RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780146|ref|YP_003064559.1| 50S ribosomal protein L1
[Candidatus Liberibacter asiaticus str. psy62]
(232 letters)
>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein,
nucleotide-binding, protein biosynthesis, translation,
zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB:
3fik_5 3kcr_5 2rdo_9 2gya_2 2gyc_2
Length = 234
Score = 262 bits (670), Expect = 5e-71
Identities = 115/229 (50%), Positives = 175/229 (76%)
Query: 3 SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62
+K++KRM+ I + +D + Y +++A+ +LKE ATA+F E+V++A+NLGID R ++Q VRG
Sbjct: 2 AKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRG 61
Query: 63 VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMM 122
+P+GTG +VRVAVF + A+ A+ AGA++VG EDL + +K G+++FD IA+PD M
Sbjct: 62 ATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAM 121
Query: 123 PLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182
+VG+LG++LGPRG+MPN +VGTVT +VA AV+ +K+G V +R++K GIIH IGKV F+
Sbjct: 122 RVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFD 181
Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231
K++EN+ A + A+ KAKP+ AKG Y+K+V++S+TMG G+ VD + S
Sbjct: 182 ADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLS 230
>1ad2_A TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant;
1.90A {Thermus thermophilus} SCOP: e.24.1.1 PDB: 1eg0_N
1vsa_A 1vsp_A 2hgj_C 2hgq_C 2hgu_C 1zho_A 1ml5_c* 1yl3_C
1giy_C 2hw8_A 2j01_C 2j03_C 2jl6_C 2jl8_C 2om7_K* 2v47_C
2wdi_C 2wdj_C 2wdl_C ...
Length = 228
Score = 243 bits (621), Expect = 3e-65
Identities = 101/227 (44%), Positives = 153/227 (67%), Gaps = 1/227 (0%)
Query: 4 KISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGV 63
K KR + + + +D + +Y + +A ++KE ATA+FDETVE+ LGIDPR ++Q VRG
Sbjct: 2 KHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGT 61
Query: 64 VTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMP 123
V++P+G G VRV A K EA EAGAD VGGE++ + + G +DFD +ATPD+M
Sbjct: 62 VSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMG 121
Query: 124 LVGR-LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182
VG LGRILGPRG++PN + GTV ++ +RE K+G ++FR++K G IHA +GK F
Sbjct: 122 AVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFP 181
Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSS 229
+K+ +N+ AF+ A+ KP AKG +++ V +++TMG ++++ S
Sbjct: 182 PEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 228
>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 352
Score = 239 bits (611), Expect = 3e-64
Identities = 103/228 (45%), Positives = 146/228 (64%)
Query: 4 KISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGV 63
SKR +I + + Y L A+ ++K+ ++ +F ET E L IDP++ +Q +R
Sbjct: 117 TRSKRFLEIQKLREIKQEYDLKTALSLMKQMSSTKFVETAEAHFRLNIDPKYNDQQLRAT 176
Query: 64 VTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMP 123
V++P GTG V++AV A K DEA+ AGADIVGGE+L E +KGG +DFD+ IAT DMM
Sbjct: 177 VSLPKGTGKTVKIAVLAQGDKIDEAKAAGADIVGGEELIEQIKGGFMDFDKLIATSDMMA 236
Query: 124 LVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFEN 183
V LGRILGPRG+MP + GTVT +VA AV E K G V+FR +K GI+H GK++FE
Sbjct: 237 KVASLGRILGPRGLMPTPKAGTVTPNVAQAVEEFKKGKVEFRVDKTGIVHIPFGKLNFEE 296
Query: 184 KKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231
+ + N+ A + +V KP+ AKG Y K +SS+MG I++++
Sbjct: 297 EDLLINLFATIKSVETNKPTGAKGVYWKSAHISSSMGPSIRLNIREML 344
>3fik_5 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary
complex, acetylation, ribonucleoprotein, ribosomal
protein, RNA-binding; 6.70A {Escherichia coli} PDB:
2rdo_9 2gya_2 2gyc_2
Length = 234
Score = 236 bits (602), Expect = 5e-63
Identities = 115/229 (50%), Positives = 175/229 (76%)
Query: 3 SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62
+K++KRM+ I + +D + Y +++A+ +LKE ATA+F E+V++A+NLGID R ++Q VRG
Sbjct: 2 AKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRG 61
Query: 63 VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMM 122
+P+GTG +VRVAVF + A+ A+ AGA++VG EDL + +K G+++FD IA+PD M
Sbjct: 62 ATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAM 121
Query: 123 PLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182
+VG+LG++LGPRG+MPN +VGTVT +VA AV+ +K+G V +R++K GIIH IGKV F+
Sbjct: 122 RVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFD 181
Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231
K++EN+ A + A+ KAKP+ AKG Y+K+V++S+TMG G+ VD + S
Sbjct: 182 ADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLS 230
>1mzp_A 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A
{Sulfolobus acidocaldarius} SCOP: e.24.1.1 PDB: 1pnu_5
1pny_5 1vor_7 1vou_7 1vow_7 1voy_7 1vp0_7 3e1b_Z 3e1d_Z
Length = 217
Score = 191 bits (487), Expect = 1e-49
Identities = 46/220 (20%), Positives = 93/220 (42%), Gaps = 15/220 (6%)
Query: 16 IDRSALYGLSDAVVMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNV 74
D+ +L + + F ++VEI + GID + + +R +V +P
Sbjct: 3 ADKESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDMKKGDLKLREIVPLPKQPSKAK 62
Query: 75 RVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQI-------DFDRCIATPDMMPLVGR 127
RV V +S + + A++A +V + + ++G + + + + M L GR
Sbjct: 63 RVLVVPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESMALAGR 122
Query: 128 L-GRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKI 186
+ G LGPRG P T D++ + K V +++ + IG + + +
Sbjct: 123 ILGPALGPRGKFPTPL--PNTADISEYINRFKRS-VLVKTKDQPQVQVFIGTEDMKPEDL 179
Query: 187 EENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVD 226
EN +A ++A+ ++ + + +TMG +KV
Sbjct: 180 AENAIAVLNAIENKAK---VETNLRNIYVKTTMGKAVKVK 216
>1i2a_A 50S ribosomal protein L1P; primary rRNA-binding protein,
translational repressor, ribosome; 1.85A
{Methanocaldococcus jannaschii} SCOP: e.24.1.1 PDB:
1cjs_A 1u63_A 1dwu_A
Length = 219
Score = 184 bits (468), Expect = 1e-47
Identities = 64/224 (28%), Positives = 97/224 (43%), Gaps = 19/224 (8%)
Query: 16 IDRSALYGLSDAVVMLKERATAR-FDETVEIAMNLG-IDPRHANQMVRGVVTMPNGTGVN 73
+DR AL AV +E A R F ++ E L ID R ++ V +P+G G
Sbjct: 1 MDREALL---QAVKEARELAKPRNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKE 57
Query: 74 VRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQ------IDFDRCIATPDMMPLVGR 127
++AV T A +A E G ++ E++ E+ K + D IA D+MPL+GR
Sbjct: 58 AKIAVIGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLMPLIGR 117
Query: 128 -LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKI 186
+G ILGPRG MP + E V + +G +++I
Sbjct: 118 YMGVILGPRGKMPK---PVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKMTDEQI 174
Query: 187 EENVLAFVSAVVKAKPSVAKGDY-VKRVTLSSTMGCGIKVDLSS 229
+N+ A ++ V K KG Y +K + TMG +KV
Sbjct: 175 VDNIEAVLNVVAKKYE---KGLYHIKDAYVKLTMGPAVKVKKEK 215
>2noq_G 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal
initiation; 7.30A {Saccharomyces cerevisiae} PDB: 1s1i_A
Length = 213
Score = 165 bits (418), Expect = 9e-42
Identities = 44/218 (20%), Positives = 86/218 (39%), Gaps = 13/218 (5%)
Query: 16 IDRSALY-GLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNV 74
I S + + + + E F ETVE+ + L ++ G + +PN N+
Sbjct: 1 ITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNM 60
Query: 75 RVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQ------IDFDRCIATPDMMPLVGR- 127
+ +F + D A+ G D + +DL ++ K + ++ IA+ ++ V R
Sbjct: 61 SICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRL 120
Query: 128 LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIE 187
LG L G P + D+ V + + + F+ +K + +G V E +
Sbjct: 121 LGPQLSKAGKFPTPV--SHNDDLYGKVTDVR-STIKFQLKKVLCLAVAVGNVEMEEDVLV 177
Query: 188 ENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKV 225
+L V+ V V + + S+MG ++
Sbjct: 178 NQILMSVNFFVSLLK--KNWQNVGSLVVKSSMGPAFRL 213
>2ftc_A Mitochondrial ribosomal protein L1; mitochondrial ribosome, large
ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}
Length = 189
Score = 162 bits (410), Expect = 7e-41
Identities = 40/191 (20%), Positives = 87/191 (45%), Gaps = 6/191 (3%)
Query: 43 VEIAMNLGIDPRHANQMVRGVVTMPNGTGVNV-RVAVFATSS-KADEAREAGADIVGGED 100
+++ +++ + + + V+++P + +VAVF ++ + A E GA GG
Sbjct: 1 LDLTLDMALGKKKNVEPFTSVLSLPYPFASEINKVAVFTENASEVKIAEENGAAFAGGTS 60
Query: 101 LFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSG 160
L + + +I D +A P++MP + RL + L + P L ++ D+ + K+G
Sbjct: 61 LIQKIWDDEIVADFYVAVPEIMPELNRLRKKLNKK--YPKLSRNSIGRDIPKMLELFKNG 118
Query: 161 A-VDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTM 219
+ E+ + I + + +I N+ A ++ V + +P G +V R L S+
Sbjct: 119 HEIKVDEERENFLQTKIATLDMSSDQIAANLQAVINEVCRHRPL-NLGPFVVRAFLRSST 177
Query: 220 GCGIKVDLSSF 230
G+ + +
Sbjct: 178 SEGLLLKIDPL 188
>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 212
Score = 136 bits (342), Expect = 5e-33
Identities = 60/212 (28%), Positives = 91/212 (42%), Gaps = 16/212 (7%)
Query: 24 LSDAVV-MLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81
+ +AV L++ F ETV++A+NL +D + V V +P GTG + VFA
Sbjct: 6 IENAVSRALEDAPERNFRETVDLAVNLRDLDLNDPSNRVDESVVLPAGTGQETTIVVFAE 65
Query: 82 SSKADEAREAGADIVGGEDLFE------IVKGGQIDFDRCIATPDMMPLVGR-LGRILGP 134
A A E D++ ++L E K D D IA +M +GR LG +LGP
Sbjct: 66 GETALRAEEVADDVLDEDELEELGGDDDAAKDLADDTDFFIAEKGLMQDIGRYLGTVLGP 125
Query: 135 RGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFV 194
RG MP D V E V RS + H +G + I +N+ +
Sbjct: 126 RGKMPEPL---DPDDDVVEVIERMKNTVQLRSGERRTFHTRVGAEDMSAENIADNIDVIL 182
Query: 195 SAVVKAKPSVAKGDY-VKRVTLSSTMGCGIKV 225
+ + KG + V + +TMG ++V
Sbjct: 183 RRL---HADLEKGPLNIDTVYVKTTMGPAMEV 211
>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A
2vpl_A
Length = 137
Score = 108 bits (271), Expect = 1e-24
Identities = 33/103 (32%), Positives = 57/103 (55%), Gaps = 11/103 (10%)
Query: 127 RLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKI 186
+LG + PR N+R G ++FR++K G IHA +GK SF +K+
Sbjct: 46 KLG--IDPRRSDQNVRGTVSLP---------HGGRIEFRNDKTGAIHAPVGKASFPPEKL 94
Query: 187 EENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSS 229
+N+ AF+ A+ KP AKG +++ V +++TMG ++++ S
Sbjct: 95 ADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 137
Score = 87.5 bits (217), Expect = 2e-18
Identities = 31/73 (42%), Positives = 49/73 (67%)
Query: 4 KISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGV 63
K KR + + + +D + +Y + +A ++KE ATA+FDETVE+ LGIDPR ++Q VRG
Sbjct: 2 KHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGT 61
Query: 64 VTMPNGTGVNVRV 76
V++P+G + R
Sbjct: 62 VSLPHGGRIEFRN 74
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 33.8 bits (77), Expect = 0.031
Identities = 39/240 (16%), Positives = 78/240 (32%), Gaps = 65/240 (27%)
Query: 9 MQQISQGIDRSALYGLSDAV-VMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMP 67
M IS + + + + L + VEI++ G ++ VV+ P
Sbjct: 338 MLSIS-NLTQEQVQDYVNKTNSHLPA------GKQVEISLVNG--AKNL------VVSGP 382
Query: 68 NGT--GVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFD----RC------ 115
+ G+N+ + S D++R I F +
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSR--------------------IPFSERKLKFSNRFLP 422
Query: 116 IATPDMMP-LVGRLGRI---LGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGI 171
+A+P LV I L + + D+ V ++ G+ D R I
Sbjct: 423 VASPFHSHLLVPASDLINKDLVKNNV--SFNAK----DIQIPVYDTFDGS-DLRVLSGSI 475
Query: 172 IHAGIGKVSFENKKIE-ENVLAF-VSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSS 229
+ + ++ E F + ++ P A G + +T + G G++V ++
Sbjct: 476 SERIVDCIIRLP--VKWETTTQFKATHILDFGPGGASG--LGVLTHRNKDGTGVRVIVAG 531
Score = 33.0 bits (75), Expect = 0.060
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 20/86 (23%)
Query: 9 MQQISQGIDRSALYGLSDAVVMLK---ERATARFDETVEIAMNLGID--PRHANQMVRGV 63
++ +S I + D ++ L E T F T I +D P A+ + GV
Sbjct: 468 LRVLSGSISER----IVDCIIRLPVKWETTTQ-FKAT-HI-----LDFGPGGASGL--GV 514
Query: 64 VTMPN--GTGVNVRVAVFATSSKADE 87
+T N GTGV V VA + D+
Sbjct: 515 LTHRNKDGTGVRVIVAGTLDINPDDD 540
Score = 29.9 bits (67), Expect = 0.48
Identities = 34/134 (25%), Positives = 52/134 (38%), Gaps = 34/134 (25%)
Query: 77 AVFATSSKADEAREAG-ADIVGGEDLFEIV--KGGQIDFDRCIATP-DMMPLVGRLGRI- 131
A FA S + A A AD++ E L E+V +G + +A P D LGR
Sbjct: 1757 ATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQ----VAVPRD------ELGRSN 1806
Query: 132 LGPRGIMPNLRVGTVTTDVATAVRE---SKSG----AVDFRSEKAGIIHAG----IGKVS 180
G I P + + + V E ++G V++ E + AG + V+
Sbjct: 1807 YGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT 1866
Query: 181 FENKKIEENVLAFV 194
NVL F+
Sbjct: 1867 --------NVLNFI 1872
>3fr7_A Putative ketol-acid reductoisomerase (OS05G0573700 protein);
rossmann fold, NADPH, knotted protein; 1.55A {Oryza
sativa japonica group} PDB: 3fr8_A* 1qmg_A* 1yve_I*
Length = 525
Score = 28.7 bits (64), Expect = 1.1
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 68 NGTGVNVRVAVFATSSKADEAREAGADIVGGE--DLFEIVKGGQIDFDRCIATPDM 121
+ + V++ + S DEAR AG G D++E V G + + D
Sbjct: 80 AKSDIVVKIGLRKGSKSFDEARAAGFTEESGTLGDIWETVSGSDL---VLLLISDA 132
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.318 0.134 0.367
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,903,653
Number of extensions: 89362
Number of successful extensions: 323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 300
Number of HSP's successfully gapped: 23
Length of query: 232
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 143
Effective length of database: 3,535,514
Effective search space: 505578502
Effective search space used: 505578502
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: 55 (25.3 bits)