RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17993
(191 letters)
>gnl|CDD|185697 cd09020, D-hex-6-P-epi_like, D-hexose-6-phosphate epimerase-like.
D-Hexose-6-phosphate epimerase Ymr099c from
Saccharomyces cerevisiae belongs to the large
superfamily of aldose-1-epimerases. Its active site is
very similar to the catalytic site of galactose
mutarotase, the best studied member of the superfamily.
It also contains the conserved glutamate and histidine
residues that have been shown in galactose mutarotase to
be critical for catalysis, the glutamate serving as the
active site base to initiate the reaction by removing
the proton from the C-1 hydroxyl group of the sugar
substrate, and the histidine as the active site acid to
protonate the C-5 ring oxygen. In addition Ymr099c
contains 2 conserved arginine residues which are
involved in phosphate binding, and exhibits
hexose-6-phosphate mutarotase activity on glucose-6-P,
galactose-6-P and mannose-6-P.
Length = 269
Score = 175 bits (445), Expect = 5e-55
Identities = 60/170 (35%), Positives = 87/170 (51%), Gaps = 5/170 (2%)
Query: 23 IFPYFARFRLTYRLILREKELHFNIGVYNPSNDLAFNFNLLLHTYLKVPDVRRCQVNGLY 82
I+P+ F L + L L + V N + F+F LHTY +V D+ + +V GL
Sbjct: 104 IWPH--AFELRLTVTLGFDTLELELTVTNTGDK-PFSFTAALHTYFRVSDIEQVRVEGLE 160
Query: 83 GCHYIDKVLDNQLFRETRETVSVSSLTDRIYQNTCQEHVVTNVVSGRKMRLQKYNFPDTV 142
G Y+DK L +Q + V+ DR+Y NT + + GR++R++K P V
Sbjct: 161 GATYLDK-LTDQREKVQGGAVTFDGEVDRVYLNTPAPLTIDDPAWGRRIRIEKSGSPSAV 219
Query: 143 IWNPW-DTGRDMKDFGDDEYPNMICVEAGHVTSPVLLHPGTTFEASQILQ 191
+WNPW + M DF DD Y M+CVEA +V PV L PG + SQ +
Sbjct: 220 VWNPWIEKAARMADFPDDGYRRMVCVEAANVADPVTLAPGESHTLSQTIS 269
>gnl|CDD|223748 COG0676, COG0676, Uncharacterized enzymes related to aldose
1-epimerase [Carbohydrate transport and metabolism].
Length = 287
Score = 102 bits (256), Expect = 1e-26
Identities = 48/154 (31%), Positives = 67/154 (43%), Gaps = 10/154 (6%)
Query: 23 IFPYFARFRLTYRLILREKELHFNIGVYNPSNDLAFNFNLLLHTYLKVPDVRRCQVNGLY 82
P+ RLT+R + L + Y +F LHTY +V D+ + +V+GL
Sbjct: 123 DEPHDFTLRLTFRF---GETLELELESYG-----EESFQAALHTYFRVGDIEQVEVSGLG 174
Query: 83 GCHYIDKVLDNQLFRETRETVSVSSLTDRIYQNTCQEHVVTNVVSGRKMRLQKYNFPDTV 142
G IDKVL+ + V+ TDRIY N V+ + R + L+ TV
Sbjct: 175 G-VCIDKVLNAEEEVTQHGIVTFPGETDRIYLNPEPCSVIVDPALNRIITLEHQGHSSTV 233
Query: 143 IWNPWDTG-RDMKDFGDDEYPNMICVEAGHVTSP 175
+WNP M D DD Y M+CVE V
Sbjct: 234 VWNPGHAKSSSMADMPDDGYQTMLCVETARVGPD 267
>gnl|CDD|216397 pfam01263, Aldose_epim, Aldose 1-epimerase.
Length = 301
Score = 97.5 bits (243), Expect = 9e-25
Identities = 35/185 (18%), Positives = 60/185 (32%), Gaps = 20/185 (10%)
Query: 24 FPYFARFRLTYRLILREKELHFNIGVYNPSNDLAFNFNLLLHTYLKVP----DVRRCQVN 79
+P R+TY L ++ I ++ FNL H Y + D+ Q+
Sbjct: 120 YPGDLEVRVTYTL---NEDNELTIEYEATNDGKPTPFNLGNHPYFNLSGHTIDIHELQIE 176
Query: 80 GLYGCHYID---------KVLDNQL-FRETRETVSVSSLTDRIYQNTCQEHVVTNVVSGR 129
D V FR+ D +Y + V+ + G
Sbjct: 177 ADEYLEVDDDLIPTGEIKDVKGTPFDFRQPTPIGEDILGLDHVYVLDPLKAVIIDPDPGS 236
Query: 130 KMRLQKY-NFPDTVIWNPWD-TGRDMKDFGDDEYPNMICVEAGHVTSP-VLLHPGTTFEA 186
+ L+ P V++ P G+ + D G + E H P ++L PG ++ A
Sbjct: 237 GIVLEVSTTQPGLVVYTPNFLKGKYLSDEGFALETQFLPDEPNHPEFPSIILKPGESYTA 296
Query: 187 SQILQ 191
Sbjct: 297 ETSYS 301
>gnl|CDD|185702 cd09025, Aldose_epim_Slr1438, Aldose 1-epimerase, similar to
Synechocystis Slr1438. Proteins similar to
Synechocystis Slr1438 are uncharacterized members of
aldose-1-epimerase superfamily. Aldose 1-epimerases or
mutarotases are key enzymes of carbohydrate metabolism,
catalyzing the interconversion of the alpha- and
beta-anomers of hexose sugars such as glucose and
galactose. This interconversion is an important step
that allows anomer specific metabolic conversion of
sugars. Studies of the catalytic mechanism of the best
known member of the family, galactose mutarotase, have
shown a glutamate and a histidine residue to be critical
for catalysis; the glutamate serves as the active site
base to initiate the reaction by removing the proton
from the C-1 hydroxyl group of the sugar substrate, and
the histidine as the active site acid to protonate the
C-5 ring oxygen.
Length = 271
Score = 39.2 bits (92), Expect = 6e-04
Identities = 45/181 (24%), Positives = 66/181 (36%), Gaps = 44/181 (24%)
Query: 24 FPYFARFRLTYRLILREKELHFNIGVYNPSN-DLAFNFNLLLHTYLKVPDVRRCQVNGLY 82
+P+ LTYR L L V+N + + F+F H Y VPD + ++
Sbjct: 114 YPFDFELELTYR--LAGNTLEIAQRVHNLGDQPMPFSFG--FHPYFAVPDKAKLSLDLPP 169
Query: 83 GCHYIDKVLDNQL-----FRETRETVSVSSLTDRIYQNTCQEHVVTNVVSGRKMRLQKYN 137
D+ D + F ET E V + +T+ G K+ L
Sbjct: 170 T-RCFDQKTDEEANTPGQFDETEEGVDLLFRPL-------GPASLTDGARGLKITLDHDE 221
Query: 138 -FPDTVIWNPWDTGRDMKDFGDDEYPNMICVEAGHVTSP----------VLLHPGTTFEA 186
F + V+W D G+D +C+E T P +LL PG T EA
Sbjct: 222 PFSNLVVWT--DKGKD-----------FVCLEPW--TGPRNALNTGERLLLLPPGETEEA 266
Query: 187 S 187
S
Sbjct: 267 S 267
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 29.5 bits (66), Expect = 1.2
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 60 FNLLLHTYLKVPDVR---------RCQVNGLYGCHYIDKVLDNQLFRETRETVSVSSLTD 110
FN+LLH Y D+R R +V GL G +VL + TR ++ + D
Sbjct: 304 FNVLLHRYSGQTDIRVGVPIANRNRAEVEGLIGFFVNTQVLRSVFDGRTRVATLLAGVKD 363
>gnl|CDD|178666 PLN03119, PLN03119, putative ADP-ribosylation factor
GTPase-activating protein AGD14; Provisional.
Length = 648
Score = 29.0 bits (64), Expect = 1.6
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 138 FPDTVIWNPWDTGRDMKDFGDDEYPNMICVEAGHVTSPVL 177
FPD++ NP D+ R++ D + + H+ S VL
Sbjct: 473 FPDSIEANPLDSSRNIHQQVDGASTSSYNTDHQHLESQVL 512
>gnl|CDD|239758 cd04091, mtEFG1_II_like, mtEFG1_C: C-terminus of mitochondrial
Elongation factor G1 (mtEFG1)-like proteins found in
eukaryotes. Eukaryotic cells harbor 2 protein synthesis
systems: one localized in the cytoplasm, the other in
the mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. Eukaryotic EF-2 operates in the
cytosolic protein synthesis machinery of eukaryotes,
EF-Gs in protein synthesis in bacteria. Eukaryotic
mtEFG1 proteins show significant homology to bacterial
EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects and
a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 81
Score = 27.2 bits (61), Expect = 1.6
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 111 RIYQNTC-QEHVVTNVVSGRKMRLQK 135
RIYQ + + NV +G+K+R+ +
Sbjct: 20 RIYQGKLKKGDTIYNVRTGKKVRVPR 45
>gnl|CDD|241493 cd13339, PH-GRAM_MTMR13, Myotubularian (MTM) related 13 protein
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase activators and Myotubularins (PH-GRAM) domain.
MTMR13 (also called SBF2/SET binding factor 2) is a
catalytically inactive phosphatase that plays a role as
an adapter for the phosphatase myotubularin to regulate
myotubularintracellular location. It contains a Leu
residue instead of a conserved Cys residue in the
dsPTPase catalytic loop which renders it catalytically
inactive as a phosphatase. MTMR13 has high sequence
similarity to MTMR5 and has recently been shown to be a
second gene mutated in type 4B Charcot-Marie-Tooth
syndrome. Both MTMR5 and MTMR13 contain an N-terminal
DENN domain, a PH-GRAM domain, an inactive PTP domain, a
SET interaction domain, a coiled-coil domain, and a
C-terminal PH domain. Myotubularin-related proteins are
a subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 184
Score = 28.4 bits (63), Expect = 1.9
Identities = 13/52 (25%), Positives = 28/52 (53%)
Query: 91 LDNQLFRETRETVSVSSLTDRIYQNTCQEHVVTNVVSGRKMRLQKYNFPDTV 142
+ NQL + +E + ++S + ++ + E V VV K +L K+ +P ++
Sbjct: 109 IQNQLQQNMQEGLQITSASFQLIKVAFDEEVSPEVVEIFKKQLMKFRYPQSI 160
>gnl|CDD|114274 pfam05543, Peptidase_C47, Staphopain peptidase C47. Staphopains
are one of four major families of proteinases secreted
by the Gram-positive Staphylococcus aureus. These
staphylococcal cysteine proteases are secreted as
preproenzymes that are proteolytically cleaved to
generate the mature enzyme.
Length = 174
Score = 27.2 bits (60), Expect = 3.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 142 VIWNPWDTGRDMKD 155
+IWNPWD G +D
Sbjct: 138 IIWNPWDNGFMTQD 151
>gnl|CDD|226515 COG4028, COG4028, Predicted P-loop ATPase/GTPase [General function
prediction only].
Length = 271
Score = 27.5 bits (61), Expect = 3.9
Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 5/55 (9%)
Query: 26 YFARFRLTYRLILREKELHFNI-----GVYNPSNDLAFNFNLLLHTYLKVPDVRR 75
F + RL + H+ I +Y P F NL L+ D
Sbjct: 101 MFYNQTVLVRLSDLIRTTHYYIPENLADLYVPLRMEVFTRNLALNPEPLSVDKLE 155
>gnl|CDD|211380 cd10981, ZnPC_S1P1, Zinc dependent phospholipase C/S1-P1
nuclease. This model describes both the bacterial and
archeal zinc-dependent phospholipase C, a domain found
in the alpha toxin of Clostridium perfringens, as well
as S1/P1 nucleases, which predominantly act on
single-stranded DNA and RNA.
Length = 238
Score = 27.4 bits (61), Expect = 4.3
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 14/65 (21%)
Query: 31 RLTYRLILREKELHFNIGVYNPSNDLAFNFNLLLHTYL-------KVPDVRRCQVNGLYG 83
T+ I R+ V+ +LA ++ LL + PD RR +G
Sbjct: 2 FGTHHKIARD-------AVFTLPPELAEFWSDLLKRNIDELLEGAVAPDKRRYDDDGEAQ 54
Query: 84 CHYID 88
H +D
Sbjct: 55 NHVLD 59
>gnl|CDD|185695 cd01081, Aldose_epim, aldose 1-epimerase superfamily. Aldose
1-epimerases or mutarotases are key enzymes of
carbohydrate metabolism; they catalyze the
interconversion of the alpha- and beta-anomers of hexose
sugars such as glucose and galactose. This
interconversion is an important step that allows anomer
specific metabolic conversion of sugars. Studies of the
catalytic mechanism of the best known member of the
family, galactose mutarotase, have shown a glutamate and
a histidine residue to be critical for catalysis; the
glutamate serves as the active site base to initiate the
reaction by removing the proton from the C-1 hydroxyl
group of the sugar substrate and the histidine as the
active site acid to protonate the C-5 ring oxygen.
Length = 284
Score = 27.4 bits (61), Expect = 5.2
Identities = 19/159 (11%), Positives = 38/159 (23%), Gaps = 28/159 (17%)
Query: 24 FPYFARFRLTYRLILREKELHFNIGVYNPSNDLAFNFNLLLHTYLKVPDV---------- 73
+P+ +TY L L V N ++ F L H Y +P V
Sbjct: 109 YPFPLELTVTYTL--DADTLTITFTVTNLGDE-PMPFGLGWHPYFGLPGVAIEDLRLRVP 165
Query: 74 -RRCQVNGLYGCHYIDKVLDNQLFRETRETVSVSSLTDRIYQNTCQEHVVTNVVSGRKMR 132
+ + + + + L D + R
Sbjct: 166 ASKVLPLDDLLPPTGELEVPGEEDFRLGRPLGGGELDDCFLLLGNDAGTAEARLEDPDSR 225
Query: 133 L---QKYNFPDTVIWNPWDTGRDMKDFGDDEYPNMICVE 168
+ + +P ++ D + +E
Sbjct: 226 ISVEFETGWPFWQVYTG-----------DGGRRGSVAIE 253
>gnl|CDD|219164 pfam06761, IcmF-related, Intracellular multiplication and human
macrophage-killing. This family represents a conserved
region within several bacterial proteins that resemble
IcmF, which has been proposed to be involved in Vibrio
cholerae cell surface reorganisation, resulting in
increased adherence to epithelial cells and increased
conjugation frequency. Note that many family members are
hypothetical proteins.
Length = 305
Score = 27.3 bits (61), Expect = 5.4
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 91 LDNQLFRETRETVSVSSLTDRIYQN 115
D++L + R+ +S L +R+YQ
Sbjct: 135 PDDELVAQARQVLSQLPLAERVYQR 159
>gnl|CDD|131928 TIGR02882, QoxB, cytochrome aa3 quinol oxidase, subunit I. This
family (QoxB) encodes subunit I of the aa3-type quinone
oxidase, one of several bacterial terminal oxidases.
This complex couples oxidation of reduced quinones with
the reduction of molecular oxygen to water and the
pumping of protons to form a proton gradient utilized
for ATP production. aa3-type oxidases contain two heme a
cofactors as well as copper atoms in the active site
[Energy metabolism, Electron transport].
Length = 643
Score = 27.1 bits (60), Expect = 6.4
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 135 KYNFPDTVIWNPWDTGRDMKDFG 157
KYNF T N +D DMK G
Sbjct: 541 KYNFAVTPDVNDYDAFWDMKKHG 563
>gnl|CDD|211826 TIGR03497, FliI_clade2, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively [Cellular processes,
Chemotaxis and motility].
Length = 413
Score = 26.9 bits (60), Expect = 6.6
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 39 REKELHFNIGVY----NPSNDLAFNFNLLLHTYLK 69
+E E NIG Y NP D A + ++++LK
Sbjct: 359 KEAEDLINIGAYKRGSNPKIDEAIRYIEKINSFLK 393
>gnl|CDD|216268 pfam01055, Glyco_hydro_31, Glycosyl hydrolases family 31. Glycosyl
hydrolases are key enzymes of carbohydrate metabolism.
Family 31 comprises of enzymes that are, or similar to,
alpha- galactosidases.
Length = 436
Score = 26.8 bits (60), Expect = 8.3
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 122 VTNVVSGRKMRLQKYNFPDTVIWNPWDTGRDMKDF--GDDEYPNM 164
V VV ++ P VIW D +DF + +P+
Sbjct: 45 VREVVD----GFREAGIPLDVIWLDIDYMDGYRDFTWDPERFPDP 85
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 0.451
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,830,061
Number of extensions: 897665
Number of successful extensions: 797
Number of sequences better than 10.0: 1
Number of HSP's gapped: 785
Number of HSP's successfully gapped: 21
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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 (21.6 bits)
S2: 56 (25.3 bits)