RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6649
(242 letters)
>gnl|CDD|216649 pfam01694, Rhomboid, Rhomboid family. This family contains
integral membrane proteins that are related to
Drosophila rhomboid protein. Members of this family are
found in bacteria and eukaryotes. Rhomboid promotes the
cleavage of the membrane-anchored TGF-alpha-like growth
factor Spitz, allowing it to activate the Drosophila EGF
receptor. Analysis has shown that Rhomboid-1 is an
intramembrane serine protease (EC:3.4.21.105).
Parasite-encoded rhomboid enzymes are also important for
invasion of host cells by Toxoplasma and the malaria
parasite.
Length = 146
Score = 68.4 bits (168), Expect = 1e-14
Identities = 41/150 (27%), Positives = 65/150 (43%), Gaps = 14/150 (9%)
Query: 61 VIQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLY 120
++Q+ RLI S F H +HL +NM++L+ G LE+I G +FL L + + SL
Sbjct: 1 LLQRGQLWRLITSMFLHAGWLHLLFNMLALLFFGIPLERILGSVRFLLLYLLSGLAGSLL 60
Query: 121 YILLAYIVFYITNDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILNINVKAIYAPWF 180
L + S ++G S +F + L L P + N A+
Sbjct: 61 SYLFSP-----------ASSPSVGASGAIFGLLGALLVLLPRNRILLFN-FPGALLLLLG 108
Query: 181 ELIIIYLLV--PNASFKGHLSGILVGLTYT 208
+++ LL P S HL G++ GL
Sbjct: 109 IILLNLLLGFLPGISNFAHLGGLIAGLLLG 138
>gnl|CDD|223777 COG0705, COG0705, Membrane associated serine protease [Amino acid
transport and metabolism].
Length = 228
Score = 52.5 bits (126), Expect = 3e-08
Identities = 46/202 (22%), Positives = 79/202 (39%), Gaps = 34/202 (16%)
Query: 27 PPATLGLVFLQSMVYLNIFRKPWSTLDVCISADA-----------VIQQRDYKRLILSAF 75
PP TL L+ L +V+L WS + + + + RLI + F
Sbjct: 17 PPVTLFLILLNILVFLLELVLGWSAIFLLTFLFRLFGLYPLNLLGALARDQLWRLITAIF 76
Query: 76 EHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDT 135
H +HL +NM++L + G LE+ G +FL + + L +L +
Sbjct: 77 LHAGFLHLLFNMLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVLFGPKGGAPS--- 133
Query: 136 SELSHCAIGFSAVLFAMKTILTRLQPDAYQQILNINVKAIYAPWFELIIIYLLV------ 189
+G S +F + L P A + + ++ P LI+I+LL
Sbjct: 134 -------LGASGAIFGLLGAYFLLFPFA---RILLLFLSLPRPALILILIWLLYSLFSGA 183
Query: 190 ----PNASFKGHLSGILVGLTY 207
P+ ++ HL G++ GL
Sbjct: 184 GSFGPSVAWSAHLGGLIGGLLL 205
>gnl|CDD|219898 pfam08551, DUF1751, Eukaryotic integral membrane protein (DUF1751).
This domain is found in eukaryotic integral membrane
proteins. YOL107W, a Saccharomyces cerervisiae protein,
has been shown to localise COP II vesicles.
Length = 99
Score = 33.7 bits (78), Expect = 0.015
Identities = 15/53 (28%), Positives = 31/53 (58%)
Query: 86 NMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSEL 138
++V+L+L G+ LE+++G + L ++ + V T+L L +++ IT L
Sbjct: 27 SLVTLLLGGKYLERLWGSKELLKFILVVNVITNLLVFLYYLLLYMITRSERYL 79
>gnl|CDD|185445 PTZ00101, PTZ00101, rhomboid-1 protease; Provisional.
Length = 278
Score = 35.2 bits (81), Expect = 0.021
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 62 IQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYY 121
I+Q + RLIL F H + H ++N+ + G LEK YG K I L T +Y
Sbjct: 97 IKQGEIHRLILPIFLHANIFHTFFNVFFQLRMGFTLEKNYGIVKI----IILYFLTGIYG 152
Query: 122 ILLAYIVFY 130
+L+ V Y
Sbjct: 153 NILSSSVTY 161
>gnl|CDD|234318 TIGR03704, PrmC_rel_meth, putative protein-(glutamine-N5)
methyltransferase, unknown substrate-specific. This
protein family is closely related to two different
families of protein-(glutamine-N5) methyltransferase.
The first is PrmB, which modifies ribosomal protein L3
in some bacteria. The second is PrmC (HemK), which
modifies peptide chain release factors 1 and 2 in most
bacteria and also in eukaryotes. The glutamine side
chain-binding motif NPPY shared by PrmB and PrmC is
N[VAT]PY in this family. The protein substrate is
unknown [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 251
Score = 31.3 bits (71), Expect = 0.39
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 66 DYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVI 111
D L++ A ++ MV + G LE + GW +F L I
Sbjct: 15 DEAALLVDAARTPGELA---AMVDRRVAGLPLEHVLGWAEFCGLRI 57
>gnl|CDD|227937 COG5650, COG5650, Predicted integral membrane protein [Function
unknown].
Length = 536
Score = 30.9 bits (70), Expect = 0.64
Identities = 14/65 (21%), Positives = 21/65 (32%)
Query: 65 RDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSLYYILL 124
R + IL G + ++ + L L +FL V +LY L
Sbjct: 297 RAWVESILLFARRGLIGVGIGISIPSFAGFYAVDPLLFIIPPLVLNVFLFVLYALYCNAL 356
Query: 125 AYIVF 129
YI
Sbjct: 357 KYIAL 361
>gnl|CDD|214819 smart00793, AgrB, Accessory gene regulator B. The accessory gene
regulator (agr) of Staphylococcus aureus is the central
regulatory system that controls the gene expression for
a large set of virulence factors. The arg locus consists
of two transcripts: RNAII and RNAIII. RNAII encodes four
genes (agrA, B, C, and D) whose gene products assemble a
quorum sensing system. At low cell density, the agr
genes are continuously expressed at basal levels. A
signal molecule, autoinducing peptide (AIP), produced
and secreted by the bacteria, accumulates outside of the
cells. When the cell density increases and the AIP
concentration reaches a threshold, it activates the agr
response, i.e. activation of secreted protein gene
expression and subsequent repression of cell
wall-associated protein genes. AgrB and AgrD are
essential for the production of the autoinducing peptide
which functions as a signal for quorum sensing. AgrB is
a transmembrane protein. AgrB is involved in the
proteolytic processing of AgrD and may have both
proteolytic enzyme activity and a transporter
facilitating the export of the processed AgrD peptide.
Length = 184
Score = 29.5 bits (67), Expect = 0.98
Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 5/93 (5%)
Query: 114 TVFTSLYYILLAYIVFYIT-NDTSELSHCAIGFSAVLFAMKTILTRLQPDAYQQILNINV 172
T+ + + ++ + +++ ++ N L IG +++ T QP +++
Sbjct: 80 TLLSIIIFVGIPFLIKFLDLNLPFILGLFLIGL-VLIYIYAPADTEKQPVIPEKLKKKLK 138
Query: 173 KAIYAPWFELIIIYLLVPNASFKGHLSGILVGL 205
K LI+I LLVPN +K S IL+G+
Sbjct: 139 KKSIILSLILILISLLVPNEPYK---SLILLGI 168
>gnl|CDD|223884 COG0814, SdaC, Amino acid permeases [Amino acid transport and
metabolism].
Length = 415
Score = 29.5 bits (67), Expect = 1.6
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 104 GKFLSLVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAV 148
GK ++I L+ F +LY +L+AYIV I N + G + +
Sbjct: 83 GKKGGILIGLSYFFALYGLLVAYIV-GIGNLLASFLGNQFGLNPL 126
>gnl|CDD|222559 pfam14126, DUF4293, Domain of unknown function (DUF4293). This
family of integral membrane proteins is functionally
uncharacterized. This family of proteins is found in
bacteria. Proteins in this family are typically between
136 and 154 amino acids in length.
Length = 111
Score = 28.2 bits (64), Expect = 1.7
Identities = 9/44 (20%), Positives = 14/44 (31%)
Query: 109 LVIFLTVFTSLYYILLAYIVFYITNDTSELSHCAIGFSAVLFAM 152
L + L AY ++ +T IG L A+
Sbjct: 45 LCRLNILLNLGLLGLFAYFFLNLSGETGATFEKGIGLFLPLVAI 88
>gnl|CDD|132952 cd06621, PKc_MAPKK_Pek1_like, Catalytic domain of fungal Pek1-like
dual-specificity MAP kinase kinases. Protein kinases
(PKs), MAP kinase kinase(MAPKK) subfamily, fungal
Pek1-like proteins, catalytic (c) domain. PKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The MAPKK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein serine/threonine kinases, protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
mitogen-activated protein (MAP) kinase signaling
pathways are important mediators of cellular responses
to extracellular signals. The pathways involve a triple
kinase core cascade comprising of the MAP kinase (MAPK),
which is phosphorylated and activated by a MAPK kinase
(MAPKK or MKK), which itself is phosphorylated and
activated by a MAPK kinase kinase (MAPKKK or MKKK).
Members of this group include the MAPKKs Pek1/Skh1 from
Schizosaccharomyces pombe and MKK2 from Saccharomyces
cerevisiae, and related proteins. Both fission yeast
Pek1 and baker's yeast MKK2 are components of the cell
integrity MAPK pathway. In fission yeast, Pek1
phosphorylates and activates the MAPK Pmk1/Spm1 and is
regulated by the MAPKKK Mkh1. In baker's yeast, the
pathway involves the MAPK Slt2, the MAPKKs MKK1 and
MKK2, and the MAPKKK Bck1. The cell integrity MAPK
cascade is activated by multiple stress conditions, and
is essential in cell wall construction, morphogenesis,
cytokinesis, and ion homeostasis.
Length = 287
Score = 28.9 bits (65), Expect = 1.9
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 137 ELSHCAIGFSAVLFAMKTILTRLQPDAYQQI---LNIN 171
++ C + + ++FA+KTI T PD +QI L IN
Sbjct: 16 SVTKCRLKNTGMIFALKTITTDPNPDLQKQILRELEIN 53
>gnl|CDD|234388 TIGR03902, rhom_GG_sort, rhomboid family GlyGly-CTERM serine
protease. This model describes a rhomboid-like
intramembrane serine protease. Its species distribution
closely matches model TIGR03501, GlyGly-CTERM, which
describes a protein targeting domain analogous to LPXTG
and PEP-CTERM. In a number of species (Ralstonia
eutropha ,R. metallidurans, R. solanacearum,
Marinobacter aquaeolei, etc) with just one GlyGly-CTERM
protein (i.e., a dedicated system), the rhombosortase
and GlyGly-CTERM genes are adjacent.
Length = 154
Score = 27.9 bits (63), Expect = 3.1
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 13/89 (14%)
Query: 62 IQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIYGWGKFLSLVIFLTVFTSL-Y 120
I + ++ RL+ F H + HL N+ L+L E+ + L L++ L++ SL
Sbjct: 11 ILEGEWWRLLTGHFVHLNWWHLLMNLAGLLLLWLLFERHLRARRLLLLLLLLSLLISLGL 70
Query: 121 YILLAYIVFYITNDTSELSHCAIGFSAVL 149
+ L + +Y +G S VL
Sbjct: 71 LLFLPSLQWY------------VGLSGVL 87
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known
are DNA polymerases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 28.5 bits (64), Expect = 3.9
Identities = 11/27 (40%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 152 MKTILTRLQPDAYQQILNINVKAIYAP 178
M+ +L RL+PD ++ I+ +N A+Y P
Sbjct: 613 MQDLLKRLKPDGFEDIIAVN--ALYRP 637
>gnl|CDD|221487 pfam12250, AftA_N, Arabinofuranosyltransferase N terminal. This
domain family is found in bacteria, and is typically
between 430 and 441 amino acids in length. This family
is the N terminal region of AftA. The enzyme catalyzes
the addition of the first key arabinofuranosyl residue
from the sugar donor
beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to
the galactan domain of the cell wall, thus priming the
galactan for further elaboration by the
arabinofuranosyltransferases. The N terminal region has
been predicted to span 11 transmembrane regions.
Length = 431
Score = 27.9 bits (62), Expect = 4.8
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 102 GWGKFLSLVIFLTVFTSLYYILLAYIVFYIT 132
GW + + +FL V + Y +LLAY F +
Sbjct: 227 GWAAVVGVGVFLGVAATFYTLLLAYAAFTLV 257
>gnl|CDD|220247 pfam09451, ATG27, Autophagy-related protein 27.
Length = 265
Score = 27.8 bits (62), Expect = 5.5
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 102 GWGKFLSLVIFLTVFTSLYYILLAYI 127
WG F L I+L +F ++Y I +++
Sbjct: 196 SWGWFTWLFIYLFLFVAIYLIGGSWL 221
>gnl|CDD|220812 pfam10566, Glyco_hydro_97, Glycoside hydrolase 97. This is the
97th family of glycosidases, in this case bacterial. The
central part of the GH97 family protein sequences
represents a typical and complete (beta/alpha)8-barrel
or catalytic TIM-barrel type domain. The N- and
C-terminal parts of the sequences, mainly consisting of
beta-strands, most probably form two additional
non-catalytic domains with as yet unknown functions. The
non-catalytic domains of glycosidases from the
alpha-galactosidase and alpha-glucosidase superfamilies
are also predominantly composed of beta-strands, and at
least some of these domains are involved in
oligomerisation and carbohydrate binding. In all known
glycosidases with the (beta-alpha)8-barrel fold, the
amino acid residues at the active site are located on
the C-termini of the beta-strands.
Length = 621
Score = 27.9 bits (62), Expect = 5.8
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 44 IFRKPWSTLDVCISADA--VIQQRDYKRLILSAFEHGDDMHLYYNMVSLILKGRQLEKIY 101
+ W T D ++D VI + D + LI G + L+ N +L + + K+Y
Sbjct: 306 SLDEGWYTPDGGKNSDMTKVISELDLQELIAYGKSKGVGIILWTNQKALYAQLDEAFKLY 365
Query: 102 G-WG 104
WG
Sbjct: 366 EKWG 369
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 27.0 bits (60), Expect = 9.6
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 155 ILTRLQPDAYQQILNIN-VKAIYAPWFELIIIYLLVPN--ASFKGHLSGILVGLTYTDTP 211
++ RL+P + LNIN A Y F + +Y P+ F+G LSGIL GL + D+
Sbjct: 38 VVDRLRPQFARIHLNINRDPARYQDLFPGLPVY---PDILPGFQGPLSGILAGLEHADSE 94
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
0.327 0.143 0.435
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,654,074
Number of extensions: 1229917
Number of successful extensions: 1803
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1791
Number of HSP's successfully gapped: 78
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.1 bits)