RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy592
(339 letters)
>gnl|CDD|216265 pfam01049, Cadherin_C, Cadherin cytoplasmic region. Cadherins are
vital in cell-cell adhesion during tissue
differentiation. Cadherins are linked to the
cytoskeleton by catenins. Catenins bind to the
cytoplasmic tail of the cadherin. Cadherins cluster to
form foci of homophilic binding units. A key determinant
to the strength of the binding that it is mediated by
cadherins is the juxtamembrane region of the cadherin.
This region induces clustering and also binds to the
protein p120ctn.
Length = 145
Score = 164 bits (418), Expect = 1e-50
Identities = 59/121 (48%), Positives = 71/121 (58%), Gaps = 6/121 (4%)
Query: 219 RRREAHIKYPGPDDDVRENIINYDDEGGGEDDMTAFDITPLQIPIGGP----HPEMNNKI 274
RRR+ +DD+RENIINYDDEGGGE+D A+DI+ L+ P+ P ++
Sbjct: 1 RRRKKEPLIIDKEDDIRENIINYDDEGGGEEDTDAYDISALRNPLDPLRRDVQPLISALP 60
Query: 275 PYGLGPMPMGVEPNVGIFIEEHKKRADADPNAPPFDDLRNYAYEGGGSTAGSLSSLASGS 334
P P +VG FI E AD DP APP+D L YAYEG GS AGSLSSL S S
Sbjct: 61 RPRPPPPPDP--GDVGDFIHEKLPEADNDPTAPPYDSLLTYAYEGRGSVAGSLSSLNSSS 118
Query: 335 S 335
S
Sbjct: 119 S 119
>gnl|CDD|238058 cd00110, LamG, Laminin G domain; Laminin G-like domains are usually
Ca++ mediated receptors that can have binding sites for
steroids, beta1 integrins, heparin, sulfatides,
fibulin-1, and alpha-dystroglycans. Proteins that
contain LamG domains serve a variety of purposes
including signal transduction via cell-surface steroid
receptors, adhesion, migration and differentiation
through mediation of cell adhesion molecules.
Length = 151
Score = 61.3 bits (149), Expect = 2e-11
Identities = 26/117 (22%), Positives = 42/117 (35%), Gaps = 31/117 (26%)
Query: 77 PVTFKPQSYIKYALSFEPDKYTTQLQLKFRTREEFGELFRLSDQHNREYAILEIKDSKLR 136
V+F SY++ P + + FRT G L Q+ ++ LE++D +L
Sbjct: 1 GVSFSGSSYVRLPTLPAPRTRLS-ISFSFRTTSPNGLLLYAGSQNGGDFLALELEDGRLV 59
Query: 137 FRYNLNNLKTDEKDIWLNAIKDSKLRFRYNLNNLKTDEKDIWLNAVAVNDGQWHFVK 193
RY+L + L++ +NDGQWH V
Sbjct: 60 LRYDLG-----SGSLVLSSK-------------------------TPLNDGQWHSVS 86
>gnl|CDD|216930 pfam02210, Laminin_G_2, Laminin G domain. This family includes the
Thrombospondin N-terminal-like domain, a Laminin G
subfamily.
Length = 124
Score = 50.1 bits (120), Expect = 7e-08
Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 29/89 (32%)
Query: 105 FRTREEFGELFRLSDQHNREYAILEIKDSKLRFRYNLNNLKTDEKDIWLNAIKDSKLRFR 164
FRT + G L + ++ LE++D +L RY+L
Sbjct: 1 FRTTQPNGLLLYAGGEDGLDFLALELEDGRLVLRYDLG---------------------- 38
Query: 165 YNLNNLKTDEKDIWLNAVAVNDGQWHFVK 193
+ + L+ +NDGQWH V
Sbjct: 39 -------SGGSVLLLSGKKLNDGQWHRVS 60
>gnl|CDD|214598 smart00282, LamG, Laminin G domain.
Length = 132
Score = 49.6 bits (119), Expect = 1e-07
Identities = 20/94 (21%), Positives = 31/94 (32%), Gaps = 29/94 (30%)
Query: 100 QLQLKFRTREEFGELFRLSDQHNREYAILEIKDSKLRFRYNLNNLKTDEKDIWLNAIKDS 159
+ FRT G L + +Y LE++D +L RY+L +
Sbjct: 1 SISFSFRTTSPNGLLLYAGSKGGGDYLALELRDGRLVLRYDLGS---------------- 44
Query: 160 KLRFRYNLNNLKTDEKDIWLNAVAVNDGQWHFVK 193
+ + +NDGQWH V
Sbjct: 45 -------------GPARLTSDPTPLNDGQWHRVA 65
>gnl|CDD|219677 pfam07974, EGF_2, EGF-like domain. This family contains EGF
domains found in a variety of extracellular proteins.
Length = 31
Score = 32.4 bits (74), Expect = 0.018
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 12/43 (27%)
Query: 29 CPATEAVCNAHSRLHCYPEHGVCVGSMHTAKCQCLPGWSGTGC 71
C A+ +CN G CV KC C G+ G C
Sbjct: 1 CSASG-ICN---------GRGTCVR--PCGKCVCDSGYQGATC 31
>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 = 31.8 bits (73), Expect = 0.029
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 44 CYPEHGVCVGSMHTAKCQCLPGWSGTGCV 72
C G CV ++ + +C C PG++G C
Sbjct: 11 CQN-GGTCVNTVGSYRCSCPPGYTGRNCE 38
>gnl|CDD|214544 smart00181, EGF, Epidermal growth factor-like domain.
Length = 35
Score = 30.6 bits (69), Expect = 0.087
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 47 EHGVCVGSMHTAKCQCLPGWSG 68
+G C+ + + C C PG++G
Sbjct: 9 SNGTCINTPGSYTCSCPPGYTG 30
>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 = 30.1 bits (68), Expect = 0.12
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 48 HGVCVGSMHTAKCQCLPGWSG 68
G CV + + +C C PG++G
Sbjct: 11 GGTCVNTPGSYRCVCPPGYTG 31
>gnl|CDD|204999 pfam12661, hEGF, Human growth factor-like EGF. hEGF, or human
growth factor-like EGF, domains have six conserved
residues disulfide-bonded into the characteristic
'ababcc' pattern. They are involved in growth and
proliferation of cells, in proteins of the Notch/Delta
pathway, neurogulin and selectins. hEGFs are also found
in mosaic proteins with four-disulfide laminin EGFs
such as aggrecan and perlecan. The core fold of the EGF
domain consists of two small beta-hairpins packed
against each other. Two major structural variants have
been identified based on the structural context of the
C-terminal Cys residue of disulfide 'c' in the
C-terminal hairpin: hEGFs and cEGFs. In hEGFs the
C-terminal thiol resides in the beta-turn, resulting in
shorter loop-lengths between the Cys residues of
disulfide 'c', typically C[8-9]XC. These shorter
loop-lengths are also typical of the four-disulfide EGF
domains, laminin ad integrin. Tandem hEGF domains have
six linking residues between terminal cysteines of
adjacent domains. hEGF domains may or may not bind
calcium in the linker region. hEGF domains with the
consensus motif CXD4X[F,Y]XCXC are hydroxylated
exclusively in the Asp residue.
Length = 13
Score = 28.1 bits (64), Expect = 0.44
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 59 KCQCLPGWSG 68
KCQC PG++G
Sbjct: 1 KCQCPPGYTG 10
>gnl|CDD|215680 pfam00053, Laminin_EGF, Laminin EGF-like (Domains III and V).
This family is like pfam00008 but has 8 conserved
cysteines instead of six.
Length = 49
Score = 28.1 bits (63), Expect = 0.87
Identities = 14/38 (36%), Positives = 15/38 (39%), Gaps = 11/38 (28%)
Query: 36 CNAHSRLH--CYPEHGVCVGSMHTAKCQCLPGWSGTGC 71
CN H L C PE G C C PG +G C
Sbjct: 3 CNPHGSLSDTCDPETGQC---------LCKPGVTGRHC 31
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 30.5 bits (68), Expect = 1.0
Identities = 22/157 (14%), Positives = 50/157 (31%), Gaps = 5/157 (3%)
Query: 89 ALSFEPDKYTTQLQLKFRTREEFGELFRLSDQHNR----EYAILEIKDSKLRFRYNLNNL 144
AL+ + L L L L D++ E+ I E +R+RY
Sbjct: 18 ALALLLLLLSLGLTLDRGLNVGIKLLPFLLDENEIEIPLEFEIEEFLIDGIRYRYGFELD 77
Query: 145 KTDEKDIWLNAIKDSKLRFRYNLNNLKTDEKDIWLNAVAVNDGQWHFVKTGSALFVTLLI 204
K D + L + + + K + + + + +L LL+
Sbjct: 78 KEDILEELLYEYRKGEELL-FERERSKESFEKSPEKKRELRGLREVLLLLNLSLSSFLLL 136
Query: 205 SPNQVLVLVFVVYSRRREAHIKYPGPDDDVRENIINY 241
+ ++L+ + + +S + + + +
Sbjct: 137 ASLEILLSILLPFSFILGNLRNLRNIELKLLDLVKRL 173
>gnl|CDD|215681 pfam00054, Laminin_G_1, Laminin G domain.
Length = 131
Score = 29.6 bits (67), Expect = 1.1
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 105 FRTREEFGELFRLSDQHNREYAILEIKDSKLRFRYNL 141
FRT E G L Q R++ LE++D +L Y+L
Sbjct: 1 FRTTEPSGLLLYNGTQTERDFLALELRDGRLEVSYDL 37
>gnl|CDD|236405 PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.
Length = 565
Score = 30.8 bits (71), Expect = 1.1
Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 109 EEFG-ELFRLSDQHNREYA 126
EE+G EL RL D+H R++
Sbjct: 87 EEYGPELLRLKDRHGRDFV 105
>gnl|CDD|114337 pfam05609, LAP1C, Lamina-associated polypeptide 1C (LAP1C). This
family contains rat LAP1C proteins and several
uncharacterized highly related sequences from both mice
and humans. LAP1s (lamina-associated polypeptide 1s) are
type 2 integral membrane proteins with a single
membrane-spanning region of the inner nuclear membrane.
LAP1s bind to both A- and B-type lamins and have a
putative role in the membrane attachment and assembly of
the nuclear lamina.
Length = 465
Score = 30.4 bits (68), Expect = 1.3
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 218 SRRREAHIKYPGPDDDVRENIINYDDEGGGEDD 250
+ R ++YP + +N ++ +EG EDD
Sbjct: 73 DKLRRPPLRYPRYEATEVQNKQSFLEEGETEDD 105
>gnl|CDD|214543 smart00180, EGF_Lam, Laminin-type epidermal growth factor-like
domai.
Length = 46
Score = 26.9 bits (60), Expect = 2.4
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 8/44 (18%)
Query: 36 CNA--HSRLHCYPEHGVCVGSMHTA--KC-QCLPG-W--SGTGC 71
C+ + C P+ G C + +C +C PG + GC
Sbjct: 3 CDPGGSASGTCDPDTGQCECKPNVTGRRCDRCAPGYYGDGPPGC 46
>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 = 26.2 bits (58), Expect = 2.5
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 48 HGVCVGSMHTAKCQCLPGWSG 68
G CV + C+C G++G
Sbjct: 10 GGTCVDTPGGYTCECPEGYTG 30
>gnl|CDD|238825 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from
retrotransposons and retroviruses which have long
terminal repeats (LTRs) in their DNA copies but not in
their RNA template. RT catalyzes DNA replication from an
RNA template, and is responsible for the replication of
retroelements. An RT gene is usually indicative of a
mobile element such as a retrotransposon or retrovirus.
RTs are present in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
Caulimoviruses.
Length = 177
Score = 28.7 bits (65), Expect = 3.0
Identities = 29/129 (22%), Positives = 45/129 (34%), Gaps = 39/129 (30%)
Query: 131 KDSKLRF-----RYNLNNLKTDE-----KDIWLNAIKDSK------LRFRYNLNNLKTDE 174
KD KLR + N D D L + +K LR Y+ + E
Sbjct: 20 KDGKLRLCVDYRKLN-KVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYH--QIPLAE 76
Query: 175 KDIWLNAVAVNDGQWHFV------KTGSALFVTLLISPNQVL-------VLVFV----VY 217
+ A G + + K A F L+ N++L V V++ VY
Sbjct: 77 ESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLM---NKILGDLLGDFVEVYLDDILVY 133
Query: 218 SRRREAHIK 226
S+ E H++
Sbjct: 134 SKTEEEHLE 142
>gnl|CDD|238012 cd00055, EGF_Lam, Laminin-type epidermal growth factor-like
domain; laminins are the major noncollagenous
components of basement membranes that mediate cell
adhesion, growth migration, and differentiation; the
laminin-type epidermal growth factor-like module occurs
in tandem arrays; the domain contains 4 disulfide bonds
(loops a-d) the first three resemble epidermal growth
factor (EGF); the number of copies of this domain in
the different forms of laminins is highly variable
ranging from 3 up to 22 copies.
Length = 50
Score = 26.2 bits (58), Expect = 3.8
Identities = 12/38 (31%), Positives = 14/38 (36%), Gaps = 11/38 (28%)
Query: 36 CNAHSRLH--CYPEHGVCVGSMHTAKCQCLPGWSGTGC 71
CN H L C P G C +C P +G C
Sbjct: 4 CNGHGSLSGQCDPGTGQC---------ECKPNTTGRRC 32
>gnl|CDD|153114 cd01056, Euk_Ferritin, eukaryotic ferritins. Eukaryotic Ferritin
(Euk_Ferritin) domain. Ferritins are the primary iron
storage proteins of most living organisms and members of
a broad superfamily of ferritin-like diiron-carboxylate
proteins. The iron-free (apoferritin) ferritin molecule
is a protein shell composed of 24 protein chains
arranged in 432 symmetry. Iron storage involves the
uptake of iron (II) at the protein shell, its oxidation
by molecular oxygen at the dinuclear ferroxidase
centers, and the movement of iron (III) into the cavity
for deposition as ferrihydrite; the protein shell can
hold up to 4500 iron atoms. In vertebrates, two types of
chains (subunits) have been characterized, H or M (fast)
and L (slow), which differ in rates of iron uptake and
mineralization. Fe(II) oxidation in the H/M subunits
take place initially at the ferroxidase center, a
carboxylate-bridged diiron center, located within the
subunit four-helix bundle. In a complementary role,
negatively charged residues on the protein shell inner
surface of the L subunits promote ferrihydrite
nucleation. Most plant ferritins combine both oxidase
and nucleation functions in one chain: they have four
interior glutamate residues as well as seven ferroxidase
center residues.
Length = 161
Score = 27.9 bits (63), Expect = 5.4
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 84 SYIKYALSFEPDKYTTQLQLKFRTREEFGELFR-LSDQHNREYAILEIKDSKLR-FRYNL 141
SY+ +++ D+ F + FR LSD+ RE+A IK R R L
Sbjct: 19 SYVYLSMAAYFDRDDV-------ALPGFAKFFRKLSDEE-REHAEKLIKYQNKRGGRVVL 70
Query: 142 NNLKTDEKDIWLNAIK 157
++K EKD W + ++
Sbjct: 71 QDIKKPEKDEWGSGLE 86
>gnl|CDD|191582 pfam06679, DUF1180, Protein of unknown function (DUF1180). This
family consists of several hypothetical mammalian
proteins of around 190 residues in length. The function
of this family is unknown.
Length = 163
Score = 28.0 bits (62), Expect = 5.5
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 8/68 (11%)
Query: 194 TGSALFVTLLISPNQVLVLVF-VVYSRRREAHIKYPGPDDDVRENI----INYDDEGGGE 248
T AL V + S ++ V V +RRR + G D EN+ + DDE +
Sbjct: 94 TQRALIVLVAFSAAVIVYFVLRTVRTRRRNKKTRKYGVLDTNAENMELTPLEQDDE---D 150
Query: 249 DDMTAFDI 256
DD T FD
Sbjct: 151 DDSTLFDA 158
>gnl|CDD|166027 PLN02386, PLN02386, superoxide dismutase [Cu-Zn].
Length = 152
Score = 27.2 bits (60), Expect = 8.2
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 247 GEDDMTAFDITPLQIPIGGPH 267
G+D F I QIP+ GP+
Sbjct: 89 GDDGTATFTIVDKQIPLTGPN 109
>gnl|CDD|219210 pfam06873, SerH, Cell surface immobilisation antigen SerH. This
family consists of several cell surface immobilisation
antigen SerH proteins which seem to be specific to
Tetrahymena thermophila. The SerH locus of Tetrahymena
thermophila is one of several paralogous loci with genes
encoding variants of the major cell surface protein
known as the immobilisation antigen (i-ag).
Length = 407
Score = 28.0 bits (62), Expect = 8.4
Identities = 19/71 (26%), Positives = 24/71 (33%), Gaps = 20/71 (28%)
Query: 29 CPATEAVCNAHSR----------LHCYP-------EHGVCVGSMHTAKCQCLPGWSGTGC 71
C A+ A C + SR L C P + C S A GW+ + C
Sbjct: 175 CVASSASCGSTSRGTTAWTDADCLLCNPTTPYLVGDKSSCAASSCAACSSSTSGWTDSDC 234
Query: 72 V---TPTSPVT 79
T SP T
Sbjct: 235 NACNTTASPST 245
>gnl|CDD|221769 pfam12784, PDDEXK_2, PD-(D/E)XK nuclease family transposase.
Members of this family belong to the PD-(D/E)XK nuclease
superfamily. These proteins are transposase proteins.
Length = 229
Score = 27.5 bits (62), Expect = 9.0
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 11/56 (19%)
Query: 109 EEFGELFRLSDQHNR-------EYAILEIKDSKLRFRYNLNNLKTDEKDIWLNAIK 157
+++ ++L ++ E +E+ +F N L+TD D WL +K
Sbjct: 124 DKYHSCYKLKEKETNKILTDDLEIHFIELP----KFNKNEEELETDTLDKWLYFLK 175
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 0.137 0.423
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,567,633
Number of extensions: 1710603
Number of successful extensions: 1292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1287
Number of HSP's successfully gapped: 33
Length of query: 339
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 241
Effective length of database: 6,590,910
Effective search space: 1588409310
Effective search space used: 1588409310
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: 59 (26.5 bits)