RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 023024
(288 letters)
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 252 bits (646), Expect = 6e-84
Identities = 166/281 (59%), Positives = 204/281 (72%), Gaps = 3/281 (1%)
Query: 3 ASFSSLSFFSSTIFLTSSSNKVPKPIQLAKPNSLINLPPKPLIVSSQLASPLPILSFTGE 62
S S F S+ +S S L P+S + L + S+L LPIL+F+GE
Sbjct: 5 TSSSLSLSFFSSSLFSSKSRNFSSKPILKLPSSSHSQTSLSLSIKSELIP-LPILNFSGE 63
Query: 63 KIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGR 122
K+GET+L+LK+A P+ ARAVVHR LIT +QNKRRGTASTLTR EVRGGGRKPY QKKTGR
Sbjct: 64 KVGETFLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGR 123
Query: 123 ARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGK 182
ARRGS +PLRPGGGV+FGPKPRDW+IK+NKKE+RLA+STAIASA +
Sbjct: 124 ARRGSQGSPLRPGGGVIFGPKPRDWTIKMNKKERRLALSTAIASAVGNSFVVEEFAE--N 181
Query: 183 FERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILD 242
FE+PKTK+FI AM+RWGLDP +K+ F +M++ ENVEKS RNI TLK+LTPR+LNLFD+L+
Sbjct: 182 FEKPKTKDFIAAMQRWGLDPAEKSLFFLMDLVENVEKSGRNIRTLKLLTPRSLNLFDVLN 241
Query: 243 AETLVLTPSTVDFLNGRYGVEFEGDGDEEEEESEAREAGEE 283
AE LV T T+ +LN RYGV+ D DEEEEE E E ++
Sbjct: 242 AEKLVFTEGTIQYLNQRYGVDTLEDEDEEEEEEEEGEEVDD 282
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
1pny_C 1vor_F 1vou_F ...
Length = 205
Score = 236 bits (604), Expect = 1e-78
Identities = 68/212 (32%), Positives = 110/212 (51%), Gaps = 10/212 (4%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRK 113
+ ++ G + E L P+ V+H + + ++RRGTAST TR +V GRK
Sbjct: 4 INVIGQNGGRTIELPL------PEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRK 57
Query: 114 PYSQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENT 173
Y QK TG AR G P GGGV FGPKPR + + ++ ++L ++ AIAS
Sbjct: 58 MYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKL 117
Query: 174 IVVEEFDGKFERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPR 233
+ V+ F KTK FI ++ GLD +K L++ EN +++RN+ + +L
Sbjct: 118 VAVDGF--DIADAKTKNFISWAKQNGLDGTEKV--LLVTDDENTRRAARNVSWVSVLPVA 173
Query: 234 TLNLFDILDAETLVLTPSTVDFLNGRYGVEFE 265
+N++DIL + LV+ + ++ + G E +
Sbjct: 174 GVNVYDILRHDRLVIDAAALEIVEEEAGEEQQ 205
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Length = 210
Score = 234 bits (598), Expect = 1e-77
Identities = 75/210 (35%), Positives = 112/210 (53%), Gaps = 9/210 (4%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRK 113
+P+LS +G + L + ++ + + +RRGTAST TRGEV GRK
Sbjct: 9 IPVLSPSGRRELAADLPAE-----INPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRK 63
Query: 114 PYSQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENT 173
+ QK TGRAR G P+ GGGVVFGPKPRD+S + KK ++ ++ A+A A
Sbjct: 64 IWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKL 123
Query: 174 IVVEEFDGKFERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPR 233
++VE F KTKEF+ + GLD + L++ +E V +++RN+ + L P
Sbjct: 124 LLVEAF--AGVNGKTKEFLAWAKEAGLDGSESV--LLVTGNELVRRAARNLPWVVTLAPE 179
Query: 234 TLNLFDILDAETLVLTPSTVDFLNGRYGVE 263
LN++DI+ E LV+ + R G E
Sbjct: 180 GLNVYDIVRTERLVMDLDAWEVFQNRIGGE 209
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 229 bits (585), Expect = 6e-76
Identities = 57/200 (28%), Positives = 100/200 (50%), Gaps = 5/200 (2%)
Query: 62 EKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTG 121
+ + + D A+VH+ ++ R+GT + TR EV G G+KP+ QK TG
Sbjct: 7 DAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTG 66
Query: 122 RARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDG 181
RAR GS ++P+ GGV F +P+D S K+NKK R A+ + ++ + IVVE+F
Sbjct: 67 RARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKF-- 124
Query: 182 KFERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDIL 241
E PKTK + ++ L+ + E+ EN+ ++RN+ + + ++ ++
Sbjct: 125 SVEAPKTKLLAQKLKDMALE---DVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLI 181
Query: 242 DAETLVLTPSTVDFLNGRYG 261
+ +V+T V +
Sbjct: 182 AFDKVVMTADAVKQVEEMLA 201
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
c.22.1.1
Length = 225
Score = 229 bits (585), Expect = 2e-75
Identities = 87/225 (38%), Positives = 121/225 (53%), Gaps = 19/225 (8%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRK 113
+ +L+ GEK+G + D V+ R + + N+R GTAST TRGEV GGGRK
Sbjct: 3 VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62
Query: 114 PYSQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENT 173
P+ QK TGRAR GS R+P+ GGVV GPKPRDWS K+NKK K+LA+ +A++
Sbjct: 63 PWPQKHTGRARHGSIRSPIWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKL 122
Query: 174 IVVEEFDGKFERPKTKEFIEAMRRWGLDPKQKATFLVM--EVSENVEKSSRNIGTLKMLT 231
+V+++ K ERPKTK E ++ L K+ L E NV+ S RN+ +K++
Sbjct: 123 LVLDDL--KLERPKTKSLKEILQNLQLSDKKTLIVLPWKEEGYMNVKLSGRNLPDVKVII 180
Query: 232 PRT---------------LNLFDILDAETLVLTPSTVDFLNGRYG 261
LN+FD+L + LVLT V + G
Sbjct: 181 ADNPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVSKIEEVLG 225
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S
ribosomal protein L3; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_D
Length = 175
Score = 207 bits (528), Expect = 1e-67
Identities = 56/178 (31%), Positives = 87/178 (48%), Gaps = 10/178 (5%)
Query: 84 HRALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVVFGPK 143
H+ + KR A T TR EVRGGGRKP+ QK TGRAR GS R+PL GGGV GP+
Sbjct: 1 HQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPR 60
Query: 144 -PRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGKFERPKTKEFIEAMRRWGLDP 202
P + + K + L + A+ A ++ +++ + + E
Sbjct: 61 GPTSYYYMLPMKVRALGLKVALTVKLAQDDLHIMDSL--ELPTGDPQYLTELAHYRRWG- 117
Query: 203 KQKATFLVM----EVSENVEKSSRNIGTLKMLTPRTLNLFDILDAETLVLTPSTVDFL 256
+ LV E+ +++ +++ + T ++ LN+ +L +TLVLT TV FL
Sbjct: 118 --DSVLLVDLTHEEMPQSIVEATSRLKTFNLIPAVGLNVHSMLKHQTLVLTLPTVAFL 173
>1vq8_C 50S ribosomal protein L4E; 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: c.22.1.1 PDB: 1k73_E*
1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E*
1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C
1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ...
Length = 246
Score = 119 bits (300), Expect = 1e-32
Identities = 49/249 (19%), Positives = 87/249 (34%), Gaps = 48/249 (19%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGT-----ASTLTRGEVR 108
I G GE L P ++ +A+ N+++ A T E
Sbjct: 3 ATIYDLDGNTDGEVDLPDVFETP-VRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61
Query: 109 GGGR-KPYSQKKTGRARRGSNRTPLRPGGGVVFGPKP-RDWSIKINKKEKRLAISTAIAS 166
G GR + + K GRARR P G PK +D S+ +N KE++LA+ +A+A+
Sbjct: 62 GSGRGQAHVPKLDGRARRV----PQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAA 117
Query: 167 AAAAENTI----VVEEF-------DGKFERPKTKEFIEAMRRWGLDP------------- 202
A A+ + D + KT+E + + +
Sbjct: 118 TADADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAG 177
Query: 203 --------KQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILDAETL----VLTP 250
++ ++ S+ ++RN+ + T +N D+ V T
Sbjct: 178 QGSARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTE 237
Query: 251 STVDFLNGR 259
S + + R
Sbjct: 238 SALAEVAER 246
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C
1s1i_D 3jyw_D
Length = 362
Score = 116 bits (290), Expect = 2e-30
Identities = 53/260 (20%), Positives = 87/260 (33%), Gaps = 50/260 (19%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKR-----RGTASTLTRGEVR 108
+ + S TGE + +VH + +NKR A T E
Sbjct: 6 VTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESW 65
Query: 109 GGGRKPYS---QKKTGRARRGSNRTPLRPGGGVVFGPKP--RDWSIKINKKEKRLAISTA 163
G GR G R G GG +F P R W++K+N EKR A ++A
Sbjct: 66 GTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASA 125
Query: 164 IASAAAAENTI-------VVEEF-----DGKFERPKTKEFIEAMRRWGLDP--------- 202
IA+ A A + + E KTKE + A++ G
Sbjct: 126 IAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSK 185
Query: 203 ---------------KQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILD----A 243
+++ +V + K+ RN+ ++ +LNL +
Sbjct: 186 KLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLG 245
Query: 244 ETLVLTPSTVDFLNGRYGVE 263
++ T + L+ +G E
Sbjct: 246 RFVIWTEAAFTKLDQVWGSE 265
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 103 bits (258), Expect = 2e-25
Identities = 44/234 (18%), Positives = 74/234 (31%), Gaps = 57/234 (24%)
Query: 82 VVHRALITDMQNKRRGTA---------STLTRGEVRGGGRKPYSQKKTGRARRGSNRTPL 132
VV NKR+ A S + G R R P G R G
Sbjct: 40 VVRFVHRLLSCNKRQPYAVSRRAGHQTSAESWGTGRAVSRIPR-VPGGGTHRAGQGAFGN 98
Query: 133 RPGGGVVFGPKP--RDWSIKINKKEKRLAISTAIAS--------------AAAAENTIVV 176
GG +F P R W ++N +R+A+++A+A+ E +V+
Sbjct: 99 MCRGGRMFAPTKTWRKWHRRVNVHLRRVAVASALAATSVPSLVLARGHRIETVPELPLVI 158
Query: 177 EEFDGKFERPKTKEFIEAMRRWGLDP-------------------------KQKATFLVM 211
D KT + I+ +++ G ++ +
Sbjct: 159 S--DSAESIEKTSQAIKILKQVGAYADAEKAKDSVGIRPGKGKMRNRRYINRKGPLIVYG 216
Query: 212 EVSENVEKSSRNIGTLKMLTPRTLNLFDIL----DAETLVLTPSTVDFLNGRYG 261
+ K+ RN+ + + LNL D+ ++ T S L YG
Sbjct: 217 TEGSKIVKAFRNLPGVDVANVERLNLLDLAPGGHLGRFVIWTESAFKKLEEVYG 270
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_C 4a1c_C 4a1e_C
Length = 410
Score = 102 bits (254), Expect = 5e-25
Identities = 39/270 (14%), Positives = 79/270 (29%), Gaps = 60/270 (22%)
Query: 49 QLASPLPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVR 108
+ + L AP +VH+ +N+++ + ++
Sbjct: 5 PQIHVHDAKEANKQTATKLTLPAVFTAP-IRTDIVHKVFTDLNKNRKQASGVKISTRGTA 63
Query: 109 G------------GGRKPYSQKKTGRARRG-SNRTPLRPGGGVVFGPKP-RDWSIKINKK 154
G + +G R G + G + K R ++N
Sbjct: 64 GMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVNVN 123
Query: 155 EKRLAISTAIASAAAA--------------ENTIVVEEFDGKFERPKTKEFIEAMRRWGL 200
+KR A++ A+A++A E V + D KTK+ + ++R G
Sbjct: 124 QKRHAVAAALAASALVPLVFARGHRISNVQELPYVFD--DSVESYEKTKQAVAFLKRVGA 181
Query: 201 DP-------------------------KQKATFLVMEVSENVEKSSRNIGTLKMLTPRTL 235
++ + + ++ RNI + + L
Sbjct: 182 YDDVLRVAETKALRAGQGKLRNRRYKLRRGPLVVYGNEKSTLTRALRNIPGVDVCNVNRL 241
Query: 236 NLFDI----LDAETLVLTPSTVDFLNGRYG 261
NL + ++ T S LN +G
Sbjct: 242 NLLQLAPGGHVGRFIIWTESAFKKLNEIFG 271
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 95.7 bits (237), Expect = 1e-22
Identities = 46/261 (17%), Positives = 82/261 (31%), Gaps = 56/261 (21%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARA-VVHRALITDMQNKRRGTA---------STLT 103
+ + S GE G+ + L + R +V+ +N R+ A S +
Sbjct: 8 ISVYSEKGESSGKN-VTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAES 66
Query: 104 RGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVVFGPKP-RDWSIKINKKEKRLAIST 162
G R R P + + GG + K R W ++N +KR AI +
Sbjct: 67 WGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICS 126
Query: 163 AIASA--------------AAAENTIVVEEFDGKFERPKTKEFIEAMRRWGLDP------ 202
A+A E +VVE D KTKE + +++
Sbjct: 127 ALACLSLPALVMSKGHRIEEVPELPLVVE--DKVEGYKKTKEAVLLLKKLKAWNDIKKVY 184
Query: 203 ------------------KQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDI---- 240
+++ ++ + K+ R + +L LN+ +
Sbjct: 185 ASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRKHPGITLLNVSKLNILKLAPGG 244
Query: 241 LDAETLVLTPSTVDFLNGRYG 261
+ T S L+ YG
Sbjct: 245 HVGRFCIWTESAFRKLDDLYG 265
>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 = 50.4 bits (120), Expect = 3e-07
Identities = 61/290 (21%), Positives = 98/290 (33%), Gaps = 102/290 (35%)
Query: 1 MAASFSSLSFFSSTI------FLTSSSNKVPKPI----QLAKPNSLINLPPKPL--IVSS 48
+A + S SFF S F I A PN+ +LPP L + +
Sbjct: 283 IAETDSWESFFVSVRKAITVLFF----------IGVRCYEAYPNT--SLPPSILEDSLEN 330
Query: 49 QLASPLPILSFTG---EKIGETYLD-LKSAAPDTARAVVHRALITDMQNKRR-----GTA 99
P P+LS + E++ + Y++ S P + V +L+ N + G
Sbjct: 331 NEGVPSPMLSISNLTQEQV-QDYVNKTNSHLPAGKQ--VEISLV----NGAKNLVVSGPP 383
Query: 100 STLT------RGEVRGGG----RKPYSQKKTGRARRGSNR-----TP-----LRPGGGVV 139
+L R G R P+S++K + SNR +P L P ++
Sbjct: 384 QSLYGLNLTLRKAKAPSGLDQSRIPFSERK----LKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 140 FGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGKFERPKTKEFIEAMRR-- 197
++ ++ N K+ + I V + FDG R + E +
Sbjct: 440 NKDLVKN-NVSFNAKD--IQIP-------------VYDTFDGSDLRVLSGSISERIVDCI 483
Query: 198 ------WGLDPKQKAT----F-------LVMEVSENVE-KSSRNI--GTL 227
W + KAT F L + N + R I GTL
Sbjct: 484 IRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTL 533
Score = 29.2 bits (65), Expect = 2.1
Identities = 28/183 (15%), Positives = 54/183 (29%), Gaps = 55/183 (30%)
Query: 138 VVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGK-----FERPK----- 187
+ FG + I+ E A+ + + +E + F K
Sbjct: 1674 IHFGG-EKGKRIR----ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSA 1728
Query: 188 TKEF------------IEAMRRWGLDPKQKATF----------L-----VMEVSENVEKS 220
T +F E ++ GL P ATF L VM +
Sbjct: 1729 T-QFTQPALTLMEKAAFEDLKSKGLIPA-DATFAGHSLGEYAALASLADVMSIES----- 1781
Query: 221 SRNIGTLKMLTPRTLNLFDILDAETLVLTPSTVDFLN-GRYGVEFEGDGDEEEEESEARE 279
++++ R + + + + L + + +N GR F + + E +
Sbjct: 1782 -----LVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKR 1836
Query: 280 AGE 282
G
Sbjct: 1837 TGW 1839
Score = 28.1 bits (62), Expect = 4.0
Identities = 22/101 (21%), Positives = 31/101 (30%), Gaps = 21/101 (20%)
Query: 1 MAASFSSLS--------FFSSTI----FLTSSSNKVPKPIQLAK-PNSLINLPPKPLIVS 47
A + S L F+ + +L + S P L P S PLI
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPS-NTPDKDYLLSIPISC------PLIGV 243
Query: 48 SQLASPLPILSFTGEKIGETYLDLKSAAPDTARAVVHRALI 88
QLA + G GE A ++ +V I
Sbjct: 244 IQLAHYVVTAKLLGFTPGE-LRSYLKGATGHSQGLVTAVAI 283
>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 = 39.5 bits (91), Expect = 0.001
Identities = 40/259 (15%), Positives = 71/259 (27%), Gaps = 75/259 (28%)
Query: 59 FTGEKIGETYLDLKSAAPDTARAVVHRALITDM----QNKRRGTASTLTRGEV-RGGGRK 113
F E + Y L S R +++T M +++ + V R +
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQ---PSMMTRMYIEQRDRLYNDNQVFAKYNVSR---LQ 135
Query: 114 PYSQKKTGRARRGSNRTPLRPGGGVV------FGPKP-------RD------------WS 148
PY + + LRP V+ G K W
Sbjct: 136 PYLKLRQALLE-------LRPAKNVLIDGVLGSG-KTWVALDVCLSYKVQCKMDFKIFW- 186
Query: 149 IKI---NKKEKRLAISTAIASAAAAENTIVVEEFDGKFERPKTKEFIEAMRRWGLDPKQK 205
+ + N E L + + T + + + +RR +
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN--IKLRIHSIQAELRRLLKSKPYE 244
Query: 206 ATFLVMEVSENVEKSSR-----NIG--TLKMLTPRTLNLFDILDAETLVLTPSTVDFLNG 258
LV+ NV ++++ N+ L LT R + D L A T S
Sbjct: 245 NCLLVLL---NV-QNAKAWNAFNLSCKIL--LTTRFKQVTDFLSAAT-TTHISLDHHSMT 297
Query: 259 RYGVEFEGDGDEEEEESEA 277
+E ++
Sbjct: 298 -----L------TPDEVKS 305
Score = 34.4 bits (78), Expect = 0.050
Identities = 46/323 (14%), Positives = 83/323 (25%), Gaps = 140/323 (43%)
Query: 1 MAASFSSLS-------FFSSTIFLTSSSNKVPKPI------------------QLAKPNS 35
+ +S + L F ++F S+ +P + +L K S
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSA--HIPTILLSLIWFDVIKSDVMVVVNKLHK-YS 415
Query: 36 LINLPPKPLIVSSQLASPLPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKR 95
L+ PK +S +P + YL+LK + +HR+++ +
Sbjct: 416 LVEKQPKESTIS------IPSI----------YLELKVKLEN--EYALHRSIVDHYNIPK 457
Query: 96 RGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVVFGPKPRD----WSI-- 149
+ P D I
Sbjct: 458 T------------------FDSDD--------------------LIPPYLDQYFYSHIGH 479
Query: 150 ---KINKKEKRLAISTAIASAAAAENTIVVEEFDGKFE--RPKTKEFIEA-MRR----WG 199
I E+ + F F R F+E +R W
Sbjct: 480 HLKNIEHPER-------------------MTLFRMVFLDFR-----FLEQKIRHDSTAWN 515
Query: 200 LDPKQKATFLVME-----VSENVEKSSRNIGTLKMLTPRTLNLFDILDAETLVLTPSTVD 254
T ++ + +N K R + + P+ E L+ + T D
Sbjct: 516 ASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKI--------EENLICSKYT-D 566
Query: 255 FLNGRYGVEFEGDGDEEEEESEA 277
L R + E + EE +
Sbjct: 567 LL--RIALMAEDEAIFEEAHKQV 587
>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 = 31.8 bits (71), Expect = 0.12
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 62 EKIGETYLDLKSAAPDTARAVVHRALI 88
+K+ + LK A D+A A+ +A +
Sbjct: 23 KKL-QA--SLKLYADDSAPALAIKATM 46
>1rqb_A Transcarboxylase 5S subunit; TIM-barrel, carbamylated lysine,
transfera; HET: KCX; 1.90A {Propionibacterium
freudenreichii subspshermanii} SCOP: a.5.7.2 c.1.10.5
PDB: 1rqe_A 1rqh_A* 1rr2_A* 1u5j_A* 1s3h_A*
Length = 539
Score = 31.5 bits (72), Expect = 0.31
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 212 EVSENVEKSSRNIGTLKMLTP-----RTLNLFDILDAETLVLTPSTVDFLNGRYGVEFEG 266
EV V + + G ++TP T +F+++ E +T D + G YG
Sbjct: 341 EVMAEVPRVRKAAGFPPLVTPSSQIVGTQAVFNVMMGEYKRMTGEFADIMLGYYG-ASPA 399
Query: 267 DGDEEEEESEAREAGEE 283
D D + + ++G++
Sbjct: 400 DRDPKVVKLAEEQSGKK 416
>3hut_A Putative branched-chain amino acid ABC transporter; extracellular
ligand-binding receptor,transport protein; 1.93A
{Rhodospirillum rubrum atcc 11170}
Length = 358
Score = 28.4 bits (64), Expect = 3.2
Identities = 9/36 (25%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 168 AAAENTIVVEEFDGKFERPKTKEFIEAMR-RWGLDP 202
A E + F P EF+ A +G P
Sbjct: 240 PAVEGVRLATAFVLGASDPVVVEFVSAYETLYGAIP 275
>3vjz_A DMP19, putative uncharacterized protein; helix bundle, DNA mimic,
gene regulation; 1.80A {Neisseria meningitidis}
Length = 166
Score = 27.3 bits (60), Expect = 3.9
Identities = 10/59 (16%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 190 EFIEAMRRWGLDP----KQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILDAE 244
+++RRW + KA L + + +E + G + F+ D
Sbjct: 80 PLADSLRRWKIKAVPKVLDKAKALYEQHGKTIETLADG-GADIPSLRKQFPEFEEWDGA 137
>1gx1_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; isoprenoid,
lyase, isoprene biosynthesis; HET: CDP; 1.8A
{Escherichia coli} SCOP: d.79.5.1 PDB: 1h47_A* 1h48_A*
3ern_A* 3eor_A* 3elc_A* 3esj_A* 3fba_A* 2amt_A* 1knj_A*
1knk_A 1u3l_A* 1u3p_A 1u40_A* 1u43_A* 1jy8_A* 2gzl_A*
1yqn_A* 3ghz_A* 3t80_A*
Length = 160
Score = 27.0 bits (61), Expect = 4.2
Identities = 9/32 (28%), Positives = 10/32 (31%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
+ PK I MR G KAT
Sbjct: 102 QAPKMLPHIPQMRVFIAEDLGCHMDDVNVKAT 133
>2pmp_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; plant enzymes,
MEP pathway, isoprenoid proteins, CMP, zinc IONS, lyase;
HET: C5P; 2.30A {Arabidopsis thaliana}
Length = 160
Score = 27.0 bits (61), Expect = 4.2
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
+RPK E +R G DP KA
Sbjct: 104 QRPKISPHKETIRSNLSKLLGADPSVVNLKAK 135
>1iv3_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; isoprenoid,
non-mevalonate, riken structural genomics/proteomics
initiative, RSGI; 1.52A {Thermus thermophilus} SCOP:
d.79.5.1 PDB: 1iv2_A 1iv4_A* 1iv1_A
Length = 152
Score = 27.0 bits (61), Expect = 4.3
Identities = 5/32 (15%), Positives = 9/32 (28%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
+RPK +A+ L +
Sbjct: 101 DRPKLGPHRKALVDSLSRLMRLPQDRIGLTFK 132
>1t0a_A 2C-methyl-D-erythritol 2,4-cyclodiphosphate synth; mixed alpha
beta, homotrimer, synthase, lyase; HET: FPP; 1.60A
{Shewanella oneidensis} SCOP: d.79.5.1 PDB: 1vh8_A*
1vha_A* 1jn1_A 3fpi_A* 3f6m_A*
Length = 159
Score = 27.0 bits (61), Expect = 4.7
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
+ PK IE MR+ D KAT
Sbjct: 103 QAPKMAPHIEDMRQVLAADLNADVADINVKAT 134
>3f0d_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; ssgcid, niaid,
isoprene biosynthe lyase, metal-binding, structural
genomics; 1.20A {Burkholderia pseudomallei} PDB: 3f0e_A
3f0f_A* 3f0g_A* 3ieq_A* 3iew_A* 3jvh_A* 3k14_A* 3k2x_A*
3ke1_A* 3mbm_A* 3p0z_A* 3p10_A* 3q8h_A* 3qhd_A* 3ikf_A*
3ike_A*
Length = 183
Score = 27.2 bits (61), Expect = 4.9
Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
+ PK I+AMR L + KA
Sbjct: 124 QAPKLAPHIDAMRANIAADLDLPLDRVNVKAK 155
>3re3_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; structural
genomics, center for structural genomics of infec
diseases, csgid; 2.65A {Francisella tularensis subsp}
Length = 162
Score = 26.7 bits (60), Expect = 5.8
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
+ PK IE MR + Q KAT
Sbjct: 107 QAPKMLPHIEKMRACLANILEIQISQINIKAT 138
>2rft_A Influenza B hemagglutinin (HA); viral protein, receptor
specificity, envelope Pro fusion protein, membrane,
transmembrane, VIR glycoprotein; HET: NAG SIA BGC GAL
NDG; 2.80A {Influenza b virus} PDB: 2rfu_A* 3bt6_A*
Length = 344
Score = 27.1 bits (59), Expect = 7.5
Identities = 4/25 (16%), Positives = 10/25 (40%)
Query: 9 SFFSSTIFLTSSSNKVPKPIQLAKP 33
FF++ + + P+ + P
Sbjct: 151 GFFATMAWAVPKNKTATNPLTVEVP 175
>3b6n_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; malaria
isoprenoid biosynthesis and prenylation pathways ISPF;
2.26A {Plasmodium vivax sai-1}
Length = 187
Score = 26.5 bits (59), Expect = 8.3
Identities = 8/32 (25%), Positives = 10/32 (31%), Gaps = 8/32 (25%)
Query: 184 ERPKTKEFIEAMRR-----WGLDPKQ---KAT 207
E PK E + R G+ Q K
Sbjct: 129 EVPKISPIREEIVRNISSALGISESQVSLKGK 160
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
0.312 0.130 0.359
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,279,488
Number of extensions: 263000
Number of successful extensions: 599
Number of sequences better than 10.0: 1
Number of HSP's gapped: 565
Number of HSP's successfully gapped: 45
Length of query: 288
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 195
Effective length of database: 4,105,140
Effective search space: 800502300
Effective search space used: 800502300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.7 bits)