: 1,605,834
Number of extensions: 83665
Number of successful extensions: 213
Number of sequences better than 10.0: 1
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 15
Length of query: 106
Length of database: 6,701,793
Length adjustment: 71
Effective length of query: 35
Effective length of database: 4,719,402
Effective search space: 165179070
Effective search space used: 165179070
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 (23.6 bits)