RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6139
(69 letters)
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to
chromosome metabolism and cell cycle control.
Length = 73
Score = 55.9 bits (135), Expect = 1e-12
Identities = 22/41 (53%), Positives = 25/41 (60%)
Query: 1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPED 41
+KKWNAVA+WSWD+E D CAICR GT P D
Sbjct: 1 RVEIKKWNAVALWSWDIEDDVCAICRNHFDGTCPECKSPGD 41
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 51.4 bits (123), Expect = 1e-10
Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 2 FTLKKWNAVAMWSWDVECDTCAICRVQVMGT 32
+KKW+AVA+WSWD+ D CAICR +MGT
Sbjct: 3 VKIKKWHAVALWSWDIPIDVCAICRNHIMGT 33
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 37.8 bits (88), Expect = 2e-05
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 3 TLKKWNAVAMWSWDV-ECDTCAICRVQVMGT 32
+K+WNAVA W+WD D C ICRV GT
Sbjct: 4 KIKEWNAVATWTWDTPSDDVCGICRVSFDGT 34
>gnl|CDD|133454 cd05312, NAD_bind_1_malic_enz, NAD(P) binding domain of malic
enzyme (ME), subgroup 1. Malic enzyme (ME), a member of
the amino acid dehydrogenase (DH)-like domain family,
catalyzes the oxidative decarboxylation of L-malate to
pyruvate in the presence of cations (typically Mg++ or
Mn++) with the concomitant reduction of cofactor NAD+ or
NADP+. ME has been found in all organisms, and plays
important roles in diverse metabolic pathways such as
photosynthesis and lipogenesis. This enzyme generally
forms homotetramers. The conversion of malate to
pyruvate by ME typically involves oxidation of malate to
produce oxaloacetate, followed by decarboxylation of
oxaloacetate to produce pyruvate and CO2. This
subfamily consists of eukaryotic and bacterial ME.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 279
Score = 32.9 bits (76), Expect = 0.006
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 30 MGTATVYPEPEDKLAFVKSFVYD 52
G AT YP PED +VKS +++
Sbjct: 256 EGLATRYPPPEDLEEYVKSQMWE 278
>gnl|CDD|215594 PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
Length = 581
Score = 26.8 bits (60), Expect = 0.91
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 30 MGTATVYPEPEDKLAFVKSFVYDYSYS 56
G AT P PED + + +S +Y Y
Sbjct: 552 EGLATRLPRPEDLVEYAESCMYSPVYR 578
>gnl|CDD|213331 cd05129, RasGAP_RAP6, Ras-GTPase Activating Domain of
Rab5-activating protein 6. Rab5-activating protein 6
(RAP6) is an endosomal protein with a role in the
regulation of receptor-mediated endocytosis. RAP6
contains a Vps9 domain, which is involved in the
activation of Rab5, and a Ras GAP domain (RGD). Rab5 is
a small GTPase required for the control of the endocytic
route, and its activity is regulated by guanine
nucleotide exchange factor, such as Rabex5, and GAPs,
such as RN-tre. Human Rap6 protein is localized on the
plasma membrane and on the endosome. RAP6 binds to Rab5
and Ras through the Vps9 and RGD domains, respectively.
Length = 365
Score = 25.4 bits (56), Expect = 2.5
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 38 EPEDKL-AFVKSFVYDYSYSEPSVPTSYSW 66
E +L A V F+ S P S W
Sbjct: 170 EFLSRLVALVNKFISSLRQSVYCFPQSLRW 199
>gnl|CDD|148618 pfam07114, DUF1370, Protein of unknown function (DUF1370). This
family consists of several hypothetical eukaryotic
proteins of around 200 residues in length. Members of
this family seem to be specific to mammals and their
function is unknown.
Length = 187
Score = 25.1 bits (55), Expect = 2.6
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 11 AMWSWDVECDTCAICRVQVMGTAT--VYP 37
+ S D+ C+TCA+ R ++G +YP
Sbjct: 86 PLLSGDLNCETCAVTRSALIGLVCGGLYP 114
>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma. The third
LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone, and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 23.8 bits (51), Expect = 4.1
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 13 WSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSF 49
+SW C CAIC++ + G T Y + + L +F
Sbjct: 20 FSWHDTCFVCAICQINLEGK-TFYSKKDKPLCKSHAF 55
>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like
family. The third LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 23.2 bits (50), Expect = 7.4
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 14 SWDVECDTCAICRVQVMGTA 33
+W C CA+C V + G
Sbjct: 21 TWHDTCFVCAVCHVNLEGQT 40
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first
LIM domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In mouse, Lmx1b functions in the developing limbs and
eyes, the kidneys, the brain, and in cranial
mesenchyme. The disruption of Lmx1b gene results kidney
and limb defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 23.1 bits (50), Expect = 7.9
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 14 SWDVECDTCAICR 26
SW EC C++C+
Sbjct: 20 SWHEECLQCSVCQ 32
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
0.320 0.131 0.452
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,399,321
Number of extensions: 227275
Number of successful extensions: 227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 11
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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 (21.9 bits)
S2: 53 (24.4 bits)