RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2553
(134 letters)
>4a17_X RPL32, 60S ribosomal protein L32; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_X 4a1c_X 4a1e_X
Length = 134
Score = 147 bits (371), Expect = 6e-47
Identities = 67/133 (50%), Positives = 97/133 (72%)
Query: 1 MSIKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYG 60
M+IKPV KI+KKR K F+R +S+ + KL SWR+P+GIDNRVRRRF+GQ M IG+
Sbjct: 1 MAIKPVAHKKIIKKRTKKFVRFESEDFAKLDSSWRRPRGIDNRVRRRFRGQRRMAKIGFA 60
Query: 61 SAKKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIR 120
S T+H+LPN F K ++ N +LE+L+M NR YC EI H +S++ + +V+RA +L +R
Sbjct: 61 SDAATKHLLPNGFKKFLIRNPADLEILLMNNRTYCGEIAHNISAQVKAALVKRAAELGVR 120
Query: 121 LTNGNARIRTEEN 133
LTN NA+++ +E+
Sbjct: 121 LTNANAKVKVQES 133
>3iz5_H 60S ribosomal protein L7A (L7AE); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_H
Length = 258
Score = 145 bits (367), Expect = 3e-46
Identities = 10/132 (7%), Positives = 27/132 (20%)
Query: 3 IKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSA 62
V ++K K+ + + RF + I
Sbjct: 2 APKRGGRAPVPAKKKTEKVTNPLFEKRPKQFGIGGALPPKKDLHRFVKWPKVVRIQRQRR 61
Query: 63 KKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLT 122
+ + L + + + + K+R +A+ +
Sbjct: 62 ILKQRLKVPPALNQFTRTLDKNLATNLFKMLLKYRPEDKAAKKERLLKRAQAEAEGKTVE 121
Query: 123 NGNARIRTEENE 134
+
Sbjct: 122 AKKPIVVKYGLN 133
>2zkr_y 60S ribosomal protein L32; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 135
Score = 144 bits (365), Expect = 6e-46
Identities = 96/132 (72%), Positives = 114/132 (86%)
Query: 3 IKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSA 62
++P+ +PKIVKKR K FIRHQSDRY K+ R+WRKP+GIDNRVRRRFKGQ LMPNIGYGS
Sbjct: 4 LRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSN 63
Query: 63 KKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLT 122
KKT+HMLP+ F K +VHNVKELEVL+M N+ YCAEI H VSSK R+ IV+RA QL+IR+T
Sbjct: 64 KKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVT 123
Query: 123 NGNARIRTEENE 134
N NAR+R+EENE
Sbjct: 124 NPNARLRSEENE 135
>3u5e_e 60S ribosomal protein L32, 60S ribosomal protein L31-A;
translation, ribosome, ribosomal R ribosomal protein,
STM1, eukaryotic ribosome; 3.00A {Saccharomyces
cerevisiae} PDB: 3izc_h 1s1i_0 3izs_h 3o5h_b 3o58_b
3u5i_e 3jyw_0
Length = 130
Score = 141 bits (356), Expect = 1e-44
Identities = 62/129 (48%), Positives = 82/129 (63%)
Query: 3 IKPVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSA 62
+ + PKIVKK K F RH SDRY ++ +WRK KGID+ VRRRF+G P IGYGS
Sbjct: 1 MASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNISQPKIGYGSN 60
Query: 63 KKTRHMLPNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLT 122
KKT+ + P+ +V NVK+LE L M + Y AEI H +S+K R I+ RA+ L I++T
Sbjct: 61 KKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNISAKNRVVILARAKALGIKVT 120
Query: 123 NGNARIRTE 131
N R+ E
Sbjct: 121 NPKGRLALE 129
>1vq8_Y 50S ribosomal protein L32E; 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: c.9.2.1 PDB: 1vq4_Y*
1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y*
1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y*
1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Length = 241
Score = 135 bits (341), Expect = 4e-41
Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 2/111 (1%)
Query: 13 KKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYGSAKKTRHMLPNH 72
+ + F R + K++ SWRKP+G ++ RR KG+ G+ S R P+
Sbjct: 123 RVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSG 182
Query: 73 FLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIRLTN 123
F +V VHNV +LE + I V ++KR I + A+ IR+ N
Sbjct: 183 FEEVRVHNVDDLE--GVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLN 231
>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 = 32.9 bits (74), Expect = 0.021
Identities = 18/130 (13%), Positives = 35/130 (26%), Gaps = 34/130 (26%)
Query: 5 PVYRPKIVKKRRKVFIRHQSDRYKKLHRSWRKPKGIDNRVRRRFKGQYLMPNIGYG---- 60
V R + K R+ + + + + G + G G
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLID-------G--------------VL--GSGKTWV 166
Query: 61 -----SAKKTRHMLPN--HFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQR 113
+ K + + +L + N E + M+Q Y + S +I R
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 114 AQQLSIRLTN 123
+ L
Sbjct: 227 IHSIQAELRR 236
Score = 30.2 bits (67), Expect = 0.22
Identities = 22/169 (13%), Positives = 44/169 (26%), Gaps = 76/169 (44%)
Query: 12 VKKRRKVF----------IRHQSDRYKKLHRSWRKPKGIDN-RVRRRFKGQYLMPN---- 56
V+K+ K ++ + + LHR +D+ + + F L+P
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHR-----SIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 57 -----IGYGSAKKTRHM-----------LPNHFL-------KV-----VVHNVKELEVLM 88
IG+ H+ FL K+ + + +
Sbjct: 472 YFYSHIGH-------HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL 524
Query: 89 MQNRKYCAEI---------------------GHAVSSKKRRDIVQRAQQ 116
Q + Y I + K D+++ A
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALM 573
>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 = 29.2 bits (65), Expect = 0.39
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 5/51 (9%)
Query: 70 PNHFLKVVVHNVKELEVLMMQNRKYCAEIGHAVSSKKRRDIVQRAQQLSIR 120
+ VV + L L + RK A G S +R + S R
Sbjct: 374 AKNL--VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS---ERKLKFSNR 419
Score = 29.2 bits (65), Expect = 0.48
Identities = 26/203 (12%), Positives = 46/203 (22%), Gaps = 92/203 (45%)
Query: 6 VYRPKIVKKRRKVFIRHQSDRYKKLHRSWRK-----PKGID-----NRVRRRFKGQYL-- 53
Y + I+ ++ +L R+ +G++ YL
Sbjct: 179 TYHVLV-----GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLS 233
Query: 54 ----MPNIG------YGSAKKTRHMLPNHFLK-----------VVV-------------- 78
P IG Y K P +V
Sbjct: 234 IPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFF 293
Query: 79 HNVKE-LEVL-------------------MMQNRKYCAEIGHAVSS-------------- 104
+V++ + VL +++ E V S
Sbjct: 294 VSVRKAITVLFFIGVRCYEAYPNTSLPPSILE---DSLENNEGVPSPMLSISNLTQEQVQ 350
Query: 105 ---KKRRDIVQRAQQLSIRLTNG 124
K + +Q+ I L NG
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNG 373
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
0.323 0.136 0.396
Gapped
Lambda K H
0.267 0.0527 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,055,369
Number of extensions: 115219
Number of successful extensions: 211
Number of sequences better than 10.0: 1
Number of HSP's gapped: 209
Number of HSP's successfully gapped: 13
Length of query: 134
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 51
Effective length of database: 4,384,350
Effective search space: 223601850
Effective search space used: 223601850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.3 bits)