RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7563
(274 letters)
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 82.8 bits (205), Expect = 2e-20
Identities = 36/83 (43%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 78 AVDFNTGLYSLNRKLIYSITGGNSREQFAVDFNTGSITVVDELDFETVQEYTLTVRATDS 137
A D ++G N K+ YSI GN F++D TG IT LD E EYTLTV ATD
Sbjct: 2 ATDADSGE---NGKVTYSILSGNDDGLFSIDPETGEITTTKPLDREEQPEYTLTVEATDG 58
Query: 138 VS-GHSAEVFVSVRVTDVNDCPP 159
S+ V++ V DVND P
Sbjct: 59 GGPPLSSTATVTITVLDVNDNAP 81
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 79.7 bits (197), Expect = 4e-19
Identities = 40/122 (32%), Positives = 52/122 (42%), Gaps = 27/122 (22%)
Query: 36 YSVSVREDIQIHSPLPLTIRAESPLNRKLIYSITGGNSREQFAVDFNTGLYSLNRKLIYS 95
Y VSV E+ + + LT+ A P D N ++ YS
Sbjct: 2 YEVSVPENAPPGTVV-LTVSATDP--------------------DSGE-----NGEVTYS 35
Query: 96 ITGGNSREQFAVDFNTGSITVVDELDFETVQEYTLTVRATDSVS-GHSAEVFVSVRVTDV 154
I GN F++D +TG IT LD E YTLTV ATD S+ V++ V DV
Sbjct: 36 IVSGNEDGLFSIDPSTGEITTAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDV 95
Query: 155 ND 156
ND
Sbjct: 96 ND 97
Score = 36.5 bits (85), Expect = 0.002
Identities = 15/26 (57%), Positives = 18/26 (69%)
Query: 166 YNVSISEAAPFGTLILKVRALDNDSG 191
Y VS+ E AP GT++L V A D DSG
Sbjct: 2 YEVSVPENAPPGTVVLTVSATDPDSG 27
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 60.0 bits (146), Expect = 7e-12
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 88 LNRKLIYSITGGNSREQFAVDFNTGSITVVDELDFETVQEYTLTVRATDSVSGH-SAEVF 146
N ++ YSI GG F +D +TG ++ LD E++ EY LTV ATDS S+
Sbjct: 27 PNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPLDRESIGEYELTVLATDSGGPPLSSTTT 86
Query: 147 VSVRVT 152
V++ V
Sbjct: 87 VTITVL 92
Score = 30.7 bits (70), Expect = 0.16
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 166 YNVSISEAAPFGTLILKVRALDNDSGKQKISSTAQIAHSFLE 207
Y+ S+ E AP GT +L V A D D G +I +S L
Sbjct: 1 YSASVPENAPVGTEVLTVTATDADLGPN-----GRIFYSILG 37
>gnl|CDD|188874 cd09768, Luminal_EIF2AK3, The Luminal domain, a dimerization
domain, of the Serine/Threonine protein kinase,
eukaryotic translation Initiation Factor 2-Alpha Kinase
3. The Luminal domain is a dimerization domain present
in eukaryotic translation Initiation Factor 2-Alpha
Kinase 3 (EIF2AK3), also called PKR-like Endoplasmic
Reticulum Kinase (PERK). EIF2AK3 is a serine/threonine
protein kinase (STK) and a type I transmembrane protein
that is localized in the endoplasmic reticulum (ER). As
a EIF2AK, it phosphorylates the alpha subunit of eIF-2,
resulting in the downregulation of protein synthesis.
eIF-2 phosphorylation is induced in response to cellular
stresses including virus infection, heat shock, nutrient
deficiency, and the accummulation of unfolded proteins,
among others. There are four distinct kinases that
phosphorylate eIF-2 and control protein synthesis:
General Control Non-derepressible-2 (GCN2), protein
kinase regulated by RNA (PKR), heme-regulated inhibitor
kinase (HRI), and PERK. PERK contains a luminal domain
bound with the chaperone BiP under unstressed conditions
and a cytoplasmic catalytic kinase domain. In response
to the accumulation of misfolded or unfolded proteins in
the ER, PERK is activated through the release of BiP,
allowing it to dimerize through its luminal domain and
autophosphorylate. It functions as the central regulator
of translational control during the Unfolded Protein
Response (UPR) pathway. In addition to the eIF-2 alpha
subunit, PERK also phosphorylates Nrf2, a leucine zipper
transcription factor which regulates cellular redox
status and promotes cell survival during the UPR.
Length = 301
Score = 31.6 bits (72), Expect = 0.36
Identities = 27/117 (23%), Positives = 41/117 (35%), Gaps = 23/117 (19%)
Query: 28 MPVFDKQFYSVSVREDIQIHSPLPLTIRAESPLNRKLIYS----ITGGNSREQFAVDFNT 83
+P D Y E I +P T AES L+ + GG + ++ T
Sbjct: 54 IPSLDGSLYQFD-GESI---EAIPFT--AESLLSSSYKLGDDSVLVGGKEVTSYGINPYT 107
Query: 84 GLYSLNRKLIYSITGGNSREQFAVDFNTGSITVVDELDFETVQEYTLTVRATDSVSG 140
G KL Y + + ++ + D V+ T TVRA D +G
Sbjct: 108 G------KLRYICSAEGCK-------SSDTEENESNDDVLIVRRTTQTVRAVDPRTG 151
>gnl|CDD|132820 cd07287, PX_RPK118_like, The phosphoinositide binding Phox Homology
domain of RPK118-like proteins. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions such as cell signaling,
vesicular trafficking, protein sorting, and lipid
modification, among others. Members of this subfamily
bear similarity to human RPK118, which contains an
N-terminal PX domain, a Microtubule Interacting and
Trafficking (MIT) domain, and a kinase domain. RPK118
binds sphingosine kinase, a key enzyme in the synthesis
of sphingosine 1-phosphate (SPP), a lipid messenger
involved in many cellular events. RPK118 may be involved
in transmitting SPP-mediated signaling. It also binds
the antioxidant peroxiredoxin-3 (PRDX3) and may be
involved in the transport of PRDX3 from the cytoplasm to
its site of function in the mitochondria. Members of
this subfamily also show similarity to sorting nexin 15
(SNX15), which contains PX and MIT domains but does not
contain a kinase domain. SNXs make up the largest group
among PX domain containing proteins. They are involved
in regulating membrane traffic and protein sorting in
the endosomal system. The PX domain of SNXs binds PIs
and targets the protein to PI-enriched membranes. SNX15
plays a role in protein trafficking processes in the
endocytic pathway and the trans-Golgi network. The PX
domain of SNX15 interacts with the PDGF receptor and is
responsible for the membrane association of the protein.
Length = 118
Score = 30.3 bits (68), Expect = 0.37
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 210 FLSLHRYMFTIGKGFFPERELLQP--------RCYRSEIEDRRRTGEEKASHSENKPYLF 261
F LH+ ++ I K + EL P R S IE+RR+ E+ S N P L+
Sbjct: 47 FKKLHKDLWQIHKNLCRQSELFPPFAKAKVFGRFDESVIEERRQCAEDLLQFSANIPALY 106
>gnl|CDD|217549 pfam03422, CBM_6, Carbohydrate binding module (family 6).
Length = 124
Score = 29.2 bits (66), Expect = 0.94
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 93 IYSITGGNSREQFAVDF-NTGSITVVDELDFETVQEYTLTVRATDSVSGHSAEVFV 147
T +AV + N G ++DF + Y+LT R + G S E+ +
Sbjct: 13 TEKTTAYGG--GYAVGYINNGDWIAYTDVDFGSGGAYSLTARVANGGGGGSIEIRL 66
>gnl|CDD|112444 pfam03627, PapG_N, PapG carbohydrate binding domain. PapG, the
adhesin of the P-pili, is situated at the tip and is
only a minor component of the whole pilus structure. A
two-domain structure has been postulated for PapG; a
carbohydrate binding N-terminus (this domain) and
chaperone binding C-terminus. The carbohydrate-binding
domain interacts with the receptor glycan.
Length = 226
Score = 29.4 bits (66), Expect = 1.4
Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 64 LIYSITGGNSREQFAVDFNTGLYSLNRKLIYSITGGN----SREQFAVDFNTGSITVV 117
L S++G N A N YS N + Y GN R QF + +NTGS T
Sbjct: 9 LFLSLSGCND--ALAGWHNVMFYSFNDYIYYP--QGNVKITDRPQFIIPWNTGSATAT 62
>gnl|CDD|214510 smart00089, PKD, Repeats in polycystic kidney disease 1 (PKD1) and
other proteins. Polycystic kidney disease 1 protein
contains 14 repeats, present elsewhere such as in
microbial collagenases.
Length = 79
Score = 26.6 bits (59), Expect = 4.1
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 122 FETVQEYTLTVRATDSVSGHSAEVFVSV 149
+ YT+T+ T++V SA V V V
Sbjct: 51 YTKPGTYTVTLTVTNAVGSASATVTVVV 78
>gnl|CDD|224488 COG1572, COG1572, Uncharacterized conserved protein [Function
unknown].
Length = 606
Score = 28.3 bits (63), Expect = 4.7
Identities = 37/172 (21%), Positives = 57/172 (33%), Gaps = 25/172 (14%)
Query: 16 EVSVNVKVIDKSMPVFDKQFYSVSVREDIQIHSPLPLTIRAESPLNRKLIYSITGGNSRE 75
EV+ V + +P+ D V D + + N+ L ++ N E
Sbjct: 388 EVTKVVDINPAELPILDL---EVVATADAGSLTQESV--------NKALTITLNIKNLGE 436
Query: 76 QFAVDFNTGLYSLN-RKLIYSITGGNSREQFAVDFNTGSITVVDELDFETVQEYTLTVRA 134
+A F L + SI G S E V N S + +TL+V
Sbjct: 437 AYASGFQVDLVLNGTIVTVDSIPGLESGESREVVVNEVSTSGGS---------HTLSVVI 487
Query: 135 --TDSVSGHSAEVFVSVRVTDVNDCPPEFPQDWYNVSISEAAPFGTLILKVR 184
+ V+ + R+ VN P+ VS FG IL +R
Sbjct: 488 DPDNDVAESNENNNEFSRILTVNTPRPDKIIL--TVSAVWIEGFGNSILTLR 537
>gnl|CDD|221532 pfam12328, Rpp20, Rpp20 subunit of nuclear RNase MRP and P. The
nuclear RNase P of Saccharomyces cerevisiae is made up
of at least nine protein subunits; Pop1, Pop3, Pop4,
Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these
subunits seem to be present also in the RNase MRP, with
the exception of Rpr2 (Rpp21) which is unique to RNase
P. Human nuclear RNase P and MRP appear to contain at
least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25,
Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although
there is recent evidence that not all of these subunits
are shared between P and MRP. Archaeal RNase P has at
least four protein subunits homologous to eukaryotic
RNase P/MRP proteins. In the yeast RNase P, Pop6 and
Pop7 (the Rpp20 homologue) interact with each other and
they are both interaction partners of Pop4; in the human
MRP Rpp25 and Rpp20 interact with each other and Rpp25
binds to Rpp29 (Pop4).
Length = 108
Score = 26.8 bits (60), Expect = 5.2
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 101 SREQFAVDFNTGSITVVDELDFETVQE 127
+ + VD TG++ VVDE+ + +
Sbjct: 64 REKNYKVDVRTGTVEVVDEIVEDEDDD 90
>gnl|CDD|214795 smart00736, CADG, Dystroglycan-type cadherin-like domains.
Cadherin-homologous domains present in metazoan
dystroglycans and alpha/epsilon sarcoglycans, yeast
Axl2p and in a very large protein from magnetotactic
bacteria. Likely to bind calcium ions.
Length = 97
Score = 26.5 bits (59), Expect = 6.5
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 123 ETVQEYTLTVRATDSVSGHSAEVFVSVRVTDVND 156
V +L V ATDS SG SA ++ V + ND
Sbjct: 64 SDVGSLSLKVTATDS-SGASASDTFTITVVNTND 96
>gnl|CDD|216908 pfam02159, Oest_recep, Oestrogen receptor.
Length = 139
Score = 27.2 bits (60), Expect = 6.8
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 223 GFFPERELLQPRCYRSEIEDRRRTGEEKASHSENK 257
RE YRS +++RR+ G E+ S +E +
Sbjct: 95 SPAAVRETSSTAFYRSSVDNRRQAGRERCSAAEER 129
>gnl|CDD|236673 PRK10340, ebgA, cryptic beta-D-galactosidase subunit alpha;
Reviewed.
Length = 1021
Score = 28.1 bits (63), Expect = 7.0
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 106 AVDFNTGSITVVDELDFETVQEYTLTV 132
A+D G + V ++L F + +YTL
Sbjct: 606 ALDLTRGELKVENKLWFTNLDDYTLHA 632
>gnl|CDD|227708 COG5421, COG5421, Transposase [DNA replication, recombination, and
repair].
Length = 480
Score = 27.8 bits (62), Expect = 7.8
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 30 VFDKQFYSVSVREDIQIH----SPLPLTI 54
V DK F S + ++I S +P TI
Sbjct: 204 VADKGFNSDNNIKNIGSKLSFISRVPATI 232
>gnl|CDD|216151 pfam00850, Hist_deacetyl, Histone deacetylase domain. Histones can
be reversibly acetylated on several lysine residues.
Regulation of transcription is caused in part by this
mechanism. Histone deacetylases catalyze the removal of
the acetyl group. Histone deacetylases are related to
other proteins.
Length = 300
Score = 27.2 bits (61), Expect = 8.6
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 198 TAQIAHSFLEIFFLSLHRYMFTIGKGFFPER 228
T +I + + +S+H+ F G GF E
Sbjct: 160 TQEIFYDDPRVLTISIHQDPFYPGTGFADET 190
>gnl|CDD|193492 cd09838, CBM6_FsXyn10D-like, Carbohydrate Binding Module Family 6
(CBM6), Fibrobacter succinogenes S85 Xyn10D-like;
appended mainly to glycoside hydrolase (GH) family 5 and
GH43 domains. This family includes carbohydrate binding
module 6 (CBM6) domains that are appended mainly to
several glycoside hydrolase (GH) families, including GH5
(cellulase) and GH43. CBM6s are non-catalytic
carbohydrate binding domains that facilitate the strong
binding of the GH catalytic modules with their
dedicated, insoluble substrates. For this subgroup,
little information is available about the specific
substrates of the appended GH domains; it includes the
CBM6 of Fibrobacter succinogenes S85 Xyn10D xylanase,
appended to a GH10 domain, and the CBM6 of Cellvibrio
japonicas Cel5G appended to a GH5 (cellulase) domain.
The GH5 (cellulase) family includes enzymes with several
known activities such as endoglucanase, beta-mannanase,
and xylanase, which are involved in the degradation of
cellulose and xylans. GH43 includes beta-xylosidases and
beta-xylanases, using aryl-glycosides as substrates.
CBM6 is an unusual CBM as it represents a chimera of two
distinct binding sites with different modes of binding:
binding site I within the loop regions and binding site
II on the concave face of the beta-sandwich fold.
Length = 139
Score = 26.4 bits (59), Expect = 9.9
Identities = 16/71 (22%), Positives = 24/71 (33%), Gaps = 8/71 (11%)
Query: 124 TVQE---YTLTVRATDSVSGHSAEVFVSVRVTDVNDCPPEFPQDWYNVSISEAAPF---G 177
V E YT++ R SG S + V +T D P W S + G
Sbjct: 62 NVAEAGTYTVSFRVASPNSGGSFRLEVDGALTGSVDVPNT--GGWQTFSTVTVSVSLTAG 119
Query: 178 TLILKVRALDN 188
+L++
Sbjct: 120 EHVLRLTFDGG 130
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
0.318 0.134 0.380
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,679,429
Number of extensions: 1291169
Number of successful extensions: 922
Number of sequences better than 10.0: 1
Number of HSP's gapped: 917
Number of HSP's successfully gapped: 26
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
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: 58 (26.2 bits)