RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11684
(198 letters)
>3r8n_P 30S ribosomal protein S16; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 1p6g_P 1p87_P* 1vs7_P* 2avy_P
2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P* 2qbb_P*
2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P* 2qoy_P*
2qp0_P* 2vho_P ...
Length = 82
Score = 64.5 bits (158), Expect = 2e-14
Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 48/107 (44%)
Query: 47 IRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHID 106
IRLAR+G RPFY +VV S
Sbjct: 4 IRLARHGAKKRPFYQVVVADS--------------------------------------- 24
Query: 107 KKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLG 153
R RN + IE++G F+P+ +E +E+ L+++RI +W+G
Sbjct: 25 --------RNARNGRFIERVGFFNPIASE-KEEGTRLDLDRIAHWVG 62
>3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 88
Score = 64.1 bits (157), Expect = 3e-14
Identities = 22/134 (16%), Positives = 40/134 (29%), Gaps = 62/134 (46%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M K +RL R G R Y IV I
Sbjct: 1 MVK-LRLKRCGRKQRAVYRIVAIDV----------------------------------- 24
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGT----SDIH 158
R RR + ++++G +DP+ ++ LN+ I +L ++
Sbjct: 25 ------------RSRREGRDLQKVGFYDPIKSQ-----TYLNVPAILDFLEKGAQPTE-- 65
Query: 159 ITSPVRELFGKLNI 172
V ++ + +
Sbjct: 66 ---TVYDILKRAEV 76
>3pys_P 30S ribosomal protein S16; ribosome, IGR, IRES, PSIV, CRPV; 3.40A
{Thermus thermophilus} PDB: 1pnx_P 1voq_P 1vos_P 1vov_P
1vox_P 1voz_P 1pns_P 3ms0_P 3mr8_P 3pyq_P 3pyn_P 3pyu_P
3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P
1i94_P* ...
Length = 83
Score = 62.5 bits (153), Expect = 1e-13
Identities = 29/134 (21%), Positives = 45/134 (33%), Gaps = 59/134 (44%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M K IRLAR+G + P Y IVV +
Sbjct: 1 MVK-IRLARFGSKHNPHYRIVVTDA----------------------------------- 24
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGT----SDIH 158
R +R+ + IE++G +DP + +++ER RYWL +D
Sbjct: 25 ------------RRKRDGKYIEKIGYYDPRKTT--PDWLKVDVERARYWLSVGAQPTD-- 68
Query: 159 ITSPVRELFGKLNI 172
R L + +
Sbjct: 69 ---TARRLLRQAGV 79
>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A
{Aquifex aeolicus} SCOP: d.27.1.1
Length = 112
Score = 62.0 bits (151), Expect = 4e-13
Identities = 23/134 (17%), Positives = 44/134 (32%), Gaps = 60/134 (44%)
Query: 43 MSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGL 102
M+ IRLA++G + P Y IVV+ +
Sbjct: 1 MAVRIRLAKFGRKHHPIYRIVVMDA----------------------------------- 25
Query: 103 AHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGT----SDIH 158
+ R + I+ LGT+DP ++ L+++ E+++ W+ S
Sbjct: 26 ------------KSPREGKYIDILGTYDPK----RKVLINVYPEKVKEWVLKGVELSH-- 67
Query: 159 ITSPVRELFGKLNI 172
+ + I
Sbjct: 68 ---RAKAILWNHGI 78
>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 = 32.1 bits (72), Expect = 0.11
Identities = 40/248 (16%), Positives = 72/248 (29%), Gaps = 85/248 (34%)
Query: 10 HNSIPLF-KHHSKMSRPMFKL------FYPASGGAKCVEGMS---KSIRLARYGCTNRPF 59
+N +F K++ +P KL PA ++G+ K+ +A C +
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKN--VLIDGVLGSGKTW-VALDVCLSYKV 176
Query: 60 YHIVVIHSSEHSVGLAHIDKK--WSSKLYVRRCVNVKSS-EHSVGLAH-IDKKWSSKITR 115
+D K W L ++ C + ++ E L + ID W+S+
Sbjct: 177 --------------QCKMDFKIFW---LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219
Query: 116 MRRNDQPIEQLGTFDP---LPNEYQEKLVSL-NIERIRYW----------LGTSDIHITS 161
I + Y+ L+ L N++ + W L T +T
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279
Query: 162 PV----------------------RELFGK-LNIDLTNL----CDLRP----------SQ 184
+ + L K L+ +L P
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339
Query: 185 WLANSNFW 192
LA + W
Sbjct: 340 GLATWDNW 347
Score = 31.4 bits (70), Expect = 0.20
Identities = 33/179 (18%), Positives = 52/179 (29%), Gaps = 63/179 (35%)
Query: 3 CKVL------------SAAHNSIPLFKHHSKMSRP--MFKLFYPASGGAKCVEGMSKSIR 48
CK+L SAA + HHS P + L K +
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL------LKYL-DCRPQ-D 317
Query: 49 LARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYVRRCVNVKSSEHSVGLAHIDKK 108
L R T P + +I + GLA D W H++
Sbjct: 318 LPREVLTTNPR-RLSII-AESIRDGLATWDN-WK---------------------HVNCD 353
Query: 109 WSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRYWLGTSDIHITSPVRELF 167
K+T + + + L P EY++ L++ HI + + L
Sbjct: 354 ---KLTTIIESS--LNVLE-----PAEYRKMFDRLSVFP-------PSAHIPTILLSLI 395
>1g9k_A Serralysin; beta jelly roll, hydrolase; 1.96A {Pseudomonas} SCOP:
b.80.7.1 d.92.1.6 PDB: 1o0q_A 1o0t_A 1om6_A 1om7_A
1om8_A 1omj_A 1h71_P
Length = 463
Score = 27.9 bits (61), Expect = 2.4
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 59 FYHIVVIHSSEHSVGLAH 76
+ + H H++GL+H
Sbjct: 162 YGRQTLTHEIGHTLGLSH 179
>2ep5_A 350AA long hypothetical aspartate-semialdehyde dehydrogenase;
oxidoreductase, structural genomics, NPPSFA; 2.40A
{Sulfolobus tokodaii}
Length = 350
Score = 27.5 bits (62), Expect = 2.6
Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 12/43 (27%)
Query: 43 MSKSIRLARYGCT------------NRPFYHIVVIHSSEHSVG 73
M+ I+++ G T P+ +V + +S +G
Sbjct: 1 MADKIKVSLLGSTGMVGQKMVKMLAKHPYLELVKVSASPSKIG 43
>3fbs_A Oxidoreductase; structural genomics, PSI2, MCSG, protein STR
initiative, midwest center for structural genomics; HET:
FAD; 2.15A {Agrobacterium tumefaciens}
Length = 297
Score = 27.5 bits (62), Expect = 3.1
Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 61 HIVVIHSSEHSVGLAHIDKKWSSK-LYVRRCVNVKSSEHSVGLAHIDKKWSSKITRMRRN 119
I VI +S ++ A + W + V + +H++ A + +++I + +
Sbjct: 143 KIGVIAASPMAIHHALMLPDWGETTFFTNGIVEPDADQHALLAARGVRVETTRIREIAGH 202
Query: 120 D 120
Sbjct: 203 A 203
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A
single chain of CSE4+SCM3+H4, fusion protein; NMR
{Saccharomyces cerevisiae}
Length = 235
Score = 26.5 bits (57), Expect = 5.7
Identities = 21/118 (17%), Positives = 36/118 (30%), Gaps = 4/118 (3%)
Query: 37 AKCVEGMSKSIRLARYGCTNRPFYHIVVIHSSEHSVGLAHIDKKWSSKLYV----RRCVN 92
AK + M K ++LAR + + + SK V+
Sbjct: 67 AKRITIMKKDMQLARRIRGQFLVPRGSMERHKLADENMRKVWSNIISKYESIEEQGDLVD 126
Query: 93 VKSSEHSVGLAHIDKKWSSKITRMRRNDQPIEQLGTFDPLPNEYQEKLVSLNIERIRY 150
+K+ E HI ++ T+ +R D E +K I + Y
Sbjct: 127 LKTGEIVEDNGHIKTLTANNSTKDKRTKYTSVLRDIIDISDEEDGDKGGVKRISGLIY 184
>2r44_A Uncharacterized protein; putative ATPase, structural genomics,
joint center for struc genomics, JCSG; HET: MSE PG4;
2.00A {Cytophaga hutchinsonii atcc 33406}
Length = 331
Score = 26.3 bits (59), Expect = 7.1
Identities = 8/12 (66%), Positives = 10/12 (83%), Gaps = 1/12 (8%)
Query: 122 PIEQLGTFDPLP 133
P+EQ GT+ PLP
Sbjct: 159 PVEQEGTY-PLP 169
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 0.134 0.427
Gapped
Lambda K H
0.267 0.0808 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,041,423
Number of extensions: 164026
Number of successful extensions: 414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 409
Number of HSP's successfully gapped: 17
Length of query: 198
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 109
Effective length of database: 4,216,824
Effective search space: 459633816
Effective search space used: 459633816
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: 55 (24.8 bits)