RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3777
(99 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 = 129 bits (326), Expect = 8e-41
Identities = 49/92 (53%), Positives = 73/92 (79%), Gaps = 3/92 (3%)
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 IVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93
VRKIS EG+ER FQ +SP++ SI VKRRG
Sbjct: 59 TVRKISNGEGVERVFQTHSPVVDSISVKRRGA 90
>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 = 127 bits (321), Expect = 1e-39
Identities = 41/93 (44%), Positives = 58/93 (62%), Gaps = 3/93 (3%)
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 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93
F VRK+SY G+ER F L+SP+I I + +RG
Sbjct: 61 FTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGR 93
>3bbo_R Ribosomal protein L19; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 233
Score = 130 bits (327), Expect = 1e-39
Identities = 29/95 (30%), Positives = 51/95 (53%), Gaps = 3/95 (3%)
Query: 1 MNLIQKIEQEEI--IRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLN 58
+++ + ++ + + +P TGD + + L V E ++R+ Y+GIVISR+N G++
Sbjct: 120 GDIMGILNKKAVHAAEELRPVPGIRTGDIVQIRLEVPEN-KRRLSVYKGIVISRQNAGIH 178
Query: 59 SNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93
+ +R+I G+E F LYSP I I V
Sbjct: 179 TTIRIRRIIAGVGVEIVFPLYSPNIKEIKVVSHRK 213
>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 = 125 bits (315), Expect = 2e-38
Identities = 38/93 (40%), Positives = 56/93 (60%), Gaps = 4/93 (4%)
Query: 1 MNLIQKIEQEEIIRLKKNIPDFVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRNKGLNSN 60
L++ IEQ+ + +PDF GDT+ V+ V EG R R QA+EG+VI+ G +
Sbjct: 10 GELLRGIEQDHT----RQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKS 65
Query: 61 FIVRKISYNEGIERTFQLYSPIISSIIVKRRGD 93
F VRKIS+ EG+ER F SP+++ + + RG
Sbjct: 66 FTVRKISFGEGVERVFPFASPLVNQVTIVERGK 98
>2ftc_K 39S ribosomal protein L19, mitochondrial; mitochondrial ribosome,
large ribosomal subunit, ribosomal R ribosome; 12.10A
{Bos taurus}
Length = 98
Score = 108 bits (271), Expect = 2e-32
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 1/76 (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 YSPIISSIIVKRRGDR 94
Y+P + I V + R
Sbjct: 60 YNPRVQEIQVVKLEKR 75
>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 = 35.4 bits (81), 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 = 26.9 bits (59), Expect = 1.1
Identities = 15/95 (15%), Positives = 34/95 (35%), Gaps = 28/95 (29%)
Query: 21 DFVTGD---TIIVNLNVIEGT-----RKRIQAY-EGIVISRR--NKGLNSNFI--VR--- 64
++ G+ + L T ++ I+ Y ++++R +K NS V
Sbjct: 94 CYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGN 153
Query: 65 -KI-----------SYNEGIERTFQLYSPIISSII 87
++ Y E + +Q Y ++ +I
Sbjct: 154 AQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLI 188
>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 = 29.1 bits (64), Expect = 0.14
Identities = 4/31 (12%), Positives = 14/31 (45%), Gaps = 13/31 (41%)
Query: 63 VRKISYNEGIERTFQLYSP-------IISSI 86
++K+ + + +LY+ I +++
Sbjct: 22 LKKL------QASLKLYADDSAPALAIKATM 46
Score = 29.1 bits (64), Expect = 0.15
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 = 27.0 bits (59), Expect = 0.95
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 41 RIQAYEGIVISRRNKGLNSNFIVRKISYNEGIERTFQLYSPIISSIIVKRRGDRNAYI 98
+ YE IS +G+ S N + + Q+ P + +RG+ +Y
Sbjct: 16 QSLNYELSFISINKQGVESLRYRHARLDNRPLAQLLQMDGPRREVV---QRGNEISYF 70
>3exz_A MAOC-like dehydratase; Q2RSA1_rhort, NESG, RRR103A, structur
genomics, PSI-2, protein structure initiative; 2.30A
{Rhodospirillum rubrum}
Length = 154
Score = 24.9 bits (55), Expect = 4.7
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 = 24.3 bits (53), Expect = 5.4
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 1 MNLIQKIEQEEIIRLKKNIP 20
M+ I IE +++ L + +
Sbjct: 4 MSYINNIEHAKVLDLTQEVM 23
>2zws_A Neutral ceramidase; prism fold and beta-sandwich fold, hydrolase,
lipid metaboli secreted; HET: PLM; 1.40A {Pseudomonas
aeruginosa} PDB: 2zxc_A*
Length = 646
Score = 24.8 bits (53), Expect = 5.9
Identities = 7/33 (21%), Positives = 12/33 (36%)
Query: 22 FVTGDTIIVNLNVIEGTRKRIQAYEGIVISRRN 54
+V D ++ V R++A V N
Sbjct: 58 YVNTDLGMIFQAVHLKVLARLKAKYPGVYDENN 90
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 0.142 0.381
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: 1,519,070
Number of extensions: 83640
Number of successful extensions: 236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 230
Number of HSP's successfully gapped: 19
Length of query: 99
Length of database: 6,701,793
Length adjustment: 65
Effective length of query: 34
Effective length of database: 4,886,928
Effective search space: 166155552
Effective search space used: 166155552
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)