RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 043596
(96 letters)
>3iz5_I 60S ribosomal protein L10 (L10E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_I 1s1i_I 3jyw_I
Length = 224
Score = 115 bits (288), Expect = 6e-34
Identities = 53/81 (65%), Positives = 63/81 (77%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKL 75
+SN+ HA+EALRRAKFKFP RQKII SRKWGFTKF+R Y++ K+E RI+ DGVNA+L
Sbjct: 140 CKESNAKHAEEALRRAKFKFPGRQKIIHSRKWGFTKFTREEYVKLKAEGRIMSDGVNAQL 199
Query: 76 FECHGPLANRQPGRAFLEATI 96
HG LA R PG+AFL TI
Sbjct: 200 LGSHGRLAKRAPGKAFLAETI 220
>4a17_H RPL10, 60S ribosomal protein L10; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_H 4a1c_H 4a1e_H
Length = 215
Score = 109 bits (274), Expect = 8e-32
Identities = 32/75 (42%), Positives = 48/75 (64%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKL 75
+ + +A +AL RAK KFP RQK++ S+KWGFTK +RA Y R +++ ++V DG N K+
Sbjct: 140 VKEPHVKYAIDALTRAKAKFPGRQKVVTSQKWGFTKLTRAQYSRLRNQKKLVTDGSNVKV 199
Query: 76 FECHGPLANRQPGRA 90
GPL+ + R
Sbjct: 200 IGERGPLSRLELFRK 214
>2zkr_h 60S ribosomal protein L10; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 214
Score = 106 bits (266), Expect = 1e-30
Identities = 34/75 (45%), Positives = 43/75 (57%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKL 75
N H EALRRAKFKFP RQKI +S+KWGFTKF+ + +E R++PDG K
Sbjct: 140 TKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRLIPDGCGVKY 199
Query: 76 FECHGPLANRQPGRA 90
GPL + +
Sbjct: 200 IPNRGPLDKWRALHS 214
>3j0l_J Ribosomal protein L10; mammalia, translation, elongation cycle,
tRNA, ribosome; 9.80A {Oryctolagus cuniculus} PDB:
3j0q_J 3izc_I 3izs_I 3o58_J 3o5h_J 3u5e_I 3u5i_I
Length = 219
Score = 103 bits (258), Expect = 2e-29
Identities = 30/69 (43%), Positives = 38/69 (55%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKL 75
DSN E LRRA++KFP +QKII+S+KWGFT R YL+ + + DG K
Sbjct: 138 TKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKF 197
Query: 76 FECHGPLAN 84
G L N
Sbjct: 198 LSKKGSLEN 206
>2pa2_A 60S ribosomal protein L10; QM protein, , structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 2.50A {Homo sapiens} SCOP: d.41.4.1
Length = 151
Score = 71.6 bits (175), Expect = 1e-17
Identities = 25/42 (59%), Positives = 29/42 (69%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANY 57
N H EALRRAKFKFP RQKI +S+KWGFTKF+ +
Sbjct: 109 TKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEF 150
>1ffk_F Ribosomal protein L10E; ribosome assembly, RNA-RNA, protein-RNA,
protein-protein; 2.40A {Haloarcula marismortui} SCOP:
d.41.4.1 PDB: 1jj2_H 1k73_J* 1k8a_J* 1k9m_J* 1kc8_J*
1kd1_J* 1kqs_H* 1m1k_J* 1m90_J* 1n8r_J* 1nji_J* 1q7y_J*
1q81_J* 1q82_J* 1q86_J* 1qvf_H 1qvg_H 1w2b_H 3cxc_H*
1giy_P ...
Length = 157
Score = 51.1 bits (122), Expect = 1e-09
Identities = 7/27 (25%), Positives = 8/27 (29%)
Query: 20 NSHHAQEALRRAKFKFPVRQKIIVSRK 46
+ A RRA K I S
Sbjct: 128 PDPAVEFAWRRAYMKVTPTVNIDSSPA 154
>1vq8_H 50S ribosomal protein L10E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: d.41.4.1 PDB: 1vq4_H*
1vq5_H* 1vq6_H* 1vq7_H* 1s72_H* 1vq9_H* 1vqk_H* 1vql_H*
1vqm_H* 1vqn_H* 1vqo_H* 1vqp_H* 2otj_H* 2otl_H* 2qa4_H*
2qex_H* 1yhq_H* 1yi2_H* 1yij_H* 1yit_H* ...
Length = 171
Score = 50.5 bits (120), Expect = 3e-09
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKIIVS 44
++ H +EA RRA K +I S
Sbjct: 138 CNVEDAEHVKEAFRRAYNKITPSCRIDSS 166
>2zjr_J 50S ribosomal protein L16; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.41.4.2 PDB: 1sm1_K* 2zjp_J* 2zjq_J
1nkw_K 3cf5_J* 3dll_J* 3pio_J* 1njm_K* 1nwx_K* 1njp_K*
1xbp_K* 1y69_K 1nwy_K* 3pip_J* 1pnu_K 1pny_K 1vor_N
1vou_N 1vow_N 1voy_N ...
Length = 142
Score = 31.1 bits (70), Expect = 0.025
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 22 HHAQEALRRAKFKFPVRQKIIVSRKW 47
A+EA R A K P++ K++ +
Sbjct: 113 EQAKEAFRLAGHKLPIQTKMVKREVY 138
>3r8s_M 50S ribosomal protein L16; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_K 1p86_K 1vs8_M 1vs6_M 2aw4_M 2awb_M 1vt2_M 2i2v_M
2j28_M 2i2t_M* 2qao_M* 2qba_M* 2qbc_M* 2qbe_M 2qbg_M
2qbi_M* 2qbk_M* 2qov_M 2qox_M 2qoz_M* ...
Length = 136
Score = 30.0 bits (67), Expect = 0.060
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 20 NSHHAQEALRRAKFKFPVRQKIIV 43
A+EA + A K P++ +
Sbjct: 109 PEELAREAFKLAAAKLPIKTTFVT 132
>3bbo_O Ribosomal protein L16; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 135
Score = 29.2 bits (65), Expect = 0.12
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 24 AQEALRRAKFKFPVRQKIIV 43
A+ A+ A K P+R + I+
Sbjct: 114 ARRAVAIAASKMPIRTQFII 133
>2ftc_I Mitochondrial ribosomal protein L16, 39S ribosomal protein L13,
mitochondrial; mitochondrial ribosome, large ribosomal
subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB:
3iy9_I
Length = 118
Score = 26.9 bits (59), Expect = 0.67
Identities = 6/25 (24%), Positives = 7/25 (28%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQK 40
G Q L + K P K
Sbjct: 94 GGRCEFEEVQGFLDQVAHKLPFAAK 118
>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 353
Score = 26.3 bits (58), Expect = 1.6
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 20/87 (22%)
Query: 15 DGTDSNSHHAQEALRRA--KFKFPVR--------QKII---VSR--KWGFTKFSRA---N 56
D DS + AQ ALRR + R +II S+ K+ F + +
Sbjct: 140 DEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAID 199
Query: 57 YLR--CKSENRIVPDGVNAKLFECHGP 81
LR + EN DGV ++ +
Sbjct: 200 RLRFISEQENVKCDDGVLERILDISAG 226
>2iv2_X Formate dehydrogenase H; oxidoreductase, 4Fe-4S, anaerobic,
complete proteome, direct protein sequencing, Fe4S4,
iron, iron sulfur cluster; HET: 2MD MGD; 2.27A
{Escherichia coli} SCOP: b.52.2.2 c.81.1.1 PDB: 1fdi_A*
1fdo_A* 1aa6_A*
Length = 715
Score = 25.2 bits (56), Expect = 4.5
Identities = 3/17 (17%), Positives = 7/17 (41%)
Query: 17 TDSNSHHAQEALRRAKF 33
TD+ ++A +
Sbjct: 408 TDAELSAVRKAFEDLEL 424
>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP,
replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP:
a.80.1.1 c.37.1.20
Length = 327
Score = 25.0 bits (55), Expect = 5.2
Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 20/84 (23%)
Query: 18 DSNSHHAQEALRRA--KFKFPVR--------QKII---VSR--KWGFTKFSRANYLR--- 59
D+ + AQ+ALRR F VR KII SR + F + +
Sbjct: 120 DALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLR 179
Query: 60 --CKSENRIVPDGVNAKLFECHGP 81
++E + + +
Sbjct: 180 YIAENEGLELTEEGLQAILYIAEG 203
>2chq_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATP ATP-binding,
nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus
fulgidus} PDB: 2chv_A
Length = 319
Score = 24.2 bits (53), Expect = 8.2
Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 21/87 (24%)
Query: 15 DGTDSNSHHAQEALRRA--KFKFPVR--------QKII---VSR--KWGFTKFSRANYLR 59
D D+ + AQ ALRR + R +II SR + F + +
Sbjct: 109 DEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKK 168
Query: 60 -----CKSEN-RIVPDGVNAKLFECHG 80
C+ E +I DG+ A ++ G
Sbjct: 169 RLLEICEKEGVKITEDGLEALIYISGG 195
>3fkd_A L-threonine-O-3-phosphate decarboxylase; structural genomic, ,
structural genomics, PSI-2, protein structure
initiative; 2.50A {Porphyromonas gingivalis}
Length = 350
Score = 24.0 bits (53), Expect = 8.5
Identities = 7/64 (10%), Positives = 16/64 (25%), Gaps = 15/64 (23%)
Query: 24 AQEALRRAKFKFPVRQKIIVSRKW---GFTKF-------SRANYLRCKSENRIVPDGVNA 73
A+ L +K + + S + + + G A
Sbjct: 236 AKFILIHPAQFTLPIRKWQRNTVDFITALNRLDGVEVHPSGTTFFLLR-----LKKGTAA 290
Query: 74 KLFE 77
+L +
Sbjct: 291 ELKK 294
>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 323
Score = 24.3 bits (53), Expect = 8.6
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 21/84 (25%)
Query: 18 DSNSHHAQEALRRA--KFKFPVR--------QKII---VSR--KWGFTKFSRANYLR--- 59
DS + AQ+ALRR + R KII S+ ++K S + L+
Sbjct: 117 DSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLL 176
Query: 60 --CKSEN-RIVPDGVNAKLFECHG 80
K E+ + DG+ A +F G
Sbjct: 177 QIIKLEDVKYTNDGLEAIIFTAEG 200
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
0.321 0.134 0.419
Gapped
Lambda K H
0.267 0.0526 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,491,962
Number of extensions: 71397
Number of successful extensions: 113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 21
Length of query: 96
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 34
Effective length of database: 4,970,691
Effective search space: 169003494
Effective search space used: 169003494
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 (21.9 bits)
S2: 51 (23.9 bits)