RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1616
(237 letters)
>4a17_D L21, RPL11, 60S ribosomal protein L11; eukaryotic ribosome,
ribosome, eukaryotic initiation factor 60S, translation,
large ribosomal subunit; 3.52A {Tetrahymena thermophila}
PDB: 4a1a_D 4a1c_D 4a1e_D
Length = 172
Score = 206 bits (526), Expect = 4e-68
Identities = 87/200 (43%), Positives = 116/200 (58%), Gaps = 47/200 (23%)
Query: 44 DKSKNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYT-RS-KGRRN 101
DK +N MREVKI KL +N CVGESGD+LT+AAKVL+ L+GQ+PVFS+ARYT RS +RN
Sbjct: 3 DKKENKMREVKIAKLVINCCVGESGDKLTKAAKVLKDLSGQEPVFSRARYTIRSFGIKRN 62
Query: 102 P---------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHLNQ 152
G++A + + + ++ ++ +
Sbjct: 63 EKMAVHVTIRGDKARDILTRGLKVKEM---------------------ELRKKNFSN--- 98
Query: 153 KIHKAQSLCLHHSGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFNVAHRRRKTG 212
+GNFGFGIQEHIDLG+KYDPS GI+G+DFYVVL RPG VA RRR T
Sbjct: 99 ------------TGNFGFGIQEHIDLGMKYDPSTGIFGMDFYVVLERPGTRVARRRRATS 146
Query: 213 IVGFQHRLTKEDAMKWFQTK 232
VG ++KE+ + WF+T+
Sbjct: 147 RVGNNQMISKEECINWFKTE 166
>2zkr_d 60S ribosomal protein L11; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 178
Score = 203 bits (519), Expect = 6e-67
Identities = 108/202 (53%), Positives = 129/202 (63%), Gaps = 47/202 (23%)
Query: 42 KKDKSKNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYT-RS-KGR 99
+ + +N MRE++IRKLCLNICVGESGDRLTRAAKVLEQLTGQ PVFSKARYT RS R
Sbjct: 4 DQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIR 63
Query: 100 RNP---------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHL 150
RN G +A ++ + KV E EL
Sbjct: 64 RNEKIAVHCTVRGAKAEEILEKGL--------------------------KVREYELRKN 97
Query: 151 NQKIHKAQSLCLHHSGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFNVAHRRRK 210
N +GNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGF++A ++R+
Sbjct: 98 N----------FSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRR 147
Query: 211 TGIVGFQHRLTKEDAMKWFQTK 232
TG +G +HR++KE+AM+WFQ K
Sbjct: 148 TGCIGAKHRISKEEAMRWFQQK 169
>3iz5_e 60S ribosomal protein L7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_e
Length = 244
Score = 202 bits (516), Expect = 2e-66
Identities = 8/202 (3%), Positives = 33/202 (16%), Gaps = 47/202 (23%)
Query: 42 KKDKSKNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYT-RS-KGR 99
+ V +V +++ + E ++ + T ++ + +
Sbjct: 3 SEAAKVAVPEKVILKRRREEVWAAEKKQKVAAEKIKAAENTKVIYARAEQYAGEYEAQDK 62
Query: 100 RNP---------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHL 150
G S + V +
Sbjct: 63 ELVQLKREARMKGGFYVSPEAKPL--------------------------FVVRIRGINA 96
Query: 151 NQKIHKAQSLCLHHSGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFNVAHRRRK 210
+ ++ + V + + +
Sbjct: 97 M----------HPKTKKILQLLRLRQIFNGVFLKVNKATINMLRRVEPYVTYGYPNLKSV 146
Query: 211 TGIVGFQHRLTKEDAMKWFQTK 232
++ +
Sbjct: 147 RELIYKRGYGKLNKQRIPLANN 168
>1vq8_D 50S ribosomal protein L5P; 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: d.77.1.1 PDB: 1vq4_D*
1vq5_D* 1vq6_D* 1vq7_D* 1s72_D* 1vq9_D* 1vqk_D* 1vql_D*
1vqm_D* 1vqn_D* 1vqo_D* 1vqp_D* 1yhq_D* 1yi2_D* 1yij_D*
1yit_D* 1yj9_D* 1yjn_D* 1yjw_D* 2otj_D* ...
Length = 177
Score = 184 bits (469), Expect = 2e-59
Identities = 54/208 (25%), Positives = 90/208 (43%), Gaps = 50/208 (24%)
Query: 37 VAKKGKKDKSKNVMREVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYTRS 96
++ + + + MRE +I K+ +++ +G G L A +L ++TGQ PV +KA+ T
Sbjct: 1 MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVG 60
Query: 97 --KGRRNP---------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTER 145
R E A F++ + ++
Sbjct: 61 EFDIREGDPIGAKVTLRDEMAEEFLQTAL-----------------------PLAELATS 97
Query: 146 ELDHLNQKIHKAQSLCLHHSGNFGFGIQEHIDL-GIKYDPSIGIYGLDFYVVLGRPGFNV 204
+ D +GNF FG++EH + +YDPSIGIYGLD V L RPG+ V
Sbjct: 98 QFDD---------------TGNFSFGVEEHTEFPSQEYDPSIGIYGLDVTVNLVRPGYRV 142
Query: 205 AHRRRKTGIVGFQHRLTKEDAMKWFQTK 232
A R + + + +HRL DA+ + ++
Sbjct: 143 AKRDKASRSIPTKHRLNPADAVAFIEST 170
>3r8s_F 50S ribosomal protein L5; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 3oat_F*
3ofc_F* 3ofz_F* 3ofr_F 3r8t_F 3i1n_F 1vs8_F 1vs6_F
1vt2_F 3i1p_F 3i1r_F 3i1t_F 3i20_F 3i22_F 3iyx_F 3iyy_F
3izt_G* 3izu_G* 3kcr_F 3orb_F* ...
Length = 177
Score = 44.1 bits (105), Expect = 6e-06
Identities = 42/165 (25%), Positives = 70/165 (42%), Gaps = 45/165 (27%)
Query: 47 KNVMREVKIRKLCLNICVGESGD---RLTRAAKVLEQLTGQQPVFSKARYTRS--KGRRN 101
+VM+ ++ K+ LN+ VGE+ L AA L ++GQ+P+ +KAR + + K R+
Sbjct: 22 NSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQG 81
Query: 102 -P--------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHLNQ 152
P GER F + L+ +A+P + F R ++ + D
Sbjct: 82 YPIGCKVTLRGERMWEFFERLITIAVPRIRDF---------------RGLSAKSFD---- 122
Query: 153 KIHKAQSLCLHHSGNFGFGIQEHIDLG-IKYDPSIGIYGLDFYVV 196
GN+ G++E I I YD + GLD +
Sbjct: 123 -----------GRGNYSMGVREQIIFPEIDYDKVDRVRGLDITIT 156
>1iq4_A 50S ribosomal protein L5; rRNA-binding, RNP motif, RNA binding
PROT; 1.80A {Geobacillus stearothermophilus} SCOP:
d.77.1.1
Length = 179
Score = 43.7 bits (104), Expect = 9e-06
Identities = 41/167 (24%), Positives = 71/167 (42%), Gaps = 49/167 (29%)
Query: 47 KNVMREVKIRKLCLNICVGE-SGDR--LTRAAKVLEQLTGQQPVFSKARYTRS----KGR 99
K++M+ KI K+ +N+ VG+ + L A + L + GQ+PV ++A+ +S + R
Sbjct: 23 KSIMQVPKIEKIVINMGVGDAVQNPKALDSAVEELTLIAGQRPVVTRAK--KSIAGFRLR 80
Query: 100 RN-P--------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHL 150
+ P GER F+ L+ ++LP F R V+++ D
Sbjct: 81 QGMPIGAKVTLRGERMYEFLDKLISVSLPRARDF---------------RGVSKKSFD-- 123
Query: 151 NQKIHKAQSLCLHHSGNFGFGIQEHIDLG-IKYDPSIGIYGLDFYVV 196
GN+ GI+E + I YD + G+D +V
Sbjct: 124 -------------GRGNYTLGIKEQLIFPEIDYDKVNKVRGMDIVIV 157
>1mji_A 50S ribosomal protein L5; ribosomal protein - 5S rRNA complex,
ribosome; 2.50A {Thermus thermophilus} SCOP: d.77.1.1
PDB: 2hgj_G 2hgq_G 2hgu_G 2j01_G 2j03_G 2jl6_G 2jl8_G
2v47_G 2v49_G 2wdi_G 2wdj_G 2wdl_G 2wdn_G 2wh2_G 2wh4_G
2wrj_G 2wrl_G 2wro_G 2wrr_G 2x9s_G ...
Length = 182
Score = 43.7 bits (104), Expect = 1e-05
Identities = 40/165 (24%), Positives = 68/165 (41%), Gaps = 45/165 (27%)
Query: 47 KNVMREVKIRKLCLNICVGE-SGDR--LTRAAKVLEQLTGQQPVFSKARYTRS--KGRRN 101
+NV ++ K+ +N +GE D L +AA+ L +TGQ+P ++A+ + S K R+
Sbjct: 26 QNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKG 85
Query: 102 -P--------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHLNQ 152
P +R F++ L+ +ALP + F R + D
Sbjct: 86 MPIGLRVTLRRDRMWIFLEKLLNVALPRIRDF---------------RGLNPNSFD---- 126
Query: 153 KIHKAQSLCLHHSGNFGFGIQEHIDLG-IKYDPSIGIYGLDFYVV 196
GN+ G++E + I YD + G+D VV
Sbjct: 127 -----------GRGNYNLGLREQLIFPEITYDMVDALRGMDIAVV 160
>3bbo_H Ribosomal protein L5; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 220
Score = 42.7 bits (101), Expect = 3e-05
Identities = 37/165 (22%), Positives = 59/165 (35%), Gaps = 45/165 (27%)
Query: 47 KNVMREVKIRKLCLNICVGE-SGDR--LTRAAKVLEQLTGQQPVFSKARYTRS--KGRRN 101
N++ K+ K+ +N +G+ S + L A L +TGQ+PV +KA+ + + K R
Sbjct: 38 SNILEVPKVVKIVVNCGIGDASQNAKGLDAAINELALITGQRPVKTKAKTSIAGFKVREG 97
Query: 102 -P--------GERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHLNQ 152
G SF+ L+ LALP F + V D
Sbjct: 98 MTLGIAVTLRGNLMYSFLDRLINLALPRTRDF---------------QGVNPNSFD---- 138
Query: 153 KIHKAQSLCLHHSGNFGFGIQEHIDLG-IKYDPSIGIYGLDFYVV 196
GN+ G +E IK + G+D +
Sbjct: 139 -----------GHGNYSVGFREQSVFPEIKPEIVGKARGMDVCIT 172
>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 = 43.1 bits (101), Expect = 5e-05
Identities = 26/171 (15%), Positives = 42/171 (24%), Gaps = 60/171 (35%)
Query: 62 ICVGESGDRLTRAA-KVLEQLT-----GQQ--PVFSKARYTRSKGRRNPGERASSFMKPL 113
I +S + + K + L + P S N E S M L
Sbjct: 283 IAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLEN-NEGVPSPM--L 339
Query: 114 VVLALPGMYLFYKYNQYKQQQQEQNRRKVTERELDHLNQKIHKAQSLCLHHSGNFGFGIQ 173
+ L ++ + ++ N H
Sbjct: 340 SISNLT--------------------QEQVQDYVNKTNS--HLPAG-------------- 363
Query: 174 EHIDLGIKYDPSIGIY-GLDFYVVLGRP----GFNVAHRRRKTGIVGFQHR 219
+ + I + G VV G P G N+ R+ K Q R
Sbjct: 364 KQV--------EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSR 406
>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 = 32.9 bits (74), Expect = 0.084
Identities = 25/179 (13%), Positives = 54/179 (30%), Gaps = 50/179 (27%)
Query: 44 DKSKNVM--REVKIRKLCLNICVGESGDRLTRAAKVLEQLTGQQP----VF----SKARY 93
D K+++ E+ +I S D ++ ++ L +Q F + Y
Sbjct: 40 DMPKSILSKEEID------HII--MSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY 91
Query: 94 --------TRSKGRRNPGERASSFMKPLVVLALPGMYLFYKYNQYKQQQQEQNRRKVTER 145
T + L +F KYN + Q + R+ +
Sbjct: 92 KFLMSPIKTEQRQPSMMTRMYIEQRDRL----YNDNQVFAKYNVSRLQPYLKLRQAL--- 144
Query: 146 ELDHLNQKIHKAQSLCLHHSGNFGFG-----IQEHIDLGIKYDPSIGIYGLDFYVVLGR 199
++ A+++ + G G G + + ++ I F++ L
Sbjct: 145 ------LELRPAKNVLID--GVLGSGKTWVALDVCLSYKVQCKMDFKI----FWLNLKN 191
>4f7g_B Talin-1; alpha-helix bundle, integrin activation, cell adhesion;
2.05A {Mus musculus} PDB: 2kbb_A 2kgx_A
Length = 216
Score = 28.6 bits (63), Expect = 1.6
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 15 VGESGDRLTRAAKTKAVDPAKPVAKKGKKDKSKNVMREVKIRKLC--LNICVGESG---- 68
+ ES +L AK +P + + +++ +M E + L LN +G
Sbjct: 137 LAESALQLLYTAKEAGGNPKQAAHTQEALEEAVQMMTEA-VEDLTTTLNEAASAAGVVGG 195
Query: 69 --DRLTRAAKVLEQLTGQQP 86
D +T+A L++ P
Sbjct: 196 MVDSITQAINQLDEGPMGDP 215
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.2 bits (62), Expect = 1.9
Identities = 3/30 (10%), Positives = 12/30 (40%), Gaps = 5/30 (16%)
Query: 124 FYK-YNQYKQQQQEQNRRK----VTERELD 148
+ + ++ ++ + NR + + D
Sbjct: 123 WNQRQSEQVEKNKINNRIADKAFYQQPDAD 152
>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2,
protein STRU initiative, northeast structural genomics
consortium, NESG; 2.50A {Bacillus halodurans} PDB:
3o3w_A
Length = 144
Score = 26.3 bits (58), Expect = 7.0
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 62 ICVGESGDRLTRAAKVLEQL 81
C G + + T+AA QL
Sbjct: 78 YCWGPACNGATKAAAKFAQL 97
>3tut_A RNA 3'-terminal phosphate cyclase; cyclase family, cyclization of
RNA 3'-phosphate ENDS, transf; HET: ATP; 1.58A
{Escherichia coli} PDB: 3tux_A* 3tv1_A* 3tw3_A* 3kgd_A*
1qmh_A* 1qmi_A
Length = 358
Score = 26.5 bits (58), Expect = 8.0
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 43 KDKSKNVMREVKIRK-LCLNICVGESGDRLTRAAKVLEQLTGQQPVFSKARYTRSKGRRN 101
S + +++ + L+ GE G ++ R+A L +TGQ + R GR
Sbjct: 9 HHHSSGHIEGRHMKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIR----AGRAK 64
Query: 102 PGERASSF 109
PG
Sbjct: 65 PGLLRQHL 72
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
0.322 0.138 0.408
Gapped
Lambda K H
0.267 0.0492 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,604,212
Number of extensions: 207826
Number of successful extensions: 464
Number of sequences better than 10.0: 1
Number of HSP's gapped: 455
Number of HSP's successfully gapped: 35
Length of query: 237
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 146
Effective length of database: 4,160,982
Effective search space: 607503372
Effective search space used: 607503372
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 (21.9 bits)
S2: 56 (25.9 bits)