RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3
[Candidatus Liberibacter asiaticus str. psy62]
(221 letters)
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Nicotiana tabacum} (F:)
Length = 259
Score = 205 bits (522), Expect = 4e-54
Identities = 83/218 (38%), Positives = 117/218 (53%), Gaps = 3/218 (1%)
Query: 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV-VHRTLDKNGYMAVQVGAGEAKVK 59
GV+A KLGM + G +PVTV+ +V +T +GY AVQVG + +
Sbjct: 42 AGVGVMATKLGMMSFFEESGTVVPVTVVGFREGNIVTQIKTEATDGYNAVQVGYRRVRDR 101
Query: 60 NVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKG 119
++KP G + P + L EFR+Q D + F G LVDV+G TIGKG
Sbjct: 102 KLTKPEMGHLEKSGIIPLRHLQEFRLQSIDGFEVTQKLDFGELFKEGDLVDVSGTTIGKG 161
Query: 120 FSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEV 179
F G +KRHNF + THG S SHR GS G PGRV+K KKM GRMGG + ++ L++
Sbjct: 162 FQGGIKRHNFKRGQMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTKRKIRKLKI 220
Query: 180 VSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCK 217
V +DD+ +I++KG +PG + + + + N
Sbjct: 221 VKIDDQLNIIMIKGALPGK-PGNLLRIAPAKIVGKNIP 257
>2j01_E 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} (E:)
Length = 206
Score = 196 bits (500), Expect = 2e-51
Identities = 91/211 (43%), Positives = 124/211 (58%), Gaps = 7/211 (3%)
Query: 3 SGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVS 62
G++ K+GMT ++ + R +PVTV+ C VV RT +K+GY AVQ+G K V+
Sbjct: 2 KGILGVKVGMTRIFR-DDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN 60
Query: 63 KPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSG 122
+P++G F+ V P + L E R + G + F G+ VDVTG + G+GF+G
Sbjct: 61 RPLKGHFAKAGVEPVRILREIRDFNPE-----GDTVTVEIFKPGERVDVTGTSKGRGFAG 115
Query: 123 AMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSV 182
MKR NF G +HG HR GS G R+ PGRV+K KKMAG G RVTV NLEVV V
Sbjct: 116 VMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDV 175
Query: 183 DDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213
+ L+LVKG VPG ++VR++ K+A
Sbjct: 176 IPEENLLLVKGAVPGP-NGGLVIVRETKKAA 205
>1vq8_B 50S ribosomal protein L3P; 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} (B:)
Length = 338
Score = 157 bits (398), Expect = 1e-39
Identities = 45/282 (15%), Positives = 72/282 (25%), Gaps = 73/282 (25%)
Query: 1 MRSGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNGYMAVQ 50
G K GMT V + +PVTV+ + V R + Y
Sbjct: 38 GVQGFAGYKAGMTHVVLVNDEPNSPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRP 97
Query: 51 VGAGEA------KVKNVSKPMRGFFSSVNVSPKKKLFEFRVQK----------------- 87
+ + + P + + +
Sbjct: 98 LTEVWTDEFHSELDRTLDVPEDHDPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPK 157
Query: 88 ----------------------DDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMK 125
D + G F G+ DV G+T GKG G +K
Sbjct: 158 KKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVK 217
Query: 126 RHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDD- 184
R + H R +P RV G+ G ++ T N ++ + +
Sbjct: 218 RWGVQKRKGKHARQGWRR-RIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEG 276
Query: 185 ---------------KRGLILVKGCVPGAKKNSWILVRDSFK 211
LVKG VPG + R + +
Sbjct: 277 DEPTVDGGFVNYGEVDGPYTLVKGSVPGP-DKRLVRFRPAVR 317
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} (B:1-29,B:91-211)
Length = 150
Score = 141 bits (356), Expect = 9e-35
Identities = 63/144 (43%), Positives = 85/144 (59%), Gaps = 4/144 (2%)
Query: 79 KLFEFRVQKDDDLLPVGSV---FSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRAT 135
K+ ++ K+D +PV V + F G+ +D TG + GKG G MKR NF G A+
Sbjct: 8 KIGMTQIWKNDRAIPVTVVLAGVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPAS 67
Query: 136 HGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCV 195
HG HR GS G R+ PGRV+K K+MAG MG RVTV+NLEVV + LILVKG +
Sbjct: 68 HGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAI 127
Query: 196 PGAKKNSWILVRDSFKSAVNCKGK 219
PGA +++R + K++ GK
Sbjct: 128 PGA-NGGLVVLRSAAKASAAKGGK 150
>3i1n_D 50S ribosomal protein L3; ribosome structure, protein-RNA
complex, acetylation, ribonucleoprotein, ribosomal
protein, RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D
2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D*
2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D*
2qov_D 2qox_D ... (D:1-30,D:102-209)
Length = 138
Score = 136 bits (344), Expect = 3e-33
Identities = 60/108 (55%), Positives = 77/108 (71%), Gaps = 1/108 (0%)
Query: 105 VGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMA 164
+ VDVTG + GKGF+G +KR NF ATHG S+SHR GS G Q PG+VFK KKMA
Sbjct: 32 DVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMA 91
Query: 165 GRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKS 212
G+MG RVTV++L+VV VD +R L+LVKG VPGA S ++V+ + K+
Sbjct: 92 GQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGA-TGSDLIVKPAVKA 138
Score = 35.4 bits (82), Expect = 0.006
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 3 SGVVARKLGMTCVYNIEGRRIPVTVLHLDN 32
G+V +K+GMT ++ +G IPVTV+ ++
Sbjct: 2 IGLVGKKVGMTRIFTEDGVSIPVTVIEVEA 31
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3;
mitochondrial ribosome, large ribosomal subunit,
ribosomal RNA; 12.10A {Bos taurus} (C:1-29,C:104-211)
Length = 137
Score = 127 bits (322), Expect = 8e-31
Identities = 50/110 (45%), Positives = 61/110 (55%), Gaps = 2/110 (1%)
Query: 104 TVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKM 163
GQ VDVT TIGKGF G MKR F G ATHG + +HR G+ D GRV+ KM
Sbjct: 30 RPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRPGAVAT-GDIGRVWPGTKM 88
Query: 164 AGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213
G+MG T L+V ++ K +I V G VPG KN + V+DS A
Sbjct: 89 PGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGH-KNCLVKVKDSKLPA 137
Score = 28.9 bits (65), Expect = 0.50
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV 36
R G++A KLGM ++ +G++ VT+L + Q V
Sbjct: 1 RVGLIALKLGMMPLWTKDGQKHVVTLLQVRPGQYV 35
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} (b:1-82,b:209-403)
Length = 277
Score = 116 bits (291), Expect = 3e-27
Identities = 26/107 (24%), Positives = 40/107 (37%), Gaps = 3/107 (2%)
Query: 93 PVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQ 152
V V +P F +++DV G+T GKG+ G R + L R G
Sbjct: 75 AVTIVETPQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL--PRKTHRGLRKVACIGA-W 131
Query: 153 DPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAK 199
P RV + AG+ G + T N ++ + + K A
Sbjct: 132 HPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNAS 178
>3jyw_C 60S ribosomal protein L3; eukaryotic ribosome, RACK1
protein, flexible fitting; 8.90A {Thermomyces
lanuginosus} PDB: 1s1i_C (C:40-78,C:206-362)
Length = 196
Score = 100 bits (251), Expect = 1e-22
Identities = 29/137 (21%), Positives = 43/137 (31%), Gaps = 34/137 (24%)
Query: 105 VGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMA 164
+++D +T G GF G R L R G P V + A
Sbjct: 41 QNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKT--HRGLRKVACIGAW-HPAHVMWSVARA 97
Query: 165 GRMGGNRVTVKNLEVVSVDD------------------------------KRGLILVKGC 194
G+ G + T N ++ V K I+VKGC
Sbjct: 98 GQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGC 157
Query: 195 VPGAKKNSWILVRDSFK 211
+PG +K + +R S
Sbjct: 158 IPGNRK-RIVTLRKSLY 173
>3i1n_D 50S ribosomal protein L3; ribosome structure, protein-RNA
complex, acetylation, ribonucleoprotein, ribosomal
protein, RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D
2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D*
2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D*
2qov_D 2qox_D ... (D:31-101)
Length = 71
Score = 87.0 bits (216), Expect = 2e-18
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 33 CQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLL 92
+V + L +GY A+QV G K V+KP G F+ V + L+EFR+ + +
Sbjct: 2 NRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRL-AEGEEF 60
Query: 93 PVGSVFSPSYF 103
VG S F
Sbjct: 61 TVGQSISVELF 71
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3;
mitochondrial ribosome, large ribosomal subunit,
ribosomal RNA; 12.10A {Bos taurus} (C:30-103)
Length = 74
Score = 83.6 bits (207), Expect = 2e-17
Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 32 NCQVVVHRTLDK--NGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDD 89
+C V+ + + + + VG + + F+ + + PK+ + F + D+
Sbjct: 2 DCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFNI-TDN 60
Query: 90 DLLPVGSVFSPSYF 103
+ G+ ++F
Sbjct: 61 AAIKPGTPLYAAHF 74
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal
subunit, ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} (B:30-90)
Length = 61
Score = 78.5 bits (194), Expect = 6e-16
Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 33 CQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDD 90
C +V +T +GY AVQ+G + V+KPM+G F+ V+P + L EFR D
Sbjct: 2 CPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDG 59
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006)
Length = 120
Score = 27.4 bits (61), Expect = 1.5
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 12/36 (33%)
Query: 94 VGSVFSPSYFTVGQLVDVT---GMTIGKGFSGAMKR 126
+ V S + LV+V GMT+ A+ R
Sbjct: 2 LADVMS-----IESLVEVVFYRGMTM----QVAVPR 28
>2qmm_A UPF0217 protein AF_1056; alpha/beta knot, SAM, structural
genomics, PSI-2, protein structure initiative; HET: SAM;
1.85A {Archaeoglobus fulgidus dsm 4304} (A:)
Length = 197
Score = 27.1 bits (60), Expect = 2.2
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 28 LHLDNCQVVVHRTLDKNGY 46
L + C V+ H LD+ +
Sbjct: 179 LLAEQCVVIAHHHLDRLQF 197
>2pcr_A Inositol-1-monophosphatase; bipolar disorder, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.60A {Aquifex aeolicus VF5}
(A:)
Length = 264
Score = 26.4 bits (57), Expect = 2.8
Identities = 10/70 (14%), Positives = 18/70 (25%)
Query: 125 KRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDD 184
N+ VS+ F + G V K ++V +
Sbjct: 90 GTKNYINGFPIFAVSVGLVKGEEPIVGAVYLPYFDKLYWGAKGLGAYVNGKRIKVKDNES 149
Query: 185 KRGLILVKGC 194
+ +V G
Sbjct: 150 LKHAGVVYGF 159
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
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,682,163
Number of extensions: 74558
Number of successful extensions: 182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 159
Number of HSP's successfully gapped: 20
Length of query: 221
Length of database: 4,956,049
Length adjustment: 85
Effective length of query: 136
Effective length of database: 2,082,624
Effective search space: 283236864
Effective search space used: 283236864
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: 53 (24.4 bits)