RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9578
(122 letters)
>3v2d_U 50S ribosomal protein L20; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_O 2hgj_T 2hgq_T 2hgu_T 1vsa_O 2j03_U 2jl6_U 2jl8_U
2v47_U 2v49_U 2wdi_U 2wdj_U 2wdl_U 2wdn_U 2wh2_U 2wh4_U
2wrj_U 2wrl_U 2wro_U 2wrr_U ...
Length = 118
Score = 184 bits (469), Expect = 5e-62
Identities = 57/117 (48%), Positives = 81/117 (69%)
Query: 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSL 60
MPR K GV R +HKK+LK AKGY+G R+ +R A++ + A YAY R+ +KR FR L
Sbjct: 1 MPRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRKRRKRDFRRL 60
Query: 61 WISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117
WI RINAA R+H + Y+TF++GLKK+ I++DRK LA +A+ + VF+ +V + K
Sbjct: 61 WIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVREPQVFAELVERAKAAQ 117
>2zjr_N 50S ribosomal protein L20; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: a.144.2.1 PDB: 1nwx_O* 1nwy_O*
1sm1_O* 1xbp_O* 1yl3_1 2b66_U 2b9n_U 2b9p_U 2zjp_N*
2zjq_N 1nkw_O 3cf5_N* 3dll_N* 3pio_N* 3pip_N* 1pnu_O
1pny_O 1vor_R 1vou_R 1vow_R ...
Length = 118
Score = 183 bits (468), Expect = 7e-62
Identities = 62/117 (52%), Positives = 82/117 (70%)
Query: 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSL 60
MPR K G+ R RHKKVLK+AKG++G R+ YR A Q +++A Y YRDRRNKKR FR L
Sbjct: 1 MPRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRL 60
Query: 61 WISRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117
WI RINA R H M Y+TF+NGLK+++I L+RK+LA IA + F ++V+ +
Sbjct: 61 WIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDASRNAR 117
>3r8s_Q 50S ribosomal protein L20; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_O 1p86_O 2awb_Q 2aw4_Q 2i2v_Q 2j28_Q 2i2t_Q*
2qao_Q* 2qba_Q* 2qbc_Q* 2qbe_Q 2qbg_Q 2qbi_Q* 2qbk_Q*
2qov_Q 2qox_Q 2qoz_Q* 2qp1_Q* 2rdo_Q 2vhm_Q ...
Length = 117
Score = 178 bits (454), Expect = 1e-59
Identities = 73/115 (63%), Positives = 96/115 (83%)
Query: 3 RVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWI 62
RVKRGV ARARHKK+LKQAKGY+G R+ VYRVA QAV+ A QYAYRDRR +KR FR LWI
Sbjct: 2 RVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWI 61
Query: 63 SRINAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117
+RINAA R++ ++Y+ F+NGLKK+S+++DRK+LA IA+ DK+ F+++V + K L
Sbjct: 62 ARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAAL 116
>3bbo_S Ribosomal protein L20; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 119
Score = 175 bits (445), Expect = 2e-58
Identities = 49/117 (41%), Positives = 69/117 (58%), Gaps = 2/117 (1%)
Query: 1 MPRVKRGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSL 60
M RVKRG AR R KK+ A + G + + R Q + A+ A+RDR +KR FR L
Sbjct: 1 MTRVKRGYIARRRRKKIRFFASSFRGAHSRLTRTIAQQKIRALVSAHRDRDRQKRDFRRL 60
Query: 61 WISRINAAVREHKM--TYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKE 115
WI+RINAA+RE + Y+ F++ L K + L+RK+LA IAI + I N+I +
Sbjct: 61 WITRINAAIRERGVYYNYSKFIHDLYKRQLLLNRKILAQIAILNPNCIYMIYNEIIK 117
>2ghj_A 50S ribosomal protein L20; folding intermediate, ribosomal protein
extension, structural protein; 2.90A {Aquifex aeolicus}
PDB: 1gyz_A
Length = 118
Score = 173 bits (440), Expect = 1e-57
Identities = 62/115 (53%), Positives = 87/115 (75%)
Query: 6 RGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRI 65
+G ++R + KK+LK AKGY G+R+ YR AK+AVM A+ Y YRDR+ +KR FR LWI+RI
Sbjct: 4 KGPSSRRKKKKILKLAKGYRGQRSRSYRRAKEAVMRALYYQYRDRKLRKREFRRLWIARI 63
Query: 66 NAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENLTNK 120
NAAVR + + Y+TF+NGLKK+ I+LDRK+LA +A+ D F +VN++KE L +
Sbjct: 64 NAAVRAYGLNYSTFINGLKKAGIELDRKILADMAVRDPQAFEQVVNKVKEALQVQ 118
>2ftc_L MRPL20 protein; mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus}
Length = 118
Score = 169 bits (431), Expect = 3e-56
Identities = 39/112 (34%), Positives = 61/112 (54%)
Query: 6 RGVTARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRI 65
R R ++VLK A+ + GR+N YR+A + V+ A + R KK+ R+LWI+RI
Sbjct: 6 RVTDRYFRIQEVLKHARHFRGRKNRCYRLAVRTVIRAFVKCTKARYLKKKNMRTLWINRI 65
Query: 66 NAAVREHKMTYNTFMNGLKKSSIQLDRKLLASIAITDKLVFSSIVNQIKENL 117
AA +EH + Y + L K ++L+RK+LA +AI + F S+
Sbjct: 66 TAASQEHGLKYPALIGNLVKCQVELNRKVLADLAIYEPKTFKSLAALASRRR 117
>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 = 30.4 bits (68), Expect = 0.13
Identities = 19/103 (18%), Positives = 30/103 (29%), Gaps = 27/103 (26%)
Query: 37 QAV-MHAMQYAYRDRRNKKRVFRSLW--------------ISRINAAVREHKMTYNTFMN 81
Q M M D + + +W I I V T
Sbjct: 1627 QEQGM-GM-----DLYKTSKAAQDVWNRADNHFKDTYGFSILDI---VIN-NPVNLTIHF 1676
Query: 82 GLKKS-SI-QLDRKLLASIAITDKLVFSSIVNQIKENLTNKAF 122
G +K I + ++ + KL I +I E+ T+ F
Sbjct: 1677 GGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTF 1719
Score = 27.3 bits (60), Expect = 1.7
Identities = 18/100 (18%), Positives = 32/100 (32%), Gaps = 27/100 (27%)
Query: 15 KKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRV---FRSLWISRINAAVRE 71
+ V +A +F Y + ++ N + F RI RE
Sbjct: 1643 QDVWNRADNHFK---DTYGFSILDIV---------INNPVNLTIHFGGEKGKRI----RE 1686
Query: 72 H--KMTYNTFMNGLKKSSIQLDRKLLASIAI-TDKLVFSS 108
+ M + T ++G K+ K+ I + F S
Sbjct: 1687 NYSAMIFETIVDGKLKT-----EKIFKEINEHSTSYTFRS 1721
>1pp9_A Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_A* 1be3_A* 1l0n_A* 1ntk_A* 1ntm_A*
1ntz_A* 1nu1_A* 1l0l_A* 1ppj_A* 1sqq_A* 1sqv_A* 1sqx_A*
2a06_A* 2fyu_A* 2ybb_A* 1sqb_A* 1sqp_A* 1qcr_A* 1bcc_A*
2bcc_A* ...
Length = 446
Score = 26.0 bits (58), Expect = 3.2
Identities = 5/42 (11%), Positives = 17/42 (40%)
Query: 14 HKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKR 55
H+++L A+ +F + Y + ++ +++
Sbjct: 205 HRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQICHRED 246
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 25.8 bits (57), Expect = 5.3
Identities = 7/57 (12%), Positives = 18/57 (31%)
Query: 19 KQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLWISRINAAVREHKMT 75
K +G+ R+ + + ++ R + R+ I R + +
Sbjct: 776 KTIRGWLMRKKYMRMRRAAITIQRYVRGHQARCYATFLRRTRAAIIIQKFQRMYVVR 832
>2i2w_A Phosphoheptose isomerase; lipopolysaccharide biosynthesis; 1.95A
{Escherichia coli} PDB: 2i22_A 1x94_A
Length = 212
Score = 25.4 bits (56), Expect = 5.4
Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 79 FMNGLKKSSIQLDRKLLASIAITDKLVFSSIVN 111
++ +R +IAI+D S + N
Sbjct: 86 LTGRYRE-----NRPGYPAIAISDVSHISCVGN 113
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 25.0 bits (55), Expect = 9.1
Identities = 7/68 (10%), Positives = 22/68 (32%), Gaps = 3/68 (4%)
Query: 9 TARARHKKVLKQAKGYFGRRNSVYRVAKQAVMHAMQYAYRDRRNKKRVFRSLW---ISRI 65
T K+ + + ++ S+ + ++Q + K+ + +S +
Sbjct: 759 TKSDYLKRANELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKTEKPPKGQEVSEL 818
Query: 66 NAAVREHK 73
A +
Sbjct: 819 EAIYNSLQ 826
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 0.132 0.367
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,722,023
Number of extensions: 88914
Number of successful extensions: 235
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 24
Length of query: 122
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,412,271
Effective search space: 176490840
Effective search space used: 176490840
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: 51 (23.5 bits)