RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 037430
(198 letters)
>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 = 295 bits (758), Expect = e-102
Identities = 175/198 (88%), Positives = 191/198 (96%)
Query: 1 MGRVIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLAR 60
MGRVIRAQRKGAGSVFKSHTHHRKGPA+FRSLDFGERNGYLKGVV +IIHDPGRGAPLA+
Sbjct: 1 MGRVIRAQRKGAGSVFKSHTHHRKGPARFRSLDFGERNGYLKGVVTDIIHDPGRGAPLAK 60
Query: 61 VTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHV 120
VTFRHPFRY QKELF+AAEGMYTGQFVYCG++ATL +GNVLP+RS+PEGAVVCNVEHHV
Sbjct: 61 VTFRHPFRYKHQKELFVAAEGMYTGQFVYCGRRATLSIGNVLPIRSVPEGAVVCNVEHHV 120
Query: 121 GDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLL 180
GDRGV ARASGDYA++ISHNPDN T+R+KLPSGAKKI+PS CRAMIGQVAGGGRTEKP+L
Sbjct: 121 GDRGVFARASGDYAIVISHNPDNGTSRIKLPSGAKKIVPSSCRAMIGQVAGGGRTEKPML 180
Query: 181 KAGNAYHKFRVKRNCWPK 198
KAGNAYHK+RVKRNCWPK
Sbjct: 181 KAGNAYHKYRVKRNCWPK 198
>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 = 289 bits (743), Expect = e-100
Identities = 127/197 (64%), Positives = 162/197 (82%)
Query: 2 GRVIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARV 61
GRVIR QRKGAGS+F SHT R+G A+ R+LD+ ER+GY++G+V +I+HD GRGAPLA+V
Sbjct: 1 GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKV 60
Query: 62 TFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVG 121
FR P++Y ++E+FIA EG++TGQF+Y GKKA+L VGNVLP+ S+PEG +V NVE G
Sbjct: 61 VFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPG 120
Query: 122 DRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLK 181
DRG LARASG+Y +II HNPD + TRV+LPSGAKK+I S R +IG +AGGGR +KPLLK
Sbjct: 121 DRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLK 180
Query: 182 AGNAYHKFRVKRNCWPK 198
AG A+HK+R+KRN WPK
Sbjct: 181 AGRAFHKYRLKRNSWPK 197
>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 = 276 bits (708), Expect = 5e-95
Identities = 127/199 (63%), Positives = 151/199 (75%), Gaps = 1/199 (0%)
Query: 1 MGRVIRAQRKG-AGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLA 59
MGRVIRAQRKG A V+KSH R PAQ+R DF ER GY++G + +I+H+PGRGAPLA
Sbjct: 1 MGRVIRAQRKGRANGVYKSHKSGRIAPAQYRVYDFAERQGYIRGCIRDIVHEPGRGAPLA 60
Query: 60 RVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHH 119
V FR P+RY KE FIAAEG Y+GQ+VYCG KA + VGNVLP+ IPEG VVCNVE
Sbjct: 61 EVAFRDPYRYKTNKEHFIAAEGQYSGQYVYCGLKAQIAVGNVLPINRIPEGTVVCNVEEK 120
Query: 120 VGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPL 179
VGDRG +RASG YA II H+ D D TR++LPSGA+K IP CRA +G VAGGGRT+KP+
Sbjct: 121 VGDRGTFSRASGCYATIIGHSEDGDKTRIRLPSGARKTIPGSCRATVGIVAGGGRTDKPI 180
Query: 180 LKAGNAYHKFRVKRNCWPK 198
LKAGN +HK+ KR WP+
Sbjct: 181 LKAGNQFHKYARKRKSWPR 199
>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 = 242 bits (620), Expect = 5e-82
Identities = 85/199 (42%), Positives = 112/199 (56%), Gaps = 11/199 (5%)
Query: 1 MGRVIRAQRKGAG-SVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLA 59
MGR I+ QR+G G S F++ +H K + R ++ + G V +I HDP R AP+A
Sbjct: 1 MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVE---DGDVIAGTVVDIEHDPARSAPVA 57
Query: 60 RVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHH 119
V F + L +A EG+ G + G A + GN LP+ IPEG VCNVE
Sbjct: 58 AVEFEDG-----DRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESS 112
Query: 120 VGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPL 179
GD G ARASG A +++H D + VKLPSG K + CRA IG VAGGGRT+KP
Sbjct: 113 PGDGGKFARASGVNAQLLTH--DRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPF 170
Query: 180 LKAGNAYHKFRVKRNCWPK 198
+KAGN +HK + + WP
Sbjct: 171 VKAGNKHHKMKARGTKWPN 189
>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 = 86.4 bits (215), Expect = 3e-22
Identities = 48/144 (33%), Positives = 76/144 (52%), Gaps = 11/144 (7%)
Query: 28 QFRSLDFGERNGY-LKGVVAEIIHDPGRGAPLARVTFRH-PFRYMKQKELFIAAEGMYTG 85
Q+R +DF +R+ + G VA I +DP R A +A + + RY+ IA + + G
Sbjct: 1 QYRIIDF-KRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYI------IAPKNLKVG 53
Query: 86 QFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDT 145
+ G A + +GN LP+ +IP G +V N+E G G L RA+G A ++ +
Sbjct: 54 MEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGK--EGKY 111
Query: 146 TRVKLPSGAKKIIPSGCRAMIGQV 169
V+L SG ++I CRA +G+V
Sbjct: 112 VIVRLASGEVRMILGKCRATVGEV 135
>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 = 87.2 bits (217), Expect = 4e-22
Identities = 62/173 (35%), Positives = 95/173 (54%), Gaps = 11/173 (6%)
Query: 28 QFRSLDFGERNGY-LKGVVAEIIHDPGRGAPLARVTFRH-PFRYMKQKELFIAAEGMYTG 85
Q+R +DF +R+ + G VA I +DP R A +A + + RY+ IA + + G
Sbjct: 1 QYRIIDF-KRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYI------IAPKNLKVG 53
Query: 86 QFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDT 145
+ G A + +GN LP+ +IP G +V N+E G G L RA+G A ++ +
Sbjct: 54 MEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGK--EGKY 111
Query: 146 TRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLKAGNAYHKFRVKRNCWPK 198
V+L SG ++I CRA +G+V GGRT+KP +KAGN +HK + + WP
Sbjct: 112 VIVRLASGEVRMILGKCRATVGEVGNGGRTDKPFVKAGNKHHKMKARGTKWPN 164
>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 = 84.5 bits (210), Expect = 3e-20
Identities = 52/159 (32%), Positives = 80/159 (50%), Gaps = 12/159 (7%)
Query: 28 QFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRH-PFRYMKQKELFIAAEGMYTGQ 86
+R +DF + VV + +DP R A +A V ++ RY+ +A +G+ G
Sbjct: 60 AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYI------LAPKGLKAGD 113
Query: 87 FVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTT 146
+ G A + GN LP+R+IP G+ V NVE G G LAR++G Y I++ D
Sbjct: 114 QIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVAR--DGAYV 171
Query: 147 RVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLKAGNA 185
++L SG + + + CRA +G+V G E L G A
Sbjct: 172 TLRLRSGEMRKVEADCRATLGEV---GNAEHMLRVLGKA 207
>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_B
Length = 136
Score = 80.3 bits (199), Expect = 7e-20
Identities = 36/146 (24%), Positives = 59/146 (40%), Gaps = 16/146 (10%)
Query: 45 VAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQFVYCGKK-----ATLMVG 99
V ++ +DP R A +A V R++ IA E M G + G
Sbjct: 1 VIQVRYDPCRSADIALVAGGSRKRWI------IATENMQAGDTILNSNHIGRMAVAAREG 54
Query: 100 NVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIP 159
+ P+ ++P G ++ NVE G RA+G V++ N T ++LPS + +
Sbjct: 55 DAHPLGALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRK--VNGTAIIQLPSKRQMQVL 112
Query: 160 SGCRAMIGQVAGGGRTEKPLLKAGNA 185
C A +G+V + G A
Sbjct: 113 ETCVATVGRV---SNVDHNKRVIGKA 135
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 269
Score = 82.9 bits (206), Expect = 9e-20
Identities = 47/157 (29%), Positives = 77/157 (49%), Gaps = 9/157 (5%)
Query: 28 QFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRH-PFRYMKQKELFIAAEGMYTGQ 86
+R +DF + G + I +DP R A + + + RY+ + G G
Sbjct: 57 LYRKIDFRRNEKDIYGKIVTIEYDPNRNAYICLIHYGDGEKRYI------LHPRGAIIGD 110
Query: 87 FVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDTT 146
+ G + + +GN LP+ +P G + N+E +G G LARA+G A +I+ + +
Sbjct: 111 TIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGRGGQLARAAGAVAKLIAK--EGKSA 168
Query: 147 RVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLKAG 183
+KLPSG ++I C A +GQV G +K L +AG
Sbjct: 169 TLKLPSGEVRLISKNCSATVGQVGNVGVNQKRLGRAG 205
>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 = 82.2 bits (204), Expect = 3e-19
Identities = 53/160 (33%), Positives = 75/160 (46%), Gaps = 13/160 (8%)
Query: 28 QFRSLDFGERNGY-LKGVVAEIIHDPGRGAPLARVTFRH-PFRYMKQKELFIAAEGMYTG 85
+R +DF + + VA I +DP R A +A + + RY+ IA +G+ G
Sbjct: 61 LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYI------IAPDGLQVG 114
Query: 86 QFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVGDRGVLARASGDYAVIISHNPDNDT 145
Q V G A + VGN LP+R IP G VV VE LARA+G A I + D
Sbjct: 115 QQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGR--EGDY 172
Query: 146 TRVKLPSGAKKIIPSGCRAMIGQVAGGGRTEKPLLKAGNA 185
++LPSG + + C A +G V G + + G A
Sbjct: 173 VILRLPSGELRKVHGECYATVGAV---GNADHKNIVLGKA 209
>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 = 33.1 bits (75), Expect = 0.055
Identities = 18/99 (18%), Positives = 30/99 (30%), Gaps = 30/99 (30%)
Query: 16 FKSHTHHRKGPAQFRSL------DFGERNGYLKG-----VVAEIIHDPGRGAP------- 57
+ S QF + +F E YL+G + A+++ +
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEF-ENC-YLEGNDIHALAAKLLQENDTTLVKTKELIK 124
Query: 58 ---LARVTFRHPFRYMKQKELFIAAE----GMYT---GQ 86
AR+ + PF LF A + GQ
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ 163
>3rhg_A Putative phophotriesterase; hydrolase, amidohydrolase, zinc binding
site, enzyme functio initiative, EFI; HET: SO4; 1.53A
{Proteus mirabilis}
Length = 365
Score = 27.0 bits (59), Expect = 3.8
Identities = 17/126 (13%), Positives = 32/126 (25%), Gaps = 19/126 (15%)
Query: 4 VIRAQRKGAGSVFKSHTHHRKGPAQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTF 63
AQ + H + G A+++
Sbjct: 184 AALAQNNNPYASMNIHMPGWQRRGDEVLDILLTEM----------------GCDPAKISL 227
Query: 64 RHPFRYMKQKE--LFIAAEGMYTGQFVYCGKKATLMVGNVLPVRSIPEGAVVCNVEHHVG 121
H K + + G++ +F G + P AV +E G
Sbjct: 228 AHSDPSGKDIDYQCKMLDRGVWL-EFDMIGLDISFPKEGAAPSVMDTVEAVATLIERGYG 286
Query: 122 DRGVLA 127
++ VL+
Sbjct: 287 NQIVLS 292
>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 = 27.1 bits (59), Expect = 4.3
Identities = 10/62 (16%), Positives = 15/62 (24%), Gaps = 17/62 (27%)
Query: 122 DRGVLARASGDYAVIISHNPDNDT---------------TRV-KLPSGAKKIIPSGCRAM 165
+ V S IS + + T R LP P ++
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL-SI 332
Query: 166 IG 167
I
Sbjct: 333 IA 334
>1hpg_A Glutamic acid specific protease; serine protease,
hydrolase-hydrolase inhibitor complex; 1.50A
{Streptomyces griseus} SCOP: b.47.1.1
Length = 187
Score = 26.0 bits (57), Expect = 7.8
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 119 HVGDRGVLARASGDYAVIISHNPDNDTTRVKLPSGAKKIIPSGCRAMIGQ-VAGGGRT 175
VG R + + DY ++ + + V L +G+ + I S A++GQ + G T
Sbjct: 49 VVGVREGTSFPTNDYGIVRYTDGSSPAGTVDLYNGSTQDISSAANAVVGQAIKKSGST 106
>4dnh_A Uncharacterized protein; structural genomics, PSI-biology, protein
structure initiati YORK structural genomics research
consortium; 2.50A {Sinorhizobium meliloti}
Length = 396
Score = 26.1 bits (57), Expect = 8.5
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 27 AQFRSLDFGERNGYLKGVVAEIIHDPGRGAPLARVTFRHPFRYMKQKELFIAAEGMYTGQ 86
A +L G + + + +P PL+R F+ P R+ K +F+A
Sbjct: 288 AALEALGSGRNGEFFE------LLEPTV--PLSRHIFKAPTRFYKTGVVFLAYLNGLQDH 339
Query: 87 FVYCGKKATLMVGNVLPVRSIP 108
FV M+G RS+
Sbjct: 340 FV--------MIGGQQSARSLV 353
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 0.139 0.430
Gapped
Lambda K H
0.267 0.0547 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,260,596
Number of extensions: 201465
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 22
Length of query: 198
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 109
Effective length of database: 4,216,824
Effective search space: 459633816
Effective search space used: 459633816
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: 55 (25.4 bits)