RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6336
(73 letters)
>gnl|CDD|176355 cd01611, GABARAP, Ubiquitin domain of GABA-receptor-associated
protein. GABARAP (GABA-receptor-associated protein)
belongs ot a large family of proteins that mediate
intracellular membrane trafficking and/or fusion.
GABARAP binds not only to GABA, type A but also to
tubulin, gephrin, and ULK1. Orthologues of GABARAP
include Gate-16 (golgi-associated ATPase enhancer), LC3
(microtubule-associated protein light chain 3), and
ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like
protein that is conjugated to the membrane
phospholipid, phosphatidylethanolamine as part of a
ubiquitin-like conjugation system essential for
autophagosome-formation.
Length = 112
Score = 126 bits (319), Expect = 5e-40
Identities = 50/67 (74%), Positives = 58/67 (86%)
Query: 5 VIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSAT 64
VIVE+ PK+ + DLDKKKYLVPSDLTVGQF ++IRKR+QLRPE ALF FVNN +PPTSAT
Sbjct: 27 VIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPTSAT 86
Query: 65 MGSLYQE 71
M LY+E
Sbjct: 87 MSQLYEE 93
>gnl|CDD|111837 pfam02991, Atg8, Autophagy protein Atg8 ubiquitin like. Light
chain 3 is proposed to function primarily as a subunit
of microtubule associated proteins 1A and 1B and that
its expression may regulate microtubule binding
activity. Autophagy is generally known as a process
involved in the degradation of bulk cytoplasmic
components that are non-specifically sequestered into
an autophagosome, where they are sequestered into
double-membrane vesicles and delivered to the
degradative organelle, the lysosome/vacuole, for
breakdown and eventual recycling of the resulting
macromolecules. The yeast proteins are involved in the
autophagosome, and Atg8 binds Atg19, via its N-terminus
and the C-terminus of Atg19.
Length = 104
Score = 119 bits (300), Expect = 3e-37
Identities = 46/67 (68%), Positives = 58/67 (86%)
Query: 5 VIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSAT 64
VI+EKA + + D+DKKKYLVP+DLTVGQF ++IRKR+QLRPE A+F FVNN +PPTSAT
Sbjct: 19 VIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNNTLPPTSAT 78
Query: 65 MGSLYQE 71
M +LY+E
Sbjct: 79 MSALYEE 85
>gnl|CDD|176356 cd01612, APG12_C, Ubiquitin-like domain of APG12. APG12_C The
carboxy-terminal ubiquitin-like domain of APG12.
Autophagy is a process in which cytoplasmic components
are delivered to the lysosome/vacuole for degradation.
Autophagy requires a ubiquitin-like protein conjugation
system, in which APG12 is covalently bound to APG5.
Length = 87
Score = 34.9 bits (81), Expect = 4e-04
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPT-S 62
+V + P L +K + + + + +RKR++L+ D+LF ++NN P+
Sbjct: 1 KVTIRFKPIGSAPILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPD 60
Query: 63 ATMGSLY 69
+G+LY
Sbjct: 61 ENVGNLY 67
>gnl|CDD|217901 pfam04110, APG12, Ubiquitin-like autophagy protein Apg12. In
yeast, 15 Apg proteins coordinate the formation of
autophagosomes. Autophagy is a bulk degradation process
induced by starvation in eukaryotic cells. The Apg12
system is one of the ubiquitin-like protein conjugation
systems conserved in eukaryotes. It was first
discovered in yeast during systematic analyses of the
apg mutants defective in autophagy. Covalent attachment
of Apg12-Apg5 is essential for autophagy.
Length = 87
Score = 33.5 bits (77), Expect = 0.001
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPT-S 62
++ + L K K+ V T ++K ++L+ D+LF +VNN P+
Sbjct: 1 KITIRLRAIGDAPILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPD 60
Query: 63 ATMGSLY 69
+G+LY
Sbjct: 61 QIVGNLY 67
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 31.7 bits (72), Expect = 0.006
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 12 KARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSLYQE 71
K ++ D + LVPS TV + K++ L PE VN I P S T+ +
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQ-QRLLVNGKILPDSLTLEDYGLQ 59
>gnl|CDD|132356 TIGR03313, Se_sel_red_Mo, probable selenate reductase,
molybdenum-binding subunit. Our comparative genomics
suggests this protein family to be a subunit of a
selenium-dependent molybdenum hydroxylase, although the
substrate is not specified. This protein is suggested by
Bebien, et al., to be the molybdenum-binding subunit of
a molydbopterin-containing selenate reductase. Xi, et
al, however, show that mutation of this gene in E. coli
conferred sensitivity to adenine, suggesting a defect in
purine interconversion. This finding, plus homology of
nearby genes in a 23-gene purine catabolism region in E.
coli to xanthine dehydrogase subunits suggests xanthine
dehydrogenase activity.
Length = 951
Score = 25.3 bits (55), Expect = 3.0
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 10 APKARIGDL--DKKKYLVPSDLTVGQF 34
APK IGD+ D + LVPSD VG +
Sbjct: 882 APK--IGDIPRDFRAVLVPSDDKVGPY 906
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
0.327 0.143 0.424
Gapped
Lambda K H
0.267 0.0681 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,950,082
Number of extensions: 313088
Number of successful extensions: 350
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 10
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
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 (21.7 bits)
S2: 53 (24.3 bits)