RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3857
(349 letters)
>gnl|CDD|239623 cd03565, VHS_Tom1, VHS domain family, Tom1 subfamily; The VHS
domain is an essential part of Tom1 (Target of myb1 -
retroviral oncogene) protein. The VHS domain has a
superhelical structure similar to the structure of the
ARM repeats and is present at the very N-termini of
proteins. It is a right-handed superhelix of eight alpha
helices. The VHS domain has been found in a number of
proteins, some of which have been implicated in
intracellular trafficking and sorting. The VHS domain of
the Tom1 protein is essential for the negative
regulation of Interleukin-1 and Tumor Necrosis
Factor-induced signaling pathways.
Length = 141
Score = 234 bits (598), Expect = 1e-77
Identities = 94/143 (65%), Positives = 115/143 (80%), Gaps = 3/143 (2%)
Query: 15 PVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMY 74
PVG IE ATD +L SE+W LNMEICDIINETEDGPKDA++A++KRL K++ +M
Sbjct: 1 PVGQLIEKATDGSLQSEDWGLNMEICDIINETEDGPKDAVRALKKRL--NGNKNHKEVML 58
Query: 75 TLTVLETCVKNCNRRFHILVCSKDFIQE-LYKLIGPKNEPPIIVQDKVLSLIQSWADAFK 133
TLTVLETCVKNC RFH+LV KDFI++ L KLI PKN PP IVQ+KVL+LIQ+WADAF+
Sbjct: 59 TLTVLETCVKNCGHRFHVLVAKKDFIKDVLVKLINPKNNPPTIVQEKVLALIQAWADAFR 118
Query: 134 DIPNLEGVNQIYQELRSKGIEFP 156
P+L GV ++Y+EL+ KGIEFP
Sbjct: 119 GSPDLTGVVEVYEELKKKGIEFP 141
>gnl|CDD|197630 smart00288, VHS, Domain present in VPS-27, Hrs and STAM.
Unpublished observations. Domain of unknown function.
Length = 133
Score = 170 bits (432), Expect = 1e-52
Identities = 66/137 (48%), Positives = 92/137 (67%), Gaps = 4/137 (2%)
Query: 16 VGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYT 75
V I+ AT P+L E+W L +EICD+IN T DGPKDA++ ++KRL K+ V +
Sbjct: 1 VERLIDKATSPSLLEEDWELILEICDLINSTPDGPKDAVRLLKKRLNN---KNPHVALLA 57
Query: 76 LTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAFKDI 135
LT+L+ CVKNC +FH+ V SK+F+ EL KLI PK P +V+ ++L LIQ WADAFK+
Sbjct: 58 LTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLP-LVKKRILELIQEWADAFKND 116
Query: 136 PNLEGVNQIYQELRSKG 152
P+L + +Y L+ KG
Sbjct: 117 PDLSQIVDVYDLLKKKG 133
>gnl|CDD|216121 pfam00790, VHS, VHS domain. Domain present in VPS-27, Hrs and
STAM.
Length = 136
Score = 160 bits (407), Expect = 5e-49
Identities = 64/139 (46%), Positives = 95/139 (68%), Gaps = 4/139 (2%)
Query: 15 PVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMY 74
P+ I+ ATDP+L E+W+L ++ICD+INETE GPK+A++ I+KR+ + V +
Sbjct: 1 PLERWIDKATDPSLREEDWSLILDICDLINETETGPKEAVRLIKKRINS---PNPHVALL 57
Query: 75 TLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPK-NEPPIIVQDKVLSLIQSWADAFK 133
LT+L+ CVKNC +FH+ + SK+F+ EL KLI K P V+ K+L LIQ WADAFK
Sbjct: 58 ALTLLDACVKNCGSKFHLEIASKEFLNELVKLIPNKPYGKPAKVKKKILELIQEWADAFK 117
Query: 134 DIPNLEGVNQIYQELRSKG 152
+ P+L+ + +Y+ L+ KG
Sbjct: 118 NDPDLKYIRDMYKLLKRKG 136
>gnl|CDD|239625 cd03568, VHS_STAM, VHS domain family, STAM subfamily; members
include STAM (Signal Transducing Adaptor Molecule), EAST
(EGFR-associated protein with SH3 and TAM domains) and
Hbp (Hrs-binding protein). Collectively, they are
referred to as STAM. All STAMs have at their N-termini a
VHS domain, which is involved in cytokine-mediated
intracellular signal transduction and has a superhelical
structure similar to the structure of ARM (Armadillo)
repeats, followed by a SH3 (Src homology 3) domain, a
well-established protein-protein interaction domain. At
the C-termini of most vertebrate STAMS, an ITAM
(Immunoreceptor Tyrosine-based Activation) motif is
present, which mediates the binding of HRS (hepatocyte
growth factor-regulated tyrosine kinase substrate) in
endocytic and exocytic machineries.
Length = 144
Score = 148 bits (377), Expect = 2e-44
Identities = 58/143 (40%), Positives = 89/143 (62%), Gaps = 5/143 (3%)
Query: 20 IEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYTLTVL 79
+E ATD L SENW L +++CD + E+G KD +KAI KRL KD V + LT+L
Sbjct: 5 VEKATDEKLTSENWGLILDVCDKVKSDENGAKDCLKAIMKRLNH---KDPNVQLRALTLL 61
Query: 80 ETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAFKDIPNLE 139
+ C +NC +RFH V S+DF QEL KLI + P V++K+ +++ WAD FK+ P+L
Sbjct: 62 DACAENCGKRFHQEVASRDFTQELKKLINDRVHPT--VKEKLREVVKQWADEFKNDPSLS 119
Query: 140 GVNQIYQELRSKGIEFPMTDLDA 162
++ +Y++L+++G + D
Sbjct: 120 LMSDLYKKLKNEGPDLVTPDEPE 142
>gnl|CDD|239620 cd03561, VHS, VHS domain family; The VHS domain is present in Vps27
(Vacuolar Protein Sorting), Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and STAM
(Signal Transducing Adaptor Molecule). It has a
superhelical structure similar to that of the ARM
(Armadillo) repeats and is present at the N-termini of
proteins involved in intracellular membrane trafficking.
There are four general groups of VHS domain containing
proteins based on their association with other domains.
The first group consists of proteins of the
STAM/EAST/Hbp family which has the domain composition
VHS-SH3-ITAM. The second consists of proteins with a
FYVE domain C-terminal to VHS. The third consists of GGA
proteins with a domain composition VHS-GAT (GGA and
TOM)-GAE (gamma-adaptin ear) domain. The fourth consists
of proteins with a VHS domain alone or with domains
other than those mentioned above. In GGA proteins, VHS
domains are involved in cargo recognition in
trans-Golgi, thereby having a general membrane
targeting/cargo recognition role in vesicular
trafficking.
Length = 133
Score = 146 bits (370), Expect = 2e-43
Identities = 53/136 (38%), Positives = 82/136 (60%), Gaps = 4/136 (2%)
Query: 16 VGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYT 75
V S IE AT P+L +WALN+E+CD+IN +GPK+A +AIRK+++ + V +
Sbjct: 1 VTSLIERATSPSLEEPDWALNLELCDLINLKPNGPKEAARAIRKKIK---YGNPHVQLLA 57
Query: 76 LTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAFKDI 135
LT+LE VKNC + FH+ V K+F+ EL K+ + V++K L LI +W+++F
Sbjct: 58 LTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAWSESFGGH 117
Query: 136 PN-LEGVNQIYQELRS 150
L G+ Y+ L+
Sbjct: 118 SEDLPGIEDAYKLLKR 133
>gnl|CDD|239626 cd03569, VHS_Hrs_Vps27p, VHS domain family, Hrs and Vps27p
subfamily; composed of Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and its
yeast homolog Vps27p (vacuolar protein sorting). The VHS
domain, an essential part of Hrs/Vps27p, has a
superhelical structure similar to the structure of ARM
(Armadillo) repeats and is present at the N-termini of
proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p,
and EEA1) zinc finger domain C-terminal to VHS, as well
as two coiled-coil domains. Hrs has been proposed to
play a role in at least three vesicle trafficking
events: exocytosis, endocytosis, and endosome to
lysosome trafficking. Hrs is involved in promoting rapid
recycling of endocytosed signaling receptors to the
plasma membrane.
Length = 142
Score = 130 bits (329), Expect = 3e-37
Identities = 58/138 (42%), Positives = 83/138 (60%), Gaps = 5/138 (3%)
Query: 19 KIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYTLTV 78
IE AT L + A +EICD+I + PK A++A++KRL K+ V +Y L +
Sbjct: 8 LIEKATSELLGEPDLASILEICDMIRSKDVQPKYAMRALKKRLLS---KNPNVQLYALLL 64
Query: 79 LETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAFKDIPNL 138
LE+CVKNC FH V S++F+ EL LI K V+ K+L LIQ+WA AF++ P L
Sbjct: 65 LESCVKNCGTHFHDEVASREFMDELKDLI--KTTKNEEVRQKILELIQAWALAFRNKPQL 122
Query: 139 EGVNQIYQELRSKGIEFP 156
+ V YQ L+++G +FP
Sbjct: 123 KYVVDTYQILKAEGHKFP 140
>gnl|CDD|238118 cd00197, VHS_ENTH_ANTH, VHS, ENTH and ANTH domain superfamily;
composed of proteins containing a VHS, ENTH or ANTH
domain. The VHS domain is present in Vps27 (Vacuolar
Protein Sorting), Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and STAM
(Signal Transducing Adaptor Molecule). It is located at
the N-termini of proteins involved in intracellular
membrane trafficking. The epsin N-terminal homology
(ENTH) domain is an evolutionarily conserved protein
module found primarily in proteins that participate in
clathrin-mediated endocytosis. A set of proteins
previously designated as harboring an ENTH domain in
fact contains a highly similar, yet unique module
referred to as an AP180 N-terminal homology (ANTH)
domain. VHS, ENTH and ANTH domains are structurally
similar and are composed of a superhelix of eight alpha
helices. ENTH adnd ANTH (E/ANTH) domains bind both
inositol phospholipids and proteins and contribute to
the nucleation and formation of clathrin coats on
membranes. ENTH domains also function in the development
of membrane curvature through lipid remodeling during
the formation of clathrin-coated vesicles. E/ANTH
domain-bearing proteins have recently been shown to
function with adaptor protein-1 and GGA adaptors at the
trans-Golgi network, which suggests that E/ANTH domains
are universal components of the machinery for
clathrin-mediated membrane budding.
Length = 115
Score = 110 bits (278), Expect = 4e-30
Identities = 50/118 (42%), Positives = 67/118 (56%), Gaps = 6/118 (5%)
Query: 16 VGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYT 75
+E AT +W L MEICD+INET GPK+A+ AI+KR+ K+ V++
Sbjct: 1 FEKTVEKATSNENMGPDWPLIMEICDLINETNVGPKEAVDAIKKRIN---NKNPHVVLKA 57
Query: 76 LTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPK---NEPPIIVQDKVLSLIQSWAD 130
LT+LE CVKNC RFH V S DF EL K K ++ V++K + L+Q WA
Sbjct: 58 LTLLEYCVKNCGERFHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQLWAS 115
>gnl|CDD|190532 pfam03127, GAT, GAT domain. The GAT domain is responsible for
binding of GGA proteins to several members of the ARF
family including ARF1 and ARF3. The GAT domain
stabilises membrane bound ARF1 in its GTP bound state,
by interfering with GAP proteins.
Length = 99
Score = 105 bits (264), Expect = 3e-28
Identities = 44/95 (46%), Positives = 58/95 (61%)
Query: 200 PEQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSDIELITELHATCKAMQERIVQLIS 259
PEQV KL +LE V+ N+ + +EML PGQE SD EL+ EL+ C++MQ RI +LI
Sbjct: 1 PEQVAKLRSELEEVKNNVKLLSEMLQEYDPGQESQSDDELLQELYERCRSMQPRIQRLIE 60
Query: 260 KYSQEDFITELLQVNDQLNNLFLRFNRYESNREAA 294
+ ED + ELLQVND LN + R+ R R
Sbjct: 61 ETEDEDALAELLQVNDDLNRVLNRYERLVKGRTGG 95
>gnl|CDD|239624 cd03567, VHS_GGA, VHS domain family, GGA subfamily; GGA
(Golgi-localized, Gamma-ear-containing, Arf-binding)
comprise a subfamily of ubiquitously expressed,
monomeric, motif-binding cargo/clathrin adaptor
proteins. The VHS domain has a superhelical structure
similar to the structure of the ARM (Armadillo) repeats
and is present at the N-termini of proteins. GGA
proteins have a multidomain structure consisting of an
N-terminal VHS domain linked by a short proline-rich
linker to a GAT (GGA and TOM) domain, which is followed
by a long flexible linker to the C-terminal appendage,
GAE (gamma-adaptin ear) domain. The VHS domain of GGA
proteins binds to the acidic-cluster dileucine (DxxLL)
motif found on the cytoplasmic tails of cargo proteins
trafficked between the trans-Golgi network and the
endosomal system.
Length = 139
Score = 85.1 bits (211), Expect = 3e-20
Identities = 43/137 (31%), Positives = 70/137 (51%), Gaps = 9/137 (6%)
Query: 20 IEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYTLTVL 79
+ AT+P+ E+W C+ IN+ +GP+ A++ + ++Q K+ + LTVL
Sbjct: 6 LNKATNPSNREEDWEAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKE---ALQALTVL 62
Query: 80 ETCVKNCNRRFHILVCSKDFIQELYKLIGPK---NEPPIIVQDKVLSLIQSWADAFKDIP 136
E C+KNC RFH V F+ EL KL+ PK + V+ K++ L+ SW P
Sbjct: 63 EACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELPHEP 122
Query: 137 NLEGVNQIYQELRSKGI 153
+ + Y L+ +GI
Sbjct: 123 K---IKEAYDMLKKQGI 136
>gnl|CDD|216488 pfam01417, ENTH, ENTH domain. The ENTH (Epsin N-terminal
homology) domain is found in proteins involved in
endocytosis and cytoskeletal machinery. The function of
the ENTH domain is unknown.
Length = 124
Score = 36.4 bits (85), Expect = 0.004
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 14 SPVGSKIEMAT--DPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTV 71
S K+ AT DP S EI + + + + ++ + KRL GK++
Sbjct: 2 SETELKVREATNNDPWGPSGTLMA--EIARLTYDYVEFF-EIMEVLWKRLNDS-GKNWRH 57
Query: 72 IMYTLTVLETCVKNCNRRF 90
+ LT+LE +KN + R
Sbjct: 58 VYKALTLLEYLLKNGSERV 76
>gnl|CDD|234221 TIGR03467, HpnE, squalene-associated FAD-dependent desaturase. The
sequences in this family are members of the pfam01593
superfamily of flavin-containing amine oxidases which
include the phytoene desaturases. These sequences also
include a FAD-dependent oxidoreductase domain,
pfam01266. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of squalene, the
condensation product of the polyisoprenoid farnesyl
pyrophosphate. This gene and its association with hopene
biosynthesis in Zymomonas mobilis has been noted in the
literature where the gene symbol hpnE was assigned. This
gene is also found in contexts where the downstream
conversion of squalene to hopenes is not evidence. The
precise nature of the reaction catalyzed by this enzyme
is unknown at this time.
Length = 411
Score = 32.0 bits (73), Expect = 0.47
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 9/80 (11%)
Query: 121 VLSLIQSWADAFKDIPNLEGVNQIYQEL-RSKGIEFPMTDLDAMAPIITPKK-----SKE 174
L+++ S A D+P E ++I EL R+ L A +I K+ +
Sbjct: 308 YLAVVISAARDLVDLPREELADRIVAELRRAFPRVAGAKPLWAR--VIKEKRATFAATPG 365
Query: 175 VASSHPVQRSKVP-MGAAGD 193
+ P R+ P + AGD
Sbjct: 366 LNRLRPGARTPWPNLFLAGD 385
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 31.0 bits (71), Expect = 0.60
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 239 LITELHATCKAMQERIVQLISK-------YSQEDFITELLQVNDQLNN 279
LI EL + + +R+++++ Y+ E+F E + + Q N
Sbjct: 137 LILELKLSPEEAYQRLLRIVEDVNAIIETYAPEEFKQEKWKFSPQKGN 184
>gnl|CDD|238376 cd00735, bacteriophage_T4-like_lysozyme, Bacteriophage T4-like
lysozymes hydrolyse the beta-1,4-glycosidic bond between
N-acetylmuramic acid (MurNAc) and N-acetylglucosamine
(GlcNAc) in peptidoglycan heteropolymers of prokaryotic
cell walls. Members include a variety of bacteriophages
(T4, RB49, RB69, Aeh1) as well as Dictyostelium. .
Length = 164
Score = 29.8 bits (67), Expect = 1.4
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 100 IQELYKLIGPKNEPPIIVQDKVLSLI-QSWADAFKDIPNLEGVNQIYQEL 148
EL K IG + +I ++V +L + A A +DI + ++ +Y++L
Sbjct: 44 NSELSKQIGREVTNGVITSEEVEALFEKDLAKAQRDIMSNPKLSPVYKKL 93
>gnl|CDD|185750 cd09237, V_ScBro1_like, Protein-interacting V-domain of
Saccharomyces cerevisiae Bro1 and related domains. This
family contains the V-shaped (V) domain of Saccharomyces
cerevisiae Bro1, and related domains. It belongs to the
V_Alix_like superfamily which also includes the V-domain
of Saccharomyces cerevisiae Rim20 (also known as PalA),
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), and related
domains. Bro1 interacts with the ESCRT (Endosomal
Sorting Complexes Required for Transport) system, and
participates in endosomal trafficking. The mammalian
Alix V-domain (belonging to a different family) contains
a binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. Bro1
also has an N-terminal Bro1-like domain, which binds
Snf7, a component of the ESCRT-III complex, and a
C-terminal proline-rich region (PRR). The C-terminal
portion (V-domain and PRR) of S. cerevisiae Bro1
interacts with Doa4, a ubiquitin thiolesterase needed to
remove ubiquitin from MVB cargoes. It interacts with a
YPxL motif in the Doa4s catalytic domain to stimulate
its deubiquitination activity.
Length = 356
Score = 30.0 bits (68), Expect = 1.7
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 284 FNRYESNREAAIGKQNPDAASKLSKKPDVAADSGPSLIDLDDDDPVDVGLNSNLSKLKFL 343
F+ + +E N + + + PSL+DLDD + L ++K L
Sbjct: 148 FSLVDPVKEDIALLLNGGSLWEELFGFSSSGSPEPSLLDLDDSQNEQ----TVLKQIKQL 203
Query: 344 QENL 347
+E L
Sbjct: 204 EELL 207
>gnl|CDD|131346 TIGR02293, TAS_TIGR02293, putative toxin-antitoxin system antitoxin
component, TIGR02293 family. Proteins in this family
are found almost exclusively in the Proteobacteria, but
also in Gloeobacter violaceus PCC 7421, a
cyanobacterium. This family was proposed by Makarova, et
al. (2009) to be the antitoxin component of a new class
of type 2 toxin-antitoxin system, or addiction module
[Cellular processes, Other].
Length = 133
Score = 29.0 bits (65), Expect = 2.0
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 194 HDERLTPEQVTKLHKDLEVVQANMAVFN------EMLNTLIPGQEHSSDIELIT 241
+RL+ E+ +L + V +A + VF + L +PG + I+L+
Sbjct: 59 AHQRLSSEESDRLARVARVWKAAVDVFGGDAEARQWLFRPVPGLGNRRPIDLLL 112
>gnl|CDD|132021 TIGR02976, phageshock_pspB, phage shock protein B. This model
describes the PspB protein of the psp (phage shock
protein) operon, as found in Escherichia coli and many
related species. Expression of a phage protein called
secretin protein IV, and a number of other stresses
including ethanol, heat shock, and defects in protein
secretion trigger sigma-54-dependent expression of the
phage shock regulon. PspB is both a regulator and an
effector protein of the phage shock response [Cellular
processes, Adaptations to atypical conditions].
Length = 75
Score = 27.3 bits (61), Expect = 3.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 234 SSDIELITELHATCKAMQERIVQL 257
+ D L+ EL+A ++ERI L
Sbjct: 38 TDDQALLQELYAKADRLEERIDTL 61
>gnl|CDD|193468 pfam12995, DUF3879, Domain of unknown function, E. rectale Gene
description (DUF3879). Based on Eubacterium rectale
gene EUBREC_1343. As seen in gene expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14
737), it appears to be upregulated in the presence of
Bacteroides thetaiotaomicron vs when isolated in
culture.
Length = 186
Score = 28.0 bits (62), Expect = 5.4
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 54 IKAIRKRLQQY-AGKDYTVIMYTLTVLETCVKNCNRRFHILVCSKDFIQELYKL 106
I+AI+ + +Y D+ L L +NCN + I+ + ++E+++L
Sbjct: 42 IQAIKNLMSRYDKDGDWINPRTGLAGLLVTDENCNSKKRIISIPESSMEEMFEL 95
>gnl|CDD|145416 pfam02252, PA28_beta, Proteasome activator pa28 beta subunit. PA28
activator complex (also known as 11s regulator of 20S
proteasome) is a ring shaped hexameric structure of
alternating alpha and beta subunits. This family
represents the beta subunit. The activator complex binds
to the 20S proteasome ana simulates peptidase activity
in and ATP-independent manner.
Length = 150
Score = 27.6 bits (62), Expect = 7.0
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 263 QEDFITELLQVNDQLNNLFLRFNRYESNREAAIGKQNPDAASKLSKKPDV 312
QE+ + EL +V + + ++Y S R D +K +K P V
Sbjct: 54 QEEVLEELTRVETKAETFQDQISKYYSER--------GDLVAKAAKYPHV 95
>gnl|CDD|219692 pfam08002, DUF1697, Protein of unknown function (DUF1697). This
family contains many hypothetical bacterial proteins.
Length = 136
Score = 27.1 bits (61), Expect = 7.4
Identities = 17/89 (19%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 45 ETEDGPKDAIKA-IRKRLQQYAGKDYTVIMYTLTVLETCVKNC--------NRRFHILVC 95
E+ + + ++A I K L++ G + V++ + L V R H+L
Sbjct: 47 ESSERDEAELEAKIEKALEERFGFEVPVLVRSAEELRAIVAANPFPWESAEPNRLHVLFL 106
Query: 96 SKDFIQE-LYKLIGPKNEP-PIIVQDKVL 122
S+ + L +L+ + + +VL
Sbjct: 107 SEPPDADELAELLAKAEGDEEVALGGRVL 135
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 27.3 bits (61), Expect = 7.6
Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 4/26 (15%)
Query: 72 IMYTLTVLETCVKNCNRRFHILVCSK 97
+ Y LT +K RRF LVC K
Sbjct: 28 VPYALT----AIKGIGRRFAYLVCKK 49
>gnl|CDD|183621 PRK12607, PRK12607, phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 313
Score = 27.9 bits (63), Expect = 7.7
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 27/68 (39%)
Query: 140 GVNQIYQELRSKGIEFP--MTDLDAM-APIITP-KKSKEVASSHPVQRSKVPMGAAGDHD 195
G ++Y G+ P + + + PIITP K++E G HD
Sbjct: 116 GKREMY------GVTLPDGLRENQKLPEPIITPTTKAEE-----------------GGHD 152
Query: 196 ERLTPEQV 203
E ++PE++
Sbjct: 153 EPISPEEI 160
>gnl|CDD|216249 pfam01025, GrpE, GrpE.
Length = 165
Score = 27.2 bits (61), Expect = 8.6
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 248 KAMQERIVQLISKYSQEDFITELLQVNDQL 277
+ ER + KY+ E F +LL V D L
Sbjct: 45 RKRTEREREEAKKYAIEKFAKDLLPVLDNL 74
>gnl|CDD|191266 pfam05397, Med15_fungi, Mediator complex subunit 15. GAL11 or
MED15 is one of the up to 32 or subunits of the Mediator
complex which is found from fungi to humans. The
Mediator complex interacts with RNA polymerase II and
other general transcription factors to form the RNA
polymerase II holoenzyme, thereby affecting
transcription through targetting of activators and
repressors. This family is found in fungi and the small
metazoan starlet anemone.
Length = 115
Score = 26.9 bits (60), Expect = 8.7
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 9/87 (10%)
Query: 199 TPEQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSDIELITELHATCKAMQERIVQLI 258
TPE +L + E V N ++ NTL P Q+ I + + + R+ LI
Sbjct: 1 TPEDPERLRQLYEEVAKNNPRLKDVTNTLSPEQK-----AAIRQQLQKNQQLFGRVDSLI 55
Query: 259 SKY----SQEDFITELLQVNDQLNNLF 281
++ E+ LLQ+
Sbjct: 56 PQFYKLTGNEENTKRLLQMRIMTKEQL 82
>gnl|CDD|215122 PLN02190, PLN02190, cellulose synthase-like protein.
Length = 756
Score = 27.9 bits (62), Expect = 8.9
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 109 PKNEPPIIVQDKVLSLI 125
P EPPIIV + VLSL+
Sbjct: 104 PVREPPIIVVNTVLSLL 120
>gnl|CDD|234670 PRK00155, ispD, 2-C-methyl-D-erythritol 4-phosphate
cytidylyltransferase; Reviewed.
Length = 227
Score = 27.4 bits (62), Expect = 9.2
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 18/80 (22%)
Query: 63 QY---AGKDYTVIMYTLTVLETCVKNCNRRFH--ILVCSKDFIQELYKLIGPKNEPPIIV 117
QY GK ++ +TL R I+V D + +L+ K+ +V
Sbjct: 24 QYLPLGGK--PILEHTLEAFLAH-----PRIDEIIVVVPPDDRPDFAELLLAKDPKVTVV 76
Query: 118 ------QDKVLSLIQSWADA 131
QD VL+ +Q+ D
Sbjct: 77 AGGAERQDSVLNGLQALPDD 96
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 28.1 bits (62), Expect = 9.3
Identities = 28/145 (19%), Positives = 66/145 (45%), Gaps = 16/145 (11%)
Query: 141 VNQIYQELRSKGIEFPMTDLDAMAPIITP--KKSKEVASSHPVQRSKVPMGAAGDHDERL 198
+ + +L+SK P L + + K+ E+ P ++S + D E+
Sbjct: 693 LQEFISDLQSKLRLAP-DKLKSTESELKKKEKRRDEMLGLAPGRQSII------DLKEKE 745
Query: 199 TPE---QVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHS----SDIELITELHATCKAMQ 251
PE ++ K+++D++ ++ ++ +L T++P +E + +D+ ++ K ++
Sbjct: 746 IPELRNKLQKVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVE 805
Query: 252 ERIVQLISKYSQEDFITELLQVNDQ 276
+I Q +K D + QVN +
Sbjct: 806 RKIAQQAAKLQGSDLDRTVQQVNQE 830
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
0.316 0.133 0.377
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,553,354
Number of extensions: 1676669
Number of successful extensions: 1862
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1846
Number of HSP's successfully gapped: 39
Length of query: 349
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 251
Effective length of database: 6,590,910
Effective search space: 1654318410
Effective search space used: 1654318410
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: 41 (21.6 bits)
S2: 59 (26.5 bits)