RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030330
(179 letters)
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 246 bits (630), Expect = 3e-84
Identities = 99/149 (66%), Positives = 119/149 (79%)
Query: 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNT 69
K +V+D + H+LGRLAS+VAKELL GQK+V VRCE++ +SG L R K+KY FLRKRMNT
Sbjct: 4 KVIVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNT 63
Query: 70 KPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129
P GP H RAP+ IFWRTVRGM+PHKTKRGAAAL RLK +EGVPAPYDKVKR+VIP AL
Sbjct: 64 NPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSAL 123
Query: 130 KVLRLQKGHKYCLLGRLASEVGWNYYDTI 158
+VLRL+ Y +LG L++ VGW Y D +
Sbjct: 124 RVLRLKPERPYTVLGDLSAHVGWKYADVV 152
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 179 bits (456), Expect = 1e-58
Identities = 83/143 (58%), Positives = 99/143 (69%), Gaps = 1/143 (0%)
Query: 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71
V+D H+LGRLAS+VAK+LLNG+KVV V E+I +SG R K+KY FLRKR T P
Sbjct: 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNP 60
Query: 72 SHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKV 131
GP RAP++IF RTVRGM+PHKT RG AAL RLK Y G+P DK KR+V+P+AL V
Sbjct: 61 RRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-V 119
Query: 132 LRLQKGHKYCLLGRLASEVGWNY 154
RL KY LG LA +GW Y
Sbjct: 120 SRLSPTRKYVTLGELAKFLGWKY 142
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 128 bits (325), Expect = 4e-39
Identities = 51/114 (44%), Positives = 62/114 (54%), Gaps = 13/114 (11%)
Query: 12 VVVDARHHMLGRLASIVAKELLN------------GQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA+ +LGRLAS VAK LL G VV V E+I ++G RQK+ Y
Sbjct: 2 HVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYY 61
Query: 60 MRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGV 113
P+ GP+H RAP +I R VRGM+P K K G AAL RLK YEG
Sbjct: 62 RHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 120 bits (304), Expect = 9e-36
Identities = 48/129 (37%), Positives = 61/129 (47%), Gaps = 15/129 (11%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA+ +LGRLAS VAK L G VV + E+I ++G R + KY
Sbjct: 2 HVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTG-KKRDQKKY 60
Query: 60 MR-FLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
R P+ R P +I R VRGM+P K K G AAL RLK Y G P P+
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLP-KNKLGRAALKRLKVYAGSPHPHA 119
Query: 119 KVKRMVIPD 127
K V+
Sbjct: 120 AQKPEVLEI 128
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 113 bits (286), Expect = 8e-33
Identities = 58/144 (40%), Positives = 81/144 (56%), Gaps = 3/144 (2%)
Query: 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71
VV+DA +LGRLAS VAK LL G++VV V E+ ++G R KY + + + P
Sbjct: 5 VVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNP 64
Query: 72 SHGPIHF-RAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALK 130
+ R P +IF RT+RGM+P+K RG AL RLK Y GVP + + VI +A
Sbjct: 65 YRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD- 123
Query: 131 VLRLQKGHKYCLLGRLASEVGWNY 154
+ RL KY LG ++ E+G +
Sbjct: 124 LSRL-STIKYVTLGEVSKELGAKF 146
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 100 bits (250), Expect = 3e-27
Identities = 47/138 (34%), Positives = 66/138 (47%), Gaps = 18/138 (13%)
Query: 12 VVVDARHHMLGRLASIVAKELLN------------GQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA +LGRLAS VAK L G V+ + E++ ++G + K Y
Sbjct: 16 YVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYY 75
Query: 60 MRFLRKRMNTKPS-HGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
P+ GP+ R P +I R VRGM+P K G AAL RLK Y G+P P+
Sbjct: 76 RHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLP-KNPLGRAALKRLKVYAGIPHPH- 133
Query: 119 KVKRMVIPDALKVLRLQK 136
P+AL++ L+
Sbjct: 134 ---EAQKPEALELKLLKG 148
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 45.4 bits (109), Expect = 1e-06
Identities = 31/123 (25%), Positives = 51/123 (41%), Gaps = 33/123 (26%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA +LGRLAS VA L G V+ + E++ ++G + K+ Y
Sbjct: 16 YVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYY 75
Query: 60 --------MRF--LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKA 109
++ + + K P ++ + V+GM+P K G A +LK
Sbjct: 76 RHSGYPGGLKEITFGELLAKK----------PERVIEKAVKGMLP-KNPLGRAMFKKLKV 124
Query: 110 YEG 112
Y G
Sbjct: 125 YAG 127
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 41.5 bits (98), Expect = 3e-05
Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 33/122 (27%)
Query: 13 VVDARHHMLGRLASIVAKELLNGQK------------VVAVRCEEICMSGGLVRQKMKYM 60
VVDA LGRLAS VA+ L K V+ + E++ ++G + QK+ Y
Sbjct: 15 VVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYR 74
Query: 61 ----------RFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAY 110
R + + R P ++ V+GM+P K + G +LK Y
Sbjct: 75 HSGYPGGLKSRTFEEMIA----------RKPERVLEHAVKGMLP-KNRLGRKLFKKLKVY 123
Query: 111 EG 112
G
Sbjct: 124 AG 125
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 39.6 bits (93), Expect = 2e-04
Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 25/118 (21%)
Query: 13 VVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYM 60
++DA+ LGRLA+ +A L G V+ + E+I ++G
Sbjct: 18 IIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTG-----NKTSQ 72
Query: 61 RFLRKRMNTKPSHGPI------HFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
+F R + +P I R P +I + V+GM+P K G +LK Y+G
Sbjct: 73 KFYV-RHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYKG 128
>gnl|CDD|119400 cd06661, GGCT_like, GGCT-like domains, also called AIG2-like
family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes
the formation of pyroglutamic acid (5-oxoproline) from
dipeptides containing gamma-glutamyl, and is a dimeric
protein. In Homo sapiens, the protein is encoded by the
gene C7orf24, and the enzyme participates in the
gamma-glutamyl cycle. Hereditary defects in the
gamma-glutamyl cycle have been described for some of the
genes involved, but not for C7orf24. The synthesis and
metabolism of glutathione
(L-gamma-glutamyl-L-cysteinylglycine) ties the
gamma-glutamyl cycle to numerous cellular processes;
glutathione acts as a ubiquitous reducing agent in
reductive mechanisms involved in protein and DNA
synthesis, transport processes, enzyme activity, and
metabolism. AIG2 (avrRpt2-induced gene) is an
Arabidopsis protein that exhibits RPS2- and
avrRpt2-dependent induction early after infection with
Pseudomonas syringae pv maculicola strain ES4326
carrying avrRpt2. avrRpt2 is an avirulence gene that can
convert virulent strains of P. syringae to avirulence on
Arabidopsis thaliana, soybean, and bean. The family also
includes bacterial tellurite-resistance proteins (trgB);
tellurium (Te) compounds are used in industrial
processes and had been used as antimicrobial agents in
the past. Some members have been described proteins
involved in cation transport (chaC).
Length = 99
Score = 27.3 bits (61), Expect = 1.9
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 101 AAALARLKAYEGVPAPYDKVKRMVIPDALKVLR 133
LARL A+EGVP Y + + V + + +
Sbjct: 61 PEDLARLDAFEGVPGGYRREEVEVELEDGEGVE 93
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 28.7 bits (64), Expect = 2.3
Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 83 KIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCL 142
+FW ++ G++ + + L L E + D +R+++P A ++R L
Sbjct: 181 DVFWSSMWGILLNDERLRTGVLNSLMREENNDSHMDWSERLILPHAGLMVR-------AL 233
Query: 143 LGRLASE 149
L
Sbjct: 234 CAGLGDN 240
>gnl|CDD|239789 cd04256, AAK_P5CS_ProBA, AAK_P5CS_ProBA: Glutamate-5-kinase (G5K)
domain of the bifunctional delta
1-pyrroline-5-carboxylate synthetase (P5CS), composed
of an N-terminal G5K (ProB) and a C-terminal glutamyl
5- phosphate reductase (G5PR, ProA), the first and
second enzyme catalyzing proline (and, in mammals,
ornithine) biosynthesis. G5K transfers the terminal
phosphoryl group of ATP to the gamma-carboxyl group of
glutamate, and is subject to feedback allosteric
inhibition by proline or ornithine. In plants, proline
plays an important role as an osmoprotectant and, in
mammals, ornithine biosynthesis is crucial for proper
ammonia detoxification, since a G5K mutation has been
shown to cause human hyperammonaemia.
Length = 284
Score = 27.4 bits (61), Expect = 4.1
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 21/74 (28%)
Query: 9 AKRVVV----------DARHHMLGRLASIV--AKELLN-GQKVVAVRCEEICMSG--GLV 53
AKR+VV D LGRLASIV EL + G++V+ V SG
Sbjct: 8 AKRIVVKLGSAVVTREDECGLALGRLASIVEQVSELQSQGREVILV------TSGAVAFG 61
Query: 54 RQKMKYMRFLRKRM 67
+Q++++ L M
Sbjct: 62 KQRLRHEILLSSSM 75
>gnl|CDD|215819 pfam00251, Glyco_hydro_32N, Glycosyl hydrolases family 32
N-terminal domain. This domain corresponds to the
N-terminal domain of glycosyl hydrolase family 32 which
forms a five bladed beta propeller structure.
Length = 305
Score = 27.2 bits (61), Expect = 5.4
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 1/21 (4%)
Query: 67 MNTKPSHGPIHFRAPAKIFWR 87
+ P HFR P K+ W
Sbjct: 117 IINPPPGYTKHFRDP-KVAWY 136
>gnl|CDD|177439 PHA02620, PHA02620, VP3; Provisional.
Length = 353
Score = 26.9 bits (59), Expect = 6.2
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 71 PSH-GPIHFRAPAKIFWRTVRGMIPHKTKR 99
P H GP F A ++ FW VR +P T +
Sbjct: 149 PRHWGPTLFSAISQAFWHLVRDDLPRLTSQ 178
>gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type
nickel import system contains the type 2 periplasmic
binding fold. This family represents the periplasmic
substrate-binding domain of nickel transport system,
which functions in the import of nickel and in the
control of chemotactic response away from nickel. The
ATP-binding cassette (ABC) type nickel transport system
is comprised of five subunits NikABCDE: the two
pore-forming integral inner membrane proteins NikB and
NikC; the two inner membrane-associated proteins with
ATPase activity NikD and NikE; and the periplasmic
nickel binding NikA, the initial nickel receptor. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA. The DppA binds dipeptides and some
tripeptides and is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which precludes
any involvement in chemotaxis. Most of other periplasmic
binding proteins are comprised of only two globular
subdomains corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 488
Score = 26.8 bits (60), Expect = 6.8
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 117 YDKVKRMVIPDAL-KVLRLQKG 137
DK+ VIPDA ++L LQ G
Sbjct: 186 IDKITVKVIPDAQTRLLALQSG 207
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.328 0.140 0.440
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,291,386
Number of extensions: 864708
Number of successful extensions: 1064
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1048
Number of HSP's successfully gapped: 27
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
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 (21.8 bits)
S2: 56 (25.3 bits)