RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 041275
(187 letters)
>2vqe_J 30S ribosomal protein S10, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
d.58.15.1 PDB: 1gix_M* 1hnw_J* 1hnx_J* 1hnz_J* 1hr0_J
1ibk_J* 1ibl_J* 1ibm_J 1jgo_M* 1jgp_M* 1jgq_M* 1ml5_M*
1xmo_J* 1xmq_J* 1xnq_J* 1xnr_J* 1yl4_M 2b64_J* 2b9m_J*
2b9o_J* ...
Length = 105
Score = 157 bits (398), Expect = 2e-50
Identities = 49/99 (49%), Positives = 72/99 (72%)
Query: 89 QKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHKDARF 148
KIRIKLR + ++ S ++I++AAR + A+ GP+PLPT+ R + V++ P HKD+R
Sbjct: 2 PKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSRE 61
Query: 149 HFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
HFE+RTH RL+DI+ P +TI+ LM LDLP GV++E+K
Sbjct: 62 HFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT 100
>3bbn_J Ribosomal protein S10; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 197
Score = 155 bits (392), Expect = 2e-48
Identities = 125/197 (63%), Positives = 139/197 (70%), Gaps = 10/197 (5%)
Query: 1 MATFSLSAAISPSLTVPISSNSKCPVFSVSFPSKNYAGNTLKL------EPLSTTNTRVF 54
MAT SLS + L + SS+ + + N + S++N RVF
Sbjct: 1 MATSSLSTIVFSPLALSNSSSFPNKPQVSNLSLHSSLSNLRRTLSHSSPSSSSSSNVRVF 60
Query: 55 SAPETLAGSESSAVEAEVPE----TLSVSSGADQMAPKQKIRIKLRSYWVPLIEDSCKQI 110
+APE L E+ L + + +DQMAPKQKIRIKLRSYWVPLIEDSCKQI
Sbjct: 61 AAPEVLESQETGPESYVEEGSETSALGIGADSDQMAPKQKIRIKLRSYWVPLIEDSCKQI 120
Query: 111 MDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHKDARFHFEIRTHQRLIDILYPTAQTID 170
MDAARTTNAKTMGPVPLPTKKRI+CVLKSPHVHKDARFHFEIRTHQRLIDILYPTAQTID
Sbjct: 121 MDAARTTNAKTMGPVPLPTKKRIFCVLKSPHVHKDARFHFEIRTHQRLIDILYPTAQTID 180
Query: 171 SLMQLDLPAGVDVEVKL 187
SLMQLDLPAGVDVEVKL
Sbjct: 181 SLMQLDLPAGVDVEVKL 197
>3r8n_J 30S ribosomal protein S10; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_J 3fih_J* 2wwl_J 3oar_J
3oaq_J 3ofb_J 3ofa_J 3ofp_J 3ofx_J 3ofy_J 3ofo_J 3r8o_J
4a2i_J 3i1m_J 1p6g_J 1p87_J* 1vs7_J* 2avy_J 2aw7_J
1vs5_J ...
Length = 98
Score = 151 bits (383), Expect = 3e-48
Identities = 51/98 (52%), Positives = 76/98 (77%)
Query: 90 KIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHKDARFH 149
+IRI+L+++ LI+ + +I++ A+ T A+ GP+PLPT+K + VL SPHV+KDAR
Sbjct: 1 RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQ 60
Query: 150 FEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
+EIRTH RL+DI+ PT +T+D+LM+LDL AGVDV++ L
Sbjct: 61 YEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL 98
>2zkq_j 40S ribosomal protein S20E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 119
Score = 136 bits (343), Expect = 6e-42
Identities = 32/107 (29%), Positives = 52/107 (48%), Gaps = 2/107 (1%)
Query: 82 ADQMAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSP- 140
+ +IRI L S V +E C ++ A+ N K GPV +PTK K+P
Sbjct: 11 VEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPC 70
Query: 141 HVHKDARFHFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
F++R H+RLID+ P+ + + + + + GV+VEV +
Sbjct: 71 GEGSKTWDRFQMRIHKRLIDLHSPS-EIVKQITSISIEPGVEVEVTI 116
>3iz6_J 40S ribosomal protein S20 (S10P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 128
Score = 132 bits (334), Expect = 2e-40
Identities = 31/107 (28%), Positives = 51/107 (47%), Gaps = 2/107 (1%)
Query: 82 ADQMAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPH 141
+ +IRI L S V +E C ++ A+ + K GPV +PTK KSP
Sbjct: 20 ESSQEVQHRIRITLSSKSVKNLEKVCGDLVKGAKDKSLKVKGPVRMPTKVLHITTRKSPC 79
Query: 142 -VHKDARFHFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
+ FE+R H+R+ID++ + + + + GV+VEV +
Sbjct: 80 GEGTNTWDRFEMRVHKRVIDLVSSA-DVVKQITSITIEPGVEVEVTI 125
>3u5c_U 40S ribosomal protein S20; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_J 3o30_N 3o2z_N 3u5g_U 1s1h_J 3jyv_J*
Length = 121
Score = 131 bits (332), Expect = 3e-40
Identities = 36/106 (33%), Positives = 50/106 (47%), Gaps = 2/106 (1%)
Query: 83 DQMAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHV 142
Q KIRI L S V +E+ I+ A N GPV LPTK K+P+
Sbjct: 14 QQQQQIIKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLKISTRKTPNG 73
Query: 143 H-KDARFHFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
+E+R H+R ID+ P Q + + Q+ + GVDVEV +
Sbjct: 74 EGSKTWETYEMRIHKRYIDLEAPV-QIVKRITQITIEPGVDVEVVV 118
>2xzm_J Ribosomal protein S10 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_J
Length = 120
Score = 127 bits (320), Expect = 2e-38
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 3/108 (2%)
Query: 82 ADQMAPKQKIRIKLRSYWVPLIEDSCKQIMD-AARTTNAKTMGPVPLPTKKRIYCVLKSP 140
++ K ++RI L + +E + +I+ A +T + GPV +PTK + V KSP
Sbjct: 10 GEEEVKKVRVRITLTCKNLKSVEKATSEIVSRAKKTEQVEVKGPVRMPTKTLVITVRKSP 69
Query: 141 HVH-KDARFHFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
FE+R ++R+ID+ + ++ + GV++E+ +
Sbjct: 70 CGEGSKTWDRFEMRIYKRIIDLTCNV-PDVKTITNFRIDPGVEIELTM 116
>3d3c_J 30S ribosomal protein S10, N utilization substance protein B; NUSB,
NUSE, phage lambda, lambda N antitermination
antitermination; 2.60A {Escherichia coli} PDB: 2kvq_E
3d3b_J* 3imq_J
Length = 87
Score = 114 bits (288), Expect = 6e-34
Identities = 39/101 (38%), Positives = 60/101 (59%), Gaps = 21/101 (20%)
Query: 87 PKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHKDA 146
Q+IRI+L+++ LI+ + +I++ A+ T A+ GP+PLPT+
Sbjct: 7 QNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRS--------------- 51
Query: 147 RFHFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
RTH RL+DI+ PT +T+D LM+LDL AGVDV++ L
Sbjct: 52 ------RTHLRLVDIVEPTEKTVDDLMRLDLAAGVDVQISL 86
>3r2c_J Protein NUSE, 30S ribosomal protein S10; cross species
NUSB-NUSE-RNA interaction; HET: PEG; 1.90A {Aquifex
aeolicus} PDB: 3r2d_J
Length = 83
Score = 113 bits (285), Expect = 1e-33
Identities = 41/103 (39%), Positives = 60/103 (58%), Gaps = 22/103 (21%)
Query: 85 MAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHK 144
M ++KIRIKLR+Y L++ S KQI++ + T GP+PLPT+K +
Sbjct: 1 ME-QEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKSEFS--------- 50
Query: 145 DARFHFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 187
R++DI+ T QTI++LM++ LPAGVDVEVK+
Sbjct: 51 ------------RILDIIRFTPQTIEALMEISLPAGVDVEVKM 81
>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 = 36.4 bits (83), Expect = 0.004
Identities = 24/154 (15%), Positives = 45/154 (29%), Gaps = 56/154 (36%)
Query: 34 KNYAGNTLK------LEPLSTTNTR-------VFSAPETLAGSESSAVEAEVPE-TLSVS 79
K+ + L L L R VF P A +P LS+
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF--PP----------SAHIPTILLSL- 394
Query: 80 SGADQMAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKS 139
W +I+ +++ ++ V K+ +
Sbjct: 395 ------------------IWFDVIKSDVMVVVNKLHK---YSL--VEKQPKESTISI--- 428
Query: 140 PHVHKDARFHFEIRT--HQRLIDILYPTAQTIDS 171
P ++ + + E H+ ++D Y +T DS
Sbjct: 429 PSIYLELKVKLENEYALHRSIVD-HYNIPKTFDS 461
Score = 32.1 bits (72), Expect = 0.11
Identities = 9/84 (10%), Positives = 27/84 (32%), Gaps = 25/84 (29%)
Query: 101 PLIED-SCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHKDARFHFEIRTHQRLI 159
+++ CK + D + + +K+ I ++ S RL
Sbjct: 28 AFVDNFDCKDVQDMPK----------SILSKEEIDHIIMSKDAVSGTL---------RLF 68
Query: 160 DIL--YPT---AQTIDSLMQLDLP 178
L + ++ +++++
Sbjct: 69 WTLLSKQEEMVQKFVEEVLRINYK 92
>1o0s_A NAD-ME, NAD-dependent malic enzyme; oxidoreductase, oxidative
decarboxylase, rossmann fold, MAla dehydrogenase; HET:
NAI; 2.00A {Ascaris suum} SCOP: c.2.1.7 c.58.1.3 PDB:
1llq_A*
Length = 605
Score = 28.6 bits (64), Expect = 1.3
Identities = 17/60 (28%), Positives = 24/60 (40%)
Query: 111 MDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHKDARFHFEIRTHQRLIDILYPTAQTID 170
MD K P + KKR +LK P ++K F R + L +L P T +
Sbjct: 17 MDEKEMALYKLYRPERVTPKKRSAELLKEPRLNKGMGFSLYERQYLGLHGLLPPAFMTQE 76
>3evp_A Circular-permutated green fluorescent protein; EGFP, chromophore,
luminescence, photoprotein, signaling protein; HET: CRO;
1.45A {Aequorea victoria}
Length = 243
Score = 26.9 bits (59), Expect = 3.7
Identities = 20/87 (22%), Positives = 26/87 (29%)
Query: 85 MAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTKKRIYCVLKSPHVHK 144
MA KQK IK IED Q+ + GPV LP + K
Sbjct: 9 MADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPN 68
Query: 145 DARFHFEIRTHQRLIDILYPTAQTIDS 171
+ R H + I +
Sbjct: 69 EKRDHMVLLEFVTAAGITLGMDELYKG 95
>1cb8_A Protein (chondroitinase AC); lyase, chondroitin degradation; HET:
MAN RAM GCU MFU; 1.90A {Pedobacter heparinus} SCOP:
a.102.3.2 b.24.1.1 b.30.5.2 PDB: 1hm2_A* 1hm3_A* 1hmu_A*
1hmw_A*
Length = 678
Score = 27.0 bits (59), Expect = 5.1
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 13 SLTVPISSNSKCPVFSVSFPSKNYAGNTLKLE 44
L++ K + FP + +AG T++L+
Sbjct: 647 VLSIRDLKTGKTNRVKIDFPQQEFAGATVELK 678
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
0.315 0.128 0.365
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,613,346
Number of extensions: 140369
Number of successful extensions: 229
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 14
Length of query: 187
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 99
Effective length of database: 4,244,745
Effective search space: 420229755
Effective search space used: 420229755
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 (21.6 bits)
S2: 54 (24.9 bits)