RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17501
(101 letters)
>gnl|CDD|216368 pfam01213, CAP_N, Adenylate cyclase associated (CAP) N terminal.
Length = 313
Score = 72.2 bits (177), Expect = 2e-16
Identities = 33/87 (37%), Positives = 53/87 (60%)
Query: 12 TASTPVTSPIHLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLT 71
T S+P + SV AF ++A ++ ++ LS KIGG+V A++V +AFQ ++ L
Sbjct: 31 TTSSPSAAVAGDPASVTAFDSLIAKNISPFVELSKKIGGEVEDQAEMVHKAFQLERALLR 90
Query: 72 VASQSKDPGQSDKMRLLQPTSDKIAAI 98
VASQS+ P Q+ + LL+P S+ I +
Sbjct: 91 VASQSQKPDQNTLLELLKPISENIIEV 117
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 25.8 bits (57), Expect = 3.9
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 8 VTPLTASTPVTSPIHLSMSVA 28
PL +TPV+ P L+ +VA
Sbjct: 84 SVPLIKTTPVSLPFDLNQTVA 104
>gnl|CDD|129314 TIGR00210, gltS, sodium--glutamate symport carrier (gltS).
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 398
Score = 25.9 bits (57), Expect = 4.6
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 30 FSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQ 67
F I+ GP+A ++ + NK+ + K V+ F+ Q
Sbjct: 170 FGGIIGGPVAKFLIIRNKLEPNCENDTKDVTIGFERPQ 207
>gnl|CDD|214414 MTH00063, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 522
Score = 25.6 bits (57), Expect = 5.6
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 13 ASTPVTSPIHLSMSVAA---FS---DIVAGPLASYIALS 45
A TPV+S +H S VAA F D + G I S
Sbjct: 186 APTPVSSLVHSSTLVAAGVWFVMRYDYLLGFSWLSIFFS 224
>gnl|CDD|241380 cd13226, PH-like_Eap45_GLUE, Eap45 GLUE (GRAM-like
ubiquitin-binding in Eap45) Pleckstrin homology-like
domain. ESCRT complexes form the main machinery driving
protein sorting from endosomes to lysosomes. Human/yeast
ESCRT-I consists of Tsg101/Vps23, Vps28/Vps28, and a
Vps37 homolog/Vps37. Human/yeast ESCRT-II is composed of
EAP20/Vps25, EAP30/Vps22, and EAP45/Vps36. Yeast
ESCRT-III consists Vps2, Vps20, Vps24, and Snf7
subunits. In contrast, there are three Human paralogs of
Snf7 (hSnf7-1/CHMP4A, hSnf7-2/CHMP4B, and
hSnf7-3/CHMP4C) and two paralogs of Vps2 (CHMP2A and
CHMP2B). Yeast ESCRT-I links directly to ESCRT-II,
through a tight interaction of Vps28 (ESCRT-I) with the
yeast-specific zinc-finger insertion within the GLUE
domain of Vps36. The Vps36 subunit (ESCRT-II) binds
ubiquitin using one of its two NZF zinc fingers in its
N-terminal region. Human Vps36, EAP45, also binds
ubiquitin despite having no NZF domain. Instead,
mammalian ESCRT-II interacts with Ub through the Eap45
GLUE domain directly. While yeast Vps36 GLUE shows a
preference for the singly phosphorylated PI(3)P, while
Eap45 GLUE preferentially binds the triply
phosphorylated phosphatidylinositol PI(3,4,5)P3.
Structurally, Eap45 GLUE only has a PH-like fold since
it lacks the secondary structure element corresponding
to the 4 strand, unlike that of yeast Vps36 GLUE.
ESCRT-II also interacts with ESCRT-III via a
EAP20(Vps25)/CHMP6(Vps20) interaction. The interactions
of ESCRT-II GLUE domain with membranes, ESCRT-I, and
ubiquitin are critical for ubiquitinated cargo
progression from early to late endosomes. 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 = 128
Score = 25.0 bits (55), Expect = 5.7
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 9/64 (14%)
Query: 5 VEEVTPLTASTPVTSPIHLSMSVAAFSDIVAGPLA----SYIALSNKIGGDVATHAKLVS 60
EE S + +HL A + GP+ SYI LS K GG + +L
Sbjct: 70 EEEAAGFGKSAKIV--LHLH---PAPPNKEPGPVQSSPYSYIKLSFKEGGQSEFYRRLSE 124
Query: 61 EAFQ 64
E +
Sbjct: 125 ELTR 128
>gnl|CDD|233173 TIGR00892, 2A0113, monocarboxylate transporter 1. [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 455
Score = 25.1 bits (55), Expect = 9.5
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 25 MSVAAFSDIVAGPLASYIA 43
+S+ F DI A P IA
Sbjct: 282 LSIIGFVDIFARPSCGLIA 300
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
0.312 0.124 0.332
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,826,352
Number of extensions: 376515
Number of successful extensions: 210
Number of sequences better than 10.0: 1
Number of HSP's gapped: 210
Number of HSP's successfully gapped: 15
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)