RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7163
(544 letters)
>gnl|CDD|197257 cd09160, PLDc_SMU_988_like_2, Putative catalytic domain, repeat 2,
of Streptococcus mutans uncharacterized protein SMU_988
and similar proteins. Putative catalytic domain, repeat
2, of Streptococcus mutans uncharacterized protein
SMU_988 and similar proteins. Although SMU_988 and
similar proteins have not been functionally
characterized, members in this subfamily show high
sequence homology to bacterial cardiolipin (CL)
synthases, which catalyze the reversible phosphatidyl
group transfer between two phosphatidylglycerol
molecules to form CL and glycerol. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
may be part of the active site and may be involved in
phosphatidyl group transfer.
Length = 176
Score = 30.9 bits (71), Expect = 1.1
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 381 EQASWVCQCDASLVQQLESDFKLTLQ--QQNSLEEWAN--WLKNVVNAVLKPF 429
E ++ + ++ DF+ TL Q+ +LEE + ++ A+L+ F
Sbjct: 122 ECGVYMYDTPV--ISDIKEDFEETLAQSQEITLEECRKRSLVTRLIGAILRLF 172
>gnl|CDD|222802 PHA00497, pol, RNA-dependent RNA polymerase.
Length = 673
Score = 31.3 bits (71), Expect = 1.4
Identities = 17/67 (25%), Positives = 23/67 (34%), Gaps = 5/67 (7%)
Query: 74 QYGSEGH-TTAGQTNSNPSPQSGNHNFLGDGSNAIPDFPE--IDLSEDCLPEDCTIEDVD 130
+Y H TT D S+ F IDL D LPE ++
Sbjct: 321 RYAYTWHHTTREDKIEKVY--EWKFAEATDVSDHDTFFSGWLIDLICDELPEMFAPWWME 378
Query: 131 TFRSIYR 137
RS++R
Sbjct: 379 LARSLHR 385
>gnl|CDD|212128 cd11663, GH119_BcIgtZ-like, putative catalytic domain of glycoside
hydrolase family 119 (GH119). The prokaryotic subgroup
is represented by IgtZ, an alpha-amylase from a Bacillus
circulans strain. The GH119 family is related to GH57, a
chiefly prokaryotic family with the majority of
thermostable enzymes coming from extremophiles (many of
these are archaeal hyperthermophiles), which exhibit the
enzyme specificities of alpha-amylase (EC 3.2.1.1),
4-alpha-glucanotransferase (EC 2.4.1.25),
amylopullulanase (EC 3.2.1.1/41), and
alpha-galactosidase (EC 3.2.1.22). GH57s cleave
alpha-glycosidic bonds by employing a retaining
mechanism, which involves a glycosyl-enzyme
intermediate, allowing transglycosylation.
Length = 363
Score = 31.1 bits (70), Expect = 1.5
Identities = 27/108 (25%), Positives = 38/108 (35%), Gaps = 26/108 (24%)
Query: 348 NHLAQAARAV-LQNSTQINQMLTDLNRVDFHNVQEQASWVCQCDASLVQQLESDFKLT-- 404
NH ++ R L N + M++ NR D NV SWV Q + Q + + +
Sbjct: 167 NHFSRTLRDYPLLNDPGSDTMVSPPNRADLQNVSTVGSWVSQPMFNEQQVVRNKYPFAST 226
Query: 405 ---------------------LQQQNSLEEWANWLKNVVNAVLKPFEG 431
+ Q S EE + V LKPFEG
Sbjct: 227 PHWVRYVDPATGAESRVVGVPVAQAESWEE--GYQGQVTADALKPFEG 272
>gnl|CDD|130844 TIGR01784, T_den_put_tspse, conserved hypothetical protein
(putative transposase or invertase). Several lines of
evidence suggest that members of this family (loaded as
a fragment mode model to find part-length matches) are
associated with transposition, inversion, or
recombination. Members are found in small numbers of
genomes, but in large copy numbers in many of those
species, including over 30 full length and fragmentary
members in Treponema denticola. The strongest
similarities are usually within rather than between
species. PSI-BLAST shows similarity to proteins
designated as possible transposases, DNA invertases
(resolvases), and recombinases. In the oral pathogenic
spirochete Treponema denticola, full-length members are
often found near transporters or other membrane
proteins. This family includes members of the putative
transposase family pfam04754.
Length = 270
Score = 30.8 bits (70), Expect = 1.7
Identities = 20/66 (30%), Positives = 24/66 (36%), Gaps = 12/66 (18%)
Query: 435 FTKAARQFL---LKWSFYSSMVIRDLTLRSAASFGSFHL----IRLLY----DEYMFYLI 483
F FL L + I+ L L S SF +L L E + Y I
Sbjct: 10 FGDENEDFLIIFLNAVLGELLDIKTLELSSQ-SFVEENLEDKFSDLDILATDSEGLHYNI 68
Query: 484 EHQVAL 489
EHQVA
Sbjct: 69 EHQVAP 74
>gnl|CDD|239780 cd04247, AAK_AK-Hom3, AAK_AK-Hom3: Amino Acid Kinase Superfamily
(AAK), AK-Hom3; this CD includes the N-terminal
catalytic domain of the aspartokinase HOM3, a
monofunctional class enzyme found in Saccharomyces
cerevisiae and other related AK domains. Aspartokinase,
the first enzyme in the aspartate metabolic pathway,
catalyzes the conversion of aspartate and ATP to
aspartylphosphate and ADP, and in fungi, is responsible
for the production of threonine, isoleucine and
methionine. S. cerevisiae has a single aspartokinase
isoenzyme type, which is regulated by feedback,
allosteric inhibition by L-threonine. Recent studies
show that the allosteric transition triggered by binding
of threonine to AK involves a large change in the
conformation of the native hexameric enzyme that is
converted to an inactive one of different shape and
substantially smaller hydrodynamic size.
Length = 306
Score = 30.1 bits (68), Expect = 2.5
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 13/61 (21%)
Query: 257 KSKLFCLSKCVPVQAFVRRVDFLFYQNLVEVL----------IPDV---LRPIPGSLTSS 303
++ LS V + + +D FY L +VL +P V +PG L S
Sbjct: 150 DAEYVDLSHIVDLDFSIEALDQTFYDELAQVLGEKITACENRVPVVTGFFGNVPGGLLSQ 209
Query: 304 I 304
I
Sbjct: 210 I 210
>gnl|CDD|240459 cd12879, SPRY3_RyR, SPRY domain 3 (SPRY3) of ryanodine receptor
(RyR). This SPRY domain (SPRY3) is the third of three
structural repeats in all three isoforms of the
ryanodine receptor (RyR), which are the major Ca2+
release channels in the membranes of sarcoplasmic
reticulum (SR). There are three RyR genes in mammals;
the skeletal RyR1, the cardiac RyR2 and the brain RyR3.
The three SPRY domains are located in the N-terminal
part of the cytoplasmic region of the RyRs, but no
specific function has been found for this third SPRY
domain of the RyRs.
Length = 151
Score = 29.2 bits (66), Expect = 3.0
Identities = 19/93 (20%), Positives = 30/93 (32%), Gaps = 19/93 (20%)
Query: 3 SKYHYYGIRVKPDSPLNNIPLSDENGG--NSKYHYYGIRVKPDSPLN-NIPLSDENGSPR 59
+Y YY +R+ P N+ + G +H Y N + DENG
Sbjct: 13 DEY-YYSVRIFPGQDPANVWV-----GWVTPDFHLYDPSFDDSKVRNVTVTKGDENG--- 63
Query: 60 GKKYKLVKTDSNSNQY---GSEGHTTAGQTNSN 89
+ ++ N Y E GQ +
Sbjct: 64 ----NVYESIKRQNCYMVCAGELLAEVGQDSGG 92
>gnl|CDD|240345 PTZ00287, PTZ00287, 6-phosphofructokinase; Provisional.
Length = 1419
Score = 30.4 bits (68), Expect = 3.4
Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 3/92 (3%)
Query: 52 SDENGSPRGKKYKLVKTDSNSNQYGSEGHTTAGQTNSNPSPQSGNHNFLGDGSNAIPDFP 111
S E + ++ S G +A ++ SGN LG +
Sbjct: 670 SSETSGAKQMDLSGSDDNNQSKG-NELGAVSATYNGTHEKSLSGNTTLLGTAYSGNGAGK 728
Query: 112 EIDLSEDCLPEDCTIEDVDTFRSIYREHCEAF 143
I + + E V+ Y +HC ++
Sbjct: 729 NILNPDSNSEDVLNSEPVN--NGFYEQHCSSY 758
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 30.0 bits (67), Expect = 3.4
Identities = 20/97 (20%), Positives = 45/97 (46%), Gaps = 11/97 (11%)
Query: 192 VPVQAFVRRVDFLFYQNLVEVLIPDAFLDAIVTLDFSTIES-----LWREFWRSQDNNNG 246
+P+ +++R + N+ ++ DAF + + F I + L+RE ++
Sbjct: 141 IPIVKYIKR---MLMSNIPTLITTDAFKKTVFEILFDIISTNDNVYLYREGYKV---TIL 194
Query: 247 DECEEEKYLSKSKLFCLSKCVPVQAFVRRVDFLFYQN 283
+ E Y+++ +L C+ C+ +Q ++ L Y N
Sbjct: 195 LKWLEYNYITEEQLLCILSCIDIQNLDKKSRLLLYSN 231
>gnl|CDD|173155 PRK14692, PRK14692, lagellar hook-associated protein FlgL;
Provisional.
Length = 749
Score = 29.9 bits (67), Expect = 4.4
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 69 DSNSNQYGSEGHTTAGQTNSNPSPQSGNHNFLGDGSNAIP-DFPEIDLSED 118
DS S Q+ + TT + P NF +N++ D P +D+ +D
Sbjct: 592 DSQSGQFPAPPFTTTSTVQNGP-------NFSFSANNSLTIDEPNVDIIKD 635
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 28.8 bits (65), Expect = 4.7
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 9/64 (14%)
Query: 108 PDFPEIDLSEDCLPEDCTIEDVDTF-RSIYREHCEAFL---DAIVTL----DFSTIESLW 159
PEI + D PE VDT R R + A + + I + ST+E +
Sbjct: 33 RVLPEITIPADVTPERVPTTIVDTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERI- 91
Query: 160 REFW 163
R W
Sbjct: 92 RTKW 95
>gnl|CDD|240106 cd04758, Commd10, COMM_Domain containing protein 10. The COMM
Domain is found at the C-terminus of a variety of
proteins; presumably all COMM_Domain containing proteins
are located in the nucleus and the COMM domain plays a
role in protein-protein interactions. Several family
members have been shown to bind and inhibit NF-kappaB.
Length = 186
Score = 28.9 bits (65), Expect = 5.1
Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 8/97 (8%)
Query: 335 GAFAQMLRRYTSLNHLAQAARAVLQNSTQINQMLTDLNRVDFHNVQE-------QASWVC 387
F ++L R HL +A R+ + + Q L D + E QA++
Sbjct: 14 EKFPRLLSRLFQKLHL-KAERSFSEEEEEKLQEAFKLLSQDLKLLLETISFILEQAAYHN 72
Query: 388 QCDASLVQQLESDFKLTLQQQNSLEEWANWLKNVVNA 424
++L QQL + L + + W ++V+
Sbjct: 73 LKPSNLQQQLRNILLLEDKASAFVNAWEAEGEDVLEK 109
>gnl|CDD|206015 pfam13844, Glyco_transf_41, Glycosyl transferase family 41. This
family of glycosyltransferases includes O-linked
beta-N-acetylglucosamine (O-GlcNAc) transferase, an
enzyme which catalyzes the addition of O-GlcNAc to
serine and threonine residues. In addition to its
function as an O-GlcNAc transferase, human OGT, also
appears to proteolytically cleave the epigenetic
cell-cycle regulator HCF-1.
Length = 468
Score = 29.4 bits (66), Expect = 5.4
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 410 SLEEWANWLKNVVNAVLK----PFEGKPNFTKAARQ 441
+L+ W N LK V N+VL P G+ N A++
Sbjct: 301 TLQMWVNILKRVPNSVLWLLRFPAVGEANIQAYAQE 336
>gnl|CDD|239867 cd04402, RhoGAP_ARHGAP20, RhoGAP_ARHGAP20: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391
and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain,
and ANXL repeats. ArhGAP20 is activated by Rap1 and
induces inactivation of Rho, which in turn leads to
neurite outgrowth. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 192
Score = 28.4 bits (64), Expect = 6.6
Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 18/89 (20%)
Query: 284 LVEVLIPDVLRPIPGSLTSSIRNFAKGVESWLTNAMQGCPQEMINIKVTAVGAFAQMLRR 343
L+ ++ D LR IPGSL SS + E W++ Q +E K+ + L R
Sbjct: 68 LLASVLKDFLRNIPGSLLSS-DLY----EEWMSALDQENEEE----KIAELQRLLDKLPR 118
Query: 344 --YTSLNHLAQAARAVLQN---STQINQM 367
L HL VL N +++ N+M
Sbjct: 119 PNVLLLKHLI----CVLHNISQNSETNKM 143
>gnl|CDD|200453 cd11314, AmyAc_arch_bac_plant_AmyA, Alpha amylase catalytic domain
found in archaeal, bacterial, and plant Alpha-amylases
(also called 1,4-alpha-D-glucan-4-glucanohydrolase).
AmyA (EC 3.2.1.1) catalyzes the hydrolysis of
alpha-(1,4) glycosidic linkages of glycogen, starch,
related polysaccharides, and some oligosaccharides. This
group includes AmyA from bacteria, archaea, water fleas,
and plants. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 302
Score = 28.7 bits (65), Expect = 8.7
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 408 QNSLEEWANWLKNVVN 423
QN L+ W NWLKN +
Sbjct: 115 QNDLKAWLNWLKNDIG 130
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
0.318 0.134 0.403
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,694,710
Number of extensions: 2651730
Number of successful extensions: 2105
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2103
Number of HSP's successfully gapped: 20
Length of query: 544
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 442
Effective length of database: 6,413,494
Effective search space: 2834764348
Effective search space used: 2834764348
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 (21.7 bits)
S2: 61 (27.5 bits)