RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8545
(547 letters)
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 80.7 bits (199), Expect = 7e-16
Identities = 63/255 (24%), Positives = 125/255 (49%), Gaps = 16/255 (6%)
Query: 16 MLSFTL-VAHWLACLWFVIADYERNRYRQDWDLGWIHTLAERLKVNVSEISHRESYITAL 74
+LS TL + H CL+++IAD RY WI + N E S YI+A+
Sbjct: 205 LLSVTLFLVHCAGCLYYLIAD----RYPHQ-GKTWIGAVIP----NFRETSLWIRYISAI 255
Query: 75 YFTCSSLTSVGFGNVSANTSAEKIFSICTMLIGALMHAVVFGNVTAIIQRMYSRRSLYQT 134
Y++ +++T+VG+G++ A + E IF I ML + A + GN+T ++ R ++
Sbjct: 256 YWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRRTMEFRN 315
Query: 135 KWRDLKEFLTLNQIPKELKQRMQDYFQTMWSLSHGIDVHETLKEFPEELRGDVSMHLHRE 194
F+ N++P LK ++ Y + + ++ + + + P+ + + HL
Sbjct: 316 SIEAASNFVGRNRLPPRLKDQILAYMCLRFK-AESLNQQQLIDQLPKSICKSICQHLFLP 374
Query: 195 ILQ-LPIFEAATQGCLKLLSLHIRNNFCAPGEYLIHKGDHLSSIYYLCNGSMEVVQNGM- 252
+++ + +F+ ++ L LL ++ + P E +I + + +Y + +G +E++ +
Sbjct: 375 VVEKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGE 434
Query: 253 ---VVAILGKGDLVG 264
VV LG GD+ G
Sbjct: 435 KERVVGTLGCGDIFG 449
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 63.9 bits (156), Expect = 1e-12
Identities = 31/135 (22%), Positives = 50/135 (37%), Gaps = 25/135 (18%)
Query: 200 IFEAATQGCLKLLSLHIRNNFCAPGEYLIHKGDHLSSIYYLCNGSMEVVQNG-----MVV 254
+F L+ L+ + GE +I +GD S+Y + +GS+EV + +V
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIV 60
Query: 255 AILGKGDLVGCDISMWLSEKNGGSAVGPGAGTGVDPIVKSSCDVKALTYCDLKSVNVVGL 314
LG GDL G + S V+ALT +L +
Sbjct: 61 GFLGPGDLFGELALLGNGP--------------------RSATVRALTDSELLVLPRSDF 100
Query: 315 VEVLRLYPEYQQEFA 329
+L+ YPE +
Sbjct: 101 RRLLQEYPELARRLL 115
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 59.7 bits (145), Expect = 6e-11
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 200 IFEAATQGCLKLLSLHIRNNFCAPGEYLIHKGDHLSSIYYLCNGSMEVVQ-----NGMVV 254
+F+ L+ L+ + GE +I +GD S Y + +G +EV + +V
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIV 60
Query: 255 AILGKGDLVG 264
LG GD G
Sbjct: 61 GTLGPGDFFG 70
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 57.6 bits (140), Expect = 8e-11
Identities = 16/61 (26%), Positives = 34/61 (55%)
Query: 59 VNVSEISHRESYITALYFTCSSLTSVGFGNVSANTSAEKIFSICTMLIGALMHAVVFGNV 118
++ E ++ ALYF+ +LT++G+G++ T A ++F+I +LIG + + +
Sbjct: 14 YSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVL 73
Query: 119 T 119
Sbjct: 74 G 74
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 48.1 bits (115), Expect = 2e-06
Identities = 29/121 (23%), Positives = 51/121 (42%), Gaps = 21/121 (17%)
Query: 4 YSQYSALILTLLMLSFTLVAHWLACLWFVIADYERNRYRQDWDLGWIHTLAERLKVNVSE 63
S S L L LL+L L+ A + + E + D + I+
Sbjct: 89 RSLKSLLNLLLLLL---LLLFIFAIIGVQLFGGELD-KCCDKNENPIN-----------G 133
Query: 64 ISHRESYITALYFTCSSLTSVGFGNV-----SANTSAEKIFSICTMLIGA-LMHAVVFGN 117
S+ +SY AL + +LT+ G+G+V T KIF + +++G L+ ++ G
Sbjct: 134 NSNFDSYGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFIILGGVLLLNLLIGV 193
Query: 118 V 118
+
Sbjct: 194 I 194
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 45.4 bits (108), Expect = 3e-06
Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 25/107 (23%)
Query: 222 APGEYLIHKGDHLSSIYYLCNGSMEVVQNG-----MVVAILGKGDLVGCDISMWLSEKNG 276
GE + +GD S+Y + +G ++V + ++A LG GD G ++++ L +
Sbjct: 5 KKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFG-ELAL-LGGE-- 60
Query: 277 GSAVGPGAGTGVDPIVKSSCDVKALTYCDLKSVNVVGLVEVLRLYPE 323
S V ALT +L + +E+L PE
Sbjct: 61 ----------------PRSATVVALTDSELLVIPREDFLELLEQDPE 91
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 36.3 bits (84), Expect = 0.023
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 197 QLPIFEAATQGCLKLLSLHIRNNFCAPGEYLIHKGDHLSSIYYLCNGSMEVVQNG----- 251
+ P+ L+LL+L + GE L +G+ S+Y + +G +++ N
Sbjct: 4 ENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTEDGRE 63
Query: 252 MVVAILGKGDLVG 264
+++ LG GD G
Sbjct: 64 IILGFLGPGDFFG 76
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 34.6 bits (80), Expect = 0.084
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 215 HIRNNFCAPGEYLIHKGDHLSSIYYLCNGSMEVV-----QNGMVVAILGKGDLVG 264
HI LIH G+ ++YY+ GS+ V+ M+++ L +GD +G
Sbjct: 21 HIHK--YPAKSTLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIG 73
>gnl|CDD|153329 cd07645, I-BAR_IMD_BAIAP2L1, Inverse (I)-BAR, also known as the
IRSp53/MIM homology Domain (IMD), of Brain-specific
Angiogenesis Inhibitor 1-Associated Protein 2-Like 1.
The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs
(I-BAR) domain, is a dimerization and lipid-binding
module that bends membranes and induces membrane
protrusions. BAIAP2L1 (Brain-specific Angiogenesis
Inhibitor 1-Associated Protein 2-Like 1) is also known
as IRTKS (Insulin Receptor Tyrosine Kinase Substrate).
It is widely expressed, serves as a substrate for the
insulin receptor, and binds the small GTPase Rac. It
plays a role in regulating the actin cytoskeleton and
colocalizes with F-actin, cortactin, VASP, and vinculin.
BAIAP2L1 expression leads to the formation of short
actin bundles, distinct from filopodia-like protrusions
induced by the expression of the related protein IRSp53.
It contains an N-terminal IMD, an SH3 domain, and a WASP
homology 2 (WH2) actin-binding motif at the C-terminus.
The IMD domain of BAIAP2L1 binds and bundles actin
filaments, and binds the small GTPase Rac.
Length = 226
Score = 33.7 bits (77), Expect = 0.18
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 364 DDEAGEGETSPLSPPSRSPLHIPMSNSPRHTKINMRGAERFRR------GELEKKSSVD 416
D A GE + +SP S+ H+ M S H K+N E F++ ELE+K+ +D
Sbjct: 48 DGVAKIGEIAAVSPVSKELGHVLMEISDVHKKLNDSLEENFKKFHREIIAELERKTDLD 106
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 33.8 bits (78), Expect = 0.24
Identities = 16/56 (28%), Positives = 35/56 (62%), Gaps = 5/56 (8%)
Query: 68 ESYITALYFTCSSLTSVGFGNVSANTSAEKIFSICTMLIGALMHAVVFG-NVTAII 122
ES TA YF+ ++++VG+G++ + + ++F+I +++G VF +++AI
Sbjct: 167 ESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILG----ITVFATSISAIF 218
>gnl|CDD|223608 COG0534, NorM, Na+-driven multidrug efflux pump [Defense
mechanisms].
Length = 455
Score = 33.7 bits (78), Expect = 0.27
Identities = 16/98 (16%), Positives = 31/98 (31%), Gaps = 4/98 (4%)
Query: 20 TLVAHWLACLW-FVIADYERNRYRQDWDLGW---IHTLAERLKVNVSEISHRESYITALY 75
T++A W+ L + ++ L E L++ + S
Sbjct: 203 TVIARWIGALLLLIYLLRKKRLLSLFKKKLLKPDRKLLKEILRLGLPIFLESLSESLGFL 262
Query: 76 FTCSSLTSVGFGNVSANTSAEKIFSICTMLIGALMHAV 113
+ +G ++A A +I S M + AV
Sbjct: 263 LLTLFVARLGTVALAAYGIALRIASFIFMPPFGIAQAV 300
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 31.1 bits (71), Expect = 0.38
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 2/63 (3%)
Query: 388 SNSPRHTKINMRGAERFRRGELEKKSSVDRLDTQVTSLHHHVATLSQE--VRNAIQALQE 445
N +H+ ++ E F L KK L+ ++ H ++ LS +Q Q
Sbjct: 45 YNPEKHSSSYLKELEYFLPSRLIKKEKSKELEKRILEAHKNLRGLSPAEAKLKYLQIAQS 104
Query: 446 LAT 448
L T
Sbjct: 105 LPT 107
>gnl|CDD|226871 COG4465, CodY, Pleiotropic transcriptional repressor
[Transcription].
Length = 261
Score = 32.4 bits (74), Expect = 0.44
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 132 YQTKWRDLKEFLTLNQIPKELKQRMQDYFQTMWSLSHGIDVHETLKEFPEELRGD 186
Y+T +K+ + P E + + ++T +L V L FP E +
Sbjct: 59 YKTNNDRVKQMFEDRKFPDEYTSALLNVYETSANL----PVDSELTIFPVENKDL 109
>gnl|CDD|217009 pfam02386, TrkH, Cation transport protein. This family consists of
various cation transport proteins (Trk) and V-type
sodium ATP synthase subunit J or translocating ATPase J
EC:3.6.1.34. These proteins are involved in active
sodium up-take utilising ATP in the process. TrkH a
member of the family from E. coli is a hydrophobic
membrane protein and determines the specificity and
kinetics of cation transport by the TrK system in E.
coli.
Length = 334
Score = 32.3 bits (74), Expect = 0.59
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 47 LGWIHTLAERLKVNVSEISHRESYITALYFTCSSLTSVGFG--NVSANTSAEKIFSICTM 104
+ + L E L V ++ + S I +F SS + GF ++S + A K+ + M
Sbjct: 138 ITIL--LLEVLVVLLASLPL-GSRILNAFFQVSSTRTAGFSTIDLSQLSPATKVLLMLLM 194
Query: 105 LIGAL 109
IG
Sbjct: 195 FIGGS 199
>gnl|CDD|213398 cd12191, gal11_coact, gall11 coactivator domain. Gall11/MED15 acts
in the general regulation of GAL structural genes and is
required for full expression for several genes in this
pathway, including GALs 1,7, and 10 in Saccharomyces
cerevisiae. GAL11 function is dependent on GCN4
functionality and binds GCN4 in a degenerate manner with
multiple orientations found at the GCN4-Gal11 interface.
Length = 90
Score = 29.6 bits (67), Expect = 1.1
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 134 TKWRDLKEFLTLNQIPKELKQRMQDYFQT 162
WR LK +L N IP + +++++ QT
Sbjct: 46 KTWRQLKAWLQQNNIPPQAMEQIKEVQQT 74
>gnl|CDD|203377 pfam06018, CodY, CodY GAF-like domain. This domain is a GAF-like
domain found at the N-terminus of several bacterial
GTP-sensing transcriptional pleiotropic repressor CodY
proteins. Presumably this domain is involved in GTP
binding. CodY has been found to repress the dipeptide
transport operon (dpp) of Bacillus subtilis in
nutrient-rich conditions. The CodY protein also has a
repressor effect on many genes in Lactococcus lactis
during growth in milk.
Length = 177
Score = 30.7 bits (70), Expect = 1.2
Identities = 21/107 (19%), Positives = 38/107 (35%), Gaps = 22/107 (20%)
Query: 96 EKIFSICTMLIGALMHAVVFGNVTA-----------IIQRM-----YSRRSLYQTKWRDL 139
EK I ++L +L V F + I+ R YS + +
Sbjct: 4 EKTRKINSILQKSLGKPVPFNEMAETLADVIECNVYIVSRKGKLLGYSLTYKTEND--RV 61
Query: 140 KEFLTLNQIPKELKQRMQDYFQTMWSLSHGIDVHETLKEFPEELRGD 186
K+F + P+E + + ++T +L + L FP E +
Sbjct: 62 KQFFEDKKFPEEYTSSLLNVYETSANL----PIDSELTVFPVENKEL 104
>gnl|CDD|233563 TIGR01766, tspaseT_teng_C, transposase, IS605 OrfB family, central
region. This model represents a region of a sequence
similarity between a family of putative transposases of
Thermoanaerobacter tengcongensis, smaller related
proteins from Bacillus anthracis, putative transposes
described by Pfam model pfam01385, and other proteins
[Mobile and extrachromosomal element functions,
Transposon functions].
Length = 82
Score = 28.5 bits (64), Expect = 1.9
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 112 AVVFGNVTAIIQRM-----YSRRSLYQTKWRDLKEFL 143
+V ++ I + + Y RR L+Q +R L +
Sbjct: 26 TIVLEDLKNIREMVDKKSKYLRRKLHQWSFRKLISKI 62
>gnl|CDD|151157 pfam10643, Cytochrome-c551, Photosystem P840 reaction-centre
cytochrome c-551. A photosynthetic reaction-centre
complex is found in certain green sulphur bacteria such
as Chlorobium vibrioforme which are anaerobic
photo-auto-trophic organisms. The primary electron donor
is P840, a probable B-Chl a dimer, and the primary
electron acceptor is a B-Chl monomer. Also on the donor
side c-type cytochromes are known to function as
electron donors to photo-oxidized P840. This family is
thus the secondary endogenous donor of the
photosynthetic reaction-centre complex and is a
membrane-bound cytochrome containing a single haem
group.
Length = 213
Score = 30.2 bits (68), Expect = 2.1
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 78 CSSLTSVGFGNVSANTSAEKI--FSICTMLIGALMHAVVFGNVTAIIQRMYSRRSLYQTK 135
C+SL +G G +S+ S + F + +I A+M A ++ + I+ R + K
Sbjct: 59 CASLIIMGLGKMSSRISDKWFLSFPLSIFVIVAVMFASLWERPSGILLSTTGRTTTLDGK 118
Query: 136 W----RDLKEFL 143
+ R LK FL
Sbjct: 119 YIRTVRQLKAFL 130
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 30.8 bits (70), Expect = 2.6
Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 21/97 (21%)
Query: 97 KIFSICTMLIGALMHAVVFGNVTAIIQRMYSRRSLYQTK------WRDLKEFLTLNQIPK 150
+C +L L+ +FG V A + Y++ + + DL+ +L N P+
Sbjct: 141 SCLGVCLLLTTVLL---LFGVVCAFVTNQYTQTGVKNSPTTMKEGVDDLRTYL--NDTPQ 195
Query: 151 ELKQRMQDYFQTMWS-----LSH-----GIDVHETLK 177
++ + +Q L G +H+ LK
Sbjct: 196 QIDHVLAQNYQETQDQVSKDLDGAGEHLGGRIHDELK 232
>gnl|CDD|233103 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, alpha region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase alpha chain and the N-terminal
region of the class I fumarase (where the C-terminal
region is homologous to the tartrate dehydratase beta
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 273
Score = 29.7 bits (67), Expect = 3.2
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 335 DLTYNIREGYEAEESDIGLPSLTLPSINEDDEAGEGETSPL 375
D+ I+E Y+ EES+I + L +I ++ E E P+
Sbjct: 19 DVVDAIKEAYDREESEIAK--INLEAILDNIEIAEKLGVPV 57
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 29.5 bits (67), Expect = 3.2
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 410 EKKSSVDRLDTQVTSLHHHVATLSQEVRNAIQALQELATTSSNVA 454
EK+ ++ LD Q+ LH V +L + ELA + + A
Sbjct: 16 EKQQQIENLDQQLRKLHASVESLVNHRK-------ELALNTGSFA 53
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 29.5 bits (67), Expect = 4.1
Identities = 11/46 (23%), Positives = 24/46 (52%)
Query: 410 EKKSSVDRLDTQVTSLHHHVATLSQEVRNAIQALQELATTSSNVAS 455
+K+ +D L++Q+ L+ + L + + A E A + + +AS
Sbjct: 28 DKRQYIDSLESQLKKLYKALELLVNQRKELASATGEFAKSLAMLAS 73
>gnl|CDD|177557 PHA03209, PHA03209, serine/threonine kinase US3; Provisional.
Length = 357
Score = 29.5 bits (66), Expect = 4.9
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 167 SHGIDVHETLKEFPEELRGDVSMHLHREILQLPIFEAA--TQ-GCLKLLSLHIRNNFCAP 223
SH + + TLK PEE D L R ++ E T+ C + ++L I
Sbjct: 273 SHLLKIISTLKVHPEEFPRDPGSRLVRGFIEYASLERQPYTRYPCFQRVNLPI------D 326
Query: 224 GEYLIHK 230
GE+L+HK
Sbjct: 327 GEFLVHK 333
>gnl|CDD|182657 PRK10698, PRK10698, phage shock protein PspA; Provisional.
Length = 222
Score = 29.0 bits (65), Expect = 5.6
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 402 ERFRR--GELEKKSSVDRLDTQVTSLHHHVATLSQEVR 437
R ++ GELE K S R Q L H A+ S++VR
Sbjct: 116 ARMKKEIGELENKLSETRARQQALMLRHQAASSSRDVR 153
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 29.3 bits (66), Expect = 5.7
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 222 APGEYLIHKGDHLSSIYYLCNGSMEVV----QNGMVVAILGKGDLVG 264
GEY++ +G+ +Y++ G EV + +L + D G
Sbjct: 37 GKGEYVVREGEPGDGLYFIWKGEAEVSGPAEEESRPEFLLKRYDYFG 83
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.7 bits (66), Expect = 5.7
Identities = 31/154 (20%), Positives = 50/154 (32%), Gaps = 21/154 (13%)
Query: 354 PSLTLPSINEDDEAGEGETSPLS---------PPSRSPLHIPMSNSPRHTKINMRGAERF 404
PS+ P NE D + L PP + +P + +G+
Sbjct: 152 PSIPSPQDNESDSDSSAQQQLLQPQGPPSIQVPPGAALAPSAPPPTPSAQAVPPQGSPIA 211
Query: 405 RRGELEKKSSVDRLDTQVTSLHHHVATLSQEVRNAIQALQELATTSSNVASNRYP--YPL 462
+ + + SLH Q + + LQ + + +P
Sbjct: 212 AQPAPQPQQPSPLSLISAPSLH------PQRLPSPHPPLQPQTASQQSPQPPAPSSRHPQ 265
Query: 463 PAHSN--PNLPHNTQCPQQRALLQRSSSHPPEMF 494
+H P +PH Q Q LQ SS+PP+ F
Sbjct: 266 SSHHGPGPPMPHALQ--QGPVFLQHPSSNPPQPF 297
>gnl|CDD|206243 pfam14073, Cep57_CLD, Centrosome localisation domain of Cep57. The
CLD or centrosome localisation domain of Cep57 is found
at the N-terminus, and lies approximately between
residues 58 and 239. This region lies within the first
alpha-helical coiled-coil segment of Cep57, and
localises to the centrosome internally to gamma-tubulin,
suggesting that it is either on both centrioles or on a
centromatrix component. This N-terminal region can also
multimerise with the N-terminus of other Cep57
molecules. The C-terminal part, Family Cep57_MT_bd,
pfam06657, is the microtubule-binding region of Cep57.
Length = 178
Score = 28.6 bits (64), Expect = 6.4
Identities = 32/134 (23%), Positives = 54/134 (40%), Gaps = 19/134 (14%)
Query: 402 ERFRRGELEKKSSVDRLDTQVTSLHHHVATLSQEVRNAIQALQELATTSSNVASNRYPYP 461
E+ RR ELE+ + D L TLS+E + + L+E + A+
Sbjct: 11 EKIRRLELERTQAEDNLQ-----------TLSREATHYKKVLEEEEQERNLAAN-----E 54
Query: 462 LPAHSNPNLPHNTQCPQQRALLQRSSSHPPEMFCWESMDQERYAHCVSQ-STQTDYPIDM 520
L + + + +LL++ + M E+ ++ER A Q S Q + D
Sbjct: 55 LTKQNKDLTSQLSSAESRCSLLEKQLEYMRRMV--ENAEKERTAVLEQQVSLQREKEHDQ 112
Query: 521 FESFVKENKLRVLE 534
+ + KL VLE
Sbjct: 113 MDVQAQLEKLEVLE 126
>gnl|CDD|233196 TIGR00933, 2a38, potassium uptake protein, TrkH family. The
proteins of the Trk family are derived from
Gram-negative and Gram-positive bacteria, yeast and
wheat. The proteins of E. coli K12 TrkH and TrkG as well
as several yeast proteins have been functionally
characterized.The E. coli TrkH and TrkG proteins are
complexed to two peripheral membrane proteins, TrkA, an
NAD-binding protein, and TrkE, an ATP-binding protein.
This complex forms the potassium uptake system
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 390
Score = 29.2 bits (66), Expect = 6.5
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 71 ITALYFTCSSLTSVGFGNVSANT--SAEKIFSICTMLIGA 108
+ + +F S+L + GF + +A + + M IG
Sbjct: 233 LLSAFFQSSTLRTAGFSTIDFAALPTATLVLLLLLMFIGG 272
>gnl|CDD|225647 COG3105, COG3105, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 138
Score = 28.2 bits (63), Expect = 6.6
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 11/80 (13%)
Query: 408 ELEKKSSVDRLDTQVTSLHHHVATLSQEVRNAIQALQEL----ATTSSNVASNRYPYPLP 463
+ E + +LD L H A ++ ++ Q Q+L A +S+++ L
Sbjct: 40 QYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDYQKLYQHMAKSSTSLLPE-----LS 94
Query: 464 AHSNP--NLPHNTQCPQQRA 481
A NP NL + +A
Sbjct: 95 AKDNPFRNLLAEEEASNDQA 114
>gnl|CDD|146915 pfam04513, Baculo_PEP_C, Baculovirus polyhedron envelope protein,
PEP, C terminus. Polyhedra are large crystalline
occlusion bodies containing nucleopolyhedrovirus
virions, and surrounded by an electron-dense structure
called the polyhedron envelope or polyhedron calyx. The
polyhedron envelope (associated) protein PEP is thought
to be an integral part of the polyhedron envelope. PEP
is concentrated at the surface of polyhedra, and is
thought to be important for the proper formation of the
periphery of polyhedra. It is thought that PEP may
stabilise polyhedra and protect them from fusion or
aggregation.
Length = 140
Score = 28.1 bits (63), Expect = 7.4
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 416 DRLDTQVTSLHHHVATLSQEVRNAIQALQE-LATTSSNVA 454
RLDT +T+L + L +RN + L L +S+V
Sbjct: 63 TRLDTLLTNLTDALNQLQDTLRNELTNLNSILNNLTSSVT 102
>gnl|CDD|202517 pfam03051, Peptidase_C1_2, Peptidase C1-like family. This family
is closely related to the Peptidase_C1 family pfam00112,
containing several prokaryotic and eukaryotic
aminopeptidases and bleomycin hydrolases.
Length = 438
Score = 28.8 bits (65), Expect = 7.6
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 490 PPEMFCWESMDQERYAHCVSQSTQTDYPIDMFESFVK 526
PPE F +E D+++ H + T P++ +E +V
Sbjct: 219 PPETFDFEYRDKDKNYHKIKDIT----PLEFYEKYVG 251
>gnl|CDD|234384 TIGR03896, cyc_nuc_ocin, bacteriocin-type transport-associated
protein. Members of this protein family are
uncharacterized and contain two copies of the cyclic
nucleotide-binding domain pfam00027. Members are
restricted to select cyanobacteria but are found
regularly in association with a transport operon that,
in turn, is associated with the production of putative
bacteriocins. The models describing the transport operon
are TIGR03794, TIGR03796, and TIGR03797.
Length = 317
Score = 28.7 bits (64), Expect = 8.5
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 224 GEYLIHKGDHLSSIYYLCNGSMEVVQN----GMVVAILGKGDLVG 264
G LIH+G + ++Y L G + + G V +G+++G
Sbjct: 169 GTILIHEGGTVDALYILLYGEASLSISPDGPGREVGSSRRGEILG 213
>gnl|CDD|179567 PRK03355, PRK03355, glycerol-3-phosphate acyltransferase;
Validated.
Length = 783
Score = 28.9 bits (65), Expect = 8.9
Identities = 18/70 (25%), Positives = 25/70 (35%), Gaps = 13/70 (18%)
Query: 390 SPRHTKINMRGAERFRRGELEKKSSVDRLDTQVTSLHHHVATLSQEVRNAIQALQELATT 449
PR K + + RFR G L K ++ T VR A + L EL
Sbjct: 180 VPRLVKPEILASARFRAG-LAKIAAKLGRPPGAT------------VREAGKMLDELVAG 226
Query: 450 SSNVASNRYP 459
S V+ +
Sbjct: 227 WSRVSVDLVS 236
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
0.319 0.133 0.404
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,563,005
Number of extensions: 2644142
Number of successful extensions: 2709
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2701
Number of HSP's successfully gapped: 46
Length of query: 547
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 445
Effective length of database: 6,413,494
Effective search space: 2854004830
Effective search space used: 2854004830
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 (21.8 bits)
S2: 61 (27.4 bits)