RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11394
(391 letters)
>gnl|CDD|202161 pfam02214, K_tetra, K+ channel tetramerisation domain. The
N-terminal, cytoplasmic tetramerisation domain (T1) of
voltage-gated K+ channels encodes molecular determinants
for subfamily-specific assembly of alpha-subunits into
functional tetrameric channels. It is distantly related
to the BTB/POZ domain pfam00651.
Length = 92
Score = 136 bits (345), Expect = 7e-40
Identities = 44/86 (51%), Positives = 59/86 (68%)
Query: 34 VVINVSGLRFETQLRTLNQFPETLLGDPARRIRYFDPLRNEYFFDRNRPSFDAILYYYQS 93
V +NV G RFET TL +FP+TLLG +R ++D NEYFFDR+ F+ IL +Y++
Sbjct: 1 VRLNVGGKRFETSKSTLTRFPDTLLGRLLKRCDFYDDDTNEYFFDRSPKHFETILNFYRT 60
Query: 94 GGRLRRPVNVPLDVFSEEIKFYELGD 119
GG+L RP V LD F EE++FY LG+
Sbjct: 61 GGKLHRPEEVCLDSFLEELEFYGLGE 86
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 51.2 bits (123), Expect = 2e-08
Identities = 14/89 (15%), Positives = 29/89 (32%), Gaps = 3/89 (3%)
Query: 34 VVINVSGLRFETQLRTLNQFPETLLGDPARRIRYFDPLRNEYFFDRNRPSFDAILYYYQS 93
V + V G +F L + + Y D + F A+L + +
Sbjct: 2 VTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKE-SDKSEIYLDDVSPEDFRALLNFLYT 60
Query: 94 GGRLRRPVNVPLDVFSEEIKFYELGDVAT 122
G+L P ++ E + ++ +
Sbjct: 61 -GKLDLPEE-NVEELLELADYLQIPGLVE 87
>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 = 41.4 bits (98), Expect = 3e-05
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 350 VVLFSSAVYFAEAGSENSFFKSIPDAFWWAVVTMTTVGYGDM 391
+VL VY++ E + DA +++ VT+TT+GYGD+
Sbjct: 5 LVLIFGTVYYSL--EEEGWGWDFLDALYFSFVTLTTIGYGDI 44
Score = 41.4 bits (98), Expect = 3e-05
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 9/62 (14%)
Query: 249 ILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPDAFWWAVVTMTTVGYGDMRCGAFFERGV 308
+L+ + G V + E G F DA +++ VT+TT+GYGD+ R +
Sbjct: 3 LLLVLIFGTVYY----SLEEEGWGWDFL----DALYFSFVTLTTIGYGDIVPLTDAGR-L 53
Query: 309 FC 310
F
Sbjct: 54 FT 55
Score = 34.1 bits (79), Expect = 0.013
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 331 SIPDAFWWAVVTMTTVGYG 349
DA +++ VT+TT+GYG
Sbjct: 24 DFLDALYFSFVTLTTIGYG 42
>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 = 41.9 bits (99), Expect = 2e-04
Identities = 23/89 (25%), Positives = 33/89 (37%), Gaps = 7/89 (7%)
Query: 222 IMPSLYCLLTSLLLYSVVMIYVHVLIPILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPD 281
+ SL LL LLL ++ I+ I+ G L + S F S +
Sbjct: 90 SLKSLLNLL--LLLLLLLFIFA-----IIGVQLFGGELDKCCDKNENPINGNSNFDSYGE 142
Query: 282 AFWWAVVTMTTVGYGDMRCGAFFERGVFC 310
A W T+TT G+GD+ V
Sbjct: 143 ALLWLFRTLTTEGWGDVMYDTLVPGTVLG 171
Score = 36.1 bits (84), Expect = 0.013
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 365 ENSFFKSIPDAFWWAVVTMTTVGYGDM 391
NS F S +A W T+TT G+GD+
Sbjct: 133 GNSNFDSYGEALLWLFRTLTTEGWGDV 159
Score = 30.7 bits (70), Expect = 0.95
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 331 SIPDAFWWAVVTMTTVGYGVVLFS 354
S +A W T+TT G+G V++
Sbjct: 139 SYGEALLWLFRTLTTEGWGDVMYD 162
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 38.8 bits (91), Expect = 0.004
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 14/81 (17%)
Query: 226 LYCLLTSLLL---------YSVVMIYVHVLIPILMYIFAGVVLFSSTVYFAEAGSDQSFF 276
YC++ + L S+ + +I I +F +Y + S
Sbjct: 112 GYCIVLLVALLIYRRDFDRSSLAAGTLFAVISITSLLFYSTF---GALYLGDGFSPP--I 166
Query: 277 KSIPDAFWWAVVTMTTVGYGD 297
+S+ AF++++VTM+TVGYGD
Sbjct: 167 ESLSTAFYFSIVTMSTVGYGD 187
Score = 38.5 bits (90), Expect = 0.004
Identities = 12/20 (60%), Positives = 18/20 (90%)
Query: 371 SIPDAFWWAVVTMTTVGYGD 390
S+ AF++++VTM+TVGYGD
Sbjct: 168 SLSTAFYFSIVTMSTVGYGD 187
Score = 35.8 bits (83), Expect = 0.036
Identities = 11/19 (57%), Positives = 17/19 (89%)
Query: 331 SIPDAFWWAVVTMTTVGYG 349
S+ AF++++VTM+TVGYG
Sbjct: 168 SLSTAFYFSIVTMSTVGYG 186
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 35.6 bits (82), Expect = 0.045
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 282 AFWWAVVTMTTVGYGDM 298
A +W++ TMTTVGYGD+
Sbjct: 254 AIYWSITTMTTVGYGDL 270
Score = 35.6 bits (82), Expect = 0.045
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 375 AFWWAVVTMTTVGYGDM 391
A +W++ TMTTVGYGD+
Sbjct: 254 AIYWSITTMTTVGYGDL 270
Score = 31.4 bits (71), Expect = 0.88
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 335 AFWWAVVTMTTVGYG 349
A +W++ TMTTVGYG
Sbjct: 254 AIYWSITTMTTVGYG 268
>gnl|CDD|240564 cd12965, CBM-Eb_CBM-Fb, carbohydrate-binding modules Eb and Fb from
SusE and SusF, respectively, and similar CBMs. Included
in this subgroup are CBM-Eb and CBM-Fb, starch-specific
carbohydrate-binding modules of SusE and SusF, cell
surface lipoproteins within the Sus (Starch-utilization
system)system of the human gut symbiont Bacteroides
thetaiotaomicron. These CBMs have no enzymatic activity.
The precise mechanistic roles of SusE and SusF in starch
metabolism are unclear. Both proteins have an N-terminal
domain which may belong to the immunoglobulin
superfamily (IgSF), followed by two or three tandem
starch-binding CBMs. SusF has three CBMs (CBM-Fa, -Fb,
and -Fc; F denotes SusF, and they are labeled
alphabetically from the N- to C- terminus). SusE has two
CBMs (CBM-Eb and -Ec, corresponding to CBM-Fb and -Fc).
Each starch-binding site contains an arc of aromatic
amino acids for hydrophobic stacking with glucose, and
hydrogen-bonding acceptors and donors for interacting
with the O-2 and O-3 of glucose. These five CBMs show
differences in their affinity for various different
starch oligosaccharides, and they contribute differently
to binding insoluble starch. CBM-Fb and CBM-Fc both bind
insoluble starch, deletion of one or the other results
in a decrease in the overall affinity of SusF for
starch. Both CBM-Eb and CBM-Ec are needed for SusE to
bind tightly to starch. Proteins in this group are
present in the species of the Gram-negative
Bacteroidetes phylum.
Length = 98
Score = 30.8 bits (70), Expect = 0.26
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 4/53 (7%)
Query: 325 CFLVGKSIPDAFWWAVVTMTTVGYGVVLFSSAVYFAEAGSENSFFKSIPDAFW 377
++ G + W MT V G F S VYF +AG+ FK W
Sbjct: 2 LYMTGSFFGNWNWDGWKEMTPVNGGDGEFWSIVYF-DAGAG---FKFNTSKAW 50
>gnl|CDD|233317 TIGR01218, Gpos_tandem_5TM, tandem five-transmembrane protein.
Members of this family of proteins, with average length
of 210, have no invariant residues but five predicted
transmembrane segments. Strangely, most members occur in
groups of consecutive paralogous genes. A striking
example is a set of eleven encoded consecutively,
head-to-tail, in Staphylococcus aureus strain COL.
Length = 208
Score = 31.0 bits (71), Expect = 0.76
Identities = 19/116 (16%), Positives = 49/116 (42%), Gaps = 7/116 (6%)
Query: 151 LFEYPESSQAARVVAIISVFVILLSIVIFCLETLPEFKHYKVFNTTTNGTKIEED--EVP 208
LF+Y + SQ+ + I+ + ILL ++ + + K++N N K +
Sbjct: 85 LFDYFDISQSIFIKIILFLISILLVYLLRIY--INKKNKKKLYNRLPNNNKRYKIKIRPT 142
Query: 209 DITDPFFLIETFLIMPSLYCLLTSLLLYS---VVMIYVHVLIPILMYIFAGVVLFS 261
F++ ++ L L L + + +++ ++ +I + ++ ++ S
Sbjct: 143 SFKYRIFILFLYIFFLGLSIFLFYLFINNGGENIILVINGIIFLFFFLLINMLPIS 198
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 31.4 bits (71), Expect = 0.83
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 14/52 (26%)
Query: 12 SQHYPGVDHFEPIPHDHDFCERVVINVSGLRFETQLRTLNQFPETLLGDPAR 63
S+H GV+ VV G R++ QLR L Q P+ ++G P R
Sbjct: 98 SKHMRGVN--------------VVALYGGQRYDVQLRALRQGPQIVVGTPGR 135
>gnl|CDD|165225 PHA02902, PHA02902, putative IMV membrane protein; Provisional.
Length = 70
Score = 28.4 bits (63), Expect = 1.4
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 166 IISVFVIL-LSIVIFCLETLPEFKHYKVFNTTTNGTKIEEDEVPDITDPFF 215
I FVIL + ++IFCL +K YK + + + D + D DP F
Sbjct: 2 AIDTFVILAVIVIIFCLLIYAAYKRYKCIPSPDDRDERFGDTLED--DPLF 50
>gnl|CDD|222193 pfam13520, AA_permease_2, Amino acid permease.
Length = 425
Score = 30.7 bits (70), Expect = 1.5
Identities = 11/47 (23%), Positives = 22/47 (46%)
Query: 238 VVMIYVHVLIPILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPDAFW 284
++ V +L+P+++ I G+VL + S +FF S +
Sbjct: 145 NILGIVKLLLPLILIILLGLVLALGGGFNLLPNSWTTFFPSGWPGVF 191
>gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16.
Length = 82
Score = 28.5 bits (64), Expect = 1.7
Identities = 9/36 (25%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 59 GDPARRIRYFDPLRNEYFFDRNRPSFDAILYYYQSG 94
G ++ ++DP++N+ + + AILY+ + G
Sbjct: 30 GRDLEKVGFYDPIKNQTYLN-----VPAILYFLEKG 60
>gnl|CDD|131075 TIGR02020, BchF, 2-vinyl bacteriochlorophyllide hydratase. This
model represents the enzyme responsible for the first
step in the modification of the ring A vinyl group of
chlorophyllide a which (in part) distinguishes
chlorophyll from bacteriochlorophyll. This enzyme is
aparrently absent from cyanobacteria (which do not use
bacteriochlorophyll) [Energy metabolism,
Photosynthesis].
Length = 145
Score = 29.0 bits (65), Expect = 2.4
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 13/70 (18%)
Query: 245 VLIPILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPDAFWWAVVTM---TTVGYGDMRCG 301
+L PI IF G + + F AG+D F+WA +++ T + G
Sbjct: 21 ILAPIQFLIFLGGLTLVTLYLFNLAGTD----------FYWATISILFKTLFLFTIFITG 70
Query: 302 AFFERGVFCR 311
AFFE+ VF +
Sbjct: 71 AFFEKEVFGK 80
>gnl|CDD|224147 COG1226, Kch, Kef-type K+ transport systems, predicted NAD-binding
component [Inorganic ion transport and metabolism].
Length = 212
Score = 29.3 bits (65), Expect = 3.1
Identities = 19/89 (21%), Positives = 29/89 (32%), Gaps = 5/89 (5%)
Query: 308 VFCRSRLRKFLLQEYSRCFLVGKSIPDAFWWAVVTMTTVGYGVVLFS-----SAVYFAEA 362
V R LL+E ++G + + A V L V A A
Sbjct: 49 VIDSDEDRVELLRELGLLVVLGDATREEVLEAAGIERARAVIVTLSDDATNVFIVLLARA 108
Query: 363 GSENSFFKSIPDAFWWAVVTMTTVGYGDM 391
+ + AV T+TTVG ++
Sbjct: 109 INPELEILARARDLDEAVETLTTVGADEV 137
Score = 28.1 bits (62), Expect = 6.1
Identities = 13/67 (19%), Positives = 21/67 (31%), Gaps = 7/67 (10%)
Query: 243 VHVLIPILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPDAFWWAVVTMTTVGYGDMRCGA 302
V V + V+L + E + AV T+TTVG ++
Sbjct: 89 VIVTLSDDATNVFIVLLARAINPELE-------ILARARDLDEAVETLTTVGADEVVPPT 141
Query: 303 FFERGVF 309
F +
Sbjct: 142 FESALLL 148
>gnl|CDD|198266 cd10403, SH2_STAP1, Src homology 2 domain found in
Signal-transducing adaptor protein 1 (STAP1). STAP1 is
a signal-transducing adaptor protein. It is composed of
a Pleckstrin homology (PH) and SH2 domains along with
several tyrosine phosphorylation sites. STAP-1 is an
ortholog of BRDG1 (BCR downstream signaling 1). STAP1
protein functions as a docking protein acting downstream
of Tec tyrosine kinase in B cell antigen receptor
signaling. The protein is phosphorylated by Tec and
participates in a positive feedback loop, increasing Tec
activity. STAP1 has been shown to interact with C19orf2,
an unconventional prefoldin RPB5 interactor. In general
SH2 domains are involved in signal transduction. They
typically bind pTyr-containing ligands via two surface
pockets, a pTyr and hydrophobic binding pocket, allowing
proteins with SH2 domains to localize to tyrosine
phosphorylated sites.
Length = 94
Score = 27.8 bits (62), Expect = 3.4
Identities = 8/25 (32%), Positives = 10/25 (40%)
Query: 184 LPEFKHYKVFNTTTNGTKIEEDEVP 208
P KHY+V + T E V
Sbjct: 46 KPRIKHYRVMSRGQGYTIELEKPVT 70
>gnl|CDD|240601 cd12918, VKOR_arc, Vitamin K epoxide reductase family in archaea
and some bacteria. This family includes vitamin K
epoxide reductase (VKOR) mostly present in archaea and
some bacteria. VKOR (also named VKORC1) is an integral
membrane protein that catalyzes the reduction of vitamin
K 2,3-epoxide and vitamin K to vitamin K hydroquinone,
an essential co-factor subsequently used in the
gamma-carboxylation of glutamic acid residues in blood
coagulation enzymes. All homologs of VKOR contain an
active site CXXC motif, which is switched between
reduced and disulfide-bonded states during the reaction
cycle. In some bacterial homologs, the VKOR domain is
fused with domains of the thioredoxin family of
oxidoreductases which may function as redox partners in
initiating the reduction cascade.
Length = 126
Score = 27.3 bits (61), Expect = 6.7
Identities = 15/79 (18%), Positives = 23/79 (29%), Gaps = 7/79 (8%)
Query: 234 LLYSVVMIYVHVLIPILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPDAFW---WAVVTM 290
LL S + Y H L + V+ V S S +P A W V +
Sbjct: 11 LLASAYLTYEHYLKRPPLACTISGVINCEKVLS----SPYSRILGVPLAVLGLAWFAVLL 66
Query: 291 TTVGYGDMRCGAFFERGVF 309
+R ++
Sbjct: 67 VLSLLAALRVRLLLGALLY 85
>gnl|CDD|217378 pfam03124, EXS, EXS family. We have named this region the EXS
family after (ERD1, XPR1, and SYG1). This family
includes C-terminus portions from the SYG1 G-protein
associated signal transduction protein from
Saccharomyces cerevisiae, and sequences that are thought
to be murine leukaemia virus (MLV) receptors (XPR1).
N-terminus portions from these proteins are aligned in
the SPX pfam03105 family. The previously noted
similarity between SYG1 and MLV receptors over their
whole sequences is thus borne out in pfam03105 and this
family. While the N-termini aligned in pfam03105 are
thought to be involved in signal transduction, the role
of the C-terminus sequences aligned in this family is
not known. This region of similarity contains several
predicted transmembrane helices. This family also
includes the ERD1 (ERD: ER retention defective) yeast
proteins. ERD1 proteins are involved in the localisation
of endogenous endoplasmic reticulum (ER) proteins. erd1
null mutants secrete such proteins even though they
possess the C-terminal HDEL ER lumen localisation label
sequence. In addition, null mutants also exhibit defects
in the Golgi-dependent processing of several
glycoproteins, which led to the suggestion that the
sorting of luminal ER proteins actually occurs in the
Golgi, with subsequent return of these proteins to the
ER via `salvage' vesicles.
Length = 337
Score = 28.4 bits (64), Expect = 6.8
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 213 PFFLIETFLIMPSLYCLLTSLLLYSVVMIYVH--VLIPILMYIFAGVVLF 260
+ +F + L L LLL + + V +P+++ + ++LF
Sbjct: 49 ELLELASFFTVLWLLSFLLYLLLEHLELTKPASWVQVPLVLLLIVLLILF 98
>gnl|CDD|225743 COG3202, COG3202, ATP/ADP translocase [Energy production and
conversion].
Length = 509
Score = 28.4 bits (64), Expect = 7.6
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 220 FLIMPSLYCLLTSLLLYSVVM----IYVHVLIPILMYIFAGVVLFSSTVYFAEAGSD 272
F I + L+ L S ++ + LI L+ + GV+ F + GS
Sbjct: 326 FQIWTGVVSLVVFLFPGSNLIRRVGWFTGALITPLVMLITGVLFFGFAFFNNSIGSI 382
>gnl|CDD|215079 PLN00151, PLN00151, potassium transporter; Provisional.
Length = 852
Score = 28.6 bits (64), Expect = 8.3
Identities = 11/57 (19%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 237 SVVMIYVHVLIPILMYIFAGVVLFSSTVYFAEAGSDQSFFKSIPDAFWWAVVTMTTV 293
S+ + + +++P L+ + G + + ++Q FF S+P + +W V + +
Sbjct: 374 SIQLAFTCLVLPCLLLAYMGQAAYLMKNPDS---AEQIFFSSVPSSLFWPVFLIANL 427
>gnl|CDD|234557 TIGR04346, DotA_TraY, conjugal transfer/type IV secretion protein
DotA/TraY. Members of this protein family include
transfer protein TraY of IncI1 plasmid R64 and DotA
(defect in organelle trafficking A) of Legionella
pneumophila.
Length = 652
Score = 28.1 bits (63), Expect = 9.3
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 222 IMPSLYCLLTSLLLYSVVMIYVHVLIPILMYIFA 255
I L+ L +L + +++ Y IP ++++ A
Sbjct: 493 ISFVLFPLALALFIMGLILAYYLPFIPFIIWMGA 526
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
0.326 0.142 0.446
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,203,775
Number of extensions: 2163975
Number of successful extensions: 3226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3211
Number of HSP's successfully gapped: 93
Length of query: 391
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 292
Effective length of database: 6,546,556
Effective search space: 1911594352
Effective search space used: 1911594352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 60 (26.8 bits)