RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9376
(320 letters)
>gnl|CDD|212566 cd11684, DHR2_DOCK, Dock Homology Region 2, a GEF domain, of
Dedicator of Cytokinesis proteins. DOCK proteins
comprise a family of atypical guanine nucleotide
exchange factors (GEFs) that lack the conventional Dbl
homology (DH) domain. As GEFs, they activate the small
GTPases Rac and Cdc42 by exchanging bound GDP for free
GTP. They are also called the CZH (CED-5, Dock180, and
MBC-zizimin homology) family, after the first family
members identified. Dock180 was first isolated as a
binding partner for the adaptor protein Crk. The
Caenorhabditis elegans protein, Ced-5, is essential for
cell migration and phagocytosis, while the Drosophila
ortholog, Myoblast city (MBC), is necessary for myoblast
fusion and dorsal closure. DOCKs are divided into four
classes (A-D) based on sequence similarity and domain
architecture: class A includes Dock1 (or Dock180), 2 and
5; class B includes Dock3 and 4; class C includes Dock6,
7, and 8; and class D includes Dock9, 10 and 11. All
DOCKs contain two homology domains: the DHR-1 (Dock
homology region-1), also called CZH1, and DHR-2 (also
called CZH2 or Docker). This alignment model represents
the DHR-2 domain of DOCK proteins, which contains the
catalytic GEF activity for Rac and/or Cdc42.
Length = 392
Score = 33.0 bits (76), Expect = 0.17
Identities = 18/102 (17%), Positives = 34/102 (33%), Gaps = 18/102 (17%)
Query: 41 ANMFKMAKKWNNAGKAFVEAANLHMKSGTKHDAACN-----------------LLDAANC 83
A++ + + A + A+L+ A A +
Sbjct: 11 ADLHEERGNYVEAALCLLLHADLYAWDLKALVPALAESLSFPEQTSFERKEALYKKAIDL 70
Query: 84 FKKTDN-EAAIDCLSKAIVIYTDMGRFTMAAKHHQTIAEIYE 124
F K E AI + I Y + + ++ H+ IA++YE
Sbjct: 71 FDKGKAWEFAIALYKELIPQYENNFDYAKLSEVHRKIAKLYE 112
>gnl|CDD|107329 cd06334, PBP1_ABC_ligand_binding_like_1, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that
are predicted to be involved in transport of amino
acids, peptides, or inorganic ions. This subgroup
includes the type I periplasmic ligand-binding domain
of uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been
determined experimentally.
Length = 351
Score = 30.3 bits (69), Expect = 1.2
Identities = 5/30 (16%), Positives = 11/30 (36%)
Query: 18 RVVFITKVGGNKIDEAIECYTRAANMFKMA 47
++ + G ++ +ECY R
Sbjct: 40 KLEWEECDTGYEVPRGVECYERLKGEDGAV 69
>gnl|CDD|217953 pfam04190, DUF410, Protein of unknown function (DUF410). This
family of proteins is from Caenorhabditis elegans and
has no known function. The protein has some GO
references indicating that the protein has a positive
regulation of growth rate and is involved in nematode
larval development.
Length = 251
Score = 30.2 bits (68), Expect = 1.3
Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 13/95 (13%)
Query: 196 EYFFRAALCHLCIDVIN-AHNAIDRYKTIYPAFQDSREYK------------LLRILIEH 242
+ RA L +LC+ A ++ Y + E L +L +
Sbjct: 142 VFIVRAVLQYLCLKNFPFAVSSFTEYTAPFIKKHPKYEKYEAKFPFTYPLLNFLHLLFDT 201
Query: 243 IEEQNVDGFTEAVKDYDSISRLDQWYTTVLLRIKK 277
I+ ++ F E Y + D + L +I +
Sbjct: 202 IDTKDKAQFLELTSSYQPSLKRDLAFIGYLAKIGQ 236
>gnl|CDD|107324 cd06329, PBP1_SBP_like_3, Periplasmic solute-binding domain of
active transport proteins. Periplasmic solute-binding
domain of active transport proteins found in bacteria
and Archaea. Members of this group are initial receptors
in the process of active transport across cellular
membrane, but their substrate specificities are not
known in detail. However, they closely resemble the
group of AmiC and active transport systems for
short-chain amides and urea (FmdDEF), and thus are
likely to exhibit a ligand-binding mode similar to that
of the amide sensor protein AmiC from Pseudomonas
aeruginosa. Moreover, this binding domain has high
sequence identity to the family of hydrophobic amino
acid transporters (HAAT), and thus it may also be
involved in transport of amino acids.
Length = 342
Score = 30.0 bits (68), Expect = 1.6
Identities = 24/82 (29%), Positives = 31/82 (37%), Gaps = 9/82 (10%)
Query: 50 WNN--AGKAFVEA---ANLHMKSGTKHDAACN---LLDAANCFKKTDNEAAIDCLSKAIV 101
N+ A +AFVEA + + A L DA TD EA L
Sbjct: 260 PNDTPANRAFVEAFKAKYGRVPDYYEGQAYNGIQMLADAIEKAGSTDPEAVAKALEGM-E 318
Query: 102 IYTDMGRFTMAAKHHQTIAEIY 123
+ T +G TM A HQ +Y
Sbjct: 319 VDTPVGPVTMRASDHQAQQPLY 340
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 29.6 bits (67), Expect = 2.3
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 126 DCVDQEKAVEHYEQAATYFKGE 147
D V +E+A+E+YEQ + KG
Sbjct: 151 DLVSRERALENYEQIKEFVKGT 172
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 28.1 bits (63), Expect = 2.3
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 131 EKAVEHYEQAATYFKGEESNSSANKCLLKVAHHAALLQNYNKAIQIYEEVGRTSLDSSLL 190
++A+E+YE+A + +A L Y +A++ YE+ D++
Sbjct: 17 DEALEYYEKALEL------DPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKA 70
Query: 191 KY 192
Y
Sbjct: 71 YY 72
Score = 26.6 bits (59), Expect = 7.1
Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 12/106 (11%)
Query: 35 ECYTRAANMFKMAKKWNNAGKAFVEAANLHMKSGTKHDAACNLLDAANCFKKTDNEAAID 94
E N++ ++ A + + +A L + A L AA +K E A++
Sbjct: 1 EALLNLGNLYYKLGDYDEALEYYEKALELD----PDNADAYYNL-AAAYYKLGKYEEALE 55
Query: 95 CLSKAIVIYTDMGRFTMAAKHHQTIAEIYETDCVDQEKAVEHYEQA 140
KA+ + D AK + + Y E+A+E YE+A
Sbjct: 56 DYEKALELDPDN------AKAYYNLGLAYYKLG-KYEEALEAYEKA 94
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 29.6 bits (67), Expect = 2.5
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 126 DCVDQEKAVEHYEQAATYFKGE 147
D V +EKA+E+YE+ + KG
Sbjct: 145 DLVSKEKALENYEEIKEFVKGT 166
>gnl|CDD|200985 pfam00081, Sod_Fe_N, Iron/manganese superoxide dismutases,
alpha-hairpin domain. superoxide dismutases (SODs)
catalyze the conversion of superoxide radicals to
hydrogen peroxide and molecular oxygen. Three
evolutionarily distinct families of SODs are known, of
which the Mn/Fe-binding family is one. In humans, there
is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe
SOD. N-terminal domain is a long alpha antiparallel
hairpin. A small fragment of YTRE_LEPBI matches well -
sequencing error?.
Length = 82
Score = 27.3 bits (61), Expect = 2.8
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 162 HHAALLQNYNKAIQIYEEVGRTSLDSSLLKYSAKEYFFRAA 202
HH + N N A++ EE + L+ +LK S F
Sbjct: 30 HHQTYVNNLNAALEGLEEARKK-LEEIILKASLGALFNNGG 69
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 29.4 bits (67), Expect = 2.8
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 126 DCVDQEKAVEHYEQAATYFKG 146
D V +E+A+E+YEQ + KG
Sbjct: 150 DLVSKERALENYEQIKEFVKG 170
>gnl|CDD|218799 pfam05893, LuxC, Acyl-CoA reductase (LuxC). This family consists
of several bacterial Acyl-CoA reductase (LuxC) proteins.
The channelling of fatty acids into the fatty aldehyde
substrate for the bacterial bioluminescence reaction is
catalyzed by a fatty acid reductase multienzyme complex,
which channels fatty acids through the thioesterase
(LuxD), synthetase (LuxE) and reductase (LuxC)
components.
Length = 400
Score = 29.2 bits (66), Expect = 3.3
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 11 QLAAALLRVVFITKVGGNKIDEAIECYTRAANMFKMAKKWNNAGKAFVEAANLHMK 66
Q A + +VVF+ G + E + AA + K A+ A +F EAA + +
Sbjct: 229 QQACSSPQVVFVESDDGITLREFAQRL--AAALEKYARILPKAVPSFDEAAAISLT 282
>gnl|CDD|153373 cd07361, MEMO_like, Memo (mediator of ErbB2-driven cell motility)
is co-precipitated with the C terminus of ErbB2, a
protein involved in cell motility. This subfamily is
composed of Memo (mediator of ErbB2-driven cell
motility) and similar proteins. Memo is a protein that
is co-precipitated with the C terminus of ErbB2, a
protein involved in cell motility. It is required for
the ErbB2-driven cell mobility and is found in protein
complexes with cofilin, ErbB2 and PLCgamma1. However,
Memo is not homologous to any known signaling proteins,
and its function in ErbB2 signaling is not known.
Structural studies show that Memo binds directly to a
specific ErbB2-derived phosphopeptide. Memo is
homologous to class III nonheme iron-dependent extradiol
dioxygenases, however, no metal binding or enzymatic
activity can be detected for Memo. This subfamily also
contains a few members containing a C-terminal
AMMECR1-like domain. The AMMECR1 protein was proposed to
be a regulatory factor that is potentially involved in
the development of AMME contiguous gene deletion
syndrome.
Length = 266
Score = 28.3 bits (64), Expect = 5.0
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 17/63 (26%)
Query: 237 RILIEHIEEQNVDGFTEAVKDYD-------SISRLDQWYTTVLLRIKKQVGRTSLDSSLL 289
R IE I + +GF E +++ I VLL K++G LL
Sbjct: 194 RKAIEAILALDPEGFYEYLRETGNTACGRGPI--------AVLLEAAKELGALKA--ELL 243
Query: 290 KYS 292
Y+
Sbjct: 244 DYA 246
>gnl|CDD|184228 PRK13671, PRK13671, hypothetical protein; Provisional.
Length = 298
Score = 28.1 bits (63), Expect = 5.7
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 240 IEHIEEQNVDGFTEAV--KDYDSISRLDQWYTTVLLRIKK 277
++I N D F K Y S SR+ + VLL+IKK
Sbjct: 260 KKNINAPNYDSFVNKCNSKRYTS-SRIKRIMLYVLLKIKK 298
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 26.6 bits (59), Expect = 5.7
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 119 IAEIYETDCVDQEKAVEHYEQAATYFK--GEESNSSANKCLLKVAHHAALLQNYNKAIQI 176
+A + D ++A+E E+A + GE+ +A L +A L +Y++A++
Sbjct: 11 LALVLRRLG-DYDEALELLEKALELARELGEDHPETAR-ALNNLARLYLALGDYDEALEY 68
Query: 177 YEEV 180
E+
Sbjct: 69 LEKA 72
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 26.1 bits (58), Expect = 6.8
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 71 HDAACNLLDAANCFKKTDNEAAIDCLSKAIVIYTDMGRFTMAAKHHQTIAEIYETDCVDQ 130
+A FK D + AI+ KA+ + D A+ + +A Y D
Sbjct: 1 DNAEALKNLGNALFKLGDYDEAIEAYEKALELDPD------NAEAYYNLALAYLKLGKDY 54
Query: 131 EKAVEHYEQA 140
E+A+E E+A
Sbjct: 55 EEALEDLEKA 64
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 28.0 bits (63), Expect = 7.7
Identities = 13/70 (18%), Positives = 23/70 (32%), Gaps = 9/70 (12%)
Query: 234 KLLRILIEHIEEQNVDGFTEAVKDYDSISRLDQWYTTVLLRIKKQVGRTSLDSSLLKYSA 293
KL + I +NV F E ++D+W +L ++ + S+
Sbjct: 26 KLRQRFIRSFPIENVQKFME---------KIDEWDIQRILPGLEKASKILESGPPNTRSS 76
Query: 294 KEYFFRAALC 303
LC
Sbjct: 77 LLLALYECLC 86
>gnl|CDD|201989 pfam01817, CM_2, Chorismate mutase type II. Chorismate mutase
EC:5.4.99.5 catalyzes the conversion of chorismate to
prephenate in the pathway of tyrosine and phenylalanine
biosynthesis. This enzyme is negatively regulated by
tyrosine, tryptophan and phenylalanine.
Length = 79
Score = 26.0 bits (58), Expect = 8.1
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 216 AIDRYKTIY--PAFQDSREYKLLRILIEHIEEQNVDGFTEAV-KDYDSISRLDQ 266
I YK P + RE ++L L+ E +D + EA+ ++ S+ +
Sbjct: 24 EIAEYKKEQGLPIYDPEREAEVLERLLREAEGPGLDEYIEAIFREIIRESKALE 77
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 0.132 0.384
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,666,712
Number of extensions: 1469891
Number of successful extensions: 1221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1212
Number of HSP's successfully gapped: 45
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
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: 59 (26.5 bits)