RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13959
(248 letters)
>3iz5_B 60S ribosomal protein L2 (L2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_B 2zkr_a
Length = 261
Score = 370 bits (953), Expect = e-131
Identities = 170/235 (72%), Positives = 200/235 (85%)
Query: 1 MGRVIRAQRKGAGSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAV 60
MGRVIRAQRKGAGSVF+SH HRKG + RSLDF ER+GYLKGVV DIIHDPGRGAPLA
Sbjct: 1 MGRVIRAQRKGAGSVFKSHTHHRKGPARFRSLDFGERNGYLKGVVTDIIHDPGRGAPLAK 60
Query: 61 VHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKT 120
V FR+P+++K KELF+A EGMYTGQFVYCG++ATL IGNV+P+ +PEG +VCN+E
Sbjct: 61 VTFRHPFRYKHQKELFVAAEGMYTGQFVYCGRRATLSIGNVLPIRSVPEGAVVCNVEHHV 120
Query: 121 GDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPIL 180
GDRG ARASG+YA VI+HNPD +R+KLPSGAKK++PS+ RAM+G VAGGGR +KP+L
Sbjct: 121 GDRGVFARASGDYAIVISHNPDNGTSRIKLPSGAKKIVPSSCRAMIGQVAGGGRTEKPML 180
Query: 181 KAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKV 235
KAG A++KY+ KRNCWPKVRGVAMNPVEHPHGGGNHQHIG ASTV+R G+KV
Sbjct: 181 KAGNAYHKYRVKRNCWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKV 235
>3jyw_B 60S ribosomal protein L2; eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
3izc_B 3izs_B 3o58_B 3o5h_B 3u5e_A 3u5i_A 1s1i_B
Length = 243
Score = 367 bits (944), Expect = e-130
Identities = 160/234 (68%), Positives = 199/234 (85%)
Query: 2 GRVIRAQRKGAGSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVV 61
GRVIR QRKGAGS+F SH + R+GA KLR+LD+AERHGY++G+V+ I+HD GRGAPLA V
Sbjct: 1 GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKV 60
Query: 62 HFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTG 121
FR+PYK++ +E+FIA EG++TGQF+Y GKKA+L +GNV+P+G +PEGTIV N+EEK G
Sbjct: 61 VFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPG 120
Query: 122 DRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILK 181
DRG LARASGNY +I HNPD +TRV+LPSGAKKVI S R ++G++AGGGR+DKP+LK
Sbjct: 121 DRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLK 180
Query: 182 AGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKV 235
AGRA +KY+ KRN WPK RGVAMNPV+HPHGGGNHQHIGKAST+ RG +G+K
Sbjct: 181 AGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKA 234
>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor
60S, translation, large ribosomal subunit; 3.52A
{Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A
Length = 264
Score = 341 bits (878), Expect = e-120
Identities = 152/236 (64%), Positives = 186/236 (78%), Gaps = 1/236 (0%)
Query: 1 MGRVIRAQRKG-AGSVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLA 59
MGRVIRAQRKG A V++SH R + R DFAER GY++G +RDI+H+PGRGAPLA
Sbjct: 1 MGRVIRAQRKGRANGVYKSHKSGRIAPAQYRVYDFAERQGYIRGCIRDIVHEPGRGAPLA 60
Query: 60 VVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEK 119
V FR+PY++KTNKE FIA EG Y+GQ+VYCG KA + +GNV+P+ +PEGT+VCN+EEK
Sbjct: 61 EVAFRDPYRYKTNKEHFIAAEGQYSGQYVYCGLKAQIAVGNVLPINRIPEGTVVCNVEEK 120
Query: 120 TGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPI 179
GDRG +RASG YAT+I H+ D +TR++LPSGA+K IP + RA VGIVAGGGR DKPI
Sbjct: 121 VGDRGTFSRASGCYATIIGHSEDGDKTRIRLPSGARKTIPGSCRATVGIVAGGGRTDKPI 180
Query: 180 LKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKV 235
LKAG +KY KR WP+VRGVAMNPV+HPHGGGNHQHIG +TV + SAG+KV
Sbjct: 181 LKAGNQFHKYARKRKSWPRVRGVAMNPVDHPHGGGNHQHIGHPATVSKWASAGQKV 236
>1vq8_A 50S ribosomal protein L2P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: b.34.5.3 b.40.4.5 PDB:
1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A*
1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A*
1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ...
Length = 240
Score = 305 bits (784), Expect = e-106
Identities = 105/236 (44%), Positives = 136/236 (57%), Gaps = 11/236 (4%)
Query: 1 MGRVIRAQRKGAG-SVFRSHNKHRKGAPKLRSLDFAERHGYLKGVVRDIIHDPGRGAPLA 59
MGR I+ QR+G G S FR+ + K + R ++ + G V DI HDP R AP+A
Sbjct: 1 MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVE---DGDVIAGTVVDIEHDPARSAPVA 57
Query: 60 VVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEK 119
V F + + L +APEG+ G + G A + GN +P+ +PEG VCN+E
Sbjct: 58 AVEFEDGDR-----RLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESS 112
Query: 120 TGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPI 179
GD G+ ARASG A ++ H D VKLPSG K + RA +G+VAGGGR DKP
Sbjct: 113 PGDGGKFARASGVNAQLLTH--DRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPF 170
Query: 180 LKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGRKV 235
+KAG H+K KA+ WP VRGVAMN V+HP GGG QH GK ++ R GRKV
Sbjct: 171 VKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKV 226
>1giy_D 50S ribosomal protein L2; ribosome assembly, protein synthesis,
LIFE; 5.50A {Thermus thermophilus} SCOP: i.1.1.1 PDB:
1ml5_d* 1yl3_D 2b66_D 2b9n_D 2b9p_D
Length = 178
Score = 121 bits (307), Expect = 7e-35
Identities = 74/185 (40%), Positives = 105/185 (56%), Gaps = 7/185 (3%)
Query: 28 KLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQF 87
+ R +DF + G V I +DP R A +A++++ + K IAP+ + G
Sbjct: 1 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYAD-----GEKRYIIAPKNLKVGME 55
Query: 88 VYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTR 147
+ G A ++IGN +P+ +P GT+V N+E K G G+L RA+G A V+ + K
Sbjct: 56 IMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGK--EGKYVI 113
Query: 148 VKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPV 207
V+L SG ++I RA VG V GGR DKP +KAG H+K KA+ WP VRGVAMN V
Sbjct: 114 VRLASGEVRMILGKCRATVGEVGNGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAV 173
Query: 208 EHPHG 212
+HP G
Sbjct: 174 DHPFG 178
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 269
Score = 118 bits (299), Expect = 1e-32
Identities = 70/195 (35%), Positives = 101/195 (51%), Gaps = 14/195 (7%)
Query: 22 HRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAP 79
HR G K R +DF + G + I +DP R A + ++H+ + K + P
Sbjct: 49 HRGGGHKRLYRKIDFRRNEKDIYGKIVTIEYDPNRNAYICLIHYGD-----GEKRYILHP 103
Query: 80 EGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAH 139
G G + G + +++GN +P+ MP GT + N+E G G+LARA+G A +IA
Sbjct: 104 RGAIIGDTIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGRGGQLARAAGAVAKLIAK 163
Query: 140 NPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKV 199
+ K +KLPSG ++I A VG V G K + +AG ++ KR P V
Sbjct: 164 --EGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQKRLGRAGSK--RWLGKR---PVV 216
Query: 200 RGVAMNPVEHPHGGG 214
RGV MNPV+HPHGGG
Sbjct: 217 RGVVMNPVDHPHGGG 231
>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_C
2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C* 3ofz_C*
3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C 2aw4_C 2awb_C
2vhm_C 2vhn_C 3bbx_C 3df2_C ...
Length = 271
Score = 118 bits (298), Expect = 2e-32
Identities = 65/195 (33%), Positives = 104/195 (53%), Gaps = 14/195 (7%)
Query: 22 HRKGAPK--LRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAP 79
H G K R +DF + VV + +DP R A +A+V +++ + +AP
Sbjct: 52 HIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKD-----GERRYILAP 106
Query: 80 EGMYTGQFVYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAH 139
+G+ G + G A ++ GN +P+ +P G+ V N+E K G G+LAR++G Y ++A
Sbjct: 107 KGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVAR 166
Query: 140 NPDTKRTRVKLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKV 199
D ++L SG + + + RA +G V + + + KAG A +++ R P V
Sbjct: 167 --DGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAA--RWRGVR---PTV 219
Query: 200 RGVAMNPVEHPHGGG 214
RG AMNPV+HPHGGG
Sbjct: 220 RGTAMNPVDHPHGGG 234
>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D 2jl8_D
2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D 2wh4_D
2wrj_D 2wrl_D 2wro_D 2wrr_D ...
Length = 276
Score = 115 bits (290), Expect = 3e-31
Identities = 61/172 (35%), Positives = 92/172 (53%), Gaps = 12/172 (6%)
Query: 43 GVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKKATLQIGNVM 102
V I +DP R A +A++H+ + K IAP+G+ GQ V G A +Q+GN +
Sbjct: 77 AKVAAIEYDPNRSARIALLHYVD-----GEKRYIIAPDGLQVGQQVVAGPDAPIQVGNAL 131
Query: 103 PVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIPSAN 162
P+ +P GT+V +E + +LARA+G A + + ++LPSG + +
Sbjct: 132 PLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGR--EGDYVILRLPSGELRKVHGEC 189
Query: 163 RAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGG 214
A VG V + + KAGR+ ++ +R P VRG AMNPV+HPHGGG
Sbjct: 190 YATVGAVGNADHKNIVLGKAGRS--RWLGRR---PHVRGAAMNPVDHPHGGG 236
>1rl2_A Protein (ribosomal protein L2); RNA-binding domain,
peptidyltransferease center, X-RAY diffraction; 2.30A
{Geobacillus stearothermophilus} SCOP: b.34.5.3 b.40.4.5
PDB: 1c04_A 487d_I
Length = 137
Score = 81.4 bits (202), Expect = 1e-19
Identities = 48/142 (33%), Positives = 75/142 (52%), Gaps = 7/142 (4%)
Query: 28 KLRSLDFAERHGYLKGVVRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQF 87
+ R +DF + G V I +DP R A +A++++ + K IAP+ + G
Sbjct: 1 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYAD-----GEKRYIIAPKNLKVGME 55
Query: 88 VYCGKKATLQIGNVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTR 147
+ G A ++IGN +P+ +P GT+V N+E K G G+L RA+G A V+ + K
Sbjct: 56 IMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGK--EGKYVI 113
Query: 148 VKLPSGAKKVIPSANRAMVGIV 169
V+L SG ++I RA VG V
Sbjct: 114 VRLASGEVRMILGKCRATVGEV 135
>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_B
Length = 136
Score = 73.0 bits (180), Expect = 1e-16
Identities = 36/144 (25%), Positives = 60/144 (41%), Gaps = 13/144 (9%)
Query: 45 VRDIIHDPGRGAPLAVVHFRNPYKFKTNKELFIAPEGMYTGQFVYCGKK-----ATLQIG 99
V + +DP R A +A+V + K IA E M G + + G
Sbjct: 1 VIQVRYDPCRSADIALVAGGS------RKRWIIATENMQAGDTILNSNHIGRMAVAAREG 54
Query: 100 NVMPVGGMPEGTIVCNLEEKTGDRGRLARASGNYATVIAHNPDTKRTRVKLPSGAKKVIP 159
+ P+G +P GT++ N+E + G + RA+G ++ ++LPS + +
Sbjct: 55 DAHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRK--VNGTAIIQLPSKRQMQVL 112
Query: 160 SANRAMVGIVAGGGRIDKPILKAG 183
A VG V+ + I KAG
Sbjct: 113 ETCVATVGRVSNVDHNKRVIGKAG 136
>3v4c_A Aldehyde dehydrogenase (NADP+); structural genomics, PSI-biology,
nysgrc, NEW YORK structura genomics research consortium;
HET: PE4; 1.91A {Sinorhizobium meliloti}
Length = 528
Score = 30.0 bits (68), Expect = 0.75
Identities = 17/54 (31%), Positives = 19/54 (35%), Gaps = 14/54 (25%)
Query: 180 LKAGRAHYKYKAKRNCWPKVRGVAMNPVEHPHGGGNHQHIGKASTVKRGTSAGR 233
KAGR N +P GV + HGG AST TS G
Sbjct: 463 RKAGRVLV------NGFPT--GVEVVD-SMVHGGPY-----PASTNFGATSVGT 502
>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 = 29.4 bits (65), Expect = 1.4
Identities = 11/66 (16%), Positives = 17/66 (25%), Gaps = 16/66 (24%)
Query: 149 KLPSGAKKVIPSANRAMVGIVAGGGRIDKPILKAGRAHYKYKAKRNCWPKVRGVAM---- 204
LP P R + I ++ G A + NC +
Sbjct: 317 DLPREVLTTNP---RRLSIIAE--------SIRDGLATWDNWKHVNCDKLTTIIESSLNV 365
Query: 205 -NPVEH 209
P E+
Sbjct: 366 LEPAEY 371
>2oez_A UPF0289 protein VP2528; immunoglobulin fold, alpha-structure,
structural genomics, P protein structure initiative;
HET: MSE; 1.97A {Vibrio parahaemolyticus} SCOP: e.68.1.1
Length = 247
Score = 28.2 bits (63), Expect = 2.1
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 10/53 (18%)
Query: 125 RLARASGNYATVIAHN-------PDTKRTRVKLPSGAKKVIP--SANRAMVGI 168
+LAR +G++ IA + R+ +P V P S ++ I
Sbjct: 174 KLARETGHFKAQIARAGFFQSDADEANILRLHIPMKY-GVYPMISGHKNRFAI 225
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.5 bits (61), Expect = 4.6
Identities = 12/29 (41%), Positives = 13/29 (44%)
Query: 135 TVIAHNPDTKRTRVKLPSGAKKVIPSANR 163
I P+T VKL GA IP A R
Sbjct: 953 VDIFEIPETGEYSVKLLKGATLYIPKALR 981
>1pp9_A Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_A* 1be3_A* 1l0n_A* 1ntk_A* 1ntm_A*
1ntz_A* 1nu1_A* 1l0l_A* 1ppj_A* 1sqq_A* 1sqv_A* 1sqx_A*
2a06_A* 2fyu_A* 2ybb_A* 1sqb_A* 1sqp_A* 1qcr_A* 1bcc_A*
2bcc_A* ...
Length = 446
Score = 26.8 bits (60), Expect = 7.7
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 130 SGNYATVIAHNPDTKRTRVKLPSGAKKVI---PSANRAMVGIVAGGGRIDKPILKAGRAH 186
+ YA + P+T+ + +L +G +V S VG+ G + G +
Sbjct: 1 TATYAQALQSVPETQVS--QLDNGL-RVASEQSSQPTCTVGVWIDAGSRYESEKNNGAGY 57
Query: 187 Y 187
+
Sbjct: 58 F 58
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 0.137 0.416
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,953,555
Number of extensions: 251279
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 423
Number of HSP's successfully gapped: 16
Length of query: 248
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 157
Effective length of database: 4,160,982
Effective search space: 653274174
Effective search space used: 653274174
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 (21.8 bits)
S2: 56 (25.3 bits)