RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16276
(215 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 190 bits (483), Expect = 3e-62
Identities = 88/94 (93%), Positives = 92/94 (97%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLA+KAARKSAP TGG+KKPHRYRPGTVALREIRRYQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQ 94
LLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQ
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQ 94
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 173 bits (439), Expect = 1e-55
Identities = 89/94 (94%), Positives = 93/94 (98%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLATKAARKSAP+TGGVKKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQ 94
LLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQ
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQ 94
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 107 bits (269), Expect = 3e-30
Identities = 49/63 (77%), Positives = 52/63 (82%), Gaps = 2/63 (3%)
Query: 34 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSAAIG 91
GG K RYRPG VALREIR+YQKST+LLIRK PFQRLVREIAQ F T DLRFQS+AI
Sbjct: 1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIM 60
Query: 92 ALQ 94
ALQ
Sbjct: 61 ALQ 63
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 87.7 bits (217), Expect = 3e-22
Identities = 51/100 (51%), Positives = 66/100 (66%), Gaps = 8/100 (8%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE 60
MAR Q ++ GK P+K+ + ++ KKPHRYRPGTVALREIR+YQKSTE
Sbjct: 1 MARRLQ-GKRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTE 53
Query: 61 LLIRKLPFQRLVREIAQDFKTD-LRFQSAAIGALQYWIEN 99
LLIRKLPF RLVREI+ + + R+ + A+ ALQ E+
Sbjct: 54 LLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATED 93
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 62.0 bits (150), Expect = 6e-13
Identities = 32/53 (60%), Positives = 40/53 (75%), Gaps = 1/53 (1%)
Query: 43 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSAAIGALQ 94
RPG AL+EI+ YQKST+LLIR+LPF RLVREI + + R+Q +AI ALQ
Sbjct: 2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQ 54
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 60.0 bits (146), Expect = 3e-12
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQYWIENSGQF 103
PG V L+EIRRYQ+ST+LL+ K P +R++R+ + R S+AI LQ +E +
Sbjct: 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEE 55
Query: 104 DLNPSSSLKIKKHRK 118
+ L RK
Sbjct: 56 IAEDAVELAEHAKRK 70
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 52.9 bits (128), Expect = 8e-10
Identities = 20/37 (54%), Positives = 25/37 (67%)
Query: 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQ 94
S+ LLI KLPF R+VRE+ + F +LR S A ALQ
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQ 37
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.7 bits (67), Expect = 0.29
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 59 TELLIRKLPFQRLVREIAQDFKT 81
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>gnl|CDD|223797 COG0725, ModA, ABC-type molybdate transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 258
Score = 31.1 bits (71), Expect = 0.37
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 67 PFQRLVREIAQDFKTDLRFQSAAIGALQYWIENSGQFDLNPSSSLKIKKHRKPTWLDYL 125
+ + ++ ++ + + GAL IE DL S+ ++D L
Sbjct: 43 ALEEIAKQFEKETGVKVEVEFGGSGALARQIEQGAPADLFISADDA--------YMDKL 93
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 31.1 bits (70), Expect = 0.43
Identities = 14/37 (37%), Positives = 17/37 (45%)
Query: 5 KQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR 41
K A+K KAP K++A K A K A K R
Sbjct: 1014 KAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAAGR 1050
Score = 27.6 bits (61), Expect = 5.3
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 2 ARTKQTARKSTGGKAP------RKQLATKAARKSAPSTGGVKKPHR 41
A K+ A+K+ KA +K A K K AP+ +KP
Sbjct: 991 AMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAA 1036
>gnl|CDD|189013 cd09606, M3B_PepF_1, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 546
Score = 29.8 bits (68), Expect = 1.00
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 25/72 (34%)
Query: 88 AAIGALQYWIENSGQFDLNPSSSLKIKKHRKPTWLDYLKTPTCALSMPNVSPLCPKTFSW 147
A +GALQ+W ++ + W DYLK S+ + +
Sbjct: 486 AQLGALQFWK--------------NSREDPEKAWEDYLK----LCSLGG-------SKPF 520
Query: 148 PDVSEESVLKFP 159
P++ + + LKFP
Sbjct: 521 PELYKAAGLKFP 532
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 27.6 bits (61), Expect = 5.1
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 2 ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTEL 61
TK A GGK P +Q T AR+ G ++ P GTV R Y + T
Sbjct: 49 HHTKTRAEVRGGGKKPWRQKGTGRARQ-----GSIRAPQWRGGGTVHGPRPREYNQRTPK 103
Query: 62 LIRKLPFQRLVREIAQD 78
+R+ + + + A+D
Sbjct: 104 KMRQAALRGALSDRARD 120
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 27.6 bits (61), Expect = 5.4
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 2 ARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVK 37
K A+K A K A +K+AP G+K
Sbjct: 882 PAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLK 917
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 26.0 bits (58), Expect = 5.5
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 59 TELLIRKLPFQRLVREIAQDFKT 81
T+L++R +PF+ +E+ + F
Sbjct: 1 TKLIVRNVPFEATKKELRELFSP 23
>gnl|CDD|200597 cd10975, CE4_CDA_like_2, Putative catalytic domain of chitin
deacetylase-like proteins. Chitin deacetylases (CDAs,
EC 3.5.1.41) are secreted metalloproteins belonging to a
family of extracellular chitin-modifying enzymes that
catalyze the N-deacetylation of chitin, a
beta-1,4-linked N-acetylglucosamine polymer, to form
chitosan, a polymer of beta-(1,4)-linked d-glucosamine
residues. CDAs have been isolated and characterized from
various bacterial and fungal species and belong to the
larger carbohydrate esterase 4 (CE4) superfamily. This
family includes many midgut-specific CDA-like proteins
mainly from insects, such as Tribolium castaneum CDAs
(TcCDA6-9). These proteins contain a putative CDA-like
catalytic domain similar to the catalytic NodB homology
domain of CE4 esterases. In addition to the CDA-like
domain, some family members have an additional
chitin-binding peritrophin-A domain (ChBD).
Length = 268
Score = 27.3 bits (61), Expect = 6.5
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 146 SWPDVSEESVLKFPTWLDYLKTPTCALSMPNVSPLCPK 183
SWP S + +P LDY T C + P CP
Sbjct: 134 SWPTQSFTNPPLWPYTLDYGSTQDCVI------PPCPT 165
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 27.4 bits (61), Expect = 7.3
Identities = 10/30 (33%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 11 STGGKAPRKQLATKAARKSAPSTGGVKKPH 40
KAPR+QL K R KK
Sbjct: 467 FGNVKAPRQQLNIK--RPEESEESEGKKQS 494
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model [Cellular processes,
Chemotaxis and motility].
Length = 678
Score = 27.2 bits (61), Expect = 7.5
Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 48 ALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 82
L + K +LL+ + QRL R+I Q + +
Sbjct: 544 TLADYAPITKDPDLLVEHVR-QRLGRQITQQYLDE 577
>gnl|CDD|213961 TIGR04348, TIGR04348, putative glycosyltransferase, TIGR04348
family. This putative glycosyltransferase is found in
marine bacteria such as Marinobacter and soil bacteria
such as Anaeromyxobacter, but does not seem to occur in
known pathogenic bacteria.
Length = 310
Score = 26.9 bits (60), Expect = 8.2
Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 26 ARKSAPSTGGVKKPHRYRPGTVAL------REIRRY---QKSTELLIRKLPFQ-RLVREI 75
AR+SA S H RP V L R+I Q+S EL R + Q R + +
Sbjct: 51 ARRSADSIAAWADAHPDRPLIVVLTGTDLYRDIHTDPEAQRSLELADRLVVLQDRGLDAL 110
Query: 76 AQDFKTDLR--FQSA 88
+ R +QSA
Sbjct: 111 PPALRAKARVIYQSA 125
>gnl|CDD|198238 cd10375, SH2_STAT4, Src homology 2 (SH2) domain found in signal
transducer and activator of transcription (STAT)
4proteins. STAT4 mediate signals from the IL-12
receptors. STAT4 is mainly phosphorylated by
IL-12-mediated signaling pathway in T cells. STAT4
expression is restricted in myeloid cells, thymus and
testis. L-12 is the major cytokine that can activate
STAT4, resulting in its tyrosine phosphorylation. The
IL-12 receptor has two chains, termed IL-12R 1 and
IL-12R 2, and ligand binding results in heterodimer
formation and activation of the receptor associated JAK
kinases, Jak2 and Tyk2. Phosphorylated STAT4
homo-dimerizes via its SH2 domain, and translocates into
nucleus where it can recognize traditional N3 STAT
target sequences in IL-12 responsive genes. STAT4 can
also be phosphorylated in response to IFN-gamma
stimulation through activation of Jak1 and Tyk2 in
human. IL-17 can also activate STAT4 in human monocytic
leukemia cell lines and IL-2 can induce Jak2 and Stat4
activation in NK cells but not in T cells. T helper 1
(Th1) cells produce IL-2 and IFNgamma, whereas Th2 cells
secrete IL-4, IL-5, IL-6 and IL-13. Th1 cells are
responsible for cell-mediated/inflammatory immunity and
can enhance defenses against infectious agents and
cancer, while Th2 cells are essential for humoral
immunity and the clearance of parasitic antigens. The
most potent factors that can promote Th1 and Th2
differentiation are the cytokines IL-12 and IL-4
respectively Although STAT4 is expressed both in Th1 and
Th2 cells, STAT4 can only be phosphorylated by IL-12
which suggests that STAT4 plays an important role in Th1
cell function or development. STAT4 activation leads to
Th1 differentiation, including the target genes of STAT4
such as ERM, a transcription factor that belongs to the
Ets family of transcription factors. The expression of
ERM is specifically induced by IL-12 in wild-type Th1
cells, but not in STAT4-deficient T cells. STAT proteins
mediate the signaling of cytokines and a number of
growth factors from the receptors of these extracellular
signaling molecules to the cell nucleus. STATs are
specifically phosphorylated by receptor-associated Janus
kinases, receptor tyrosine kinases, or cytoplasmic
tyrosine kinases. The phosphorylated STAT molecules
dimerize by reciprocal binding of their SH2 domains to
the phosphotyrosine residues. These dimeric STATs
translocate into the nucleus, bind to specific DNA
sequences, and regulate the transcription of their
target genes. However there are a number of
unphosphorylated STATs that travel between the cytoplasm
and nucleus and some STATs that exist as dimers in
unstimulated cells that can exert biological functions
independent of being activated. There are seven
mammalian STAT family members which have been
identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A
and STAT5B), and STAT6. There are 6 conserved domains in
STAT: N-terminal domain (NTD), coiled-coil domain (CCD),
DNA-binding domain (DBD), alpha-helical linker domain
(LD), SH2 domain, and transactivation domain (TAD). NTD
is involved in dimerization of unphosphorylated STATs
monomers and for the tetramerization between STAT1,
STAT3, STAT4 and STAT5 on promoters with two or more
tandem STAT binding sites. It also plays a role in
promoting interactions with transcriptional
co-activators such as CREB binding protein (CBP)/p300,
as well as being important for nuclear import and
deactivation of STATs involving tyrosine
de-phosphorylation. CCD interacts with other proteins,
such as IFN regulatory protein 9 (IRF-9/p48) with STAT1
and c-JUN with STAT3 and is also thought to participate
in the negative regulation of these proteins. Distinct
genes are bound to STATs via their DBD domain. This
domain is also involved in nuclear translocation of
activated STAT1 and STAT3 phosphorylated dimers upon
cytokine stimulation. LD links the DNA-binding and SH2
domains and is important for the transcriptional
activation of STAT1 in response to IFN-gamma. It also
plays a role in protein-protein interactions and has
also been implicated in the constitutive
nucleocytoplasmic shuttling of unphosphorylated STATs in
resting cells. The SH2 domain is necessary for receptor
association and tyrosine phosphodimer formation.
Residues within this domain may be particularly
important for some cellular functions mediated by the
STATs as well as residues adjacent to this domain. The
TAD interacts with several proteins, namely
minichromosome maintenance complex component 5 (MCM5),
breast cancer 1 (BRCA1) and CBP/p300. TAD also contains
a modulatory phosphorylation site that regulates STAT
activity and is necessary for maximal transcription of a
number of target genes. The conserved tyrosine residue
present in the C-terminus is crucial for dimerization
via interaction with the SH2 domain upon the interaction
of the ligand with the receptor. STAT activation by
tyrosine phosphorylation also determines nuclear import
and retention, DNA binding to specific DNA elements in
the promoters of responsive genes, and transcriptional
activation of STAT dimers. In addition to the SH2 domain
there is a coiled-coil domain, a DNA binding domain, and
a transactivation domain in the STAT proteins. In
general SH2 domains are involved in signal transduction.
They typically bind pTyr-containing ligands via two
surface pockets, a pTyr and hydrophobic binding pocket,
allowing proteins with SH2 domains to localize to
tyrosine phosphorylated sites.
Length = 148
Score = 26.4 bits (58), Expect = 8.3
Identities = 23/81 (28%), Positives = 31/81 (38%), Gaps = 16/81 (19%)
Query: 113 IKKHRKPTWLDYL----------------KTPTCALSMPNVSPLCPKTFSWPDVSEESVL 156
IKKH P W+D K P L + S L TF+W D SE +
Sbjct: 9 IKKHILPLWIDGYIMGFVSKEKERLLLKDKMPGTFLLRFSESHLGGITFTWVDQSENGEV 68
Query: 157 KFPTWLDYLKTPTCALSMPNV 177
+F + Y K AL ++
Sbjct: 69 RFHSVEPYNKGRLSALPFADI 89
>gnl|CDD|225055 COG2144, COG2144, Selenophosphate synthetase-related proteins
[General function prediction only].
Length = 324
Score = 27.0 bits (60), Expect = 9.1
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 49 LREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 82
L ++ + E ++RK P + VRE +F
Sbjct: 3 LEDLISELRLFEGILRKNPIKDAVREFLDEFYGA 36
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 0.402
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,813,327
Number of extensions: 974091
Number of successful extensions: 806
Number of sequences better than 10.0: 1
Number of HSP's gapped: 801
Number of HSP's successfully gapped: 37
Length of query: 215
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 122
Effective length of database: 6,812,680
Effective search space: 831146960
Effective search space used: 831146960
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: 57 (25.8 bits)