RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10453
(184 letters)
>gnl|CDD|220651 pfam10248, Mlf1IP, Myelodysplasia-myeloid leukemia factor
1-interacting protein. This entry is the conserved
central region of a group of proteins that are putative
transcriptional repressors. The structure contains a
putative 14-3-3 binding motif involved in the
subcellular localisation of various regulatory
molecules, and it may be that interaction with the
transcription factor DREF could be regulated through
this motif. DREF regulates proliferation-related genes
in Drosophila. Mlf1IP is expressed in both the nuclei
and the cytoplasm and thus may have multi-functions.
Length = 177
Score = 137 bits (346), Expect = 2e-41
Identities = 56/86 (65%), Positives = 71/86 (82%), Gaps = 4/86 (4%)
Query: 84 KVYQATSSTRSAPGGIRETKKAVCDSRTGVKKLAIGHAIGDKEHIIEREQNLRSGEQEER 143
KVYQATS TR+APGGIRET+K V DS +G++K+AIGH IGD+ HIIER QN R+G+QEER
Sbjct: 96 KVYQATSQTRTAPGGIRETRKTVRDSESGLEKMAIGHHIGDRAHIIERSQNRRTGDQEER 155
Query: 144 QDFINLDEGIDNEESEAFNQEWRQKA 169
QDFINLDE E+ AF++EW+++
Sbjct: 156 QDFINLDES----EAAAFDEEWQREV 177
>gnl|CDD|143611 cd07587, ML_beta-AS, mammalian-like beta-alanine synthase
(beta-AS) and similar proteins (class 5 nitrilases).
This subgroup includes mammalian-like beta-AS (EC
3.5.1.6, also known as beta-ureidopropionase or
N-carbamoyl-beta-alanine amidohydrolase). This enzyme
catalyzes the third and final step in the catabolic
pyrimidine catabolic pathway responsible for the
degradation of uracil and thymine, the hydrolysis of
N-carbamyl-beta-alanine and
N-carbamyl-beta-aminoisobutyrate to the beta-amino
acids, beta-alanine and beta-aminoisobutyrate
respectively. This subgroup belongs to a larger
nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as
1-13), this subgroup corresponds to class 5. Members of
this superfamily generally form homomeric complexes,
the basic building block of which is a homodimer.
Beta-ASs from this subgroup are found in various
oligomeric states, dimer (human), hexamer (calf liver),
decamer (Arabidopsis and Zea mays), and in the case of
Drosophila melanogaster beta-AS, as a homooctamer
assembled as a left-handed helical turn, with the
possibility of higher order oligomers formed by adding
dimers at either end. Rat beta-AS changes its
oligomeric state (hexamer, trimer, dodecamer) in
response to allosteric effectors. Eukaryotic
Saccharomyces kluyveri beta-AS belongs to a different
superfamily.
Length = 363
Score = 33.1 bits (76), Expect = 0.060
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 16 ILGAPAEAREFIEVASDVMRERQFDLQGWEITGDPETEKPTSL--LGLLWNKV 66
+ G + E E A D+ +E F+L+G++ PE +P + +GL+ NK+
Sbjct: 21 LYGEEVKPLELPESALDLAKENDFELKGYKFEAAPEQTRPPRIVRVGLIQNKI 73
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 29.6 bits (67), Expect = 0.73
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 14/71 (19%)
Query: 62 LWNKVEDTLSVSIESLKEM----QYQKVYQATSSTRSAP---GGIRETKKAVCDSRTGVK 114
W++VE T +S E LK+ + +Y + A GG E +AV + R VK
Sbjct: 47 HWDRVEATEKMSDEQLKDRTEIFERDSLYVNNDTAFCARLSCGGAIEACRAVAEGR--VK 104
Query: 115 K-LAI----GH 120
A+ GH
Sbjct: 105 NAFAVVRPPGH 115
>gnl|CDD|173442 PTZ00153, PTZ00153, lipoamide dehydrogenase; Provisional.
Length = 659
Score = 28.7 bits (64), Expect = 1.9
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 66 VEDTLSVSIESLKEMQYQKVYQATSSTRSAPGGIRETKKAVCDSRTGVK 114
V+ S +S KE + + + AT ST + P I +K+V S T VK
Sbjct: 259 VDKNTIKSEKSGKEFKVKNIIIATGSTPNIPDNIEVDQKSVFTSDTAVK 307
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 28.6 bits (64), Expect = 2.0
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 11/73 (15%)
Query: 114 KKLAIGHAI---------GDKEHIIEREQNLRSGEQEERQDFINLDEGIDNEESEAFNQE 164
++ I H I KE I + L + E+E Q +L++ + +E E +E
Sbjct: 490 QRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLL--KEQEKLKKE 547
Query: 165 WRQKAREAQLLQH 177
Q+ E + +
Sbjct: 548 LEQEMEELKERER 560
>gnl|CDD|176765 cd08787, CARD_NOD2_1_CARD15, Caspase activation and recruitment
domain of NOD2, repeat 1. Caspase activation and
recruitment domain (CARD) similar to that found in
human NOD2 (CARD15), repeat 1. NOD2 is a member of the
Nod-like receptor (NLR) family, which plays a central
role in the innate immune response. NLRs typically
contain an N-terminal effector domain, a central
nucleotide-binding domain and a C-terminal
ligand-binding region of several leucine-rich repeats
(LRRs). In NOD2, as well as NOD1, the N-terminal
effector domain is a CARD. NOD2 contains two N-terminal
CARD repeats. Mutations in NOD2 have been associated
with Crohns disease and Blau syndrome. Nod2-CARDs have
been shown to interact with the CARD domain of the
downstream effector RICK (RIP2, CARDIAK), a
serine/threonine kinase. In general, CARDs are death
domains (DDs) found associated with caspases. They are
known to be important in the signaling pathways for
apoptosis, inflammation, and host-defense mechanisms.
DDs are protein-protein interaction domains found in a
variety of domain architectures. Their common feature
is that they form homodimers by self-association or
heterodimers by associating with other members of the
DD superfamily including PYRIN and DED (Death Effector
Domain). They serve as adaptors in signaling pathways
and can recruit other proteins into signaling
complexes.
Length = 87
Score = 27.2 bits (60), Expect = 2.1
Identities = 9/42 (21%), Positives = 19/42 (45%)
Query: 40 DLQGWEITGDPETEKPTSLLGLLWNKVEDTLSVSIESLKEMQ 81
D +G+ + G P + LL ++NK E + + ++
Sbjct: 38 DYEGFHVLGQPLSHNARQLLDTVYNKGEWACQKFLAAAQQAL 79
>gnl|CDD|177792 PLN00202, PLN00202, beta-ureidopropionase.
Length = 405
Score = 27.9 bits (62), Expect = 3.9
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 17 LGAPAEAREFIEVASDVMRERQFDLQGWEITGDPETEKPTSL--LGLLWNKV 66
G P E E A + + FDLQ + T D E + + +GL+ N +
Sbjct: 45 CGRPVEMIALPEAAKALSKAHDFDLQAFRFTADKEQLRAPRVVRVGLIQNSI 96
>gnl|CDD|240355 PTZ00314, PTZ00314, inosine-5'-monophosphate dehydrogenase;
Provisional.
Length = 495
Score = 27.2 bits (61), Expect = 5.6
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 100 RETKKAVCDSRTGVKKLAIGHAIGDKEHIIEREQNL 135
R A DS +L +G AI + IER L
Sbjct: 217 RGYPNASLDSN---GQLLVGAAISTRPEDIERAAAL 249
>gnl|CDD|225227 COG2352, Ppc, Phosphoenolpyruvate carboxylase [Energy production
and conversion].
Length = 910
Score = 26.9 bits (60), Expect = 7.6
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 117 AIGHAIGDK-EHIIEREQNLRSGEQEERQDFINLDEGIDNEE----SEAFNQ 163
A G AI + E I + + R+G+Q +RQ+ + N+E + AF+Q
Sbjct: 27 AEGEAILELVETIRKLSKESRAGDQADRQELEATLANLSNDEAIPVARAFSQ 78
>gnl|CDD|238822 cd01644, RT_pepA17, RT_pepA17: Reverse transcriptase (RTs) in
retrotransposons. This subfamily represents the RT
domain of a multifunctional enzyme. C-terminal to the RT
domain is a domain homologous to aspartic proteinases
(corresponding to Merops family A17) encoded by
retrotransposons and retroviruses. RT catalyzes DNA
replication from an RNA template and is responsible for
the replication of retroelements.
Length = 213
Score = 26.1 bits (58), Expect = 9.2
Identities = 17/72 (23%), Positives = 24/72 (33%), Gaps = 17/72 (23%)
Query: 14 DDILGAPAEAREFIEVASDV--------MRERQFDLQGWEITGDPETEKPTS-------- 57
DDIL + E + VA + R++ E+ D E+
Sbjct: 142 DDILVSTDTLNEAVNVAKRLIALLKKGGFNLRKWASNSQEVLDDLPEERVLLDRDSDVTE 201
Query: 58 -LLGLLWNKVED 68
LGL WN D
Sbjct: 202 KTLGLRWNPKTD 213
>gnl|CDD|236084 PRK07739, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 507
Score = 26.5 bits (59), Expect = 9.6
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 131 REQNLRSGEQEERQDFINLDEGIDNEESE-----AFNQEW 165
R +N + G E + D ++ E I NE S+ +Q W
Sbjct: 86 RRENNKLGYWETKADALSQMEDIMNEPSDTGLNKVLDQFW 125
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
0.313 0.131 0.368
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,406,158
Number of extensions: 858236
Number of successful extensions: 663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 661
Number of HSP's successfully gapped: 37
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.3 bits)