RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13511
(88 letters)
>gnl|CDD|236653 PRK10137, PRK10137, alpha-glucosidase; Provisional.
Length = 786
Score = 32.4 bits (74), Expect = 0.018
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 13/67 (19%)
Query: 14 SFLETSGPLNDTYLPL---------YETDAGRRVYDATLASVRENFPQYVEEIEGTADGA 64
S LET ++ L L E G+ + D T+A +P Y +I T DG
Sbjct: 146 SLLETK-ITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIA---GEYPDYQRKISATRDGL 201
Query: 65 KVPFHKM 71
KV F K+
Sbjct: 202 KVTFGKV 208
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 27.0 bits (60), Expect = 1.1
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 38 VYDATLASVRENFPQYVEEIEGTADGAKVP 67
VYD T + + P ++EE E + +VP
Sbjct: 82 VYDVTNMASFHSLPSWIEECEQHSLPNEVP 111
>gnl|CDD|235992 PRK07328, PRK07328, histidinol-phosphatase; Provisional.
Length = 269
Score = 26.1 bits (58), Expect = 2.3
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 26 YLPLYETDAGRRVYDATLASVRENFPQYVEEIEGT 60
+LP+Y R D LA E P YV E+E
Sbjct: 40 HLPMYFLPPEWR--DPGLAMRLEELPFYVSEVERL 72
>gnl|CDD|238859 cd01821, Rhamnogalacturan_acetylesterase_like,
Rhamnogalacturan_acetylesterase_like subgroup of
SGNH-hydrolases. Rhamnogalacturan acetylesterase removes
acetyl esters from rhamnogalacturonan substrates, and
renders them susceptible to degradation by
rhamnogalacturonases. Rhamnogalacturonans are highly
branched regions in pectic polysaccharides, consisting
of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide
units, with many rhamnose residues substituted by
neutral oligosaccharides such as arabinans, galactans
and arabinogalactans. Extracellular enzymes
participating in the degradation of plant cell wall
polymers, such as Rhamnogalacturonan acetylesterase,
would typically be found in saprophytic and plant
pathogenic fungi and bacteria.
Length = 198
Score = 25.6 bits (57), Expect = 3.3
Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 4/50 (8%)
Query: 32 TDAGRRVYDATLASVRENFPQYVEEIEGTADGAKVPF---HKMSRKLKER 78
T RR +D V + Y + A VP + SR L E
Sbjct: 114 TPVTRRTFDEG-GKVEDTLGDYPAAMRELAAEEGVPLIDLNAASRALYEA 162
>gnl|CDD|129561 TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase, mitochondrial.
Unlike all other known phenylalanyl-tRNA synthetases,
the mitochondrial form demonstrated from yeast is
monomeric. It is similar to but longer than the alpha
subunit (PheS) of the alpha 2 beta 2 form found in
Bacteria, Archaea, and eukaryotes, and shares the
characteristic motifs of class II aminoacyl-tRNA
ligases. This model models the experimental example from
Saccharomyces cerevisiae (designated MSF1) and its
orthologs from other eukaryotic species [Protein
synthesis, tRNA aminoacylation].
Length = 460
Score = 25.8 bits (56), Expect = 3.6
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 3 SRGRTFSGIIKSFLETSG------PLNDTYLPLYETDAGRRVYDATLASVRENFPQYVEE 56
G S IKS S ++ T+ P++ G + T A + E P Y+E+
Sbjct: 123 QGGLDDSDNIKSGFLISADVYRRDEIDKTHYPVFHQADGAAIRKRTKADLFEKEPGYIEK 182
Query: 57 IEGTADGAKVPFHKMSRKL 75
E G + +K + K+
Sbjct: 183 FEEDIRGTEADLNKENVKI 201
>gnl|CDD|221872 pfam12954, DUF3843, Protein of unknown function (DUF3843). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 325
Score = 25.4 bits (56), Expect = 4.5
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 9 SGIIKSFLETSGPLNDTYLPLYETD 33
G+ +SF+ L YLP Y
Sbjct: 67 LGLWRSFITAHKRLYGKYLPFYTLT 91
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 25.4 bits (55), Expect = 5.2
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 36 RRVYDATLASVRENFPQYVEEIEGTADGAKVPFHKMSR 73
++ ++A L ++ E P+YV+ I T D K+P +SR
Sbjct: 133 KQSFNALLKTLEEP-PEYVKFILATTDYHKIPVTILSR 169
>gnl|CDD|181372 PRK08307, PRK08307, stage III sporulation protein SpoAB;
Provisional.
Length = 171
Score = 24.8 bits (55), Expect = 5.9
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 71 MSRKLKERPTELRSL 85
+++ KERP +LR L
Sbjct: 20 YAKRYKERPRQLREL 34
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I. All proteins in this family for
which functions are known are DNA polymerases Many also
have an exonuclease motif. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 887
Score = 25.0 bits (55), Expect = 6.1
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 17/67 (25%)
Query: 31 ETDAGRRVY----DATLASVRE-------NFPQYVEEIEGT-ADGAKVPFHKMSRKLKER 78
ET GRR Y ++ +VRE N P I+G+ AD K+ K+ ++LKER
Sbjct: 775 ETLFGRRRYIPDINSRNRNVREAAERMAINAP-----IQGSAADIMKIAMIKLDKRLKER 829
Query: 79 PTELRSL 85
+ R L
Sbjct: 830 KLKARLL 836
>gnl|CDD|215129 PLN02216, PLN02216, protein SRG1.
Length = 357
Score = 24.4 bits (53), Expect = 9.1
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 47 RENFPQYVEEIEGTADGAKVPFHKMSRKLKERPTELRSL 85
R+ Y E++ A K+ F KM+ L+ +P E+ L
Sbjct: 168 RDTLETYSAEVKSIA---KILFAKMASALEIKPEEMEKL 203
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
0.315 0.132 0.369
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,396,781
Number of extensions: 350197
Number of successful extensions: 274
Number of sequences better than 10.0: 1
Number of HSP's gapped: 274
Number of HSP's successfully gapped: 17
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
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: 42 (22.0 bits)
S2: 53 (24.2 bits)