RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17338
(130 letters)
>gnl|CDD|109891 pfam00853, Runt, Runt domain.
Length = 134
Score = 191 bits (486), Expect = 3e-64
Identities = 76/94 (80%), Positives = 86/94 (91%)
Query: 23 RTLDSLLAEHPGELTRTGCPHVVCTVLPTHWRSNKTLPVAFKVVALGDVMDGTIVTIRAG 82
R++ +LAEHPGEL +TG P+ +C+VLP+HWRSNKTLPVAFKVVALG+V DGT+VTIRAG
Sbjct: 1 RSVVEVLAEHPGELVKTGSPNFLCSVLPSHWRSNKTLPVAFKVVALGEVPDGTMVTIRAG 60
Query: 83 NDENYCGELRNCTAVMKNQVAKFNDLRFVGRSGR 116
NDENYC ELRN TAVMKNQVAKFNDLRFVGRSGR
Sbjct: 61 NDENYCAELRNATAVMKNQVAKFNDLRFVGRSGR 94
>gnl|CDD|224135 COG1214, COG1214, Inactive homolog of metal-dependent proteases,
putative molecular chaperone [Posttranslational
modification, protein turnover, chaperones].
Length = 220
Score = 30.1 bits (68), Expect = 0.23
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 77 VTIRAGNDENYCGELRNCTAVMKNQVAKFNDLR 109
V I A E Y E + + + V +L
Sbjct: 115 VAIDARRGEVYWAEYQRSGGLEEEAVLSAEELF 147
>gnl|CDD|198029 smart00961, RuBisCO_small, Ribulose bisphosphate carboxylase,
small chain. RuBisCO (ribulose-1,5-bisphosphate
carboxylase/oxygenase) is a bifunctional enzyme that
catalyses both the carboxylation and oxygenation of
ribulose-1,5-bisphosphate (RuBP), thus fixing carbon
dioxide as the first step of the Calvin cycle. RuBisCO
is the major protein in the stroma of chloroplasts, and
in higher plants exists as a complex of 8 large and 8
small subunits. The function of the small subunit is
unknown. While the large subunit is coded for by a
single gene, the small subunit is coded for by several
different genes, which are distributed in a tissue
specific manner. They are transcriptionally regulated
by light receptor phytochrome. which results in RuBisCO
being more abundant during the day when it is required.
Length = 96
Score = 27.9 bits (63), Expect = 0.81
Identities = 15/23 (65%), Positives = 18/23 (78%), Gaps = 2/23 (8%)
Query: 16 SAEVLAERTLDSLLAEHPGELTR 38
+AEVLAE L++ LAEHPGE R
Sbjct: 56 AAEVLAE--LEACLAEHPGEYVR 76
>gnl|CDD|214805 smart00756, VKc, Family of likely enzymes that includes the
catalytic subunit of vitamin K epoxide reductase.
Bacterial homologues are fused to members of the
thioredoxin family of oxidoreductases.
Length = 142
Score = 28.1 bits (63), Expect = 0.91
Identities = 8/52 (15%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 53 WRSNKTLPVAFKVVALGDVMDGTIVTIRAGNDENY---C--GELRNCTAVMK 99
R + + + ++ L + T + D +Y C + +C V+
Sbjct: 1 PRWTRWILLILGLIGLLASLYLTYEKLTLLEDPDYVASCDINPVVSCGKVLS 52
>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 = 27.8 bits (63), Expect = 1.8
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR DE
Sbjct: 153 IVAPSDMMDGRVAAIREALDEA 174
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). SLT11 can facilitate the cooperative formation
of U2/U6 helix II in association with stem II in the
yeast spliceosome by utilizing its RNA-annealing and
-binding activities. .
Length = 86
Score = 26.6 bits (59), Expect = 2.0
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 3/34 (8%)
Query: 16 SAEVLAERTLDSLL---AEHPGELTRTGCPHVVC 46
+AE A ++ L G L GCP V
Sbjct: 50 AAEKFAAAISENGLNAGLSRGGLLVLEGCPLRVA 83
>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 = 27.0 bits (61), Expect = 2.7
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR D
Sbjct: 160 IVAPSDMMDGRVGAIREALDAA 181
>gnl|CDD|181159 PRK07890, PRK07890, short chain dehydrogenase; Provisional.
Length = 258
Score = 26.8 bits (60), Expect = 3.3
Identities = 23/89 (25%), Positives = 33/89 (37%), Gaps = 16/89 (17%)
Query: 19 VLAERTLDSLLAEHPGELTRTG---------------CPHVVCTVLPTHWRSNKTLPVAF 63
VLA RT L E E+ G C ++V L R + + AF
Sbjct: 33 VLAART-AERLDEVAAEIDDLGRRALAVPTDITDEDQCANLVALALERFGRVDALVNNAF 91
Query: 64 KVVALGDVMDGTIVTIRAGNDENYCGELR 92
+V ++ + D RA + N G LR
Sbjct: 92 RVPSMKPLADADFAHWRAVIELNVLGTLR 120
>gnl|CDD|238187 cd00307, RuBisCO_small_like, Ribulose bisphosphate
carboxylase/oxygenase (Rubisco), small subunit and
related proteins. Rubisco is a bifunctional enzyme
catalyzes the initial steps of two opposing metabolic
pathways: photosynthetic carbon fixation and the
competing process of photorespiration. Rubisco Form I,
present in plants and green algae, is composed of eight
large and eight small subunits. The nearly identical
small subunits are encoded by a family of nuclear
genes. After translation, the small subunits are
translocated across the chloroplast membrane, where an
N-terminal signal peptide is cleaved off. While the
large subunits contain the catalytic activities, it has
been shown that the small subunits are important for
catalysis by enhancing the catalytic rate through
inducing conformational changes in the large subunits.
This superfamily also contains specific proteins from
cyanobacteria. CcmM plays a role in a CO2 concentrating
mechanism, which cyanobacteria need to to overcome the
low specificity of their Rubisco and fusions to Rubisco
activase, a type of chaperone, which promotes and
maintains the catalytic activity of Rubisco. CcmM
contains an N-terminal carbonic anhydrase fused to four
copies of the Rubisco-small subunit domain.
Length = 84
Score = 25.7 bits (57), Expect = 3.6
Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 16 SAEVLAERTLDSLLAEHPGELTR 38
A+VLA L++ LAEHPGE R
Sbjct: 44 EAQVLAA--LEACLAEHPGEYVR 64
>gnl|CDD|215945 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.
Length = 322
Score = 26.6 bits (60), Expect = 3.9
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR DE
Sbjct: 161 IVAPSDMMDGRVGAIREALDEA 182
>gnl|CDD|236450 PRK09283, PRK09283, delta-aminolevulinic acid dehydratase;
Validated.
Length = 323
Score = 26.5 bits (60), Expect = 4.7
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR DE
Sbjct: 161 IVAPSDMMDGRVGAIREALDEA 182
>gnl|CDD|163657 cd07414, MPP_PP1_PPKL, PP1, PPKL (PP1 and kelch-like) enzymes, and
related proteins, metallophosphatase domain. PP1
(protein phosphatase type 1) is a serine/threonine
phosphatase that regulates many cellular processes
including: cell-cycle progression, protein synthesis,
muscle contraction, carbohydrate metabolism,
transcription and neuronal signaling, through its
interaction with at least 180 known targeting proteins.
PP1 occurs in all tissues and regulates many pathways,
ranging from cell-cycle progression to carbohydrate
metabolism. Also included here are the PPKL (PP1 and
kelch-like) enzymes including the PPQ, PPZ1, and PPZ2
fungal phosphatases. These PPKLs have a large
N-terminal kelch repeat in addition to a C-terminal
phosphoesterase domain. The PPP (phosphoprotein
phosphatase) family, to which PP1 belongs, is one of two
known protein phosphatase families specific for serine
and threonine. The PPP family also includes: PP2A, PP2B
(calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE,
PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain
is defined by three conserved motifs (-GDXHG-, -GDXVDRG-
and -GNHE-). The PPP enzyme family is ancient with
members found in all eukaryotes, and in most bacterial
and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 293
Score = 26.2 bits (58), Expect = 6.1
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 86 NYCGELRNCTAVM 98
NYCGE N A+M
Sbjct: 264 NYCGEFDNAGAMM 276
>gnl|CDD|223191 COG0113, HemB, Delta-aminolevulinic acid dehydratase [Coenzyme
metabolism].
Length = 330
Score = 26.0 bits (58), Expect = 7.8
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 65 VVALGDVMDGTIVTIRAGNDEN 86
+VA D+MDG + IR DE
Sbjct: 166 IVAPSDMMDGRVGAIREALDEA 187
>gnl|CDD|239796 cd04268, ZnMc_MMP_like, Zinc-dependent metalloprotease, MMP_like
subfamily. This group contains matrix
metalloproteinases (MMPs), serralysins, and the
astacin_like family of proteases.
Length = 165
Score = 25.5 bits (56), Expect = 8.9
Identities = 9/39 (23%), Positives = 11/39 (28%), Gaps = 2/39 (5%)
Query: 51 THWRSNKTLPVAFKVVALGDVMDGTIVTIRAGNDENYCG 89
W NK + FK D D IR +
Sbjct: 25 EAW--NKAFAIGFKNANDVDPADIRYSVIRWIPYNDGTW 61
>gnl|CDD|220240 pfam09435, DUF2015, Fungal protein of unknown function (DUF2015).
This is a fungal family of uncharacterized proteins.
Length = 124
Score = 25.0 bits (55), Expect = 9.1
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 80 RAGNDENYCGELRNCTAVMKNQVAKFNDLRFVGRSGREAHNNKAPD 125
RAG D+ E++ +MK Q F++ R + R NN PD
Sbjct: 75 RAGLDDAAKREIQR---IMKRQRVSFDEARLIYTERRFGKNNIGPD 117
>gnl|CDD|184080 PRK13483, PRK13483, enterobactin receptor protein; Provisional.
Length = 660
Score = 25.9 bits (57), Expect = 9.3
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 36 LTRTGCPHVVCTVLPTHWRSNKT 58
+TR CP CT P + ++ T
Sbjct: 490 ITRVACPATQCTDGPNQFGADPT 512
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 0.399
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: 6,410,135
Number of extensions: 541689
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 444
Number of HSP's successfully gapped: 22
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (23.9 bits)