RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 022045
(303 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 = 352 bits (905), Expect = e-121
Identities = 249/314 (79%), Positives = 277/314 (88%), Gaps = 15/314 (4%)
Query: 1 MSHRKFEHPRHGSLGFLPRKRASRHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 60
MSHRKFEHPRHGSLGFLPRKR SRHRGKVK+FPKDD KPC LTAFLGYKAGMTHIVR+V
Sbjct: 1 MSHRKFEHPRHGSLGFLPRKRCSRHRGKVKSFPKDDQQKPCHLTAFLGYKAGMTHIVREV 60
Query: 61 EKPGSKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRRRFYK 120
EKPGSKLHKKETCEAVTIIETPPLV+VG+V YVKTPRGLR+L +VWAQHL+E+VRRRFYK
Sbjct: 61 EKPGSKLHKKETCEAVTIIETPPLVIVGLVAYVKTPRGLRTLNSVWAQHLSEDVRRRFYK 120
Query: 121 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIR---------------KKAH 165
NWCKSKKKAFTKY KY++D GKK+IQ QLEKMKKY T++R KKAH
Sbjct: 121 NWCKSKKKAFTKYALKYDSDAGKKEIQLQLEKMKKYATIVRVIAHTQIRKMKGLKQKKAH 180
Query: 166 LMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 225
LMEIQVNGG++A KVD+ Y FFEK++P++AVFQKDEM+DIIGVTKGKGYEGVVTRWGVTR
Sbjct: 181 LMEIQVNGGTIADKVDYGYKFFEKEVPVEAVFQKDEMVDIIGVTKGKGYEGVVTRWGVTR 240
Query: 226 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMT 285
LPRKTHRGLRKVACIGAWHPARVS+TVARAGQNGYHHRTEMNKKIYK+GK+ QESH A T
Sbjct: 241 LPRKTHRGLRKVACIGAWHPARVSYTVARAGQNGYHHRTEMNKKIYKMGKSGQESHEACT 300
Query: 286 EFDRSVYLLSSLMG 299
EFDR+ ++ + G
Sbjct: 301 EFDRTEKDITPMGG 314
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 403
Score = 337 bits (865), Expect = e-115
Identities = 204/312 (65%), Positives = 250/312 (80%), Gaps = 20/312 (6%)
Query: 1 MSHRKFEHPRHGSLGFLPRKRASRHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 60
MSHRKF PRHGSLGFLPRKR+SRHRGKVK+FPKDD SKP LTAFLGYKAGMTHIVR+V
Sbjct: 1 MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDSSKPVHLTAFLGYKAGMTHIVREV 60
Query: 61 EKPGSKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRRRFYK 120
++PGSK++KKE EAVTI+ETPP+V+VG+VGYV+TPRGLR+ T++A+H+++E +RRFYK
Sbjct: 61 DRPGSKVNKKEVVEAVTIVETPPMVIVGIVGYVETPRGLRTFKTIFAEHISDECKRRFYK 120
Query: 121 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIR--------------KKAHL 166
NW KSKKKAFTKY KK++ DGKK ++ MKKYC VIR KKAHL
Sbjct: 121 NWHKSKKKAFTKYCKKWQDADGKKQLERDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL 180
Query: 167 MEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRL 226
ME+QVNGG+VA+K+D+A E+Q+P+ VF +DEMID+IGVTKGKGY+GV +RW +L
Sbjct: 181 MEVQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL 240
Query: 227 PRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKA------SQES 280
PRKTHRGLRKVACIGAWHPARV+F+VARAGQ GYHHRTE+NKKIYK+G+
Sbjct: 241 PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK 300
Query: 281 HSAMTEFDRSVY 292
++A T++D S
Sbjct: 301 NNASTDYDLSDK 312
>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 = 325 bits (835), Expect = e-111
Identities = 168/304 (55%), Positives = 225/304 (74%), Gaps = 19/304 (6%)
Query: 1 MSHRKFEHPRHGSLGFLPRKRASRHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 60
MSHRKFE PRHGSLGF PR+R HRG+ ++FPKDDPSK LTAF G+KAGMTHI+R+V
Sbjct: 1 MSHRKFEAPRHGSLGFRPRRRTRHHRGRCRSFPKDDPSKKPHLTAFTGFKAGMTHILREV 60
Query: 61 EKPGSKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRRRFYK 120
++ GS+ +KKE EAVT+IE PP+ +VGVVGY+ TPRGLR+L TVWA+ ++ ++RFYK
Sbjct: 61 DRSGSRHNKKEVVEAVTVIECPPMTIVGVVGYIDTPRGLRALTTVWAKTIDNNTKKRFYK 120
Query: 121 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIR--------------KKAHL 166
NW S KKAFT + K ++ +K L++++KYC+V+R KK H+
Sbjct: 121 NWANSNKKAFTHHEKNFD----QKAQDLLLKRIEKYCSVVRVIAHTNMSKLNLRQKKNHI 176
Query: 167 MEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRL 226
+EIQVNGG VA+KV FA EK++ +D++F ++EM+D++GVTKGKG+ GV+ R+GV L
Sbjct: 177 LEIQVNGGKVAEKVAFAKSLLEKEVKVDSIFAENEMLDVLGVTKGKGFAGVIKRFGVKHL 236
Query: 227 PRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMTE 286
+KTHRG RKV CIGAWHP+R+ FTV RAGQ GYHHRTE NKK+Y++GK ++ +A T
Sbjct: 237 QKKTHRGYRKVGCIGAWHPSRIRFTVPRAGQLGYHHRTETNKKVYRVGKG-DDASNASTA 295
Query: 287 FDRS 290
D +
Sbjct: 296 GDVT 299
>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 = 322 bits (825), Expect = e-109
Identities = 195/313 (62%), Positives = 243/313 (77%), Gaps = 17/313 (5%)
Query: 1 MSHRKFEHPRHGSLGFLPRKRASRHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDV 60
MSHRK+E PRHG LGFLPRKRA+ R +VKAFPKDD SKP LT+FLGYKAGMT IVRD+
Sbjct: 1 MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL 60
Query: 61 EKPGSKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRRRFYK 120
++PGSK HK+E EAVT+++TPP+VVVGVVGYV+TPRGLRSL TVWA+HL++EV+RRFYK
Sbjct: 61 DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK 120
Query: 121 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIR--------------KKAHL 166
NW KSKKKAFTKY+ KY D I+ +L ++KKY +V+R KKAHL
Sbjct: 121 NWYKSKKKAFTKYSAKYAQDGAG--IERELARIKKYASVVRVLVHTQIRKTPLAQKKAHL 178
Query: 167 MEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRL 226
EIQ+NGGS+++KVD+A FEK + +D+VF+++EMID I VTKG G+EGV RWG +L
Sbjct: 179 AEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKL 238
Query: 227 PRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMTE 286
PRKTHRGLRKVACIGAWHPA V ++VARAGQ GYH RT +N KIY++GK E++ T
Sbjct: 239 PRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEAN-GATS 297
Query: 287 FDRSVYLLSSLMG 299
FDR+ ++ + G
Sbjct: 298 FDRTKKTITPMGG 310
>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 = 307 bits (787), Expect = e-104
Identities = 98/278 (35%), Positives = 142/278 (51%), Gaps = 6/278 (2%)
Query: 5 KFEHPRHGSLGFLPRKRASRHRGKVKAFPKDDPSKPCRLTAFLGYKAGMTHIVRDVEKPG 64
+ PR GSLGF PRKR++ + ++P DD + F GYKAGMTH+V ++P
Sbjct: 3 QPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPG--VQGFAGYKAGMTHVVLVNDEPN 60
Query: 65 SKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRRRFYKNWCK 124
S E VT+IETPP+ V + Y TP G R L VW + E+ R
Sbjct: 61 SPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDH 120
Query: 125 SKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRKKAHLMEIQVNGGSVAQKVDFAY 184
A + +E D +V +KK +ME +V GGSV+ ++D A
Sbjct: 121 DPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHAL 180
Query: 185 GFFE--KQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTHRG--LRKVACI 240
E + ++ +F+ E D+ GVTKGKG +G V RWGV + K R R++ +
Sbjct: 181 DIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNL 240
Query: 241 GAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQ 278
G W+P+RV TV + GQ GYH RTE+NK++ +G+ +
Sbjct: 241 GPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDE 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 = 51.0 bits (123), Expect = 7e-08
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 195 AVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWHPARVSFT 251
A F+ + +D+ T GKG++GV+ RWG P TH + R+ + RV
Sbjct: 101 AHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQP-ATHGQTKTHRRPGAVATGDIGRVWPG 159
Query: 252 VARAGQNGYHHRTEMNKKIYK 272
G+ G +RTE K+++
Sbjct: 160 TKMPGKMGNIYRTEYGLKVWR 180
>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 = 5e-07
Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 196 VFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-PARVSFT 251
+F+ E +D+ G +KG+G+ GV+ RW P +H + R IG P RV
Sbjct: 95 IFKPGERVDVTGTSKGRGFAGVMKRWNFAGGP-DSHGAHKIHRHPGSIGNRKTPGRVYKG 153
Query: 252 VARAGQNGYHHRTEMNKKIYK 272
AG G T MN ++
Sbjct: 154 KKMAGHYGAERVTVMNLEVVD 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 = 47.9 bits (115), Expect = 7e-07
Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 196 VFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-PARVSFT 251
+F + E ID G +KGKG +GV+ RW P +H + R+ IG P RV
Sbjct: 95 IFAEGEKIDATGTSKGKGTQGVMKRWNFAGGP-ASHGSKKWHRRPGSIGQRKTPGRVYKG 153
Query: 252 VARAGQNGYHHRTEMNKKIYK 272
AG G T N ++ +
Sbjct: 154 KRMAGHMGMERVTVQNLEVVE 174
>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 = 47.9 bits (115), Expect = 9e-07
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 14/114 (12%)
Query: 163 KAHLMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWG 222
L E ++ G +F G + I ++ +F + +D+ G +KGKG+ G V RW
Sbjct: 76 GRGLWEFRLAEGE-----EFTVG---QSISVE-LFADVKKVDVTGTSKGKGFAGTVKRWN 126
Query: 223 VTRLPRKTH---RGLRKVACIGAWH-PARVSFTVARAGQNGYHHRTEMNKKIYK 272
TH R IG P +V AGQ G T + + +
Sbjct: 127 FRTQD-ATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVR 179
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 259
Score = 48.0 bits (115), Expect = 1e-06
Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 12/113 (10%)
Query: 163 KAHLMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWG 222
HL E ++ + ++ +F++ +++D+ G T GKG++G + R
Sbjct: 119 LRHLQEFRLQSIDGFEVTQ--------KLDFGELFKEGDLVDVSGTTIGKGFQGGIKRHN 170
Query: 223 VTRLPRKTH--RGLRKVACIGAWH-PARVSFTVARAGQNGYHHRTEMNKKIYK 272
R TH + R++ IGA P RV G+ G R KI 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 = 40.6 bits (94), Expect = 6e-04
Identities = 30/252 (11%), Positives = 68/252 (26%), Gaps = 75/252 (29%)
Query: 71 ETCEAVTIIETPPLVVVGV----VGYVKTPRG----LRSLCTV----WAQHLNEEVRRRF 118
+ C + + + + +P L+ L W + +
Sbjct: 169 DVCLSYKVQCKMDF---KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 119 YKNWCKSKKKAFTKYTKKYET-----DD--GKKDIQAQLEKMKKYCTVI---RKKAHLME 168
+ +++ + K +K YE + K A C ++ R K
Sbjct: 226 RIHSIQAELRRLLK-SKPYENCLLVLLNVQNAKAWNA----FNLSCKILLTTRFK----- 275
Query: 169 IQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRW---GVTR 225
V + A DE+ + ++ ++
Sbjct: 276 ------QVTDFLSAATTTHISLDHHSMTLTPDEV------------KSLLLKYLDCRPQD 317
Query: 226 LPRKTHRGL-RKVACIGAW---HPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESH 281
LPR+ R+++ I A + + H +N KL + S
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATW---------DNWKH---VNCD--KLTTIIESSL 363
Query: 282 SAMTEFD-RSVY 292
+ + + R ++
Sbjct: 364 NVLEPAEYRKMF 375
Score = 33.3 bits (75), Expect = 0.098
Identities = 31/163 (19%), Positives = 47/163 (28%), Gaps = 55/163 (33%)
Query: 29 VKAFPKDDPSKPCR---------LTAFLGYKAGMTHIVRDVEKPGSKLHKKETCE----- 74
AF + S C+ +T FL A THI D L E
Sbjct: 259 WNAF---NLS--CKILLTTRFKQVTDFLS-AATTTHISLDHHSMT--LTPDEVKSLLLKY 310
Query: 75 -AVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRRRFYKNWCKSKKKAFTKY 133
+ P V+ PR L S+ A+ + + + + NW
Sbjct: 311 LDCRPQDLPREVLTT------NPRRL-SII---AESIRDGLAT--WDNW----------- 347
Query: 134 TKKYETDDGKKDIQAQLEK-----MKKY---CTVIRKKAHLME 168
K D I++ L +K +V AH+
Sbjct: 348 -KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389
Score = 29.4 bits (65), Expect = 1.9
Identities = 31/196 (15%), Positives = 63/196 (32%), Gaps = 49/196 (25%)
Query: 8 HPRHGSLGFLPRKRASRHR------GKVKAFPKDDPSKPCR---LTAFLGYKAGMTHIVR 58
+ L + HR K F DD P + +G+ H
Sbjct: 429 PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH-----H--- 480
Query: 59 DVEKPGSKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVW---AQHLNEEVR 115
L E E +T+ +V + +++ + +R T W LN +
Sbjct: 481 --------LKNIEHPERMTLF---RMVFLD-FRFLE--QKIRHDSTAWNASGSILNTLQQ 526
Query: 116 RRFYKNWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRKKAHLMEIQVNGGS 175
+FYK + KYE + + A L+ + K + + +++ +
Sbjct: 527 LKFYKPY-------ICDNDPKYE-----RLVNAILDFLPKIEENLICSKYTDLLRI---A 571
Query: 176 VAQKVDFAYGFFEKQI 191
+ + + + KQ+
Sbjct: 572 LMAEDEAIFEEAHKQV 587
Score = 27.5 bits (60), Expect = 7.3
Identities = 16/126 (12%), Positives = 37/126 (29%), Gaps = 30/126 (23%)
Query: 93 VKTPRGLRSLCTVWAQHLNEEVRR---RFY------KNWCKSKKKAFTKYTKKYETDDGK 143
P L L +W + +V + + K +S + Y + + +
Sbjct: 385 AHIPTIL--LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 144 KDIQAQL----EKMKKYCTVIRKKA------------HLMEIQVNGGSVA--QKVDFAYG 185
+ + K + + HL I+ + + + V +
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIE-HPERMTLFRMVFLDFR 501
Query: 186 FFEKQI 191
F E++I
Sbjct: 502 FLEQKI 507
>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 = 31.1 bits (69), Expect = 0.22
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 126 KKKAFTKYT---KKYETDDGKK-DIQAQLE 151
+K+A K K Y D I+A +E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.9 bits (69), Expect = 0.30
Identities = 8/60 (13%), Positives = 20/60 (33%), Gaps = 7/60 (11%)
Query: 96 PRGLRSLCTVWAQHLNEEVRRRFYKNWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKK 155
P +R W + + ++ + + K + ++ + 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 = 31.0 bits (70), Expect = 0.49
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 119 YKNWCKSKKKAFTKYTKKYETDDGKKDIQAQ--LEKMKKYCT 158
YKN+ +KK + T KY+ + K+ + + +K+ C
Sbjct: 227 YKNYILTKKTEYEIQTNKYDNEFKNKNSNDKDAPDYLKEKCN 268
>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 = 0.74
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 119 YKNWCKSKKKAFTKYTKKYETDDGKKDIQAQL-EKMKKY 156
YK + KK+ + K KYE K L E +
Sbjct: 291 YKKYISEKKQEWDKQKTKYENKYVGKSASDLLKENYPEC 329
>3vuv_A Erythrocyte membrane protein, putative; duffy binding-like domain,
erythrocyte binding, merozoite SU malaria, cell
adhesion; 2.11A {Plasmodium falciparum}
Length = 339
Score = 30.2 bits (68), Expect = 0.85
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 5/44 (11%)
Query: 119 YKNWCKSKKKAF----TKYTKKYETDDGKKDIQAQLEKMKKYCT 158
Y+ W +K + KY K + E + + C
Sbjct: 279 YEEWYNKRKTEWTEQSIKYNNDKINYTDIKTLSPS-EYLIEKCP 321
>3vuu_A Erythrocyte membrane protein, putative; duffy binding-like domain,
erythrocyte binding, merozoite SU malaria, cell
adhesion; 2.09A {Plasmodium falciparum}
Length = 305
Score = 30.2 bits (68), Expect = 0.87
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 5/44 (11%)
Query: 119 YKNWCKSKKKAF----TKYTKKYETDDGKKDIQAQLEKMKKYCT 158
Y+ W +K + KY K + E + + C
Sbjct: 245 YEEWYNKRKTEWTEQSIKYNNDKINYTDIKTLSPS-EYLIEKCP 287
>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 = 29.4 bits (67), Expect = 1.5
Identities = 7/47 (14%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 90 VGYVKTPRGLRSL----CTVWAQHLNEEVRRRFYKNWCKSKKKAFTK 132
V + ++SL V+ ++++ R++ W K+ ++ +
Sbjct: 456 VKIWDSLDSVKSLLRRSDAVFHSKMDDKKRKKKTSEWNKAVERTLIQ 502
>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 = 29.1 bits (65), Expect = 1.7
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 119 YKNWCKSKKKAFTKYTKKYETDDGKKDIQ 147
Y W KK + + K+ + + +Q
Sbjct: 231 YDQWITRKKNQWDVLSNKFISVKNAEKVQ 259
>2wau_A VAR2CSA, erythrocyte membrane protein 1 (pfemp1); chondroitin
sulphate A, membrane protein DBL, malaria; 3.00A
{Plasmodium falciparum}
Length = 302
Score = 28.6 bits (64), Expect = 2.4
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 119 YKNWCKSKKKAFTKYTKKYETDDGKKDIQAQ--LEKMKKYC 157
Y N+ KKK + +Y+ + + + + E K C
Sbjct: 226 YSNFILIKKKEYQSLNSQYDMNYKETKAEKKESPEYFKDKC 266
>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 = 28.4 bits (63), Expect = 3.1
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 119 YKNWCKSKKKAF----TKYTKKYETDDGKKDIQAQLEKMKKYC 157
YK W KK+ + +Y + + ++ K + + K + Y
Sbjct: 525 YKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYL 567
>3u61_A DNA polymerase accessory protein 62; AAA+, ATP hydrolase, clamp
loader, sliding clamp, primer-TEM DNA, DNA binding
protein-DNA complex; HET: DNA ADP 08T; 3.20A
{Enterobacteria phage T4} PDB: 3u5z_A* 3u60_A*
Length = 199
Score = 27.6 bits (61), Expect = 4.3
Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 5/59 (8%)
Query: 106 WAQHLNEEVRRRFYKNWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRKKA 164
L++E + + K + K+ K E ++ + K V A
Sbjct: 84 IGSGLSDEAHFNYLMAAVP-RGKRYGKWAKLVE----DSTEVLIIKLLAKRYQVNTNDA 137
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_A
Length = 329
Score = 27.8 bits (63), Expect = 4.9
Identities = 9/51 (17%), Positives = 20/51 (39%), Gaps = 14/51 (27%)
Query: 157 CTVIRKKAHL-MEIQVNGG---------SVAQKVDFAYGFFEKQIPIDAVF 197
C + + A + M I+V G +++ + G + +DA +
Sbjct: 131 CHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGR----LLVDACY 177
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble;
2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Length = 235
Score = 27.4 bits (62), Expect = 5.7
Identities = 9/51 (17%), Positives = 20/51 (39%), Gaps = 14/51 (27%)
Query: 157 CTVIRKKAHL-MEIQVNGG---------SVAQKVDFAYGFFEKQIPIDAVF 197
C + + A + M I+V G +++ + G + +DA +
Sbjct: 131 CHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGR----LLVDACY 177
>2xu0_A Erythrocyte membrane protein 1; adhesion, virulence,
duffy-binding-like-DO; 2.06A {Plasmodium falciparum palo
alto}
Length = 487
Score = 27.4 bits (61), Expect = 6.6
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 119 YKNWCKSKKKAFTKYTKKYET 139
Y W K + F K KY
Sbjct: 380 YNEWIVKKLEEFYKQNLKYSM 400
>2yk0_A Erythrocyte membrane protein 1; adhesin, pfemp1; 2.80A {Plasmodium
falciparum}
Length = 790
Score = 27.2 bits (60), Expect = 9.1
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 119 YKNWCKSKKKAFTKYTKKYET 139
Y W K + F K KY
Sbjct: 383 YNEWIVKKLEEFYKQNLKYSM 403
>1q8c_A Hypothetical protein Mg027; structural genomics, NUSB, GI 3 BSGC
structure funded by NIH, protein structure initiative;
2.00A {Mycoplasma genitalium} SCOP: a.79.1.2
Length = 151
Score = 26.3 bits (57), Expect = 9.4
Identities = 17/67 (25%), Positives = 30/67 (44%)
Query: 105 VWAQHLNEEVRRRFYKNWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRKKA 164
+ A L + + R W K KAF++ ++ ++ ++ QLE KY + KK
Sbjct: 39 IQADFLEYDTKERQLNEWQKLIVKAFSENIFSFQKKIEEQQLKNQLEIQTKYNKISGKKI 98
Query: 165 HLMEIQV 171
L+ V
Sbjct: 99 DLLTTAV 105
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 0.135 0.410
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: 4,794,796
Number of extensions: 290758
Number of successful extensions: 642
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 37
Length of query: 303
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 210
Effective length of database: 4,105,140
Effective search space: 862079400
Effective search space used: 862079400
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)