RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029253
(196 letters)
>gnl|CDD|215430 PLN02800, PLN02800, imidazoleglycerol-phosphate dehydratase.
Length = 261
Score = 215 bits (549), Expect = 7e-71
Identities = 113/172 (65%), Positives = 127/172 (73%), Gaps = 5/172 (2%)
Query: 15 SSTSSRRLLVKPKTNLSRKLLPISTQYCSSTRRMNSLTTPRASLNPDGDSKHNNGSASTS 74
S++SS L++PK + LLP SS S S +AS+S
Sbjct: 4 SASSSAAQLLRPKLS-FIDLLPRRAAIVSSPSSSLPRFLRMESQLRQSIS----CAASSS 58
Query: 75 SAVDSGRIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRA 134
S+ GRIGEVKRVTKETNVSVKIN+DG+GVADSST IPFLDHMLDQLASHGLFDVHV+A
Sbjct: 59 SSNALGRIGEVKRVTKETNVSVKINLDGTGVADSSTGIPFLDHMLDQLASHGLFDVHVKA 118
Query: 135 TGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSL 186
TGD+ IDDHHTNEDV LAIGTALL+ALGDRKGINRFGDF+APLDEALI V L
Sbjct: 119 TGDLWIDDHHTNEDVALAIGTALLKALGDRKGINRFGDFSAPLDEALIEVVL 170
Score = 27.1 bits (60), Expect = 5.5
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 115 LDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQA 160
++H L ++ VH+R + HH E A G AL Q
Sbjct: 197 VEHFFQSLVNNSGMTVHIRQLAAGK-NSHHIIEATAKAFGRALRQC 241
>gnl|CDD|234873 PRK00951, hisB, imidazoleglycerol-phosphate dehydratase; Validated.
Length = 195
Score = 193 bits (493), Expect = 4e-63
Identities = 63/106 (59%), Positives = 83/106 (78%)
Query: 81 RIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRATGDIHI 140
R EV+R TKET++SV++N+DG+G +D T + FLDHMLDQ A HGLFD+ V+A GD+HI
Sbjct: 3 RTAEVERKTKETDISVELNLDGTGKSDIDTGVGFLDHMLDQFARHGLFDLTVKAKGDLHI 62
Query: 141 DDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSL 186
DDHHT EDVG+ +G AL +ALGD+KGI R+G P+DEAL V++
Sbjct: 63 DDHHTVEDVGIVLGQALKEALGDKKGIRRYGHAYVPMDEALARVAV 108
>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 = 184 bits (470), Expect = 1e-59
Identities = 54/104 (51%), Positives = 75/104 (72%)
Query: 83 GEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRATGDIHIDD 142
E++R TKET++ V++N+DG+G + T I F DHML A HG FD+ V+A GD+ +DD
Sbjct: 1 AEIERKTKETDIEVELNLDGTGKSKIDTGIGFFDHMLTLFARHGGFDLTVKAKGDLEVDD 60
Query: 143 HHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSL 186
HHT EDVG+ +G AL +ALGD+KGI R+G P+DEAL V++
Sbjct: 61 HHTVEDVGIVLGQALKKALGDKKGIRRYGSALVPMDEALARVAV 104
>gnl|CDD|223209 COG0131, HisB, Imidazoleglycerol-phosphate dehydratase [Amino acid
transport and metabolism].
Length = 195
Score = 176 bits (449), Expect = 2e-56
Identities = 59/106 (55%), Positives = 77/106 (72%)
Query: 81 RIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRATGDIHI 140
R EV R TKET++ V +++DG+G + T + F DHMLDQLA HG FD+ V A GD+HI
Sbjct: 4 RTAEVTRKTKETDIEVSLDLDGTGKSKIDTGVGFFDHMLDQLARHGGFDLEVSAKGDLHI 63
Query: 141 DDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSL 186
DDHHT ED G+A+G AL +ALGD++GI RFG P+DEAL V++
Sbjct: 64 DDHHTVEDTGIALGQALKEALGDKRGIRRFGSAYVPMDEALARVAV 109
>gnl|CDD|235471 PRK05446, PRK05446, imidazole glycerol-phosphate
dehydratase/histidinol phosphatase; Provisional.
Length = 354
Score = 164 bits (419), Expect = 5e-50
Identities = 55/109 (50%), Positives = 73/109 (66%), Gaps = 1/109 (0%)
Query: 78 DSGRIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRATGD 137
R V R TKET++ V++ +D G + +T I F DHMLDQ+A+HG F + ++ GD
Sbjct: 163 KRDRYAHVVRNTKETDIDVEVWLDREGKSKINTGIGFFDHMLDQIATHGGFRLEIKVKGD 222
Query: 138 IHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSL 186
+HIDDHHT ED LA+G AL QALGD++GI RFG F P+DE L +L
Sbjct: 223 LHIDDHHTVEDTALALGEALKQALGDKRGIGRFG-FVLPMDECLARCAL 270
>gnl|CDD|189563 pfam00475, IGPD, Imidazoleglycerol-phosphate dehydratase.
Length = 145
Score = 143 bits (363), Expect = 4e-44
Identities = 48/77 (62%), Positives = 58/77 (75%)
Query: 110 TCIPFLDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINR 169
T I F DHML+Q A HG FD+ V+A GD+ IDDHHT EDVG+ +G AL QALGD+KGI R
Sbjct: 1 TGIGFFDHMLEQFAKHGGFDLTVKAKGDLEIDDHHTVEDVGIVLGQALKQALGDKKGIRR 60
Query: 170 FGDFTAPLDEALIHVSL 186
FG T P+DEAL V++
Sbjct: 61 FGSATVPMDEALAEVAV 77
>gnl|CDD|184171 PRK13598, hisB, imidazoleglycerol-phosphate dehydratase;
Provisional.
Length = 193
Score = 93.7 bits (233), Expect = 4e-24
Identities = 45/106 (42%), Positives = 63/106 (59%)
Query: 81 RIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFLDHMLDQLASHGLFDVHVRATGDIHI 140
R + R TKET + V +++D G ST +PF +HML L ++ V AT +
Sbjct: 3 RNANITRETKETKIEVFLDIDRKGEIKVSTPVPFFNHMLITLLTYMNSTATVSATDKLPY 62
Query: 141 DDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEALIHVSL 186
DDHH EDV + +G A+ +ALGD++GI RF P+DEAL+ VSL
Sbjct: 63 DDHHIVEDVAITLGLAIKEALGDKRGIKRFSHQIIPMDEALVLVSL 108
>gnl|CDD|133065 cd06915, NTP_transferase_WcbM_like, WcbM_like is a subfamily of
nucleotidyl transferases. WcbM protein of Burkholderia
mallei is involved in the biosynthesis, export or
translocation of capsule. It is a subfamily of
nucleotidyl transferases that transfer nucleotides onto
phosphosugars.
Length = 223
Score = 29.1 bits (66), Expect = 1.3
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 113 PFLDHMLDQLASHGLFDV 130
PFL+++L+ LA G+ +
Sbjct: 30 PFLEYLLEYLARQGISRI 47
>gnl|CDD|178201 PLN02591, PLN02591, tryptophan synthase.
Length = 250
Score = 28.9 bits (65), Expect = 1.6
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 150 GLAIGTALLQALGDRK----GINRFGDFTAPLDEAL 181
G+ +G+A+++ALG+ K G+ R L AL
Sbjct: 214 GVIVGSAMVKALGEAKSPEEGLKRLEKLAKSLKAAL 249
>gnl|CDD|224584 COG1670, RimL, Acetyltransferases, including N-acetylases of
ribosomal proteins [Translation, ribosomal structure and
biogenesis].
Length = 187
Score = 28.0 bits (62), Expect = 2.6
Identities = 13/63 (20%), Positives = 21/63 (33%)
Query: 122 LASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPLDEAL 181
L+ A +D + + ALL + G++R P +EA
Sbjct: 85 LSDIDRAANGDLAEIGYWLDPEYWGKGYATEALRALLDYAFEELGLHRIEATVDPENEAS 144
Query: 182 IHV 184
I V
Sbjct: 145 IRV 147
>gnl|CDD|238510 cd01040, globin, Globins are heme proteins, which bind and
transport oxygen. This family summarizes a diverse set
of homologous protein domains, including: (1) tetrameric
vertebrate hemoglobins, which are the major protein
component of erythrocytes and transport oxygen in the
bloodstream, (2) microorganismal flavohemoglobins, which
are linked to C-terminal FAD-dependend reductase
domains, (3) homodimeric bacterial hemoglobins, such as
from Vitreoscilla, (4) plant leghemoglobins (symbiotic
hemoglobins, involved in nitrogen metabolism in plant
rhizomes), (5) plant non-symbiotic hexacoordinate
globins and hexacoordinate globins from bacteria and
animals, such as neuroglobin, (6) invertebrate
hemoglobins, which may occur in tandem-repeat
arrangements, and (7) monomeric myoglobins found in
animal muscle tissue.
Length = 140
Score = 27.0 bits (60), Expect = 3.9
Identities = 17/67 (25%), Positives = 22/67 (32%), Gaps = 5/67 (7%)
Query: 114 FLDHMLDQLASHGLFDVHVRATGDIHIDDHHTNEDVGLAIGTALLQALGDRKGINRFGDF 173
LD + L + G H E L G ALL+ L + G DF
Sbjct: 67 ALDEAIKNLDDLEALKALLAKLGRKHAKRGVDPEHFKL-FGEALLEVLAEVLG----DDF 121
Query: 174 TAPLDEA 180
T + A
Sbjct: 122 TPEVKAA 128
>gnl|CDD|133014 cd02523, PC_cytidylyltransferase, Phosphocholine
cytidylyltransferases catalyze the synthesis of
CDP-choline. This family contains proteins similar to
prokaryotic phosphocholine (P-cho)
cytidylyltransferases. Phosphocholine (PC)
cytidylyltransferases catalyze the transfer of a
cytidine monophosphate from CTP to phosphocholine to
form CDP-choline. PC is the most abundant phospholipid
in eukaryotic membranes and it is also important in
prokaryotic membranes. For pathogenic prokaryotes, the
cell surface PC facilitates the interaction with host
surface and induces attachment and invasion. In addition
cell wall PC serves as scaffold for a group of
choline-binding proteins that are secreted from the
cells. Phosphocholine (PC) cytidylyltransferase is a key
enzyme in the prokaryotic choline metabolism pathway. It
has been hypothesized to consist of a choline transport
system, a choline kinase, CTP:phosphocholine
cytidylyltransferase, and a choline phosphotransferase
that transfers P-Cho from CDP-Cho to either lipoteichoic
acid or lipopolysaccharide.
Length = 229
Score = 27.6 bits (62), Expect = 4.2
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 112 IPFLDHMLDQLASHGLFDVHV 132
P L+ ++ L G+ D+ +
Sbjct: 29 KPLLERQIETLKEAGIDDIVI 49
>gnl|CDD|215454 PLN02845, PLN02845, Branched-chain-amino-acid aminotransferase-like
protein.
Length = 336
Score = 27.3 bits (61), Expect = 4.8
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 111 CIPFLDHMLDQLASHGLFDVHVRATGDIHIDDHH 144
IP DHM+ + HG+FD G ++ D H
Sbjct: 56 VIPLDDHMVHR--GHGVFDTATIRDGHLYELDAH 87
>gnl|CDD|187655 cd08952, KR_1_SDR_x, ketoreductase (KR), subgroup 1, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
KR domains found in many multidomain PKSs, including six
of seven Sorangium cellulosum PKSs (encoded by
spiDEFGHIJ) which participate in the synthesis of the
polyketide scaffold of the cytotoxic spiroketal
polyketide spirangien. These seven PKSs have either a
single PKS module (SpiF), two PKR modules
(SpiD,-E,-I,-J), or three PKS modules (SpiG,-H). This
subfamily includes the single KR domain of SpiF, the
first KR domains of SpiE,-G,H,-I,and #J, the third KR
domain of SpiG, and the second KR domain of SpiH. The
second KR domains of SpiE,-G, I, and #J, and the KR
domains of SpiD, belong to a different KR_FAS_SDR
subfamily. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) 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. Extended SDRs have additional
elements in the C-terminal region, 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 KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 480
Score = 27.5 bits (62), Expect = 5.2
Identities = 14/37 (37%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 141 DDHHTNEDVGLAIGTALLQALGDRKGINRFGDFTAPL 177
H GLA AL+QALGD APL
Sbjct: 103 HPDHPAVPAGLAATLALVQALGDA-------GVDAPL 132
>gnl|CDD|112770 pfam03971, IDH, Monomeric isocitrate dehydrogenase.
NADP(+)-dependent isocitrate dehydrogenase (ICD) is an
important enzyme of the intermediary metabolism, as it
controls the carbon flux within the citric acid cycle
and supplies the cell with 2-oxoglutarate EC:1.1.1.42
and NADPH for biosynthetic purposes.
Length = 735
Score = 27.5 bits (61), Expect = 5.6
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 5/80 (6%)
Query: 61 DGDSKHNNGSASTSSAVD-----SGRIGEVKRVTKETNVSVKINVDGSGVADSSTCIPFL 115
GD + S + + A + G+VK + + +D ++ + F
Sbjct: 174 GGDFFGSEKSMTLAQAGMVRIEFVAKDGKVKVLKDPVALQAGEIIDAMVMSKKALADFFE 233
Query: 116 DHMLDQLASHGLFDVHVRAT 135
+ M D + LF +HV+AT
Sbjct: 234 EQMQDAKETGVLFSLHVKAT 253
>gnl|CDD|237413 PRK13528, PRK13528, outer membrane receptor FepA; Provisional.
Length = 727
Score = 27.4 bits (61), Expect = 6.5
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 9/33 (27%)
Query: 62 GDSKHNNGSASTSSAVDSGRIGEVKRVTKETNV 94
GD++++N SA T S SG KETN
Sbjct: 280 GDTQNSNSSAVTESLAKSG---------KETNR 303
>gnl|CDD|215210 PLN02370, PLN02370, acyl-ACP thioesterase.
Length = 419
Score = 26.9 bits (59), Expect = 7.5
Identities = 21/66 (31%), Positives = 26/66 (39%), Gaps = 8/66 (12%)
Query: 4 SVPARLVHLSISSTSSRRLLVK------PKTNLSRKLLPISTQYCSSTRRMNSLTTPRAS 57
S A L + S SS L VK PK N S L S + + + S PR
Sbjct: 27 SGSASLGGIKSKSASSGALQVKANAQAPPKINGSPVGLTGSVEIVKTDEDVVSSPAPRTF 86
Query: 58 LN--PD 61
+N PD
Sbjct: 87 INQLPD 92
>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated.
Length = 83
Score = 25.4 bits (56), Expect = 7.5
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 75 SAVDSGRIGEVKRVTKETNVSVKINVDG 102
S D G+IGEV ++ K++N K+ V G
Sbjct: 19 SGSDKGKIGEVLKIIKKSN---KVIVKG 43
>gnl|CDD|240513 cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26. RPL26 and
its bacterial paralogs RPL24 have a KOW motif at their N
terminal. KOW domain is known as an RNA-binding motif
that is shared so far among some families of ribosomal
proteins, the essential bacterial transcriptional
elongation factor NusG, the eukaryotic chromatin
elongation factor Spt5, the higher eukaryotic KIN17
proteins and Mtr4. RPL26 makes a very minor
contributions to the biogenesis, structure, and function
of 60s ribosomal subunits. However, RPL24 is essential
to generate the first intermediate during 50s ribosomal
subunits assembly. RPL26 have an extra-ribosomal
function to enhances p53 translation after DNA damage.
Length = 65
Score = 24.8 bits (55), Expect = 8.8
Identities = 8/25 (32%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 78 DSGRIGEVKRVTKETNVSVKINVDG 102
D G+ G+V +V ++ N ++ V+G
Sbjct: 11 DKGKQGKVLKVDRKKN---RVIVEG 32
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
0.317 0.132 0.375
Gapped
Lambda K H
0.267 0.0618 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,483,331
Number of extensions: 845528
Number of successful extensions: 807
Number of sequences better than 10.0: 1
Number of HSP's gapped: 806
Number of HSP's successfully gapped: 32
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
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: 56 (25.6 bits)