RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031794
(153 letters)
>3u5e_X 60S ribosomal protein L25; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 2wwa_K 2ww9_K 3izc_X
3izs_X 2wwb_K 3o5h_W 3o58_W 3u5i_X 1s1i_T 3jyw_T
Length = 142
Score = 171 bits (434), Expect = 7e-56
Identities = 83/141 (58%), Positives = 106/141 (75%), Gaps = 1/141 (0%)
Query: 13 PKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQ 72
P A+AT KAV G T KKA K+RTS TF PKTLK R PKY + P N+LD Y+
Sbjct: 3 PSAKATAAKKAVVKG-TNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYK 61
Query: 73 ILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGTKK 132
+++ P+T+E+AMKK+ED N LVF V ++A+K +IK AVK++YE+ KVNTL+RP+GTKK
Sbjct: 62 VIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKK 121
Query: 133 AYVRLTPDYDALDVANKIGII 153
AYVRLT DYDALD+AN+IG I
Sbjct: 122 AYVRLTADYDALDIANRIGYI 142
>3iz5_X 60S ribosomal protein L23A (L23P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_X 2go5_4 2j37_4
Length = 152
Score = 170 bits (432), Expect = 1e-55
Identities = 123/153 (80%), Positives = 134/153 (87%), Gaps = 1/153 (0%)
Query: 1 MAPKVDSSKKGDPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRI 60
MAPK K QA KVAKAVKSG + K+K+KK+RTSVTFHRPKTLKK R+PKYPR+
Sbjct: 1 MAPKAAVKKADGKTQQALKVAKAVKSG-SIKRKSKKIRTSVTFHRPKTLKKARDPKYPRV 59
Query: 61 SAPPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKK 120
SAP RNKLD YQILKYPLTTESAMKKIEDNNTLVFIVD++ADK+KIK AVKKMY+IQ KK
Sbjct: 60 SAPGRNKLDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKK 119
Query: 121 VNTLIRPDGTKKAYVRLTPDYDALDVANKIGII 153
VNTLIRPDG KKAYV+LTPDYDALDVANKIGII
Sbjct: 120 VNTLIRPDGKKKAYVKLTPDYDALDVANKIGII 152
>4a17_R RPL23A, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_R 4a1c_R 4a1e_R
Length = 150
Score = 160 bits (405), Expect = 2e-51
Identities = 65/152 (42%), Positives = 87/152 (57%), Gaps = 5/152 (3%)
Query: 5 VDSSKKGDPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAP- 63
++ K +A AK K G K T V F RPKTL+ + PKY R
Sbjct: 1 MNKENKTQAVNKAKNTAKVAKKG--SSITKHKTYTGVRFFRPKTLQLAKAPKYSRTVRAH 58
Query: 64 --PRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKV 121
LD++ ++K PLTTE AMKK+ED NT+VF V R+ K +IK A +K+Y ++ + V
Sbjct: 59 LKVSGHLDNHSVVKTPLTTEKAMKKMEDENTMVFYVHNRSTKPQIKSAFEKLYNVKVRSV 118
Query: 122 NTLIRPDGTKKAYVRLTPDYDALDVANKIGII 153
NTL G KKAY+RL D D+L +ANKIG+I
Sbjct: 119 NTLNTITGNKKAYIRLAADSDSLTLANKIGLI 150
>2zkr_s 60S ribosomal protein L23A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 156
Score = 159 bits (404), Expect = 3e-51
Identities = 108/157 (68%), Positives = 121/157 (77%), Gaps = 5/157 (3%)
Query: 1 MAPKV----DSSKKGDPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPK 56
MAPK + K + KA+A K KAV G K KK+RTS TF RPKTL+ R PK
Sbjct: 1 MAPKAKKEAPAPPKAEAKAKALKAKKAVLKG-VHSHKKKKIRTSPTFRRPKTLRLRRQPK 59
Query: 57 YPRISAPPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEI 116
YPR SAP RNKLDHY I+K+PLTTESAMKKIEDNNTLVFIVD++A+K +IK AVKK+Y+I
Sbjct: 60 YPRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDI 119
Query: 117 QTKKVNTLIRPDGTKKAYVRLTPDYDALDVANKIGII 153
KVNTLIRPDG KKAYVRL PDYDALDVANKIGII
Sbjct: 120 DVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII 156
>3bbo_V Ribosomal protein L23; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 198
Score = 159 bits (402), Expect = 2e-50
Identities = 57/149 (38%), Positives = 83/149 (55%), Gaps = 7/149 (4%)
Query: 4 KVDSSKKGDPKAQATKVAKAVKSGPTFKKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAP 63
K + + + + +PKT KK + KYPR
Sbjct: 52 KSFNFHDAVTPMNKPSFGRDLMVAQA-TEAVAPTTEEAATSQPKTSKKAKKLKYPR---- 106
Query: 64 PRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNT 123
LD YQIL+ P+ TE+A+K I D N+L+F VD+RADK+ I++A+ + ++ +KVNT
Sbjct: 107 --RILDVYQILQSPIITEAAIKNIADENSLLFTVDVRADKKMIREAISNFFGVKVRKVNT 164
Query: 124 LIRPDGTKKAYVRLTPDYDALDVANKIGI 152
LIRPDGTKKAY+ L +Y+A ++A KIGI
Sbjct: 165 LIRPDGTKKAYIMLNKEYNASELAKKIGI 193
>1vq8_S 50S ribosomal protein L23P; 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.12.1.1 PDB: 1vq4_S*
1vq5_S* 1vq6_S* 1vq7_S* 1s72_S* 1vq9_S* 1vqk_S* 1vql_S*
1vqm_S* 1vqn_S* 1vqo_S* 1vqp_S* 1yhq_S* 1yi2_S* 1yij_S*
1yit_S* 1yj9_S* 1yjn_S* 1yjw_S* 2otj_S* ...
Length = 85
Score = 127 bits (320), Expect = 2e-39
Identities = 36/82 (43%), Positives = 55/82 (67%)
Query: 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPDGT 130
+ ++K+P TE AM ++ N L F VD RA K ++ DAV++ Y++ ++VNT DG
Sbjct: 3 WDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGE 62
Query: 131 KKAYVRLTPDYDALDVANKIGI 152
KKA VRL+ D DA +VA++IG+
Sbjct: 63 KKAVVRLSEDDDAQEVASRIGV 84
>3r8s_T 50S ribosomal protein L23; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_T 2wwq_T 3oat_T* 3oas_T* 3ofd_T 3ofc_T 3ofr_T*
3ofz_T* 3og0_T 3ofq_T 3r8t_T 2j28_T 3e1b_M 3e1d_M 3iy9_T
3i1n_T 1p85_R 1p86_R 1vs8_T 1vs6_T ...
Length = 93
Score = 62.2 bits (152), Expect = 9e-14
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 13/90 (14%)
Query: 66 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLI 125
+ ++L+ P +E A +E +NT+V V A K +IK AV+K++E++ + VNTL+
Sbjct: 3 REERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLV 62
Query: 126 RP-------------DGTKKAYVRLTPDYD 142
KKAYV L +
Sbjct: 63 VKGKVKRHGQRIGRRSDWKKAYVTLKEGQN 92
>2zjr_Q 50S ribosomal protein L23; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.12.1.1 PDB: 1sm1_R* 2aar_R 2d3o_R
2zjp_Q* 2zjq_Q 1nkw_R 3cf5_Q* 3dll_Q* 3pio_Q* 3pip_Q*
1nwy_R* 1nwx_R* 1xbp_R* 1pnu_R 1pny_R 1vor_U 1vou_U
1vow_U 1voy_U 1vp0_U
Length = 95
Score = 61.0 bits (149), Expect = 3e-13
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 14/88 (15%)
Query: 68 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP 127
+ HY IL+ P+ +E A +E F V +A K +IKDA+++ + ++ ++T+ P
Sbjct: 1 MSHYDILQAPVISEKAYSAME-RGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVP 59
Query: 128 -------------DGTKKAYVRLTPDYD 142
+ KKA VRL
Sbjct: 60 GKRKRVGRFIGQRNDRKKAIVRLAEGQS 87
>3tve_T 50S ribosomal protein L23; RNA, ribosome, tRNA, translation, mRNA;
3.10A {Thermus thermophilus} PDB: 3pyr_T 3pyo_T 3pyv_T
3pyt_T 3tvh_T 1n88_A 1vsa_R 1vsp_R 2hgj_W 2hgq_W 2hgu_W
2j01_X 2j03_X 2jl6_X 2jl8_X 2v47_X 2v49_X 2wdi_X 2wdj_X
2wdl_X ...
Length = 92
Score = 59.1 bits (144), Expect = 1e-12
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 14/85 (16%)
Query: 71 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRP--- 127
Y ++ P+ +E A F V +A K +IK+AV+ ++++ KVNTL
Sbjct: 3 YDVILAPVLSEKAYAGFA-EGKYTFWVHPKATKTEIKNAVETAFKVKVVKVNTLHVRGKK 61
Query: 128 ----------DGTKKAYVRLTPDYD 142
KKA V++ P
Sbjct: 62 KRLGRYLGKRPDRKKAIVQVAPGQK 86
>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 = 36.0 bits (82), Expect = 0.003
Identities = 25/136 (18%), Positives = 42/136 (30%), Gaps = 36/136 (26%)
Query: 43 FHRPKTLKKDRNPK-------YPRISAPPRNK-------LDHYQILK-YPLTTESA---- 83
H+ ++K Y + N+ +DHY I K +
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD 470
Query: 84 ----------MKKIE-----DNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTLIRPD 128
+K IE +VF +D R ++KI+ + +NTL +
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVF-LDFRFLEQKIR-HDSTAWNASGSILNTLQQLK 528
Query: 129 GTKKAYVRLTPDYDAL 144
K P Y+ L
Sbjct: 529 FYKPYICDNDPKYERL 544
>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 = 30.3 bits (67), Expect = 0.17
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 13/33 (39%)
Query: 31 KKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAP 63
K+ KK++ S+ + D SAP
Sbjct: 19 KQALKKLQASLKLYAD-----D--------SAP 38
>3mag_A VP39; methylated adenine, methyltransferase, RNA CAP analog, poly
(A) polymerase, mRNA processing, transcription; HET: SAH
3MA; 1.80A {Vaccinia virus} SCOP: c.66.1.25 PDB: 1bky_A*
1jsz_A* 1v39_A* 1p39_A* 1vp9_A* 2vp3_A* 1eam_A* 1jte_A*
1jtf_A* 4dcg_A* 3mct_A* 1b42_A* 1eqa_A* 1av6_A* 3er9_A*
2gaf_A 3er8_A 2ga9_A* 3erc_A*
Length = 307
Score = 27.8 bits (61), Expect = 1.3
Identities = 13/72 (18%), Positives = 26/72 (36%), Gaps = 5/72 (6%)
Query: 58 PRISAPPRNKLDHYQILKYPLTTESA--MKKIEDNNTLVFIVDIRA---DKRKIKDAVKK 112
R P N L ++ + E +KK + ++ I D+R+ +
Sbjct: 96 GRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSKRGGNEPSTADLLS 155
Query: 113 MYEIQTKKVNTL 124
Y +Q ++ L
Sbjct: 156 NYALQNVMISIL 167
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; HET: MES; 1.30A {Geobacillus
stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A*
Length = 119
Score = 25.2 bits (55), Expect = 5.9
Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 11/65 (16%)
Query: 84 MKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQT-------KKVNTLIRPDGTKKAYVR 136
M+++E V IV+ R+DK+K+ + + I ++ L Y+
Sbjct: 1 MRRVEK----VIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGYDVYLL 56
Query: 137 LTPDY 141
D
Sbjct: 57 ADADE 61
>1t8t_A Heparan sulfate D-glucosaminyl 3-O- sulfotransferase 3A1;
alpha-beta motif, substrate-binding cleft; HET: A3P CIT;
1.85A {Homo sapiens} SCOP: c.37.1.5 PDB: 1t8u_A*
Length = 271
Score = 25.9 bits (56), Expect = 6.2
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 31 KKKAKKMRTSVTFHRPKTLKKDRNPKYPRISAPPRNKL-DHYQ 72
K ++ + RP L K + +P I +L + Y+
Sbjct: 211 TKGFPCLKKAEGSSRPHCLGKTKGRTHPEIDREVVRRLREFYR 253
>1xfd_A DIP, dipeptidyl aminopeptidase-like protein 6, dipeptidylpeptidase
6; DPPX, DPP6, KV4, KV, KAF, membrane protein; HET: NDG
NAG BMA MAN; 3.00A {Homo sapiens} SCOP: b.70.3.1
c.69.1.24
Length = 723
Score = 26.0 bits (57), Expect = 7.7
Identities = 8/86 (9%), Positives = 25/86 (29%), Gaps = 22/86 (25%)
Query: 65 RNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKRKIKDAVKKMYEIQTKKVNTL 124
K++ + ++Y ++ D +F ++ + + +I +L
Sbjct: 55 GKKIESLRAIRYEIS--------PDREYALFSYNVEPIYQHSYTGYYVLSKIPHGDPQSL 106
Query: 125 IR--------------PDGTKKAYVR 136
P G + ++
Sbjct: 107 DPPEVSNAKLQYAGWGPKGQQLIFIF 132
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
0.314 0.130 0.362
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,227,757
Number of extensions: 124430
Number of successful extensions: 289
Number of sequences better than 10.0: 1
Number of HSP's gapped: 272
Number of HSP's successfully gapped: 39
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: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.7 bits)