RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046110
(130 letters)
>gnl|CDD|178175 PLN02561, PLN02561, triosephosphate isomerase.
Length = 253
Score = 119 bits (299), Expect = 2e-34
Identities = 46/60 (76%), Positives = 51/60 (85%)
Query: 33 KISNWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIYRDTV 92
K+S+W NVVLAYEPVW IGTGKVA PAQAQEVH ELRKWL NV+ EVAA+TRIIY +V
Sbjct: 154 KVSDWANVVLAYEPVWAIGTGKVATPAQAQEVHDELRKWLHKNVSPEVAATTRIIYGGSV 213
>gnl|CDD|240365 PTZ00333, PTZ00333, triosephosphate isomerase; Provisional.
Length = 255
Score = 106 bits (266), Expect = 2e-29
Identities = 38/56 (67%), Positives = 44/56 (78%)
Query: 33 KISNWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
WDN+V+AYEPVW IGTGKVA P QAQEVHA +RKWL + V A+VA +TRIIY
Sbjct: 157 SDEAWDNIVIAYEPVWAIGTGKVATPEQAQEVHAFIRKWLAEKVGADVAEATRIIY 212
>gnl|CDD|166070 PLN02429, PLN02429, triosephosphate isomerase.
Length = 315
Score = 92.2 bits (228), Expect = 1e-23
Identities = 39/59 (66%), Positives = 47/59 (79%)
Query: 34 ISNWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIYRDTV 92
+ +WDN+V+AYEPVW IGTGKVA P QAQEVH +R WLK NV+ EVA+ TRIIY +V
Sbjct: 214 VPSWDNIVVAYEPVWAIGTGKVASPQQAQEVHVAVRGWLKKNVSEEVASKTRIIYGGSV 272
>gnl|CDD|238190 cd00311, TIM, Triosephosphate isomerase (TIM) is a glycolytic
enzyme that catalyzes the interconversion of
dihydroxyacetone phosphate and
D-glyceraldehyde-3-phosphate. The reaction is very
efficient and requires neither cofactors nor metal ions.
TIM, usually homodimeric, but in some organisms
tetrameric, is ubiqitous and conserved in function
across eukaryotes, bacteria and archaea.
Length = 242
Score = 86.8 bits (216), Expect = 5e-22
Identities = 31/56 (55%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 33 KISNWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
+ + VV+AYEPVW IGTGK A P QAQEVHA +RK L + EVA RI+Y
Sbjct: 150 GVEDLAPVVIAYEPVWAIGTGKTASPEQAQEVHAFIRKLLAEL-YGEVAEKVRILY 204
>gnl|CDD|234589 PRK00042, tpiA, triosephosphate isomerase; Provisional.
Length = 250
Score = 80.2 bits (199), Expect = 2e-19
Identities = 30/50 (60%), Positives = 35/50 (70%), Gaps = 1/50 (2%)
Query: 39 NVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
N+V+AYEPVW IGTGK A P QAQEVHA +R L + EVA RI+Y
Sbjct: 160 NLVIAYEPVWAIGTGKTATPEQAQEVHAFIRAVLAELYG-EVAEKVRILY 208
>gnl|CDD|215732 pfam00121, TIM, Triosephosphate isomerase.
Length = 242
Score = 77.6 bits (192), Expect = 1e-18
Identities = 32/54 (59%), Positives = 40/54 (74%), Gaps = 1/54 (1%)
Query: 35 SNWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
W N+++AYEPVW IGTGKVA P QAQEVHA +RK+L + + EVA RI+Y
Sbjct: 153 EEWKNLIIAYEPVWAIGTGKVATPEQAQEVHAFIRKYLAEL-SKEVAEEVRILY 205
>gnl|CDD|237572 PRK13962, PRK13962, bifunctional phosphoglycerate
kinase/triosephosphate isomerase; Provisional.
Length = 645
Score = 76.3 bits (188), Expect = 3e-17
Identities = 31/53 (58%), Positives = 37/53 (69%)
Query: 40 VVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIYRDTV 92
VV+AYEPVW IGTGKVA P QAQEVHA +RK + + E A RI+Y +V
Sbjct: 556 VVIAYEPVWAIGTGKVATPEQAQEVHAFIRKLVAELYGEEAARKVRILYGGSV 608
>gnl|CDD|223227 COG0149, TpiA, Triosephosphate isomerase [Carbohydrate transport
and metabolism].
Length = 251
Score = 70.7 bits (174), Expect = 8e-16
Identities = 29/55 (52%), Positives = 36/55 (65%), Gaps = 2/55 (3%)
Query: 34 ISNWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
+S N+V+AYEPVW IGTGK A PA A+EVHA +R L + AE RI+Y
Sbjct: 155 LSPEANIVIAYEPVWAIGTGKSASPADAEEVHAFIRAVLAELFGAE--EKVRILY 207
>gnl|CDD|184749 PRK14566, PRK14566, triosephosphate isomerase; Provisional.
Length = 260
Score = 70.7 bits (173), Expect = 8e-16
Identities = 28/57 (49%), Positives = 40/57 (70%), Gaps = 1/57 (1%)
Query: 36 NWDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIYRDTV 92
+DN ++AYEP+W +GTGK A P QAQEVHA +RK L + V+ + + RI+Y +V
Sbjct: 166 AFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIRKRLSE-VSPFIGENIRILYGGSV 221
>gnl|CDD|129513 TIGR00419, tim, triosephosphate isomerase. Triosephosphate
isomerase (tim/TPIA) is the glycolytic enzyme that
catalyzes the reversible interconversion of
glyceraldehyde 3-phosphate and dihydroxyacetone
phosphate. The active site of the enzyme is located
between residues 240-258 of the model
([AV]-Y-E-P-[LIVM]-W-[SA]-I-G-T-[GK]) with E being the
active site residue. There is a slight deviation from
this sequence within the archeal members of this family
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 205
Score = 64.1 bits (156), Expect = 1e-13
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 37 WDNVVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
+ V+A EP +IGTG PAQ + VH +R EV S R++
Sbjct: 129 LEPDVVAVEPPELIGTGIPVSPAQPEVVHGSVR------AVKEVNESVRVLC 174
>gnl|CDD|173031 PRK14567, PRK14567, triosephosphate isomerase; Provisional.
Length = 253
Score = 47.3 bits (112), Expect = 3e-07
Identities = 24/49 (48%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 40 VVLAYEPVWVIGTGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIY 88
VV+AYEPVW IGTG VA Q QE H +R L V+ +A + +I+Y
Sbjct: 160 VVIAYEPVWAIGTGVVASLEQIQETHQFIRSLLA-KVDERLAKNIKIVY 207
>gnl|CDD|184898 PRK14905, PRK14905, triosephosphate isomerase/PTS system
glucose/sucrose-specific transporter subunit IIB;
Provisional.
Length = 355
Score = 35.8 bits (82), Expect = 0.003
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 42 LAYEPVWVIGTGKVAVPAQ-AQEVHAELRKWLKDNVNAEVAASTRIIYRDTV-INSTLQL 99
+AYEPVW IG G + A+ A E HA +++ L + + AE + ++Y +V + + +L
Sbjct: 172 IAYEPVWAIGEGGIPASAEYADEKHAIIKQCLFE-LFAEESKKIPVLYGGSVNLENANEL 230
Query: 100 NIQYYYPNLFI 110
++ + LFI
Sbjct: 231 IMKPHIDGLFI 241
>gnl|CDD|237758 PRK14565, PRK14565, triosephosphate isomerase; Provisional.
Length = 237
Score = 31.3 bits (71), Expect = 0.092
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 41 VLAYEPVWVIGTGKV 55
++AYEPVW IG +
Sbjct: 156 IIAYEPVWAIGGSTI 170
>gnl|CDD|185389 PRK15492, PRK15492, triosephosphate isomerase; Provisional.
Length = 260
Score = 31.5 bits (71), Expect = 0.097
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 42 LAYEPVWVIGTGKVAVPAQ-AQEVHAELRKWLKDNVNAEVAASTRIIYRDTV-INSTLQL 99
+AYEPVW IG + A A E HA +++ L + + + + Y +V + +L
Sbjct: 171 IAYEPVWAIGEAGIPASADYADEKHAVIKQCLIE-LFGDAGDDIPVFYGGSVNAENANEL 229
Query: 100 NIQYYYPNLFI 110
Q + LFI
Sbjct: 230 FGQPHIDGLFI 240
>gnl|CDD|203672 pfam07533, BRK, BRK domain. The function of this domain is
unknown. It is often found associated with helicases
and transcription factors.
Length = 45
Score = 27.6 bits (62), Expect = 0.32
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 45 EPVWVI--GTGKVAVPAQAQEVHAELRKWLKDNVNAEVAAS 83
E V VI TGK A ++ +L +WL++N EV
Sbjct: 6 ERVPVINRKTGKRLTGDDAPKLK-DLERWLQENPGYEVDPR 45
>gnl|CDD|197800 smart00592, BRK, domain in transcription and CHROMO domain
helicases.
Length = 45
Score = 26.2 bits (58), Expect = 1.3
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 45 EPVWVIG--TGKVAVPAQAQEVHAELRKWLKDNVNAEVAAS 83
E V VI TGK A + +L +WL++N EVA
Sbjct: 4 ERVPVINRETGKKLTGDDAPKAK-DLERWLEENPEYEVAPR 43
>gnl|CDD|227307 COG4973, XerC, Site-specific recombinase XerC [DNA replication,
recombination, and repair].
Length = 299
Score = 28.1 bits (63), Expect = 1.3
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 36 NWDNVVLAYEPVWVIGTG--KVAVPAQAQEVHAELRKWLK 73
+ +V L V V+G G + VP + V A L WL
Sbjct: 158 DLKHVDLDEGEVRVMGKGNKERRVPVGRKAVEA-LEHWLA 196
>gnl|CDD|181961 PRK09569, PRK09569, type I citrate synthase; Reviewed.
Length = 437
Score = 27.4 bits (61), Expect = 2.7
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 52 TGKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIYRDT 91
TG+V Q QEV AE +K + NV V + R + RD+
Sbjct: 95 TGEVPTQEQVQEVVAEWKK--RQNVPQYVIDAIRALPRDS 132
>gnl|CDD|185763 cd09240, BRO1_Alix, Protein-interacting, N-terminal, Bro1-like
domain of mammalian Alix and related domains. This
family contains the N-terminal, Bro1-like domain of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), also called apoptosis-linked gene-2
interacting protein 1 (AIP1). It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of His-Domain type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Alix
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4,
in the case of Alix. The Alix Bro1-like domain can also
bind human immunodeficiency virus type 1 (HIV-1)
nucleocapsid and Rab5-specfic GAP (RabGAP5, also known
as Rab-GAPLP). In addition to this Bro1-like domain,
Alix has a middle V-shaped (V) domain. The Alix V-domain
is a dimerization domain, and carries a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in the superfamily. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1) and the
apoptotic protein ALG-2.
Length = 346
Score = 26.9 bits (60), Expect = 3.4
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 59 AQAQEV---HAELRKWLKDNVNAEVAASTRIIYRDT 91
AQAQEV A K +KD + A++AA Y D
Sbjct: 191 AQAQEVFYLKATRDK-MKDAIIAKLAAQAADYYGDA 225
>gnl|CDD|130395 TIGR01328, met_gam_lyase, methionine gamma-lyase. This model
describes a methionine gamma-lyase subset of a family of
PLP-dependent trans-sulfuration enzymes. The member from
the parasite Trichomonas vaginalis is described as
catalyzing alpha gamma- and alpha-beta eliminations and
gamma-replacement reactions on methionine, cysteine, and
some derivatives. Likewise, the enzyme from Pseudomonas
degrades cysteine as well as methionine [Energy
metabolism, Amino acids and amines].
Length = 391
Score = 26.4 bits (58), Expect = 4.8
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 8/33 (24%)
Query: 67 ELRKWLKDNVNAEVAASTRIIYRDTVINSTLQL 99
E++ +KDN T+I+Y +T N T++L
Sbjct: 136 EVKAHIKDN--------TKIVYFETPANPTMKL 160
>gnl|CDD|184997 PRK15037, PRK15037, D-mannonate oxidoreductase; Provisional.
Length = 486
Score = 25.8 bits (56), Expect = 8.5
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 53 GKVAVPAQAQEVHAELRKWLKDNVNAEVAASTRIIYRDTVINSTLQL 99
KVAV AQ +L W+++NV RI+ T TLQ
Sbjct: 195 AKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAAT--PETLQE 239
>gnl|CDD|176888 cd08879, RHO_alpha_C_AntDO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of Pseudomonas resinovorans
strain CA10 anthranilate 1,2-dioxygenase and related
aromatic ring hydroxylating dioxygenases. C-terminal
catalytic domain of the oxygenase alpha subunit of
anthranilate 1,2-dioxygenase (AntDO) and related
Rieske-type non-heme iron aromatic ring-hydroxylating
oxygenases (RHOs, also known as aromatic ring
hydroxylating dioxygenases). RHOs utilize non-heme
Fe(II) to catalyze the addition of hydroxyl groups to
the aromatic ring, an initial step in the oxidative
degradation of aromatic compounds. RHOs are composed of
either two or three protein components, and are
comprised of an electron transport chain (ETC) and an
oxygenase. The ETC transfers reducing equivalents from
the electron donor to the oxygenase component, which in
turn transfers electrons to the oxygen molecules. The
oxygenase components are oligomers, either (alpha)n or
(alpha)n(beta)n. The alpha subunits are the catalytic
components and have an N-terminal domain, which binds a
Rieske-like 2Fe-2S cluster, and the C-terminal catalytic
domain which binds the non-heme Fe(II). The Fe(II) is
co-ordinated by conserved His and Asp residues.
Oxygenases belonging to this subgroup include the alpha
subunits of AntDO, aniline dioxygenase, Acinetobacter
calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate
1,2-dioxygenase from Pseudomonas cepacia 2CBS,
2,4,5-trichlorophenoxyacetic acid oxygenase from
Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic
acid oxygenase from Bradyrhizobium sp. strain HW13,
p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase
form Pseudomonas cepacia 2CBS, and Pseudomonas putida
IacC, which may be involved in the catabolism of the
plant hormone indole 3-acetic acid. This subfamily
belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 237
Score = 25.4 bits (56), Expect = 8.7
Identities = 18/49 (36%), Positives = 20/49 (40%), Gaps = 10/49 (20%)
Query: 62 QEVHAELRKWLKDNVNAEVAASTRIIYRDTVINSTLQLNIQYYYPNLFI 110
+ AE R L E A R I R N LNI +PNLFI
Sbjct: 85 KPPIAEYRAALVAAHGEERA---RRILRGRGRN----LNI---FPNLFI 123
>gnl|CDD|99857 cd06103, ScCS-like, Saccharomyces cerevisiae (Sc) citrate synthase
(CS)-like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) with oxaloacetate (OAA) to form
citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). Some CS proteins
function as 2-methylcitrate synthase (2MCS). 2MCS
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and OAA to form 2-methylcitrate and CoA during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). This group includes three S.
cerevisiae CS proteins, ScCit1,-2,-3. ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA; in addition to having activity with AcCoA, it
plays a part in the construction of the TCA cycle
metabolon. Yeast cells deleted for Cit1 are
hyper-susceptible to apoptosis induced by heat and aging
stress. ScCit2 is a peroxisomal CS involved in the
glyoxylate cycle; in addition to having activity with
AcCoA, it may have activity with PrCoA. ScCit3 is a
mitochondrial CS and functions in the metabolism of
PrCoA; it is a dual specificity CS and 2MCS, having
similar catalytic efficiency with both AcCoA and PrCoA.
The pattern of expression of the ScCIT3 gene follows
that of the ScCIT1 gene and its expression is increased
in the presence of a ScCIT1 deletion. Included in this
group is the Tetrahymena 14 nm filament protein which
functions as a CS in mitochondria and as a cytoskeletal
component in cytoplasm and Geobacter sulfurreducens
(GSu) CS. GSuCS is dimeric and eukaryotic-like; it lacks
2MCS activity and is inhibited by ATP. In contrast to
eukaryotic and other prokaryotic CSs, GSuCIT is not
stimulated by K+ ions. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS.
Length = 426
Score = 25.7 bits (57), Expect = 8.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 48 WVIGTGKVAVPAQAQEVHAELRK 70
W++ TG+V Q E+ E K
Sbjct: 89 WLLLTGEVPTEEQVDELSKEWAK 111
>gnl|CDD|233575 TIGR01783, TonB-siderophor, TonB-dependent siderophore receptor.
This subfamily model encompasses a wide variety of
TonB-dependent outer membrane siderophore receptors. It
has no overlap with TonB receptors known to transport
other substances, but is likely incomplete due to lack
of characterizations. It is likely that genuine
siderophore receptors will be identified which score
below the noise cutoff to this model at which point the
model should be updated [Transport and binding proteins,
Cations and iron carrying compounds, Transport and
binding proteins, Porins].
Length = 651
Score = 25.8 bits (57), Expect = 9.0
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 94 NSTLQLNIQYYYPNLFIELTLAFSIRYQGDVFS 126
T L Y P LTL ++Y G +
Sbjct: 548 KHTASLWASYAPPVGDNGLTLGGGVQYTGKAYV 580
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
0.325 0.141 0.435
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,686,003
Number of extensions: 583792
Number of successful extensions: 723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 720
Number of HSP's successfully gapped: 36
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)