RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11046
(550 letters)
>gnl|CDD|211376 cd09265, AP_Syp1_like_MHD, Mu-homology domain (MHD) of endocytic
adaptor protein (AP), Syp1. This family corresponds to
the MHD found in the metazoan counterparts of yeast
Syp1, which includes two ubiquitously expressed
membrane-sculpting F-BAR domain-containing Fer/Cip4
homology domain-only proteins 1 and 2 (FCH domain only 1
and 2, or FCHo1/FCHo2), neuronal-specific SH3-containing
GRB2-like protein 3-interacting protein 1 (SGIP1), and
related uncharacterized proteins. FCHo1/FCHo2 represent
key initial proteins ultimately controlling cellular
nutrient uptake, receptor regulation, and synaptic
vesicle retrieval. They are required for plasma membrane
clathrin-coated vesicle (CCV) budding and marked sites
of CCV formation. They bind specifically to the plasma
membrane and recruit the scaffold proteins eps15 and
intersectin, which subsequently engage the adaptor
complex AP2 and clathrin, leading to coated vesicle
formation. Both FCHo1/FCHo2 contain an N-terminal
EFC/F-BAR domain that induces membrane tabulation, a
proline-rich domain (PRD) in the middle region, and a
C-terminal MHD responsible for the binding of eps15 and
intersectin. Another mammalian neuronal-specific
protein, neuronal-specific transcript Scr homology 3
(SH3)-domain growth factor receptor-bound 2 (GRB2)-like
(endophilin) interacting protein 1 [SGIP1] does not
contain EFC/F-BAR domain, but does have a PRD and a
C-terminal MHD and has been classified into this family
as well. SGIP1 is an endophilin-interacting protein that
plays an obligatory role in the regulation of energy
homeostasis. It is also involved in clathrin-mediated
endocytosis by interacting with phospholipids and eps15.
Length = 258
Score = 367 bits (943), Expect = e-125
Identities = 147/263 (55%), Positives = 190/263 (72%), Gaps = 5/263 (1%)
Query: 282 PLAVAFHEIIHSYFRGTDETRCQVKMSGDMMLSFPAGIVSILTSNPSPAQLKFKVSNISH 341
P+AVAF E +H+YF+GTD T+C VK++G++M+SFPAGIV LTSNPSPA L F++ N S
Sbjct: 1 PVAVAFTETVHAYFKGTDSTKCIVKITGEVMMSFPAGIVRALTSNPSPAPLSFRLKNASR 60
Query: 342 IENMLPNKQLINIEENKLDKSSDSMTCEFNMSALSSLLRKQCEQNPSASYFNVDILKYQI 401
IE++LPN QLI + +++ FNM+AL++ L+KQ EQNP ASY+NVD+LKYQ+
Sbjct: 61 IESVLPNAQLI--FSDPSQSDAETKDFWFNMTALTTWLKKQAEQNPDASYYNVDVLKYQV 118
Query: 402 KSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNNHAMGSPSPLLNVVLAVPVDGEVTNVQ 461
PG +S P QL ++WKCEP+ TDL+VDYKYN AM +PLLNV +VPVDG VTNVQ
Sbjct: 119 SP-PGPQSPPLQLTSYWKCEPSSTDLRVDYKYNTDAMAIATPLLNVQFSVPVDGGVTNVQ 177
Query: 462 AKPNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARFELKNGPGTPSTIATQFNCEGTTL 521
++PN W E NR WK ++S+ G G +KAR L GP PS +A QF EGTTL
Sbjct: 178 SEPNATWNAEQNRLSWKLPEISR--NGGGSGSLKARLSLSEGPSKPSQLAVQFQSEGTTL 235
Query: 522 SGAEFELIGPGYRVSLVKRKFMS 544
SG +FEL+G GYR+SLVKR+F S
Sbjct: 236 SGVDFELVGSGYRLSLVKRRFAS 258
>gnl|CDD|211378 cd09267, FCHo2_MHD, mu-homology domain (MHD) of F-BAR
domain-containing Fer/Cip4 homology domain-only protein
2 (FCH domain only 2 or FCHo2) and similar proteins.
This family corresponds to the MHD found in the
ubiquitously expressed mammalian membrane-sculpting
FCHo2 and similar proteins. FCHo2 represents a key
initial protein that ultimately controls cellular
nutrient uptake, receptor regulation, and synaptic
vesicle retrieval. It is required for plasma membrane
clathrin-coated vesicle (CCV) budding and marks sites of
CCV formation. It binds specifically to the plasma
membrane and recruits the scaffold proteins eps15 and
intersectin, which subsequently engages the adaptor
complex AP2 and clathrin, leading to coated vesicle
formation. FCHo2 contains an N-terminal EFC/F-BAR
domain, a proline-rich domain (PRD) in the middle
region, and a C-terminal MHD. The crescent-shaped
EFC/F-BAR domain can form an antiparallel dimer
structure that binds PtdIns(4,5)P2-enriched membranes
and can polymerize into rings to generate membrane
tubules. The MHD is structurally related to the
cargo-binding mu2 subunit of adaptor complex 2 (AP-2)
and is responsible for the binding of eps15 and
intersectin.
Length = 267
Score = 294 bits (754), Expect = 1e-96
Identities = 137/267 (51%), Positives = 189/267 (70%), Gaps = 7/267 (2%)
Query: 282 PLAVAFHEIIHSYFRGTDETRCQVKMSGDMMLSFPAGIVSILTSNPSPAQLKFKVSNISH 341
P+AVA E +++YF+G D T+C VK++GDM +SFP+GI+ + TSNPSPA L F++ N S
Sbjct: 1 PVAVALTESVNAYFKGADPTKCIVKITGDMTVSFPSGIIKVFTSNPSPAVLCFRLKNTSR 60
Query: 342 IENMLPNKQLINIEENKLDKSSDSMTCEF--NMSALSSLLRKQCEQNPSASYFNVDILKY 399
+E +LPN QL+ + ++ SDS T +F NM A++ L+K EQNP+ASY+NVDILKY
Sbjct: 61 LEQILPNAQLLYSDPSQ----SDSNTKDFWMNMQAVTVYLKKSSEQNPAASYYNVDILKY 116
Query: 400 QIKSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNNHAMGSPSPLLNVVLAVPVDGEVTN 459
Q+ S G +S P L +WKC + TDL+VDYKYN AM PSPL NV + VPVDG VTN
Sbjct: 117 QVSSN-GIQSTPLNLATYWKCSASTTDLRVDYKYNPEAMQPPSPLSNVQVLVPVDGGVTN 175
Query: 460 VQAKPNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARFELKNGPGTPSTIATQFNCEGT 519
+Q+ P W E +A+WK + +S+ SEN G G ++A+FEL GP P+T+A QF EG+
Sbjct: 176 MQSLPPAIWNAEQMKALWKLSSISEKSENGGSGSLRAKFELSEGPSKPATLAVQFFSEGS 235
Query: 520 TLSGAEFELIGPGYRVSLVKRKFMSGK 546
TLSG + EL+G GYR+SL K++F +G+
Sbjct: 236 TLSGVDMELVGTGYRLSLNKKRFATGR 262
>gnl|CDD|211377 cd09266, SGIP1_MHD, mu-homology domain (MHD) of Scr homology 3
(SH3)-domain growth factor receptor-bound 2 (GRB2)-like
(endophilin) interacting protein 1 (also known as
endophilin-3-interacting protein, SGIP1) and similar
proteins. This family corresponds to the MHD found in
mammalian neuronal-specific transcript SGIP1 and similar
proteins. Unlike other members in this family, SGIP1
does not contain EFC/F-BAR domain, but does have a
proline-rich domain (PRD) and a C-terminal MHD. It is an
endophilin-interacting protein that plays an obligatory
role in the regulation of energy homeostasis, and is
also involved in clathrin-mediated endocytosis by
interacting with phospholipids and eps15.
Length = 261
Score = 261 bits (667), Expect = 7e-84
Identities = 130/264 (49%), Positives = 177/264 (67%), Gaps = 8/264 (3%)
Query: 282 PLAVAFHEIIHSYFRGTDETRCQVKMSGDMMLSFPAGIVSILTSNPSPAQLKFKVSNISH 341
P+A AF E +++YF+G D ++C VK++G+M+LSFPAGI +NPSPA L F+++N S
Sbjct: 1 PVAAAFTETVNAYFKGADPSKCIVKITGEMVLSFPAGITRHFANNPSPAVLTFRITNYSR 60
Query: 342 IENMLPNKQLINIEENKLDKSSDSMTCEF--NMSALSSLLRKQCEQNPSASYFNVDILKY 399
+E++LPN QL+ + + SD+ T EF NM L + L+K EQ P A+Y+NVD+LKY
Sbjct: 61 LEHVLPNPQLLCCDNTQ----SDANTKEFWVNMPNLMTHLKKVSEQKPQATYYNVDMLKY 116
Query: 400 QIKSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNNHAMGSPSPLLNVVLAVPVDGEVTN 459
Q+ S G +S P L W+CEP TDL++DYKYN AM +P L NV VPVDG VT
Sbjct: 117 QV-SAQGIQSTPLNLAVSWRCEPASTDLRIDYKYNTDAMTTPVALNNVQFLVPVDGGVTK 175
Query: 460 VQAK-PNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARFELKNGPGTPSTIATQFNCEG 518
+QA P W E R +WK D+SQ SEN G+G + ARF+L GP P+ +A QF EG
Sbjct: 176 LQAVLPPAVWNAEQQRILWKIPDISQKSENGGVGSLLARFQLSEGPSKPAPLAVQFTSEG 235
Query: 519 TTLSGAEFELIGPGYRVSLVKRKF 542
+TLSG + EL+G GYR SL+K++F
Sbjct: 236 STLSGCDIELVGAGYRFSLIKKRF 259
>gnl|CDD|211379 cd09268, FCHo1_MHD, mu-homology domain (MHD) of F-BAR
domain-containing Fer/Cip4 homology domain-only protein
1 (FCH domain only 1 or FCHo1, also known as KIAA0290)
and similar proteins. This family corresponds to the
MHD found in ubiquitously expressed mammalian
membrane-sculpting FCHo1 and similar proteins. FCHo1
represents a key initial protein that ultimately
controls cellular nutrient uptake, receptor regulation,
and synaptic vesicle retrieval. It is required for
plasma membrane clathrin-coated vesicle (CCV) budding
and marks sites of CCV formation. It binds specifically
to the plasma membrane and recruits the scaffold
proteins eps15 and intersectin, which subsequently
engage the adaptor complex AP2 and clathrin, leading to
coated vesicle formation. FCHo1 contains an N-terminal
EFC/F-BAR domain, a proline-rich domain (PRD) in the
middle region, and a C-terminal MHD. The crescent-shaped
EFC/F-BAR domain can form an antiparallel dimer
structure that binds PtdIns(4,5)P2-enriched membranes
and can polymerize into rings to generate membrane
tubules. The MHD is structurally related to the
cargo-binding mu2 subunit of adaptor complex 2 (AP-2)
and is responsible for the binding of eps15 and
intersectin. Unlike other F-BAR domain containing
proteins, FCHo1 has neither the Src homology 3 (SH3)
domain nor any other known domain for interaction with
dynamin and actin cytoskeleton. However, it can
periodically accumulate at the budding site of clathrin.
FCHo1 may utilize a unique action mode for vesicle
formation as compared with other F-BAR proteins.
Length = 259
Score = 239 bits (611), Expect = 2e-75
Identities = 104/261 (39%), Positives = 163/261 (62%), Gaps = 4/261 (1%)
Query: 282 PLAVAFHEIIHSYFRGTDETRCQVKMSGDMMLSFPAGIVSILTSNPSPAQLKFKVSNISH 341
P+A AF E +H+YFRG C ++++G++ +SFPAGI+ + S P+P L F++ + SH
Sbjct: 1 PVAAAFTEYVHAYFRGGALEGCLLRITGELTMSFPAGILRVFASTPTPPVLSFRLVHTSH 60
Query: 342 IENMLPNKQLINIEENKLDKSSDSMTCEFNMSALSSLLRKQCEQNPSASYFNVDILKYQI 401
+E+ PN +L+ + ++ D ++ NM AL+S L++ EQNP ASY+NV +LKYQ+
Sbjct: 61 VEHFAPNSELLFSDPSQSD--PNTKDFWLNMPALTSYLQRMAEQNPQASYYNVTLLKYQV 118
Query: 402 KSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNNHAMGSPSPLLNVVLAVPVDGEVTNVQ 461
SK G + P L A W+C PT TD+ +DY+ N A + L +V + +P+D TN+Q
Sbjct: 119 -SKSGPSAAPLYLSATWQCGPTSTDVSLDYRQNP-ATAPATFLTDVQILLPLDEPFTNLQ 176
Query: 462 AKPNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARFELKNGPGTPSTIATQFNCEGTTL 521
++P W E R W+ S +E+ G G + A ++ + P P++ A QF EG+TL
Sbjct: 177 SQPPAAWNAEERRLHWQLPHESAGNEHDGSGRLCASWQPLHAPSRPTSAAAQFTSEGSTL 236
Query: 522 SGAEFELIGPGYRVSLVKRKF 542
SG + EL+G GYR+SLVK++F
Sbjct: 237 SGVDIELVGSGYRMSLVKKRF 257
>gnl|CDD|220677 pfam10291, muHD, Muniscin C-terminal mu homology domain. The
muniscins are a family of endocytic adaptors that is
conserved from yeast to humans.This C-terminal domain is
structurally similar to mu homology domains, and is the
region of the muniscin proteins involved in the
interactions with the endocytic adaptor-scaffold
proteins Ede1-eps15. This interaction influences
muniscin localisation. The muniscins provide a combined
adaptor-membrane-tubulation activity that is important
for regulating endocytosis.
Length = 251
Score = 237 bits (608), Expect = 5e-75
Identities = 96/274 (35%), Positives = 142/274 (51%), Gaps = 34/274 (12%)
Query: 280 TIPLAVAFHEIIHSYFRGTDETRCQVKMSGDMMLSFPAGIVSILTSNPSPAQLKFKVSNI 339
T L + E +++YF+G ++ VK+ G++ LS+PAGIV+ T+ PA L F+++N
Sbjct: 1 TPGLNASIAETVNAYFKGGQVSK--VKVVGEIALSYPAGIVASFTN---PAPLNFRLNNF 55
Query: 340 SHIENMLPNKQLINIEENKLDKSSDSMTCEFNMSALSSLLRKQCEQNPSASYFNVDILKY 399
S +E +LPN I E+ SD + EF ++ + +L R + LKY
Sbjct: 56 SRLEKVLPNPAFIFPEQ------SDDESGEFKVN-MQALTRSKTLGA----------LKY 98
Query: 400 QIKSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNN-HAMGSPSPLLNVVLAVPVDG-EV 457
Q+ + SCP L WKCEP T L +DYK N A S LLN+V++V +DG V
Sbjct: 99 QVH----SASCPLILHPVWKCEPHQTSLILDYKLNPSPASSSSLVLLNLVVSVNLDGSRV 154
Query: 458 TNVQAKPNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARFELKNGP-GTPSTIATQFNC 516
T+ Q+KP + E NR W+ + S + G G + ARF + G P + +F
Sbjct: 155 TSAQSKPQGTFNKEKNRITWRLPEPLVLS-DGGEGKLIARFMTEGGGSEKPGGVQVKFEI 213
Query: 517 EGTTLSGAEFELIG----PGYRVSLVKRKFMSGK 546
EG TLSG EL+G +R KR+ +SGK
Sbjct: 214 EGPTLSGLGIELVGSEGDEDWREVPTKRRLVSGK 247
>gnl|CDD|211368 cd09257, AP_muniscins_like_MHD, Mu-homology domain (MHD) of
muniscins adaptor proteins (AP) and similar proteins.
This family corresponds to the MHD found in muniscins, a
novel family of endocytic adaptor proteins. The term,
muniscins, has been assigned to name the MHD of proteins
with both EFC/F-BAR domain and MHD. These two domains
are responsible for the membrane-tubulation activity
associated with transmembrane cargo proteins. Members in
this family include an endocytic adaptor Syp1, the
mammalian FCH domain only proteins (FCHo1/2),
SH3-containing GRB2-like protein 3-interacting protein 1
(SGIP1), and related uncharacterized proteins. Syp1 is a
poorly characterized yeast protein with multiple
biological functions. Syp1 contains an N-terminal
EFC/F-BAR domain that induces membrane tabulation, a
proline-rich domain (PRD) in the middle region, and a
C-terminal MHD that can directly binds to the endocytic
adaptor/scaffold protein Ede1 or a transmembrane stress
sensor cargo protein Mid2. Thus, Syp1 represents a novel
type of endocytic adaptor protein that participates in
endocytosis, promotes vesicle tabulation, and
contributes to cell polarity and stress response. Syp1
shares the same domain architecture with its two
ubiquitously expressed mammalian counterparts, the
membrane-sculpting F-BAR domain-containing Fer/Cip4
homology domain-only proteins 1 and 2 (FCHo1/2). FCHo1/2
represent key initial proteins ultimately controlling
cellular nutrient uptake, receptor regulation, and
synaptic vesicle retrieval. They are required for plasma
membrane clathrin-coated vesicle (CCV) budding and
marked sites of CCV formation. They bind specifically to
the plasma membrane and recruit the scaffold proteins
eps15 and intersectin, which subsequently engage the
adaptor complex AP2 and clathrin, leading to coated
vesicle formation. Another mammalian neuronal-specific
protein, neuronal-specific transcript Scr homology 3
(SH3)-domain growth factor receptor-bound 2 (GRB2)-like
(endophilin) interacting protein 1 [SGIP1] does not
contain EFC/F-BAR domain, but does have a PRD and a
C-terminal MHD and has been classified into this family
as well. SGIP1 is an endophilin-interacting protein that
plays an obligatory role in the regulation of energy
homeostasis. It is also involved in clathrin-mediated
endocytosis by interacting with phospholipids and eps15.
Length = 246
Score = 105 bits (265), Expect = 7e-26
Identities = 67/272 (24%), Positives = 108/272 (39%), Gaps = 39/272 (14%)
Query: 282 PLAVAFHEIIHSYFRGTDETRCQVKMSGDMMLSFPAGIVSILTSNPSPAQLKFKVSNISH 341
+++A E +++ F+G+ C V + G + + P+ V P PA ++++ S
Sbjct: 1 TVSLALTEELNAEFKGSSL--CSVGVEGSVQVKVPSSGVK-----PKPAPFNLRLNDASA 53
Query: 342 -IENMLPNKQLINIEENKLDKSSDSMTCEFNMSALSSLLRKQCEQNPSASYFNVDILKYQ 400
+EN + N I ++ S T EF ++ AS ILKY
Sbjct: 54 SVENAILNVAFIE----SVESPGISSTGEFLVN---------TTAVRVASEVGSPILKYS 100
Query: 401 IKSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNNHAMGSPSPLLNVVLAVPVDGE-VTN 459
SK P ++ + + V Y N P PL NV + V V G T+
Sbjct: 101 CSSK--LRPVPLRVQTRVRTSGNQCSVMVQYVSNPSL---PGPLSNVTVIVNVPGGAGTS 155
Query: 460 VQAKPNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARFELKNGPGT-----PSTIATQF 514
+++ P+ W E WK ++ N G ++ARFE GP + +
Sbjct: 156 LKSSPSAIWDREKRELTWKLPEIGV---NGEKGSLRARFEADAGPSLAAEKLQFPVLVRC 212
Query: 515 NCEGTTLSGAEFELIGPGYRV----SLVKRKF 542
G+TLSG E E+ LVKR+F
Sbjct: 213 LSSGSTLSGIELEVAALDEENATAGVLVKRRF 244
>gnl|CDD|211375 cd09264, AP_Syp1_MHD, mu-homology domain (MHD) of adaptor protein
(AP), Syp1, and related proteins. This family
corresponds to the MHD found in a novel endocytic
adaptor Syp1 and related proteins. Syp1 is a poorly
characterized yeast protein with multiple biological
functions. It was originally identified as a suppressor
of a yeast profiling deletion and later as a suppressor
of arf3delta (Arf3 is the yeast homologue of Arf6, a
mammalian regulator of endocytosis). Syp1 can bind to
septins and physically link with cell polarity factors.
It also directly binds to the endocytic adaptor/scaffold
protein Ede1, and plays a role in endocytosis. Further
studies show that Syp1 is itself an endocytic adaptor
protein contributing to stress responses. Its
mu-homology domain at the C-terminus binds to the cargo
protein Mid2, a transmembrane stress sensor protein, and
mediates Mid2 internalization. In addition, Syp1
contains an EFC/F-BAR domain which can induce membrane
tabulation.
Length = 253
Score = 60.8 bits (148), Expect = 3e-10
Identities = 53/236 (22%), Positives = 89/236 (37%), Gaps = 37/236 (15%)
Query: 325 SNPSPAQLKFKVSNISHIENMLPNKQLINIEENKLDKSSDSMTCEFNMSALSSLLRKQCE 384
+ + + +++N +E + PN + + E+ ++ S +L K
Sbjct: 37 AVGPTSPIHVRLNNFEVLEKVAPNPTFV--------EQVPVSPNEYTLN-PSLILSKT-- 85
Query: 385 QNPSASYFNVDILKYQIK--SKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNN--HAMGS 440
+ KYQ+ A P + WK EP L + YK N S
Sbjct: 86 ---------LGAFKYQVHLDPSNVAAYAPIIVTPVWKFEPHQASLILFYKLNPSFRLSTS 136
Query: 441 PSPLLNVVLAVPVDG--EVTNVQAKPNVQWLPETNRAIWKFTDLSQHSENHGIGCVKARF 498
L N+VL+V +DG + T+ Q+KP + E +R W+ D + + ARF
Sbjct: 137 ALTLENLVLSVALDGSVQATSAQSKPQGSFSREKSRITWRLPDPLV--LDDSEEKLIARF 194
Query: 499 ELKNGPGTPS--------TIATQFNCEGTTLSGAEFELIGPGYRVSLVKRKFMSGK 546
G G+ + I+ G TLS +E E ++ R +SGK
Sbjct: 195 MT-EGLGSEAPGGVEVRFEISGPNVGSGLTLSSSEPENEPGTWKEVPTVRTLVSGK 249
>gnl|CDD|211360 cd07954, AP_MHD_Cterm, C-terminal domain of adaptor protein (AP)
complexes medium mu subunits and its homologs (MHD).
This family corresponds to the C-terminal domain of
heterotetrameric AP complexes medium mu subunits and its
homologs existing in monomeric stonins, delta-subunit of
the heteroheptameric coat protein I (delta-COPI), a
protein encoded by a pro-death gene referred as MuD
(also known as MUDENG, mu-2 related death-inducing
gene), an endocytic adaptor syp1, the mammalian FCH
domain only proteins (FCHo1/2), SH3-containing GRB2-like
protein 3-interacting protein 1 (SGIP1), and related
proteins. AP complexes participate in the formation of
intracellular coated transport vesicles and select cargo
molecules for incorporation into the coated vesicles in
the late secretory and endocytic pathways. Stonins have
been characterized as clathrin-dependent AP-2 mu chain
related factors and may act as cargo-specific sorting
adaptors in endocytosis. Coat protein complex I
(COPI)-coated vesicles function in the early secretory
pathway. They mediate the retrograde transport from the
Golgi to the ER, and intra-Golgi transport. MuD is
distantly related to the C-terminal domain of mu2
subunit of AP-2. It is able to induce cell death by
itself and plays an important role in cell death in
various tissues. Syp1 represents a novel type of
endocytic adaptor protein that participates in
endocytosis, promotes vesicle tabulation, and
contributes to cell polarity and stress responses. It
shares the same domain architecture with its two
ubiquitously expressed mammalian counterparts, FCHo1/2,
which represent key initial proteins ultimately
controlling cellular nutrient uptake, receptor
regulation, and synaptic vesicle retrieval. They bind
specifically to the plasma membrane and recruit the
scaffold proteins eps15 and intersectin, which
subsequently engage the adaptor complex AP2 and
clathrin, leading to coated vesicle formation. Another
mammalian neuronal-specific protein SGIP1 does have a
C-terminal MHD and has been classified into this family
as well. It is an endophilin-interacting protein that
plays an obligatory role in the regulation of energy
homeostasis. It is also involved in clathrin-mediated
endocytosis by interacting with phospholipids and eps15.
Length = 239
Score = 50.5 bits (121), Expect = 6e-07
Identities = 30/163 (18%), Positives = 55/163 (33%), Gaps = 23/163 (14%)
Query: 386 NPSASYFNVDILKYQIKSKPGAESCPFQLVAHWKCEPTHTDLKVDYKYNNHAMGSPSPLL 445
P F + + Y+ + P + E ++ V K +
Sbjct: 77 IPPDGEFEL--MSYRTVLEEPI--LPITIFPVVSEEGGRLEVTVKLKLS---ESLQLTAE 129
Query: 446 NVVLAVPVDGEVTNVQAKPNVQ---WLPETNRAIWKFTDLSQHSENHGIGCVKARFELKN 502
NV + +P+ VT++ +KP+ + PE N +W+ + + + A FEL
Sbjct: 130 NVEVHIPLPSGVTSLSSKPSDGQAKFDPEKNALVWRIKRIPVGGKEQ---SLSATFELGG 186
Query: 503 GPGTPS----TIATQFNCEGTTLSGA------EFELIGPGYRV 535
++ F TT SG F+ PG+
Sbjct: 187 LAHECPEEAPPVSLSFEIPETTGSGIQVRSLQVFDEKNPGHDP 229
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 32.8 bits (75), Expect = 0.60
Identities = 28/142 (19%), Positives = 47/142 (33%), Gaps = 12/142 (8%)
Query: 146 SASTEDKPDHVDPTEPPLGLLSGNTPPPSSSTSTEKTTSDSSSTSKYTNLGDLFSEVGEI 205
S+S+ + P+ G + P +SS+S+ S SSSTS S
Sbjct: 286 SSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSS--------SSESSR 337
Query: 206 VPALPPKQTARMTPTLTSSTISLPRPPSRRSEGRGHISPLNSTLTRSESEFKTSGVSTTN 265
A+ P + +P+ S P S R R +P + + + + +
Sbjct: 338 GAAVSPGPSPSRSPSP-SRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAG 396
Query: 266 SSR---GPSPLTIGMSDTIPLA 284
+R G PL
Sbjct: 397 RARRRDATGRFPAGRPRPSPLD 418
>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 = 31.7 bits (71), Expect = 1.1
Identities = 34/142 (23%), Positives = 45/142 (31%), Gaps = 12/142 (8%)
Query: 146 SASTEDKPDHVDPTEPPLGLLSGNTPPPSSSTSTEKTTSDSSSTSKYTNLGDLFSEVGEI 205
+ T D P+ PT +G+ + T PP+ +TS TS + N V
Sbjct: 516 TQKTSDTPNATSPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEESPVN-NTNTPVVTSA 574
Query: 206 VPALPPKQTARMTPTLTSSTISLPRPPSR-----RSEGRGHISPLNSTL------TRSES 254
L T T +S T P PS RS L S E+
Sbjct: 575 PSVLTSAVTTGQHGTGSSPTSQQPGIPSSSHSTPRSNSTSTTPLLTSAHPTGGENITEET 634
Query: 255 EFKTSGVSTTNSSRGPSPLTIG 276
S + S GP P T
Sbjct: 635 PSVPSTTHVSTLSPGPGPGTTS 656
Score = 31.7 bits (71), Expect = 1.4
Identities = 30/147 (20%), Positives = 45/147 (30%), Gaps = 4/147 (2%)
Query: 128 KINGLAELNHALMKTMGDSASTEDKPDHVDPTEPPLGLLSGNTPPPSSSTSTEKTTSDSS 187
K + + G + ST D P PT L +T P S +TS + +
Sbjct: 445 KTTAVPTTPSLPPASTGPTVSTAD-PTSGTPTGTTSSTLPEDTSPTSRTTSATPNATSPT 503
Query: 188 STSKYTNLGDLFSEVGEIVPALPPKQTA--RMTPTLTSSTISLPRPPSRRSEGRGHISPL 245
N ++ P +T T TS P+ S SP+
Sbjct: 504 PAVTTPNATSPTTQKTSDTPNATSPTPIVIGVTTTATSPPTGTTSVPNATSPQVTEESPV 563
Query: 246 NSTLTRSESEFKTSGVST-TNSSRGPS 271
N+T T + + S T G
Sbjct: 564 NNTNTPVVTSAPSVLTSAVTTGQHGTG 590
>gnl|CDD|215130 PLN02217, PLN02217, probable pectinesterase/pectinesterase
inhibitor.
Length = 670
Score = 31.6 bits (71), Expect = 1.2
Identities = 30/118 (25%), Positives = 44/118 (37%), Gaps = 27/118 (22%)
Query: 163 LGLLSGN------TPPPSSSTSTEKTTSDSSSTSKYTNLGDLFSEVGEIVPALPPKQTAR 216
GL +GN TP S+++S +SDS ST + P+ P
Sbjct: 559 PGLFAGNPGSTNSTPTGSAASSNTTFSSDSPSTV--------------VAPSTSPPAGHL 604
Query: 217 MTPTLTSSTISLPR--PP-----SRRSEGRGHISPLNSTLTRSESEFKTSGVSTTNSS 267
+P T S I P PP S + S + T + S + V++T SS
Sbjct: 605 GSPPATPSKIVSPSTSPPASHLGSPSTTPSSPESSIKVASTETASPESSIKVASTESS 662
>gnl|CDD|216789 pfam01924, HypD, Hydrogenase formation hypA family. HypD is
involved in hydrogenase formation. It contains many
possible metal binding residues, which may bind to
nickel. Transposon Tn5 insertions into hypD resulted in
R. leguminosarum mutants that lacked any hydrogenase
activity in symbiosis with peas.
Length = 355
Score = 30.5 bits (70), Expect = 2.2
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 34 PEVDEEGYRIRPKEEMWDAEKFYSSSDSDSDDDR 67
+ + G ++R + +DAEK + D + DD +
Sbjct: 272 GVIPDSGLKLREEYAAFDAEKRFDLPDIEVDDPK 305
>gnl|CDD|221321 pfam11928, DUF3446, Domain of unknown function (DUF3446). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 80 to 99 amino acids in length. This domain is
found associated with pfam00096. This domain has a
single completely conserved residue P that may be
functionally important.
Length = 84
Score = 28.7 bits (64), Expect = 2.2
Identities = 21/52 (40%), Positives = 28/52 (53%)
Query: 164 GLLSGNTPPPSSSTSTEKTTSDSSSTSKYTNLGDLFSEVGEIVPALPPKQTA 215
GL+ + PPPSSS S+ ++S SSS S + SE I A PP +A
Sbjct: 26 GLVGMSNPPPSSSPSSSSSSSSSSSQSPPLSCSVHQSEPSPIYSAAPPYSSA 77
>gnl|CDD|233689 TIGR02023, BchP-ChlP, geranylgeranyl reductase. This model
represents a group of geranylgeranyl reductases specific
for the biosyntheses of bacteriochlorophyll and
chlorophyll. It is unclear whether the processes of
isoprenoid ligation to the chlorin ring and reduction of
the geranylgeranyl chain to a phytyl chain are
necessarily ordered the same way in all species (see
introduction to ) [Biosynthesis of cofactors, prosthetic
groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 388
Score = 30.1 bits (68), Expect = 2.7
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 10/60 (16%)
Query: 258 TSGVSTTNSSRGPSPLTIGMSDTIPLAVAFHEIIH------SYFRGTDETRCQVKMSGDM 311
V + + P +G+ +P +A+ E I +Y E V G++
Sbjct: 144 ADVVIGADGANSPVAKELGLPKNLPRVIAYQERIKLPDDKMAY----YEELADVYYGGEV 199
>gnl|CDD|235665 PRK05996, motB, flagellar motor protein MotB; Validated.
Length = 423
Score = 30.1 bits (68), Expect = 3.0
Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 8/62 (12%)
Query: 140 MKTMGDSASTEDKPDHVDPTEPPLGLLSGNTPPPSSSTSTEKTTSDSSSTSKYTNLGDLF 199
+K D A E KP E SS+ + + TT S + Y+ DLF
Sbjct: 83 LKDPVDGAEGEQKPGKSKFEE-------DQRVEGSSAVTGDDTTRTSGDQTNYSE-ADLF 134
Query: 200 SE 201
Sbjct: 135 RN 136
>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3). All proteins in this
family for which funcitons are known are DNA-DNA
helicases that funciton in the initiation of
transcription and nucleotide excision repair as part of
the TFIIH complex. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 705
Score = 30.1 bits (68), Expect = 4.1
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 138 ALMKTMGDSASTEDKPDHVDPTEPPLGLLSGNTPPPSSSTSTEKTTSDSSSTSKYTNLGD 197
A + +G + ++D P H+ E L L+ +ST + +D S NLG+
Sbjct: 456 AFPRNLGFNPVSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRND---PSLVRNLGE 512
Query: 198 LFSEVGEIVP 207
L E +I+P
Sbjct: 513 LLVEFSKIIP 522
>gnl|CDD|223020 PHA03246, PHA03246, large tegument protein UL36; Provisional.
Length = 3095
Score = 29.6 bits (66), Expect = 5.4
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 29 SEAPTPEVDEEGYRIRPKEEMWDAEKFYSSSDSDSDDDRDH 69
+EA + E + P + ++E SS+DSDSDD R
Sbjct: 2978 TEAESGENKFNNVNVDPIRKRSESESL-SSTDSDSDDSRST 3017
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 28.8 bits (65), Expect = 6.8
Identities = 13/59 (22%), Positives = 18/59 (30%), Gaps = 6/59 (10%)
Query: 98 NLTLSPL--SVKERRNSIDINPEVNFSQSPHKKINGLAELNHALMKTMGDSASTEDKPD 154
L S +V + N GL EL AL K +G S + +
Sbjct: 11 YLGDSGTLPAVAKAEKDALAGGTRNLYGPTD----GLPELREALAKFLGRSPVLKLDRE 65
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family
is long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 29.0 bits (65), Expect = 8.1
Identities = 22/144 (15%), Positives = 34/144 (23%), Gaps = 14/144 (9%)
Query: 94 VTAGNLTLSPLSVKERRNSIDINPEVNFSQSPHKKINGLAELNHALMKTMGDSASTEDKP 153
+A LT S + + P V + + L + + + + T K
Sbjct: 110 PSARRLTRSEGVARHEMEDLAGRPVVKPDADRQLRQDILNKSSSSRRPPVSKEEGTSSKM 169
Query: 154 DHVDPTEPPLGLLSGNTPPPSSSTSTEKTTSDSSSTSKYTNLGDLFSEVGEIVPALPPKQ 213
L ++ S S S + N P P
Sbjct: 170 PATALASAALFKDDEIRQEVDAARS--DQASQSRLSRSRGN------------PPAIPPD 215
Query: 214 TARMTPTLTSSTISLPRPPSRRSE 237
A P LT S E
Sbjct: 216 AAPRQPMLTRSAGGRFEGEDENLE 239
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
0.310 0.127 0.366
Gapped
Lambda K H
0.267 0.0621 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,694,253
Number of extensions: 2477025
Number of successful extensions: 1771
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1728
Number of HSP's successfully gapped: 57
Length of query: 550
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 448
Effective length of database: 6,413,494
Effective search space: 2873245312
Effective search space used: 2873245312
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 61 (27.5 bits)