RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780262|ref|YP_003064675.1| 30S ribosomal protein S10
[Candidatus Liberibacter asiaticus str. psy62]
(104 letters)
>gnl|CDD|144070 pfam00338, Ribosomal_S10, Ribosomal protein S10p/S20e. This family
includes small ribosomal subunit S10 from prokaryotes
and S20 from eukaryotes.
Length = 97
Score = 120 bits (303), Expect = 1e-28
Identities = 50/95 (52%), Positives = 69/95 (72%)
Query: 10 ICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEM 69
I LK++D ++L+S ++ IV K+ G ++ GPIP P R TV RSPHVDKKSR+Q EM
Sbjct: 3 IKLKSYDHKLLESYVKFIVEAAKRLGIKVSGPIPLPTKRLRVTVLRSPHVDKKSREQFEM 62
Query: 70 RIYKRLLYIIKPTPQTVDALMKLDIAAGVNVVIKL 104
R +KRL+ I TP+TVDAL+++D+ GV+V IKL
Sbjct: 63 RTHKRLIDIYDATPETVDALLRIDLPEGVDVEIKL 97
>gnl|CDD|30400 COG0051, RpsJ, Ribosomal protein S10 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 116 bits (291), Expect = 2e-27
Identities = 57/98 (58%), Positives = 73/98 (74%)
Query: 7 RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQ 66
+I I LK+FD R+LD REIV T K++G+ + GPIP P R TV RSPH +K SR+Q
Sbjct: 5 KIRIRLKSFDHRLLDQVCREIVETAKRTGADVKGPIPLPTKRERVTVLRSPHGEKDSREQ 64
Query: 67 LEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNVVIKL 104
EMR +KRL+ I+ PTP+TVDALM+LD+ AGV+V IKL
Sbjct: 65 FEMRTHKRLIDIVDPTPKTVDALMRLDLPAGVDVEIKL 102
>gnl|CDD|177057 CHL00135, rps10, ribosomal protein S10; Validated.
Length = 101
Score = 101 bits (254), Expect = 4e-23
Identities = 43/96 (44%), Positives = 67/96 (69%)
Query: 5 NIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSR 64
N +I I LK+F+ +L+SS ++I+ T ++ + VGPIP P R + V RSPHVDK SR
Sbjct: 6 NAKIRIKLKSFNHELLNSSCKKIIDTASRTNATAVGPIPLPTKRRIYCVLRSPHVDKDSR 65
Query: 65 DQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100
+ E+R +KR++ I P+ +T+D+LMKLD+ GV++
Sbjct: 66 EHFEIRTHKRIIDIYYPSSETIDSLMKLDLPPGVDI 101
>gnl|CDD|38531 KOG3321, KOG3321, KOG3321, Mitochondrial ribosomal protein S10
[Translation, ribosomal structure and biogenesis].
Length = 175
Score = 60.8 bits (147), Expect = 9e-11
Identities = 29/84 (34%), Positives = 43/84 (51%)
Query: 7 RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQ 66
+ I L+ D +LDS I T G I GP P P+ R+T+ RSP + KKS++
Sbjct: 48 LVAIELRGHDKAVLDSYTDFICRTAYYLGIPIKGPEPLPKKRERWTLLRSPFIHKKSKEN 107
Query: 67 LEMRIYKRLLYIIKPTPQTVDALM 90
E R + RL+ + T T+D +
Sbjct: 108 YERRTHSRLIELYSVTGSTLDTFL 131
>gnl|CDD|36118 KOG0900, KOG0900, KOG0900, 40S ribosomal protein S20 [Translation,
ribosomal structure and biogenesis].
Length = 121
Score = 52.7 bits (126), Expect = 2e-08
Identities = 26/100 (26%), Positives = 50/100 (50%), Gaps = 2/100 (2%)
Query: 2 TSRNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPH-VD 60
T +I I L + + L+ ++V K+ ++ GP+ P + + T ++P
Sbjct: 16 TPEIHKIRITLTSQKVKSLEKVCADLVRGAKEKNLKVKGPVRLPTKVLKITTRKTPCGEG 75
Query: 61 KKSRDQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100
K+ D+ EMR++KRL+ + P+ + V + + I GV V
Sbjct: 76 SKTWDRFEMRVHKRLIDLHSPS-EIVKQITSISIEPGVEV 114
>gnl|CDD|144019 pfam00274, Glycolytic, Fructose-bisphosphate aldolase class-I.
Length = 348
Score = 28.8 bits (65), Expect = 0.30
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 23 SMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD 60
+ R+++ TT G I G I F ++ + T + P VD
Sbjct: 44 AYRQLLFTTPGLGEYISGVILFEETLYQKTDDGKPFVD 81
>gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 27.6 bits (61), Expect = 0.88
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 21 DSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMR-IYKRL 75
+ EI ++ G I+G IP+ + I VN P V+ S++ + ++L
Sbjct: 225 NLGDSEIEEYCEEEGIPILGEIPYDKDIPEAYVNGEPFVEPDSKEAEAILEEAEKL 280
>gnl|CDD|146362 pfam03686, UPF0146, Uncharacterized protein family (UPF0146). The
function of this family of proteins is unknown.
Length = 127
Score = 27.0 bits (60), Expect = 1.2
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 68 EMRIYK--RLLYIIKPTPQTVDALMKLDIAAGVNVVIK 103
+ IY+ L+Y I+P P+ A++ + A G + IK
Sbjct: 64 NISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIK 101
>gnl|CDD|31447 COG1255, COG1255, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 129
Score = 26.8 bits (59), Expect = 1.5
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 68 EMRIYK--RLLYIIKPTPQTVDALMKLDIAAGVNVVIK 103
+ IY+ L+Y I+P P+ A++ + A G + IK
Sbjct: 64 NISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIK 101
>gnl|CDD|29941 cd00948, FBP_aldolase_I_a, Fructose-1,6-bisphosphate aldolase.
The enzyme catalyzes the cleavage of fructose
1,6-bisphosphate to glyceraldehyde 3-phosphate and
dihydroxyacetone phosphate (DHAP). This family includes
proteins found in vertebrates, plants, and bacterial
plant pathogens. Mutations in the aldolase genes in
humans cause hemolytic anemia and hereditary fructose
intolerance. The enzyme is a member of the class I
aldolase family, which utilizes covalent catalysis
through a Schiff base formed between a lysine residue
of the enzyme and ketose substrates..
Length = 330
Score = 26.3 bits (58), Expect = 1.8
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 25 REIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD 60
RE++ TT G I G I F ++ + T + P VD
Sbjct: 48 RELLFTTPGLGQYISGVILFEETLYQKTDDGKPFVD 83
>gnl|CDD|132784 cd06874, PX_KIF16B_SNX23, The phosphoinositide binding Phox
Homology domain of KIF16B kinesin or Sorting Nexin 23.
The PX domain is a phosphoinositide (PI) binding module
present in many proteins with diverse functions such as
cell signaling, vesicular trafficking, protein sorting,
and lipid modification, among others. KIF16B, also
called sorting nexin 23 (SNX23), is a family-3 kinesin
which harbors an N-terminal kinesin motor domain
containing ATP and microtubule binding sites, a
ForkHead Associated (FHA) domain, and a C-terminal PX
domain. The PX domain of KIF16B binds to
phosphatidylinositol-3-phosphate (PI3P) in early
endosomes and plays a role in the transport of early
endosomes to the plus end of microtubules. By
regulating early endosome plus end motility, KIF16B
modulates the balance between recycling and degradation
of receptors. SNXs make up the largest group among PX
domain containing proteins. They are involved in
regulating membrane traffic and protein sorting in the
endosomal system. The PX domain of SNXs binds PIs and
targets the protein to PI-enriched membranes. SNXs
differ from each other in PI-binding specificity and
affinity, and the presence of other protein-protein
interaction domains, which help determine subcellular
localization and specific function in the endocytic
pathway.
Length = 127
Score = 25.8 bits (57), Expect = 2.3
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 39 VGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQ 84
V + FP ++ N+S V K+ R QLE + + P
Sbjct: 55 VAALEFPP--KKLFGNKSERVAKERRRQLE-TYLRNFFSVCLKLPA 97
>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 25.2 bits (55), Expect = 3.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 81 PTPQTVDALMKLDIAAGVNVVI 102
P PQT + LM L+I N++I
Sbjct: 124 PQPQTREHLMALEIIGIKNIII 145
>gnl|CDD|176674 cd07251, Glo_EDI_BRP_like_10, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 121
Score = 25.2 bits (56), Expect = 3.6
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 82 TPQTVDALMKLDIAAGVNVV 101
+ + VDA++ AAG +V
Sbjct: 74 SEEEVDAVLARAAAAGATIV 93
>gnl|CDD|29575 cd02647, nuc_hydro_TvIAG, nuc_hydro_ TvIAG: Nucleoside
hydrolases similar to the
Inosine-adenosine-guanosine-preferring nucleoside
hydrolase from Trypanosoma vivax. Nucleoside
hydrolases cleave the N-glycosidic bond in nucleosides
generating ribose and the respective base. Nucleoside
hydrolases vary in their substrate specificity. This
group contains eukaryotic and bacterial proteins
similar to the purine specific
inosine-adenosine-guanosine-preferring nucleoside
hydrolase (IAG-NH) from T. vivax. T. vivax IAG-NH is
of the order of a thousand to ten thousand fold more
specific towards the naturally occurring purine
nucleosides, than towards the pyrimidine nucleosides. .
Length = 312
Score = 25.3 bits (55), Expect = 3.7
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 19 ILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNR 55
++D + + K GS PFPRS RR
Sbjct: 52 LIDRLGQRDAIPVGKGGS--RAVNPFPRSWRRDAAFS 86
>gnl|CDD|146287 pfam03568, Peptidase_C50, Peptidase family C50.
Length = 339
Score = 24.6 bits (54), Expect = 5.4
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 36 SQIVGPIPFPRSIRRFTVNRSPHVDK------KSRDQLEMRIYKRLLYIIKPTPQTVDAL 89
I+ + R + +RSP + + SRD E + II+ ++V
Sbjct: 3 EIIISKDTKTLLLSRLSPDRSPIILRLPLDRHNSRDLDESTLLDEFRRIIEEDNESVTTK 62
Query: 90 MK 91
K
Sbjct: 63 NK 64
>gnl|CDD|176211 cd08249, enoyl_reductase_like, enoyl_reductase_like. Member
identified as possible enoyl reductase of the MDR
family. 2-enoyl thioester reductase (ETR) catalyzes the
NADPH-dependent dependent conversion of trans-2-enoyl
acyl carrier protein/coenzyme A (ACP/CoA) to
acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl
thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which
contacts a mononucleotide. The N-terminal catalytic
domain has a distant homology to GroES. These proteins
typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site, and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding
induces a conformational closing of this cleft.
Coenzyme binding typically precedes and contributes to
substrate binding. Candida tropicalis enoyl thioester
reductase (Etr1p) catalyzes the NADPH-dependent
reduction of trans-2-enoyl thioesters in mitochondrial
fatty acid synthesis. Etr1p forms homodimers with each
subunit containing a nucleotide-binding Rossmann fold
domain and a catalytic domain.
Length = 339
Score = 24.9 bits (55), Expect = 5.8
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 24 MREIVLTTKKSGSQIVGPIPFP 45
+ VLT G +V +P P
Sbjct: 1 QKAAVLTGPGGGLLVVVDVPVP 22
>gnl|CDD|144549 pfam00995, Sec1, Sec1 family.
Length = 558
Score = 24.5 bits (54), Expect = 6.1
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 76 LYIIKPTPQTVDALMK 91
+Y I+PT + VD ++
Sbjct: 47 IYFIRPTKENVDRIID 62
>gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid
receptor, a member of the nuclear receptor superfamily.
The ligand binding domain of the glucocorticoid
receptor (GR): GR is a ligand-activated transcription
factor belonging to the nuclear receptor superfamily.
It binds with high affinity to cortisol and other
glucocorticoids. GR is expressed in almost every cell
in the body and regulates genes controlling a wide
variety of processes including the development,
metabolism, and immune response of the organism. In the
absence of hormone, the glucocorticoid receptor (GR) is
complexes with a variety of heat shock proteins in the
cytosol. The binding of the glucocorticoids results in
release of the heat shock proteins and transforms it to
its active state. One mechanism of action of GR is by
direct activation of gene transcription. The activated
form of GR forms dimers, translocates into the nucleus,
and binds to specific hormone responsive elements,
activating gene transcription. GR can also function as
a repressor of other gene transcription activators,
such as NF-kappaB and AF-1 by directly binding to them,
and bloc king the expression of their activated genes.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
GR has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD). The LBD
also functions for dimerization and chaperone protein
association.
Length = 247
Score = 24.1 bits (52), Expect = 7.7
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 15 FDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIY 72
+DS + DS+ R + G Q+V + + ++I F R+ H+D DQ+ + Y
Sbjct: 18 YDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGF---RNLHLD----DQMTLLQY 68
>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
2). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP
is released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma
is a member of the same family as eubacterial IF2, but
the two proteins are only distantly related. This
family includes translation initiation, elongation, and
release factors.
Length = 203
Score = 24.1 bits (53), Expect = 8.7
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 81 PTPQTVDALMKLDIAAGVNVVI 102
P PQT + L L+I +++I
Sbjct: 121 PQPQTSEHLAALEIMGLKHIII 142
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
0.326 0.139 0.393
Gapped
Lambda K H
0.267 0.0673 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,203,312
Number of extensions: 54490
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 26
Length of query: 104
Length of database: 6,263,737
Length adjustment: 71
Effective length of query: 33
Effective length of database: 4,729,498
Effective search space: 156073434
Effective search space used: 156073434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.5 bits)