RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 047709
(93 letters)
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 146 bits (370), Expect = 6e-44
Identities = 64/101 (63%), Positives = 76/101 (75%), Gaps = 13/101 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLPP-------------KKATYDDIKAAHKEASQGEMKGIFGY 47
VGKVLP LNGKLTGMAFR+P K A+Y+D+KAA K AS+G +KGI GY
Sbjct: 300 VGKVLPELNGKLTGMAFRVPTPNVSVVDLTCRLEKSASYEDVKAAIKYASEGPLKGILGY 359
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSD 88
++DVVS DFVGD+RSSIFDAKAGI LS +F KLVSWYD++
Sbjct: 360 TDEDVVSNDFVGDSRSSIFDAKAGIGLSASFMKLVSWYDNE 400
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 138 bits (350), Expect = 1e-41
Identities = 59/104 (56%), Positives = 75/104 (72%), Gaps = 13/104 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
VGKV+P LNGKLTGMAFR+P K A Y++I AA K+A++G +KGI GY
Sbjct: 219 VGKVIPELNGKLTGMAFRVPVPDVSVVDLTCKLAKPAKYEEIVAAVKKAAEGPLKGILGY 278
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSDAAF 91
+D+VVS+DFV D RSSIFD KAGI+L+D F KLVSWYD++ +
Sbjct: 279 TDDEVVSSDFVHDKRSSIFDVKAGIALNDTFVKLVSWYDNEWGY 322
>gnl|CDD|217235 pfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase,
C-terminal domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
C-terminal domain is a mixed alpha/antiparallel beta
fold.
Length = 157
Score = 131 bits (333), Expect = 4e-41
Identities = 53/98 (54%), Positives = 66/98 (67%), Gaps = 13/98 (13%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
VG VLP L GKLTGMAFR+P K T +++ AA KEA++G +KGI GY
Sbjct: 60 VGLVLPELKGKLTGMAFRVPTPNVSVVDLTVELEKPVTVEEVNAALKEAAEGALKGILGY 119
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWY 85
E+ +VS+DFVGD SSIFDAKA I L+ NF K+V+WY
Sbjct: 120 TEEPLVSSDFVGDPHSSIFDAKATIVLNGNFVKVVAWY 157
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 130 bits (327), Expect = 2e-38
Identities = 70/104 (67%), Positives = 80/104 (76%), Gaps = 13/104 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLPP-------------KKATYDDIKAAHKEASQGEMKGIFGY 47
VGKVLPSLNGKLTGM+FR+P K ATYD+IK A KE S+G++KGI GY
Sbjct: 221 VGKVLPSLNGKLTGMSFRVPTVDVSVVDLTVRLEKAATYDEIKKAIKEESEGKLKGILGY 280
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSDAAF 91
EDDVVSTDFVGDNRSSIFDAKAGI+LSD F KLVSWYD++ +
Sbjct: 281 TEDDVVSTDFVGDNRSSIFDAKAGIALSDKFVKLVSWYDNEWGY 324
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 122 bits (309), Expect = 2e-35
Identities = 52/99 (52%), Positives = 61/99 (61%), Gaps = 13/99 (13%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
VG VLP L GKLTGMA R+P K+ T ++I AA K AS+ +KGI GY
Sbjct: 216 VGLVLPELKGKLTGMAIRVPTPNVSVVDLTVELEKEVTVEEINAALKAASEIGLKGILGY 275
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYD 86
ED +VS+DF GD SSIFDA A I L N KLV+WYD
Sbjct: 276 TEDPLVSSDFNGDPHSSIFDASATIVLGGNLVKLVAWYD 314
>gnl|CDD|233453 TIGR01534, GAPDH-I, glyceraldehyde-3-phosphate dehydrogenase, type
I. This model represents glyceraldehyde-3-phosphate
dehydrogenase (GAPDH), the enzyme responsible for the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in glycolysis
and gluconeogenesis. Forms exist which utilize NAD (EC
1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In
some species, NAD- and NADP- utilizing forms exist,
generally being responsible for reactions in the
anabolic and catabolic directions respectively. Two PFAM
models cover the two functional domains of this protein;
pfam00044 represents the N-terminal NAD(P)-binding
domain and pfam02800 represents the C-terminal catalytic
domain. An additional form of gap gene is found in gamma
proteobacteria and is responsible for the conversion of
erythrose-4-phosphate (E4P) to 4-phospho-erythronate in
the biosynthesis of pyridoxine. This pathway of
pyridoxine biosynthesis appears to be limited, however,
to a relatively small number of bacterial species
although it is prevalent among the gamma-proteobacteria.
This enzyme is described by TIGR001532. These sequences
generally score between trusted and noise to this GAPDH
model due to the close evolutionary relationship. There
exists the possiblity that some forms of GAPDH may be
bifunctional and act on E4P in species which make
pyridoxine and via hydroxythreonine and lack a separate
E4PDH enzyme (for instance, the GAPDH from Bacillus
stearothermophilus has been shown to posess a limited
E4PD activity as well as a robust GAPDH activity). There
are a great number of sequences in the databases which
score between trusted and noise to this model, nearly
all of them due to fragmentary sequences. It seems that
study of this gene has been carried out in many species
utilizing PCR probes which exclude the extreme ends of
the consenses used to define this model. The noise level
is set relative not to E4PD, but the next closest
outliers, the class II GAPDH's (found in archaea,
TIGR01546) and aspartate semialdehyde dehydrogenase
(ASADH, TIGR01296) both of which have highest-scoring
hits around -225 to the prior model [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 326
Score = 120 bits (302), Expect = 1e-34
Identities = 48/106 (45%), Positives = 67/106 (63%), Gaps = 15/106 (14%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
+GKVLP L GKLTGMA R+P K T +++ AA KEA++GE+KG+ GY
Sbjct: 215 IGKVLPELAGKLTGMAIRVPTPNVSLVDLVVNLEKDVTVEEVNAALKEAAEGELKGVLGY 274
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGI--SLSDNFEKLVSWYDSDAAF 91
ED++VS+DF+G SSI DA A L D+ K+V+WYD++ +
Sbjct: 275 TEDELVSSDFIGSPYSSIVDATATKVTGLGDSLVKVVAWYDNEWGY 320
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 118 bits (297), Expect = 5e-34
Identities = 64/104 (61%), Positives = 77/104 (74%), Gaps = 13/104 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLPP-------------KKATYDDIKAAHKEASQGEMKGIFGY 47
VGKVLP LNGKLTGMAFR+P K ATY+ IKAA K A++GEMKG+ GY
Sbjct: 215 VGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGY 274
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSDAAF 91
EDDVVSTDF G+ +S+FDAKAGI+L+DNF KLVSWYD++ +
Sbjct: 275 TEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGY 318
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 94.0 bits (233), Expect = 2e-24
Identities = 49/110 (44%), Positives = 68/110 (61%), Gaps = 21/110 (19%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
VG V+PS GKLTGM+FR+P + + +I AA K ASQ MKGI G+
Sbjct: 233 VGMVIPSTKGKLTGMSFRVPTPDVSVVDLTFRATRDTSIQEIDAAIKRASQTYMKGILGF 292
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDN------FEKLVSWYDSDAAF 91
+D++VS DF+ DNRSSI+D+KA +L +N F K+VSWYD++ +
Sbjct: 293 TDDELVSADFINDNRSSIYDSKA--TLQNNLPGERRFFKIVSWYDNEWGY 340
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 82.9 bits (205), Expect = 2e-20
Identities = 36/101 (35%), Positives = 56/101 (55%), Gaps = 13/101 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
+ KVLP LNGKL GMA R+P + T ++I A K A+ G +KGI +
Sbjct: 216 LAKVLPHLNGKLHGMALRVPTPNVSLVDLVVDVKRDVTVEEINEAFKTAANGALKGILEF 275
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSD 88
E+ +VS DF + S+I D + + + D K+++WYD++
Sbjct: 276 SEEPLVSIDFNTNTHSAIIDGLSTMVMGDRKVKVLAWYDNE 316
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 74.4 bits (183), Expect = 2e-17
Identities = 37/98 (37%), Positives = 55/98 (56%), Gaps = 13/98 (13%)
Query: 4 VLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGYIED 50
+ P L GKL G A R+P + T +++ A KEA++GE+KGI GY E
Sbjct: 219 IFPELKGKLNGHAVRVPLANASLTDCVFEVERDTTVEEVNALLKEAAEGELKGILGYEER 278
Query: 51 DVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSD 88
+VS D+ D RSSI DA + + ++ KL +WYD++
Sbjct: 279 PLVSIDYKTDPRSSIVDALSTMVVNGTQVKLYAWYDNE 316
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 68.0 bits (166), Expect = 4e-15
Identities = 33/101 (32%), Positives = 55/101 (54%), Gaps = 13/101 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLPP-------------KKATYDDIKAAHKEASQGEMKGIFGY 47
V V+P L GKL G+A R+P K+ + + K+AS+G +KGI Y
Sbjct: 218 VALVIPELKGKLNGIALRVPTPNVSVVDLVVQVEKRTITEQVNEVLKDASEGPLKGILEY 277
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSD 88
+ +VS+D+ G + SSI DA + + + K+++WYD++
Sbjct: 278 SDLPLVSSDYRGTDASSIVDASLTMVMGGDMVKVIAWYDNE 318
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 66.9 bits (163), Expect = 1e-14
Identities = 34/101 (33%), Positives = 57/101 (56%), Gaps = 13/101 (12%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-------------PKKATYDDIKAAHKEASQGEMKGIFGY 47
V VLP+L GKL G+A R+P KK +++ AA ++A++ E+KGI
Sbjct: 276 VALVLPNLKGKLNGIALRVPTPNVSVVDLVVQVEKKTFAEEVNAAFRDAAEKELKGILAV 335
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSD 88
++ +VS DF + SS D+ + + D+ K+V+WYD++
Sbjct: 336 CDEPLVSVDFRCSDVSSTIDSSLTMVMGDDMVKVVAWYDNE 376
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 66.8 bits (163), Expect = 1e-14
Identities = 36/102 (35%), Positives = 54/102 (52%), Gaps = 14/102 (13%)
Query: 1 VGKVLPSLNGKLTGMAFRLP--------------PKKATYDDIKAAHKEASQGEMKGIFG 46
V VLP L GKL G+A R+P K T +D+ AA ++A+ G +KGI
Sbjct: 293 VSLVLPQLKGKLNGIALRVPTPNVSVVDLVVNVEKKGITAEDVNAAFRKAADGPLKGILA 352
Query: 47 YIEDDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSD 88
+ +VS DF + SS DA + + D+ K+V+WYD++
Sbjct: 353 VCDVPLVSVDFRCSDVSSTIDASLTMVMGDDMVKVVAWYDNE 394
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 64.9 bits (159), Expect = 6e-14
Identities = 32/101 (31%), Positives = 50/101 (49%), Gaps = 16/101 (15%)
Query: 1 VGKVLPSLNGKLTGMAFRLP-P------------KKATYDDIKAAHKEAS-QGEMKGIFG 46
V K LP L GKLTG A R+P P K+ + +++ ++ S ++
Sbjct: 353 VAKALPELAGKLTGNAIRVPTPNVSMAILNLNLEKETSREELNEYLRQMSLHSPLQNQID 412
Query: 47 YIED-DVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYD 86
Y + +VVS+DFVG + + D++A I + N L WYD
Sbjct: 413 YTDSTEVVSSDFVGSRHAGVVDSQATIV-NGNRAVLYVWYD 452
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 51.8 bits (124), Expect = 2e-09
Identities = 26/107 (24%), Positives = 52/107 (48%), Gaps = 15/107 (14%)
Query: 1 VGKVLPSLNGKLTGMAFRLPPKK-------------ATYDDIKAAHKEASQGEMKGIFGY 47
V K+LP L G+++G AF++P KK + + + +A EA+ + G+
Sbjct: 219 VCKLLPHLVGRISGSAFQVPVKKGCAIDMLVRTKQPVSKEVVDSALAEAASDRLNGVLCI 278
Query: 48 IEDDVVSTDFVGDNRSSIFDAKAGISLSD-NFEKLVSWYDSDAAFEK 93
+ D++S D + + + +DA + S + K+V W+D + +
Sbjct: 279 SKRDMISVDCIPNGK-LCYDATSSSSSREGEVHKMVLWFDVECYYAA 324
>gnl|CDD|130595 TIGR01532, E4PD_g-proteo, erythrose-4-phosphate dehydrogenase.
This model represents the small clade of dehydrogenases
in gamma-proteobacteria which utilize NAD+ to oxidize
erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a
precursor for the de novo synthesis of pyridoxine via
4-hydroxythreonine and D-1-deoxyxylulose. This enzyme
activity appears to have evolved from
glyceraldehyde-3-phosphate dehydrogenase, whose
substrate differs only in the lack of one carbon
relative to E4P. Accordingly, this model is very close
to the corresponding models for GAPDH, and those
sequences which hit above trusted here invariably hit
between trusted and noise to the GAPDH model
(TIGR01534). Similarly, it may be found that there are
species outside of the gamma proteobacteria which
synthesize pyridoxine and have more than one aparrent
GAPDH gene of which one may have E4PD activity - this
may necessitate a readjustment of these models.
Alternatively, some of the GAPDH enzymes may prove to be
bifunctional in certain species [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridoxine].
Length = 325
Score = 47.2 bits (112), Expect = 1e-07
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 13/102 (12%)
Query: 3 KVLPSLNGKLTGMAFRLPPKKATYDDI--------KAAH-----KEASQGEMKGIFGYIE 49
+ P N + +A R+P T D+ KA ++A+QG ++GI Y E
Sbjct: 218 RFFPQFNDRFEAIAVRVPTVNVTAIDLSVTVKKPVKANEVNLLLQKAAQGALRGIVDYTE 277
Query: 50 DDVVSTDFVGDNRSSIFDAKAGISLSDNFEKLVSWYDSDAAF 91
+VS DF D S+I D + K + W D++ F
Sbjct: 278 LPLVSVDFNHDPHSAIVDGTQTRVSGAHLVKTLVWCDNEWGF 319
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 45.0 bits (107), Expect = 5e-07
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 13/80 (16%)
Query: 1 VGKVLPSLNGKLTGMAFRLPP-------------KKATYDDIKAAHKEASQGEMKGIFGY 47
+ ++ P N + ++ R+P K +++ ++A+QG GI Y
Sbjct: 218 ITRIFPQFNDRFEAISVRVPTINVTAIDLSVTVKKPVKVNEVNQLLQKAAQGAFHGIVDY 277
Query: 48 IEDDVVSTDFVGDNRSSIFD 67
E +VS DF D S+I D
Sbjct: 278 TELPLVSIDFNHDPHSAIVD 297
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin
D or UBD).
Length = 350
Score = 27.7 bits (62), Expect = 0.85
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 12 LTGMAFRLPPKKATYDDIKAAHKEASQGEMK 42
L RLP + AT D++ H E EMK
Sbjct: 35 LLERCLRLPSRLATEDELLLCHSEEHLDEMK 65
>gnl|CDD|233714 TIGR02082, metH, 5-methyltetrahydrofolate--homocysteine
methyltransferase. This family represents
5-methyltetrahydrofolate--homocysteine methyltransferase
(EC 2.1.1.13), one of at least three different enzymes
able to convert homocysteine to methionine by
transferring a methyl group on to the sulfur atom. It is
also called the vitamin B12(or cobalamine)-dependent
methionine synthase. Other methionine synthases include
5-methyltetrahydropteroyltriglutamate--homocysteine
S-methyltransferase (MetE, EC 2.1.1.14, the
cobalamin-independent methionine synthase) and
betaine-homocysteine methyltransferase [Amino acid
biosynthesis, Aspartate family].
Length = 1178
Score = 26.7 bits (59), Expect = 1.8
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 5 LPSLNGKLTGMAFRLPPKKATYDDIKAAHKEASQGEMKG 43
+L+ + FR TYD++ A+ E ++G + G
Sbjct: 126 TATLSPDVERPGFR----NVTYDELVDAYTEQAKGLLDG 160
>gnl|CDD|177623 PHA03387, gp37, spherodin-like protein; Provisional.
Length = 267
Score = 26.5 bits (59), Expect = 1.9
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 45 FGYIEDDVVSTDFVG---DNRSSIFDAKAGISL 74
F +I+ +VV ++RS++F K+G+
Sbjct: 99 FEHIKRNVVPHTLCAAGANDRSAVFGDKSGMDE 131
>gnl|CDD|223719 COG0646, MetH, Methionine synthase I (cobalamin-dependent),
methyltransferase domain [Amino acid transport and
metabolism].
Length = 311
Score = 26.1 bits (58), Expect = 2.7
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 10 GKLTGMAFRLPPKKATYDDIKAAHKEASQGEMKG 43
G P T+D++ A++E +G + G
Sbjct: 122 GPTNKTLSISPDFAVTFDELVEAYREQVEGLIDG 155
>gnl|CDD|198347 cd07769, FGGY_GK, Glycerol kinases; a subfamily of the FGGY family
of carbohydrate kinases. This subfamily includes
glycerol kinases (GK; EC 2.7.1.30) and glycerol
kinase-like proteins from all three kingdoms of living
organisms. Glycerol is an important intermediate of
energy metabolism and it plays fundamental roles in
several vital physiological processes. GKs are involved
in the entry of external glycerol into cellular
metabolism. They catalyze the rate-limiting step in
glycerol metabolism by transferring a phosphate from ATP
to glycerol thus producing glycerol 3-phosphate (G3P) in
the cytoplasm. Human GK deficiency, called
hyperglycerolemia, is an X-linked recessive trait
associated with psychomotor retardation, osteoporosis,
spasticity, esotropia, and bone fractures. Under
different conditions, GKs from different species may
exist in different oligomeric states. The monomer of GKs
is composed of two large domains separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain. The high affinity ATP binding site of GKs is
created only by a substrate-induced conformational
change. Based on sequence similarity, some GK-like
proteins from metazoa, which have lost their GK
enzymatic activity, are also included in this CD.
Members in this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 484
Score = 26.0 bits (58), Expect = 3.0
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 3 KVLPSLNGKLTGMAFRLPPKKATY 26
K + S +G LT +A++L P K Y
Sbjct: 274 KPVISEHGLLTTIAYKLGPGKPVY 297
>gnl|CDD|237286 PRK13125, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 244
Score = 25.8 bits (57), Expect = 4.0
Identities = 7/21 (33%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 19 LPPKKATYDD--IKAAHKEAS 37
+PPK YD I+ +H++
Sbjct: 38 IPPKYPKYDGPVIRKSHRKVK 58
>gnl|CDD|182254 PRK10124, PRK10124, putative UDP-glucose lipid carrier transferase;
Provisional.
Length = 463
Score = 25.8 bits (57), Expect = 4.3
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 40 EMKGIFGYIEDDVVSTDFVGDNRSSIFDAKAG 71
E+ G++ + VS D+ G+ + + DAKAG
Sbjct: 171 EVVGVYHDPKPGGVSNDWAGNLQQLVEDAKAG 202
>gnl|CDD|215166 PLN02295, PLN02295, glycerol kinase.
Length = 512
Score = 25.4 bits (56), Expect = 5.1
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 3 KVLPSLNGKLTGMAFRLPPKKAT 25
+V+PS +G LT +A++L P T
Sbjct: 281 EVVPSKHGLLTTVAYKLGPDAPT 303
>gnl|CDD|240453 cd12873, SPRY_DDX1, SPRY domain associated with DEAD box gene DDX1.
This SPRY domain is associated with the DEAD box gene,
DDX1, an RNA-dependent ATPase involved in HIV-1 Rev
function and virus replication. It is suggested that
DDX1 acts as a cellular cofactor by promoting
oligomerization of Rev on the Rev response element
(RRE). DDX1 RNA is overexpressed in breast cancer, data
showing a strong and independent association between
poor prognosis and deregulation of the DEAD box protein
DDX1, thus potentially serving as an effective
prognostic biomarker for early recurrence in primary
breast cancer. DDX1 also interacts with RelA and
enhances nuclear factor kappaB-mediated transcription.
DEAD-box proteins are associated with all levels of RNA
metabolism and function, and have been implicated in
translation initiation, transcription, RNA splicing,
ribosome assembly, RNA transport, and RNA decay.
Length = 155
Score = 24.5 bits (54), Expect = 7.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 7 SLNGKLTGMAFRLPPK 22
S NGK G+AF +PPK
Sbjct: 115 SKNGKDLGVAFDIPPK 130
>gnl|CDD|153089 cd02888, RNR_II_dimer, Class II ribonucleotide reductase, dimeric
form. Ribonucleotide reductase (RNR) catalyzes the
reductive synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class are found to be
homodimers. Adenosylcobalamin interacts directly with an
active site cysteine to form the reactive cysteine
radical.
Length = 464
Score = 24.9 bits (55), Expect = 7.9
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 21 PKKATYDDIKAAHKEASQGEMKGI 44
P AT +D++A + A + +KGI
Sbjct: 435 PNDATVEDVEAVYLLAWKLGLKGI 458
>gnl|CDD|233900 TIGR02504, NrdJ_Z, ribonucleoside-diphosphate reductase,
adenosylcobalamin-dependent. This model represents a
group of adenosylcobalamin(B12)-dependent ribonucleotide
reductases (Class II RNRs) related to the characterized
species from Pyrococcus , Thermoplasma , Corynebacterium
and Deinococcus. RNR's are responsible for the
conversion of the ribose sugar of RNA into the
deoxyribose sugar of DNA. This is the rate-limiting step
of DNA biosynthesis. This model identifies genes in a
wide range of deeply branching bacteria. All are
structurally related to the class I (non-heme iron
dependent) RNRs. In most species this gene is known as
NrdJ, while in mycobacteria it is called NrdZ [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 589
Score = 24.6 bits (54), Expect = 8.7
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 21 PKKATYDDIKAAHKEASQGEMKGI 44
P AT +D+KA + EA + +KGI
Sbjct: 553 PSDATVEDVKAVYLEAWKLGLKGI 576
>gnl|CDD|182774 PRK10846, PRK10846, bifunctional folylpolyglutamate synthase/
dihydrofolate synthase; Provisional.
Length = 416
Score = 24.7 bits (54), Expect = 9.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 55 TDFVGDNRSSIFDAKAGI 72
TD++G +R SI KAGI
Sbjct: 174 TDWLGPDRESIGREKAGI 191
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
0.314 0.133 0.381
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,760,028
Number of extensions: 385360
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 35
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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: 42 (21.9 bits)
S2: 53 (24.2 bits)