RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3395
(775 letters)
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 336 bits (862), Expect = e-110
Identities = 155/190 (81%), Positives = 173/190 (91%)
Query: 7 LEQLIPIVNKLQDAFTQLGVPMQMDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVT 66
+E+LIP+VNKLQDAF+ LG +DLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVT
Sbjct: 1 MEELIPLVNKLQDAFSALGQSCDLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVT 60
Query: 67 RRPLVLQLINSMTEYAEFLHCKGKKFVDFDEVRREIEAETDRITGSNKGISNVPINLRVY 126
RRPL+LQLI S TEYAEFLHCKGKKF DFDEVR EIEAETDR+TG+NKGIS +PINLRVY
Sbjct: 61 RRPLILQLIKSKTEYAEFLHCKGKKFTDFDEVRNEIEAETDRVTGTNKGISGIPINLRVY 120
Query: 127 SPNVLNITLIDLPGLTKVPVGDQPIDIEQQIKDMLFQFITKETCLILAVTPANTDLATSD 186
SP+VLN+TLIDLPG+TKV VGDQP DIE QIK M+ QFI++E CLILAVTPANTDLA SD
Sbjct: 121 SPHVLNLTLIDLPGITKVAVGDQPPDIEYQIKKMIKQFISREECLILAVTPANTDLANSD 180
Query: 187 ALQIAKQVDP 196
AL++AK+VDP
Sbjct: 181 ALKLAKEVDP 190
Score = 129 bits (325), Expect = 1e-33
Identities = 59/72 (81%), Positives = 64/72 (88%)
Query: 196 PDVLNLTLVDLPGMTKVPIGDQPADIEYQIKSMILQFIKRDNCLILAVTPANSDLANSDA 255
P VLNLTL+DLPG+TKV +GDQP DIEYQIK MI QFI R+ CLILAVTPAN+DLANSDA
Sbjct: 122 PHVLNLTLIDLPGITKVAVGDQPPDIEYQIKKMIKQFISREECLILAVTPANTDLANSDA 181
Query: 256 LKLAKEVDPPGL 267
LKLAKEVDP GL
Sbjct: 182 LKLAKEVDPQGL 193
>gnl|CDD|206738 cd08771, DLP_1, Dynamin_like protein family includes dynamins and
Mx proteins. The dynamin family of large
mechanochemical GTPases includes the classical dynamins
and dynamin-like proteins (DLPs) that are found
throughout the Eukarya. These proteins catalyze membrane
fission during clathrin-mediated endocytosis. Dynamin
consists of five domains; an N-terminal G domain that
binds and hydrolyzes GTP, a middle domain (MD) involved
in self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific, mediates
uptake of synaptic vesicles in presynaptic terminals;
dynamin-2 is expressed ubiquitously and similarly
participates in membrane fission; mutations in the MD,
PH and GED domains of dynamin 2 have been linked to
human diseases such as Charcot-Marie-Tooth peripheral
neuropathy and rare forms of centronuclear myopathy.
Dynamin 3 participates in megakaryocyte progenitor
amplification, and is also involved in cytoplasmic
enlargement and the formation of the demarcation
membrane system. This family also includes
interferon-induced Mx proteins that inhibit a wide range
of viruses by blocking an early stage of the replication
cycle. Dynamin oligomerizes into helical structures
around the neck of budding vesicles in a GTP
hydrolysis-dependent manner.
Length = 278
Score = 307 bits (789), Expect = 4e-99
Identities = 139/285 (48%), Positives = 183/285 (64%), Gaps = 23/285 (8%)
Query: 31 DLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLINSMT--------EYA 82
DLPQI VVG QS+GKSSVLE VGRDFLPRGSGI TRRPL LQL S + E+
Sbjct: 2 DLPQIVVVGDQSSGKSSVLEALVGRDFLPRGSGICTRRPLELQLRRSPSESDEDEKEEWG 61
Query: 83 EFLHCKGKKFVDFDEVRREIEAETDRITGSNKGISNVPINLRVYSPNVLNITLIDLPGLT 142
EFLH K K+F DF+E+R EIE ETDR+ G NKGIS PI L + SP+V N+TL+DLPGL
Sbjct: 62 EFLHLKSKEFTDFEELREEIEKETDRVAGENKGISPEPIRLEIESPDVPNLTLVDLPGLI 121
Query: 143 KVPVGDQPIDIEQQIKDMLFQFITKETCLILAVTPANTDLATSDALQIAKQVDPDVLNLT 202
KVPVGDQP DIE+QI+ M+ +I+ +ILAV PAN DLA S+AL++A++VDP+
Sbjct: 122 KVPVGDQPEDIEEQIRSMVKSYISNPRSIILAVVPANVDLANSEALKLAREVDPEGERTI 181
Query: 203 LVDLPGMTKVPIGDQPADIEYQIKSMILQFIKRDNCLILA----VTPANSDLANSDALKL 258
V +TK+ + D D E ++L + L L V + D+ + +++
Sbjct: 182 GV----LTKLDLMDPGTDAE----DILLLLQGKVIPLKLGYVGVVNRSQKDIDSGKSIEE 233
Query: 259 AKEVDPP--GLHPSYRHL-ADRLGTPYLQRVLNQQLTNHIRDTLP 300
A E + HP Y+ L A R+GTP L++ L++ L HIR++LP
Sbjct: 234 ALEAEEEFFETHPWYKLLPASRVGTPALRKRLSKLLQKHIRESLP 278
>gnl|CDD|216255 pfam01031, Dynamin_M, Dynamin central region. This region lies
between the GTPase domain, see pfam00350, and the
pleckstrin homology (PH) domain, see pfam00169.
Length = 296
Score = 295 bits (758), Expect = 3e-94
Identities = 107/243 (44%), Positives = 154/243 (63%), Gaps = 2/243 (0%)
Query: 268 HPSYRHLADRLGTPYLQRVLNQQLTNHIRDTLPGLRDRLQKQLLTLEKDVEQFKHFRPDD 327
HP YR LA+R GTPYL + LNQ+L NHIR +LP L+ ++ K+L EK++E++ P+D
Sbjct: 47 HPHYRTLAERCGTPYLAKKLNQELVNHIRKSLPDLKSQINKKLQETEKELERYGDDPPED 106
Query: 328 PSIKTKAMLQMIQQLQSDFERTIEGSGSAQINTMELSGGAKINRLFHERFPFEIVKMEFD 387
P+ K +L +I DF+ I+G ++T ELSGGA+I +FHE FP + ++
Sbjct: 107 PAEKGAFLLDLITAFNQDFKNLIDGE-EDDLSTNELSGGARIRYIFHEWFPKLLKSIDPF 165
Query: 388 EKELRREIAFAIRNIHGIRVGLFTPDMAFEAIVKKQISRLKEPALKCVDLVVAELSNVVR 447
EK EI AIRN G R+ LF P+ AFE +VKKQI RL+EPALKCVDLV EL +
Sbjct: 166 EKLSDEEIRTAIRNYRGRRLPLFVPEKAFELLVKKQIKRLEEPALKCVDLVYEELRRIFL 225
Query: 448 -ICTDKMSRYPRLREETERIITSYVRNREQQCKEQIVLLVDCELAYMNTNHEDFIGFANV 506
I + ++SR+P L+E + ++ +R + + ++ + L+D ELAY+NTNH DFIG
Sbjct: 226 KIASKELSRFPNLKEAIKEVVEDILREQLEPTEKMVRDLIDMELAYINTNHPDFIGGLQA 285
Query: 507 MFS 509
+
Sbjct: 286 VKK 288
>gnl|CDD|241287 cd01256, PH_dynamin, Dynamin pleckstrin homology (PH) domain.
Dynamin is a GTPase that regulates endocytic vesicle
formation. It has an N-terminal GTPase domain, followed
by a PH domain, a GTPase effector domain and a
C-terminal proline arginine rich domain. Dynamin-like
proteins, which are found in metazoa, plants and yeast
have the same domain architecture as dynamin, but lack
the 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 = 112
Score = 253 bits (649), Expect = 5e-81
Identities = 88/112 (78%), Positives = 104/112 (92%)
Query: 526 NQVIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQ 585
NQVIRKGW+ I+N+G MKGGS++YWFVLT+E++SW+KDEEE+EKKYMLPLD LKLRDVE+
Sbjct: 1 NQVIRKGWLTINNIGFMKGGSKEYWFVLTAESLSWYKDEEEKEKKYMLPLDNLKLRDVEK 60
Query: 586 GFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRAGVYPEK 637
GFMS +H FALFN + RNVYKDYKQLELSCE Q++VDSWKASFLRAGVYPE+
Sbjct: 61 GFMSSKHIFALFNTDQRNVYKDYKQLELSCETQEEVDSWKASFLRAGVYPER 112
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 192 bits (489), Expect = 3e-57
Identities = 87/171 (50%), Positives = 108/171 (63%), Gaps = 22/171 (12%)
Query: 35 IAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQL--------INSMTEYAEFLH 86
IAVVG QSAGKSSVL +GRD LPRG G TRRPLVL+L EY + L
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDGL- 59
Query: 87 CKGKKFVDFDEVRREIEAETDRITGSNKGISNVPINLRVYSPNVLNITLIDLPGLTKVPV 146
KKF DF E+R EIE ETD+I+G+ KGIS+ PI L + SP V +TL+D PGL V V
Sbjct: 60 ---KKFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVPGLTLVDTPGLDSVAV 116
Query: 147 GDQPIDIEQQIKDMLFQFITKETCLILAVTPANTDLATSDALQIAKQVDPD 197
GDQ D+ ++I +ILAV AN DL+TS+AL +A++VDP+
Sbjct: 117 GDQ---------DLTEEYIKPA-DIILAVVDANHDLSTSEALFLAREVDPN 157
>gnl|CDD|202159 pfam02212, GED, Dynamin GTPase effector domain.
Length = 90
Score = 115 bits (291), Expect = 7e-31
Identities = 35/90 (38%), Positives = 52/90 (57%)
Query: 660 ERQVETIRNLVDSYMKIVTKTCRDLVPKTIMLLIINNAKDFINGELLAHLYASGDQAAMM 719
E +VE IR L+ SY IV K D +PK IM ++N +K+ + ELL LY D ++
Sbjct: 1 ELEVEEIRRLLKSYFNIVRKRIADQIPKAIMYFLVNESKESLQKELLQLLYKKEDLDELL 60
Query: 720 EESPEEALKREEMLRMYHACKEALRIIGDV 749
+E PE A KR+E+ + K+A I+ +V
Sbjct: 61 KEDPEIAQKRKELKKRLERLKKAREILAEV 90
>gnl|CDD|128597 smart00302, GED, Dynamin GTPase effector domain.
Length = 92
Score = 111 bits (281), Expect = 2e-29
Identities = 39/92 (42%), Positives = 56/92 (60%)
Query: 658 QLERQVETIRNLVDSYMKIVTKTCRDLVPKTIMLLIINNAKDFINGELLAHLYASGDQAA 717
+ ++E I++LV SY IV+KT D VPK IM L++N +KD + ELLA LY
Sbjct: 1 YEDSELEEIKSLVKSYFTIVSKTLADQVPKAIMYLLVNESKDSLQNELLALLYKEELLDE 60
Query: 718 MMEESPEEALKREEMLRMYHACKEALRIIGDV 749
++EE PE A KR+E+ + K+A +II V
Sbjct: 61 LLEEDPEIASKRKELKKRLELLKKARQIIAAV 92
>gnl|CDD|223771 COG0699, COG0699, Predicted GTPases (dynamin-related) [General
function prediction only].
Length = 546
Score = 118 bits (297), Expect = 9e-28
Identities = 100/469 (21%), Positives = 179/469 (38%), Gaps = 70/469 (14%)
Query: 79 TEYAEFLHCKGKKFVDFDEVRREIEAETDRITGSNKGISNVPINLRVYSPNVLNITLIDL 138
TE EF H +F+DF VR E E ET + G N GI+ V I L++ + +L +T +DL
Sbjct: 1 TEEFEFTHAPIFRFLDFSRVRSEKEKETLKDDGRNSGITEVIIELKIAAERLLQLTDVDL 60
Query: 139 PGLTKVPVGDQPIDIEQQIKDMLFQFITKETCLILAVTPANTDLATSDALQIAKQVDPDV 198
PGL KVP+ +P DI Q+ + + I E LIL N D ++++ ++ D
Sbjct: 61 PGLRKVPLSLEPEDIAQEDELLDLGKIEIENALILLGIAPNADEEAELSIEVIREADRVP 120
Query: 199 LNLTLVDLPGMTKVPIGDQPADIEYQIKSMILQFIKRDNCLILAVTPANSDLANSDALKL 258
+ ++ G T + + + + + L + L + L
Sbjct: 121 TKINFLN--GGTNLTLI------------LGNGDVLVVDALETDI-----QLLKTALEAL 161
Query: 259 AKEVDPPGLHPSYRHLADRLGTPYLQRVLNQQLTNHIRDTLP--GLRDRLQKQLLTLEKD 316
KE++ HP + PYL+++L++ L H+R L+D +Q E +
Sbjct: 162 VKELEYFAEHPLLEDNEKLVLLPYLKKLLSKILELHLRLLPKYDKLQDVIQLSQDLFENE 221
Query: 317 VEQFKHFRPDDPSIKTKAMLQMIQQLQSDFERTIEGSGSAQINTMELSGGAKINRLFHER 376
V L +IQ L + G+ R
Sbjct: 222 V------------------LAVIQTLLKRLSELVRGA----------------------R 241
Query: 377 FPFEIVKMEFDEKELRREIAFAIRNIHGIRVGLFTPDMAFEAIVKKQISRLKEPALKCVD 436
I+ E+ + G R L + + +V+ I + + +
Sbjct: 242 IRLNIILFSDLEEVSDSPVLLKELASKGERPSLLSGLTLLDTLVETPIGQFDTQINQLLR 301
Query: 437 LVVAELSNVVRIC-----TDKMSRYPRLREETERIITSYVRNREQQCKEQIVLLVDCELA 491
+++EL VRI + S +P+L E E ++ + + ++ ++D E
Sbjct: 302 KLISEL---VRILLKELESASSSPFPKLSEALEEVVNQLKNKVDSGLESGLLAIIDIEER 358
Query: 492 YMNTNHEDFIGFANVMFSAQQTTDNSNKAGRKLG-NQVIRKGWMCIHNL 539
Y+NT H F+ + DN R L +++ M +++L
Sbjct: 359 YINTKHPLFLSLRQAAAILSKVLDNLEALLRSLDDSRLRELSDMGLNSL 407
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 57.1 bits (138), Expect = 3e-10
Identities = 20/107 (18%), Positives = 43/107 (40%), Gaps = 11/107 (10%)
Query: 528 VIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKD--EEEREKKYMLPLDGLKLRDVEQ 585
VI++GW+ + + + +FVL + ++KD + K +PL G ++ V
Sbjct: 1 VIKEGWL-LKKGSGGRKSWKKRYFVLFDGVLLYYKDSKKSSSRPKGSIPLSGCQVTKVPD 59
Query: 586 GFMS-RRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRA 631
R++ F + + L E++++ W + A
Sbjct: 60 SEDGKRKNCFEIRTGDRE-------TFLLQAESEEERKEWVKAIRSA 99
>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 = 56.0 bits (135), Expect = 1e-09
Identities = 20/108 (18%), Positives = 49/108 (45%), Gaps = 12/108 (11%)
Query: 528 VIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREK---KYMLPLDGLKLRDVE 584
VI++GW+ G K + +FVL + + ++K +++++ K + L G +R+
Sbjct: 1 VIKEGWL-YKKSGGGKKSWKKRYFVLFNSTLLYYKSKKDKKSYKPKGSIDLSGCTVREAP 59
Query: 585 QGF-MSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRA 631
+ H F + + + + L E++++ + W + +A
Sbjct: 60 DPDSSKKPHCFEIKTSDRKTLL-------LQAESEEEREKWVEALRKA 100
>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 = 48.5 bits (115), Expect = 3e-07
Identities = 23/98 (23%), Positives = 47/98 (47%), Gaps = 12/98 (12%)
Query: 530 RKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKY--MLPL-DGLKLRDVEQG 586
++GW+ +K + WFVL + + ++K +++ KK ++PL DGL++ V
Sbjct: 1 KEGWLKKRGGKGLKS-WKKRWFVLFDDVLLYYKSKKDSSKKPKGLIPLSDGLEVELVSS- 58
Query: 587 FMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSW 624
+ + F L P+ Y L E++++ + W
Sbjct: 59 -SGKPNCFELVTPDRGRTY------YLQAESEEEREEW 89
>gnl|CDD|241402 cd13248, PH_PEPP1_2_3, Phosphoinositol 3-phosphate binding proteins
1, 2, and 3 pleckstrin homology (PH) domain. PEPP1
(also called PLEKHA4/PH domain-containing family A
member 4 and RHOXF1/Rhox homeobox family member 1), and
related homologs PEPP2 (also called PLEKHA5/PH
domain-containing family A member 5) and PEPP3 (also
called PLEKHA6/PH domain-containing family A member 6),
have PH domains that interact specifically with
PtdIns(3,4)P3. Other proteins that bind PtdIns(3,4)P3
specifically are: TAPP1 (tandem PH-domain-containing
protein-1) and TAPP2], PtdIns3P AtPH1, and Ptd-
Ins(3,5)P2 (centaurin-beta2). All of these proteins
contain at least 5 of the 6 conserved amino acids that
make up the putative phosphatidylinositol 3,4,5-
trisphosphate-binding motif (PPBM) located at their
N-terminus. 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 = 104
Score = 46.5 bits (111), Expect = 2e-06
Identities = 22/103 (21%), Positives = 41/103 (39%), Gaps = 19/103 (18%)
Query: 528 VIRKGWMCIHNLGIMKGGS-----RDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRD 582
V+ GW+ H G GS + WFVL + ++KD EE + + L +
Sbjct: 7 VVFSGWL--HKQG----GSGLKNWKKRWFVLKDNCLYYYKDPEEEKALGSILLPSYTISP 60
Query: 583 V-EQGFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSW 624
++R+ F + R Y + + Q++++ W
Sbjct: 61 ASPSDEINRKFAFKAEHAGMRTYY-------FAADTQEEMEQW 96
>gnl|CDD|241427 cd13273, PH_SWAP-70, Switch-associated protein-70 Pleckstrin
homology (PH) domain. SWAP-70 (also called
Differentially expressed in FDCP 6/DEF-6 or IRF4-binding
protein) functions in cellular signal transduction
pathways (in conjunction with Rac), regulates cell
motility through actin rearrangement, and contributes to
the transformation and invasion activity of mouse embryo
fibroblasts. Metazoan SWAP-70 is found in B lymphocytes,
mast cells, and in a variety of organs. Metazoan SWAP-70
contains an N-terminal EF-hand motif, a centrally
located PH domain, and a C-terminal coiled-coil domain.
The PH domain of Metazoan SWAP-70 contains a
phosphoinositide-binding site and a nuclear localization
signal (NLS), which localize SWAP-70 to the plasma
membrane and nucleus, respectively. The NLS is a
sequence of four Lys residues located at the N-terminus
of the C-terminal a-helix; this is a unique
characteristic of the Metazoan SWAP-70 PH domain. The
SWAP-70 PH domain binds PtdIns(3,4,5)P3 and
PtdIns(4,5)P2 embedded in lipid bilayer vesicles. There
are additional plant SWAP70 proteins, but these are not
included in this hierarchy. Rice SWAP70 (OsSWAP70)
exhibits GEF activity toward the its Rho GTPase, OsRac1,
and regulates chitin-induced production of reactive
oxygen species and defense gene expression in rice.
Arabidopsis SWAP70 (AtSWAP70) plays a role in both PAMP-
and effector-triggered immunity. Plant SWAP70 contains
both DH and PH domains, but their arrangement is the
reverse of that in typical DH-PH-type Rho GEFs, wherein
the DH domain is flanked by a C-terminal 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 = 110
Score = 43.8 bits (104), Expect = 2e-05
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 528 VIRKGWMCIHNLGIMKGGS-----RDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRD 582
VI+KG++ K G R+ WFVL ++S++K E+ +EKK + LD +
Sbjct: 8 VIKKGYL-------WKKGHLLPTWRERWFVLKPNSLSYYKSEDLKEKKGEIALDSNCCVE 60
Query: 583 VEQGFMSRRHTFALFNPE 600
++ F + P+
Sbjct: 61 SLPDREGKKCRFCVKTPD 78
>gnl|CDD|241283 cd01252, PH_GRP1-like, General Receptor for
Phosphoinositides-1-like Pleckstrin homology (PH)
domain. GRP1/cytohesin3 and the related proteins ARNO
(ARF nucleotide-binding site opener)/cytohesin-2 and
cytohesin-1 are ARF exchange factors that contain a
pleckstrin homology (PH) domain thought to target these
proteins to cell membranes through binding
polyphosphoinositides. The PH domains of all three
proteins exhibit relatively high affinity for
PtdIns(3,4,5)P3. Within the Grp1 family, diglycine (2G)
and triglycine (3G) splice variants, differing only in
the number of glycine residues in the PH domain,
strongly influence the affinity and specificity for
phosphoinositides. The 2G variants selectively bind
PtdIns(3,4,5)P3 with high affinity,the 3G variants bind
PtdIns(3,4,5)P3 with about 30-fold lower affinity and
require the polybasic region for plasma membrane
targeting. These ARF-GEFs share a common, tripartite
structure consisting of an N-terminal coiled-coil
domain, a central domain with homology to the yeast
protein Sec7, a PH domain, and a C-terminal polybasic
region. The Sec7 domain is autoinhibited by conserved
elements proximal to the PH domain. GRP1 binds to the
DNA binding domain of certain nuclear receptors
(TRalpha, TRbeta, AR, ER, but not RXR), and can repress
thyroid hormone receptor (TR)-mediated transactivation
by decreasing TR-complex formation on thyroid hormone
response elements. ARNO promotes sequential activation
of Arf6, Cdc42 and Rac1 and insulin secretion. Cytohesin
acts as a PI 3-kinase effector mediating biological
responses including cell spreading and adhesion,
chemotaxis, protein trafficking, and cytoskeletal
rearrangements, only some of which appear to depend on
their ability to activate ARFs. 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 = 118
Score = 41.5 bits (98), Expect = 2e-04
Identities = 26/114 (22%), Positives = 53/114 (46%), Gaps = 26/114 (22%)
Query: 528 VIRKGWMCIHNLGIMKGGSR-----DYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRD 582
R+GW+ +K G R WF+LT + +F+ ++E + ++PL+ L +R+
Sbjct: 3 PDREGWL-------LKLGGRVKSWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSVRE 55
Query: 583 VEQGFMSRRHTFALFNP------------EGRNVYKDYKQLELSCENQDDVDSW 624
VE + F L++P +G+ V ++ +S ++++D W
Sbjct: 56 VED--SKKPFCFELYSPSNEVIKACKTDSDGKVVEGNHTVYRISAATEEEMDEW 107
>gnl|CDD|241452 cd13298, PH1_PH_fungal, Fungal proteins Pleckstrin homology (PH)
domain, repeat 1. The functions of these fungal
proteins are unknown, but they all contain 2 PH domains.
This cd represents the first PH repeat. 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 = 106
Score = 39.5 bits (93), Expect = 6e-04
Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 18/95 (18%)
Query: 550 WFVLTSENISWFKDEEEREKKYMLPLDGL----KLRDVEQGFMSRRHTFALFNPEGRNVY 605
WFVL +S++KDE+E + + ++ L L L+D + R++ FA++ P +N +
Sbjct: 26 WFVLRPCQLSYYKDEKEYKLRRVINLSELTAVAPLKDKK-----RKNVFAIYTPS-KNYH 79
Query: 606 KDYKQLELSCENQDDVDSWKASFLRAGVYPEKSTD 640
++ D + W +R +
Sbjct: 80 -------FQASSEKDANEW-VEAIREESRSRDEEE 106
>gnl|CDD|241425 cd13271, PH2_TAPP1_2, Tandem PH-domain-containing proteins 1 and 2
Pleckstrin homology (PH) domain, C-terminal repeat. The
binding of TAPP1 (also called PLEKHA1/pleckstrin
homology domain containing, family A (phosphoinositide
binding specific) member 1) and TAPP2 (also called
PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4,
5)P3, function as negative regulators of insulin and
PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin
complex). TAPP1 and TAPP2 contain two sequential PH
domains in which the C-terminal PH domain specifically
binds PtdIns(3,4)P2 with high affinity. The N-terminal
PH domain does not interact with any phosphoinositide
tested. They also contain a C-terminal PDZ-binding motif
that interacts with several PDZ-binding proteins,
including PTPN13 (known previously as PTPL1 or FAP-1) as
well as the scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. 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 = 114
Score = 39.6 bits (93), Expect = 7e-04
Identities = 26/113 (23%), Positives = 48/113 (42%), Gaps = 22/113 (19%)
Query: 522 RKLGNQVIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLR 581
+ G VI+ G+ C+ + K R Y F+L IS++K E ++E PL + L+
Sbjct: 2 QPAGRNVIKSGY-CVKQGAVRKNWKRRY-FILDDNTISYYKSETDKE-----PLRTIPLK 54
Query: 582 DV-------EQGFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKAS 627
+V + R + F + R Y + ++ +D+ SW +
Sbjct: 55 EVLKVHECLSGDLLMRDNLFEIIT-TSRTFY-------IQADSPEDMHSWIKA 99
>gnl|CDD|241430 cd13276, PH_AtPH1, Arabidopsis thaliana Pleckstrin homolog (PH) 1
(AtPH1) PH domain. AtPH1 is expressed in all plant
tissue and is proposed to be the plant homolog of human
pleckstrin. Pleckstrin consists of two PH domains
separated by a linker region, while AtPH has a single PH
domain with a short N-terminal extension. AtPH1 binds
PtdIns3P specifically and is thought to be an adaptor
molecule since it has no obvious catalytic functions. 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 = 117
Score = 38.9 bits (91), Expect = 0.001
Identities = 28/125 (22%), Positives = 49/125 (39%), Gaps = 27/125 (21%)
Query: 530 RKGWMCIHNLGIMKGGS----RDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDV-- 583
+ GW+ +GGS R WFVL + +FKDE+ + P + L D
Sbjct: 9 KAGWLT------KQGGSIKTWRRRWFVLKQGKLFYFKDEDPDSE----PRGVIDLSDCLT 58
Query: 584 ---EQGFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRAGVYPEKSTD 640
+ ++ F + PE R Y L +++ + + W ++ RA V +S
Sbjct: 59 VKSAEEATNKEFAFEVSTPE-RTFY-------LIADSEKEKEEWISAIGRAIVKLSRSKG 110
Query: 641 QSNGD 645
+
Sbjct: 111 TIDEV 115
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 40.3 bits (95), Expect = 0.002
Identities = 41/221 (18%), Positives = 76/221 (34%), Gaps = 75/221 (33%)
Query: 31 DLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLINSMTEYAEFLHCKGK 90
DLP+IA G + GKSS++ + L R S P QLIN
Sbjct: 23 DLPEIAFAGRSNVGKSSLINALTNQKNLARTSK----TPGRTQLIN-------------- 64
Query: 91 KFVDFDEVRREIEAETDRITGSNKGISNVPINLRVYSPNVLNITLIDLP--GLTKVPVGD 148
F + D+ R L+DLP G KV
Sbjct: 65 -FFEVDDELR----------------------------------LVDLPGYGYAKV---- 85
Query: 149 QPIDIEQQIKDMLFQFITKETCLILAV-------TPANTDLATSDALQIAKQVDPDVLNL 201
P +++++ K ++ +++ K L V P + D + ++ ++ V
Sbjct: 86 -PKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDR---EMIEFLLELGIPV--- 138
Query: 202 TLVDLPGMTKVPIGDQPADIEYQIKSMILQFIKRDNCLILA 242
+V L K+ ++ + ++ + + D ++L
Sbjct: 139 -IVVLTKADKLKKSERNKQLN-KVAEELKKPPPDDQWVVLF 177
>gnl|CDD|241413 cd13259, PH5_ARAP, ArfGAP with RhoGAP domain, ankyrin repeat and PH
domain Pleckstrin homology (PH) domain, repeat 5. ARAP
proteins (also called centaurin delta) are
phosphatidylinositol 3,4,5-trisphosphate-dependent
GTPase-activating proteins that modulate actin
cytoskeleton remodeling by regulating ARF and RHO family
members. They bind phosphatidylinositol
3,4,5-trisphosphate (PtdIns(3,4,5)P3) and
phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2)
binding. There are 3 mammalian ARAP proteins: ARAP1,
ARAP2, and ARAP3. All ARAP proteins contain a N-terminal
SAM (sterile alpha motif) domain, 5 PH domains, an
ArfGAP domain, 2 ankyrin domain, A RhoGap domain, and a
Ras-associating domain. This hierarchy contains the five
PH domain in ARAP. 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 = 121
Score = 38.1 bits (89), Expect = 0.003
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 548 DYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQGFMSRRHTFALFNPEGRNVYKD 607
+ +FVL E + +K+ + + + PL LK+ ++ R G V +
Sbjct: 36 ERYFVLRDEKLLLYKEVKSSKPEKEWPLKSLKV------YLGIRKKLKPPTSWGFTVILE 89
Query: 608 YKQLELSCENQDDVDSWKASFLRA 631
+Q L C+ Q+++ W AS L A
Sbjct: 90 KQQWYLCCDTQEELWEWMASILSA 113
>gnl|CDD|241451 cd13297, PH3_MyoX-like, Myosin X-like Pleckstrin homology (PH)
domain, repeat 3. MyoX, a MyTH-FERM myosin, is a
molecular motor that has crucial functions in the
transport and/or tethering of integrins in the
actin-based extensions known as filopodia, microtubule
binding, and in netrin-mediated axon guidance. It
functions as a dimer. MyoX walks on bundles of actin,
rather than single filaments, unlike the other
unconventional myosins. MyoX is present in organisms
ranging from humans to choanoflagellates, but not in
Drosophila and Caenorhabditis elegans.MyoX consists of a
N-terminal motor/head region, a neck made of 3 IQ
motifs, and a tail consisting of a coiled-coil domain, a
PEST region, 3 PH domains, a myosin tail homology 4
(MyTH4), and a FERM domain at its very C-terminus. The
first PH domain in the MyoX tail is a split-PH domain,
interupted by the second PH domain such that PH 1a and
PH 1b flanks PH 2. The third PH domain (PH 3) follows
the PH 1b domain. This cd contains the third MyoX PH
repeat. PLEKHH3/Pleckstrin homology (PH) domain
containing, family H (with MyTH4 domain) member 3 is
also part of this CD and like MyoX contains a FERM
domain, a MyTH4 domain, and a single PH domain. Not much
is known about the function of PLEKHH3. 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 = 123
Score = 37.3 bits (87), Expect = 0.005
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 525 GNQVIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYM--LPLDGL 578
+VI KGW+ + WFVLT ++ ++K ER + L L+ L
Sbjct: 10 DQEVIEKGWLLKEGGKGGNLTKKKRWFVLTPNSLDYYKS-SERNALKLGSLVLNSL 64
>gnl|CDD|241455 cd13301, PH1_Pleckstrin_2, Pleckstrin 2 Pleckstrin homology (PH)
domain, repeat 1. Pleckstrin is a protein found in
platelets. This name is derived from platelet and
leukocyte C kinase substrate and the KSTR string of
amino acids. Pleckstrin 2 contains two PH domains and a
DEP (dishvelled, egl-10, and pleckstrin) domain. Unlike
pleckstrin 1, pleckstrin 2 does not contain obvious
sites of PKC phosphorylation. Pleckstrin 2 plays a role
in actin rearrangement, large lamellipodia and
peripheral ruffle formation, and may help orchestrate
cytoskeletal arrangement. The PH domains of pleckstrin 2
are thought to contribute to lamellipodia formation.
This cd contains the first PH domain repeat. 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 = 108
Score = 35.4 bits (82), Expect = 0.018
Identities = 20/110 (18%), Positives = 46/110 (41%), Gaps = 19/110 (17%)
Query: 527 QVIRKGWMC-----IHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLR 581
V+++G++ ++N WFVL + + ++K + + K M+ L G +
Sbjct: 2 GVLKEGFLVKKGHVVNNWKAR-------WFVLLEDKLEYYKKKTDSSPKGMILLKGCTIT 54
Query: 582 DVEQGFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRA 631
+ R F L +G++ + L ++++ D+W +A
Sbjct: 55 SPCLEYEKRPLVFKLTTAKGQDHF-------LQACSREERDAWAKDITKA 97
>gnl|CDD|241294 cd01263, PH_anillin, Anillin Pleckstrin homology (PH) domain.
Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin
homology domain-containing family K) is an actin binding
protein involved in cytokinesis. It interacts with
GTP-bound Rho proteins and results in the inhibition of
their GTPase activity. Dysregulation of the Rho signal
transduction pathway has been implicated in many forms
of cancer. Anillin proteins have a N-terminal HRI
domain/ACC (anti-parallel coiled-coil) finger domain or
Rho-binding domain binds small GTPases from the Rho
family. The C-terminal PH domain helps target anillin to
ectopic septin containing foci. 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 = 119
Score = 35.0 bits (81), Expect = 0.033
Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 17/93 (18%)
Query: 549 YWFVLTSENISWFK--DEEEREKKYMLPLDGLKLRD--------VEQGFMSRRHTFALFN 598
W VL +S++K ++EE++K P+ + LR + +R +TF L
Sbjct: 23 RWCVLRGGYLSFWKYPEDEEKKK----PIGSIDLRKCINEKVEPASRELCARPNTFELET 78
Query: 599 PEGRNVYKDYKQLE---LSCENQDDVDSWKASF 628
+ + LS + +++ W +
Sbjct: 79 LRPAEDSDGTNEKKRVLLSADTKEERIEWLDAL 111
>gnl|CDD|241470 cd13316, PH_Boi, Boi family Pleckstrin homology domain. Yeast Boi
proteins Boi1 and Boi2 are functionally redundant and
important for cell growth with Boi mutants displaying
defects in bud formation and in the maintenance of cell
polarity.They appear to be linked to Rho-type GTPase,
Cdc42 and Rho3. Boi1 and Boi2 display two-hybrid
interactions with the GTP-bound ("active") form of
Cdc42, while Rho3 can suppress of the lethality caused
by deletion of Boi1 and Boi2. These findings suggest
that Boi1 and Boi2 are targets of Cdc42 that promote
cell growth in a manner that is regulated by Rho3. Boi
proteins contain a N-terminal SH3 domain, followed by a
SAM (sterile alpha motif) domain, a proline-rich region,
which mediates binding to the second SH3 domain of Bem1,
and C-terminal PH domain. The PH domain is essential for
its function in cell growth and is important for
localization to the bud, while the SH3 domain is needed
for localization to the neck. 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 = 95
Score = 34.3 bits (79), Expect = 0.038
Identities = 21/105 (20%), Positives = 42/105 (40%), Gaps = 16/105 (15%)
Query: 531 KGWMCIHNLGIMKGGSRDYW----FVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQG 586
GWM +G W FVL + + K E + ++K ++ L G ++ +
Sbjct: 2 SGWMK------KRGERYGTWKTRYFVLKGTRLYYLKSENDSKEKGLIDLTGHRVTVDDSN 55
Query: 587 FMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRA 631
R+ F L P V+ Y + + ++ + W + ++A
Sbjct: 56 SKPGRYGFKLVPPAVEKVH--Y----FAVDEKEVLREWMKALMKA 94
>gnl|CDD|241480 cd13326, PH_CNK_insect-like, Connector enhancer of KSR (Kinase
suppressor of ras) (CNK) pleckstrin homology (PH)
domain. CNK family members function as protein
scaffolds, regulating the activity and the subcellular
localization of RAS activated RAF. There is a single CNK
protein present in Drosophila and Caenorhabditis elegans
in contrast to mammals which have 3 CNK proteins (CNK1,
CNK2, and CNK3). All of the CNK members contain a
sterile a motif (SAM), a conserved region in CNK (CRIC)
domain, and a PSD-95/DLG-1/ZO-1 (PDZ) domain, and a PH
domain. A CNK2 splice variant CNK2A also has a PDZ
domain-binding motif at its C terminus and Drosophila
CNK (D-CNK) also has a domain known as the
Raf-interacting region (RIR) that mediates binding of
the Drosophila Raf kinase. This cd contains CNKs from
insects, spiders, mollusks, and nematodes. 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 = 90
Score = 33.9 bits (78), Expect = 0.041
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 550 WFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQGFMSRRHTFALFNPEGRNVYKDYK 609
WFVL N+ F+ +E + ++ L G + + SR++ F +++ G Y
Sbjct: 22 WFVLKGSNLYGFRSQESTKADCVIFLPGFTVSPAPE-VKSRKYAFKVYHT-GTVFY---- 75
Query: 610 QLELSCENQDDVDSW 624
+ E+Q+D+ W
Sbjct: 76 ---FAAESQEDMKKW 87
>gnl|CDD|241529 cd13378, PH_RhoGAP2, Rho GTPase activating protein 2 Pleckstrin
homology (PH) domain. RhoGAP2 (also called RhoGap22 or
ArhGap22) are involved in cell polarity, cell morphology
and cytoskeletal organization. They activate a GTPase
belonging to the RAS superfamily of small GTP-binding
proteins. The encoded protein is insulin-responsive, is
dependent on the kinase Akt, and requires the
Akt-dependent 14-3-3 binding protein which binds
sequentially to two serine residues resulting in
regulation of cell motility. Members here contain an
N-terminal PH domain followed by a RhoGAP domain and
either a BAR or TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) 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 = 116
Score = 33.4 bits (76), Expect = 0.098
Identities = 27/108 (25%), Positives = 51/108 (47%), Gaps = 8/108 (7%)
Query: 528 VIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQGF 587
V++ GW+ IMK + WFVL + + ++KDEEE + + + L G ++ ++
Sbjct: 3 VLKAGWL-KKQRSIMKNWQQR-WFVLRGDQLFYYKDEEETKPQGCISLQGSQVNELPPNP 60
Query: 588 MSR-RHTFALFNPEG----RNVYKDYKQLELSCENQDDVDSWKASFLR 630
+H F + P G V +++ L +Q D++ W + R
Sbjct: 61 EEPGKHLFEI-LPGGAGDREKVPMNHEAFLLMANSQSDMEDWVKAIRR 107
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The
dynamin family of large mechanochemical GTPases
includes the classical dynamins and dynamin-like
proteins (DLPs) that are found throughout the Eukarya.
This family also includes bacterial DLPs. These
proteins catalyze membrane fission during
clathrin-mediated endocytosis. Dynamin consists of five
domains; an N-terminal G domain that binds and
hydrolyzes GTP, a middle domain (MD) involved in
self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific,
mediates uptake of synaptic vesicles in presynaptic
terminals; dynamin-2 is expressed ubiquitously and
similarly participates in membrane fission; mutations
in the MD, PH and GED domains of dynamin 2 have been
linked to human diseases such as Charcot-Marie-Tooth
peripheral neuropathy and rare forms of centronuclear
myopathy. Dynamin 3 participates in megakaryocyte
progenitor amplification, and is also involved in
cytoplasmic enlargement and the formation of the
demarcation membrane system. This family also includes
mitofusins (MFN1 and MFN2 in mammals) that are involved
in mitochondrial fusion. Dynamin oligomerizes into
helical structures around the neck of budding vesicles
in a GTP hydrolysis-dependent manner.
Length = 180
Score = 34.4 bits (80), Expect = 0.11
Identities = 17/39 (43%), Positives = 23/39 (58%)
Query: 35 IAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQ 73
+AVVG SAGKS++L +G + LP G T VL+
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVITVLR 41
>gnl|CDD|213262 cd03295, ABC_OpuCA_Osmoprotection, ATP-binding cassette domain of
the osmoprotectant transporter. OpuCA is a the ATP
binding component of a bacterial solute transporter that
serves a protective role to cells growing in a
hyperosmolar environment. ABC (ATP-binding cassette)
transporter nucleotide-binding domain; ABC transporters
are a large family of proteins involved in the transport
of a wide variety of different compounds, like sugars,
ions, peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition, to the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 242
Score = 34.2 bits (79), Expect = 0.16
Identities = 39/121 (32%), Positives = 47/121 (38%), Gaps = 37/121 (30%)
Query: 353 SGSAQINTMELSGGAKINRLFH----ERFPFEIVKMEFDEKELRREIAFAIRNIHGIRVG 408
SGS + TM++ INRL E F E D ELRR+I + I+ I G
Sbjct: 36 SGSGKTTTMKM-----INRLIEPTSGEIFIDGEDIREQDPVELRRKIGYVIQQI-----G 85
Query: 409 LFTPDMAFE---AIV--------KKQISRLKEPALKCVDLVVAELSNVVRICTDKMSRYP 457
LF P M E A+V +K R E L V L AE RYP
Sbjct: 86 LF-PHMTVEENIALVPKLLKWPKEKIRERADE-LLALVGLDPAEF----------ADRYP 133
Query: 458 R 458
Sbjct: 134 H 134
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
Miro is one of few Rho subfamilies that lack this
feature.
Length = 180
Score = 33.8 bits (78), Expect = 0.16
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 37 VVGGQSAGKSSVLENFVGRDF 57
V+G + +GKS++L+ F+GR F
Sbjct: 9 VLGAKGSGKSALLQAFLGRSF 29
>gnl|CDD|241453 cd13299, PH2_PH_fungal, Fungal proteins Pleckstrin homology (PH)
domain, repeat 2. The functions of these fungal
proteins are unknown, but they all contain 2 PH domains.
This cd represents the second PH repeat. 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 = 102
Score = 32.2 bits (74), Expect = 0.22
Identities = 17/84 (20%), Positives = 41/84 (48%), Gaps = 11/84 (13%)
Query: 547 RDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQGFMSR--RHTFALFNPEGRNV 604
+ YW VL + ++S++KD+ E ++P+D + + VE +S+ + + PE
Sbjct: 24 KKYWLVLRNRSLSFYKDQSEYSPVKIIPIDDI-IDVVELDPLSKSKKWCLQIITPE---- 78
Query: 605 YKDYKQLELSCENQDDVDSWKASF 628
K++ ++++ + W +
Sbjct: 79 ----KRIRFCADDEESLIKWLGAL 98
>gnl|CDD|132749 cd06951, NR_LBD_Dax1_like, The ligand binding domain of DAX1
protein, a nuclear receptor lacking DNA binding domain.
The ligand binding domain of DAX1-like proteins: This
orphan nuclear receptor family includes DAX1
(dosage-sensitive sex reversal adrenal hypoplasia
congenita critical region on chromosome X gene 1) and
the Small Heterodimer Partner (SHP). Both receptors have
a typical ligand binding domain, but lack the DNA
binding domain, typical to almost all of the nuclear
receptors. They function as a transcriptional
coregulator by directly interacting with other nuclear
receptors. DAX1 and SHP can form heterodimers with each
other, as well as with many other nuclear receptors. In
addition, DAX1 can also form homodimers. DAX1 plays an
important role in the normal development of several
hormone-producing tissues. SHP has shown to regulate a
variety of target genes.
Length = 222
Score = 33.6 bits (77), Expect = 0.24
Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 8/51 (15%)
Query: 263 DPPGLHPSYRHLADRLGTPYLQRVLNQQLTNHIRDTLPGLRDRLQKQLLTL 313
PP L P Y LQ+ Q L H T P + R + LL L
Sbjct: 149 VPPLLCPHYIE--------ALQKEAQQALNEHTMMTRPLEQLRSARLLLML 191
>gnl|CDD|241436 cd13282, PH1_PLEKHH1_PLEKHH2, Pleckstrin homology (PH) domain
containing, family H (with MyTH4 domain) members 1 and 2
(PLEKHH1) PH domain, repeat 1. PLEKHH1 and PLEKHH2
(also called PLEKHH1L) are thought to function in
phospholipid binding and signal transduction. There are
3 Human PLEKHH genes: PLEKHH1, PLEKHH2, and PLEKHH3.
There are many isoforms, the longest of which contain a
FERM domain, a MyTH4 domain, two PH domains, a peroximal
domain, a vacuolar domain, and a coiled coil stretch.
The FERM domain has a cloverleaf tripart structure
(FERM_N, FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe,
B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3 within the
FERM domain is part of the PH domain family. 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 = 96
Score = 31.9 bits (73), Expect = 0.28
Identities = 28/110 (25%), Positives = 44/110 (40%), Gaps = 31/110 (28%)
Query: 519 KAG--RKLGNQVIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYM--LP 574
KAG KLG +V K W + WFVL + + ++K + +K +
Sbjct: 1 KAGYLTKLGGKV--KTW-------------KRRWFVLKNGELFYYKSPNDVIRKPQGQIA 45
Query: 575 LDGLKLRDVEQGFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSW 624
LDG E TF + E R Y L+ ++++D+D W
Sbjct: 46 LDGS----CEIARAEGAQTFEIVT-EKRTYY-------LTADSENDLDEW 83
>gnl|CDD|240145 cd05014, SIS_Kpsf, KpsF-like protein. KpsF is an
arabinose-5-phosphate isomerase which contains SIS
(Sugar ISomerase) domains. SIS domains are found in many
phosphosugar isomerases and phosphosugar binding
proteins. KpsF catalyzes the reversible reaction of
ribulose 5-phosphate to arabinose 5-phosphate. This is
the second step in the CMP-Kdo biosynthesis pathway.
Length = 128
Score = 32.1 bits (74), Expect = 0.32
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 229 ILQFIKRDNCLILAVT-PANSDLA-NSDA---LKLAKEVDPPGLHP 269
+L +KR I+A+T NS LA SD L + +E P GL P
Sbjct: 66 LLPHLKRRGAPIIAITGNPNSTLAKLSDVVLDLPVEEEACPLGLAP 111
>gnl|CDD|241442 cd13288, PH_Ses, Sesquipedalian family Pleckstrin homology (PH)
domain. The sesquipedalian family has 2 mammalian
members: Ses1 and Ses2, which are also callled 7 kDa
inositol polyphosphate phosphatase-interacting protein 1
and 2. They play a role in endocytic trafficking and are
required for receptor recycling from endosomes, both to
the trans-Golgi network and the plasma membrane. Members
of this family form homodimers and heterodimers.
Sesquipedalian interacts with inositol polyphosphate
5-phosphatase OCRL-1 (INPP5F) also known as Lowe
oculocerebrorenal syndrome protein, a phosphatase enzyme
that is involved in actin polymerization and is found in
the trans-Golgi network and INPP5B. Sesquipedalian
contains a single 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 = 120
Score = 31.8 bits (73), Expect = 0.36
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 10/84 (11%)
Query: 550 WFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQGFMSRRHTFAL-FNPEGRNVYKDY 608
WFVL + +F+ + +RE ++ L+G + E + FA+ F+ G Y
Sbjct: 28 WFVLKGNLLFYFEKKGDREPLGVIVLEGCTVELSEDE---EPYAFAIRFDGPGSRSYV-- 82
Query: 609 KQLELSCENQDDVDSWKASFLRAG 632
L+ E+Q+D++SW + RA
Sbjct: 83 ----LAAESQEDMESWMKALSRAS 102
>gnl|CDD|115805 pfam07175, Osteoregulin, Osteoregulin. This family represents a
conserved region approximately 180 residues long within
osteoregulin, a bone-remodelling protein expressed
highly in osteocytes within trabecular and cortical
bone. A conserved RGD motif is found towards the
C-terminal end of this region, and this is potentially
involved in integrin recognition.
Length = 163
Score = 32.7 bits (74), Expect = 0.42
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 15/96 (15%)
Query: 614 SCENQDDVDSWKASFLRAGVYPEKSTDQSNGDEGGTEGTSSMDPQLERQVETIRNLVDSY 673
S NQ+++ + LRA VYP+ + ++ G E G + + Q +RN+
Sbjct: 8 SSGNQENIHNG----LRASVYPKPTVNK--GTEDGDDAILHLHDQERYGAALLRNITQPV 61
Query: 674 MKIVTKT------CRDLVPKTIMLLI---INNAKDF 700
+VT ++ P++++ +I +N AK
Sbjct: 62 KSLVTGIELLGEENKEKTPQSVLSVIPADVNYAKAH 97
>gnl|CDD|241433 cd13279, PH_Cla4_Ste20, Pleckstrin homology (PH) domain. Budding
yeast contain two main p21-activated kinases (PAKs),
Cla4 and Ste20. The yeast Ste20 protein kinase is
involved in pheromone response, though the function of
Ste20 mammalian homologs is unknown. Cla4 is involved in
budding and cytokinesis and interacts with Cdc42, a
GTPase required for polarized cell growth as is Pak.
Cla4 and Ste20 kinases share a function in localizing
cell growth with respect to the septin ring. They both
contain a PH domain, a Cdc42/Rac interactive binding
(CRIB) domain, and a C-terminal Protein Kinase catalytic
(PKc) 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 = 91
Score = 31.1 bits (71), Expect = 0.48
Identities = 16/99 (16%), Positives = 42/99 (42%), Gaps = 13/99 (13%)
Query: 528 VIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDVEQGF 587
V++ GW+ + G++ + VL +++ ++K+E +P L+D+
Sbjct: 1 VVKSGWVSVKEDGLLSFRWSKRYLVLREQSLDFYKNESSSSASLSIP-----LKDISNVS 55
Query: 588 MS--RRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSW 624
+ + + F + K + +S ++ D++ W
Sbjct: 56 RTDLKPYCFEIVRKSST------KSIYISVKSDDELYDW 88
>gnl|CDD|241528 cd13377, PH_SynGAP_2, Synaptic Ras-GTPase activating protein
Pleckstrin homology (PH) domain. SynGAP is a member of
the RasSynGAP family along with DOC-2/DAB2-interacting
protein (DAB2IP) and neuronal growth-associated protein
(nGAP/RASAL2). SynGAP, a neuronal Ras-GAP, has been
shown display both Ras-GAP activity and Ras-related
protein (Rap)-GAP activity. Saccharomyces cerevisiae
Bud2 and GAP1 members CAPRI (Ca2+-promoted Ras
inactivator) and RASAL (Ras-GTPase-activating-like
protein) also possess this dual activity. Human
DOC-2/DAB2-interacting protein (DAB2IP) is encoded by a
tumor suppressor gene and a newly recognized member of
the Ras-GTPase-activating family. Members here include
nematodes, insects, arthropods, and cnidarians. PH
domains are only found in eukaryotes. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. 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 = 129
Score = 31.7 bits (72), Expect = 0.52
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 9/65 (13%)
Query: 573 LPLDGLKLRDVEQGFMSRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRAG 632
G++L + + R H F + P + +C ++ + D W S LR
Sbjct: 68 EGPAGVRLHPLHPSVLGRPHCFQVSTPTDTTYF--------ACRSRQERDKWIES-LRKS 118
Query: 633 VYPEK 637
+ P++
Sbjct: 119 IQPDR 123
>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 = 30.4 bits (69), Expect = 0.81
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 7/43 (16%)
Query: 589 SRRHTFALFNPEGRNVYKDYKQLELSCENQDDVDSWKASFLRA 631
R H+F L + D LEL+ ++ + W S ++
Sbjct: 64 DRPHSFEL-------ILTDRPSLELAAPDEYEASEWLQSLCQS 99
>gnl|CDD|226054 COG3523, IcmF, Type VI protein secretion system component VasK
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1188
Score = 32.8 bits (75), Expect = 1.0
Identities = 36/179 (20%), Positives = 63/179 (35%), Gaps = 33/179 (18%)
Query: 230 LQFIKRDNCLILAVTPANSDLANSDALKLAKE-----VDPPGLHPSY-----RHLADRLG 279
+ L +A L DA + A + P L + + +
Sbjct: 481 ATQLDDLVPLQVADDDLLQVLPLLDAARDATAAFALFRERPPLLARFGLYQGDAIGPGVA 540
Query: 280 TPYLQRVLNQQLTNHIRDTLPGLRDRLQKQLLTLEKDVEQFKHFRPDDPSIKTKAML--- 336
Y +R+L Q L LP L +RL+ L D E+ ++K ML
Sbjct: 541 DTY-RRLLEQVL-------LPRLVNRLENALNAAPADSEELYD------ALKAYLMLGGK 586
Query: 337 ------QMIQQLQSDFERTIEGSGSAQINTMELSGGAKINRLFHERFPFEIVKMEFDEK 389
++Q + D+E + G G+ M L+ A ++ L + K+E D++
Sbjct: 587 SGRDADFLVQWMAQDWENSYPGQGNVPGEQMLLASYAHLDALLARELGDQDPKIEPDDE 645
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity.
The Ras superfamily is divided into at least four
families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf
families. This superfamily also includes proteins like
the GTP translation factors, Era-like GTPases, and
G-alpha chain of the heterotrimeric G proteins. Members
of the Ras superfamily regulate a wide variety of
cellular functions: the Ras family regulates gene
expression, the Rho family regulates cytoskeletal
reorganization and gene expression, the Rab and
Sar1/Arf families regulate vesicle trafficking, and the
Ran family regulates nucleocytoplasmic transport and
microtubule organization. The GTP translation factor
family regulates initiation, elongation, termination,
and release in translation, and the Era-like GTPase
family regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 31.3 bits (71), Expect = 1.1
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 36 AVVGGQSAGKSSVLENFVGRDFLPRGS-GIVTRRP 69
VVG GKSS+L +G + TR P
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDP 35
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains
(pfam00036), that may bind calcium. They are also
larger than classical small GTPases. It has been
proposed that they are involved in mitochondrial
homeostasis and apoptosis.
Length = 116
Score = 30.5 bits (69), Expect = 1.2
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 35 IAVVGGQSAGKSSVLENFVGRDFLPRGSGI 64
+ V+G + +GKSS+L VG +F P I
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEI 31
>gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal. This
model represents the archaeal branch of the MinD family.
MinD, a weak ATPase, works in bacteria with MinC as a
generalized cell division inhibitor and, through
interaction with MinE, prevents septum placement
inappropriate sites. Often several members of this
family are found in archaeal genomes, and the function
is uncharacterized. More distantly related proteins
include flagellar biosynthesis proteins and ParA
chromosome partitioning proteins. The exact roles of the
various archaeal MinD homologs are unknown.
Length = 251
Score = 31.6 bits (72), Expect = 1.3
Identities = 30/98 (30%), Positives = 44/98 (44%), Gaps = 19/98 (19%)
Query: 192 KQVDPDVLNLTLVDLPGMTKVPIGDQPADIEYQIKSMILQFIKRDNCLILAVTPANSDLA 251
++ DPD L L ++ T + D PA +E + + D L+L V P S +
Sbjct: 91 RKADPDKLEDVLKEIIDDTDFLLIDAPAGLE---RDAVTALAAADE-LLLVVNPEISSI- 145
Query: 252 NSDALKLAKEVDPPGLHPSYRHLADRLGTPYLQRVLNQ 289
+DALK K V A++LGT L VLN+
Sbjct: 146 -TDALKT-KIV------------AEKLGTAILGVVLNR 169
>gnl|CDD|241291 cd01260, PH_CNK_mammalian-like, Connector enhancer of KSR (Kinase
suppressor of ras) (CNK) pleckstrin homology (PH)
domain. CNK family members function as protein
scaffolds, regulating the activity and the subcellular
localization of RAS activated RAF. There is a single CNK
protein present in Drosophila and Caenorhabditis elegans
in contrast to mammals which have 3 CNK proteins (CNK1,
CNK2, and CNK3). All of the CNK members contain a
sterile a motif (SAM), a conserved region in CNK (CRIC)
domain, and a PSD-95/DLG-1/ZO-1 (PDZ) domain, and, with
the exception of CNK3, a PH domain. A CNK2 splice
variant CNK2A also has a PDZ domain-binding motif at its
C terminus and Drosophila CNK (D-CNK) also has a domain
known as the Raf-interacting region (RIR) that mediates
binding of the Drosophila Raf kinase. This cd contains
CNKs from mammals, chickens, amphibians, fish, and
crustacea. 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 = 114
Score = 30.0 bits (68), Expect = 1.5
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 17/89 (19%)
Query: 547 RDYWFVLTSENISWFKDEEEREKKYMLPLDGL-KLRD--VEQGFMSRR-HTFALFNPEGR 602
+ YWFVL ++ W+ + ++ EK +G L D +E+ ++ + F +P+
Sbjct: 34 KRYWFVLKGSSLYWYNNPQD-EKA-----EGFINLPDFKIERASECKKKYAFKASHPK-- 85
Query: 603 NVYKDYKQLELSCENQDDVDSWKASFLRA 631
K + EN DD++ W + + A
Sbjct: 86 -----IKTFYFAAENLDDMNKWLSKLITA 109
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 31.6 bits (72), Expect = 1.8
Identities = 39/228 (17%), Positives = 81/228 (35%), Gaps = 17/228 (7%)
Query: 283 LQRVLNQQLTNHIRDTLPGLRDRLQKQLLTLEKDVEQFKHFRPDDPSIKTKAMLQMIQQL 342
L+ L + + LR L QL L + + F DD L Q +
Sbjct: 668 LKDKLELAIAERKQQAETQLRQ-LDAQLKQLLEQQQAFLEALKDDFRELRTERLAKWQVV 726
Query: 343 QSDFERTIEGSGSAQINTMELSGGAKINRLFHERFPFEIVKMEFDE---KELRREIAFAI 399
+ + + + SA I A++ L +++ E+ ++ D KEL+R+I
Sbjct: 727 EGELDNQL-AQLSAAIEAARTQAKARLKEL-KKQYDRELASLDVDPNTVKELKRQIEELE 784
Query: 400 RNIHGIRVGLFTPDMA-FEAIVKKQISRLKEPALKCVDLVVAELSNVVRICTDKMSRYPR 458
I I V P++ + A +++ + + +L + + R
Sbjct: 785 TTIERIAV--RRPEVREYRAFMQETWLHRDSLREE-RPNLAIQLRELESSAEELQQELTR 841
Query: 459 LREETERIITSYVRNREQQCKEQIVLL------VDCELAYMNTNHEDF 500
L ++T+ + R + ++Q+ L + E+ + E
Sbjct: 842 LIKDTKLRRKKLEQER-KALEKQLDQLDELLRGLRDEMRQLAELKEPA 888
>gnl|CDD|241429 cd13275, PH_M-RIP, Myosin phosphatase-RhoA Interacting Protein
Pleckstrin homology (PH) domain. M-RIP is proposed to
play a role in myosin phosphatase regulation by RhoA.
M-RIP contains 2 PH domains followed by a Rho binding
domain (Rho-BD), and a C-terminal myosin binding subunit
(MBS) binding domain (MBS-BD). The amino terminus of
M-RIP with its adjacent PH domains and polyproline
motifs mediates binding to both actin and Galpha. M-RIP
brings RhoA and MBS into close proximity where M-RIP can
target RhoA to the myosin phosphatase complex to
regulate the myosin phosphorylation state. M-RIP does
this via its C-terminal coiled-coil domain which
interacts with the MBS leucine zipper domain of myosin
phosphatase, while its Rho-BD, directly binds RhoA in a
nucleotide-independent manner. 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 = 29.2 bits (66), Expect = 2.2
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 13/44 (29%)
Query: 530 RKGWMCIHNLGIMKGGS----RDYWFVLTSENISWFKDE--EER 567
+KGW+ MK + +WFVL ++ +++D EE
Sbjct: 1 KKGWL-------MKQDEDGEWKKHWFVLRDASLRYYRDSVAEEA 37
>gnl|CDD|212116 cd10805, YdjC_like_1, uncharacterized YdjC-like family proteins
from bacteria. The subfamily contains many hypothetical
proteins, and belongs to the YdjC-like family of
uncharacterized proteins from bacteria. The YdjC-family
is represented by an uncharacterised protein YdjC (also
known as ChbG) encoded by the chb
(N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel
operon in Escherichia coli, which encodes enzymes
involved in growth on an N,N'-diacetylchitobiose carbon
source. The molecular function of this subfamily is
unclear.
Length = 251
Score = 30.6 bits (70), Expect = 2.5
Identities = 11/28 (39%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 87 CKGKKFVDFDEVRREIEAETDR---ITG 111
+G+ FV+++EV EIEA+ +R + G
Sbjct: 94 AEGEDFVNYEEVYLEIEAQVERFIELVG 121
>gnl|CDD|241272 cd01239, PH_PKD, Protein kinase D (PKD/PKCmu) pleckstrin homology
(PH) domain. Protein Kinase C family is composed of
three members, PKD1 (PKCmu), PKD2 and PKD3 (PKCnu). Like
the C-type protein kinases (PKCs), PKDs are activated by
diacylglycerol (DAG). They are involved in vesicular
transport, cell proliferation, survival, migration and
immune responses. PKD consists of tandem C1 domains,
followed by a PH domain and a kinase domain. While the
PKD PH domain has not been shown to bind phosphorylated
inositol lipids and is not required for membrane
translocation, it is required for nuclear export. 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 = 127
Score = 29.7 bits (67), Expect = 2.7
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 8/52 (15%)
Query: 522 RKLGNQVIRKGWMCIH--NLGIMKGGSRDYWFVLTSENISWFKDEEEREKKY 571
++ ++V+++GWM +H N + R YW L ++ I+ F++E +Y
Sbjct: 2 KRRSSKVLKEGWM-VHYTNKDPQR--KRHYW-RLDTKCITLFQNET--TSRY 47
>gnl|CDD|241417 cd13263, PH_RhoGap25-like, Rho GTPase activating protein 25 and
related proteins Pleckstrin homology (PH) domain.
RhoGAP25 (also called ArhGap25) like other RhoGaps are
involved in cell polarity, cell morphology and
cytoskeletal organization. They act as GTPase activators
for the Rac-type GTPases by converting them to an
inactive GDP-bound state and control actin remodeling by
inactivating Rac downstream of Rho leading to suppress
leading edge protrusion and promotes cell retraction to
achieve cellular polarity and are able to suppress RAC1
and CDC42 activity in vitro. Overexpression of these
proteins induces cell rounding with partial or complete
disruption of actin stress fibers and formation of
membrane ruffles, lamellipodia, and filopodia. This
hierarchy contains RhoGAP22, RhoGAP24, and RhoGAP25.
Members here contain an N-terminal PH domain followed by
a RhoGAP domain and either a BAR or TATA Binding Protein
(TBP) Associated Factor 4 (TAF4) 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 = 114
Score = 29.3 bits (66), Expect = 3.2
Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 528 VIRKGWMCIHNLGIMKGGSRDYWFVLTSENISWFKDEEEREKKYMLPLDGLKLRDV 583
VI+ GW+ GI+K R WFVL + + ++KDE+E + + +PL G ++++
Sbjct: 3 VIKSGWLKKQG-GIVKNWQRR-WFVLRGDQLYYYKDEDESKPQGCIPLPGNTVKEL 56
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.4 bits (67), Expect = 4.7
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 35 IAVVGGQSAGKSSVLENF----------VGRDFLPRGSGI 64
I + GG S GK+++LE GR+++
Sbjct: 2 IVITGGPSTGKTTLLEALAARGYPVVPEYGREYIEEQLAD 41
>gnl|CDD|212684 cd11734, Ssq1_like_NBD, Nucleotide-binding domain of Saccharomyces
cerevisiae Ssq1 and similar proteins. Ssq1p (also
called Stress-seventy subfamily Q protein 1, Ssc2p,
Ssh1p, mtHSP70 homolog) belongs to the heat shock
protein 70 (HSP70) family of chaperones that assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Typically, HSP70s
have a nucleotide-binding domain (NBD) and a
substrate-binding domain (SBD). The nucleotide sits in a
deep cleft formed between the two lobes of the NBD. The
two subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). S. cerevisiae Ssq1p is a mitochondrial
chaperone that is involved in iron-sulfur (Fe/S) center
biogenesis. Ssq1p plays a role in the maturation of
Yfh1p, a nucleus-encoded mitochondrial protein involved
in iron homeostasis (and a homolog of human frataxin,
implicated in the neurodegenerative disease,
Friedreich's ataxia).
Length = 373
Score = 29.8 bits (67), Expect = 5.4
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 421 KKQISRLKEPALKC-VDLVVAELS--NVVRICTDKMSRYPRLREETERIITSYVRNREQQ 477
KK I R+KE A K ++L +E S + + K R R E E++ S +
Sbjct: 251 KKAIQRIKEAAEKAKIELSSSEESVIELPYLDGPKHLRITITRREFEQLRKSICKRTIYP 310
Query: 478 CKE 480
CK+
Sbjct: 311 CKQ 313
>gnl|CDD|241271 cd01238, PH_Btk, Bruton's tyrosine kinase pleckstrin homology (PH)
domain. Btk is a member of the Tec family of
cytoplasmic protein tyrosine kinases that includes BMX,
IL2-inducible T-cell kinase (Itk) and Tec. Btk plays a
role in the maturation of B cells. Tec proteins general
have an N-terminal PH domain, followed by a Tek homology
(TH) domain, a SH3 domain, a SH2 domain and a kinase
domain. The Btk PH domain binds phosphatidylinositol
3,4,5-trisphosphate and responds to signalling via
phosphatidylinositol 3-kinase. The PH domain is also
involved in membrane anchoring which is confirmed by the
discovery of a mutation of a critical arginine residue
in the BTK PH domain. This results in severe human
immunodeficiency known as X-linked agammaglobulinemia
(XLA) in humans and a related disorder is mice.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 = 140
Score = 28.7 bits (65), Expect = 5.6
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 16/81 (19%)
Query: 550 WFVLTSENISWFKD--EEEREKKYMLPLDGLKLRDVEQ----GFMSRRHTFALFNPEGRN 603
WFVLT ++S+++ + ++K + L +K VE+ R++ F +
Sbjct: 24 WFVLTKSSLSYYEGDGGKRGKEKGSIDLSKIKC--VEEVKDDASFERKYPFQV------- 74
Query: 604 VYKDYKQLELSCENQDDVDSW 624
VY DY L + +++D D W
Sbjct: 75 VYDDY-TLYVFAPSEEDRDEW 94
>gnl|CDD|225532 COG2985, COG2985, Predicted permease [General function prediction
only].
Length = 544
Score = 30.1 bits (68), Expect = 5.6
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 11/71 (15%)
Query: 71 VLQLINSMTEYAEFLHCKGKKFVDFDEVRREIEAETDRITGSNKGISNVPINLRVYSPNV 130
+L +I + V+ D ++I E T I V +PN+
Sbjct: 166 ILGIILGAWLLPKLFK------VNLDTEAQQIARERGLDTVYLPVI-----RAYVVNPNL 214
Query: 131 LNITLIDLPGL 141
+ L DLP L
Sbjct: 215 DGLNLRDLPIL 225
>gnl|CDD|179654 PRK03818, PRK03818, putative transporter; Validated.
Length = 552
Score = 29.4 bits (67), Expect = 8.4
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 120 PINLRVYSPNVLNITLIDLPGLTKVPV 146
IN+RV +PN+ + D+P L
Sbjct: 206 TINIRVENPNLHGKAIKDVPILNGDKF 232
>gnl|CDD|234469 TIGR04098, biosyn_clust_1, biosynthesis cluster domain. Radical
SAM family TIGR04043 is a marker for a widespread
eight-gene probable biosynthetic cluster of unknown
function. This protein family describes a domain that
occurs as an additional protein for some of those
clusters, but also as the N-terminal domain of large,
multidomain polyketide synthases and in other contexts.
Length = 270
Score = 28.9 bits (65), Expect = 8.7
Identities = 24/103 (23%), Positives = 35/103 (33%), Gaps = 22/103 (21%)
Query: 215 GDQPADIEYQIKSMILQFIKRDNCLILAVTPANSDLANSDALKLAKEVDPPGLHPSYRHL 274
G AD+E ++ +F++R V +N LA V PPG HL
Sbjct: 97 GRPVADVE-----LLSRFVRRT------VPGSNRSLA---------RVSPPGFR--GAHL 134
Query: 275 ADRLGTPYLQRVLNQQLTNHIRDTLPGLRDRLQKQLLTLEKDV 317
+R+ + PG R LL LE +
Sbjct: 135 PLLPAQYSPRRIRARARRAGAFGMHPGPPGRDVPDLLALEYEP 177
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 29.2 bits (66), Expect = 9.3
Identities = 22/84 (26%), Positives = 33/84 (39%), Gaps = 12/84 (14%)
Query: 25 GVPMQMDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLINSMTEYAEF 84
G Q+DLP+ G A +L++ DF V R PLV +++ + Y
Sbjct: 277 GDITQIDLPRGVKSGLHPA--LEILKHVEDIDFAGFNLKDVVRHPLVGRIVGAYEAYERL 334
Query: 85 LHCKGKKFVDFDEVRREIEAETDR 108
+ DEV RE+ R
Sbjct: 335 V----------DEVLRELLGMGVR 348
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 27.6 bits (62), Expect = 9.7
Identities = 22/103 (21%), Positives = 42/103 (40%), Gaps = 13/103 (12%)
Query: 108 RITGSNKGI-SNVP-----INLRVYSPNVLNITLIDLPGLTKVPVGDQPIDIEQQIKDML 161
+TG+ I S+ P L V I L+D PGL + + ++ + + +
Sbjct: 18 ALTGAKVAIVSDYPGTTRDPILGVLGLG-RQIILVDTPGLIEGASEGKGVEGFNRFLEAI 76
Query: 162 FQFITKETCLILAVTPANTDLATSDALQIAKQVDPDVLNLTLV 204
+E LIL V A+ L D +I ++++ ++
Sbjct: 77 -----READLILLVVDASEGLTEDD-EEILEELEKLPKKPIIL 113
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
0.319 0.136 0.392
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,273,371
Number of extensions: 4075633
Number of successful extensions: 4382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4360
Number of HSP's successfully gapped: 76
Length of query: 775
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 671
Effective length of database: 6,324,786
Effective search space: 4243931406
Effective search space used: 4243931406
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.1 bits)