RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6849
(439 letters)
>gnl|CDD|99895 cd05834, HDGF_related, The PWWP domain is an essential part of
the Hepatoma Derived Growth Factor (HDGF) family of
proteins, and is necessary for DNA binding by HDGF.
This family of endogenous nuclear-targeted mitogens
includes HRP (HDGF-related proteins 1, 2, 3, 4, or
HPR1, HPR2, HPR3, HPR4, respectively) and lens
epithelium-derived growth factor, LEDGF. Members of the
HDGF family have been linked to human diseases, and
HDGF is a prognostic factor in several types of cancer.
The PWWP domain, named for a conserved Pro-Trp-Trp-Pro
motif, is a small domain consisting of 100-150 amino
acids. The PWWP domain is found in numerous proteins
that are involved in cell division, growth and
differentiation. Most PWWP-domain proteins seem to be
nuclear, often DNA-binding, proteins that function as
transcription factors regulating a variety of
developmental processes.
Length = 83
Score = 117 bits (295), Expect = 2e-32
Identities = 43/81 (53%), Positives = 56/81 (69%)
Query: 6 RKFKTNDKVFAKVRGYPPWPARIEGLADETPNRLKYHIFFYGTRETGICRQDELFPYTEF 65
++FK D VFAKV+GYP WPAR++ D P KY ++F+GT ET + ++LFPYTE
Sbjct: 1 KQFKAGDLVFAKVKGYPAWPARVDEPEDWKPPGKKYPVYFFGTHETAFLKPEDLFPYTEN 60
Query: 66 KDKYGKGVKRKFFTEALQEIE 86
K K+GK KRK F EA+ EIE
Sbjct: 61 KKKFGKPKKRKGFNEAVWEIE 81
>gnl|CDD|151906 pfam11467, LEDGF, Lens epithelium-derived growth factor (LEDGF).
LEDGF is a chromatin-associated protein that protects
cells from stress-induced apoptosis. It is the binding
partner of HIV-1 integrase in human cells. The integrase
binding domain (IBD) of LEDGF is a compact right-handed
bundle composed of five alpha-helices. The residues
essential for the interaction with the integrase are
present in the inter-helical loop regions of the bundle
structure.
Length = 106
Score = 75.1 bits (185), Expect = 1e-16
Identities = 38/115 (33%), Positives = 66/115 (57%), Gaps = 22/115 (19%)
Query: 309 IKDSIGLEHADCDECLKALDDLINLPITPLVLKKHPEIVDTCRRLQRYTGNIAEWTMTEE 368
IK S+ L++AD ++CL+AL++L +L +T +L+K+PE V T ++++RY GN
Sbjct: 11 IKFSLKLDNADVEKCLEALEELGSLQVTSQILQKNPECVATLKKIRRYKGN--------- 61
Query: 369 EAEVFTQKASQVRAKADHVYNKFKNLFTVPAGET---FWDTFSKQLVTFNDVTRN 420
+ KA +YNKFK++F + GE+ FW+ S++ F + +N
Sbjct: 62 ---------QDIMDKATMIYNKFKSMF-LGEGESVQSFWENKSEEEQKFEEEAKN 106
>gnl|CDD|216154 pfam00855, PWWP, PWWP domain. The PWWP domain is named after a
conserved Pro-Trp-Trp-Pro motif. The domain binds to
Histone-4 methylated at lysine-20, H4K20me, suggesting
that it is methyl-lysine recognition motif. Removal of
two conserved aromatic residues in a hydrophobic cavity
created by this domain within the full-lemgth protein,
Pdp1, abolishes the interaction o f the protein with
H4K20me3. In fission yeast, Set9 is the sole enzyme
that catalyzes all three states of H4K20me, and
Set9-mediated H4K20me is required for efficient
recruitment of checkpoint protein Crb2 to sites of DNA
damage. The methylation of H4K20 is involved in a
diverse array of cellular processes, such as organising
higher-order chromatin, maintaining genome stability,
and regulating cell-cycle progression.
Length = 74
Score = 69.7 bits (171), Expect = 4e-15
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 7 KFKTNDKVFAKVRGYPPWPARIEGLADETPNRL----KYHIFFYGTRETGICRQDELFPY 62
FK D V+AK++G+P WPARI ETP + + + F+G +T L P
Sbjct: 1 DFKPGDLVWAKMKGFPWWPARIVSQK-ETPTSIRKDNRVKVQFFGDHKTAWVSPKRLKPL 59
Query: 63 TEFKDKYGKGVKRK 76
+K+ K KRK
Sbjct: 60 DVDIEKFHKDRKRK 73
>gnl|CDD|99894 cd05162, PWWP, The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes. The function of the PWWP
domain is still not known precisely; however, based on
the fact that other regions of PWWP-domain proteins are
responsible for nuclear localization and DNA-binding,
is likely that the PWWP domain acts as a site for
protein-protein binding interactions, influencing
chromatin remodeling and thereby regulating
transcriptional processes. Some PWWP-domain proteins
have been linked to cancer or other diseases; some are
known to function as growth factors.
Length = 87
Score = 69.7 bits (171), Expect = 6e-15
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 8 FKTNDKVFAKVRGYPPWPARIEGLADETPNRL------KYHIFFYGTRETGICRQDELFP 61
F+ D V+AK++GYP WPA + ++ K + F+G + + L P
Sbjct: 1 FRPGDLVWAKMKGYPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFGDKTFAWVGAERLKP 60
Query: 62 YTEFKDKYGKGVKRKFFTEALQEIE 86
+TE K+ K KRK F +A E
Sbjct: 61 FTEHKESEAKQSKRKGFKKAYDEAL 85
>gnl|CDD|99897 cd05836, N_Pac_NP60, The PWWP domain is an essential part of the
cytokine-like nuclear factor n-pac protein, or NP60,
which enhances the activity of MAP2K4 and MAP2K6
kinases to phosphorylate p38-alpha. In a variety of
cell lines, NP60 has been shown to localize to the
nucleus. In addition to the PWWP domain, NP60 also
contains an AT-hook and a C-terminal NAD-binding
domain. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding proteins, that
function as transcription factors regulating a variety
of developmental processes.
Length = 86
Score = 53.6 bits (129), Expect = 2e-09
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 8 FKTNDKVFAKVRGYPPWPARI--EGLADETPNRLK--YHIFFYGTRETGICRQDELFPYT 63
K D V+AK++G+PPWP RI + P + +FF+G+ +++ + PY
Sbjct: 1 LKLGDLVWAKMKGFPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSENHAWIKEENIKPYH 60
Query: 64 EFKDKYGKGVKRKFFTEALQEIE 86
E K++ K K F +A+ IE
Sbjct: 61 EHKEEMIKLNKGARFQQAVDAIE 83
>gnl|CDD|214603 smart00293, PWWP, domain with conserved PWWP motif. conservation
of Pro-Trp-Trp-Pro residues.
Length = 63
Score = 49.7 bits (119), Expect = 4e-08
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 8 FKTNDKVFAKVRGYPPWPARIEGLADETPNRLK-------YHIFFYGTRETGICRQDELF 60
FK D V+AK++G+P WPA + N +K Y + F+G ++T +LF
Sbjct: 1 FKPGDLVWAKMKGFPWWPALVISPKMTPDNIMKRKSDENLYPVLFFGDKDTAWIPSSKLF 60
Query: 61 PYT 63
P T
Sbjct: 61 PLT 63
>gnl|CDD|99896 cd05835, Dnmt3b_related, The PWWP domain is an essential
component of DNA methyltransferase 3 B (Dnmt3b) which
is responsible for establishing DNA methylation
patterns during embryogenesis and gametogenesis. In
tumorigenesis, DNA methylation by Dnmt3b is known to
play a role in the inactivation of tumor suppressor
genes. In addition, a point mutation in the PWWP
domain of Dnmt3b has been identified in patients with
ICF syndrome (immunodeficiency, centromeric
instability, and facial anomalies), a rare autosomal
recessive disorder characterized by hypomethylation of
classical satellite DNA. The PWWP domain, named for a
conserved Pro-Trp-Trp-Pro motif, is a small domain
consisting of 100-150 amino acids. The PWWP domain is
found in numerous proteins that are involved in cell
division, growth and differentiation. Most PWWP-domain
proteins seem to be nuclear, often DNA-binding,
proteins that function as transcription factors
regulating a variety of developmental processes.
Length = 87
Score = 47.4 bits (113), Expect = 3e-07
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 8 FKTNDKVFAKVRGYPPWPAR---IEGLADETPNRLKYHIFFYGTRETGICRQDELFPYTE 64
F D V+ K++G+P WP R I + P + ++G+ D+L P++E
Sbjct: 1 FNVGDLVWGKIKGFPWWPGRVVSITVTSKRPPVVGMRWVTWFGSGTFSEVSVDKLSPFSE 60
Query: 65 F------KDKYGKGVKRKFFTEALQE 84
F ++ KG+ +K EAL+
Sbjct: 61 FFKAFSRYNRKKKGLYKKAIYEALEV 86
>gnl|CDD|99899 cd05838, WHSC1_related, The PWWP domain was first identified in
the WHSC1 (Wolf-Hirschhorn syndrome candidate 1)
protein, a protein implicated in Wolf-Hirschhorn
syndrome (WHS). When translocated, WHSC1 plays a role
in lymphoid multiple myeloma (MM) disease, also known
as plasmacytoma. WHCS1 proteins typically contain two
copies of the PWWP domain. The PWWP domain, named for
a conserved Pro-Trp-Trp-Pro motif, is a small domain
consisting of 100-150 amino acids. The PWWP domain is
found in numerous proteins that are involved in cell
division, growth and differentiation. Most PWWP-domain
proteins seem to be nuclear, often DNA-binding,
proteins that function as transcription factors
regulating a variety of developmental processes.
Length = 95
Score = 45.0 bits (107), Expect = 3e-06
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 10/87 (11%)
Query: 8 FKTNDKVFAKVRGYPPWPARIEGLADETPNRL-KYH------IFFYGTRETGICRQDELF 60
D V+AK+ + WPA I + PN H + F+GT + + +F
Sbjct: 1 PLYGDIVWAKLGNFRWWPAIICDPREVPPNIQVLRHCIGEFCVMFFGTHDYYWVHRGRVF 60
Query: 61 PYTEFKDKYGKGVKR---KFFTEALQE 84
PY E + + K K F +AL+E
Sbjct: 61 PYQEGDKGFKEQTKSYLAKRFRKALEE 87
>gnl|CDD|99901 cd05840, SPBC215_ISWI_like, The PWWP domain is a component of the
S. pombe hypothetical protein SPBC215, as well as ISWI
complex protein 4. The ISWI (imitation switch)
proteins are ATPases responsible for chromatin
remodeling in eukaryotes, and SPBC215 is proposed to
also bind chromatin. The PWWP domain, named for a
conserved Pro-Trp-Trp-Pro motif, is a small domain
consisting of 100-150 amino acids. The PWWP domain is
found in numerous proteins that are involved in cell
division, growth and differentiation. Most PWWP-domain
proteins seem to be nuclear, often DNA-binding,
proteins that function as transcription factors
regulating a variety of developmental processes.
Length = 93
Score = 40.4 bits (95), Expect = 1e-04
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 8 FKTNDKVFAKVRGYPPWPARI 28
F+ D+V AKV+G+P WPA +
Sbjct: 1 FQPGDRVLAKVKGFPAWPAIV 21
>gnl|CDD|99903 cd06080, MUM1_like, Mutated melanoma-associated antigen 1 (MUM-1)
is a melanoma-associated antigen (MAA). MUM-1 belongs
to the mutated or aberrantly expressed type of MAAs,
along with antigens such as CDK4, beta-catenin,
gp100-in4, p15, and N-acetylglucosaminyltransferase V.
It is highly expressed in several types of human
cancers. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 80
Score = 39.3 bits (92), Expect = 2e-04
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 5/81 (6%)
Query: 8 FKTNDKVFAKVRGYPPWPARIEGLADETPNRLKYHIFFYGTRET-GICRQDELFPYTEFK 66
F+ ND V+AK++GYP WPA I + + K + F G + + +
Sbjct: 1 FEKNDLVWAKIQGYPWWPAVI---KSISRKKQKARVNFIGDNMQSEKKGIRVVKRWLKHF 57
Query: 67 DKYGKGVKRKFFTEAL-QEIE 86
D K E+ Q I+
Sbjct: 58 DCTEKQKLTNKAKESYEQAIQ 78
>gnl|CDD|99902 cd05841, BS69_related, The PWWP domain is part of BS69 protein, a
nuclear protein that specifically binds adenoviral E1A
and Epstein-Barr viral EBNA2 proteins, suppressing
their transactivation functions. BS69 is a
multi-domain protein, containing bromo, PHD, PWWP, and
MYND domains. The specific role of the PWWP domain
within BS69 is not clearly identified, but BS69
functions in chromatin remodeling, consistent with
other PWWP-containing proteins. The PWWP domain, named
for a conserved Pro-Trp-Trp-Pro motif, is a small
domain consisting of 100-150 amino acids. The PWWP
domain is found in numerous proteins that are involved
in cell division, growth and differentiation. Most
PWWP-domain proteins seem to be nuclear, often
DNA-binding, proteins that function as transcription
factors regulating a variety of developmental
processes.
Length = 83
Score = 33.1 bits (76), Expect = 0.034
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 14 VFAKVRGYPPWPARIEGLADETPNRLKYHI-FFYGTRETGICRQDELFPYTEFKDKYGKG 72
V+AK++G+P WPA++ + D + + FF G + + + P + + +
Sbjct: 13 VWAKLKGFPYWPAKVMRVEDN-----QVDVRFFGGQHDRAWIPSNNIQPIS--TEIPQQL 65
Query: 73 VKRKF--FTEALQEIEC 87
VK++ F +A+ E+E
Sbjct: 66 VKKRSRGFNKAMDELEL 82
>gnl|CDD|99898 cd05837, MSH6_like, The PWWP domain is present in MSH6, a
mismatch repair protein homologous to bacterial MutS.
The PWWP domain of histone-lysine N-methyltransferase,
also known as Nuclear SET domain-containing protein 3,
is also included. Mutations in MSH6 have been linked to
increased cancer susceptibility, particularly in
hereditary nonpolyposis colorectal cancer in humans.
The role of the PWWP domain in MSH6 is not clear; MSH6
orthologs found in S. cerevisiae, Caenorhabditis
elegans and Arabidopsis thaliana lack the PWWP domain.
Histone methyltransferases (HMTases) induce the
posttranslational methylation of lysine residues in
histones and play a role in apoptosis. In the HMTase
Whistle, the PWWP domain is necessary for HMTase
activity. The PWWP domain, named for a conserved
Pro-Trp-Trp-Pro motif, is a small domain consisting of
100-150 amino acids. The PWWP domain is found in
numerous proteins that are involved in cell division,
growth and differentiation. Most PWWP-domain proteins
seem to be nuclear, often DNA-binding, proteins that
function as transcription factors regulating a variety
of developmental processes.
Length = 110
Score = 32.7 bits (75), Expect = 0.081
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 9/50 (18%)
Query: 7 KFKTNDKVFAKVRGYPPWPARIE---------GLADETPNRLKYHIFFYG 47
K++ D V+AKV GYP WP + +YH+ F+G
Sbjct: 2 KYQVGDLVWAKVSGYPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFG 51
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 32.7 bits (74), Expect = 0.52
Identities = 34/113 (30%), Positives = 55/113 (48%), Gaps = 17/113 (15%)
Query: 223 LLDINKFTPPENCKTEKSINLWKMNKINEFKQIREKVEEGEPVKEEYAKIIEEQCQPEVQ 282
LLD K N + N++ + K+N+ K+I ++V +EY K IEE ++
Sbjct: 1331 LLDAQKHNSDINLYLNEIANIYNILKLNKIKKIIDEV-------KEYTKEIEEN-NKNIK 1382
Query: 283 AELEANEKALKT---QLKLEVCILDIDLRIKDSIGLEHADCDECLKALDDLIN 332
EL+ +EK +K + LE C I+ + D D DEC+K + +L N
Sbjct: 1383 DELDKSEKLIKKIKDDINLEECKSKIESTLDDK------DIDECIKKIKELKN 1429
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 32.0 bits (73), Expect = 0.69
Identities = 26/145 (17%), Positives = 53/145 (36%), Gaps = 21/145 (14%)
Query: 254 QIREKVEEGEPVKEEYAKIIEEQCQPEVQAELEANEKALKTQLKLEVCILDIDL-RIKDS 312
IR ++EE V+ + + +VQ + E ++ +K QL+ ++ + L I++
Sbjct: 356 SIRSELEE---VEARLDALTGKH--QDVQRKYERLKQKIKEQLERDLEKNNERLAAIREE 410
Query: 313 IGLEHADCDECLKALDDLINLPITPLVLKKHPEIVDTCRRLQRYTGNIAEW-------TM 365
+ A +E L+AL+ + L + ++ + T
Sbjct: 411 KDRQKAAIEEDLQALE-------SQLRQQLEAGKLEFNEEEYELELRLGRLKQRLDSATA 463
Query: 366 TEEEAEVFTQKASQVRAKADHVYNK 390
T EE E + KA +
Sbjct: 464 TPEELEQLEINDEALE-KAQEEQEQ 487
>gnl|CDD|234636 PRK00105, cobT, nicotinate-nucleotide--dimethylbenzimidazole
phosphoribosyltransferase; Reviewed.
Length = 335
Score = 31.6 bits (73), Expect = 0.79
Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 26/70 (37%)
Query: 303 LDIDLRIKDSIGLEHADCDECLKALDDLINLPITPLVLKKHPEIVDTCRRLQRYTGNIA- 361
DL + D +G+ D E P +++ R+ R TGNIA
Sbjct: 92 AGADLEVVD-LGV---DAPE-------------------PLPGLIN--MRVARGTGNIAK 126
Query: 362 EWTMTEEEAE 371
E MT EEAE
Sbjct: 127 EPAMTREEAE 136
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 31.0 bits (71), Expect = 1.2
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 17/72 (23%)
Query: 247 NKINEFKQIREKVEEGEPVKEEYAKIIEEQCQPEVQAELEANEKALKTQL-KLEV----- 300
K++ +++R+++++ E E ++ EE+ E AE EA KAL+ +L LE+
Sbjct: 63 AKLDTLEELRQRLDDLE----ELLELAEEEDDEETLAEAEAELKALEKKLAALELERLLS 118
Query: 301 -------CILDI 305
IL I
Sbjct: 119 GEYDANNAILTI 130
>gnl|CDD|99900 cd05839, BR140_related, The PWWP domain is found in the BR140
family, which includes peregrin and BR140-like proteins
1 and 2. BR140 is the only family to contain the PWWP
domain at the C terminus, with PHD and bromo domains in
the N-terminal region. In myeloid leukemias, BR140 is
disrupted by chromosomal translocations, similar to
translocations of WHSC1 in lymphoid multiple myeloma.
The PWWP domain, named for a conserved Pro-Trp-Trp-Pro
motif, is a small domain consisting of 100-150 amino
acids. The PWWP domain is found in numerous proteins
that are involved in cell division, growth and
differentiation. Most PWWP-domain proteins seem to be
nuclear, often DNA-binding proteins, that function as
transcription factors regulating a variety of
developmental processes.
Length = 111
Score = 29.0 bits (65), Expect = 1.6
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 12 DKVFAKVRGYPPWPARI 28
V+AK RGYP +PA I
Sbjct: 5 TLVWAKCRGYPSYPALI 21
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 30.2 bits (69), Expect = 1.8
Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 14/98 (14%)
Query: 246 MNKINEFKQIREKVEEGEP-----------VKEEYAKIIEEQCQPEVQAELEANEKALKT 294
++K+ E+ R+K + G P + Y + +++A+ E K
Sbjct: 54 LSKLYEYIDQRKKCDRGCPNYAKGYQPKLVMNGGYIDVSYLPTPEKIEADEEKAIKKRIQ 113
Query: 295 QLKLEVCILDIDLRIKDSIGLEHADCDECLKALDDLIN 332
+ + +L L I L+ D + L A D +
Sbjct: 114 SIYMPKDLLQASL---ADIDLDDRDRLDALMAALDFLE 148
>gnl|CDD|213983 cd12108, Hr-like, Hemerythrin-like domain. Hemerythrin (Hr) like
domains have the same four alpha helix bundle and a
similar, but slightly different active site structure
than hemerythrin. They are non-heme diiron binding
proteins mainly found in bacteria and eukaryotes. Like
Hr, they may be involved in oxygen transport or like
human FBXL5 (F-box and leucine-rich repeat protein 5), a
member of this group, play a role in cellular iron
homeostasis.
Length = 130
Score = 28.9 bits (65), Expect = 2.4
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 311 DSIGLEHADCDECLKALDDLINLPITPLVLKKHPEIVDTCRRLQRYTGNIAEWTMTEEEA 370
D++ EHA+ DE L L+ L+ + + E+ L+ + EEE
Sbjct: 72 DALEAEHAEIDELLARLEALLPA-LLAGDAEDAEELAAALEALRTALRE----HLDEEEE 126
Query: 371 EVF 373
E+F
Sbjct: 127 ELF 129
>gnl|CDD|220453 pfam09875, DUF2102, Uncharacterized protein conserved in archaea
(DUF2102). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 104
Score = 28.4 bits (64), Expect = 2.9
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 6 RKFKTNDKVFAKVRGYPPWPARI 28
RK N +F K RG+PP R
Sbjct: 52 RKLDPN-HIFIKDRGFPPGDPRR 73
>gnl|CDD|235861 PRK06782, PRK06782, flagellar motor switch protein; Reviewed.
Length = 528
Score = 29.8 bits (67), Expect = 3.7
Identities = 25/121 (20%), Positives = 47/121 (38%), Gaps = 6/121 (4%)
Query: 219 GKLVLLDINKFTPPENCKTEKSINLWKMNKINEFKQIREKVEEGEPVKEEYAKIIEEQCQ 278
G L+ + + P K + L+ M K E ++I + E E V E + IE +
Sbjct: 389 GDLLQTKMYQILPISEAKEMVRLLLYPMVK--EEEEIATEEIEPEKVVEPVVQPIEFKEV 446
Query: 279 PEVQAELEANEKALKTQLKLEVCILDIDLRIKDSIGLEHADCDECLKALDDLINLPITPL 338
+++ + ++V I+D + L+ + LD+ I+ PI
Sbjct: 447 KQMEPVYMDTSILQDVPMNVKVVFGSTKKTIQDILSLQENEVVV----LDEDIDEPIRIY 502
Query: 339 V 339
V
Sbjct: 503 V 503
>gnl|CDD|225109 COG2199, COG2199, c-di-GMP synthetase (diguanylate cyclase, GGDEF
domain) [Signal transduction mechanisms].
Length = 181
Score = 28.6 bits (64), Expect = 4.3
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 286 EANEKALKTQLKLEVCILDID--LRIKDSIGLEHADCDECLKAL 327
A +A + L + +LD+D +I D+ G HA DE L+ +
Sbjct: 40 RALARARRHGEPLALLLLDLDHFKQINDTYG--HAAGDEVLREV 81
>gnl|CDD|226454 COG3945, COG3945, Uncharacterized conserved protein [Function
unknown].
Length = 189
Score = 28.6 bits (64), Expect = 4.8
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 247 NKINEFKQIREKVEEGEPVKEEYAKIIEE 275
N++N ++ E + E YAK++EE
Sbjct: 153 NEVNSECFRFDEETFKETIHERYAKLLEE 181
>gnl|CDD|149180 pfam07960, CBP4, CBP4. The CBP4 in S. cerevisiae is essential for
the expression and activity of ubiquinol-cytochrome c
reductase. This family appears to be fungal specific.
Length = 128
Score = 27.0 bits (60), Expect = 9.6
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 236 KTEKSINLWKMNKI------NEFKQIREKVEEGEPVKEEYAKIIEEQCQPEVQAELEANE 289
K++K I WK I + +K + E KEE +I EE + Q+E E
Sbjct: 71 KSDKPI--WKTGPIESPWEKKRNVREFQKTKAEEAQKEELERIREELEEARAQSEEMRKE 128
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
0.314 0.132 0.389
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,275,541
Number of extensions: 2157010
Number of successful extensions: 1624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1609
Number of HSP's successfully gapped: 60
Length of query: 439
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 339
Effective length of database: 6,502,202
Effective search space: 2204246478
Effective search space used: 2204246478
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (26.9 bits)