RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780145|ref|YP_003064558.1| 50S ribosomal protein L10
[Candidatus Liberibacter asiaticus str. psy62]
(172 letters)
>gnl|CDD|88597 cd05797, Ribosomal_L10, Ribosomal protein L10 family, L10
subfamily; composed of bacterial 50S ribosomal protein
and eukaryotic mitochondrial 39S ribosomal protein, L10.
L10 occupies the L7/L12 stalk of the ribosome. The
N-terminal domain (NTD) of L10 interacts with L11
protein and forms the base of the L7/L12 stalk, while
the extended C-terminal helix binds to two or three
dimers of the NTD of L7/L12 (L7 and L12 are identical
except for an acetylated N-terminus). The L7/L12 stalk
is known to contain the binding site for elongation
factors G and Tu (EF-G and EF-Tu, respectively);
however, there is disagreement as to whether or not L10
is involved in forming the binding site. The stalk is
believed to be associated with GTPase activities in
protein synthesis. In a neuroblastoma cell line, L10 has
been shown to interact with the SH3 domain of Src and to
activate the binding of the Nck1 adaptor protein with
skeletal proteins such as the Wiskott-Aldrich Syndrome
Protein (WASP) and the WASP-interacting protein (WIP).
These bacteria and eukaryotic sequences have no
additional C-terminal domain, present in other
eukaryotic and archaeal orthologs..
Length = 157
Score = 149 bits (378), Expect = 3e-37
Identities = 61/157 (38%), Positives = 98/157 (62%), Gaps = 1/157 (0%)
Query: 2 NRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIA 61
NR+ K ++EL + + S+VVA Y+G++VAQ+ +LRK++REAG +KV KN L K A
Sbjct: 1 NREKKEEIVAELKEKLKEAKSVVVADYRGLTVAQLTELRKELREAGVKLKVVKNTLAKRA 60
Query: 62 IRDTSIRGISDLFVGQSLIVYS-DSPVIAPKISVSFSNDNNEFRVLGGVVEKGVLNQDSI 120
+ T + DL G + I +S + PV A K+ F+ +N + + GGVVE VL+ + +
Sbjct: 61 LEGTGFEDLDDLLKGPTAIAFSEEDPVAAAKVLKDFAKENKKLEIKGGVVEGKVLDAEEV 120
Query: 121 KQIASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQ 157
K +A LP E + A ++ +Q+ AT+LVR+L P ++
Sbjct: 121 KALAKLPSREELLAQLLGLLQAPATKLVRVLNAPASK 157
>gnl|CDD|88594 cd00379, Ribosomal_L10_P0, Ribosomal protein L10 family; composed
of the large subunit ribosomal protein called L10 in
bacteria, P0 in eukaryotes, and L10e in archaea, as well
as uncharacterized P0-like eukaryotic proteins. In all
three kingdoms, L10 forms a tight complex with multiple
copies of the small acidic protein L12(e). This complex
forms a stalk structure on the large subunit of the
ribosome. The N-terminal domain (NTD) of L10 interacts
with L11 protein and forms the base of the L7/L12 stalk,
while the extended C-terminal helix binds to two or
three dimers of the NTD of L7/L12 (L7 and L12 are
identical except for an acetylated N-terminus). The
L7/L12 stalk is known to contain the binding site for
elongation factors G and Tu (EF-G and EF-Tu,
respectively); however, there is disagreement as to
whether or not L10 is involved in forming the binding
site. The stalk is believed to be associated with GTPase
activities in protein synthesis. In a neuroblastoma cell
line, L10 has been shown to interact with the SH3 domain
of Src and to activate the binding of the Nck1 adaptor
protein with skeletal proteins such as the
Wiskott-Aldrich Syndrome Protein (WASP) and the
WASP-interacting protein (WIP). Some eukaryotic P0
sequences have an additional C-terminal domain
homologous with acidic proteins P1 and P2..
Length = 155
Score = 124 bits (313), Expect = 1e-29
Identities = 47/155 (30%), Positives = 84/155 (54%), Gaps = 1/155 (0%)
Query: 4 QGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIR 63
+ K + EL ++ S+VV Y+G++VAQ+ +LRK++RE+G +KV KN L++ A++
Sbjct: 1 EKKEELVEELKELLKKYKSVVVVDYRGLTVAQLTELRKELRESGAKLKVGKNTLMRRALK 60
Query: 64 DTSIRGISDLFVGQSLIVYS-DSPVIAPKISVSFSNDNNEFRVLGGVVEKGVLNQDSIKQ 122
T + L G + + ++ + PV K+ F+ +N + GGVV VL+ +
Sbjct: 61 GTGFEELKPLLKGPTALAFTNEDPVEVAKVLKDFAKENKKLFAKGGVVAGKVLDPAGVTA 120
Query: 123 IASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQ 157
+A LP E + A +I +++ +L RLL
Sbjct: 121 LAKLPSREELLAMLIGLLKAPIAKLARLLNALGIG 155
>gnl|CDD|30593 COG0244, RplJ, Ribosomal protein L10 [Translation, ribosomal
structure and biogenesis].
Length = 175
Score = 123 bits (310), Expect = 3e-29
Identities = 56/173 (32%), Positives = 97/173 (56%), Gaps = 2/173 (1%)
Query: 1 MNRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKI 60
+ R+ K ++EL ++ S S+V+ Y+G++VAQ+ +LRKK+REAG +KV KN L++
Sbjct: 3 LAREWKKELVAELKELIKESPSVVIVDYRGLTVAQLTELRKKLREAGAKLKVVKNTLLRR 62
Query: 61 AIRDTSIRGISDLFVGQSLIVYSDS-PVIAPKISVSFSNDNNE-FRVLGGVVEKGVLNQD 118
A+ + + G+ DL G + I +S+ PV A K+ F+ + + + GGV E VL
Sbjct: 63 ALEEAGLEGLDDLLKGPTAIAFSNEDPVAAAKLLKDFAKEAGDKAPIKGGVPEGKVLGAA 122
Query: 119 SIKQIASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAFVDKNQQ 171
+ +A LP E + ++ +Q+ AT+L+R L +V + A +K
Sbjct: 123 EVIALAKLPSKEELVVMLLGVLQAPATKLLRALKAVPDKVGLKLLAAYEKGVV 175
>gnl|CDD|144164 pfam00466, Ribosomal_L10, Ribosomal protein L10.
Length = 100
Score = 97.6 bits (244), Expect = 1e-21
Identities = 35/99 (35%), Positives = 61/99 (61%), Gaps = 2/99 (2%)
Query: 1 MNRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKI 60
M R+ K + EL ++ S+VV Y+G++VAQ+ +LRKK+REAG +KV KN L++
Sbjct: 1 MTREKKEEIVEELKELLKEYKSVVVVDYRGLTVAQLTELRKKLREAGAELKVGKNTLMRR 60
Query: 61 AIRDTSIR-GISDLFVGQSLIVYSDSPVIAP-KISVSFS 97
A+ T G+S+L G + +++++ +A K+ F+
Sbjct: 61 ALEGTGEEEGLSELLKGPTALIFTNEDPVAVAKVLKKFA 99
>gnl|CDD|88595 cd05795, Ribosomal_P0_L10e, Ribosomal protein L10 family, P0 and
L10e subfamily; composed of eukaryotic 60S ribosomal
protein P0 and the archaeal P0 homolog, L10e. P0 or
L10e forms a tight complex with multiple copies of the
small acidic protein L12(e). This complex forms a stalk
structure on the large subunit of the ribosome. The
stalk is known to contain the binding site for
elongation factors G and Tu (EF-G and EF-Tu,
respectively); however, there is disagreement as to
whether or not L10 is involved in forming the binding
site. The stalk is believed to be associated with
GTPase activities in protein synthesis. In a
neuroblastoma cell line, L10 has been shown to interact
with the SH3 domain of Src and to activate the binding
of the Nck1 adaptor protein with skeletal proteins such
as the Wiskott-Aldrich Syndrome Protein (WASP) and the
WASP-interacting protein (WIP). These eukaryotic and
archaeal P0 sequences have an additional C-terminal
domain homologous with acidic proteins P1 and P2..
Length = 175
Score = 40.5 bits (95), Expect = 3e-04
Identities = 12/87 (13%), Positives = 39/87 (44%), Gaps = 6/87 (6%)
Query: 4 QGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIR 63
+ K + +L+++ S +++ + Q++ +R+ +R + + KN L++ A+R
Sbjct: 1 EWKKEYVEKLTELLKSYPKVLIVDADNVGSKQLQKIRRSLRGKAE-ILMGKNTLIRRALR 59
Query: 64 D-----TSIRGISDLFVGQSLIVYSDS 85
+ + + G ++++
Sbjct: 60 NLGDENPELEKLLPYLKGNVGFIFTNG 86
>gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding
TIM barrel domain of Type III PLP-Dependent Enzymes,
Yggs-like proteins. This subfamily contains mainly
uncharacterized proteobacterial proteins with similarity
to the hypothetical Escherichia coli protein YggS, a
homolog of yeast YBL036c, which is homologous to a
Pseudomonas aeruginosa gene that is co-transcribed with
a known proline biosynthetic gene. Like yeast YBL036c,
Yggs is a single domain monomeric protein with a typical
TIM-barrel fold. Its structure, which shows a
covalently-bound PLP cofactor, is similar to the
N-terminal domain of the fold type III PLP-dependent
enzymes, bacterial alanine racemase and eukaryotic
ornithine decarboxylase, which are two-domain dimeric
proteins. YggS has not been characterized extensively
and its biological function is still unkonwn.
Length = 224
Score = 28.3 bits (64), Expect = 1.0
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 117 QDSIKQIASLPDLEGIRAGIISAIQSNATRLV 148
Q+++++I +L DL+ I I IQSN T+L+
Sbjct: 58 QEALEKIEALRDLQDIEWHFIGPIQSNKTKLI 89
>gnl|CDD|32910 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 1480
Score = 28.1 bits (62), Expect = 1.4
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 139 AIQSNATRLVRLLGTPQTQVVRAISAFVDKNQQ 171
A +++ +R L + + ++ RA+S + NQQ
Sbjct: 829 AFEADPEAEIRQLNSRRNELERALSNHENDNQQ 861
>gnl|CDD|146015 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160
kDa) subunit. CPSF is involved in mRNA polyadenylation
and binds the AAUAAA conserved sequence in pre-mRNA.
CPSF has also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA
binding.
Length = 319
Score = 27.6 bits (62), Expect = 2.1
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 54 KNRLVKIAIRDTSIRGISDLFVGQSLIVYSDS 85
K++L+ A DT I + L V + I+ D
Sbjct: 115 KDKLLPKAFLDTPITYVVSLKVFGNRIIVGDL 146
>gnl|CDD|35507 KOG0286, KOG0286, KOG0286, G-protein beta subunit [General function
prediction only].
Length = 343
Score = 27.2 bits (60), Expect = 2.5
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 64 DTSIRGISDLFVGQSLIVYSDSPVIAPKISVSFSNDNNEFRVL-GGVVEKGVLNQDSIKQ 122
D + R + DL Q L VYS +I SV+FS R+L G + D++K
Sbjct: 250 DATCR-LYDLRADQELAVYSHDSIICGITSVAFSKSG---RLLFAGYDDFTCNVWDTLKG 305
>gnl|CDD|30673 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General
function prediction only].
Length = 228
Score = 26.4 bits (58), Expect = 4.2
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 117 QDSIKQIASLPDLEGIRAGIISAIQSNATRLV 148
Q+++ +I +L DL I I +QSN +LV
Sbjct: 59 QEALDKIEALKDLPDIEWHFIGPLQSNKVKLV 90
>gnl|CDD|33490 COG3694, COG3694, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 260
Score = 25.6 bits (56), Expect = 7.4
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 55 NRLVKIAIRDTSIRGISDLFVGQSLIVYSDS--PVIAPKI 92
N +++R SI + DL +G L+VY+ + KI
Sbjct: 105 NSQFNVSVRTFSIWRVPDLLIGVGLLVYAVKSIVLTPTKI 144
>gnl|CDD|29350 cd01166, KdgK, 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates
2-keto-3-deoxygluconate (KDG) to form
2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the
common intermediate product, that allows organisms to
channel D-glucuronate and/or D-galacturinate into the
glycolysis and therefore use polymers, like pectin and
xylan as carbon sources..
Length = 294
Score = 25.6 bits (56), Expect = 7.5
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 27 HYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSIR 68
H GI++A + R+ + EA ++ AK R V ++ D + R
Sbjct: 129 HLSGITLALSESAREALLEA---LEAAKARGVTVSF-DLNYR 166
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.316 0.133 0.349
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,788,014
Number of extensions: 88740
Number of successful extensions: 234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 231
Number of HSP's successfully gapped: 16
Length of query: 172
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 85
Effective length of database: 4,383,754
Effective search space: 372619090
Effective search space used: 372619090
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 (21.6 bits)
S2: 54 (24.5 bits)