RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16108
(94 letters)
>gnl|CDD|202484 pfam02953, zf-Tim10_DDP, Tim10/DDP family zinc finger. Putative
zinc binding domain with four conserved cysteine
residues. This domain is found in the human disease
protein TIMM8A. Members of this family such as Tim9 and
Tim10 are involved in mitochondrial protein import.
Members of this family seem to be localised to the
mitochondrial intermembrane space.
Length = 66
Score = 63.4 bits (155), Expect = 4e-15
Identities = 26/60 (43%), Positives = 34/60 (56%)
Query: 17 QINTFKEFLLQYNKITEICFKDCVNHFISREITKKEESCAVNCLEKYMKMTSRISMRMQE 76
Q F NK+TE CFK CV F ++K EESC C+EKY+ +R+S R+QE
Sbjct: 6 QELQKANFQELINKLTENCFKKCVTKFPGSSLSKGEESCLDRCVEKYLDANNRVSKRLQE 65
>gnl|CDD|221269 pfam11854, DUF3374, Protein of unknown function (DUF3374). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 665 to 712 amino acids in
length.
Length = 675
Score = 29.6 bits (67), Expect = 0.18
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 67 TSRISMRMQEFQMLQNEQMLAASGGN 92
+R+S R+ +M Q+E L A+
Sbjct: 285 RTRVSGRLSYGRMTQDEAFLPATYAL 310
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA
polymerase I (RNAP I) is a multi-subunit protein complex
responsible for the synthesis of rRNA precursor. It
consists of at least 14 different subunits, and the
largest one is homologous to subunit Rpb1 of yeast RNAP
II and subunit beta' of bacterial RNAP. Rpa1 is also
known as Rpa190 in yeast. Structure studies suggest that
different RNAP complexes share a similar crab-claw-shape
structure. The C-terminal domain of Rpb1, the largest
subunit of RNAP II, makes up part of the foot and jaw
structures of RNAP II. The similarity between this
domain and the C-terminal domain of Rpb1, its
counterpart in RNAP II, suggests a similar functional
and structural role.
Length = 309
Score = 27.2 bits (61), Expect = 1.4
Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 15 KTQINTFKEFLLQYNKITEICFKDCVNHFISREITKKEESCAVNCLEKYMKMTSRISMRM 74
+ T K +++ + D V EI K E L K+ ++T ++ +
Sbjct: 76 AERAETLK------KRLSRVTLSDVVEKVEVTEILKTIERVFKKLLGKWCEVTIKLPLSS 129
Query: 75 QEFQMLQNEQMLA 87
+ +L + LA
Sbjct: 130 PKLLLLSIVEKLA 142
>gnl|CDD|215091 PLN00179, PLN00179, acyl- [acyl-carrier protein] desaturase.
Length = 390
Score = 25.8 bits (57), Expect = 3.3
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 60 LEKYMKMTSRISMRMQE 76
L KY+ ++ R+ MR E
Sbjct: 175 LNKYLYLSGRVDMRQIE 191
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 25.1 bits (55), Expect = 3.7
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 5 LNEAQQNEMMKTQINTFKEFLLQYNK------ITEICFKD 38
+ EAQ E +QI K LL YN+ I I FK
Sbjct: 11 VTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKR 50
>gnl|CDD|212080 cd11511, SLC6sbd_BGT1, Na(+)- and Cl(-)-dependent betaine/GABA
transporter-1, and related proteins; solute-binding
domain. BGT1 is a relatively low-affinity transporter
of gamma-aminobutyric acid (GABA), and can also
transport betaine. GABA is the main inhibitory
neurotransmitter within the mammalian CNS. Human BGT1 is
encoded by the SLC6A12 gene, and is similar to mouse
GAT2. Mouse GAT2 plays a role in transporting GABA
across the blood-brain barrier. In addition to being
expressed in cells of the central nervous system, BGT1
is expressed in peripheral tissues, including kidney,
liver, and heart. An association has been shown between
the SLC6A12 gene and the occurrence of
aspirin-intolerant asthma, and BGT1 is a drug target for
antiepileptic drugs. This subgroup belongs to the solute
carrier 6 (SLC6) transporter family.
Length = 541
Score = 25.7 bits (56), Expect = 4.9
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 25 LLQYNKITEICFKDCV 40
L YNK T C++DC+
Sbjct: 271 LGSYNKYTNNCYRDCI 286
>gnl|CDD|178032 PLN02410, PLN02410, UDP-glucoronosyl/UDP-glucosyl transferase
family protein.
Length = 451
Score = 25.4 bits (55), Expect = 5.4
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 23 EFLLQYNKITEICFKDCVNHFISREITKKEESCAV 57
EFL + NK ++ FKDC+ + ++ E +C V
Sbjct: 78 EFLHKLNKECQVSFKDCLGQLVLQQ--GNEIACVV 110
>gnl|CDD|136007 PRK06698, PRK06698, bifunctional
5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase/phosphatase; Validated.
Length = 459
Score = 25.0 bits (54), Expect = 7.5
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 10 QNEMMKTQINTFKEFLLQYNKITEICFKDCVNHFISREI 48
+NEM++ I L Q +KI E+ D +H S ++
Sbjct: 237 ENEMLQALIFDMDGTLFQTDKILELSLDDTFDHLRSLQL 275
>gnl|CDD|220558 pfam10087, DUF2325, Uncharacterized protein conserved in bacteria
(DUF2325). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 96
Score = 24.5 bits (54), Expect = 7.7
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 12/40 (30%)
Query: 34 ICFKDCVNHFISREITKKE-----------ESCAVNCLEK 62
I F DCV+H ++ K+E S +++ LE+
Sbjct: 51 IVFTDCVSHDAMWKV-KEEAKRRGIPVVYSRSRSLSALER 89
>gnl|CDD|218759 pfam05811, DUF842, Eukaryotic protein of unknown function (DUF842).
This family consists of a number of conserved
eukaryotic proteins of unknown function. The sequences
carry three sets of CxxxC motifs, which might suggest a
type of zinc-finger formation.
Length = 131
Score = 24.6 bits (54), Expect = 8.2
Identities = 8/30 (26%), Positives = 17/30 (56%)
Query: 47 EITKKEESCAVNCLEKYMKMTSRISMRMQE 76
+ K+ E C C++K++ + I RM++
Sbjct: 100 DAAKEMERCVNKCVDKHVNLLPEIVKRMKK 129
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
0.319 0.128 0.362
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,301,850
Number of extensions: 324372
Number of successful extensions: 335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 29
Length of query: 94
Length of database: 10,937,602
Length adjustment: 61
Effective length of query: 33
Effective length of database: 8,232,008
Effective search space: 271656264
Effective search space used: 271656264
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: 53 (24.4 bits)