RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4600
(108 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of
Eumetazoan signaling molecules, often in tandem
arrangements. May be responsible for specific
protein-protein interactions, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of PDZ domains an
N-terminal beta-strand forms the peptide-binding groove
base, a circular permutation with respect to PDZ
domains found in proteases.
Length = 82
Score = 46.4 bits (111), Expect = 3e-08
Identities = 23/51 (45%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 41 ITTVSFTKGPGFKGLGFSIVGGKDSPKGIMGIYVKTIFPTGQAADTGSLKE 91
+ TV+ K PG GLGFS+ GGKDS GI+V + P G A+ G L+
Sbjct: 1 VRTVTLRKDPG-GGLGFSLRGGKDSG---GGIFVSRVEP-GGPAERGGLRV 46
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 39.7 bits (93), Expect = 2e-05
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 41 ITTVSFTKGPGFKGLGFSIVGGKDSPKGIMGIYVKTIFPTGQAADTG 87
V KG G GLGFS+VGGKD G+ V ++ P AA G
Sbjct: 2 PRLVELEKGGG--GLGFSLVGGKDEGG---GVVVSSVVPGSPAAKAG 43
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 31.8 bits (73), Expect = 0.016
Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 48 KGPGFKGLGFSIVGGKDSPKGIMGIYVKTIFPTGQAADTGSLKED 92
+ G GLGFS+VGG D G GI+V + P G AA+ G L+E
Sbjct: 5 EKSGRGGLGFSLVGGSD---GDPGIFVSEVLP-GGAAEAGGLQEG 45
>gnl|CDD|216269 pfam01056, Myc_N, Myc amino-terminal region. The myc family
belongs to the basic helix-loop-helix leucine zipper
class of transcription factors, see pfam00010. Myc forms
a heterodimer with Max, and this complex regulates cell
growth through direct activation of genes involved in
cell replication. Mutations in the C-terminal 20
residues of this domain cause unique changes in the
induction of apoptosis, transformation, and G2 arrest.
Length = 329
Score = 32.2 bits (73), Expect = 0.030
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 8 EENEDQEQEEDEDEEEESQFCTLRRAGKSASFTITTVSFTKG 49
E ED+E+EE+E+EEEE T+ + +S+S + S +
Sbjct: 227 ESEEDEEEEEEEEEEEEIDVVTVEK-RRSSSNRKASTSESIT 267
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 31.9 bits (73), Expect = 0.039
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 6 FQEENEDQEQEEDEDEEEESQFCTLRRAGKSASFTITTVSFT 47
+EE+E+ E +DED+EEE + ++ KSA T + + FT
Sbjct: 353 DEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRSELPFT 394
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.9 bits (72), Expect = 0.042
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 870 EEEEEEEEEEEEEEEEEEEE 889
Score = 30.3 bits (68), Expect = 0.16
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 866 EEEEEEEEEEEEEEEEEEEE 885
Score = 30.3 bits (68), Expect = 0.18
Identities = 11/20 (55%), Positives = 19/20 (95%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE++
Sbjct: 872 EEEEEEEEEEEEEEEEEENE 891
Score = 30.0 bits (67), Expect = 0.21
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 865 EEEEEEEEEEEEEEEEEEEE 884
Score = 29.6 bits (66), Expect = 0.30
Identities = 10/20 (50%), Positives = 17/20 (85%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEE +
Sbjct: 873 EEEEEEEEEEEEEEEEENEE 892
Score = 29.2 bits (65), Expect = 0.41
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 867 EEEEEEEEEEEEEEEEEEEE 886
Score = 29.2 bits (65), Expect = 0.44
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 864 EEEEEEEEEEEEEEEEEEEE 883
Score = 29.2 bits (65), Expect = 0.44
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 868 EEEEEEEEEEEEEEEEEEEE 887
Score = 28.4 bits (63), Expect = 0.75
Identities = 11/20 (55%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E++E+EE+E+EEEE +
Sbjct: 869 EEEEEEEEEEEEEEEEEEEE 888
Score = 28.4 bits (63), Expect = 0.78
Identities = 9/18 (50%), Positives = 17/18 (94%)
Query: 9 ENEDQEQEEDEDEEEESQ 26
++E++E+EE+E+EEEE +
Sbjct: 862 DSEEEEEEEEEEEEEEEE 879
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 29.5 bits (66), Expect = 0.35
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 4 FAFQEENEDQEQEEDEDEEEESQFC 28
A QE E++ EE+E+EEEE +
Sbjct: 434 MASQESEEEESVEEEEEEEEEEEEE 458
Score = 25.3 bits (55), Expect = 8.2
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE E +E+E +++EEEE
Sbjct: 457 EEEQESEEEEGEDEEEEEEV 476
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to
be DNA-binding and may be a transcription factor.
Length = 238
Score = 28.1 bits (63), Expect = 0.71
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 5 AFQEENEDQEQEEDEDEEEE 24
F+EE +D+E E +E+EEEE
Sbjct: 33 LFEEEEDDEEFEIEEEEEEE 52
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 28.1 bits (63), Expect = 0.76
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 7 QEENEDQEQEEDEDEEEE 24
++E E+QE EE+E+EEEE
Sbjct: 347 KDEEEEQEDEEEEEEEEE 364
Score = 27.3 bits (61), Expect = 1.8
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 8 EENEDQEQEEDEDEEEESQ 26
EE ED+E+EE+E+E EE +
Sbjct: 351 EEQEDEEEEEEEEEPEEPE 369
Score = 26.6 bits (59), Expect = 2.7
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 7 QEENEDQEQEEDEDEEEE 24
QE+ E++E+EE+ +E E
Sbjct: 353 QEDEEEEEEEEEPEEPEP 370
Score = 26.6 bits (59), Expect = 2.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 6 FQEENEDQEQEEDEDEEEE 24
EE E++E+E +E E EE
Sbjct: 354 EDEEEEEEEEEPEEPEPEE 372
Score = 26.6 bits (59), Expect = 2.9
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 7 QEENEDQEQEEDEDEEEE 24
+EE ++ E+EE+E+EE E
Sbjct: 349 EEEEQEDEEEEEEEEEPE 366
Score = 25.8 bits (57), Expect = 4.9
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 8 EENEDQEQEEDEDEEEESQ 26
E+ +++E+EE+E+ EE
Sbjct: 352 EQEDEEEEEEEEEPEEPEP 370
Score = 25.8 bits (57), Expect = 5.7
Identities = 9/18 (50%), Positives = 16/18 (88%)
Query: 7 QEENEDQEQEEDEDEEEE 24
++E+E++E+EE+E EE E
Sbjct: 352 EQEDEEEEEEEEEPEEPE 369
Score = 25.0 bits (55), Expect = 9.0
Identities = 9/18 (50%), Positives = 17/18 (94%)
Query: 8 EENEDQEQEEDEDEEEES 25
+++E++EQE++E+EEEE
Sbjct: 346 QKDEEEEQEDEEEEEEEE 363
Score = 25.0 bits (55), Expect = 9.5
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
EE E +++EE+E+EEE +
Sbjct: 348 DEEEEQEDEEEEEEEEEPEE 367
>gnl|CDD|205321 pfam13140, DUF3980, Domain of unknown function (DUF3980). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is
approximately 90 amino acids in length.
Length = 87
Score = 27.1 bits (60), Expect = 0.86
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 40 TITTVSFTKGPGFKGLGFSIVGG 62
++T SF G GF+ + S G
Sbjct: 29 AVSTGSFINGSGFQSISVSGAGA 51
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 27.7 bits (61), Expect = 1.1
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 6 FQEENEDQEQEEDEDEEEESQFCTLRRAGK 35
F E +E+ E E+E EEEE++ + +RA K
Sbjct: 767 FAESSEEDESSEEEKEEEENKEVSAKRAKK 796
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 27.3 bits (61), Expect = 1.3
Identities = 7/22 (31%), Positives = 17/22 (77%)
Query: 6 FQEENEDQEQEEDEDEEEESQF 27
++ ED+E+E+DE++++E +
Sbjct: 114 SDDDEEDEEEEDDEEDDDEDES 135
Score = 26.9 bits (60), Expect = 1.7
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 8 EENEDQEQEEDEDEEEESQ 26
EE+++++ +EDE EEEES
Sbjct: 123 EEDDEEDDDEDESEEEESP 141
Score = 26.1 bits (58), Expect = 2.7
Identities = 9/19 (47%), Positives = 18/19 (94%)
Query: 8 EENEDQEQEEDEDEEEESQ 26
EE+E++E +E++D+E+ES+
Sbjct: 118 EEDEEEEDDEEDDDEDESE 136
Score = 26.1 bits (58), Expect = 3.2
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 8 EENEDQEQEEDEDEEEE 24
EE ED E+++DEDE EE
Sbjct: 121 EEEEDDEEDDDEDESEE 137
Score = 25.4 bits (56), Expect = 5.0
Identities = 5/19 (26%), Positives = 17/19 (89%)
Query: 7 QEENEDQEQEEDEDEEEES 25
+ +++++++EE++DEE++
Sbjct: 113 ESDDDEEDEEEEDDEEDDD 131
>gnl|CDD|233389 TIGR01382, PfpI, intracellular protease, PfpI family. The member
of this family from Pyrococcus horikoshii has been
solved to 2 Angstrom resolution. It is an
ATP-independent intracellular protease that
crystallizes as a hexameric ring. Cys-101 is proposed
as the active site residue in a catalytic triad with
the adjacent His-102 and a Glu residue from an adjacent
monomer. A member of this family from Bacillus
subtilis, GSP18, has been shown to be expressed in
response to several forms of stress. A role in the
degradation of small peptides has been suggested. A
closely related family consists of the thiamine
biosynthesis protein ThiJ and its homologs [Protein
fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 166
Score = 27.4 bits (61), Expect = 1.3
Identities = 19/82 (23%), Positives = 28/82 (34%), Gaps = 14/82 (17%)
Query: 19 EDEEEESQFCTLRRAGKSASFTITTVSFTKGPGFKGLGFSIVGGKDSPKGIMGI----YV 74
ED E LR AG + TVS G G+S+ I + Y
Sbjct: 11 EDSELLYPLDRLREAG----HEVDTVSKEAGTTVGKHGYSV----TVDATIDEVNPEEYD 62
Query: 75 KTIFPTGQAADTGSLKEDTDYK 96
+ P G+A + L+ +
Sbjct: 63 ALVIPGGRAPEY--LRLNNKAV 82
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 27.7 bits (61), Expect = 1.5
Identities = 10/20 (50%), Positives = 17/20 (85%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
++E+ED + EED++EEEE +
Sbjct: 158 EDEDEDDDDEEDDEEEEEEE 177
Score = 26.5 bits (58), Expect = 3.3
Identities = 8/20 (40%), Positives = 17/20 (85%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+E+ED++ +++ED+EEE +
Sbjct: 156 DDEDEDEDDDDEEDDEEEEE 175
Score = 25.4 bits (55), Expect = 8.2
Identities = 7/19 (36%), Positives = 17/19 (89%)
Query: 6 FQEENEDQEQEEDEDEEEE 24
F +++D++++ED+D+EE+
Sbjct: 151 FVIDDDDEDEDEDDDDEED 169
Score = 25.4 bits (55), Expect = 9.3
Identities = 6/21 (28%), Positives = 18/21 (85%)
Query: 4 FAFQEENEDQEQEEDEDEEEE 24
F +++ED+++++D++E++E
Sbjct: 151 FVIDDDDEDEDEDDDDEEDDE 171
Score = 25.4 bits (55), Expect = 9.7
Identities = 8/20 (40%), Positives = 18/20 (90%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
++E++D E++++E+EEEE +
Sbjct: 160 EDEDDDDEEDDEEEEEEEEE 179
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 26.5 bits (59), Expect = 1.7
Identities = 8/18 (44%), Positives = 15/18 (83%)
Query: 8 EENEDQEQEEDEDEEEES 25
E+ E++E+EE+++E EE
Sbjct: 79 EKKEEEEEEEEKEESEEE 96
Score = 24.9 bits (55), Expect = 5.8
Identities = 8/18 (44%), Positives = 15/18 (83%)
Query: 7 QEENEDQEQEEDEDEEEE 24
+++ E++E+EE E+ EEE
Sbjct: 79 EKKEEEEEEEEKEESEEE 96
>gnl|CDD|235430 PRK05362, PRK05362, phosphopentomutase; Provisional.
Length = 394
Score = 27.0 bits (61), Expect = 1.8
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 62 GKDSPKG---IMGIYVKTIFPT 80
GKD+P G IMG+ V F
Sbjct: 83 GKDTPTGHWEIMGVPVLFPFGY 104
>gnl|CDD|188150 TIGR01515, branching_enzym, alpha-1,4-glucan:alpha-1,4-glucan
6-glycosyltransferase. This model describes the
glycogen branching enzymes which are responsible for the
transfer of chains of approx. 7 alpha(1--4)-linked
glucosyl residues to other similar chains (in new
alpha(1--6) linkages) in the biosynthesis of glycogen.
This enzyme is a member of the broader amylase family of
starch hydrolases which fold as (beta/alpha)8 barrels,
the so-called TIM-barrel structure. All of the sequences
comprising the seed of this model have been
experimentally characterized. (For instance,). This
model encompasses both bacterial and eukaryotic species.
No archaea have this enzyme, although Aquifex aolicus
does. Two species, Bacillus thuringiensis and
Clostridium perfringens have two sequences each which
are annotated as amylases. These annotations are
aparrently in error. GP|18143720 from C. perfringens,
for instance, contains the note "674 aa, similar to
gp:A14658_1 amylase (1,4-alpha-glucan branching enzyme
(EC 2.4.1.18) ) from Bacillus thuringiensis (648 aa);
51.1% identity in 632 aa overlap." A branching enzyme
from Porphyromonas gingivales, OMNI|PG1793, appears to
be more closely related to the eukaryotic species
(across a deep phylogenetic split) and may represent an
instance of lateral transfer from this species' host. A
sequence from Arabidopsis thaliana, GP|9294564, scores
just above trusted, but appears either to contain
corrupt sequence or, more likely, to be a pseudogene as
some of the conserved catalytic residues common to the
alpha amylase family are not conserved here [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 618
Score = 27.1 bits (60), Expect = 2.1
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 18 DEDEEEESQFCTLRRAGKSASFTITTVSFTKGP 50
D D++E+S F +RRA K + +FT
Sbjct: 523 DVDDDEQSVFSFIRRAKKHGEALVIICNFTPVV 555
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 26.9 bits (60), Expect = 2.6
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 5 AFQEENEDQEQEEDEDEEEES 25
A+++ ED + +E+ DEE+E
Sbjct: 119 AYRDLEEDDDDDEESDEEDEE 139
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The
CAF-1 or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression
in addition to DNA-based checkpoints.
Length = 76
Score = 25.6 bits (57), Expect = 2.6
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 7 QEENEDQEQEEDEDEEEE 24
+EE ED E E++EDEEE+
Sbjct: 51 EEEGEDLESEDEEDEEED 68
Score = 24.1 bits (53), Expect = 8.4
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 9 ENEDQEQEEDEDEEEESQF 27
E+ED+E EE++D+++ F
Sbjct: 58 ESEDEEDEEEDDDDDMDGF 76
>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 26.7 bits (59), Expect = 2.9
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 9 ENEDQEQEEDEDEEEESQ 26
+ED++Q+EDEDE+E+
Sbjct: 892 ADEDEDQDEDEDEDEDED 909
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel,
four-helix bundle structure with a large hydrophobic
patch in which 23 residues of one monomer form van der
Waals contacts with the other monomer. This CENP-B
dimer configuration may be suitable for capturing two
distant CENP-B boxes during centromeric heterochromatin
formation.
Length = 101
Score = 25.9 bits (56), Expect = 2.9
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE++D E EED+DE+++
Sbjct: 18 EEEDDDDEDEEDDDEDDDED 37
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 26.4 bits (59), Expect = 3.0
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 7 QEENEDQEQEEDEDEEEE 24
+EE E++E+EE+E EEE
Sbjct: 303 EEEEEEEEEEEEEPSEEE 320
Score = 26.0 bits (58), Expect = 4.3
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 7 QEENEDQEQEEDEDEEEES 25
+EE E++E+EE+E+ EE
Sbjct: 302 EEEEEEEEEEEEEEPSEEE 320
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 26.6 bits (59), Expect = 3.1
Identities = 17/80 (21%), Positives = 24/80 (30%), Gaps = 10/80 (12%)
Query: 8 EENEDQEQEEDEDEEEESQFCTLRRAGKSASFTITTVSFTKGPGFKGLGFSIVGGKDS-- 65
D E+E D EE + Q + AG + + G G+ S
Sbjct: 356 TPGNDDEKEPDPQEEADGQGSSTDPAGDIFRIRVLAPPQARARG--------ASGRRSRT 407
Query: 66 PKGIMGIYVKTIFPTGQAAD 85
G YV+ G D
Sbjct: 408 RSDSRGRYVRARRNRGPPDD 427
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 25.8 bits (57), Expect = 3.4
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 7 QEENEDQEQEEDEDEEEES 25
+EE E++E+EE+E+E EE
Sbjct: 77 EEEEEEEEEEEEEEESEEE 95
Score = 24.6 bits (54), Expect = 7.7
Identities = 10/18 (55%), Positives = 16/18 (88%)
Query: 8 EENEDQEQEEDEDEEEES 25
EE E++E+EE+E+ EEE+
Sbjct: 79 EEEEEEEEEEEEESEEEA 96
>gnl|CDD|227458 COG5129, MAK16, Nuclear protein with HMG-like acidic region
[General function prediction only].
Length = 303
Score = 26.2 bits (57), Expect = 3.6
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 8 EENEDQEQEEDEDEEEESQFCTLRRAGKSASFT 40
EE E E E DEDE+E+++ +R A +
Sbjct: 247 EEEESSESESDEDEDEDNKGKIRKRKTDDAKKS 279
>gnl|CDD|129314 TIGR00210, gltS, sodium--glutamate symport carrier (gltS).
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 398
Score = 26.3 bits (58), Expect = 4.0
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 25 SQFCTLRRAGKS-ASFTITTVSFTKGPGFKGLGFSIVGGKDSPKGIMG 71
+ F +L + GK F T V F G+G + + G+ G++
Sbjct: 81 ANFKSLLKGGKPLLIFLATAVGFLVIQNAVGIGMASLLGQAPLMGLLA 128
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 26.3 bits (58), Expect = 4.6
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 8 EENEDQEQEEDEDEEEESQ 26
EE ED+E+EE+EDE+E
Sbjct: 391 EEEEDEEEEEEEDEDEGPS 409
>gnl|CDD|217741 pfam03806, ABG_transport, AbgT putative transporter family.
Length = 502
Score = 25.8 bits (57), Expect = 5.4
Identities = 22/95 (23%), Positives = 34/95 (35%), Gaps = 5/95 (5%)
Query: 5 AFQEENEDQEQEEDEDEEEESQFCTLRRAGKSASFTITTVSFTKGPGFKGLGFSIVGG-K 63
+Q + E+ E + LR AG + TI ++ T P L G
Sbjct: 232 PYQGSLDADEKPELASHITAEEKKGLRWAGVAFVVTIALLALTVIPENGPLRDPETGSVA 291
Query: 64 DSP--KGIMGIYVKTIFPTGQA--ADTGSLKEDTD 94
SP K I+ + + G TG++K D
Sbjct: 292 GSPFMKSIVPLIMLLFLVPGLVYGRVTGTIKNSKD 326
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 25.5 bits (56), Expect = 6.6
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 7 QEENEDQEQEEDEDEEEESQ 26
+EE ++ +Q + +D EE Q
Sbjct: 286 EEEPDEPDQTDPDDGEETDQ 305
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 25.3 bits (55), Expect = 7.2
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 8 EENEDQEQEEDEDEEEESQ 26
EE+ D E+ EDE E +ES
Sbjct: 345 EESTD-EESEDEVEIDESV 362
>gnl|CDD|240369 PTZ00340, PTZ00340, O-sialoglycoprotein endopeptidase-like
protein; Provisional.
Length = 345
Score = 25.4 bits (56), Expect = 7.2
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 30 LRRAGKSASFT---ITTVSFTKGPG 51
++ A + A T I+ + +TKGPG
Sbjct: 57 VKEALEEAKITPSDISLICYTKGPG 81
>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region. The precise
function of this eukaryotic protein family is unknown.
The yeast orthologues have been implicated in cell
cycle progression and biogenesis of 60S ribosomal
subunits. The Schistosoma mansoni Mak16 has been shown
to target protein transport to the nucleolus.
Length = 97
Score = 24.4 bits (53), Expect = 8.2
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 5 AFQEENEDQEQEEDEDEEEESQ 26
+E E+ E+EE+E+EEE+
Sbjct: 56 EAEESEENDEEEEEEEEEEDEG 77
>gnl|CDD|226238 COG3715, ManY, Phosphotransferase system,
mannose/fructose/N-acetylgalactosamine-specific
component IIC [Carbohydrate transport and metabolism].
Length = 265
Score = 25.3 bits (56), Expect = 8.5
Identities = 4/16 (25%), Positives = 9/16 (56%)
Query: 57 FSIVGGKDSPKGIMGI 72
F+I G+ P+ + +
Sbjct: 83 FAITSGQGIPEAALAL 98
>gnl|CDD|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast
Rrp6p, human polymyositis/scleroderma autoantigen
100kDa, and similar proteins. Yeast Rrp6p and its human
homolog, the polymyositis/scleroderma autoantigen 100kDa
(PM/Scl-100), are exosome-associated proteins involved
in the degradation and processing of precursors to
stable RNAs. Both proteins contain a DEDDy-type
DnaQ-like 3'-5' exonuclease domain possessing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. The motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. PM/Scl-100, an
autoantigen present in the nucleolar compartment of the
cell, reacts with autoantibodies produced by about 50%
of patients with polymyositis-scleroderma overlap
syndrome.
Length = 192
Score = 24.9 bits (55), Expect = 8.6
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 71 GIYVKTIFPTGQAAD 85
G+YV +F TGQAA
Sbjct: 97 GLYVVNLFDTGQAAR 111
>gnl|CDD|204918 pfam12436, USP7, Ubiquitin-specific protease 7. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam00443, pfam00917. USP7 regulates
the turnover of p53.
Length = 35
Score = 23.2 bits (51), Expect = 8.6
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 6 FQEENEDQEQEEDEDEEEE 24
+EE E++E+ E EE
Sbjct: 13 LEEEREERERRRKEREEAH 31
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 25.3 bits (55), Expect = 9.1
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 6 FQEENEDQEQEEDEDEEEES 25
+ E++D E D +EE
Sbjct: 269 YGYESDDDEGSSSNDYDEEE 288
>gnl|CDD|212055 cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporter SGLT1;solute
binding domain. Human SGLT1 (hSGLT1) is a
high-affinity/low-capacity glucose transporter, which
can also transport galactose. In the transport
mechanism, two Na+ ions first bind to the extracellular
side of the transporter and induce a conformational
change in the glucose binding site. This results in an
increased affinity for glucose. A second conformational
change in the transporter follows, bringing the Na+ and
glucose binding sites to the inner surface of the
membrane. Glucose is then released, followed by the Na+
ions. In the process, hSGLT1 is also able to transport
water and urea and may be a major pathway for transport
of these across the intestinal brush-border membrane.
hSGLT1 is encoded by the SLC5A1 gene and expressed
mostly in the intestine, but also in the trachea,
kidney, heart, brain, testis, and prostate. The
WHO/UNICEF oral rehydration solution (ORS) for the
treatment of secretory diarrhea contains salt and
glucose. The glucose, along with sodium ions, is
transported by hSGLT1 and water is either co-transported
along with these or follows by osmosis. Mutations in
SGLT1 are associated with intestinal glucose galactose
malabsorption (GGM). Up-regulation of intestinal SGLT1
may protect against enteric infections. SGLT1 is
expressed in colorectal, head and neck, and prostate
tumors. Epidermal growth factor receptor (EGFR)
functions in cell survival by stabilizing SGLT1, and
thereby maintaining intracellular glucose levels. SGLT1
is predicted to have 14 membrane-spanning regions. This
subgroup belongs to the solute carrier 5
(SLC5)transporter family.
Length = 635
Score = 25.2 bits (55), Expect = 9.8
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 7 QEENEDQEQEEDEDEEEESQFCTLRRA 33
+ ED+++ E E +EE + R+A
Sbjct: 550 DDWTEDEDENEMETDEERKKPGCCRKA 576
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
0.309 0.130 0.358
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,334,605
Number of extensions: 448817
Number of successful extensions: 1685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1519
Number of HSP's successfully gapped: 224
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.3 bits)