RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15130
(263 letters)
>gnl|CDD|214968 smart01004, ALAD, Delta-aminolevulinic acid dehydratase. This
entry represents porphobilinogen (PBG) synthase (PBGS,
or 5-aminoaevulinic acid dehydratase, or ALAD, ), which
functions during the second stage of tetrapyrrole
biosynthesis. This enzyme catalyses a Knorr-type
condensation reaction between two molecules of ALA to
generate porphobilinogen, the pyrrolic building block
used in later steps. The structure of the enzyme is
based on a TIM barrel topology made up of eight
identical subunits, where each subunit binds to a metal
ion that is essential for activity, usually zinc (in
yeast, mammals and certain bacteria) or magnesium (in
plants and other bacteria). A lysine has been implicated
in the catalytic mechanism. The lack of PBGS enzyme
causes a rare porphyric disorder known as ALAD
porphyria, which appears to involve conformational
changes in the enzyme.
Length = 321
Score = 78.6 bits (195), Expect = 6e-17
Identities = 28/56 (50%), Positives = 33/56 (58%), Gaps = 11/56 (19%)
Query: 160 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHFEANEKAM 215
A D+++GAD +MVKPALPYLDII VK P+ YQ VSG E AM
Sbjct: 234 ALDIAEGADMVMVKPALPYLDIIRRVKDEFD-LPVAAYQ-----VSG-----EYAM 278
>gnl|CDD|215945 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.
Length = 322
Score = 78.2 bits (194), Expect = 7e-17
Identities = 29/56 (51%), Positives = 33/56 (58%), Gaps = 11/56 (19%)
Query: 160 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHFEANEKAM 215
A D+ +GAD +MVKPALPYLDII VK R P+ YQ VSG E AM
Sbjct: 235 ALDIEEGADMVMVKPALPYLDIIRRVKDRFD-LPVAAYQ-----VSG-----EYAM 279
>gnl|CDD|236450 PRK09283, PRK09283, delta-aminolevulinic acid dehydratase;
Validated.
Length = 323
Score = 76.6 bits (190), Expect = 3e-16
Identities = 28/56 (50%), Positives = 32/56 (57%), Gaps = 11/56 (19%)
Query: 160 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHFEANEKAM 215
A D+ +GAD +MVKPALPYLDII VK P+ YQ VSG E AM
Sbjct: 235 ALDIEEGADMVMVKPALPYLDIIRRVKDEFN-LPVAAYQ-----VSG-----EYAM 279
>gnl|CDD|240128 cd04824, eu_ALAD_PBGS_cysteine_rich, Porphobilinogen synthase
(PBGS), which is also called delta-aminolevulinic acid
dehydratase (ALAD), catalyzes the condensation of two
5-aminolevulinic acid (ALA) molecules to form the
pyrrole porphobilinogen (PBG), which is the second step
in the biosynthesis of tetrapyrroles, such as heme,
vitamin B12 and chlorophyll. This reaction involves the
formation of a Schiff base link between the substrate
and the enzyme. PBGSs are metalloenzymes, some of which
have a second, allosteric metal binding site, beside the
metal ion binding site in their active site. Although
PBGS is a family of homologous enzymes, its metal ion
utilization at catalytic site varies between zinc and
magnesium and/or potassium. PBGS can be classified into
two groups based on differences in their active site
metal binding site. The eukaryotic PBGSs represented by
this model, which contain a cysteine-rich zinc binding
motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their
activity, they do not contain an additional allosteric
metal binding site and do not bind magnesium.
Length = 320
Score = 74.3 bits (183), Expect = 2e-15
Identities = 28/51 (54%), Positives = 33/51 (64%), Gaps = 5/51 (9%)
Query: 158 AQARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHF 208
A RDVS+GAD +MVKP PYLDI+ E K +HP PL VY VSG +
Sbjct: 230 AVERDVSEGADMIMVKPGTPYLDIVREAKDKHPDLPLAVYH-----VSGEY 275
>gnl|CDD|238226 cd00384, ALAD_PBGS, Porphobilinogen synthase (PBGS), which is also
called delta-aminolevulinic acid dehydratase (ALAD),
catalyzes the condensation of two 5-aminolevulinic acid
(ALA) molecules to form the pyrrole porphobilinogen
(PBG), which is the second step in the biosynthesis of
tetrapyrroles, such as heme, vitamin B12 and
chlorophyll. This reaction involves the formation of a
Schiff base link between the substrate and the enzyme.
PBGSs are metalloenzymes, some of which have a second,
allosteric metal binding site, beside the metal ion
binding site in their active site. Although PBGS is a
family of homologous enzymes, its metal ion utilization
at catalytic site varies between zinc and magnesium
and/or potassium. PBGS can be classified into two groups
based on differences in their active site metal binding
site. They either contain a cysteine-rich zinc binding
site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an
aspartate-rich magnesium binding site (consensus
DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding
site appears more common. Most members represented by
this model also have a second allosteric magnesium
binding site (consensus RX~164DX~65EXXXD, missing in a
eukaryotic subfamily with cysteine-rich zinc binding
site).
Length = 314
Score = 73.7 bits (182), Expect = 3e-15
Identities = 26/56 (46%), Positives = 31/56 (55%), Gaps = 11/56 (19%)
Query: 160 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHFEANEKAM 215
D+ +GAD LMVKPAL YLDII +V+ R P+ Y VSG E AM
Sbjct: 227 ELDIEEGADILMVKPALAYLDIIRDVRERFD-LPVAAYN-----VSG-----EYAM 271
>gnl|CDD|223191 COG0113, HemB, Delta-aminolevulinic acid dehydratase [Coenzyme
metabolism].
Length = 330
Score = 71.0 bits (175), Expect = 2e-14
Identities = 28/56 (50%), Positives = 31/56 (55%), Gaps = 11/56 (19%)
Query: 160 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHFEANEKAM 215
D+ +GAD LMVKPALPYLDII VK P+ YQ VSG E AM
Sbjct: 240 ELDIEEGADILMVKPALPYLDIIRRVKEEFNL-PVAAYQ-----VSG-----EYAM 284
>gnl|CDD|240127 cd04823, ALAD_PBGS_aspartate_rich, Porphobilinogen synthase (PBGS),
which is also called delta-aminolevulinic acid
dehydratase (ALAD), catalyzes the condensation of two
5-aminolevulinic acid (ALA) molecules to form the
pyrrole porphobilinogen (PBG), which is the second step
in the biosynthesis of tetrapyrroles, such as heme,
vitamin B12 and chlorophyll. This reaction involves the
formation of a Schiff base link between the substrate
and the enzyme. PBGSs are metalloenzymes, some of which
have a second, allosteric metal binding site, beside the
metal ion binding site in their active site. Although
PBGS is a family of homologous enzymes, its metal ion
utilization at catalytic site varies between zinc and
magnesium and/or potassium. PBGS can be classified into
two groups based on differences in their active site
metal binding site. All of PBGS_aspartate_rich contain
an aspartate rich metal binding site with the general
sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an
allosteric magnesium binding sequence RX~164DX~65EXXXD
and are activated by magnesium and/or potassium, but not
by zinc. PBGSs_aspartate_rich are found in some
bacterial species and photosynthetic organisms such as
vascular plants, mosses and algae, but not in archaea.
Length = 320
Score = 66.8 bits (164), Expect = 7e-13
Identities = 27/56 (48%), Positives = 32/56 (57%), Gaps = 11/56 (19%)
Query: 160 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHFEANEKAM 215
A D+++GAD +MVKP +PYLDII VK P F YQ VSG E AM
Sbjct: 232 ALDIAEGADMVMVKPGMPYLDIIRRVKDEFGV-PTFAYQ-----VSG-----EYAM 276
>gnl|CDD|172020 PRK13384, PRK13384, delta-aminolevulinic acid dehydratase;
Provisional.
Length = 322
Score = 52.4 bits (126), Expect = 5e-08
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 162 DVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQERCITVSGHF 208
D ++GAD LMVKP PYLD++S ++ PL YQ V G +
Sbjct: 238 DEAEGADILMVKPGTPYLDVLSRLRQETH-LPLAAYQ-----VGGEY 278
>gnl|CDD|215237 PLN02433, PLN02433, uroporphyrinogen decarboxylase.
Length = 345
Score = 34.1 bits (79), Expect = 0.058
Identities = 13/24 (54%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 175 ALPYLD-IISEVKSRHPAYPLFVY 197
+ PYL+ I+ EVK+RHP PL +Y
Sbjct: 215 SKPYLEKIVDEVKARHPDVPLILY 238
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 30.3 bits (69), Expect = 0.13
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 198 QERCITVSGHFEANEKAMEMILEKI 222
+ER + ++G E EKA E+ILE +
Sbjct: 44 EERVVEITGPPENVEKAAELILEIL 68
>gnl|CDD|115378 pfam06716, DUF1201, Protein of unknown function (DUF1201). This
family consists of several Sugar beet yellow virus
(SBYV) putative membrane-binding proteins of around 54
residues in length. The function of this family is
unknown.
Length = 54
Score = 30.3 bits (68), Expect = 0.14
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 14 MSCLVSSRLVLSCLVLSCLVLSCLPAFLWWV-------QTCAMQRAKHLHCTL 59
M C++ S L+L+ L CL L CL F+W+V T A+ H T+
Sbjct: 1 MDCVLRSYLLLAFGFLICLFLFCLVVFIWFVYKQILFRNTAPSNEARFNHSTV 53
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 29.1 bits (66), Expect = 0.36
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 198 QERCITVSGHFEANEKAMEMIL 219
+ER +T++G EA EKA E+IL
Sbjct: 43 EERIVTITGTPEAVEKAKELIL 64
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 65
Score = 28.2 bits (64), Expect = 0.89
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 198 QERCITVSGHFEANEKAMEMIL 219
ER +T+SG A +KA+ +IL
Sbjct: 44 TERVVTISGKPSAVQKALLLIL 65
>gnl|CDD|148808 pfam07410, Phage_Gp111, Streptococcus thermophilus bacteriophage
Gp111 protein. This family consists of several
Streptococcus thermophilus bacteriophage Gp111 proteins
of around 110 residues in length. The function of this
family is unknown.
Length = 116
Score = 29.1 bits (64), Expect = 1.1
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 95 ALHDAW-QTRPIQTSATHIKDIRQKTANLSDTHKRLLQCSKTLLQLNFLKHVQTNE 149
AL AW + TS K I +K C++ +L L+F K V+ NE
Sbjct: 26 ALKMAWSDAKGSNTSLAEFKAIEEKLREAGGKEYSAHNCNRMILTLDFAKEVKFNE 81
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 26.8 bits (60), Expect = 2.1
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 199 ERCITVSGHFEANEKAMEMI 218
+ +T+SG E EKA E+I
Sbjct: 40 DDTVTISGTPEQVEKAKELI 59
>gnl|CDD|227095 COG4753, COG4753, Response regulator containing CheY-like receiver
domain and AraC-type DNA-binding domain [Signal
transduction mechanisms].
Length = 475
Score = 28.1 bits (63), Expect = 6.0
Identities = 16/114 (14%), Positives = 32/114 (28%), Gaps = 10/114 (8%)
Query: 117 QKTANLSDTHKRLLQCSKTLLQLNFLKHVQTNEFHCIARCIAQARDVSQGADFLMVKPAL 176
+K L H+ L + +K + + +Q+ A + +L
Sbjct: 134 EKLLTLLIGHEPLEELAKKIYKWEGATGIQSQLADSQRTLKDLAEHLELSPSYLSQLFKE 193
Query: 177 PYLDIISEVKSRHPAYPLFVYQERCITVS------GHFEANEKAMEMILEKIAE 224
I E A +QE + +E+ +L+ E
Sbjct: 194 EVGLFILERFLIRSAP----FQEYGLLRKRLEQAKLLLVTSEQVSIYVLKVYRE 243
>gnl|CDD|182036 PRK09700, PRK09700, D-allose transporter ATP-binding protein;
Provisional.
Length = 510
Score = 27.8 bits (62), Expect = 6.9
Identities = 12/24 (50%), Positives = 20/24 (83%)
Query: 114 DIRQKTANLSDTHKRLLQCSKTLL 137
D+ +K ANLS +HK++L+ +KTL+
Sbjct: 138 DLDEKVANLSISHKQMLEIAKTLM 161
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 0.134 0.417
Gapped
Lambda K H
0.267 0.0905 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,445,916
Number of extensions: 1092650
Number of successful extensions: 1323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1323
Number of HSP's successfully gapped: 24
Length of query: 263
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 168
Effective length of database: 6,723,972
Effective search space: 1129627296
Effective search space used: 1129627296
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 (21.7 bits)
S2: 58 (25.8 bits)