RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3429
(192 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 97.9 bits (245), Expect = 2e-27
Identities = 33/57 (57%), Positives = 40/57 (70%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+ RT FT +QL LEK+F + +Y S ER E + L LTE QVK+WFQNRRAK KR
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 84.6 bits (210), Expect = 3e-22
Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
R+ RT FT +QL LEK+F++ Y S ER E + L L+E QVK+WFQNRRAK K
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 84.2 bits (209), Expect = 4e-22
Identities = 34/59 (57%), Positives = 40/59 (67%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100
R+ RT FT +QL LEK+F + Y S ER E + L LTE QVKIWFQNRRAK KR +
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 57.4 bits (139), Expect = 7e-11
Identities = 26/78 (33%), Positives = 41/78 (52%)
Query: 29 PKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIW 88
KL P + R T +QL+ LE++F Y S R + S L++ V+IW
Sbjct: 39 MKLERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIW 98
Query: 89 FQNRRAKAKRLQEAEIEK 106
FQN+RAK K+ + ++E+
Sbjct: 99 FQNKRAKEKKKRSGKVEQ 116
>gnl|CDD|224194 COG1275, TehA, Tellurite resistance protein and related permeases
[Inorganic ion transport and metabolism].
Length = 329
Score = 30.4 bits (69), Expect = 0.47
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 141 LLHHPHPFSALLGRHPAMAHFMPAAPM 167
L+ +P+ A L HP ++ F+P P+
Sbjct: 63 LIKYPNTVIADL-NHPVVSSFVPTFPI 88
>gnl|CDD|191634 pfam06886, TPX2, Targeting protein for Xklp2 (TPX2). This family
represents a conserved region approximately 60 residues
long within the eukaryotic targeting protein for Xklp2
(TPX2). Xklp2 is a kinesin-like protein localised on
centrosomes throughout the cell cycle and on spindle
pole microtubules during metaphase. In Xenopus, it has
been shown that Xklp2 protein is required for centrosome
separation and maintenance of spindle bi-polarity. TPX2
is a microtubule-associated protein that mediates the
binding of the C-terminal domain of Xklp2 to
microtubules. It is phosphorylated during mitosis in a
microtubule-dependent way.
Length = 57
Score = 28.1 bits (63), Expect = 0.54
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARP 117
+RAEF L E ++ + A+ K +E I++++ + A P
Sbjct: 9 KRAEFDKKLEEKEKALEAEKEEAEARQKEEEEEAIKQLRKELVPKANP 56
>gnl|CDD|223624 COG0550, TopA, Topoisomerase IA [DNA replication, recombination,
and repair].
Length = 570
Score = 29.5 bits (67), Expect = 1.1
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 25 KGDPPKLNVNLRKHKPNRKPRTPFTT---QQLLSLEKKFREKQYLSIAER 71
KG P K+ V++ K R P PFTT QQ S + F K+ + IA++
Sbjct: 238 KGKPAKV-VSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQK 286
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 115 and 181 amino acids in length. There are two
completely conserved residues (F and G) that may be
functionally important.
Length = 110
Score = 27.8 bits (62), Expect = 1.9
Identities = 11/71 (15%), Positives = 15/71 (21%), Gaps = 11/71 (15%)
Query: 117 PHPLYGPGPSPHLHQYFQHASPEALLHHPHPFSALLGRHPAMAHFMPAAPMPQNSPPGGS 176
+P P+ Q + P P P PQ P
Sbjct: 9 QYPPQNQQQQPYQQQPYHQQMPPPPYSPPQ-----------QQQGHFMPPQPQPYPKQSP 57
Query: 177 DMKASPPRPSP 187
+ P S
Sbjct: 58 QQQQPPQFSSF 68
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 28.4 bits (64), Expect = 2.3
Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 16/95 (16%)
Query: 19 LLSDSNKGDP--PKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSS 76
L N G+P +++ R ++ R+ + FT +++ EK+ E + I ER E +S
Sbjct: 292 LSGLKNSGEPSLKEIH-EARLNEEERELKKKFT-EKIREKEKRLEELEQNLIEERKELNS 349
Query: 77 SLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSA 111
L K E +EK+K +
Sbjct: 350 KL------------EEIQKKLEDLEKRLEKLKSNK 372
>gnl|CDD|240287 PTZ00142, PTZ00142, 6-phosphogluconate dehydrogenase; Provisional.
Length = 470
Score = 28.2 bits (63), Expect = 3.1
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 7/57 (12%)
Query: 88 WFQNRRAKAKRLQEAEIEKIKMSAI---AAARPHPLYGPGPSP----HLHQYFQHAS 137
W+ N + KR +E I + M AR P PG + H+ + S
Sbjct: 104 WYLNTERRIKRCEEKGILYLGMGVSGGEEGARYGPSLMPGGNKEAYDHVKDILEKCS 160
>gnl|CDD|217631 pfam03595, C4dic_mal_tran, C4-dicarboxylate transporter/malic acid
transport protein. This family of transporters have ten
alpha helical transmembrane segments. The structure of a
bacterial homologue of SLAC1 shows it to have a trimeric
arrangement. The pore is composed of five helices with a
conserved phe residue involved in gating. One homologue,
Mae1 from the yeast Schizosaccharomyces pombe, functions
as a malate uptake transporter; another, Ssu1 from
Saccharomyces cerevisiae and other fungi including
Aspergillus fumigatus, is characterized as a sulphite
efflux pump; and TehA from Escherichia coli is
identified as a tellurite resistance protein by virtue
of its association in the tehA/tehB operon. Many
homologues are incorrectly annotated as tellurite
resistance/dicarboxylate transporter (TDT) proteins.
Length = 314
Score = 27.9 bits (63), Expect = 3.6
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 141 LLHHPHPFSALLGRHPAMAHFMPAAPM 167
+ +P A L RHP F PM
Sbjct: 57 FIRYPKAVKAEL-RHPVRGSFFGTFPM 82
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.0 bits (62), Expect = 3.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 163 PAAPMPQNSPPGGSDMKASPPRPSPSPT 190
P P+P +PP D PPRP+P P+
Sbjct: 2551 PPPPLPPAAPPAAPDRSVPPPRPAPRPS 2578
>gnl|CDD|202276 pfam02541, Ppx-GppA, Ppx/GppA phosphatase family. This family
consists of the N-terminal region of exopolyphosphatase
(Ppx) EC:3.6.1.11 and guanosine pentaphosphate
phospho-hydrolase (GppA) EC:3.6.1.40.
Length = 285
Score = 27.3 bits (61), Expect = 4.4
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 22/70 (31%)
Query: 60 FREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK----------AKRLQEAEIEKIKM 109
REK+ + +AE + L N A A+ LQ +E I+
Sbjct: 14 AREKRKVRLAEGLNSTGRL------------NEEAIERTISALKEFAEILQGFGVENIRA 61
Query: 110 SAIAAARPHP 119
A +A R
Sbjct: 62 VATSALRDAV 71
>gnl|CDD|212672 cd10230, HYOU1-like_NBD, Nucleotide-binding domain of human HYOU1
and similar proteins. This subgroup includes human
HYOU1 (also known as human hypoxia up-regulated 1,
GRP170; HSP12A; ORP150; GRP-170; ORP-150; the human
HYOU1 gene maps to11q23.1-q23.3) and Saccharomyces
cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian
HYOU1 functions as a nucleotide exchange factor (NEF)
for HSPA5 (alos known as BiP, Grp78 or HspA5) and may
also function as a HSPA5-independent chaperone. S.
cerevisiae Lhs1p, does not have a detectable endogenous
ATPase activity like canonical HSP70s, but functions as
a NEF for Kar2p; it's interaction with Kar2p is
stimulated by nucleotide-binding. In addition, Lhs1p has
a nucleotide-independent holdase activity that prevents
heat-induced aggregation of proteins in vitro. This
subgroup belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as NEFs, to
remove ADP from their HSP70 chaperone partners during
the ATP hydrolysis cycle. HSP70 chaperones assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 388
Score = 27.5 bits (62), Expect = 4.8
Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 18/56 (32%)
Query: 56 LEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSA 111
L K+F EK + R N RA AK L+EA K +SA
Sbjct: 249 LAKEFEEKHKAKVDVR------------------TNPRAMAKLLKEANRAKEVLSA 286
>gnl|CDD|132648 TIGR03609, S_layer_CsaB, polysaccharide pyruvyl transferase CsaB.
The CsaB protein (cell surface anchoring B) of Bacillus
anthracis adds a pyruvoyl group to
peptidoglycan-associated polysaccharide. This addition
is required for proteins with an S-layer homology domain
(pfam00395) to bind. Within the larger group of proteins
described by pfam04230, this model represents a distinct
clade that nearly exactly follows the phylogenetic
distribution of the S-layer homology domain (pfam00395)
[Cell envelope, Surface structures, Protein fate,
Protein and peptide secretion and trafficking].
Length = 298
Score = 26.8 bits (60), Expect = 6.5
Identities = 9/57 (15%), Positives = 16/57 (28%), Gaps = 1/57 (1%)
Query: 13 LILSSPLLSDSNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIA 69
+L P + V+LR R + L L++ L +
Sbjct: 157 WLLPPEPWPGGEPLPEPVIVVSLRPWPLLDVSRLLRLLRALDRLQRD-TGAFVLFLP 212
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 27.0 bits (61), Expect = 7.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 66 LSIAERAEFSSSLHLTETQVKI 87
LSI E EF +L L+E + KI
Sbjct: 437 LSIGEALEFFENLKLSEQEAKI 458
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 26.7 bits (59), Expect = 8.2
Identities = 22/142 (15%), Positives = 35/142 (24%), Gaps = 31/142 (21%)
Query: 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARPHPLYGPG 124
Y+++A+R E ++ F + + ++L A P YG G
Sbjct: 357 YVALAQRKE------QRRAHLQDQFMQLQPRMRQLPMG------SPMGGAMGQPPYYGQG 404
Query: 125 PSPHLHQYFQ----------------HASPEALLHHPHPFSALLGRHPAMAHFMPAAPMP 168
P + P L + A P
Sbjct: 405 PQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQ---KPPMQP 461
Query: 169 QNSPPGGSDMKASPPRPSPSPT 190
PP + S P P T
Sbjct: 462 VMYPPNYQSLPLSQDLPQPQST 483
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryote. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAF orthologs
and paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 26.5 bits (59), Expect = 8.4
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 49 TTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIK 108
+QL LE+ RE++ E E L + + + KAK +Q+ E E+++
Sbjct: 112 VRKQLRFLEQLEREEEEKRDEEERE----RLLRAAKSRSEQSRLKQKAKEMQKEEDEEMR 167
Query: 109 MSAI-AAAR 116
A A A
Sbjct: 168 HRAANATAL 176
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 24.0 bits (53), Expect = 9.3
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 65 YLSIAERAEFSSSLHLTETQVKIWFQNRR 93
Y S E++E + L+ Q+ WF N R
Sbjct: 10 YPSEEEKSELARQTGLSRKQIDNWFINAR 38
>gnl|CDD|235877 PRK06850, PRK06850, hypothetical protein; Provisional.
Length = 507
Score = 26.5 bits (59), Expect = 9.9
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 50 TQQLLSLEKKFREKQYLS-IAERAE--FSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEK 106
++LL LE+++R S I ++ E + ++ R + + +IEK
Sbjct: 433 VRKLLDLERQYRGLSRRSGIYDKLEKILKQD-WRSLEEIAQNAALLRKLKDAIHQGDIEK 491
Query: 107 IK 108
I+
Sbjct: 492 IE 493
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
0.316 0.131 0.393
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,143,463
Number of extensions: 941026
Number of successful extensions: 1477
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1401
Number of HSP's successfully gapped: 92
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
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 (21.6 bits)
S2: 56 (25.5 bits)