RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17538
(164 letters)
>gnl|CDD|185763 cd09240, BRO1_Alix, Protein-interacting, N-terminal, Bro1-like
domain of mammalian Alix and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), also called apoptosis-linked gene-2
interacting protein 1 (AIP1). It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4,
in the case of Alix. The Alix Bro1-like domain can also
bind human immunodeficiency virus type 1 (HIV-1)
nucleocapsid and Rab5-specfic GAP (RabGAP5, also known
as Rab-GAPLP). In addition to this Bro1-like domain,
Alix has a middle V-shaped (V) domain. The Alix V-domain
is a dimerization domain, and carries a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1) and the
apoptotic protein ALG-2.
Length = 346
Score = 240 bits (615), Expect = 3e-80
Identities = 89/166 (53%), Positives = 118/166 (71%), Gaps = 5/166 (3%)
Query: 2 AEFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKH 61
A F++VPLKK ++VD++KPL+ I + + E+ D E + +KLR AV + +KH
Sbjct: 1 ASFISVPLKKSSEVDLVKPLEKFIKNTYSSGEEQAD-YKEAIKELNKLRNNAVCRPLDKH 59
Query: 62 ESSLEVIYSYYDHLVSLESKIFPATVN---IPFRWKDAFNKGSLFGGRISLTVCSLAWER 118
ESSLE++ YYD L ++E K FP + + + F WKDAF+KGSLFGG L + SL +E+
Sbjct: 60 ESSLELLLRYYDQLCAIEPK-FPFSESQIQVTFTWKDAFDKGSLFGGSKKLALSSLGYEK 118
Query: 119 VCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKST 164
VCVLFNIAALQS IA Q+LDTDEGLKLAAK+ Q +AGIFN+LK T
Sbjct: 119 VCVLFNIAALQSQIAAEQNLDTDEGLKLAAKLFQQAAGIFNHLKET 164
>gnl|CDD|217365 pfam03097, BRO1, BRO1-like domain. This domain is found in a
number proteins including Rhophilin and BRO1. It is
known to have a role in endosomal targeting. ESCRT-III
subunit Snf7 binds to a conserved hydrophobic patch in
the BRO1 domain that is required for protein complex
formation and for the protein-sorting function of BRO1.
Length = 374
Score = 152 bits (385), Expect = 2e-45
Identities = 66/161 (40%), Positives = 89/161 (55%), Gaps = 9/161 (5%)
Query: 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHES 63
L +PLK+ +VD+ KPLK+ I + D + + L +KLR AV ES
Sbjct: 1 LLPLPLKETKEVDLSKPLKDYILSTYGEDPSLFE---DDLAELNKLRQDAVNVPGSPDES 57
Query: 64 SLEVIYSYYDHLVSLESKIFPATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLF 123
LE++Y YY L +LE + + + F W DAF+ GS +T SLA+E+ VLF
Sbjct: 58 GLELLYRYYGQLEALEKRFPDDQLGVEFTWYDAFDTGS------PVTQSSLAFEKASVLF 111
Query: 124 NIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKST 164
N+AAL S IA +Q+ DTDEGLK A Q +AG F YLK
Sbjct: 112 NLAALYSQIAASQNRDTDEGLKAACDYFQKAAGAFEYLKEN 152
>gnl|CDD|214990 smart01041, BRO1, BRO1-like domain. This domain is found in a
number proteins including Rhophilin and BRO1. It is
known to have a role in endosomal targeting. ESCRT-III
subunit Snf7 binds to a conserved hydrophobic patch in
the BRO1 domain that is required for protein complex
formation and for the protein-sorting function of BRO1.
Length = 381
Score = 134 bits (338), Expect = 3e-38
Identities = 60/163 (36%), Positives = 89/163 (54%), Gaps = 13/163 (7%)
Query: 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHES 63
+ +PLK+ +VD KPLK+ I + D+ + +++ ++LR AA + ES
Sbjct: 1 LIPLPLKETKEVDFSKPLKDYIKETYSEDSSSYE---DEIAELNRLRQAARTP--SRDES 55
Query: 64 SLEVIYSYYDHLVSLESKIFPAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCV 121
LE++ YY L +LE + P + + F W D+ + G T SLA+E+ V
Sbjct: 56 GLELLLKYYGQLEALELRFPPPEGQLKLSFTWYDSLDTGV------PSTQSSLAFEKASV 109
Query: 122 LFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKST 164
LFN+ AL S IA Q+ DT+EGLK A K Q +AG+FNYLK
Sbjct: 110 LFNLGALYSQIAAEQNRDTEEGLKEACKAFQQAAGVFNYLKEN 152
>gnl|CDD|185764 cd09241, BRO1_ScRim20-like, Protein-interacting, N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Rim20 and
related proteins. This family contains the N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Rim20 (also
known as PalA) and related proteins. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox,
Saccharomyces cerevisiae Bro1, Ustilago maydis Rim23
(also known as PalC), and related domains. Alix, HD-PTP,
Brox, Bro1, Rim20, and Rim23, interact with the ESCRT
(Endosomal Sorting Complexes Required for Transport)
system. Rim20 and Rim23 participate in the response to
the external pH via the Rim101 pathway. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: Snf7 in the case of Rim20. RIM20, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain is a dimerization domain that
also contains a binding site for the retroviral late
assembly (L) domain YPXnL motif, which is partially
conserved in the V-domain superfamily. Rim20 localizes
to endosomes under alkaline pH conditions. By binding
Snf7, it may bring the protease Rim13 (a YPxL-containing
transcription factor) into proximity with Rim101, and
thus aid in the proteolytic activation of the latter.
Rim20 and other intermediates in the Rim101 pathway play
roles in the pathogenesis of fungal corneal infection
during Candida albicans keratitis.
Length = 355
Score = 103 bits (259), Expect = 5e-27
Identities = 52/161 (32%), Positives = 78/161 (48%), Gaps = 11/161 (6%)
Query: 3 EFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHE 62
L++P K+ VD+ L+N I+ + + + L KLR A+ E
Sbjct: 1 NLLSIPFKRTLPVDLKDALRNYISNHYFQTPSSFE---DDLAEIDKLRNDAINP--EPSV 55
Query: 63 SSLEVIYSYYDHLVSLESKIFPATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVL 122
+ L ++ YY LV L K FP + F W G G +SL+ SL +ER +L
Sbjct: 56 NGLSLLKEYYAQLVVLSKK-FPD-DQLEFTWYPTL--GYKSSGPVSLS--SLKFERANIL 109
Query: 123 FNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKS 163
+N+ AL S +A +++ TDEGLK A Q+SAG F Y+
Sbjct: 110 YNLGALYSQLALSENRYTDEGLKRACSYFQASAGCFEYILQ 150
>gnl|CDD|185765 cd09242, BRO1_ScBro1_like, Protein-interacting, N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Bro1 and
related proteins. This family contains the N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Bro1 and
related proteins. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
proteins Rhophilin-1 and -2, Brox, Saccharomyces
cerevisiae Rim20 (also known as PalA), Ustilago maydis
Rim23 (also known as PalC), and related domains. Alix,
HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the
ESCRT (Endosomal Sorting Complexes Required for
Transport) system. Bro1 participates in endosomal
trafficking. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. Bro1-like domains bind components
of the ESCRT-III complex: Snf7 in the case of Bro1. Snf7
binds to a conserved hydrophobic patch on the middle of
the concave side of the Bro1 domain. RIM20, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain contains a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. The
Alix V-domain is also a dimerization domain. The
C-terminal portion (V-domain and proline rich-region) of
Bro1 interacts with Doa4, a protease that
deubiquitinates integral membrane proteins sorted into
the lumenal vesicles of late-endosomal multivesicular
bodies. It interacts with a YPxL motif in the Doa4
catalytic domain to stimulate its deubiquitination
activity.
Length = 348
Score = 97.4 bits (243), Expect = 9e-25
Identities = 49/161 (30%), Positives = 76/161 (47%), Gaps = 13/161 (8%)
Query: 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHES 63
+++PLK +VD KPL + + + + + E++ F +LR A V E+
Sbjct: 1 LISLPLKDTEEVDWKKPLSSYLKRSYGSSTFYYE---EEIAEFDRLRQDAN-GVLAD-ET 55
Query: 64 SLEVIYSYYDHLVSLESKIFPATV--NIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCV 121
+++Y YY L LE + + F W DAF K SLA+E+ V
Sbjct: 56 GRDLLYKYYGQLELLELRFPFNNKELKVDFTWYDAFYKSKKV------KQHSLAFEKASV 109
Query: 122 LFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLK 162
LFNI AL S +A + + ++ LK A LQ +AG F Y+
Sbjct: 110 LFNIGALLSQLAAEKYREDEDDLKEAITNLQQAAGCFQYIN 150
>gnl|CDD|185769 cd09246, BRO1_Alix_like_1, Protein-interacting, N-terminal,
Bro1-like domain of an Uncharacterized family of the
BRO1_Alix_like superfamily. This domain family is
comprised of uncharacterized proteins. It belongs to the
BRO1_Alix_like superfamily which includes the Bro1-like
domains of mammalian Alix (apoptosis-linked gene-2
interacting protein X), His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and
Rim23 interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP and Bro1 function in
endosomal trafficking, with HD-PTP having additional
functions in cell migration. Rim20 and Rim23 play roles
in the response to the external pH via the Rim101
pathway. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. Bro1-like domains bind components
of the ESCRT-III complex: CHMP4 (in the case of Alix,
Brox and HD-PTP) and Snf7 (in the case of yeast Bro1 and
Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and
Rhophilin can bind human immunodeficiency virus type 1
(HIV-1) nucleocapsid. In addition to this Bro1-like
domain, Alix, Bro1, Rim20, HD_PTP, and proteins
belonging to this uncharacterized family, also have a
V-shaped (V) domain. The Alix V-domain is a dimerization
domain, and contains a binding site for the retroviral
late assembly (L) domain YPXnL motif, which is partially
conserved in the BRO1_Alix_like superfamily. Many
members of this superfamily also have a proline-rich
region (PRR), a protein interaction domain.
Length = 353
Score = 89.0 bits (221), Expect = 1e-21
Identities = 48/163 (29%), Positives = 80/163 (49%), Gaps = 15/163 (9%)
Query: 5 LAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESS 64
L++ KK VD++ PL+ I+ + + + L +LR+ + EKH +S
Sbjct: 2 LSIHRKKTETVDLVSPLRAYISETYSER--EAQDAEDDLAELQQLRSEVR-TLQEKHAAS 58
Query: 65 LEVIYSYYDHLVSLESKIFPAT-----VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERV 119
E++ YY L ++ES+ FP + + F W DAF + T ++ +E+
Sbjct: 59 RELLLRYYRALCAVESR-FPISEESGHARVSFSWYDAF-RPHRKA-----TQANVHFEKA 111
Query: 120 CVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLK 162
VLFN+ AL S + Q T EG+K A Q++AG F +L+
Sbjct: 112 AVLFNLGALSSQLGLQQDRTTAEGIKQACHAFQAAAGAFAHLR 154
>gnl|CDD|185761 cd09034, BRO1_Alix_like, Protein-interacting Bro1-like domain of
mammalian Alix and related domains. This superfamily
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also
known as PalA) from Saccharomyces cerevisiae, and
related domains. Alix, HD-PTP, Brox, Bro1 and Rim20
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1),
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP functions in cell
migration and endosomal trafficking, Bro1 in endosomal
trafficking, and Rim20 in the response to the external
pH via the Rim101 pathway. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4
(in the case of Alix, HD-PTP, and Brox) and Snf7 (in the
case of yeast Bro1, and Rim20). The single domain
protein human Brox, and the isolated Bro1-like domains
of Alix, HD-PTP and Rhophilin can bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V)
domain, which in the case of Alix, has been shown to be
a dimerization domain and to contain a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in this superfamily. Alix,
HD-PTP and Bro1 also have a proline-rich region (PRR);
the Alix PRR binds multiple partners. Rhophilin-1, and
-2, in addition to this Bro1-like domain, have an
N-terminal Rho-binding domain and a C-terminal PDZ
(PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded
by the PTPN23 gene, a tumor suppressor gene candidate
frequently absent in human kidney, breast, lung, and
cervical tumors. This protein has a C-terminal,
catalytically inactive tyrosine phosphatase domain.
Length = 345
Score = 87.8 bits (218), Expect = 3e-21
Identities = 54/169 (31%), Positives = 81/169 (47%), Gaps = 20/169 (11%)
Query: 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHES 63
F+ +PLKK +VD+ PL I + + + SKLR V E++
Sbjct: 1 FIGLPLKKTKEVDVKVPLSKFIPKNYGELEATAV--EDLIEKLSKLRNNIV---TEQNND 55
Query: 64 S-----LEVIYSYYDHLVSLESKIFPA--TVNIPFRWKDAFNKGSLFGGRISLTVCSLAW 116
+ LE + Y +L+ LE K+ N+ F W D+F+ + S T SL +
Sbjct: 56 TTCENLLEALKEYLPYLLGLEKKLPFQKLRDNVEFTWTDSFDTK-----KESAT--SLRY 108
Query: 117 ERVCVLFNIAALQSAIAQAQ-SLDTDEGLKLAAKMLQSSAGIFNYLKST 164
E + +LFN+AAL S +A + ++E LK A K LQ +AG F YLK
Sbjct: 109 ELLSILFNLAALASQLANEKLITGSEEDLKQAIKSLQKAAGYFEYLKEH 157
>gnl|CDD|185762 cd09239, BRO1_HD-PTP_like, Protein-interacting, N-terminal,
Bro1-like domain of mammalian His-Domain type N23
protein tyrosine phosphatase and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian His-Domain type N23 protein tyrosine
phosphatase (HD-PTP) and related domains. It belongs to
the BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), RhoA-binding proteins
Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains. Alix,
also known as apoptosis-linked gene-2 interacting
protein 1 (AIP1), HD-PTP, Brox, Bro1, Rim20, and Rim23,
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. HD-PTP participates in
cell migration and endosomal trafficking. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of HD-PTP. The Bro1-like
domain of HD-PTP can also bind human immunodeficiency
virus type 1 (HIV-1) nucleocapsid. HD-PTP, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain contains a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the V-domain
superfamily. HD-PTP is encoded by the PTPN23 gene, a
tumor suppressor gene candidate frequently absent in
human kidney, breast, lung, and cervical tumors. This
family also contains Drosophila Myopic which promotes
epidermal growth factor receptor (EGFR) signaling, and
Caenorhabditis elegans (enhancer of glp-1) EGO-2 which
promotes Notch signaling.
Length = 361
Score = 77.5 bits (191), Expect = 2e-17
Identities = 45/163 (27%), Positives = 71/163 (43%), Gaps = 17/163 (10%)
Query: 5 LAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESS 64
L + LK + LK I + E ++ +E+L +LR AV +
Sbjct: 9 LWLQLKSSGEFTFQPALKKYILENY---GEDPELYSEELKSLEQLRQEAV--NPPRDFEG 63
Query: 65 LEVIYSYYDHLVSLESKIFPAT----VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVC 120
V+ YY L L+S+ FP +PF W D F+ + T + +E
Sbjct: 64 CSVLKRYYGQLHLLQSR-FPMGAGQEAAVPFTWTDIFSGSEV-------THEDIKFEEAS 115
Query: 121 VLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKS 163
VL+NI AL S + + D++EG+K+A Q +A F YL+
Sbjct: 116 VLYNIGALHSQLGASDKRDSEEGMKVACTHFQCAAWAFAYLRE 158
>gnl|CDD|185767 cd09244, BRO1_Rhophilin, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin and related domains.
This family contains the Bro1-like domain of
RhoA-binding proteins, Rhophilin-1 and -2, and related
domains. It belongs to the BRO1_Alix_like superfamily
which also includes the Bro1-like domains of mammalian
Alix (apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20
(also known as PalA) from Saccharomyces cerevisiae,
Ustilago maydis Rim23 (also known as PalC), and related
domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound
RhoA. Bro1-like domains are boomerang-shaped, and part
of the domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 and -2, contain an N-terminal Rho-binding
domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. Their PDZ domains have limited homology.
Rhophilin-1 and -2 have different activities. The
Drosophila knockout of Rhophilin-1 is embryonic lethal,
suggesting an essential role in embryonic development.
Roles of Rhophilin-2 may include limiting stress fiber
formation or increasing the turnover of F-actin in the
absence of high levels of RhoA signaling activity. The
isolated Bro1-like domain of Rhophilin-1 binds human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. This
family lacks the V-shaped (V) domain found in many
members of the BRO1_Alix _like superfamily.
Length = 350
Score = 76.6 bits (189), Expect = 4e-17
Identities = 49/160 (30%), Positives = 82/160 (51%), Gaps = 18/160 (11%)
Query: 9 LKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVI 68
LK+ ++D ++P K+ I + D + +++ F+ LR A + + E+ +E++
Sbjct: 6 LKETKEIDFMEPFKDFILEHYSEDPSLYE---DEIADFTDLRQAM--RTPSRDEAGIELL 60
Query: 69 YSYYDHLVSLESKIFPAT--VNIPFRWKDAFNKGSLFGGRISLTVC--SLAWERVCVLFN 124
+ YY+ L +E + FP + I F W D SL G + S+A+E+ VLFN
Sbjct: 61 FEYYNQLYFVERRFFPPDRSLGIYFHWYD-----SLTG----VPSVQRSVAFEKASVLFN 111
Query: 125 IAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKST 164
I AL + I Q T+EG++ A Q +AG FNYL+
Sbjct: 112 IGALYTQIGAKQDRTTEEGIEAAVDAFQRAAGAFNYLREN 151
>gnl|CDD|185772 cd09249, BRO1_Rhophilin_2, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-2. This subfamily
contains the Bro1-like domain of RhoA-binding protein,
Rhophilin-2. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-1, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-2, binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-2 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. Roles for Rhophilin-2 may include limiting
stress fiber formation or increasing the turnover of
F-actin in the absence of high levels of RhoA signaling
activity. Rhophilin-2 lacks the V-shaped (V) domain
found in many members of the BRO1_Alix_like superfamily.
Length = 385
Score = 72.6 bits (178), Expect = 1e-15
Identities = 52/161 (32%), Positives = 80/161 (49%), Gaps = 20/161 (12%)
Query: 9 LKKPTDVDIIKPLKNLIALQFPND-NEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEV 67
LK+ DVD PLK+ I + D +E D + + ++L RT + + E+ +E+
Sbjct: 6 LKETKDVDFSVPLKDFILEHYSEDGSEYEDEIADLMDLRQACRTPS------RDEAGVEL 59
Query: 68 IYSYYDHLVSLESKIFPAT--VNIPFRWKDAFNKGSLFGGRISLTVC--SLAWERVCVLF 123
+ SY+ L LE++ FP T + I F W D+F + V +L E+ +LF
Sbjct: 60 LMSYFSQLGFLENRFFPPTRQMGILFTWYDSFT---------GVPVSQQNLLLEKASILF 110
Query: 124 NIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKST 164
NI AL + I + T GL+ A Q +AG+ NYLK T
Sbjct: 111 NIGALYTQIGTRCNRQTQAGLESAVDAFQRAAGVLNYLKET 151
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-1 binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 70.7 bits (173), Expect = 5e-15
Identities = 49/157 (31%), Positives = 80/157 (50%), Gaps = 16/157 (10%)
Query: 9 LKKPTDVDIIKPLKNLIALQFPNDNEKLDI-LNEKLNLFSKLRTAAVWKVFEKHESSLEV 67
LK+ ++D+ PLK LI+ F D + + E +L +RT + + E+ LE+
Sbjct: 6 LKETKELDLPTPLKELISEHFGEDGTSYEAEIRELEDLRQAMRTPS------RSEAGLEL 59
Query: 68 IYSYYDHLVSLESKIFP--ATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNI 125
+ +YY+ L L+++ FP ++ + F W D SL G + +LA+E+ VLFNI
Sbjct: 60 LMAYYNQLCFLDARFFPPAKSLGLFFHWYD-----SLTG--VPAQQRALAFEKGSVLFNI 112
Query: 126 AALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLK 162
AL + I Q EG + A Q +AG F+ L+
Sbjct: 113 GALHTQIGARQDRSCTEGTRRAIDAFQRAAGAFSLLR 149
>gnl|CDD|185770 cd09247, BRO1_Alix_like_2, Protein-interacting Bro1-like domain of
an Uncharacterized family of the BRO1_Alix_like
superfamily. This domain family is comprised of
uncharacterized proteins. It belongs to the
BRO1_Alix_like superfamily which includes the Bro1-like
domains of mammalian Alix (apoptosis-linked gene-2
interacting protein X), His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and
Rim23 interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP and Bro1 function in
endosomal trafficking, with HD-PTP having additional
functions in cell migration. Rim20 and Rim23 play roles
in the response to the external pH via the Rim101
pathway. Bro1-like domains are boomerang-shaped, and
part of the domain is a tetratricopeptide repeat
(TPR)-like structure. These domains bind components of
the ESCRT-III complex: CHMP4 (in the case of Alix, Brox
and HD-PTP) and Snf7 (in the case of yeast Bro1 and
Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and
Rhophilin can bind human immunodeficiency virus type 1
(HIV-1) nucleocapsid. This family lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_like
superfamily.
Length = 346
Score = 32.0 bits (73), Expect = 0.10
Identities = 26/99 (26%), Positives = 36/99 (36%), Gaps = 7/99 (7%)
Query: 65 LEVIYSYYDHLVSLESKIFPATVNIP--FRWKDAFNKGSLFGGRISLTVCSLAWERVCVL 122
L + Y L +L + +N FRW G + SL +E VL
Sbjct: 60 LPYLEGYLPALENLVNHRDKVQLNEQLSFRWTSGLGSS---KGPKAFQSDSLRFELGMVL 116
Query: 123 FNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161
F A A D K AA L+ +AG+F +L
Sbjct: 117 FLYGAALRERASEVLPTED--FKEAATHLRRAAGVFEFL 153
>gnl|CDD|185766 cd09243, BRO1_Brox_like, Protein-interacting Bro1-like domain of
human Brox1 and related proteins. This family contains
the Bro1-like domain of a single-domain protein, human
Brox, and related domains. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1
and Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of Brox. Human Brox can bind
to human immunodeficiency virus type 1 (HIV-1)
nucleocapsid. In addition to a Bro1-like domain, Brox
also has a C-terminal thioester-linkage site for
isoprenoid lipids (CaaX motif). This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 353
Score = 31.5 bits (72), Expect = 0.14
Identities = 28/88 (31%), Positives = 44/88 (50%), Gaps = 14/88 (15%)
Query: 79 ESKIFPATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAAL----QSAIAQ 134
ESK+ I F+W D SL G S+ ++ +E +LFN+A S +A
Sbjct: 78 ESKLRYL---INFKWTD-----SLLGNEPSVQQDAI-FELASMLFNVALWYTKHASKLAG 128
Query: 135 AQSLDTDEGLKLAAKMLQSSAGIFNYLK 162
+ + DE K K L+++AGIF ++K
Sbjct: 129 KEDITEDEA-KDVHKSLRTAAGIFQFVK 155
>gnl|CDD|212581 cd11708, DHR2_DOCK5, Dock Homology Region 2, a GEF domain, of Class
A Dedicator of Cytokinesis 5. Dock5 is an atypical
guanine nucleotide exchange factor (GEF) that lacks the
conventional Dbl homology (DH) domain. As a GEF, it
activates small GTPases by exchanging bound GDP for free
GTP. It functions upstream of Rac1 to regulate
osteoclast function. DOCK proteins are divided into four
classes (A-D) based on sequence similarity and domain
architecture; class A includes Dock1, 2 and 5. All DOCKs
contain two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock5, which
contains the catalytic GEF activity for Rac and/or
Cdc42. Class A DOCKs, like Dock5, are specific GEFs for
Rac and they contain an SH3 domain at the N-terminal
region and a PxxP motif at the C-terminus.
Length = 400
Score = 30.7 bits (69), Expect = 0.32
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 10 KKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKL 43
+ P D + I+ LK LIALQ P E + I EKL
Sbjct: 341 EHPEDQEKIELLKQLIALQMPLLAEGIRIHGEKL 374
>gnl|CDD|185768 cd09245, BRO1_UmRIM23-like, Protein-interacting, Bro1-like domain
of Ustilago maydis Rim23 (PalC), and related domains.
This family contains the Bro1-like domain of Ustilago
maydis Rim23 (also known as PalC), and related proteins.
It belongs to the BRO1_Alix_like superfamily which
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, and related
domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Rim20 and Rim23
participate in the response to the external pH via the
Rim101 pathway. Through its Bro1-like domain, Rim23
allows the interaction between the endosomal and plasma
membrane complexes. Bro1-like domains are
boomerang-shape, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure.
Intermediates in the Rim101 pathway may play roles in
the pathogenesis of fungal corneal infection during
Candida albicans keratitis. This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 413
Score = 30.8 bits (70), Expect = 0.32
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 109 LTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161
+ +LA + L +I+ A DE LK A K+L +AGIF+YL
Sbjct: 125 YALSNLARSILAPLGA-YETDRSISDASRKQRDERLKAATKLLCKAAGIFDYL 176
>gnl|CDD|200432 TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.
This clade of aminotransferases is a member of the
pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family
is named after the instance in Leptospira interrogans
serovar Lai, str. 56601, where it is the 31st gene in
the 91-gene lipopolysaccharide biosynthesis locus.
Members of this family are generally found within a
subcluster of seven or more genes including an
epimerase/dehydratase, four genes homologous to the
elements of the neuraminic (sialic) acid biosynthesis
cluster (NeuABCD) and a nucleotidyl transferase.
Together it is very likely that these enzymes direct the
biosynthesis of a nine-carbon sugar analogous to
CMP-neuraminic acid. These seven genes form the core of
the cassette, although they are often accompanied by
additional genes that may further modify the product
sugar.
Length = 359
Score = 29.4 bits (67), Expect = 0.69
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 9/64 (14%)
Query: 24 LIALQFPNDNEKLDILNEKLNLFSKLRTAAVWK------VFEKHESS-LEVIYSYYDHLV 76
L AL + ++ ++L E LN + ++T +W ++ L V + + L+
Sbjct: 297 LNALLLDSKLDRDELL-EALNE-NGIQTRPLWTLMHELPMYRDCPRDDLPVAENLEERLI 354
Query: 77 SLES 80
+L S
Sbjct: 355 NLPS 358
>gnl|CDD|212580 cd11707, DHR2_DOCK1, Dock Homology Region 2, a GEF domain, of Class
A Dedicator of Cytokinesis 1. Dock1, also called
Dock180, is an atypical guanine nucleotide exchange
factor (GEF) that lacks the conventional Dbl homology
(DH) domain. As a GEF, it activates small GTPases by
exchanging bound GDP for free GTP. Dock1 interacts with
the scaffold protein Elmo and the resulting complex
functions upstream of Rac in many biological events
including phagocytosis of apoptotic cells, cell
migration and invasion. In the nervous system, it
mediates attractive responses to netrin-1 and thus,
plays a role in axon outgrowth and pathfinding. DOCK
proteins are divided into four classes (A-D) based on
sequence similarity and domain architecture; class A
includes Dock1, 2 and 5. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate. This
alignment model represents the DHR-2 domain of Dock1,
which contains the catalytic GEF activity for Rac and/or
Cdc42. Class A DOCKs, like Dock1, are specific GEFs for
Rac and they contain an SH3 domain at the N-terminal
region and a PxxP motif at the C-terminus.
Length = 400
Score = 28.5 bits (63), Expect = 1.9
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 9 LKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKL 43
+ P D + I+ LK+LIA Q P E + I EK+
Sbjct: 340 QEHPEDHEKIEKLKDLIAWQIPFLAEGIRIHGEKV 374
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 28.2 bits (63), Expect = 2.5
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 46 FSKLRTAAVWKVFEKHESSLEVIY-SYYDHLVSLESKIFPATVNI 89
F RT A +V + +VI+ +++ HLV L ++F A V I
Sbjct: 1071 FDDERTRATLEVLRELSKRTQVIFFTHHRHLVPLAKEVFGAAVQI 1115
>gnl|CDD|112355 pfam03532, OMS28_porin, OMS28 porin.
Length = 253
Score = 27.4 bits (60), Expect = 3.0
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 14 DVDIIKPLKNLIALQFPNDNEKL---DILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYS 70
+ +I+KP N++ DN+KL D +N+ L+ +K+ K+ ESSLE++ S
Sbjct: 26 NANILKPQSNVLEHSDQKDNKKLDQKDQVNQALDTINKVTEDVSSKLEGVRESSLELVES 85
>gnl|CDD|203820 pfam07956, DUF1690, Protein of Unknown function (DUF1690). Family
of uncharacterized fungal proteins.
Length = 142
Score = 27.1 bits (60), Expect = 3.3
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 33 NEKLDILNEKLNLFSKLRTAAVWKVFEKHES 63
NEK++ L EKL FSKL K ++ E
Sbjct: 81 NEKIESLTEKLEEFSKLEEKEKSKKLKEVED 111
>gnl|CDD|211385 cd11299, O-FucT_plant, GDP-fucose protein O-fucosyltransferase,
plant specific subfamily. Some members of this
plant-specific family of O-fucosyltransferases have been
annotated as auxin-independent growth promotors. The
function of the protein seems unclear.
O-fucosyltransferase-like proteins are GDP-fucose
dependent enzymes with similarities to the family 1
glycosyltransferases (GT1). They are soluble ER proteins
that may be proteolytically cleaved from a
membrane-associated preprotein, and are involved in the
O-fucosylation of protein substrates, the core
fucosylation of growth factor receptors, and other
processes.
Length = 290
Score = 27.1 bits (61), Expect = 4.3
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 21/70 (30%)
Query: 18 IKPLKNLIALQFPNDNEKLDILN-EKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLV 76
+ PL+++ FPN K + E+L FS H S L + D++V
Sbjct: 220 LDPLRSI----FPNLYTKETLATAEELAPFSG------------HSSRLAAL----DYIV 259
Query: 77 SLESKIFPAT 86
LES +F T
Sbjct: 260 CLESDVFVPT 269
>gnl|CDD|227623 COG5307, COG5307, SEC7 domain proteins [General function prediction
only].
Length = 1024
Score = 26.6 bits (59), Expect = 8.2
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 16 DIIKPLKNLIALQFPNDNEKLDILNEKLNLFSK-------LRTAAVWKVFEKHESSLEV 67
D++ LK I L F + EKL+IL KL L + L A+ + E + ++V
Sbjct: 959 DLLAALKEFIEL-FNSIFEKLEILAGKLILLHQCLNNCDQLGLGAIETLEEILWNKIDV 1016
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.134 0.389
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,194,951
Number of extensions: 726741
Number of successful extensions: 686
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 29
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.0 bits)