RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13118
(286 letters)
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 176 bits (446), Expect = 1e-52
Identities = 113/143 (79%), Positives = 128/143 (89%)
Query: 16 VGVARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGH 75
+ ARPLI+VYSEK E +G+ VTLP+VFKAPIRPD+VNFVH NL KN+RQPYAVS+ AGH
Sbjct: 1 MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH 60
Query: 76 QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQR 135
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCR GRMFAPT+ WRRWHR+VN Q+
Sbjct: 61 QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK 120
Query: 136 RYAMVSAIAASSVPALVMSKGHQ 158
RYA+ SA+A S+PALVMSKGH+
Sbjct: 121 RYAICSALACLSLPALVMSKGHR 143
Score = 140 bits (353), Expect = 6e-39
Identities = 96/129 (74%), Positives = 112/129 (86%)
Query: 155 KGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNV 214
GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCR GRMFAPT+ WRRWHR+VN
Sbjct: 58 AGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNT 117
Query: 215 NQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAW 274
Q+RYA+ SA+A S+PALVMSKGH I++VPE PLVV DK++ YKKTK+A + L ++KAW
Sbjct: 118 TQKRYAICSALACLSLPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAW 177
Query: 275 NDVLKVQSS 283
ND+ KV +S
Sbjct: 178 NDIKKVYAS 186
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C
1s1i_D 3jyw_D
Length = 362
Score = 167 bits (423), Expect = 9e-50
Identities = 92/141 (65%), Positives = 116/141 (82%)
Query: 18 VARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQT 77
++RP +TV+S E T + LP+VF APIRPD+V+ V +++KN RQ YAVS+ AGHQT
Sbjct: 1 MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT 60
Query: 78 SAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRY 137
SAESWGTGRAVARIPRV GGGT RSGQGAFGNMCR GRMFAPT+ WR+W+ KVN N++RY
Sbjct: 61 SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY 120
Query: 138 AMVSAIAASSVPALVMSKGHQ 158
A SAIAA++V +LV+++GH+
Sbjct: 121 ATASAIAATAVASLVLARGHR 141
Score = 133 bits (336), Expect = 6e-37
Identities = 82/130 (63%), Positives = 103/130 (79%)
Query: 154 SKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVN 213
GHQTSAESWGTGRAVARIPRV GGGT RSGQGAFGNMCR GRMFAPT+ WR+W+ KVN
Sbjct: 55 KAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVN 114
Query: 214 VNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKA 273
N++RYA SAIAA++V +LV+++GH ++ +PE PLVVS ++ +KTK+A L + A
Sbjct: 115 HNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGA 174
Query: 274 WNDVLKVQSS 283
+D+LKV S
Sbjct: 175 HSDLLKVLKS 184
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 161 bits (407), Expect = 6e-47
Identities = 93/143 (65%), Positives = 118/143 (82%), Gaps = 3/143 (2%)
Query: 19 ARPLITVYSEKNEPTGQ---TVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGH 75
RPL++V + + + ++ L VF+AP+RPDVV FVH+ LS N RQPYAVS+ AGH
Sbjct: 5 TRPLVSVKALEGDMATDNSSSLALAEVFRAPLRPDVVRFVHRLLSCNKRQPYAVSRRAGH 64
Query: 76 QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQR 135
QTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCR GRMFAPT+ WR+WHR+VNV+ R
Sbjct: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVNVHLR 124
Query: 136 RYAMVSAIAASSVPALVMSKGHQ 158
R A+ SA+AA+SVP+LV+++GH+
Sbjct: 125 RVAVASALAATSVPSLVLARGHR 147
Score = 131 bits (329), Expect = 1e-35
Identities = 83/128 (64%), Positives = 104/128 (81%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCR GRMFAPT+ WR+WHR+VNV+
Sbjct: 63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVNVH 122
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
RR A+ SA+AA+SVP+LV+++GH I+ VPE PLV+SD + +KT QA L ++ A+
Sbjct: 123 LRRVAVASALAATSVPSLVLARGHRIETVPELPLVISDSAESIEKTSQAIKILKQVGAYA 182
Query: 276 DVLKVQSS 283
D K + S
Sbjct: 183 DAEKAKDS 190
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_C 4a1c_C 4a1e_C
Length = 410
Score = 155 bits (392), Expect = 9e-45
Identities = 80/146 (54%), Positives = 103/146 (70%), Gaps = 6/146 (4%)
Query: 19 ARPLITVYSEKN--EPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDA--- 73
+RP I V+ K + T +TLP+VF APIR D+V+ V +L+KN +Q V
Sbjct: 3 SRPQIHVHDAKEANKQTATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRGT 62
Query: 74 -GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNV 132
G SAESWGTGRAVARIPRV G GTHRSGQ AFGN CR GRMFAP + +RR HR+VNV
Sbjct: 63 AGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVNV 122
Query: 133 NQRRYAMVSAIAASSVPALVMSKGHQ 158
NQ+R+A+ +A+AAS++ LV ++GH+
Sbjct: 123 NQKRHAVAAALAASALVPLVFARGHR 148
Score = 137 bits (345), Expect = 7e-38
Identities = 77/130 (59%), Positives = 99/130 (76%)
Query: 154 SKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVN 213
+ G SAESWGTGRAVARIPRV G GTHRSGQ AFGN CR GRMFAP + +RR HR+VN
Sbjct: 62 TAGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVN 121
Query: 214 VNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKA 273
VNQ+R+A+ +A+AAS++ LV ++GH I +V E P V D ++ Y+KTKQA FL R+ A
Sbjct: 122 VNQKRHAVAAALAASALVPLVFARGHRISNVQELPYVFDDSVESYEKTKQAVAFLKRVGA 181
Query: 274 WNDVLKVQSS 283
++DVL+V +
Sbjct: 182 YDDVLRVAET 191
>1vq8_C 50S ribosomal protein L4E; 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.22.1.1 PDB: 1k73_E*
1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E*
1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C
1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ...
Length = 246
Score = 135 bits (342), Expect = 5e-39
Identities = 40/135 (29%), Positives = 64/135 (47%), Gaps = 8/135 (5%)
Query: 23 ITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESW 82
T+Y G V LP VF+ P+R D++ + N +Q Y + AG +T AES+
Sbjct: 3 ATIYDLDGNTDG-EVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61
Query: 83 GTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSA 142
G+GR A +P++ G GR P + + +N +R+ A+ SA
Sbjct: 62 GSGRGQAHVPKLDGR-------ARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSA 114
Query: 143 IAASSVPALVMSKGH 157
+AA++ LV +GH
Sbjct: 115 LAATADADLVADRGH 129
Score = 112 bits (280), Expect = 7e-30
Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 8/130 (6%)
Query: 154 SKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVN 213
G +T AES+G+GR A +P++ G GR P + + +N
Sbjct: 51 YAGLRTPAESFGSGRGQAHVPKLDGRA-------RRVPQAVKGRSAHPPKTEKDRSLDLN 103
Query: 214 VNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKA 273
+R+ A+ SA+AA++ LV +GH D E P+VVSD ++ KT++ L +
Sbjct: 104 DKERQLAVRSALAATADADLVADRGHEF-DRDEVPVVVSDDFEDLVKTQEVVSLLEALDV 162
Query: 274 WNDVLKVQSS 283
D+ + +
Sbjct: 163 HADIDRADET 172
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
c.22.1.1
Length = 225
Score = 40.1 bits (94), Expect = 4e-04
Identities = 30/131 (22%), Positives = 44/131 (33%), Gaps = 26/131 (19%)
Query: 23 ITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAG--HQTSAE 80
+ + + K E G VF DV+ N R A +K G +
Sbjct: 3 VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62
Query: 81 SW---GTGRAVA---RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQ 134
W TGRA R P R G G + P R W +K+N
Sbjct: 63 PWPQKHTGRARHGSIRSPIWRHG----------------GVVHGPKP--RDWSKKLNKKM 104
Query: 135 RRYAMVSAIAA 145
++ A+ SA++
Sbjct: 105 KKLALRSALSV 115
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 39.1 bits (91), Expect = 0.001
Identities = 28/131 (21%), Positives = 44/131 (33%), Gaps = 26/131 (19%)
Query: 23 ITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAG--HQTSAE 80
+ + + E G+T VV+ +N R+ A + +
Sbjct: 55 LPILNFSGEKVGETFLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRK 114
Query: 81 SW---GTGRAVA---RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQ 134
+ TGRA P GG G +F P R W K+N +
Sbjct: 115 PYPQKKTGRARRGSQGSPLRPGG----------------GVIFGPKP--RDWTIKMNKKE 156
Query: 135 RRYAMVSAIAA 145
RR A+ +AIA+
Sbjct: 157 RRLALSTAIAS 167
Score = 28.7 bits (64), Expect = 2.0
Identities = 28/120 (23%), Positives = 38/120 (31%), Gaps = 38/120 (31%)
Query: 165 GTGRAVA---RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAM 221
TGRA P GGG +F P R W K+N +RR A+
Sbjct: 120 KTGRARRGSQGSPLRPGGG----------------VIFGPKP--RDWTIKMNKKERRLAL 161
Query: 222 VSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQ-EYKKTKQATIFLHRIKAWNDVLKV 280
+AIA++ V +V E KTK + R + K
Sbjct: 162 STAIASA---------------VGNSFVVEEFAENFEKPKTKDFIAAMQRWG-LDPAEKS 205
>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 = 31.5 bits (70), Expect = 0.14
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 10/35 (28%)
Query: 128 RKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAE 162
+K+ + + YA S PAL + + + E
Sbjct: 23 KKLQASLKLYA------DDSAPALAI----KATME 47
Score = 30.7 bits (68), Expect = 0.31
Identities = 7/27 (25%), Positives = 12/27 (44%), Gaps = 6/27 (22%)
Query: 210 RKVNVNQRRYAMVSAIAASSVPALVMS 236
+K+ + + YA S PAL +
Sbjct: 23 KKLQASLKLYA------DDSAPALAIK 43
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Length = 210
Score = 30.7 bits (70), Expect = 0.37
Identities = 24/118 (20%), Positives = 38/118 (32%), Gaps = 26/118 (22%)
Query: 36 TVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAG--HQTSAESW---GTGRAVA- 89
L + A I P ++ V + R+ A +K G + + W TGRA
Sbjct: 17 RRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHG 76
Query: 90 --RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAA 145
P GGG +F P R + + R+ + A+A
Sbjct: 77 DIGAPIFVGGG----------------VVFGPKP--RDYSYTLPKKVRKKGLAMAVAD 116
Score = 28.4 bits (64), Expect = 2.2
Identities = 19/117 (16%), Positives = 31/117 (26%), Gaps = 35/117 (29%)
Query: 165 GTGRAVA---RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAM 221
TGRA P GGG +F P R + + R+ +
Sbjct: 69 HTGRARHGDIGAPIFVGGG----------------VVFGPKP--RDYSYTLPKKVRKKGL 110
Query: 222 VSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWNDVL 278
A+A +G ++ +V KTK+ +
Sbjct: 111 AMAVADR------AREGKLL--------LVEAFAGVNGKTKEFLAWAKEAGLDGSES 153
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S
ribosomal protein L3; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_D
Length = 175
Score = 29.1 bits (66), Expect = 0.94
Identities = 20/123 (16%), Positives = 36/123 (29%), Gaps = 34/123 (27%)
Query: 165 GTGRAVA---RIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAM 221
GTGRA R P RGGG P R ++ + + R +
Sbjct: 36 GTGRARHGSIRSPLWRGGG----------------VAHGP-RGPTSYYYMLPMKVRALGL 78
Query: 222 VSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWNDVLKVQ 281
A+ +++ + ++ + T H + + VL V
Sbjct: 79 KVALTVK------LAQDDLH--------IMDSLELPTGDPQYLTELAHYRRWGDSVLLVD 124
Query: 282 SSG 284
+
Sbjct: 125 LTH 127
>1mdl_A Mandelate racemase; isomerase, mandelate pathway, magnesium; HET:
RMN SMN; 1.85A {Pseudomonas aeruginosa} SCOP: c.1.11.2
d.54.1.1 PDB: 1mdr_A* 3uxk_A* 3uxl_A* 1dtn_A* 1mra_A*
2mnr_A 1mns_A
Length = 359
Score = 29.5 bits (67), Expect = 1.1
Identities = 4/32 (12%), Positives = 9/32 (28%)
Query: 114 GRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAA 145
AP + ++ + + A A
Sbjct: 75 NEPLAPVSLEAMLAKRFCLAGYTGLIRMAAAG 106
Score = 29.5 bits (67), Expect = 1.1
Identities = 4/32 (12%), Positives = 9/32 (28%)
Query: 196 GRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAA 227
AP + ++ + + A A
Sbjct: 75 NEPLAPVSLEAMLAKRFCLAGYTGLIRMAAAG 106
>3toy_A Mandelate racemase/muconate lactonizing enzyme FA protein; enolase,
magnesium binding site, lyase; HET: P4C; 1.80A
{Bradyrhizobium SP} PDB: 3tte_A*
Length = 383
Score = 27.2 bits (61), Expect = 7.0
Identities = 4/32 (12%), Positives = 12/32 (37%)
Query: 114 GRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAA 145
G+ P + + K + + + A++
Sbjct: 98 GKALVPVDLMKAMDAKFRLLGWQGLVGMAVSG 129
Score = 27.2 bits (61), Expect = 7.0
Identities = 4/32 (12%), Positives = 12/32 (37%)
Query: 196 GRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAA 227
G+ P + + K + + + A++
Sbjct: 98 GKALVPVDLMKAMDAKFRLLGWQGLVGMAVSG 129
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 0.132 0.413
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: 4,380,534
Number of extensions: 254001
Number of successful extensions: 613
Number of sequences better than 10.0: 1
Number of HSP's gapped: 604
Number of HSP's successfully gapped: 31
Length of query: 286
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 193
Effective length of database: 4,105,140
Effective search space: 792292020
Effective search space used: 792292020
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: 57 (26.3 bits)