RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15166
(90 letters)
>gnl|CDD|193604 cd09829, PET_testin, The PET domain of Testin. The PET domain of
Testin: Testin contains a PET domain at the N-terminus
and three C-terminal LIM domains. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at cell-cell
contact areas, and at focal adhesion plaques. Testin
interacts with a variety of cytoskeletal proteins,
including zyxin, mena, VASP, talin, and actin and is
involved in cell motility and adhesion events. Knockout
mice experiments reveal a tumor repressor function of
Testin. The PET domain is a protein-protein interaction
domain and is usually found in conjunction with LIM
domain, which is also involved in protein-protein
interactions. The PET containing proteins serve as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 88
Score = 81.9 bits (203), Expect = 3e-22
Identities = 30/56 (53%), Positives = 43/56 (76%), Gaps = 2/56 (3%)
Query: 28 AAEYMQQLPAGKLPISGSDGALYRRQQLEKQVPLHDLNANLCHNLTADEIKCEKME 83
A YM+ LP K PI+GS+GA YR++QL+KQ+PLHD + +LCH L+ +E+K +ME
Sbjct: 15 ARYYMELLPKEKQPIAGSEGAQYRKKQLQKQLPLHDQDPSLCHELSENEVK--QME 68
>gnl|CDD|191489 pfam06297, PET, PET Domain. This domain is suggested to be
involved in protein-protein interactions. The family is
found in conjunction with pfam00412.
Length = 106
Score = 63.9 bits (156), Expect = 6e-15
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 26 KQAAEYMQQLPAGKLPISGSDGALYRRQQLEKQVPLHDLNANLCHNLTADEIK 78
+ YM+ LP K+P+ GS+G YRR+QL Q+P HD + CH L+ +E+K
Sbjct: 31 ELVHRYMELLPEEKVPVVGSEGEKYRRRQLLHQLPPHDQDPRYCHGLSEEEVK 83
>gnl|CDD|193601 cd09027, PET, PET ((Prickle Espinas Testin) domain is involved in
protein-protein interactions. PET domain is involved
in protein-protein interactions and is usually found in
conjunction with LIM domain, which is also a
protein-protein interaction domain. The PET containing
proteins serve as adaptors or scaffolds to support the
assembly of multimeric protein complexes. The PET
domain has been found at the N-terminal of four known
groups of proteins: prickle, testin, LIMPETin/LIM-9 and
overexpressed breast tumor protein (OEBT). Prickle has
been implicated in regulation of cell movement through
its association with the Dishevelled (Dsh) protein in
the planar cell polarity (PCP) pathway. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at cell contact
areas, and at focal adhesion plaques. It interacts with
a variety of cytoskeletal proteins, including zyxin,
mena, VASP, talin, and actin, and is involved in cell
motility and adhesion events. Knockout mice experiments
reveal tumor repressor function of Testin.
LIMPETin/LIM-9 contains an N-terminal PET domain and 6
LIM domains at the C-terminal. In Schistosoma mansoni,
where LIMPETin was first identified, it is down
regulated in sexually mature adult females compared to
sexually immature adult females and adult males. Its
differential expression indicates that it is a
transcription regulator. In C. elegans, LIM-9 may play
a role in regulating the assembly and maintenance of
the muscle A-band by forming a protein complex with
SCPL-1 and UNC-89 and other proteins. OEBT displays a
PET domain with two LIM domains, and is predicted to be
localized in the nucleus with a possible role in cancer
differentiation.
Length = 82
Score = 53.2 bits (128), Expect = 5e-11
Identities = 22/52 (42%), Positives = 31/52 (59%)
Query: 27 QAAEYMQQLPAGKLPISGSDGALYRRQQLEKQVPLHDLNANLCHNLTADEIK 78
+Y + LP K+P GS+GA YRR+QL Q+P HDL+ C L+ +E
Sbjct: 14 LIEQYFECLPKEKVPRLGSEGAKYRRRQLLYQLPAHDLDPRYCDALSEEERA 65
>gnl|CDD|193605 cd09830, PET_LIMPETin_LIM-9, The PET domain of protein LIMPETin
and LIM-9. The PET domain of protein LIMPETin and
LIM-9: Members of this family contain an N-terminal
PETdomain and five to six LIM domains at the
C-terminus. Four of the six LIM domains are highly
homologous to the four-and-half LIM (FHL) domain family
while the other two show sequence similarity to LIM
domains of the Testin family. Thus, proteins of this
family may be the recombinant product of genes coding
testin and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Thus, proteins of this family may be the
recombinant product of genes coding Testin and FHL
proteins. SmLIMPETin is down regulated in sexually
mature adult Schistosoma females compared to sexually
immature adult females and adult males. Its
differential expression indicates that it is a
transcription regulator. In C. elegans, LIM-9 binds to
UNC-97 and UNC-96, components of sarcomeric muscle
M-lines. LIM-9 also forms a complex with SCPL-1 and
UNC-89, whose function is to organize sarcomeric
A-bands, especially the M-line of muscle. Thus, it
might play a role in regulating the assembly and
maintenance of muscle A-band. The PET domain is a
protein-protein interaction domain and is usually found
in conjunction with LIM domain, which is also involved
in protein-protein interactions. The PET containing
proteins serve as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 83
Score = 51.9 bits (125), Expect = 2e-10
Identities = 21/47 (44%), Positives = 27/47 (57%)
Query: 30 EYMQQLPAGKLPISGSDGALYRRQQLEKQVPLHDLNANLCHNLTADE 76
+YM LP K+P GS G YR +QL Q+P DL+ C +L DE
Sbjct: 17 DYMSSLPNEKVPKLGSPGERYREKQLILQLPKQDLSLAYCKHLEEDE 63
>gnl|CDD|193602 cd09827, PET_Prickle, The PET domain of Prickle. The PET domain
of Prickle: Prickle contains an N-terminal PET domain
and three C-terminal LIM domains. Prickle has been
implicated in regulation of cell movement in the planar
cell polarity (PCP) pathway which requires the
conserved Frizzled/Dishevelled (Dsh); Prickle interacts
with Dishevelled, thereby modulating the activity of
Frizzled/Dishevelled and the PCP signaling. Two forms
of Prickle have been identified, namely Prickle 1 and
Prickle 2. These are differentially expressed; Prickle
1 is found in fetal heart and hematological
malignancies, while Prickle 2 is expressed in fetal
brain, adult cartilage, pancreatic islet, and some
types of timorous cells. The PET domain is a
protein-protein interaction domain, usually found in
conjunction with the LIM domain, which is also involved
in protein-protein interactions. The PET containing
proteins serve as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 97
Score = 45.8 bits (109), Expect = 5e-08
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 26 KQAAEYMQQLPAGKLPISGSDGALYRRQQLEKQVPLHDLNANLCHNLTADEIK 78
+Q Y LP K+P S G YR +QL Q+P HD C++L+ +E +
Sbjct: 22 EQVHAYFSCLPEDKVPYVNSPGEKYRIKQLLHQLPPHDNEVRYCNSLSEEEKR 74
>gnl|CDD|237539 PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
Length = 746
Score = 26.6 bits (59), Expect = 1.8
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 6 AGKLPISGSDGAL-YRRQQLEKQAAEYMQQLP 36
+LPI+ D AL RRQ L + + +
Sbjct: 490 DSQLPITFDDPALESRRQALLNKENTHERTER 521
Score = 25.8 bits (57), Expect = 3.5
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 37 AGKLPISGSDGAL-YRRQQLEKQVPLHDLNANLCHNLTAD 75
+LPI+ D AL RRQ L + H+ H
Sbjct: 490 DSQLPITFDDPALESRRQALLNKENTHERTERPEHRGRTG 529
>gnl|CDD|206633 pfam14468, DUF4427, Protein of unknown function (DUF4427). This
domain is often found at the C-terminal of proteins with
pfam10899 domain, for instance in STY1911 protein from a
multiple drug resistant Salmonella enterica serovar
Typhi CT18.
Length = 132
Score = 26.0 bits (57), Expect = 2.1
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 8 KLPISGSDGALYRRQQLEKQAAEYMQQ---LPAGKLPISGSD 46
KLP+ GS L +++ + K+ A ++ Q L G + GS+
Sbjct: 70 KLPLFGSRWPLRQKETMAKEVARWLTQRFGLECGYFSVLGSE 111
>gnl|CDD|214343 CHL00035, psbC, photosystem II 44 kDa protein.
Length = 473
Score = 26.2 bits (58), Expect = 2.6
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 25 EKQAAEYMQQLPAGKL 40
E+++AEYM P G L
Sbjct: 389 ERRSAEYMTHAPLGSL 404
>gnl|CDD|182018 PRK09651, PRK09651, RNA polymerase sigma factor FecI; Provisional.
Length = 172
Score = 25.5 bits (56), Expect = 3.3
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 18 LYRRQQLEKQAAEYMQQLPAGKLPISGSDGALYRRQQLE 56
L+RR LEK E + +P G P R QLE
Sbjct: 75 LFRRNALEKAYLEMLALMPEGGAP-----SPEERESQLE 108
>gnl|CDD|216732 pfam01837, DUF39, Domain of unknown function DUF39. This presumed
domain is about is about 360 residues long. The function
of this domain is unknown. It is found in some proteins
that have two C-terminal CBS pfam00571 domains. There
are also proteins that contain two inserted Fe4S domains
near the C-terminal end of the domain. The protein
MTH_855 has been misannotated as an inosine
monophosphate dehydrogenase based on the similarity to
the CBS domains.
Length = 335
Score = 25.9 bits (58), Expect = 3.3
Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 35 LPAGK---LPISGSDGALYRRQQLEKQVPLHDLN-ANLC 69
L AGK L G Y R++LE + L DLN A L
Sbjct: 96 LVAGKEVELKAEGYGTDCYPRRELETTITLDDLNQARLF 134
>gnl|CDD|238283 cd00512, MM_CoA_mutase, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM)-like family; contains
proteins similar to MCM, and the large subunit of
Streptomyces coenzyme B12-dependent isobutyryl-CoA
mutase (ICM). MCM catalyzes the isomerization of
methylmalonyl-CoA to succinyl-CoA. The reaction proceeds
via radical intermediates beginning with a
substrate-induced homolytic cleavage of the Co-C bond of
coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
higher animals, MCM is involved in the breakdown of
odd-chain fatty acids, several amino acids, and
cholesterol. Methylobacterium extorquens MCM
participates in the glyoxylate regeneration pathway. In
M. extorquens, MCM forms a complex with MeaB; MeaB may
protect MCM from irreversible inactivation. In some
bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Examples include Propionbacterium
shermanni MCM during propionic acid fermentation, E.coli
MCM in a pathway for the conversion of succinate to
propionate and Streptomyces MCM in polyketide
biosynthesis. P. shermanni and Streptomyces
cinnamonensis MCMs are alpha/beta heterodimers, with
both subunits being homologous members of this family.
It has been shown for P. shermanni MCM that only the
alpha subunit binds coenzyme B12 and substrates. Human
MCM is a homodimer with two active sites. Mouse and
E.coli MCMs are also homodimers. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA (intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis). In humans, impaired activity of MCM results
in methylmalonic aciduria, a disorder of propionic acid
metabolism.
Length = 399
Score = 25.9 bits (57), Expect = 3.7
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 19 YRRQQLEKQAAEYMQQLPAGKLPISG 44
Y + +++ AAE ++ +GK PI G
Sbjct: 359 YVKGVIDESAAERQARIESGKQPIVG 384
>gnl|CDD|129739 TIGR00654, PhzF_family, phenazine biosynthesis protein PhzF family.
Members of this family show a distant global similarity
to diaminopimelate epimerases, which can be taken as the
outgroup. One member of this family has been shown to
act as an enzyme in the biosynthesis of the antibiotic
phenazine in Pseudomonas aureofaciens. The function in
other species is unclear [Cellular processes, Toxin
production and resistance].
Length = 297
Score = 25.6 bits (56), Expect = 3.8
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 5 PAGKLPISG--SDGALYRRQQLEK--QAAEYMQQLPAGKLPISGSDGALYRRQQLEKQVP 60
P +LP +G + G+ Y + K A +Q+ AG +P++ ++ R LE+ +P
Sbjct: 67 PRSELPFAGHPTIGSCYALLEFTKLTTATTLVQECKAGAVPVTINEKNGDLRISLEQPMP 126
Query: 61 L 61
Sbjct: 127 D 127
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 25.3 bits (55), Expect = 5.0
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 3 QLPAGKLPISGSDGALYRRQQLEKQAAEYMQQL 35
LPA LPI +D AL++R LE A E +QL
Sbjct: 212 GLPA--LPIQYADYALWQRSWLE--AGEQERQL 240
>gnl|CDD|219398 pfam07394, DUF1501, Protein of unknown function (DUF1501). This
family contains a number of hypothetical bacterial
proteins of unknown function approximately 400 residues
long.
Length = 393
Score = 24.6 bits (54), Expect = 9.5
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 56 EKQVPLHDLNANLCHNLTADE 76
E V +HDL+A + H L D
Sbjct: 348 ENPVHVHDLHATILHLLGIDH 368
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
0.317 0.132 0.383
Gapped
Lambda K H
0.267 0.0601 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,545,202
Number of extensions: 362285
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 422
Number of HSP's successfully gapped: 27
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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 (21.6 bits)
S2: 53 (24.5 bits)