RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13418
(159 letters)
>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_B
Length = 136
Score = 78.4 bits (194), Expect = 1e-19
Identities = 52/112 (46%), Positives = 77/112 (68%)
Query: 48 RTANLALVGSGDFLKLILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIVC 107
R+A++ALV G + I+ATENM+AGD + S I R+ V A+EGDA+P+GALP+G+++
Sbjct: 10 RSADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGDAHPLGALPVGTLIN 69
Query: 108 CVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
VE PG GA Y RAAG L+R ++ ++QLPSK ++ V + C+A V +
Sbjct: 70 NVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETCVATVGR 121
>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 = 80.7 bits (200), Expect = 2e-19
Identities = 41/141 (29%), Positives = 62/141 (43%), Gaps = 12/141 (8%)
Query: 20 DFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDFLK-LILATENMKAGDILKT 78
+ D V+ I PA R+A +A V D + LILA E + GD L+
Sbjct: 30 HRKVEDGDVIAG---TVVDIEHDPA---RSAPVAAVEFEDGDRRLILAPEGVGVGDELQV 83
Query: 79 SMFIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHDRVV 138
+ G+ P+ +P G VC VE PG+G +ARA+G + L+ + V
Sbjct: 84 G---VSAEI--APGNTLPLAEIPEGVPVCNVESSPGDGGKFARASGVNAQLLTHDRNVAV 138
Query: 139 LQLPSKHEVAVDKHCMAVVAQ 159
++LPS +D C A +
Sbjct: 139 VKLPSGEMKRLDPQCRATIGV 159
>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 = 78.8 bits (195), Expect = 8e-19
Identities = 30/120 (25%), Positives = 53/120 (44%), Gaps = 13/120 (10%)
Query: 48 RTANLALVGSGD------FLKLILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALP 101
R A LA V D ++ +A E + G + + + G+ P+G++P
Sbjct: 53 RGAPLAKVVFRDPYKYRLREEIFIANEGVHTGQFI---YAGKKASL--NVGNVLPLGSVP 107
Query: 102 MGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHD--RVVLQLPSKHEVAVDKHCMAVVAQ 159
G+IV VE+ PG+ ARA+GN ++ D + ++LPS + + V+
Sbjct: 108 EGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGV 167
>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 = 79.2 bits (196), Expect = 8e-19
Identities = 32/120 (26%), Positives = 53/120 (44%), Gaps = 13/120 (10%)
Query: 48 RTANLALVGSGDFLK------LILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALP 101
R A LA V + L +A E M G + R + G+ P+ ++P
Sbjct: 54 RGAPLAKVTFRHPFRYKHQKELFVAAEGMYTGQFVYCG---RRATL--SIGNVLPIRSVP 108
Query: 102 MGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHD--RVVLQLPSKHEVAVDKHCMAVVAQ 159
G++VC VE G+ +ARA+G+ ++ D ++LPS + V C A++ Q
Sbjct: 109 EGAVVCNVEHHVGDRGVFARASGDYAIVISHNPDNGTSRIKLPSGAKKIVPSSCRAMIGQ 168
>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 = 77.6 bits (192), Expect = 3e-18
Identities = 29/120 (24%), Positives = 51/120 (42%), Gaps = 13/120 (10%)
Query: 48 RTANLALVGSGDFLK------LILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALP 101
R A LA V D + +A E +G + + + G+ P+ +P
Sbjct: 55 RGAPLAEVAFRDPYRYKTNKEHFIAAEGQYSGQYVYCG---LKAQI--AVGNVLPINRIP 109
Query: 102 MGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHD--RVVLQLPSKHEVAVDKHCMAVVAQ 159
G++VC VE+ G+ ++RA+G T++ D + ++LPS + C A V
Sbjct: 110 EGTVVCNVEEKVGDRGTFSRASGCYATIIGHSEDGDKTRIRLPSGARKTIPGSCRATVGI 169
>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 = 66.7 bits (164), Expect = 5e-15
Identities = 35/113 (30%), Positives = 58/113 (51%), Gaps = 6/113 (5%)
Query: 48 RTANLALVGSGDFLK-LILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIV 106
R+AN+AL+ D K I+A +N+K G + + P + K G+A P+ +P+G++V
Sbjct: 27 RSANIALINYADGEKRYIIAPKNLKVGMEIMSG---PDADI--KIGNALPLENIPVGTLV 81
Query: 107 CCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
+E PG G RAAG S ++ V+++L S + C A V +
Sbjct: 82 HNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGE 134
>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 = 69.1 bits (170), Expect = 6e-15
Identities = 48/153 (31%), Positives = 72/153 (47%), Gaps = 13/153 (8%)
Query: 8 GGGIKEDIHWVHDFRRGPTDDSPPLEERVIQIIPSPAPTVRTANLALVGSGDFLK-LILA 66
GGG K + DF+R P I+ P+ R+A +AL+ D K I+A
Sbjct: 55 GGGHKRLYRII-DFKRWDKVGIPAKVAA-IEYDPN-----RSARIALLHYVDGEKRYIIA 107
Query: 67 TENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNS 126
+ ++ G + P P+ + G+A P+ +P+G++V VE P +GA ARAAG S
Sbjct: 108 PDGLQVGQQVVAG---PDAPI--QVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTS 162
Query: 127 CTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
+ D V+L+LPS V C A V
Sbjct: 163 AQIQGREGDYVILRLPSGELRKVHGECYATVGA 195
>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 = 67.5 bits (166), Expect = 2e-14
Identities = 38/113 (33%), Positives = 58/113 (51%), Gaps = 6/113 (5%)
Query: 48 RTANLALVGSGDFLKL-ILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIV 106
R+AN+ALV D + ILA + +KAGD +++ + K G+ P+ +P+GS V
Sbjct: 86 RSANIALVLYKDGERRYILAPKGLKAGDQIQSG---VDAAI--KPGNTLPMRNIPVGSTV 140
Query: 107 CCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
VE PG+G AR+AG +V V L+L S V+ C A + +
Sbjct: 141 HNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGE 193
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 269
Score = 67.5 bits (166), Expect = 2e-14
Identities = 35/113 (30%), Positives = 52/113 (46%), Gaps = 6/113 (5%)
Query: 48 RTANLALVGSGDFLK-LILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIV 106
R A + L+ GD K IL GD + + +P+ K G+A P+ +P+G+ +
Sbjct: 83 RNAYICLIHYGDGEKRYILHPRGAIIGDTIVSG---TEVPI--KMGNALPLTDMPLGTAI 137
Query: 107 CCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
+E G G ARAAG L+ L+LPS + K+C A V Q
Sbjct: 138 HNIEITLGRGGQLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATVGQ 190
>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 = 65.2 bits (160), Expect = 4e-14
Identities = 35/113 (30%), Positives = 58/113 (51%), Gaps = 6/113 (5%)
Query: 48 RTANLALVGSGDFLK-LILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVGALPMGSIV 106
R+AN+AL+ D K I+A +N+K G + + P + K G+A P+ +P+G++V
Sbjct: 27 RSANIALINYADGEKRYIIAPKNLKVGMEIMSG---PDADI--KIGNALPLENIPVGTLV 81
Query: 107 CCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQLPSKHEVAVDKHCMAVVAQ 159
+E PG G RAAG S ++ V+++L S + C A V +
Sbjct: 82 HNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGE 134
>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 = 28.3 bits (62), Expect = 1.2
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 8/64 (12%)
Query: 9 GGIKEDIHWVHDFRRGPTDDSPPLEERVIQII---PSPAPTVRTANLALVGSGDFLKLIL 65
G I + + ++ D+ P E V I+ P NL D L++ L
Sbjct: 518 GSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEE-----NLICSKYTDLLRIAL 572
Query: 66 ATEN 69
E+
Sbjct: 573 MAED 576
>2zf9_A SCAE cell-surface anchored scaffoldin protein; dockerin-binding
module, anchoring module, alpha helix, beta structural
protein; HET: MSE; 1.95A {Ruminococcus flavefaciens}
Length = 194
Score = 26.0 bits (56), Expect = 5.8
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 56 GSGDFLKLILATENMKAGDILKTSMFIPRIPVRAKEGDAYPVG 98
+ F +T N K G + F+ ++P A+ GD Y V
Sbjct: 107 DNSFFTATGSSTNNGKDGVLW---SFVLQVPADAQPGDKYDVQ 146
>2lon_A HIG1 domain family member 1B; membrane protein, helical bundle; NMR
{Homo sapiens}
Length = 99
Score = 25.3 bits (55), Expect = 6.1
Identities = 9/60 (15%), Positives = 21/60 (35%), Gaps = 7/60 (11%)
Query: 81 FIPRIPVRAKEGDAYPVGALPMGSIVCCVEKFPGEGAHYARAAGNSCTLVRTLHDRVVLQ 140
++ + +E P+G + + R+ G++ + +H RV Q
Sbjct: 17 VSEKLLRKTRESPLVPIGLGGCLVVAAY-------RIYRLRSRGSTKMSIHLIHTRVAAQ 69
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 25.8 bits (57), Expect = 7.7
Identities = 6/31 (19%), Positives = 14/31 (45%), Gaps = 10/31 (32%)
Query: 15 IHWVHDFRRGPTDDSPPLEE-----RVIQII 40
+H+++D RGP +E + ++
Sbjct: 154 LHYLNDPERGPV-----VESVTIRAKRRNLL 179
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 0.139 0.422
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,548,626
Number of extensions: 148851
Number of successful extensions: 261
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 30
Length of query: 159
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,300,587
Effective search space: 313942851
Effective search space used: 313942851
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: 53 (24.1 bits)