RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2293
(832 letters)
>gnl|CDD|241263 cd01229, PH_Ect2, Epithelial cell transforming 2 (Ect2) pleckstrin
homology (PH) domain. Ect2, a mammalian ortholog of
Drosophila pebble, plays a role in neuronal
differentiation and brain development. Pebble and Ect2
have been identified as Rho-family guanine nucleotide
exchange factors (GEF) that mediate activation of Rho
during cytokinesis, but are proposed to play slightly
different roles. 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 = 180
Score = 168 bits (427), Expect = 4e-48
Identities = 74/182 (40%), Positives = 114/182 (62%), Gaps = 12/182 (6%)
Query: 585 IRTVMTFLNENKQRQDNQRSLFDIYQDIENCPPQLINSHRSFVLKCDVIELS-NMLSHRG 643
++ VMT +NE+K++ + Q +FDI +IE CPP L++SHRSFV + +V+EL ++ S RG
Sbjct: 1 LKEVMTHINEDKRKTEGQAQMFDIVNEIEGCPPTLLSSHRSFVSRLEVVELGDSLKSGRG 60
Query: 644 DCITLFLFTDVVEVCKKRSKYVNVLKSPNTSKMSLSTYKTQAKHPID-KTYKHIKLLSMT 702
D + LFLF+D++E+CKKRS KSP S T + K YKHIKL+ ++
Sbjct: 61 DSLALFLFSDLLEICKKRSSVKGTAKSPRGS--------TGSGLRESKKKYKHIKLMPLS 112
Query: 703 SIKKVYNVEDEAHDNDRQIFALRCRGSDEVIETTYSFNIIDDTLDKMSFLRELCRQASAV 762
+IK+V ++ + ++ + +FAL R E+ E YSF I+D+ DK FL+ LC+Q +
Sbjct: 113 NIKRVIDITE--TEDCQNVFALLFRSPTELKEKLYSFQILDEETDKEKFLKTLCKQIANT 170
Query: 763 YC 764
C
Sbjct: 171 VC 172
>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 = 161 bits (410), Expect = 8e-46
Identities = 67/191 (35%), Positives = 108/191 (56%), Gaps = 13/191 (6%)
Query: 405 VFKELCQTESNYVNVLRVLIEHFKNPLEEKLNTNECILNQAEMKIIFGDLCPIFDTHKDL 464
V +EL QTE +YV L++L+E F PL E IL++ E+K IF ++ I + H++
Sbjct: 1 VIQELLQTERSYVRDLKILVEVFLKPLRESP-----ILSEEEIKTIFSNIEEILELHQEF 55
Query: 465 LKDLKYLEQNYSDSVSIGEVFVKHCTAFKKVYPPFINFFQDSNSLLKE-KEKNSRFLAFL 523
L++L+ + + D IG++F+K F KVY + + + + LLK+ ++KN RF FL
Sbjct: 56 LEELEERLEEWPDIQRIGDIFLKFA-PFFKVYSTYCSNYPRALELLKKLRKKNPRFAKFL 114
Query: 524 KLCYMNLRDLGLPEIDKQTLPDLLIRPVQRLGSISLLLNDILKNTSKSSTDHQKLSEALD 583
K C + P L LI+PVQR+ LLL ++LK+T D++ L +AL+
Sbjct: 115 KECEAS------PLCRGLDLNSFLIKPVQRIPRYPLLLKELLKHTPPDHPDYEDLKKALE 168
Query: 584 GIRTVMTFLNE 594
I+ V + +NE
Sbjct: 169 AIKEVASQINE 179
>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 = 138 bits (350), Expect = 1e-37
Identities = 69/191 (36%), Positives = 111/191 (58%), Gaps = 12/191 (6%)
Query: 405 VFKELCQTESNYVNVLRVLIEHFKNPLEEKLNTNECILNQAEMKIIFGDLCPIFDTHKDL 464
V KEL QTE NYV L++L+E F PL+++L +L+ E++ +FG++ I++ H+D
Sbjct: 1 VLKELLQTERNYVRDLKLLVEVFLKPLKKELK----LLSPNELETLFGNIEEIYEFHRDF 56
Query: 465 LKDL-KYLEQNYSDSVSIGEVFVKHCTAFKKVYPPFINFFQDSNSLLKEKEKNSRFLAFL 523
L +L + +E+ IG+VF+K F K+Y + + D+ LLK+ +KN RF FL
Sbjct: 57 LDELEERIEEWDDSVERIGDVFLKLEE-FFKIYSEYCSNHPDALELLKKLKKNPRFQKFL 115
Query: 524 KLCYMNLRDLGLPEIDKQTLPDLLIRPVQRLGSISLLLNDILKNTSKSSTDHQKLSEALD 583
K + P+ + TL LL++PVQRL LLL ++LK+T + D + L +AL
Sbjct: 116 KEIESS------PQCRRLTLESLLLKPVQRLTKYPLLLKELLKHTPEDHEDREDLKKALK 169
Query: 584 GIRTVMTFLNE 594
I+ + +NE
Sbjct: 170 AIKELANQVNE 180
>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 = 130 bits (330), Expect = 6e-35
Identities = 65/194 (33%), Positives = 105/194 (54%), Gaps = 15/194 (7%)
Query: 402 RHQVFKELCQTESNYVNVLRVLIEHFKNPLEEKLNTNECILNQAEMKIIFGDLCPIFDTH 461
R +V KEL QTE NYV L++L+E F PL++ L+ E++++FG++ I++ H
Sbjct: 1 RQEVIKELLQTERNYVRDLKLLVEVFLKPLDK----ELLPLSPEEVELLFGNIEEIYEFH 56
Query: 462 KDLLKDLK-YLEQNYSDSVSIGEVFVKHCTAFKKVYPPFINFFQDSNSLLKE-KEKNSRF 519
+ LK L+ +E+ IG+VF+K F K+Y + + D+ LLK+ K+ N F
Sbjct: 57 RIFLKSLEERVEEWDKSGPRIGDVFLKLA-PFFKIYSEYCSNHPDALELLKKLKKFNKFF 115
Query: 520 LAFLKLCYMNLRDLGLPEIDKQTLPDLLIRPVQRLGSISLLLNDILKNTSKSSTDHQKLS 579
FL+ + L LL++PVQRL LLL ++LK+T D + L
Sbjct: 116 QEFLEKAESECG--------RLKLESLLLKPVQRLTKYPLLLKELLKHTPDGHEDREDLK 167
Query: 580 EALDGIRTVMTFLN 593
+AL+ I+ V + +N
Sbjct: 168 KALEAIKEVASQVN 181
>gnl|CDD|193214 pfam12738, PTCB-BRCT, twin BRCT domain. This is a BRCT domain that
appears in duplicate in most member sequences. BRCT
domains are peptide- and phosphopeptide-binding modules.
BRCT domains are present in a number of proteins
involved in DNA checkpoint controls and DNA repair.
Length = 63
Score = 63.4 bits (155), Expect = 1e-12
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 151 IVICITGFRNKQETMKLIDITKHMGGKLRKEMNYQVTHLIANCVSGEKYKYAMGFRVPVL 210
+VIC++G+ L + + +G + K++ +VTHLI GEKY+ A + +PV+
Sbjct: 1 LVICVSGYSGDDRK-YLQKLIEALGAEYSKDLTKKVTHLICKRGEGEKYEKAKKWGIPVV 59
Query: 211 T 211
+
Sbjct: 60 S 60
Score = 29.1 bits (66), Expect = 1.3
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 252 GFSEEDEEQLQELLLSNGGK--PSLSSDEPLTTHVVVDDSK 290
G+S +D + LQ+L+ + G + L+ TH++ +
Sbjct: 7 GYSGDDRKYLQKLIEALGAEYSKDLTKK---VTHLICKRGE 44
>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1),
carboxy-terminal domain. The BRCT domain is found within
many DNA damage repair and cell cycle checkpoint
proteins. The unique diversity of this domain
superfamily allows BRCT modules to interact forming
homo/hetero BRCT multimers, BRCT-non-BRCT interactions,
and interactions within DNA strand breaks.
Length = 72
Score = 49.6 bits (119), Expect = 8e-08
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 150 NIVICITGFRNKQETMKLIDITKHMGGKLRKEMNYQVTHLIANCVSGEK-YKYAMGFRVP 208
+ ITG +E +L ++ + +GGK+ ++ + TH+I +G K A+ +P
Sbjct: 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIP 60
Query: 209 VLTKEFVLSAWE 220
++T E++L +
Sbjct: 61 IVTPEWLLDCLK 72
Score = 32.7 bits (75), Expect = 0.090
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 253 FSEEDEEQLQELLLSNGGK--PSLSSDEPLTTHVVVD-DSKVTCMPNVPCTSTYVVKARW 309
E+ ++L+EL+ GGK S+S TTHV+V D+ + +V W
Sbjct: 10 LPSEERDELKELIEKLGGKVTSSVSKK---TTHVIVGSDAGPKKLLKAIKLGIPIVTPEW 66
Query: 310 FWMSIQ 315
++
Sbjct: 67 LLDCLK 72
>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain.
Length = 78
Score = 48.1 bits (115), Expect = 4e-07
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 148 MQNIVICITGFRNKQETMKLIDITKHMGGKLRKEMN-YQVTHLIANCVSGEKYKYAMGFR 206
+ ITG +K+E +L ++ + +GGK+ ++ TH+I G K +
Sbjct: 4 FKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKAIA 63
Query: 207 --VPVLTKEFVL 216
+P++ +E++L
Sbjct: 64 LGIPIVKEEWLL 75
Score = 38.1 bits (89), Expect = 0.001
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 241 KLFQGAKVNFFG-FSEEDEEQLQELLLSNGGKPSLSSDEPLTTHVVVDD--SKVTCMPNV 297
KLF+G G F +E+ ++L+EL+ + GGK + S TTHV+V +
Sbjct: 2 KLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKA 61
Query: 298 PCTSTYVVKARWFW 311
+VK W
Sbjct: 62 IALGIPIVKEEWLL 75
>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain. The BRCT domain
is found predominantly in proteins involved in cell
cycle checkpoint functions responsive to DNA damage. The
BRCT domain of XRCC1 forms a homodimer in the crystal
structure. This suggests that pairs of BRCT domains
associate as homo- or heterodimers. BRCT domains are
often found as tandem-repeat pairs. Structures of the
BRCA1 BRCT domains revealed a basis for a widely
utilised head-to-tail BRCT-BRCT oligomerisation mode.
This conserved tandem BRCT architecture facilitates
formation of the canonical BRCT phospho-peptide
interaction cleft at a groove between the BRCT domains.
Disease associated missense and nonsense mutations in
the BRCA1 BRCT domains disrupt peptide binding by
directly occluding this peptide binding groove, or by
disrupting key conserved BRCT core folding determinants.
Length = 77
Score = 45.1 bits (107), Expect = 3e-06
Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 148 MQNIVICITGFRNKQETMKLIDITKHMGGKLRKEMNYQVTHLIA-NCVSGEKYKYAMGFR 206
+ ITG + + +L ++ + +GGK+ ++ + TH+I K A+
Sbjct: 6 FKGKTFVITGLDSLERE-ELEELIEKLGGKVTDSLSKKTTHVIVGENAGTLKLLKAIALG 64
Query: 207 VPVLTKEFVL 216
+P++T+E++L
Sbjct: 65 IPIVTEEWLL 74
Score = 38.1 bits (89), Expect = 0.001
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 12/82 (14%)
Query: 239 KLKLFQGAKVNFFGFSEEDEEQLQELLLSNGGKPSLSSDEPLTTHVVVDDSKVT------ 292
K KLF+G G + E+L+EL+ GGK + S TTHV+V ++ T
Sbjct: 2 KEKLFKGKTFVITGLDSLEREELEELIEKLGGKVTDSLS-KKTTHVIVGENAGTLKLLKA 60
Query: 293 CMPNVPCTSTYVVKARWFWMSI 314
+P +V W I
Sbjct: 61 IALGIP-----IVTEEWLLDCI 77
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 45.7 bits (108), Expect = 1e-04
Identities = 68/274 (24%), Positives = 110/274 (40%), Gaps = 33/274 (12%)
Query: 402 RHQVFKELCQTESNYVNVLRVLIEHFKNPLEEKLNTNECILNQAEMKII---FGDLCPIF 458
R + E+ TE ++V L L + + PLEE + I A I F ++ I+
Sbjct: 485 RQEAIYEVIYTERDFVKDLEYLRDTWIKPLEE----SNIIPENARRNFIKHVFANINEIY 540
Query: 459 DTHKDLLKDLKYLEQNYSDSV-SIGEVFVKHCTAFKKVYPPFINFFQDSN----SLLKEK 513
+ LLK L Q S V I ++F+ + F+ PFI + +EK
Sbjct: 541 AVNSKLLKALTN-RQCLSPIVNGIADIFLDYVPKFE----PFIKYGASQPYAKYEFEREK 595
Query: 514 EKNSRFLAFLKLCYMNLRDLGLPEIDKQTLPDLLIRPVQRLGSISLLLNDILKNTSKSST 573
N F F L E K L L +P RL LLL ++LK T +
Sbjct: 596 SVNPNFARFDHEV------ERLDESRKLELDGYLTKPTTRLARYPLLLEEVLKFTDPDNP 649
Query: 574 DHQKLSEALDGIRTVMTFLNENKQRQDNQRSLFDIYQDIENCPPQLINSH---RSFVLKC 630
D + + + +D +R ++ LN + +N+ LF + Q + P+ +N +
Sbjct: 650 DTEDIPKVIDMLREFLSRLNFESGKAENRGDLFHLNQQL-LFKPEYVNLGLNDEYRKIIF 708
Query: 631 DVI-----ELSNMLSHRGDCITLFLFTDVVEVCK 659
+ + S RGD I FL +++ CK
Sbjct: 709 KGVLKRKAKSKTDGSLRGD-IQFFLLDNMLLFCK 741
>gnl|CDD|241256 cd01221, PH_ephexin, Ephexin Pleckstrin homology (PH) domain.
Ephexin-1 (also called NGEF/ neuronal guanine nucleotide
exchange factor) plays a role in the homeostatic
modulation of presynaptic neurotransmitter release.
Specific functions are still unknown for Ephexin-2 (also
called RhoGEF19) and Ephexin-3 (also called Rho guanine
nucleotide exchange factor 5/RhoGEF5, Transforming
immortalized mammary oncogene/p60 TIM, and
NGEF/neuronalGEF). Ephexin-4 (also called RhoGEF16) acts
downstream of EphA2 to promote ligand-independent breast
cancer cell migration and invasion toward epidermal
growth factor through activation of RhoG. This in turn
results in the activation of RhoG which recruits ELMO2
and Dock4 to form a complex with EphA2 at the tips of
cortactin-rich protrusions in migrating breast cancer
cells. Ephexin-5 is the specific GEF for RhoA activation
and the regulation of vascular smooth muscle
contractility. It interacts with EPHA4 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. The
members of the Ephexin family contains a RhoGEF (DH)
followed by a PH domain and an SH3 domain. The ephexin
PH domain is believed to act with the DH domain in
mediating protein-protein interactions. 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 = 130
Score = 29.5 bits (67), Expect = 2.9
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 646 ITLFLFTDVVEVCKKRS 662
+ LFLF D++ + KK+S
Sbjct: 41 VYLFLFNDLLLITKKKS 57
>gnl|CDD|237044 PRK12294, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 272
Score = 29.0 bits (65), Expect = 9.1
Identities = 31/132 (23%), Positives = 48/132 (36%), Gaps = 26/132 (19%)
Query: 504 QDSNSLLKEKEKNSRFLAFLKLCYMNLRDLGLPE-IDKQTL--PDLLIRPVQRLG----- 555
+S L+ KE + FL + L D + E +D + L DL Q++G
Sbjct: 2 NNSEQLIALKESETAFLKYFNKADYELVDFSVIEKLDWKQLNHEDL-----QQMGERSFW 56
Query: 556 ----SISLLLND----ILKNTSKSSTDHQKLSEALDGIR-----TVMTFLNENKQRQDNQ 602
I L ND +L+ S T K++ A IR + N + Q
Sbjct: 57 QHEHQIYALRNDFTDQLLRYYSMYPTAATKVAYAGLIIRNNEAAVQVGIENYAPSLANVQ 116
Query: 603 RSLFDIYQDIEN 614
+S Q I+
Sbjct: 117 QSFKLFIQFIQQ 128
>gnl|CDD|226288 COG3765, WzzB, Chain length determinant protein [Cell envelope
biogenesis, outer membrane].
Length = 347
Score = 29.3 bits (66), Expect = 9.1
Identities = 24/111 (21%), Positives = 40/111 (36%), Gaps = 11/111 (9%)
Query: 495 VYPPFINFFQDSNSLLKEKEKNSRFLAFLKLCYMNLRDLGLPEIDKQTLPDLLIRPVQRL 554
Y FI F S+SL + + Y + G +ID L L+ +
Sbjct: 95 AYSEFIKQFSSSDSLREFWLQTD---------YYKQKLTGESKIDAALLDRLINNISFKP 145
Query: 555 GSISLLLNDILKNTSKSSTDHQK-LSEALDGIRT-VMTFLNENKQRQDNQR 603
G L N + T++++ D Q L + + V L +N + R
Sbjct: 146 GGFDLATNLTVSFTAETAEDAQDLLRGYIAFVSQKVAQELLDNLKDAIALR 196
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 0.133 0.388
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 41,055,760
Number of extensions: 4005237
Number of successful extensions: 3374
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3350
Number of HSP's successfully gapped: 27
Length of query: 832
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 727
Effective length of database: 6,280,432
Effective search space: 4565874064
Effective search space used: 4565874064
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: 63 (28.0 bits)