RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 047952
(354 letters)
>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 = 64.9 bits (159), Expect = 1e-13
Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 4/78 (5%)
Query: 73 VYLAAYLGGGSLSFYAVNSQIEGLKTNEILDSIYFCIVTMTTVGYGDLVPNSVVSKLLSC 132
+ L L G++ +Y++ + G + LD++YF VT+TT+GYGD+VP + +L +
Sbjct: 1 ILLLLVLIFGTV-YYSLEEEGWGW---DFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTI 56
Query: 133 AFVFTGMGLVGMFLSKAA 150
++ G+ L +FL+
Sbjct: 57 IYILIGIPLFLLFLAVLG 74
Score = 54.9 bits (133), Expect = 5e-10
Identities = 22/74 (29%), Positives = 32/74 (43%)
Query: 191 IMLVLELVLILVGTIFLVVVEKMSFVDAFYCVCSTITTLGYGDKSFSTTGGRAFGVVWIS 250
I+L+L L+ V F+DA Y T+TT+GYGD T GR F +++I
Sbjct: 1 ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYIL 60
Query: 251 SSTMTLAQFFLYVA 264
F +
Sbjct: 61 IGIPLFLLFLAVLG 74
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 46.6 bits (111), Expect = 1e-05
Identities = 26/65 (40%), Positives = 34/65 (52%), Gaps = 15/65 (23%)
Query: 75 LAAYLGGGSLSFYAV----------NSQIEGLKTNEILDSIYFCIVTMTTVGYGDLVPNS 124
L A + SL FY+ + IE L T + YF IVTM+TVGYGD+VP S
Sbjct: 138 LFAVISITSLLFYSTFGALYLGDGFSPPIESLST-----AFYFSIVTMSTVGYGDIVPVS 192
Query: 125 VVSKL 129
++L
Sbjct: 193 ESARL 197
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 39.5 bits (92), Expect = 0.002
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 104 SIYFCIVTMTTVGYGDLVPNSVVSKLLSCAFVFTGMGLVGMFLSKAADYLVDKQEILLVK 163
+IY+ I TMTTVGYGDL + + + ++ +GL YL+ L+V+
Sbjct: 254 AIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTA--------YLIGNMTNLVVE 305
Query: 164 ALHR 167
R
Sbjct: 306 GTRR 309
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse superfamily
of calcium sensors and calcium signal modulators; most
examples in this alignment model have 2 active canonical
EF hands. Ca2+ binding induces a conformational change
in the EF-hand motif, leading to the activation or
inactivation of target proteins. EF-hands tend to occur
in pairs or higher copy numbers.
Length = 63
Score = 35.2 bits (82), Expect = 0.003
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 293 DIDEDGVVSAAEFIIYKLKEMG-KISQEDIALVMEEFQDLDFDQSGTLSPSDL 344
D D DG +SA E LK +G +S+E+I ++ E D D G + +
Sbjct: 10 DKDGDGTISADELKAA-LKSLGEGLSEEEIDEMIREV---DKDGDGKIDFEEF 58
>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 = 37.6 bits (88), Expect = 0.008
Identities = 30/162 (18%), Positives = 56/162 (34%), Gaps = 21/162 (12%)
Query: 83 SLSFYAVNSQIEGLKTNEILDSIYFCIVTMTTVGYG--DLVPNSVVSKLLSCAFVFTGMG 140
+ + +L S +F T+ T G+ D + +L +F G
Sbjct: 214 LFLLLERGNTLYSYSFGALLLSAFFQSSTLRTAGFSTIDFAALPTATLVLLLLLMFIGGC 273
Query: 141 LV----GMFLSKAADYLVDKQEILLVKALHRYQKVG--PTDILKEIETNKVRYKCIIMLV 194
G+ + A +L+K ++R + G P I K K I++ V
Sbjct: 274 SGSTAGGIKTTTFA---------ILLKQVYREIRRGIHPRIIFSRRIGGKTIDKAILISV 324
Query: 195 LEL----VLILVGTIFLVVVEKMSFVDAFYCVCSTITTLGYG 232
LI + +I ++ F+ + + V S T+G
Sbjct: 325 WSFFLVFALIFLLSILELISSGYDFLTSLFEVVSAFGTVGLS 366
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 33.8 bits (78), Expect = 0.055
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 293 DIDEDGVVSAAEFIIYKLKEMG-KISQEDIALVMEEFQDLDFDQSGTLS 340
D D DG +S E LK +G ++S E++ + ++ D D G +
Sbjct: 102 DKDHDGYISIGELRRV-LKSLGERLSDEEVE---KLLKEYDEDGDGEID 146
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 31.2 bits (71), Expect = 0.097
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 290 EAADIDEDGVVSAAEFIIYKLKEMGKISQEDIALVMEE-FQDLDFDQSGTLSPSDL 344
+ D D DG + E K++ E++ ++E F ++D D G +S +
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEF 56
>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 = 31.5 bits (72), Expect = 0.43
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 101 ILDSIYFCIVTMTTVGYGDL-----VPNSVVSKLLSCAF-VFTGMGLVGMFL 146
+++ + T+TT G+GD+ VP +V+ K+ F + G+ L+ + +
Sbjct: 140 YGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFIILGGVLLLNLLI 191
Score = 27.3 bits (61), Expect = 9.4
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 213 MSFVDAFYCVCSTITTLGYGD-----KSFSTTGGRAFGVVWI 249
S+ +A + T+TT G+GD T G+ F V++I
Sbjct: 138 DSYGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFI 179
>gnl|CDD|216963 pfam02293, AmiS_UreI, AmiS/UreI family transporter. This family
includes UreI and proton gated urea channel as well as
putative amide transporters.
Length = 166
Score = 30.3 bits (69), Expect = 0.80
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 220 YCVCSTITTLGYGDKSFSTTGGRAFGVVWI 249
+ + IT L Y SF++ FGV+W+
Sbjct: 90 FSLFVAITALPYAIVSFTSGEDPWFGVIWL 119
>gnl|CDD|223246 COG0168, TrkG, Trk-type K+ transport systems, membrane components
[Inorganic ion transport and metabolism].
Length = 499
Score = 30.4 bits (69), Expect = 1.6
Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 6/90 (6%)
Query: 190 IIMLVLELVLILVGTIFLVVVEKMSFVDAFYCVCSTITTLGY--GDKSFSTTGGRAFGVV 247
+ ++ L+L ++ + ++ M DA + S G+ D S G +
Sbjct: 175 KTLWLIYLLLTILLALAFILAG-MPLFDAIFHSMSAFNNGGFSTHDASIGYFNGSPL-IN 232
Query: 248 WISSSTMTL--AQFFLYVAEFNTEKRQKAL 275
I + + L F ++ K K L
Sbjct: 233 LIITILIILGGIGFPVHYRLLIWIKSLKFL 262
Score = 29.6 bits (67), Expect = 2.5
Identities = 25/143 (17%), Positives = 49/143 (34%), Gaps = 29/143 (20%)
Query: 104 SIYFCIVTMTT-VGYGDLVPNSVVSKLLSCAFVF-------TGMG--------LVGMFLS 147
S F T DL + +L +F T G L+
Sbjct: 311 SAIFQTGFTRTGFNTVDLSQWPPATLVLLMLLMFIGGSPGSTAGGIKTTRFAVLLKALKR 370
Query: 148 KAADYLVDKQEILLVKALHRYQKVGPTDILKEIETNKVRYKCIIMLVLELVLILVGTIFL 207
+ L ++ VK + + D +++ + L L+++++G + L
Sbjct: 371 ELRR-LGHPNAVISVKI---FGRAIDEDTIRKA---------LAFFFLYLLILIIGALIL 417
Query: 208 VVVEKMSFVDAFYCVCSTITTLG 230
++ F+DA + V S T+G
Sbjct: 418 ILTGYDPFIDALFEVVSAFGTVG 440
>gnl|CDD|176238 cd08277, liver_alcohol_DH_like, Liver alcohol dehydrogenase.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48) , then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 29.6 bits (67), Expect = 2.2
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 13/87 (14%)
Query: 59 SLFGKPRPNFKRVLVYLAAYLGGGSLSFYAVNSQIEGLKTNEILDSIYFCIVTMT-TVGY 117
+ GK + +LG + S Y V + K + + C++ + GY
Sbjct: 124 TCKGKK----------IYHFLGTSTFSQYTVVDENYVAKIDPAAPLEHVCLLGCGFSTGY 173
Query: 118 GDLVPNSVVSKLLSCAFVFTGMGLVGM 144
G + V + A VF G+G VG+
Sbjct: 174 GAAWNTAKVEPGSTVA-VF-GLGAVGL 198
>gnl|CDD|216761 pfam01882, DUF58, Protein of unknown function DUF58. This family
of prokaryotic proteins have no known function.
Caldicellulosiruptor saccharolyticus PepX, a protein of
unknown function in the family, has been misannotated as
alpha-dextrin 6-glucanohydrolase.
Length = 85
Score = 26.8 bits (60), Expect = 5.6
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 261 LYVAEFNTEKRQKALVNWVLTRKMTHVDLEAADIDEDGVVSAAEFIIYKLKEMG 314
L V EF E+ ++ + M + ++E +SAA + Y+L G
Sbjct: 30 LMVKEFEAERAAPVVLLLDASPSM-GFGSTESKLEE--ALSAAASLAYELLRQG 80
>gnl|CDD|240454 cd12874, SPRY_PRY, PRY/SPRY domain, also known as B30.2. This
domain contains residues in the N-terminus that form a
distinct PRY domain structure such that the B30.2 domain
consists of PRY and SPRY subdomains. B30.2 domains
comprise the C-terminus of three protein families: BTNs
(receptor glycoproteins of immunoglobulin superfamily);
several TRIM proteins (composed of
RING/B-box/coiled-coil core); Stonutoxin (secreted
poisonous protein of the stonefish Synanceia horrida).
While SPRY domains are evolutionarily ancient, B30.2
domains are a more recent adaptation where the SPRY/PRY
combination is a possible component of immune defense.
Among the TRIM proteins, also known as the N-terminal
RING finger/B-box/coiled coil (RBCC) family, only
Classes I and IV contain the B30.2 domain that has
evolved under positive selection. Class IV TRIM proteins
include multiple members involved in antiviral immunity
at various levels of interferon signaling cascade.
Length = 167
Score = 27.8 bits (62), Expect = 6.4
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 58 ESLFGKPRPNFKRVLVYLAAYLGGGSLSFYAVNS 91
L P +RV V+L GSLSFY V+S
Sbjct: 109 TPLDVTVGP--ERVGVFLD--FDVGSLSFYNVSS 138
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 24.9 bits (56), Expect = 6.8
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 289 LEAADIDEDGVVSAAEF 305
D + DG +S E
Sbjct: 5 FRQFDTNGDGKISKEEL 21
>gnl|CDD|235786 PRK06369, nac, nascent polypeptide-associated complex protein;
Reviewed.
Length = 115
Score = 26.8 bits (60), Expect = 7.8
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 299 VVSAAEFIIYKLKEMGKISQEDIALVME 326
+V E + + ++ +I +EDI LV E
Sbjct: 58 IVGEPEEVEKEAEKEVEIPEEDIELVAE 85
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 27.9 bits (63), Expect = 7.9
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 285 THVDLEAADIDEDGVVSAAE-FIIYKLKEMGKISQEDIALVMEEFQDLD 332
+D E A D + V+ AE I Y K++ + +++ + + +L
Sbjct: 224 WMLDPEMAFADLNDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELK 272
>gnl|CDD|173804 cd07478, Peptidases_S8_CspA-like, Peptidase S8 family domain in
CspA-like proteins. GSP (germination-specific protease)
converts the spore peptidoglycan hydrolase (SleC)
precursor to an active enzyme during germination of
Clostridium perfringens S40 spores. Analysis of an
enzyme fraction of GSP showed that it was composed of a
gene cluster containing the processed forms of products
of cspA, cspB, and cspC which are positioned in a tandem
array just upstream of the 5' end of sleC. The amino
acid sequences deduced from the nucleotide sequences of
the csp genes showed significant similarity and showed a
high degree of homology with those of the catalytic
domain and the oxyanion binding region of
subtilisin-like serine proteases. Members of the
peptidases S8 and S35 clan include endopeptidases,
exopeptidases and also a tripeptidyl-peptidase. The S8
family has an Asp/His/Ser catalytic triad similar to
that found in trypsin-like proteases, but do not share
their three-dimensional structure and are not homologous
to trypsin. The S53 family contains a catalytic triad
Glu/Asp/Ser. The stability of these enzymes may be
enhanced by calcium, some members have been shown to
bind up to 4 ions via binding sites with different
affinity. Some members of this clan contain disulfide
bonds. These enzymes can be intra- and extracellular,
some function at extreme temperatures and pH values.
Length = 455
Score = 28.0 bits (63), Expect = 8.9
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 12/50 (24%)
Query: 298 GVVSAAEFIIYKLKEMGKISQEDIALVMEEFQDLDFDQSGTLSPSDLFLA 347
GV AE I+ KLK+ K + E ++D+ F Q +D+ LA
Sbjct: 100 GVAPEAELIVVKLKQAKKY-------LREFYEDVPFYQE-----TDIMLA 137
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 0.136 0.386
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,939,296
Number of extensions: 1756859
Number of successful extensions: 1821
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1815
Number of HSP's successfully gapped: 42
Length of query: 354
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 256
Effective length of database: 6,590,910
Effective search space: 1687272960
Effective search space used: 1687272960
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)