RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780260|ref|YP_003064673.1| 50S ribosomal protein L4 [Candidatus Liberibacter asiaticus str. psy62] (207 letters) >2j01_F 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (F:) Length = 210 Score = 196 bits (499), Expect = 2e-51 Identities = 65/206 (31%), Positives = 102/206 (49%) Query: 1 MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYT 60 M E++V + + +L V+RWQ ++R G + +K R EVAY+ Sbjct: 1 MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS 60 Query: 61 GSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCS 120 G K++ QK TGRARH F GGG FGP P + LPKKVR L A++D+ Sbjct: 61 GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE 120 Query: 121 NDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQG 180 +++++ KTK + + L + + + + AARN+P + L +G Sbjct: 121 GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG 180 Query: 181 INVYDILRCSKLVLSKSAIEALEDRF 206 +NVYDI+R +LV+ A E ++R Sbjct: 181 LNVYDIVRTERLVMDLDAWEVFQNRI 206 >2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (C:) Length = 205 Score = 181 bits (461), Expect = 5e-47 Identities = 70/206 (33%), Positives = 113/206 (54%), Gaps = 6/206 (2%) Query: 1 MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYT 60 M +++V +G ++ + G+L V+ WQ +R G + ++ R++V+ T Sbjct: 1 MAQINVIGQNGGRTI------ELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKT 54 Query: 61 GSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCS 120 G KMY QKGTG ARH +SV F GGG AFGP P + LP++VR L L A++ + Sbjct: 55 GRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEG 114 Query: 121 NDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQG 180 ++ +D + KTK ++ + L + D N + AARN+ +++LPV G Sbjct: 115 GKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAG 174 Query: 181 INVYDILRCSKLVLSKSAIEALEDRF 206 +NVYDILR +LV+ +A+E +E+ Sbjct: 175 VNVYDILRHDRLVIDAAALEIVEEEA 200 >1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon; HET: CIT; 1.70A {Thermotoga maritima} (A:) Length = 225 Score = 174 bits (442), Expect = 7e-45 Identities = 68/223 (30%), Positives = 116/223 (52%), Gaps = 19/223 (8%) Query: 3 ELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGS 62 ++ + N+ GE G + +S+ +F + P ++ R + Q +R G + +K R EV+ G Sbjct: 2 QVDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGR 61 Query: 63 KMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSND 122 K + QK TGRARH S +R GG GP P L KK++ LALR ALS K+ N Sbjct: 62 KPWPQKHTGRARHGSIRSPIWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENK 121 Query: 123 IMVIDNLVSKECKTKYLVTRFRALDLSNA----LIIDGCQLDRNFQLAARNIPNINLL-- 176 ++V+D+L + KTK L + L LS+ ++ + N +L+ RN+P++ ++ Sbjct: 122 LLVLDDLKLERPKTKSLKEILQNLQLSDKKTLIVLPWKEEGYMNVKLSGRNLPDVKVIIA 181 Query: 177 -------------PVQGINVYDILRCSKLVLSKSAIEALEDRF 206 + G+NV+D+L+ LVL++ + +E+ Sbjct: 182 DNPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVSKIEEVL 224 >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 1s1i_D (H:1-138) Length = 138 Score = 107 bits (268), Expect = 2e-24 Identities = 19/132 (14%), Positives = 40/132 (30%), Gaps = 10/132 (7%) Query: 3 ELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKR--------IGCSKSKGR 54 +++V +L GE +F+ + I+ V + KR G S Sbjct: 5 QVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAES 64 Query: 55 SEVAYTGSKMYVQKGTGRARH-SSKSVSQFRGGGKAFGP-VPIIGVHALPKKVRSLALRH 112 +++ G G R + RGG + + A Sbjct: 65 WGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATAS 124 Query: 113 ALSDKFCSNDIM 124 A++ ++ ++ Sbjct: 125 AIAATAVASLVL 136 >3i1n_E 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_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* 2qp1_E* ... (E:20-116) Length = 97 Score = 100 bits (251), Expect = 2e-22 Identities = 29/97 (29%), Positives = 44/97 (45%) Query: 25 ALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFR 84 + ++ +V+ + R G K R+EV +G K + QKGTGRAR S +R Sbjct: 1 GRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWR 60 Query: 85 GGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSN 121 GG F P + KK+ AL+ LS+ + Sbjct: 61 SGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQD 97 >3i1n_E 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_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* 2qp1_E* ... (E:1-19,E:117-201) Length = 104 Score = 95.2 bits (237), Expect = 6e-21 Identities = 26/96 (27%), Positives = 53/96 (55%), Gaps = 1/96 (1%) Query: 111 RHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNI 170 + AL+ + ++V++ + KTK L + + + L + LII G +LD N LAARN+ Sbjct: 9 QSALTVSETTFRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITG-ELDENLFLAARNL 67 Query: 171 PNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRF 206 +++ GI+ ++ K+V++ A++ +E+ Sbjct: 68 HKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML 103 >3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (G:77-171) Length = 95 Score = 94.8 bits (236), Expect = 7e-21 Identities = 33/91 (36%), Positives = 43/91 (47%) Query: 28 PQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGG 87 + ++ R L KR G + + R+EV G K Y QK TGRAR S+ GGG Sbjct: 3 KARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGSQGSPLRPGGG 62 Query: 88 KAFGPVPIIGVHALPKKVRSLALRHALSDKF 118 FGP P + KK R LAL A++ Sbjct: 63 VIFGPKPRDWTIKMNKKERRLALSTAIASAV 93 >1vq8_C 50S ribosomal protein L4E; 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} (C:24-132) Length = 109 Score = 92.5 bits (230), Expect = 4e-20 Identities = 17/107 (15%), Positives = 35/107 (32%), Gaps = 3/107 (2%) Query: 28 PQQGILARVLRWQSWRKRIG--CSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRG 85 + ++ + +R ++ + G A + Q + ++ V Q Sbjct: 3 VRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKLDGRARRVPQAVK 62 Query: 86 GGKAFGPVPIIGVH-ALPKKVRSLALRHALSDKFCSNDIMVIDNLVS 131 G A P L K R LA+R AL+ ++ + + Sbjct: 63 GRSAHPPKTEKDRSLDLNDKERQLAVRSALAATADADLVADRGHEFD 109 >2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (c:29-146) Length = 118 Score = 85.2 bits (211), Expect = 6e-18 Identities = 17/111 (15%), Positives = 34/111 (30%), Gaps = 10/111 (9%) Query: 32 ILARVLRWQSWRKRIG-----CSKSKGRSEVAYTG---SKMYVQKGTGRARH-SSKSVSQ 82 I+ V R + + +E TG +++ +G G R + Sbjct: 8 IVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNM 67 Query: 83 FRGGGKAFGPVPIIGVH-ALPKKVRSLALRHALSDKFCSNDIMVIDNLVSK 132 RGG H + + A+ AL+ +M + + + Sbjct: 68 CRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALACLSLPALVMSKGHRIEE 118 >3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (G:172-293) Length = 122 Score = 77.9 bits (192), Expect = 8e-16 Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 6/88 (6%) Query: 124 MVIDNLVS--KECKTKYLVTRFRALDLSN---ALIIDGCQLDRNFQLAARNIPNINLLPV 178 V++ ++ KTK + + L +L L N + + RNI + LL Sbjct: 2 FVVEEFAENFEKPKTKDFIAAMQRWGLDPAEKSLFFLM-DLVENVEKSGRNIRTLKLLTP 60 Query: 179 QGINVYDILRCSKLVLSKSAIEALEDRF 206 + +N++D+L KLV ++ I+ L R+ Sbjct: 61 RSLNLFDVLNAEKLVFTEGTIQYLNQRY 88 >2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_D (D:104-175) Length = 72 Score = 77.0 bits (190), Expect = 2e-15 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 3/71 (4%) Query: 137 KYLVTRFRALDLS-NALIIDGC--QLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLV 193 +YL + L++D ++ ++ A + NL+P G+NV+ +L+ LV Sbjct: 2 QYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTFNLIPAVGLNVHSMLKHQTLV 61 Query: 194 LSKSAIEALED 204 L+ + LED Sbjct: 62 LTLPTVAFLED 72 >1vq8_C 50S ribosomal protein L4E; 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} (C:1-23,C:133-246) Length = 137 Score = 72.3 bits (177), Expect = 5e-14 Identities = 17/112 (15%), Positives = 35/112 (31%), Gaps = 27/112 (24%) Query: 121 NDIMVIDNLVSKECKTKYLVTRFRALDLSNALI-----------------------IDGC 157 +V+ + KT+ +V+ ALD+ + Sbjct: 26 EVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGSARGRKYRRPASILF 85 Query: 158 QLDRNFQLAARNIPNINLLPVQGINVYDILRCSKL----VLSKSAIEALEDR 205 AARN+ ++ +N D+ V ++SA+ + +R Sbjct: 86 VTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAER 137 >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 = 32.4 bits (74), Expect = 0.039 Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 10/32 (31%) Query: 122 DIMVIDNLVSKECKTKYLVTRF-RALDLSNAL 152 D+M I++LV +V F R + + A+ Sbjct: 4 DVMSIESLVE-------VV--FYRGMTMQVAV 26 >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 1s1i_D (H:139-362) Length = 224 Score = 29.0 bits (65), Expect = 0.55 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 4/45 (8%) Query: 166 AARNIPNINLLPVQGINVYDILRCSKL----VLSKSAIEALEDRF 206 A RN+P + V +N+ + + L + +++A L+ + Sbjct: 80 ALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAAFTKLDQVW 124 >1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} (A:) Length = 256 Score = 25.3 bits (54), Expect = 6.1 Identities = 7/55 (12%), Positives = 13/55 (23%), Gaps = 2/55 (3%) Query: 151 ALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYD--ILRCSKLVLSKSAIEALE 203 QL ++ + N +L SKL + + Sbjct: 6 YDEDRKTQLIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYD 60 >1jmx_B Amine dehydrogenase; oxidoreductase; HET: TRQ HEC; 1.90A {Pseudomonas putida} (B:86-187) Length = 102 Score = 25.2 bits (55), Expect = 6.3 Identities = 6/32 (18%), Positives = 13/32 (40%) Query: 11 GEDKGVISVSEDIFALKPQQGILARVLRWQSW 42 +D + DI+ + + G L ++W Sbjct: 71 ADDGSLYVAGPDIYKMDVKTGKYTVALPLRNW 102 >3bik_B Programmed cell death protein 1; CO-stimulation, receptor-ligand complex, immunoglobulin- like beta-sandwich, T cell, B cell, programmed death; 2.65A {Mus musculus} (B:) Length = 134 Score = 24.9 bits (55), Expect = 7.9 Identities = 5/47 (10%), Positives = 11/47 (23%), Gaps = 6/47 (12%) Query: 39 WQSW-RKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHS-SKSVSQF 83 +W R + A + + R + + F Sbjct: 41 MLNWNRLSPS----NQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDF 83 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 0.397 Gapped Lambda K H 0.267 0.0678 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,505,363 Number of extensions: 63332 Number of successful extensions: 134 Number of sequences better than 10.0: 1 Number of HSP's gapped: 120 Number of HSP's successfully gapped: 18 Length of query: 207 Length of database: 4,956,049 Length adjustment: 84 Effective length of query: 123 Effective length of database: 2,116,429 Effective search space: 260320767 Effective search space used: 260320767 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 (21.9 bits) S2: 52 (23.9 bits)