RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3772
(119 letters)
>3r8s_P 50S ribosomal protein L19; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_N 1p86_N 2awb_P 2gya_N 2gyc_N 2aw4_P 2i2v_P 2j28_P
2i2t_P* 2qao_P* 2qba_P* 2qbc_P* 2qbe_P 2qbg_P 2qbi_P*
2qbk_P* 2qov_P 2qox_P 2qoz_P* 2qp1_P* ...
Length = 114
Score = 171 bits (435), Expect = 5e-57
Identities = 66/115 (57%), Positives = 95/115 (82%), Gaps = 3/115 (2%)
Query: 2 NLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNF 61
N+I+++EQE+ +K+++P F GDT+ V + V+EG++KR+QA+EG+VI+ RN+GL+S F
Sbjct: 2 NIIKQLEQEQ---MKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAF 58
Query: 62 IVRKISYNEGIERTFQLYSPIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKL 116
VRKIS EG+ER FQ +SP++ SI VKRRG VR+AKLYYLR+ +GK+ARIKE+L
Sbjct: 59 TVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLRERTGKAARIKERL 113
>3v2d_T 50S ribosomal protein L19; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_S 2hgj_S 2hgu_S 2j03_T 2jl6_T 2jl8_T 2v47_T 2v49_T
2wdi_T 2wdj_T 2wdl_T 2wdn_T 2wh2_T 2wh4_T 2wrj_T 2wrl_T
2wro_T 2wrr_T 2x9s_T 2x9u_T ...
Length = 146
Score = 168 bits (428), Expect = 2e-55
Identities = 52/119 (43%), Positives = 74/119 (62%), Gaps = 3/119 (2%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
LI+ +E ++ ++P+F GDT+ V+ V EG R RIQ +EGIVI R G N+
Sbjct: 4 GALIKLVESRY---VRTDLPEFRPGDTVRVSYKVKEGNRTRIQDFEGIVIRIRRNGFNTT 60
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKLLKK 119
F VRK+SY G+ER F L+SP+I I + +RG RRAKLY++R S + R K + +K
Sbjct: 61 FTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAKLYFIRNLSDREIRRKLRADRK 119
>3bbo_R Ribosomal protein L19; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 233
Score = 167 bits (423), Expect = 9e-54
Identities = 38/115 (33%), Positives = 64/115 (55%), Gaps = 3/115 (2%)
Query: 1 MNLIQKIEQEEI--IRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLN 58
+++ + ++ + + +P TGD + + L V E ++R+ Y+GIVISR+N G++
Sbjct: 120 GDIMGILNKKAVHAAEELRPVPGIRTGDIVQIRLEVPEN-KRRLSVYKGIVISRQNAGIH 178
Query: 59 SNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGDVRRAKLYYLRKCSGKSARIK 113
+ +R+I G+E F LYSP I I V VR+A+LYYLR + + K
Sbjct: 179 TTIRIRRIIAGVGVEIVFPLYSPNIKEIKVVSHRKVRKARLYYLRDKLPRLSTFK 233
>2zjr_M 50S ribosomal protein L19; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.34.5.6 PDB: 1nwx_N* 1nwy_N* 1sm1_N*
1xbp_N* 2zjp_M* 2zjq_M 1nkw_N 3cf5_M* 3dll_M* 3pio_M*
3pip_M* 1pnu_N 1pny_N 1vor_Q 1vou_Q 1vow_Q 1voy_Q 1vp0_Q
Length = 166
Score = 164 bits (416), Expect = 2e-53
Identities = 54/119 (45%), Positives = 75/119 (63%), Gaps = 4/119 (3%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
L++ IEQ+ + +PDF GDT+ V+ V EG R R QA+EG+VI+ G +
Sbjct: 10 GELLRGIEQDHT----RQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKS 65
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKLLKK 119
F VRKIS+ EG+ER F SP+++ + + RG VRRAKLYYLR+ GK+ARIK +
Sbjct: 66 FTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRELRGKAARIKSDRSRV 124
>2ftc_K 39S ribosomal protein L19, mitochondrial; mitochondrial ribosome,
large ribosomal subunit, ribosomal R ribosome; 12.10A
{Bos taurus}
Length = 98
Score = 144 bits (365), Expect = 2e-46
Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 1/98 (1%)
Query: 19 IPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQL 78
IP+F G + V +I + GI I R +GL + FI+R + +G+E F+L
Sbjct: 1 IPEFYVGSILRVTTADPYA-SGKISQFLGICIQRSGRGLGATFILRNVIEGQGVEICFEL 59
Query: 79 YSPIISSIIVKRRGDVRRAKLYYLRKCSGKSARIKEKL 116
Y+P + I V + L YLR + + +
Sbjct: 60 YNPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDVNM 97
>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 = 36.2 bits (83), Expect = 0.001
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 17/68 (25%)
Query: 6 KIEQEEIIRLKKNIPDFVTGDTI-IVNLNVIEGTRKRIQAYEGIVISRRNKGLNS----- 59
QE + + + + TG + IVN NV E Q V + + L++
Sbjct: 1820 SFSQEALQYVVERVGK-RTGWLVEIVNYNV-ENQ----Q----YVAAGDLRALDTVTNVL 1869
Query: 60 NFI-VRKI 66
NFI ++KI
Sbjct: 1870 NFIKLQKI 1877
Score = 28.5 bits (63), Expect = 0.57
Identities = 20/146 (13%), Positives = 48/146 (32%), Gaps = 41/146 (28%)
Query: 3 LIQKIEQEEIIR----LKKNIPDFVTG-----D--TIIVNLNVIEGT-----RKRIQAY- 45
+ +E ++ + L + +F D + L T ++ I+ Y
Sbjct: 68 VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYI 127
Query: 46 EGIVISRR--NKGLNSNFI--VR----KI-----------SYNEGIERTFQLYSPIISSI 86
++++R +K NS V ++ Y E + +Q Y ++ +
Sbjct: 128 TARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDL 187
Query: 87 IVKRRGDVRRAKLYYLRKCSGKSARI 112
I L L + + + ++
Sbjct: 188 I-----KFSAETLSELIRTTLDAEKV 208
>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 = 28.4 bits (62), Expect = 0.42
Identities = 3/19 (15%), Positives = 10/19 (52%), Gaps = 6/19 (31%)
Query: 63 VRKISYNEGIERTFQLYSP 81
++K+ + + +LY+
Sbjct: 22 LKKL------QASLKLYAD 34
Score = 28.4 bits (62), Expect = 0.49
Identities = 4/33 (12%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 8 EQEEIIRLKKNI----PDFVTGDTIIVNLNVIE 36
E++ + +L+ ++ D + + + +E
Sbjct: 18 EKQALKKLQASLKLYADD--SAPALAIKAT-ME 47
>3m4w_A Sigma-E factor regulatory protein RSEB; RSEA, RSEB, RSEP, stress
response, sigma factor, periplasm, membrane,
transmembrane; 2.30A {Escherichia coli} PDB: 2p4b_A
2v43_A 2v42_A
Length = 295
Score = 26.2 bits (57), Expect = 2.5
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 41 RIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGDV 94
+ YE IS +G+ S N + + Q+ P + +RG+
Sbjct: 16 QSLNYELSFISINKQGVESLRYRHARLDNRPLAQLLQMDGPRREVV---QRGNE 66
>3exz_A MAOC-like dehydratase; Q2RSA1_rhort, NESG, RRR103A, structur
genomics, PSI-2, protein structure initiative; 2.30A
{Rhodospirillum rubrum}
Length = 154
Score = 25.3 bits (56), Expect = 4.6
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 25 GDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
GD + V V+ T + + IV ++ LN
Sbjct: 95 GDELHVETTVLAITPSKSRPDRAIVTC-QSDTLNQR 129
>1yhf_A Hypothetical protein SPY1581; structural genomics, conserved
hypothetical protein, PSI, PR structure initiative;
2.00A {Streptococcus pyogenes} SCOP: b.82.1.9
Length = 115
Score = 25.1 bits (55), Expect = 5.0
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 1 MNLIQKIEQEEIIRLKKNIP 20
M+ I IE +++ L + +
Sbjct: 4 MSYINNIEHAKVLDLTQEVM 23
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
0.322 0.140 0.377
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,850,853
Number of extensions: 105197
Number of successful extensions: 256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 250
Number of HSP's successfully gapped: 23
Length of query: 119
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,440,192
Effective search space: 168727296
Effective search space used: 168727296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.3 bits)