RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032581
(137 letters)
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 170 bits (432), Expect = 4e-55
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 29 YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
YIGHLKER+LK+QM +DPTE IRKAVLRMLPRN+LRDDRDRKLRIF GSEHPFGD+PLEP
Sbjct: 82 YIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGDKPLEP 141
Query: 89 YVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKNRKKEVEAEVTA 137
+VMPPR+VRE+RPR RRAMIR QKKAE + Q+ + RK +KKEVE EVTA
Sbjct: 142 FVMPPRQVREMRPRARRAMIRAQKKAEQREQAANEKRKGKKKEVEVEVTA 191
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 71.3 bits (176), Expect = 8e-17
Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 27 YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
YR Y G LKE T E + + P I KAV MLP+N L +KL+++ G+EHP
Sbjct: 75 YRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHP 131
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 69.9 bits (172), Expect = 2e-16
Identities = 23/63 (36%), Positives = 33/63 (52%)
Query: 27 YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPL 86
Y G LK T K +ER P + +AV MLP+NKL ++L+++ GS HP +
Sbjct: 64 TGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAAQKP 123
Query: 87 EPY 89
E
Sbjct: 124 EVL 126
>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 = 63.5 bits (155), Expect = 8e-14
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 28 RYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 81
Y G LK RT +E + R P + AV MLP+N+L +KL+++ GSEHP
Sbjct: 77 GYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPH 130
>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 = 61.8 bits (151), Expect = 2e-13
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 27 YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 77
Y G LK T R P +++AV MLP+NKL ++L+++ G+
Sbjct: 64 TGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 114
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 52.6 bits (127), Expect = 1e-09
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 27 YRYIGHLKERTLKEQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
Y G LK T + R P + +AV MLP+N L ++L+++ G HP
Sbjct: 78 SGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHP 132
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 45.0 bits (107), Expect = 8e-07
Identities = 20/50 (40%), Positives = 25/50 (50%)
Query: 31 GHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
G LK T +E R P I KAV MLP+ L KL+++ G HP
Sbjct: 83 GGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHP 132
>gnl|CDD|218715 pfam05719, GPP34, Golgi phosphoprotein 3 (GPP34). This family
consists of several eukaryotic GPP34 like proteins.
GPP34 localises to the Golgi complex and is conserved
from yeast to humans. The cytosolic-ally exposed
location of GPP34 predict a role for a novel coat
protein in Golgi trafficking.
Length = 205
Score = 28.4 bits (64), Expect = 0.94
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 34 KERTLKEQMERDPTEAIRKAVL-RMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMP 92
+ R++K+ +ER +R+ V ++ R LR ++ R L +FP + +P D
Sbjct: 73 RPRSVKDWLERLSGRGLRERVAAGLVARGILRREKRRFLGLFPTTRYPLVD--------- 123
Query: 93 PRRVRELRPRVRRA 106
P LR R+R A
Sbjct: 124 PAAEAALRARLRAA 137
>gnl|CDD|216872 pfam02096, 60KD_IMP, 60Kd inner membrane protein.
Length = 193
Score = 27.5 bits (62), Expect = 2.0
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 94 RRVRELRPRVRRAMIREQKKAEMQQSNKDMRKNRKKE 130
+++EL+P ++ I+E+ K + Q+ ++M K K+
Sbjct: 30 AKMQELQPEIKE--IQEKYKDDPQKLQQEMMKLYKEH 64
>gnl|CDD|215152 PLN02269, PLN02269, Pyruvate dehydrogenase E1 component subunit
alpha.
Length = 362
Score = 27.8 bits (62), Expect = 2.2
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 11/44 (25%)
Query: 22 EMSVSYRYIGHLKE------RTLKE----QMERDPTEAIRKAVL 55
EM +YRY GH RT E + ERDP E +RK +L
Sbjct: 255 EMD-TYRYHGHSMSDPGSTYRTRDEISGVRQERDPIERVRKLLL 297
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 27.9 bits (62), Expect = 2.2
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 26 SYRYIGHLKERTLKEQMERD---PT-EAIRKAVLRML 58
Y +IGH K R KE + R+ PT RKA LRM+
Sbjct: 200 RYMFIGHQKGRNTKENIMRNFGMPTPHGYRKA-LRMM 235
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 26.8 bits (60), Expect = 3.0
Identities = 12/33 (36%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 103 VRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEV 135
+R+A+ EQ K+E++Q K + + K+E+E V
Sbjct: 112 MRKALQAEQGKSELEQEIKKL-EEEKEELEKRV 143
>gnl|CDD|148609 pfam07100, ASRT, Anabaena sensory rhodopsin transducer. The family
of bacterial Anabaena sensory rhodopsin transducers are
likely to bind sugars or related metabolites. The entire
protein is comprised of a single globular domain with an
eight-stranded beta-sandwich fold. There are a few
characteristics which define this beta-sandwich fold as
being distinct from other so-named folds, and these are:
1) a well conserved tryptophan, usually following a
polar residue, present at the start of the first strand;
this tryptophan appears to be central to a hydrophobic
interaction required to hold the two beta-sheets of the
sandwich together, and 2) a nearly absolutely conserved
asparagine located at the end of the second beta-strand,
that hydrogen bonds with the backbone carbonyls of the
residues 2 and 4 positions downstream from it, thereby
stabilising the characteristic tight turn between
strands 2 and 3 of the structure.
Length = 120
Score = 26.5 bits (59), Expect = 3.1
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 11/40 (27%)
Query: 66 DRDRKLRI--FPGSEHPFGDR-PLEPY--VMPPRRVRELR 100
D D L+I + F DR P+ PY +P RR R LR
Sbjct: 38 DEDAHLKITVY------FEDRDPVGPYEVTVPARRTRHLR 71
>gnl|CDD|203307 pfam05693, Glycogen_syn, Glycogen synthase. This family consists
of the eukaryotic glycogen synthase proteins GYS1, GYS2
and GYS3. Glycogen synthase (GS) is the enzyme
responsible for the synthesis of -1,4-linked glucose
chains in glycogen. It is the rate limiting enzyme in
the synthesis of the polysaccharide, and its activity
is highly regulated through phosphorylation at multiple
sites and also by allosteric effectors, mainly glucose
6-phosphate (G6P).
Length = 633
Score = 27.4 bits (61), Expect = 3.1
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 21 DEMSVSYRYIGHLKERTLKEQMER--DPTEAIRKAVLRM 57
DE Y +G E T + ++E +++ + M
Sbjct: 26 DEYGDQYCLLGPYNEHTARTEVEELEPENPSLKATLDSM 64
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 27.2 bits (61), Expect = 3.2
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 6/57 (10%)
Query: 22 EMSVSYRYIGHLKE------RTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLR 72
+ V+ + LKE E +E A+++A+L +L L D +
Sbjct: 80 ALEVAEEILESLKEKLVGKKVKRGEDVEEIVKNALKEALLEVLSVGDLFDLIEEIKS 136
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 26.9 bits (60), Expect = 3.8
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 28 RYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRD 65
+IG + R L +QMER ++ + K V R +P ++ +
Sbjct: 495 EFIGIQETRYLLDQMERKYSDLV-KEVQRQIPLQRIAE 531
>gnl|CDD|223682 COG0609, FepD, ABC-type Fe3+-siderophore transport system, permease
component [Inorganic ion transport and metabolism].
Length = 334
Score = 26.5 bits (59), Expect = 4.6
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 2 ISIYVVFFILRNLFILSLNDEMSVS 26
I + ++ F+ R L ILSL DE++ S
Sbjct: 204 IGLLLLLFLSRKLNILSLGDELAKS 228
>gnl|CDD|239950 cd04513, Glycosylasparaginase, Glycosylasparaginase catalyzes the
hydrolysis of the glycosylamide bond of
asparagine-linked glycoproteins. This enzyme is an
amidase located inside lysosomes. Mutation of this gene
in humans causes a genetic disorder known as
aspartylglycosaminuria (AGU). The glycosylasparaginase
precursor undergoes autoproteolysis through an N-O or
N-S acyl rearrangement of the peptide bond, which leads
to the cleavage of a peptide bond between an Asp and a
Thr. This proteolysis step generates an exposed
N-terminal catalytic threonine and activates the enzyme.
Length = 263
Score = 26.4 bits (59), Expect = 4.6
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 40 EQMER--DPTEAIRKAVLRMLPRNKLRD 65
E M + P EA +A+ R+ D
Sbjct: 207 EYMRQGMSPKEACLEAIKRIAKHFDGPD 234
>gnl|CDD|220884 pfam10826, DUF2551, Protein of unknown function (DUF2551). This
Archaeal family of proteins has no known function.
Length = 83
Score = 25.3 bits (56), Expect = 4.7
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 38 LKEQMERDPTEAIRKAVLRMLPRNK 62
LK+ + RD IR+AVLR+ + K
Sbjct: 1 LKKYLSRDKN-GIRRAVLRLFLKVK 24
>gnl|CDD|153361 cd07677, F-BAR_FCHSD2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH and double SH3
domains 2 (FCHSD2). F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. FCH and double SH3 domains 2 (FCHSD2)
contains an N-terminal F-BAR domain and two SH3 domains
at the C-terminus. It has been characterized only in
silico, and its biological function is still unknown.
F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 260
Score = 26.6 bits (58), Expect = 5.0
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 92 PPRRVRELRPRVRRAMIREQKK--AEMQQSNKDMRKNRKKEVEAEVTA 137
P R VR + + + + + K AE+Q++ KD+ K +KK E E A
Sbjct: 100 PARTVRLYKEQQLKRCVDQLTKIQAELQETVKDLAKGKKKYFETEQMA 147
>gnl|CDD|219699 pfam08016, PKD_channel, Polycystin cation channel. This family
contains the cation channel region of PKD1 and PKD2
proteins.
Length = 423
Score = 26.1 bits (58), Expect = 6.3
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 4 IYVVFFILRNLFILSLNDEMSV 25
+++V FIL NLF+ +ND
Sbjct: 401 VFLVIFILLNLFLAIINDSYVE 422
>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 = 25.5 bits (56), Expect = 8.0
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 44 RDPTEAIRKAVLRMLPRNKLRDDRD-RKLRIFPGSEHPFGDRPLE 87
R P+ R+ V MLP R R+L+++ G +
Sbjct: 68 RAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRV 112
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
0.323 0.138 0.388
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,353,789
Number of extensions: 693962
Number of successful extensions: 1143
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1134
Number of HSP's successfully gapped: 77
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.5 bits)