RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031308
(161 letters)
>3r8s_N 50S ribosomal protein L17; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_N 2wwq_N 3oat_N* 3oas_N* 3ofd_N 3ofc_N 3ofr_N*
3ofz_N* 3og0_N 3ofq_N 3r8t_N 3i1n_N 1p85_L 1p86_L 1vs8_N
1vs6_N 2aw4_N 2awb_N 1vt2_N 2i2v_N ...
Length = 120
Score = 163 bits (414), Expect = 7e-53
Identities = 55/114 (48%), Positives = 75/114 (65%), Gaps = 1/114 (0%)
Query: 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARR 62
R+LNR + HR +M R M LV+HE I+TT+ KAKE+RR+ + ++ L K S+ R
Sbjct: 6 SGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRL 65
Query: 63 AAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFVDR 116
A A R ++++ KLF EL R+ RAGGYTR+L+ R GD APMAYI+ VDR
Sbjct: 66 AFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIE-LVDR 118
>2zjr_K 50S ribosomal protein L17; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.188.1.1 PDB: 1nwx_L* 1nwy_L*
1sm1_L* 1xbp_L* 2zjp_K* 2zjq_K 1nkw_L 3cf5_K* 3dll_K*
3pio_K* 3pip_K* 1pnu_L 1pny_L 1vor_O 1vou_O 1vow_O
1voy_O 1vp0_O
Length = 116
Score = 151 bits (385), Expect = 1e-48
Identities = 42/108 (38%), Positives = 63/108 (58%)
Query: 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARR 62
RKLNR + R+++ R + L++ RI+TT+ KAKE+R + ++ K G L + R
Sbjct: 6 AGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRL 65
Query: 63 AAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYI 110
A + DV+ K+ E+A +Y +R GGYTR+LR R GD MA I
Sbjct: 66 VAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALI 113
>1gd8_A 50S ribosomal protein L17; two domains, ribosomal protein S8-like
domain, Trp repressor-like domain, helix-turn-helix
motif; 2.30A {Thermus thermophilus} SCOP: d.188.1.1 PDB:
1vsa_L 1vsp_L 1yl3_0 2b66_R 2b9n_R 2b9p_R 2hgj_Q 2hgq_Q
2hgu_Q 2j01_R 2j03_R 2jl6_R 2jl8_R 2v47_R 2v49_R 2wdi_R
2wdj_R 2wdl_R 2wdn_R 2wh2_R ...
Length = 118
Score = 149 bits (380), Expect = 7e-48
Identities = 49/114 (42%), Positives = 70/114 (61%), Gaps = 2/114 (1%)
Query: 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARR 62
RKLNR + HR+++ R L+ H RI TTV KAKE+R D+++ L K G L A R
Sbjct: 6 SGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDHLIHLAKRGDLHARRL 65
Query: 63 AAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRS-RIRVGDAAPMAYIDRFVD 115
++ ++ KLF E+A RY+DR GGYTR+L+ R GD AP+A ++ V+
Sbjct: 66 VLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKLAERRRGDGAPLALVE-LVE 118
>3bbo_P Ribosomal protein L17; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 205
Score = 151 bits (384), Expect = 2e-47
Identities = 52/109 (47%), Positives = 73/109 (66%)
Query: 2 TKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAAR 61
K KLNRP R ++LR + +QL+KH RI+TT A+A+ VR+ D M+ + K+GSL R
Sbjct: 94 RKVPKLNRPPDQRRALLRGLTTQLLKHGRIKTTKARARAVRKYVDKMITMAKDGSLHKRR 153
Query: 62 RAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYI 110
+A F+ ++H LF E+ RY +R GGYTR++R+ R GD APMAYI
Sbjct: 154 QALGFIYEKQIVHALFAEVPDRYGERNGGYTRIIRTLPRRGDNAPMAYI 202
>2cqm_A Ribosomal protein L17 isolog; alpha and beta (A+B), structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.188.1.1 PDB: 2ftc_J 3iy9_S
Length = 122
Score = 145 bits (368), Expect = 6e-46
Identities = 41/109 (37%), Positives = 60/109 (55%), Gaps = 3/109 (2%)
Query: 11 TGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCA--ARRAAAFVR 68
+ +LR +++ LV+HERIE A+ E+R A+ ++ GK G R A ++
Sbjct: 2 SSGSSGLLRNLLTGLVRHERIEAPWARVDEMRGYAEKLIDYGKLGDTNERAMRMADFWLT 61
Query: 69 GDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFVDRE 117
D+I KLF LA RYKD+ GGYTR+L+ R D A MA I+ +
Sbjct: 62 EKDLIPKLFQVLAPRYKDQTGGYTRMLQIPNRSLDRAKMAVIE-YKGNC 109
>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 = 32.5 bits (73), Expect = 0.053
Identities = 24/128 (18%), Positives = 41/128 (32%), Gaps = 36/128 (28%)
Query: 21 MVSQLVKHERIETTVAKAKEV---RRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLF 77
M ++ E I+ + V RL ++ +E FV ++V
Sbjct: 41 MPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM-------VQKFV--EEV----- 86
Query: 78 TELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFVDRENELRQ-----SKPAVPQPPP 132
L YK L S I+ P ++++ + L +K V + P
Sbjct: 87 --LRINYK--------FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136
Query: 133 ----RAAL 136
R AL
Sbjct: 137 YLKLRQAL 144
Score = 32.1 bits (72), Expect = 0.076
Identities = 23/163 (14%), Positives = 43/163 (26%), Gaps = 42/163 (25%)
Query: 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARR 62
F K N LR + +L + + + D ++ GK +
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRPAKNV--LI----------DGVLGSGKT-WV----- 166
Query: 63 AAAFVRGDDVIHKLFTE---LAYRYKDRAGG--------YTRLLRSRIRVGDAAPMAYID 111
A V K+ + L + + ++ + D
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD-HSSNIKL 225
Query: 112 RFVDRENELR---QSKPAVPQPPPRAAL---DPWTRSRLTKNF 148
R + ELR +SKP L + ++ F
Sbjct: 226 RIHSIQAELRRLLKSKPY-----ENCLLVLLNVQN-AKAWNAF 262
>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 = 30.0 bits (67), Expect = 0.33
Identities = 25/151 (16%), Positives = 48/151 (31%), Gaps = 40/151 (26%)
Query: 20 TMVSQLVKHERIETTVAKAKEV-------RRLADNMVQLGKEGSL--CAARRAAAFV--- 67
+ ++L++ +TT+ K KE+ R +A +L A V
Sbjct: 103 ALAAKLLQEN--DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
Query: 68 --RGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFVDRENELRQSKP 125
+G+ F EL Y+ Y L+ I + +EL ++
Sbjct: 161 GGQGN--TDDYFEELRDLYQT----YHVLVG-----------DLIKFSAETLSELIRTTL 203
Query: 126 AVPQPPPRAALDP--WTRSRLTKNFAPPKQE 154
+ + L+ W L P ++
Sbjct: 204 DAEKVFTQ-GLNILEW----LENPSNTPDKD 229
>1aj8_A Citrate synthase; hyperthermostable, lyase; HET: COA CIT; 1.90A
{Pyrococcus furiosus} SCOP: a.103.1.1
Length = 371
Score = 27.5 bits (62), Expect = 2.1
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAA 60
+ + + H M LRT++S L + +EV R+ ++ K ++ A
Sbjct: 76 VIEIMEALPKNTHPMGALRTIISYLGNIDDSGDIPVTPEEVYRIGISV--TAKIPTIVAN 133
>3o8j_A 2-methylcitrate synthase; short chain fatty acids, propionate
metabolism, 2-methylcitr cycle, PRPC or 2-MCS, GLTA or
CS, 2-methy synthase; 2.41A {Salmonella enterica}
Length = 404
Score = 26.7 bits (60), Expect = 4.0
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAA 60
H M ++RT VS L E R +AD + L S+
Sbjct: 116 PAASHPMDVMRTGVSALGCTLP-EKEGHTVSGARDIADKL--LASLSSILLY 164
>2ibp_A Citrate synthase; disulfide bond, homodimer, thermophilic, C
transferase; 1.60A {Pyrobaculum aerophilum}
Length = 409
Score = 26.8 bits (60), Expect = 4.1
Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 17/82 (20%)
Query: 10 PTGHRMSMLRTMVSQLVK--HERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFV 67
H M L V+ + + A + + + KE + A +
Sbjct: 105 AKAHPMFALEAAVAAEGAYDEDNQKLIEALSVGRYKAEE------KELAYRIAEK----- 153
Query: 68 RGDDVIHKLFTELAYRYKDRAG 89
++ K+ T +AY Y+ G
Sbjct: 154 ----LVAKMPTIVAYHYRFSRG 171
>2qzs_A Glycogen synthase; glycosyl-transferase, GT-B fold, rossmann fold,
closed-form, ADP and glucose binding, glycogen
biosynthesis; HET: GLC ADP 250; 2.20A {Escherichia coli}
PDB: 2r4t_A* 2r4u_A* 3guh_A* 3cx4_A* 3cop_A* 3d1j_A
Length = 485
Score = 26.7 bits (60), Expect = 4.2
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 69 GDDVIHKLFTELAYRYKDRAGGY 91
GD V+ + F A Y + G
Sbjct: 330 GDPVLQEGFLAAAAEYPGQVGVQ 352
>1vgp_A 373AA long hypothetical citrate synthase; open form, transferase;
2.70A {Sulfolobus tokodaii}
Length = 373
Score = 26.3 bits (59), Expect = 4.8
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL 25
+ KF + R M +LRT VS L
Sbjct: 78 IIKFLREVRKDAQPMDILRTAVSLL 102
>1rzu_A Glycogen synthase 1; glycosyl-transferase, GT-B fold, rossmann
fold, ADP-binding, transferase; HET: ADP; 2.30A
{Agrobacterium tumefaciens} SCOP: c.87.1.8 PDB: 1rzv_A
Length = 485
Score = 26.4 bits (59), Expect = 4.9
Identities = 6/23 (26%), Positives = 8/23 (34%)
Query: 69 GDDVIHKLFTELAYRYKDRAGGY 91
GD + A R+ R G
Sbjct: 329 GDVALEGALLAAASRHHGRVGVA 351
>1vgm_A 378AA long hypothetical citrate synthase; open form, transferase;
2.00A {Sulfolobus tokodaii}
Length = 378
Score = 26.4 bits (59), Expect = 5.3
Identities = 6/47 (12%), Positives = 13/47 (27%), Gaps = 2/47 (4%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL--VKHERIETTVAKAKEVRRLA 45
+ + M+ T L + + K V+ +A
Sbjct: 80 VISTIFSMPRNCDAIGMMETAFGILASIYDPKWNRATNKELAVQIIA 126
>3h11_B Caspase-8; cell death, apoptosis, caspase, alternative splicing,
HOST- virus interaction, polymorphism, cytoplasm,
disease mutation; 1.90A {Homo sapiens} PDB: 2k7z_A
1i4e_B 2fun_B 2c2z_B*
Length = 271
Score = 26.3 bits (57), Expect = 5.8
Identities = 5/22 (22%), Positives = 5/22 (22%), Gaps = 1/22 (4%)
Query: 138 PWTRSRLTKNFA-PPKQEKSSD 158
P L K P E
Sbjct: 248 PQPTFTLRKKLVFPSDVEHHHH 269
>3hwk_A Methylcitrate synthase; niaid, ssgcid, structural genomics, seattle
structural genomics center for infectious disease,
tubercluosis; 2.30A {Mycobacterium tuberculosis}
Length = 414
Score = 26.0 bits (58), Expect = 6.0
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL--VKHERIETTVAKAKEVRRLA 45
M H M ++RT +S L + + +AK +R +A
Sbjct: 124 MLSLLAKLPDNCHPMDVVRTAISYLGAEDPDEDDAAANRAKAMRMMA 170
>2abw_A PDX2 protein, glutaminase; PLP-synthase, vitamin B6, malaria,
transferase; HET: PG4; 1.62A {Plasmodium falciparum}
SCOP: c.23.16.1 PDB: 4ads_G
Length = 227
Score = 25.8 bits (56), Expect = 6.1
Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 9/62 (14%)
Query: 31 IETTVAKAKEVRRLADNMVQLGKEGSLCAARR----AAAF---VRGDDVIHKLFTELAYR 83
I ++ +V LA + + A + F + + F E
Sbjct: 158 IREILSDEVKV--LATFSHESYGPNIIAAVEQNNCLGTVFHPELLPHTAFQQYFYEKVKN 215
Query: 84 YK 85
YK
Sbjct: 216 YK 217
>1iom_A Citrate synthase; open form, riken structural genomics/proteomics
in RSGI, structural genomics, lyase; 1.50A {Thermus
thermophilus} SCOP: a.103.1.1 PDB: 1ixe_A*
Length = 377
Score = 25.9 bits (58), Expect = 6.1
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAA 60
+ + K + H MS LRT VS+ + + + ++ + K ++ AA
Sbjct: 78 LLESFKRYPVSAHPMSFLRTAVSEFGMLDP-TEGDISREALYEKGLDL--IAKFATIVAA 134
>1o7x_A Citrate synthase; lyase, tricarboxylic acid cycle; 2.7A {Sulfolobus
solfataricus} SCOP: a.103.1.1
Length = 377
Score = 25.9 bits (58), Expect = 6.1
Identities = 3/25 (12%), Positives = 7/25 (28%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL 25
+ L + +L + L
Sbjct: 79 VLDTIYLMPKEADAIGLLEVGTAAL 103
>2ifc_A Citrate synthase; oxaloacetate, EC 2.3.3.1, transferase; 1.70A
{Thermoplasma acidophilum} PDB: 2r9e_A* 2r26_A*
Length = 385
Score = 26.0 bits (58), Expect = 6.6
Identities = 2/25 (8%), Positives = 8/25 (32%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL 25
+ + ++M V+ +
Sbjct: 83 VINAIRQLPRESDAVAMQMAAVAAM 107
>1kf6_A Fumarate reductase flavoprotein; respiration, fumarate reductace,
succinate dehydrogenase, CO quinol, quinone,
oxidoreductase; HET: FAD HQO CE1 1PE; 2.70A {Escherichia
coli} SCOP: a.7.3.1 c.3.1.4 d.168.1.1 PDB: 1kfy_A*
1l0v_A* 2b76_A* 3cir_A* 3p4p_A* 3p4q_A* 3p4r_A* 3p4s_A*
Length = 602
Score = 26.1 bits (58), Expect = 6.6
Identities = 6/22 (27%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 11 TGHRMSMLRTMVSQLVKHERIE 32
TG ML T+ ++ +I+
Sbjct: 132 TGF--HMLHTLFQTSLQFPQIQ 151
>2c6x_A Citrate synthase 1; tricarboxylic acid cycle, transferase,
allosteric enzyme, enzyme thermostability; HET: COZ CIT;
3.4A {Bacillus subtilis}
Length = 363
Score = 26.0 bits (58), Expect = 7.0
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL 25
+ + + MS+LRT+VS L
Sbjct: 76 IERLIQSLPNNMDDMSVLRTVVSAL 100
>1a59_A Citrate synthase; cold-activity; HET: COA CIT; 2.09A {Antarctic
bacterium ds2-3r} SCOP: a.103.1.1
Length = 378
Score = 26.0 bits (58), Expect = 7.3
Identities = 8/25 (32%), Positives = 10/25 (40%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL 25
+ L H M + RT VS L
Sbjct: 80 VKGAIDLLSTACHPMDVARTAVSVL 104
>3tqg_A 2-methylcitrate synthase; energy metabolism, transferase; 2.30A
{Coxiella burnetii}
Length = 375
Score = 25.5 bits (57), Expect = 8.8
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 1 MTKFRKLNRPTGHRMSMLRTMVSQL 25
+ + + H M ++RT S L
Sbjct: 82 LKDTLERIPASSHPMDVMRTGCSML 106
>3lho_A Putative hydrolase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: PG4; 1.80A {Shewanella frigidimarina}
Length = 267
Score = 25.3 bits (55), Expect = 9.6
Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 8/86 (9%)
Query: 12 GHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEG--------SLCAARRA 63
G+R + ++ L + ERIE K+ + ++ K S A +
Sbjct: 160 GYRANHFTVSINDLPEFERIEDVNQALKQAGFVLNSSGGEVKGSPEVLLEQSSTMADKVV 219
Query: 64 AAFVRGDDVIHKLFTELAYRYKDRAG 89
F GD I F E A RY G
Sbjct: 220 VNFTDGDVEIPSCFYEFARRYPMANG 245
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
0.320 0.133 0.383
Gapped
Lambda K H
0.267 0.0562 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,477,161
Number of extensions: 147640
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 469
Number of HSP's successfully gapped: 42
Length of query: 161
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 75
Effective length of database: 4,300,587
Effective search space: 322544025
Effective search space used: 322544025
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: 53 (24.6 bits)