RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 027581
(221 letters)
>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 = 138 bits (350), Expect = 5e-41
Identities = 36/79 (45%), Positives = 50/79 (63%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ + N E G + ++ VF++ D++ R V QL+ R+ GT STKT EVSG G+K
Sbjct: 3 VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62
Query: 161 PWRQKGTGRARHGTLRGPQ 179
PW QK TGRARHG++R P
Sbjct: 63 PWPQKHTGRARHGSIRSPI 81
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 138 bits (349), Expect = 3e-40
Identities = 35/125 (28%), Positives = 53/125 (42%), Gaps = 3/125 (2%)
Query: 58 ASRKFSTTILTPDSSEGAFPSDLLLK---KTVLTPDITIGLHQDLVIPVTNFFNEDKGFM 114
S F ++ L S +L T + + +P+ NF E G
Sbjct: 9 LSLSFFSSSLFSSKSRNFSSKPILKLPSSSHSQTSLSLSIKSELIPLPILNFSGEKVGET 68
Query: 115 VLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGT 174
L + ++HR + L +++GT ST T +EV G G+KP+ QK TGRAR G+
Sbjct: 69 FLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGS 128
Query: 175 LRGPQ 179
P
Sbjct: 129 QGSPL 133
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 134 bits (340), Expect = 7e-40
Identities = 29/72 (40%), Positives = 46/72 (63%)
Query: 108 NEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGT 167
+ + + ++ F + ++H+VV A +QGT + KT +EV+G+GKKPWRQKGT
Sbjct: 6 KDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGT 65
Query: 168 GRARHGTLRGPQ 179
GRAR G+++ P
Sbjct: 66 GRARSGSIKSPI 77
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
1pny_C 1vor_F 1vou_F ...
Length = 205
Score = 128 bits (325), Expect = 1e-37
Identities = 28/63 (44%), Positives = 40/63 (63%)
Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
++ + ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG
Sbjct: 14 TIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRS 73
Query: 177 GPQ 179
P
Sbjct: 74 VPT 76
>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 = 127 bits (321), Expect = 7e-37
Identities = 38/79 (48%), Positives = 47/79 (59%), Gaps = 5/79 (6%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
IPV + G LA D I ++ VVRWQLAKR++GT STKT EV+ +G+K
Sbjct: 9 IPVLSP----SGRRELAAD-LPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRK 63
Query: 161 PWRQKGTGRARHGTLRGPQ 179
W QK TGRARHG + P
Sbjct: 64 IWPQKHTGRARHGDIGAPI 82
>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 = 112 bits (283), Expect = 1e-31
Identities = 26/49 (53%), Positives = 33/49 (67%)
Query: 131 HRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ 179
H+V WQ ++ TKT +EV G G+KPW QKGTGRARHG++R P
Sbjct: 1 HQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPL 49
>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 = 84.3 bits (208), Expect = 5e-20
Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 11/85 (12%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHS-----TKTISEVS 155
+ + G + L DVF+ P+R D+I + VR A R+Q S +T +E
Sbjct: 3 ATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61
Query: 156 GTGK-KPWRQKGTGRARHGTLRGPQ 179
G+G+ + K GRAR R PQ
Sbjct: 62 GSGRGQAHVPKLDGRAR----RVPQ 82
>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 = 82.9 bits (204), Expect = 6e-19
Identities = 22/89 (24%), Positives = 31/89 (34%), Gaps = 8/89 (8%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQG-----THSTKTISEVS 155
+ V + E + VF PIR DI+H V ++Q +T +E
Sbjct: 6 VTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESW 65
Query: 156 GTGKKPW---RQKGTGRARHGTLRGPQGW 181
GTG+ R G G R G
Sbjct: 66 GTGRAVARIPRVGGGGTGRSGQGAFGNMC 94
>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 = 72.2 bits (176), Expect = 4e-15
Identities = 19/94 (20%), Positives = 29/94 (30%), Gaps = 13/94 (13%)
Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGT-- 157
V + + L VF PIR DI+H+V R+Q + + +G
Sbjct: 9 VHDAKEANKQTATKLTLP-AVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRGTAGMGH 67
Query: 158 ----------GKKPWRQKGTGRARHGTLRGPQGW 181
+ R G+G R G
Sbjct: 68 SAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQC 101
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 69.5 bits (169), Expect = 4e-14
Identities = 21/91 (23%), Positives = 30/91 (32%), Gaps = 10/91 (10%)
Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQG---------THSTKT 150
+I V + E G V VF PIR DI++ V +Q S ++
Sbjct: 7 LISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAES 66
Query: 151 ISEVSGTGKKPWRQKGTGRARHGTLRGPQGW 181
+ P R +G G R G
Sbjct: 67 WGTGRAVARIP-RVRGGGTHRSGQGAFGNMC 96
>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 = 66.0 bits (160), Expect = 7e-13
Identities = 17/71 (23%), Positives = 25/71 (35%), Gaps = 8/71 (11%)
Query: 119 DVFDVPIRKDIIHRVVRWQLAKRQQ-------GTHSTKTISEVSGTG-KKPWRQKGTGRA 170
+VF P+R D++ V R ++Q H T S +G + R G G
Sbjct: 30 EVFRAPLRPDVVRFVHRLLSCNKRQPYAVSRRAGHQTSAESWGTGRAVSRIPRVPGGGTH 89
Query: 171 RHGTLRGPQGW 181
R G
Sbjct: 90 RAGQGAFGNMC 100
>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 = 55.8 bits (134), Expect = 2e-09
Identities = 50/180 (27%), Positives = 73/180 (40%), Gaps = 52/180 (28%)
Query: 35 PP-DLYV---------ACSGDNLFPLKSGLSFLASRK--FST---TILTPDSSEGAFPSD 79
PP LY A SG + +S + F + RK FS + +P F S
Sbjct: 382 PPQSLYGLNLTLRKAKAPSGLD----QSRIPF-SERKLKFSNRFLPVASP------FHSH 430
Query: 80 LL------LKKTVLTPDITIGLHQDLVIPVTNFFN-EDKGFMVLAGDVFDVPIRKDIIHR 132
LL + K ++ +++ +D+ IPV + F+ D VL+G + + I II
Sbjct: 431 LLVPASDLINKDLVKNNVSFN-AKDIQIPVYDTFDGSD--LRVLSGSISER-IVDCIIRL 486
Query: 133 VVRWQLAKRQQGTHSTKTI-----SEVSGTGKKPWRQK-GTGRAR---HGTL-RGPQGWY 182
V+W+ + + TH I SG G R K GTG R GTL P Y
Sbjct: 487 PVKWETTTQFKATH----ILDFGPGGASGLGVLTHRNKDGTG-VRVIVAGTLDINPDDDY 541
Score = 40.8 bits (95), Expect = 2e-04
Identities = 28/181 (15%), Positives = 47/181 (25%), Gaps = 56/181 (30%)
Query: 26 SLTSRSIRS----PPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLL 81
+L+ S+ P + S L+ F T D E P++L+
Sbjct: 10 TLSHGSLEHVLLVPTASFFIAS-----QLQE--QFNKILPEPTEGFAADD-EPTTPAELV 61
Query: 82 LK----KTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQ 137
K + L +G ++ F L G DI H + +
Sbjct: 62 GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENC----YLEG--------NDI-HALAA-K 107
Query: 138 LAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYKVE 197
L + T ++ Y AR A++P K
Sbjct: 108 LLQENDTTLV----------------------KTKELIKN----YITARIMAKRPFDKKS 141
Query: 198 Q 198
Sbjct: 142 N 142
>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 = 36.0 bits (82), Expect = 0.008
Identities = 24/147 (16%), Positives = 47/147 (31%), Gaps = 33/147 (22%)
Query: 18 AFGRYESPSLTSRSIR-SPPDL-YVACSGDNLFPLKSGLSFLAS--RKFSTTI-----LT 68
E SL + + P DL + + P + LS +A R T +
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTTN---PRR--LSIIAESIRDGLATWDNWKHVN 351
Query: 69 PDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNED-----KGFMVL-AGDVFD 122
D S L VL P + L + F ++ +
Sbjct: 352 CDKLTTIIESSL----NVLEPAEYRKMFDRLSV-----FPPSAHIPTILLSLIWFDVIKS 402
Query: 123 VPIRKDIIHRVVRWQLAKRQ--QGTHS 147
+ +++++ ++ L ++Q + T S
Sbjct: 403 DVM--VVVNKLHKYSLVEKQPKESTIS 427
>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 = 32.2 bits (72), Expect = 0.056
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 8/36 (22%)
Query: 51 KSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTV 86
K L L + S + DS+ P+ L +K T+
Sbjct: 19 KQALKKLQA---SLKLYADDSA----PA-LAIKATM 46
>1iye_A Branched-chain amino acid aminotransferase; hexamer, PLP; HET: PGU;
1.82A {Escherichia coli} SCOP: e.17.1.1 PDB: 1i1l_A*
1i1m_A* 1iyd_A* 1i1k_A* 1a3g_A*
Length = 309
Score = 29.1 bits (66), Expect = 1.1
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 20/66 (30%)
Query: 39 YVA-CSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQ 97
Y++ +G+NLF +K G + TP + A P +T D I L +
Sbjct: 191 YISEGAGENLFEVKDG-----------VLFTPPFTSSALPG--------ITRDAIIKLAK 231
Query: 98 DLVIPV 103
+L I V
Sbjct: 232 ELGIEV 237
>3csw_A BCAT, putative branched-chain-amino-acid aminotransfera; TM0831,
putative branched-chain amino acid aminotransferase;
HET: PLP CIT; 2.15A {Thermotoga maritima MSB8}
Length = 285
Score = 27.1 bits (61), Expect = 4.0
Identities = 17/70 (24%), Positives = 22/70 (31%), Gaps = 28/70 (40%)
Query: 39 YVA-CSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDIT----I 93
V S N+F +K G ++TP G IT I
Sbjct: 173 QVCEGSFSNVFLVKEG-----------KLITPSLDSGILDG------------ITRENVI 209
Query: 94 GLHQDLVIPV 103
L + L IPV
Sbjct: 210 KLAKSLEIPV 219
>2vx2_A Enoyl-COA hydratase domain-containing protein 3; isomerase, fatty
acid metabolism, transit peptide, lipid Met crontonase,
mitochondrion, CAsp; 2.3A {Homo sapiens}
Length = 287
Score = 26.8 bits (60), Expect = 5.4
Identities = 7/30 (23%), Positives = 10/30 (33%), Gaps = 3/30 (10%)
Query: 49 PLKSGLSFLASRKFSTTILTPDSSEG--AF 76
L + S+ + D EG AF
Sbjct: 249 DLGTAYYL-TSQAMVDNLALRDGQEGITAF 277
>2zgi_A Putative 4-amino-4-deoxychorismate lyase; TTHA0621, PLP cofactor,
pyridoxal enzyme, structural NPPSFA; HET: PLP PGE; 1.93A
{Thermus thermophilus}
Length = 246
Score = 26.3 bits (59), Expect = 6.7
Identities = 4/34 (11%), Positives = 9/34 (26%), Gaps = 12/34 (35%)
Query: 39 YVA-CSGDNLFPLKSGLSFLASRKFSTTILTPDS 71
+V S + + G T+ +
Sbjct: 156 HVVDGSRTSPLLFREG-----------TLYLLEG 178
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
0.320 0.135 0.411
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: 3,398,898
Number of extensions: 193726
Number of successful extensions: 401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 394
Number of HSP's successfully gapped: 20
Length of query: 221
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 131
Effective length of database: 4,188,903
Effective search space: 548746293
Effective search space used: 548746293
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 (21.8 bits)
S2: 55 (25.6 bits)