RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13700
(166 letters)
>gnl|CDD|149675 pfam08694, UFC1, Ubiquitin-fold modifier-conjugating enzyme 1.
Ubiquitin-like (UBL) post-translational modifiers are
covalently linked to most, if not all, target protein(s)
through an enzymatic cascade analogous to
ubiquitylation, consisting of E1 (activating), E2
(conjugating), and E3 (ligating) enzymes. Ubiquitin-fold
modifier 1 (Ufm1) a ubiquitin-like protein is activated
by a novel E1-like enzyme, Uba5, by forming a
high-energy thioester bond. Activated Ufm1 is then
transferred to its cognate E2-like enzyme, Ufc1, in a
similar thioester linkage. This family represents the
E2-like enzyme.
Length = 161
Score = 301 bits (772), Expect = e-107
Identities = 119/161 (73%), Positives = 142/161 (88%)
Query: 3 ESSKKTLSSIPLLKTKAGPRDKDLWPKRLKEEYVALIEYVKNNKAADNDWFRLESNKEGT 62
E++K T+S IPLLKT AGPRD + W +RLKEEY ALI+YV+NNK+ADNDWFRLESNKEGT
Sbjct: 1 EATKSTVSRIPLLKTNAGPRDGEKWIQRLKEEYQALIKYVENNKSADNDWFRLESNKEGT 60
Query: 63 KWFGSCWFFYNQLKYEFQIEFDIPITFPTTAPELALPELDGKTAKMYRGGKICLSDHFKP 122
+WFG CW+ +N KYEF +EFDIP+T+P T PE+ALPELDGKTAKMYRGGKICL+ HFKP
Sbjct: 61 RWFGKCWYVHNLKKYEFDLEFDIPVTYPATPPEIALPELDGKTAKMYRGGKICLTIHFKP 120
Query: 123 LWARNVPKFGIAHAMALGLGPWLAVEIPALVDAGIIKYQEK 163
LWARNVPKFGIAHA+ALGL PWLAVEIP L++ G+IK+++
Sbjct: 121 LWARNVPKFGIAHALALGLAPWLAVEIPDLIEKGVIKHKDD 161
>gnl|CDD|220127 pfam09149, DUF1935, Domain of unknown function (DUF1935).
Members of this family are found in various bacterial
and eukaryotic hypothetical proteins, as well as in the
cysteine protease calpain. Their exact function has
not, as yet, been defined.
Length = 97
Score = 30.6 bits (70), Expect = 0.11
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 7/32 (21%)
Query: 53 FRLESNKEGTKWFGSCWFFYNQ-LKYEFQIEF 83
FR+ K G W FYN YE +
Sbjct: 23 FRIVDEKGGR------WAFYNDTKDYEMHVTV 48
>gnl|CDD|237377 PRK13405, bchH, magnesium chelatase subunit H; Provisional.
Length = 1209
Score = 30.0 bits (68), Expect = 0.70
Identities = 13/42 (30%), Positives = 15/42 (35%)
Query: 97 ALPELDGKTAKMYRGGKICLSDHFKPLWARNVPKFGIAHAMA 138
A+PELDG T M GG+ A MA
Sbjct: 371 AIPELDGATGPMVFGGRSDGVACTGCDRGCKFSGNDAARDMA 412
>gnl|CDD|238117 cd00195, UBCc, Ubiquitin-conjugating enzyme E2, catalytic (UBCc)
domain. This is part of the ubiquitin-mediated protein
degradation pathway in which a thiol-ester linkage forms
between a conserved cysteine and the C-terminus of
ubiquitin and complexes with ubiquitin protein ligase
enzymes, E3. This pathway regulates many fundamental
cellular processes. There are also other E2s which form
thiol-ester linkages without the use of E3s as well as
several UBC homologs (TSG101, Mms2, Croc-1 and similar
proteins) which lack the active site cysteine essential
for ubiquitination and appear to function in DNA repair
pathways which were omitted from the scope of this CD.
Length = 141
Score = 28.7 bits (65), Expect = 0.84
Identities = 26/109 (23%), Positives = 37/109 (33%), Gaps = 29/109 (26%)
Query: 28 PKRLKEEYVALIEYVKNNKAADNDWFRLESNKEG-TKWFGSCWFF------YNQLKYEFQ 80
KRL++E L K E +E +W G+ Y ++
Sbjct: 1 SKRLQKELKDL-------KKDPPSGISAEPVEENLLEWHGT--IRGPPDTPYEGGIFKLD 51
Query: 81 IEFDIPITFPTTAPELALPELDGKTAKMY-----RGGKICLSDHFKPLW 124
IEF P +P P++ K+Y GKICLS W
Sbjct: 52 IEF--PEDYPFKPPKVRF------VTKIYHPNVDENGKICLSILKTHGW 92
>gnl|CDD|180598 PRK06512, PRK06512, thiamine-phosphate pyrophosphorylase;
Provisional.
Length = 221
Score = 27.7 bits (62), Expect = 2.2
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 134 AHAMALGLGPWLA--VEIPALVDAG 156
AH L L W A +EIP +V AG
Sbjct: 148 AHPRNLSLAEWWAEMIEIPCIVQAG 172
>gnl|CDD|193490 cd04085, delta_endotoxin_C, delta-endotoxin C-terminal domain may
be associated with carbohydrate binding functionality.
Delta-endotoxin C-terminal domain (delta endotoxin
domain III) is part of the activated region of delta
endotoxins, which are insecticidal toxins produced
during sporulation by Bacillus species of bacteria. The
activated endotoxin binds to the gut epithelium and
causes cell lysis leading to death. This activated
region of the delta endotoxin is composed of three
structural domains. The N-terminal helical domain (I) is
involved in membrane insertion and pore formation, while
the second and third domains (II and III) are involved
in receptor binding. Domain III structurally resembles
the carbohydrate binding domain 6 (CBM6) and it is
possible that insect specificity is determined by
protein-protein or protein-carbohydrate interactions
mediated by both domains II and III of the toxin.
Delta-endotoxins are of great interest for development
of new bioinsecticides and in the control of mosquitoes.
Length = 145
Score = 27.2 bits (61), Expect = 2.8
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 73 NQLKYE-FQ-IEFDIPITFPTTAPELAL 98
+ L YE FQ +EF P TF ++ + +
Sbjct: 97 DNLTYESFQYVEFSTPFTFSESSNTITI 124
>gnl|CDD|220909 pfam10935, DUF2637, Protein of unknown function (DUF2637). This
family of proteins has no known function.
Length = 139
Score = 27.0 bits (60), Expect = 3.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 136 AMALGLGPWLAVEIPALVDAGII 158
A+A G LA P ++D I+
Sbjct: 26 AIAAGGPGSLAWLFPLVIDGLIL 48
>gnl|CDD|147539 pfam05404, TRAP-delta, Translocon-associated protein, delta subunit
precursor (TRAP-delta). This family consists of several
eukaryotic translocon-associated protein, delta subunit
precursors (TRAP-delta or SSR-delta). The exact function
of this protein is unknown.
Length = 167
Score = 27.0 bits (60), Expect = 4.1
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 121 KPLWARNVPKFGIAHAMALGLGPWLAVEIPALVDAGIIKY 160
KPL+ NV G GPW++ EI A V ++ Y
Sbjct: 123 KPLFTVNVDHRGAYK------GPWVSSEILAAVIVVLVAY 156
>gnl|CDD|193444 pfam12971, NAGLU_N, Alpha-N-acetylglucosaminidase (NAGLU)
N-terminal domain. Alpha-N-acetylglucosaminidase, a
lysosomal enzyme required for the stepwise degradation
of heparan sulfate. Mutations on the
alpha-N-acetylglucosaminidase (NAGLU) gene can lead to
Mucopolysaccharidosis type IIIB (MPS IIIB; or
Sanfilippo syndrome type B) characterized by
neurological dysfunction but relatively mild somatic
manifestations. The structure shows that the enzyme is
composed of three domains. This N-terminal domain has
an alpha-beta fold.
Length = 85
Score = 25.7 bits (57), Expect = 5.0
Identities = 5/29 (17%), Positives = 10/29 (34%)
Query: 29 KRLKEEYVALIEYVKNNKAADNDWFRLES 57
+RL E+ + + D F +
Sbjct: 10 ERLLPEHAGQFRFEVIESSDGLDCFEISG 38
>gnl|CDD|240068 cd04717, BAH_polybromo, BAH, or Bromo Adjacent Homology domain,
as present in polybromo and yeast RSC1/2. The human
polybromo protein (BAF180) is a component of the
SWI/SNF chromatin-remodeling complex PBAF. It is
thought that polybromo participates in transcriptional
regulation. Saccharomyces cerevisiae RSC1 and RSC2 are
part of the 15-subunit nucleosome remodeling RSC
complex. BAH domains are found in a variety of proteins
playing roles in transcriptional silencing and the
remodeling of chromatin. It is assumed that in most or
all of these instances the BAH domain mediates
protein-protein interactions.
Length = 121
Score = 25.6 bits (57), Expect = 7.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 53 FRLESNKEGTKWFGSCWFF 71
RL +++G K+F CWF+
Sbjct: 27 ERLWKDEDGEKFFFGCWFY 45
>gnl|CDD|153115 cd01057, AAMH_A, Aromatic and Alkene Monooxygenase Hydroxylase,
subunit A, ferritin-like diiron-binding domain.
Aromatic and Alkene Monooxygenase Hydroxylases, subunit
A (AAMH_A). Subunit A of the soluble hydroxylase of
multicomponent, aromatic and alkene monooxygenases are
members of a superfamily of ferritin-like iron-storage
proteins. AAMH exists as a hexamer (an
alpha2-beta2-gamma2 homodimer) with each alpha-subunit
housing one nonheme diiron center embedded in a
four-helix bundle. The N-terminal domain of the alpha-
and noncatalytic beta-subunits possess nearly identical
folds, however, the beta-subunit lacks critical diiron
ligands and a C-terminal domain found in the
alpha-subunit. Methane monooxygenase is a multicomponent
enzyme found in methanotrophic bacteria that catalyzes
the hydroxylation of methane and higher alkenes (as
large as octane). Phenol monooxygenase, found in a
diverse group of bacteria, catalyses the hydroxylation
of phenol, chloro- and methyl-phenol and naphthol. Both
enzyme systems consist of three components: the
hydroxylase, a coupling protein and a reductase. In the
MMO hydroxylase, dioxygen and substrate interact with
the diiron center in a hydrophobic cavity at the active
site. The reductase component and protein coupling
factor provide electrons from NADH for reducing the
oxidized binuclear iron-oxo cluster to its reduced form.
Reaction with dioxygen produces a peroxy-bridged complex
and dehydration leads to the formation of complex Q,
which is thought to be the oxygenating species that
carries out the insertion of an oxygen atom into a C-H
bond of the substrate. The toluene monooxygenase
systems, toluene 2-, 3-, and 4-monooxygenase, are
similar to MMO but with an additional component, a
Rieske-type ferredoxin. The alkene monooxygenase from
Xanthobacter strain Py2 is closely related to aromatic
monooxygenases and catalyzes aromatic monohydroxylation
of benzene, toluene, and phenol. Alkane
omega-hydroxylase (AlkB) and xylene monooxygenase are
members of a distinct class of integral membrane diiron
proteins and are not included in this CD.
Length = 465
Score = 26.5 bits (59), Expect = 7.8
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 3/45 (6%)
Query: 47 AADNDWFRLESNKEGT-KWFGSCWFFYNQLKYEFQIEFDIPITFP 90
+ +WF E G K++G W + E + E P T P
Sbjct: 338 PEEMEWF--EEKYPGWYKYYGKFWEEIRKNAAEGKRELFYPETLP 380
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 26.3 bits (58), Expect = 8.5
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 90 PTTAPELALPELDGKTAKMY 109
PT L++ E+DGK K+Y
Sbjct: 235 PTRQEGLSMFEVDGKKNKVY 254
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 26.7 bits (59), Expect = 8.7
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 41 YVKNNKAADNDWFRLESNKEGTKWFGSCWFF 71
+V + R E+N +W GSCW++
Sbjct: 564 WVNTVDPSSGKPARRETNTM-PQWAGSCWYY 593
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
0.318 0.136 0.431
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: 8,566,132
Number of extensions: 773540
Number of successful extensions: 658
Number of sequences better than 10.0: 1
Number of HSP's gapped: 657
Number of HSP's successfully gapped: 25
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
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: 55 (24.9 bits)