RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029751
(188 letters)
>3iz5_V 60S ribosomal protein L17 (L22P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_V
Length = 171
Score = 233 bits (595), Expect = 2e-79
Identities = 138/161 (85%), Positives = 147/161 (91%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPF 60
MVKYS+E +NPTKS KA G DLRVHFKNTRE A A+RKL L KAKRYLEDV+AHKQAIPF
Sbjct: 1 MVKYSREANNPTKSSKAMGRDLRVHFKNTRETAFAIRKLPLGKAKRYLEDVIAHKQAIPF 60
Query: 61 TRFCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+C GVGRTAQAK+R+ NGQGRWP KSA+FILDLLKNAESNAEVKGLDVD LY+SHIQV
Sbjct: 61 RRYCGGVGRTAQAKSRHSNGQGRWPAKSARFILDLLKNAESNAEVKGLDVDTLYVSHIQV 120
Query: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKKE 161
NQAQKQRRRTYRAHGRINPYMSSPCHIEL LSEKEEPVKKE
Sbjct: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELILSEKEEPVKKE 161
>3u5e_P L20A, YL17, 60S ribosomal protein L17-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_I
2ww9_I 2wwb_I 3o5h_Q 3o58_Q 3u5i_P 1s1i_N 3izc_V 3izs_V
3jyw_N
Length = 184
Score = 216 bits (551), Expect = 1e-72
Identities = 98/161 (60%), Positives = 113/161 (70%), Gaps = 1/161 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPF 60
M +Y NP KS ARGS LRV FKNTRE A A+ LTKA++YLE V+ H++AIPF
Sbjct: 1 MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF 60
Query: 61 TRFCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
RF +GRTAQ K + RWP KS KF+ LL+NA +NAE KGLD LY+SHIQV
Sbjct: 61 RRFNSSIGRTAQGKEFG-VTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKKE 161
NQA KQRRRTYRAHGRIN Y SSP HIEL ++EKEE V K
Sbjct: 120 NQAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKA 160
>2zkr_r 60S ribosomal protein L17; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 184
Score = 213 bits (543), Expect = 2e-71
Identities = 109/175 (62%), Positives = 137/175 (78%), Gaps = 1/175 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPF 60
MV+YS +P+NPTKSCK+RGS+LRVHFKNTRE A A++ + + KA +YL+DV KQ +PF
Sbjct: 1 MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF 60
Query: 61 TRFCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+ GVGR AQAK QGRWP KSA+F+L +LKNAESNAE+KGLDVD+L I HIQV
Sbjct: 61 RRYNGGVGRCAQAKQWG-WTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKKEVGSLVKVRSVNYRK 175
N+A K RRRTYRAHGRINPYMSSPCHIE+ L+EKE+ V K + + + ++ +K
Sbjct: 120 NKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKK 174
>4a17_Q RPL17, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_Q 4a1c_Q 4a1e_Q
Length = 183
Score = 210 bits (537), Expect = 2e-70
Identities = 90/174 (51%), Positives = 110/174 (63%), Gaps = 1/174 (0%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPFT 61
YS+EP N K+ K SDLRVHFKNT E A++ L+L AKRYL+ V+ K+ IPFT
Sbjct: 4 TNYSREPANQAKAVKTSASDLRVHFKNTYEVVRAIKGLNLENAKRYLKAVIDRKRCIPFT 63
Query: 62 RFCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
RF +GRTAQA QGRWPVKS K IL LL N +NA+ K L+ L I H QVN
Sbjct: 64 RFTGCIGRTAQAH-EFGRTQGRWPVKSVKVILGLLDNLSANAQAKSLNTANLVIQHGQVN 122
Query: 122 QAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEEPVKKEVGSLVKVRSVNYRK 175
+AQK RRRTYRAHGRINPY++S CH+E+ E V+KE + +K
Sbjct: 123 RAQKGRRRTYRAHGRINPYLNSGCHVEIFAQEVAAKVRKEAPKDAAKKVPKTKK 176
>1vq8_R 50S ribosomal protein L22P; 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.55.1.1 PDB: 1vq4_R*
1vq5_R* 1vq6_R* 1vq7_R* 1s72_R* 1vq9_R* 1vqk_R* 1vql_R*
1vqm_R* 1vqn_R* 1vqo_R* 1vqp_R* 1yhq_R* 1yi2_R* 1yij_R*
1yit_R* 1yjn_R* 1yjw_R* 2otj_R* 2otl_R* ...
Length = 155
Score = 206 bits (526), Expect = 3e-69
Identities = 51/155 (32%), Positives = 85/155 (54%), Gaps = 4/155 (2%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQAIPFT 61
+ YS E D P + KA + ++ FK+++ A ++ + +A YLE V+ Q +PF
Sbjct: 3 ISYSVEAD-PDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFK 61
Query: 62 RFCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
+ GVG ++ + GR+P K++K LDLL+NA NA+ +G D +A+ I H+ +
Sbjct: 62 QHNSGVGHKSKVDGWD---AGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAH 118
Query: 122 QAQKQRRRTYRAHGRINPYMSSPCHIELTLSEKEE 156
+ +Q+ R RA GR + + S +EL L E E
Sbjct: 119 KVGEQQGRKPRAMGRASAWNSPQVDVELILEEPEV 153
>2zjr_P 50S ribosomal protein L22; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.55.1.1 PDB: 1j5a_L* 1jzy_L* 1jzz_L*
1k01_L* 1nkw_Q 1nwx_Q* 1nwy_Q* 1ond_Q* 1sm1_Q* 1xbp_Q*
2zjp_P* 2zjq_P 1jzx_L 3cf5_P* 3dll_P* 3pio_P* 3pip_P*
1pnu_Q 1pny_Q 1vor_T ...
Length = 134
Score = 58.0 bits (141), Expect = 1e-11
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
P +++ + +L +A++NA + D L++ V+ +R RA G N
Sbjct: 61 PRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKR 120
Query: 144 PCHIELTLSEKEE 156
HI + ++EK
Sbjct: 121 TSHITIIVAEKGN 133
>1i4j_A 50S ribosomal protein L22; mutant, erythromycin resistance, RNA
binding, RNA binding protein; 1.80A {Thermus
thermophilus} SCOP: d.55.1.1 PDB: 1bxe_A 1giy_S 1ml5_s*
1vsa_Q 1vsp_Q 1yl3_S 2b66_W 2b9n_W 2b9p_W 2hgj_V 2hgq_V
2hgu_V 2j01_W 2j03_W 2jl6_W 2jl8_W 2v47_W 2v49_W 2wdi_W
2wdj_W ...
Length = 110
Score = 57.1 bits (139), Expect = 2e-11
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 4/73 (5%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
+ A F+ +L++A +NA D LY+ V++ RA GR +
Sbjct: 40 NKRGAYFVAKVLESAAANAVNNHDALEDRLYVKAAYVDEGPAVLP---RARGRADIIKKR 96
Query: 144 PCHIELTLSEKEE 156
HI + L EK
Sbjct: 97 TSHITVILGEKHG 109
>3r8s_S 50S ribosomal protein L22; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_Q 1p86_Q 1vs8_S 1vs6_S 2aw4_S 2awb_S 1vt2_S 2i2v_S
2j28_S 2i2t_S* 2qao_S* 2qba_S* 2qbc_S* 2qbe_S 2qbg_S
2qbi_S* 2qbk_S* 2qov_S 2qox_S 2qoz_S* ...
Length = 110
Score = 56.7 bits (138), Expect = 3e-11
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
K+A + +L++A +NAE G D+D L ++ I V++ +R RA GR + +
Sbjct: 40 NKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKR 99
Query: 144 PCHIELTLSEK 154
HI + +S++
Sbjct: 100 TSHITVVVSDR 110
>3bbo_U Ribosomal protein L22; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 199
Score = 55.5 bits (134), Expect = 4e-10
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSS 143
P ++ I L+ +A +NA K + L IS +VN+ ++ RA GR +
Sbjct: 69 PYRACYPIFKLIYSAAANASHNKQFNKANLIISKAEVNKGITLKKVKPRARGRSYMILRP 128
Query: 144 PCHIELTLSEKEE 156
CHI + L +
Sbjct: 129 TCHITIVLRDITH 141
>2ftc_M Mitochondrial ribosomal protein L22 isoform A; mitochondrial
ribosome, large ribosomal subunit, ribosomal R ribosome;
12.10A {Bos taurus} PDB: 3iy9_M
Length = 110
Score = 52.9 bits (128), Expect = 8e-10
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 85 PVKSAKFILDLLKNAESNAEV-KGLDV-DALYISHIQVNQAQKQRRRTYRAHGRINPYMS 142
K AK I ++L A+ A ++ LYI+ + Q +R Y GR
Sbjct: 36 DKKGAKIIKEVLLEAQDMAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIMEK 95
Query: 143 SPCHIELTLSEKEEP 157
CH + L E P
Sbjct: 96 VYCHYFVKLVEGPPP 110
>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 = 32.5 bits (73), Expect = 0.080
Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 28/84 (33%)
Query: 90 KFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINPYMSSPCHIEL 149
K + D+ K+ S E+ HI + T R
Sbjct: 36 KDVQDMPKSILSKEEID----------HI-IMSKDAV-SGTLRL-------------FWT 70
Query: 150 TLSEKEEPVKKEVGSLVKVRSVNY 173
LS++EE V+K V +++ +NY
Sbjct: 71 LLSKQEEMVQKFVEEVLR---INY 91
Score = 32.1 bits (72), Expect = 0.097
Identities = 32/187 (17%), Positives = 61/187 (32%), Gaps = 41/187 (21%)
Query: 1 MVKYS---KEPDNPTKSCKARGSDLRVHFKNTREAAHALRKL--SLTKAKRYLEDVMAHK 55
+ KYS K+P T S + +L+V +N A H R + K + D
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLEN-EYALH--RSIVDHYNIPKTFDSD----D 463
Query: 56 QAIPFTR--FCRGVGRTAQAKNRNPNGQGRWPVKSAKFILDL------LKNAESNAEVKG 107
P+ F +G + R + F LD +++ + G
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHP----ERMTLFRMVF-LDFRFLEQKIRHDSTAWNASG 518
Query: 108 LDVDAL-----YISHIQVNQAQKQRR--------RTYRAHGRINPYMSSPCHIELTLSEK 154
++ L Y +I N + +R + + Y + + L +
Sbjct: 519 SILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYT---DLLRIALMAE 575
Query: 155 EEPVKKE 161
+E + +E
Sbjct: 576 DEAIFEE 582
>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 = 30.0 bits (67), Expect = 0.60
Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 13/85 (15%)
Query: 9 DNPTKSCKARGSDLRVHFKNTREAAHALRKLSLTKAKRYLEDVMAHKQ-----AIPFTR- 62
D + D+++ +T + + LR LS + ++R + D + F
Sbjct: 442 DLVKNNVSFNAKDIQIPVYDTFDGSD-LRVLSGSISER-IVDCIIRLPVKWETTTQFKAT 499
Query: 63 ----FCRG-VGRTAQAKNRNPNGQG 82
F G +RN +G G
Sbjct: 500 HILDFGPGGASGLGVLTHRNKDGTG 524
>2jdq_A Importin alpha-1 subunit; transport, PB2 subunit, nuclear
protein, protein transport, armadillo repeats; 2.2A
{Homo sapiens} PDB: 3tj3_A
Length = 450
Score = 26.0 bits (57), Expect = 8.1
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 30 REAAHALRKLSLTKAKRYLEDVMAHKQAIP 59
A RKL + +++V++ +
Sbjct: 38 LSATQKFRKLLSKEPNPPIDEVISTPGVVA 67
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
0.319 0.132 0.388
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,738,020
Number of extensions: 151863
Number of successful extensions: 344
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 25
Length of query: 188
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 100
Effective length of database: 4,244,745
Effective search space: 424474500
Effective search space used: 424474500
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 (21.8 bits)
S2: 54 (24.5 bits)