RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13042
(127 letters)
>gnl|CDD|221257 pfam11838, DUF3358, Domain of unknown function (DUF3358). This
domain is functionally uncharacterized. This domain is
found in eukaryotes and bacteria. This domain is found
to the C-terminus of an aminopeptidase domain.
Length = 323
Score = 65.4 bits (160), Expect = 9e-14
Identities = 20/82 (24%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 26 GEEEWKKMWAKFREESNPQEQIKMLGGLSSVKEPKLLEKFLEMAKDEKNIRSQDYFTVIV 85
G +E+ ++ A+++ + + L L++V +P+L K L D+ ++ +QD V+
Sbjct: 183 GAKEYDQILAEYKNDPTADGKEAALRALAAVPDPELKAKALNFLLDDDSVSNQDIRAVMA 242
Query: 86 -MVAGNPKGLPVAWDYVKKNWD 106
+ N G + W +V++N+D
Sbjct: 243 GLRRSNQAGRELLWPWVERNFD 264
>gnl|CDD|232842 TIGR00132, gatA, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
A subunit. In many species, Gln--tRNA ligase is
missing. tRNA(Gln) is misacylated with Glu after which a
heterotrimeric amidotransferase converts Glu to Gln.
This model represents the amidase chain of that
heterotrimer, encoded by the gatA gene. In the Archaea,
Asn--tRNA ligase is also missing. This amidase subunit
may also function in the conversion of Asp-tRNA(Asn) to
Asn-tRNA(Asn), presumably with a different recognition
unit to replace gatB. Both Methanococcus jannaschii and
Methanobacterium thermoautotrophicum have both authentic
gatB and a gatB-related gene, but only one gene like
gatA. It has been shown that gatA can be expressed only
when gatC is also expressed. In most species expressing
the amidotransferase, the gatC ortholog is about 90
residues in length, but in Mycoplasma genitalium and
Mycoplasma pneumoniae the gatC equivalent is as the
C-terminal domain of a much longer protein. Not
surprisingly, the Mycoplasmas also represent the most
atypical lineage of gatA orthology. This orthology group
is more narrowly defined here than in Proc Natl Acad Aci
USA 94, 11819-11826 (1997). In particular, a Rhodococcus
homolog found in association with nitrile hydratase
genes and described as an enantiomer-selective amidase
active on several 2-aryl propionamides, is excluded
here. It is likely, however, that the amidase subunit
GatA is not exclusively a part of the Glu-tRNA(Gln)
amidotransferase heterotrimer and restricted to that
function in all species [Protein synthesis, tRNA
aminoacylation].
Length = 460
Score = 27.3 bits (61), Expect = 2.5
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 1/42 (2%)
Query: 59 PKLLEKFLEMAKDEKNIRSQDYFTVIVMVAGNPKG-LPVAWD 99
P L K E D + D TV +AG P +P
Sbjct: 389 PTLPFKIGEKLDDPLEMYLSDILTVPANLAGLPAISVPCGVK 430
>gnl|CDD|130543 TIGR01478, STEVOR, variant surface antigen, stevor family. This
model represents the stevor branch of the rifin/stevor
family (pfam02009) of predicted variant surface antigens
as found in Plasmodium falciparum. This model is based
on a set of stevor sequences kindly provided by Matt
Berriman from the Sanger Center. This is a global model
and assesses a penalty for incomplete sequence.
Additional fragmentary sequences may be found with the
fragment model and a cutoff of 8 bits.
Length = 295
Score = 26.7 bits (59), Expect = 3.3
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 13/53 (24%)
Query: 36 KFREESNPQEQI---------KMLGGL----SSVKEPKLLEKFLEMAKDEKNI 75
K++E +P EQ+ K GG S E +LLEK+ EM DE +I
Sbjct: 74 KYQETHDPYEQLQELVEKNRTKSTGGNGAEPMSTIEKELLEKYEEMFGDESHI 126
>gnl|CDD|200492 cd11355, AmyAc_Sucrose_phosphorylase, Alpha amylase catalytic
domain found in sucrose phosphorylase (also called
sucrose glucosyltransferase, disaccharide
glucosyltransferase, and sucrose-phosphate alpha-D
glucosyltransferase). Sucrose phosphorylase is a
bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do not have the conserved calcium ion present in
other alpha amylase family enzymes. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 433
Score = 26.8 bits (60), Expect = 3.8
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 9 EAQVLKVYRRKTRMENV----GEEEWKKMWAKFREE 40
E + K+YRR+ + +K+W F EE
Sbjct: 122 EEDLDKIYRRRPGAPFTTITFADGSTEKVWTTFTEE 157
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 26.1 bits (58), Expect = 5.7
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 70 KDEKNIRSQDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLGRLVTY 114
++E + V++ G P+ L A ++ GR+V
Sbjct: 191 EEELRLTGGGGADVVIDAVGGPETLAQALRLLRPG----GRIVVV 231
>gnl|CDD|198114 smart01046, c-SKI_SMAD_bind, c-SKI Smad4 binding domain. c-SKI
is an oncoprotein that inhibits TGF-beta signaling
through interaction with Smad proteins. This domain
binds to Smad4.
Length = 95
Score = 25.0 bits (55), Expect = 6.7
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 5/37 (13%)
Query: 7 GFEAQVLKVYRRKTRMENVGEEE-----WKKMWAKFR 38
GF++ + Y + E E ++M KF
Sbjct: 59 GFDSANWRSYLHVAKDYGTEEREKLEQLLEEMKEKFN 95
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 25.8 bits (57), Expect = 8.0
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 83 VIVMVAGNPKGLPVAWDYVKKNWDYLGR 110
V+ A +G+ WD ++++ ++L
Sbjct: 207 VLTTSAVTGEGIDELWDAIEEHREFLTA 234
>gnl|CDD|233745 TIGR02141, modB_ABC, molybdate ABC transporter, permease protein.
This model describes the permease protein, ModB, of the
molybdate ABC transporter. This system has been
characterized in E. coli , Staphylococcus carnosus
Rhodobacter capsulatus and Azotobacter vinlandii.
Molybdate is chemically similar to sulfate, thiosulfate,
and selenate. These related substrates, and sometimes
molybdate itself, can be transported by the homologous
sulfate receptor. Some apparent molybdenum transport
operons include a permease related to this ModB,
although less similar than some sulfate permease
proteins and not included in this model [Transport and
binding proteins, Anions].
Length = 208
Score = 25.3 bits (56), Expect = 9.2
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 81 FTVIVMVAGNPKG----LPVA-WDYVKKNWDYLGRLV 112
F +M AGN G +P+A +D V+ +++ +L
Sbjct: 152 FGATLMFAGNIPGETQTIPLAIYDAVESDYELAHQLS 188
>gnl|CDD|217098 pfam02550, AcetylCoA_hydro, Acetyl-CoA hydrolase/transferase
N-terminal domain. This family contains several
enzymes which take part in pathways involving
acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes
the formation of acetate from acetyl-CoA, CoA
transferase (CAT1) EC:2.8.3.- produces succinyl-CoA,
and acetate-CoA transferase EC:2.8.3.8 utilises
acyl-CoA and acetate to form acetyl-CoA.
Length = 198
Score = 25.2 bits (55), Expect = 9.9
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 27 EEEWKKMWAKFREESNPQEQIKML--GGLSSVKEPKLLEKFLEMAKDEKN 74
+E++++ E ++ E + GG + K + K+L K E
Sbjct: 2 QEQYERKLISPEEAASLVEIGMHIERGGFTFAGTAKAIPKYLAKRKVELV 51
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 0.135 0.402
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,572,673
Number of extensions: 572021
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: 26
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
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: 53 (24.3 bits)