RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030945
(168 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 = 176 bits (448), Expect = 9e-58
Identities = 78/140 (55%), Positives = 102/140 (72%)
Query: 29 PKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQI 88
P +A KAV G KKA K+RTS TF PKTLK R PKY + P N+LD Y++
Sbjct: 3 PSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKV 62
Query: 89 LKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGTKKA 148
++ P+T+E+AMKK+ED N LVF V ++A+K +IK AVK++Y++ KVNTL+RP+GTKKA
Sbjct: 63 IEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKA 122
Query: 149 YVRLTPDSDALDVANKIGII 168
YVRLT D DALD+AN+IG I
Sbjct: 123 YVRLTADYDALDIANRIGYI 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 = 176 bits (447), Expect = 2e-57
Identities = 124/152 (81%), Positives = 131/152 (86%)
Query: 17 MAPPKGETKKADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRIS 76
MAP K QALK AKAVKSG +K+KKIRTSVTFHRPKTLKK R+PKYPR+S
Sbjct: 1 MAPKAAVKKADGKTQQALKVAKAVKSGSIKRKSKKIRTSVTFHRPKTLKKARDPKYPRVS 60
Query: 77 APPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKV 136
AP RNKLD YQILKYPLTTESAMKKIEDNNTLVFIVD++ADKKKIK AVKKMYDIQAKKV
Sbjct: 61 APGRNKLDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKKV 120
Query: 137 NTLIRPDGTKKAYVRLTPDSDALDVANKIGII 168
NTLIRPDG KKAYV+LTPD DALDVANKIGII
Sbjct: 121 NTLIRPDGKKKAYVKLTPDYDALDVANKIGII 152
>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 = 169 bits (430), Expect = 2e-54
Identities = 57/147 (38%), Positives = 83/147 (56%), Gaps = 6/147 (4%)
Query: 21 KGETKKADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPR 80
A + + + + + +PKT KK + KYPR
Sbjct: 53 SFNFHDAVTPMNKPSFGRDLMVAQATEAVAPTTEEAATSQPKTSKKAKKLKYPR------ 106
Query: 81 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 140
LD YQIL+ P+ TE+A+K I D N+L+F VD+RADKK I++A+ + ++ +KVNTLI
Sbjct: 107 RILDVYQILQSPIITEAAIKNIADENSLLFTVDVRADKKMIREAISNFFGVKVRKVNTLI 166
Query: 141 RPDGTKKAYVRLTPDSDALDVANKIGI 167
RPDGTKKAY+ L + +A ++A KIGI
Sbjct: 167 RPDGTKKAYIMLNKEYNASELAKKIGI 193
>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 = 166 bits (421), Expect = 1e-53
Identities = 68/148 (45%), Positives = 90/148 (60%), Gaps = 4/148 (2%)
Query: 24 TKKADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAP---PR 80
K +A TAK K G + K K T V F RPKTL+ + PKY R
Sbjct: 4 ENKTQAVNKAKNTAKVAKKGSSITK-HKTYTGVRFFRPKTLQLAKAPKYSRTVRAHLKVS 62
Query: 81 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 140
LD++ ++K PLTTE AMKK+ED NT+VF V R+ K +IK A +K+Y+++ + VNTL
Sbjct: 63 GHLDNHSVVKTPLTTEKAMKKMEDENTMVFYVHNRSTKPQIKSAFEKLYNVKVRSVNTLN 122
Query: 141 RPDGTKKAYVRLTPDSDALDVANKIGII 168
G KKAY+RL DSD+L +ANKIG+I
Sbjct: 123 TITGNKKAYIRLAADSDSLTLANKIGLI 150
>2zkr_s 60S ribosomal protein L23A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 156
Score = 165 bits (419), Expect = 3e-53
Identities = 109/156 (69%), Positives = 119/156 (76%), Gaps = 4/156 (2%)
Query: 17 MAP----PKGETKKADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKY 72
MAP KA+ K +ALK KAV G K KKIRTS TF RPKTL+ R PKY
Sbjct: 1 MAPKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKY 60
Query: 73 PRISAPPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQ 132
PR SAP RNKLDHY I+K+PLTTESAMKKIEDNNTLVFIVD++A+K +IK AVKK+YDI
Sbjct: 61 PRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDID 120
Query: 133 AKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 168
KVNTLIRPDG KKAYVRL PD DALDVANKIGII
Sbjct: 121 VAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII 156
>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 = 130 bits (330), Expect = 1e-40
Identities = 37/82 (45%), Positives = 55/82 (67%)
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRPDGT 145
+ ++K+P TE AM ++ N L F VD RA K ++ DAV++ YD+ ++VNT DG
Sbjct: 3 WDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGE 62
Query: 146 KKAYVRLTPDSDALDVANKIGI 167
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 = 64.5 bits (158), Expect = 1e-14
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 13/90 (14%)
Query: 81 NKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLI 140
+ ++L+ P +E A +E +NT+V V A K +IK AV+K+++++ + VNTL+
Sbjct: 3 REERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLV 62
Query: 141 RP-------------DGTKKAYVRLTPDSD 157
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 = 62.9 bits (154), Expect = 5e-14
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 14/88 (15%)
Query: 83 LDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP 142
+ HY IL+ P+ +E A +E F V +A K +IKDA+++ + ++ ++T+ P
Sbjct: 1 MSHYDILQAPVISEKAYSAME-RGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVP 59
Query: 143 -------------DGTKKAYVRLTPDSD 157
+ 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 = 61.8 bits (151), Expect = 1e-13
Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 86 YQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIKDAVKKMYDIQAKKVNTLIRP--- 142
Y ++ P+ +E A F V +A K +IK+AV+ + ++ KVNTL
Sbjct: 3 YDVILAPVLSEKAYAGFA-EGKYTFWVHPKATKTEIKNAVETAFKVKVVKVNTLHVRGKK 61
Query: 143 ----------DGTKKAYVRLTPDSD 157
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 = 35.6 bits (81), Expect = 0.005
Identities = 17/109 (15%), Positives = 31/109 (28%), Gaps = 28/109 (25%)
Query: 58 FHRPKTLKKDRNPK-------YPRISAPPRNK-------LDHYQILK-YPLTTESAMKKI 102
H+ ++K Y + N+ +DHY I K +
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI--PPY 468
Query: 103 EDNNTLVFIVD--IRADKKKIKDAVKKMY-D---IQAKKVNTLIRPDGT 145
D I + + + ++ D ++ K IR D T
Sbjct: 469 LDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK-----IRHDST 512
>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 = 28.8 bits (63), Expect = 0.70
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 18/45 (40%)
Query: 122 KDAVKKMYDIQAKKVNTLIRPDGTKKAYVRLTPDS-DALDVANKI 165
K A+KK+ + K Y DS AL + +
Sbjct: 19 KQALKKL--------------QASLKLY---ADDSAPALAIKATM 46
Score = 28.0 bits (61), Expect = 1.1
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 14/33 (42%)
Query: 47 KKA-KKIRTSVTFHRPKTLKKDRNPKYPRISAP 78
K+A 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 = 28.6 bits (63), Expect = 1.1
Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 5/72 (6%)
Query: 73 PRISAPPRNKLDHYQILKYPLTTESA--MKKIEDNNTLVFIVDIRA---DKKKIKDAVKK 127
R P N L ++ + E +KK + ++ I D+R+ + +
Sbjct: 96 GRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSKRGGNEPSTADLLS 155
Query: 128 MYDIQAKKVNTL 139
Y +Q ++ L
Sbjct: 156 NYALQNVMISIL 167
>2vpn_A Periplasmic substrate binding protein; ectoine, hydroxyectoine,
trap-transporter, periplasmic binding protein,
transport; HET: 4CS; 1.55A {Halomonas elongata} PDB:
2vpo_A* 3gyy_A
Length = 316
Score = 27.6 bits (62), Expect = 1.7
Identities = 5/42 (11%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 96 ESAMKKIEDNNTLVFIVDI-RADKKKIKDAVKKMYDIQAKKV 136
E +++KI+ + V + + + K+ ++ + +
Sbjct: 251 EESLEKIKAASDEVTVTRLNDEQIQAFKERAPQVEEKFIEMT 292
>3fxb_A Trap dicarboxylate transporter, DCTP subunit; periplasmic substrate
binding protein, selectivity helix, TR membrane; HET:
4CS; 2.90A {Silicibacter pomeroyi dss-3}
Length = 326
Score = 26.5 bits (59), Expect = 4.9
Identities = 4/42 (9%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 96 ESAMKKIEDNNTLVFIVDI-RADKKKIKDAVKKMYDIQAKKV 136
++ + KI + + + + + K+A ++ +
Sbjct: 265 DTELAKIMEAKPEMQVTVLTDEQRSCFKEAAAEVEAKFIEMT 306
>1vpt_A VP39; RNA CAP, poly(A) polymerase, methyltransferase; HET: SAM;
1.80A {Vaccinia virus} SCOP: c.66.1.25 PDB: 1vp3_A*
Length = 348
Score = 25.9 bits (56), Expect = 7.8
Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 5/72 (6%)
Query: 73 PRISAPPRNKLDHYQILKYPLTTESA--MKKIEDNNTLVFIVDIRA---DKKKIKDAVKK 127
R P N L ++ + E +KK + ++ I D+ + + +
Sbjct: 111 GRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVASAAGGNEPSTADLLS 170
Query: 128 MYDIQAKKVNTL 139
Y +Q ++ L
Sbjct: 171 NYALQNVMISIL 182
>3vbb_A Seryl-tRNA synthetase, cytoplasmic; coiled-coil, ligase; 2.89A
{Homo sapiens}
Length = 522
Score = 25.8 bits (57), Expect = 9.1
Identities = 14/79 (17%), Positives = 24/79 (30%), Gaps = 1/79 (1%)
Query: 63 TLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFIVDIRADKKKIK 122
L K +N I + K P S D + + I+ + I
Sbjct: 52 NLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLID 111
Query: 123 DAVKKMYDIQAKKVNTLIR 141
+A+ K D + K+
Sbjct: 112 EAILKC-DAERIKLEAERF 129
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
0.317 0.132 0.372
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: 2,523,534
Number of extensions: 140752
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 42
Length of query: 168
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 81
Effective length of database: 4,272,666
Effective search space: 346085946
Effective search space used: 346085946
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 (21.7 bits)
S2: 54 (25.1 bits)