RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032125
(147 letters)
>2xzm_I RPS16E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_I
Length = 145
Score = 197 bits (503), Expect = 2e-66
Identities = 86/144 (59%), Positives = 119/144 (82%)
Query: 4 AAPKTESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGRHR 63
+ K + VQ FGRKK AVAV + G+GL+K+NG PI+++ P+IL+ K +EPILLLG+ +
Sbjct: 2 SQQKPQLVQTFGRKKNAVAVASVRPGKGLLKVNGSPIDMINPQILQAKIYEPILLLGQQK 61
Query: 64 FNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVA 123
F +D+RIRV+G G+TSQ+YAIRQ+++K +VA++ KYVDE SK+EIK+ L++YDR+LLVA
Sbjct: 62 FANLDIRIRVRGSGYTSQVYAIRQALSKGIVAYHAKYVDENSKREIKEQLMQYDRSLLVA 121
Query: 124 DPRRCEPKKFGGRGARARFQKSYR 147
DPRR EPKK GGRGAR++ QK+YR
Sbjct: 122 DPRRMEPKKCGGRGARSKMQKAYR 145
>3u5c_Q RP61R, 40S ribosomal protein S16-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_I 3o30_J 3o2z_J 3u5g_Q 1s1h_I
3jyv_I*
Length = 143
Score = 195 bits (497), Expect = 2e-65
Identities = 95/141 (67%), Positives = 116/141 (82%)
Query: 7 KTESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGRHRFNG 66
SVQ FG+KK+A AV + K G+GLIK+NG PI LVEPEILRFK +EP+LL+G +F+
Sbjct: 3 AVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSN 62
Query: 67 VDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPR 126
+D+R+RV GGGH SQ+YAIRQ+IAK LVA++QKYVDEQSK E+K YDRTLL+AD R
Sbjct: 63 IDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADSR 122
Query: 127 RCEPKKFGGRGARARFQKSYR 147
R EPKKFGG+GAR+RFQKSYR
Sbjct: 123 RPEPKKFGGKGARSRFQKSYR 143
>3iz6_I 40S ribosomal protein S16 (S9P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 149
Score = 194 bits (494), Expect = 5e-65
Identities = 118/146 (80%), Positives = 128/146 (87%)
Query: 2 ATAAPKTESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGR 61
A P +VQCFGRKKTAVAV+YCK GRGLIK+NG PIEL+ PE+LR KAFEPILL GR
Sbjct: 4 ALTRPPPGTVQCFGRKKTAVAVSYCKPGRGLIKVNGVPIELIRPEMLRLKAFEPILLAGR 63
Query: 62 HRFNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLL 121
RF +DMRIRV+GGG TSQIYAIRQ+IAKALVA+YQKYVDE SKKE+KDI RYDRTLL
Sbjct: 64 SRFKDIDMRIRVRGGGKTSQIYAIRQAIAKALVAYYQKYVDEASKKEVKDIFARYDRTLL 123
Query: 122 VADPRRCEPKKFGGRGARARFQKSYR 147
VADPRRCEPKKFGGRGARARFQKSYR
Sbjct: 124 VADPRRCEPKKFGGRGARARFQKSYR 149
>2zkq_i 40S ribosomal protein S16E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 146
Score = 191 bits (488), Expect = 4e-64
Identities = 106/141 (75%), Positives = 124/141 (87%)
Query: 7 KTESVQCFGRKKTAVAVTYCKRGRGLIKINGCPIELVEPEILRFKAFEPILLLGRHRFNG 66
+SVQ FGRKKTA AV +CKRG GLIK+NG P+E++EP L++K EP+LLLG+ RF G
Sbjct: 6 PLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAG 65
Query: 67 VDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPR 126
VD+R+RVKGGGH +QIYAIRQSI+KALVA+YQKYVDE SKKEIKDIL++YDRTLLVADPR
Sbjct: 66 VDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPR 125
Query: 127 RCEPKKFGGRGARARFQKSYR 147
RCE KKFGG GARAR+QKSYR
Sbjct: 126 RCESKKFGGPGARARYQKSYR 146
>3r8n_I 30S ribosomal protein S9; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_I 3fih_I* 3iy8_I 2wwl_I 3oar_I 3oaq_I
3ofb_I 3ofa_I 3ofp_I 3ofx_I 3ofy_I 3ofo_I 3r8o_I 4a2i_I
2qal_I* 1p6g_I 1p87_I 2aw7_I 2avy_I 2i2u_I ...
Length = 127
Score = 79.4 bits (197), Expect = 3e-20
Identities = 45/134 (33%), Positives = 64/134 (47%), Gaps = 14/134 (10%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAFEPILLLGRHRFNGVDMRIRV 73
GR+K++ A + K G G I IN +E E R +P+ L+ +D+ I V
Sbjct: 7 GRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMV--EKLDLYITV 64
Query: 74 KGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKF 133
KGGG + Q AIR I +AL+ + DE + E++ + D R+ E KK
Sbjct: 65 KGGGISGQAGAIRHGITRALMEY-----DESLRSELR------KAGFVTRDARQVERKKV 113
Query: 134 GGRGARARFQKSYR 147
G R AR R Q S R
Sbjct: 114 GLRKARRRPQFSKR 127
>3bbn_I Ribosomal protein S9; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 197
Score = 81.3 bits (201), Expect = 3e-20
Identities = 37/135 (27%), Positives = 53/135 (39%), Gaps = 15/135 (11%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPIE--LVEPEILRFKAFEPILLLGRHRFNGVDMRIR 72
GR+K A+A + G G IN + L + P+ LG D+ ++
Sbjct: 76 GRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYVKTPLATLGYE--TNYDVFVK 133
Query: 73 VKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKK 132
GGG + Q AI +A+AL+ + +K LL D R E KK
Sbjct: 134 AHGGGLSGQAQAISLGVARALLKV-----SASHRAPLK------QEGLLTRDSRIVERKK 182
Query: 133 FGGRGARARFQKSYR 147
G + AR Q S R
Sbjct: 183 PGLKKARKAPQFSKR 197
>2vqe_I 30S ribosomal protein S9, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.14.1.1
PDB: 1gix_L* 1hnw_I* 1hnx_I* 1hnz_I* 1hr0_I 1i94_I*
1i95_I* 1i96_I* 1i97_I* 1ibk_I* 1ibl_I* 1ibm_I 1j5e_I
1jgo_L* 1jgp_L* 1jgq_L* 1ml5_L* 1n32_I* 1n33_I* 1n34_I
...
Length = 128
Score = 79.1 bits (196), Expect = 4e-20
Identities = 41/134 (30%), Positives = 59/134 (44%), Gaps = 14/134 (10%)
Query: 15 GRKKTAVAVTYCKRGRGLIKINGCPIELVEP-EILRFKAFEPILLLGRHRFNGVDMRIRV 73
GR+K AVA + + G G + +NG + A EP+ + D I V
Sbjct: 8 GRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDAL--GRFDAYITV 65
Query: 74 KGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKF 133
+GGG + QI AI+ IA+ALV + + + ++K L D R E KK+
Sbjct: 66 RGGGKSGQIDAIKLGIARALVQY-----NPDYRAKLK------PLGFLTRDARVVERKKY 114
Query: 134 GGRGARARFQKSYR 147
G AR Q S R
Sbjct: 115 GKHKARRAPQYSKR 128
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 37.1 bits (85), Expect = 9e-04
Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 13/68 (19%)
Query: 44 EPEILRFKAFEPILLLGRHRFNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDE 103
EPE +R K R R++ R+ K L + Q+ E
Sbjct: 83 EPESIR-KW--------REEQ---RKRLQELDAASKVMEQEWREKAKKDLEEWNQRQ-SE 129
Query: 104 QSKKEIKD 111
Q +K +
Sbjct: 130 QVEKNKIN 137
>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 = 32.7 bits (74), Expect = 0.035
Identities = 20/131 (15%), Positives = 42/131 (32%), Gaps = 27/131 (20%)
Query: 9 ESVQCFGRKKTAVAVT--YCKRGRG----LIKINGCPIELVEPEILRFKAFEPILLLGRH 62
+ + ++ + G ++ I+ E V+ + + + P G+
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLP---AGKQ 365
Query: 63 ----RFNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSK----KEIKDILV 114
NG + V G +Y + ++ KA +QS+ +
Sbjct: 366 VEISLVNGAKNLV-V--SGPPQSLYGLNLTLRKAKAPSGL----DQSRIPFSERKLKFSN 418
Query: 115 RYDRTLLVADP 125
R+ L VA P
Sbjct: 419 RF---LPVASP 426
Score = 31.9 bits (72), Expect = 0.065
Identities = 20/149 (13%), Positives = 40/149 (26%), Gaps = 64/149 (42%)
Query: 39 PIELVEPEILRFKAFEPILLLGRHRFNGVDMRIRVKGGGHTSQIYAIRQSIAKALVAFYQ 98
P ELV +F + V + G Q+ + L F
Sbjct: 57 PAELV----GKFLGY-------------VSSLVEPSKVGQFDQV------LNLCLTEFEN 93
Query: 99 KYV---------------DEQSKKEIKDILVRYDRTLLVADPRRCEPKK----------- 132
Y+ ++ + + K+++ Y ++A +
Sbjct: 94 CYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGN 153
Query: 133 ------FGGRGA--------RARFQKSYR 147
FGG+G R + ++Y
Sbjct: 154 AQLVAIFGGQGNTDDYFEELRDLY-QTYH 181
>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 = 29.1 bits (64), Expect = 0.55
Identities = 20/119 (16%), Positives = 32/119 (26%), Gaps = 36/119 (30%)
Query: 14 FGRKKTAVAVTYCKRGRGLIKINGCPI------ELVEPEILRFKAFEPILLLGRHRFNGV 67
G KT VA+ C + I PE + E + L
Sbjct: 161 SG--KTWVALDVC-LSYKVQCKMDFKIFWLNLKNCNSPETV----LEMLQKLLY------ 207
Query: 68 DMRIRVKGGGHTSQIYAIRQSIAKALVAFYQKYVDEQSKKEIKDILV--RYDRTLLVAD 124
+I + I+ I + E++ +L Y+ LLV
Sbjct: 208 --QIDPNWTSRSDHSSNIKLRI-------------HSIQAELRRLLKSKPYENCLLVLL 251
>1eum_A Ferritin 1; ECFTNA, metal binding protein; 2.05A {Escherichia coli}
SCOP: a.25.1.1
Length = 165
Score = 26.8 bits (60), Expect = 2.2
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQ--SKKEIKDILVRYDR 118
T +I + A F Q YV EQ +K K I+ +
Sbjct: 98 TQKINELA-HAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSL 143
>3bvf_A Ferritin; iron storage, metal-binding, oxidoreductase; 1.50A
{Helicobacter pylori} PDB: 3bve_A 3bvi_A 3bvk_A 3bvl_A
3egm_A
Length = 181
Score = 26.5 bits (59), Expect = 3.0
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQ--SKKEIKDILVRYDR 118
+ I I A A F Q YV EQ + KDIL + +
Sbjct: 112 SESINNIVD-HAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIEL 157
>1s3q_A Ferritin; ferroxidase, four helix bundle, iron storage, metal
binding; 2.10A {Archaeoglobus fulgidus} SCOP: a.25.1.1
PDB: 1sq3_A 3kx9_A
Length = 173
Score = 26.4 bits (59), Expect = 3.3
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQSK--KEIKDILVRYDR 118
T +I+ + +A A F Q YV EQ + DI+ +
Sbjct: 100 TKRIHELV-EMAMQEKDFATYNFLQWYVAEQVEEEASALDIVEKLRL 145
>3oj5_A Ferritin family protein; ferroxidase, cytosol, oxidoreductase;
2.85A {Mycobacterium tuberculosis} PDB: 3qd8_A
Length = 189
Score = 26.1 bits (58), Expect = 3.8
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQSK--KEIKDILVRYDR 118
T Q+ + +A+ F Q ++ EQ + + ++ DR
Sbjct: 103 TDQVGRLTA-VARDEGDFLGEQFMQWFLQEQIEEVALMATLVRVADR 148
>3qz3_A Ferritin; structural genomics, the center for structural genomics
of I diseases, csgid, cytoplasmic, oxidoreductase; 2.10A
{Vibrio cholerae o1 biovar el tor}
Length = 184
Score = 26.1 bits (58), Expect = 4.4
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQSK--KEIKDILVRYDR 118
T QI + +A + F Q YV EQ + K K IL + +
Sbjct: 107 TQQINKLA-HVAFTSQDYSTFNFLQWYVAEQHEEEKLFKGILDKLEL 152
>2jd6_0 Ferritin homolog, ferritin; metal transport, iron, pores, archaeon,
entry channels, thermostability, hyperthermophIle,
ferroxidase center; 2.75A {Pyrococcus furiosus} PDB:
2jd7_0 2jd8_0 2x17_0
Length = 174
Score = 26.0 bits (58), Expect = 4.6
Identities = 10/47 (21%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQSK--KEIKDILVRYDR 118
+ IY + ++A+ + AF + +++EQ + +K IL +
Sbjct: 98 SKSIYELA-ALAEEEKDYSTRAFLEWFINEQVEEEASVKKILDKLKF 143
>4g22_A Hydroxycinnamoyl-COA shikimate/quinate
hydroxycinnamoyltransferase; BAHD superfamily; 1.70A
{Coffea canephora} PDB: 4g2m_A 4g0b_A
Length = 439
Score = 26.2 bits (58), Expect = 4.8
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 75 GGGHTSQIYAIRQSIAKALVAFY 97
G + ++ ++++ALV FY
Sbjct: 51 GSSNFFDAKVLKDALSRALVPFY 73
>1krq_A Ferritin; H-chain like four-helix bundle, binding protein; 2.70A
{Campylobacter jejuni} SCOP: a.25.1.1
Length = 167
Score = 25.7 bits (57), Expect = 5.6
Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQ--SKKEIKDILVRYDR 118
T I + + F Q YV EQ + + I+ +
Sbjct: 98 TKSINTLV-EHMLTHKDYSTFNFLQWYVSEQHEEEALFRGIVDKIKL 143
>1vlg_A Ferritin; TM1128, structural genomics, JCSG, protein structu
initiative, PSI, joint center for structural genomics,
META protein; 2.00A {Thermotoga maritima} SCOP: a.25.1.1
PDB: 1z4a_A*
Length = 176
Score = 25.7 bits (57), Expect = 6.3
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQSK--KEIKDILVRYDR 118
T IY I +A A V+F + +VDEQ + ++++IL ++
Sbjct: 112 TQSIYNIL-ELASEEKDHATVSFLKWFVDEQVEEEDQVREILDLLEK 157
>2p5i_A BH3822 protein; PFAM03099, structural genomics, PSI-2, protein
structure initiative, NEW YORK structural genomix
research consortium; 2.21A {Bacillus halodurans c-125}
SCOP: d.104.1.3
Length = 288
Score = 25.3 bits (55), Expect = 7.6
Identities = 9/47 (19%), Positives = 14/47 (29%), Gaps = 14/47 (29%)
Query: 45 PEILRFKAFEPILLLGRH--------------RFNGVDMRIRVKGGG 77
P LR ++LG + D+ +R GG
Sbjct: 49 PPTLRAWVHHNTVVLGIQDSRLPQIKAGIEALKGFQHDVIVRNSGGL 95
>3e6s_A Ferritin; iron storage, ferroxidase, oxidoreductase; 1.95A
{Pseudo-nitzschia multiseries} PDB: 3e6r_A
Length = 168
Score = 25.3 bits (56), Expect = 7.6
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 79 TSQIYAIRQSIAK-----ALVAFYQKYVDEQSK--KEIKDILVRYDR 118
T + + A A++AF + +Q +I IL +
Sbjct: 99 TRSLLNLA-EAASTCHDFAVMAFLNPFHLQQVNEEDKIGSILAKVTD 144
>3ahn_A Oligopeptidase, PZ peptidase A; hydrolase, hydrolase-hydrolase
inhibitor complex; HET: 3A1; 1.80A {Geobacillus SP} PDB:
3ahm_A* 3aho_A* 2h1n_A 2h1j_A
Length = 564
Score = 25.5 bits (56), Expect = 7.7
Identities = 12/66 (18%), Positives = 21/66 (31%), Gaps = 2/66 (3%)
Query: 82 IYAIRQSIAKALVAFYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARAR 141
+ R+ + K +V K + Q ++ + L YD P K
Sbjct: 233 VAKFRKQVEKHIVPIAVKLRERQRERIGVEKLKYYDE--AFVFPTGNPMPKGDANWIIEN 290
Query: 142 FQKSYR 147
+K Y
Sbjct: 291 GKKMYE 296
>2e1v_A Acyl transferase; BAHD superfamily, seleno-methionine derivative,
dendranthema morifolium, DMAT; 1.80A {Chrysanthemum x
morifolium} PDB: 2e1u_A 2e1t_A
Length = 454
Score = 25.3 bits (55), Expect = 9.1
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 84 AIRQSIAKALVAFY 97
I+ S++ L FY
Sbjct: 64 NIKHSLSITLKHFY 77
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
0.325 0.140 0.414
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,265,927
Number of extensions: 132481
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 420
Number of HSP's successfully gapped: 35
Length of query: 147
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 62
Effective length of database: 4,328,508
Effective search space: 268367496
Effective search space used: 268367496
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: 53 (24.3 bits)