RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 041511
(147 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 = 129 bits (327), Expect = 1e-40
Identities = 38/79 (48%), Positives = 58/79 (73%)
Query: 41 QMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDP 100
+++++ G VVS+KM+KS+VVA++R H +Y +++KRT+K HDENNEC IGD V +
Sbjct: 1 KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRE 60
Query: 101 SRPLSKHKHWLVAEILKKA 119
RPLSK K W + +++KA
Sbjct: 61 CRPLSKTKSWTLVRVVEKA 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 = 127 bits (322), Expect = 1e-39
Identities = 38/93 (40%), Positives = 56/93 (60%), Gaps = 4/93 (4%)
Query: 41 QMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDP 100
Q K VG VVS+KM K++ V V+ H +Y + VK + K+ AHDE+NE +GD V++
Sbjct: 1 QRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIME 60
Query: 101 SRPLSKHKHWLVAEILKKARIYVPPSADNAAAA 133
+RPLS K + + EI++KA + A AA
Sbjct: 61 TRPLSATKRFRLVEIVEKA----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 = 127 bits (320), Expect = 4e-39
Identities = 33/79 (41%), Positives = 53/79 (67%)
Query: 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSR 102
K + G+VVS+KMQK+V V V+R F H +Y + +KR+ K++AHD + +GD V + SR
Sbjct: 4 KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 63
Query: 103 PLSKHKHWLVAEILKKARI 121
P+SK K + V +++ R+
Sbjct: 64 PISKRKRFRVLRLVESGRM 82
>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 = 124 bits (313), Expect = 1e-37
Identities = 31/77 (40%), Positives = 46/77 (59%)
Query: 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDENNECNIGDRVRLDPSR 102
K++ G VV K+V V V RL H Y R V+ K+ AHD +N+ +GD VRL+ SR
Sbjct: 61 KTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKSR 120
Query: 103 PLSKHKHWLVAEILKKA 119
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 = 111 bits (280), Expect = 2e-32
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH-DENNECNIGDRVRLDPS 101
K + G VVS KM +++V+ L + YNRY KR H +GD V +
Sbjct: 69 KILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQC 128
Query: 102 RPLSKHKHWLVAEILKKA 119
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 = 110 bits (276), Expect = 6e-32
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH-DENNECNIGDRVR 97
+ K + GLV+S KM ++V++ D L + + YNRY KR H GD +
Sbjct: 64 SIRGKIIKGLVISTKMNRTVIIRRDYLHYVRKYNRYEKRHRNIPVHISPCFSVKEGDILV 123
Query: 98 LDPSRPLSKHKHWLVAEILKKARI 121
RP+SK + +++ I
Sbjct: 124 AGQCRPISKTVRFNALQVVPNEII 147
>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 = 108 bits (272), Expect = 3e-31
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 39 PSQMKSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAH-DENNECNIGDRVR 97
+ + + G S KM ++++V + L K Y RY KR S AH GD V
Sbjct: 66 SIRGRIIAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHVI 125
Query: 98 LDPSRPLSKHKHWLVAEILKKA 119
+ RPLSK + V +++
Sbjct: 126 IGQCRPLSKTVRFNVLKVIPAG 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 = 107 bits (270), Expect = 5e-31
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 43 KSVVGLVVSNKMQKSVVVAVDRLFHHKVYNRYVKRTSKFMAHDEN--NECNIGDRVRLDP 100
+ + G+V KMQ+++V+ D L + + YNR+ KR H + IGD V +
Sbjct: 71 RILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGE 130
Query: 101 SRPLSKHKHWLVAEILKKA 119
RPLSK + V ++ K A
Sbjct: 131 CRPLSKTVRFNVLKVTKAA 149
>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 = 36.6 bits (84), Expect = 0.002
Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 29/85 (34%)
Query: 14 FLSCAVD-LRQLLW--------------PPSVSSLSIQIG---PSQMKSVVGLVVSNKMQ 55
F + L + PPS+ S++ PS M S+ L Q
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL-----TQ 346
Query: 56 KSVVVAVDRLFHHKVYNRYVKRTSK 80
+ V V++ N ++ +
Sbjct: 347 EQVQDYVNKT------NSHLPAGKQ 365
>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 = 31.7 bits (71), Expect = 0.075
Identities = 22/178 (12%), Positives = 45/178 (25%), Gaps = 71/178 (39%)
Query: 11 HHRFLSCAV--------DLRQLLWPPSVSSLSIQIGPSQMKSVVGLVVSNK------MQK 56
HH + D+ + V + + KS++ S + M K
Sbjct: 3 HHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL----SKEEIDHIIMSK 58
Query: 57 SVVVAVDRLF------HHKVYNRYV----KRTSKFMA---HDENNE-------------- 89
V RLF ++ ++V + KF+ E +
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR 118
Query: 90 -CNIGDRV-------------------RLDPSRPLSKH------KHWLVAEILKKARI 121
N L P++ + K W+ ++ ++
Sbjct: 119 LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKV 176
>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 = 29.5 bits (65), Expect = 0.25
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 8/30 (26%)
Query: 116 LKKA----RIYVPPSADNAAAAAVSNPETE 141
LKK ++Y S A A A+ E
Sbjct: 22 LKKLQASLKLYADDS---APALAI-KATME 47
>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 = 27.5 bits (61), Expect = 1.8
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 106 KHKHWLVAEILKKARIYVPPSADNAAAAA 134
K + +++ V P+ +N A AA
Sbjct: 200 KQNNLAYTKLISADGKPVSPTEENFANAA 228
>2p4q_A 6-phosphogluconate dehydrogenase, decarboxylating; rossmann fold,
oxidoreductase; HET: FLC; 2.37A {Saccharomyces
cerevisiae}
Length = 497
Score = 26.4 bits (59), Expect = 4.3
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 39 PSQMKS---VVGLVVSNKMQKSVVV-AVDRLFHHKVYNRYVKRTSKFMAHDENNECNIG 93
M + ++GL V M +++++ A D F YNR + F+A++ + IG
Sbjct: 6 HHHMSADFGLIGLAV---MGQNLILNAADHGFTVCAYNRTQSKVDHFLANEAKGKSIIG 61
>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 = 25.9 bits (57), Expect = 5.4
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 112 VAEILKKARIYVPPSADNAAAAA 134
A++ + ++ P A + AAA
Sbjct: 239 EAQLGNSSGNFLLPDAQSIQAAA 261
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 0.129 0.384
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: 2,293,689
Number of extensions: 120256
Number of successful extensions: 274
Number of sequences better than 10.0: 1
Number of HSP's gapped: 268
Number of HSP's successfully gapped: 17
Length of query: 147
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 62
Effective length of database: 4,328,508
Effective search space: 268367496
Effective search space used: 268367496
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: 53 (24.4 bits)