RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780254|ref|YP_003064667.1| 50S ribosomal protein L16
[Candidatus Liberibacter asiaticus str. psy62]
(138 letters)
>gnl|CDD|176985 CHL00044, rpl16, ribosomal protein L16.
Length = 135
Score = 178 bits (455), Expect = 3e-46
Identities = 73/135 (54%), Positives = 97/135 (71%), Gaps = 1/135 (0%)
Query: 1 MLRQPKNTKYPKQFKGRIKGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMK 60
ML PK TK+ KQ +GR+KG++ G+RICFG +AL+A E I S +IEA RRAI+R +
Sbjct: 1 ML-SPKRTKFRKQHRGRMKGISYRGNRICFGRYALQALEPAWITSRQIEAGRRAITRYAR 59
Query: 61 RAGRVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRAFR 120
R G++WI +FPD PVT +P E RMG GKG+ E WV VKPGRIL+E+ GVSE +AR A +
Sbjct: 60 RGGKIWIRIFPDKPVTMRPAETRMGSGKGSPEYWVAVVKPGRILYEMGGVSETIARAAIK 119
Query: 121 LGAAKLSVVTKFIQR 135
+ A K+ + T+FI
Sbjct: 120 IAAYKMPIKTQFIIS 134
>gnl|CDD|144001 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 169 bits (431), Expect = 2e-43
Identities = 76/129 (58%), Positives = 92/129 (71%), Gaps = 1/129 (0%)
Query: 5 PKNTKYPKQFKGRI-KGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMKRAG 63
PK TKY K KGR+ G A G+++ FG++ LKA E RI + +IEAAR AI+R +KR G
Sbjct: 1 PKRTKYRKYQKGRLEYGGAVPGNKLAFGDYGLKALEPGRITARQIEAARIAINRYLKRGG 60
Query: 64 RVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRAFRLGA 123
++WI VFPD PVT KP E RMGKGKG E W RVKPG+ILFEI GVSEEVA+ A R A
Sbjct: 61 KLWIRVFPDKPVTKKPAETRMGKGKGKPEGWAARVKPGQILFEIGGVSEEVAKEALRRAA 120
Query: 124 AKLSVVTKF 132
+KL + TK
Sbjct: 121 SKLPIKTKI 129
>gnl|CDD|30546 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 155 bits (393), Expect = 4e-39
Identities = 79/140 (56%), Positives = 97/140 (69%), Gaps = 2/140 (1%)
Query: 1 MLRQPKNTKYPKQFKGRIKGV--AKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRG 58
+ QPK TKY KQ KGR G+ AKGG+++ FG + L A E +I + +IEAAR A +R
Sbjct: 1 HMLQPKRTKYRKQHKGRGPGITIAKGGNKVFFGEYGLVALEPGQITARQIEAARIAANRY 60
Query: 59 MKRAGRVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRA 118
+KR G +WI VFPD P+T KP E RMGKGKG E W RVKPGR+LFEI GV EE+AR A
Sbjct: 61 LKRGGGLWIRVFPDKPLTEKPGEDRMGKGKGKPEGWAARVKPGRVLFEIAGVPEELAREA 120
Query: 119 FRLGAAKLSVVTKFIQRVVE 138
R AAKL V TKF+ R+ +
Sbjct: 121 LRRAAAKLPVKTKFVIRIEK 140
>gnl|CDD|38632 KOG3422, KOG3422, KOG3422, Mitochondrial ribosomal protein L16
[Translation, ribosomal structure and biogenesis].
Length = 221
Score = 123 bits (309), Expect = 2e-29
Identities = 55/136 (40%), Positives = 80/136 (58%), Gaps = 4/136 (2%)
Query: 4 QPKNTKYPKQFKGRI-KGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMK-- 60
P+ TKY K +GR+ +G ++ G+ + FG + L+A+ + S++ EA R +R M
Sbjct: 41 APERTKYRKIQRGRVPRGGSERGTELIFGRYGLRAKSGGILDSAQFEAMRLTRARKMNPR 100
Query: 61 RAGRVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDG-VSEEVARRAF 119
G++W P++PVT K E RMG GKG ++ WV RVK GRILFE+ G V EE AR+A
Sbjct: 101 NNGKIWRRPAPNLPVTVKGNETRMGGGKGAIDHWVARVKAGRILFEMGGDVEEEEARQAL 160
Query: 120 RLGAAKLSVVTKFIQR 135
A KL +F+
Sbjct: 161 LQAAHKLPFKYEFVSE 176
>gnl|CDD|88606 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an
essential protein in the large ribosomal subunit of
bacteria, mitochondria, and chloroplasts. Large subunits
that lack L16 are defective in peptidyl transferase
activity, peptidyl-tRNA hydrolysis activity, association
with the 30S subunit, binding of aminoacyl-tRNA and
interaction with antibiotics. L16 is required for the
function of elongation factor P (EF-P), a protein
involved in peptide bond synthesis through the
stimulation of peptidyl transferase activity by the
ribosome. Mutations in L16 and the adjoining bases of
23S rRNA confer antibiotic resistance in bacteria,
suggesting a role for L16 in the formation of the
antibiotic binding site. The GTPase RbgA (YlqF) is
essential for the assembly of the large subunit, and it
is believed to regulate the incorporation of L16. L10e
is the archaeal and eukaryotic cytosolic homolog of
bacterial L16. L16 and L10e exhibit structural
differences at the N-terminus..
Length = 112
Score = 120 bits (302), Expect = 1e-28
Identities = 61/112 (54%), Positives = 78/112 (69%), Gaps = 2/112 (1%)
Query: 24 GGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMKR-AGRVWICVFPDVPVTAKPTEV 82
G+++ FG + L A E RI + ++EAAR AI+R +K+ G++WI VFPD PVT KP E
Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYLKKKGGKLWIRVFPDHPVTKKPLET 60
Query: 83 RMGKGKGNVEKWVCRVKPGRILFEIDGVS-EEVARRAFRLGAAKLSVVTKFI 133
RMGKGKG E WV RVKPG+ILFE+ GV EEVA+ A R A KL + TK +
Sbjct: 61 RMGKGKGKPEGWVARVKPGQILFEVRGVPEEEVAKEALRRAAKKLPIKTKIV 112
>gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 30.3 bits (69), Expect = 0.18
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 2/63 (3%)
Query: 73 VPVTAKPTEVRMGKGKG-NVEKWVCRVKPGRILFE-IDGVSEEVARRAFRLGAAKLSVVT 130
P T +P +R+G+ G K G FE + EE+ ++ + +
Sbjct: 29 GPTTRRPLVLRLGEEPGAIPGAVKVEYKDGLKKFEDFSELREEIEDETDKISGTGKGISS 88
Query: 131 KFI 133
+ I
Sbjct: 89 EPI 91
>gnl|CDD|39457 KOG4256, KOG4256, KOG4256, Kinetochore component [Cell cycle control,
cell division, chromosome partitioning].
Length = 2209
Score = 27.1 bits (59), Expect = 1.9
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 91 VEKWVC-RVKPGRILFEIDGVSEEVARRAFRLGAAKLS 127
+EK +C KPG L E + + E+ A + G AK S
Sbjct: 1873 LEKGLCISEKPGEDLSEEEELEEDEALARLKDGIAKFS 1910
>gnl|CDD|147618 pfam05536, Neurochondrin, Neurochondrin. This family contains
several eukaryotic neurochondrin proteins. Neurochondrin
induces hydroxyapatite resorptive activity in bone
marrow cells resistant to bafilomycin A1, an inhibitor
of macrophage- and osteoclast-mediated resorption.
Expression of the gene is localized to chondrocyte,
osteoblast, and osteocyte in the bone and to the
hippocampus and Purkinje cell layer of cerebellum in the
brain.
Length = 542
Score = 26.6 bits (59), Expect = 2.1
Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 12/54 (22%)
Query: 41 NRIGSSEIEAARRAISRGMKRAGRVWICVFPDVPVTAKP----------TEVRM 84
+++ S+ + A + + + G WI F V EVR+
Sbjct: 242 SKLTPSQRDPALKLAANLLSALGPQWI--FAGDKVPNSKFLLLLLNLACVEVRV 293
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a
homodimer. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Sorbitol and aldose reductase are NAD(+) binding
proteins of the polyol pathway, which interconverts
glucose and fructose. Sorbitol dehydrogenase is
tetrameric and has a single catalytic zinc per subunit.
Length = 351
Score = 26.0 bits (58), Expect = 3.4
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 17 RIKGVAKGGSRICFGN--------FALKAQEANRIGSSEIEAARRAISR 57
R G G + + G ALKA A++I SE ARR ++
Sbjct: 166 RRSGFKPGDTALVLGAGPIGLLTILALKAAGASKIIVSEPSEARRELAE 214
>gnl|CDD|88404 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase.
Members of this family contain the SIS (Sugar ISomerase)
domain. The SIS domain is found in many phosphosugar
isomerases and phosphosugar binding proteins. The
bacterial cell wall sugar N-acetylmuramic acid carries a
unique D-lactyl ether substituent at the C3 position.
The etherase catalyzes the cleavage of the lactyl ether
bond of N-acetylmuramic acid 6-phosphate..
Length = 257
Score = 25.1 bits (55), Expect = 7.0
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 82 VRMGKGKGNV--------EKWVCRVKPGRILFEIDGVSEEVARRAF 119
+R+GK GN+ EK R RI+ E GVS + A A
Sbjct: 201 IRLGKVYGNLMVDVRATNEKLRERAI--RIVMEATGVSRDEAEAAL 244
>gnl|CDD|73393 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). Imidazole glycerol phosphate synthase
(IGPS) catalyzes the fifth step of histidine
biosynthesis, the formation of the imidazole ring. IGPS
converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria..
Length = 243
Score = 25.1 bits (55), Expect = 7.3
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 111 SEEVARRAFRLGAAKLSVVTKFIQR 135
S E ARR R GA K+S+ + ++
Sbjct: 82 SLEDARRLLRAGADKVSINSAAVEN 106
>gnl|CDD|29363 cd01941, YeiC_kinase_like, YeiC-like sugar kinase. Found in
eukaryotes and bacteria, YeiC-like kinase is part of the
ribokinase/pfkB sugar kinase superfamily. Its
oligomerization state is unknown at this time..
Length = 288
Score = 24.9 bits (54), Expect = 7.9
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 100 PGRILFEIDGVSEEVARRAFRLG 122
PG + GV +A RLG
Sbjct: 27 PGHVKQSPGGVGRNIAENLARLG 49
>gnl|CDD|107326 cd06331, PBP1_AmiC_like, Type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF). This group
includes the type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF), found in
bacteria and Archaea. AmiC controls expression of the
amidase operon by a ligand-triggered conformational
switch. In the absence of ligand or presence of
butyramide (repressor), AmiC (the ligand sensor and
negative regulator) adopts an open conformation and
inhibits the transcription antitermination function of
AmiR by direct protein-protein interaction. In the
presence of inducing ligands such as acetamide, AmiC
adopts a closed conformation which disrupts a silencing
AmiC-AmiR complex and the expression of amidase and
other genes of the operon is induced. FmdDEF is
predicted to be an ATP-dependent transporter and closely
resembles the periplasmic binding protein and the two
transmembrane proteins present in various hydrophobic
amino acid-binding transport systems.
Length = 333
Score = 24.4 bits (54), Expect = 9.4
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 37 AQEANRIGSSEIEAARRAISRGMKRA--GRVWI 67
A + GS++ EA R A+ A G V I
Sbjct: 287 AAAVEKAGSTDPEAVRAALEGVSFDAPQGPVRI 319
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
0.322 0.137 0.409
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,617,352
Number of extensions: 78492
Number of successful extensions: 233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 228
Number of HSP's successfully gapped: 22
Length of query: 138
Length of database: 6,263,737
Length adjustment: 84
Effective length of query: 54
Effective length of database: 4,448,581
Effective search space: 240223374
Effective search space used: 240223374
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 (23.8 bits)