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)