RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13048
(188 letters)
>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 = 71.5 bits (176), Expect = 6e-16
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 17/104 (16%)
Query: 59 HAQKFNMYVHYCRNKPDSNALLVQHGG--PLFEELQKKHRVDH-----PVSAYLIKPVQR 111
A F +Y YC N P + LL + P F + K+ ++++LIKPVQR
Sbjct: 79 FAPFFKVYSTYCSNYPRALELLKKLRKKNPRFAKFLKECEASPLCRGLDLNSFLIKPVQR 138
Query: 112 ITKYQLLLKDLQGEIK-------GQGEIKDGLEVMLSVPRKAND 148
I +Y LLLK+L +K ++K LE + V + N+
Sbjct: 139 IPRYPLLLKEL---LKHTPPDHPDYEDLKKALEAIKEVASQINE 179
>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 = 67.7 bits (166), Expect = 2e-14
Identities = 32/100 (32%), Positives = 48/100 (48%), Gaps = 9/100 (9%)
Query: 57 EAHAQKFNMYVHYCRNKPDSNALLVQH--GGPLFEELQKKHR---VDHPVSAYLIKPVQR 111
A F +Y YC N PD+ LL + F+E +K + + L+KPVQR
Sbjct: 82 LKLAPFFKIYSEYCSNHPDALELLKKLKKFNKFFQEFLEKAESECGRLKLESLLLKPVQR 141
Query: 112 ITKYQLLLKDL----QGEIKGQGEIKDGLEVMLSVPRKAN 147
+TKY LLLK+L + + ++K LE + V + N
Sbjct: 142 LTKYPLLLKELLKHTPDGHEDREDLKKALEAIKEVASQVN 181
>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 = 63.1 bits (154), Expect = 8e-13
Identities = 27/102 (26%), Positives = 49/102 (48%), Gaps = 10/102 (9%)
Query: 57 EAHAQKFNMYVHYCRNKPDSNALLVQ--HGGPLFEELQKKHR----VDHPVSAYLIKPVQ 110
+ F +Y YC N PD+ LL + + L++ + + L+KPVQ
Sbjct: 79 LKLEEFFKIYSEYCSNHPDALELLKKLKKNPRFQKFLKEIESSPQCRRLTLESLLLKPVQ 138
Query: 111 RITKYQLLLKDL----QGEIKGQGEIKDGLEVMLSVPRKAND 148
R+TKY LLLK+L + + + ++K L+ + + + N+
Sbjct: 139 RLTKYPLLLKELLKHTPEDHEDREDLKKALKAIKELANQVNE 180
>gnl|CDD|241394 cd13240, PH1_Kalirin_Trio_like, Triple functional domain pleckstrin
homology pleckstrin homology (PH) domain, repeat 1.
RhoGEFs, Kalirin and Trio, the mammalian homologs of
Drosophila Trio and Caenorhabditis elegans UNC-73
regulate a novel step in secretory granule maturation.
Their signaling modulates the extent to which regulated
cargo enter and remain in the regulated secretory
pathway. This allows for fine tuning of peptides
released by a single secretory cell type with impaired
signaling leading to pathological states. Trio plays an
essential role in regulating the actin cytoskeleton
during axonal guidance and branching. Kalirin and Trio
are encoded by separate genes in mammals and by a single
one in invertebrates. Kalirin and Trio share the same
complex multidomain structure and display several splice
variants. The longest Kalirin and Trio proteins have a
Sec14 domain, a stretch of spectrin repeats, a
RhoGEF(DH)/PH cassette (also called GEF1), an SH3
domain, a second RhoGEF(DH)/PH cassette (also called
GEF2), a second SH3 domain, Ig/FNIII domains, and a
kinase domain. The first RhoGEF(DH)/PH cassette
catalyzes exchange on Rac1 and RhoG while the second
RhoGEF(DH)/PH cassette is specific for RhoA. Kalirin and
Trio are closely related to p63RhoGEF and have PH
domains of similar function. 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.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 = 123
Score = 52.7 bits (127), Expect = 2e-09
Identities = 18/28 (64%), Positives = 25/28 (89%)
Query: 160 DVNIDAMGEVVLQDALQVWDPKQLIRKE 187
D +++++GEV+LQD+ QVWDPKQLIRK
Sbjct: 6 DESLESLGEVILQDSFQVWDPKQLIRKG 33
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 30.7 bits (70), Expect = 0.28
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 131 EIKDGLEVMLSVPRKANDALHLSLLEAPADVNIDAMGEVV 170
EI DG+ + V R A+ V ID +G +
Sbjct: 58 EIGDGVIEIKCVARDPRAAVVS------NVVKIDPVGACI 91
>gnl|CDD|102471 PRK06628, PRK06628, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 290
Score = 28.0 bits (62), Expect = 2.7
Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 2/90 (2%)
Query: 96 RVDHPVSAYLIKPVQRITKYQLLLKDLQGEIKGQGEIKDGLEVMLSVPRKANDALHLSLL 155
+ ++P L+ + K +L+ K +G IK+ +++ V +K ND + + L
Sbjct: 146 KANNPYVNKLVNESRAGDKLRLIPKGPEGSRALVRAIKESESIVMLVDQKMNDGIEVPFL 205
Query: 156 EAPADVNIDAMGEVVLQDALQVWDPKQLIR 185
PA + A+ ++ LQ + P Q+IR
Sbjct: 206 GHPA-MTASAIAKIALQYKYPII-PCQIIR 233
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
0.314 0.132 0.372
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: 9,404,266
Number of extensions: 859026
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 527
Number of HSP's successfully gapped: 15
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.3 bits)