RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9055
(284 letters)
>gnl|CDD|217613 pfam03556, Cullin_binding, Cullin binding. This domain binds to
cullins and to Rbx-1, components of an E3 ubiquitin
ligase complex for neddylation. Neddylation is the
process by which the C-terminal glycine of the
ubiquitin-like protein Nedd8 is covalently linked to
lysine residues in a protein through an isopeptide bond.
The structure of this domain is composed entirely of
alpha helices.
Length = 117
Score = 176 bits (448), Expect = 4e-56
Identities = 69/117 (58%), Positives = 87/117 (74%), Gaps = 2/117 (1%)
Query: 156 IEKLKMRLPSLEAELK-DNLKFKDFYQFTFNYAKNPGQKGLDLDMAITYWNIVLQGR-FK 213
IEKLK +LP L +ELK D KFKD Y+FTF++A+ GQK LDL+ AI YW ++ R F
Sbjct: 1 IEKLKAKLPELRSELKSDPEKFKDLYRFTFDFAREEGQKSLDLETAIEYWKLLFGSRTFP 60
Query: 214 FLHLWCTFLQEHHKRSIPKDTWNLLLDFATATNEDMSNYDEEGAWPVLIDDFVEWAQ 270
L W FL+E HK+SI KDTWN+LL+F+ +ED+SNYDEEGAWP LID+FVEW +
Sbjct: 61 LLDQWIEFLEEKHKKSISKDTWNMLLEFSKTIDEDLSNYDEEGAWPSLIDEFVEWLK 117
>gnl|CDD|227444 COG5113, UFD2, Ubiquitin fusion degradation protein 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 929
Score = 30.0 bits (67), Expect = 1.9
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 36 KLDLASDNYFQNPSAYYK-EQKSSVDRKKLESLYSKYKDAS 75
K+D+ YF NP K E K +VD K L+S Y+K + S
Sbjct: 330 KIDMVDKIYFNNPRVDIKEETKLNVDEKSLDSFYTKPAEGS 370
>gnl|CDD|146254 pfam03513, Cloacin_immun, Cloacin immunity protein.
Length = 82
Score = 27.4 bits (61), Expect = 2.7
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 142 SLEAELKDNLNCDSIEKLKMRLPSLEAELKDNLKF-KDFYQFTFNY 186
SL LKDN+N + K +P L+ K+ ++ K++YQ +F+Y
Sbjct: 34 SLGLPLKDNINNGGFDVEKEWVPLLQPHFKNKIETDKNWYQISFDY 79
>gnl|CDD|153358 cd07674, F-BAR_FCHO1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only 1
protein. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
FCH domain Only 1 (FCHO1) may be involved in
clathrin-coated vesicle formation. It contains an
N-terminal F-BAR domain and a C-terminal domain of
unknown function named SAFF which is also present in
FCHO2 and endophilin interacting protein 1. 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 = 261
Score = 28.8 bits (64), Expect = 2.9
Identities = 31/138 (22%), Positives = 56/138 (40%), Gaps = 8/138 (5%)
Query: 22 GELTAINCLSQNDWKLDLASDNYFQNPSAYYKEQKSSVDRKKLESLYSKYKDASEPDKIL 81
G L A+ L L + +NY + ++ V +K+LE K K A+E +
Sbjct: 110 GTLEAVQSLQVQSQHLQKSRENYHSKCVEQERLRREGVPQKELEKAELKTKKAAESLRGS 169
Query: 82 VEGIMKFLDDLSLSPESKLVLIIAWRFKAAAQCEFSRDEFMNGMLELGCDSIEKLKMRLP 141
VE + D E K+ L A +F+ + M +++ S+E +++
Sbjct: 170 VEKYNRARGDF----EQKM-LESAQKFQDIEETHLRH---MKLLIKGYSHSVEDTHVQIG 221
Query: 142 SLEAELKDNLNCDSIEKL 159
+ E K N+ +E L
Sbjct: 222 QVHEEFKQNVENVGVENL 239
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 28.1 bits (63), Expect = 4.9
Identities = 13/48 (27%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 131 DSIEKLKMRLPSLEAELKDNLNCDSIEKLKMRLPSLEAELKDNLKFKD 178
+ I++ K L + E+++ + + +E+L+ ++ LE +LK L KD
Sbjct: 60 EDIKEAKEILEESDPEMRE-MAKEELEELEEKIEELEEQLKVLLLPKD 106
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 28.3 bits (64), Expect = 5.6
Identities = 14/54 (25%), Positives = 22/54 (40%)
Query: 133 IEKLKMRLPSLEAELKDNLNCDSIEKLKMRLPSLEAELKDNLKFKDFYQFTFNY 186
+ K + RL LE LK LN D + L + L + L+ F + +
Sbjct: 340 LGKAEARLHILEGLLKAILNIDEVINLIRSSDEAKKALIEELEKLGFSEIQADA 393
>gnl|CDD|239545 cd03462, 1,2-CCD, chlorocatechol 1,2-dioxygenases (1,2-CCDs) (type
II enzymes) are homodimeric intradiol dioxygenases that
degrade chlorocatechols via the addition of molecular
oxygen and the subsequent cleavage between two adjacent
hydroxyl groups. This reaction is part of the modified
ortho-cleavage pathway which is a central oxidative
bacterial pathway that channels chlorocatechols, derived
from the degradation of chlorinated benzoic acids,
phenoxyacetic acids, phenols, benzenes, and other
aromatics into the energy-generating tricarboxylic acid
pathway.
Length = 247
Score = 27.7 bits (62), Expect = 6.8
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 254 EEGAWPVLIDDFVEWAQPQVKAANQPTST 282
E G WP+L+D F +VKA + ST
Sbjct: 42 EAGEWPLLLDVFFNSTIEEVKARKRRGST 70
>gnl|CDD|192987 pfam12325, TMF_TATA_bd, TATA element modulatory factor 1 TATA
binding. This is the C-terminal conserved coiled coil
region of a family of TATA element modulatory factor 1
proteins conserved in eukaryotes. The proteins bind to
the TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding of
TATA binding protein. TMF1_TATA_bd is the most conserved
part of the TMFs. TMFs are evolutionarily conserved
golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells. The Rab6-binding
domain appears to be the same region as this C-terminal
family.
Length = 121
Score = 26.4 bits (59), Expect = 9.9
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 136 LKMRLPSLEAELKDNLN---------CDSIEKLKMRLPSLEAELKD 172
LK L LEAE +D + + +LK + LE EL+D
Sbjct: 36 LKDELARLEAE-RDEARQEIVKLTEENEELRELKKEIEELEKELED 80
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
0.317 0.133 0.398
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,182,559
Number of extensions: 1336849
Number of successful extensions: 1201
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1196
Number of HSP's successfully gapped: 28
Length of query: 284
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 188
Effective length of database: 6,679,618
Effective search space: 1255768184
Effective search space used: 1255768184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)