RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033482
(118 letters)
>3iz6_J 40S ribosomal protein S20 (S10P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 128
Score = 133 bits (335), Expect = 1e-41
Identities = 97/122 (79%), Positives = 105/122 (86%), Gaps = 5/122 (4%)
Query: 1 MAYAA-MKPTKPGLEEAQEQIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRM 59
+AYA MK K G E +QE H+IRITLSSK+VKNLEKVC DLV+GAKDK L+VKGPVRM
Sbjct: 6 VAYAPPMKSGKIGFESSQEVQHRIRITLSSKSVKNLEKVCGDLVKGAKDKSLKVKGPVRM 65
Query: 60 PTKVLHITTRKSPCGEGTNTWDRFELRVHKRVIDLFSSPD----ITSITIEPGVEVEVTI 115
PTKVLHITTRKSPCGEGTNTWDRFE+RVHKRVIDL SS D ITSITIEPGVEVEVTI
Sbjct: 66 PTKVLHITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSADVVKQITSITIEPGVEVEVTI 125
Query: 116 AD 117
+D
Sbjct: 126 SD 127
>2zkq_j 40S ribosomal protein S20E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 119
Score = 129 bits (326), Expect = 2e-40
Identities = 79/118 (66%), Positives = 96/118 (81%), Gaps = 4/118 (3%)
Query: 5 AMKPTKPGLEEAQEQIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVL 64
A K T E + IH+IRITL+S+NVK+LEKVC DL+RGAK+K L+VKGPVRMPTK L
Sbjct: 2 AFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTL 61
Query: 65 HITTRKSPCGEGTNTWDRFELRVHKRVIDLFSSPD----ITSITIEPGVEVEVTIADS 118
ITTRK+PCGEG+ TWDRF++R+HKR+IDL S + ITSI+IEPGVEVEVTIAD+
Sbjct: 62 RITTRKTPCGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA 119
>3u5c_U 40S ribosomal protein S20; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_J 3o30_N 3o2z_N 3u5g_U 1s1h_J 3jyv_J*
Length = 121
Score = 123 bits (311), Expect = 4e-38
Identities = 61/117 (52%), Positives = 81/117 (69%), Gaps = 4/117 (3%)
Query: 6 MKPTKPGLEEAQEQIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLH 65
K E+ Q+QI KIRITL+S VK LE V +++V+ A+ L KGPVR+PTKVL
Sbjct: 5 QKEKVEEQEQQQQQIIKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLK 64
Query: 66 ITTRKSPCGEGTNTWDRFELRVHKRVIDLFSSPD----ITSITIEPGVEVEVTIADS 118
I+TRK+P GEG+ TW+ +E+R+HKR IDL + IT ITIEPGV+VEV +A +
Sbjct: 65 ISTRKTPNGEGSKTWETYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVVASN 121
>2xzm_J Ribosomal protein S10 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_J
Length = 120
Score = 118 bits (298), Expect = 3e-36
Identities = 61/119 (51%), Positives = 85/119 (71%), Gaps = 7/119 (5%)
Query: 4 AAMKPTKPGLEEAQEQIHKIRITLSSKNVKNLEKVCTDLV-RGAKDKRLRVKGPVRMPTK 62
A K TK G EE + ++RITL+ KN+K++EK +++V R K +++ VKGPVRMPTK
Sbjct: 2 DATKETKKGEEEVK--KVRVRITLTCKNLKSVEKATSEIVSRAKKTEQVEVKGPVRMPTK 59
Query: 63 VLHITTRKSPCGEGTNTWDRFELRVHKRVIDLFSSPD----ITSITIEPGVEVEVTIAD 117
L IT RKSPCGEG+ TWDRFE+R++KR+IDL + IT+ I+PGVE+E+T+
Sbjct: 60 TLVITVRKSPCGEGSKTWDRFEMRIYKRIIDLTCNVPDVKTITNFRIDPGVEIELTMTA 118
>2vqe_J 30S ribosomal protein S10, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
d.58.15.1 PDB: 1gix_M* 1hnw_J* 1hnx_J* 1hnz_J* 1hr0_J
1ibk_J* 1ibl_J* 1ibm_J 1jgo_M* 1jgp_M* 1jgq_M* 1ml5_M*
1xmo_J* 1xmq_J* 1xnq_J* 1xnr_J* 1yl4_M 2b64_J* 2b9m_J*
2b9o_J* ...
Length = 105
Score = 110 bits (276), Expect = 6e-33
Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 6/101 (5%)
Query: 20 IHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLHITTRKSPCGEGTNT 79
+ KIRI L + K L+ +V A+ +V GP+ +PT+V T + P + ++
Sbjct: 1 MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPF-KHKDS 59
Query: 80 WDRFELRVHKRVIDLFSSPD-----ITSITIEPGVEVEVTI 115
+ FELR H R++D+ + + ++ + GVE+E+
Sbjct: 60 REHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT 100
>3r8n_J 30S ribosomal protein S10; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_J 3fih_J* 2wwl_J 3oar_J
3oaq_J 3ofb_J 3ofa_J 3ofp_J 3ofx_J 3ofy_J 3ofo_J 3r8o_J
4a2i_J 3i1m_J 1p6g_J 1p87_J* 1vs7_J* 2avy_J 2aw7_J
1vs5_J ...
Length = 98
Score = 105 bits (265), Expect = 2e-31
Identities = 24/99 (24%), Positives = 54/99 (54%), Gaps = 6/99 (6%)
Query: 22 KIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLHITTRKSPCGEGTNTWD 81
+IRI L + + + +++ ++V AK +V+GP+ +PT+ T SP + D
Sbjct: 1 RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISP-HVNKDARD 59
Query: 82 RFELRVHKRVIDLFSSPD-----ITSITIEPGVEVEVTI 115
++E+R H R++D+ + + + + GV+V++++
Sbjct: 60 QYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL 98
>3bbn_J Ribosomal protein S10; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 197
Score = 108 bits (271), Expect = 3e-31
Identities = 33/118 (27%), Positives = 51/118 (43%), Gaps = 7/118 (5%)
Query: 4 AAMKPTKPGLEEAQE-QIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTK 62
+ G + Q KIRI L S V +E C ++ A+ + GPV +PTK
Sbjct: 81 SETSALGIGADSDQMAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKTMGPVPLPTK 140
Query: 63 VLHITTRKSPCGEGTNTWDRFELRVHKRVIDLFSSPD-----ITSITIEPGVEVEVTI 115
KSP + FE+R H+R+ID+ + + + GV+VEV +
Sbjct: 141 KRIFCVLKSPHVHKDARF-HFEIRTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL 197
>3d3c_J 30S ribosomal protein S10, N utilization substance protein B; NUSB,
NUSE, phage lambda, lambda N antitermination
antitermination; 2.60A {Escherichia coli} PDB: 2kvq_E
3d3b_J* 3imq_J
Length = 87
Score = 67.1 bits (164), Expect = 4e-16
Identities = 20/103 (19%), Positives = 46/103 (44%), Gaps = 27/103 (26%)
Query: 19 QIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLHITTRKSPCGEGTN 78
Q +IRI L + + + +++ ++V AK +V+GP+ +PT+
Sbjct: 7 QNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTR---------------- 50
Query: 79 TWDRFELRVHKRVIDLFSSPD-----ITSITIEPGVEVEVTIA 116
R H R++D+ + + + + GV+V++++
Sbjct: 51 ------SRTHLRLVDIVEPTEKTVDDLMRLDLAAGVDVQISLG 87
>3r2c_J Protein NUSE, 30S ribosomal protein S10; cross species
NUSB-NUSE-RNA interaction; HET: PEG; 1.90A {Aquifex
aeolicus} PDB: 3r2d_J
Length = 83
Score = 53.6 bits (129), Expect = 6e-11
Identities = 21/100 (21%), Positives = 39/100 (39%), Gaps = 27/100 (27%)
Query: 21 HKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLHITTRKSPCGEGTNTW 80
KIRI L + + + L++ ++ K VKGP+ +PT+
Sbjct: 4 EKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRK----------------- 46
Query: 81 DRFELRVHKRVIDLFSSPD-----ITSITIEPGVEVEVTI 115
R++D+ + I++ GV+VEV +
Sbjct: 47 -----SEFSRILDIIRFTPQTIEALMEISLPAGVDVEVKM 81
>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 = 34.1 bits (77), Expect = 0.006
Identities = 20/113 (17%), Positives = 33/113 (29%), Gaps = 38/113 (33%)
Query: 22 KIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPT---------KVLHITTRKSP 72
KI +T K V TD + A + + T K L + P
Sbjct: 267 KILLTTRFKQV-------TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319
Query: 73 ---CG--------------EGTNTWDRFELRVHKRVIDLFSSPDITSI-TIEP 107
+G TWD ++ ++ + S S+ +EP
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES----SLNVLEP 368
>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 = 33.1 bits (75), Expect = 0.015
Identities = 22/163 (13%), Positives = 51/163 (31%), Gaps = 68/163 (41%)
Query: 13 LEEAQEQIHKIRITLSSKNVKNLEKVCTDLVRGAKD-KRLRVKG---------------- 55
EE ++ +++ L +K + ++L+R D +++ +G
Sbjct: 170 FEELRD-LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK 228
Query: 56 ------PVRMP----TKVLH-ITTRK----SP------------CGEG---------TNT 79
P+ P ++ H + T K +P +G T++
Sbjct: 229 DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDS 288
Query: 80 WDRFE--------------LRVHKRVIDLFSSPDITSITIEPG 108
W+ F +R ++ + P I ++E
Sbjct: 289 WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENN 331
>3ib7_A ICC protein; metallophosphoesterase, alpha-beta fold,
swapped-dimer, HYDR; HET: BTB; 1.60A {Mycobacterium
tuberculosis} PDB: 3ib8_A* 2hy1_A 2hyp_A 2hyo_A
Length = 330
Score = 26.0 bits (57), Expect = 3.6
Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 6/62 (9%)
Query: 48 DKRLRVKGPVRMPTKVLHIT-----TRKSPCGEGTNTWDRFELRVHKRVIDLFSSPDITS 102
+ RLR R +LHI+ + DR + +++ PD
Sbjct: 13 EHRLRAAEHPRPDYVLLHISDTHLIGGDRRLYGAVDADDRLG-ELLEQLNQSGLRPDAIV 71
Query: 103 IT 104
T
Sbjct: 72 FT 73
>1hc1_A Arthropodan hemocyanin; oxygen transport; 3.20A {Panulirus
interruptus} SCOP: a.85.1.1 a.86.1.1 b.1.18.3 PDB:
1hc2_A 1hc3_A 1hc4_A 1hc5_A 1hc6_A 1hcy_A*
Length = 657
Score = 26.0 bits (57), Expect = 4.2
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 77 TNTWDRFELRVHKRVIDLFSS-----PDITSITIE-PGVEVE 112
T T D R+HK + ++F P T +E G+ V
Sbjct: 373 TATRDPSFFRLHKYMDNIFKKHTDSFPPYTHDNLEFSGMVVN 414
>1n91_A ORF, hypothetical protein; alpha+beta, northeast structural
genomics consortium, PSI, P structure initiative, NESG;
NMR {Escherichia coli} SCOP: d.206.1.1 PDB: 1yh5_A
Length = 108
Score = 25.2 bits (55), Expect = 4.4
Identities = 5/34 (14%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 41 DLVRGAK--DKRLRVKGPVRMPTKVLHITTRKSP 72
+ +G K++++ P ++P +V + +
Sbjct: 71 VIEKGELGRHKQIKIINPQQIPPEVAALINLEHH 104
>3d03_A Phosphohydrolase; glycerophosphodiesterase, metallohydrolase,
phosphatase, metal ION; 1.90A {Enterobacter aerogenes}
SCOP: d.159.1.11 PDB: 2zoa_A 2zo9_B 2dxn_A 2dxl_A
Length = 274
Score = 25.5 bits (56), Expect = 4.5
Identities = 6/41 (14%), Positives = 12/41 (29%), Gaps = 1/41 (2%)
Query: 64 LHITTRKSPCGEGTNTWDRFELRVHKRVIDLFSSPDITSIT 104
H +R + V ++ L PD ++
Sbjct: 9 THFRSRGEKLYGFIDVNAANA-DVVSQLNALRERPDAVVVS 48
>2ifr_A Scytalidopepsin B; enzyme-transition state analog complex,
hydrolase-hydrolase complex; HET: TA2; 1.95A
{Scytalidium lignicola} SCOP: b.29.1.20 PDB: 1s2b_A*
1s2k_A* 2ifw_A*
Length = 206
Score = 25.3 bits (55), Expect = 5.0
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 96 SSPDITSITIEPGVEVEVTI 115
S D + ITI G +++++
Sbjct: 74 VSDDFSGITISEGDSIQMSV 93
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
0.316 0.132 0.380
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,775,233
Number of extensions: 94168
Number of successful extensions: 232
Number of sequences better than 10.0: 1
Number of HSP's gapped: 215
Number of HSP's successfully gapped: 19
Length of query: 118
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 37
Effective length of database: 4,440,192
Effective search space: 164287104
Effective search space used: 164287104
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 (21.6 bits)
S2: 51 (23.7 bits)