RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7247
(104 letters)
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been
linked to a number of Rab proteins through their
association with mutual effectors, suggesting a
coordinate role in endocytic regulation. Eukaryotic EHDs
comprise four members (EHD1-4) in mammals and single
members in Caenorhabditis elegans (Rme-1), Drosophila
melanogaster (Past1) as well as several eukaryotic
parasites. EHD1 regulates trafficking of multiple
receptors from the endocytic recycling compartment (ERC)
to the plasma membrane; EHD2 regulates trafficking from
the plasma membrane by controlling Rac1 activity; EHD3
regulates endosome-to-Golgi transport, and preserves
Golgi morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from
the endocytic recycling compartment to the plasma
membrane. In D. melanogaster, deletion of the Past1 gene
leads to infertility as well as premature death of adult
flies. Arabidopsis thaliana also has homologs of EHD
proteins (AtEHD1 and AtEHD2), possibly involved in
regulating endocytosis and signaling.
Length = 241
Score = 69.6 bits (171), Expect = 6e-16
Identities = 28/44 (63%), Positives = 35/44 (79%)
Query: 9 IWDQPFRYDLNRKLFEDEEQDLFKDLQTLPKNAIIRKLNDVIKR 52
WDQP+ D NRKLF +EE DL +DL +LP+NA +RKLND+IKR
Sbjct: 198 FWDQPYEPDTNRKLFLEEEIDLLRDLNSLPRNAALRKLNDLIKR 241
>gnl|CDD|237526 PRK13837, PRK13837, two-component VirA-like sensor kinase;
Provisional.
Length = 828
Score = 30.0 bits (68), Expect = 0.20
Identities = 14/50 (28%), Positives = 20/50 (40%)
Query: 44 RKLNDVIKRARLAKVHAFIIGALRAEMPSTFPLELQLELENNRVENNRVE 93
RK K L+++ I LR +P L+ + E VE N E
Sbjct: 511 RKGERNTKPFDLSELVTEIAPLLRVSLPPGVELDFDQDQEPAVVEGNPAE 560
>gnl|CDD|220537 pfam10042, DUF2278, Uncharacterized conserved protein (DUF2278).
Members of this family of hypothetical bacterial
proteins have no known function.
Length = 206
Score = 29.5 bits (67), Expect = 0.23
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 38 PKNAIIRKLNDVIKRARLAKVHAFIIGAL 66
P N I L +++RA ++ G
Sbjct: 116 PDNDINDDLEPLLQRAIDEDATLYVFGEP 144
>gnl|CDD|212672 cd10230, HYOU1-like_NBD, Nucleotide-binding domain of human HYOU1
and similar proteins. This subgroup includes human
HYOU1 (also known as human hypoxia up-regulated 1,
GRP170; HSP12A; ORP150; GRP-170; ORP-150; the human
HYOU1 gene maps to11q23.1-q23.3) and Saccharomyces
cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian
HYOU1 functions as a nucleotide exchange factor (NEF)
for HSPA5 (alos known as BiP, Grp78 or HspA5) and may
also function as a HSPA5-independent chaperone. S.
cerevisiae Lhs1p, does not have a detectable endogenous
ATPase activity like canonical HSP70s, but functions as
a NEF for Kar2p; it's interaction with Kar2p is
stimulated by nucleotide-binding. In addition, Lhs1p has
a nucleotide-independent holdase activity that prevents
heat-induced aggregation of proteins in vitro. This
subgroup belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as NEFs, to
remove ADP from their HSP70 chaperone partners during
the ATP hydrolysis cycle. HSP70 chaperones assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
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 also
regulated by J-domain proteins.
Length = 388
Score = 28.3 bits (64), Expect = 0.61
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 3 ETPCTI---IWDQPFRYDLNRKLFEDEEQDLFKDLQTLPKNAI------IRKLNDVI 50
E P +I D F+ + R FE+ DLF+ K A+ ++ ++ V
Sbjct: 289 EAPVSIESLYDDIDFKTKITRAEFEELCADLFERAVAPIKKALESAGLTLKDIDSVE 345
>gnl|CDD|234729 PRK00331, PRK00331, glucosamine--fructose-6-phosphate
aminotransferase; Reviewed.
Length = 604
Score = 27.7 bits (63), Expect = 1.2
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 22 LFEDEEQDLFKDLQTLPK--NAIIRKLNDVIKR--ARLAKVHAFI-IG 64
L +EE DL +L+ LP ++ L + I+ A + +G
Sbjct: 422 LSAEEEADLVHELRELPALIEQVL-DLKEQIEELAEDFADARNALFLG 468
>gnl|CDD|219860 pfam08486, SpoIID, Stage II sporulation protein. This domain is
found in the stage II sporulation protein SpoIID.
SpoIID is necessary for membrane migration as well as
for some of the earlier steps in engulfment during
bacterial endospore formation. The domain is also found
in amidase enhancer proteins. Amidases, like SpoIID,
are cell wall hydrolases.
Length = 95
Score = 26.7 bits (60), Expect = 1.4
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 61 FIIGALRAEMPSTFPLE 77
++ G + AEMP+++PLE
Sbjct: 19 YLKGVVAAEMPASWPLE 35
>gnl|CDD|235673 PRK06018, PRK06018, putative acyl-CoA synthetase; Provisional.
Length = 542
Score = 27.0 bits (60), Expect = 1.7
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 17/65 (26%)
Query: 18 LNRKLFED---------EEQDLFKDLQTLPKNAIIRKLNDVIKRARLAKVHAFIIGALRA 68
+N +LF + E++ + DL +P I+ K+ D +L V +++ A
Sbjct: 94 VNPRLFPEQIAWIINHAEDRVVITDLTFVP---ILEKIAD-----KLPSVERYVVLTDAA 145
Query: 69 EMPST 73
MP T
Sbjct: 146 HMPQT 150
>gnl|CDD|234042 TIGR02870, spore_II_D, stage II sporulation protein D. Stage II
sporulation protein D (SpoIID) is a protein of the
endospore formation program in a number of lineages in
the Firmicutes (low-GC Gram-positive bacteria). It is
expressed in the mother cell compartment, under control
of Sigma-E. SpoIID, along with SpoIIM and SpoIIP, is
one of three major proteins involved in engulfment of
the forespore by the mother cell [Cellular processes,
Sporulation and germination].
Length = 338
Score = 26.6 bits (59), Expect = 2.5
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 61 FIIGALRAEMPSTFPLE 77
++ G + +EMP+ F +E
Sbjct: 77 YVKGVVASEMPAEFEIE 93
>gnl|CDD|240363 PTZ00331, PTZ00331, alpha/beta hydrolase; Provisional.
Length = 212
Score = 25.8 bits (57), Expect = 3.9
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 29 DLFKDLQTLPKNAIIRK 45
L KDL + IIRK
Sbjct: 99 QLHKDLVVERIDIIIRK 115
>gnl|CDD|218135 pfam04537, Herpes_UL55, Herpesvirus UL55 protein. In infected
cells, UL55 is associated with the nuclear matrix, and
found adjacent to compartments containing the capsid
protein ICP35. UL55 was not detected in assembled
virions. It is thought that UL55 may play a role in
virion assembly or maturation.
Length = 170
Score = 25.9 bits (57), Expect = 4.3
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 56 AKVHAFIIGALRAEMPSTFPLELQLELEN--NRVENNRVEK 94
+HAF G + PS P L ++L+N + + N R+ K
Sbjct: 60 GDLHAFFFGLSTDDSPSMSP--LIVDLQNFASLLNNQRLLK 98
>gnl|CDD|232919 TIGR00322, diphth2_R, diphthamide biosynthesis enzyme Dph1/Dph2
domain. Archaea and Eukaryotes, but not Eubacteria,
share the property of having a covalently modified
residue,
2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine,
as a part of a cytosolic protein. The modified His,
termed diphthamide, is part of translation elongation
factor EF-2 and is the site for ADP-ribosylation by
diphtheria toxin. This model includes both Dph1 and Dph2
from Saccharomyces cerevisiae, although only Dph2 is
found in the Archaea (see TIGR03682). Dph2 has been
shown to act analogously to the radical SAM (rSAM)
family (pfam04055), with 4Fe-4S-assisted cleavage of
S-adenosylmethionine to create a free radical, but a
different organic radical than in rSAM.
Length = 319
Score = 26.0 bits (58), Expect = 4.3
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 14 FRYDLNRKLFEDEEQDLFKDLQTLPKNAIIRKLNDVIKRARLAKVHAFIIGAL 66
+ YD +EE D K ++R+ +I++A+ AK I+G L
Sbjct: 201 YVYDPYSGELTEEEYDANK---------LLRRRYALIEKAKDAKKVGIIVGTL 244
>gnl|CDD|212667 cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70 family.
HSP70 (70-kDa heat shock protein) family chaperones
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). Some HSP70 family members are not
chaperones but instead, function as NEFs to remove ADP
from their HSP70 chaperone partners during the ATP
hydrolysis cycle, some may function as both chaperones
and NEFs.
Length = 369
Score = 25.7 bits (57), Expect = 5.0
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 8/44 (18%)
Query: 14 FRYDLNRKLFEDEEQDLFKDLQTLPKNAIIRKLNDVIKRARLAK 57
+L R+ FE+ + L + I + V+ A L
Sbjct: 285 LEVELTREEFEELIRPLLE--------RTIDLVERVLADAGLKP 320
>gnl|CDD|212679 cd10237, HSPA13-like_NBD, Nucleotide-binding domain of human HSPA13
and similar proteins. Human HSPA13 (also called 70-kDa
heat shock protein 13, STCH, "stress 70 protein
chaperone, microsome-associated, 60kD", "stress 70
protein chaperone, microsome-associated, 60kDa"; the
gene encoding HSPA13 maps to 21q11.1) 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). STCH contains an NBD but lacks an SBD.
STCH may function to regulate cell proliferation and
survival, and modulate the TRAIL-mediated cell death
pathway. The HSPA13 gene is a candidate stomach cancer
susceptibility gene; a mutation in the NBD coding region
of HSPA13 has been identified in stomach cancer cells.
The NBD of HSPA13 interacts with the ubiquitin-like
proteins Chap1 and Chap2, implicating HSPA13 in
regulating cell cycle and cell death events. HSPA13 is
induced by the Ca2+ ionophore A23187.
Length = 417
Score = 25.9 bits (57), Expect = 5.0
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 14 FRYDLNRKLFEDEEQDLFKDLQTLPKNAIIRKLNDV 49
F Y+L R FE +DLF+ + LP I L +
Sbjct: 315 FEYELTRDEFETLNEDLFQKI-LLP---IEAVLAEG 346
>gnl|CDD|224234 COG1315, COG1315, Uncharacterized conserved protein [Function
unknown].
Length = 543
Score = 25.5 bits (56), Expect = 5.8
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 21 KLFEDEEQDLFKDLQTLPKNAIIRKLNDVI--KRARLAKVHAFIIGALRAEMPSTFPLEL 78
L E+ + L K L L K I K N + K + L V+ I LR + ++
Sbjct: 420 SLHEERLKKLTKLLVALVKVKIESKKNILPPDKESLLTAVNNTKI-TLRNSIEK---IKA 475
Query: 79 QLELENNRVENNRVEKS 95
+LE +E +E S
Sbjct: 476 ELEGLQEELEVVGIEGS 492
>gnl|CDD|216748 pfam01866, Diphthamide_syn, Putative diphthamide synthesis protein.
Human DPH1 is a candidate tumour suppressor gene. DPH2
from yeast, which confers resistance to diphtheria
toxin, has been found to be involved in diphthamide
synthesis. Diphtheria toxin inhibits eukaryotic protein
synthesis by ADP-ribosylating diphthamide, a
posttranslationally modified histidine residue present
in EF2. The exact function of the members of this family
is unknown.
Length = 300
Score = 25.2 bits (56), Expect = 6.5
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 11/53 (20%)
Query: 14 FRYDLNRKLFEDEEQDLFKDLQTLPKNAIIRKLNDVIKRARLAKVHAFIIGAL 66
+ YD E+ + D +R+ I++A+ AK I+G
Sbjct: 172 YAYDPYSLEVEEYDADKM-----------LRRRYAAIEKAKDAKSFGIIVGTK 213
>gnl|CDD|227023 COG4678, COG4678, Muramidase (phage lambda lysozyme) [Carbohydrate
transport and metabolism].
Length = 180
Score = 25.1 bits (55), Expect = 8.3
Identities = 11/72 (15%), Positives = 27/72 (37%), Gaps = 8/72 (11%)
Query: 9 IWDQPFRYDLNRKLFEDEEQDLFKDLQTLPKNAI---IR--KLNDVIKRARLAKVHAFII 63
+ L+ K F E QD + + I+ +++ ++ +L+ A +
Sbjct: 97 RTWDDYAPQLHLKDFSPESQDAVA-YRWIRDRDALADIQAGRIDQALR--KLSNTWASLY 153
Query: 64 GALRAEMPSTFP 75
G ++ + P
Sbjct: 154 GIEYNQIERSLP 165
>gnl|CDD|219797 pfam08326, ACC_central, Acetyl-CoA carboxylase, central region.
The region featured in this family is found in various
eukaryotic acetyl-CoA carboxylases, N-terminal to the
catalytic domain (pfam01039). This enzyme (EC:6.4.1.2)
is involved in the synthesis of long-chain fatty acids,
as it catalyzes the rate-limiting step in this process.
Length = 707
Score = 25.0 bits (55), Expect = 9.2
Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 27/89 (30%)
Query: 24 EDEEQDLFKDLQTLPKNAIIRKLNDVIKRARLAKVHAFIIGALRAEMPSTF--------- 74
+++L L+ AI+++ + ++ A + +V FI+G P F
Sbjct: 452 FGSDEELIARLE-----AILKENKEELRAAGVRRV-TFIVGRDEGRYPKYFTFRASDEYE 505
Query: 75 ----------PLELQLELENNRVENNRVE 93
L QLEL R+ N ++
Sbjct: 506 EDPIIRHIEPALAFQLEL--GRLSNFDIK 532
>gnl|CDD|224650 COG1736, DPH2, Diphthamide synthase subunit DPH2 [Translation,
ribosomal structure and biogenesis].
Length = 347
Score = 25.0 bits (55), Expect = 9.6
Identities = 8/53 (15%), Positives = 16/53 (30%), Gaps = 9/53 (16%)
Query: 14 FRYDLNRKLFEDEEQDLFKDLQTLPKNAIIRKLNDVIKRARLAKVHAFIIGAL 66
F D +E+ + + ++ I +A AK I+
Sbjct: 204 FAIDPYSGKVREEDPE--------ADRFLRKRYA-AISKALDAKSFGIIVSTK 247
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
0.321 0.136 0.394
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,361,307
Number of extensions: 462819
Number of successful extensions: 515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 37
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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 (21.9 bits)
S2: 53 (24.2 bits)