RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7264
(206 letters)
>gnl|CDD|238033 cd00078, HECTc, HECT domain; C-terminal catalytic domain of a
subclass of Ubiquitin-protein ligase (E3). It binds
specific ubiquitin-conjugating enzymes (E2), accepts
ubiquitin from E2, transfers ubiquitin to substrate
lysine side chains, and transfers additional ubiquitin
molecules to the end of growing ubiquitin chains.
Length = 352
Score = 135 bits (342), Expect = 1e-38
Identities = 61/144 (42%), Positives = 84/144 (58%), Gaps = 7/144 (4%)
Query: 33 KQV-IIREYFLKFIPKKLVSYRLSPST-KLLLCGTSDYSIADLLAHHV--VASSFPHPKL 88
+QV R+ F + IP++L+S +P +LL+CG+ D + DL + S P
Sbjct: 206 EQVEAFRDGFSEVIPEELLSL-FTPEELELLICGSEDIDLEDLKKNTEYKGGYSSDSP-T 263
Query: 89 LQWFWTALQNFTTEERARLLQFTTGSSQLPPGGFAQLKPKFSISYI-QAHNSLPVAHTCS 147
+QWFW L++FT EER + LQF TGSS+LP GGFA L PKF+I + + LP AHTC
Sbjct: 264 IQWFWEVLESFTNEERKKFLQFVTGSSRLPVGGFADLNPKFTIRRVGSPDDRLPTAHTCF 323
Query: 148 NQLCLPTYDNYEKFEKALITAIKA 171
N L LP Y + E + L+ AI
Sbjct: 324 NLLKLPPYSSKEILREKLLYAINE 347
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 131 bits (332), Expect = 1e-37
Identities = 63/172 (36%), Positives = 87/172 (50%), Gaps = 32/172 (18%)
Query: 37 IREYFLKFIPKKLVSYRLSPST-KLLLCGTSDYSIADLLAHHVVASSF-PHPKLLQWFWT 94
RE F IPK+L+S +P +LL+CG+ + + DL + + + ++WFW
Sbjct: 157 FREGFYSVIPKELLSL-FTPEELELLICGSPEIDVEDLKKNTEYDGGYSKNSPTIKWFWE 215
Query: 95 ALQNFTTEERARLLQFTTGSSQLPPGGFAQLKPKFSISYIQAHNSLPVAHTCSNQLCLPT 154
L+ FT EER + L+F TGSS+LP GGF +L K +I + LP AHTC N+L LP
Sbjct: 216 VLEEFTQEERRKFLKFVTGSSRLPLGGFKKL--KITIQRKDDDDRLPTAHTCFNRLKLPP 273
Query: 155 YDNYEKFEKALITAIKALSSNQLCLPTYDNYEKFEKALITAINEGSEGFGLA 206
Y + E EK L+ AI EGSEGFGL+
Sbjct: 274 YSSKEIL-----------------------KEK----LLIAIEEGSEGFGLS 298
>gnl|CDD|214523 smart00119, HECTc, Domain Homologous to E6-AP Carboxyl Terminus
with. E3 ubiquitin-protein ligases. Can bind to E2
enzymes.
Length = 328
Score = 131 bits (331), Expect = 3e-37
Identities = 56/141 (39%), Positives = 82/141 (58%), Gaps = 3/141 (2%)
Query: 33 KQV-IIREYFLKFIPKKLVSYRLSPSTKLLLCGTSDYSIADLLAHHVVASSFPH-PKLLQ 90
KQ+ RE F + IP+ L+ +LL+CG+ + + DL ++ + + ++
Sbjct: 183 KQLEAFREGFSEVIPENLLKLFDPEELELLICGSPEIDVDDLKSNTEYKGGYSANSQTIK 242
Query: 91 WFWTALQNFTTEERARLLQFTTGSSQLPPGGFAQLKPKFSISYIQA-HNSLPVAHTCSNQ 149
WFW +++FT EER +LLQF TGSS+LP GGFA L PKF+I + LP AHTC N+
Sbjct: 243 WFWEVVESFTNEERRKLLQFVTGSSRLPVGGFAALSPKFTIRKAGSDDERLPTAHTCFNR 302
Query: 150 LCLPTYDNYEKFEKALITAIK 170
L LP Y + E + L+ AI
Sbjct: 303 LKLPPYSSKEILREKLLLAIN 323
>gnl|CDD|227354 COG5021, HUL4, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 872
Score = 110 bits (276), Expect = 4e-28
Identities = 44/136 (32%), Positives = 63/136 (46%), Gaps = 7/136 (5%)
Query: 41 FLKFIPKKLVSYRLSPSTKLLLCGTSDYSIADLLAHHVVASSF-PHPKLLQWFWTALQNF 99
F + IP L+ +LL+ G + D + + ++ WFW + F
Sbjct: 728 FSEIIPPDLLQIFDESELELLIGGIPEDIDIDDWKSNTAYHGYTEDSPIIVWFWEIISEF 787
Query: 100 TTEERARLLQFTTGSSQLPPGGFAQLKPKFSISYIQAHN------SLPVAHTCSNQLCLP 153
EERA+LLQF TG+S++P GF L+ + LP AHTC N+L LP
Sbjct: 788 DFEERAKLLQFVTGTSRIPINGFKDLQGSDGVRKFTIEKGGTDDDRLPSAHTCFNRLKLP 847
Query: 154 TYDNYEKFEKALITAI 169
Y + EK L+TAI
Sbjct: 848 EYSSKEKLRSKLLTAI 863
>gnl|CDD|237267 PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1;
Provisional.
Length = 896
Score = 34.1 bits (79), Expect = 0.037
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 15/39 (38%)
Query: 81 SSFPHPKLLQWFWTALQNFTTEERARLLQFTTGSSQLPP 119
SS+PHP L+ FW QF TGS + P
Sbjct: 186 SSYPHPWLMPDFW---------------QFPTGSMGIGP 209
>gnl|CDD|236500 PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed.
Length = 891
Score = 32.0 bits (74), Expect = 0.20
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 81 SSFPHPKLLQWFW 93
SS+PHP L+ FW
Sbjct: 178 SSYPHPWLMPDFW 190
>gnl|CDD|233117 TIGR00759, aceE, pyruvate dehydrogenase E1 component, homodimeric
type. Most members of this family are pyruvate
dehydrogenase complex, E1 component. Note: this family
was classified as subfamily rather than equivalog
because it includes a counterexample from Pseudomonas
putida, MdeB, that is active as an E1 component of an
alpha-ketoglutarate dehydrogenase complex rather than a
pyruvate dehydrogase complex. The second pyruvate
dehydrogenase complex E1 protein from Alcaligenes
eutrophus, PdhE, complements an aceE mutant of E. coli
but is not part of a pyruvate dehydrogenase complex
operon, is more similar to the Pseudomonas putida MdeB
than to E. coli AceE, and may have also have a different
primary specificity.
Length = 885
Score = 30.1 bits (68), Expect = 0.95
Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 15/39 (38%)
Query: 81 SSFPHPKLLQWFWTALQNFTTEERARLLQFTTGSSQLPP 119
SS+PHP L+ FW QF T S L P
Sbjct: 172 SSYPHPWLMPDFW---------------QFPTVSMGLGP 195
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 29.2 bits (66), Expect = 1.1
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 7/40 (17%)
Query: 154 TYDNYEKFEKALITAIKALSSNQLCLPTYDNYEKFEKALI 193
T +++E+ KAL + S+ +Y F + LI
Sbjct: 136 TKEDFEELRKALAKKLTKYESS-------PHYAGFLEDLI 168
>gnl|CDD|238975 cd02017, TPP_E1_EcPDC_like, Thiamine pyrophosphate (TPP) family, E1
of E. coli PDC-like subfamily, TPP-binding module;
composed of proteins similar to the E1 component of the
Escherichia coli pyruvate dehydrogenase multienzyme
complex (PDC). PDC catalyzes the oxidative
decarboxylation of pyruvate and the subsequent
acetylation of coenzyme A to acetyl-CoA. The E1
component of PDC catalyzes the first step of the
multistep process, using TPP and a divalent cation as
cofactors. E. coli PDC is a homodimeric enzyme.
Length = 386
Score = 29.6 bits (67), Expect = 1.2
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 15/44 (34%)
Query: 76 HHVVASSFPHPKLLQWFWTALQNFTTEERARLLQFTTGSSQLPP 119
SS+PHP L+ FW +F T S L P
Sbjct: 96 GGGGLSSYPHPWLMPDFW---------------EFPTVSMGLGP 124
>gnl|CDD|219289 pfam07083, DUF1351, Protein of unknown function (DUF1351). This
family consists of several bacterial and phage proteins
of around 230 residues in length. The function of this
family is unknown.
Length = 220
Score = 29.2 bits (66), Expect = 1.2
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 9/49 (18%)
Query: 156 DNYEKFEKALITAIKALSSNQLCLPTYDNYE--KFEKA----LITAINE 198
++E+FEKA+ + + T +NY+ K E+A LI A+N+
Sbjct: 15 LDFEEFEKAIDEVVAKYKG---YVVTEENYKDDKKERAELNKLIKALND 60
>gnl|CDD|225329 COG2609, AceE, Pyruvate dehydrogenase complex, dehydrogenase (E1)
component [Energy production and conversion].
Length = 887
Score = 29.6 bits (67), Expect = 1.3
Identities = 15/40 (37%), Positives = 17/40 (42%), Gaps = 15/40 (37%)
Query: 80 ASSFPHPKLLQWFWTALQNFTTEERARLLQFTTGSSQLPP 119
SS+PHPKL+ FW QF T S L P
Sbjct: 174 LSSYPHPKLMPDFW---------------QFPTVSMGLGP 198
>gnl|CDD|176114 cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of
LysR-type transcriptional regulator CrgA and its related
homologs, contains the type 2 periplasmic binding
domain. This CD includes the substrate binding domain
of LysR-type transcriptional regulator (LTTR) CrgA and
its related homologs. The LTTRs are acting as both
auto-repressors and activators of target promoters,
controlling operons involved in a wide variety of
cellular processes such as amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of nitrogen-fixing bacteria,
and synthesis of virulence factors, to name a few. In
contrast to the tetrameric form of other LTTRs, CrgA
from Neisseria meningitides assembles into an octameric
ring, which can bind up to four 63-bp DNA
oligonucleotides. Phylogenetic cluster analysis further
showed that the CrgA-like regulators form a subclass of
the LTTRs that function as octamers. The CrgA is an
auto-repressor of its own gene and activates the
expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 27.4 bits (62), Expect = 4.2
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 10/51 (19%)
Query: 49 LVSYRLSPSTKLLLCGTSDY--------SIADLLAHHVVASSFPHPKLLQW 91
LV+ RL P + +L + Y + DL H + P + L+W
Sbjct: 62 LVARRLGPV-RRVLVASPAYLARHGTPQTPEDLARHRCLGYRLP-GRPLRW 110
>gnl|CDD|214004 cd12805, Allergen_V_VI, Group V, VI major allergens from grass,
including Phlp 5, Phlp 6, Pha a 5 and Lol p 5. This
family contains major allergens from various grass
pollen, including Phl p 5 and Phl p 6 (timothy grass),
Lol p 5 (rye grass) and Pha a 5 (canary grass). They
induce allergic rhinitis and bronchial asthma in
millions of allergic patients worldwide. These group V
and group VI grass-pollen allergens belong to a new
class of protease-resistant four-helix-bundle domains,
which also have internal helix-turn-helix homology
pointing to a special type of four-helix bundle
topology, defined as twinned two-helix bundle. IgE
binding experiments with recombinant Phl p 6 fragments
indicated that the N terminus of the allergen is
required for IgE recognition. Immunotherapy treatment
for these allergies generally involves administration of
grass pollen extracts which induce an initial rise in
specific immunoglobulin E (sIgE) production followed by
a progressive decline during the treatment.
Length = 85
Score = 26.3 bits (58), Expect = 4.5
Identities = 12/47 (25%), Positives = 17/47 (36%)
Query: 160 KFEKALITAIKALSSNQLCLPTYDNYEKFEKALITAINEGSEGFGLA 206
K + + A K + D Y+ FE A AI S +A
Sbjct: 1 KLIEKINAAFKQAYAAAAAAAPADKYKVFEAAFKKAITAASAAAKVA 47
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 27.6 bits (61), Expect = 5.0
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 139 SLPVAHTCSNQLCLPTYDNYEKFEKALITAIKA--LSSNQLCLPTYDNYEKFEKALITAI 196
LP + + S+ C PT E+ + K L++ L DNY+++E++++ +
Sbjct: 551 RLPKSSSSSSSCCCPTKKKPEQDPSEIYRDAKREDLNAAIFNLREIDNYDEYERSMLISQ 610
Query: 197 NEGSEGFGLA 206
+ FGL+
Sbjct: 611 MSFEKTFGLS 620
>gnl|CDD|236175 PRK08180, PRK08180, feruloyl-CoA synthase; Reviewed.
Length = 614
Score = 27.5 bits (62), Expect = 5.2
Identities = 16/48 (33%), Positives = 19/48 (39%), Gaps = 8/48 (16%)
Query: 69 SIADLLAHHVVASSFPHPKLLQWFWTALQNFTTEERARLLQFTTGSSQ 116
+A LLA +A HP + F L ARL TGSS
Sbjct: 521 RLAGLLADASLAEVLAHPAVRAAFRERL--------ARLNAQATGSST 560
>gnl|CDD|236845 PRK11099, PRK11099, putative inner membrane protein; Provisional.
Length = 399
Score = 27.6 bits (62), Expect = 5.8
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 5 HVSYVAY--LIHMNGTPLSRPRKVIV 28
HV Y +I + GTPL+R +++
Sbjct: 55 HVEEWGYFKIIGLEGTPLTRIDGMMI 80
>gnl|CDD|221265 pfam11850, DUF3370, Protein of unknown function (DUF3370). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 452 to 532 amino acids in
length.
Length = 439
Score = 27.2 bits (61), Expect = 5.9
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 72 DLLAHHVVASSFPHPKLLQWFWTALQNFTTEERARLLQFTTGSSQL 117
DL +HHV A S P + N R L+F GSS L
Sbjct: 81 DLFSHHVYAPSDPEKLRTLYLGVIAHNPGD--RPVTLKFLQGSSYL 124
>gnl|CDD|180486 PRK06246, PRK06246, fumarate hydratase; Provisional.
Length = 280
Score = 27.1 bits (61), Expect = 6.5
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 161 FEKALITAIKALSSNQLCLPTYD-NYEKFEKALITAINE---GSEGFG 204
F+KA A KAL + D E+ L+ IN+ G G G
Sbjct: 196 FDKAAKLAKKALLRP-IGERNPDPEIAALEEELLEEINKLGIGPMGLG 242
>gnl|CDD|237094 PRK12410, PRK12410, glutamylglutaminyl-tRNA synthetase;
Provisional.
Length = 433
Score = 27.3 bits (61), Expect = 6.9
Identities = 10/42 (23%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 156 DNYEKFEKALITAIKALSSNQLCLPTYDNYEKFEKALITAIN 197
D E+F++ +AL S + ++++E+F+K L+
Sbjct: 356 DINEEFKEECKILKEALKS----MDFFEDFEEFKKELMQKSG 393
>gnl|CDD|198292 cd03183, GST_C_Theta, C-terminal, alpha helical domain of Class
Theta Glutathione S-transferases. Glutathione
S-transferase (GST) C-terminal domain family, Class
Theta subfamily; composed of eukaryotic class Theta GSTs
and bacterial dichloromethane (DCM) dehalogenase. GSTs
are cytosolic dimeric proteins involved in cellular
detoxification by catalyzing the conjugation of
glutathione (GSH) with a wide range of endogenous and
xenobiotic alkylating agents, including carcinogens,
therapeutic drugs, environmental toxins and products of
oxidative stress. The GST fold contains an N-terminal
thioredoxin-fold domain and a C-terminal alpha helical
domain, with an active site located in a cleft between
the two domains. GSH binds to the N-terminal domain
while the hydrophobic substrate occupies a pocket in the
C-terminal domain. Mammalian class Theta GSTs show poor
GSH conjugating activity towards the standard
substrates, CDNB and ethacrynic acid, differentiating
them from other mammalian GSTs. GSTT1-1 shows similar
cataytic activity as bacterial DCM dehalogenase,
catalyzing the GSH-dependent hydrolytic dehalogenation
of dihalomethanes. This is an essential process in
methylotrophic bacteria to enable them to use
chloromethane and DCM as sole carbon and energy sources.
The presence of polymorphisms in human GSTT1-1 and its
relationship to the onset of diseases including cancer
is the subject of many studies. Human GSTT2-2 exhibits a
highly specific sulfatase activity, catalyzing the
cleavage of sulfate ions from aralkyl sufate esters, but
not from the aryl or alkyl sulfate esters.
Length = 126
Score = 26.4 bits (59), Expect = 7.3
Identities = 14/39 (35%), Positives = 15/39 (38%), Gaps = 9/39 (23%)
Query: 62 LCGTSDYSIADLLA-----HHVVA--SSF-PHPKLLQWF 92
L G + SIADL A A F PKL W
Sbjct: 68 LAG-DEISIADLSAICEIMQPEAAGYDVFEGRPKLAAWR 105
>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
Length = 337
Score = 26.9 bits (60), Expect = 7.3
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 102 EERARLLQFTTGSSQL 117
E R +++ TTGS+QL
Sbjct: 92 EARKNIIRITTGSTQL 107
>gnl|CDD|221296 pfam11894, DUF3414, Protein of unknown function (DUF3414). This
family of proteins are functionally uncharacterized. This
protein is found in eukaryotes. Proteins in this family
are typically between 764 to 2011 amino acids in length.
This protein has a conserved LLG sequence motif.
Length = 1612
Score = 27.3 bits (61), Expect = 8.5
Identities = 15/89 (16%), Positives = 24/89 (26%), Gaps = 13/89 (14%)
Query: 25 KVIVNLCP-----KQVIIREYFLKFIPKKLVSYRLSPSTKLLLCGTS-------DYSIAD 72
+V++ CP + I E +PK L +
Sbjct: 1245 QVLLTDCPLSGDVRSNFILEILQAILPKLEDYIDSDVEFAEELASLALTLFALLRQDRPT 1304
Query: 73 LLAHHVVASSFPHPKLLQWFWTALQNFTT 101
L V S +L Q F T + +
Sbjct: 1305 GLDAIDVG-SLIDSRLHQLFKTCIDGILS 1332
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 0.135 0.407
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,443,879
Number of extensions: 950141
Number of successful extensions: 795
Number of sequences better than 10.0: 1
Number of HSP's gapped: 785
Number of HSP's successfully gapped: 30
Length of query: 206
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 114
Effective length of database: 6,857,034
Effective search space: 781701876
Effective search space used: 781701876
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: 57 (25.7 bits)