RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17173
(1108 letters)
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 210 bits (538), Expect = 6e-62
Identities = 95/247 (38%), Positives = 156/247 (63%), Gaps = 11/247 (4%)
Query: 779 ILIAHPVEIARQLTLLEFDYFRSVKPSELVGSVWTKKNKAEYSP-NLIKIMKHTTNFTRW 837
+L+ P E+A QLTLL+F+ FR + PSEL+GSVW K++K SP NL ++ + W
Sbjct: 1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNW 60
Query: 838 LEKIIVEAENFDERLAIMTRIIEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALP 897
+ I++ +R ++++ I++ ++LNNFN ++A+ SA+ S+ + RL+ T++ LP
Sbjct: 61 VATEILKQTTPKDRAELLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLP 120
Query: 898 TRLQKVLEDAREL--NGDHFKKYQEKLRNIN-PPCIPFFGMYLTNILHIEEGNPDFLPDS 954
++ +K+ E+ EL ++K Y+E L + N PPCIPF G+ L ++ I+EGNPDFL +
Sbjct: 121 SKYKKLFEELEELLSPERNYKNYREALSSCNLPPCIPFLGVLLKDLTFIDEGNPDFLEN- 179
Query: 955 KLINFTKRRKVAEIISEIQQYQNEPYCLSVVPIY-REFFENLSPFEGIDDNEMCNILFEQ 1013
L+NF KRR++AEI+ EI+Q Q++PY L + + L + +D+ E L++
Sbjct: 180 GLVNFEKRRQIAEILREIRQLQSQPYNLRPNRSDIQSLLQQL--LDHLDEEE---ELYQL 234
Query: 1014 SLLIEPR 1020
SL IEPR
Sbjct: 235 SLKIEPR 241
>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases. Small GTP-binding proteins of the Ras
superfamily function as molecular switches in fundamental
events such as signal transduction, cytoskeleton dynamics
and intracellular trafficking.
Guanine-nucleotide-exchange factors (GEFs) positively
regulate these GTP-binding proteins in response to a
variety of signals. GEFs catalyze the dissociation of GDP
from the inactive GTP-binding proteins. GTP can then bind
and induce structural changes that allow interaction with
effectors.
Length = 237
Score = 208 bits (531), Expect = 4e-61
Identities = 93/242 (38%), Positives = 151/242 (62%), Gaps = 11/242 (4%)
Query: 779 ILIAHPVEIARQLTLLEFDYFRSVKPSELVGSVWTKKNKAEY-SPNLIKIMKHTTNFTRW 837
L P E+A QLTLL+F+ FR ++P EL+GS+W+KK+K + SPNL + ++ N + W
Sbjct: 1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNIHLSPNLERFIERFNNLSNW 60
Query: 838 LEKIIVEAENFDERLAIMTRIIEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALP 897
+ I+ N +R ++++ I++ ++LNNFN ++A+ SA+ S+ + RL+ T++ L
Sbjct: 61 VASEILLCTNPKKRARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLS 120
Query: 898 TRLQKVLEDAREL--NGDHFKKYQEKLRNI--NPPCIPFFGMYLTNILHIEEGNPDFLPD 953
++L+K+ E+ EL +FK Y++ L+++ NPPC+PF G+YL ++ + EGNPDFL
Sbjct: 121 SKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFLGVYLKDLTFLHEGNPDFLEG 180
Query: 954 SKLINFTKRRKVAEIISEIQQYQNEPYCLSVVPIYREFFENLSPFEGIDDNEMCNILFEQ 1013
L+NF KRRK+AEI+ EI+Q Q+ Y L+ F L + NE L+E
Sbjct: 181 -NLVNFEKRRKIAEILREIRQLQSNSYELNRDEDILAFLWKLLE---LILNED--ELYEL 234
Query: 1014 SL 1015
SL
Sbjct: 235 SL 236
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 196 bits (501), Expect = 9e-58
Identities = 74/184 (40%), Positives = 117/184 (63%), Gaps = 4/184 (2%)
Query: 783 HPVEIARQLTLLEFDYFRSVKPSELVGSVWTKKNKAEYSPNLIKIMKHTTNFTRWLEKII 842
P+E+ARQLTL+E + F ++ P EL+ S W KK+ SPN+ + +RW+ I
Sbjct: 4 DPLELARQLTLIESELFSAIDPRELLDSAWGKKDSKL-SPNIEAFISRFNQLSRWVATEI 62
Query: 843 VEAENFDERLAIMTRIIEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALPTRLQK 902
+ E+ +R ++ + I++ ++LNNFN ++A+ S + S+ + RL+ T++ + + +K
Sbjct: 63 LSEEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLNSSPISRLKKTWELVSKKYKK 122
Query: 903 VLEDAREL--NGDHFKKYQEKLRNINPPCIPFFGMYLTNILHIEEGNPDFLPDSKLINFT 960
+LE+ EL +FK Y+E L+ NPPCIPF G+YL ++ IEEGNPDFL + LINF
Sbjct: 123 LLEELEELMSPSKNFKNYREALKKANPPCIPFLGLYLKDLTFIEEGNPDFLDNG-LINFE 181
Query: 961 KRRK 964
KRRK
Sbjct: 182 KRRK 185
>gnl|CDD|241292 cd01261, PH_SOS, Son of Sevenless (SOS) Pleckstrin homology (PH)
domain. SOS is a Ras guanine nucleotide exchange
factor. SOS is thought to transmit signals from
activated receptor tyrosine kinases to the Ras signaling
pathway. SOS contains a histone domain, Dbl-homology
(DH), a PH domain, Rem domain, Cdc25 domain, and a Grb2
binding domain. The SOS PH domain binds to
phosphatidylinositol-4,5-bisphosphate (PIP2) and
phosphatidic acid (PA). SOS is dependent on Ras binding
to the allosteric site via its histone domain for both a
lower level of activity (Ras GDP) and maximal activity
(Ras GTP). The DH domain blocks the allosteric Ras
binding site in SOS. The PH domain is closely associated
with the DH domain and the action of the DH-PH unit
gates a reciprocal interaction between Ras and SOS. The
C-terminal proline-rich domain of SOS binds to the
adapter protein Grb2 which localizes the Sos protein to
the plasma membrane and diminishes the negative effect
of the C-terminal domain on the guanine nucleotide
exchange activity of the CDC25-homology domain of SOS.
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 = 109
Score = 122 bits (308), Expect = 9e-33
Identities = 53/111 (47%), Positives = 74/111 (66%), Gaps = 6/111 (5%)
Query: 443 EFYREDTLMKYDGKSNRLTERKVYFFDGVLILCKSNKKISVTVPINVVSSQYEFKCKEMY 502
EF E TL K G R TER ++ FDG+L+LCKSN+ + + S+ E++ KE
Sbjct: 5 EFIMEGTLTKV-GAGKRSTERHLFLFDGLLLLCKSNQSSTASG-----QSKPEYRLKEKI 58
Query: 503 FLRKVEINDYENTDDIKNAFEIAPRDQPSIIIVTKSPEDKKSWFSDLIMVN 553
F+RKVEIND E+TD++KNAFEI PRD+PS I+ KS E+K +W + L+ +
Sbjct: 59 FIRKVEINDLEDTDELKNAFEIVPRDEPSYILFAKSAEEKNNWMAALVTLQ 109
>gnl|CDD|100121 cd06224, REM, Guanine nucleotide exchange factor for Ras-like
GTPases; N-terminal domain (RasGef_N), also called REM
domain (Ras exchanger motif). This domain is common in
nucleotide exchange factors for Ras-like small GTPases
and is typically found immediately N-terminal to the
RasGef (Cdc25-like) domain. REM contacts the GTPase and
is assumed to participate in the catalytic activity of
the exchange factor. Proteins with the REM domain
include Sos1 and Sos2, which relay signals from
tyrosine-kinase mediated signalling to Ras, RasGRP1-4,
RasGRF1,2, CNrasGEF, and RAP-specific nucleotide
exchange factors, to name a few.
Length = 122
Score = 108 bits (271), Expect = 1e-27
Identities = 51/137 (37%), Positives = 75/137 (54%), Gaps = 16/137 (11%)
Query: 611 TLHKLIERLTYH-IYADPAFIGTFLTTYRSFTTPTELLDLLIDRFNVPDPNKVFENNNAD 669
TL LIE LT DP+F+ TFL TYRSFTTPTELL+ LI+R+ + P +
Sbjct: 1 TLEALIEHLTSTFDMPDPSFVSTFLLTYRSFTTPTELLEKLIERYEIAPP--------EN 52
Query: 670 IEESILREDIIRYKKELCQPVQFRVLNVFRQWVQHHFYDFQRDQNLLEKLKSFLLNEISG 729
+E + + + P++ RVLNV R WV+++ YDF D+ LLE L+ FL +
Sbjct: 53 LEYNDWDKKKSK-------PIRLRVLNVLRTWVENYPYDFFDDEELLELLEEFLNRLVQE 105
Query: 730 KSLRKWADIVLNLIQRK 746
+L + +L + +
Sbjct: 106 GALLQELKKLLRKLLKL 122
>gnl|CDD|214571 smart00229, RasGEFN, Guanine nucleotide exchange factor for
Ras-like GTPases; N-terminal motif. A subset of guanine
nucleotide exchange factor for Ras-like small GTPases
appear to possess this domain N-terminal to the RasGef
(Cdc25-like) domain. The recent crystal structureof Sos
shows that this domain is alpha-helical and plays a
"purely structural role" (Nature 394, 337-343).
Length = 127
Score = 102 bits (255), Expect = 2e-25
Identities = 52/143 (36%), Positives = 71/143 (49%), Gaps = 20/143 (13%)
Query: 605 PLIKGATLHKLIERLTYHIY-ADPAFIGTFLTTYRSFTTPTELLDLLIDRFNVPDPNKVF 663
LIKG TL LIE LT ADP+F+ TFL TYRSF T ELL LL+ R+N P
Sbjct: 3 GLIKGGTLEALIEHLTEAFDKADPSFVETFLLTYRSFITTQELLQLLLYRYNAIPPE--- 59
Query: 664 ENNNADIEESILREDIIRYKKELCQPVQFRVLNVFRQWVQHHFYDFQRDQNLLEKLKSFL 723
+K + V+ RVLN+ R WV++++ DF+ D L+ L F
Sbjct: 60 ---------------SWVEEKVNPRRVKNRVLNILRTWVENYWEDFEDDPKLISFLLEF- 103
Query: 724 LNEISGKSLRKWADIVLNLIQRK 746
L + + +LNL++R
Sbjct: 104 LELVDDEKYPGLVTSLLNLLRRL 126
>gnl|CDD|216026 pfam00618, RasGEF_N, RasGEF N-terminal motif. A subset of guanine
nucleotide exchange factor for Ras-like small GTPases
appear to possess this motif/domain N-terminal to the
RasGef (Cdc25-like) domain.
Length = 94
Score = 88.6 bits (220), Expect = 4e-21
Identities = 44/117 (37%), Positives = 60/117 (51%), Gaps = 25/117 (21%)
Query: 607 IKGATLHKLIERLTYH-IYADPAFIGTFLTTYRSFTTPTELLDLLIDRFNVPDPNKVFEN 665
+KG TL L+E LT D +F+ TFL TYRSFTTP ELL+LL++RF P +
Sbjct: 2 VKGGTLEALVEHLTSTDDMLDDSFLETFLLTYRSFTTPGELLELLLERFLSPPLGLSY-- 59
Query: 666 NNADIEESILREDIIRYKKELCQPVQFRVLNVFRQWVQHHFYDFQRDQNLLEKLKSF 722
Q ++ RVLNV R+W++++ DF D LL L+ F
Sbjct: 60 ----------------------QEIRIRVLNVLRKWIENYNSDFVDDPELLSLLEEF 94
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 79.7 bits (197), Expect = 6e-17
Identities = 44/176 (25%), Positives = 80/176 (45%), Gaps = 7/176 (3%)
Query: 213 VVNDFVAEEKLFIRELKLILKIFYEELNKITPLKEIKEVHSLFEIIEEIYNLTVCLLGAV 272
V+ + + E+ ++R+LKL++++F + L K L E+ +LF IEEIY L +
Sbjct: 1 VLKELLQTERNYVRDLKLLVEVFLKPLKKELKLLSPNELETLFGNIEEIYEFHRDFLDEL 60
Query: 273 EDISEMSSDDHC-IGSCFEEFAEDAEFDVYEKLLHNIVNQKSIEVLSMHVTQPSILNTLQ 331
E+ E D IG F + E F +Y + N ++E+L P L+
Sbjct: 61 EERIEEWDDSVERIGDVFLKLEEF--FKIYSEYCSNH--PDALELLKKLKKNPRFQKFLK 116
Query: 332 FAGYGFKECVKYYLPNLLMSPLYHCNLYFEYIK-IFHSLTDSSKDKECLEQAQGLL 386
+ C + L +LL+ P+ Y +K + + +D+E L++A +
Sbjct: 117 EIESSPQ-CRRLTLESLLLKPVQRLTKYPLLLKELLKHTPEDHEDREDLKKALKAI 171
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 77.7 bits (192), Expect = 2e-16
Identities = 44/180 (24%), Positives = 80/180 (44%), Gaps = 10/180 (5%)
Query: 210 YEQVVNDFVAEEKLFIRELKLILKIFYEELNKITPLKEIKEVHSLFEIIEEIYNLTVCLL 269
++V+ + + E+ ++R+LKL++++F + L+K +EV LF IEEIY L
Sbjct: 1 RQEVIKELLQTERNYVRDLKLLVEVFLKPLDKELLPLSPEEVELLFGNIEEIYEFHRIFL 60
Query: 270 GAVEDISEMSSDDH-CIGSCFEEFAEDAEFDVYEKLLHNIVNQKSIEVLSMHVTQPSILN 328
++E+ E IG F + A F +Y + N ++E+L
Sbjct: 61 KSLEERVEEWDKSGPRIGDVFLKLAPF--FKIYSEYCSNH--PDALELLK---KLKKFNK 113
Query: 329 TLQFAGYGF-KECVKYYLPNLLMSPLYHCNLYFEYIK-IFHSLTDSSKDKECLEQAQGLL 386
Q EC + L +LL+ P+ Y +K + D +D+E L++A +
Sbjct: 114 FFQEFLEKAESECGRLKLESLLLKPVQRLTKYPLLLKELLKHTPDGHEDREDLKKALEAI 173
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 59.2 bits (144), Expect = 6e-10
Identities = 42/174 (24%), Positives = 74/174 (42%), Gaps = 12/174 (6%)
Query: 213 VVNDFVAEEKLFIRELKLILKIFYEELNKITPLKEIKEVHSLFEIIEEIYNLTVCLLGAV 272
V+ + + E+ ++R+LK+++++F + L + L E +E+ ++F IEEI L L +
Sbjct: 1 VIQELLQTERSYVRDLKILVEVFLKPLRESPILSE-EEIKTIFSNIEEILELHQEFLEEL 59
Query: 273 EDISEMSSDDHCIGSCFEEFAEDAEFDVYEKLLHNIVNQKSIEVLSMHVTQPSILNTLQF 332
E+ E D IG F +FA F VY N +++E+L +
Sbjct: 60 EERLEEWPDIQRIGDIFLKFAPF--FKVYSTYCSNY--PRALELLKKLRKKNPRFAKFLK 115
Query: 333 AGYGFKECVKYYLPNLLMSPLYHCNLYF----EYIKIFHSLTDSSKDKECLEQA 382
C L + L+ P+ Y E +K D E L++A
Sbjct: 116 ECEASPLCRGLDLNSFLIKPVQRIPRYPLLLKELLK---HTPPDHPDYEDLKKA 166
>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 = 53.3 bits (128), Expect = 1e-08
Identities = 22/112 (19%), Positives = 41/112 (36%), Gaps = 15/112 (13%)
Query: 444 FYREDTLMKY-DGKSNRLTERKVYFFDGVLILCKSNKKISVTVPINVVSSQYEFKCKEMY 502
+E L K G +R F+ L+ KS K + +K K
Sbjct: 1 VIKEGWLYKKSGGGKKSWKKRYFVLFNSTLLYYKSKKD------------KKSYKPKGSI 48
Query: 503 FLRKVEINDYENTDDI--KNAFEIAPRDQPSIIIVTKSPEDKKSWFSDLIMV 552
L + + + D + FEI D+ ++++ +S E+++ W L
Sbjct: 49 DLSGCTVREAPDPDSSKKPHCFEIKTSDRKTLLLQAESEEEREKWVEALRKA 100
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 50.2 bits (120), Expect = 2e-07
Identities = 24/105 (22%), Positives = 41/105 (39%), Gaps = 15/105 (14%)
Query: 450 LMKYDGKSNRLTERKVYFFDGVLILCKSNKKISVTVPINVVSSQYEFKCKEMYFLRKVEI 509
L K G +R FDGVL+ K S + + K L ++
Sbjct: 8 LKKGSGGRKSWKKRYFVLFDGVLLYYKD-------------SKKSSSRPKGSIPLSGCQV 54
Query: 510 NDYENTDDIK--NAFEIAPRDQPSIIIVTKSPEDKKSWFSDLIMV 552
+++D K N FEI D+ + ++ +S E++K W +
Sbjct: 55 TKVPDSEDGKRKNCFEIRTGDRETFLLQAESEEERKEWVKAIRSA 99
>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
nucleosome is an octamer containing two H2A, H2B, H3,
and H4 subunits. The H2A subunit performs essential
roles in maintaining structural integrity of the
nucleosome, chromatin condensation, and binding of
specific chromatin-associated proteins.
Length = 115
Score = 47.7 bits (114), Expect = 1e-06
Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 6/93 (6%)
Query: 101 KQALEKGKKKSS------LVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLLK 154
K +K KK S L + R+ L+K Y +V +Y AAVL+Y+ A++L+
Sbjct: 1 KGGGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLE 60
Query: 155 LVGNYVKNIRKVDISIQDIDVAMYADKALLELF 187
L GN ++ +K I+ + + +A+ D+ L +L
Sbjct: 61 LAGNAARDNKKKRITPRHLQLAVRNDEELNKLL 93
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 47.4 bits (113), Expect = 3e-06
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 100 AKQALEKGKKKSSLVIS----------IDRVQNILQKEFYFRKVETNMVLYYAAVLDYVA 149
K GK +S + RV L+K Y ++V +Y AAVL+Y+
Sbjct: 3 GKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLT 62
Query: 150 ADLLKLVGNYVKNIRKVDISIQDIDVAMYADKAL 183
A++L+L GN K+ +K I+ + I +A+ D+ L
Sbjct: 63 AEVLELAGNAAKDNKKKRITPRHIQLAIRNDEEL 96
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 45.9 bits (108), Expect = 1e-05
Identities = 26/88 (29%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 100 AKQALEKGKKKSSLVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLLKLVGNY 159
K+A+ + K+ L + R+ L+K Y ++ +Y AAVL+Y+ A++L+L GN
Sbjct: 11 GKKAVSR-SAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNA 69
Query: 160 VKNIRKVDISIQDIDVAMYADKALLELF 187
++ +K I + I +A+ D+ L +L
Sbjct: 70 ARDNKKNRIVPRHIQLAIRNDEELGKLL 97
>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
Length = 132
Score = 46.0 bits (109), Expect = 1e-05
Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 7/93 (7%)
Query: 101 KQALEKGKKKSS-------LVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLL 153
K+ G KK++ L + R+ L+ Y +V +Y AAVL+Y+AA++L
Sbjct: 6 KRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVL 65
Query: 154 KLVGNYVKNIRKVDISIQDIDVAMYADKALLEL 186
+L GN ++ +K I + I +A+ D+ L +L
Sbjct: 66 ELAGNAARDNKKSRIVPRHIQLAVRNDEELSKL 98
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 45.0 bits (107), Expect = 1e-05
Identities = 23/78 (29%), Positives = 47/78 (60%)
Query: 110 KSSLVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLLKLVGNYVKNIRKVDIS 169
++ L + R+ +L+K Y ++V +Y AAVL+Y+ A++L+L GN ++ +K I+
Sbjct: 5 RAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRIT 64
Query: 170 IQDIDVAMYADKALLELF 187
+ + +A+ D+ L +L
Sbjct: 65 PRHLQLAIRNDEELNKLL 82
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 44.9 bits (106), Expect = 2e-05
Identities = 26/88 (29%), Positives = 49/88 (55%), Gaps = 4/88 (4%)
Query: 100 AKQALEKGKKKSS----LVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLLKL 155
K A + + S L+ + RV+ +L+K Y ++ +Y AAVL+Y+AA++L+L
Sbjct: 8 GKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILEL 67
Query: 156 VGNYVKNIRKVDISIQDIDVAMYADKAL 183
GN ++ +K I + + +A+ D+ L
Sbjct: 68 AGNAARDNKKKRIIPRHLQLAIRNDEEL 95
>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
Length = 139
Score = 44.2 bits (104), Expect = 4e-05
Identities = 24/78 (30%), Positives = 44/78 (56%)
Query: 110 KSSLVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLLKLVGNYVKNIRKVDIS 169
K+ L + R+ L+ Y +V +Y +AVL+Y+AA++L+L GN ++ +K I
Sbjct: 25 KAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIV 84
Query: 170 IQDIDVAMYADKALLELF 187
+ I +A+ D+ L +L
Sbjct: 85 PRHIQLAVRNDEELSKLL 102
>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
Length = 134
Score = 42.6 bits (100), Expect = 1e-04
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 7/62 (11%)
Query: 101 KQALEKGKKKSS-------LVISIDRVQNILQKEFYFRKVETNMVLYYAAVLDYVAADLL 153
KQA +K K S L+ + RV ++L++ Y R++ + +Y AAVL+Y+ A+LL
Sbjct: 5 KQAKKKASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELL 64
Query: 154 KL 155
+L
Sbjct: 65 EL 66
>gnl|CDD|241255 cd01220, PH1_FARP1-like, FERM, RhoGEF and pleckstrin
domain-containing protein 1 and related proteins
Pleckstrin Homology (PH) domain, repeat 1. Members here
include FARP1 (also called Chondrocyte-derived
ezrin-like protein; PH domain-containing family C member
2), FARP2 (also called FIR/FERM domain including RhoGEF;
FGD1-related Cdc42-GEF/FRG), and FARP6 (also called Zinc
finger FYVE domain-containing protein 24). They are
members of the Dbl family guanine nucleotide exchange
factors (GEFs) which are upstream positive regulators of
Rho GTPases. Little is known about FARP1 and FARP6,
though FARP1 has increased expression in differentiated
chondrocytes. FARP2 is thought to regulate neurite
remodeling by mediating the signaling pathways from
membrane proteins to Rac. It is found in brain, lung,
and testis, as well as embryonic hippocampal and
cortical neurons. FARP1 and FARP2 are composed of a
N-terminal FERM domain, a proline-rich (PR) domain,
Dbl-homology (DH), and two C-terminal PH domains. FARP6
is composed of Dbl-homology (DH), and two C-terminal PH
domains separated by a FYVE domain. This hierarchy
contains 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 = 123
Score = 39.2 bits (92), Expect = 0.002
Identities = 33/133 (24%), Positives = 59/133 (44%), Gaps = 18/133 (13%)
Query: 421 KIHELKKNVDGVDVRDLRPYLEEFYREDTLMKYDGKSNRLTERKVYFFDGVLIL-CKSNK 479
K+ EL++++ G+D ++P EF RE L+K K L +R + F VLI +
Sbjct: 1 KLCELQRDLIGID-NLVQP-GREFIREGCLLKLSKKG--LQQRMFFLFSDVLIYTSRG-- 54
Query: 480 KISVTVPINVVSSQYEFKCKEMYFLRKVEINDYENTDDIKNAFEIAPRDQPSIIIVTKSP 539
+S +FK LR + + + E + + F I ++ ++ + S
Sbjct: 55 ----------PTSTLQFKVHGQLPLRGLMVEESEPEMGVPHCFTIYGGNR-ALTVAASSE 103
Query: 540 EDKKSWFSDLIMV 552
E+K+ W DL
Sbjct: 104 EEKERWLEDLSRA 116
>gnl|CDD|241258 cd01224, PH_Collybistin_ASEF, Collybistin/APC-stimulated guanine
nucleotide exchange factor pleckstrin homology (PH)
domain. Collybistin (also called PEM2) is homologous to
the Dbl proteins ASEF (also called ARHGEF4/RhoGEF4) and
SPATA13 (Spermatogenesis-associated protein 13; also
called ASEF2). It activates CDC42 specifically and not
any other Rho-family GTPases. Collybistin consists of an
SH3 domain, followed by a RhoGEF/DH and PH domain. In
Dbl proteins, the DH and PH domains catalyze the
exchange of GDP for GTP in Rho GTPases, allowing them to
signal to downstream effectors. It induces submembrane
clustering of the receptor-associated peripheral
membrane protein gephyrin, which is thought to form a
scaffold underneath the postsynaptic membrane linking
receptors to the cytoskeleton. It also acts as a tumor
suppressor that links adenomatous polyposis coli (APC)
protein, a negative regulator of the Wnt signaling
pathway and promotes the phosphorylation and degradation
of beta-catenin, to Cdc42. Autoinhibition of collybistin
is accomplished by the binding of its SH3 domain with
both the RhoGEF and PH domains to block access of Cdc42
to the GTPase-binding site. Inactivation promotes cancer
progression. 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 = 36.8 bits (86), Expect = 0.016
Identities = 34/141 (24%), Positives = 61/141 (43%), Gaps = 27/141 (19%)
Query: 416 LQSLEKIHELKKNVDGVDVRDLRPYLEEFYREDTLMKYDGKSNRLTERKVYFFDGVLILC 475
L++LEK+ + +++G + DL E L K K ER + FD L+ C
Sbjct: 1 LENLEKLAAWQSSIEGWEGEDLLDRSSELIHSGELSKISSKGKA-QERTFFLFDHQLVYC 59
Query: 476 KSNKKISVTVPINVVSSQYEFKCKEMYFLRKVEINDYENTDD---------IKNAFEI-- 524
K K + + +K + L +EI E+ +D +KNA++I
Sbjct: 60 K--KDL-------LKRDNLIYKGR--IDLDNMEI---EDLEDGKDKDSGVTVKNAWKIYN 105
Query: 525 APRDQPSIIIVTKSPEDKKSW 545
+++ ++ KS E+K+ W
Sbjct: 106 TSKNK-WYLLCAKSAEEKQRW 125
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 34.1 bits (79), Expect = 0.043
Identities = 14/74 (18%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 108 KKKSSLVISIDRVQNILQKEFYFRK-VETNMVLYYAAVLDYVAADLLKLVGNYVKNIRKV 166
+ L + RV L++ FY + + + L+ + ++L+ G ++ ++
Sbjct: 2 SRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRK 61
Query: 167 DISIQDIDVAMYAD 180
I+ +DI +A+ D
Sbjct: 62 TITPRDIQLAVRLD 75
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 34.9 bits (80), Expect = 0.065
Identities = 26/108 (24%), Positives = 52/108 (48%), Gaps = 4/108 (3%)
Query: 80 MEGKIKKYFPNPISEWTFNEAKQALEKGKKKSS---LVISIDRVQNILQKEFYFR-KVET 135
M GK K + + + +K +SS L + R+ L++ +V
Sbjct: 1 MSGKGGKGLLAAKTTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGA 60
Query: 136 NMVLYYAAVLDYVAADLLKLVGNYVKNIRKVDISIQDIDVAMYADKAL 183
+Y AA+L+Y+ A++L+L GN K+++ I+ + + +A+ D+ L
Sbjct: 61 TAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEEL 108
>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 = 0.082
Identities = 24/104 (23%), Positives = 41/104 (39%), Gaps = 15/104 (14%)
Query: 446 REDTLMKYDGKSNRL-TERKVYFFDGVLILCKSNKKISVTVPINVVSSQYEFKCKEMYFL 504
+E L K GK + +R FD VL+ KS KK S P ++ + + +
Sbjct: 1 KEGWLKKRGGKGLKSWKKRWFVLFDDVLLYYKS-KKDSSKKPKGLIPLSDGLEVELVSSS 59
Query: 505 RKVEINDYENTDDIKNAFEIAPRDQP-SIIIVTKSPEDKKSWFS 547
K N FE+ D+ + + +S E+++ W
Sbjct: 60 GK------------PNCFELVTPDRGRTYYLQAESEEEREEWLE 91
>gnl|CDD|241540 cd13389, PH1_FGD5_FGD6, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia proteins 5 and 6
Pleckstrin Homology (PH) domain. FGD5 regulates
promotes angiogenesis of vascular endothelial growth
factor (VEGF) in vascular endothelial cells, including
network formation, permeability, directional movement,
and proliferation. The specific function of FGD6 is
unknown. In general, FGDs have a RhoGEF (DH) domain,
followed by a PH domain, a FYVE domain and a C-terminal
PH domain. All FGDs are guanine nucleotide exchange
factors that activate the Rho GTPase Cdc42, an important
regulator of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the PH
domain is involved in intracellular targeting of the DH
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 = 125
Score = 34.2 bits (79), Expect = 0.084
Identities = 22/107 (20%), Positives = 37/107 (34%), Gaps = 15/107 (14%)
Query: 443 EFYREDTLMKYDGKSNRLTERKVYFFDGVLILCKSNKKISVTVPINVVSSQYEFKCKEMY 502
+E LMK K + R ++ F+ VL+ + + E M
Sbjct: 13 VLIKEGELMKVSRKE--MQPRYLFLFNDVLLYTTPVQSGVGKYKLK-----NELPLSGM- 64
Query: 503 FLRKVEINDYENTDDIKNAFEIAPRDQPSIIIVTKSPEDKKSWFSDL 549
KV + + E N F+I + S + S E++ W L
Sbjct: 65 ---KVSLPEDEEY---SNEFQIESTKR-SFTLSASSAEERDEWVKAL 104
>gnl|CDD|241259 cd01225, PH_Cool_Pix, Cloned out of library/PAK-interactive
exchange factor pleckstrin homology (PH) domain. There
are two forms of Pix proteins: alpha Pix (also called
Rho guanine nucleotide exchange factor (GEF) 6/90Cool-2)
and beta Pix (GEF7/p85Cool-1). betaPix contains an
N-terminal SH3 domain, a RhoGEF/DH domain, a PH domain,
a GIT1 binding domain (GBD), and a C-terminal
coiled-coil (CC) domain. alphaPix differs in that it
contains a calponin homology (CH) domain, which
interacts with beta-parvin, N-terminal to the SH3
domain. alphaPix is an exchange factor for Rac1 and
Cdc42 and mediates Pak activation on cell adhesion to
fibronectin. Mutations in alphaPix can cause X-linked
mental retardation. alphaPix also interacts with
Huntington's disease protein (htt), and enhances the
aggregation of mutant htt (muthtt) by facilitating
SDS-soluble muthtt-muthtt interactions. The DH-PH domain
of a Pix was required for its binding to htt. In the
majority of Rho GEF proteins, the DH-PH domain is
responsible for the exchange activity. 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 = 100
Score = 32.3 bits (74), Expect = 0.27
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 509 INDYENTDDIKNAFEIAPRDQPSIIIVTKSPEDKKSWFSDL 549
+N E+T+ IK+AFEI+ I+++ S D++ W L
Sbjct: 54 VNRLEDTEGIKHAFEISGPMIERIVVICNSSNDQQEWIEHL 94
>gnl|CDD|241393 cd13239, PH_Obscurin, Obscurin pleckstrin homology (PH) domain.
Obscurin (also called Obscurin-RhoGEF; Obscurin-myosin
light chain kinase/Obscurin-MLCK) is a giant muscle
protein that is concentrated at the peripheries of
Z-disks and M-lines. It binds small ankyrin I, a
component of the sarcoplasmic reticulum (SR) membrane.
It is associated with the contractile apparatus through
binding with titin and sarcomeric myosin. It plays
important roles in the organization and assembly of the
myofibril and the SR. Obscurin has been observed as
alternatively-spliced isoforms. The major isoform in
sleletal muscle, approximately 800 kDa in size, is
composed of many adhesion modules and signaling domains.
It harbors 49 Ig and 2 FNIII repeats at the N-terminues,
a complex middle region with additional Ig domains, an
IQ motif, and a conserved SH3 domain near RhoGEF and PH
domains, and a non-modular C-terminus with
phosphorylation motifs. The obscurin gene also encodes
two kinase domains, which are not part of the 800 kDa
form of the protein, but is part of smaller spliced
products that present in heart muscle. 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 = 125
Score = 32.8 bits (75), Expect = 0.33
Identities = 25/117 (21%), Positives = 46/117 (39%), Gaps = 18/117 (15%)
Query: 441 LEEFYREDTLMKYDG-----KSNRLTERKVYFFDGVLILCKSNKKISVTVPINVVSSQYE 495
L E R+ ++G S++ R V+ F +++CK + P +
Sbjct: 12 LGEPIRQGHFTVWEGAPGVRTSSKGHHRHVFLFKNCIVICKPKRDSRTDTPTYI------ 65
Query: 496 FKCKEMYFLRKVEINDYENTDDIKNAFEIAPRDQPSIIIVT---KSPEDKKSWFSDL 549
K L +++ND DD AFE+ + S+ T ++ K SW ++
Sbjct: 66 --FKNKMKLNDIDVNDTVEGDD--RAFELWHEREDSVRKYTLQARTIIVKNSWVKEI 118
>gnl|CDD|237801 PRK14719, PRK14719, bifunctional
RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase;
Provisional.
Length = 360
Score = 33.4 bits (76), Expect = 0.76
Identities = 13/42 (30%), Positives = 27/42 (64%)
Query: 393 LSKISLEKNGKNACVRNYNRVKHLQSLEKIHELKKNVDGVDV 434
+S + + +GK A + N +R+ L+++HE++K+VD + V
Sbjct: 143 ISNVGMTLDGKLATIENDSRISGENDLKRVHEIRKDVDAIMV 184
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 30.2 bits (68), Expect = 1.1
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 233 KIFYEELNKITPLKEIKEVHSLFEIIEEIY 262
K+F LNK KE++EV S + +E+IY
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIY 30
>gnl|CDD|220149 pfam09234, DUF1963, Domain of unknown function (DUF1963). This
domain is found in a set of hypothetical bacterial
proteins. Its exact function has not, as yet, been
described.
Length = 221
Score = 31.2 bits (71), Expect = 2.2
Identities = 22/103 (21%), Positives = 43/103 (41%), Gaps = 16/103 (15%)
Query: 178 YADKALLELFFQEDDDPVYLEPQVQSNNVVLHYEQVVN---------DFVAEEKLFIREL 228
+ ++ +L+ F DDD P+ Q+ V+++E ++ DF + F EL
Sbjct: 42 FPEEGILQFFIDLDDDDWGDSPEDQTGFRVIYFEDIIEDLLPKDLIEDFSFLKAPFEGEL 101
Query: 229 KLILKIFYE-------ELNKITPLKEIKEVHSLFEIIEEIYNL 264
KL + E + + ++ E+IEE+Y+
Sbjct: 102 KLPFEKSDEPISEDDYSFEQEYESEILELEEEDEELIEELYDE 144
>gnl|CDD|241397 cd13243, PH_PLEKHG1_G2_G3, Pleckstrin homology domain-containing
family G members 1, 2, and 3 pleckstrin homology (PH)
domain. PLEKHG1 (also called ARHGEF41), PLEKHG2 (also
called ARHGEF42 or CLG/common-site lymphoma/leukemia
guanine nucleotide exchange factor2), and PLEKHG3 (also
called ARHGEF43) have RhoGEF DH/double-homology domains
in tandem with a PH domain which is involved in
phospholipid binding. They function as a guanine
nucleotide exchange factor (GEF) and are involved in the
regulation of Rho protein signal transduction. Mutations
in PLEKHG1 have been associated panic disorder (PD), an
anxiety disorder characterized by panic attacks and
anticipatory anxiety. 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 = 147
Score = 30.4 bits (69), Expect = 2.6
Identities = 28/136 (20%), Positives = 50/136 (36%), Gaps = 31/136 (22%)
Query: 412 RVKHLQSLEKIHELKKNVDGVDVRDLRPYLEEFYREDTLMKYDGKSNRLTERKVYFFDGV 471
R++ +QSL +DG DL Y E E + K+ RL ++ FD +
Sbjct: 30 RLQEIQSL---------LDGWLGPDLTTYGE-LVLEGSFRVQGAKNERL----LFLFDKM 75
Query: 472 LILCKSNKKISVTVPINVVSSQYEFKCKEMYFLRKVEINDYENTDDIKNAFEIAPRDQP- 530
L++ K + K + + + D + +F++ P D P
Sbjct: 76 LLITKKREDDH-------------LVYKTHIMCSNLMLVESIPKDPL--SFQVLPFDNPK 120
Query: 531 -SIIIVTKSPEDKKSW 545
+ K+ E K+ W
Sbjct: 121 AQYTLQAKNLEQKRLW 136
>gnl|CDD|150276 pfam09547, Spore_IV_A, Stage IV sporulation protein A (spore_IV_A).
SpoIVA is designated stage IV sporulation protein A. It
acts in the mother cell compartment and plays a role in
spore coat morphogenesis. A comparative genome analysis
of all sequenced genomes of Firmicutes shows that the
proteins are strictly conserved among the sub-set of
endospore-forming species.
Length = 492
Score = 31.0 bits (71), Expect = 3.6
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 7/64 (10%)
Query: 219 AEEKLFIRELKLILKIFYEELNKITPLKEIKEVHSLFEIIEEIYNLTVCLLGAVEDISEM 278
AEE++ I ELK I K F LN P E E L + +EE Y++ V + + ++M
Sbjct: 168 AEERV-IEELKEIGKPFIILLNSQRPYSE--ETKELRDELEEKYDVPVLPV----NCAQM 220
Query: 279 SSDD 282
+ +D
Sbjct: 221 TEED 224
>gnl|CDD|224348 COG1431, COG1431, Argonaute homolog, implicated in RNA metabolism
[Translation, ribosomal structure and biogenesis].
Length = 685
Score = 31.0 bits (70), Expect = 4.7
Identities = 25/134 (18%), Positives = 48/134 (35%), Gaps = 7/134 (5%)
Query: 638 RSFTTPTELLDLLIDRFNVPDPNKVFENNNADIEESILREDIIR-YKKELCQPVQFRVLN 696
P+ L++ + + ++V+ +N I E I K E+ + V++
Sbjct: 178 NGVNQPSSLVNPTKSQISGRRVDEVWHIHNIGISEFIYDSPHFSSIKSEVDNNIDTGVVD 237
Query: 697 VFRQWVQHHFYDFQRDQNLLEKLKSFLLNEISGKSLRKWADIVLNLIQRKELD-LEKEIT 755
+ D + L LKS+L+ EI ++ DI+ N +D L +
Sbjct: 238 GI---LLVLPEDVLYNTPLYYPLKSYLILEIPSRNEVY--DILSNRKLLFYIDNLLVQFV 292
Query: 756 FAFNNSPPPIEVHV 769
P + V
Sbjct: 293 SKLRGKPWILNVDP 306
>gnl|CDD|225979 COG3448, COG3448, CBS-domain-containing membrane protein [Signal
transduction mechanisms].
Length = 382
Score = 30.6 bits (69), Expect = 4.9
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 859 IEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALPTRLQKVL 904
I M L+ L+ +G +A+T+ +G AV+RL + F P L ++
Sbjct: 117 IGAMFALRCLHPPSGAVALTAVLGGPAVHRLGYNFVLWPVALNSLI 162
>gnl|CDD|241253 cd01218, PH_Phafin2-like, Phafin2 (also called EAPF, FLJ13187,
ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain.
Phafin2 is differentially expressed in the liver cancer
cell and regulates the structure and function of the
endosomes through Rab5-dependent processes. Phafin2
modulates the cell's response to extracellular
stimulation by modulating the receptor density on the
cell surface. Phafin2 contains a PH domain and a FYVE
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 = 123
Score = 29.1 bits (66), Expect = 5.9
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 504 LRKVEINDYENTDDIKNAFEIAPRDQPSIIIVTKSPEDKKSWFSDL 549
L V+I D E+T ++KN ++I + S ++ + +K W +
Sbjct: 76 LEDVKIEDLEDTGELKNGWQIISPKK-SFVVYAATATEKSEWMDHI 120
>gnl|CDD|130572 TIGR01508, rib_reduct_arch,
2,
5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
1'-reductase, archaeal. This model represents a
specific reductase of riboflavin biosynthesis in the
Archaea, diaminohydroxyphosphoribosylaminopyrimidine
reductase. It should not be confused with bacterial
5-amino-6-(5-phosphoribosylamino)uracil reductase. The
intermediate
2,
5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
in riboflavin biosynthesis is reduced first, and then
deaminated, in both Archaea and Fungi, opposite the
order in Bacteria. The subsequent deaminase is not
presently known and is not closely homologous to the
deaminase domain (3.5.4.26) fused to the reductase
domain (1.1.1.193) similar to this protein but found in
most bacteria.
Length = 210
Score = 29.8 bits (67), Expect = 6.5
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 388 PLQISLSKISLEKNGKNACVRNYNRVKHLQSLEKIHELKKNVDGVDV 434
P I +SL+ GK A + +R+ + L ++HE++ VD + V
Sbjct: 1 PYVIVNVAMSLD--GKLATINRDSRISCEEDLIRVHEIRAEVDAIMV 45
>gnl|CDD|241257 cd01223, PH_Vav, Vav pleckstrin homology (PH) domain. Vav acts as
a guanosine nucleotide exchange factor (GEF) for Rho/Rac
proteins. They control processes including T cell
activation, phagocytosis, and migration of cells. The
Vav subgroup of Dbl GEFs consists of three family
members (Vav1, Vav2, and Vav3) in mammals. Vav1 is
preferentially expressed in the hematopoietic system,
while Vav2 and Vav3 are described by broader expression
patterns. Mammalian Vav proteins consist of a calponin
homology (CH) domain, an acidic region, a catalytic Dbl
homology (DH) domain, a PH domain, a zinc finger
cysteine rich domain (C1/CRD), and an SH2 domain,
flanked by two SH3 domains. In invertebrates such as
Drosophila and C. elegans, Vav is missing the N-terminal
SH3 domain. The DH domain is involved in RhoGTPase
recognition and selectivity and stimulates the
reorganization of the switch regions for GDP/GTP
exchange. The PH domain is implicated in directing
membrane localization, allosteric regulation of guanine
nucleotide exchange activity, and as a phospholipid-
dependent regulator of GEF activity. Vavs bind
RhoGTPases including Rac1, RhoA, RhoG, and Cdc42, while
other members of the GEF family are specific for a
single RhoGTPase. This promiscuity is thought to be a
result of its CRD. 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.polarized. PH domains also have
diverse functions. They are often involved in targeting
proteins to the plasma membrane, but only a few (less
than 10%) display strong specificity in binding inositol
phosphates. 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 kinases, tyrosine kinases,
regulators of G-proteins, endocytotic GTPases, adaptors,
cytoskeletal associated molecules, and in lipid
associated enzymes.
Length = 127
Score = 28.8 bits (65), Expect = 6.7
Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 20/97 (20%)
Query: 456 KSNRLTERKVYFFDGVLILCKSNKKISVTVPINVVSSQYEFKCKEMYFLRKVEINDYENT 515
+ + +R + FD VL++CK + QYE+ KE+ L + +I D +
Sbjct: 31 EDQKKKDRYAFLFDKVLLVCKRLR-----------GDQYEY--KEIINLSEYKIEDDPSR 77
Query: 516 DDIKNA-------FEIAPRDQPSIIIVTKSPEDKKSW 545
+K + + + + + K+ E KK W
Sbjct: 78 RTLKRDKRWSYQFLLVHKQGKTAYTLYAKTEELKKKW 114
>gnl|CDD|241423 cd13269, PH_alsin, Alsin Pleckstrin homology (PH) domain. The ALS2
gene encodes alsin, a GEF, that has dual specificity for
Rac1 and Rab5 GTPases. Alsin mutations in the form of
truncated proteins are responsible for motor function
disorders including juvenile-onset amyotrophic lateral
sclerosis, familial juvenile primary lateral sclerosis,
and infantile-onset ascending hereditary spastic
paralysis. The alsin protein is widely expressed in the
developing CNS including neurons of the cerebral cortex,
brain stem, spinal cord, and cerebellum. Alsin contains
a regulator of chromosome condensation 1 (RCC1) domain,
a Rho guanine nucleotide exchanging factor (RhoGEF)
domain, a PH domain, a Membrane Occupation and
Recognition Nexus (MORN), a vacuolar protein sorting 9
(Vps9) domain, and a Dbl homology (DH) domain. Alsin
interacts with Rab5 through its Vps9 domain and through
this interaction modulates early endosome fusion and
trafficking. The GEF activity of alsin towards Rab5 is
regulated by Rac1 function. The GEF activity of alsin
for Rac1 occurs via its DH domain and this interaction
plays a role in promoting spinal motor neuron survival
via multiple Rac-dependent signaling pathways. 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 = 28.5 bits (64), Expect = 6.7
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 504 LRKVEINDYENTDDIKNAFEIAPRDQPSIIIVTKSPEDKKSWF 546
L + + + D +NA +I + S +V +P++K W
Sbjct: 52 LATLWVEPIPDEDSGQNALKI-TTPEESFTLVASTPQEKAEWL 93
>gnl|CDD|200569 cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of
Streptococcus mutans polysaccharide deacetylase PgdA,
Bacillus subtilis YheN, and similar proteins. This
family is represented by a putative polysaccharide
deacetylase PgdA from the oral pathogen Streptococcus
mutans (SmPgdA) and Bacillus subtilis YheN (BsYheN),
which are members of the carbohydrate esterase 4 (CE4)
superfamily. SmPgdA is an extracellular metal-dependent
polysaccharide deacetylase with a typical CE4 fold, with
metal bound to a His-His-Asp triad. It possesses
de-N-acetylase activity toward a hexamer of
chitooligosaccharide N-acetylglucosamine, but not
shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. SmPgdA plays a role in
tuning cell surface properties and in interactions with
(salivary) agglutinin, an essential component of the
innate immune system, most likely through deacetylation
of an as-yet-unidentified polysaccharide. SmPgdA shows
significant homology to the catalytic domains of
peptidoglycan deacetylases from Streptococcus pneumoniae
(SpPgdA) and Listeria monocytogenes (LmPgdA), both of
which are involved in the bacterial defense mechanism
against human mucosal lysozyme. The Bacillus subtilis
genome contains six polysaccharide deacetylase gene
homologs: pdaA, pdaB (previously known as ybaN), yheN,
yjeA, yxkH and ylxY. The biological function of BsYheN
is still unknown. This family also includes many
uncharacterized polysaccharide deacetylases mainly found
in bacteria.
Length = 189
Score = 29.4 bits (67), Expect = 8.0
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 12/49 (24%)
Query: 302 EKLLHNIVNQ---KSIEVLSMHVTQ---------PSILNTLQFAGYGFK 338
E+++ N++ Q K++ V+ MH T P I+ L+ GY FK
Sbjct: 140 EQIVQNVIKQVKNKNVIVILMHDTAGKETTVEALPEIIKYLKEQGYEFK 188
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.8 bits (68), Expect = 9.5
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 20/73 (27%)
Query: 899 RLQKVLEDARELNGDHFKKYQEKLRNINPPCIPFFGMYLTNILHIEEGNPDFLPDSKLIN 958
R +K + A+EL+ +H K EKLR I + L PDS++I
Sbjct: 331 RFRKAVRKAKELDIEHPK--LEKLREI-----------VKEQLGKN-------PDSRIIV 370
Query: 959 FTKRRKVAEIISE 971
FT+ R AE I +
Sbjct: 371 FTQYRDTAEKIVD 383
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.137 0.399
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 58,056,010
Number of extensions: 5987005
Number of successful extensions: 5407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5377
Number of HSP's successfully gapped: 76
Length of query: 1108
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1001
Effective length of database: 6,191,724
Effective search space: 6197915724
Effective search space used: 6197915724
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 64 (28.4 bits)