RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11060
(155 letters)
>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 = 36.1 bits (84), Expect = 3e-04
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 87 CVGPDTCLNGGTCKPYLVDETQHRFNCTCPSGYHGKICE 125
C + C NGGTC T + C+CP GY G+ CE
Sbjct: 5 CASGNPCQNGGTCVN-----TVGSYRCSCPPGYTGRNCE 38
Score = 34.1 bits (79), Expect = 0.002
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 52 YSPCK-HGSCVDKRAGYFCDCPPTYGGKNC 80
+PC+ G+CV+ Y C CPP Y G+NC
Sbjct: 8 GNPCQNGGTCVNTVGSYRCSCPPGYTGRNC 37
>gnl|CDD|214542 smart00179, EGF_CA, Calcium-binding EGF-like domain.
Length = 39
Score = 31.1 bits (71), Expect = 0.021
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 53 SPCKHGS-CVDKRAGYFCDCPPTY-GGKNC 80
+PC++G CV+ Y C+CPP Y G+NC
Sbjct: 9 NPCQNGGTCVNTVGSYRCECPPGYTDGRNC 38
Score = 30.3 bits (69), Expect = 0.052
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 87 CVGPDTCLNGGTCKPYLVDETQHRFNCTCPSGYH-GKICE 125
C + C NGGTC T + C CP GY G+ CE
Sbjct: 5 CASGNPCQNGGTCVN-----TVGSYRCECPPGYTDGRNCE 39
>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 = 30.5 bits (69), Expect = 0.035
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 54 PCKH-GSCVDKRAGYFCDCPPTYGGKN 79
PC + G+CVD GY C+CP Y GK
Sbjct: 6 PCSNGGTCVDTPGGYTCECPEGYTGKR 32
Score = 28.6 bits (64), Expect = 0.20
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 93 CLNGGTCKPYLVDETQHRFNCTCPSGYHGK 122
C NGGTC +T + C CP GY GK
Sbjct: 7 CSNGGTCV-----DTPGGYTCECPEGYTGK 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 = 29.8 bits (67), Expect = 0.074
Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 5/36 (13%)
Query: 87 CVGPDTCLNGGTCKPYLVDETQHRFNCTCPSGYHGK 122
C + C NGGTC T + C CP GY G
Sbjct: 2 CAASNPCSNGGTCVN-----TPGSYRCVCPPGYTGD 32
Score = 27.4 bits (61), Expect = 0.42
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 49 PCAYS-PCKH-GSCVDKRAGYFCDCPPTYGGKN 79
CA S PC + G+CV+ Y C CPP Y G
Sbjct: 1 ECAASNPCSNGGTCVNTPGSYRCVCPPGYTGDR 33
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 29.4 bits (66), Expect = 0.081
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 53 SPCKHGSCVDKRAGYFCDCPPTY-GGKNCS 81
PC +G+C++ Y C CPP Y G K C
Sbjct: 6 GPCSNGTCINTPGSYTCSCPPGYTGDKRCE 35
Score = 24.8 bits (54), Expect = 4.0
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 93 CLNGGTCKPYLVDETQHRFNCTCPSGYHG-KICE 125
C +GG C T + C+CP GY G K CE
Sbjct: 2 CASGGPCSNGTCINTPGSYTCSCPPGYTGDKRCE 35
>gnl|CDD|221680 pfam12637, TSCPD, TSCPD domain. This family of proteins is found
in bacteria, archaea and viruses. The domain is found in
isolation in many proteins where it has a conserved
C-terminal motif TSCPD after which the domain is named.
Most copies of the domain possess 4 conserved cysteines
that may be part of an Iron-sulfur cluster. This domain
is found at the C-terminus of some
ribonucleoside-diphosphate reductase enzymes.
Length = 94
Score = 26.8 bits (60), Expect = 2.4
Identities = 8/39 (20%), Positives = 12/39 (30%), Gaps = 7/39 (17%)
Query: 109 HRFNCTCPSGY-------HGKICEKITTMSFSGGSHIML 140
++ C S Y G E + +GG L
Sbjct: 1 YKTKGGCGSLYITVNFDEDGGPFEVFINVGKAGGCAGNL 39
>gnl|CDD|238512 cd01061, RNase_T2_euk, Ribonuclease T2 (RNase T2) is a widespread
family of secreted RNases found in every organism
examined thus far. This family includes RNase Rh, RNase
MC1, RNase LE, and self-incompatibility RNases
(S-RNases). Plant T2 RNases are expressed during leaf
senescence in order to scavenge phosphate from
ribonucleotides. They are also expressed in response to
wounding or pathogen invasion. S-RNases are thought to
prevent self-fertilization by acting as selective
cytotoxins of "self" pollen. Generally, RNases have two
distinct binding sites: the primary site (B1 site) and
the subsite (B2 site), for nucleotides located at the
5'- and 3'- terminal ends of the sessil bond,
respectively. This CD includes the eukaryotic RNase T2
family members.
Length = 195
Score = 27.3 bits (61), Expect = 3.3
Identities = 9/24 (37%), Positives = 11/24 (45%), Gaps = 1/24 (4%)
Query: 60 CVDKRAGYFCDCPPTYGGKNCSVE 83
C DK+ G F DCP C +
Sbjct: 169 CFDKKGGEFIDCPRP-PKSTCPDD 191
>gnl|CDD|233736 TIGR02122, TRAP_TAXI, TRAP transporter solute receptor, TAXI
family. This family is one of at least three major
families of extracytoplasmic solute receptor (ESR) for
TRAP (Tripartite ATP-independent Periplasmic
Transporter) transporters. The others are the DctP
(TIGR00787) and SmoM (pfam03480) families. These
transporters are secondary (driven by an ion gradient)
but composed of three polypeptides, although in some
species the 4-TM and 12-TM integral membrane proteins
are fused. Substrates for this transporter family are
not fully characterized but, besides C4 dicarboxylates,
may include mannitol and other compounds [Transport and
binding proteins, Unknown substrate].
Length = 320
Score = 27.3 bits (61), Expect = 3.9
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 6 DGGIRTLDLLHGKQFSIGT-NSVLNVIML 33
D GI+T+ L GK+ ++G S +
Sbjct: 130 DSGIKTVADLKGKRVAVGAPGSGTELNAR 158
>gnl|CDD|173113 PRK14650, PRK14650, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 302
Score = 27.1 bits (60), Expect = 4.3
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 12/64 (18%)
Query: 96 GGTCKPYL----VDETQHRFNCTCPSGYHGKICEKITTMSFSGGSHIMLNTTREEGYDIS 151
GG K +L + + +H F I EKI GGS+I++N E + I
Sbjct: 30 GGISKLFLTPKTIKDAEHIFKAA--------IEEKIKIFILGGGSNILINDEEEIDFPII 81
Query: 152 FILH 155
+ H
Sbjct: 82 YTGH 85
>gnl|CDD|215222 PLN02397, PLN02397, aspartate transaminase.
Length = 423
Score = 26.8 bits (60), Expect = 4.6
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 6/26 (23%)
Query: 34 KSDYRLIIRPLYSLCPCAYSPCKHGS 59
KS +LI RP+YS +P HG+
Sbjct: 295 KSQLKLIARPMYS------NPPIHGA 314
>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase.
Length = 455
Score = 27.1 bits (60), Expect = 4.8
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 9/42 (21%)
Query: 78 KNCSVELTGCVGPDT------CLNGGTCKPYLVDETQHRFNC 113
K C +EL C+ CL +P DET+ + C
Sbjct: 119 KECRLELAKCIANPKCAANVACLQTCNGRP---DETECQIKC 157
>gnl|CDD|218407 pfam05061, Pox_A11, Poxvirus A11 Protein. Family of conserved
Chordopoxvirinae A11 family proteins. Conserved region
spans entire protein in the majority of family members.
Length = 309
Score = 26.7 bits (59), Expect = 5.2
Identities = 8/41 (19%), Positives = 12/41 (29%), Gaps = 3/41 (7%)
Query: 70 DCPPTYGGKNCSVELTGCVGPDTCLNGGTCKPYLVDETQHR 110
P + + V P T N + +V Q R
Sbjct: 63 SLIP---DDDSPRTIIEHVSPQTKFNDDSDPSEIVLAEQQR 100
>gnl|CDD|224164 COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin
structure and dynamics].
Length = 515
Score = 26.6 bits (59), Expect = 7.6
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 12/35 (34%)
Query: 50 CAYSPCKHGSCVDKRAGYFC------DCPPTYGGK 78
+ C HG CV FC D P +Y G+
Sbjct: 72 TSPHGCPHGRCV------FCPGGPDKDSPQSYTGE 100
>gnl|CDD|240390 PTZ00376, PTZ00376, aspartate aminotransferase; Provisional.
Length = 404
Score = 26.4 bits (59), Expect = 8.1
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 6/28 (21%)
Query: 32 MLKSDYRLIIRPLYSLCPCAYSPCKHGS 59
+ S +LIIRP+YS SP HG+
Sbjct: 275 NVLSQLKLIIRPMYS------SPPIHGA 296
>gnl|CDD|215505 PLN02935, PLN02935, Bifunctional NADH kinase/NAD(+) kinase.
Length = 508
Score = 26.3 bits (58), Expect = 8.9
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 8 GIRTLDLLHGKQFSIGTNSVLNVIMLKSDYRL 39
GI + ++L SVLN +M K+ ++L
Sbjct: 121 GICSHEVLQDGSTDSDNRSVLNKVMRKASFKL 152
>gnl|CDD|238220 cd00374, RNase_T2, Ribonuclease T2 (RNase T2) is a widespread
family of secreted RNases found in every organism
examined thus far. This family includes RNase Rh, RNase
MC1, RNase LE, and self-incompatibility RNases
(S-RNases). Plant T2 RNases are expressed during leaf
senescence in order to scavenge phosphate from
ribonucleotides. They are also expressed in response to
wounding or pathogen invasion. S-RNases are thought to
prevent self-fertilization by acting as selective
cytotoxins of "self" pollen.
Length = 195
Score = 25.9 bits (57), Expect = 10.0
Identities = 10/22 (45%), Positives = 10/22 (45%), Gaps = 1/22 (4%)
Query: 60 CVDKRAGYFCDCPPTYGGKNCS 81
C DK A F DCP G C
Sbjct: 169 CFDKDALKFIDCPTP-GKSTCP 189
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
0.324 0.142 0.471
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,519,182
Number of extensions: 622325
Number of successful extensions: 446
Number of sequences better than 10.0: 1
Number of HSP's gapped: 440
Number of HSP's successfully gapped: 43
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.2 bits)