RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 027746
(219 letters)
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 269
Score = 208 bits (531), Expect = 8e-68
Identities = 76/168 (45%), Positives = 99/168 (58%), Gaps = 10/168 (5%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
P+ + D I+ V I ++G+ +PL M +GT IHNIE+ G+GG+L RAAG AK
Sbjct: 103 PRGAIIGDTIVSG-TEVPI--KMGNALPLTDMPLGTAIHNIEITLGRGGQLARAAGAVAK 159
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVR 166
++ KE ++LPSG +LI C AT+G V N K+L +AG RWLG+RPVVR
Sbjct: 160 LIAKE--GKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQKRLGRAGSKRWLGKRPVVR 217
Query: 167 GVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPCKSGYKTASPKKK 214
GV MNPVDHPHGGGEGR+ TPWG P G ++ K
Sbjct: 218 GVVMNPVDHPHGGGEGRAPIGRKS---PTTPWGYPAL-GRRSRKRNKY 261
>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D 2jl8_D
2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D 2wh4_D
2wrj_D 2wrl_D 2wro_D 2wrr_D ...
Length = 276
Score = 208 bits (531), Expect = 1e-67
Identities = 76/167 (45%), Positives = 101/167 (60%), Gaps = 11/167 (6%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
P V +++ I Q+G+ +PL + +GT++H +E+ P +G KL RAAGTSA+
Sbjct: 108 PDGLQVGQQVVAG-PDAPI--QVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQ 164
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVR 166
I +E + ++RLPSG + + C AT+G V N H L KAG+SRWLGRRP VR
Sbjct: 165 IQGRE--GDYVILRLPSGELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVR 222
Query: 167 GVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPCKSGYKTASPKK 213
G AMNPVDHPHGGGEGR+ GR +PWG K G KT +K
Sbjct: 223 GAAMNPVDHPHGGGEGRAPR----GRPPASPWGWQTK-GLKTRKRRK 264
>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_C
2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C* 3ofz_C*
3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C 2aw4_C 2awb_C
2vhm_C 2vhn_C 3bbx_C 3df2_C ...
Length = 271
Score = 205 bits (523), Expect = 2e-66
Identities = 72/171 (42%), Positives = 103/171 (60%), Gaps = 12/171 (7%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
PK D+I I + G+ +P+ + +G+ +HN+E+ PG+GG+L R+AGT +
Sbjct: 106 PKGLKAGDQIQSG-VDAAI--KPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQ 162
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRRPVVR 166
I+ ++ ++ +RL SG + ++ CRAT+G V N H + L KAG +RW G RP VR
Sbjct: 163 IVARD--GAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVR 220
Query: 167 GVAMNPVDHPHGGGEGRSKSSGNHGRCSLTPWGKPCKSGYKTASPKKKKKL 217
G AMNPVDHPHGGGEGR+ G+ +TPWG K G KT S K+ K
Sbjct: 221 GTAMNPVDHPHGGGEGRNF-----GKHPVTPWGVQTK-GKKTRSNKRTDKF 265
>1vq8_A 50S ribosomal protein L2P; 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.34.5.3 b.40.4.5 PDB:
1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A*
1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A*
1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ...
Length = 240
Score = 188 bits (481), Expect = 1e-60
Identities = 53/154 (34%), Positives = 78/154 (50%), Gaps = 13/154 (8%)
Query: 69 QIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKIL-KEPTSSFCLVRLPSGNEK 127
G+ +PLA + G + N+E +PG GGK RA+G +A++L + + +V+LPSG K
Sbjct: 90 APGNTLPLAEIPEGVPVCNVESSPGDGGKFARASGVNAQLLTHD--RNVAVVKLPSGEMK 147
Query: 128 LIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRR-----PVVRGVAMNPVDHPHGGGEG 182
+D +CRATIG V+ K KAG + P VRGVAMN VDHP GGG
Sbjct: 148 RLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGGGR 207
Query: 183 RSKSSGNHGRCSLTPWGKPCKSGYKTASPKKKKK 216
+ S++ P + + K+ +
Sbjct: 208 QHPG----KPKSISRNAPPGR-KVGDIASKRTGR 236
>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor
60S, translation, large ribosomal subunit; 3.52A
{Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A
Length = 264
Score = 186 bits (474), Expect = 3e-59
Identities = 50/155 (32%), Positives = 73/155 (47%), Gaps = 11/155 (7%)
Query: 69 QIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKIL-KEPTSSFCLVRLPSGNEK 127
+G+ +P+ + GT++ N+E G G RA+G A I+ +RLPSG K
Sbjct: 98 AVGNVLPINRIPEGTVVCNVEEKVGDRGTFSRASGCYATIIGHSEDGDKTRIRLPSGARK 157
Query: 128 LIDTRCRATIGTVSNPSHGAKKLRKAGQS-----RWLGRRPVVRGVAMNPVDHPHGGGEG 182
I CRAT+G V+ K + KAG R P VRGVAMNPVDHPHGGG
Sbjct: 158 TIPGSCRATVGIVAGGGRTDKPILKAGNQFHKYARKRKSWPRVRGVAMNPVDHPHGGGNH 217
Query: 183 RSKSSGNHGRCSLTPWGKPCKSGYKTASPKKKKKL 217
+ G +++ W + + ++ +
Sbjct: 218 Q--HIG--HPATVSKWASAGQ-KVGLRAARRTGLV 247
>3iz5_B 60S ribosomal protein L2 (L2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_B 2zkr_a
Length = 261
Score = 183 bits (468), Expect = 2e-58
Identities = 47/153 (30%), Positives = 76/153 (49%), Gaps = 8/153 (5%)
Query: 69 QIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKIL-KEPTSSFCLVRLPSGNEK 127
IG+ +P+ + G ++ N+E + G G RA+G A ++ P + ++LPSG +K
Sbjct: 97 SIGNVLPIRSVPEGAVVCNVEHHVGDRGVFARASGDYAIVISHNPDNGTSRIKLPSGAKK 156
Query: 128 LIDTRCRATIGTVSNPSHGAKKLRKAGQS--RWLGRR---PVVRGVAMNPVDHPHGGGEG 182
++ + CRA IG V+ K + KAG + ++ +R P VRGVAMNPV+HPHGGG
Sbjct: 157 IVPSSCRAMIGQVAGGGRTEKPMLKAGNAYHKYRVKRNCWPKVRGVAMNPVEHPHGGGNH 216
Query: 183 RSKSSGNHGRCSLTPWGKPCKSGYKTASPKKKK 215
+ P G+ + +
Sbjct: 217 QH-IGHASTVRRDAPPGQKVG-LIAARRTGRLR 247
>3jyw_B 60S ribosomal protein L2; eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
3izc_B 3izs_B 3o58_B 3o5h_B 3u5e_A 3u5i_A 1s1i_B
Length = 243
Score = 178 bits (454), Expect = 2e-56
Identities = 49/151 (32%), Positives = 73/151 (48%), Gaps = 11/151 (7%)
Query: 69 QIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAKIL-KEPTSSFCLVRLPSGNEK 127
+G+ +PL + GTI+ N+E PG G L RA+G I+ P + VRLPSG +K
Sbjct: 96 NVGNVLPLGSVPEGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKK 155
Query: 128 LIDTRCRATIGTVSNPSHGAKKLRKAGQSRWL-----GRRPVVRGVAMNPVDHPHGGGEG 182
+I + R IG ++ K L KAG++ P RGVAMNPVDHPHGGG
Sbjct: 156 VISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNH 215
Query: 183 RSKSSGNHGRCSLTPWGKPCKSGYKTASPKK 213
+ +++ + + ++
Sbjct: 216 QHIG----KASTISRGAVSGQ-KAGLIAARR 241
>1giy_D 50S ribosomal protein L2; ribosome assembly, protein synthesis,
LIFE; 5.50A {Thermus thermophilus} SCOP: i.1.1.1 PDB:
1ml5_d* 1yl3_D 2b66_D 2b9n_D 2b9p_D
Length = 178
Score = 169 bits (430), Expect = 9e-54
Identities = 63/137 (45%), Positives = 83/137 (60%), Gaps = 11/137 (8%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
PK V +IM DI +IG+ +PL + +GT++HNIE+ PG+GG+LVRAAGTSA+
Sbjct: 47 PKNLKVGMEIMSG-PDADI--KIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQ 103
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAGQSRWLGRR---- 162
+L KE + +VRL SG ++I +CRAT+G V N K KAG +
Sbjct: 104 VLGKE--GKYVIVRLASGEVRMILGKCRATVGEVGNGGRTDKPFVKAGNKHHKMKARGTK 161
Query: 163 -PVVRGVAMNPVDHPHG 178
P VRGVAMN VDHP G
Sbjct: 162 WPNVRGVAMNAVDHPFG 178
>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_B
Length = 136
Score = 117 bits (296), Expect = 5e-34
Identities = 35/112 (31%), Positives = 56/112 (50%), Gaps = 9/112 (8%)
Query: 48 PKKETVRDKIM----RQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAG 103
+ D I+ V + G PL + +GT+I+N+E PG+G + +RAAG
Sbjct: 29 TENMQAGDTILNSNHIGRMAVAA--REGDAHPLGALPVGTLINNVESEPGRGAQYIRAAG 86
Query: 104 TSAKIL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSNPSHGAKKLRKAG 154
T +L K + +++LPS + + C AT+G VSN H + + KAG
Sbjct: 87 TCGVLLRKV--NGTAIIQLPSKRQMQVLETCVATVGRVSNVDHNKRVIGKAG 136
>1rl2_A Protein (ribosomal protein L2); RNA-binding domain,
peptidyltransferease center, X-RAY diffraction; 2.30A
{Geobacillus stearothermophilus} SCOP: b.34.5.3 b.40.4.5
PDB: 1c04_A 487d_I
Length = 137
Score = 105 bits (264), Expect = 3e-29
Identities = 46/96 (47%), Positives = 65/96 (67%), Gaps = 6/96 (6%)
Query: 48 PKKETVRDKIMRQMAHVDINSQIGSCMPLACMRIGTIIHNIEVNPGQGGKLVRAAGTSAK 107
PK V +IM DI +IG+ +PL + +GT++HNIE+ PG+GG+LVRAAGTSA+
Sbjct: 47 PKNLKVGMEIM-SGPDADI--KIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQ 103
Query: 108 IL-KEPTSSFCLVRLPSGNEKLIDTRCRATIGTVSN 142
+L KE + +VRL SG ++I +CRAT+G V N
Sbjct: 104 VLGKE--GKYVIVRLASGEVRMILGKCRATVGEVGN 137
>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 = 31.0 bits (69), Expect = 0.30
Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 14/83 (16%)
Query: 14 FNRLLCPSVLNNNTTYRYQSSETELVGDPSKQ---EKPKKETVRDKIMRQMAHV------ 64
FN L C +L TT R++ L + + D++ +
Sbjct: 262 FN-LSCKILL---TT-RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316
Query: 65 DINSQIGSCMPLACMRIGTIIHN 87
D+ ++ + P I I +
Sbjct: 317 DLPREVLTTNPRRLSIIAESIRD 339
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
0.316 0.131 0.397
Gapped
Lambda K H
0.267 0.0485 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,223,797
Number of extensions: 180304
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 290
Number of HSP's successfully gapped: 15
Length of query: 219
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 129
Effective length of database: 4,188,903
Effective search space: 540368487
Effective search space used: 540368487
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.6 bits)