RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 038172
(323 letters)
>3iz5_C 60S ribosomal protein L3 (L3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_C
Length = 389
Score = 365 bits (938), Expect = e-126
Identities = 262/303 (86%), Positives = 288/303 (95%)
Query: 21 MSHRKFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 80
MSHRKFEHPRHGSLGFLPRKR +RHRGKVK+FPKDD KPC LTAFLGYKAGMTHIVR+V
Sbjct: 1 MSHRKFEHPRHGSLGFLPRKRCSRHRGKVKSFPKDDQQKPCHLTAFLGYKAGMTHIVREV 60
Query: 81 EKPGSKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRGLRSLNTVWAQHLSEEVRRRFYK 140
EKPGSKLHKKETCEAVTIIETPP+++VG+V YVKTPRGLR+LN+VWAQHLSE+VRRRFYK
Sbjct: 61 EKPGSKLHKKETCEAVTIIETPPLVIVGLVAYVKTPRGLRTLNSVWAQHLSEDVRRRFYK 120
Query: 141 NWCKSKKKAFTKYSKQYETDEGKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAH 200
NWCKSKKKAFTKY+ +Y++D GKK IQ QLEK+KKYA++VRV+AHTQIRKMKGLKQKKAH
Sbjct: 121 NWCKSKKKAFTKYALKYDSDAGKKEIQLQLEKMKKYATIVRVIAHTQIRKMKGLKQKKAH 180
Query: 201 LMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 260
LMEIQVNGGTIA+KVDY Y FFEK++PV+AVFQKDEM+DIIGVTKGKGYEGVVTRWGVTR
Sbjct: 181 LMEIQVNGGTIADKVDYGYKFFEKEVPVEAVFQKDEMVDIIGVTKGKGYEGVVTRWGVTR 240
Query: 261 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYKLGKGGQESHTGIT 320
LPRKTHRGLRKVACIGAWHPARVS+TVARAGQNGYHHRTEMNKK+YK+GK GQESH T
Sbjct: 241 LPRKTHRGLRKVACIGAWHPARVSYTVARAGQNGYHHRTEMNKKIYKMGKSGQESHEACT 300
Query: 321 EFD 323
EFD
Sbjct: 301 EFD 303
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 403
Score = 347 bits (892), Expect = e-119
Identities = 207/309 (66%), Positives = 259/309 (83%), Gaps = 7/309 (2%)
Query: 21 MSHRKFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 80
MSHRKF PRHGSLGFLPRKR++RHRGKVK+FPKDD SKP LTAFLGYKAGMTHIVR+V
Sbjct: 1 MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDSSKPVHLTAFLGYKAGMTHIVREV 60
Query: 81 EKPGSKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRGLRSLNTVWAQHLSEEVRRRFYK 140
++PGSK++KKE EAVTI+ETPPM++VG+VGYV+TPRGLR+ T++A+H+S+E +RRFYK
Sbjct: 61 DRPGSKVNKKEVVEAVTIVETPPMVIVGIVGYVETPRGLRTFKTIFAEHISDECKRRFYK 120
Query: 141 NWCKSKKKAFTKYSKQYETDEGKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAH 200
NW KSKKKAFTKY K+++ +GKK ++ +KKY V+RV+AHTQ+R + L+QKKAH
Sbjct: 121 NWHKSKKKAFTKYCKKWQDADGKKQLERDFSSMKKYCQVIRVIAHTQMRLLP-LRQKKAH 179
Query: 201 LMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 260
LME+QVNGGT+AEK+D+A E+Q+PV VF +DEMID+IGVTKGKGY+GV +RW +
Sbjct: 180 LMEVQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKK 239
Query: 261 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYKLGKG------GQE 314
LPRKTHRGLRKVACIGAWHPARV+F+VARAGQ GYHHRTE+NKK+YK+G+G
Sbjct: 240 LPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLI 299
Query: 315 SHTGITEFD 323
+ T++D
Sbjct: 300 KNNASTDYD 308
>3u5e_B 60S ribosomal protein L3; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 3o5h_C 3o58_C 3u5i_B
3izc_C 3izs_C 1s1i_C 3jyw_C
Length = 387
Score = 332 bits (851), Expect = e-113
Identities = 210/303 (69%), Positives = 250/303 (82%), Gaps = 4/303 (1%)
Query: 21 MSHRKFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 80
MSHRK+E PRHG LGFLPRKRAA R +VKAFPKDD SKP LT+FLGYKAGMT IVRD+
Sbjct: 1 MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL 60
Query: 81 EKPGSKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRGLRSLNTVWAQHLSEEVRRRFYK 140
++PGSK HK+E EAVT+++TPP++VVGVVGYV+TPRGLRSL TVWA+HLS+EV+RRFYK
Sbjct: 61 DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK 120
Query: 141 NWCKSKKKAFTKYSKQYETDEGKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAH 200
NW KSKKKAFTKYS +Y + I+ +L +IKKYASVVRVL HTQIRK L QKKAH
Sbjct: 121 NWYKSKKKAFTKYSAKYA--QDGAGIERELARIKKYASVVRVLVHTQIRKTP-LAQKKAH 177
Query: 201 LMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 260
L EIQ+NGG+I+EKVD+A FEK + VD+VF+++EMID I VTKG G+EGV RWG +
Sbjct: 178 LAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKK 237
Query: 261 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYKLGKGGQESHTGIT 320
LPRKTHRGLRKVACIGAWHPA V ++VARAGQ GYH RT +N K+Y++GKG E++ G T
Sbjct: 238 LPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEAN-GAT 296
Query: 321 EFD 323
FD
Sbjct: 297 SFD 299
>4a17_B RPL3, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_B 4a1c_B 4a1e_B
Length = 391
Score = 331 bits (850), Expect = e-113
Identities = 179/303 (59%), Positives = 232/303 (76%), Gaps = 6/303 (1%)
Query: 21 MSHRKFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 80
MSHRKFE PRHGSLGF PR+R HRG+ ++FPKDDPSK LTAF G+KAGMTHI+R+V
Sbjct: 1 MSHRKFEAPRHGSLGFRPRRRTRHHRGRCRSFPKDDPSKKPHLTAFTGFKAGMTHILREV 60
Query: 81 EKPGSKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRGLRSLNTVWAQHLSEEVRRRFYK 140
++ GS+ +KKE EAVT+IE PPM +VGVVGY+ TPRGLR+L TVWA+ + ++RFYK
Sbjct: 61 DRSGSRHNKKEVVEAVTVIECPPMTIVGVVGYIDTPRGLRALTTVWAKTIDNNTKKRFYK 120
Query: 141 NWCKSKKKAFTKYSKQYETDEGKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAH 200
NW S KKAFT + K ++ +K+ L++I+KY SVVRV+AHT + K L+QKK H
Sbjct: 121 NWANSNKKAFTHHEKNFD----QKAQDLLLKRIEKYCSVVRVIAHTNMSK-LNLRQKKNH 175
Query: 201 LMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 260
++EIQVNGG +AEKV +A EK++ VD++F ++EM+D++GVTKGKG+ GV+ R+GV
Sbjct: 176 ILEIQVNGGKVAEKVAFAKSLLEKEVKVDSIFAENEMLDVLGVTKGKGFAGVIKRFGVKH 235
Query: 261 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYKLGKGGQESHTGIT 320
L +KTHRG RKV CIGAWHP+R+ FTV RAGQ GYHHRTE NKKVY++GK G ++ T
Sbjct: 236 LQKKTHRGYRKVGCIGAWHPSRIRFTVPRAGQLGYHHRTETNKKVYRVGK-GDDASNAST 294
Query: 321 EFD 323
D
Sbjct: 295 AGD 297
>1vq8_B 50S ribosomal protein L3P; 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.43.3.2 PDB: 1vq4_B*
1vq5_B* 1vq6_B* 1vq7_B* 1s72_B* 1vq9_B* 1vqk_B* 1vql_B*
1vqm_B* 1vqn_B* 1vqo_B* 1vqp_B* 1yhq_B* 1yi2_B* 1yij_B*
1yit_B* 1yj9_B* 1yjn_B* 1yjw_B* 2otj_B* ...
Length = 338
Score = 309 bits (793), Expect = e-105
Identities = 99/293 (33%), Positives = 148/293 (50%), Gaps = 21/293 (7%)
Query: 25 KFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDVEKPG 84
+ PR GSLGF PRKR+ + ++P DD + F GYKAGMTH+V ++P
Sbjct: 3 QPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPG--VQGFAGYKAGMTHVVLVNDEPN 60
Query: 85 SKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRGLRSLNTVWAQHLSEEVRRRFYKNWCK 144
S E VT+IETPPM V + Y TP G R L VW E+ R
Sbjct: 61 SPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDH 120
Query: 145 SKKKAFTKYSKQYETDEGKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAHLMEI 204
A + +E +R++ HT + + +KK +ME
Sbjct: 121 DPDAAEEQIRDAHE---------------AGDLGDLRLITHTVPDAVPSVPKKKPDVMET 165
Query: 205 QVNGGTIAEKVDYAYGFFE--KQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLP 262
+V GG++++++D+A E + ++ +F+ E D+ GVTKGKG +G V RWGV +
Sbjct: 166 RVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRK 225
Query: 263 RKTHRG--LRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYKLGKGGQ 313
K R R++ +G W+P+RV TV + GQ GYH RTE+NK++ +G+G +
Sbjct: 226 GKHARQGWRRRIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDE 278
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial
ribosome, large ribosomal subunit, ribosomal R ribosome;
12.10A {Bos taurus}
Length = 211
Score = 52.5 bits (127), Expect = 2e-08
Identities = 26/113 (23%), Positives = 44/113 (38%), Gaps = 13/113 (11%)
Query: 198 KAHLMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWG 257
K + + + G + F+ + +D+ T GKG++GV+ RWG
Sbjct: 78 KQTVKIFNI-----TDNAAIKPG---TPLYAA-HFRPGQYVDVTAKTIGKGFQGVMKRWG 128
Query: 258 VTRLPRKTH---RGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYK 307
P TH + R+ + RV G+ G +RTE KV++
Sbjct: 129 FKGQP-ATHGQTKTHRRPGAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWR 180
>3r8s_D 50S ribosomal protein L3; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_B
1p86_B 1vs8_D 1vs6_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vt2_D
2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D
2qbg_D 2qbi_D* 2qbk_D* 2qov_D ...
Length = 209
Score = 49.4 bits (119), Expect = 3e-07
Identities = 31/114 (27%), Positives = 46/114 (40%), Gaps = 14/114 (12%)
Query: 198 KAHLMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWG 257
L E ++ AE ++ G + I V+ +F + +D+ G +KGKG+ G V RW
Sbjct: 76 GRGLWEFRL-----AEGEEFTVG---QSISVE-LFADVKKVDVTGTSKGKGFAGTVKRWN 126
Query: 258 VTRLPRKTH---RGLRKVACIGAWH-PARVSFTVARAGQNGYHHRTEMNKKVYK 307
TH R IG P +V AGQ G T + V +
Sbjct: 127 FRTQD-ATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVR 179
>3v2d_E 50S ribosomal protein L3; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_C 2hgj_E 2hgq_E 2hgu_E 1vsa_C 2j03_E 2jl6_E 2jl8_E
2v47_E 2v49_E 2wdi_E 2wdj_E 2wdl_E 2wdn_E 2wh2_E 2wh4_E
2wrj_E 2wrl_E 2wro_E 2wrr_E ...
Length = 206
Score = 48.7 bits (117), Expect = 4e-07
Identities = 27/87 (31%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 225 QIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-P 280
+ V+ +F+ E +D+ G +KG+G+ GV+ RW P +H + R IG P
Sbjct: 90 TVTVE-IFKPGERVDVTGTSKGRGFAGVMKRWNFAGGP-DSHGAHKIHRHPGSIGNRKTP 147
Query: 281 ARVSFTVARAGQNGYHHRTEMNKKVYK 307
RV AG G T MN +V
Sbjct: 148 GRVYKGKKMAGHYGAERVTVMNLEVVD 174
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.43.3.2 PDB: 1nwx_B* 1nwy_B* 1sm1_B*
1xbp_B* 2ogm_B* 2ogn_B* 2ogo_B* 2zjp_B* 2zjq_B 1nkw_B
3cf5_B* 3dll_B* 3pio_B* 3pip_B* 1pnu_B 1pny_B 1vor_E
1vou_E 1vow_E 1voy_E ...
Length = 211
Score = 48.3 bits (116), Expect = 6e-07
Identities = 29/87 (33%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 225 QIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-P 280
+ VD +F + E ID G +KGKG +GV+ RW P +H + R+ IG P
Sbjct: 90 SVNVD-IFAEGEKIDATGTSKGKGTQGVMKRWNFAGGP-ASHGSKKWHRRPGSIGQRKTP 147
Query: 281 ARVSFTVARAGQNGYHHRTEMNKKVYK 307
RV AG G T N +V +
Sbjct: 148 GRVYKGKRMAGHMGMERVTVQNLEVVE 174
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 259
Score = 48.8 bits (117), Expect = 7e-07
Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 12/113 (10%)
Query: 198 KAHLMEIQVNGGTIAEKVDYAYGFFEKQIPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWG 257
HL E ++ E ++ +F++ +++D+ G T GKG++G + R
Sbjct: 119 LRHLQEFRLQSIDGFEVTQ--------KLDFGELFKEGDLVDVSGTTIGKGFQGGIKRHN 170
Query: 258 VTRLPRKTH--RGLRKVACIGAWH-PARVSFTVARAGQNGYHHRTEMNKKVYK 307
R TH + R++ IGA P RV G+ G R K+ K
Sbjct: 171 FKRGQ-MTHGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTKRKIRKLKIVK 222
>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 = 38.3 bits (88), Expect = 0.003
Identities = 30/188 (15%), Positives = 55/188 (29%), Gaps = 54/188 (28%)
Query: 2 SLPALEHNESVAAAAQRRRMSHRKFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPC 61
++ A RR + + +E+ L L ++ AF + S C
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYEN----CLLVL---LNVQNAKAWNAF---NLS--C 266
Query: 62 R---------LTAFLGYKAGMTHIVRDVEKPGSKLHKKETCE------AVTIIETPPMMV 106
+ +T FL A THI D L E + P ++
Sbjct: 267 KILLTTRFKQVTDFLS-AATTTHISLDHHSMT--LTPDEVKSLLLKYLDCRPQDLPREVL 323
Query: 107 VGVVGYVKTPRGLRSLNTVWAQHLSEEVRRRFYKNWCKSKKKAFTKYSKQYETDEGKKSI 166
PR L+ + + + + + NW K D+ I
Sbjct: 324 TT------NPR---RLSIIAES-IRDGLAT--WDNW------------KHVNCDKLTTII 359
Query: 167 QAQLEKIK 174
++ L ++
Sbjct: 360 ESSLNVLE 367
Score = 34.4 bits (78), Expect = 0.048
Identities = 23/152 (15%), Positives = 45/152 (29%), Gaps = 49/152 (32%)
Query: 77 VRDVEKPGSKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRGLRSLNTVW---------A 127
+DV+ + KE + II + +L W
Sbjct: 35 CKDVQDMPKSILSKEEID--HIIMSKD-------------AVSGTLRLFWTLLSKQEEMV 79
Query: 128 QHLSEEVRRRFYKNW--------CKSKKKAFTKYSKQYETDEGKKSIQAQLEKIKKYASV 179
Q EEV R Y + + Y +Q + + + KY +V
Sbjct: 80 QKFVEEVLRINY-KFLMSPIKTEQRQPSMMTRMYIEQRD------RLYNDNQVFAKY-NV 131
Query: 180 VRVLAHTQIRKMKGLKQKKAHLMEIQVNGGTI 211
R+ + ++R+ L+E++ +
Sbjct: 132 SRLQPYLKLRQ---------ALLELRPAKNVL 154
Score = 33.3 bits (75), Expect = 0.11
Identities = 32/209 (15%), Positives = 64/209 (30%), Gaps = 57/209 (27%)
Query: 8 HNESVAAAAQRRRMSHRKFEHPRHGSLGFLPRKRAARHR------GKVKAFPKDDPSKPC 61
H S+ +++ + L A HR K F DD P
Sbjct: 412 HKYSLV---EKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPY 468
Query: 62 R---LTAFLGYKAGMTHIVRDVEKPGSKLHKKETCEAVTIIETPPMMVVGVVGYVKTPRG 118
+ +G+ H L E E +T+ M+ + +++ +
Sbjct: 469 LDQYFYSHIGH-----H-----------LKNIEHPERMTLF---RMVFLD-FRFLE--QK 506
Query: 119 LRSLNTVW---AQHLSEEVRRRFYKNWCKSKKKAFTKYSKQYET---DEGKKSIQAQLEK 172
+R +T W L+ + +FYK + + + + I +
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICS---- 562
Query: 173 IKKYASVVRVL-----------AHTQIRK 190
KY ++R+ AH Q+++
Sbjct: 563 --KYTDLLRIALMAEDEAIFEEAHKQVQR 589
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.2 bits (72), Expect = 0.12
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 146 KKKAFTKYS---KQYETDEGKK-SIQAQLE 171
+K+A K K Y D +I+A +E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
Score = 30.7 bits (68), Expect = 0.35
Identities = 5/16 (31%), Positives = 12/16 (75%), Gaps = 2/16 (12%)
Query: 163 KKSIQAQLE-KIKKYA 177
K++++ +L+ +K YA
Sbjct: 19 KQALK-KLQASLKLYA 33
>3bqk_A Pfemp1 protein, erythrocyte membrane protein 1; malaria, pregnancy,
VAR2CSA encoded pfemp1 protein, DBL3X DO chondroitin
sulphate A; 1.80A {Plasmodium falciparum} PDB: 3bqi_A
3bql_A 3cml_A 3cpz_A
Length = 360
Score = 30.4 bits (68), Expect = 0.71
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 139 YKNWCKSKKKAFTKYSKQYETD-EGKKSIQAQLEKIKKYAS 178
YK + KK+ + K +YE GK + E + S
Sbjct: 291 YKKYISEKKQEWDKQKTKYENKYVGKSASDLLKENYPECIS 331
>2w40_A Glycerol kinase, putative; closed conformation, malaria,
transferase, sugar kinase/HSP70/actin superfamily, open
conformation; 1.49A {Plasmodium falciparum} PDB: 2w41_A*
Length = 503
Score = 30.6 bits (70), Expect = 0.83
Identities = 7/47 (14%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 110 VGYVKTPRGLRSLN----TVWAQHLSEEVRRRFYKNWCKSKKKAFTK 152
V + ++SL V+ + ++ R++ W K+ ++ +
Sbjct: 456 VKIWDSLDSVKSLLRRSDAVFHSKMDDKKRKKKTSEWNKAVERTLIQ 502
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 1.3
Identities = 8/60 (13%), Positives = 20/60 (33%), Gaps = 7/60 (11%)
Query: 116 PRGLRSLNTVWAQHLSEEVRRRFYKNWCKSKKKAFTKYSKQYETDEGKKSIQAQLEKIKK 175
P +R W + + ++ + + + + +E + Q+EK K
Sbjct: 84 PESIRK----WREEQRKRLQELDAA---SKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136
>2y8d_A Erythrocyte membrane protein 1; DBL epsilon, pfemp1, malaria; 1.84A
{Plasmodium falciparum}
Length = 306
Score = 29.4 bits (66), Expect = 1.4
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 139 YKNWCKSKKKAFTKYSKQYETDEGKKSIQ 167
YKN+ +KK + + +Y+ + K+
Sbjct: 227 YKNYILTKKTEYEIQTNKYDNEFKNKNSN 255
>3rrc_A Duffy receptor; duffy binding like, receptor recognition, duffy
antigen RECE chemokines, cell invasion; HET: EDO; 1.95A
{Plasmodium vivax} PDB: 2c6j_A
Length = 317
Score = 29.5 bits (66), Expect = 1.6
Identities = 6/29 (20%), Positives = 13/29 (44%)
Query: 139 YKNWCKSKKKAFTKYSKQYETDEGKKSIQ 167
Y W KK + S ++ + + + +Q
Sbjct: 231 YDQWITRKKNQWDVLSNKFISVKNAEKVQ 259
>1zro_A Erythrocyte binding antigen region II; EBA-175, RII, DBL, invasion,
HOST, malaria, disease, glycophorin, glycan, sialic
acid; HET: SO4; 2.25A {Plasmodium falciparum} SCOP:
a.264.1.1 a.264.1.1 PDB: 1zrl_A*
Length = 602
Score = 29.2 bits (65), Expect = 2.1
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 139 YKNWCKSKKKAFTKYSKQYETDEGKKS 165
YK W KK+ + K +KQY+ + +
Sbjct: 525 YKEWISKKKEEYNKQAKQYQEYQKGNN 551
>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A
2vpl_A
Length = 137
Score = 27.6 bits (62), Expect = 3.2
Identities = 3/23 (13%), Positives = 6/23 (26%), Gaps = 1/23 (4%)
Query: 98 IIETPPMM-VVGVVGYVKTPRGL 119
I +V + K +
Sbjct: 19 IYTIDEAAHLVKELATAKFDETV 41
>2ash_A Queuine tRNA-ribosyltransferase; TM1561, tRNA-guanine, struc
genomics, joint center for structural genomics, JCSG;
1.90A {Thermotoga maritima}
Length = 381
Score = 28.3 bits (64), Expect = 3.7
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 98 IIETPPMMVVGVVGYVK--TPRGLRSLNT 124
+ETP M VG VK TPR L
Sbjct: 35 AVETPVFMPVGTNASVKLLTPRDLEEAGA 63
>2o36_A ThiMet oligopeptidase; thermolysin-like domain, substrate-binding
channel, hydrolase; 1.95A {Homo sapiens} PDB: 1s4b_P
Length = 674
Score = 28.4 bits (64), Expect = 4.0
Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 138 FYKNWCKSKKKAFTKYSKQYETDEGKKSI-QAQLEKIKK 175
+NW +++ + S+ Y T ++ + LEK+ +
Sbjct: 492 MLENWV-WEQEPLLRMSRHYRTGS---AVPRELLEKLIE 526
>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein,
nucleotide-binding, protein biosynthesis, translation,
zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB:
3fik_5 3izt_C* 3izu_C* 3j01_5 3j0t_C* 3j0w_C* 3j0y_C*
3j11_C* 3j12_C* 3j14_C* 3kcr_5 2rdo_9 2gya_2 2gyc_2
Length = 234
Score = 28.0 bits (63), Expect = 4.1
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 98 IIETPPMM-VVGVVGYVKTPRGL 119
+I +P M VVG +G V PRGL
Sbjct: 114 VIASPDAMRVVGQLGQVLGPRGL 136
>3qoy_A 50S ribosomal protein L1; beta-alpha-beta, structural constituent
of ribosome, rRNA BI regulation of translation,
translation, ribosomal RNA; 2.10A {Aquifex aeolicus}
Length = 242
Score = 27.7 bits (62), Expect = 4.3
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 98 IIETPPMM-VVGVVGYVKTPRGL 119
I TP MM V +G + PRGL
Sbjct: 118 AIATPEMMPKVAKLGRILGPRGL 140
>3bld_A Queuine tRNA-ribosyltransferase; TGT, PREQ1, glycosyltransferase,
metal-binding, queuosine biosynthesis, tRNA processing;
HET: PRF; 1.19A {Zymomonas mobilis} PDB: 3bl3_A* 1ozq_A*
1ozm_A* 1r5y_A* 1enu_A* 1f3e_A* 1k4h_A* 1n2v_A* 1p0b_A*
1p0d_A 1p0e_A* 1pud_A 1q2r_A* 1q2s_A* 1q4w_A* 1q63_A*
1q65_A* 1q66_A* 1k4g_A* 1s38_A* ...
Length = 386
Score = 27.9 bits (63), Expect = 4.4
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 98 IIETPPMMVVGVVGYVK--TPRGLRSLNT 124
+I TP M VG VK P +R+
Sbjct: 36 VIRTPAFMPVGTAATVKALKPETVRATGA 64
>2wau_A VAR2CSA, erythrocyte membrane protein 1 (pfemp1); chondroitin
sulphate A, membrane protein DBL, malaria; 3.00A
{Plasmodium falciparum}
Length = 302
Score = 27.9 bits (62), Expect = 4.5
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 139 YKNWCKSKKKAFTKYSKQYETDEGKKSIQ 167
Y N+ KKK + + QY+ + + +
Sbjct: 226 YSNFILIKKKEYQSLNSQYDMNYKETKAE 254
>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 352
Score = 28.0 bits (62), Expect = 5.0
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 98 IIETPPMM-VVGVVGYVKTPRGL 119
+I T MM V +G + PRGL
Sbjct: 228 LIATSDMMAKVASLGRILGPRGL 250
>2o3e_A Neurolysin; thermolysin-like domain, substrate-binding channel,
hydrolase; 2.20A {Rattus norvegicus} PDB: 1i1i_P
Length = 678
Score = 28.0 bits (63), Expect = 5.3
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 5/39 (12%)
Query: 138 FYKNWCKSKKKAFTKYSKQYETDEGKKSI-QAQLEKIKK 175
+NW + K SK Y+ I LEK+
Sbjct: 508 MLENWV-WDVDSLRKLSKHYKDGH---PITDELLEKLVA 542
>3vuv_A Erythrocyte membrane protein, putative; duffy binding-like domain,
erythrocyte binding, merozoite SU malaria, cell
adhesion; 2.11A {Plasmodium falciparum}
Length = 339
Score = 27.5 bits (61), Expect = 5.4
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 139 YKNWCKSKKKAF----TKYSKQYETDEGKKSIQAQLEKIKKYAS 178
Y+ W +K + KY+ K++ E + +
Sbjct: 279 YEEWYNKRKTEWTEQSIKYNNDKINYTDIKTLSPS-EYLIEKCP 321
>2zbw_A Thioredoxin reductase; redox protein, oxidoreductase, structural
genomics, NPPSFA, project on protein structural and
functional analyses; HET: FAD; 2.10A {Thermus
thermophilus}
Length = 335
Score = 27.6 bits (62), Expect = 5.6
Identities = 12/89 (13%), Positives = 31/89 (34%), Gaps = 18/89 (20%)
Query: 162 GKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAHLMEIQVNGGTIAEKVDYAYGF 221
++ +L K + + VL ++R+++G ++ + ++ +A +VD
Sbjct: 189 AHEASVKELMKAHE-EGRLEVLTPYELRRVEGDERVRWAVVFHNQTQEELALEVDAVLIL 247
Query: 222 F-----------------EKQIPVDAVFQ 233
+ +I VD
Sbjct: 248 AGYITKLGPLANWGLALEKNKIKVDTTMA 276
>3vuu_A Erythrocyte membrane protein, putative; duffy binding-like domain,
erythrocyte binding, merozoite SU malaria, cell
adhesion; 2.09A {Plasmodium falciparum}
Length = 305
Score = 27.5 bits (61), Expect = 6.0
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 139 YKNWCKSKKKAF----TKYSKQYETDEGKKSIQAQLEKIKKYAS 178
Y+ W +K + KY+ K++ E + +
Sbjct: 245 YEEWYNKRKTEWTEQSIKYNNDKINYTDIKTLSPS-EYLIEKCP 287
>3ab1_A Ferredoxin--NADP reductase; oxidoreductase, electron transport,
FAD, flavoprotein; HET: FAD; 2.39A {Chlorobaculum
tepidum}
Length = 360
Score = 27.3 bits (61), Expect = 7.9
Identities = 9/89 (10%), Positives = 24/89 (26%), Gaps = 18/89 (20%)
Query: 162 GKKSIQAQLEKIKKYASVVRVLAHTQIRKMKGLKQKKAHLMEIQVNGGTIAEKVDYAYGF 221
G ++E+ + + V T++ ++ + +G + D
Sbjct: 200 GHGKTAHEVERARA-NGTIDVYLETEVASIEESNGVLTRVHLRSSDGSKWTVEADRLLIL 258
Query: 222 F-----------------EKQIPVDAVFQ 233
E + VD+ +
Sbjct: 259 IGFKSNLGPLARWDLELYENALVVDSHMK 287
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
0.319 0.134 0.402
Gapped
Lambda K H
0.267 0.0501 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,139,713
Number of extensions: 314852
Number of successful extensions: 739
Number of sequences better than 10.0: 1
Number of HSP's gapped: 729
Number of HSP's successfully gapped: 45
Length of query: 323
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 229
Effective length of database: 4,077,219
Effective search space: 933683151
Effective search space used: 933683151
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: 57 (26.3 bits)