RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8268
(61 letters)
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha, beta
and gamma subunits of the AP-1, AP-2 and AP-3 adaptor
protein complexes. The adaptor protein (AP) complexes
are involved in the formation of clathrin-coated pits
and vesicles. The N-terminal region of the various
adaptor proteins (APs) is constant by comparison to the
C-terminal which is variable within members of the AP-2
family; and it has been proposed that this constant
region interacts with another uniform component of the
coated vesicles.
Length = 522
Score = 44.1 bits (105), Expect = 4e-07
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 8 MVKLYLTNPAQTT--LLCQYLLSLARYDQ-NYDIRDRARLLRQLLFPAP 53
+VKL LT P + L+ Q +LSLA D + ++RDRA +LL A
Sbjct: 474 LVKLSLTFPDEEVQNLIVQVVLSLATQDSSDLELRDRAVEYLRLLSLAD 522
>gnl|CDD|151527 pfam11082, DUF2880, Protein of unknown function (DUF2880). This
bacterial family of proteins has no known function.
Length = 79
Score = 27.7 bits (61), Expect = 0.14
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 2 PVACRRMVKLYLTNPAQ 18
PVAC + VK L NP Q
Sbjct: 33 PVACMKAVKAALPNPDQ 49
>gnl|CDD|217454 pfam03252, Herpes_UL21, Herpesvirus UL21. The UL21 protein appears
to be a dispensable component in herpesviruses.
Length = 515
Score = 25.4 bits (56), Expect = 1.7
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 15 NPAQTTLLCQYLLSLARYDQNYDI 38
+P Q L QY+LS Y
Sbjct: 331 SPCQKFALLQYILSRWGLPNCYGA 354
>gnl|CDD|178074 PLN02455, PLN02455, fructose-bisphosphate aldolase.
Length = 358
Score = 25.1 bits (55), Expect = 2.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 43 RLLRQLLFPAPGA 55
+ LR+LLF APGA
Sbjct: 53 QALRELLFTAPGA 65
>gnl|CDD|236618 PRK09736, PRK09736, 5-methylcytosine-specific restriction enzyme
subunit McrC; Provisional.
Length = 352
Score = 24.9 bits (55), Expect = 2.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 26 LLSLARYDQNYDIRDRARLL 45
L L R+D + DI+DR R L
Sbjct: 113 LELLIRHDIDKDIKDRLRSL 132
>gnl|CDD|233982 TIGR02715, amido_AtzE, amidohydrolase, AtzE family. Members of
this protein family are aminohydrolases related to, but
distinct from, glutamyl-tRNA(Gln) amidotransferase
subunit A. The best characterized member is the biuret
hydrolase of Pseudomonas sp. ADP, which hydrolyzes
ammonia from the three-nitrogen compound biuret to yield
allophanate. Allophanate is also an intermediate in urea
degradation by the urea carboxylase/allophanate
hydrolase pathway, an alternative to urease [Unknown
function, Enzymes of unknown specificity].
Length = 452
Score = 24.7 bits (54), Expect = 3.0
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 23 CQYLLSLARYDQNYDIRDRARLLRQLLFPAP 53
+L +L Q++D R RLL L PA
Sbjct: 310 NLHLDALRTRPQDFDPATRDRLLAGALLPAS 340
>gnl|CDD|239658 cd03687, Dehydratase_LU, Dehydratase large subunit. This family
contains the large (alpha) subunit of B12-dependent
glycerol dehydratases (GDHs) and B12-dependent diol
dehydratases (DDHs). GDH is isofunctional with DDH.
These enzymes can each catalyze the conversion of
1,2-propanediol, glycerol, and 1,2-ethanediol to the
corresponding aldehydes via a coenzyme B12
(adenosylcobalamin)-dependent radical mechanism. Both
enzymes exhibit a subunit composition of
alpha2beta2gamma2. The enzymes differ in substrate
specificity; glycerol is the preferred substrate for GDH
and 1,2-propanediol for DDH. GDH shows almost equal
affinity for both (R) and (S)-isomers while DDH prefers
the (S) isomer. GDH plays a key role in the
dihydroxyacetone (DHA) pathway and DDH in the anaerobic
degradation of 1,2-diols. The radical mechanism has been
well studied for Klebsiella oxytoca DDH and involves
binding of 1,2-propanediol to the enzyme to induce
hemolytic cleavage of the Co-C5' bond of the coenzyme to
form cob(II)alamin and the adenosyl radical. Hydrogen
abstraction from the substrate follows producing a
substrate generated radical and 5'-deoxyadenosine.
Rearrangement to the product radical is then followed by
abstraction of a hydrogen atom from 5'-deoxyadenosine to
produce the hydrated propionaldehyde and regenerate the
adenosyl radical. After the Co-C5' bond is reformed and
the hydrated aldehyde dehydrated, the process is
complete. GDH has a higher affinity for coenzyme B12
than DDH. Both GDH and DDH are activated by various
monovalent cations with K+, NH4+, and Rb+ being the most
effective. However, DDH differs from GDH in that it is
partially active with Cs+ and Na+. In general, the alpha
and beta subunits for both enzymes are on different
chains. However, for a subset of the GDHs, alpha and
beta subunits appear to be on a single chain.
Length = 545
Score = 24.8 bits (54), Expect = 3.5
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 37 DIRDRARLLRQLLFPAPGAEIIS 59
DIR AR L QLL PG + I
Sbjct: 335 DIRRTARTLMQLL---PGTDFIF 354
>gnl|CDD|200451 cd00551, AmyAc_family, Alpha amylase catalytic domain family. 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; and 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 this 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 = 260
Score = 24.4 bits (53), Expect = 3.8
Identities = 11/36 (30%), Positives = 14/36 (38%)
Query: 26 LLSLARYDQNYDIRDRARLLRQLLFPAPGAEIISYF 61
L L Y + R +L LL PG +I Y
Sbjct: 219 LADLVSYKIVELRKARLKLALALLLTLPGTPMIYYI 254
>gnl|CDD|184465 PRK14032, PRK14032, citrate synthase; Provisional.
Length = 447
Score = 24.1 bits (53), Expect = 5.7
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 9/39 (23%)
Query: 27 LSLARYDQNYDIRDRARLLRQLL-----FPAPGAEIISY 60
L+L YD N D +LRQ + FP + Y
Sbjct: 147 LALYSYDDNPDDTSIDNVLRQSISLIARFPT----LAVY 181
>gnl|CDD|177589 PHA03348, PHA03348, tegument protein UL21; Provisional.
Length = 526
Score = 23.4 bits (51), Expect = 8.3
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 15 NPAQTTLLCQYLLSLARY 32
+P Q LCQY+LS
Sbjct: 332 SPLQKFALCQYILSRWGL 349
>gnl|CDD|234014 TIGR02786, addB_alphas, double-strand break repair protein AddB,
alphaproteobacterial type. AddAB is a system well
described in the Firmicutes as a replacement for RecBCD
in many prokaryotes for the repair of double stranded
break DNA damage. More recently, a distantly related
gene pair conserved in many alphaproteobacteria was
shown also to function in double-stranded break repair
in Rhizobium etli. This family consists of AddB proteins
of the alphaproteobacteial type [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1021
Score = 23.5 bits (51), Expect = 8.5
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 33 DQNYDIRDRARLLRQLLFPAPGAE 56
+ +R R RL+ + L PA +
Sbjct: 299 PADRGLRKRERLVSEALRPAETTD 322
>gnl|CDD|168315 PRK05962, PRK05962, amidase; Validated.
Length = 424
Score = 23.6 bits (51), Expect = 8.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 29 LARYDQNYDIRDRARLLRQLLFPAPG 54
LA D N DIR + L R++ P
Sbjct: 291 LADLDANVDIRVKRPLSRRIKVPLEA 316
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
0.331 0.143 0.433
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,186,204
Number of extensions: 224264
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 15
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.1 bits)