RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11810
(93 letters)
>gnl|CDD|220215 pfam09379, FERM_N, FERM N-terminal domain. This domain is the
N-terminal ubiquitin-like structural domain of the FERM
domain.
Length = 79
Score = 58.0 bits (141), Expect = 6e-13
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 25 VTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKIHK 83
V +D +LEF + + TG++L DQ + +GLRE +FGLQ+ D + + W+ L KK+ K
Sbjct: 1 VRLLDGTQLEFTVDKSATGQELLDQVCQRLGLREKDYFGLQFNDKKNERIWLDLDKKLRK 60
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized
plasmamembrane domains. Some PDZ domain containing
proteins bind one or more of this family. Now includes
JAKs.
Length = 201
Score = 57.3 bits (139), Expect = 1e-11
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 23 VRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDL-TWIKLYKK 80
++V +D LEF + +TT ++L + + +G+RE +FGLQ+ D DL W+ K
Sbjct: 2 LKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLRHWLDPAKT 61
Query: 81 I 81
+
Sbjct: 62 L 62
>gnl|CDD|238715 cd01434, EFG_mtEFG1_IV, EFG_mtEFG1_IV: domains similar to domain
IV of the bacterial translational elongation factor
(EF) EF-G. Included in this group is a domain of
mitochondrial Elongation factor G1 (mtEFG1) proteins
homologous to domain IV of EF-G. Eukaryotic cells
harbor 2 protein synthesis systems: one localized in
the cytoplasm, the other in the mitochondria. Most
factors regulating mitochondrial protein synthesis are
encoded by nuclear genes, translated in the cytoplasm,
and then transported to the mitochondria. The
eukaryotic system of elongation factor (EF) components
is more complex than that in prokaryotes, with both
cytoplasmic and mitochondrial elongation factors and
multiple isoforms being expressed in certain species.
During the process of peptide synthesis and tRNA site
changes, the ribosome is moved along the mRNA a
distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic mtEFG1 proteins show significant homology to
bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects
and a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 116
Score = 26.6 bits (60), Expect = 1.2
Identities = 10/16 (62%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 8 VTLTFG--HPVDSYEM 21
VTL G H VDS EM
Sbjct: 83 VTLYDGSYHDVDSSEM 98
>gnl|CDD|131155 TIGR02100, glgX_debranch, glycogen debranching enzyme GlgX. This
family consists of the GlgX protein from the E. coli
glycogen operon and probable equivalogs from other
prokaryotic species. GlgX is not required for glycogen
biosynthesis, but instead acts as a debranching enzyme
for glycogen catabolism. This model distinguishes GlgX
from pullanases and other related proteins that also
operate on alpha-1,6-glycosidic linkages. In the wide
band between the trusted and noise cutoffs are
functionally similar enzymes, mostly from plants, that
act similarly but usually are termed isoamylase [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 688
Score = 25.8 bits (57), Expect = 3.4
Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 8/45 (17%)
Query: 40 TTGKQLFDQTVKTIGLR--------EVWFFGLQYADSRGDLTWIK 76
+L T K I LR E +F G AD D+TW+
Sbjct: 550 EGDDELLAFTKKLIALRKAHPVLRRERFFDGRNEADGLKDVTWLN 594
>gnl|CDD|238931 cd01971, Nitrogenase_VnfN_like, Nitrogenase_vnfN_like: VnfN subunit
of the VnfEN complex-like. This group in addition to
VnfN contains a subset of the beta subunit of the
nitrogenase MoFe protein and NifN-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protien
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 427
Score = 25.5 bits (56), Expect = 5.1
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 36 IQHTTTGKQLFDQTVKTIGLRE---VWFFGLQ-YADS--RGDLTWIK 76
H K + DQ V +E V +G Y D RGDL IK
Sbjct: 133 AGHEIVLKAIIDQYVGQSEEKEPGLVNLWGPVPYQDPFWRGDLEEIK 179
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 25.2 bits (56), Expect = 5.4
Identities = 8/16 (50%), Positives = 9/16 (56%), Gaps = 2/16 (12%)
Query: 8 VTLTFG--HPVDSYEM 21
TL G H VDS E+
Sbjct: 562 ATLYDGSYHDVDSSEL 577
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar to
bacterial alanine racemases. They exist as homodimers
with active sites that lie at the interface between the
TIM barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity. Also members of this subfamily are proteins
with homology to ODC but do not possess any catalytic
activity, the Antizyme inhibitor (AZI) and ODC-paralogue
(ODC-p). AZI binds to the regulatory protein Antizyme
with a higher affinity than ODC and prevents ODC
degradation. ODC-p is a novel ODC-like protein, present
only in mammals, that is specifically exressed in the
brain and testes. ODC-p may function as a
tissue-specific antizyme inhibitory protein.
Length = 362
Score = 25.1 bits (56), Expect = 6.6
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 7/29 (24%)
Query: 12 FGHPVDS-------YEMNVRVTTMDAELE 33
F +P S E+ VR+ T D+E E
Sbjct: 74 FANPCKSISDIRYAAELGVRLFTFDSEDE 102
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 25.1 bits (56), Expect = 6.6
Identities = 10/16 (62%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 8 VTLTFG--HPVDSYEM 21
VTL G H VDS EM
Sbjct: 565 VTLFDGSYHDVDSSEM 580
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
0.322 0.135 0.411
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,535,594
Number of extensions: 350921
Number of successful extensions: 230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 230
Number of HSP's successfully gapped: 12
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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: 53 (24.2 bits)