RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5716
(294 letters)
>gnl|CDD|239860 cd04395, RhoGAP_ARHGAP21, RhoGAP_ARHGAP21: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP21-like proteins. ArhGAP21 is a multi-domain
protein, containing RhoGAP, PH and PDZ domains, and is
believed to play a role in the organization of the
cell-cell junction complex. It has been shown to
function as a GAP of Cdc42 and RhoA, and to interact
with alpha-catenin and Arf6. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 196
Score = 229 bits (586), Expect = 9e-76
Identities = 96/176 (54%), Positives = 121/176 (68%), Gaps = 20/176 (11%)
Query: 138 IGVPLQHC--VSVNLLCPFLFP-----------------RVPGNTAAVSSLTEAVNKGLD 178
GVPL C S N P + RVPGN AA+S+L E +N+G
Sbjct: 2 FGVPLDDCPPSSENPYVPLIVEVCCNIVEARGLETVGIYRVPGNNAAISALQEELNRGGF 61
Query: 179 ASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLV 238
L QDPRW DVNV+SSLLKSFFR+LP+ L T ELYP FI+A++IEDP R+ +++L+
Sbjct: 62 DIDL-QDPRWRDVNVVSSLLKSFFRKLPEPLFTNELYPDFIEANRIEDPVERLKELRRLI 120
Query: 239 HELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDDNMVTMVS 294
H LP+HH++TLK++++HLK V DNSEVNKME RNLAI+FGPTLVR DDNM TMV+
Sbjct: 121 HSLPDHHYETLKHLIRHLKTVADNSEVNKMEPRNLAIVFGPTLVRTSDDNMETMVT 176
>gnl|CDD|216027 pfam00620, RhoGAP, RhoGAP domain. GTPase activator proteins
towards Rho/Rac/Cdc42-like small GTPases.
Length = 152
Score = 158 bits (401), Expect = 2e-48
Identities = 67/153 (43%), Positives = 92/153 (60%), Gaps = 8/153 (5%)
Query: 141 PLQHCVSV----NLLCPFLFPRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISS 196
++ CV L +F RV G+ + + L EA + G ++ D DV+V++S
Sbjct: 3 IVEKCVEFLEKRGLDTEGIF-RVSGSASRIKELREAFDSG---EDVDLDLEEEDVHVVAS 58
Query: 197 LLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHL 256
LLK F R LP+ LLT ELY FI+A K ED R+ +++L+ +LP + TL+Y+L HL
Sbjct: 59 LLKLFLRELPEPLLTFELYEEFIEAAKSEDEEERVEALRELLRKLPPANRDTLRYLLAHL 118
Query: 257 KRVVDNSEVNKMEARNLAIMFGPTLVRAGDDNM 289
RV NSEVNKM A NLAI+FGPTL+R DD
Sbjct: 119 NRVAQNSEVNKMNAHNLAIVFGPTLLRPPDDES 151
>gnl|CDD|214618 smart00324, RhoGAP, GTPase-activator protein for Rho-like GTPases.
GTPase activator proteins towards Rho/Rac/Cdc42-like
small GTPases. etter domain limits and outliers.
Length = 174
Score = 150 bits (380), Expect = 4e-45
Identities = 61/161 (37%), Positives = 95/161 (59%), Gaps = 8/161 (4%)
Query: 136 SNIGVPLQHCVSV----NLLCPFLFPRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDV 191
I + ++ C+ L ++ RV G+ + V L +A + G D + + DV
Sbjct: 1 KPIPIIVEKCIEYLEKRGLDTEGIY-RVSGSKSRVKELRDAFDSGPDPDLDLSE---YDV 56
Query: 192 NVISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKY 251
+ ++ LLK F R LP+ L+T ELY FI+A K+ED R+ +++L+ LP + TL+Y
Sbjct: 57 HDVAGLLKLFLRELPEPLITYELYEEFIEAAKLEDETERLRALRELLSLLPPANRATLRY 116
Query: 252 ILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDDNMVTM 292
+L HL RV ++SE NKM ARNLAI+FGPTL+R D + ++
Sbjct: 117 LLAHLNRVAEHSEENKMTARNLAIVFGPTLLRPPDGEVASL 157
>gnl|CDD|238090 cd00159, RhoGAP, RhoGAP: GTPase-activator protein (GAP) for
Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small
GTPases. Small GTPases (G proteins) cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when bound
to GDP. The Rho family of small G proteins, which
includes Cdc42Hs, activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. G proteins generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude. The
RhoGAPs are one of the major classes of regulators of
Rho G proteins.
Length = 169
Score = 146 bits (370), Expect = 1e-43
Identities = 56/144 (38%), Positives = 83/144 (57%), Gaps = 5/144 (3%)
Query: 149 NLLCPFLFPRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDS 208
L +F RV G+ + + L + ++G D D DV+ ++SLLK + R LP+
Sbjct: 15 GLNTEGIF-RVSGSASKIEELKKKFDRGEDI----DDLEDYDVHDVASLLKLYLRELPEP 69
Query: 209 LLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKM 268
L+ ELY FI+ KIED R+ +K+L+ LP + LKY+L+ L ++ NSEVNKM
Sbjct: 70 LIPFELYDEFIELAKIEDEEERIEALKELLKSLPPENRDLLKYLLKLLHKISQNSEVNKM 129
Query: 269 EARNLAIMFGPTLVRAGDDNMVTM 292
A NLAI+F PTL+R D + +
Sbjct: 130 TASNLAIVFAPTLLRPPDSDDELL 153
>gnl|CDD|239863 cd04398, RhoGAP_fRGD1, RhoGAP_fRGD1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein
for Rho3 and Rho4 and plays a role in low-pH response.
Small GTPases cluster into distinct families, and all
act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 192
Score = 128 bits (324), Expect = 2e-36
Identities = 54/136 (39%), Positives = 84/136 (61%), Gaps = 1/136 (0%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRW-SDVNVISSLLKSFFRRLPDSLLTTELYP 216
R+ GN + V+ L E +K +L + SD++ ++SLLK FFR LP+ LLT L
Sbjct: 39 RLSGNVSRVNKLKELFDKDPLNVLLISPEDYESDIHSVASLLKLFFRELPEPLLTKALSR 98
Query: 217 HFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIM 276
FI+A KIED + R + L+++LP+ ++ TL+ ++ HL R+ ++ VN+M NLAI+
Sbjct: 99 EFIEAAKIEDESRRRDALHGLINDLPDANYATLRALMFHLARIKEHESVNRMSVNNLAII 158
Query: 277 FGPTLVRAGDDNMVTM 292
+GPTL+ A DN M
Sbjct: 159 WGPTLMNAAPDNAADM 174
>gnl|CDD|239868 cd04403, RhoGAP_ARHGAP27_15_12_9, RhoGAP_ARHGAP27_15_12_9:
GTPase-activator protein (GAP) domain for Rho-like
GTPases found in ARHGAP27 (also called CAMGAP1),
ARHGAP15, 12 and 9-like proteins; This subgroup of
ARHGAPs are multidomain proteins that contain RhoGAP,
PH, SH3 and WW domains. Most members that are studied
show GAP activity towards Rac1, some additionally show
activity towards Cdc42. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 187
Score = 128 bits (323), Expect = 2e-36
Identities = 55/139 (39%), Positives = 82/139 (58%), Gaps = 5/139 (3%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV GN A + L AV+ D + D +W D++VI+ LK FFR LP+ L L+
Sbjct: 39 RVSGNLAVIQKLRFAVDH--DEKLDLDDSKWEDIHVITGALKLFFRELPEPLFPYSLFND 96
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
F+ A K+ D R++ +K L+ LP+ + TLK + +HL RV+++ E N+M +NLAI+F
Sbjct: 97 FVAAIKLSDYEQRVSAVKDLIKSLPKPNHDTLKMLFRHLCRVIEHGEKNRMTTQNLAIVF 156
Query: 278 GPTLVRAGDDN---MVTMV 293
GPTL+R + V MV
Sbjct: 157 GPTLLRPEQETGNIAVHMV 175
>gnl|CDD|239837 cd04372, RhoGAP_chimaerin, RhoGAP_chimaerin: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain of chimaerins. Chimaerins are a family
of phorbolester- and diacylglycerol-responsive GAPs
specific for the Rho-like GTPase Rac. Chimaerins exist
in two alternative splice forms that each contain a
C-terminal GAP domain, and a central C1 domain which
binds phorbol esters, inducing a conformational change
that activates the protein; one splice form is lacking
the N-terminal Src homology-2 (SH2) domain. Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 194
Score = 117 bits (294), Expect = 4e-32
Identities = 50/134 (37%), Positives = 82/134 (61%), Gaps = 1/134 (0%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV G + + A ++ + + + + D+NVI+ LK +FR LP ++T + YP
Sbjct: 39 RVSGFAEEIEDVKMAFDRDGEKADISAT-VYPDINVITGALKLYFRDLPIPVITYDTYPK 97
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
FI A KI +P R+ + + + LP H++TL+Y+++HLKRV + + NKM A NL I+F
Sbjct: 98 FIDAAKISNPDERLEAVHEALMLLPPAHYETLRYLMEHLKRVTLHEKDNKMNAENLGIVF 157
Query: 278 GPTLVRAGDDNMVT 291
GPTL+R +D+ +T
Sbjct: 158 GPTLMRPPEDSALT 171
>gnl|CDD|239869 cd04404, RhoGAP-p50rhoGAP, RhoGAP-p50rhoGAP: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP,
also known as RhoGAP-1, contains a C-terminal RhoGAP
domain and an N-terminal Sec14 domain which binds
phosphatidylinositol 3,4,5-trisphosphate
(PtdIns(3,4,5)P3). It is ubiquitously expressed and
preferentially active on Cdc42. This subgroup also
contains closely related ARHGAP8. Small GTPases cluster
into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 195
Score = 113 bits (284), Expect = 1e-30
Identities = 45/132 (34%), Positives = 75/132 (56%), Gaps = 5/132 (3%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R NT V + + N G + + DV++ + +LK+F R LP+ LLT +LY
Sbjct: 46 RRSANTQVVKEVQQKYNMGEPVDFDQYE----DVHLPAVILKTFLRELPEPLLTFDLYDD 101
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
+ ++ R+ +K+L+ LPE ++Q LKY+++ L +V +S+ NKM NLA++F
Sbjct: 102 IVGFLNVDK-EERVERVKQLLQTLPEENYQVLKYLIKFLVQVSAHSDQNKMTNSNLAVVF 160
Query: 278 GPTLVRAGDDNM 289
GP L+ A D +M
Sbjct: 161 GPNLLWAKDASM 172
>gnl|CDD|239851 cd04386, RhoGAP_nadrin, RhoGAP_nadrin: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
Nadrin-like proteins. Nadrin, also named Rich-1, has
been shown to be involved in the regulation of
Ca2+-dependent exocytosis in neurons and recently has
been implicated in tight junction maintenance in
mammalian epithelium. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 203
Score = 106 bits (265), Expect = 1e-27
Identities = 51/162 (31%), Positives = 85/162 (52%), Gaps = 7/162 (4%)
Query: 135 GSNIGVPLQHCVSVNLLCPF----LFPRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSD 190
G I +P++ CV L LF RV G + + L A++ G L D +SD
Sbjct: 17 GREIALPIEACVMCLLETGMNEEGLF-RVGGGASKLKRLKAALDAG--TFSLPLDEFYSD 73
Query: 191 VNVISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLK 250
+ ++S LKS+ R LPD LLT LY ++QA D R+ I +++++LP + L+
Sbjct: 74 PHAVASALKSYLRELPDPLLTYNLYEDWVQAANKPDEDERLQAIWRILNKLPRENRDNLR 133
Query: 251 YILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDDNMVTM 292
Y+++ L ++ S+ NKM N+AI+ P L+ A ++ +
Sbjct: 134 YLIKFLSKLAQKSDENKMSPSNIAIVLAPNLLWAKNEGSLAE 175
>gnl|CDD|239839 cd04374, RhoGAP_Graf, RhoGAP_Graf: GTPase-activator protein (GAP)
domain for Rho-like GTPases found in GRAF (GTPase
regulator associated with focal adhesion kinase); Graf
is a multi-domain protein, containing SH3 and PH
domains, that binds focal adhesion kinase and influences
cytoskeletal changes mediated by Rho proteins. Graf
exhibits GAP activity toward RhoA and Cdc42, but only
weakly activates Rac1. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 203
Score = 105 bits (264), Expect = 1e-27
Identities = 47/137 (34%), Positives = 77/137 (56%), Gaps = 2/137 (1%)
Query: 158 RVPGNTAAVSSLTEAV--NKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELY 215
RV G + V L K ++ D ++ I+S LK++ R LP+ L+T EL+
Sbjct: 51 RVVGVNSKVQKLLSLGLDPKTSTPGDVDLDNSEWEIKTITSALKTYLRNLPEPLMTYELH 110
Query: 216 PHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAI 275
FI A K E+ +R+ I LVH+LPE + + L+ +++HL V D+S+ N M NL +
Sbjct: 111 NDFINAAKSENLESRVNAIHSLVHKLPEKNREMLELLIKHLTNVSDHSKKNLMTVSNLGV 170
Query: 276 MFGPTLVRAGDDNMVTM 292
+FGPTL+R ++ + +
Sbjct: 171 VFGPTLLRPQEETVAAI 187
>gnl|CDD|239865 cd04400, RhoGAP_fBEM3, RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP]
protein for Rho-like small GTPases) domain of fungal
BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and
is specifically involved in the control of the initial
assembly of the septin ring in yeast bud formation.
Small GTPases cluster into distinct families, and all
act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 190
Score = 104 bits (262), Expect = 2e-27
Identities = 39/125 (31%), Positives = 70/125 (56%), Gaps = 2/125 (1%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R+ G+ + + L E N D + + DV+ ++ LLK + R LP +L EL+
Sbjct: 46 RLSGSASVIKQLKERFNTEYDVDLF-SSSLYPDVHTVAGLLKLYLRELPTLILGGELHND 104
Query: 218 FIQ-ADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIM 276
F + ++ D + R +K LV +LP+ ++ L + L++++++S+VNKM RN+ I+
Sbjct: 105 FKRLVEENHDRSQRALELKDLVSQLPQANYDLLYVLFSFLRKIIEHSDVNKMNLRNVCIV 164
Query: 277 FGPTL 281
F PTL
Sbjct: 165 FSPTL 169
>gnl|CDD|239852 cd04387, RhoGAP_Bcr, RhoGAP_Bcr: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain of Bcr
(breakpoint cluster region protein)-like proteins. Bcr
is a multidomain protein with a variety of enzymatic
functions. It contains a RhoGAP and a Rho GEF domain, a
Ser/Thr kinase domain, an N-terminal oligomerization
domain, and a C-terminal PDZ binding domain, in addition
to PH and C2 domains. Bcr is a negative regulator of:
i) RacGTPase, via the Rho GAP domain, ii) the
Ras-Raf-MEK-ERK pathway, via phosphorylation of the Ras
binding protein AF-6, and iii) the Wnt signaling pathway
through binding beta-catenin. Bcr can form a complex
with beta-catenin and Tcf1. The Wnt signaling pathway
is involved in cell proliferation, differentiation, and
cell renewal. Bcr was discovered as a fusion partner of
Abl. The Bcr-Abl fusion is characteristic for a large
majority of chronic myelogenous leukemias (CML). Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 196
Score = 100 bits (250), Expect = 1e-25
Identities = 50/127 (39%), Positives = 73/127 (57%), Gaps = 4/127 (3%)
Query: 158 RVPGNTAAVSSLTEAVN-KGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYP 216
R+ G + +L A + D SV+ + DVN I+ LK +FR LP+ L T ELYP
Sbjct: 39 RISGVATDIQALKAAFDTNNKDVSVMLSE---MDVNAIAGTLKLYFRELPEPLFTDELYP 95
Query: 217 HFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIM 276
+F + + DP + + + L+ LP+ + T ++L HLKRV + EVNKM NLA +
Sbjct: 96 NFAEGIALSDPVAKESCMLNLLLSLPDPNLVTFLFLLHHLKRVAEREEVNKMSLHNLATV 155
Query: 277 FGPTLVR 283
FGPTL+R
Sbjct: 156 FGPTLLR 162
>gnl|CDD|239838 cd04373, RhoGAP_p190, RhoGAP_p190: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain of p190-like
proteins. p190, also named RhoGAP5, plays a role in
neuritogenesis and axon branch stability. p190 shows a
preference for Rho, over Rac and Cdc42, and consists of
an N-terminal GTPase domain and a C-terminal GAP domain.
The central portion of p190 contains important
regulatory phosphorylation sites. Small GTPases cluster
into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 185
Score = 99.5 bits (248), Expect = 2e-25
Identities = 46/132 (34%), Positives = 75/132 (56%), Gaps = 3/132 (2%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV GN + SL + ++ + ++ +D VN ++ LKSFF LPD L+ ++
Sbjct: 38 RVSGNKTHLDSLQKQFDQDHNLDLVSKD---FTVNAVAGALKSFFSELPDPLIPYSMHLE 94
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
++A KI D R+ +K+L+ + P +F KY++ HL +V NS+VN M + NL+I F
Sbjct: 95 LVEAAKINDREQRLHALKELLKKFPPENFDVFKYVITHLNKVSQNSKVNLMTSENLSICF 154
Query: 278 GPTLVRAGDDNM 289
PTL+R +M
Sbjct: 155 WPTLMRPDFTSM 166
>gnl|CDD|239850 cd04385, RhoGAP_ARAP, RhoGAP_ARAP: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain present in
ARAPs. ARAPs (also known as centaurin deltas) contain,
besides the RhoGAP domain, an Arf GAP, ankyrin repeat
ras-associating, and PH domains. Since their ArfGAP
activity is PIP3-dependent, ARAPs are considered
integration points for phosphoinositide, Arf and Rho
signaling. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 184
Score = 99.3 bits (248), Expect = 2e-25
Identities = 49/130 (37%), Positives = 77/130 (59%), Gaps = 2/130 (1%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R G ++V L EA K DA ++ V+ ++ +LK F R LPD LLT+EL+
Sbjct: 38 RKNGKNSSVKKLLEAFRK--DARSVQLREGEYTVHDVADVLKRFLRDLPDPLLTSELHAE 95
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
+I+A ++E+ R+A K+L+ LP + TLK ++ HL RV +S+ N+M NLA++F
Sbjct: 96 WIEAAELENKDERIARYKELIRRLPPINRATLKVLIGHLYRVQKHSDENQMSVHNLALVF 155
Query: 278 GPTLVRAGDD 287
GPTL + +
Sbjct: 156 GPTLFQTDEH 165
>gnl|CDD|239842 cd04377, RhoGAP_myosin_IX, RhoGAP_myosin_IX: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in class IX myosins. Class IX
myosins contain a characteristic head domain, a neck
domain, a tail domain which contains a C6H2-zinc binding
motif and a RhoGAP domain. Class IX myosins are
single-headed, processive myosins that are partly
cytoplasmic, and partly associated with membranes and
the actin cytoskeleton. Class IX myosins are implicated
in the regulation of neuronal morphogenesis and function
of sensory systems, like the inner ear. There are two
major isoforms, myosin IXA and IXB with several splice
variants, which are both expressed in developing
neurons. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 186
Score = 96.7 bits (241), Expect = 2e-24
Identities = 44/129 (34%), Positives = 76/129 (58%), Gaps = 4/129 (3%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R G+ + L + ++ D+ LE P ++VI+S+LK + R LP+ L+T ELY +
Sbjct: 38 RKSGSANKIKELRQGLDTDPDSVNLEDYP----IHVITSVLKQWLRELPEPLMTFELYEN 93
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
F++A ++E+ R+ + ++ +LP + TL+ ++ HL RV EVN+M A LAI+F
Sbjct: 94 FLRAMELEEKQERVRALYSVLEQLPRANLNTLERLIFHLVRVALQEEVNRMSANALAIVF 153
Query: 278 GPTLVRAGD 286
P ++R D
Sbjct: 154 APCILRCPD 162
>gnl|CDD|239849 cd04384, RhoGAP_CdGAP, RhoGAP_CdGAP: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP
domain and a C-terminal proline-rich region, and it is
active on both Cdc42 and Rac1 but not RhoA. CdGAP is
recruited to focal adhesions via the interaction with
the scaffold protein actopaxin (alpha-parvin). Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 195
Score = 94.9 bits (236), Expect = 1e-23
Identities = 37/103 (35%), Positives = 63/103 (61%)
Query: 182 LEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHEL 241
L +D D++ +SSL K +FR LP+ LLT +LY F +A R+ I ++ +L
Sbjct: 63 LTKDVYIQDIHSVSSLCKLYFRELPNPLLTYQLYEKFSEAVSAASDEERLEKIHDVIQQL 122
Query: 242 PEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRA 284
P H++TL+++++HL R+ + M A+NLAI++ P L+R+
Sbjct: 123 PPPHYRTLEFLMRHLSRLAKYCSITNMHAKNLAIVWAPNLLRS 165
>gnl|CDD|239847 cd04382, RhoGAP_MgcRacGAP, RhoGAP_MgcRacGAP: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in MgcRacGAP proteins. MgcRacGAP
plays an important dual role in cytokinesis: i) it is
part of centralspindlin-complex, together with the
mitotic kinesin MKLP1, which is critical for the
structure of the central spindle by promoting microtuble
bundling. ii) after phosphorylation by aurora B
MgcRacGAP becomes an effective regulator of RhoA and
plays an important role in the assembly of the
contractile ring and the initiation of cytokinesis.
MgcRacGAP-like proteins contain a N-terminal C1-like
domain, and a C-terminal RhoGAP domain. Small GTPases
cluster into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 193
Score = 92.4 bits (230), Expect = 1e-22
Identities = 44/125 (35%), Positives = 68/125 (54%), Gaps = 5/125 (4%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV G+ V +L E +G L + D++VI LK F R L + L+T L+
Sbjct: 40 RVSGSEREVKALKEKFLRGKTVPNLSK----VDIHVICGCLKDFLRSLKEPLITFALWKE 95
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
F++A +I D A + + + ELP+ + TL +++ HL+RV S KM+ NLA +F
Sbjct: 96 FMEAAEILDEDNSRAALYQAISELPQPNRDTLAFLILHLQRVAQ-SPECKMDINNLARVF 154
Query: 278 GPTLV 282
GPT+V
Sbjct: 155 GPTIV 159
>gnl|CDD|239856 cd04391, RhoGAP_ARHGAP18, RhoGAP_ARHGAP18: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP18-like proteins. The function of ArhGAP18 is
unknown. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 216
Score = 92.0 bits (229), Expect = 2e-22
Identities = 45/126 (35%), Positives = 63/126 (50%), Gaps = 6/126 (4%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNV--ISSLLKSFFRRLPDSLLTTELY 215
R+PG+ V L + L+A E W V +SLLK F R LP LLT E
Sbjct: 45 RIPGSAQRVKFLCQE----LEAKFYEGTFLWDQVKQHDAASLLKLFIRELPQPLLTVEYL 100
Query: 216 PHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAI 275
P F + ++ + LV LPE + TLK +L+ L++VVD+ E NKM N+A+
Sbjct: 101 PAFYSVQGLPSKKDQLQALNLLVLLLPEANRDTLKALLEFLQKVVDHEEKNKMNLWNVAM 160
Query: 276 MFGPTL 281
+ P L
Sbjct: 161 IMAPNL 166
>gnl|CDD|239843 cd04378, RhoGAP_GMIP_PARG1, RhoGAP_GMIP_PARG1: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain of GMIP (Gem interacting protein) and
PARG1 (PTPL1-associated RhoGAP1). GMIP plays important
roles in neurite growth and axonal guidance, and
interacts with Gem, a member of the RGK subfamily of the
Ras small GTPase superfamily, through the N-terminal
half of the protein. GMIP contains a C-terminal RhoGAP
domain. GMIP inhibits RhoA function, but is inactive
towards Rac1 and Cdc41. PARG1 interacts with Rap2, also
a member of the Ras small GTPase superfamily whose exact
function is unknown, and shows strong preference for
Rho. Small GTPases cluster into distinct families, and
all act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 203
Score = 90.9 bits (226), Expect = 5e-22
Identities = 57/153 (37%), Positives = 78/153 (50%), Gaps = 21/153 (13%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVL-EQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYP 216
RV G+ A V L +A G D L E P + ISS+LK F R+LP+ L+ LY
Sbjct: 39 RVSGSKARVEKLCQAFENGKDLVELSELSP-----HDISSVLKLFLRQLPEPLILFRLYN 93
Query: 217 HFI------QADKIEDPATRMAT--------IKKLVHELPEHHFQTLKYILQHLKRVVDN 262
FI Q D ED A +K L+ +LP ++ TL++++ HL RV +
Sbjct: 94 DFIALAKEIQRDTEEDKAPNTPIEVNRIIRKLKDLLRQLPASNYNTLQHLIAHLYRVAEQ 153
Query: 263 SEVNKMEARNLAIMFGPTLVRAGD-DNMVTMVS 294
E NKM NL I+FGPTL+R D V++ S
Sbjct: 154 FEENKMSPNNLGIVFGPTLIRPRPGDADVSLSS 186
>gnl|CDD|239841 cd04376, RhoGAP_ARHGAP6, RhoGAP_ARHGAP6: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP6-like proteins. ArhGAP6 shows GAP activity
towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is
often deleted in microphthalmia with linear skin defects
syndrome (MLS); MLS is a severe X-linked developmental
disorder. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 206
Score = 89.4 bits (222), Expect = 2e-21
Identities = 46/141 (32%), Positives = 72/141 (51%), Gaps = 16/141 (11%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV + V L E ++G+D VL+++ DV ++LLK FFR +PD LL ELY
Sbjct: 32 RVGSSKKRVRQLREEFDRGIDV-VLDENHSVHDV---AALLKEFFRDMPDPLLPRELYTA 87
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEV-----------N 266
FI +E P ++ ++ L++ LP + TL +L+ L V +++ N
Sbjct: 88 FIGTALLE-PDEQLEALQLLIYLLPPCNCDTLHRLLKFLHTVAEHAADSIDEDGQEVSGN 146
Query: 267 KMEARNLAIMFGPTLVRAGDD 287
KM + NLA +FGP L+
Sbjct: 147 KMTSLNLATIFGPNLLHKQKS 167
>gnl|CDD|239867 cd04402, RhoGAP_ARHGAP20, RhoGAP_ARHGAP20: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391
and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain,
and ANXL repeats. ArhGAP20 is activated by Rap1 and
induces inactivation of Rho, which in turn leads to
neurite outgrowth. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 192
Score = 88.9 bits (221), Expect = 2e-21
Identities = 42/130 (32%), Positives = 74/130 (56%), Gaps = 5/130 (3%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R N A L E +N G++ L+ +P V +++S+LK F R +P SLL+++LY
Sbjct: 38 RRSANAKACKELKEKLNSGVEV-DLKAEP----VLLLASVLKDFLRNIPGSLLSSDLYEE 92
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
++ A E+ ++A +++L+ +LP + LK+++ L + NSE NKM+A NLA+
Sbjct: 93 WMSALDQENEEEKIAELQRLLDKLPRPNVLLLKHLICVLHNISQNSETNKMDAFNLAVCI 152
Query: 278 GPTLVRAGDD 287
P+L+
Sbjct: 153 APSLLWPPAS 162
>gnl|CDD|239846 cd04381, RhoGap_RalBP1, RhoGap_RalBP1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain present
in RalBP1 proteins, also known as RLIP, RLIP76 or
cytocentrin. RalBP1 plays an important role in
endocytosis during interphase. During mitosis, RalBP1
transiently associates with the centromere and has been
shown to play an essential role in the proper assembly
of the mitotic apparatus. RalBP1 is an effector of the
Ral GTPase which itself is an effector of Ras. RalBP1
contains a RhoGAP domain, which shows weak activity
towards Rac1 and Cdc42, but not towards Ral, and a Ral
effector domain binding motif. Small GTPases cluster
into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 182
Score = 84.0 bits (208), Expect = 1e-19
Identities = 42/151 (27%), Positives = 76/151 (50%), Gaps = 10/151 (6%)
Query: 135 GSNIGVPLQHCV----SVNLLCPFLFPRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSD 190
G ++ + + C+ + C ++ +V G + V L A N+ ++ E +P
Sbjct: 17 GIDLPLVFRECIDYVEKHGMKCEGIY-KVSGIKSKVDELKAAYNRRESPNLEEYEP---- 71
Query: 191 VNVISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLK 250
++SLLK + R LP+ LLT EL P F +A A R +++L+ ELPE + L
Sbjct: 72 -PTVASLLKQYLRELPEPLLTKELMPRFEEACGRPTEAEREQELQRLLKELPECNRLLLA 130
Query: 251 YILQHLKRVVDNSEVNKMEARNLAIMFGPTL 281
+++ H+ V+ KM +N++I+ PT+
Sbjct: 131 WLIVHMDHVIAQELETKMNIQNISIVLSPTV 161
>gnl|CDD|239873 cd04408, RhoGAP_GMIP, RhoGAP_GMIP: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain of GMIP (Gem
interacting protein). GMIP plays important roles in
neurite growth and axonal guidance, and interacts with
Gem, a member of the RGK subfamily of the Ras small
GTPase superfamily, through the N-terminal half of the
protein. GMIP contains a C-terminal RhoGAP domain. GMIP
inhibits RhoA function, but is inactive towards Rac1 and
Cdc41. Small GTPases cluster into distinct families, and
all act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 200
Score = 84.5 bits (209), Expect = 1e-19
Identities = 49/148 (33%), Positives = 76/148 (51%), Gaps = 18/148 (12%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVL-EQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYP 216
R+ G+ A V L +A G D L P + I+S+LK F + LP+ +L +LY
Sbjct: 39 RISGSKARVEKLCQAFENGRDLVDLSGHSP-----HDITSVLKHFLKELPEPVLPFQLYD 93
Query: 217 HFI------QADKIEDPATR------MATIKKLVHELPEHHFQTLKYILQHLKRVVDNSE 264
FI Q D + + + ++K+L+ LP ++ TL++++ HL RV + E
Sbjct: 94 DFIALAKELQRDSEKAAESPSIVENIIRSLKELLGRLPVSNYNTLRHLMAHLYRVAERFE 153
Query: 265 VNKMEARNLAIMFGPTLVRAGDDNMVTM 292
NKM NL I+FGPTL+R V+M
Sbjct: 154 DNKMSPNNLGIVFGPTLLRPLVGGDVSM 181
>gnl|CDD|239848 cd04383, RhoGAP_srGAP, RhoGAP_srGAP: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain present
in srGAPs. srGAPs are components of the intracellular
part of Slit-Robo signalling pathway that is important
for axon guidance and cell migration. srGAPs contain an
N-terminal FCH domain, a central RhoGAP domain and a
C-terminal SH3 domain; this SH3 domain interacts with
the intracellular proline-rich-tail of the Roundabout
receptor (Robo). This interaction with Robo then
activates the rhoGAP domain which in turn inhibits Cdc42
activity. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 188
Score = 83.2 bits (206), Expect = 2e-19
Identities = 39/130 (30%), Positives = 66/130 (50%), Gaps = 2/130 (1%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV G+ V+ + A +G D L D D+N ++ +LK +FR L + L E +
Sbjct: 41 RVSGSQVEVNDIKNAFERGEDP--LADDQNDHDINSVAGVLKLYFRGLENPLFPKERFED 98
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
+ K+E+P R+ I++++ LP ++Y+ L + S+ N M+ NLAI F
Sbjct: 99 LMSCVKLENPTERVHQIREILSTLPRSVIIVMRYLFAFLNHLSQFSDENMMDPYNLAICF 158
Query: 278 GPTLVRAGDD 287
GPTL+ +
Sbjct: 159 GPTLMPVPEG 168
>gnl|CDD|239858 cd04393, RhoGAP_FAM13A1a, RhoGAP_FAM13A1a: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
FAM13A1, isoform a-like proteins. The function of
FAM13A1a is unknown. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by up several orders of magnitude.
Length = 189
Score = 82.5 bits (204), Expect = 5e-19
Identities = 42/141 (29%), Positives = 68/141 (48%), Gaps = 12/141 (8%)
Query: 155 LFPRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTEL 214
LF RV GN V L + ++ G + + ++ DV +SLL+ F + LP+ L+ L
Sbjct: 41 LF-RVNGNAETVEWLRQRLDSGEEVDLSKEA----DVCSAASLLRLFLQELPEGLIPASL 95
Query: 215 YPHFIQ--AD-KIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEAR 271
+Q D ED R ++ L+ +LP ++ LK++ L V N+M A
Sbjct: 96 QIRLMQLYQDYNGEDEFGR--KLRDLLQQLPPVNYSLLKFLCHFLSNVASQHHENRMTAE 153
Query: 272 NLAIMFGPTL--VRAGDDNMV 290
NLA +FGP + V ++M
Sbjct: 154 NLAAVFGPDVFHVYTDVEDMK 174
>gnl|CDD|239874 cd04409, RhoGAP_PARG1, RhoGAP_PARG1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally
cloned as an interaction partner of PTPL1, an
intracellular protein-tyrosine phosphatase. PARG1
interacts with Rap2, also a member of the Ras small
GTPase superfamily whose exact function is unknown, and
shows strong preference for Rho. Small GTPases cluster
into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 211
Score = 80.6 bits (199), Expect = 3e-18
Identities = 47/148 (31%), Positives = 71/148 (47%), Gaps = 26/148 (17%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RV G + V L +A G D L + + IS++LK + R+LP+ L+ LY
Sbjct: 39 RVNGAKSRVEKLCQAFENGKDLVELSE----LSPHDISNVLKLYLRQLPEPLILFRLYNE 94
Query: 218 FI------QADKIEDPATRMAT----------------IKKLVHELPEHHFQTLKYILQH 255
FI Q A + + K L+ +LP ++ TL++++ H
Sbjct: 95 FIGLAKESQHVNETQEAKKNSDKKWPNMCTELNRILLKSKDLLRQLPAPNYNTLQFLIVH 154
Query: 256 LKRVVDNSEVNKMEARNLAIMFGPTLVR 283
L RV + +E NKM A NL I+FGPTL+R
Sbjct: 155 LHRVSEQAEENKMSASNLGIIFGPTLIR 182
>gnl|CDD|239855 cd04390, RhoGAP_ARHGAP22_24_25, RhoGAP_ARHGAP22_24_25:
GTPase-activator protein (GAP) domain for Rho-like
GTPases found in ARHGAP22, 24 and 25-like proteins;
longer isoforms of these proteins contain an additional
N-terminal pleckstrin homology (PH) domain. ARHGAP25
(KIA0053) has been identified as a GAP for Rac1 and
Cdc42. Short isoforms (without the PH domain) of
ARHGAP24, called RC-GAP72 and p73RhoGAP, and of
ARHGAP22, called p68RacGAP, has been shown to be
involved in angiogenesis and endothelial cell capillary
formation. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 199
Score = 77.9 bits (192), Expect = 3e-17
Identities = 42/137 (30%), Positives = 68/137 (49%), Gaps = 6/137 (4%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R+PG V L +A + G S +DV+ ++SLLK + R LP+ ++ Y
Sbjct: 45 RLPGQANLVKQLQDAFDAGERPSF----DSDTDVHTVASLLKLYLRELPEPVIPWAQYED 100
Query: 218 FIQADKIEDPATRMATIK--KLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAI 275
F+ ++ + K V LP+ ++ L YI + L V NS VNKM +NLA
Sbjct: 101 FLSCAQLLSKDEEKGLGELMKQVSILPKVNYNLLSYICRFLDEVQSNSSVNKMSVQNLAT 160
Query: 276 MFGPTLVRAGDDNMVTM 292
+FGP ++R ++ T+
Sbjct: 161 VFGPNILRPKVEDPATI 177
>gnl|CDD|239862 cd04397, RhoGAP_fLRG1, RhoGAP_fLRG1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
fungal LRG1-like proteins. Yeast Lrg1p is required for
efficient cell fusion, and mother-daughter cell
separation, possibly through acting as a RhoGAP
specifically regulating 1,3-beta-glucan synthesis. Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 213
Score = 77.8 bits (192), Expect = 4e-17
Identities = 45/138 (32%), Positives = 69/138 (50%), Gaps = 12/138 (8%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVI--SSLLKSFFRRLPDSLLTTELY 215
R GN + LTE ++K + P S N + ++LLK F R LPD LLT +LY
Sbjct: 50 RKNGNIRRLKELTEEIDKNPT-----EVPDLSKENPVQLAALLKKFLRELPDPLLTFKLY 104
Query: 216 PHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRV-----VDNSEVNKMEA 270
+I + KIED R + + LP++H T++ + LK V +D +KM+
Sbjct: 105 RLWISSQKIEDEEERKRVLHLVYCLLPKYHRDTMEVLFSFLKWVSSFSHIDEETGSKMDI 164
Query: 271 RNLAIMFGPTLVRAGDDN 288
NLA + P ++ + DN
Sbjct: 165 HNLATVITPNILYSKTDN 182
>gnl|CDD|239859 cd04394, RhoGAP-ARHGAP11A, RhoGAP-ARHGAP11A: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain of ArhGAP11A-like proteins. The mouse
homolog of human ArhGAP11A has been detected as a gene
exclusively expressed in immature ganglion cells,
potentially playing a role in retinal development. The
exact function of ArhGAP11A is unknown. Small GTPases
cluster into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 202
Score = 76.0 bits (187), Expect = 1e-16
Identities = 31/94 (32%), Positives = 50/94 (53%)
Query: 194 ISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYIL 253
++ LLK FFR LP+ LL +L+ ++A ++ R + L LP+ H TL+Y
Sbjct: 72 VAGLLKQFFRELPEPLLPYDLHEALLKAQELPTDEERKSATLLLTCLLPDEHVNTLRYFF 131
Query: 254 QHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGDD 287
L V NKM++ NLA++F P L ++ +
Sbjct: 132 SFLYDVAQRCSENKMDSSNLAVIFAPNLFQSEEG 165
>gnl|CDD|239871 cd04406, RhoGAP_myosin_IXA, RhoGAP_myosin_IXA: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in myosins IXA. Class IX myosins
contain a characteristic head domain, a neck domain and
a tail domain which contains a C6H2-zinc binding motif
and a Rho-GAP domain. Class IX myosins are
single-headed, processive myosins that are partly
cytoplasmic, and partly associated with membranes and
the actin cytoskeleton. Class IX myosins are implicated
in the regulation of neuronal morphogenesis and function
of sensory systems, like the inner ear. There are two
major isoforms, myosin IXA and IXB with several splice
variants, which are both expressed in developing
neurons. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 186
Score = 74.7 bits (183), Expect = 3e-16
Identities = 37/129 (28%), Positives = 71/129 (55%), Gaps = 4/129 (3%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R G+T + L + ++ ++ L+ +++VI+S+ K + R LP+ L+T ELY
Sbjct: 38 RKSGSTNKIKELRQGLDTDANSVNLDD----YNIHVIASVFKQWLRDLPNPLMTFELYEE 93
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
F++A +++ + + ++ +L H TL+ ++ HL R+ E N+M A LAI+F
Sbjct: 94 FLRAMGLQERRETVRGVYSVIDQLSRTHLNTLERLIFHLVRIALQEETNRMSANALAIVF 153
Query: 278 GPTLVRAGD 286
P ++R D
Sbjct: 154 APCILRCPD 162
>gnl|CDD|239844 cd04379, RhoGAP_SYD1, RhoGAP_SYD1: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain present in
SYD-1_like proteins. Syd-1, first identified and best
studied in C.elegans, has been shown to play an
important role in neuronal development by specifying
axonal properties. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 207
Score = 72.1 bits (177), Expect = 4e-15
Identities = 37/100 (37%), Positives = 53/100 (53%), Gaps = 3/100 (3%)
Query: 190 DVNVISSLLKSFFRRLPDSLLTTELYPHFIQA---DKIEDPATRMATIKKLVHELPEHHF 246
D+NVI+ +LK + R LP+ L+T +LY ++A D T ++ LP
Sbjct: 72 DINVITGVLKDYLRELPEPLITPQLYEMVLEALAVALPNDVQTNTHLTLSIIDCLPLSAK 131
Query: 247 QTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPTLVRAGD 286
TL +L HL V+ NSE NKM +NLA+ FGP L+
Sbjct: 132 ATLLLLLDHLSLVLSNSERNKMTPQNLAVCFGPVLMFCSQ 171
>gnl|CDD|241284 cd01253, PH_ARHGAP21-like, ARHGAP21 and related proteins pleckstrin
homology (PH) domain. ARHGAP family genes encode
Rho/Rac/Cdc42-like GTPase activating proteins with a
RhoGAP domain. These proteins functions as a
GTPase-activating protein (GAP) for RHOA and CDC42.
ARHGAP21 controls the Arp2/3 complex and F-actin
dynamics at the Golgi complex by regulating the activity
of the small GTPase Cdc42. It is recruited to the Golgi
by to GTPase, ARF1, through its PH domain and its
helical motif. It is also required for CTNNA1
recruitment to adherens junctions. ARHGAP21 and it
related proteins all contains a PH domain and a RhoGAP
domain. Some of the members have additional N-terminal
domains including PDZ, SH3, and SPEC. The ARHGAP21 PH
domain interacts with the GTPbound forms of both ARF1
and ARF6 ARF-binding domain/ArfBD. The members here
include: ARHGAP15, ARHGAP21, and ARHGAP23. PH domains
have diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 113
Score = 69.7 bits (171), Expect = 5e-15
Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 1 MTGSCERIDIGHNCVEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQTHA 60
S +RIDI V++A YTKRK+V RL++ S +E L QA+D M WI+ +Q ++
Sbjct: 52 AEDSEQRIDIRSCIVDIAYSYTKRKNVFRLTT-SDGSEYLFQAEDRDDMLGWIKAIQENS 110
>gnl|CDD|239872 cd04407, RhoGAP_myosin_IXB, RhoGAP_myosin_IXB: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in myosins IXB. Class IX myosins
contain a characteristic head domain, a neck domain and
a tail domain which contains a C6H2-zinc binding motif
and a Rho-GAP domain. Class IX myosins are
single-headed, processive myosins that are partly
cytoplasmic, and partly associated with membranes and
the actin cytoskeleton. Class IX myosins are implicated
in the regulation of neuronal morphogenesis and function
of sensory systems, like the inner ear. There are two
major isoforms, myosin IXA and IXB with several splice
variants, which are both expressed in developing neurons
Small GTPases cluster into distinct families, and all
act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 186
Score = 70.4 bits (172), Expect = 1e-14
Identities = 39/137 (28%), Positives = 72/137 (52%), Gaps = 6/137 (4%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R G+ + L + + + LE P ++ I+ LLK + R LP+ L+T Y
Sbjct: 38 RKSGSANRMKELHQLLQADPENVKLENYP----IHAITGLLKQWLRELPEPLMTFAQYND 93
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEVNKMEARNLAIMF 277
F++A ++ + ++ I +++ +LP + TL+ ++ HL +V +VN+M LAI+F
Sbjct: 94 FLRAVELPEKQEQLQAIYRVLEQLPTANHNTLERLIFHLVKVALEEDVNRMSPNALAIVF 153
Query: 278 GPTLVRAGD--DNMVTM 292
P L+R D D + +M
Sbjct: 154 APCLLRCPDSSDPLTSM 170
>gnl|CDD|239857 cd04392, RhoGAP_ARHGAP19, RhoGAP_ARHGAP19: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP19-like proteins. The function of ArhGAP19 is
unknown. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 208
Score = 65.6 bits (160), Expect = 8e-13
Identities = 43/137 (31%), Positives = 63/137 (45%), Gaps = 15/137 (10%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
R PGN+A L + +N G D + D +++LK F LP+ LLT YP
Sbjct: 31 RKPGNSARQQELRDLLNSGTDLDLESGGFHAHDC---ATVLKGFLGELPEPLLTHAHYPA 87
Query: 218 FIQ-AD-----------KIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVDNSEV 265
+Q AD D + ++ L+ LPE + LK IL L + + +
Sbjct: 88 HLQIADLCQFDEKGNKTSAPDKERLLEALQLLLLLLPEENRNLLKLILDLLYQTAKHEDK 147
Query: 266 NKMEARNLAIMFGPTLV 282
NKM A NLA++F P L+
Sbjct: 148 NKMSADNLALLFTPHLI 164
>gnl|CDD|239854 cd04389, RhoGAP_KIAA1688, RhoGAP_KIAA1688: GTPase-activator protein
(GAP) domain for Rho-like GTPases found in KIAA1688-like
proteins; KIAA1688 is a protein of unknown function that
contains a RhoGAP domain and a myosin tail homology 4
(MyTH4) domain. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 187
Score = 64.7 bits (158), Expect = 1e-12
Identities = 39/137 (28%), Positives = 63/137 (45%), Gaps = 13/137 (9%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDSLLTTELYPH 217
RVPG+ V+ L V++ D +V +SLLK + R L + L+ LY
Sbjct: 45 RVPGDIDEVNELKLRVDQWD-----YPLSGLEDPHVPASLLKLWLRELEEPLIPDALYQQ 99
Query: 218 FIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVV--DNSEVNKMEARNLAI 275
I A EDP ++V +LP + L Y++ L+ +N KM+ NLA+
Sbjct: 100 CISAS--EDP----DKAVEIVQKLPIINRLVLCYLINFLQVFAQPENVAHTKMDVSNLAM 153
Query: 276 MFGPTLVRAGDDNMVTM 292
+F P ++R D+ +
Sbjct: 154 VFAPNILRCTSDDPRVI 170
>gnl|CDD|239840 cd04375, RhoGAP_DLC1, RhoGAP_DLC1: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain of DLC1-like
proteins. DLC1 shows in vitro GAP activity towards RhoA
and CDC42. Beside its C-terminal GAP domain, DLC1 also
contains a SAM (sterile alpha motif) and a START
(StAR-related lipid transfer action) domain. DLC1 has
tumor suppressor activity in cell culture. Small GTPases
cluster into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 220
Score = 63.6 bits (155), Expect = 6e-12
Identities = 29/88 (32%), Positives = 49/88 (55%)
Query: 194 ISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYIL 253
++ +LK +FR LP+ LLT +L FI + R+ ++ + LP+ + + L+ +L
Sbjct: 75 VADMLKQYFRDLPEPLLTNKLSETFIAIFQYVPKEQRLEAVQCAILLLPDENREVLQTLL 134
Query: 254 QHLKRVVDNSEVNKMEARNLAIMFGPTL 281
L V NS+ N+M A NLA+ P+L
Sbjct: 135 YFLSDVAANSQENQMTATNLAVCLAPSL 162
>gnl|CDD|241307 cd10571, PH_beta_spectrin, Beta-spectrin pleckstrin homology (PH)
domain. Beta spectrin binds actin and functions as a
major component of the cytoskeleton underlying cellular
membranes. Beta spectrin consists of multiple spectrin
repeats followed by a PH domain, which binds to
inositol-1,4,5-trisphosphate. The PH domain of
beta-spectrin is thought to play a role in the
association of spectrin with the plasma membrane of
cells. PH domains have diverse functions, but in general
are involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 105
Score = 53.4 bits (129), Expect = 3e-09
Identities = 22/49 (44%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 12 HNCV-EVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQTH 59
V EVA DY K+KHV RL S +E L QA D M W++ LQ
Sbjct: 58 SGAVCEVASDYKKKKHVFRLRL-SDGSEYLFQAKDEEEMNDWVQKLQAA 105
>gnl|CDD|239861 cd04396, RhoGAP_fSAC7_BAG7, RhoGAP_fSAC7_BAG7: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain of fungal SAC7 and BAG7-like proteins.
Both proteins are GTPase activating proteins of Rho1,
but differ functionally in vivo: SAC7, but not BAG7, is
involved in the control of Rho1-mediated activation of
the PKC-MPK1 pathway. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 225
Score = 54.3 bits (131), Expect = 1e-08
Identities = 37/151 (24%), Positives = 58/151 (38%), Gaps = 22/151 (14%)
Query: 158 RVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNV--ISSLLKSFFRRLPDSLLTTELY 215
RV G++ + L + D + W V +S+L+ + LP+ L+ +LY
Sbjct: 55 RVAGSSKRIRELQLIFSTPPDYG---KSFDWDGYTVHDAASVLRRYLNNLPEPLVPLDLY 111
Query: 216 PHF-----------------IQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKR 258
F I D + + L+ LP + Q L Y+L L
Sbjct: 112 EEFRNPLRKRPRILQYMKGRINEPLNTDIDQAIKEYRDLITRLPNLNRQLLLYLLDLLAV 171
Query: 259 VVDNSEVNKMEARNLAIMFGPTLVRAGDDNM 289
NS+ N M A NLA +F P ++ D M
Sbjct: 172 FARNSDKNLMTASNLAAIFQPGILSHPDHEM 202
>gnl|CDD|239853 cd04388, RhoGAP_p85, RhoGAP_p85: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain present in the
p85 isoforms of the regulatory subunit of the class IA
PI3K (phosphatidylinositol 3'-kinase). This domain is
also called Bcr (breakpoint cluster region protein)
homology (BH) domain. Class IA PI3Ks are heterodimers,
containing a regulatory subunit (p85) and a catalytic
subunit (p110) and are activated by growth factor
receptor tyrosine kinases (RTKs); this activation is
mediated by the p85 subunit. p85 isoforms, alpha and
beta, contain a C-terminal p110-binding domain flanked
by two SH2 domains, an N-terminal SH3 domain, and a
RhoGAP domain flanked by two proline-rich regions. Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 200
Score = 52.6 bits (126), Expect = 3e-08
Identities = 33/139 (23%), Positives = 61/139 (43%), Gaps = 11/139 (7%)
Query: 150 LLCPFLF-PRVPGNTAAVSSLTEAVNKGLDASVLEQDPRWSDVNVISSLLKSFFRRLPDS 208
L L+ + + + + + +D LEQ DV ++ LK + LP+
Sbjct: 31 LESSTLYRTQSSSSLTELRQILDCDAASVD---LEQ----FDVAALADALKRYLLDLPNP 83
Query: 209 LLTTELYPHFIQADKIEDPATRMATIKKLVHE---LPEHHFQTLKYILQHLKRVVDNSEV 265
++ +Y I + + A + + + LP ++ TL+Y+L+H R+ +S
Sbjct: 84 VIPAPVYSEMISRAQEVQSSDEYAQLLRKLIRSPNLPHQYWLTLQYLLKHFFRLCQSSSK 143
Query: 266 NKMEARNLAIMFGPTLVRA 284
N + AR LA +F P L R
Sbjct: 144 NLLSARALAEIFSPLLFRF 162
>gnl|CDD|241449 cd13295, PH_EFA6, Exchange Factor for ARF6 Pleckstrin homology (PH)
domain. EFA6 (also called PSD/pleckstrin and Sec7
domain containing) is an guanine nucleotide exchange
factor for ADP ribosylation factor 6 (ARF6), which is
involved in membrane recycling. EFA6 has four
structurally related polypeptides: EFA6A, EFA6B, EFA6C
and EFA6D. It consists of a N-terminal proline rich
region (PR), a SEC7 domain, a PH domain, a PR, a
coiled-coil region, and a C-terminal PR. The EFA6 PH
domain regulates its association with the plasma
membrane. EFA6 activates Arf6 through its Sec7 catalytic
domain and modulates this activity through its
C-terminal domain, which rearranges the actin
cytoskeleton in fibroblastic cell lines. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 126
Score = 43.8 bits (104), Expect = 1e-05
Identities = 25/61 (40%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 5 CERIDIGHNCVEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQTHAIAQS 64
I + H+ E A DYTK+ HV RL + + E L QA DT M WI + A A S
Sbjct: 63 RNAISVHHSLAEKATDYTKKPHVFRLQT-ADWREFLFQASDTEEMQSWIEAINLVAAAFS 121
Query: 65 A 65
A
Sbjct: 122 A 122
>gnl|CDD|239864 cd04399, RhoGAP_fRGD2, RhoGAP_fRGD2: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein
for Cdc42 and Rho5. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 212
Score = 43.9 bits (104), Expect = 3e-05
Identities = 28/136 (20%), Positives = 58/136 (42%), Gaps = 15/136 (11%)
Query: 169 LTEAVNKGLDASVLEQDPRWSDVN--VISSLLKSFFRRLPDSLLTTE-------LYPHFI 219
L +NK ++ ++S+LK + LPDSL+ + LY +
Sbjct: 56 LRNLLNKPKKPD--KEVIILKKFEPSTVASVLKLYLLELPDSLIPHDIYDLIRSLYSAY- 112
Query: 220 QADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVVD---NSEVNKMEARNLAIM 276
+ + R+ ++ + +LP+ H TL I+ H R+++ E + A LA
Sbjct: 113 PPSQEDSDTARIQGLQSTLSQLPKSHIATLDAIITHFYRLIEITKMGESEEEYADKLATS 172
Query: 277 FGPTLVRAGDDNMVTM 292
++R ++++T+
Sbjct: 173 LSREILRPIIESLLTI 188
>gnl|CDD|239845 cd04380, RhoGAP_OCRL1, RhoGAP_OCRL1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain present
in OCRL1-like proteins. OCRL1 (oculocerebrorenal
syndrome of Lowe 1)-like proteins contain two conserved
domains: a central inositol polyphosphate 5-phosphatase
domain and a C-terminal Rho GAP domain, this GAP domain
lacks the catalytic residue and therefore maybe
inactive. OCRL-like proteins are type II inositol
polyphosphate 5-phosphatases that can hydrolyze lipid
PI(4,5)P2 and PI(3,4,5)P3 and soluble Ins(1,4,5)P3 and
Ins(1,3,4,5)P4, but their individual specificities vary.
The functionality of the RhoGAP domain is still unclear.
Small GTPases cluster into distinct families, and all
act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 220
Score = 42.3 bits (100), Expect = 9e-05
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 4/83 (4%)
Query: 201 FFRRLPDSLLTTELYPHFIQADKIEDPATRMATIKKLVHELPEHHFQTLKYILQHLKRVV 260
F LPD ++ LY ++A + + + LP H Y+ L+ ++
Sbjct: 114 FLESLPDPIIPYSLYERLLEAVA--NNEEDKRQV--IRISLPPVHRNVFVYLCSFLRELL 169
Query: 261 DNSEVNKMEARNLAIMFGPTLVR 283
S ++ LA +FG L+R
Sbjct: 170 SESADRGLDENTLATIFGRVLLR 192
>gnl|CDD|239866 cd04401, RhoGAP_fMSB1, RhoGAP_fMSB1: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
fungal MSB1-like proteins. Msb1 was originally
identified as a multicopy suppressor of temperature
sensitive cdc42 mutation. Msb1 is a positive regulator
of the Pkc1p-MAPK pathway and 1,3-beta-glucan synthesis,
both pathways involve Rho1 regulation. Small GTPases
cluster into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific groups
of GAPs that enhance the rate of GTP hydrolysis by
several orders of magnitude.
Length = 198
Score = 38.1 bits (89), Expect = 0.002
Identities = 27/101 (26%), Positives = 43/101 (42%), Gaps = 5/101 (4%)
Query: 182 LEQDPRWSDVNVISSLLKSFFRRLPDSLLT-TELYPHFIQADKIED-PATRMATIKKLVH 239
L + R++D + + +LK + RLP S + E+Y F ++ + PA +
Sbjct: 61 LLDELRYADPHTLILVLKWIWSRLPGSKVIWWEVYEEFKARERRSNYPADAFLDLLPQC- 119
Query: 240 ELPEH-HFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGP 279
L H L L + +S VN M R L+ M GP
Sbjct: 120 -LSSPAHASILYDFFDLLSSIAAHSSVNGMSGRKLSKMAGP 159
>gnl|CDD|241231 cd00821, PH, Pleckstrin homology (PH) domain. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They
share little sequence conservation, but all have a
common fold, which is electrostatically polarized. Less
than 10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 92
Score = 33.9 bits (77), Expect = 0.015
Identities = 7/47 (14%), Positives = 14/47 (29%)
Query: 8 IDIGHNCVEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIR 54
I + + + + L +P LQA+ W+
Sbjct: 45 IPLSDGLEVELVSSSGKPNCFELVTPDRGRTYYLQAESEEEREEWLE 91
>gnl|CDD|241387 cd13233, PH_ARHGAP9-like, Beta-spectrin pleckstrin homology (PH)
domain. ARHGAP family genes encode Rho/Rac/Cdc42-like
GTPase activating proteins with RhoGAP domain. The
ARHGAP members here all have a PH domain upstream of
their C-terminal RhoGAP domain. Some have additional
N-terminal SH3 and WW domains. The members here include:
ARHGAP9, ARHGAP12, ARHGAP15, and ARHGAP27. ARHGAP27 and
ARHGAP12 shared the common-domain structure, consisting
of SH3, WW, PH, and RhoGAP domains. The PH domain of
ArhGAP9 employs a non-canonical phosphoinositide binding
mechanism, a variation of the spectrin-
Ins(4,5)P2-binding mode, that gives rise to a unique PI
binding profile, namely a preference for both PI(4,5)P2
and the PI 3-kinase products PI(3,4,5)P3 and PI(3,4)P2.
This lipid binding mechanism is also employed by the PH
domain of Tiam1 and Slm1. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 110
Score = 32.6 bits (75), Expect = 0.056
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 15 VEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQTHAIAQ 63
+E A + + RK+V +LS+ + TE LLQ+D+ + W ++ I +
Sbjct: 64 IEWAKEKSSRKNVFQLST-VTGTEYLLQSDNDTEIQEWFDAIKR-VIQR 110
>gnl|CDD|224364 COG1447, CelC, Phosphotransferase system cellobiose-specific
component IIA [Carbohydrate transport and metabolism].
Length = 105
Score = 32.2 bits (74), Expect = 0.068
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 38 ELLLQADDTLTMAHWIRDLQTHAIAQSASESNISP 72
EL+ +A+D L AH +QT I + AS I
Sbjct: 40 ELIQEANDALNEAH---HVQTKLIQKEASGEKIEV 71
>gnl|CDD|238133 cd00215, PTS_IIA_lac, PTS_IIA, PTS system, lactose/cellobiose
specific IIA subunit. The bacterial
phosphoenolpyruvate: sugar phosphotransferase system
(PTS) is a multi-protein system involved in the
regulation of a variety of metabolic and
transcriptional processes. This family is one of four
structurally and functionally distinct group IIA PTS
system cytoplasmic enzymes, necessary for the uptake of
carbohydrates across the cytoplasmic membrane and their
phosphorylation. This family of proteins normally
function as a homotrimer, stabilized by a centrally
located metal ion. Separation into subunits is thought
to occur after phosphorylation.
Length = 97
Score = 31.0 bits (71), Expect = 0.17
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 38 ELLLQADDTLTMAHWIRDLQTHAIAQSASESNISP 72
ELL +A+D+L AH QT + Q AS +
Sbjct: 36 ELLEEANDSLNEAH---HAQTKLLQQEASGEKVEV 67
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 30.5 bits (69), Expect = 0.26
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 23 KRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQ 57
KRK+ + + T LLQA+ W++ ++
Sbjct: 64 KRKNCFEIRTGDRET-FLLQAESEEERKEWVKAIR 97
>gnl|CDD|214574 smart00233, PH, Pleckstrin homology domain. Domain commonly
found in eukaryotic signalling proteins. The domain
family possesses multiple functions including the
abilities to bind inositol phosphates, and various
proteins. PH domains have been found to possess
inserted domains (such as in PLC gamma, syntrophins)
and to be inserted within other domains. Mutations in
Brutons tyrosine kinase (Btk) within its PH domain
cause X-linked agammaglobulinaemia (XLA) in patients.
Point mutations cluster into the positively charged end
of the molecule around the predicted binding site for
phosphatidylinositol lipids.
Length = 102
Score = 30.2 bits (68), Expect = 0.42
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 6 ERIDIGHNCVEVA--CDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQ 57
ID+ V A D +K+ H + + T LLLQA+ W+ L+
Sbjct: 46 GSIDLSGCTVREAPDPDSSKKPHCFEIKTSDRKT-LLLQAESEEEREKWVEALR 98
>gnl|CDD|219720 pfam08101, DUF1708, Domain of unknown function (DUF1708). This is
a yeast domain of unknown function.
Length = 381
Score = 31.2 bits (71), Expect = 0.59
Identities = 20/91 (21%), Positives = 33/91 (36%), Gaps = 4/91 (4%)
Query: 190 DVNVISSLLKSFFRRLPDSLLTTELYPHFIQADKIEDPATR-MATIKKLVHELPEH-HFQ 247
D + S LK + RLP ++ + Y F + ++ TI L H
Sbjct: 30 DPFTLISALKYCWSRLPGGVIGWDAYKLFKRKEEDSGYPRDAFLTIMPKC--LSSPAHAS 87
Query: 248 TLKYILQHLKRVVDNSEVNKMEARNLAIMFG 278
+ L + NS+ N + R L+ M
Sbjct: 88 IVYDFFDLLVAIAANSKSNGLSGRKLSRMAS 118
>gnl|CDD|223816 COG0745, OmpR, Response regulators consisting of a CheY-like
receiver domain and a winged-helix DNA-binding domain
[Signal transduction mechanisms / Transcription].
Length = 229
Score = 30.3 bits (69), Expect = 0.82
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 198 LKSFFRRLPDSLLTTELYPHFIQADKIE-DPATRMATIKKLVHELPEHHFQTLKYILQHL 256
L++ RR + + + + DP TR T+ L F+ L+ + +H
Sbjct: 112 LRALLRRNAGA--SRAEASEVLVFGDLTLDPDTRTVTLNGRELTLTPKEFELLELLARHP 169
Query: 257 KRVVDNSE 264
RV+ +
Sbjct: 170 GRVLSREQ 177
>gnl|CDD|241404 cd13250, PH_ACAP, ArfGAP with coiled-coil, ankyrin repeat and PH
domains Pleckstrin homology (PH) domain. ACAP (also
called centaurin beta) functions both as a Rab35
effector and as an Arf6-GTPase-activating protein (GAP)
by which it controls actin remodeling and membrane
trafficking. ACAP contain an NH2-terminal
bin/amphiphysin/Rvs (BAR) domain, a
phospholipid-binding domain, a PH domain, a GAP domain,
and four ankyrin repeats. The AZAPs constitute a family
of Arf GAPs that are characterized by an NH2-terminal
pleckstrin homology (PH) domain and a central Arf GAP
domain followed by two or more ankyrin repeats. On the
basis of sequence and domain organization, the AZAP
family is further subdivided into four subfamilies: 1)
the ACAPs contain an NH2-terminal bin/amphiphysin/Rvs
(BAR) domain (a phospholipid-binding domain that is
thought to sense membrane curvature), a single PH
domain followed by the GAP domain, and four ankyrin
repeats; 2) the ASAPs also contain an NH2-terminal BAR
domain, the tandem PH domain/GAP domain, three ankyrin
repeats, two proline-rich regions, and a COOH-terminal
Src homology 3 domain; 3) the AGAPs contain an
NH2-terminal GTPase-like domain (GLD), a split PH
domain, and the GAP domain followed by four ankyrin
repeats; and 4) the ARAPs contain both an Arf GAP
domain and a Rho GAP domain, as well as an NH2-terminal
sterile-a motif (SAM), a proline-rich region, a
GTPase-binding domain, and five PH domains. PMID
18003747 and 19055940 Centaurin can bind to
phosphatidlyinositol (3,4,5)P3. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold,
which is electrostatically polarized. Less than 10% of
PH domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 98
Score = 28.3 bits (64), Expect = 1.3
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 34 SSNTELLLQADDTLTMAHWIRDLQTHAIA 62
S +LQA+ WI+ +Q AIA
Sbjct: 67 SPTKSYMLQAESEEDRQAWIQAIQA-AIA 94
>gnl|CDD|131681 TIGR02633, xylG, D-xylose ABC transporter, ATP-binding protein.
Several bacterial species have enzymes xylose isomerase
and xylulokinase enzymes for xylose utilization. Members
of this protein family are the ATP-binding cassette
(ABC) subunit of the known or predicted high-affinity
xylose ABC transporter for xylose import. These genes,
which closely resemble other sugar transport ABC
transporter genes, typically are encoded near xylose
utilization enzymes and regulatory proteins. Note that
this form of the transporter contains two copies of the
ABC transporter domain (pfam00005) [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 500
Score = 29.4 bits (66), Expect = 2.8
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 15 VEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQTHAIA 62
VE+A K+ +L L PSS+ L +T + IRDL+ H +A
Sbjct: 150 VEIAKALNKQARLLILDEPSSS----LTEKETEILLDIIRDLKAHGVA 193
>gnl|CDD|241463 cd13309, PH_SKIP, SifA and kinesin-interacting protein Pleckstrin
homology (PH) domain. SKIP (also called
PLEKHM2/Pleckstrin homology domain-containing family M
member 2) is a soluble cytosolic protein that contains a
RUN domain and a PH domain separated by a unstructured
linker region. SKIP is a target of the Salmonella
effector protein SifA and the SifA-SKIP complex
regulates kinesin-1 on the bacterial vacuole. The PH
domain of SKIP binds to the N-terminal region of SifA
while the N-terminus of SKIP is proposed to bind the TPR
domain of the kinesin light chain. The opposite side of
the SKIP PH domain is proposed to bind
phosphoinositides. TSifA, SKIP, SseJ, and RhoA family
GTPases are also thought to promote host membrane
tubulation. Recently, it was shown that the lysosomal
GTPase Arl8 binds to the kinesin-1 linker SKIP and that
both are required for the normal intracellular
distribution of lysosomes. Interestingly, two kinesin
light chain binding motifs (WD) in SKIP have now been
identified to match a consensus sequence for a kinesin
light chain binding site found in several proteins
including calsyntenin-1/alcadein, caytaxin, and vaccinia
virus A36. SKIP has also been shown to interact with
Rab1A. PH domains have diverse functions, but in general
are involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 103
Score = 27.7 bits (62), Expect = 2.9
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 36 NTELLLQADDTLTMAHWIRDLQTHAIAQSAS 66
L L A D + W+ ++ QSAS
Sbjct: 76 RPSLELAAPDEYEASEWL-----QSLCQSAS 101
>gnl|CDD|217884 pfam04086, SRP-alpha_N, Signal recognition particle, alpha subunit,
N-terminal. SRP is a complex of six distinct
polypeptides and a 7S RNA that is essential for
transferring nascent polypeptide chains that are
destined for export from the cell to the translocation
apparatus of the endoplasmic reticulum (ER) membrane.
SRP binds hydrophobic signal sequences as they emerge
from the ribosome, and arrests translation.
Length = 272
Score = 28.9 bits (65), Expect = 2.9
Identities = 16/80 (20%), Positives = 24/80 (30%), Gaps = 4/80 (5%)
Query: 61 IAQSASESNISPASGQKNRKFASASTSPRKSSATEATLPPSPKSKTWKGRVAKQFRRIQA 120
+ + ES S + R F S +K+ + P K R Q
Sbjct: 94 LRELEKESKKQAKSPKAMRTF-EESKKSKKTVDSMIERKPKEPGLKRKQRKKAQESATSP 152
Query: 121 ---GAGSPNSPHPPYPPGSN 137
+ +PNS P P
Sbjct: 153 ESSPSSTPNSSRPSTPHLLK 172
Score = 27.4 bits (61), Expect = 9.8
Identities = 11/39 (28%), Positives = 14/39 (35%), Gaps = 2/39 (5%)
Query: 75 GQKNRKFASASTSPRKSSATEATL--PPSPKSKTWKGRV 111
G R +A S SS E + +PK K R
Sbjct: 176 GPSRRAKKAAKLSSTASSGDEKSPKSKAAPKKAGKKMRK 214
>gnl|CDD|241435 cd13281, PH_PLEKHD1, Pleckstrin homology (PH) domain containing,
family D (with coiled-coil domains) member 1 PH domain.
Human PLEKHD1 (also called UPF0639, pleckstrin homology
domain containing, family D (with M protein repeats)
member 1) is a single transcript and contains a single
PH domain. PLEKHD1 is conserved in human, chimpanzee, ,
dog, cow, mouse, chicken, zebrafish, and Caenorhabditis
elegans. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 139
Score = 27.7 bits (62), Expect = 4.0
Identities = 10/45 (22%), Positives = 16/45 (35%)
Query: 13 NCVEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQ 57
C A R + +S P ++L AD W+ L+
Sbjct: 71 GCSIEAGRDPGRPYCFLISHPDFKGSIILAADSEEEQESWLDMLR 115
>gnl|CDD|233365 TIGR01347, sucB, 2-oxoglutarate dehydrogenase complex
dihydrolipoamide succinyltransferase (E2 component).
This model describes the TCA cycle 2-oxoglutarate system
E2 component, dihydrolipoamide succinyltransferase. It
is closely related to the pyruvate dehydrogenase E2
component, dihydrolipoamide acetyltransferase. The seed
for this model includes mitochondrial and Gram-negative
bacterial forms. Mycobacterial candidates are highly
derived, differ in having and extra copy of the
lipoyl-binding domain at the N-terminus. They score
below the trusted cutoff, but above the noise cutoff and
above all examples of dihydrolipoamide acetyltransferase
[Energy metabolism, TCA cycle].
Length = 403
Score = 28.5 bits (64), Expect = 4.7
Identities = 26/141 (18%), Positives = 43/141 (30%), Gaps = 16/141 (11%)
Query: 16 EVACDYTKRKHVLRLSSPSSN--TELLLQADDTLTMAHWIRDLQTHAIA--QSASESNIS 71
E + K VL + SP+ E+L + DT+ + L+ A ++S
Sbjct: 32 ENIVEIETDKVVLEVPSPADGVLQEILFKEGDTVESGQVLAILEEGNDATAAPPAKSGEE 91
Query: 72 PASGQKNR---------KFASASTSPRKSSATEATLPPSPKSKTWKGRVAKQFRRIQAGA 122
S S + R+ + + GRV K+ I
Sbjct: 92 KEETPAASAAAAPTAAANRPSLSPAARRLAKEHGIDLSAVPGTGVTGRVTKE--DIIKKT 149
Query: 123 GSPNSPHPPYPPGSNIGVPLQ 143
+P S P P + P
Sbjct: 150 EAPASAQQP-APAAAAKAPAN 169
>gnl|CDD|181856 PRK09436, thrA, bifunctional aspartokinase I/homoserine
dehydrogenase I; Provisional.
Length = 819
Score = 28.6 bits (65), Expect = 5.1
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 60 AIAQSASESNIS 71
AIAQ +SE +IS
Sbjct: 429 AIAQGSSERSIS 440
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 28.6 bits (64), Expect = 5.6
Identities = 21/122 (17%), Positives = 31/122 (25%), Gaps = 1/122 (0%)
Query: 13 NCVEVACDYTKRKHVLRLSSPSSNTELLLQADDTLTMAHWIRDLQTHAIAQSASESNISP 72
N V + +L + P R ++ A +AS +
Sbjct: 760 NPSLVPAKLAEALALLEPAEPQRGAGSSPPVRAEAAFRRPGRLRRSGPAADAASRTASKR 819
Query: 73 ASGQKNRKFASASTSPRKSSATEATLPPSPKSKTWKGRVAKQFRRIQAGAGSPNSPHPPY 132
S S S+ P + A PP +S G P PP
Sbjct: 820 KSRSHTPDGGSESSGPARPPGAAAR-PPPARSSESSKSKPAAAGGRARGKNGRRRPRPPE 878
Query: 133 PP 134
P
Sbjct: 879 PR 880
>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional.
Length = 943
Score = 28.5 bits (63), Expect = 5.9
Identities = 20/67 (29%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 74 SGQKNRKFASASTSPRKS----SATEATLPPSPKSKTWKGRVAKQFRRIQAGAGSPNSPH 129
K+ K P+K SA T P SPK + K +R ++ SP P
Sbjct: 580 EFPKDPKHPKDPEEPKKPKRPRSAQRPTRPKSPK-LPELLDIPKSPKRPESPK-SPKRPP 637
Query: 130 PPYPPGS 136
PP P S
Sbjct: 638 PPQRPSS 644
>gnl|CDD|202178 pfam02255, PTS_IIA, PTS system, Lactose/Cellobiose specific IIA
subunit. The bacterial phosphoenolpyruvate: sugar
phosphotransferase system (PTS) is a multi-protein
system involved in the regulation of a variety of
metabolic and transcriptional processes. The
lactose/cellobiose-specific family are one of four
structurally and functionally distinct group IIA PTS
system enzymes. This family of proteins normally
function as a homotrimer, stabilised by a centrally
located metal ion. Separation into subunits is thought
to occur after phosphorylation.
Length = 96
Score = 26.6 bits (60), Expect = 6.5
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 38 ELLLQADDTLTMAHWIRDLQTHAIAQSASESNISP 72
ELL +A++ L AH + QT I + A +
Sbjct: 35 ELLEEANEALLEAH---NAQTKLIQKEAGGEKVEV 66
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 27.9 bits (63), Expect = 7.4
Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 232 ATIKKLVHELPEH----HFQTLKYILQHLKRVVDNSEVNKMEARNLAIMFGPT 280
+KL+ L EH +Y+L+ L ++ + ++ + + GPT
Sbjct: 178 EIAEKLLKLLLEHMPPRERTAWRYLLELLANMIPVRVEDILKQGGVVALVGPT 230
>gnl|CDD|237941 PRK15315, PRK15315, outer membrane protein RatA; Provisional.
Length = 1865
Score = 28.1 bits (62), Expect = 7.4
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 83 SASTSPR--KSSATEATLPPSPKSKTWKGRVAKQFRRIQAGAGSPNSPHPPYP 133
+ STS R S+ TE L P + W+ R + A A +P++P P P
Sbjct: 89 ATSTSMRAVNSTDTEGDLFSDPPTIAWENRQPPAMGLVWADAATPDTPLSPQP 141
>gnl|CDD|205978 pfam13805, Pil1, Eisosome component PIL1. In the budding yeast, S.
cerevisiae, Pil1 and another cytoplasmic protein, Lsp1,
together form large immobile assemblies at the plasma
membrane that mark sites for endocytosis, called
eisosomes. Endocytosis functions to recycle plasma
membrane components, to regulate cell-surface expression
of signalling receptors and to internalise nutrients in
all eukaryotic cells.
Length = 271
Score = 27.5 bits (61), Expect = 8.4
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 87 SPRKSSATEATLPPSPKSKTWKGR------VAKQFRRIQAGAGSP 125
+ R +A++ PP P S T GR ++ FR+ AGA P
Sbjct: 9 NSRAPTASQLQNPPPPPSSTKSGRFFGKGPLSHSFRKNAAGAFGP 53
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
0.316 0.129 0.382
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,362,426
Number of extensions: 1308549
Number of successful extensions: 1487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1447
Number of HSP's successfully gapped: 78
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
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: 59 (26.5 bits)