RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 016469
(389 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 = 500 bits (1287), Expect = e-178
Identities = 341/389 (87%), Positives = 368/389 (94%)
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 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRVLAHTQIRKMKGLKQKKAH 180
NWCKSKKKAFTKY KY++D GKK+IQ QLEKMKKY T++RV+AHTQIRKMKGLKQKKAH
Sbjct: 121 NWCKSKKKAFTKYALKYDSDAGKKEIQLQLEKMKKYATIVRVIAHTQIRKMKGLKQKKAH 180
Query: 181 LMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 240
LMEIQVNGG++A KVD+ Y FFEK++P++AVFQKDEM+DIIGVTKGKGYEGVVTRWGVTR
Sbjct: 181 LMEIQVNGGTIADKVDYGYKFFEKEVPVEAVFQKDEMVDIIGVTKGKGYEGVVTRWGVTR 240
Query: 241 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMT 300
LPRKTHRGLRKVACIGAWHPARVS+TVARAGQNGYHHRTEMNKKIYK+GK+ QESH A T
Sbjct: 241 LPRKTHRGLRKVACIGAWHPARVSYTVARAGQNGYHHRTEMNKKIYKMGKSGQESHEACT 300
Query: 301 EFDRTEKDITPMGGFPHYGVVNEDYLLIKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL 360
EFDRTEKDITPMGGFPHYGVV DYL+IKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL
Sbjct: 301 EFDRTEKDITPMGGFPHYGVVKGDYLMIKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL 360
Query: 361 KFIDTSSKFGHGRFQTTQEKAKYYGRLKA 389
KFIDTSSKFGHGRFQTT EK K+YGRLKA
Sbjct: 361 KFIDTSSKFGHGRFQTTDEKQKFYGRLKA 389
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 403
Score = 480 bits (1236), Expect = e-170
Identities = 265/395 (67%), Positives = 328/395 (83%), Gaps = 7/395 (1%)
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 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRVLAHTQIRKMKGLKQKKAH 180
NW KSKKKAFTKY KK++ DGKK ++ MKKYC VIRV+AHTQ+R + L+QKKAH
Sbjct: 121 NWHKSKKKAFTKYCKKWQDADGKKQLERDFSSMKKYCQVIRVIAHTQMRLLP-LRQKKAH 179
Query: 181 LMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 240
LME+QVNGG+VA+K+D+A E+Q+P+ VF +DEMID+IGVTKGKGY+GV +RW +
Sbjct: 180 LMEVQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKK 239
Query: 241 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKA------SQE 294
LPRKTHRGLRKVACIGAWHPARV+F+VARAGQ GYHHRTE+NKKIYK+G+
Sbjct: 240 LPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLI 299
Query: 295 SHSAMTEFDRTEKDITPMGGFPHYGVVNEDYLLIKGCCVGPKKRVVTLRQSLLKQTSRLA 354
++A T++D ++K I P+GGF HYG V D++++KGC VG KKRV+TLR+SLL QT R A
Sbjct: 300 KNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRA 359
Query: 355 LEEIKLKFIDTSSKFGHGRFQTTQEKAKYYGRLKA 389
LE+I LKFIDT+SKFGHGRFQT +EK + G LK
Sbjct: 360 LEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKK 394
>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 = 463 bits (1193), Expect = e-164
Identities = 232/389 (59%), Positives = 304/389 (78%), Gaps = 6/389 (1%)
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 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRVLAHTQIRKMKGLKQKKAH 180
NW S KKAFT + K ++ +K L++++KYC+V+RV+AHT + K L+QKK H
Sbjct: 121 NWANSNKKAFTHHEKNFD----QKAQDLLLKRIEKYCSVVRVIAHTNMSK-LNLRQKKNH 175
Query: 181 LMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 240
++EIQVNGG VA+KV FA EK++ +D++F ++EM+D++GVTKGKG+ GV+ R+GV
Sbjct: 176 ILEIQVNGGKVAEKVAFAKSLLEKEVKVDSIFAENEMLDVLGVTKGKGFAGVIKRFGVKH 235
Query: 241 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMT 300
L +KTHRG RKV CIGAWHP+R+ FTV RAGQ GYHHRTE NKK+Y++GK ++ +A T
Sbjct: 236 LQKKTHRGYRKVGCIGAWHPSRIRFTVPRAGQLGYHHRTETNKKVYRVGKG-DDASNAST 294
Query: 301 EFDRTEKDITPMGGFPHYGVVNEDYLLIKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL 360
D T+K ITP+GGFPHYGVV D+++IKGCCVGPKKRV+TLR+S++ QT A E I L
Sbjct: 295 AGDVTDKAITPLGGFPHYGVVKNDFIMIKGCCVGPKKRVLTLRKSIIPQTHGAAKEIINL 354
Query: 361 KFIDTSSKFGHGRFQTTQEKAKYYGRLKA 389
KFIDTSSK GHGRFQT +EK K++GR +
Sbjct: 355 KFIDTSSKIGHGRFQTVEEKDKFFGRDRT 383
>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 = 462 bits (1190), Expect = e-163
Identities = 255/389 (65%), Positives = 312/389 (80%), Gaps = 4/389 (1%)
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 NWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRVLAHTQIRKMKGLKQKKAH 180
NW KSKKKAFTKY+ KY D I+ +L ++KKY +V+RVL HTQIRK L QKKAH
Sbjct: 121 NWYKSKKKAFTKYSAKYAQDGAG--IERELARIKKYASVVRVLVHTQIRKTP-LAQKKAH 177
Query: 181 LMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTR 240
L EIQ+NGGS+++KVD+A FEK + +D+VF+++EMID I VTKG G+EGV RWG +
Sbjct: 178 LAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKK 237
Query: 241 LPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMT 300
LPRKTHRGLRKVACIGAWHPA V ++VARAGQ GYH RT +N KIY++GK E++ T
Sbjct: 238 LPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEAN-GAT 296
Query: 301 EFDRTEKDITPMGGFPHYGVVNEDYLLIKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL 360
FDRT+K ITPMGGF HYG + D++++KGC G +KR+VTLR+SL TSR ALEE+ L
Sbjct: 297 SFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSL 356
Query: 361 KFIDTSSKFGHGRFQTTQEKAKYYGRLKA 389
K+IDT+SKFG GRFQT EK + G LK
Sbjct: 357 KWIDTASKFGKGRFQTPAEKHAFMGTLKK 385
>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 = 387 bits (994), Expect = e-134
Identities = 118/370 (31%), Positives = 176/370 (47%), Gaps = 38/370 (10%)
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 SKKKAFTKYTKKYETDDGKKDIQAQLEKMKKYCTVIRVLAHTQIRKMKGLKQKKAHLMEI 184
A + + +R++ HT + + +KK +ME
Sbjct: 121 DPDAAEEQIRDAH---------------EAGDLGDLRLITHTVPDAVPSVPKKKPDVMET 165
Query: 185 QVNGGSVAQKVDFAYGFFE--KQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLP 242
+V GGSV+ ++D A E + ++ +F+ E D+ GVTKGKG +G V RWGV +
Sbjct: 166 RVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRK 225
Query: 243 RKTHRG--LRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQESHSAMT 300
K R R++ +G W+P+RV TV + GQ GYH RTE+NK++ +G+
Sbjct: 226 GKHARQGWRRRIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGE---------- 275
Query: 301 EFDRTEKDITPMGGFPHYGVVNEDYLLIKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL 360
+ T GGF +YG V+ Y L+KG GP KR+V R ++ E+
Sbjct: 276 -----GDEPTVDGGFVNYGEVDGPYTLVKGSVPGPDKRLVRFRPAVRPNDQPRLDPEV-- 328
Query: 361 KFIDTSSKFG 370
+++ S G
Sbjct: 329 RYVSNESNQG 338
>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 = 56.3 bits (137), Expect = 2e-09
Identities = 32/142 (22%), Positives = 55/142 (38%), Gaps = 35/142 (24%)
Query: 210 AVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWHPARVSFT 266
A F+ + +D+ T GKG++GV+ RWG P TH + R+ + RV
Sbjct: 101 AHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQP-ATHGQTKTHRRPGAVATGDIGRVWPG 159
Query: 267 VARAGQNGYHHRTEMNKKIYKLGKASQESHSAMTEFDRTEKDITPMGGFPHYGVVNEDYL 326
G+ G +RTE K++++ T+ +I +
Sbjct: 160 TKMPGKMGNIYRTEYGLKVWRI---------------NTKHNI----------------I 188
Query: 327 LIKGCCVGPKKRVVTLRQSLLK 348
+ G G K +V ++ S L
Sbjct: 189 YVNGSVPGHKNCLVKVKDSKLP 210
>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 = 51.4 bits (124), Expect = 7e-08
Identities = 34/139 (24%), Positives = 55/139 (39%), Gaps = 36/139 (25%)
Query: 211 VFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-PARVSFT 266
+F+ E +D+ G +KG+G+ GV+ RW P +H + R IG P RV
Sbjct: 95 IFKPGERVDVTGTSKGRGFAGVMKRWNFAGGP-DSHGAHKIHRHPGSIGNRKTPGRVYKG 153
Query: 267 VARAGQNGYHHRTEMNKKIYKLGKASQESHSAMTEFDRTEKDITPMGGFPHYGVVNEDYL 326
AG G T MN ++ + E+++ L
Sbjct: 154 KKMAGHYGAERVTVMNLEVVDV---------------IPEENL----------------L 182
Query: 327 LIKGCCVGPKKRVVTLRQS 345
L+KG GP +V +R++
Sbjct: 183 LVKGAVPGPNGGLVIVRET 201
>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 = 51.4 bits (124), Expect = 7e-08
Identities = 34/148 (22%), Positives = 53/148 (35%), Gaps = 36/148 (24%)
Query: 211 VFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-PARVSFT 266
+F + E ID G +KGKG +GV+ RW P +H + R+ IG P RV
Sbjct: 95 IFAEGEKIDATGTSKGKGTQGVMKRWNFAGGP-ASHGSKKWHRRPGSIGQRKTPGRVYKG 153
Query: 267 VARAGQNGYHHRTEMNKKIYKLGKASQESHSAMTEFDRTEKDITPMGGFPHYGVVNEDYL 326
AG G T N ++ ++ E+ +
Sbjct: 154 KRMAGHMGMERVTVQNLEVVEI-------------------------------RAGENLI 182
Query: 327 LIKGCCVGPKKRVVTLRQSLLKQTSRLA 354
L+KG G +V LR + ++
Sbjct: 183 LVKGAIPGANGGLVVLRSAAKASAAKGG 210
>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 = 50.6 bits (122), Expect = 1e-07
Identities = 29/139 (20%), Positives = 48/139 (34%), Gaps = 36/139 (25%)
Query: 211 VFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTH---RGLRKVACIGAWH-PARVSFT 266
+F + +D+ G +KGKG+ G V RW TH R IG P +V
Sbjct: 100 LFADVKKVDVTGTSKGKGFAGTVKRWNFRTQD-ATHGNSLSHRVPGSIGQNQTPGKVFKG 158
Query: 267 VARAGQNGYHHRTEMNKKIYKLGKASQESHSAMTEFDRTEKDITPMGGFPHYGVVNEDYL 326
AGQ G T + + ++ E+++ L
Sbjct: 159 KKMAGQMGNERVTVQSLDVVRV---------------DAERNL----------------L 187
Query: 327 LIKGCCVGPKKRVVTLRQS 345
L+KG G + ++ +
Sbjct: 188 LVKGAVPGATGSDLIVKPA 206
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 259
Score = 51.1 bits (123), Expect = 2e-07
Identities = 33/171 (19%), Positives = 61/171 (35%), Gaps = 43/171 (25%)
Query: 178 KAHLMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQKDEMIDIIGVTKGKGYEGVVTRWG 237
HL E ++ + ++ +F++ +++D+ G T GKG++G + R
Sbjct: 119 LRHLQEFRLQSIDGFEVTQ--------KLDFGELFKEGDLVDVSGTTIGKGFQGGIKRHN 170
Query: 238 VTRLPRKTH--RGLRKVACIGAWH-PARVSFTVARAGQNGYHHRTEMNKKIYKLGKASQE 294
R TH + R++ IGA P RV G+ G R KI K+
Sbjct: 171 FKRGQ-MTHGSKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTKRKIRKLKIVKI------ 223
Query: 295 SHSAMTEFDRTEKDITPMGGFPHYGVVNEDYLLIKGCCVGPKKRVVTLRQS 345
+ +I ++IKG G ++ + +
Sbjct: 224 ---------DDQLNI----------------IMIKGALPGKPGNLLRIAPA 249
>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 = 40.0 bits (93), Expect = 0.001
Identities = 67/444 (15%), Positives = 119/444 (26%), Gaps = 181/444 (40%)
Query: 2 SHRKFEHPRHGSLGFLPRKRASRHRGK-----VKAFPKDDPSKPCRLTAFL-GYKAGMTH 55
+FE+ +L G +++ + + + Y
Sbjct: 87 CLTEFEN------CYL--------EGNDIHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 56 IVRDVEKPG-SKLHKKETCEAVTIIETPPLVVVGVVG------YVK-------TPRGL-R 100
R +K S L + ++ + G G Y + T L
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLV-----AIFG--GQGNTDDYFEELRDLYQTYHVLVG 185
Query: 101 SLCTVWAQHLNEEVRRRFYKNWCKSKKKAFTKYTKKYETDDGKKDIQAQLEKMKK----- 155
L A+ L+E +R + A +T+ +I LE
Sbjct: 186 DLIKFSAETLSELIR---------TTLDAEKVFTQGL-------NILEWLENPSNTPDKD 229
Query: 156 YCTVIRVLAHTQIR-KMKGLKQKKAHLMEIQVNGGSVAQKVDFAYGFFEKQIPIDAVFQK 214
Y L I + G+ Q AH + A+ + F G
Sbjct: 230 Y------LLSIPISCPLIGVIQL-AHYV-------VTAKLLGFTPG-------------- 261
Query: 215 DEMIDII-GVTKGKGYEGVVTRWGVTRLPRKTHRGLRKVACIGA---WHPARVSFTVARA 270
E+ + G T G +G+VT I W SF
Sbjct: 262 -ELRSYLKGAT-GHS-QGLVT-----------------AVAIAETDSWE----SF----- 292
Query: 271 GQNGYHHRTEMNKKIYKLGKASQESH-------SAMTEF-DRTEKDITPM---------- 312
+ + ++ +G E++ S + + + E +PM
Sbjct: 293 ----FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQ 348
Query: 313 ---------GGFP-----HYGVVNEDYLLIKGCCVGPKKRVVT--------LRQSLLKQT 350
P +VN G K VV+ L +L K
Sbjct: 349 VQDYVNKTNSHLPAGKQVEISLVN-----------GAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 351 SRLALEEIKLKFIDTSSKFGHGRF 374
+ L++ ++ F + KF + RF
Sbjct: 398 APSGLDQSRIPFSERKLKFSN-RF 420
Score = 34.6 bits (79), Expect = 0.066
Identities = 27/142 (19%), Positives = 42/142 (29%), Gaps = 53/142 (37%)
Query: 277 HRTEMNKKIYKLGKASQESHSAMTEFDRTEKDITPMGGF---------P-----HYG--- 319
M +YK S +A ++R + GF P H+G
Sbjct: 1627 QEQGMGMDLYK------TSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEK 1680
Query: 320 --VVNEDYLLIK------GCC--------VGPKKRVVTLR--QSLLKQT----------S 351
+ E+Y + G + T R + LL T
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 352 RLALEEIKLKF-IDTSSKF-GH 371
+ A E++K K I + F GH
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGH 1762
>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 = 33.7 bits (76), Expect = 0.11
Identities = 27/146 (18%), Positives = 49/146 (33%), Gaps = 41/146 (28%)
Query: 57 VRDVEKPGSKLHKKETCEAVTIIETPPLVVVGVVGYVKTPRGLRSLCTVWAQHLNEEVRR 116
+DV+ + KE + II + V T R +L + EE+ +
Sbjct: 35 CKDVQDMPKSILSKEEID--HIIMSKDAVS-------GTLRLFWTLLSK-----QEEMVQ 80
Query: 117 RFYK-------NWCKSKKKAFTK----YTKKYET--DDGKKDIQAQLEKMKKYCTVIRVL 163
+F + + S K + T+ Y D D Q KY V R+
Sbjct: 81 KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ----VFAKY-NVSRLQ 135
Query: 164 AHTQIRKMKGLKQKKAHLMEIQVNGG 189
+ ++R+ L+E++
Sbjct: 136 PYLKLRQ---------ALLELRPAKN 152
Score = 32.1 bits (72), Expect = 0.33
Identities = 32/185 (17%), Positives = 60/185 (32%), Gaps = 46/185 (24%)
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 RRFYKNW-CKSKK------KAFTKYTKKYETD---DGKKDIQAQLEKMKKYCTVIRVLAH 165
+FYK + C + A + K E + D+ ++ M + + AH
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL-LRIALMAEDEAIFEE-AH 584
Query: 166 TQIRK 170
Q+++
Sbjct: 585 KQVQR 589
Score = 29.8 bits (66), Expect = 1.8
Identities = 28/148 (18%), Positives = 42/148 (28%), Gaps = 52/148 (35%)
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 156
K D I++ L +K
Sbjct: 348 -KHVNCDKLTTIIESSLNVLEPAEYRKM 374
Score = 29.1 bits (64), Expect = 3.2
Identities = 20/138 (14%), Positives = 36/138 (26%), Gaps = 39/138 (28%)
Query: 93 VKTPRGLRSLCTVWAQHLNEEVRRRFYKNWCKSK---KKAFTKYTKKYETDDGKKDIQAQ 149
P L L +W + +V N +K + T +++ +
Sbjct: 385 AHIPTIL--LSLIWFDVIKSDVMV--VVNKLHKYSLVEKQPKEST--ISIPSIYLELKVK 438
Query: 150 LEKMKKYCTVIRVLAHTQI----RKMKGLKQKKA---------------HLMEIQVNGGS 190
LE H I K HL I+ +
Sbjct: 439 LENEYA--------LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIE-HPER 489
Query: 191 VA--QKVDFAYGFFEKQI 206
+ + V + F E++I
Sbjct: 490 MTLFRMVFLDFRFLEQKI 507
>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 = 32.5 bits (74), Expect = 0.27
Identities = 33/159 (20%), Positives = 52/159 (32%), Gaps = 46/159 (28%)
Query: 109 HLNEEVRRRFYKNWCKSKKKAFTKYTKKYETDDGK----KDIQAQLEKMKKYCTVIRVLA 164
+ N ++ R Y W ++ + KD++A+ E +L
Sbjct: 863 YHNGNLKGRPYTGW--------------VDSKTKEPVDDKDVKAKYET--------SILE 900
Query: 165 HTQIRK-----MKGLK-QKKAHLMEIQVNGGSVAQKVDFAYGFFE--KQIPIDAVFQKDE 216
H+ IR G +KK + E+ V D FE K+ Q +
Sbjct: 901 HSGIRLIEPELFNGYNPEKKEMIQEVIVEE-------DLE--PFEASKETAEQFKHQHGD 951
Query: 217 MIDIIGVTKGKGYEGVVTRW-GVTRLPRKTHRGLRKVAC 254
+DI + + E V G T K R R VA
Sbjct: 952 KVDIFEI--PETGEYSVKLLKGATLYIPKALRFDRLVAG 988
>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 = 0.34
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 = 0.46
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 = 30.2 bits (68), Expect = 0.94
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 = 30.0 bits (67), Expect = 1.4
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 119 YKNWCKSKKKAFTKYTKKYETDDGKKD 145
YK + KK+ + K KYE K
Sbjct: 291 YKKYISEKKQEWDKQKTKYENKYVGKS 317
>3vuv_A Erythrocyte membrane protein, putative; duffy binding-like domain,
erythrocyte binding, merozoite SU malaria, cell
adhesion; 2.11A {Plasmodium falciparum}
Length = 339
Score = 29.8 bits (67), Expect = 1.6
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 = 29.4 bits (66), Expect = 1.7
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 = 2.2
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 = 28.7 bits (64), Expect = 3.0
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 = 28.3 bits (63), Expect = 4.5
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 = 28.0 bits (62), Expect = 5.7
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
>2yrn_A Neuron navigator 2 isoform 4; calponin homolgy domain, helicase,
all alpha, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 129
Score = 27.1 bits (60), Expect = 6.0
Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 112 EEVRRRFYKNWCKSKKKAFTK----YTKKYETDDGKKDIQAQLEKMKKYCTVIRVLAHTQ 167
+R+ + + +K+ +T Y K +D+Q + +I+V+A+ +
Sbjct: 5 SSGKRKPVIHGLEDQKRIYTDWANHYLAKSGHKRLIRDLQQDVTDGVLLAQIIQVVANEK 64
Query: 168 IRKMKGLKQKKAHLME 183
I + G + ++ ++E
Sbjct: 65 IEDINGCPKNRSQMIE 80
>2ov8_A STAL; sulfotransferase, structural genomics, montr kingston
bacterial structural genomics initiative, BSGI, UN
function; 2.58A {Streptomyces toyocaensis} PDB: 2ovb_A
2ovf_A*
Length = 288
Score = 27.3 bits (61), Expect = 9.4
Identities = 13/69 (18%), Positives = 32/69 (46%), Gaps = 11/69 (15%)
Query: 119 YKNWCKSKKKAFTKYTK---KYETDDGKKDIQAQLEKMKKYC------TVIRVLAHTQIR 169
++W S ++F +YE D +KD + +L K+ + V +A+ +
Sbjct: 160 IRSWTDSVHESFPNAAVLAVRYE--DLRKDPEGELWKVVDFLELGGRDGVADAVANCTLE 217
Query: 170 KMKGLKQKK 178
+M+ ++++
Sbjct: 218 RMREMEERS 226
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
0.321 0.136 0.411
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: 6,148,091
Number of extensions: 375574
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 767
Number of HSP's successfully gapped: 44
Length of query: 389
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 294
Effective length of database: 4,049,298
Effective search space: 1190493612
Effective search space used: 1190493612
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: 58 (26.7 bits)