RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5981
(131 letters)
>gnl|CDD|100087 cd03085, PGM1, Phosphoglucomutase 1 (PGM1) catalyzes the
bidirectional interconversion of glucose-1-phosphate
(G-1-P) and glucose-6-phosphate (G-6-P) via a glucose
1,6-diphosphate intermediate, an important metabolic
step in prokaryotes and eukaryotes. In one direction,
G-1-P produced from sucrose catabolism is converted to
G-6-P, the first intermediate in glycolysis. In the
other direction, conversion of G-6-P to G-1-P generates
a substrate for synthesis of UDP-glucose which is
required for synthesis of a variety of cellular
constituents including cell wall polymers and
glycoproteins. The PGM1 family also includes a
non-enzymatic PGM-related protein (PGM-RP) thought to
play a structural role in eukaryotes, as well as
pp63/parafusin, a phosphoglycoprotein that plays an
important role in calcium-regulated exocytosis in
ciliated protozoans. PGM1 belongs to the
alpha-D-phosphohexomutase superfamily which includes
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Other members of this superfamily include
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 548
Score = 185 bits (472), Expect = 2e-57
Identities = 72/115 (62%), Positives = 86/115 (74%), Gaps = 2/115 (1%)
Query: 6 VTVETKVFDGQKPGTSGLRKPTKTFQQEHYTENFIQSILTALGD-KLKGSVLVVGGDGRY 64
TV TK ++GQKPGTSGLRK K FQQ +Y ENF+QSI AL KLKG+ LVVGGDGRY
Sbjct: 1 QTVPTKPYEGQKPGTSGLRKKVKVFQQPNYLENFVQSIFNALPPEKLKGATLVVGGDGRY 60
Query: 65 FGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALIRK-HILGRLVKVPSSNP 118
+ A+ IIKI+AANGV K++VGQNG+LSTPAVSA+IRK G ++ S NP
Sbjct: 61 YNKEAIQIIIKIAAANGVGKVVVGQNGLLSTPAVSAVIRKRKATGGIILTASHNP 115
>gnl|CDD|177942 PLN02307, PLN02307, phosphoglucomutase.
Length = 579
Score = 160 bits (406), Expect = 2e-47
Identities = 68/123 (55%), Positives = 86/123 (69%), Gaps = 5/123 (4%)
Query: 1 MSFKSVTVETKVFDGQKPGTSGLRKPTKTFQQEHYTENFIQSILTAL-GDKLKGSVLVVG 59
SFK +V TK +GQKPGTSGLRK K F QE+Y NF+Q++ AL +K+KG+ LV+G
Sbjct: 8 ASFKVSSVPTKPIEGQKPGTSGLRKKVKVFMQENYLANFVQALFNALPAEKVKGATLVLG 67
Query: 60 GDGRYFGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALIRKHIL----GRLVKVPS 115
GDGRYF A+ IIKI+AANGV ++ VGQNG+LSTPAVSA+IR+ G + S
Sbjct: 68 GDGRYFNKEAIQIIIKIAAANGVRRVWVGQNGLLSTPAVSAVIRERDGSKANGGFILTAS 127
Query: 116 SNP 118
NP
Sbjct: 128 HNP 130
>gnl|CDD|223111 COG0033, Pgm, Phosphoglucomutase [Carbohydrate transport and
metabolism].
Length = 524
Score = 126 bits (319), Expect = 3e-35
Identities = 40/127 (31%), Positives = 54/127 (42%), Gaps = 7/127 (5%)
Query: 1 MSFKSVTVETKVFDGQKPGTSGLRKPTKTFQ-QEHYTENFIQSILTALGDKLKGSVLVVG 59
+ T + K GTSG R F E++ FIQ+I + G LVVG
Sbjct: 1 QYYMIKPDPTNPYQDVKFGTSGHRGSALVFTFNENHILAFIQAIADYRAEGGIGGPLVVG 60
Query: 60 GDGRYFGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALIRKHIL------GRLVKV 113
GD + A+ +++ AANGV ++ GQ G TPA S I H +V
Sbjct: 61 GDTHALSEPAIQSALEVLAANGVEVIVQGQGGFTPTPAASHAILTHNGKYKALADGIVLT 120
Query: 114 PSSNPSR 120
PS NP
Sbjct: 121 PSHNPPE 127
>gnl|CDD|236050 PRK07564, PRK07564, phosphoglucomutase; Validated.
Length = 543
Score = 123 bits (312), Expect = 3e-34
Identities = 37/103 (35%), Positives = 51/103 (49%), Gaps = 7/103 (6%)
Query: 7 TVETKVFDGQKPGTSGLRKPTKTFQQEHYTENFIQSILTALGD--KLKGSV--LVVGGDG 62
T F K GTSG R + Q + EN I +I A+ + +G L VGGD
Sbjct: 29 PDPTNPFQDVKFGTSGHRGSS---LQPSFNENHILAIFQAICEYRGKQGITGPLFVGGDT 85
Query: 63 RYFGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALIRKH 105
+ A+ +++ AANGV +IVG+ G TPAVS I K+
Sbjct: 86 HALSEPAIQSALEVLAANGVGVVIVGRGGYTPTPAVSHAILKY 128
>gnl|CDD|217263 pfam02878, PGM_PMM_I, Phosphoglucomutase/phosphomannomutase,
alpha/beta/alpha domain I.
Length = 138
Score = 74.2 bits (183), Expect = 5e-18
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 15 GQKPGTSGLRKPTKTFQ-QEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKI 73
Q GTSG+R + + Q+I + L K G +VVG D RY +
Sbjct: 1 RQLFGTSGIRGKVGVGELTPEFALKLGQAIASYLRAKAGGGKVVVGRDTRYSSRELARAL 60
Query: 74 IKISAANGVAKLIVGQNGILSTPAVSALIRKH 105
AANGV +++ G+L TPA+S RK
Sbjct: 61 AAGLAANGVEVILL---GLLPTPALSFATRKL 89
>gnl|CDD|234431 TIGR03990, Arch_GlmM, phosphoglucosamine mutase. The MMP1680
protein from Methanococcus maripaludis has been
characterized as the archaeal protein responsible for
the second step of UDP-GlcNAc biosynthesis. This GlmM
protein catalyzes the conversion of
glucosamine-6-phosphate to glucosamine-1-phosphate. The
first-characterized bacterial GlmM protein is modeled by
TIGR01455. These two families are members of the larger
phosphoglucomutase/phosphomannomutase family
(characterized by three domains: pfam02878, pfam02879
and pfam02880), but are not nearest neighbors to each
other. This model also includes a number of sequences
from non-archaea in the Bacteroides, Chlorobi,
Chloroflexi, Planctomycetes and Spirochaetes lineages.
Evidence supporting their inclusion in this equivalog as
having the same activity comes from genomic context and
phylogenetic profiling. A large number of these
organisms are known to produce exo-polysaccharide and
yet only appeared to contain the GlmS enzyme of the
GlmSMU pathway for UDP-GlcNAc biosynthesis
(GenProp0750). In some organisms including Leptospira,
this archaeal GlmM is found adjacent to the GlmS as well
as a putative GlmU non-orthologous homolog. Phylogenetic
profiling of the GlmS-only pattern using PPP identifies
members of this archaeal GlmM family as the
highest-scoring result [Central intermediary metabolism,
Amino sugars].
Length = 443
Score = 40.2 bits (95), Expect = 1e-04
Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 7/87 (8%)
Query: 19 GTSGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKIIKISA 78
GTSG+R E T + A G L+G +VVG D R G + + +I
Sbjct: 5 GTSGIRGIV----GEELTPELALKVGKAFGTYLRGGKVVVGRDTRTSGPMLENAVIAGLL 60
Query: 79 ANGVAKLIVGQNGILSTPAVSALIRKH 105
+ G V GI TP + +R+
Sbjct: 61 STGCD---VVDLGIAPTPTLQYAVREL 84
>gnl|CDD|224034 COG1109, {ManB}, Phosphomannomutase [Carbohydrate transport and
metabolism].
Length = 464
Score = 36.9 bits (86), Expect = 0.001
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 18/94 (19%)
Query: 19 GTSGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVL---VVGGDGRYFGDV---AVDK 72
GT G+R E T F + ALG L+ VVG D R ++ A+
Sbjct: 11 GTDGIRGVAG----EELTPEFALKLGRALGSVLRKKGAPKVVVGRDTRLSSEMLAAALAA 66
Query: 73 IIKISAANGV-AKLIVGQNGILSTPAVSALIRKH 105
+ + G+ + G++ TPAV+ RK
Sbjct: 67 GL---TSAGIDVYDL----GLVPTPAVAFATRKL 93
>gnl|CDD|100089 cd03087, PGM_like1, This archaeal PGM-like
(phosphoglucomutase-like) protein of unknown function
belongs to the alpha-D-phosphohexomutase superfamily
which includes several related enzymes that catalyze a
reversible intramolecular phosphoryl transfer on their
sugar substrates. The alpha-D-phosphohexomutases include
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Members of this superfamily include the
phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 439
Score = 36.4 bits (85), Expect = 0.002
Identities = 31/102 (30%), Positives = 44/102 (43%), Gaps = 9/102 (8%)
Query: 19 GTSGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKIIK-IS 77
GTSG+R E T + ALG L G +VVG D R G + + +I +
Sbjct: 3 GTSGIRGVV----GEELTPELALKVGKALGTYLGGGTVVVGRDTRTSGPMLKNAVIAGLL 58
Query: 78 AANGVAKLIVGQNGILSTPAVSALIRKHILGRLVKVPSSNPS 119
+A I GI+ TPA+ +RK ++ S NP
Sbjct: 59 SAGCDVIDI----GIVPTPALQYAVRKLGDAGVMITASHNPP 96
>gnl|CDD|188111 TIGR01132, pgm, phosphoglucomutase, alpha-D-glucose
phosphate-specific. This enzyme interconverts
alpha-D-glucose-1-P and alpha-D-glucose-6-P [Energy
metabolism, Sugars].
Length = 544
Score = 33.7 bits (77), Expect = 0.016
Identities = 34/112 (30%), Positives = 49/112 (43%), Gaps = 17/112 (15%)
Query: 19 GTSGLRKP--TKTFQQEHYTENFIQSILTALGD-KLKGSV---LVVGGDGRYFGDVAVDK 72
GTSG R TF + H I +I A+ + + + L +G D + A
Sbjct: 43 GTSGHRGSALRGTFNEPH-----ILAIAQAIAEYRAAQGITGPLYIGKDTHALSEPAFIS 97
Query: 73 IIKISAANGVAKLIVGQNGILSTPAVSALIRKHILGR------LVKVPSSNP 118
++++ AANGV ++ NG TPAVS I H +V PS NP
Sbjct: 98 VLEVLAANGVEVIVQENNGFTPTPAVSHAILTHNKKGEPLADGIVITPSHNP 149
>gnl|CDD|100096 cd05803, PGM_like4, This PGM-like (phosphoglucomutase-like) domain
is located C-terminal to a mannose-1-phosphate
guanyltransferase domain in a protein of unknown
function that is found in both prokaryotes and
eukaryotes. This domain belongs to the
alpha-D-phosphohexomutase superfamily which includes
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Members of this superfamily include the
phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 445
Score = 33.1 bits (76), Expect = 0.026
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 3/85 (3%)
Query: 21 SGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKIIKISAAN 80
SG+R ++ + T ++ KG +VVG DGR G + +I A
Sbjct: 5 SGIRGIVGEGLTPEVITRYVAAFATWQPERTKGGKIVVGRDGRPSGPMLEKIVIGALLAC 64
Query: 81 GVAKLIVGQNGILSTPAVSALIRKH 105
G V GI TP V L+R+
Sbjct: 65 GCD---VIDLGIAPTPTVQVLVRQS 86
>gnl|CDD|100094 cd05801, PGM_like3, This bacterial PGM-like
(phosphoglucomutase-like) protein of unknown function
belongs to the alpha-D-phosphohexomutase superfamily.
The alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Other
members of this superfamily include phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 522
Score = 30.7 bits (70), Expect = 0.18
Identities = 35/113 (30%), Positives = 50/113 (44%), Gaps = 18/113 (15%)
Query: 19 GTSGLRKP--TKTFQQEHYTENFIQSILTALGD--KLKG--SVLVVGGDGRYFGDVAVDK 72
GTSG R +F + H I +I A+ D K +G L +G D + A
Sbjct: 24 GTSGHRGSSLKGSFNEAH-----ILAISQAICDYRKSQGITGPLFLGKDTHALSEPAFIS 78
Query: 73 IIKISAANGVAKLIVGQNGILSTPAVSALIRKHILGR-------LVKVPSSNP 118
+++ AANGV +I +G TP +S I + GR +V PS NP
Sbjct: 79 ALEVLAANGVEVIIQQNDGYTPTPVISHAILTYNRGRTEGLADGIVITPSHNP 131
>gnl|CDD|184619 PRK14322, glmM, phosphoglucosamine mutase; Provisional.
Length = 429
Score = 29.6 bits (66), Expect = 0.51
Identities = 32/100 (32%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 19 GTSGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKIIKISA 78
GT G+R E T+ + ALG+ + ++VG D R GD I
Sbjct: 7 GTDGIRG----VFGETLTDELAFKVGKALGEIVGEGKVIVGKDTRVSGDSLEAAISAGLT 62
Query: 79 ANGVAKLIVGQNGILSTPAVSALIRKHILGRLVKVPSSNP 118
+ GV L+ G IL TPAV+ L R +V S NP
Sbjct: 63 SMGVDVLLCG---ILPTPAVALLTRITRSFGVVISASHNP 99
>gnl|CDD|238848 cd01715, ETF_alpha, The electron transfer flavoprotein (ETF) serves
as a specific electron acceptor for various
mitochondrial dehydrogenases. ETF transfers electrons to
the main respiratory chain via ETF-ubiquinone
oxidoreductase. ETF is an heterodimer that consists of
an alpha and a beta subunit which binds one molecule of
FAD per dimer . A similar system also exists in some
bacteria. The homologous pair of proteins (FixA/FixB)
are essential for nitrogen fixation. The alpha subunit
of ETF is structurally related to the bacterial nitrogen
fixation protein fixB which could play a role in a redox
process and feed electrons to ferredoxin.
Length = 168
Score = 28.7 bits (65), Expect = 0.70
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 19/76 (25%)
Query: 44 LTALGDKLKGSV-LVVGGDGRYFGDVAVDKIIKISAANGVAKLIVGQNGILS-------T 95
KL G V +V G G + + A G K++V ++ L+
Sbjct: 20 AVTAARKLGGEVTALVIGSG-------AEAVAAALKAYGADKVLVAEDPALAHYLAEPYA 72
Query: 96 PAVSALIRK----HIL 107
PA+ AL +K HIL
Sbjct: 73 PALVALAKKEKPSHIL 88
>gnl|CDD|131393 TIGR02340, chap_CCT_alpha, T-complex protein 1, alpha subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
alpha chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 536
Score = 27.8 bits (62), Expect = 1.9
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 37 ENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKI--IKISAANGVAKLIVGQNGILS 94
E I T++ K+ +G D +F ++ VD + +K + NG K + IL
Sbjct: 142 EALINVAKTSMSSKI------IGLDSDFFSNIVVDAVLAVKTTNENGEIKYPIKAVNILK 195
Query: 95 TPAVSAL 101
SA
Sbjct: 196 AHGKSAR 202
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 27.7 bits (62), Expect = 2.1
Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 15/77 (19%)
Query: 39 FIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKIIKISAANGVAKLIVGQNGILSTPAV 98
F S+ +LKG +VVGG G V AA+ A+ G+ S A+
Sbjct: 11 FYASVEERDNPELKGKPVVVGGGAPR-GVV--------LAASYEARA----FGVRS--AM 55
Query: 99 SALIRKHILGRLVKVPS 115
+ R + P
Sbjct: 56 PLFEALKLCPRAIVAPP 72
>gnl|CDD|239451 cd03335, TCP1_alpha, TCP-1 (CTT or eukaryotic type II) chaperonin
family, alpha subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 527
Score = 27.6 bits (62), Expect = 2.2
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 36 TENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKI--IKISAANGVAKLIVGQNGIL 93
E+ I T++ K+ +G D +F ++ VD I +K + G K + IL
Sbjct: 137 KESLINVAKTSMSSKI------IGADSDFFANMVVDAILAVKTTNEKGKTKYPIKAVNIL 190
Query: 94 STPAVSA 100
SA
Sbjct: 191 KAHGKSA 197
>gnl|CDD|163520 TIGR03808, RR_plus_rpt_1, twin-arg-translocated uncharacterized
repeat protein. Members of this protein family have a
Sec-independent twin-arginine tranlocation (TAT) signal
sequence, which enables tranfer of proteins folded
around prosthetic groups to cross the plasma membrane.
These proteins have four copies of a repeat of about 23
amino acids that resembles the beta-helix repeat.
Beta-helix refers to a structural motif in which
successive beta strands wind around to stack parallel in
a right-handed helix, as in AlgG and related enzymes of
carbohydrate metabolism. The twin-arginine motif
suggests that members of this protein family bind some
unknown cofactor.
Length = 455
Score = 27.5 bits (61), Expect = 2.6
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 57 VVGGDGRYFGDVAV-DKIIK-------ISAANGVAKLIVGQNGILSTP 96
+V G G+Y DVA+ +I+ +S +G +V N I TP
Sbjct: 372 IVAGWGKYLRDVAISGNVIRNAFVGIGVSVVDGAGTALVNNNVISETP 419
>gnl|CDD|163144 TIGR03123, one_C_unchar_1, probable H4MPT-linked C1 transfer
pathway protein. This protein family was identified, by
the method of partial phylogenetic profiling, as related
to the use of tetrahydromethanopterin (H4MPT) as a C-1
carrier. Characteristic markers of the H4MPT-linked C1
transfer pathway include formylmethanofuran
dehydrogenase subunits, methenyltetrahydromethanopterin
cyclohydrolase, etc. Tetrahydromethanopterin, a
tetrahydrofolate analog, occurs in methanogenic archaea,
bacterial methanotrophs, planctomycetes, and a few other
lineages [Central intermediary metabolism, One-carbon
metabolism].
Length = 318
Score = 27.3 bits (61), Expect = 2.7
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 40 IQSILTALGDKLKGSVLVVGGDGRYF-GDVAVDKIIKISAANGVA 83
++ IL A+ V V DG + + A+ + ++AAN +A
Sbjct: 74 VEFILAAVESAFGSPVSVFASDGGFVSAEEALTNPLDVAAANWLA 118
>gnl|CDD|223662 COG0589, UspA, Universal stress protein UspA and related
nucleotide-binding proteins [Signal transduction
mechanisms].
Length = 154
Score = 26.8 bits (59), Expect = 2.9
Identities = 13/69 (18%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 65 FGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALIRKHILGRLVKVPSSNPSRTIR- 123
G + ++I++++ ++VG G + + +LG S + +R
Sbjct: 97 EGSPSAEEILELAEEEDADLIVVGSRGRSG-------LSRLLLG-------SVAEKVLRH 142
Query: 124 -PCPLLITK 131
PCP+L+ +
Sbjct: 143 APCPVLVVR 151
>gnl|CDD|102357 PRK06395, PRK06395, phosphoribosylamine--glycine ligase;
Provisional.
Length = 435
Score = 27.2 bits (60), Expect = 2.9
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 71 DKIIKISAANGVAKLIVGQNGILSTPAVSALIRKHI 106
D I + N V + VG + +L+TP V+ L+++ I
Sbjct: 55 DLIEDFALKNNVDIVFVGPDPVLATPLVNNLLKRGI 90
>gnl|CDD|172797 PRK14321, glmM, phosphoglucosamine mutase; Provisional.
Length = 449
Score = 26.7 bits (59), Expect = 4.1
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 15 GQKPGTSGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKII 74
G+ GTSG+R+ E T + ALG L G +VVG D R ++ + +I
Sbjct: 2 GKYFGTSGIREVV----NEKLTPELALKVGLALGTYLGGGKVVVGKDTRTSSEMLKNALI 57
Query: 75 KISAANGVAKLIVG 88
+ GV + +G
Sbjct: 58 SGLLSTGVDVIDIG 71
>gnl|CDD|215177 PLN02311, PLN02311, chalcone isomerase.
Length = 271
Score = 26.5 bits (58), Expect = 4.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 64 YFGDVAVDKIIKISAANGVAKLIV 87
+FGD V +K S ANG+A +
Sbjct: 248 FFGDSPVSPSLKASVANGLATTLK 271
>gnl|CDD|220422 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members
of this family include various bacterial predicted ABC
class ATPases.
Length = 447
Score = 26.4 bits (59), Expect = 4.6
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 54 SVLVVGGDGRYFGDVAVDKII-----KISAANGVAKLIVGQNG 91
++LVVGG G Y DVA D +I + AK I +
Sbjct: 390 TILVVGGSGDYL-DVA-DTVIQMDDYRPKDVTEEAKEIAEELP 430
>gnl|CDD|184641 PRK14352, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 482
Score = 26.4 bits (59), Expect = 5.3
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 40 IQSILTALGDKLKGSVLVVGGD 61
+Q L AL G+V+V GD
Sbjct: 87 VQCALEALPADFDGTVVVTAGD 108
>gnl|CDD|220979 pfam11101, DUF2884, Protein of unknown function (DUF2884). Some
members in this bacterial family of proteins are
annotated as YggN which currently has no known function.
Length = 228
Score = 26.1 bits (58), Expect = 5.9
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 31 QQEHYTENFIQSILTALGDKLKGSVLVVGGDGR 63
E + I SIL ALG ++ S G
Sbjct: 139 AIEQLVQQSIGSILIALGSEMMSS----EGGNN 167
>gnl|CDD|151062 pfam10502, Peptidase_S26, Signal peptidase, peptidase S26. This is
a family of membrane signal serine endopeptidases which
function in the processing of newly-synthesised secreted
proteins. Peptidase S26 removes the hydrophobic,
N-terminal, signal peptides as proteins are translocated
across membranes. The active site residues take the form
of a catalytic dyad that is Ser, Lys in subfamily S26A;
the Ser is the nucleophile in catalysis, and the Lys is
the general base.
Length = 138
Score = 25.7 bits (57), Expect = 6.3
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 61 DGRYFGDVAVDKII 74
D RYFG V II
Sbjct: 117 DSRYFGPVPASAII 130
>gnl|CDD|188239 TIGR02650, RNase_Z_T_toga, ribonuclease Z, Thermotoga type.
Members of this protein family are ribonuclease Z as
found in the genus Thermotoga, where the enzyme cleaves
after the CCA, in contrast to the activities
characterized for other enzymes also designated
ribonuclease Z. In other systems, cleavage occurs
5-prime to the location of the CCA sequence, and CCA is
added subsequently. A species may lack ribonuclease Z if
all tRNA genes encode the CCA sequence, or if the CCA is
exposed by exonuclease activity rather than endonuclease
activity. Note that members of this sequence family
differ considerably from the majority of RNase Z
sequences [Transcription, RNA processing].
Length = 277
Score = 26.1 bits (57), Expect = 7.0
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 14/84 (16%)
Query: 36 TENFIQSILTALGDKL-------KGSVLVV-------GGDGRYFGDVAVDKIIKISAANG 81
TE + + ILT GD L +G+ L++ D RY A+D++++ A G
Sbjct: 176 TEEYHKKILTISGDSLALDPEEIEGTELLIHECTFLDARDRRYKNHAAIDEVMESVKAAG 235
Query: 82 VAKLIVGQNGILSTPAVSALIRKH 105
V K+I+ + ++I+K+
Sbjct: 236 VKKVILYHISTRYIRQIKSVIKKY 259
>gnl|CDD|237103 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
Length = 426
Score = 26.0 bits (58), Expect = 7.1
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 46 ALGDKLKGS--VLVVGGDGRYFGDVAVDKIIKIS 77
A GDK+ G+ VL G RY G + V K +K
Sbjct: 350 AYGDKVIGTNHVLPTSGAARYTGGLWVGKFLKTV 383
>gnl|CDD|131641 TIGR02592, cas_Cas5h, CRISPR-associated protein Cas5, subtype
I-B/HMARI. This is a CRISPR-associated protein unique
to the hmari subtype of cas genes and CRISPR repeat,
which is the only subtype present in Haloarcula
marismortui ATCC 43049. The hmari type, though uncommon,
is also found in the Aquificae, Thermotogae, Firmicutes,
and Dictyoglomi [Mobile and extrachromosomal element
functions, Other].
Length = 241
Score = 26.0 bits (57), Expect = 7.3
Identities = 26/94 (27%), Positives = 37/94 (39%), Gaps = 6/94 (6%)
Query: 17 KPGTSGLRKPTKTFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAVDKIIKI 76
+ RKP T ++T + LG L G+VL G + Y K I I
Sbjct: 8 SGPYAFFRKPYTTTS--YFTYGNVHRT-ALLG--LIGAVLGYGKEEIYDEFYEKLKKIAI 62
Query: 77 SAANGVAKLIVGQNGILSTPAVSALIRKHILGRL 110
+ KL + + I+ST A K + GRL
Sbjct: 63 QVVPPLRKLYIDKK-IVSTKADVGYASKELGGRL 95
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM
of some eukaryotic DnaJ homolog subfamily C member 17
and similar proteins. DnaJ/Hsp40 (heat shock protein
40) proteins are highly conserved and play crucial
roles in protein translation, folding, unfolding,
translocation, and degradation. They act primarily by
stimulating the ATPase activity of Hsp70s, an important
chaperonine family. Members in this family contains an
N-terminal DnaJ domain or J-domain, which mediates the
interaction with Hsp70. They also contains a RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
C-terminus, which may play an essential role in RNA
binding. .
Length = 74
Score = 24.9 bits (55), Expect = 7.3
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 8/36 (22%)
Query: 31 QQEHYTENFIQSILTALGD--------KLKGSVLVV 58
Y+E+ ++ I + GD K KGS +V
Sbjct: 12 GNGDYSEDELRKIFSKYGDVSDVVVSSKKKGSAIVE 47
>gnl|CDD|223457 COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate
transport and metabolism].
Length = 486
Score = 26.1 bits (58), Expect = 7.3
Identities = 13/41 (31%), Positives = 15/41 (36%)
Query: 29 TFQQEHYTENFIQSILTALGDKLKGSVLVVGGDGRYFGDVA 69
FQ E Y NF+ LG + G DGR A
Sbjct: 208 GFQTESYARNFLDLCSRLLGVTGDADIRFNGADGRIVKVGA 248
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 26.0 bits (58), Expect = 7.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 33 EHYTENFIQSILTALGDKLKGSV-----LVVGGDG 62
E + + +++L ALG K+ GSV VV G+
Sbjct: 607 EGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGEN 641
>gnl|CDD|238945 cd01987, USP_OKCHK, USP domain is located between the N-terminal
sensor domain and C-terminal catalytic domain of this
Osmosensitive K+ channel histidine kinase family. The
family of KdpD sensor kinase proteins regulates the
kdpFABC operon responsible for potassium transport. The
USP domain is homologous to the universal stress protein
Usp Usp is a small cytoplasmic bacterial protein whose
expression is enhanced when the cell is exposed to
stress agents. Usp enhances the rate of cell survival
during prolonged exposure to such conditions, and may
provide a general "stress endurance" activity.
Length = 124
Score = 25.2 bits (56), Expect = 7.8
Identities = 13/66 (19%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 47 LGDKLKGSVLVVGGDGRYFGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALIRKHI 106
L ++L V+ + GD + I++ + + V +++VG++ L R +
Sbjct: 57 LAEELGAEVVTLPGDDV------AEAIVEFAREHNVTQIVVGKS---RRSRWRELFRGSL 107
Query: 107 LGRLVK 112
+ RL++
Sbjct: 108 VDRLLR 113
>gnl|CDD|179615 PRK03634, PRK03634, rhamnulose-1-phosphate aldolase; Provisional.
Length = 274
Score = 25.7 bits (57), Expect = 8.2
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 10/84 (11%)
Query: 33 EHYTENFIQSI----LTALGDKLKGSVLVVGGDGRYFGDVAVDK-----IIKISAANGVA 83
Y ++F Q L+ +L G+ +V G G++F +V +D +I+I +
Sbjct: 43 APYGDDFHQQPRYIPLSQPMPELAGTYFLVTGSGKFFRNVQLDPAANLGVIRIDSDGAGY 102
Query: 84 KLIVG-QNGILSTPAVSALIRKHI 106
++ G NG T + A + HI
Sbjct: 103 HILWGLTNGGKPTSELPAHLMSHI 126
>gnl|CDD|227628 COG5316, COG5316, Uncharacterized conserved protein [Function
unknown].
Length = 421
Score = 26.0 bits (57), Expect = 8.4
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 95 TPAVSALIRKHILGRLVKVPSSNPSRTIR 123
T AV+ IR+ + G +V V S P +R
Sbjct: 367 TDAVTVEIRELVYGDVVIVDSEVPKGNLR 395
>gnl|CDD|215151 PLN02267, PLN02267, enoyl-CoA hydratase/isomerase family protein.
Length = 239
Score = 25.4 bits (56), Expect = 8.5
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 38 NFIQSILTAL----GDKLKGSVLVVGGDGRYF 65
I SI +AL GSVL+ +G++F
Sbjct: 26 TLIDSIRSALRQVKSQATPGSVLITTAEGKFF 57
>gnl|CDD|131673 TIGR02624, rhamnu_1P_ald, rhamnulose-1-phosphate aldolase. Members
of this family are the enzyme RhaD,
rhamnulose-1-phosphate aldolase.
Length = 270
Score = 25.5 bits (56), Expect = 9.3
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 50 KLKGSVLVVGGDGRYFGDVAVDK-----IIKISAANGVAKLIVG-QNGILSTPAVSALIR 103
+L +V G G++F +V + I+++S L+ G +G + T + A
Sbjct: 63 ELANKYFLVTGSGKFFRNVEENPAENLGILRVSEDGASVHLLWGLTDGGVPTSELPA--- 119
Query: 104 KHILGRLVKVPSSNPSRTIRPC 125
H + + ++ +R I C
Sbjct: 120 -HFMSHIARLKVDPENRVIMHC 140
>gnl|CDD|223436 COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 25.2 bits (56), Expect = 9.5
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 46 ALGDKLKGSVLV----VGGDGRYFGDVAVDKIIKISAANGV 82
AL +KL+G + G DG+ FG V I + A G
Sbjct: 67 ALKEKLEGKTVEIAVKAGEDGKLFGSVTSKDIAEALKAAGF 107
>gnl|CDD|214006 cd12807, Esterase_713, Novel bacterial esterase 713 that cleaves
esters on halogenated cyclic compounds. This family
contains proteins similar to a novel bacterial esterase
(esterase 713) with the alpha/beta hydrolase fold that
cleaves esters on halogenated cyclic compounds. This
Alcaligenes esterase, however, does not contain the
GXSXXG pentapeptide around the active site serine
residue as seen in other esterase families. This enzyme
is active as a dimer though its natural substrate is
unknown. It has two distinct disulfide bridges; one
formed between adjacent cysteines appears to facilitate
the correct formation of the oxyanion cleft in the
catalytic site. Esterase 713 also resembles human
pancreatic lipase in its location of the acidic residue
of the catalytic triad. It is possibly exported from the
cytosol to the periplasmic space. A large majority of
sequences in this family have yet to be characterized.
Length = 315
Score = 25.4 bits (56), Expect = 9.6
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 36 TENFIQSILTALGDKLKGSVLVVGGDGRYFGDVAV 70
T N + L AL DKL G+VL+ F A
Sbjct: 173 TPNPTPNALAALADKLGGAVLLGHSQSGPFPLEAA 207
>gnl|CDD|237672 PRK14318, glmM, phosphoglucosamine mutase; Provisional.
Length = 448
Score = 25.7 bits (57), Expect = 9.6
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 55 VLVVGGDGRYFGDVAVDKIIKISAANGVAKLIVGQNGILSTPAVSALI 102
V VVG D R G+ + A+ GV L VG +L TPAV+ L
Sbjct: 46 VAVVGRDPRASGEFLEAAVSAGLASAGVDVLRVG---VLPTPAVAYLT 90
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 25.3 bits (56), Expect = 9.8
Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 9/45 (20%)
Query: 85 LIVGQNGILSTPAVSALIRK-----HILGRLVKVPSSNPSRTIRP 124
I G G L P VSAL+ +L R PSS S +P
Sbjct: 3 AIAGATGTLGGPIVSALLASPGFTVTVLTR----PSSTSSNEFQP 43
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 25.0 bits (56), Expect = 9.9
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 46 ALGDKLKGSVLV----VGGDGRYFGDVAVDKIIKISAANGV 82
AL +KL+G + G DG+ FG V I + G+
Sbjct: 67 ALAEKLEGLTVTIKAKAGEDGKLFGSVTTKDIAEALKKQGI 107
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 0.136 0.382
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,482,545
Number of extensions: 581110
Number of successful extensions: 724
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 63
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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: 53 (24.2 bits)