RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031778
(153 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 = 207 bits (528), Expect = 7e-70
Identities = 124/150 (82%), Positives = 132/150 (88%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
MVKYS+E +NPTKS KA G DLRVHFKNTRETA AIRKLPL KAKRYLEDV+AHKQAIPF
Sbjct: 1 MVKYSREANNPTKSSKAMGRDLRVHFKNTRETAFAIRKLPLGKAKRYLEDVIAHKQAIPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+CGGVGRTAQAK+RH NGQGRWP KSA+FILDLLKNAESNAEVKGLDVD LY+SHIQV
Sbjct: 61 RRYCGGVGRTAQAKSRHSNGQGRWPAKSARFILDLLKNAESNAEVKGLDVDTLYVSHIQV 120
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
NQAQKQRRRTYRAHGRIN H+ LI
Sbjct: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELI 150
>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 = 190 bits (485), Expect = 3e-63
Identities = 88/150 (58%), Positives = 103/150 (68%), Gaps = 1/150 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
M +Y NP KS ARGS LRV FKNTRETA AI LTKA++YLE V+ H++AIPF
Sbjct: 1 MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
RF +GRTAQ K + RWP KS KF+ LL+NA +NAE KGLD LY+SHIQV
Sbjct: 61 RRFNSSIGRTAQGKE-FGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
NQA KQRRRTYRAHGRIN+ H+ L+
Sbjct: 120 NQAPKQRRRTYRAHGRINKYESSPSHIELV 149
>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 = 189 bits (480), Expect = 2e-62
Identities = 82/149 (55%), Positives = 95/149 (63%), Gaps = 1/149 (0%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
YS+EP N K+ K SDLRVHFKNT E AI+ L L AKRYL+ V+ K+ IPFT
Sbjct: 4 TNYSREPANQAKAVKTSASDLRVHFKNTYEVVRAIKGLNLENAKRYLKAVIDRKRCIPFT 63
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
RF G +GRTAQA QGRWPVKS K IL LL N +NA+ K L+ L I H QVN
Sbjct: 64 RFTGCIGRTAQAH-EFGRTQGRWPVKSVKVILGLLDNLSANAQAKSLNTANLVIQHGQVN 122
Query: 122 QAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
+AQK RRRTYRAHGRIN H+ +
Sbjct: 123 RAQKGRRRTYRAHGRINPYLNSGCHVEIF 151
>2zkr_r 60S ribosomal protein L17; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 184
Score = 187 bits (476), Expect = 9e-62
Identities = 95/139 (68%), Positives = 113/139 (81%), Gaps = 1/139 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
MV+YS +P+NPTKSCK+RGS+LRVHFKNTRETA AI+ + + KA +YL+DV KQ +PF
Sbjct: 1 MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+ GGVGR AQAK QGRWP KSA+F+L +LKNAESNAE+KGLDVD+L I HIQV
Sbjct: 61 RRYNGGVGRCAQAKQ-WGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINR 139
N+A K RRRTYRAHGRIN
Sbjct: 120 NKAPKMRRRTYRAHGRINP 138
>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 = 184 bits (469), Expect = 4e-61
Identities = 46/138 (33%), Positives = 75/138 (54%), Gaps = 4/138 (2%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
+ YS E D P + KA + ++ FK+++ A I+ +A YLE V+ Q +PF
Sbjct: 3 ISYSVEAD-PDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFK 61
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
+ GVG ++ GR+P K++K LDLL+NA NA+ +G D +A+ I H+ +
Sbjct: 62 QHNSGVGHKSKVDGWD---AGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAH 118
Query: 122 QAQKQRRRTYRAHGRINR 139
+ +Q+ R RA GR +
Sbjct: 119 KVGEQQGRKPRAMGRASA 136
>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 = 47.8 bits (115), Expect = 3e-08
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINR 139
K+A + +L++A +NAE G D+D L ++ I V++ +R RA GR +R
Sbjct: 40 NKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADR 95
>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 = 46.8 bits (112), Expect = 1e-07
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINR 139
P +++ + +L +A++NA + D L++ V+ +R RA G N
Sbjct: 61 PRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANI 116
>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 = 45.9 bits (110), Expect = 2e-07
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 85 PVKSAKFILDLLKNAESNAEVK-GLDVDALYISHIQVNQAQKQRRRTYRAHGRINR 139
+ A F+ +L++A +NA D LY+ V++ RA GR +
Sbjct: 40 NKRGAYFVAKVLESAAANAVNNHDALEDRLYVKAAYVDEGPAVLP---RARGRADI 92
>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 = 44.8 bits (107), Expect = 4e-07
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 85 PVKSAKFILDLLKNAESNAEV-KGLDV-DALYISHIQVNQAQKQRRRTYRAHGRINRM 140
K AK I ++L A+ A ++ LYI+ + Q +R Y GR M
Sbjct: 36 DKKGAKIIKEVLLEAQDMAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIM 93
>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 = 45.5 bits (108), Expect = 8e-07
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 85 PVKSAKFILDLLKNAESNAEV-KGLDVDALYISHIQVNQAQKQRRRTYRAHGRINR 139
P ++ I L+ +A +NA K + L IS +VN+ ++ RA GR
Sbjct: 69 PYRACYPIFKLIYSAAANASHNKQFNKANLIISKAEVNKGITLKKVKPRARGRSYM 124
>3r6w_A FMN-dependent NADH-azoreductase 1; nitrofurazone, P. aeruginosa,
nitroreductase, flavodoxin, oxidoreductase; HET: FMN
NFZ; 2.08A {Pseudomonas aeruginosa} PDB: 3lt5_A* 2v9c_A*
3keg_A*
Length = 212
Score = 27.3 bits (60), Expect = 1.9
Identities = 8/42 (19%), Positives = 16/42 (38%)
Query: 77 HPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHI 118
P G+ + A+ L + A A V +V + + +
Sbjct: 10 SPRGERSQSRRLAEVFLAAYREAHPQARVARREVGRVPLPAV 51
>1t5b_A Acyl carrier protein phosphodiesterase; structural genomics, FMN,
alpha/beta/alpha sandwich, PSI, protein structure
initiative; HET: FMN; 1.40A {Salmonella typhimurium}
SCOP: c.23.5.3 PDB: 1tik_A 2z98_A* 2d5i_A* 1v4b_A*
2z9b_A* 2z9c_A* 2z9d_A*
Length = 201
Score = 26.6 bits (58), Expect = 3.8
Identities = 3/43 (6%), Positives = 12/43 (27%)
Query: 77 HPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQ 119
+ + ++ + E+ D+ A + +
Sbjct: 10 SILAGYSQSGQLTDYFIEQWREKHVADEITVRDLAANPVPVLD 52
>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 = 26.7 bits (58), Expect = 3.8
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 16/65 (24%)
Query: 90 KFILDLLKNAESNAEVKGLDVDALYISHIQVNQA--------QKQRRRTYRAHG---RIN 138
K + D+ K+ S E +D + +S V+ KQ + RIN
Sbjct: 36 KDVQDMPKSILSKEE-----IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN 90
Query: 139 RMFLV 143
FL+
Sbjct: 91 YKFLM 95
Score = 26.0 bits (56), Expect = 8.0
Identities = 26/146 (17%), Positives = 48/146 (32%), Gaps = 30/146 (20%)
Query: 1 MVKYS---KEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRY--LEDVMAHK 55
+ KYS K+P T S + +L+V +N H R + Y + +
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYA-LH--RSI----VDHYNIPKTFDSDD 463
Query: 56 QAIPFTR--FCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDL------LKNAESNAEVKG 107
P+ F +G + R + F LD +++ + G
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHP----ERMTLFRMVF-LDFRFLEQKIRHDSTAWNASG 518
Query: 108 LDVDAL-----YISHIQVNQAQKQRR 128
++ L Y +I N + +R
Sbjct: 519 SILNTLQQLKFYKPYICDNDPKYERL 544
>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 = 26.6 bits (58), Expect = 4.7
Identities = 13/87 (14%), Positives = 28/87 (32%), Gaps = 17/87 (19%)
Query: 9 DNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQA----------- 57
D + D+++ +T +R L + ++R + D +
Sbjct: 442 DLVKNNVSFNAKDIQIPVYDT-FDGSDLRVLSGSISER-IVDCIIRLPVKWETTTQFKAT 499
Query: 58 --IPFTRFCGGVGRTAQAKNRHPNGQG 82
+ F GG +R+ +G G
Sbjct: 500 HILDFGP--GGASGLGVLTHRNKDGTG 524
>2ks9_A Substance-P receptor; water, autodock, NK1, neuropeptide
receptor-NEU complex; NMR {Homo sapiens} PDB: 2ksa_A
2ksb_A
Length = 364
Score = 26.2 bits (58), Expect = 5.7
Identities = 8/39 (20%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 113 LYISHIQVNQAQKQRRRTYRAHGRINRMFLV---LFHLC 148
L+ S I + + + + A ++ +M +V F +C
Sbjct: 223 LWASEIPGDSSDRYHEQV-SAKRKVVKMMIVVVCTFAIC 260
>2qyf_B MAD2L1-binding protein; MAD2 family, spindle assembly checkpoint,
cell cycle, cell division, mitosis, nucleus,
phosphorylation; 2.30A {Homo sapiens}
Length = 240
Score = 25.9 bits (56), Expect = 6.5
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 11/64 (17%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKN--TRET-AHAIRKLPLTKAKRYLEDVMAHKQA 57
M ++EP N +++ R + V F ++E +L L+ +M +Q
Sbjct: 1 MTSSTQEPLNASEAFCPRDCMVPVVFPGPVSQEGCCQFTCEL--------LKHIMYQRQQ 52
Query: 58 IPFT 61
+P
Sbjct: 53 LPLP 56
>2q3e_A UDP-glucose 6-dehydrogenase; hexamer, structural genomics, S
genomics consortium, SGC, oxidoreductase; HET: NAD UPG;
2.00A {Homo sapiens} PDB: 2qg4_A* 3khu_A* 3itk_A*
3tdk_A* 3ptz_A* 3prj_A* 3tf5_A
Length = 467
Score = 25.2 bits (56), Expect = 10.0
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 90 KFILDLLKNAESNAEVKGLDVDALYISH-IQVNQAQKQR 127
K +L+L+ E+ L A Y I +N Q++R
Sbjct: 280 KDVLNLVYLCEAL----NLPEVARYWQQVIDMNDYQRRR 314
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
0.324 0.136 0.413
Gapped
Lambda K H
0.267 0.0576 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,260,657
Number of extensions: 121812
Number of successful extensions: 373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 20
Length of query: 153
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 68
Effective length of database: 4,328,508
Effective search space: 294338544
Effective search space used: 294338544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.5 bits)