RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9686
(769 letters)
>gnl|CDD|238066 cd00119, LYZ1, C-type lysozyme (1, 4-beta-N-acetylmuramidase, LYZ)
and alpha-lactalbumin (lactose synthase B protein, LA).
They have a close evolutionary relationship and similar
tertiary structure, however, functionally they are quite
different. Lysozymes have primarily bacteriolytic
function; hydrolysis of peptidoglycan of prokaryotic
cell walls and transglycosylation. LA is a
calcium-binding metalloprotein that is expressed
exclusively in the mammary gland during lactation. LA is
the regulatory subunit of the enzyme lactose synthase.
The association of LA with the catalytic component of
lactose synthase, galactosyltransferase, alters the
acceptor substrate specificity of this
glycosyltransferase, facilitating biosynthesis of
lactose.
Length = 123
Score = 130 bits (328), Expect = 2e-35
Identities = 51/127 (40%), Positives = 67/127 (52%), Gaps = 9/127 (7%)
Query: 279 KRFGACELAKFLVRQRGIARRDVPTWVCIATKESNRNSNARSPKNGNGSRDHGIFQINDK 338
K F CELAK L R + WVC+A ES N+ A + N +GS D+G+FQIN K
Sbjct: 1 KIFTRCELAKELKRLGLYPGISLANWVCLAEHESGFNTQAVN-NNNDGSTDYGLFQINSK 59
Query: 339 YWCT-ASGPAGKECHAKCSSFEDNNITDDVACVVKIHSQTQRARGNGFQAWSTYH-YCNT 396
YWC P+G CH CS D++ITDD+ C KI + Q GF AW + +C
Sbjct: 60 YWCNDGKTPSGNICHISCSKLLDDDITDDIKCAKKIVKEHQ-----GFDAWVAWKNHCQ- 113
Query: 397 NSKVSTY 403
+S +
Sbjct: 114 GRDLSQW 120
Score = 91.2 bits (227), Expect = 7e-22
Identities = 33/80 (41%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 15 GSRDHGIFQINDKYWCT-ASGPAGKECHAKCSSFEDNNITDDVACVVKIHSQTQRARGNG 73
GS D+G+FQIN KYWC P+G CH CS D++ITDD+ C KI + Q G
Sbjct: 47 GSTDYGLFQINSKYWCNDGKTPSGNICHISCSKLLDDDITDDIKCAKKIVKEHQ-----G 101
Query: 74 FQAWSTYH-YCNTNSKVSTY 92
F AW + +C +S +
Sbjct: 102 FDAWVAWKNHCQ-GRDLSQW 120
>gnl|CDD|197612 smart00263, LYZ1, Alpha-lactalbumin / lysozyme C.
Length = 127
Score = 110 bits (276), Expect = 2e-28
Identities = 49/130 (37%), Positives = 62/130 (47%), Gaps = 13/130 (10%)
Query: 279 KRFGACELAKFLVRQR--GIARRDVPTWVCIATKESNRNSNARSPKNGNGSRDHGIFQIN 336
K F CELA+ L R G + WVC+A ES N+ A + NG S D+GIFQIN
Sbjct: 1 KVFTRCELARELKRLGLDGYRGISLANWVCLAFHESGYNTQATNYNNGG-STDYGIFQIN 59
Query: 337 DKYWCTASG--PAGKECHAKCSSFEDNNITDDVACVVKIHSQTQRARGNGFQAWSTYH-Y 393
KYWC + C CS D++ITDDV C KI S G AW + +
Sbjct: 60 SKYWCNDGKTPGSVNACGISCSKLLDDDITDDVKCAKKIVSD------QGIDAWVAWKNH 113
Query: 394 CNTNSKVSTY 403
C +S +
Sbjct: 114 CQ-GEDLSQW 122
Score = 81.6 bits (202), Expect = 2e-18
Identities = 31/86 (36%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 15 GSRDHGIFQINDKYWCTASG--PAGKECHAKCSSFEDNNITDDVACVVKIHSQTQRARGN 72
GS D+GIFQIN KYWC + C CS D++ITDDV C KI S
Sbjct: 49 GSTDYGIFQINSKYWCNDGKTPGSVNACGISCSKLLDDDITDDVKCAKKIVSD------Q 102
Query: 73 GFQAWSTYH-YCNTNSKVSTYYSSSF 97
G AW + +C +S +
Sbjct: 103 GIDAWVAWKNHCQ-GEDLSQWIRGCG 127
>gnl|CDD|200968 pfam00062, Lys, C-type lysozyme/alpha-lactalbumin family.
Alpha-lactalbumin is the regulatory subunit of lactose
synthase, changing the substrate specificity of
galactosyltransferase from N-acetylglucosamine to
glucose. C-type lysozymes are secreted bacteriolytic
enzymes that cleave the peptidoglycan of bacterial cell
walls. Structure is a multi-domain, mixed alpha and beta
fold, containing four conserved disulfide bonds.
Length = 125
Score = 100 bits (252), Expect = 3e-25
Identities = 51/131 (38%), Positives = 66/131 (50%), Gaps = 13/131 (9%)
Query: 279 KRFGACELAKFLVRQ--RGIARRDVPTWVCIATKESNRNSNARSPKNGNGSRDHGIFQIN 336
K F CELA+ L R G + WVC+A ES N+ A + N NGS D+GIFQIN
Sbjct: 1 KVFTRCELARELKRLGMDGYRGISLANWVCLAFHESGYNTQATN-NNNNGSTDYGIFQIN 59
Query: 337 DKYWCTAS-GPAGK-ECHAKCSSFEDNNITDDVACVVKIHSQTQRARGNGFQAWSTY-HY 393
KYWC P K C CS D++ITDD+ C KI Q G AW + ++
Sbjct: 60 SKYWCNDGKTPGSKNACGISCSKLLDDDITDDIMCAKKILRDPQ-----GIDAWVAWKNH 114
Query: 394 CNTNSKVSTYD 404
C+ +S +
Sbjct: 115 CSE--DLSQWR 123
Score = 70.8 bits (174), Expect = 1e-14
Identities = 31/72 (43%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 15 GSRDHGIFQINDKYWCTAS-GPAGK-ECHAKCSSFEDNNITDDVACVVKIHSQTQRARGN 72
GS D+GIFQIN KYWC P K C CS D++ITDD+ C KI Q
Sbjct: 49 GSTDYGIFQINSKYWCNDGKTPGSKNACGISCSKLLDDDITDDIMCAKKILRDPQ----- 103
Query: 73 GFQAWSTY-HYC 83
G AW + ++C
Sbjct: 104 GIDAWVAWKNHC 115
>gnl|CDD|238011 cd00054, EGF_CA, Calcium-binding EGF-like domain, present in a
large number of membrane-bound and extracellular (mostly
animal) proteins. Many of these proteins require calcium
for their biological function and calcium-binding sites
have been found to be located at the N-terminus of
particular EGF-like domains; calcium-binding may be
crucial for numerous protein-protein interactions. Six
conserved core cysteines form three disulfide bridges as
in non calcium-binding EGF domains, whose structures are
very similar. EGF_CA can be found in tandem repeat
arrangements.
Length = 38
Score = 36.8 bits (86), Expect = 0.001
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 694 CVTLNPCQNNATCVASPGDKQITCLCLKGFEGPH 727
C + NPCQN TCV + G C C G+ G +
Sbjct: 5 CASGNPCQNGGTCVNTVGS--YRCSCPPGYTGRN 36
Score = 32.2 bits (74), Expect = 0.055
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 518 CA-GRPCRNNGTCTPVSGGVVNFTCTCPSG 546
CA G PC+N GTC G + C+CP G
Sbjct: 5 CASGNPCQNGGTCVNTVGS---YRCSCPPG 31
Score = 30.3 bits (69), Expect = 0.22
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 650 CVTLNPCQNNATCVASPGDKQITCLCLKG 678
C + NPCQN TCV + G C C G
Sbjct: 5 CASGNPCQNGGTCVNTVGS--YRCSCPPG 31
>gnl|CDD|238010 cd00053, EGF, Epidermal growth factor domain, found in epidermal
growth factor (EGF) presents in a large number of
proteins, mostly animal; the list of proteins currently
known to contain one or more copies of an EGF-like
pattern is large and varied; the functional significance
of EGF-like domains in what appear to be unrelated
proteins is not yet clear; a common feature is that
these repeats are found in the extracellular domain of
membrane-bound proteins or in proteins known to be
secreted (exception: prostaglandin G/H synthase); the
domain includes six cysteine residues which have been
shown to be involved in disulfide bonds; the main
structure is a two-stranded beta-sheet followed by a
loop to a C-terminal short two-stranded sheet;
Subdomains between the conserved cysteines vary in
length; the region between the 5th and 6th cysteine
contains two conserved glycines of which at least one
is present in most EGF-like domains; a subset of
these bind calcium.
Length = 36
Score = 36.3 bits (84), Expect = 0.002
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 694 CVTLNPCQNNATCVASPGDKQITCLCLKGFEGPHR 728
C NPC N TCV +PG C+C G+ G
Sbjct: 2 CAASNPCSNGGTCVNTPGS--YRCVCPPGYTGDRS 34
Score = 32.1 bits (73), Expect = 0.053
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 522 PCRNNGTCTPVSGGVVNFTCTCPSG 546
PC N GTC G + C CP G
Sbjct: 7 PCSNGGTCVNTPGS---YRCVCPPG 28
Score = 30.5 bits (69), Expect = 0.22
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 650 CVTLNPCQNNATCVASPGDKQITCLCLKG 678
C NPC N TCV +PG C+C G
Sbjct: 2 CAASNPCSNGGTCVNTPGS--YRCVCPPG 28
>gnl|CDD|215652 pfam00008, EGF, EGF-like domain. There is no clear separation
between noise and signal. pfam00053 is very similar, but
has 8 instead of 6 conserved cysteines. Includes some
cytokine receptors. The EGF domain misses the N-terminus
regions of the Ca2+ binding EGF domains (this is the
main reason of discrepancy between swiss-prot domain
start/end and Pfam). The family is hard to model due to
many similar but different sub-types of EGF domains.
Pfam certainly misses a number of EGF domains.
Length = 32
Score = 35.9 bits (83), Expect = 0.002
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 694 CVTLNPCQNNATCVASPGDKQITCLCLKGFEGPH 727
C NPC N TCV +PG TC C +G+ G
Sbjct: 1 CSPNNPCSNGGTCVDTPGG--YTCECPEGYTGKR 32
Score = 32.0 bits (73), Expect = 0.052
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 650 CVTLNPCQNNATCVASPGDKQITCLCLKGGT 680
C NPC N TCV +PG TC C +G T
Sbjct: 1 CSPNNPCSNGGTCVDTPGG--YTCECPEGYT 29
Score = 31.3 bits (71), Expect = 0.10
Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 522 PCRNNGTCTPVSGGVVNFTCTCPSGGQGQ 550
PC N GTC GG +TC CP G G+
Sbjct: 6 PCSNGGTCVDTPGG---YTCECPEGYTGK 31
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 33.4 bits (77), Expect = 0.021
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 694 CVTLNPCQNNATCVASPGDKQITCLCLKGFEGPHR 728
C + NPCQN TCV + G C C G+
Sbjct: 5 CASGNPCQNGGTCVNTVGS--YRCECPPGYTDGRN 37
Score = 31.1 bits (71), Expect = 0.14
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 518 CA-GRPCRNNGTCTPVSGGVVNFTCTCPSG 546
CA G PC+N GTC G + C CP G
Sbjct: 5 CASGNPCQNGGTCVNTVGS---YRCECPPG 31
Score = 29.9 bits (68), Expect = 0.34
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 650 CVTLNPCQNNATCVASPGDKQITCLCLKG 678
C + NPCQN TCV + G C C G
Sbjct: 5 CASGNPCQNGGTCVNTVGS--YRCECPPG 31
>gnl|CDD|150167 pfam09404, DUF2003, Eukaryotic protein of unknown function
(DUF2003). This is a family of proteins of unknown
function which adopt an alpha helical and beta sheet
structure.
Length = 447
Score = 34.2 bits (78), Expect = 0.27
Identities = 12/51 (23%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 572 QYYFRRKSTSPHKSRGQGQSGLEITPVYLWLMKMKTLVMVQ--YYLQQNIS 620
Q + R++ T H GQ Q ++ ++LWL +++ +++ + +Y + +S
Sbjct: 229 QTFERQRETRKHLFGGQSQKAVQPPHLFLWLQRLQAMLLAKFSFYFHEALS 279
Score = 33.1 bits (75), Expect = 0.66
Identities = 9/30 (30%), Positives = 20/30 (66%)
Query: 546 GGQGQSGLEITPVYLWLMKLKTLVMVQYYF 575
GGQ Q ++ ++LWL +L+ +++ ++ F
Sbjct: 243 GGQSQKAVQPPHLFLWLQRLQAMLLAKFSF 272
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 29.0 bits (65), Expect = 0.60
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 694 CVTLNPCQNNATCVASPGDKQITCLCLKGFEGPHR 728
C + PC N TC+ +PG TC C G+ G R
Sbjct: 2 CASGGPCSNG-TCINTPGS--YTCSCPPGYTGDKR 33
>gnl|CDD|219771 pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA)
PRD domain. Mga is a DNA-binding protein that activates
the expression of several important virulence genes in
group A streptococcus in response to changing
environmental conditions. This corresponds to the PRD
like region.
Length = 217
Score = 31.1 bits (71), Expect = 1.4
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 13/88 (14%)
Query: 188 KISD-PIFTDRFRDRIWFLALLINLS----SFFVSVPLMLISLEIFKELNGLNFRIKVFS 242
KI+D P+ + FR F +L+ L+ FFV +P + ++FK+L L ++
Sbjct: 17 KITDVPMNFEEFR----FFKILLALNWKRKGFFVEIP----NSKLFKQLKKLFIYDELMK 68
Query: 243 HCRNEGRPQSAMHFSPIAACLLVLVYCT 270
P + S L L+Y T
Sbjct: 69 SVSQLFEPHFNLTLSEDDLDYLFLIYLT 96
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to
the RRM1 of hnRNP A0 which is a low abundance hnRNP
protein that has been implicated in mRNA stability in
mammalian cells. It has been identified as the
substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 79
Score = 29.4 bits (66), Expect = 1.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 58 CVVKIHSQTQRARGNGFQAWSTYHYCN 84
CVV + T+R+RG GF +S+ +
Sbjct: 32 CVVMVDPNTKRSRGFGFITFSSADEAD 58
Score = 29.4 bits (66), Expect = 1.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 369 CVVKIHSQTQRARGNGFQAWSTYHYCN 395
CVV + T+R+RG GF +S+ +
Sbjct: 32 CVVMVDPNTKRSRGFGFITFSSADEAD 58
>gnl|CDD|238157 cd00254, LT_GEWL, Lytic Transglycosylase (LT) and Goose Egg White
Lysozyme (GEWL) domain. Members include the soluble and
insoluble membrane-bound LTs in bacteria, the LTs in
bacteriophage lambda, as well as, the eukaryotic
"goose-type" lysozymes (GEWL). LTs catalyze the
cleavage of the beta-1,4-glycosidic bond between
N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine
(GlcNAc), as do "goose-type" lysozymes. However, in
addition to this, they also make a new glycosidic bond
with the C6 hydroxyl group of the same muramic acid
residue.
Length = 113
Score = 30.1 bits (68), Expect = 1.7
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 4/34 (11%)
Query: 307 IATKESNRNSNARSPKNGNGSRDHGIFQINDKYW 340
I +ES N NA +G+ G+ Q
Sbjct: 7 IIRQESGFNPNAV----NSGAGAVGLMQFMPSTA 36
>gnl|CDD|189996 pfam01464, SLT, Transglycosylase SLT domain. This family is
distantly related to pfam00062. Members are found in
phages, type II, type III and type IV secretion systems.
Length = 117
Score = 29.6 bits (67), Expect = 2.2
Identities = 16/66 (24%), Positives = 22/66 (33%), Gaps = 14/66 (21%)
Query: 300 DVPTWVCIATKESNRNSNARSPKNGNGSRDHGIFQINDKYWCTASGPAGKECHAKCSSFE 359
D IA +ES N NA S G+ QI TA S
Sbjct: 13 DPSLLAAIAQQESGFNPNAISGSG-----ALGLMQIMPS---TAKA------LGLKGSPG 58
Query: 360 DNNITD 365
++++ D
Sbjct: 59 EDDLFD 64
>gnl|CDD|219677 pfam07974, EGF_2, EGF-like domain. This family contains EGF
domains found in a variety of extracellular proteins.
Length = 31
Score = 27.0 bits (60), Expect = 3.1
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 4/34 (11%)
Query: 694 CVTLNPCQNNATCVASPGDKQITCLCLKGFEGPH 727
C C TCV G C+C G++G
Sbjct: 1 CSASGICNGRGTCVRPCG----KCVCDSGYQGAT 30
>gnl|CDD|216585 pfam01582, TIR, TIR domain. The Toll/interleukin-1 receptor (TIR)
homology domain is an intracellular signalling domain
found in MyD88, interleukin 1 receptor and the Toll
receptor. It contains three highly-conserved regions,
and mediates protein-protein interactions between the
Toll-like receptors (TLRs) and signal-transduction
components. TIR-like motifs are also found in plant
proteins thought to be involved in resistance to
disease. When activated, TIR domains recruit cytoplasmic
adaptor proteins MyD88 and TOLLIP (Toll interacting
protein). In turn, these associate with various kinases
to set off signalling cascades.
Length = 135
Score = 28.8 bits (65), Expect = 5.5
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 8/45 (17%)
Query: 441 FISYSSTH-------HISKMANKFKFNLFKDHADDM-GTCTWEKL 477
F+S+S H+ K + L D D++ G E L
Sbjct: 2 FVSFSGKDDRDTFVSHLLKELEEKGIKLCIDDRDELPGESILENL 46
>gnl|CDD|205157 pfam12947, EGF_3, EGF domain. This family includes a variety of
EGF-like domain homologues. This family includes the
C-terminal domain of the malaria parasite MSP1 protein.
Length = 36
Score = 26.3 bits (59), Expect = 5.9
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 699 PCQNNATCVASPGDKQITCLCLKGFEG 725
C NATC + G TC C G+ G
Sbjct: 7 GCHPNATCTNTGG--SFTCTCKSGYTG 31
>gnl|CDD|219026 pfam06432, GPI2, Phosphatidylinositol
N-acetylglucosaminyltransferase.
Glycosylphosphatidylinositol (GPI) represents an
important anchoring molecule for cell surface proteins.
The first step in its synthesis is the transfer of
N-acetylglucosamine (GlcNAc) from
UDP-N-acetylglucosamine to phosphatidylinositol (PI).
This step involves products of three or four genes in
both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG
A, PIG H and PIG C), respectively.
Length = 268
Score = 29.1 bits (66), Expect = 7.5
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 198 FRDRIWFLALLINLSSFFVSV--PLMLISLEIFK-ELNG 233
LALL L+ F+S PL I L+ +K E++G
Sbjct: 227 LLTLSPILALLFLLTVLFISFVCPLWFIRLQKYKNEIHG 265
>gnl|CDD|220520 pfam10011, DUF2254, Predicted membrane protein (DUF2254). Members
of this family of bacterial proteins comprises various
hypothetical and putative membrane proteins. Their exact
function, has not, as yet, been defined.
Length = 369
Score = 29.1 bits (66), Expect = 8.6
Identities = 9/41 (21%), Positives = 16/41 (39%)
Query: 198 FRDRIWFLALLINLSSFFVSVPLMLISLEIFKELNGLNFRI 238
R +WF L L + ++ L+ + L F+I
Sbjct: 1 LRRSLWFRPTLYALLAVLLAFVAPLLDRLLPSSLLPWLFKI 41
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
0.321 0.134 0.428
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,946,877
Number of extensions: 3428066
Number of successful extensions: 2454
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2432
Number of HSP's successfully gapped: 41
Length of query: 769
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 665
Effective length of database: 6,324,786
Effective search space: 4205982690
Effective search space used: 4205982690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 63 (28.0 bits)