RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6887
(70 letters)
>gnl|CDD|215675 pfam00044, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD
binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 148
Score = 67.9 bits (167), Expect = 2e-16
Identities = 24/44 (54%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
VVAIND + + YL KYDS HG+F+GEV+ D + L+VNG K
Sbjct: 27 VVAINDLT-DPETLAYLLKYDSVHGRFDGEVEVDEDGLIVNGKK 69
Score = 49.8 bits (120), Expect = 2e-09
Identities = 28/72 (38%), Positives = 37/72 (51%), Gaps = 20/72 (27%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV--------AINDPF------IGVDYMVYLFKYD 46
+ YL KYDS HG+F+GEV+ D + L+V A DP +GVD +V +
Sbjct: 39 LAYLLKYDSVHGRFDGEVEVDEDGLIVNGKKIKVFAERDPAELPWGELGVDIVV-----E 93
Query: 47 STHGKFNGEVKA 58
ST G F KA
Sbjct: 94 ST-GVFTTAEKA 104
>gnl|CDD|214851 smart00846, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase,
NAD binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 149
Score = 66.8 bits (164), Expect = 5e-16
Identities = 24/44 (54%), Positives = 30/44 (68%), Gaps = 1/44 (2%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
VVAIND +Y+ YL KYDS HG+F G V+ +G+ LVVNG
Sbjct: 27 VVAINDL-TDPEYLAYLLKYDSVHGRFPGTVEVEGDGLVVNGKA 69
Score = 49.9 bits (120), Expect = 2e-09
Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 20/72 (27%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV--------AINDP------FIGVDYMVYLFKYD 46
+ YL KYDS HG+F G V+ +G+ LVV A DP +GVD +V +
Sbjct: 39 LAYLLKYDSVHGRFPGTVEVEGDGLVVNGKAIKVFAERDPANLPWGELGVDIVV-----E 93
Query: 47 STHGKFNGEVKA 58
T G F KA
Sbjct: 94 CT-GGFTTREKA 104
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 67.6 bits (165), Expect = 3e-15
Identities = 25/45 (55%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKA-DGNFLVVNGNK 69
VVA+NDPFI YM Y+FKYDSTHG F G + D + L +NG +
Sbjct: 112 VVAVNDPFIDAKYMAYMFKYDSTHGNFKGTINVVDDSTLEINGKQ 156
Score = 40.2 bits (94), Expect = 1e-05
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 1 MVYLFKYDSTHGKFNGEVKA 20
M Y+FKYDSTHG F G +
Sbjct: 125 MAYMFKYDSTHGNFKGTINV 144
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 60.3 bits (147), Expect = 1e-12
Identities = 26/52 (50%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 18 VKADGNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
++ DG+ VVAIND DY+ +L KYDS HG+F+GEV+ + LVVNG
Sbjct: 21 LERDGDIEVVAINDL-TDPDYLAHLLKYDSVHGRFDGEVEVKDDALVVNGKG 71
Score = 41.0 bits (97), Expect = 7e-06
Identities = 28/72 (38%), Positives = 37/72 (51%), Gaps = 20/72 (27%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV--------AINDP------FIGVDYMVYLFKYD 46
+ +L KYDS HG+F+GEV+ + LVV A DP +GVD +V +
Sbjct: 41 LAHLLKYDSVHGRFDGEVEVKDDALVVNGKGIKVLAERDPANLPWADLGVDIVV-----E 95
Query: 47 STHGKFNGEVKA 58
T GKF G KA
Sbjct: 96 CT-GKFTGREKA 106
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 59.8 bits (145), Expect = 1e-12
Identities = 24/48 (50%), Positives = 29/48 (60%)
Query: 22 GNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
+ VVAINDPF+ +DYM YL KYDS HG EV FL++ K
Sbjct: 25 EDVEVVAINDPFMTLDYMCYLLKYDSVHGSLPAEVSVTDGFLMIGSKK 72
Score = 35.2 bits (81), Expect = 0.001
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV 27
M YL KYDS HG EV FL++
Sbjct: 42 MCYLLKYDSVHGSLPAEVSVTDGFLMI 68
>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 = 59.6 bits (145), Expect = 2e-12
Identities = 26/45 (57%), Positives = 32/45 (71%), Gaps = 1/45 (2%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNKT 70
VVAIND ++Y+ YL KYDS HG+F GEV AD + LVVNG +
Sbjct: 28 VVAINDL-TDLEYLAYLLKYDSVHGRFEGEVTADEDGLVVNGKEV 71
Score = 44.2 bits (105), Expect = 5e-07
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 21/75 (28%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV---------AINDP------FIGVDYMVYLFKY 45
+ YL KYDS HG+F GEV AD + LVV + DP +GVD ++
Sbjct: 40 LAYLLKYDSVHGRFEGEVTADEDGLVVNGKEVISVFSERDPSDLPWKALGVDIVI----- 94
Query: 46 DSTHGKFNGEVKADG 60
+ T GKF + K +G
Sbjct: 95 ECT-GKFRDKEKLEG 108
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 50.9 bits (121), Expect = 2e-09
Identities = 24/44 (54%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
+VAIND + DYM Y+ KYDSTHG+F+G V+ L+VNG K
Sbjct: 29 IVAIND-LLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKK 71
Score = 35.5 bits (81), Expect = 6e-04
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV 27
M Y+ KYDSTHG+F+G V+ L+V
Sbjct: 41 MAYMLKYDSTHGRFDGTVEVKDGHLIV 67
>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 = 48.7 bits (116), Expect = 1e-08
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 24 FLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGN 68
VVAIN+ M +L KYD++HG+F EV+ D + L V +
Sbjct: 27 ITVVAINE-LADAAGMAHLLKYDTSHGRFAWEVRQDRDQLFVGDD 70
Score = 39.5 bits (92), Expect = 3e-05
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV 27
M +L KYD++HG+F EV+ D + L V
Sbjct: 41 MAHLLKYDTSHGRFAWEVRQDRDQLFV 67
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 48.2 bits (115), Expect = 2e-08
Identities = 20/49 (40%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
Query: 21 DGNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
+ F +VAIN + + + +L KYD+ HGKF+G V+A + L+V+G K
Sbjct: 24 ESAFEIVAINASY-PSETLAHLIKYDTVHGKFDGTVEAFEDHLLVDGKK 71
Score = 35.9 bits (83), Expect = 6e-04
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV 27
+ +L KYD+ HGKF+G V+A + L+V
Sbjct: 41 LAHLIKYDTVHGKFDGTVEAFEDHLLV 67
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 45.1 bits (106), Expect = 2e-07
Identities = 17/27 (62%), Positives = 23/27 (85%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKF 52
+VA+NDPFI +YM Y+FKYDS HG++
Sbjct: 32 LVAVNDPFITTEYMTYMFKYDSVHGQW 58
Score = 26.6 bits (58), Expect = 0.92
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 1 MVYLFKYDSTHGKF 14
M Y+FKYDS HG++
Sbjct: 45 MTYMFKYDSVHGQW 58
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 40.8 bits (96), Expect = 8e-06
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 7/43 (16%)
Query: 26 VVAIN---DPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVV 65
VVAIN D + M +L KYD++HG+F +V+ + + L V
Sbjct: 31 VVAINELADA----EGMAHLLKYDTSHGRFAWDVRQERDQLFV 69
Score = 37.0 bits (86), Expect = 2e-04
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV 27
M +L KYD++HG+F +V+ + + L V
Sbjct: 43 MAHLLKYDTSHGRFAWDVRQERDQLFV 69
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 40.5 bits (95), Expect = 1e-05
Identities = 17/43 (39%), Positives = 29/43 (67%)
Query: 27 VAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNGNK 69
V INDP + +L ++DS HG+++ EV A+G+ +V+NG +
Sbjct: 30 VQINDPAGDAATLAHLLEFDSVHGRWHHEVTAEGDAIVINGKR 72
Score = 30.1 bits (68), Expect = 0.060
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVVAINDPFIGV 36
+ +L ++DS HG+++ EV A+G+ +V IN I
Sbjct: 42 LAHLLEFDSVHGRWHHEVTAEGDAIV--INGKRIRT 75
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 36.8 bits (85), Expect = 2e-04
Identities = 20/43 (46%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 19 KADGNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGN 61
+ D VVAIND GV +L KYDST G F+ +VK G+
Sbjct: 82 RKDSPLDVVAINDTG-GVKQASHLLKYDSTLGTFDADVKPVGD 123
Score = 28.0 bits (62), Expect = 0.30
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 3 YLFKYDSTHGKFNGEVKADGN 23
+L KYDST G F+ +VK G+
Sbjct: 103 HLLKYDSTLGTFDADVKPVGD 123
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 36.8 bits (85), Expect = 3e-04
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 19 KADGNFLVVAIN---DPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNG 67
+ + +VAIN DP +L KYDS GK N ++ AD N + VNG
Sbjct: 23 RENSQLELVAINDTSDPRTNA----HLLKYDSMLGKLNADISADENSITVNG 70
Score = 29.9 bits (67), Expect = 0.066
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 3 YLFKYDSTHGKFNGEVKADGNFLVV 27
+L KYDS GK N ++ AD N + V
Sbjct: 44 HLLKYDSMLGKLNADISADENSITV 68
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 33.5 bits (76), Expect = 0.003
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 26 VVAINDPFIGVDYMVYLFKYDSTHGKFNGEVK--------ADGNFLVVNGNK 69
VVA+ D +Y Y KYD+ HG+ V+ + LVVNG++
Sbjct: 34 VVAVVDMSTNAEYFAYQMKYDTVHGRPKYTVETTKSSPSVKTDDVLVVNGHR 85
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 33.4 bits (77), Expect = 0.004
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 42 LFKYDSTHGKFNGEVKAD--GNFLVVNGN 68
L + DS HG FNG + D N ++ NGN
Sbjct: 177 LLRRDSVHGPFNGTITVDEENNAIIANGN 205
Score = 32.6 bits (75), Expect = 0.008
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 11/48 (22%)
Query: 4 LFKYDSTHGKFNGEVKAD---------GNFL-VVAINDPFIGVDYMVY 41
L + DS HG FNG + D GN++ V+ N P VDY Y
Sbjct: 177 LLRRDSVHGPFNGTITVDEENNAIIANGNYIQVIYANSP-EEVDYTAY 223
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 32.9 bits (75), Expect = 0.005
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 20 ADGNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNG-EVKADGNFLVVNG 67
D VVA+ND + + Y+ Y+ + +S +G ++ G +V+NG
Sbjct: 23 TDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRVVGEQIVLNG 71
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 31.8 bits (72), Expect = 0.014
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 19 KADGNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVK-ADGNFLVVNGN 68
+ D VV +ND GV +L KYDS G F +VK D + V+G
Sbjct: 97 RKDSPLDVVVVNDSG-GVKNASHLLKYDSMLGTFKADVKIVDDETISVDGK 146
Score = 26.0 bits (57), Expect = 1.8
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 9/39 (23%)
Query: 3 YLFKYDSTHGKFNGEVK--------ADGNFL-VVAINDP 32
+L KYDS G F +VK DG + VV+ DP
Sbjct: 118 HLLKYDSMLGTFKADVKIVDDETISVDGKPIKVVSNRDP 156
>gnl|CDD|218125 pfam04519, Bactofilin, Polymer-forming cytoskeletal. This is a
family of bactofilins, a functionally diverse class of
cytoskeletal, polymer-forming, proteins that is widely
conserved among bacteria. In the example species C.
crescentus, two bactofilins assemble into a
membrane-associated laminar structure that shows
cell-cycle-dependent polar localisation and acts as a
platform for the recruitment of a cell wall
biosynthetic enzyme involved in polar morphogenesis.
Bactofilins display distinct subcellular distributions
and dynamics in different bacterial species, suggesting
that they are versatile structural elements that have
adopted a range of different cellular functions.
Length = 101
Score = 25.5 bits (57), Expect = 1.8
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 22/56 (39%)
Query: 12 GKFNGEVKADGNFLVVAINDPFIGVDYMVYLFKYDSTHGKFNGEVKADGNFLVVNG 67
GK G + ++G LV+ G+ GE+KAD +++NG
Sbjct: 25 GKVEGNITSEGT-LVI-------------------GEGGRVEGEIKADE--VIING 58
>gnl|CDD|153419 cd07914, IGPD, Imidazoleglycerol-phosphate dehydratase.
Imidazoleglycerol-phosphate dehydratase (IGPD; EC
4.2.1.19) catalyzes the dehydration of imidazole
glycerol phosphate to imidazole acetol phosphate, the
sixth step of histidine biosynthesis in plants and
microorganisms where the histidine is synthesized de
novo. There is an internal repeat in the protein domain
that is related by pseudo-dyad symmetry, perhaps as a
result of an ancient gene duplication. The apo-form of
IGPD exists as a catalytically inactive trimer which,
in the presence of specific divalent metal cations such
as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+),
nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles
to form a biologically active high molecular weight
metalloenzyme; a 24-mer with 4-3-2 symmetry. Each
24-mer has 24 active sites, and contains around 1.5
metal ions per monomer, each monomer contributing
residues to three separate active sites. IGPD enzymes
are monofunctional in fungi, plants, archaea and some
eubacteria while they are encoded as bifunctional
enzymes in other eubacteria, such that the enzyme is
fused to histidinol-phosphate phosphatase, the
penultimate enzyme of the histidine biosynthesis
pathway. The histidine biosynthesis pathway is a
potential target for development of herbicides, and
IGPD is a target for the triazole phosphonate
herbicides.
Length = 190
Score = 23.9 bits (53), Expect = 7.6
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 37 DYMVYLFKYDSTHGKFNGEVKADG 60
D+M+ LF + HG F+ VKA G
Sbjct: 34 DHMLTLF---ARHGGFDLTVKAKG 54
>gnl|CDD|233128 TIGR00792, gph, sugar (Glycoside-Pentoside-Hexuronide)
transporter. The Glycoside-Pentoside-Hexuronide
(GPH):Cation Symporter Family (TC 2.A.2) GPH:cation
symporters catalyze uptake of sugars in symport with a
monovalent cation (H+ or Na+). Members of this family
includes transporters for melibiose, lactose,
raffinose, glucuronides, pentosides and isoprimeverose.
Mutants of two groups of these symporters (the
melibiose permeases of enteric bacteria, and the
lactose permease of Streptococcus thermophilus) have
been isolated in which altered cation specificity is
observed or in which sugar transport is uncoupled from
cation symport (i.e., uniport is catalyzed). The
various members of the family can use Na+, H+ or Li,
Na+ or Li+, H+ or Li+, or only H+ as the symported
cation. All of these proteins possess twelve putative
transmembrane a-helical spanners [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 437
Score = 24.1 bits (53), Expect = 7.7
Identities = 15/58 (25%), Positives = 19/58 (32%), Gaps = 13/58 (22%)
Query: 1 MVYLFKYDSTHGKFNGEVKADGNFLVV----AINDPFIG--VDYMVYLFKYDSTHGKF 52
YL + + FLV AI DP +G VD + GKF
Sbjct: 19 STYLLFFYTDVL-GLSAAFVGTLFLVARILDAITDPIMGNIVDRT------RTRWGKF 69
>gnl|CDD|130314 TIGR01247, drrB, daunorubicin resistance ABC transporter membrane
protein. This model describes daunorubicin resistance
ABC transporter, membrane associated protein in
bacteria and archaea. The protein associated with effux
of the drug, daunorubicin. This transport system belong
to the larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP
hydrolysis to substrate translocation. The minimal
configuration of bacterial ABC transport system: an
ATPase or ATP binding subunit; An integral membrane
protein; a hydrophilic polypetpide, which likely
functions as substrate binding protein. In eukaryotes
proteins of similar function include p-gyco proteins,
multidrug resistance protein etc [Transport and binding
proteins, Other].
Length = 236
Score = 23.6 bits (51), Expect = 9.6
Identities = 10/18 (55%), Positives = 10/18 (55%), Gaps = 2/18 (11%)
Query: 28 AINDPFI--GVDYMVYLF 43
A P I GVDYM YL
Sbjct: 34 AFRFPMIFGGVDYMTYLV 51
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 0.143 0.429
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,557,161
Number of extensions: 269719
Number of successful extensions: 255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 45
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
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 (21.8 bits)
S2: 53 (24.0 bits)