RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6334
(63 letters)
>gnl|CDD|153114 cd01056, Euk_Ferritin, eukaryotic ferritins. Eukaryotic Ferritin
(Euk_Ferritin) domain. Ferritins are the primary iron
storage proteins of most living organisms and members of
a broad superfamily of ferritin-like diiron-carboxylate
proteins. The iron-free (apoferritin) ferritin molecule
is a protein shell composed of 24 protein chains
arranged in 432 symmetry. Iron storage involves the
uptake of iron (II) at the protein shell, its oxidation
by molecular oxygen at the dinuclear ferroxidase
centers, and the movement of iron (III) into the cavity
for deposition as ferrihydrite; the protein shell can
hold up to 4500 iron atoms. In vertebrates, two types of
chains (subunits) have been characterized, H or M (fast)
and L (slow), which differ in rates of iron uptake and
mineralization. Fe(II) oxidation in the H/M subunits
take place initially at the ferroxidase center, a
carboxylate-bridged diiron center, located within the
subunit four-helix bundle. In a complementary role,
negatively charged residues on the protein shell inner
surface of the L subunits promote ferrihydrite
nucleation. Most plant ferritins combine both oxidase
and nucleation functions in one chain: they have four
interior glutamate residues as well as seven ferroxidase
center residues.
Length = 161
Score = 80.3 bits (199), Expect = 2e-21
Identities = 37/62 (59%), Positives = 47/62 (75%), Gaps = 3/62 (4%)
Query: 2 QALLELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADLLTNVRRVG---EGLGIFVFD 58
Q+LL+LH LAS H D + DFLESEFL+EQV+SIK LA +TN++RVG GLG ++FD
Sbjct: 100 QSLLDLHKLASEHNDPHLADFLESEFLEEQVESIKKLAGYITNLKRVGKPQSGLGEYLFD 159
Query: 59 KE 60
K
Sbjct: 160 KY 161
>gnl|CDD|153098 cd00904, Ferritin, Ferritin iron storage proteins. Ferritins are
the primary iron storage proteins of most living
organisms and members of a broad superfamily of
ferritin-like diiron-carboxylate proteins. The iron-free
(apoferritin) ferritin molecule is a protein shell
composed of 24 protein chains arranged in 432 symmetry.
Iron storage involves the uptake of iron (II) at the
protein shell, its oxidation by molecular oxygen at the
dinuclear ferroxidase centers, and the movement of iron
(III) into the cavity for deposition as ferrihydrite;
the protein shell can hold up to 4500 iron atoms. In
vertebrates, two types of chains (subunits) have been
characterized, H or M (fast) and L (slow), which differ
in rates of iron uptake and mineralization. Bacterial
non-heme ferritins are composed only of H chains. Fe(II)
oxidation in the H/M subunits take place initially at
the ferroxidase center, a carboxylate-bridged diiron
center, located within the subunit four-helix bundle. In
a complementary role, negatively charged residues on the
protein shell inner surface of the L subunits promote
ferrihydrite nucleation. Most plant ferritins combine
both oxidase and nucleation functions in one chain: they
have four interior glutamate residues as well as seven
ferroxidase center residues.
Length = 160
Score = 57.7 bits (139), Expect = 2e-12
Identities = 32/61 (52%), Positives = 41/61 (67%), Gaps = 3/61 (4%)
Query: 2 QALLELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADLLTNVRRVG---EGLGIFVFD 58
QALL+LH LAS KD + DFLES FL EQV IK + D+LTN+ R+ G G ++FD
Sbjct: 100 QALLDLHELASEEKDPHLCDFLESHFLDEQVKEIKQVGDILTNLERLNGQQAGSGEYLFD 159
Query: 59 K 59
+
Sbjct: 160 R 160
>gnl|CDD|224445 COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and
metabolism].
Length = 167
Score = 37.6 bits (88), Expect = 7e-05
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 6 ELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADLLTNVRRVGE-GLGIFVFDKELKS 63
EL +A KD +FL+ F+ EQV+ K +L + G G G+++ DKELK+
Sbjct: 103 ELAEVAREEKDYATFNFLQ-WFVAEQVEEEKLFKTILDKLELAGNDGEGLYLIDKELKN 160
>gnl|CDD|215791 pfam00210, Ferritin, Ferritin-like domain. This family contains
ferritins and other ferritin-like proteins such as
members of the DPS family and bacterioferritins.
Length = 142
Score = 36.9 bits (86), Expect = 1e-04
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 2 QALLELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADLLTNVRRV 48
++L EL LA D DFLE FL+EQ + L LL ++R+
Sbjct: 97 ESLRELIELAEEEGDYATADFLE-WFLEEQEEHEWFLEALLEKLKRI 142
>gnl|CDD|153113 cd01055, Nonheme_Ferritin, nonheme-containing ferritins. Nonheme
Ferritin domain, found in archaea and bacteria, is a
member of a broad superfamily of ferritin-like
diiron-carboxylate proteins. The ferritin protein shell
is composed of 24 protein subunits arranged in 432
symmetry. Each protein subunit, a four-helix bundle with
a fifth short terminal helix, contains a dinuclear
ferroxidase center (H type). Unique to this group of
proteins is a third metal site in the ferroxidase
center. Iron storage involves the uptake of iron (II) at
the protein shell, its oxidation by molecular oxygen at
the ferroxidase centers, and the movement of iron (III)
into the cavity for deposition as ferrihydrite.
Length = 156
Score = 35.5 bits (83), Expect = 3e-04
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 2 QALLELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADLLTNVRRVGE-GLGIFVFDKE 60
+++ L +LA KD +FL+ F++EQV+ D+L ++ G+ G G+++ DKE
Sbjct: 97 ESINNLVDLALEEKDYATFNFLQ-WFVKEQVEEEALARDILDKLKLAGDDGGGLYMLDKE 155
Query: 61 L 61
L
Sbjct: 156 L 156
>gnl|CDD|233269 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
periplasmic protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 250
Score = 27.3 bits (61), Expect = 0.37
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 10 LASNHKDANFTD--FLESEFLQ-EQVDSIKSLADLLTNVRRVGEGLGIFVF--DKELK 62
L + DA FTD L FL+ K + +T+ + G+G GI + D ELK
Sbjct: 169 LKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKGDTELK 226
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 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 = 315
Score = 25.6 bits (57), Expect = 1.4
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 32 VDSIKSLADLLTNVRRVGEGLGIFVFDKE 60
VD+ ++LAD L + G GI VFD E
Sbjct: 238 VDN-EALADALNEGKIAGA--GIDVFDME 263
>gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein. Members
of this protein family are about 265 residues long and
each contains an S4 RNA-binding domain of about 48
residues. The member from the Cyanobacterium,
Synechocystis sp. PCC 6803, was detected as a novel
polypeptide in a highly purified preparation of active
photosystem II (Kashino, et al., 2002). The
phylogenetic distribution, including Cyanobacteria and
Arabidopsis, supports a role in photosystem II,
although the high bit score cutoffs for this model
reflect similar sequences in non-photosynthetic
organisms such as Carboxydothermus hydrogenoformans, a
Gram-positive bacterium [Energy metabolism,
Photosynthesis].
Length = 257
Score = 25.7 bits (57), Expect = 1.5
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 1 MQALLELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADL 41
++ LL+L A + ++DFL + +E + +L DL
Sbjct: 16 LERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDL 56
>gnl|CDD|179803 PRK04260, PRK04260, acetylornithine aminotransferase; Provisional.
Length = 375
Score = 24.8 bits (54), Expect = 3.7
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 20 TDFLE-----SEFLQEQVDSIKSLADLLTNVRRVGEGLGI 54
FLE +LQEQ+ + +T VR +G +GI
Sbjct: 284 AGFLEQALENGNYLQEQLQKALQDKETVTTVRGLGYMIGI 323
>gnl|CDD|217050 pfam02460, Patched, Patched family. The transmembrane protein
Patched is a receptor for the morphogene Sonic Hedgehog.
This protein associates with the smoothened protein to
transduce hedgehog signals.
Length = 801
Score = 24.6 bits (54), Expect = 3.8
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 3 ALLELHNLASNHKDANFTDFLESEFLQEQVDSIKSLADLLTNV 45
L E +A + + N T F E +Q+ +I L D + ++
Sbjct: 613 LLQEWRGVADEYPEFNVTVFDEDSPFLDQILTI--LPDTIQSI 653
>gnl|CDD|224588 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
proteins [Cell division and chromosome partitioning].
Length = 858
Score = 24.8 bits (54), Expect = 3.9
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 19 FTDFLESEFLQEQVDSIKSLADLLTNVRRVGEGLGIFVFD 58
+ EF + + + A+LL ++ R+G LGI +
Sbjct: 385 HLFLIADEFAELKSEH-PDFAELLVSIARLGRSLGIHLIL 423
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 24.5 bits (54), Expect = 4.2
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 17 ANFTDFLESEFLQEQVDSIKSLAD 40
AN FL E +Q + S++ LA
Sbjct: 85 ANLAAFLTVERMQSPIQSLEDLAK 108
>gnl|CDD|217683 pfam03709, OKR_DC_1_N, Orn/Lys/Arg decarboxylase, N-terminal
domain. This domain has a flavodoxin-like fold, and is
termed the "wing" domain because of its position in the
overall 3D structure.
Length = 111
Score = 23.7 bits (52), Expect = 6.8
Identities = 6/26 (23%), Positives = 10/26 (38%)
Query: 32 VDSIKSLADLLTNVRRVGEGLGIFVF 57
+ LL +RR L +F+
Sbjct: 44 LSWDDEARGLLDEIRRRNFDLPVFLL 69
>gnl|CDD|239790 cd04257, AAK_AK-HSDH, AAK_AK-HSDH: Amino Acid Kinase Superfamily
(AAK), AK-HSDH; this CD includes the N-terminal
catalytic domain of aspartokinase (AK) of the
bifunctional enzyme AK - homoserine dehydrogenase
(HSDH). These aspartokinases are found in bacteria (E.
coli AKI-HSDHI, ThrA and E. coli AKII-HSDHII, MetL) and
higher plants (Z. mays AK-HSDH). AK and HSDH are the
first and third enzymes in the biosynthetic pathway of
the aspartate family of amino acids. AK catalyzes the
phosphorylation of Asp to P-aspartyl phosphate. HSDH
catalyzes the NADPH-dependent conversion of Asp
3-semialdehyde to homoserine. ThrA and MetL are involved
in threonine and methionine biosynthesis, respectively.
In E. coli, ThrA is subject to allosteric regulation by
the end product L-threonine and the native enzyme is
reported to be tetrameric. As with bacteria, plant AK
and HSDH are feedback inhibited by pathway end products.
Maize AK-HSDH is a Thr-sensitive 180-kD enzyme.
Arabidopsis AK-HSDH is an alanine-activated,
threonine-sensitive enzyme whose ACT domains, located
C-terminal to the AK catalytic domain, were shown to be
involved in allosteric activation.
Length = 294
Score = 23.7 bits (52), Expect = 7.4
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 18/66 (27%)
Query: 3 ALLELHNLASNHKDAN--------------FTDFL----ESEFLQEQVDSIKSLADLLTN 44
LLEL LAS+ DA T+ L +E L + ++ L DLL
Sbjct: 46 LLLELAELASSGDDAYEDILQELESKHLDLITELLSGDAAAELLSALGNDLEELKDLLEG 105
Query: 45 VRRVGE 50
+ +GE
Sbjct: 106 IYLLGE 111
>gnl|CDD|224925 COG2014, COG2014, Uncharacterized conserved protein [Function
unknown].
Length = 250
Score = 23.6 bits (51), Expect = 9.3
Identities = 11/51 (21%), Positives = 26/51 (50%)
Query: 13 NHKDANFTDFLESEFLQEQVDSIKSLADLLTNVRRVGEGLGIFVFDKELKS 63
+ ++AN+ D L+ +++ I ++ VR + E ++VF++ K
Sbjct: 97 DLEEANWFDILDLIQRDDKIKMIAEFGNMPPVVRTLKEKFEVYVFERNPKL 147
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
0.318 0.135 0.361
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,127,973
Number of extensions: 221777
Number of successful extensions: 283
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 23
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
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 (24.1 bits)