RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6888
(69 letters)
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 61.8 bits (150), Expect = 3e-13
Identities = 24/28 (85%), Positives = 26/28 (92%)
Query: 32 TAHLAGGAKKVIISAPSADAPMFVCGVN 59
+AHL GGAKKV+ISAPSADAPMFV GVN
Sbjct: 192 SAHLKGGAKKVVISAPSADAPMFVVGVN 219
>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 = 54.8 bits (133), Expect = 2e-11
Identities = 20/33 (60%), Positives = 24/33 (72%), Gaps = 1/33 (3%)
Query: 33 AHLAGGAKKVIISAPSAD-APMFVCGVNLDKFE 64
AHL GAKKVIISAP+ D P FV GVN + ++
Sbjct: 106 AHLKAGAKKVIISAPAKDDDPTFVYGVNHEDYD 138
>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 = 50.6 bits (122), Expect = 8e-10
Identities = 23/32 (71%), Positives = 25/32 (78%), Gaps = 1/32 (3%)
Query: 33 AHLAGGAKKVIISAPSADA-PMFVCGVNLDKF 63
AHL GAKKVIISAPS DA P FV GVN D++
Sbjct: 106 AHLKAGAKKVIISAPSKDADPTFVYGVNHDEY 137
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 51.6 bits (123), Expect = 1e-09
Identities = 23/32 (71%), Positives = 27/32 (84%)
Query: 33 AHLAGGAKKVIISAPSADAPMFVCGVNLDKFE 64
AHL GGAKKV+ISAPS DAPMFV GVN +++
Sbjct: 114 AHLKGGAKKVVISAPSKDAPMFVVGVNEHEYK 145
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 51.4 bits (123), Expect = 2e-09
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 30 LQTAHLAGGAKKVIISAP-SADAPMFVCGVNLDKFEWKEV 68
AHL GGAKKVI+SAP D P++V GVN +++ +
Sbjct: 106 KAQAHLKGGAKKVIMSAPPKDDTPIYVMGVNHTQYDKSQR 145
>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 = 49.2 bits (118), Expect = 8e-09
Identities = 17/28 (60%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 33 AHLAGGAKKVIISAPSA-DAPMFVCGVN 59
HL GAKKV+ISAPS D V GVN
Sbjct: 108 GHLEAGAKKVLISAPSKGDVKTIVYGVN 135
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 44.1 bits (105), Expect = 5e-07
Identities = 18/34 (52%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 33 AHL-AGGAKKVIISAPSADA-PMFVCGVNLDKFE 64
HL AGGAKKV+ISAP D V GVN + ++
Sbjct: 108 KHLKAGGAKKVLISAPGKDDVATVVYGVNHNYYD 141
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 39.9 bits (93), Expect = 2e-05
Identities = 18/33 (54%), Positives = 24/33 (72%), Gaps = 2/33 (6%)
Query: 34 HLAGGAKKVIISAPS--ADAPMFVCGVNLDKFE 64
H+ GAKKVII+AP+ AD P +V GVN D ++
Sbjct: 185 HIQAGAKKVIITAPAKGADIPTYVVGVNEDDYD 217
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 39.1 bits (91), Expect = 3e-05
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 34 HLAGGAKKVIISAPSADAPMFVCGVNLDK 62
H+ GGAK V ++ SADAP + G N ++
Sbjct: 112 HVTGGAKGVFVAGQSADAPTVMAGSNDER 140
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 39.1 bits (91), Expect = 3e-05
Identities = 16/31 (51%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 34 HLAGGAKKVIISAPS-ADAPMFVCGVNLDKF 63
H+ GAKKV+I+AP D P +V GVN D +
Sbjct: 170 HIQAGAKKVLITAPGKGDIPTYVVGVNADDY 200
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 37.4 bits (86), Expect = 1e-04
Identities = 17/36 (47%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 34 HLAGGAKKVIISAPSAD-APMFVCGVNLDKFEWKEV 68
H+ GAKKV+++ PS D PMFV G N DK+ +++
Sbjct: 109 HITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDI 144
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 37.3 bits (86), Expect = 2e-04
Identities = 18/27 (66%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 34 HLAGGAKKVIISAP-SADAPMFVCGVN 59
HL GGAKKV+ISAP S A V GVN
Sbjct: 124 HLKGGAKKVVISAPASGGAKTIVMGVN 150
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 34.6 bits (80), Expect = 0.001
Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 4/30 (13%)
Query: 33 AHLAGGAKKVIISAPSA---DAPMFVCGVN 59
AH+A GAKKV+ S P + DA + V GVN
Sbjct: 110 AHIAAGAKKVLFSHPGSNDLDATV-VYGVN 138
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 33.3 bits (76), Expect = 0.003
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 32 TAHLAGGAKKVIISAP--SADAPMFVCGVNLDKFE 64
+ H+ GAKKV+I+AP D +V GVN +++
Sbjct: 108 SKHIQAGAKKVLITAPGKGEDIGTYVVGVNHHEYD 142
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 32.0 bits (73), Expect = 0.010
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 33 AHLAGGAKKVIISAPSADAPM-FVCGVNLDKF 63
H+ GAKKVI++AP + + V GVN D+
Sbjct: 108 LHVEAGAKKVILTAPGKNEDVTIVVGVNEDQL 139
>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 = 27.9 bits (62), Expect = 0.33
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 33 AHLAGGAKKVIISAPSA---DAPMFVCGVNLDKFEWKE 67
AH+A GAKKV+ S P A DA + V GVN D+ +
Sbjct: 108 AHIAAGAKKVLFSHPGASDLDATI-VYGVNQDQLRAEH 144
>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
Provisional.
Length = 606
Score = 27.4 bits (61), Expect = 0.45
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 31 QTAHLAGGAKKVIISAPSADAPMFVCG 57
Q L G +K+ A SAD PM VCG
Sbjct: 439 QVHTLLKGLEKI---AASADIPMLVCG 462
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 27.2 bits (61), Expect = 0.49
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 34 HL-AGGAKKVIISAPS-ADAPMFVCGVN 59
HL + G KV+++AP D V GVN
Sbjct: 246 HLKSKGVAKVLLTAPGKGDIKNIVHGVN 273
>gnl|CDD|179184 PRK00961, PRK00961, H(2)-dependent
methylenetetrahydromethanopterin dehydrogenase;
Provisional.
Length = 342
Score = 26.7 bits (59), Expect = 0.96
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 34 HLAGGAKKVIISAPSADA-PMFVCGVNLDKFEWKEV 68
HLA G +V++S P P FV +D F++KEV
Sbjct: 52 HLAPGVDEVVVSDPCFAEEPGFVV---IDDFDYKEV 84
>gnl|CDD|223072 PHA03393, odv-e66, occlusion-derived virus envelope protein E66;
Provisional.
Length = 682
Score = 26.0 bits (58), Expect = 1.3
Identities = 8/49 (16%), Positives = 14/49 (28%)
Query: 16 FLIFLVLFLSVNNILQTAHLAGGAKKVIISAPSADAPMFVCGVNLDKFE 64
+I +++ L +N P +LD FE
Sbjct: 12 VVIIIIILLWQSNNNNNTPNPPNPPPNPPPPPPPPPTPEDYHDDLDTFE 60
>gnl|CDD|182860 PRK10949, PRK10949, protease 4; Provisional.
Length = 618
Score = 25.0 bits (55), Expect = 3.1
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 10/55 (18%)
Query: 16 FLIFLVL-----FLSVNNILQTAHLAGGA-----KKVIISAPSADAPMFVCGVNL 60
F IFL+L ++ V+N + GA VI+ PS+ + G L
Sbjct: 30 FFIFLILVGVGIWMQVSNGDTPETASRGALLLDISGVIVDKPSSSNKLSQLGRQL 84
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 24.7 bits (54), Expect = 4.3
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 29 ILQTAHLAGGAKKVIISAPSADAPMF--VCGVNLDKFE 64
+LQ A+L G K+V+++AP + + V GVN F+
Sbjct: 104 LLQ-AYLDQGVKRVVVTAPVKEEGVLNIVMGVNDHLFD 140
>gnl|CDD|240328 PTZ00247, PTZ00247, adenosine kinase; Provisional.
Length = 345
Score = 24.2 bits (53), Expect = 6.3
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 5 VRDEIKSTSFKFLIFLVLFLSVNNILQTAHLA 36
V++ IK+ +L L +S NN+LQ A A
Sbjct: 153 VQEAIKTAQLYYLEGFFLTVSPNNVLQVAKHA 184
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 23.7 bits (52), Expect = 9.6
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 23 FLSVNNILQTAHLAGGAKKVIISAP 47
L ++N+ T H+AG + V +P
Sbjct: 275 LLKLDNVTLTPHIAGATRDVAERSP 299
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
0.328 0.141 0.415
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: 3,452,652
Number of extensions: 250510
Number of successful extensions: 410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 402
Number of HSP's successfully gapped: 26
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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 (21.8 bits)
S2: 53 (24.0 bits)