RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14113
(543 letters)
>gnl|CDD|188822 cd09438, LIM3_Ajuba_like, The third LIM domain of Ajuba-like
proteins. The third LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. 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 = 62
Score = 126 bits (319), Expect = 2e-35
Identities = 44/62 (70%), Positives = 51/62 (82%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
CAACG+ I P EG+EET+RVVSMDKD+HV+CY CEDCGLQL DE RCYPL G L+C +
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRCYPLDGHLLCHS 60
Query: 525 CH 526
CH
Sbjct: 61 CH 62
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. 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 = 126 bits (318), Expect = 2e-35
Identities = 47/53 (88%), Positives = 51/53 (96%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA+CGHLIMEMILQA+GKSYHPGCFRCC+CNECLDGVPFTVDV+N IYCV DY
Sbjct: 1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
Score = 47.0 bits (112), Expect = 3e-07
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAF-YNVHGRVYCEEDY 372
C CG + QA+G YH CF CC C L G F +V +YC +DY
Sbjct: 1 CAVCGHLIME--MILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. 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 = 54
Score = 117 bits (294), Expect = 4e-32
Identities = 44/54 (81%), Positives = 47/54 (87%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG+ V GA QACQAMGNLYHTNCF CCSCGR LRGKAFYNV+G+VYCEEDY
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
Score = 42.4 bits (100), Expect = 1e-05
Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 418 QAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
QAMG YH CF CC C L G F +V+ K+YC DY
Sbjct: 16 QAMGNLYHTNCFTCCSCGRTLRGKAF-YNVNGKVYCEEDY 54
Score = 28.9 bits (65), Expect = 0.73
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
C CGKG+ G + + +M +H +C+ C CG L K Y + G++ C
Sbjct: 1 CVKCGKGVY---GASQACQ--AMGNLYHTNCFTCCSCGRTLR---GKAFYNVNGKVYC 50
>gnl|CDD|188743 cd09357, LIM3_Zyxin_like, The third LIM domain of Zyxin-like
family. The third LIM domain of Zyxin like family: This
family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and
Trip6 LIM proteins. Members of Zyxin family contain
three tandem C-terminal LIM domains, and a proline-rich
N-terminal region. Zyxin proteins are detected
primarily in focal adhesion plaques. They function as
scaffolds, participating in the assembly of multiple
interactions and signal transduction networks, which
regulate cell adhesion, spreading, and motility. They
can also shuffle into nucleus. In nucleus, zyxin
proteins affect gene transcription by interaction with a
variety of nuclear proteins, including several
transcription factors, playing regulating roles in cell
proliferation, differentiation and apoptosis. 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 = 63
Score = 95.2 bits (237), Expect = 4e-24
Identities = 32/63 (50%), Positives = 48/63 (76%), Gaps = 1/63 (1%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKR-CYPLQGRLMCR 523
C+ CG+ I P G +ETVR+V++D+ FHV+CY CEDCG+ L+ E + + CYPL G L+C+
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCK 60
Query: 524 ACH 526
+C+
Sbjct: 61 SCN 63
Score = 31.2 bits (71), Expect = 0.15
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 405 CAICGHLIM------EMI-LQAMGKSYHPGCFRCCLCNECL 438
C++CG IM E + + A+ +S+H C++C C L
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLL 41
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at the
N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. 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 = 60
Score = 85.3 bits (211), Expect = 1e-20
Identities = 31/60 (51%), Positives = 45/60 (75%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPK 464
C++C I++ IL+A GK YHP CF C +C + LDG+PFTVD N+I+C+ D+H+ FAP+
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60
Score = 33.7 bits (77), Expect = 0.019
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAF-YNVHGRVYCEEDY 372
C C + + + +A G YH CF C CG++L G F + +++C ED+
Sbjct: 1 CSVCSKPILD--RILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDF 53
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. 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 = 79.9 bits (197), Expect = 6e-19
Identities = 28/53 (52%), Positives = 39/53 (73%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C++C IME IL+A GK+YHP CF C +C+ LDG+PFTVD +I+C+ D+
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
Score = 36.0 bits (83), Expect = 0.002
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAF-YNVHGRVYCEEDY 372
C C + + + +A G YH +CF C C R+L G F + G+++C ED+
Sbjct: 1 CSVCSKPIME--RILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
>gnl|CDD|188820 cd09436, LIM3_TRIP6, The third LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The third LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. 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 = 66
Score = 79.7 bits (196), Expect = 1e-18
Identities = 32/66 (48%), Positives = 48/66 (72%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
C+ C + I P G EETVR+V++D+DFHV CY CEDCG L++ ++ CYPL G ++C+A
Sbjct: 1 CSVCKEPIMPAPGQEETVRIVALDRDFHVQCYRCEDCGSLLSEGDNQGCYPLDGHILCKA 60
Query: 525 CHLSHL 530
C+ + +
Sbjct: 61 CNSARI 66
>gnl|CDD|188821 cd09437, LIM3_LPP, The third LIM domain of lipoma preferred partner
(LPP). The third LIM domain of lipoma preferred partner
(LPP): LPP is a member of the zyxin LIM protein family
and contains three LIM zinc-binding domains at the
C-terminal and proline-rich region at the N-terminal.
LPP initially identified as the most frequent
translocation partner of HMGA2 (High Mobility Group A2)
in a subgroup of benign tumors of adipose tissue
(lipomas). It was also shown to be rearranged in a
number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP), Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. 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 = 68
Score = 77.5 bits (191), Expect = 8e-18
Identities = 32/63 (50%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKR-CYPLQGRLMCR 523
C C I P G +ETVRVV++D+ FHV CY CEDCGL L+ E + R CYPL ++C+
Sbjct: 1 CCVCKLPIMPEPGQDETVRVVALDRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLCK 60
Query: 524 ACH 526
+C+
Sbjct: 61 SCN 63
>gnl|CDD|188819 cd09435, LIM3_Zyxin, The third LIM domain of Zyxin. The third LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cellsubstratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. 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 = 67
Score = 76.1 bits (187), Expect = 3e-17
Identities = 31/63 (49%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKR-CYPLQGRLMCR 523
C C + I P G +ETVRVV+++K+FH+ CY CEDCG L+ E D C+PL G ++C
Sbjct: 1 CCVCSEPIMPEPGRDETVRVVALEKNFHMKCYKCEDCGRPLSIEADDNGCFPLDGHVLCM 60
Query: 524 ACH 526
CH
Sbjct: 61 KCH 63
>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin. The second
LIM domain of Zyxin: Zyxin exhibits three copies of the
LIM domain, an extensive proline-rich domain and a
nuclear export signal. Localized at sites of
cellsubstratum adhesion in fibroblasts, Zyxin interacts
with alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. 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 o r
scaffolds to support the assembly of multimeric protein.
Length = 60
Score = 72.7 bits (178), Expect = 3e-16
Identities = 31/60 (51%), Positives = 41/60 (68%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPK 464
CA+C I + +L+A GKSYHP CF C +C L+G F VD N+ +CVNDYHR +AP+
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60
Score = 34.5 bits (79), Expect = 0.009
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAF 359
C C +K+T + +A G YH CF C C L G++F
Sbjct: 1 CAVCDQKITD--RMLKATGKSYHPQCFTCVVCKCPLEGESF 39
>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner
(LPP). The first LIM domain of lipoma preferred partner
(LPP): LPP is a member of the zyxin LIM protein family
and contains three LIM zinc-binding domains at the
C-terminal and proline-rich region at the N-terminal.
LPP initially identified as the most frequent
translocation partner of HMGA2 (High Mobility Group A2)
in a subgroup of benign tumors of adipose tissue
(lipomas). It was also shown to be rearranged in a
number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. 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 = 54
Score = 68.6 bits (168), Expect = 6e-15
Identities = 29/54 (53%), Positives = 34/54 (62%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CGEKV G G C AM +YH +CF C C L+GK FY + G+ YCEEDY
Sbjct: 1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
Score = 35.1 bits (81), Expect = 0.004
Identities = 18/39 (46%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 419 AMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
AM + YH CF C C L G PF +D K YC DY
Sbjct: 17 AMDQVYHISCFTCHQCQINLQGKPF-YALDGKPYCEEDY 54
Score = 33.6 bits (77), Expect = 0.020
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
C CG+ V G E +MD+ +H+ C+ C C + L +P Y L G+ C
Sbjct: 1 CVKCGE---KVLG--EGSGCTAMDQVYHISCFTCHQCQINLQGKP---FYALDGKPYC 50
>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The first LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. 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 = 54
Score = 67.4 bits (165), Expect = 2e-14
Identities = 25/54 (46%), Positives = 31/54 (57%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CGE V G G C AM ++H +CF C +C LRG+ FY V + YCE Y
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 41.2 bits (97), Expect = 4e-05
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
C CG+ + EGT +MD+ FHVDC+ C C +L +P Y ++ + C
Sbjct: 1 CGRCGENVV-GEGTG----CTAMDQVFHVDCFTCMTCNGKLRGQP---FYAVEKKAYCEP 52
Query: 525 CH 526
C+
Sbjct: 53 CY 54
Score = 35.1 bits (81), Expect = 0.005
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
C CG ++ AM + +H CF C CN L G PF V+ K YC
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYA-VEKKAYC 50
>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the filamin-binding
LIM protein-1 (FBLP-1). The second LIM domain of the
filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains
a proline-rich domain near its N terminus and two LIM
domains at its C terminus. FBLP-1 mRNA was detected in a
variety of tissues and cells including platelets and
endothelial cells. FBLP-1 binds to Filamins. The
association between filamin B and FBLP-1 may play an
unknown role in cytoskeletal function, cell adhesion,
and cell motility. As in other LIM domains, this domain
family is 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.
Length = 53
Score = 63.6 bits (155), Expect = 4e-13
Identities = 24/53 (45%), Positives = 33/53 (62%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C +I E I++A+GK YHP CF C C + F VD N++YC++DY
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
Score = 42.0 bits (99), Expect = 2e-05
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAF-YNVHGRVYCEEDY 372
C C +T +A+G YH CF C +CGR + ++F + VYC +DY
Sbjct: 1 CAKCQGVITE--HIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
Score = 30.1 bits (68), Expect = 0.28
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDE 508
CA C IT E +R ++ K +H C+ C CG ++ DE
Sbjct: 1 CAKCQGVIT-----EHIIR--ALGKGYHPPCFTCVTCGRRIGDE 37
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are identified
in a diverse group of proteins with wide variety of
biological functions, including gene expression
regulation, cell fate determination, cytoskeleton
organization, tumor formation and development. LIM
domains function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. They perform
their functions through interactions with other protein
partners. LIM domains are 50-60 amino acids in size and
share two characteristic highly conserved zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. The consensus
sequence of LIM domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 63.1 bits (154), Expect = 5e-13
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG+ + G + +A+G +H CF C CG+ L G +FY G+ YCE+ Y
Sbjct: 1 CAGCGKPIEG-RELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 62.3 bits (152), Expect = 1e-12
Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 405 CAICGHLIM-EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA CG I +L+A+GK +HP CF+C +C + L G F D K YC Y
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYE-KDGKPYCEKCY 53
Score = 50.0 bits (120), Expect = 3e-08
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
CA CGK I E + ++ K +H +C+ C CG L + Y G+ C
Sbjct: 1 CAGCGKPI------EGRELLRALGKKWHPECFKCSVCGKPLGGDS---FYEKDGKPYCEK 51
Query: 525 CH 526
C+
Sbjct: 52 CY 53
>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin. The first LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cell substratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. 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 = 87
Score = 63.3 bits (154), Expect = 1e-12
Identities = 29/80 (36%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 294 KIEELTRQLEEEMEK-QEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGR 352
++E LT+QL ++M+ E +C CG+ ++ A +A+G+L+H CF C C +
Sbjct: 8 ELEMLTQQLMQDMDHPPAAEAATNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQ 67
Query: 353 ALRGKAFYNVHGRVYCEEDY 372
L+G+ FY++ G+ YCEE Y
Sbjct: 68 QLQGQQFYSLEGKPYCEECY 87
Score = 33.3 bits (76), Expect = 0.049
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 462 APKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLM 521
A CG P+ T+ VR ++ FHV C+ C C QL + + Y L+G+
Sbjct: 28 AATNELCGICGQPLSRTQPAVR--ALGHLFHVTCFTCHQCEQQLQGQ---QFYSLEGKPY 82
Query: 522 CRACH 526
C C+
Sbjct: 83 CEECY 87
Score = 31.4 bits (71), Expect = 0.20
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 401 TAEKCAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
T E C ICG + + ++A+G +H CF C C + L G F ++ K YC Y
Sbjct: 30 TNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQF-YSLEGKPYCEECY 87
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 62.0 bits (151), Expect = 1e-12
Identities = 18/54 (33%), Positives = 32/54 (59%)
Query: 318 ICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEED 371
C CG+ + G + +A+G ++H CF C +CG+ L G F+ G++YC++
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 57.8 bits (140), Expect = 5e-11
Identities = 24/55 (43%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 404 KCAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVND 456
KCA CG I E +L+A+GK +HP CF+C C + L G F D K+YC +
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEK-DGKLYCKDC 54
Score = 51.2 bits (123), Expect = 9e-09
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 464 KCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
KCA CGK I E + ++ K +H +C+ C CG L+ + G+L C+
Sbjct: 1 KCAGCGKPIYGTE-----RVLRALGKVWHPECFKCATCGKPLS---GDTFFEKDGKLYCK 52
Query: 524 AC 525
C
Sbjct: 53 DC 54
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 57.0 bits (138), Expect = 1e-10
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDYL 373
C CG+ + +A+G ++H CF C CG+ L F+ G++YC+ DY
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYF 55
Score = 55.8 bits (135), Expect = 2e-10
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMF 461
CA CG I E++ +A+GK +HP CFRC +C + L F D K+YC +DY ++F
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFE-KDGKLYCKHDYFKLF 58
Score = 50.0 bits (120), Expect = 3e-08
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
CA CGK I E R + K +H +C+ C CG L + G+L C+
Sbjct: 1 CAGCGKPIYD---RELVRRA--LGKVWHPECFRCAVCGKPLG---PGDFFEKDGKLYCKH 52
Query: 525 CHL 527
+
Sbjct: 53 DYF 55
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the nucleus
to suppress Rac/Cdc42-dependent cyclin D1 expression.
LIMK1 is expressed in all tissues and is localized to
focal adhesions in the cell. LIMK1 can form homodimers
upon binding of HSP90 and is activated by Rho effector
Rho kinase and MAPKAPK2. LIMK1 is important for normal
central nervous system development, and its deletion has
been implicated in the development of the human genetic
disorder Williams syndrome. Moreover, LIMK1 up-regulates
the promoter activity of urokinase type plasminogen
activator and induces its mRNA and protein expression in
breast cancer cells. The LIM domains have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All 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 = 74
Score = 53.0 bits (127), Expect = 4e-09
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 303 EEEMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNV 362
EE M EEEG +C +CG+ + GQ QA+ + +H +CF CC CG +L +Y
Sbjct: 8 EERM--GEEEGNVLPVCASCGQSIYD-GQYLQALNSDWHADCFRCCECGASL-SHWYYEK 63
Query: 363 HGRVYCEEDY 372
GR++C++DY
Sbjct: 64 DGRLFCKKDY 73
Score = 40.3 bits (94), Expect = 1e-04
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIM-EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA CG I LQA+ +H CFRCC C L + + D +++C DY
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYY--EKDGRLFCKKDY 73
Score = 37.6 bits (87), Expect = 0.001
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 463 PKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
P CA+CG+ I + + +++ D+H DC+ C +CG L+ Y GRL C
Sbjct: 20 PVCASCGQSIY------DGQYLQALNSDWHADCFRCCECGASLS----HWYYEKDGRLFC 69
Query: 523 R 523
+
Sbjct: 70 K 70
>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. 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 = 59
Score = 52.3 bits (126), Expect = 4e-09
Identities = 19/54 (35%), Positives = 24/54 (44%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C E + + G LYH CF+C C + FY GR YCE D+
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDF 54
Score = 38.1 bits (89), Expect = 5e-04
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 405 CAIC--GHLIMEMILQAMGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYCVNDYHRMF 461
C C G E I+ + G+ YH CF C C + DG+ + + + + YC +D+ +F
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFY--EFEGRKYCEHDFQVLF 58
Query: 462 A 462
A
Sbjct: 59 A 59
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a cytoskeleton
adaptor protein, which is preferentially expressed in
hematopoietic cells. Leupaxin belongs to the paxillin
focal adhesion protein family. Same as other members of
the family, it has four leucine-rich LD-motifs in the
N-terminus and four LIM domains in the C-terminus. It
may function in cell type-specific signaling by
associating with interaction partners PYK2, FAK, PEP and
p95PKL. When expressed in human leukocytic cells,
leupaxin significantly suppressed integrin-mediated cell
adhesion to fibronectin and the tyrosine phosphorylation
of paxillin. These findings indicate that leupaxin may
negatively regulate the functions of paxillin during
integrin signaling. 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 = 49.9 bits (119), Expect = 3e-08
Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 317 GICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
G C +C + + AGQ A+G +H F+CC CG+ L + F+ +G+ YCEEDY
Sbjct: 1 GDCASCQKPI--AGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
Score = 46.4 bits (110), Expect = 5e-07
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYH 458
CA C I ++ A+G+++HP F CC C + L PF + + + YC DYH
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPF-FERNGQAYCEEDYH 55
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong 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. Mouse Lmx1a is
expressed in multiple tissues, including the roof plate
of the neural tube, the developing brain, the otic
vesicles, the notochord, and the pancreas. In mouse,
mutations in Lmx1a result in failure of the roof plate
to develop. Lmx1a may act upstream of other roof plate
markers such as MafB, Gdf7, Bmp6, and Bmp7. Further
characterization of these mice reveals numerous defects
including disorganized cerebellum, hippocampus, and
cortex; altered pigmentation; female sterility, skeletal
defects, and behavioral abnormalities. In the 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 = 55
Score = 47.8 bits (114), Expect = 1e-07
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL-RGKAFYNVHGRVYCEEDY 372
C C EK+ + +A+ N+YH CF CC C R L +G F G++ C+ DY
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
Score = 37.8 bits (88), Expect = 6e-04
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 414 EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
E++++A+ YH CF CC+C L V + ++ C +DY
Sbjct: 12 ELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin
like protein family. The first LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. 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 = 53
Score = 47.7 bits (114), Expect = 1e-07
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYH 458
CA C I+ ++ A+GK++HP F C C L F + D + YC DYH
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNF-FERDGQPYCEKDYH 53
Score = 46.6 bits (111), Expect = 4e-07
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + + GQ A+G +H F+C C L K F+ G+ YCE+DY
Sbjct: 1 CAACKKPI--VGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma
subfamily with unknown function. The third LIM domain
of an Enigma subfamily with unknown function: The Enigma
LIM domain family is comprised of three characterized
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.
They serve as adaptor proteins, where the PDZ domain
tethers the protein to the cytoskeleton and the LIM
domains, recruit signaling proteins to implement
corresponding functions. The members of the enigma
family have been implicated in regulating or organizing
cytoskeletal structure, as well as involving multiple
signaling pathways. 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 = 47.9 bits (114), Expect = 1e-07
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C +CG + + +A+ N YH+ CF C C L G++FY GR +C+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
Score = 31.0 bits (70), Expect = 0.14
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPF 443
C CG I + ++A+ +YH CF C CN L+G F
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSF 41
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second 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 = 52
Score = 47.5 bits (113), Expect = 2e-07
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C +K+ G + A+ +H +CF+C +C + + F+ G YCE+DY
Sbjct: 1 CARCHKKILG--EVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 33.6 bits (77), Expect = 0.015
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C I+ ++ A+ +++H CF C C + + F ++ D + YC DY
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHME-DGEPYCEKDY 52
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The second
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 = 52
Score = 47.7 bits (113), Expect = 2e-07
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C +K+TG + A+ +H +CF C +C +R +AFY G YCE DY
Sbjct: 1 CAKCKKKITG--EIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 31.9 bits (72), Expect = 0.077
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C I I+ A+ ++H CF C C + F ++ + YC DY
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYME-EGAPYCERDY 52
>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 = 46.3 bits (110), Expect = 5e-07
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
CH C + + +A+G+ +H CF+C C L G+ FY+ + C
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 32.0 bits (73), Expect = 0.068
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPF 443
C C I + L+A+G ++H CF C +C+ L+G F
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTF 41
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only
protein 4). The second LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact with
Smad proteins, and associate with the promoter of the
PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential role
for LMO4 as a negative regulator of BRCA1 in sporadic
breast cancer. LMO4 also forms complex to both ERa
(oestrogen receptor alpha), MTA1 (metastasis tumor
antigen 1), and HDACs (histone deacetylases), implying
that LMO4 is also a component of the MTA1 corepressor
complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All 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 = 45.9 bits (109), Expect = 6e-07
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL-RGKAFYNVHGRVYCEED 371
C CG+ + + +A GN+YH CF C +C L G F+ V+G ++CE D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54
Score = 40.2 bits (94), Expect = 7e-05
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLC-NECLDGVPFTVDVDNKIYCVND 456
C+ CG I E++++A G YH CF C C N+ + G F V+ ++C +D
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHY-VNGSLFCEHD 54
Score = 35.9 bits (83), Expect = 0.002
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
C+ACG+ I +E +R +H+ C+ C C QL P R + + G L C
Sbjct: 1 CSACGQSIP---ASELVMRA--QGNVYHLKCFTCSTCHNQLV--PGDRFHYVNGSLFC 51
>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated
LIM protein) family. This family represents the LIM
domain of ALP (actinin-associated LIM protein) family.
Four proteins: ALP, CLP36, RIL, and Mystique have been
classified into the ALP subfamily of LIM domain
proteins. Each member of the subfamily contains an
N-terminal PDZ domain and a C-terminal LIM domain.
Functionally, these proteins bind to alpha-actinin
through their PDZ domains and bind or other signaling
molecules through their LIM domains. ALP proteins have
been implicated in cardiac and skeletal muscle
structure, function and disease, platelet, and
epithelial cell motility. 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 = 52
Score = 44.7 bits (106), Expect = 2e-06
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C CG + G +A H CF+C CG L+ K ++ + +YCE
Sbjct: 1 CDKCGNGI--VGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCE 49
Score = 41.6 bits (98), Expect = 2e-05
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
C CG+ I+ ++++A K+ HP CF C C L + +++++YC
Sbjct: 1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFF-IEDELYC 48
Score = 35.4 bits (82), Expect = 0.003
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
C CG GI V V + DK+ H +C++C DCGL L
Sbjct: 1 CDKCGNGIV-------GVVVKARDKNRHPECFVCADCGLNL 34
>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM
(abLIM) proteins. The first LIM domain of actin binding
LIM (abLIM) proteins: Three homologous members of the
abLIM protein family have been identified; abLIM-1,
abLIM-2 and abLIM-3. The N-terminal of abLIM consists of
four tandem repeats of LIM domains and the C-terminal of
acting binding LIM protein is a villin headpiece domain,
which has strong actin binding activity. The abLIM-1,
which is expressed in retina, brain, and muscle tissue,
has been indicated to function as a tumor suppressor.
AbLIM-2 and -3, mainly expressed in muscle and neuronal
tissue, bind to F-actin strongly. They may serve as a
scaffold for signaling modules of the actin cytoskeleton
and thereby modulate transcription. It has shown that
LIM domains of abLIMs interact with STARS (striated
muscle activator of Rho signaling), which directly binds
actin and stimulates serum-response factor
(SRF)-dependent transcription. All LIM domains are 50-60
amino acids in size and share two characteristic highly
conserved 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 = 52
Score = 44.6 bits (106), Expect = 2e-06
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C+ CG+K G+ + +H CF C CG L F+ G YC +DY
Sbjct: 1 CYKCGKKC--KGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
Score = 36.9 bits (86), Expect = 0.001
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG +L+ K +H CF C +C L F V + + YC +DY
Sbjct: 1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVK-EGEYYCTDDY 52
Score = 28.8 bits (65), Expect = 0.75
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
C CGK +G E +RV DK FH+ C+ C+ CG L
Sbjct: 1 CYKCGK---KCKG--EVLRV--QDKYFHIKCFTCKVCGCDL 34
>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH. The
second LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
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 = 52
Score = 44.2 bits (105), Expect = 2e-06
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPF 443
C CG ++ +++AM ++HP CFRC +CN+ L + F
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGF 39
Score = 38.1 bits (89), Expect = 4e-04
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
C CGE V G + +AM N +H +CF C C + L F GR C
Sbjct: 1 CGKCGEFVIG--RVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50
Score = 33.5 bits (77), Expect = 0.019
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 483 RVV-SMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRACH 526
RV+ +M+ ++H DC+ CE C +L D + GR +C C+
Sbjct: 11 RVIKAMNNNWHPDCFRCEICNKELADIGFVKN---AGRALCHPCN 52
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM domains
at the C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also 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. ENH
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 = 52
Score = 44.2 bits (104), Expect = 3e-06
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C K+ G + A+ +H +CF+C +C +R F+ G YCE DY
Sbjct: 1 CGRCQRKILG--EVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 32.7 bits (74), Expect = 0.039
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C I+ ++ A+ +++H CF C C+ + F ++ D + YC DY
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLE-DGEPYCETDY 52
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
The PINCH LIM4 domain recognizes the third SH3 domain of
another adaptor protein, Nck2. This step is an important
component of integrin signaling event. 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 assem
bly of multimeric protein complexes.
Length = 54
Score = 43.9 bits (104), Expect = 4e-06
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 318 ICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
IC C + G + A+G +H F+C C + G Y G YCE Y
Sbjct: 2 ICGACRRPIEG--RVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 33.1 bits (76), Expect = 0.023
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 5/39 (12%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPF 443
C C I ++ A+GK +H F C C PF
Sbjct: 3 CGACRRPIEGRVVTALGKHWHVEHFVCAKC-----EKPF 36
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. 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 it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. 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
complexes.
Length = 58
Score = 43.7 bits (104), Expect = 5e-06
Identities = 23/64 (35%), Positives = 27/64 (42%), Gaps = 17/64 (26%)
Query: 405 CAICGHLIM--EMILQAM----GKSYHPGCFRCCLCNECLDGVPFTVDV-----DNKIYC 453
C C I E+ + A +HPGCF C CNE L VD+ D KIYC
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELL------VDLIYFYHDGKIYC 54
Query: 454 VNDY 457
Y
Sbjct: 55 GRHY 58
Score = 30.6 bits (70), Expect = 0.23
Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 14/63 (22%)
Query: 319 CHTCGEKVTG---------AGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C C E + AG+ +H CF+C +C L ++ G++YC
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDAC-----WHPGCFVCETCNELLVDLIYFYHDGKIYCG 55
Query: 370 EDY 372
Y
Sbjct: 56 RHY 58
>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 = 43.1 bits (101), Expect = 7e-06
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
CH C K+ + +A+G +H CF+C C L GK FY+ + C+
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCK 51
Score = 29.6 bits (66), Expect = 0.52
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 417 LQAMGKSYHPGCFRCCLCNECLDGVPF 443
L+A+G S+H CF C +C L+G F
Sbjct: 15 LEALGFSWHDTCFVCAICQINLEGKTF 41
>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH). The
first LIM domain of Arrowhead (AWH): Arrowhead 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. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. 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 = 54
Score = 42.4 bits (100), Expect = 1e-05
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG I + +L+ G+S+H C RCC+C L+ P D +IYC DY
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
Score = 27.7 bits (62), Expect = 2.2
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL-RGKAFYNVHGRVYCEEDY 372
C CGE +T + G +H +C CC C L R + + ++YC+ DY
Sbjct: 1 CTGCGEPITDR-FLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP,
actinin-associated LIM protein. This family represents
the LIM domain of ALP, actinin-associated LIM protein.
ALP contains an N-terminal PDZ domain, a C-terminal LIM
domain and an ALP-subfamily-specific 34-amino-acid motif
termed ALP-like motif (AM), which contains a putative
consensus protein kinase C (PKC) phosphorylation site
and two alpha-helices. ALP proteins are found in heart
and in skeletal muscle. ALP may act as a signaling
molecule which is regulated by PKC-dependent signaling.
ALP plays an essential role in the development of RV
(right ventricle) chamber. 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 = 53
Score = 41.8 bits (98), Expect = 2e-05
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C CG + G +A H CF+C C L+ K ++ V G++YCE
Sbjct: 1 CDKCGSGIVGT--VVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49
Score = 33.3 bits (76), Expect = 0.023
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
C CG GI GT R DK H +C++C DC L L K + ++G+L C A
Sbjct: 1 CDKCGSGIV---GTVVKAR----DKYRHPECFVCSDCNLNLK---QKGYFFVEGQLYCEA 50
Score = 31.4 bits (71), Expect = 0.085
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
C CG I+ +++A K HP CF C CN L + V+ ++YC
Sbjct: 1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFF-VEGQLYC 48
>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM
(abLIM) proteins. The third LIM domain of actin binding
LIM (abLIM) proteins: Three homologous members of the
abLIM protein family have been identified; abLIM-1,
abLIM-2 and abLIM-3. The N-terminal of abLIM consists of
four tandem repeats of LIM domains and the C-terminal of
acting binding LIM protein is a villin headpiece domain,
which has strong actin binding activity. The abLIM-1,
which is expressed in retina, brain, and muscle tissue,
has been indicated to function as a tumor suppressor.
AbLIM-2 and -3, mainly expressed in muscle and neuronal
tissue, bind to F-actin strongly. They may serve as a
scaffold for signaling modules of the actin cytoskeleton
and thereby modulate transcription. It has shown that
LIM domains of abLIMs interact with STARS (striated
muscle activator of Rho signaling), which directly binds
actin and stimulates serum-response factor
(SRF)-dependent transcription. All LIM domains are 50-60
amino acids in size and share two characteristic highly
conserved 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 = 52
Score = 41.5 bits (98), Expect = 2e-05
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG+++ GQA A+ +H CF C CG+ L G+ + G+ YCE DY
Sbjct: 1 CAGCGQEIKN-GQALLALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52
Score = 37.3 bits (87), Expect = 8e-04
Identities = 21/61 (34%), Positives = 25/61 (40%), Gaps = 17/61 (27%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECL-------DGVPFTVDVDNKIYCVND 456
CA CG I L A+ K +H CF+C C + L DG P YC D
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMGKDGKP---------YCERD 51
Query: 457 Y 457
Y
Sbjct: 52 Y 52
Score = 32.7 bits (75), Expect = 0.033
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDE 508
CA CG+ I + ++++DK +HV C+ C++CG LT E
Sbjct: 1 CAGCGQEIKNGQA------LLALDKQWHVWCFKCKECGKVLTGE 38
>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM
domains protein (FHL). The second LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. 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 = 41.5 bits (98), Expect = 2e-05
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG IM ++ GK +H CF C C + + F + D+KIYCV Y
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSF-IPKDDKIYCVPCY 54
Score = 41.1 bits (97), Expect = 4e-05
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG+ + + + G +H CF C C + + K+F ++YC
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYC 50
>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule
interacting with CasL) like family. The LIM domain of
Mical (molecule interacting with CasL) like family:
Known members of this family includes LIM domain
containing proteins; Mical (molecule interacting with
CasL), pollen specific protein SF3, Eplin, xin
actin-binding repeat-containing protein 2 (XIRP2) and
Ltd-1. The members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth and mobility. Eplin has
also found to be tumor suppressor. 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 = 41.5 bits (98), Expect = 3e-05
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG+ V + A G L+H +CF C C + LR + ++ G++YC
Sbjct: 1 CAVCGKTVYPM-ERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49
Score = 32.2 bits (74), Expect = 0.046
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 405 CAICGHLIMEM-ILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
CA+CG + M L A GK +H CFRC CN+ L + ++ K+YC
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYAS-LEGKLYC 49
Score = 30.7 bits (70), Expect = 0.15
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
CA CGK + P+E R+V+ K FH C+ C C L L+G+L C+
Sbjct: 1 CAVCGKTVYPME------RLVADGKLFHKSCFRCSHCNKTLR--LGNYAS-LEGKLYCK 50
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain, and
a short consensus C-terminal region. It is the smallest
molecule in the ALP LIM domain containing protein
family. RIL was identified in rat fibroblasts and in
human lymphocytes. The LIM domain interacts with the
AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. 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 = 53
Score = 41.5 bits (97), Expect = 3e-05
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C CG + G +A LYH CF+C CG L+ + ++ + ++YCE
Sbjct: 1 CTRCGNGIVGT--IVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYCE 49
Score = 37.6 bits (87), Expect = 6e-04
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 7/41 (17%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
C CG GI V + DK +H +C+MC+DCGL L
Sbjct: 1 CTRCGNGIV-------GTIVKARDKLYHPECFMCDDCGLNL 34
Score = 36.4 bits (84), Expect = 0.002
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVN 455
C CG+ I+ I++A K YHP CF C C L + +D ++YC
Sbjct: 1 CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFF-IDEQLYCET 50
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong 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. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain , the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. 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 = 54
Score = 41.2 bits (97), Expect = 3e-05
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA CG I + L A+ + +H C +CC C LD D IYC DY
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
Score = 36.5 bits (85), Expect = 0.001
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGK-AFYNVHGRVYCEEDY 372
C CGEK+ A+ +H +C CC C L + + ++ G +YC+EDY
Sbjct: 1 CAGCGEKIQDRFYLL-AVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase
). The first LIM domain of LIMK (LIM domain Kinase ):
LIMK protein family is comprised of two members LIMK1
and LIMK2. LIMK contains two LIM domains, a PDZ domain
and a kinase domain. LIMK is involved in the regulation
of actin polymerization and microtubule disassembly.
LIMK influences architecture of the actin cytoskeleton
by regulating the activity of the cofilin family
proteins cofilin1, cofilin2, and destrin. The mechanism
of the activation is to phosphorylates cofilin on serine
3 and inactivates its actin-severing activity, and
altering the rate of actin depolymerisation. LIMKs can
function in both cytoplasm and nucleus and are expressed
in all tissues. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. However, LIMK1 and LIMk2 have different
cellular locations. While LIMK1 localizes mainly at
focal adhesions, LIMK2 is found in cytoplasmic punctae,
suggesting that they may have different cellular
functions. The LIM domains of LIMK have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All 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 = 53
Score = 40.9 bits (96), Expect = 4e-05
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 405 CAIC-GHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C G ++ +QA+ + +H CFRC +C++ L F + D K+YC DY
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYF--EKDGKLYCRKDY 52
Score = 36.3 bits (84), Expect = 0.002
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C K+ Q QA+ +H +CF C C +L ++ G++YC +DY
Sbjct: 1 CAGCRGKIL-DSQYVQALNQDWHCDCFRCSVCSDSLSNW-YFEKDGKLYCRKDY 52
Score = 29.4 bits (66), Expect = 0.57
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
CA C I + V+ + ++D+H DC+ C C L++ + G+L CR
Sbjct: 1 CAGCRGKILD----SQYVQAL--NQDWHCDCFRCSVCSDSLSNW----YFEKDGKLYCR 49
>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like
family. The first 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 = 52
Score = 40.8 bits (96), Expect = 4e-05
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C +I L A+G+S+HP F C C+ L + F V+ +YC Y
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGF-VEEKGSLYCELCY 52
Score = 34.3 bits (79), Expect = 0.009
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + + G A+G +H F C C +L F G +YCE Y
Sbjct: 1 CAHCNQVIRGP--FLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 46.1 bits (109), Expect = 5e-05
Identities = 44/219 (20%), Positives = 55/219 (25%), Gaps = 41/219 (18%)
Query: 74 SAKPGPVSPSGSSKDSNSPRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPH---LRS 130
A P P D PR P P A PP P
Sbjct: 2590 DAPPQSARPRAPVDDRGDPRGPAPPSPLP---------PDTHAPDPPPPSPSPAANEPDP 2640
Query: 131 GSHSSVGSQDSKHSSPRGSYVSNDINAFQFDRKAQPQVPQGLKYIRDYPPYEAPPVYENI 190
+V + P VS A + R AQ P + A P ++
Sbjct: 2641 HPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-----PQRPRRRAARPTVGSL 2695
Query: 191 QELNKPPKPGPQVPVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQV 250
L PP P P P A A P+ + + Q
Sbjct: 2696 TSLADPPPPPP------------------TP--EPAPHALVSATPLPPGPAAA----RQA 2731
Query: 251 SSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPT 289
S + P+P P P TP G T P P
Sbjct: 2732 SPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPA 2770
Score = 39.2 bits (91), Expect = 0.006
Identities = 47/266 (17%), Positives = 82/266 (30%), Gaps = 28/266 (10%)
Query: 31 RAPAPPPVDYKQYERGNIIASSKFATPKSVDNLPLADVYRSNGSAKPGPVSPSGSSKDSN 90
APA P ++ S+ + P D + +A P SP+G
Sbjct: 2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP--- 2829
Query: 91 SPRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPHLRSGSHSSVGSQDSKHSSPRGSY 150
P ++ T P P ++ P R S ++ + + P
Sbjct: 2830 PPTSAQPTAPPPPPGPPPPSLPLGGSVAPGG----DVRRRPPSRSPAAKPAAPARPPVRR 2885
Query: 151 VSNDINAFQFDRKAQPQVPQGLKYIRDYPPYEAPPVYENIQELNKPPKPGPQVPVFGGEH 210
++ + + A P P +APP + + PP+P P P
Sbjct: 2886 LARPAVSRSTESFALPPDQP-----ERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQ 2940
Query: 211 RQMA----IALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKT 266
+A A P + VP + A P ++V P + +P+ S
Sbjct: 2941 PPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAV-----PRFRVPQPAPSREAPASSTPP 2995
Query: 267 P-------VTPYGKNLLPYNVTPPRP 285
V+ + +L + T P P
Sbjct: 2996 LTGHSLSRVSSWASSLALHEETDPPP 3021
Score = 39.2 bits (91), Expect = 0.008
Identities = 46/282 (16%), Positives = 72/282 (25%), Gaps = 37/282 (13%)
Query: 17 PVGAIESFLVEGTSRAPAPPPVDYKQYERGNIIASSKFATPKSVDNLPLADVYRSNGSAK 76
P + + + PPP + ++ + A + R A
Sbjct: 2629 PSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAA 2688
Query: 77 PGPVSPSGSSKDSNSPRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPHLRSGSHSSV 136
V S D P + P L +A PP P + ++
Sbjct: 2689 RPTVGSLTSLADPPPPPPTPEPAPHALV---------SATPLPP----GPAAARQASPAL 2735
Query: 137 GSQDSKHSSPRGSYVSNDINAFQFDRKAQPQVPQGLKYIRDYPPYEAPPVYENIQELNKP 196
+ + + P G R A+P G PP APP
Sbjct: 2736 PAAPAPPAVPAGPATPGGPA-----RPARPPTTAG-------PPAPAPPA-------APA 2776
Query: 197 PKPGPQVPVFGGEHRQMAI-ALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVD 255
P ++ + +L SP + + P +S
Sbjct: 2777 AGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQP 2836
Query: 256 TTPSPSPSPKTPVTPYGKNLLP----YNVTPPRPMGPTEAER 293
T P P P P P P G ++ P P R A
Sbjct: 2837 TAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAP 2878
Score = 31.8 bits (72), Expect = 1.3
Identities = 55/291 (18%), Positives = 82/291 (28%), Gaps = 53/291 (18%)
Query: 17 PVGAIESFLVEGTSRAPAPPPVDYKQYERGNIIASSKFATPKSVDNLPLADVYRSNGSAK 76
VG++ S + P PPP + + A V PL + A
Sbjct: 2691 TVGSLTSL-----ADPPPPPP-------------TPEPAPHALVSATPLPPGPAAARQAS 2732
Query: 77 P-------------GPVSPSGSSKDSNSPRASVATVPSPLYENVDYYNGRNAALTPPYYH 123
P GP +P G ++ + P + P+P A PP
Sbjct: 2733 PALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAP---------PAAPAAGPPRRL 2783
Query: 124 QLPHLRSGSHSSVGSQDSKHSSPRGSYVSNDINAFQFDRKAQPQVPQGLKYIRDYPPYEA 183
P + S S S + + V A +P PP
Sbjct: 2784 TRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPP 2843
Query: 184 PPVYENIQELNKPPKPGPQVPVFGGEHR-----QMAIALTSPPVYSRANTVTSKAVPVKT 238
P ++ P G P GG+ R + A + P + AV T
Sbjct: 2844 GPPPPSL------PLGGSVAP--GGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRST 2895
Query: 239 ATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPT 289
+ + P P P P+ P P + P P P+ PT
Sbjct: 2896 ESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946
>gnl|CDD|188816 cd09432, LIM6_LIMPETin, The sixth LIM domain of protein LIMPETin.
The sixth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
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. Its differential expression indicates that it is a
transcription regulator. 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 = 56
Score = 40.5 bits (95), Expect = 6e-05
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQA--CQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
C CG+ +TG G +H +CF C C +L GK F GR+ C +
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPD 54
Score = 37.5 bits (87), Expect = 8e-04
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 465 CAACGKGITPVEGTEETVRVVSM-DKDFHVDCYMCEDCGLQL------TDEPDKRC 513
CAACGK IT + GT + +S D+ +H DC+ C C L TD C
Sbjct: 1 CAACGKPITGIGGT----KFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52
Score = 28.2 bits (63), Expect = 1.6
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 10/46 (21%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCA 466
+ +H CF C C L G F D R+ P CA
Sbjct: 21 DRHWHNDCFNCAGCRTSLVGKGFI----------TDGGRILCPDCA 56
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The first LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain 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 = 57
Score = 40.4 bits (95), Expect = 6e-05
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAF---YNVHGRVY--CEEDY 372
C CG+ +TG Q +A+G++YH +CF C CG+ + K F CE DY
Sbjct: 1 CAKCGKPITG--QFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSEQVPLCETDY 57
Score = 35.4 bits (82), Expect = 0.004
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 7/38 (18%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCG 502
CA CGK IT + VR ++ +H+DC+ C DCG
Sbjct: 1 CAKCGKPITG-----QFVR--ALGDVYHLDCFTCHDCG 31
Score = 35.4 bits (82), Expect = 0.004
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIY----CVNDY 457
CA CG I ++A+G YH CF C C + + F VD + C DY
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSEQVPLCETDY 57
>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8.
The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong 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. Studies using mutant mice have
revealed roles for Lhx7 and Lhx8 in the development of
cholinergic neurons in the telencephalon and in basal
forebrain development. Mice lacking alleles of the
LIM-homeobox gene Lhx7 or Lhx8 display dramatically
reduced number of forebrain cholinergic neurons. In
addition, Lhx7 mutation affects male and female mice
differently, with females appearing more affected than
males. 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 = 55
Score = 40.4 bits (94), Expect = 6e-05
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVHGRVYCEEDY 372
C CG + +A GN+YH CF C SC R L G+ F V +V C Y
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
Score = 30.0 bits (67), Expect = 0.38
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYC 453
C+ CG I + + +A G YH CF C C L G F + V+ K+ C
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFAL-VEEKVLC 51
>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight cons erved 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 = 40.4 bits (94), Expect = 8e-05
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 318 ICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+C C + + AGQ AMG +H F+C C + + F+ G+ YCE+DY
Sbjct: 1 VCGACKKPI--AGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
Score = 35.8 bits (82), Expect = 0.003
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYH 458
C C I ++ AMGK++HP F C C E + F + D + YC DYH
Sbjct: 2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNF-FERDGQPYCEKDYH 54
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. 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 = 52
Score = 40.3 bits (94), Expect = 8e-05
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C ++I L A+G+S+HP F C C+ L V F V+ N +YC N Y
Sbjct: 1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSF-VEEQNNVYCENCY 52
Score = 26.9 bits (59), Expect = 3.7
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 335 AMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
A+G +H F C C +L +F VYCE Y
Sbjct: 15 ALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. 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 it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. 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
complexes.
Length = 57
Score = 40.1 bits (94), Expect = 8e-05
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTN--CFICCSCGRALRGKAFYNVHGRVYC 368
C CGE + Q G +H CF C +C ++L G+ F +G+++C
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
Score = 29.3 bits (66), Expect = 0.64
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 421 GKSYH--PGCFRCCLCNECLDGVPFTVDVDNKIYC 453
G+ +H CF C C + L G PF + +I+C
Sbjct: 19 GQHWHATEECFCCSNCKKSLLGQPFLP-KNGQIFC 52
>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6. The second LIM
domain of Lhx6. Lhx6 is a member of 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. Lhx6 functions in
brain and nervous system. It is expressed at high
levels in several regions of the embryonic mouse CNS,
including the telencephalon and hypothalamus, and the
first branchial arch. Lhx6 is proposed to have a role in
patterning of the mandible and maxilla, and in signaling
during odontogenesis. In brain sections, knockdown of
Lhx6 gene blocks the normal migration of neurons to the
cortex. 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 complexes.
Length = 55
Score = 40.1 bits (93), Expect = 1e-04
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVHGRVYCEEDY 372
C CG ++ + +A GN YH CF C SC R L G+ F V +V C Y
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55
Score = 29.3 bits (65), Expect = 0.64
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYC 453
CA CG I + + +A G +YH CF C C L G F + V+ K+ C
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGL-VEEKVLC 51
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. 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 = 55
Score = 40.0 bits (93), Expect = 1e-04
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
CH C V + +A+G+ +H CFIC C L G+ FY+ + C++
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 52
Score = 30.0 bits (67), Expect = 0.32
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 417 LQAMGKSYHPGCFRCCLCNECLDGVPF 443
++A+G ++H CF C +C+ L+G PF
Sbjct: 15 IEALGHTWHDTCFICAVCHVNLEGQPF 41
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. 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 = 53
Score = 39.6 bits (93), Expect = 1e-04
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + + A+ +H CF+C C + +F+ G YCE Y
Sbjct: 1 CGGCNKPILE--NYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
Score = 36.9 bits (86), Expect = 0.001
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFT----VDVDNKIYCVNDYH 458
C C I+E + A+ +HP CF +C EC PF + + YC YH
Sbjct: 1 CGGCNKPILENYISALNTQWHPECF---VCREC--HKPFINGSFFEHEGLPYCETHYH 53
>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1. The Lim domain of DA1:
DA1 contains one copy of LIM domain and a domain of
unknown function. DA1 is predicted as an ubiquitin
receptor, which sets final seed and organ size by
restricting the period of cell proliferation. The LIM
domain 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 = 39.5 bits (93), Expect = 1e-04
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEED 371
C C G G+ A+G ++H CF C +C + + F V G +
Sbjct: 1 CAGCK-SEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFS-VSGNDPYHKS 51
Score = 37.2 bits (87), Expect = 8e-04
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 405 CAICGHLIMEMI-LQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIY 452
CA C I L A+G +HP CFRC C + + F+V N Y
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVS-GNDPY 48
>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin. The
second LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners PYK2,
FAK, PEP and p95PKL. When expressed in human leukocytic
cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. 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 = 52
Score = 39.4 bits (92), Expect = 1e-04
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C I++ +L AM +++HP F C C E L G ++ D K YC D+
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGE-LFGDEGFLERDGKPYCRRDF 52
Score = 30.9 bits (70), Expect = 0.16
Identities = 12/38 (31%), Positives = 16/38 (42%)
Query: 335 AMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
AM +H F C CG + F G+ YC D+
Sbjct: 15 AMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH)
family. The third LIM domain of the Enigma Homolog
(ENH) family: ENH was initially identified in rat brain.
Same as enigma, it contains three LIM domains at the
C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also 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. ENH
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 = 39.2 bits (91), Expect = 2e-04
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
CH C + + +A+G+ +H CF+C C +L G+ F++ + C++
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKK 52
Score = 33.8 bits (77), Expect = 0.017
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 414 EMILQAMGKSYHPGCFRCCLCNECLDGVPF 443
+ L+A+G ++H CF C +C E L+G F
Sbjct: 12 DRFLEALGHTWHDTCFVCSVCCESLEGQTF 41
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family.
The second LIM domain of Lhx3-Lhx4 family: Lhx3 and
Lhx4 belong 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. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription.Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. 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 = 56
Score = 38.9 bits (91), Expect = 2e-04
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYCVNDY 457
CA C I +++ +A YH CF C +C L+ G F + D+++ C DY
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
Score = 34.2 bits (79), Expect = 0.011
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVH-GRVYCEEDY 372
C C E + +A N+YH CF C C R L G FY + R+ C++DY
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
Score = 30.8 bits (70), Expect = 0.17
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
CA C +GI P + VR D +H++C+ C C QL
Sbjct: 1 CAGCDEGIPP----TQVVRRAQ-DNVYHLECFACFMCKRQL 36
>gnl|CDD|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM
(abLIM) proteins. The second LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to function
as a tumor suppressor. AbLIM-2 and -3, mainly expressed
in muscle and neuronal tissue, bind to F-actin strongly.
They may serve as a scaffold for signaling modules of
the actin cytoskeleton and thereby modulate
transcription. It has shown that LIM domains of abLIMs
interact with STARS (striated muscle activator of Rho
signaling), which directly binds actin and stimulates
serum-response factor (SRF)-dependent transcription. All
LIM domains are 50-60 amino acids in size and share two
characteristic highly conserved 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 = 56
Score = 38.9 bits (91), Expect = 2e-04
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 404 KCAICGHLIMEMILQAMGKSYHPGCFRCCLC 434
KC C + ++ A+GK+YHP CF C +C
Sbjct: 3 KCDSCQDFVEGEVVSALGKTYHPKCFVCSVC 33
Score = 35.0 bits (81), Expect = 0.006
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGR 352
C +C + V G + A+G YH CF+C C +
Sbjct: 4 CDSCQDFVEG--EVVSALGKTYHPKCFVCSVCRQ 35
>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein
2 (CRP2). The second LIM domain of Cysteine Rich
Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. 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 = 38.6 bits (89), Expect = 3e-04
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG+ V A + A G +H NCF C CG++L G +YC+ Y
Sbjct: 1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
Score = 32.8 bits (74), Expect = 0.038
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
C+ CG + E I+ A GK +H CFRC C + L+ T + + +IYC
Sbjct: 1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLT-EKEGEIYC 49
Score = 29.7 bits (66), Expect = 0.39
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 13/64 (20%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCG--LQLTDEPDKRCYPLQGRLMC 522
C+ CG + E +++ K +H +C+ C CG L+ T +K +G + C
Sbjct: 1 CSRCGDSVYAAE------KIMGAGKPWHKNCFRCAKCGKSLESTTLTEK-----EGEIYC 49
Query: 523 RACH 526
+ C+
Sbjct: 50 KGCY 53
>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM
domains protein 1 (FHL1). The second LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. 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 = 58
Score = 38.6 bits (90), Expect = 3e-04
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C + + Q + GN++H +CF C +C + + K+F+ YC
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO modulates
the activity of LIM-homeodomain protein Apterous (Ap),
which regulates the formation of the dorsal-ventral axis
of the Drosophila wing. Biochemical analysis shows that
dLMO protein influences the activity of Apterous by
binding of its cofactor Chip. Further studies shown that
dLMO proteins might function in an evolutionarily
conserved mechanism involved in patterning the
appendages. All 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 = 38.3 bits (89), Expect = 3e-04
Identities = 23/57 (40%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNE--CLDGVPFTVDVDNKIYCVNDY 457
CA C I EM+++A YH CF C CN C+ G F + +NKI C DY
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCV-GDRFYL-CENKILCEYDY 55
Score = 37.5 bits (87), Expect = 8e-04
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCG-RALRGKAFYNVHGRVYCEEDY 372
C C + + +A N+YH CF C C R G FY ++ CE DY
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55
>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin.
The first LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
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. Its differential expression indicates that it is a
transcription regulator. 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 = 58
Score = 38.1 bits (89), Expect = 4e-04
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 405 CAICGHLI----MEMILQAMGKS--YHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C + + + G+S +HP CFRC C E L + + V D++IYC Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVH-DDQIYCERHY 58
Score = 28.5 bits (64), Expect = 1.3
Identities = 19/59 (32%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 319 CHTCGEKVTGAGQACQA----MGNLYHTNCFICCSCGRALRGKAFYNVH-GRVYCEEDY 372
C C E + A A L+H CF C +C L Y VH ++YCE Y
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLT-YCVHDDQIYCERHY 58
>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin. The
third LIM domain of Leupaxin: Leupaxin is a cytoskeleton
adaptor protein, which is preferentially expressed in
hematopoietic cells. Leupaxin belongs to the paxillin
focal adhesion protein family. Same as other members of
the family, it has four leucine-rich LD-motifs in the
N-terminus and four LIM domains in the C-terminus. It
may function in cell type-specific signaling by
associating with interaction partners PYK2, FAK, PEP and
p95PKL. When expressed in human leukocytic cells,
leupaxin significantly suppressed integrin-mediated cell
adhesion to fibronectin and the tyrosine phosphorylation
of paxillin. These findings indicate that leupaxin may
negatively regulate the functions of paxillin during
integrin signaling. 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 = 53
Score = 37.9 bits (88), Expect = 5e-04
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG V A ++H CF+C C + +F+ + GR CE Y
Sbjct: 1 CSGCGRPVKE--NYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52
Score = 32.5 bits (74), Expect = 0.039
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFT----VDVDNKIYCVNDYH 458
C+ CG + E L A +HP CF +C++CL PFT ++D + C YH
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECF---VCSDCLK--PFTDGSFFELDGRPLCELHYH 53
>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein
(CRP). The second LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residu es,
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 = 37.6 bits (87), Expect = 7e-04
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG+ V A + A G +H NCF C CG++L + G +YC+ Y
Sbjct: 1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 36.0 bits (83), Expect = 0.003
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
C CG + E I+ A GK +H CFRC C + L+ D D +IYC
Sbjct: 1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLA-DKDGEIYC 49
Score = 30.2 bits (68), Expect = 0.25
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 13/64 (20%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCG--LQLTDEPDKRCYPLQGRLMC 522
C CGK + E +++ K +H +C+ C CG L+ T DK G + C
Sbjct: 1 CPRCGKSVYAAE------KIIGAGKPWHKNCFRCAKCGKSLESTTLADK-----DGEIYC 49
Query: 523 RACH 526
+ C+
Sbjct: 50 KGCY 53
>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM
domains protein 1 (FHL1). The third LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. 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 = 53
Score = 36.7 bits (85), Expect = 0.001
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + +T G Q +H+ CF+C SC + L G+ F V + YC + Y
Sbjct: 1 CVKCNKPITSGGVTYQDQP--WHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52
Score = 30.6 bits (69), Expect = 0.18
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C I + + +H CF C C++ L G FT V+++ YCV+ Y
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTA-VEDQYYCVDCY 52
>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The second LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or cofactors.
For example, LMO1 interacts with the the bHLH domain of
bHLH transcription factor, TAL1 (T-cell acute
leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the
expression of TAL1/SCL target genes. LMO3 facilitates
p53 binding to its response elements, which suggests
that LMO3 acts as a co-repressor of p53, suppressing
p53-dependent transcriptional regulation. In addition,
LMO3 interacts with neuronal transcription factor, HEN2,
and acts as an oncogene in neuroblastoma. Another
binding partner of LMO3 is calcium- and integrin-binding
protein CIB, which binds via the second LIM domain
(LIM2) of LMO3. One role of the CIB/LMO3 complex is to
inhibit cell proliferation. Although LMO1 and LMO3 are
highly homologous proteins, they play different roles in
the regulation of the pituitary glycoprotein hormone
alpha-subunit (alpha GSU) gene. Alpha GSU promoter
activity was markedly repressed by LMO1 but activated by
LMO3. All 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 = 36.9 bits (85), Expect = 0.001
Identities = 23/57 (40%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNE--CLDGVPFTVDVDNKIYCVNDY 457
CA C LI EM+++A YH CF C LCN+ C+ F +N I C DY
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFL--KNNMILCQMDY 55
Score = 33.1 bits (75), Expect = 0.025
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCG-RALRGKAFYNVHGRVYCEEDY 372
C C + + +A N+YH +CF C C R G F+ + + C+ DY
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55
Score = 27.3 bits (60), Expect = 2.7
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDC 501
CAAC K I E + + + D +H+DC+ C+ C
Sbjct: 1 CAACSKLIPAFE-----MVMRAKDNVYHLDCFACQLC 32
>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma. The first
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 = 52
Score = 36.7 bits (85), Expect = 0.001
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + + G + A+G YH F C C + L F+ G ++C + Y
Sbjct: 1 CAQCNKIIRG--RYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
Score = 34.8 bits (80), Expect = 0.006
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLD 439
CA C +I L A+G+SYHP F C C + LD
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLD 35
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first LIM
domain of Lhx3a: Lhx3a is a member of 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. Lhx3a is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. 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 = 56
Score = 36.7 bits (85), Expect = 0.001
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 10/62 (16%)
Query: 463 PKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
PKCA C I ++V DK +H C C DC QLTD +C+ G++ C
Sbjct: 2 PKCAGCDHPIF----DRFILKVQ--DKPWHSKCLKCVDCQAQLTD----KCFSRGGQVYC 51
Query: 523 RA 524
+
Sbjct: 52 KE 53
Score = 33.6 bits (77), Expect = 0.017
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 404 KCAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
KCA C H I + IL+ K +H C +C C L F+ ++YC D+
Sbjct: 3 KCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCFS--RGGQVYCKEDF 55
Score = 30.1 bits (68), Expect = 0.35
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H+ C C C L K ++ G+VYC+ED+
Sbjct: 24 WHSKCLKCVDCQAQLTDKC-FSRGGQVYCKEDF 55
>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM
(abLIM) proteins. The fourth LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to function
as a tumor suppressor. AbLIM-2 and -3, mainly expressed
in muscle and neuronal tissue, bind to F-actin strongly.
They may serve as a scaffold for signaling modules of
the actin cytoskeleton and thereby modulate
transcription. It has shown that LIM domains of abLIMs
interact with STARS (striated muscle activator of Rho
signaling), which directly binds actin and stimulates
serum-response factor (SRF)-dependent transcription. All
LIM domains are 50-60 amino acids in size and share two
characteristic highly conserved 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 = 56
Score = 36.6 bits (85), Expect = 0.002
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNE 436
C C I +L+A GK YHP C RC C +
Sbjct: 1 CEACDKFITGKVLEAGGKHYHPTCARCSRCGQ 32
>gnl|CDD|188804 cd09420, LIM3_Prickle, The third LIM domain of Prickle. The third
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle 1
and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. 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 = 59
Score = 36.6 bits (85), Expect = 0.002
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 319 CHTCGEKVTGAGQACQAM-GNLYHT--NCFICCSCGRALRGKAFYNVHGRVYC 368
C TCGE + G Q G +H CF C C ++L G+ F G++YC
Sbjct: 3 CDTCGEHI-GVDQGQMTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYC 54
Score = 26.6 bits (59), Expect = 5.1
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 428 CFRCCLCNECLDGVPFTVDVDNKIYC 453
CF C C + L G PF + +IYC
Sbjct: 30 CFCCAQCKKSLLGRPF-LPKQGQIYC 54
>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9
family. The second LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong 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. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain, the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. 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 = 59
Score = 36.1 bits (84), Expect = 0.002
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVH-GRVYCEEDY 372
+H NCF C +C + L + + G VYC Y
Sbjct: 26 FHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
Score = 30.3 bits (69), Expect = 0.27
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 464 KCAACGKGITPVEGTEETVRVVSMDKD--FHVDCYMCEDCGLQLT 506
+CA C GI+ E +V +D FH++C+ C C LT
Sbjct: 4 RCARCHLGISASE-------LVMRARDLVFHLNCFTCATCNKPLT 41
Score = 29.2 bits (66), Expect = 0.60
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 404 KCAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYCVNDY 457
+CA C I E++++A +H CF C CN+ L G F + D +YC Y
Sbjct: 4 RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMR-DGLVYCRLHY 59
>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the
Paxillin-like protein family. The fourth LIM domain of
the Paxillin like protein family: This family consists
of paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. 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 = 52
Score = 36.2 bits (84), Expect = 0.002
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
CA CG I + AMG+ +HP F C C + L F + D+K YC
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFK-EQDDKPYC 48
Score = 33.5 bits (77), Expect = 0.020
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 319 CHTCGEKVTGAGQAC-QAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG+ +TG C AMG +H F+C C + L F + YC +
Sbjct: 1 CAGCGKPITGR---CITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of 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. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All 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 = 52
Score = 35.9 bits (83), Expect = 0.002
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 487 MDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
+D+ +H C C DC LT+ +C+ +G+L CR
Sbjct: 17 LDRAWHAKCVQCCDCKCPLTE----KCFSREGKLYCR 49
Score = 33.9 bits (78), Expect = 0.013
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C I++ +L + +++H C +CC C L F+ + K+YC ND+
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFS--REGKLYCRNDF 52
Score = 27.4 bits (61), Expect = 2.5
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H C CC C L K F + G++YC D+
Sbjct: 21 WHAKCVQCCDCKCPLTEKCF-SREGKLYCRNDF 52
>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4. The second LIM
domain of Lhx4. Lhx4 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. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. 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 = 56
Score = 36.2 bits (83), Expect = 0.003
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL-RGKAFYNVH-GRVYCEEDY 372
C C + + +A +YH +CF C C R L G FY + GR+ C+EDY
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56
Score = 30.0 bits (67), Expect = 0.33
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDF--HVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
C AC +GI P + VV +DF H+ C+ C C QL D+ GRL+C
Sbjct: 1 CTACQQGIPPTQ-------VVRKAQDFVYHLHCFACIICSRQLA-TGDEFYLMEDGRLVC 52
Query: 523 R 523
+
Sbjct: 53 K 53
Score = 28.8 bits (64), Expect = 0.87
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYCVNDY 457
C C I +++ +A YH CF C +C+ L G F + D ++ C DY
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. 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 = 64
Score = 36.3 bits (84), Expect = 0.003
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 319 CHTCGEKVTGAGQACQAM---GNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEED 371
C C +TG G+ + G+ +H CF C C L K F +G++YC +
Sbjct: 5 CSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
Score = 27.8 bits (62), Expect = 2.4
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 462 APKCAACGKGITPVEGTEETVRVVSM-DKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRL 520
A KC+ C IT G + VV+ +H C+ C+ C L L +KR G++
Sbjct: 2 AKKCSGCQNPIT---GFGKGTNVVNYEGSSWHDYCFNCKKCSLNLA---NKRFVFHNGQI 55
Query: 521 MCRAC 525
C C
Sbjct: 56 YCSDC 60
>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting
with CasL). The LIM domain of Mical (molecule
interacting with CasL): MICAL is a large, multidomain,
cytosolic protein with a single LIM domain, a calponin
homology (CH) domain and a flavoprotein monooxygenase
domain. In Drosophila, MICAL is expressed in axons,
interacts with the neuronal A (PlexA) receptor and is
required for Semapho-rin 1a (Sema-1a)-PlexA-mediated
repulsive axon guidance. The LIM domain and calporin
homology domain are known for interactions with the
cytoskeleton, cytoskeletal adaptor proteins, and other
signaling proteins. The flavoprotein monooxygenase (MO)
is required for semaphorin-plexin repulsive axon
guidance during axonal pathfinding in the Drosophila
neuromuscular system. In addition, MICAL was
characterized to interact with Rab13 and Rab8 to
coordinate the assembly of tight junctions and adherens
junctions in epithelial cells. Thus, MICAL was also
named junctional Rab13-binding protein (JRAB). 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 = 55
Score = 35.7 bits (83), Expect = 0.003
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR--GKAFYNVHGRVYCEEDY 372
C+ C ++V + A G +H +CF C CG LR AF G+ YC+ +
Sbjct: 1 CYFCKKRVYVMERLS-AEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55
Score = 30.0 bits (68), Expect = 0.33
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 412 IMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDN-KIYC 453
+ME L A G +H CF+C C L + D D+ K YC
Sbjct: 10 VMER-LSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYC 51
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The second LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain 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 = 35.4 bits (82), Expect = 0.003
Identities = 15/53 (28%), Positives = 22/53 (41%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG + + A+G+ YH F C +C + + KIYC Y
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
Score = 33.9 bits (78), Expect = 0.015
Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVH-GRVYCEEDY 372
C CG + G A+G YH F C C Y H G++YC Y
Sbjct: 1 CFKCGGALRG--SYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of 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. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All 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 = 56
Score = 35.4 bits (82), Expect = 0.003
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYCVNDY 457
CA C I +++ +A K +H CF C +C + L G + +NK C DY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
Score = 35.0 bits (81), Expect = 0.006
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
CA C +GI+P + VR + DK FH++C+ C C QL+
Sbjct: 1 CAGCDQGISP----NDLVRR-ARDKVFHLNCFTCMVCRKQLS 37
Score = 34.6 bits (80), Expect = 0.008
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR--GKAFYNVHGRVYCEEDY 372
C C + ++ +A ++H NCF C C + L + + + C+EDY
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The first
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. 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 = 59
Score = 35.7 bits (83), Expect = 0.004
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 11/38 (28%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDV-----DNKIYC 453
G +HP CF C C E L VD+ D K+YC
Sbjct: 23 GACWHPACFVCSTCKELL------VDLIYFYQDGKVYC 54
Score = 34.9 bits (81), Expect = 0.006
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 319 CHTCGEKVTGAGQACQA----MGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CGE+++G A A G +H CF+C +C L ++ G+VYC
Sbjct: 1 CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCKELLVDLIYFYQDGKVYC 54
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong 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. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription. Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. 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 = 52
Score = 35.1 bits (81), Expect = 0.004
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H C C CG L K F +G VYC++D+
Sbjct: 21 WHAKCLKCNDCGAQLTDKCFAR-NGHVYCKDDF 52
Score = 33.2 bits (76), Expect = 0.021
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 487 MDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
+D+ +H C C DCG QLTD +C+ G + C+
Sbjct: 17 LDRTWHAKCLKCNDCGAQLTD----KCFARNGHVYCK 49
Score = 30.9 bits (70), Expect = 0.15
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C I++ IL+ + +++H C +C C L F + +YC +D+
Sbjct: 1 CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFA--RNGHVYCKDDF 52
>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin
like protein family. The second LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. 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 = 52
Score = 35.1 bits (81), Expect = 0.004
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 335 AMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
A+ +H F C CG+ + F+ G+ YC EDY
Sbjct: 15 ALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 34.7 bits (80), Expect = 0.006
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C I++ + A+ K++HP F C C + F + D K YC DY
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFH-EKDGKPYCREDY 52
>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like
family. The second LIM domain of Testin-like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. 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 it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. 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
complexes.
Length = 56
Score = 35.3 bits (82), Expect = 0.004
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 404 KCAICGHLI-MEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYH 458
+CA C LI QA GK++H F C C+E L G + + + K YC++ Y
Sbjct: 2 RCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLR-EGKPYCLDCYE 56
Score = 31.8 bits (73), Expect = 0.064
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C E + +G+ QA G +H F C C L G+ + G+ YC
Sbjct: 3 CAACDE-LIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51
Score = 27.6 bits (62), Expect = 2.2
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 463 PKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
P+CAAC + I E T+ K++H+ + C C L + R +G+ C
Sbjct: 1 PRCAACDELIFSGEYTQA------EGKNWHLKHFCCFQCDEPLGGQ---RYVLREGKPYC 51
Query: 523 RACH 526
C+
Sbjct: 52 LDCY 55
>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9. The second LIM
domain of Lhx9: Lhx9 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. Lhx9 is highly
homologous to Lhx2. It is expressed in several regions
of the developing mouse brain, the spinal cord, the
pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles exhibit
numerous urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
have reduced levels of the Sf1 nuclear receptor that is
required for gonadogenesis, and recent studies have
shown that Lhx9 is able to activate the Sf1/FtzF1 gene.
Lhx9 null mice are phenotypically female, even those
that are genotypically male. 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 = 59
Score = 35.1 bits (80), Expect = 0.005
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 401 TAEKCAIC--GHLIMEMILQAMGKSYHPGCFRCCLCNECLD-GVPFTVDVDNKIYC 453
+ ++CA C G EM+++A YH CF C CN+ L G F + DN +YC
Sbjct: 1 SVQRCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMK-DNLVYC 55
Score = 31.2 bits (70), Expect = 0.14
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVHGRVYC 368
C C ++ + +A ++YH +CF C +C + L G F VYC
Sbjct: 5 CARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYC 55
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All 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 = 53
Score = 34.9 bits (81), Expect = 0.005
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDV-DNKIYCVNDY 457
GKS+H CF C +CN+ LD T+ D +IYC + Y
Sbjct: 18 GKSWHKSCFTCAVCNKRLD--STTLAEHDGEIYCKSCY 53
Score = 26.0 bits (58), Expect = 9.0
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 13/42 (30%)
Query: 319 CHTCG------EKVTGAGQACQAMGNLYHTNCFICCSCGRAL 354
C CG E+V AG++ +H +CF C C + L
Sbjct: 1 CPRCGKSVYAAEEVIAAGKS-------WHKSCFTCAVCNKRL 35
Score = 26.0 bits (58), Expect = 9.2
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 17/66 (25%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL----TDEPDKRCYPLQGRL 520
C CGK + E V++ K +H C+ C C +L E D Y
Sbjct: 1 CPRCGKSVYAAE------EVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIY------ 48
Query: 521 MCRACH 526
C++C+
Sbjct: 49 -CKSCY 53
>gnl|CDD|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM
domains protein 3 (FHL3). The second LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. 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 = 58
Score = 35.2 bits (81), Expect = 0.006
Identities = 14/50 (28%), Positives = 23/50 (46%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG+ V + + G +H +CFIC C + + ++F YC
Sbjct: 4 CVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53
Score = 30.6 bits (69), Expect = 0.20
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 402 AEKCAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
+ KC CG +M L+ G+++H CF C C + + F D D YCV Y
Sbjct: 1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEH-YCVPCY 57
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. 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 = 59
Score = 35.1 bits (81), Expect = 0.006
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 422 KSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
+ +H GCF+C C L PF D + C Y
Sbjct: 24 RHWHEGCFKCFKCQRSLVDKPFAAK-DEDLLCTECY 58
Score = 29.7 bits (67), Expect = 0.41
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H CF C C R+L K F + C E Y
Sbjct: 26 WHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
>gnl|CDD|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9. The first LIM
domain of Lhx9: Lhx9 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. Lhx9 is highly
homologous to Lhx2. It is expressed in several regions
of the developing mouse brain, the spinal cord, the
pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles exhibit
numerous urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
have reduced levels of the Sf1 nuclear receptor that is
required for gonadogenesis, and recent studies have
shown that Lhx9 is able to activate the Sf1/FtzF1 gene.
Lhx9 null mice are phenotypically female, even those
that are genotypically male. 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 = 54
Score = 34.6 bits (79), Expect = 0.006
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA CG I + L A+ K +H C +CC C L+ D IYC DY
Sbjct: 1 CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
Score = 31.9 bits (72), Expect = 0.064
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
CA CG I+ + ++++DK +H+ C C +C +L E + C+ G + C+
Sbjct: 1 CAGCGGKIS------DRYYLLAVDKQWHLRCLKCCEC--KLALESELTCFAKDGSIYCK 51
Score = 31.6 bits (71), Expect = 0.082
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGK-AFYNVHGRVYCEEDY 372
C CG K++ A+ +H C CC C AL + + G +YC+EDY
Sbjct: 1 CAGCGGKISDR-YYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 54
>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH). The
second LIM domain of Arrowhead (AWH): Arrowhead 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. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. 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 = 55
Score = 34.7 bits (80), Expect = 0.006
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVHGRVYCEEDY 372
C C ++ + +A ++YH CF C +C R L G+ F + RV C+ Y
Sbjct: 1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55
Score = 28.9 bits (65), Expect = 0.78
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL-TDEPDKRCYPLQ-GRLMC 522
CA C + I+ + VR + D +H+ C+ C+ C QL T E + L R++C
Sbjct: 1 CAKCSRNISA----SDWVRR-ARDHVYHLACFACDACKRQLSTGEE----FALIEDRVLC 51
Query: 523 RA 524
+A
Sbjct: 52 KA 53
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated in
roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. 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 = 59
Score = 34.9 bits (80), Expect = 0.007
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 319 CHTCGEKVTGAGQACQA----MGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG ++ G A A +G +H CF C SC L ++ G++YC
Sbjct: 1 CQQCGRQICGGDIAVFASRAGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYC 54
Score = 29.5 bits (66), Expect = 0.65
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 420 MGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYC 453
+G +HP CF+C C E L D + F D KIYC
Sbjct: 22 LGACWHPQCFQCASCQELLVDLIYFY--QDGKIYC 54
>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2
(CRP2). The first LIM domain of Cysteine Rich Protein 2
(CRP2): The CRP family members include CRP1, CRP2,
CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation, and
involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network. CRP2 specifically
binds to protein inhibitor of activated STAT-1 (PIAS1)
and a novel human protein designed CRP2BP (for CRP2
binding partner). PIAS1 specifically inhibits the STAT-1
pathway and CRP2BP is homologous to members of the
histone acetyltransferase family raising the possibility
that CRP2 is a modulator of cytokine-controlled pathways
or is functionally active in the transcriptional
regulatory network. 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 = 34.6 bits (79), Expect = 0.008
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 404 KCAICGHLIMEMI-LQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
KC CG + +Q G+S+H CF C +C + LD + D +IYC + Y
Sbjct: 1 KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIH-DQEIYCKSCY 54
Score = 28.0 bits (62), Expect = 1.8
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG V A + Q G +H CF+C C + L +YC+ Y
Sbjct: 2 CGACGRTVYHA-EEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54
>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2. The first LIM
domain of Lhx2: Lhx2 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 animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. The Lhx2 protein has been shown to bind to
the mouse M71 olfactory receptor promoter. Similar to
other LIM domains, this domain family is 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.
Length = 64
Score = 34.6 bits (79), Expect = 0.009
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA CG I + L A+ K +H C +CC C L+ D IYC DY
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
Score = 34.6 bits (79), Expect = 0.011
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 313 GEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGK-AFYNVHGRVYCEED 371
+ +C CG K++ A+ +H C CC C L + ++ G +YC+ED
Sbjct: 5 SDRAALCAGCGGKISDR-YYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKED 63
Query: 372 Y 372
Y
Sbjct: 64 Y 64
Score = 31.9 bits (72), Expect = 0.091
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
CA CG I+ + ++++DK +H+ C C +C L L E + C+ G + C+
Sbjct: 11 CAGCGGKIS------DRYYLLAVDKQWHMRCLKCCECKLNL--ESELTCFSKDGSIYCK 61
>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin. The first
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. 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 it is involved in cell motility and
adhesion events. Knockout mice experiments reveal that
tumor repressor function of Testin. 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 = 58
Score = 34.4 bits (79), Expect = 0.009
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 319 CHTCGEKVTGAGQACQA----MGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C+ C + + A A L+H CF+C +CG L ++ +G++YC Y
Sbjct: 1 CYCCKQPMKEGDPAVYAERAGYDKLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58
Score = 29.3 bits (66), Expect = 0.54
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 422 KSYHPGCFRCCLCNECL 438
K +HP CF C C E L
Sbjct: 24 KLWHPACFVCSTCGELL 40
>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1. The
first LIM domain of Prickle 1. Prickle contains three
C-terminal LIM domains and a N-terminal PET domain
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
mainly expressed in fetal brain, adult cartilage,
pancreatic islet, and some types of timorous cells. In
addition, Prickle 1 regulates cell movements during
gastrulation and neuronal migration through interaction
with the noncanonical Wnt11/Wnt5 pathway in zebrafish.
Mutations in prickle 1 have been linked to progressive
myoclonus epilepsy. 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 = 59
Score = 34.5 bits (79), Expect = 0.010
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 319 CHTCGEKVTGAGQACQAM----GNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG K+ G A A G +H +CF+C +C L ++ G+++C
Sbjct: 1 CEQCGIKINGGEVAVFASRAGPGVCWHPSCFVCFTCNELLVDLIYFYQDGKIHC 54
Score = 29.9 bits (67), Expect = 0.38
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
G +HP CF C CNE L + + D KI+C
Sbjct: 23 GVCWHPSCFVCFTCNELLVDLIYFYQ-DGKIHC 54
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. 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 = 33.8 bits (77), Expect = 0.012
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
GK +H CFRC +C + L+ T D D ++YC
Sbjct: 18 GKPWHKTCFRCAICGKSLESTTVT-DKDGELYC 49
Score = 32.7 bits (74), Expect = 0.036
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 324 EKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
EKV G G+ +H CF C CG++L + G +YC+ Y
Sbjct: 12 EKVMGGGKP-------WHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
Score = 27.3 bits (60), Expect = 3.4
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 13/64 (20%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCG--LQLTDEPDKRCYPLQGRLMC 522
C CGK + E +V+ K +H C+ C CG L+ T DK G L C
Sbjct: 1 CPRCGKSVYAAE------KVMGGGKPWHKTCFRCAICGKSLESTTVTDK-----DGELYC 49
Query: 523 RACH 526
+ C+
Sbjct: 50 KVCY 53
>gnl|CDD|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase
domains protein (Ltd-1). The LIM domain of LIM and
transglutaminase domains protein (Ltd-1): This family
includes mouse Ky protein and Caenorhabditis elegans
Ltd-1 protein. The members of this family consists a
N-terminal Lim domain and a C-terminal transglutaminase
domain. The mouse Ky protein has putative function in
muscle development. The mouse with ky mutant exhibits
combined posterior and lateral curvature of the spine.
The Ltd-1 gene in C. elegans is expressed in developing
hypodermal cells from the twofold stage embryo through
adulthood. These data define the ltd-1 gene as a novel
marker for C. elegans epithelial cell 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 = 55
Score = 33.9 bits (78), Expect = 0.013
Identities = 20/52 (38%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVH--GRVYC 368
C CG+ A ++ G YH CF C CG L K F V G VYC
Sbjct: 1 CPRCGKTAYPA-ESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYC 51
Score = 33.2 bits (76), Expect = 0.027
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFT-VDVDNKIYCVND 456
G YH GCF+C C L FT V D ++YC
Sbjct: 18 GTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
Score = 32.4 bits (74), Expect = 0.051
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
C CGK P E V +H C+ C +CG +L+
Sbjct: 1 CPRCGKTAYPAE------SVDKDGTFYHKGCFKCRECGTRLS 36
>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4. The first LIM
domain of Lhx4. Lhx4 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. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. 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 = 52
Score = 33.8 bits (77), Expect = 0.013
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H++C C C L + F G VYC+ED+
Sbjct: 21 WHSSCLKCADCQMQLAERCFSRA-GNVYCKEDF 52
Score = 29.9 bits (67), Expect = 0.30
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 405 CAICG-HLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C H++ + IL+ + + +H C +C C L F+ +YC D+
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFS--RAGNVYCKEDF 52
Score = 28.8 bits (64), Expect = 0.83
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 487 MDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
+D+ +H C C DC +QL + RC+ G + C+
Sbjct: 17 LDRHWHSSCLKCADCQMQLAE----RCFSRAGNVYCK 49
>gnl|CDD|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog (ENH)
family. The first LIM domain of the Enigma Homolog
(ENH) family: ENH was initially identified in rat brain.
Same as enigma, it contains three LIM domains at the
C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also 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. ENH
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 = 52
Score = 33.8 bits (77), Expect = 0.014
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
CA C +I L A+GKS+HP F C C + + F V+ +YC
Sbjct: 1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGF-VEEKGALYC 48
>gnl|CDD|188832 cd09448, LIM_CLP36, This family represents the LIM domain of CLP36.
This family represents the LIM domain of CLP36. CLP36
has also been named as CLIM1, Elfin, or PDLIM1. CLP36
contains a C-terminal LIM domain and an N-terminal PDZ
domain. CLP36 is highly expressed in heart and is
present in many other tissues including lung, liver,
spleen, and blood. CLP36 has been implicated in many
processes including hypoxia and regulation of actin
stress fibers. CLP36 co-localizes with alpha-actinin-2
at the Z-lines in myocardium. In addition, CLP36 binds
to alpha-actinin-1 and alpha-actinin-4, and associates
with F-actin filaments and stress fibers. CLP36 might be
involved in not only the function of sarcomeres in
muscle cells, but also in actin stress fiber-mediated
cellular processes, such as cell shape, migration,
polarit, and cytokinesis in non-muscle cells. 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 = 52
Score = 33.7 bits (77), Expect = 0.014
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
C CG + G + H C++C CG L+ K + V ++YCE+
Sbjct: 1 CDKCGSGIVGV--FVKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYCEK 50
Score = 30.7 bits (69), Expect = 0.16
Identities = 17/41 (41%), Positives = 19/41 (46%), Gaps = 7/41 (17%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
C CG GI V V DK H +CY+C DCG L
Sbjct: 1 CDKCGSGIV-------GVFVKIRDKPRHPECYVCTDCGTNL 34
Score = 27.2 bits (60), Expect = 3.1
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECL--DGVPFTVDVDNKIYC 453
C CG I+ + ++ K HP C+ C C L G F V+++IYC
Sbjct: 1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKGHFF---VEDQIYC 48
>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin. The
third LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. 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 = 53
Score = 33.7 bits (77), Expect = 0.015
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 9/58 (15%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFT----VDVDNKIYCVNDYH 458
C C I+E + A+ +HP CF +C EC PF + D + YC YH
Sbjct: 1 CGGCARAILENYISALNTLWHPECF---VCRECF--TPFVNGSFFEHDGQPYCEAHYH 53
Score = 32.9 bits (75), Expect = 0.029
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 335 AMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
A+ L+H CF+C C +F+ G+ YCE Y
Sbjct: 15 ALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
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. Its differential expression indicates that it is a
transcription regulator. 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 = 33.6 bits (77), Expect = 0.018
Identities = 16/50 (32%), Positives = 22/50 (44%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CGE + + G +H CF CC C + + K+F VYC
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50
Score = 30.5 bits (69), Expect = 0.22
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
G+ +H CF CC C + + F + D+ +YCV Y
Sbjct: 19 GQQWHEKCFCCCECKQPIGTKSF-IPKDDDVYCVPCY 54
>gnl|CDD|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL)-like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. 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 = 33.2 bits (76), Expect = 0.021
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVH-GRVYC 368
C +CG+ V + A ++YH NCF C C + L+ Y H G +YC
Sbjct: 1 CRSCGKPVYKMEEI-IAEKHIYHKNCFRCKDCNKQLKVDN-YQSHEGNLYC 49
Score = 29.4 bits (66), Expect = 0.53
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
C +CGK + +E +++ +H +C+ C+DC QL
Sbjct: 1 CRSCGKPVYKME------EIIAEKHIYHKNCFRCKDCNKQLK 36
>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 = 33.1 bits (76), Expect = 0.023
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C I + +L+ +S+H C +C +C + L + D K+YC DY
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYFRD--RKLYCKQDY 52
>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein
(TLP). The LIM domain of thymus LIM protein (TLP) like
proteins: This family includes the LIM domains of TLP
and CRIP (Cysteine-Rich Intestinal Protein). TLP is the
distant member of the CRP family of proteins. TLP has
two isomers (TLP-A and TLP-B) and sharing approximately
30% with each of the three other CRPs. Like CRP1, CRP2
and CRP3/MLP, TLP has two LIM domains, connected by a
flexible linker region. Unlike the CRPs, TLP lacks the
nuclear targeting signal (K/R-K/R-Y-G-P-K) and is
localized solely in the cytoplasm. TLP is specifically
expressed in the thymus in a subset of cortical
epithelial cells. TLP has a role in development of
normal thymus and in controlling the development and
differentiation of thymic epithelial cells. CRIP is a
short LIM protein with only one LIM domain. CRIP gene is
developmentally regulated and can be induced by
glucocorticoid hormones during the first three postnatal
weeks. The domain shows close sequence homology to LIM
domain of thymus LIM protein. However, unlike the TLP
proteins which have two LIM domains, the members of this
family have only one LIM domain. 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 = 53
Score = 33.1 bits (76), Expect = 0.023
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTD 507
C CGK PV E + S+ +D+H C CE C LT
Sbjct: 1 CPKCGK---PVYFAE---KKTSLGRDWHKPCLRCEKCKKTLTP 37
Score = 33.1 bits (76), Expect = 0.026
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 405 CAICGHLIMEM-ILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG + ++G+ +H C RC C + L + + + K YC Y
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHS-EHEGKPYCNKCY 53
Score = 28.5 bits (64), Expect = 0.98
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG+ V A + ++G +H C C C + L G+ YC
Sbjct: 1 CPKCGKPVYFAEKK-TSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYC 49
>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2. The second LIM
domain of Lhx2: Lhx2 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 animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. The Lhx2 protein has been shown to bind to
the mouse M71 olfactory receptor promoter. Similar to
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 = 59
Score = 33.1 bits (75), Expect = 0.025
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 401 TAEKCAIC--GHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
+ ++CA C G EM+++A YH CF C CN+ L DN +YC
Sbjct: 1 SVQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYC 55
Score = 31.6 bits (71), Expect = 0.088
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL-RGKAFYNVHGRVYC 368
C C ++ + +A +YH NCF C +C + L G F VYC
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYC 55
Score = 27.0 bits (59), Expect = 3.9
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 464 KCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
+CA C GI+ +E +R + D +H++C+ C C LT
Sbjct: 4 RCARCHLGIS---ASEMVMR--ARDLVYHLNCFTCTTCNKMLT 41
>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. 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 = 55
Score = 33.2 bits (76), Expect = 0.027
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 405 CAICG---HLIMEMILQAMGKSYHPGCFRCCLCNECL 438
CA CG HL+ + GK YH CFRC C+ L
Sbjct: 1 CAACGQHVHLVQRHL--VDGKLYHRNCFRCKECSSTL 35
Score = 32.0 bits (73), Expect = 0.074
Identities = 15/36 (41%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL 354
C CG+ V Q G LYH NCF C C L
Sbjct: 1 CAACGQHVHLV-QRHLVDGKLYHRNCFRCKECSSTL 35
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. The consensus sequence of LIM domain
has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 33.2 bits (76), Expect = 0.027
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
C +CG V A + G +YH CF C CG L +FY YC E
Sbjct: 5 CASCGLPVFLA-ERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYCCE 55
Score = 30.1 bits (68), Expect = 0.35
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 464 KCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
CA+CG + E R++ K +H C+ C CG+QLT
Sbjct: 4 PCASCGLPVFLAE------RLLIEGKVYHRTCFKCARCGVQLT 40
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first LIM
domain of Lmx1a: Lmx1a 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. Mouse Lmx1a is
expressed in multiple tissues, including the roof plate
of the neural tube, the developing brain, the otic
vesicles, the notochord, and the pancreas. Human Lmx1a
can be found in pancreas, skeletal muscle, adipose
tissue, developing brain, mammary glands, and pituitary.
The functions of Lmx1a in the developing nervous system
were revealed by studies of mutant mouse. In mouse,
mutations in Lmx1a result in failure of the roof plate
to develop. Lmx1a may act upstream of other roof plate
markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further
characterization of these mice reveals numerous defects
including disorganized cerebellum, hippocampus, and
cortex; altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within pancreatic
cells, the Lmx1a protein interacts synergistically with
the bHLH transcription factor E47 to activate the
insulin gene enhancer/promoter. 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 = 52
Score = 32.8 bits (75), Expect = 0.029
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 338 NLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+L+H C C SC L FY ++YC+EDY
Sbjct: 19 SLWHERCLQCASCKEPLETTCFYRDK-KLYCKEDY 52
Score = 31.7 bits (72), Expect = 0.069
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIMEMILQAMGKS-YHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C +I + L + S +H C +C C E L+ F D K+YC DY
Sbjct: 1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCFY--RDKKLYCKEDY 52
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
fetal brain, adult cartilage, pancreatic islet, and some
types of timorous cells. Mutations in prickle 1 have
been linked to progressive myoclonus epilepsy. 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 = 59
Score = 33.0 bits (75), Expect = 0.029
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 319 CHTCGEKVTGAGQACQAM----GNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG ++ G A A G +H CF+C C L ++ G++YC
Sbjct: 1 CEQCGGQINGGDIAVFASRAGHGVCWHPQCFVCSVCNELLVDLIYFYQDGKIYC 54
Score = 31.8 bits (72), Expect = 0.095
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
G +HP CF C +CNE L + + D KIYC
Sbjct: 23 GVCWHPQCFVCSVCNELLVDLIYFYQ-DGKIYC 54
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. 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 = 59
Score = 33.0 bits (75), Expect = 0.029
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 398 FQQTAEKCA-ICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVND 456
F T ++C + GH E+ + + YH CFRC C+ L PFT D ++ C +
Sbjct: 1 FANTCDECKELIGHDSRELYYE--DRHYHEHCFRCFRCDRSLADEPFTCQ-DEELLCNDC 57
Query: 457 Y 457
Y
Sbjct: 58 Y 58
Score = 28.0 bits (62), Expect = 1.7
Identities = 14/54 (25%), Positives = 21/54 (38%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C E + + YH +CF C C R+L + F + C + Y
Sbjct: 5 CDECKELIGHDSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58
>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function. The
first Lim domain of a LIM domain containing protein: The
functions of the proteins are unknown. The members of
this family contain two copies of LIM domain. The LIM
domain 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 = 58
Score = 33.0 bits (76), Expect = 0.034
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 424 YHPGCFRCCLCNECLDGVPFTVDV---DNKIYCVNDYH 458
+H CF C C F+V D+K YC YH
Sbjct: 24 WHRECFVCTTCG---CPFQFSVPCYVLDDKPYCQQHYH 58
Score = 30.3 bits (69), Expect = 0.29
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 319 CHTCGEKVTGAGQACQAMGNL---YHTNCFICCSCGRALRGKA-FYNVHGRVYCEEDY 372
C CG ++ G + G L +H CF+C +CG + Y + + YC++ Y
Sbjct: 1 CRKCGLEIEGKSISS-KDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>gnl|CDD|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein
Lost in Neoplasm (Eplin). The Lim domain of Epithelial
Protein Lost in Neoplasm (Eplin): Epithelial Protein
Lost in Neoplasm is a cytoskeleton-associated tumor
suppressor whose expression inversely correlates with
cell growth, motility, invasion and cancer mortality.
Eplin interacts and stabilizes F-actin filaments and
stress fibers, which correlates with its ability to
suppress anchorage independent growth. In epithelial
cells, Eplin is required for formation of the F-actin
adhesion belt by binding to the E-cadherin-catenin
complex through alpha-catenin. Eplin is expressed in two
isoforms, a longer Eplin-beta and a shorter Eplin-alpha.
Eplin-alpha mRNA is detected in various tissues and cell
lines, but is absent or down regulated in cancer cells.
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 = 32.5 bits (74), Expect = 0.035
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 339 LYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+YH +CF C C L + ++HG +YC+ +
Sbjct: 20 IYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53
Score = 27.9 bits (62), Expect = 1.6
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 417 LQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
L A + YH CFRC CN L + + IYC
Sbjct: 14 LVANQQIYHNSCFRCSYCNTKLSLGTYA-SLHGNIYC 49
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerization.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All 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 = 53
Score = 32.5 bits (74), Expect = 0.038
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG ++ + + +H +CF C C L +Y G++YC + Y
Sbjct: 1 CTGCGGRIQ-DSFHYRVVQEAWHNSCFQCSVCQDLLT-NWYYEKDGKLYCHKHY 52
Score = 31.8 bits (72), Expect = 0.085
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIMEMILQAM-GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG I + + +++H CF+C +C + L + + D K+YC Y
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYY--EKDGKLYCHKHY 52
Score = 26.8 bits (59), Expect = 5.3
Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 10/59 (16%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
C CG I RVV + +H C+ C C LT+ Y G+L C
Sbjct: 1 CTGCGGRIQD----SFHYRVV--QEAWHNSCFQCSVCQDLLTN----WYYEKDGKLYCH 49
>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH. The
third LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
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 = 51
Score = 32.3 bits (74), Expect = 0.038
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCV 454
C C +I E L+ G YHP F C C + L ++ ++YC+
Sbjct: 1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTAD--ARELKGELYCL 48
Score = 26.2 bits (58), Expect = 7.2
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C + Q + G+ YH F C +CG+ L A + G +YC
Sbjct: 1 CQKCHAIIEE--QHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYC 47
>gnl|CDD|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only
protein 2). The first LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex that
is capable of transcriptional activation. LMOs have also
been shown to be involved in oncogenesis. LMO1 and LMO2
are activated in T-cell acute lymphoblastic leukemia by
distinct chromosomal translocations. LMO2 was also shown
to be involved in erythropoiesis and is required for the
hematopoiesis in the adult animals. All 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 = 56
Score = 32.5 bits (74), Expect = 0.039
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFIC--CSCGRALRGKAFYNVHGRVYCEEDYL 373
C C + + G +A+ +H +C C C C G+ Y GR C DYL
Sbjct: 1 CGGCQQNI-GDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 56
Score = 31.4 bits (71), Expect = 0.13
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 486 SMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRACHL 527
++D+ +H DC C+ CG +L E +R Y GR +CR +L
Sbjct: 16 AIDQYWHEDCLSCDLCGCRL-GEVGRRLYYKLGRKLCRRDYL 56
>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin. The
fourth LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners PYK2,
FAK, PEP and p95PKL. When expressed in human leukocytic
cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. 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 = 52
Score = 32.4 bits (74), Expect = 0.043
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C +CG +TG + A+G +H F+C C R L +F G+ YC
Sbjct: 1 CGSCGLPITG--RCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48
Score = 28.2 bits (63), Expect = 1.4
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLC 434
C CG I + A+G+ +HP F C C
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFC 30
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein
SF3. The first Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. 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 = 63
Score = 32.4 bits (74), Expect = 0.052
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 401 TAEKCAICGHLI--MEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYH 458
T +KC C + ++ L A G YH CFRC C L ++ ++ +YC +
Sbjct: 1 TTQKCKACDKTVYLVDQ-LSADGVVYHKSCFRCSHCKGTLKLSNYS-SMEGVLYCKPHFE 58
Query: 459 RMF 461
++F
Sbjct: 59 QLF 61
Score = 27.8 bits (62), Expect = 2.1
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 335 AMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
A G +YH +CF C C L+ + ++ G +YC
Sbjct: 20 ADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYC 53
>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein
(LASP)-like proteins. The LIM domain of LIM and SH3
Protein (LASP) like proteins: This family contains two
types of LIM containing proteins; LASP and N-RAP. LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains, but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. N-RAP is a
muscle-specific protein concentrated at myotendinous
junctions in skeletal muscle and intercalated disks in
cardiac muscle. LIM domain is found at the N-terminus of
N-RAP and the C-terminal of N-RAP contains a region with
multiple of nebulin repeats. N-RAP functions as a
scaffolding protein that organizes alpha-actinin and
actin into symmetrical I-Z-I structures in developing
myofibrils. Nebulin repeat is known as actin binding
domain. The N-RAP is hypothesized to form antiparallel
dimerization via its LIM domain. 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 = 32.2 bits (73), Expect = 0.055
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
CA CGK + P E +V +DK +H C+ CE C + L
Sbjct: 1 CARCGKIVYPTE------KVNCLDKTWHKACFHCEVCKMTLN 36
>gnl|CDD|225689 COG3147, DedD, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 226
Score = 35.2 bits (81), Expect = 0.055
Identities = 29/107 (27%), Positives = 37/107 (34%), Gaps = 9/107 (8%)
Query: 166 PQVPQGLKYIRDYPPYEAPPVYENIQELNKPPKPGPQVPVFGGEHRQMAIA-LTSPPVYS 224
P PQG + P V +Q + P +P V + A A + PV
Sbjct: 44 PPKPQGDRDEPR----VLPAV---VQVVALPTQPPEGVAQEIQDAGDAAAASVDPQPVAQ 96
Query: 225 RANTVTSKAVPVKTATSLSVTPNYQ-VSSPVDTTPSPSPSPKTPVTP 270
T VPV T V P Q + V P+P P PK P
Sbjct: 97 PPVESTPAGVPVAAQTPKPVKPPKQPPAGAVPAKPTPKPEPKPVAEP 143
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. 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 s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 32.3 bits (73), Expect = 0.059
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C + + + + GN +H CFIC C + + K+F + +C
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50
>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1
(CRP1). The first LIM domain of Cysteine Rich Protein 1
(CRP1): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and
CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1 can associate with the actin cytoskeleton
and are capable of interacting with alpha-actinin and
zyxin. CRP1 was shown to regulate actin filament
bundling by interaction with alpha-actinin and direct
binding to actin filaments. 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 = 56
Score = 32.3 bits (73), Expect = 0.060
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 403 EKCAICGHLI-MEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
+KC +C + +Q G+S+H CF C +C + LD V +IYC + Y
Sbjct: 1 KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVH-GEEIYCKSCY 55
Score = 27.3 bits (60), Expect = 3.5
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHG-RVYCEEDY 372
C C + V A + Q G +H +CF+C C + L VHG +YC+ Y
Sbjct: 3 CGVCQKTVYFA-EEVQCEGRSFHKSCFLCMVCKKNLDSTTV-AVHGEEIYCKSCY 55
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. 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 = 56
Score = 31.9 bits (73), Expect = 0.062
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 465 CAACGKGITPVEGTEETVRVVSM-DKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
CAAC K IT + G + +S ++ +H DC+ C C + L + + ++C
Sbjct: 1 CAACTKPITGLGGA----KFISFEERQWHSDCFNCGKCSVSLVGQG---FLTQRDEILCP 53
Query: 524 AC 525
C
Sbjct: 54 EC 55
Score = 26.9 bits (60), Expect = 3.7
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 12/59 (20%)
Query: 319 CHTCGEKVTGAG-------QACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
C C + +TG G + Q +H++CF C C +L G+ F + C E
Sbjct: 1 CAACTKPITGLGGAKFISFEERQ-----WHSDCFNCGKCSVSLVGQGFLTQRDEILCPE 54
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains ,but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. 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 = 32.0 bits (73), Expect = 0.066
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
CA CGK + P E ++ +DK +H C+ CE CG+ L
Sbjct: 1 CARCGKTVYPTE------KLNCLDKIWHKGCFKCEVCGMTLN 36
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first LIM domain of Four and a
half LIM domains protein 1 (FHL1): FHL1 is heavily
expressed in skeletal and cardiac muscles. It plays
important roles in muscle growth, differentiation, and
sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. 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 = 32.0 bits (73), Expect = 0.069
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 421 GKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
+ +H CFRC C + L PF DNKI C
Sbjct: 19 NRYWHETCFRCAKCYKPLANEPFVA-KDNKILC 50
>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only
protein 4). The first LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact with
Smad proteins, and associate with the promoter of the
PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential role
for LMO4 as a negative regulator of BRCA1 in sporadic
breast cancer. LMO4 also forms complex to both ERa
(oestrogen receptor alpha), MTA1 (metastasis tumor
antigen 1), and HDACs (histone deacetylases), implying
that LMO4 is also a component of the MTA1 corepressor
complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All 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 = 32.0 bits (73), Expect = 0.070
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
CA CG I + + ++D+ +H C C C QL + CY G ++C+
Sbjct: 1 CAGCGGKIV------DRFLLHALDRYWHNGCLKCSCCQAQLGE-IGSSCYTKGGMILCKN 53
Score = 31.2 bits (71), Expect = 0.12
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGV-PFTVDVDNKIYCVNDY 457
CA CG I++ +L A+ + +H GC +C C L + I C NDY
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
Score = 29.7 bits (67), Expect = 0.46
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR--GKAFYNVHGRVYCEEDY 372
C CG K+ A+ +H C C C L G + Y G + C+ DY
Sbjct: 1 CAGCGGKIVDR-FLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga GTPase-Activating
Proteins. The second LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain 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 = 31.7 bits (72), Expect = 0.075
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGR 352
C CG+K+ + Y ++CF C C R
Sbjct: 1 CKNCGKKIDDTA-ILLSSDEAYCSDCFRCRRCSR 33
Score = 31.7 bits (72), Expect = 0.075
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 15/65 (23%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTD---EPDKRCYPLQGRLM 521
C CGK I ++T ++S D+ + DC+ C C +TD KR L
Sbjct: 1 CKNCGKKI------DDTAILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRG------LF 48
Query: 522 CRACH 526
C +CH
Sbjct: 49 CMSCH 53
Score = 30.1 bits (68), Expect = 0.25
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 405 CAICGHLIMEM-ILQAMGKSYHPGCFRCCLCNE 436
C CG I + IL + ++Y CFRC C+
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSR 33
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
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. Its differential expression indicates that it is a
transcription regulator. 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 = 59
Score = 31.8 bits (72), Expect = 0.086
Identities = 22/61 (36%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 398 FQQTAEKCA-ICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVND 456
F E+C+ I G I L K +H CF C C L PF D +IYC N
Sbjct: 1 FANQCEECSKIIG--IDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKAD-RIYCGNC 57
Query: 457 Y 457
Y
Sbjct: 58 Y 58
Score = 29.8 bits (67), Expect = 0.39
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H CF+C C +L K F + R+YC Y
Sbjct: 26 WHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58
Score = 29.1 bits (65), Expect = 0.69
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 461 FAPKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEP 509
FA +C C K I ++ + + + DK +H C++C C + L D+P
Sbjct: 1 FANQCEECSKIIG-IDSKDLSYK----DKHWHEACFLCSKCKISLVDKP 44
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family. Mlp60A
exhibits only one LIM domain linked to a glycin-rich
region. Mlp84B and Mlp60A are muscle specific proteins
and have been implicated in muscle differentiation.
While Mlp84B transcripts are enriched at the terminal
ends of muscle fibers, Mlp60A transcripts are found
throughout the muscle fibers. All 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 = 31.7 bits (72), Expect = 0.092
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 404 KCAICGHLIM---EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
KC CG + E + A G +H CF+C +CN+ LD + + ++YC
Sbjct: 1 KCPKCGKSVYAAEERL--AGGYKWHKMCFKCGMCNKLLDSTNCA-EHEGELYC 50
Score = 30.1 bits (68), Expect = 0.29
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 9/63 (14%)
Query: 464 KCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCR 523
KC CGK V EE + + +H C+ C C L D + + +G L C+
Sbjct: 1 KCPKCGKS---VYAAEERL---AGGYKWHKMCFKCGMCNKLL-DSTNCAEH--EGELYCK 51
Query: 524 ACH 526
CH
Sbjct: 52 QCH 54
Score = 29.0 bits (65), Expect = 0.73
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 318 ICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C CG+ V A + A G +H CF C C + L G +YC
Sbjct: 1 KCPKCGKSVYAA-EERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYC 50
>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain
Kinase ). The second LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates cofilin
on serine 3 and inactivates its actin-severing activity,
and altering the rate of actin depolymerization. LIMKs
can function in both cytoplasm and nucleus and are
expressed in all tissues. Both LIMK1 and LIMK2 can act
in the nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. However, LIMK1 and LIMk2 have different
cellular locations. While LIMK1 localizes mainly at
focal adhesions, LIMK2 is found in cytoplasmic punctae,
suggesting that they may have different cellular
functions. The LIM domains of LIMK have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All 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 = 31.6 bits (72), Expect = 0.100
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYCVNDY 457
C C +I ++ A +HP CF C C + DG + + +K+YC Y
Sbjct: 1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIGDGDSYALVERSKLYCGVCY 54
Score = 26.2 bits (58), Expect = 7.6
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCG 351
CH C + +TG A + +H CF C SC
Sbjct: 1 CHGCSQIITGP--VMVAGDHKFHPECFSCSSCK 31
>gnl|CDD|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain
Kinase 1). The second LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the nucleus
to suppress Rac/Cdc42-dependent cyclin D1 expression.
LIMK1 is expressed in all tissues and is localized to
focal adhesions in the cell. LIMK1 can form homodimers
upon binding of HSP90 and is activated by Rho effector
Rho kinase and MAPKAPK2. LIMK1 is important for normal
central nervous system development, and its deletion has
been implicated in the development of the human genetic
disorder Williams syndrome. Moreover, LIMK1 up-regulates
the promoter activity of urokinase type plasminogen
activator and induces its mRNA and protein expression in
breast cancer cells. The LIM domains have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All 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 = 31.4 bits (71), Expect = 0.10
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNV--HGRVYCEEDY 372
CH C E +T G A YH CF C CG + Y + H ++YC Y
Sbjct: 1 CHGCSETIT-TGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYCGHCY 55
Score = 27.9 bits (62), Expect = 1.8
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 410 HLIMEMILQAMGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYC 453
+ +++ A + YHP CF C C + DG + + +K+YC
Sbjct: 7 TITTGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYC 51
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 35.1 bits (81), Expect = 0.10
Identities = 26/163 (15%), Positives = 43/163 (26%), Gaps = 24/163 (14%)
Query: 117 LTPPYYHQLPHLRSGSHSSVGSQDSKHSSPRGSYVSNDINAFQFDRKAQPQVPQGLKY-- 174
TPP S S + S+ S+ ++ Q +A
Sbjct: 646 KTPP---SRAPPASLSKPASSPDASQTSASFDLDPDFELATHQSVPEAALASGSAPAPPP 702
Query: 175 ---IRDYPPYEAPPVYENIQELNKPPKPGPQVPVFG----GEHRQMAIALTSPP-VYSRA 226
D PP+E P + + G E + + T P V + A
Sbjct: 703 VPDPYDRPPWEEAPEVASANDGPNNAAEGNLSESVEDASNSELQAVEQQATHQPQVQAEA 762
Query: 227 NTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVT 269
+ S +T+ S DT + +T
Sbjct: 763 QSPASTTALTQTS-----------SEVQDTELNLVLLSSGSIT 794
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The third LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain 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 = 56
Score = 31.5 bits (72), Expect = 0.11
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGV---PFTVDVDNKIYCVN 455
CA CG I + ++ K +H CF C C+ + + D +I C N
Sbjct: 1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54
Score = 29.6 bits (67), Expect = 0.41
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 340 YHTNCFICCSCGRALRGK----AFYNVHGRVYCEE 370
+H CF C C R + + AF N R+ C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54
>gnl|CDD|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3
(CRP3/MLP). The first LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. CRP3/MLP interacts with
cytoskeletal protein beta-spectrin. CRP3/MLP also
interacts with the basic helix-loop-helix myogenic
transcriptio n factors MyoD, myogenin, and MRF4 thereby
increasing their affinity for specific DNA regulatory
elements. 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 = 31.3 bits (70), Expect = 0.12
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + V A + Q G +H CFIC +C +AL +YC+ Y
Sbjct: 2 CGACEKTVYHA-EEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54
Score = 31.3 bits (70), Expect = 0.13
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 404 KCAICGHLIMEMI-LQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
KC C + +Q G+S+H CF C C + LD +++IYC Y
Sbjct: 1 KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAH-ESEIYCKTCY 54
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost
in Neoplasm (Eplin) like proteins. The Lim domain of
Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of the
F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising F-actin.
Xirp2 is expressed in muscles and is significantly
induced in the heart in response to systemic
administration of angiotensin II. Xirp2 is an important
effector of the Ang II signaling pathway in the heart.
The expression of Xirp2 is activated by myocyte enhancer
factor (MEF)2A, whose transcriptional activity is
stimulated by angiotersin II. Thus, Xirp2 plays
important pathological roles in the angiotensin II
induced hypertension. 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 = 30.9 bits (70), Expect = 0.13
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H +CF C C L + ++HGR+YC+ +
Sbjct: 21 FHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53
Score = 29.8 bits (67), Expect = 0.35
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
C C K + P+E R+++ ++FH C+ CE C +L+
Sbjct: 1 CTVCQKRVYPME------RLIADKQNFHKSCFRCEHCNSKLS 36
>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein
(CRP). The first LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific 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 = 53
Score = 31.1 bits (70), Expect = 0.14
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 405 CAICGHLIMEMI-LQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C + +Q G+S+H CF C +C + LD +++IYC + Y
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAH-EDEIYCKSCY 53
Score = 29.2 bits (65), Expect = 0.72
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + V A + Q G +H +CF+C C + L +YC+ Y
Sbjct: 1 CGACEKTVYHA-EEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCKSCY 53
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain 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 = 55
Score = 30.8 bits (70), Expect = 0.15
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL 354
C C E +T G A + G+ +H +CF C C + L
Sbjct: 1 CVGCKESIT-EGHAYELGGDRWHIHCFKCYKCDKKL 35
Score = 27.7 bits (62), Expect = 2.2
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPD 510
C C + IT E + D+ +H+ C+ C C +L+ + +
Sbjct: 1 CVGCKESIT-----EGHAYELGGDR-WHIHCFKCYKCDKKLSCDSN 40
>gnl|CDD|128804 smart00531, TFIIE, Transcription initiation factor IIE.
Length = 147
Score = 33.1 bits (76), Expect = 0.16
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 293 RKIEELTRQLEEEMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCG 351
K++++ ++LE+++E + Y C C K T +A L F C CG
Sbjct: 78 YKLDKMRKRLEDKLEDETNNAYYK--CPNCQSKYT----FLEANQLLDMDGTFTCPRCG 130
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. 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 = 52
Score = 30.7 bits (69), Expect = 0.20
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 335 AMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
A+ +H F C CG + F+ G+ YC +DY
Sbjct: 15 ALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
Score = 30.3 bits (68), Expect = 0.25
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C C I++ ++ A+ +++HP F C C F + D K YC DY
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFH-EKDGKAYCRKDY 52
>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM
domain only protein 1 and 3). The first LIM domain of
LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1
and LMO3 are highly homologous and belong to the LMO
protein family. LMO1 and LMO3 are nuclear protein that
plays important roles in transcriptional regulation and
development. As LIM domains lack intrinsic DNA-binding
activity, nuclear LMOs are involved in transcriptional
regulation by forming complexes with other transcription
factors or cofactors. For example, LMO1 interacts with
the the bHLH domain of bHLH transcription factor, TAL1
(T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation. In
addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the second
LIM domain (LIM2) of LMO3. One role of the CIB/LMO3
complex is to inhibit cell proliferation. Although LMO1
and LMO3 are highly homologous proteins, they play
different roles in the regulation of the pituitary
glycoprotein hormone alpha-subunit (alpha GSU) gene.
Alpha GSU promoter activity was markedly repressed by
LMO1 but activated by LMO3. All 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 = 30.6 bits (69), Expect = 0.20
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVD-NKIYCVNDY 457
CA C I + +L+A+ + +H C +C C+ L V T+ N I C DY
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin.
The fifth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
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. Its differential expression indicates that it is a
transcription regulator. 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 = 52
Score = 30.5 bits (69), Expect = 0.21
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C C + + G + +H CF C +C ++L G+ F + + YC + +
Sbjct: 1 CSKCNKIINSGGVTYK--NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 29.4 bits (66), Expect = 0.60
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C+ C +I + + +H CF C C++ L G FT D K YC + +
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFT-SRDEKPYCADCF 52
>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma
subfamily with unknown function. The first LIM domain
of an Enigma subfamily with unknown function: The Enigma
LIM domain family is comprised of three characterized
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.
They serve as adaptor proteins, where the PDZ domain
tethers the protein to the cytoskeleton and the LIM
domains, recruit signaling proteins to implement
corresponding functions. The members of the Enigma
family have been implicated in regulating or organizing
cytoskeletal structure, as well as involving multiple
signaling pathways. 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 = 30.5 bits (69), Expect = 0.22
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICC--SCGRALRGKAFYNVHGRVYCE 369
C +C +++ G A+G ++ + FIC SC R L+ F G++YCE
Sbjct: 1 CESCNQQIRGP--FITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCE 51
Score = 27.8 bits (62), Expect = 2.0
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCC--LCNECLDGVPFTVDVDNKIYC 453
C C I + A+GK + P F C C L + F V+ ++YC
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGF-VEEKGQLYC 50
>gnl|CDD|188818 cd09434, LIM4_FHL3, The fourth LIM domain of Four and a half LIM
domains protein 3 (FHL3). The fourth LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. 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 = 56
Score = 30.5 bits (69), Expect = 0.24
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
CAAC K IT G V D+ +H C+ C C + L +P +++CR
Sbjct: 1 CAACNKPIT---GFGGGKYVSFEDRQWHQPCFKCSRCSVSLV---GAGFFPDGDQILCRD 54
Query: 525 C 525
C
Sbjct: 55 C 55
Score = 28.6 bits (64), Expect = 0.93
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 319 CHTCGEKVTGAGQA--CQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C + +TG G +H CF C C +L G F+ ++ C
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILC 52
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 34.2 bits (78), Expect = 0.24
Identities = 30/135 (22%), Positives = 45/135 (33%), Gaps = 20/135 (14%)
Query: 180 PYEAPPVYEN-IQELNKPPKPGPQVPVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKT 238
P V + + ++ P V A+ SPPV S A A V T
Sbjct: 1127 PVIKSVVTQAPVVQVTISVAPAAPV----------LPAVVSPPVVSAA-----PAQSVAT 1171
Query: 239 ATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAERKIEEL 298
A +++ ++ PV + PS P + M AE K
Sbjct: 1172 AVAMAPVAEVPIAVPVQQSVDYMPSVAQAAAPQASVNDS---AIQQVMMEVVAE-KTGYP 1227
Query: 299 TRQLEEEMEKQEEEG 313
T LE EM+ + + G
Sbjct: 1228 TEMLELEMDMEADLG 1242
>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b. The second
LIM domain of Lhx3b. Lhx3b is a member of 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. Lhx3b is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. 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 = 57
Score = 30.4 bits (68), Expect = 0.28
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 10/63 (15%)
Query: 464 KCAACGKGITPVEGTEETVRVVSMDKDF--HVDCYMCEDCGLQLTDEPDKRCYPLQGRLM 521
KCAAC +GI P + VV +DF H+ C+ C C QL D+ RL+
Sbjct: 1 KCAACQQGIPPTQ-------VVRRAQDFVYHLHCFACIVCKRQLA-TGDEFYLMEDSRLV 52
Query: 522 CRA 524
C+A
Sbjct: 53 CKA 55
Score = 29.3 bits (65), Expect = 0.64
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL-RGKAFYNVH-GRVYCEEDY 372
C C + + +A +YH +CF C C R L G FY + R+ C+ DY
Sbjct: 2 CAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57
Score = 28.5 bits (63), Expect = 1.2
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 404 KCAIC--GHLIMEMILQAMGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYCVNDY 457
KCA C G +++ +A YH CF C +C L G F + D+++ C DY
Sbjct: 1 KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57
>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only
protein 2). The second LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex that
is capable of transcriptional activation. LMOs have also
been shown to be involved in oncogenesis. LMO1 and LMO2
are activated in T-cell acute lymphoblastic leukemia by
distinct chromosomal translocations. LMO2 was also shown
to be involved in erythropoiesis and is required for the
hematopoiesis in the adult animals. All 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 = 56
Score = 30.0 bits (67), Expect = 0.32
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVHGRVYCEED 371
C +C +++ + +YH CF C +C + G + ++ + CE+D
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54
Score = 28.1 bits (62), Expect = 1.6
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 405 CAICGHLI--MEMILQAMGKSYHPGCFRCCLCNE 436
CA C I EM ++ K YH CF+C C +
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQK 34
Score = 28.1 bits (62), Expect = 1.6
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDC 501
CA+C K I E T+RV DK +H++C+ C C
Sbjct: 1 CASCDKRI---RAYEMTMRV--KDKVYHLECFKCAAC 32
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group 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. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Isl2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All 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 = 30.1 bits (68), Expect = 0.33
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALR-GKAFYNVHGRVYCEEDY 372
C C + + +A +YH CF C +C R L G F ++C+ D+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55
Score = 28.9 bits (65), Expect = 0.76
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLC 434
CA C + +++A K YH CFRC C
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSAC 32
Score = 26.6 bits (59), Expect = 5.1
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 11/64 (17%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT--DEPDKRCYPLQGRLMC 522
CA C + + + +R K +H++C+ C C QL DE R L C
Sbjct: 1 CAKCQQSFSK---NDFVMRA--RTKIYHIECFRCSACSRQLIPGDEFALR----DDGLFC 51
Query: 523 RACH 526
+A H
Sbjct: 52 KADH 55
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 33.2 bits (76), Expect = 0.38
Identities = 35/287 (12%), Positives = 68/287 (23%), Gaps = 24/287 (8%)
Query: 42 QYERGNIIASSKFATPKSVDNLPLADVYRSNGSAKPGPVSP----------SGSSKDSNS 91
+Y + A S +S A P + K
Sbjct: 76 RYNQNAPGAPSVGPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKPEPQ 135
Query: 92 PRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPHLRSGSHSSV--GSQDSKHSSPRGS 149
P + + P P + Q P L + G + + P+
Sbjct: 136 PPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQG 195
Query: 150 YVSNDINAFQFDRKAQPQVPQGLKYIRDYPPYEAPPVYENIQELNKPPKPGPQVPVFGGE 209
+ + Q Q P +AP +L + P P Q G
Sbjct: 196 PPEQ---PPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLS 252
Query: 210 HRQMAIALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVT 269
+ P + +A P Q + P P P+
Sbjct: 253 QQMPPPPPQPPQ--QQQQPPQPQAQPPPQNQPTPHPGLPQGQNA--PLPPPQQPQLLPLV 308
Query: 270 PYGKNLLPYNVTPPRPMGPTEAERKIEELTRQLEEEMEKQEEEGEYF 316
+ + + ++ +R+ +EE ++ + +
Sbjct: 309 QQPQGQQRGPQFREQLVQLSQQQREA-----LSQEEAKRAKRRHKIV 350
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 32.9 bits (75), Expect = 0.45
Identities = 17/104 (16%), Positives = 31/104 (29%), Gaps = 4/104 (3%)
Query: 212 QMAI--ALTSPPVYSRANTVTSKAVPVKTAT-SLSVTPNYQVSSPVDTTPSPSPSPKTPV 268
++A+ AL P + T+ A T + S P ++ + P TP
Sbjct: 352 ELAVIEALLVPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKE-PVRETATPP 410
Query: 269 TPYGKNLLPYNVTPPRPMGPTEAERKIEELTRQLEEEMEKQEEE 312
+ + P P + + +EEE
Sbjct: 411 PVPPRPVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPKEEE 454
Score = 30.9 bits (70), Expect = 2.2
Identities = 18/90 (20%), Positives = 27/90 (30%), Gaps = 6/90 (6%)
Query: 215 IALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKN 274
A ++ P + A + K +TAT V P P P P
Sbjct: 383 PAPSTRPKAAAAANIPPKEPVRETATPPPVPP------RPVAPPVPHTPESAPKLTRAAI 436
Query: 275 LLPYNVTPPRPMGPTEAERKIEELTRQLEE 304
+ P P E E+ + LE+
Sbjct: 437 PVDEKPKYTPPAPPKEEEKALIADGDVLEQ 466
>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP. The LIM domain of
N-RAP: N-RAP is a muscle-specific protein concentrated
at myotendinous junctions in skeletal muscle and
intercalated disks in cardiac muscle. LIM domain is
found at the N-terminus of N-RAP and the C-terminal of
N-RAP contains a region with multiple of nebulin
repeats. N-RAP functions as a scaffolding protein that
organizes alpha-actinin and actin into symmetrical I-Z-I
structures in developing myofibrils. Nebulin repeat is
known as actin binding domain. The N-RAP is hypothesized
to form antiparallel dimerization via its LIM domain. 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 = 29.5 bits (66), Expect = 0.45
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
CA CG G+ P E ++ +D+ +H C+ CE C + LT
Sbjct: 1 CARCGYGVYPAE------KINCIDQTWHKACFHCEVCKMMLT 36
>gnl|CDD|226406 COG3889, COG3889, Predicted solute binding protein [General
function prediction only].
Length = 872
Score = 32.9 bits (75), Expect = 0.48
Identities = 24/120 (20%), Positives = 36/120 (30%), Gaps = 15/120 (12%)
Query: 166 PQVPQGLKYIRDYPPYEAPPVYENIQELNKPPKPG--PQVPVFGGEHRQMAIALTSPPVY 223
+ K +A VY +++ G P A +
Sbjct: 709 TTLSSEAKNPDTVKIGQALTVYGSLEVFPAGENWGFIPTTKRVKVRIMDPASGTGTSITT 768
Query: 224 SRANTVTSKAVPVKTATSLSVTP------NYQVSSPVDT-------TPSPSPSPKTPVTP 270
S T P KT T+LS + + +S V T T + SPSP +P
Sbjct: 769 SGTFTAEVPQSPTKTETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSP 828
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 33.0 bits (76), Expect = 0.53
Identities = 18/107 (16%), Positives = 29/107 (27%), Gaps = 17/107 (15%)
Query: 245 TPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAERKIEELTRQLEE 304
Q+ + P+ P A ++ E
Sbjct: 858 ERAAQLETG-SYAPASDADLIAEAAASAAPAAPSAAPKEANSEAAPAPKEA----HSSTE 912
Query: 305 EMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCG 351
+E Q E +C TCG K+ G +C++C CG
Sbjct: 913 LLELQLGEAADAPLCPTCGTKMVRNG------------SCYVCEGCG 947
>gnl|CDD|235761 PRK06266, PRK06266, transcription initiation factor E subunit
alpha; Validated.
Length = 178
Score = 31.5 bits (72), Expect = 0.56
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 11/63 (17%)
Query: 292 ERKIEELTRQLEEEMEKQEEEGEYFGICHTCGEKVTGAGQACQAMGNLYHTNCFICCSCG 351
++K E ++L+E++E EEE F C C + T +AM F C CG
Sbjct: 95 KKKKMEELKKLKEQLE--EEENNMFFFCPNCHIRFTFD----EAM-----EYGFRCPQCG 143
Query: 352 RAL 354
L
Sbjct: 144 EML 146
>gnl|CDD|188803 cd09419, LIM3_Testin, The third LIM domain of Testin. The third
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. 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 it is involved in cell motility and adhesion events.
Knockout mice experiments reveal that tumor repressor
function of Testin. 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 = 59
Score = 29.5 bits (66), Expect = 0.59
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 342 TNCFICCSCGRALRGKAFYNVHGRVYC 368
CF+C C + L G+ F V G V+C
Sbjct: 26 PECFLCSCCSKCLIGQKFMPVEGMVFC 52
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. 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.
Isl proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may be able to bind to the
insulin gene enhancer to promote gene activation. All
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 = 29.1 bits (65), Expect = 0.70
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 405 CAIC--GHLIMEMILQAMGKSYHPGCFRCCLCN-ECLDGVPFTVDVDNKIYCVNDY 457
CA C G +++++A YH CFRC +C+ + L G F + ++++ C D+
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLR-EHELLCRADH 55
Score = 28.7 bits (64), Expect = 0.85
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRAL 354
C C + + +A ++YH CF C C R L
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQL 36
Score = 28.7 bits (64), Expect = 1.1
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMCRA 524
CA C G + ++ +R + D +H++C+ C C QL P + L+CRA
Sbjct: 1 CAQCRLGFS---SSDLVMR--ARDSVYHIECFRCSVCSRQLL--PGDEFCLREHELLCRA 53
Query: 525 CH 526
H
Sbjct: 54 DH 55
>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin. The
fourth LIM domain of Paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. 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 = 52
Score = 28.8 bits (64), Expect = 0.74
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C C + +TG + AMG +H F+C C + L F + + YC
Sbjct: 1 CSGCQKPITG--RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCH 49
Score = 28.0 bits (62), Expect = 1.6
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYC 453
C+ C I + AMGK +HP F C C + L+ F + ++K YC
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFK-EQNDKPYC 48
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first LIM
domain of Lhx3b. Lhx3b is a member of 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. Lhx3b is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. 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 = 55
Score = 29.1 bits (65), Expect = 0.78
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 463 PKCAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLTDEPDKRCYPLQGRLMC 522
P CA C + I + + +D+ +H C C DC QL + +C+ + C
Sbjct: 2 PLCAGCNQHIV------DRFILKVLDRHWHSKCLKCSDCQTQLAE----KCFSRGDSVYC 51
Query: 523 R 523
+
Sbjct: 52 K 52
Score = 28.7 bits (64), Expect = 0.96
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 405 CAICG-HLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
CA C H++ IL+ + + +H C +C C L F+ + +YC +D+
Sbjct: 4 CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFS--RGDSVYCKDDF 55
>gnl|CDD|238958 cd02000, TPP_E1_PDC_ADC_BCADC, Thiamine pyrophosphate (TPP) family,
E1 of PDC_ADC_BCADC subfamily, TPP-binding module;
composed of proteins similar to the E1 components of the
human pyruvate dehydrogenase complex (PDC), the acetoin
dehydrogenase complex (ADC) and the branched chain
alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). PDC catalyzes the
irreversible oxidative decarboxylation of pyruvate to
produce acetyl-CoA in the bridging step between
glycolysis and the citric acid cycle. ADC participates
in the breakdown of acetoin while BCADC participates in
the breakdown of branched chain amino acids. BCADC
catalyzes the oxidative decarboxylation of
4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and
3-methyl-2-oxobutanoate (branched chain 2-oxo acids
derived from the transamination of leucine, valine and
isoleucine).
Length = 293
Score = 31.7 bits (73), Expect = 0.80
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 298 LTRQLEEEMEKQEEEGEYFGICHTC-GEKVTGAGQACQAMGN 338
L R+ +E + + +G+ G H G++ G A+
Sbjct: 7 LIRRFDERLLELYRQGKIGGFYHLSIGQEAVAVG-VAAALRP 47
>gnl|CDD|218215 pfam04696, Pinin_SDK_memA, pinin/SDK/memA/ protein conserved
region. Members of this family have very varied
localisations within the eukaryotic cell. pinin is known
to localise at the desmosomes and is implicated in
anchoring intermediate filaments to the desmosomal
plaque. SDK2/3 is a dynamically localised nuclear
protein thought to be involved in modulation of
alternative pre-mRNA splicing. memA is a tumour marker
preferentially expressed in human melanoma cell lines. A
common feature of the members of this family is that
they may all participate in regulating protein-protein
interactions.
Length = 131
Score = 30.5 bits (69), Expect = 0.82
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 289 TEAERKIEELTRQLEEEMEKQEEE 312
E E+K+EE +Q EE+ K++ E
Sbjct: 38 AEIEQKLEEQEKQEREELRKEKRE 61
>gnl|CDD|188833 cd09449, LIM_Mystique, The LIM domain of Mystique, a subfamily of
ALP LIM domain proteins. The LIM domain of Mystique, a
subfamily of ALP LIM domain proteins: Mystique is the
most recently identified member of the ALP protein
family. It also interacts with alpha-actinin, as other
ALP proteins do. Mystique promotes cell attachment and
migration and suppresses anchorage-independent growth.
The LIM domain of Mystique is required for the
suppression function. Moreover, Mystique functions as an
ubiquitin E3 ligase acting on STAT proteins to cause
their proteosome mediated degradation. As in all LIM
domains, this domain 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
complexes.
Length = 53
Score = 28.7 bits (64), Expect = 0.86
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 319 CHTCGEKVTGAGQACQAMGNLY-HTNCFICCSCGRALRGKAFYNVHGRVYCE 369
C CG + QA + Y H C+ C CG L+ + + +++CE
Sbjct: 1 CEKCGTSI--VTQAVRIQEGRYRHPGCYTCTDCGLNLKMRGHFWAGEKMFCE 50
Score = 26.8 bits (59), Expect = 5.3
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
C CG I + VR+ + H CY C DCGL L
Sbjct: 1 CEKCGTSIV-----TQAVRI-QEGRYRHPGCYTCTDCGLNL 35
>gnl|CDD|167649 PRK03963, PRK03963, V-type ATP synthase subunit E; Provisional.
Length = 198
Score = 31.3 bits (71), Expect = 0.89
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 290 EAERKIEELTRQLEEEMEKQEEEGE 314
EAE+KIE + + ++E EK +EE
Sbjct: 14 EAEQKIEYILEEAQKEAEKIKEEAR 38
>gnl|CDD|188812 cd09428, LIM2_FHL5, The second LIM domain of Four and a half LIM
domains protein 5 (FHL5). The second LIM domain of Four
and a half LIM domains protein 5 (FHL5): FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors , which are highly expressed in
male germ cells and is required for post-meiotic gene
expression. FHL5 associates with CREM and confers a
powerful transcriptional activation function. Activation
by CREB has known to occur upon phosphorylation at an
essential regulatory site and the subsequent interaction
with the ubiquitous coactivator CREB-binding protein
(CBP). However, the activation by FHL5 is independent of
phosphorylation and CBP association. It represents a new
route for transcriptional activation by CREM and CREB.
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 = 28.7 bits (64), Expect = 0.91
Identities = 13/50 (26%), Positives = 22/50 (44%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C + + + + GN +H CF+C SC + + K + YC
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50
Score = 26.3 bits (58), Expect = 6.8
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 405 CAICGHLIM--EMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCV 454
C C IM L+ G +H CF C C + + P + +NK YCV
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPL-ITKENKNYCV 51
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. 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 = 52
Score = 28.8 bits (65), Expect = 0.91
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 424 YHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
+H CF C C + L G FT D YCV+ +
Sbjct: 20 WHKECFVCTGCKKQLAGQRFT-SRDEYPYCVDCF 52
Score = 26.1 bits (58), Expect = 6.6
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 340 YHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
+H CF+C C + L G+ F + YC + +
Sbjct: 20 WHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
>gnl|CDD|188817 cd09433, LIM4_FHL2, The fourth LIM domain of Four and a half LIM
domains protein 2 (FHL2). The fourth LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. 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 s upport the assembly of multimeric protein
complexes.
Length = 58
Score = 28.8 bits (64), Expect = 0.93
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQL 505
CA C P+ G T + ++ +H DC+ C+ C L L
Sbjct: 1 CAGC---TNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL 38
Score = 26.5 bits (58), Expect = 5.6
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 319 CHTCGEKVTGAGQA--CQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEE 370
C C ++G G +H +CF C C +L G+ F + C E
Sbjct: 1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPE 54
>gnl|CDD|188801 cd09417, LIM2_LIMPETin_like, The second LIM domain of protein
LIMPETin and related proteins. The second LIM domain of
protein LIMPETin: LIMPETin contains 6 LIM domains at the
C-terminal and an N-terminal PET domain. Four of the six
LIM domains are highly homologous to the four and half
LIM domain protein family and two of them show sequence
similarity to the LIM domains of the testin family.
Thus, LIMPETin 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. Its differential expression indicates that it is a
transcription regulator. 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 = 56
Score = 28.7 bits (64), Expect = 1.2
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 418 QAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
+AM K +H G F C C+E L G + + D YC+ Y
Sbjct: 17 KAMNKDWHSGHFCCWQCDESLTGQRYVLR-DEHPYCIKCY 55
>gnl|CDD|146016 pfam03179, V-ATPase_G, Vacuolar (H+)-ATPase G subunit. This family
represents the eukaryotic vacuolar (H+)-ATPase
(V-ATPase) G subunit. V-ATPases generate an acidic
environment in several intracellular compartments.
Correspondingly, they are found as membrane-attached
proteins in several organelles. They are also found in
the plasma membranes of some specialised cells.
V-ATPases consist of peripheral (V1) and membrane
integral (V0) heteromultimeric complexes. The G subunit
is part of the V1 subunit, but is also thought to be
strongly attached to the V0 complex. It may be involved
in the coupling of ATP degradation to H+ translocation.
Length = 105
Score = 29.5 bits (67), Expect = 1.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 289 TEAERKIEELTRQLEEEMEKQEEE 312
EAE++IEE Q E E ++ E E
Sbjct: 36 EEAEKEIEEYRAQREAEFKEFEAE 59
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short protein with
only one LIM domain. CRIP gene is developmentally
regulated and can be induced by glucocorticoid hormones
during the first three postnatal weeks. The domain shows
close sequence homology to LIM domain of thymus LIM
protein. However, unlike the TLP proteins which have two
LIM domains, the members of this family have only one
LIM domain. 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 = 28.3 bits (63), Expect = 1.4
Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
C C K + E RV S+ KD+H C CE CG LT
Sbjct: 1 CPKCDKEVYFAE------RVTSLGKDWHRPCLKCEKCGKTLT 36
>gnl|CDD|225029 COG2118, COG2118, DNA-binding protein [General function prediction
only].
Length = 116
Score = 29.6 bits (67), Expect = 1.5
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 292 ERKIEELTRQ--LEEEMEKQEEEGE 314
RK+ EL RQ LEE+ E QEE+
Sbjct: 11 RRKLAELQRQAKLEEQREAQEEQAR 35
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 30.3 bits (69), Expect = 1.6
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 290 EAERKIEELTRQLEEEMEKQEEEGE 314
E +++I EL Q+E+ + +EE E
Sbjct: 80 ELKQRIAELQAQIEKLKKGREETEE 104
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents a
LIM domain subfamily of Eplin-like family. This family
shows highest homology to the LIM domains on Eplin and
XIRP2 protein families. Epithelial Protein Lost in
Neoplasm is a cytoskeleton-associated tumor suppressor
whose expression inversely correlates with cell growth,
motility, invasion and cancer mortality. Xirp2 is
expressed in muscles and is an important effector of the
Ang II signaling pathway in the heart. 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 = 27.6 bits (61), Expect = 2.0
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 465 CAACGKGITPVEGTEETVRVVSMDKDFHVDCYMCEDCGLQLT 506
C++C K + P+E R+V+ FH C+ C+ C +L+
Sbjct: 1 CSSCQKTVYPME------RLVADKLVFHNSCFCCKHCNAKLS 36
Score = 27.6 bits (61), Expect = 2.1
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 339 LYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
++H +CF C C L ++ +HG YC+ +
Sbjct: 20 VFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53
>gnl|CDD|233897 TIGR02499, HrpE_YscL_not, type III secretion apparatus protein,
HrpE/YscL family. This model is related to pfam06188,
but is broader. pfam06188 describes HrpE-like proteins,
components of bacterial type III secretion systems
primarily in bacteria that infect plants. This model
includes also the homologous proteins of animal
pathogens, such as YscL of Yersinia pestis. This model
excludes the related protein FliH of the bacterial
flagellar apparatus (see pfam02108) [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 166
Score = 30.0 bits (68), Expect = 2.1
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 290 EAERKIEELTRQLEEEMEKQEEEG 313
A ++ E + EEE E + G
Sbjct: 21 AARQRAEAILADAEEEAEASRQLG 44
>gnl|CDD|224849 COG1938, COG1938, Archaeal enzymes of ATP-grasp superfamily
[General function prediction only].
Length = 244
Score = 30.4 bits (69), Expect = 2.2
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 290 EAER---KIEELTRQLEEEMEKQEEEGEY 315
EAE ++E+L QLE+E E+ E E E
Sbjct: 212 EAEEIEEQLEKLAEQLEKEEERVEREEEP 240
>gnl|CDD|129469 TIGR00373, TIGR00373, transcription factor E. This family of
proteins is, so far, restricted to archaeal genomes. The
family appears to be distantly related to the N-terminal
region of the eukaryotic transcription initiation factor
IIE alpha chain [Transcription, Transcription factors].
Length = 158
Score = 29.8 bits (67), Expect = 2.2
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 292 ERKIEELTRQLEEEMEKQEEEGEYFGICHTCGEKVT 327
+RK+EE ++L E++E E F IC + T
Sbjct: 87 KRKLEETAKKLREKLEF--ETNNMFFICPNMCVRFT 120
>gnl|CDD|189476 pfam00261, Tropomyosin, Tropomyosin.
Length = 237
Score = 30.3 bits (69), Expect = 2.3
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 290 EAERKIEELTRQL---EEEMEKQEEEGE 314
EA+RK EE+ R+L E ++E+ EE E
Sbjct: 110 EADRKYEEVARKLVVVEGDLERAEERAE 137
>gnl|CDD|148265 pfam06557, DUF1122, Protein of unknown function (DUF1122). This
family consists of several hypothetical archaeal and
bacterial proteins of unknown function.
Length = 170
Score = 29.7 bits (67), Expect = 2.3
Identities = 8/30 (26%), Positives = 17/30 (56%)
Query: 284 RPMGPTEAERKIEELTRQLEEEMEKQEEEG 313
+P+ +R++ EL +++ + K EE G
Sbjct: 139 KPLSEEAEKRQLRELLDEVKNFIGKFEESG 168
>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6. The first LIM
domain of Lhx6. Lhx6 is a member of 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. Lhx6 functions in the
brain and nervous system. It is expressed at high
levels in several regions of the embryonic mouse CNS,
including the telencephalon and hypothalamus, and the
first branchial arch. Lhx6 is proposed to have a role in
patterning of the mandible and maxilla, and in signaling
during odontogenesis. In brain sections, knockdown of
Lhx6 gene blocks the normal migration of neurons to the
cortex. 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 complexes.
Length = 54
Score = 27.7 bits (61), Expect = 2.3
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 405 CAICGHLIME-MILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C+ CG I++ +L+ +H C C +C L + +I+C DY
Sbjct: 1 CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 54
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 30.7 bits (70), Expect = 2.4
Identities = 18/87 (20%), Positives = 22/87 (25%), Gaps = 9/87 (10%)
Query: 189 NIQELNKPPKPGPQVPVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKTATSLSVTPNY 248
I E+ P P A S P +A T S +
Sbjct: 364 FISEIANASAPANPTPAPNPSPPP-APIQPSAPKTKQAATTPSPPPAKASPPI------- 415
Query: 249 QVSSPVDTTPSPSPSPKTPVTPYGKNL 275
T PSP+P P NL
Sbjct: 416 -PVPAEPTEPSPTPPANAANAPPSLNL 441
>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM
domains protein 2 (FHL2). The third LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. 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 s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 27.6 bits (61), Expect = 2.4
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C + +T G + +H CF+C C + L G+ F + YC
Sbjct: 1 CVQCKKPITTGGVTYRDQP--WHKECFVCTGCKKQLSGQRFTSRDDFAYC 48
Score = 26.1 bits (57), Expect = 9.7
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 405 CAICGHLIMEMILQAMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFA 462
C C I + + +H CF C C + L G FT D+ YC+N + ++A
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSR-DDFAYCLNCFCNLYA 57
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 30.5 bits (69), Expect = 2.5
Identities = 18/121 (14%), Positives = 38/121 (31%), Gaps = 9/121 (7%)
Query: 193 LNKPPKPGPQV---PVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQ 249
+ GP+ PVF A P + A+ S++ ++
Sbjct: 367 DDASGGRGPKQHIKPVFTQ-----PAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPA 421
Query: 250 VSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAERKIEELTRQLEEEMEKQ 309
+ P + P+ P P + + + P + + P + T + +E +Q
Sbjct: 422 GTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEKKI-PVSKVSSLGPSTLRPIQEKAEQ 480
Query: 310 E 310
Sbjct: 481 A 481
>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX
protein family. The first LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group 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. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Is l2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All 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 = 27.3 bits (61), Expect = 2.7
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 405 CAICGHLIME-MILQ-AMGKSYHPGCFRCCLCNECLDGVPFTVDVDNKIYCVNDY 457
C CG I + IL+ A +H C +C C + LD D K YC DY
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at their
amino terminus. This family represents the rest of these
proteins.
Length = 244
Score = 30.1 bits (68), Expect = 2.7
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 291 AERKIEELTRQLEEEMEKQEEEGE 314
++EE R+LEEE EEE E
Sbjct: 55 KADELEEENRRLEEEAAASEEERE 78
>gnl|CDD|152702 pfam12267, DUF3614, Protein of unknown function (DUF3614). This
family of proteins is found in viruses. Proteins in this
family are typically between 162 and 495 amino acids in
length.
Length = 173
Score = 29.5 bits (66), Expect = 2.7
Identities = 27/125 (21%), Positives = 40/125 (32%), Gaps = 14/125 (11%)
Query: 173 KYIRDYPPYEAPPVYENIQELNKPPKPGPQVPVFGGEHRQMAIALTSPPVYSRANTVTSK 232
+Y R Y A + + K +V + A ++ P A+ VT +
Sbjct: 12 RYERHYD---ASMEDVGLSWVRKSRVSFVEVFALR-RRSRSARSVLRFPP---ASVVTEE 64
Query: 233 AVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAE 292
+VP + S V VS V PS +P + V EA
Sbjct: 65 SVPALVSPSRIVVKKVPVSVEV---SPPSRGASSPRVDSVRGSGWIVVGGVV----HEAL 117
Query: 293 RKIEE 297
KI E
Sbjct: 118 NKIRE 122
>gnl|CDD|221466 pfam12220, U1snRNP70_N, U1 small nuclear ribonucleoprotein of 70kDa
MW N terminal. This domain is found in eukaryotes. This
domain is about 90 amino acids in length. This domain is
found associated with pfam00076. This domain is part of
U1 snRNP, which is the pre-mRNA binding protein of the
penta-snRNP spliceosome complex. It extends over a
distance of 180 A from its RNA binding domain, wraps
around the core domain of U1 snRNP consisting of the
seven Sm proteins and finally contacts U1-C, which is
crucial for 5'-splice-site recognition.
Length = 94
Score = 28.4 bits (64), Expect = 2.8
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 253 PVDTTP-SPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAERKIEELTRQLEEEMEKQEE 311
P+D P +P T V Y Y PP T E++ E + E+ +K EE
Sbjct: 24 PLDKAPEKRKTNPITGVAQYLSEFKDYKDEPPPEPTETWLEKREREKREKKEKLEKKLEE 83
Query: 312 E 312
E
Sbjct: 84 E 84
>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator. This protein is
found in a wide range of eukaryotes. It is a nuclear
protein and is suggested to be DNA binding. In plants,
this family is essential for correct circadian clock
functioning by acting as a light-quality regulator
coordinating the activities of blue and red light
signalling pathways during plant growth - inhibiting
growth in red light but promoting growth in blue light.
Length = 233
Score = 30.0 bits (68), Expect = 2.8
Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 2/58 (3%)
Query: 256 TTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPT-EAERKIEELTRQLEEEMEKQEEE 312
S + V P K + N + P E K EL +L EE K++E
Sbjct: 31 VPKESSEPDEANVNPNKKKIGK-NPSVDTSFLPDKAREEKEAELREELREEFLKKQEA 87
>gnl|CDD|216421 pfam01299, Lamp, Lysosome-associated membrane glycoprotein (Lamp).
Length = 305
Score = 30.1 bits (68), Expect = 2.9
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 243 SVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVT 281
+ S TPSPSP+P G Y+VT
Sbjct: 79 TRCEADTPSPTTVATPSPSPTPVPSSPAVGN----YSVT 113
>gnl|CDD|227652 COG5349, COG5349, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 126
Score = 28.9 bits (65), Expect = 3.0
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 10/55 (18%)
Query: 368 CEEDYLYSGFQQTAEKCAICGHLIMEMYSGFQQTAEKCA-----ICGHLIMEMIL 417
C E L+ GF + C CG + GF + A I GH+++ + L
Sbjct: 27 CGEGRLFRGFLKVVPACEACGL---DY--GFADADDGPAYFVILIVGHIVVGLAL 76
>gnl|CDD|188849 cd09465, LIM2_LIMK2, The second LIM domain of LIMK2 (LIM domain
Kinase 2). The second LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerisation.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All 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 = 59
Score = 27.2 bits (60), Expect = 3.1
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNV--HGRVYC 368
CH C +TG A A YH CF C SC + Y + H +YC
Sbjct: 6 CHGCSLLMTGP--AMVAGEYKYHPECFACMSCKVIIEDGDTYALVQHTTLYC 55
Score = 27.2 bits (60), Expect = 3.7
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 403 EKCAICGHLIMEMILQAMGKSYHPGCFRCCLCNECL-DGVPFTVDVDNKIYC 453
E C C L+ + A YHP CF C C + DG + + +YC
Sbjct: 4 ELCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVIIEDGDTYALVQHTTLYC 55
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 29.3 bits (66), Expect = 3.3
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 290 EAERKIEELTRQLEEEMEKQEEEGE 314
E E EE ++ EEE K+ EE
Sbjct: 44 EEEELEEEREKKKEEEERKEREEQA 68
>gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast
subunit 62; Provisional.
Length = 576
Score = 30.3 bits (68), Expect = 3.5
Identities = 15/73 (20%), Positives = 26/73 (35%)
Query: 220 PPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYN 279
PP T + V + +S+ P+ ++ +P P+ P++PY
Sbjct: 449 PPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAPPPANMRPLSPYAVYDDLKP 508
Query: 280 VTPPRPMGPTEAE 292
T P P P
Sbjct: 509 PTSPSPAAPVGKV 521
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 29.9 bits (68), Expect = 3.5
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 290 EAERKIEELTRQLEEEMEKQEE 311
E ER++ L Q EE +++EE
Sbjct: 179 EKEREVARLRAQQEEAEDEREE 200
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 30.3 bits (68), Expect = 3.6
Identities = 23/115 (20%), Positives = 40/115 (34%), Gaps = 13/115 (11%)
Query: 196 PPKPGPQVPVFGGEHRQMAIALTSPPVYSRANT-----VTSKAVPVKTATSLSVTPNYQV 250
PPK ++ + + P + NT T+K P + S T
Sbjct: 79 PPKSSSEMEGEMLAPQATVGRDEATPSIAMENTPSPPRRTAKITPTTPKNNYSPTAAGTE 138
Query: 251 SSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMG------PTEAERKIEELT 299
DT +PS + ++ G+ + P+P G PT+ K+ + T
Sbjct: 139 RVKEDTPATPSRALNHYISTSGRQRV--KSYTPKPRGEVKSSSPTQTREKVRKYT 191
Score = 28.8 bits (64), Expect = 8.4
Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 15/90 (16%)
Query: 212 QMAIALT--SPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVD--TTPSPSPSPKTP 267
Q+ I++ S P ++A+T K ++ S + P +++S +PS +P TP
Sbjct: 324 QVTISIMTGSSPAETKASTAAWK---IRNPLSRTSAPAVRIASATFRGLEKNPSTAPSTP 380
Query: 268 VTPYGKNLLPYNV--------TPPRPMGPT 289
TP + +L V P P P+
Sbjct: 381 ATPRVRAVLTTQVHHCVVVKPAPAVPTTPS 410
>gnl|CDD|146815 pfam04368, DUF507, Protein of unknown function (DUF507). Bacterial
protein of unknown function.
Length = 183
Score = 29.1 bits (66), Expect = 3.8
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 290 EAERKIEELTRQLEEEMEKQEEEGEYFGI 318
ER ++E R++ +E+ EEE E+ +
Sbjct: 47 AKERALDERAREI---LEENEEEIEFMNV 72
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 29.8 bits (67), Expect = 3.9
Identities = 33/210 (15%), Positives = 52/210 (24%), Gaps = 14/210 (6%)
Query: 82 PSGSSKDSNSPRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPHLRSGSHSSVGSQDS 141
P S + A+ A V P A PP + + +V + +
Sbjct: 365 PGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPA 424
Query: 142 KHSSPRGSYVSNDINAFQFDRKAQPQVPQGLKYIRDYP-PYEAPPVYENIQELNKPPKPG 200
+ S A R+A + P G P A
Sbjct: 425 RRSPAP--------EALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAA 476
Query: 201 PQVPVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKTATS-----LSVTPNYQVSSPVD 255
P A A PP + + P + + P+ + P D
Sbjct: 477 AAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDD 536
Query: 256 TTPSPSPSPKTPVTPYGKNLLPYNVTPPRP 285
+ +P+P P V P P
Sbjct: 537 AFETLAPAPAAAPAPRAAAATEPVVAPRPP 566
>gnl|CDD|216919 pfam02181, FH2, Formin Homology 2 Domain.
Length = 372
Score = 29.6 bits (67), Expect = 4.1
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 290 EAERKIEELTRQLEEEMEKQEEEGEYFG 317
EAE K+++L L+E ME +E EYFG
Sbjct: 322 EAEEKLDKLESLLKEAMELFKELTEYFG 349
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 29.9 bits (68), Expect = 4.1
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 296 EELTRQLEEEMEKQEE 311
EE TR+LEE+M+K EE
Sbjct: 1138 EERTRKLEEKMDKVEE 1153
>gnl|CDD|115340 pfam06677, Auto_anti-p27, Sjogren's syndrome/scleroderma
autoantigen 1 (Autoantigen p27). This family consists
of several Sjogren's syndrome/scleroderma autoantigen 1
(Autoantigen p27) sequences. It is thought that the
potential association of anti-p27 with anti-centromere
antibodies suggests that autoantigen p27 might play a
role in mitosis.
Length = 41
Score = 26.5 bits (59), Expect = 4.1
Identities = 9/39 (23%), Positives = 12/39 (30%), Gaps = 4/39 (10%)
Query: 371 DYLYSGFQQTAEKCAICGHLIMEMYSGFQQTAEKCAICG 409
+ L G E C CG + + G C C
Sbjct: 7 ELLLKGATMLDEHCPKCGTPLFRLKDG----KVFCPSCE 41
>gnl|CDD|184285 PRK13733, PRK13733, conjugal transfer protein TraV; Provisional.
Length = 171
Score = 29.0 bits (65), Expect = 4.2
Identities = 14/71 (19%), Positives = 20/71 (28%), Gaps = 3/71 (4%)
Query: 233 AVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTP---PRPMGPT 289
+T +VT S T +P P + V P P+ P
Sbjct: 67 EGNFRTMPVQTVTATTPSGSRPAVTATPEQKLLAPRPLFTAAREVKTVVPVSSVTPVTPP 126
Query: 290 EAERKIEELTR 300
R E+ R
Sbjct: 127 RPLRTGEQTAR 137
>gnl|CDD|220979 pfam11101, DUF2884, Protein of unknown function (DUF2884). Some
members in this bacterial family of proteins are
annotated as YggN which currently has no known function.
Length = 228
Score = 29.2 bits (66), Expect = 4.6
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 289 TEAERKIEELTRQLEEEMEKQEEEGEYFG 317
T E++++ L +++EEEME Q + E
Sbjct: 169 TAFEQRMDGLGQEIEEEMESQSQALEAKA 197
>gnl|CDD|224346 COG1429, CobN, Cobalamin biosynthesis protein CobN and related
Mg-chelatases [Coenzyme metabolism].
Length = 1388
Score = 29.7 bits (67), Expect = 4.7
Identities = 11/57 (19%), Positives = 18/57 (31%), Gaps = 1/57 (1%)
Query: 218 TSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPV-DTTPSPSPSPKTPVTPYGK 273
+P + + V TA+S S + + PS VT G+
Sbjct: 1292 FAPASATPGAPESVGTTAVSTASSASSATVTGSDAGSGADSTGPSLGAAGSVTGAGE 1348
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and
repair].
Length = 1187
Score = 29.7 bits (67), Expect = 5.4
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 296 EELTRQLEEEMEKQEE 311
EE TR+LEE M+K EE
Sbjct: 1152 EERTRRLEEIMDKVEE 1167
>gnl|CDD|216406 pfam01275, Myelin_PLP, Myelin proteolipid protein (PLP or
lipophilin).
Length = 244
Score = 29.0 bits (65), Expect = 5.5
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 10/56 (17%)
Query: 427 GCFRCCLCNECLDGVPFTVDVDNKIYCVNDYHRMFAPKCAACGKGITPVEGTEETV 482
GCF CC+ CL GVP+ + I C FA CG G + GTE+ +
Sbjct: 1 GCFECCI--RCLGGVPYASLIAT-ILC-------FAGVALFCGCGHEALTGTEKLI 46
>gnl|CDD|215126 PLN02204, PLN02204, diacylglycerol kinase.
Length = 601
Score = 29.5 bits (66), Expect = 5.8
Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 77 PGPVSPSGSSKDSNSPRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPHLRSGSHSSV 136
P P SPS S S R S +V P + N ++ L ++ + R+ + S
Sbjct: 246 PYPPSPS-DSVHSVQSRGSS-SVHEPNETVHECDNEDHSPLLSDSVQEVMNFRTENGSCE 303
Query: 137 GSQDSKHSSP 146
G QDS P
Sbjct: 304 GDQDSDFPFP 313
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 29.3 bits (65), Expect = 6.2
Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 29/104 (27%)
Query: 185 PVYENIQELNKPPKPGPQVPVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKTATSLSV 244
P E + LN P P+ ++ T T P T ++
Sbjct: 98 PKQEEQKSLNISATPAPK--------------------QEQSQTTTESTTP---KTKVTT 134
Query: 245 TPNYQVSSPVDTTPSPSP-SP-----KTPVTPYGKNLLPYNVTP 282
P+ P+ +T S +P SP +T +TP ++L Y P
Sbjct: 135 PPSTNTPQPMQSTKSDTPQSPTIKQAQTDMTPKYEDLRAYYTKP 178
>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage [Cellular processes, DNA transformation].
Length = 410
Score = 29.3 bits (66), Expect = 6.2
Identities = 10/34 (29%), Positives = 14/34 (41%)
Query: 281 TPPRPMGPTEAERKIEELTRQLEEEMEKQEEEGE 314
P+ E R++EEL +L E E E
Sbjct: 138 EYPKTDEEKELLREVEELESRLATEPSPAPELEE 171
>gnl|CDD|225442 COG2888, COG2888, Predicted Zn-ribbon RNA-binding protein with a
function in translation [Translation, ribosomal
structure and biogenesis].
Length = 61
Score = 26.6 bits (59), Expect = 6.2
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 12/56 (21%)
Query: 459 RMFAPKCAACGKGITPVE----------GTEETVRVVSMDKDFHVDCYMCEDCGLQ 504
P C +CG+ I P E G E R K + Y C CG +
Sbjct: 6 MKDPPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLGNP--YRCPKCGFE 59
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein
SF3. The second Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. 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 = 61
Score = 26.7 bits (59), Expect = 6.3
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 13/60 (21%)
Query: 319 CHTCG------EKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYCEEDY 372
C CG EKVT G + YH +CF C G + + GR+YC+ +
Sbjct: 1 CVACGKTVYPIEKVTVEGTS-------YHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHH 53
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 29.4 bits (66), Expect = 7.0
Identities = 31/196 (15%), Positives = 63/196 (32%), Gaps = 6/196 (3%)
Query: 71 SNGSAKPGPVSPSGSSKDSNSPRASVATVPSPLYENVDYYNGRNAALTPPYYHQLPHLRS 130
S + S ++ +SP + SP E A+ PP +
Sbjct: 158 SPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASA 217
Query: 131 GSHSSVGSQDSKHSSPRGSYVSNDINAFQFDRKAQPQVPQGLKYIRDYPPYEAPPVYENI 190
S + + + + S S+ + + + P R P ++E
Sbjct: 218 SSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLP----RPAPITLPTRIWEAS 273
Query: 191 QELNKPPKPGPQVPVFGGEHRQMAIALTSPPVYSRANTVTS--KAVPVKTATSLSVTPNY 248
+PGP R + + +SP ++ + + + ++S S + +
Sbjct: 274 GWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSS 333
Query: 249 QVSSPVDTTPSPSPSP 264
+ S +P PSPS
Sbjct: 334 ESSRGAAVSPGPSPSR 349
>gnl|CDD|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle. The
second LIM domain of Prickle: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Two forms of prickles have
been identified; namely prickle 1 and prickle 2. Prickle
1 and prickle 2 are differentially expressed. While
prickle 1 is expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. 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 = 56
Score = 26.2 bits (58), Expect = 7.6
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 319 CHTCGEKVTGAGQACQAMGNLYHTNCFICCSCGRALRGKAFYNVHGRVYC 368
C C E + A + +A G +H F C C L G+ + GR YC
Sbjct: 3 CSACDE-IIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
>gnl|CDD|218881 pfam06070, Herpes_UL32, Herpesvirus large structural phosphoprotein
UL32. The large phosphorylated protein (UL32-like) of
herpes viruses is the polypeptide most frequently
reactive in immuno-blotting analyses with antisera when
compared with other viral proteins.
Length = 777
Score = 29.1 bits (65), Expect = 8.3
Identities = 42/252 (16%), Positives = 68/252 (26%), Gaps = 29/252 (11%)
Query: 46 GNIIASSKFATPKSVDNLPLADVYRSNGSAKPGPVSPSGSSKDSNSPRASVATVPSPLYE 105
G+ A S N L D+ R GS K V G+S P S + P+ E
Sbjct: 325 GSGFAPEPLIKTDSRSNDTLVDLGRGGGSLKLDSVDAPGTSSYLFEPGLSPS--PNSGKE 382
Query: 106 NVDYYNGRNAALTPPYYHQLPH-LRSGSHSSVGSQDSKHSSPRGSYVSNDINAFQFDRKA 164
N L +V +S + + A D ++
Sbjct: 383 MPGILTTENLDLPLASTDSTEMDPEDKRGGAVKINNSGILAWG---LKTPGLAVN-DERS 438
Query: 165 QPQVPQGLKYIRDYP-PYEAPPVYENIQELNKPPKPGPQVPVFGGEHRQMAIALTSPPVY 223
G+ + D P P + I ++ P K P
Sbjct: 439 IAVSSDGITDVLDPPSPLRLHSSDKVIDSVSPPSKRRVSAPASR-----------LDDAK 487
Query: 224 SRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPP 283
T T ++ + S + + D S P + +PP
Sbjct: 488 RPEVTATPES---SGSDSEGGASGREDETSSDAESVVSIKELRPRIGFINK------SPP 538
Query: 284 RPMGPTEAERKI 295
P P ++ R +
Sbjct: 539 -PKSPPKSRRTL 549
>gnl|CDD|225629 COG3087, FtsN, Cell division protein [Cell division and chromosome
partitioning].
Length = 264
Score = 28.7 bits (64), Expect = 8.6
Identities = 15/113 (13%), Positives = 24/113 (21%), Gaps = 11/113 (9%)
Query: 192 ELNKPPKPGPQVPVFGGEHRQMAIALTSP----PVYSRANTVTSKAVPVKTATSLSVTPN 247
+ + P E RQ+ + P ++ S
Sbjct: 85 AVKDAERLTP-------EQRQLLEQMEVDQKAQPTQLGEQPEQARIEEQPRTQSQKAQSQ 137
Query: 248 YQVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAERKIEELTR 300
P P P PV P P + + + TR
Sbjct: 138 ATTVQTQPVKPKPRPEKPQPVAPAPAPEPVEKAPKAEAAPPPKPKAEDAAETR 190
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 28.5 bits (64), Expect = 8.7
Identities = 22/109 (20%), Positives = 33/109 (30%), Gaps = 10/109 (9%)
Query: 165 QPQVPQGLKYIRDYPPYEAPPVYENIQ---------ELNKPPKPGPQVPVFGGEHRQMAI 215
P Q + R P ++ P Y + Q E PP+ P+ P
Sbjct: 74 APANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPR-PAQPAPQPVQQP 132
Query: 216 ALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSP 264
A P V+ + P + P Q P + +P P P
Sbjct: 133 AYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEP 181
>gnl|CDD|234101 TIGR03074, PQQ_membr_DH, membrane-bound PQQ-dependent
dehydrogenase, glucose/quinate/shikimate family. This
protein family has a phylogenetic distribution very
similar to that coenzyme PQQ biosynthesis enzymes, as
shown by partial phylogenetic profiling. Members of this
family have several predicted transmembrane helices in
the N-terminal region, and include the quinoprotein
glucose dehydrogenase (EC 1.1.5.2) of Escherichia coli
and the quinate/shikimate dehydrogenase of Acinetobacter
sp. ADP1 (EC 1.1.99.25). Sequences closely related
except for the absense of the N-terminal hydrophobic
region, scoring in the gray zone between the trusted and
noise cutoffs, include PQQ-dependent glycerol (EC
1.1.99.22) and and other polyol (sugar alcohol)
dehydrogenases.
Length = 764
Score = 28.8 bits (65), Expect = 8.8
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 18 VGAIESFLVEGTSRAPAPPPVDYKQYERGNIIASSKFA-----TPKSVDNLPLADVYRS 71
VGA+++ + + APA P D+ Y G A +++ P +V NL +A Y +
Sbjct: 116 VGALDTEVPATAAAAPAVPAGDWAAY--GRTQAGQRYSPLDQINPDNVGNLKVAWTYHT 172
>gnl|CDD|147601 pfam05505, Ebola_NP, Ebola nucleoprotein. This family consists of
Ebola and Marburg virus nucleoproteins. These proteins
are responsible for encapsidation of genomic RNA. It has
been found that nucleoprotein DNA vaccines can offer
protection from the virus.
Length = 717
Score = 28.8 bits (64), Expect = 9.0
Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 11/86 (12%)
Query: 26 VEGTSRAPAPPPVDYKQYERGNIIASSKFATPKSVDNLPLADVYRSNGSAKPGPVSPSGS 85
V+ T AP P PV Y+ + + I P P + + PS
Sbjct: 578 VDLTEVAP-PAPV-YRDEKEQDEIP-----HPAQNPQDPTGSIGNVDSDILRSNSKPSAP 630
Query: 86 SKDSNSPRASVATVPSPLYENVDYYN 111
+++ + P ++ ++YY+
Sbjct: 631 LEET---YMHLLRTQGP-FDAINYYH 652
>gnl|CDD|138835 PRK12279, PRK12279, 50S ribosomal protein L22/unknown domain fusion
protein; Provisional.
Length = 311
Score = 28.5 bits (63), Expect = 9.1
Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 15/66 (22%)
Query: 249 QVSSPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAE--RKIEELTRQLEEEM 306
+ + V+T PS V P + E ++ +++ + +E+
Sbjct: 134 EPKAKVETKKVAKPSKVE-------------VKPVEKDENVDPELLKREQQVLKVVEKTA 180
Query: 307 EKQEEE 312
++EEE
Sbjct: 181 SQKEEE 186
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse gyrase,
found in both archaeal and bacterial thermophiles. This
enzyme, a fusion of a type I topoisomerase domain and a
helicase domain, introduces positive supercoiling to
increase the melting temperature of DNA double strands.
Generally, these gyrases are encoded as a single
polypeptide. An exception was found in Methanopyrus
kandleri, where enzyme is split within the topoisomerase
domain, yielding a heterodimer of gene products
designated RgyB and RgyA [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1171
Score = 29.0 bits (65), Expect = 9.2
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 296 EELTRQLEEEMEKQEE 311
E+ TR+LEE M+K E
Sbjct: 1137 EDRTRELEEAMDKIER 1152
>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer
membranes [Cell envelope biogenesis, outer membrane].
Length = 244
Score = 28.2 bits (63), Expect = 9.3
Identities = 11/58 (18%), Positives = 17/58 (29%)
Query: 252 SPVDTTPSPSPSPKTPVTPYGKNLLPYNVTPPRPMGPTEAERKIEELTRQLEEEMEKQ 309
T P P P+ P P P P P E + ++ + + K
Sbjct: 48 VLEAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKP 105
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 29.0 bits (64), Expect = 9.4
Identities = 19/111 (17%), Positives = 32/111 (28%), Gaps = 9/111 (8%)
Query: 201 PQVPVFGGEHRQMAIALTSPPVYSRANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSP 260
P +P TS T +S + TS + + +SP +P
Sbjct: 453 PSLPPASTGPTVSTADPTSGTP---TGTTSSTLPEDTSPTSRTTSATPNATSPTPAVTTP 509
Query: 261 SPSPKTPV--TPYGKNLLPYNV----TPPRPMGPTEAERKIEELTRQLEEE 305
+ + T + P + T PT + Q+ EE
Sbjct: 510 NATSPTTQKTSDTPNATSPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEE 560
>gnl|CDD|165513 PHA03255, PHA03255, BDLF3; Provisional.
Length = 234
Score = 28.3 bits (62), Expect = 9.8
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 218 TSPPVYS----RANTVTSKAVPVKTATSLSVTPNYQVSSPVDTTPSPSPSP---KTPVTP 270
TS V S R+++ TS + AT+L+ T + + +S T + P+ + P
Sbjct: 120 TSTGVTSNVTTRSSSTTSATTRITNATTLAPTLSSKGTSNATKTTAELPTVPDERQPSLS 179
Query: 271 YG 272
YG
Sbjct: 180 YG 181
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 0.134 0.419
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,185,961
Number of extensions: 2564656
Number of successful extensions: 4629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4460
Number of HSP's successfully gapped: 495
Length of query: 543
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 441
Effective length of database: 6,413,494
Effective search space: 2828350854
Effective search space used: 2828350854
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: 61 (27.3 bits)