RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 028623
(206 letters)
>3iz5_K 60S ribosomal protein L13A (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_K
Length = 206
Score = 225 bits (575), Expect = 1e-75
Identities = 182/206 (88%), Positives = 199/206 (96%)
Query: 1 MVSGSGICAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYM 60
MVSGSG+CAKRVVVDARHHMLGRLAS++AKELLNGQ+VVVVRCEEIC+SGGLVRQKMKY+
Sbjct: 1 MVSGSGVCAKRVVVDARHHMLGRLASIVAKELLNGQRVVVVRCEEICMSGGLVRQKMKYL 60
Query: 61 RFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKT 120
RFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKT RG AALARLKAYEGVP PYD+T
Sbjct: 61 RFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTARGEAALARLKAYEGVPPPYDRT 120
Query: 121 KRMVIPDALKVLRLQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLA 180
KRMVIPDALKVLRLQ GH+YCLLG+LS EVGWNY DTI+ELE+KRKE+A+V+Y+RRKQLA
Sbjct: 121 KRMVIPDALKVLRLQPGHRYCLLGQLSKEVGWNYADTIRELEEKRKEKAKVSYDRRKQLA 180
Query: 181 KLRVKAEKAAEERLGPQLEIIAPIKY 206
KLRVKAEKAAEE+LG QLEI+APIKY
Sbjct: 181 KLRVKAEKAAEEKLGTQLEILAPIKY 206
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 216 bits (553), Expect = 1e-72
Identities = 89/178 (50%), Positives = 113/178 (63%)
Query: 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71
VV+D + H++GRLASV+AK+LLNGQK+VVVR EE+ ISG R K+KY FLRK
Sbjct: 1 VVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNK 60
Query: 72 SHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKV 131
+ GP HFRAP++I ++ +RGM+ HKT RG AAL RLK +EG+P PYDK KR+V+P AL+V
Sbjct: 61 TRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRV 120
Query: 132 LRLQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEKA 189
LRL+ G KY LG+LS+ VGW A A A A A
Sbjct: 121 LRLKPGRKYTTLGKLSTSVGWKAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 178
>4a17_I RPL13A, 60S ribosomal protein L13A; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_I 4a1c_I 4a1e_I
Length = 198
Score = 211 bits (538), Expect = 4e-70
Identities = 98/200 (49%), Positives = 133/200 (66%), Gaps = 2/200 (1%)
Query: 7 ICAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKR 66
+ K VV+DA+ H+LGRLAS +AKELL+GQ++VVVR E I ISG L R ++K+ FL K
Sbjct: 1 MFDKLVVIDAKGHLLGRLASYVAKELLSGQRIVVVRTEAINISGSLFRNRVKFSEFLNKW 60
Query: 67 MNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIP 126
MN P G HFRAP++I WR +RGM+PHKT +GAAAL RLK +EG+P PYD+ K+ V+
Sbjct: 61 MNHNPRRGVQHFRAPSRIFWRAVRGMLPHKTPKGAAALERLKIFEGIPTPYDRVKKQVVV 120
Query: 127 DALKVLRLQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKA 186
DALKV RL+ C LG LS+ VGW I++LE+KR+ RA+ ++++ + A R K
Sbjct: 121 DALKVQRLRNSRPVCKLGDLSASVGWGKQTLIEKLEEKRRARAKTYHDKKVKQADARKKE 180
Query: 187 EKAAEERLGPQLEIIAPIKY 206
A L + +A Y
Sbjct: 181 LAAPA--LKAIKDKLAQFGY 198
>3izc_K 60S ribosomal protein RPL16 (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_K
3o58_P 3o5h_P 3u5e_O 3u5i_O
Length = 199
Score = 205 bits (522), Expect = 1e-67
Identities = 99/191 (51%), Positives = 130/191 (68%), Gaps = 1/191 (0%)
Query: 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNT 69
VV+D + H++GRLASV+AK+LLNGQK+VVVR EE+ ISG R K+KY FLRK
Sbjct: 5 PVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAF 64
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDAL 129
+ GP HFRAP++I ++ +RGM+ HKT RG AAL RLK +EG+P PYDK KR+V+P AL
Sbjct: 65 NKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQAL 124
Query: 130 KVLRLQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEK- 188
+VLRL+ G KY LG+LS+ VGW Y D + +LE KRK + Y +++ K A
Sbjct: 125 RVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVASANAT 184
Query: 189 AAEERLGPQLE 199
AAE + QL
Sbjct: 185 AAESDVAKQLA 195
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 203 bits (517), Expect = 7e-67
Identities = 109/193 (56%), Positives = 146/193 (75%)
Query: 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNT 69
+ +V+D R H+LGRLA+++AK++L G+KVVVVRCE I ISG R K+ Y+ FLRKRMNT
Sbjct: 5 QVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNT 64
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDAL 129
PS GP FRAP++I WRT+RGM+PHKTKRG AAL RLK ++G+P PYDK KRMV+P AL
Sbjct: 65 NPSRGPYDFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAAL 124
Query: 130 KVLRLQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEKA 189
KV+RL+ K+ LGRL+ EVGW Y LE+KRKE+A++ Y ++KQL +LR +AEK
Sbjct: 125 KVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKN 184
Query: 190 AEERLGPQLEIIA 202
E+++ E++
Sbjct: 185 VEKKIDKYTEVLK 197
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 200 bits (510), Expect = 1e-66
Identities = 50/143 (34%), Positives = 76/143 (53%), Gaps = 2/143 (1%)
Query: 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71
+++A +LGRLAS +AK LL G++VV+V E+ I+G KY + R T P
Sbjct: 2 RIINADGLILGRLASRVAKMLLEGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNP 61
Query: 72 SHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKV 131
GP + + +I+ RTIRGM+P KT RG A RLK Y G+P + + I +A
Sbjct: 62 RRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETIVEAHVS 121
Query: 132 LRLQKGHKYCLLGRLSSEVGWNY 154
+ KY +G ++ +G +
Sbjct: 122 RLSRP--KYVTVGEVAKFLGGKF 142
>1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M
1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I*
1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K*
1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
Length = 145
Score = 183 bits (468), Expect = 4e-60
Identities = 50/145 (34%), Positives = 77/145 (53%), Gaps = 9/145 (6%)
Query: 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNT 69
V+VDAR ++GR+AS +A++ L+G+ V VV E I+G + KY KR++
Sbjct: 8 ADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKY----EKRVDI 63
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDAL 129
+G + + P I RTIRGM+PHK +RG A ++ Y G PYD+ ++ +L
Sbjct: 64 GNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLG--NPYDEDGEVLDGTSL 121
Query: 130 KVLRLQKGHKYCLLGRLSSEVGWNY 154
L K+ LG +S +G N
Sbjct: 122 DRL---SNIKFVTLGEISETLGANK 143
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus}
Length = 148
Score = 51.8 bits (125), Expect = 6e-09
Identities = 26/119 (21%), Positives = 43/119 (36%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
++D + G+LA++ + L G VV++ I SG QK+ Y
Sbjct: 19 YLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKV-Y 77
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
R+ + +H R P I+ I GM+P K + RL +
Sbjct: 78 SSHTGYPGGFRQV-----TAAQLHLRDPVAIVKLAIYGMLP-KNLHRRTMMERLHLFPD 130
>3r8s_J 50S ribosomal protein L13; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H
1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J
2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ...
Length = 142
Score = 49.8 bits (120), Expect = 3e-08
Identities = 29/119 (24%), Positives = 52/119 (43%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
VVDA LGRLA+ LA+ L G ++V+ +++ ++G K+ Y
Sbjct: 16 YVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKV-Y 74
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
+++ + + R P +++ ++GM+P K G A +LK Y G
Sbjct: 75 YHHTGHIGGIKQA-----TFEEMIARRPERVIEIAVKGMLP-KGPLGRAMFRKLKVYAG 127
>3v2d_N 50S ribosomal protein L13; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N
2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 2wrj_N 2wrl_N
2wro_N 2wrr_N 2x9s_N 2x9u_N ...
Length = 140
Score = 49.8 bits (120), Expect = 3e-08
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
V++DA LGRLA+ +A L G VVVV ++I ++G + QK+ Y
Sbjct: 14 VLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI-Y 72
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
R+ L+K + P ++L ++GM+P K G RLK Y G
Sbjct: 73 TRYSGYPGGLKKI-----PLEKMLATHPERVLEHAVKGMLP-KGPLGRRLFKRLKVYAG 125
>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A
{Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N
Length = 163
Score = 49.5 bits (119), Expect = 4e-08
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
V++DA LGRLA+ +A L G VVVV ++I ++G + QK+ Y
Sbjct: 37 VLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI-Y 95
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
R+ L+K + P ++L ++GM+P K G RLK Y G
Sbjct: 96 TRYSGYPGGLKKI-----PLEKMLATHPERVLEHAVKGMLP-KGPLGRRLFKRLKVYAG 148
>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H*
1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 3pio_G*
3pip_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K
Length = 174
Score = 49.2 bits (118), Expect = 8e-08
Identities = 32/119 (26%), Positives = 54/119 (45%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
VVVDA LGRLA+++A + G VVV+ ++ ++G + K+ Y
Sbjct: 42 VVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKV-Y 100
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
R+ L+ + + P +++ + GM+P K ++G A RLK Y G
Sbjct: 101 TRYTGYQGGLKTE-----TAREALSKHPERVIEHAVFGMLP-KGRQGRAMHTRLKVYAG 153
>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 250
Score = 48.6 bits (116), Expect = 3e-07
Identities = 34/119 (28%), Positives = 54/119 (45%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
VVDA +LGR+AS +A + G V+VV +++ +SG QK+ Y
Sbjct: 115 YVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKL-Y 173
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
R L++ + + R P +I+ +RGM+P K + G LK Y+G
Sbjct: 174 RRHSGRPGGLKEE-----TFDQLQKRIPERIIEHAVRGMLP-KGRLGRYLFNHLKVYKG 226
>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 = 37.5 bits (86), Expect = 0.002
Identities = 33/217 (15%), Positives = 60/217 (27%), Gaps = 68/217 (31%)
Query: 8 CAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRM 67
C ++++ R V + L+ + + S L ++K L K +
Sbjct: 266 C--KILL------TTRFKQVT--DFLSAATTTHISLDHH--SMTLTPDEVK--SLLLKYL 311
Query: 68 NTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMV--- 124
+ +P P R R + +I + G A K DK ++
Sbjct: 312 DCRPQDLP---REVLTTNPRRL-SIIAESIRDGLATWDNWKHVN-----CDKLTTIIESS 362
Query: 125 ------------------------IP-DALKVL-----------RLQKGHKYCLLGRLSS 148
IP L ++ + K HKY L+ +
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422
Query: 149 EVGWNYYDTIKELEKKRKERAQV------AYERRKQL 179
E + EL+ K + + Y K
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF 459
Score = 33.3 bits (75), Expect = 0.047
Identities = 26/154 (16%), Positives = 52/154 (33%), Gaps = 51/154 (33%)
Query: 18 HHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYM--RFLRKRMNTKPSHGP 75
HH+ K + + +++ + R M ++ RFL +++ H
Sbjct: 479 HHL---------KNIEHPERMTLFR--------------MVFLDFRFLEQKIR----HDS 511
Query: 76 IHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQ 135
+ A IL L +LK Y+ D ++ L L
Sbjct: 512 TAWNASGSIL----------------NTLQQLKFYKPYICDNDPKYERLVNAILDFLPKI 555
Query: 136 KGH----KYCLLGR--LSSEVGWNYYDTIKELEK 163
+ + KY L R L +E + + K++++
Sbjct: 556 EENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
>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 = 37.3 bits (86), Expect = 0.003
Identities = 40/235 (17%), Positives = 70/235 (29%), Gaps = 76/235 (32%)
Query: 9 AKRVVVDARHHMLGRLA-SVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRF----- 62
A+ V A +H S+L + N + + E G +R+ M F
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGE---KGKRIRENYSAMIFETIVD 1698
Query: 63 -------LRKRMNTKPSHGPIHFRAPAKIL-----------------WRTIR--GMIPHK 96
+ K +N + FR+ +L + ++ G+IP
Sbjct: 1699 GKLKTEKIFKEINEHSTS--YTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPAD 1756
Query: 97 TKRGA-------AALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCLLGRLSSE 149
A AALA + V M I ++V+ + G
Sbjct: 1757 -ATFAGHSLGEYAALA---SLADV---------MSIESLVEVVFYR--------GMTMQV 1795
Query: 150 VGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEKAAEERLGPQ----LEI 200
+ E R +A + A +A + ER+G + +EI
Sbjct: 1796 A-------VPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEI 1843
Score = 35.0 bits (80), Expect = 0.015
Identities = 43/225 (19%), Positives = 72/225 (32%), Gaps = 85/225 (37%)
Query: 1 MVSGSGICAKRV--VVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISG------GL 52
M+S S + ++V V+ + L + L+NG K +VV SG GL
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPA-GKQVEISLVNGAKNLVV-------SGPPQSLYGL 389
Query: 53 VRQKMKYMRFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALAR-LKAYE 111
LRK +AP+ + + IP ++R R L
Sbjct: 390 NLT-------LRKA------------KAPSGL----DQSRIPF-SERKLKFSNRFLP--- 422
Query: 112 GVPAPY-----DKTKRMVIPDALKVLRLQKGHKYCLLGRLSSEVGWNY-------YDTI- 158
V +P+ ++ D +K + V +N YDT
Sbjct: 423 -VASPFHSHLLVPASDLINKDLVK-----------------NNVSFNAKDIQIPVYDTFD 464
Query: 159 -KELEKKRKERAQVAYERRKQLAKLRVKAEKAAEER------LGP 196
+L R ++ + +L VK E + + GP
Sbjct: 465 GSDL---RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGP 506
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.7 bits (79), Expect = 0.009
Identities = 11/48 (22%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 156 DTIKELEKKRKER-AQVAYERRKQLAKLRVKAEKAAEE---RLGPQLE 199
++I++ +++++R ++ + + R KA+K EE R Q+E
Sbjct: 85 ESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVE 132
Score = 33.2 bits (75), Expect = 0.029
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 160 ELEKKRKERAQVAYERRKQLAKLRVKAEKAAEE 192
E E RK R E+RK+L +L ++ +E
Sbjct: 83 EPESIRKWRE----EQRKRLQELDAASKVMEQE 111
Score = 29.4 bits (65), Expect = 0.58
Identities = 6/33 (18%), Positives = 15/33 (45%)
Query: 162 EKKRKERAQVAYERRKQLAKLRVKAEKAAEERL 194
EK +K+ + + +Q+ K ++ A +
Sbjct: 114 EKAKKDLEEWNQRQSEQVEKNKINNRIADKAFY 146
>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 = 30.3 bits (67), Expect = 0.24
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 22/49 (44%)
Query: 157 TIKELEKKRKERAQVAYERRKQLAKLRVKAEKAAEERLGPQLEIIAPIK 205
+K+L+ A L++ A+ +A P L I A ++
Sbjct: 21 ALKKLQ-----------------ASLKLYADDSA-----PALAIKATME 47
Score = 26.1 bits (56), Expect = 5.8
Identities = 8/22 (36%), Positives = 9/22 (40%), Gaps = 5/22 (22%)
Query: 98 KRGAAAL-ARLKAYEGVP--AP 116
K+ L A LK Y AP
Sbjct: 19 KQALKKLQASLKLYA--DDSAP 38
Score = 26.1 bits (56), Expect = 7.2
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 187 EKAAEERLGPQLEIIAP 203
EK A ++L L++ A
Sbjct: 18 EKQALKKLQASLKLYAD 34
>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent
proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A*
1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E*
1ht1_E* 1ht2_E*
Length = 444
Score = 30.8 bits (70), Expect = 0.32
Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 174 ERRKQLAKLRVKAEKAAEERLGPQLEIIAP 203
R++++AK R +AE AEER+ L+ + P
Sbjct: 111 VRQQEIAKNRARAEDVAEERI---LDALLP 137
>2wd5_A Structural maintenance of chromosomes protein 1A; DNA damage, cell
cycle, cell division; 2.70A {Mus musculus}
Length = 233
Score = 28.1 bits (63), Expect = 1.7
Identities = 9/48 (18%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 159 KELEKKRKERAQVAYERRKQLAKLR-VKAEKAAEERLGPQLEIIAPIK 205
+E+E ++ ++ E + + +L + ++ R + EI+ IK
Sbjct: 1 EEVEMAKRRIDEINKELNQVMEQLGDARIDRQESSRQQRKAEIMESIK 48
>2ch5_A NAGK protein; transferase, N-acetylglucosamine, glcnac, sugar
kinase, RIBO H fold, sugar kinase/HSP70/actin
superfamily, domain rotati conformation; HET: NAG NDG;
1.9A {Homo sapiens} SCOP: c.55.1.5 c.55.1.5 PDB: 2ch6_A*
Length = 347
Score = 28.1 bits (62), Expect = 2.4
Identities = 13/114 (11%), Positives = 29/114 (25%), Gaps = 8/114 (7%)
Query: 9 AKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMN 68
++ + A LGR + E+ + I G + + +
Sbjct: 234 SRYIFRKAGEM-LGRHIVAVLPEI-DPVLFQGKIGLPILCVGSVWKSWELLKEGFLLALT 291
Query: 69 TKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKR 122
+F + ++ + G A+L +P Y
Sbjct: 292 QGREIQAQNFFSSFTLMKLRHSSAL------GGASLGARHIGHLLPMDYSANAI 339
>3haj_A Human pacsin2 F-BAR; pacsin,syndapin,FAP52,F-BAR, alternative
splicing, coiled coil, cytoplasmic vesicle, endocytosis,
phosphoprotein, polymorphism; 2.78A {Homo sapiens}
Length = 486
Score = 27.4 bits (59), Expect = 3.4
Identities = 7/36 (19%), Positives = 14/36 (38%)
Query: 156 DTIKELEKKRKERAQVAYERRKQLAKLRVKAEKAAE 191
+L ERA++ +QL + + + E
Sbjct: 36 RLCSDLMNCLHERARIEKAYAQQLTEWARRWRQLVE 71
>3uo9_A Glutaminase kidney isoform, mitochondrial; hydrolase-hydrolase
inhibitor complex; HET: 04A; 2.30A {Homo sapiens} PDB:
3unw_A* 3ss3_A 3ss4_A 3ss5_A*
Length = 534
Score = 27.4 bits (60), Expect = 4.3
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 142 LLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKA 186
L S ++ YD ++ KK R + ++R L ++
Sbjct: 447 FCHDLVSLCNFHNYDNLRHFAKKLDPR-REGGDQRHSFGPLDYES 490
>1lnq_A MTHK channels, potassium channel related protein; rossman fold,
helix bundle, membrane protein; 3.30A
{Methanothermobacter thermautotrophicusorganism_taxid}
SCOP: c.2.1.9 d.286.1.1 f.14.1.1 PDB: 3rbz_A
Length = 336
Score = 27.0 bits (60), Expect = 4.8
Identities = 6/41 (14%), Positives = 13/41 (31%), Gaps = 4/41 (9%)
Query: 10 KRVVVDARHHML----GRLASVLAKELLNGQKVVVVRCEEI 46
+ V H++ +EL + V+ E +
Sbjct: 108 GLIDVAKSRHVVICGWSESTLECLRELRGSEVFVLAEDENV 148
>4ad9_A Lactb2, beta-lactamase-like protein 2; hydrolase, metallo-beta
lactamase, mitochondria; 2.60A {Homo sapiens}
Length = 289
Score = 26.3 bits (58), Expect = 6.5
Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 6/54 (11%)
Query: 71 PSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPA-PYDKTKRM 123
P HGP+ A AK I+ I H+ R L + + K +
Sbjct: 198 PGHGPVIHNAEAK-----IQQYISHRNIREQQILTLFRENFEKSFTVMELVKII 246
>3q0i_A Methionyl-tRNA formyltransferase; structural genomics, center for
structural genomics of infec diseases, csgid; 1.89A
{Vibrio cholerae}
Length = 318
Score = 26.3 bits (59), Expect = 7.4
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIP 94
I++ A + R IR P
Sbjct: 212 SKEEARINWSDAATHIERCIRAFNP 236
>3qwe_A GMIP, GEM-interacting protein; structural genomics consortium, SGC,
protein binding; 2.40A {Homo sapiens}
Length = 279
Score = 26.3 bits (57), Expect = 7.4
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 158 IKELEKKRKERAQVAYERRKQLAKLRVKAEKA 189
E+EK RKE + + +K++ + +A
Sbjct: 107 RTEIEKWRKEFKEQWMKEQKRMNEAVQALRRA 138
>3rfo_A Methionyl-tRNA formyltransferase; structural genomics, center for
structural genomics of infec diseases, csgid, alpha-beta
structure, cytosol; HET: PGE; 2.40A {Bacillus anthracis}
Length = 317
Score = 26.3 bits (59), Expect = 7.9
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIP 94
K I + + ++ IRG+ P
Sbjct: 209 KREQEKIDWTKTGEEVYNHIRGLNP 233
>1fmt_A Methionyl-tRNA FMet formyltransferase; initiator tRNA, translation
initiation; 2.00A {Escherichia coli} SCOP: b.46.1.1
c.65.1.1 PDB: 2fmt_A* 3r8x_A
Length = 314
Score = 25.9 bits (58), Expect = 8.8
Identities = 7/25 (28%), Positives = 8/25 (32%)
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIP 94
I + A L R IR P
Sbjct: 208 SKEEARIDWSLSAAQLERCIRAFNP 232
>3tqq_A Methionyl-tRNA formyltransferase; protein synthesis; 2.00A
{Coxiella burnetii}
Length = 314
Score = 25.9 bits (58), Expect = 9.7
Identities = 6/25 (24%), Positives = 10/25 (40%)
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIP 94
+ I +R A + R +R P
Sbjct: 207 QKQEALIDWRKSAVEIARQVRAFNP 231
>3epq_A Putative fructokinase; SCRK, ADP binding, PSI2, MCSG, structural
GENO protein structure initiative, midwest center for
structural genomics; HET: MLY MSE MLZ ADP; 1.66A
{Bacillus subtilis} PDB: 1xc3_A 3ohr_A* 3lm9_A*
Length = 302
Score = 26.1 bits (57), Expect = 9.7
Identities = 20/126 (15%), Positives = 42/126 (33%), Gaps = 18/126 (14%)
Query: 1 MVSGSGICAKRVVVDAR----HHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQK 56
+ SG I A+ A + +A+ L ++++ I + GG+++Q
Sbjct: 181 LASGPAIEARWGXKAADLSDIAQVWELEGYYIAQALAQY--ILILAPXXIILGGGVMQQX 238
Query: 57 ---MKYMRFLRKRMNTKPSHGPIHFRAPAKILWRTIR---GMIPHKTKRGAAALARLKAY 110
+++ K MN+ + I+ + G+I G LA
Sbjct: 239 QVFSYIYQYVPKIMNSYLDFSELSDDISDYIVPPRLGSNAGII------GTLVLAHQALQ 292
Query: 111 EGVPAP 116
+
Sbjct: 293 AEAASG 298
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
0.323 0.137 0.402
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,334,368
Number of extensions: 205041
Number of successful extensions: 646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 613
Number of HSP's successfully gapped: 79
Length of query: 206
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 117
Effective length of database: 4,216,824
Effective search space: 493368408
Effective search space used: 493368408
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 (22.0 bits)
S2: 55 (24.9 bits)