RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5867
(287 letters)
>gnl|CDD|176484 cd08366, APC10, APC10 subunit of the anaphase-promoting complex
(APC) that mediates substrate ubiquitination. This
model represents the single domain protein APC10, a
subunit of the anaphase-promoting complex (APC), which
is a multi-subunit E3 ubiquitin ligase. E3 ubiquitin
ligases mediate substrate ubiquitination (or
ubiquitylation), a vital component of the ubiquitin-26S
proteasome pathway for selective proteolytic
degradation. The APC (also known as the cyclosome), is a
cell cycle-regulated E3 ubiquitin ligase that controls
important transitions in mitosis and the G1 phase by
ubiquitinating regulatory proteins, thereby targeting
them for degradation. In mitosis, the APC initiates
sister chromatid separation by ubiquitinating the
anaphase inhibitor securin and triggers exit from
mitosis by ubiquitinating cyclin B. The C-terminus of
APC10 binds to CDC27/APC3, an APC subunit that contains
multiple tetratrico peptide repeats. APC10 domains are
homologous to the DOC1 domains present in the HECT
(Homologous to the E6-AP Carboxyl Terminus) E3 ubiquitin
ligase protein, and the Cullin-RING (Really Interesting
New Gene) E3 ubiquitin ligase complex. The APC10/DOC1
domain forms a beta-sandwich structure that is related
in architecture to the galactose-binding domain-like
fold; their sequences are quite dissimilar, however, and
are not included here.
Length = 139
Score = 244 bits (624), Expect = 2e-82
Identities = 91/162 (56%), Positives = 116/162 (71%), Gaps = 24/162 (14%)
Query: 21 REVGSQAIWSLSSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICIYRQ 80
RE+GS A+WSLSS KPG GVDQLRDD +DTYWQSDG PHL+N+QF +KT + + +Y
Sbjct: 1 REIGSLAVWSLSSAKPGNGVDQLRDDSLDTYWQSDGPQPHLINIQFSKKTDISAVALY-- 58
Query: 81 LPHLVNVQFRRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEPSGW 140
DYKLDESYTPS++S+RAGT+ +DLQE+ V+L EP+GW
Sbjct: 59 ---------------------LDYKLDESYTPSKISIRAGTSPHDLQEVRTVELEEPNGW 97
Query: 141 VKIPIKDIH-DKPIRTYMIQIAVMSNHQNGRDTHMRQIKVYS 181
V IP++D KP+RT+ +QIA++SNHQNGRDTH+RQIKVY
Sbjct: 98 VHIPLEDNRDGKPLRTFFLQIAILSNHQNGRDTHIRQIKVYG 139
Score = 116 bits (294), Expect = 1e-32
Identities = 42/70 (60%), Positives = 58/70 (82%), Gaps = 1/70 (1%)
Query: 197 QQVSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIKDIH-DKPIRTYMIQIAVMSNHQNGRD 255
++S+RAGT+ +DLQE+ V+L EP+GWV IP++D KP+RT+ +QIA++SNHQNGRD
Sbjct: 70 SKISIRAGTSPHDLQEVRTVELEEPNGWVHIPLEDNRDGKPLRTFFLQIAILSNHQNGRD 129
Query: 256 THMRQIKVYS 265
TH+RQIKVY
Sbjct: 130 THIRQIKVYG 139
>gnl|CDD|217458 pfam03256, APC10, Anaphase-promoting complex, subunit 10 (APC10).
Length = 175
Score = 231 bits (590), Expect = 7e-77
Identities = 96/184 (52%), Positives = 125/184 (67%), Gaps = 24/184 (13%)
Query: 8 EKDPVMEERLGRIREVGSQAIWSLSSCKPGFGVD-QLRDDCMDTYWQSDGQLPHLVNVQF 66
DP E G +RE+G A+WSLSSCK G GVD LRDD +DTYWQSDG PHLVN+QF
Sbjct: 9 FGDPSQRELAGFMREIGGLAVWSLSSCKHGNGVDHLLRDDNLDTYWQSDGSQPHLVNIQF 68
Query: 67 RRKTTVQDICIYRQLPHLVNVQFRRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDL 126
+KT + + IY DYKLDESYTPS++ VRAGT FNDL
Sbjct: 69 SKKTDISYVAIY-----------------------LDYKLDESYTPSKIRVRAGTGFNDL 105
Query: 127 QEIEVVDLNEPSGWVKIPIKDIHDKPIRTYMIQIAVMSNHQNGRDTHMRQIKVYSPVQQH 186
QE++ +++ EP+GWV IP++D +KP+RT+M+QIAV++NHQNGRDTH+RQI++Y PV ++
Sbjct: 106 QEVKTLEVGEPTGWVHIPLRDGREKPLRTFMLQIAVLANHQNGRDTHVRQIRIYGPVIEY 165
Query: 187 PSTM 190
Sbjct: 166 SEVP 169
Score = 119 bits (300), Expect = 3e-33
Identities = 43/78 (55%), Positives = 64/78 (82%)
Query: 197 QQVSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIKDIHDKPIRTYMIQIAVMSNHQNGRDT 256
++ VRAGT FNDLQE++ +++ EP+GWV IP++D +KP+RT+M+QIAV++NHQNGRDT
Sbjct: 92 SKIRVRAGTGFNDLQEVKTLEVGEPTGWVHIPLRDGREKPLRTFMLQIAVLANHQNGRDT 151
Query: 257 HMRQIKVYSPVQQHPSTM 274
H+RQI++Y PV ++
Sbjct: 152 HVRQIRIYGPVIEYSEVP 169
>gnl|CDD|227485 COG5156, DOC1, Anaphase-promoting complex (APC), subunit 10 [Cell
division and chromosome partitioning / Posttranslational
modification, protein turnover, chaperones].
Length = 189
Score = 130 bits (327), Expect = 4e-37
Identities = 64/193 (33%), Positives = 95/193 (49%), Gaps = 27/193 (13%)
Query: 19 RIREVGSQAIWSLSSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICIY 78
R+ V A W LSS K G + +L DD MDTYWQSDG PH + + F ++ +Q + ++
Sbjct: 22 RMINVTHLAEWRLSSFKRGHPLRELLDDNMDTYWQSDGVQPHSIQISFDKRRYIQSVQLF 81
Query: 79 RQLPHLVNVQFRRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEPS 138
+ DESYTPS++ VRAG D++EI V++ EP
Sbjct: 82 LS-----------------------FTQDESYTPSKIGVRAGLTREDVREISSVEVVEPE 118
Query: 139 GWVKIPIKD-IHDKPIRTYMIQIAVMSNHQNGRDTHMRQIKVYSPVQQHPSTMFTTVECQ 197
GWV + + D D ++ I + + SNHQ G+D+H+R IK+Y P + + +E
Sbjct: 119 GWVTLSVADKREDDLLKCIYILVVINSNHQEGKDSHVRHIKIYEPSTEEI---YYKIEWA 175
Query: 198 QVSVRAGTNFNDL 210
Q F D
Sbjct: 176 QTLPETNNVFQDA 188
Score = 68.5 bits (167), Expect = 6e-14
Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 199 VSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIKD-IHDKPIRTYMIQIAVMSNHQNGRDTH 257
+ VRAG D++EI V++ EP GWV + + D D ++ I + + SNHQ G+D+H
Sbjct: 95 IGVRAGLTREDVREISSVEVVEPEGWVTLSVADKREDDLLKCIYILVVINSNHQEGKDSH 154
Query: 258 MRQIKVYSPVQQHP 271
+R IK+Y P +
Sbjct: 155 VRHIKIYEPSTEEI 168
>gnl|CDD|176482 cd08159, APC10-like, APC10-like DOC1 domains in E3 ubiquitin
ligases that mediate substrate ubiquitination. This
family contains the single domain protein, APC10, a
subunit of the anaphase-promoting complex (APC), as well
as the DOC1 domain of multi-domain proteins present in
E3 ubiquitin ligases. E3 ubiquitin ligases mediate
substrate ubiquitination (or ubiquitylation), a
component of the ubiquitin-26S proteasome pathway for
selective proteolytic degradation. The APC, a
multi-protein complex (or cyclosome), is a cell
cycle-regulated, E3 ubiquitin ligase that controls
important transitions in mitosis and the G1 phase by
ubiquitinating regulatory proteins, thereby targeting
them for degradation. APC10-like DOC1 domains such as
those present in HECT (Homologous to the E6-AP Carboxyl
Terminus) and Cullin-RING (Really Interesting New Gene)
E3 ubiquitin ligase proteins, HECTD3, and CUL7,
respectively, are also included in this hierarchy. CUL7
is a member of the Cullin-RING ligase family and
functions as a molecular scaffold assembling a
SCF-ROC1-like E3 ubiquitin ligase complex consisting of
Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box
protein 1) and promotes ubiquitination. CUL7 is a
multi-domain protein with a C-terminal cullin domain
that binds ROC1 and a centrally positioned APC10/DOC1
domain. HECTD3 contains a C-terminal HECT domain which
contains the active site for ubiquitin transfer onto
substrates, and an N-terminal APC10 domain which is
responsible for substrate recognition and binding. An
APC10/DOC1 domain homolog is also present in HERC2 (HECT
domain and RLD2), a large multi-domain protein with
three RCC1-like domains (RLDs), additional internal
domains including zinc finger ZZ-type and Cyt-b5
(Cytochrome b5-like Heme/Steroid binding) domains, and a
C-terminal HECT domain. Recent studies have shown that
the protein complex HERC2-RNF8 coordinates
ubiquitin-dependent assembly of DNA repair factors on
damaged chromosomes. Also included in this hierarchy is
an uncharacterized APC10/DOC1-like domain found in a
multi-domain protein, which also contains CUB, zinc
finger ZZ-type, and EF-hand domains. The APC10/DOC1
domain forms a beta-sandwich structure that is related
in architecture to the galactose-binding domain-like
fold; their sequences are quite dissimilar, however, and
are not included here.
Length = 129
Score = 71.3 bits (175), Expect = 1e-15
Identities = 40/154 (25%), Positives = 66/154 (42%), Gaps = 29/154 (18%)
Query: 27 AIWSLSSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICIYRQLPHLVN 86
A +SS V +L D DTYWQSDG H +
Sbjct: 5 ASIEVSSNP--LPVSRLTDGNYDTYWQSDGSQGS----------------------HWIR 40
Query: 87 VQFRRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIK 146
+ ++ ++ + I+ D D SY PS V V G + +DL+E++ V++ +GWV +
Sbjct: 41 LFMKKDVLIRVLAIFVDMA-DSSYMPSLVVVYGGHSPSDLRELKDVNIRPSNGWVALLED 99
Query: 147 DIHDKPIRTYMIQIAVMSNHQNGRDTHMRQIKVY 180
D P I+I + +G DT +R +++
Sbjct: 100 DTLKCPY----IEIRIKRCRSDGIDTRIRGLRLL 129
Score = 44.0 bits (104), Expect = 8e-06
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 197 QQVSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIKDIHDKPIRTYMIQIAVMSNHQNGRDT 256
V V G + +DL+E++ V++ +GWV + D P I+I + +G DT
Sbjct: 66 SLVVVYGGHSPSDLRELKDVNIRPSNGWVALLEDDTLKCPY----IEIRIKRCRSDGIDT 121
Query: 257 HMRQIKVY 264
+R +++
Sbjct: 122 RIRGLRLL 129
>gnl|CDD|176483 cd08365, APC10-like1, APC10-like DOC1 domains of E3 ubiquitin
ligases that mediate substrate ubiquitination. This
model represens the APC10-like DOC1 domain of
multi-domain proteins present in E3 ubiquitin ligases.
E3 ubiquitin ligases mediate substrate ubiquitination
(or ubiquitylation), a component of the ubiquitin-26S
proteasome pathway for selective proteolytic
degradation. APC10/DOC1 domains such as those present in
HECT (Homologous to the E6-AP Carboxyl Terminus) and
Cullin-RING (Really Interesting New Gene) E3 ubiquitin
ligase proteins, HECTD3, and CUL7, respectively, are
also included here. CUL7 is a member of the Cullin-RING
ligase family and functions as a molecular scaffold
assembling a SCF-ROC1-like E3 ubiquitin ligase complex
consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1
(RING-box protein 1) and promotes ubiquitination. CUL7
is a multi-domain protein with a C-terminal cullin
domain that binds ROC1 and a centrally positioned
APC10/DOC1 domain. HECTD3 contains a C-terminal HECT
domain which contains the active site for ubiquitin
transfer onto substrates, and an N-terminal APC10/DOC1
domain which is responsible for substrate recognition
and binding. An APC10/DOC1 domain homolog is also
present in HERC2 (HECT domain and RLD2), a large
multi-domain protein with three RCC1-like domains
(RLDs), additional internal domains including zinc
finger ZZ-type and Cyt-b5 (Cytochrome b5-like
Heme/Steroid binding) domains, and a C-terminal HECT
domain. Recent studies have shown that the protein
complex HERC2-RNF8 coordinates ubiquitin-dependent
assembly of DNA repair factors on damaged chromosomes.
Also included in this hierarchy is an uncharacterized
APC10/DOC1-like domain found in a multi-domain protein,
which also contains CUB, zinc finger ZZ-type, and
EF-hand domains. The APC10/DOC1 domain forms a
beta-sandwich structure that is related in architecture
to the galactose-binding domain-like fold; their
sequences are quite dissimilar, however, and are not
included here.
Length = 131
Score = 44.8 bits (106), Expect = 4e-06
Identities = 36/141 (25%), Positives = 58/141 (41%), Gaps = 28/141 (19%)
Query: 40 VDQLRDDCMDTYWQSDG-QLPHLVNVQFRRKTTVQDICIYRQLPHLVNVQFRRKTTVQDI 98
+L D TYWQSDG Q H + ++ + V R L V+
Sbjct: 17 ASRLTDGNTSTYWQSDGSQGSHWIRLKMKPDVLV------RHLSLAVDAT---------- 60
Query: 99 CIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIKDIHDKPIRTYMI 158
D SY P RV V G + ++LQE+ V++ PS + + + D I I
Sbjct: 61 --------DSSYMPQRVVVAGGRSASNLQELRDVNIP-PSVTGYVTL--LEDATISQPYI 109
Query: 159 QIAVMSNHQNGRDTHMRQIKV 179
+I + +G DT + +++
Sbjct: 110 EIRIKRCRSDGIDTRIHGLRI 130
>gnl|CDD|176488 cd08667, APC10-ZZEF1, APC10/DOC1-like domain of uncharacterized
Zinc finger ZZ-type and EF-hand domain-containing
protein 1 (ZZEF1) and homologs. This model represents
the APC10/DOC1-like domain present in the
uncharacterized Zinc finger ZZ-type and EF-hand
domain-containing protein 1 (ZZEF1) of Mus musculus.
Members of this family contain EF-hand, APC10, CUB, and
zinc finger ZZ-type domains. ZZEF1-like APC10 domains
are homologous to the APC10 subunit/DOC1 domains present
in E3 ubiquitin ligases, which mediate substrate
ubiquitination (or ubiquitylation), and are components
of the ubiquitin-26S proteasome pathway for selective
proteolytic degradation.
Length = 131
Score = 42.6 bits (100), Expect = 3e-05
Identities = 32/141 (22%), Positives = 61/141 (43%), Gaps = 30/141 (21%)
Query: 40 VDQLRDDCMDTYWQSDGQL-PHLVNVQFRRKTTVQDICIYRQLPHLVNVQFRRKTTVQDI 98
+D++ D TYWQSDG H + ++ + ++ + I
Sbjct: 16 IDRMTDGETSTYWQSDGSARSHWIRLKMKPDVVLRHLSIAVA------------------ 57
Query: 99 CIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDL-NEPSGWVKIPIKDIHDKPIRTYM 157
D+SY P +V+V G + + LQE+ V + + +G+V + + + I +
Sbjct: 58 ------ATDQSYMPQQVTVSVGRSASSLQEVRDVHIPSNVTGYVTL----LENANISYLV 107
Query: 158 IQIAVMSNHQNGRDTHMRQIK 178
+QI + H +G DT + +K
Sbjct: 108 VQINIKRCHSDGCDTRIHGLK 128
Score = 31.0 bits (70), Expect = 0.32
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 197 QQVSVRAGTNFNDLQEIEVVDL-NEPSGWVKIPIKDIHDKPIRTYMIQIAVMSNHQNGRD 255
QQV+V G + + LQE+ V + + +G+V + + + I ++QI + H +G D
Sbjct: 66 QQVTVSVGRSASSLQEVRDVHIPSNVTGYVTL----LENANISYLVVQINIKRCHSDGCD 121
Query: 256 THMRQIK 262
T + +K
Sbjct: 122 TRIHGLK 128
>gnl|CDD|176487 cd08666, APC10-HECTD3, APC10-like DOC1 domain of HECTD3, a HECT E3
ubiquitin ligase protein that mediates substrate
ubiquitination. This model represents the APC10/DOC1
domain present in HECTD3, a HECT (Homologous to the
E6-AP Carboxyl Terminus) E3 ubiquitin ligase protein.
HECT E3 ubiquitin ligases mediate substrate
ubiquitination (or ubiquitylation), and are a component
of the ubiquitin-26S proteasome pathway for selective
proteolytic degradation. They also regulate the
trafficking of many receptors, channels, transporters
and viral proteins. HECTD3 (HECT domain-containing
protein3) contains a C-terminal HECT domain with the
active site for ubiquitin transfer onto substrates, and
an N-terminal APC10/DOC1 domain, which is responsible
for substrate recognition and binding. HECTD3
specifically recognizes the Trio-binding protein, Tara
(Trio-associated repeat on actin), implicated in
regulating actin cytoskeletal, cell motility and cell
growth. Tara also binds to TRF1 and may participate in
telomere maintenance and/or mitotic regulation through
interacting with TRF1. HECTD3 interacts with and
promotes the ubiquitination of Syntaxin 8, an endosomal
syntaxin proposed to mediate distinct steps of endosomal
protein trafficking. HECTD3-mediated Syntaxin 8
degradation has been suggested to contribute to the
pathophysiology of neurodegenerative diseases.
Length = 134
Score = 40.5 bits (95), Expect = 2e-04
Identities = 38/151 (25%), Positives = 64/151 (42%), Gaps = 29/151 (19%)
Query: 30 SLSSCKPGFGVDQLRDDCMDTYWQSDGQLPHLVNVQFRRKTTVQDICIYRQLPHLVNVQF 89
+SS F V L D DTYW+SDG Q H + +
Sbjct: 11 EVSSYTDDFNVSCLTDGDPDTYWESDGS----------------------QGQHWIRLHM 48
Query: 90 RRKTTVQDICIYTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEPS-GWVKIPIKDI 148
++ T ++ + + D D++Y P RV+V G ++L+++ V ++E G V I +
Sbjct: 49 KKGTIIKKLLLTVDAT-DDNYMPKRVAVYGGEG-DNLKKLNDVSIDETLIGDVCI----L 102
Query: 149 HDKPIRTYMIQIAVMSNHQNGRDTHMRQIKV 179
D +I+I + G D +R IK+
Sbjct: 103 EDMTTHLPVIEIRIKECKDEGIDVRIRGIKI 133
>gnl|CDD|176486 cd08665, APC10-CUL7, APC10-like DOC1 domain of CUL7, subunit of the
SCF-ROC1-like E3 ubiquitin ligase complex that mediates
substrate ubiquitination. This model represents the
APC10/DOC1 domain present in CUL7, a subunit of the
SCF-ROC1-like E3 Ubiquitin (Ub) ligase complex, which
mediates substrate ubiquitination (or ubiquitylation),
and is a component of the ubiquitin-26S proteasome
pathway for selective proteolytic degradation. CUL7 is
a member of the Cullin-RING ligase family and functions
as a molecular scaffold assembling the SCF-ROC1-like E3
Ub ligase complex consisting of the adapter protein
Skp1, CUL7, the WD40 repeat-containing F-box Fbw8 (also
known as Fbx29), and ROC1 (RING-box protein 1). CUL7 is
a large protein with a C-terminal cullin domain that
binds ROC1 and additional domains, including an
APC10/DOC1 domain. While the Fbw8 protein is responsible
for substrate protein recognition, the ROC1 RING domain
recruits an Ub-charged E2 Ub-conjugating enzyme for
substrate ubiquitination. It remains to be determined
how CUL7 binds to the Skp1-Fbw8 heterodimer. The CUL7 E3
Ub ligase has been implicated in the proteasomal
degradation of the cellular proteins, cyclin D1, an
important regulator of the G1 to S-phase cell cycle
progression, and insulin receptor substrate 1, a
critical component of the signaling pathways downstream
of the insulin and insulin-like growth factor 1
receptor. CUL7 appears to be an important regulator of
placental development. Germ line mutations of CUL7 are
linked to 3-M syndrome and Yakuts short stature
syndrome.
Length = 131
Score = 36.4 bits (84), Expect = 0.004
Identities = 36/141 (25%), Positives = 59/141 (41%), Gaps = 30/141 (21%)
Query: 41 DQLRDDCMDTYWQSDGQL-PHLVNVQFRRKTTVQDICIYRQLPHLVNVQFRRKTTVQDIC 99
++L D TYW+S+G H +N+ R + RQL LV +
Sbjct: 17 NKLTDGNPKTYWESNGSTGSHYINIHMHRGVVI------RQLYMLVASE----------- 59
Query: 100 IYTDYKLDESYTPSRVSVRAGTNFNDLQ-EIEVVDLNEPSGWVKIPIKDIHDKPIRTYMI 158
D SY P+RV V G + + + E+ V+++ + V + PI I
Sbjct: 60 -------DSSYMPARVVVLGGDSPSCITTELNAVNVSPTASRVVLLENMTRFWPI----I 108
Query: 159 QIAVMSNHQNGRDTHMRQIKV 179
QI + Q G DT +R +++
Sbjct: 109 QIRIKRCQQGGIDTRVRGLEI 129
>gnl|CDD|176485 cd08664, APC10-HERC2, APC10-like DOC1 domain present in HERC2 (HECT
domain and RLD2). This model represents the APC10/DOC1
domain present in HERC2 (HECT domain and RLD2), a large
multi-domain protein with three RCC1-like domains
(RLDs), additional internal domains including a zinc
finger ZZ-type and Cyt-b5 (Cytochrome b5-like
Heme/Steroid binding) domains, and a C-terminal HECT
(Homologous to the E6-AP Carboxyl Terminus) domain. The
APC10/DOC1 domain of HERC2 is a homolog of the APC10
subunit and the DOC1 domain present in E3 ubiquitin
ligases which mediate substrate ubiquitination (or
ubiquitylation), a component of the ubiquitin-26S
proteasome pathway for selective proteolytic
degradation. As suggested by structural relationships
between HERC2 and other proteins such as HERC1, the
proposed role for HERC2 in protein trafficking and
degradation pathways is consistent with observations
that mutations in HERC2 lead to neuromuscular secretory
vesicle and sperm acrosome defects, other developmental
abnormalities, and juvenile lethality of jdf2 mice.
Recent studies have shown that the protein complex,
HERC2-RNF8, coordinates ubiquitin-dependent assembly of
DNA repair factors on damaged chromosomes.
Length = 152
Score = 32.7 bits (75), Expect = 0.087
Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 23/90 (25%)
Query: 46 DCMDTYWQSDGQLPHLVNVQFRRKTTVQDICIYRQLPHLVNVQFRRKTTVQDICIYTDYK 105
D +YWQS G Q H + ++ + + I D
Sbjct: 45 DGSGSYWQSSGS----------------------QGKHWIRLELHPDVLIHSLKIIVD-P 81
Query: 106 LDESYTPSRVSVRAGTNFNDLQEIEVVDLN 135
D SY PS V V G + N L+E++ +++N
Sbjct: 82 ADSSYMPSLVVVSGGDSLNSLKELKTINVN 111
>gnl|CDD|198455 cd10487, EphR_LBD_A10, Ligand Binding Domain of Ephrin type-A
Receptor 10. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphA10, which contains an inactive tyr kinase
domain, may function to attenuate signals of
co-clustered active receptors. EphA10 is mainly
expressed in the testis. EphRs contain a ligand binding
domain and two fibronectin repeats extracellularly, a
transmembrane segment, and a cytoplasmic tyrosine kinase
domain. Binding of the ephrin ligand to EphR requires
cell-cell contact since both are anchored to the plasma
membrane. The resulting downstream signals occur
bidirectionally in both EphR-expressing cells (forward
signaling) and ephrin-expressing cells (reverse
signaling). Ephrin/EphR interaction results in cell-cell
repulsion or adhesion.
Length = 173
Score = 30.0 bits (67), Expect = 0.98
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 138 SGWVKIPIKDIHDKPIRTYMIQIAVMSNHQN 168
+GW +I D H KPIRTY + VM +QN
Sbjct: 22 NGWEEISGVDEHYKPIRTYQV-CNVMEPNQN 51
Score = 30.0 bits (67), Expect = 0.98
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 222 SGWVKIPIKDIHDKPIRTYMIQIAVMSNHQN 252
+GW +I D H KPIRTY + VM +QN
Sbjct: 22 NGWEEISGVDEHYKPIRTYQV-CNVMEPNQN 51
>gnl|CDD|226159 COG3633, SstT, Na+/serine symporter [Amino acid transport and
metabolism].
Length = 407
Score = 30.1 bits (68), Expect = 1.4
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 152 PIRTYMIQIAVMSNHQNGRDTHMRQIKV 179
P+ +++ +A ++NH+ G+ T++R I V
Sbjct: 57 PVLVFILVMASIANHKKGQKTNIRPIIV 84
Score = 30.1 bits (68), Expect = 1.4
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 236 PIRTYMIQIAVMSNHQNGRDTHMRQIKV 263
P+ +++ +A ++NH+ G+ T++R I V
Sbjct: 57 PVLVFILVMASIANHKKGQKTNIRPIIV 84
>gnl|CDD|216481 pfam01404, Ephrin_lbd, Ephrin receptor ligand binding domain. The
Eph receptors, which bind to ephrins pfam00812 are a
large family of receptor tyrosine kinases. This family
represents the amino terminal domain which binds the
ephrin ligand.
Length = 178
Score = 29.6 bits (67), Expect = 1.4
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 137 PSGWVKIPIKDIHDKPIRTYMIQIA-VMSNHQNG 169
GW ++ D + +PIRTY Q+ VM +QN
Sbjct: 21 SGGWEEVSGVDENGRPIRTY--QVCNVMEPNQNN 52
Score = 29.6 bits (67), Expect = 1.4
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 221 PSGWVKIPIKDIHDKPIRTYMIQIA-VMSNHQNG 253
GW ++ D + +PIRTY Q+ VM +QN
Sbjct: 21 SGGWEEVSGVDENGRPIRTY--QVCNVMEPNQNN 52
>gnl|CDD|176911 cd08902, START_STARD4-like, Lipid-binding START domain of mammalian
STARD4 and related proteins. This subgroup includes the
steroidogenic acute regulatory protein (StAR)-related
lipid transfer (START) domains of mammalian STARD4 and
related domains. It belongs to the START domain family,
and in turn to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. STARD4 plays an important role in
steroidogenesis, trafficking cholesterol into
mitochondria. It specifically binds cholesterol, and
demonstrates limited binding to another sterol,
7alpha-hydroxycholesterol. STARD4 is ubiquitously
expressed, with highest levels in liver and kidney.
Length = 202
Score = 29.2 bits (65), Expect = 2.1
Identities = 14/59 (23%), Positives = 23/59 (38%)
Query: 101 YTDYKLDESYTPSRVSVRAGTNFNDLQEIEVVDLNEPSGWVKIPIKDIHDKPIRTYMIQ 159
+ D+ Y +S + + + V N P GW +P+KD + T IQ
Sbjct: 112 FVDFSYTTQYEDGLLSCGVSIEYEEARPNFVRGFNHPCGWFCVPLKDNPSHSLLTGYIQ 170
>gnl|CDD|198441 cd10473, EphR_LBD_A, Ligand Binding Domain of Ephrin type-A
Receptors. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphRs contain a ligand binding domain and two
fibronectin repeats extracellularly, a transmembrane
segment, and a cytoplasmic tyrosine kinase domain.
Binding of the ephrin ligand to EphR requires cell-cell
contact since both are anchored to the plasma membrane.
The resulting downstream signals occur bidirectionally
in both EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling). Ephrin/EphR
interaction mainly results in cell-cell repulsion or
adhesion, making it important in neural development and
plasticity, cell morphogenesis, cell-fate determination,
embryonic development, tissue patterning, and
angiogenesis.
Length = 173
Score = 28.9 bits (65), Expect = 2.3
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 137 PSGWVKIPIKDIHDKPIRTYMIQIAVMSNHQN 168
P+GW +I D PIRTY + VM +QN
Sbjct: 21 PNGWEEISEMDEDYTPIRTYQV-CNVMEPNQN 51
Score = 28.9 bits (65), Expect = 2.3
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 221 PSGWVKIPIKDIHDKPIRTYMIQIAVMSNHQN 252
P+GW +I D PIRTY + VM +QN
Sbjct: 21 PNGWEEISEMDEDYTPIRTYQV-CNVMEPNQN 51
>gnl|CDD|184190 PRK13628, PRK13628, serine/threonine transporter SstT; Provisional.
Length = 402
Score = 28.7 bits (65), Expect = 3.8
Identities = 9/26 (34%), Positives = 19/26 (73%)
Query: 152 PIRTYMIQIAVMSNHQNGRDTHMRQI 177
PI +++ +A ++NH+ G+ T++R I
Sbjct: 57 PILVFVLVMASIANHKKGQKTNIRPI 82
Score = 28.7 bits (65), Expect = 3.8
Identities = 9/26 (34%), Positives = 19/26 (73%)
Query: 236 PIRTYMIQIAVMSNHQNGRDTHMRQI 261
PI +++ +A ++NH+ G+ T++R I
Sbjct: 57 PILVFVLVMASIANHKKGQKTNIRPI 82
>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional.
Length = 435
Score = 27.6 bits (62), Expect = 9.0
Identities = 10/31 (32%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 137 PSGWVKIPIKDIHDK---PIRTYMIQIAVMS 164
P+ WV++P+ +IH P+ Y + I ++S
Sbjct: 136 PNIWVRVPLTEIHQGDFSPLFRYTLAIGLLS 166
Score = 27.6 bits (62), Expect = 9.0
Identities = 10/31 (32%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 221 PSGWVKIPIKDIHDK---PIRTYMIQIAVMS 248
P+ WV++P+ +IH P+ Y + I ++S
Sbjct: 136 PNIWVRVPLTEIHQGDFSPLFRYTLAIGLLS 166
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
0.321 0.134 0.407
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,448,493
Number of extensions: 1329549
Number of successful extensions: 868
Number of sequences better than 10.0: 1
Number of HSP's gapped: 850
Number of HSP's successfully gapped: 36
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.2 bits)