RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8038
(157 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 = 186 bits (475), Expect = 3e-62
Identities = 80/149 (53%), Positives = 94/149 (63%), Gaps = 37/149 (24%)
Query: 5 YKEEHPFEKRKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLI 64
+KE HPFEKRKAE E+IR KYPDR+PVIVE+ PK+ + DLDKKKYLVPSDLTVGQF ++I
Sbjct: 1 FKERHPFEKRKAEVERIRAKYPDRIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYII 60
Query: 65 RKRVQLRPEDALFFFVNNVIPPTSATMGSLYQVIVEKAPKARIGDLDKKKYLVPSDLTVG 124
RKR+QLRPE ALF FVNN +PPTSATM LY+
Sbjct: 61 RKRIQLRPEKALFLFVNNSLPPTSATMSQLYE---------------------------- 92
Query: 125 QFYFLIRKREHHEEDFFLYIAYSDENVYG 153
EH +ED FLY+ YS E +G
Sbjct: 93 ---------EHKDEDGFLYMTYSSEETFG 112
>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 = 160 bits (408), Expect = 3e-52
Identities = 70/141 (49%), Positives = 87/141 (61%), Gaps = 37/141 (26%)
Query: 13 KRKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRP 72
KR+AE EKIR KYPDR+PVI+EKA + + D+DKKKYLVP+DLTVGQF ++IRKR+QLRP
Sbjct: 1 KRQAESEKIREKYPDRIPVIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRP 60
Query: 73 EDALFFFVNNVIPPTSATMGSLYQVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRK 132
E A+F FVNN +PPTSATM +LY+
Sbjct: 61 EKAIFLFVNNTLPPTSATMSALYE------------------------------------ 84
Query: 133 REHHEEDFFLYIAYSDENVYG 153
E +ED FLY+ YS EN +G
Sbjct: 85 -EEKDEDGFLYMVYSGENTFG 104
>gnl|CDD|173572 PTZ00380, PTZ00380, microtubule-associated protein (MAP);
Provisional.
Length = 121
Score = 40.5 bits (94), Expect = 4e-05
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 5 YKEEHPFEKRKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYL-VPSDLTVGQFYFL 63
Y +P E R+AE +++ KYP V V+VE A KA K +L +P D TV +
Sbjct: 4 YHSSNPVEARRAECARLQAKYPGHVAVVVEAAEKAG----SKVHFLALPRDATVAELEAA 59
Query: 64 IRK 66
+R+
Sbjct: 60 VRQ 62
>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 = 34.2 bits (79), Expect = 0.004
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 31 VIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPT-SA 89
V + P L +K + + + + +RKR++L+ D+LF ++NN P+
Sbjct: 2 VTIRFKPIGSAPILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDE 61
Query: 90 TMGSLY 95
+G+LY
Sbjct: 62 NVGNLY 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 = 33.2 bits (76), Expect = 0.010
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 37 PKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPT-SATMGSLY 95
L K K+ V T ++K ++L+ D+LF +VNN P+ +G+LY
Sbjct: 8 AIGDAPILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLY 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 = 30.6 bits (69), Expect = 0.072
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 38 KARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 93
K ++ D + LVPS TV + K++ L PE VN I P S T+
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQ-QRLLVNGKILPDSLTLED 55
Score = 26.3 bits (58), Expect = 2.6
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 104 KARIGDLDKKKYLVPSDLTVGQFYFLIRKREH-HEEDFFLYIAYSD 148
K ++ D + LVPS TV + K+ E L +
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKI 46
>gnl|CDD|235892 PRK06938, PRK06938, diaminobutyrate--2-oxoglutarate
aminotransferase; Provisional.
Length = 464
Score = 30.4 bits (69), Expect = 0.32
Identities = 10/44 (22%), Positives = 25/44 (56%)
Query: 7 EEHPFEKRKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYL 50
P +R++ E R YP R+P+ +++A + D++ ++++
Sbjct: 23 SNSPLLERQSRRESNARSYPRRIPLALKRARGIYVEDVEGRQFI 66
>gnl|CDD|235889 PRK06931, PRK06931, diaminobutyrate--2-oxoglutarate
aminotransferase; Provisional.
Length = 459
Score = 29.3 bits (66), Expect = 0.76
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 14 RKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYL 50
R+AE E R YP ++P+ + KA + D++ +YL
Sbjct: 25 RQAEFESNVRSYPRKLPLAIAKAQGVWVTDVEGNQYL 61
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 28.1 bits (63), Expect = 1.8
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 3 FQYKEEHPFEKRKAEGEKIRRKYPDRVPVIV 33
++P+E+ KAE E++ R ++P+ V
Sbjct: 142 PGQNFKNPYEQSKAEAEQLVRAAATQIPLTV 172
>gnl|CDD|236553 PRK09535, btuC, corrinoid ABC transporter permease; Reviewed.
Length = 366
Score = 28.2 bits (63), Expect = 2.2
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 83 VIPPTSATMGSLYQVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKREHHE 137
++ PTSA G+ + V + AR G + +V + L F +L+R RE H
Sbjct: 313 ILLPTSALAGASFLVATDTV--ARSGPAEVPVGIVTAALGAPFFLYLLRTREVHA 365
>gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 449
Score = 27.6 bits (61), Expect = 2.8
Identities = 18/75 (24%), Positives = 33/75 (44%)
Query: 2 KFQYKEEHPFEKRKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFY 61
+ Q+ F+ + EG +RK PD VP V+ A ++ DL + +G+ Y
Sbjct: 329 EVQFDMAFMFKYSEREGTMAKRKLPDNVPEEVKSARLTKLVDLQTSISHEQNRARIGRVY 388
Query: 62 FLIRKRVQLRPEDAL 76
++ + + E L
Sbjct: 389 SILIENTSRKSEKQL 403
>gnl|CDD|129792 TIGR00709, dat, 2,4-diaminobutyrate 4-transaminases. This family
consists of L-diaminobutyric acid transaminases. This
general designation covers both 2.6.1.76
(diaminobutyrate-2-oxoglutarate transaminase, which
uses glutamate as the amino donor in DABA
biosynthesis), and 2.6.1.46 (diaminobutyrate--pyruvate
transaminase, which uses alanine as the amino donor).
Most members with known function are 2.6.1.76, and at
least some annotations as 2.6.1.46 in current databases
at time of model revision are incorrect. A distinct
branch of this family contains examples of 2.6.1.76
nearly all of which are involved in ectoine
biosynthesis. A related enzyme is 4-aminobutyrate
aminotransferase (EC 2.6.1.19), also called GABA
transaminase. These enzymes all are pyridoxal
phosphate-containing class III aminotransferase
[Central intermediary metabolism, Other].
Length = 442
Score = 27.6 bits (61), Expect = 3.5
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 14 RKAEGEKIRRKYPDRVPVIVEKAPKARIGDLDKKKYL 50
R+ E E R YP ++P KA + D++ K+YL
Sbjct: 6 RQNEMESNVRSYPRKLPTAFAKAQGCWVTDVEGKEYL 42
>gnl|CDD|215273 PLN02495, PLN02495, oxidoreductase, acting on the CH-CH group of
donors.
Length = 385
Score = 27.1 bits (60), Expect = 4.9
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 8 EHPFEKRKAEGEKIRRKYPDRVPV--IVEKAPKA 39
+ PFE AE ++++ +YPDR+ + I+E+ K
Sbjct: 94 DRPFETMLAEFKQLKEEYPDRILIASIMEEYNKD 127
>gnl|CDD|130741 TIGR01680, Veg_Stor_Prot, vegetative storage protein. The proteins
represented by this model are close relatives of the
plant acid phosphatases (TIGR01675), are limited to
members of the Phaseoleae including Glycine max
(soybean) and Phaseolus vulgaris (kidney bean). These
proteins are highly expressed in the leaves of
repeatedly depodded plants. VSP differs most strinkingly
from the acid phosphatases in the lack of the conserved
nucleophilic aspartate residue in the N-terminus, thus,
they should be inactive as phosphatases. This issue was
confused by the publication in 1992 of an article
claiming activity for the Glycine max VSP. In 1994 this
assertion was refuted by the separation of the activity
from the VSP.
Length = 275
Score = 26.6 bits (58), Expect = 6.4
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 95 YQVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKREHHEEDFFLY---------IA 145
++ I E+ A ++ ++Y S Q YF R E HE+D FL+ I
Sbjct: 58 FETIPEECVDATAEYIEGEQYRSDSKTVNQQAYFFARDLEVHEKDTFLFNIDGTALSNIP 117
Query: 146 YSDENVYGASQ 156
Y ++ YG+ +
Sbjct: 118 YYKKHGYGSEK 128
>gnl|CDD|233853 TIGR02407, ectoine_ectB, diaminobutyrate--2-oxoglutarate
aminotransferase. Members of this family of class III
pyridoxal-phosphate-dependent aminotransferases are
diaminobutyrate--2-oxoglutarate aminotransferase (EC
2.6.1.76) that catalyze the first step in ectoine
biosynthesis from L-aspartate beta-semialdehyde. This
family is readily separated phylogenetically from
enzymes with the same substrate and product but
involved in other process such as siderophore
(SP|Q9Z3R2) or 1,3-diaminopropane (SP|P44951)
biosynthesis. The family TIGR00709 previously included
both groups but has now been revised to exclude the
ectoine biosynthesis proteins of this family. Ectoine
is a compatible solute particularly effective in
conferring salt tolerance [Cellular processes,
Adaptations to atypical conditions].
Length = 412
Score = 26.5 bits (59), Expect = 8.2
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 23 RKYPDRVPVIVEKAPKARIGDLDKKKYL 50
R Y P + EKA + + D D K+Y+
Sbjct: 11 RSYCRSFPTVFEKAKGSTLWDEDGKEYI 38
>gnl|CDD|213287 cd05920, 23DHB-AMP_lg, 2,3-dihydroxybenzoate-AMP ligase.
2,3-dihydroxybenzoate-AMP ligase activates
2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP
with the release of pyrophosphate. However, it can also
catalyze the ATP-PPi exchange for 2,3-DHB analogs, such
as salicyclic acid (o-hydrobenzoate), as well as 2,4-DHB
and 2,5-DHB, but with less efficiency. Proteins in this
family are the stand-alone adenylation components of
non-ribosomal peptide synthases (NRPSs) involved in the
biosynthesis of siderophores, which are low molecular
weight iron-chelating compounds synthesized by many
bacteria to aid in the acquisition of this vital trace
elements. In Escherichia coli, the
2,3-dihydroxybenzoate-AMP ligase is called EntE, the
adenylation component of the enterobactin NRPS system.
Length = 483
Score = 26.4 bits (59), Expect = 8.7
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 24 KYPDRVPVIVEKAPKARIGDLDKKK 48
K PDR+ +V+ P +G +DKK
Sbjct: 459 KLPDRL-EVVDSLPLTPVGKVDKKA 482
>gnl|CDD|223100 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 26.0 bits (58), Expect = 9.4
Identities = 8/39 (20%), Positives = 14/39 (35%), Gaps = 2/39 (5%)
Query: 2 KFQYKEE--HPFEKRKAEGEKIRRKYPDRVPVIVEKAPK 38
F+ EE F + G K + + +K P+
Sbjct: 285 PFEVPEEVYAAFRAVEERGAKAEAAWNELFAAYKKKYPE 323
>gnl|CDD|233968 TIGR02668, moaA_archaeal, probable molybdenum cofactor biosynthesis
protein A, archaeal. This model describes an archaeal
family related, and predicted to be functionally
equivalent, to molybdenum cofactor biosynthesis protein
A (MoaA) of bacteria (see TIGR02666) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 302
Score = 26.1 bits (58), Expect = 9.7
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 9/59 (15%)
Query: 4 QYKEEHPFEKRKAEGEKIRRKYPDRVPVIVE----KAPKARIGDL-DKKKYLVPSDLTV 57
Q E P EGEK +KY + + I E A + R + ++ KY +P + V
Sbjct: 181 QLIELMPPG----EGEKEFKKYHEDIDPIEEELEKMADRVRTRRMHNRPKYFIPGGVEV 235
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
0.321 0.141 0.407
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,549,080
Number of extensions: 819483
Number of successful extensions: 806
Number of sequences better than 10.0: 1
Number of HSP's gapped: 803
Number of HSP's successfully gapped: 30
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
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 (21.8 bits)
S2: 55 (24.9 bits)