RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780258|ref|YP_003064671.1| 50S ribosomal protein L2
[Candidatus Liberibacter asiaticus str. psy62]
(278 letters)
>2j01_D 50S ribosomal protein L2; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} (D:49-276)
Length = 228
Score = 224 bits (573), Expect = 7e-60
Identities = 123/229 (53%), Positives = 161/229 (70%), Gaps = 3/229 (1%)
Query: 49 VTMRFRGGGHKNRYRLVDFKRGE-YGLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAP 107
+T+RFRGGGHK YR++DFKR + G+ V +EYDPNR+A IAL+ Y +G YI+AP
Sbjct: 1 ITVRFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAP 60
Query: 108 QRLSVGDKVISSDSAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVE 167
L VG +V++ A ++ GNA+PLRFIPVG++VH VE++P KG +++R+AG+ A++
Sbjct: 61 DGLQVGQQVVAGPDA-PIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQG 119
Query: 168 RDRSRALLRLSSGEMRFVHSSCMASIGAVSNQDHSNVNHAKAGRARWLGMRSHVRGVAMN 227
R+ +LRL SGE+R VH C A++GAV N DH N+ KAGR+RWLG R HVRG AMN
Sbjct: 120 REGDYVILRLPSGELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMN 179
Query: 228 PVDHPHGGGEGKTSGGRNPCSPWGKLTKGKRTRS-NKSTDVFIARSRHK 275
PVDHPHGGGEG+ GR P SPWG TKG +TR K + FI R K
Sbjct: 180 PVDHPHGGGEGRAPRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK 228
>1rl2_A Protein (ribosomal protein L2); RNA-binding domain,
peptidyltransferease center, X-RAY diffraction; 2.30A
{Geobacillus stearothermophilus} (A:)
Length = 137
Score = 166 bits (421), Expect = 3e-42
Identities = 67/138 (48%), Positives = 103/138 (74%), Gaps = 1/138 (0%)
Query: 61 RYRLVDFKRGEYGLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVISSD 120
+YR++DFKR + G+ G V +EYDPNR+A IALI+Y++G YI+AP+ L VG ++ S
Sbjct: 1 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGXEIXSGP 60
Query: 121 SAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLSSG 180
A D+K GNA+PL IPVG++VHN+E+KPG+GGQ+ R+AG+ A+++ ++ ++RL+SG
Sbjct: 61 DA-DIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASG 119
Query: 181 EMRFVHSSCMASIGAVSN 198
E+R + C A++G V N
Sbjct: 120 EVRXILGKCRATVGEVGN 137
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
(E:62-198)
Length = 137
Score = 165 bits (419), Expect = 6e-42
Identities = 56/138 (40%), Positives = 90/138 (65%), Gaps = 1/138 (0%)
Query: 66 DFKRGEYGLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVISSDSAVDV 125
DF+R E + G + +EYDPNR A+I LI Y +G YIL P+ +GD ++S +
Sbjct: 1 DFRRNEKDIYGKIVTIEYDPNRNAYICLIHYGDGEKRYILHPRGAIIGDTIVSGTEV-PI 59
Query: 126 KPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLSSGEMRFV 185
K GNA+PL +P+G+ +HN+E+ G+GGQ++R+AG+ A+L+ ++ A L+L SGE+R +
Sbjct: 60 KMGNALPLTDMPLGTAIHNIEITLGRGGQLARAAGAVAKLIAKEGKSATLKLPSGEVRLI 119
Query: 186 HSSCMASIGAVSNQDHSN 203
+C A++G V N +
Sbjct: 120 SKNCSATVGQVGNVGVNQ 137
>1vq8_A 50S ribosomal protein L2P; ribosome 50S, protein-protein
complex, RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} (A:1-168)
Length = 168
Score = 160 bits (407), Expect = 1e-40
Identities = 59/165 (35%), Positives = 93/165 (56%), Gaps = 2/165 (1%)
Query: 40 KGGRNNTGRVTMRFRGGGHKNRYRLVDFKR-GEYGLEGVVKRLEYDPNRTAFIALISYSN 98
+ GR T FR H+ + L K + G V +E+DP R+A +A + + +
Sbjct: 4 RIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVEFED 63
Query: 99 GSLAYILAPQRLSVGDKVISSDSAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRS 158
G ILAP+ + VGD++ SA ++ PGN +PL IP G V NVE PG GG+ +R+
Sbjct: 64 GDRRLILAPEGVGVGDELQVGVSA-EIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFARA 122
Query: 159 AGSYARLVERDRSRALLRLSSGEMRFVHSSCMASIGAVSNQDHSN 203
+G A+L+ DR+ A+++L SGEM+ + C A+IG V+ ++
Sbjct: 123 SGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTD 167
>2zkr_a 60S ribosomal protein L8; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 1s1i_B (a:1-177)
Length = 177
Score = 157 bits (398), Expect = 1e-39
Identities = 43/176 (24%), Positives = 84/176 (47%), Gaps = 10/176 (5%)
Query: 35 RGLCSKGGRNNTGRVTMRFRGGGHKNRYRLVDFKRGEYGLEGVVKRLEYDPNRTAFIALI 94
+ G + R ++ R G + R VDF ++G+VK + +DP R A +A +
Sbjct: 4 VIRGQRKGAGSVFRAHVKHRKGAAR--LRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV 61
Query: 95 SYSNGS-----LAYILAPQRLSVGDKVISSDSAVDVKPGNAMPLRFIPVGSIVHNVEMKP 149
+ + +A + + G V A + GN +P+ +P G+IV +E KP
Sbjct: 62 VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKA-QLNIGNVLPVGTMPEGTIVCCLEEKP 120
Query: 150 GKGGQISRSAGSYARLVER--DRSRALLRLSSGEMRFVHSSCMASIGAVSNQDHSN 203
G G+++R++G+YA ++ + + ++L SG + + S+ A +G V+ +
Sbjct: 121 GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRID 176
>3i1n_C 50S ribosomal protein L2; ribosome structure, protein-RNA
complex, acetylation, ribonucleoprotein, ribosomal
protein, RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1vs8_C 2aw4_C 2awb_C 2vhm_C
2vhn_C 3bbx_C 3df2_C 3df4_C 1vs6_C 3i1p_C 3i1r_C 3i1t_C
3i20_C 3i22_C 2qam_C* 1p85_A 1p86_A 2i2v_C 2i2t_C*
2qao_C* ... (C:70-200,C:260-273)
Length = 145
Score = 155 bits (394), Expect = 4e-39
Identities = 74/130 (56%), Positives = 96/130 (73%), Gaps = 1/130 (0%)
Query: 73 GLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVISSDSAVDVKPGNAMP 132
G+ VV+RLEYDPNR+A IAL+ Y +G YILAP+ L GD++ S A +KPGN +P
Sbjct: 4 GIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDA-AIKPGNTLP 62
Query: 133 LRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLSSGEMRFVHSSCMAS 192
+R IPVGS VHNVEMKPGKGGQ++RSAG+Y ++V RD + LRL SGEMR V + C A+
Sbjct: 63 MRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRAT 122
Query: 193 IGAVSNQDHS 202
+G V N +H+
Sbjct: 123 LGEVGNAEHN 132
>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome,
large ribosomal subunit, ribosomal RNA; 12.10A {Bos
taurus} PDB: 3iy9_B (B:28-136)
Length = 109
Score = 132 bits (333), Expect = 7e-32
Identities = 38/109 (34%), Positives = 65/109 (59%), Gaps = 4/109 (3%)
Query: 106 APQRLSVGDKVISSDSA----VDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGS 161
A + + GD +++S+ V + G+A PL +PVG++++NVE +PG+G Q R+AG+
Sbjct: 1 ATENMQAGDTILNSNHIGRMAVAAREGDAHPLGALPVGTLINNVESEPGRGAQYIRAAGT 60
Query: 162 YARLVERDRSRALLRLSSGEMRFVHSSCMASIGAVSNQDHSNVNHAKAG 210
L+ + A+++L S V +C+A++G VSN DH+ KAG
Sbjct: 61 CGVLLRKVNGTAIIQLPSKRQMQVLETCVATVGRVSNVDHNKRVIGKAG 109
>1giy_D 50S ribosomal protein L2; ribosome assembly, protein
synthesis, LIFE; 5.50A {Thermus thermophilus} (D:57-140)
Length = 84
Score = 112 bits (281), Expect = 7e-26
Identities = 37/83 (44%), Positives = 59/83 (71%)
Query: 119 SDSAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLS 178
S D+K GNA+PL IPVG++VHN+E+KPG+GGQ+ R+AG+ A+++ ++ ++RL+
Sbjct: 2 SGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLA 61
Query: 179 SGEMRFVHSSCMASIGAVSNQDH 201
SGE+R + C A++G V N
Sbjct: 62 SGEVRMILGKCRATVGEVGNGGR 84
>1giy_D 50S ribosomal protein L2; ribosome assembly, protein
synthesis, LIFE; 5.50A {Thermus thermophilus} (D:1-56)
Length = 56
Score = 86.6 bits (215), Expect = 3e-18
Identities = 29/56 (51%), Positives = 43/56 (76%)
Query: 61 RYRLVDFKRGEYGLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKV 116
+YR++DFKR + G+ G V +EYDPNR+A IALI+Y++G YI+AP+ L VG ++
Sbjct: 1 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEI 56
>3i1n_C 50S ribosomal protein L2; ribosome structure, protein-RNA
complex, acetylation, ribonucleoprotein, ribosomal
protein, RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1vs8_C 2aw4_C 2awb_C
2vhm_C 2vhn_C 3bbx_C 3df2_C 3df4_C 1vs6_C 3i1p_C 3i1r_C
3i1t_C 3i20_C 3i22_C 2qam_C* 1p85_A 1p86_A 2i2v_C
2i2t_C* 2qao_C* ... (C:1-69,C:201-230)
Length = 99
Score = 84.1 bits (208), Expect = 2e-17
Identities = 35/69 (50%), Positives = 40/69 (57%)
Query: 1 MALKNFNPDTSGRRQLVMVDRNSLHSGKPIKSLTRGLCSKGGRNNTGRVTMRFRGGGHKN 60
MA+ P + GRR +V V LH GKP L GGRNN GR+T R GGGHK
Sbjct: 1 MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ 60
Query: 61 RYRLVDFKR 69
YR+VDFKR
Sbjct: 61 AYRIVDFKR 69
Score = 52.5 bits (126), Expect = 6e-08
Identities = 18/31 (58%), Positives = 19/31 (61%)
Query: 201 HSNVNHAKAGRARWLGMRSHVRGVAMNPVDH 231
KAG ARW G+R VRG AMNPVDH
Sbjct: 69 RMLRVLGKAGAARWRGVRPTVRGTAMNPVDH 99
>3cih_A Putative alpha-rhamnosidase; structural genomics, protein
structure initiative II, NYSGXRC, (alpha/alpha)6 barrel
domain; 2.33A {Bacteroides thetaiotaomicron vpi-5482}
(A:39-51,A:168-298)
Length = 144
Score = 27.9 bits (62), Expect = 1.4
Identities = 10/54 (18%), Positives = 15/54 (27%), Gaps = 4/54 (7%)
Query: 42 GRNNTGRVTMRFRGGGHKNRYR----LVDFKRGEYGLEGVVKRLEYDPNRTAFI 91
G+ G +T++ G K + K Y LE I
Sbjct: 45 GKETFGFITLKNLSGKGKIDLYYGESPEEAKDKAYCETLDKLLLEPGQITDLAI 98
>1phz_A Protein (phenylalanine hydroxylase); aromatic amino acid
hydroxylase, phosphorylation, intrasteric regulation,
allosteric regulation; 2.20A {Rattus norvegicus}
(A:1-131)
Length = 131
Score = 26.8 bits (59), Expect = 3.1
Identities = 3/22 (13%), Positives = 8/22 (36%)
Query: 72 YGLEGVVKRLEYDPNRTAFIAL 93
+ ++L T++I
Sbjct: 6 LENGVLSRKLSDFGQETSYIED 27
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.317 0.134 0.396
Gapped
Lambda K H
0.267 0.0578 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,059,570
Number of extensions: 88407
Number of successful extensions: 162
Number of sequences better than 10.0: 1
Number of HSP's gapped: 151
Number of HSP's successfully gapped: 14
Length of query: 278
Length of database: 4,956,049
Length adjustment: 87
Effective length of query: 191
Effective length of database: 2,015,014
Effective search space: 384867674
Effective search space used: 384867674
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 (21.7 bits)
S2: 54 (24.9 bits)