RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4231
(247 letters)
>gnl|CDD|218120 pfam04511, DER1, Der1-like family. The endoplasmic reticulum (ER)
of the yeast Saccharomyces cerevisiae contains of
proteolytic system able to selectively degrade misfolded
lumenal secretory proteins. For examination of the
components involved in this degradation process, mutants
were isolated. They could be divided into four
complementation groups. The mutations led to
stabilisation of two different substrates for this
process. The mutant classes were called 'der' for
'degradation in the ER'. DER1 was cloned by
complementation of the der1-2 mutation. The DER1 gene
codes for a novel, hydrophobic protein, that is
localised to the ER. Deletion of DER1 abolished
degradation of the substrate proteins. The function of
the Der1 protein seems to be specifically required for
the degradation process associated with the ER.
Interestingly this family seems distantly related to the
Rhomboid family of membrane peptidases. Suggesting that
this family may also mediate degradation of misfolded
proteins (Bateman A pers. obs.).
Length = 192
Score = 184 bits (468), Expect = 1e-58
Identities = 82/193 (42%), Positives = 111/193 (57%), Gaps = 4/193 (2%)
Query: 12 PFFTRWWLALTIAFTIGGRFGLLRGSDLILIYDLFVNNFHIWRPITALFYYPLSPANGFH 71
P TR+W T+ TI GR L+ L+ ++L F IWR +T+LFY+ GFH
Sbjct: 2 PPVTRYWTLATVLLTILGRLNLISPLKLVFNWELVFKKFQIWRLLTSLFYFG---NTGFH 58
Query: 72 FLMNCYFLYSYSGLLEKGLFDGKPADYAFMLLFNWVCCVVIALLADIYFLMNPMVLSVMY 131
FL N YFLY YS +LE G F G+ ADY +ML+F V + L+ + YFL + ++Y
Sbjct: 59 FLFNLYFLYRYSSMLENGSFRGRAADYLYMLIFGAVLITIFGLIVNAYFLGQGLTAMIVY 118
Query: 132 VWCQLNKDANVTFMFRTQFKAMYLPWVLFACNLILFGGGVM-ELIGILIGHLYFFLTFKY 190
VW + N D V F +FKA YLPWVL + +L + +L+GIL+GHLY+F Y
Sbjct: 119 VWSRKNADVQVNFFGLIRFKASYLPWVLLGFSFLLGNRSSLVDLMGILVGHLYYFFKDVY 178
Query: 191 PQEMGGPALLSTP 203
P+ GG LL TP
Sbjct: 179 PRLPGGKDLLKTP 191
>gnl|CDD|227611 COG5291, COG5291, Predicted membrane protein [Function unknown].
Length = 313
Score = 92.7 bits (230), Expect = 3e-22
Identities = 59/205 (28%), Positives = 96/205 (46%), Gaps = 15/205 (7%)
Query: 12 PFFTRWWLALTIAFTIGGRFGLLRGSDLILIYDLFVNNFHIWRPITALFYYPLSPANGFH 71
P TR+ L A TI L+ + LF+ IWR T+ Y+
Sbjct: 20 PPITRYMTLLISAVTILVYVDLVSPWYSLYYSPLFLKRLQIWRLFTSFLYFG---KPTLD 76
Query: 72 FLMNCYFLYSYSGLLEKGLFDGKPADYAFMLLFNWVCCVVIALLADIYFLMNPMVLS--- 128
M+ YFLY YS +LE+G F+ +Y + LL +VI +++IY ++ + S
Sbjct: 77 MFMHVYFLYRYSRMLEEGCFNTSLVEYFWYLLV---ISLVIFAISNIYGGISALGTSFSA 133
Query: 129 -VMYVWCQLNKDANVTFMFRTQFKAMYLPWVLFACNLILFGGG--VMELIGILIGHLYFF 185
+ Y+W + N A + F YLP++L + L G + +++G ++GHL+ +
Sbjct: 134 TITYIWSKRNPRAIIQFFGFISVPGKYLPFILLGFSF-LSRRGISIDDVLGFVVGHLFHY 192
Query: 186 LTFKYPQEMGGPALLSTPAFMYKWF 210
YP M G +LSTP ++ K F
Sbjct: 193 FGDIYP--MIGRDILSTPCWVKKLF 215
>gnl|CDD|177594 PHA03356, PHA03356, tegument protein UL11; Provisional.
Length = 93
Score = 29.5 bits (66), Expect = 0.44
Identities = 10/31 (32%), Positives = 12/31 (38%)
Query: 211 PNERTTVHGFGQVPRRPAEPTSAGGRSWGRG 241
P R G+ P RP+ P S R W
Sbjct: 50 PELRVVTQPPGRQPPRPSGPPSRHTRHWSPS 80
>gnl|CDD|225146 COG2237, COG2237, Predicted membrane protein [Function unknown].
Length = 364
Score = 29.6 bits (67), Expect = 1.5
Identities = 27/109 (24%), Positives = 38/109 (34%), Gaps = 21/109 (19%)
Query: 17 WWLALTIAFTIGGRF-GLLRGSDLILIYDLFVNNFHIWRPITALFYYPLSPANGFHFLMN 75
WW L I T+ G F L+ G + + Y + FY FL+
Sbjct: 267 WWFTLAILTTMVGIFFDLIIGGKVRIEY--------LKISF---FYL------IIAFLVY 309
Query: 76 CYFLYSYSGLLEKGLFDGKPADYAFMLLFNWVCCVVIALLADIYFLMNP 124
F Y L L +P A L+ + V+I L IYF +
Sbjct: 310 GAFGYILELLTIYSLSPEQP--SALFLVAGVIISVIIILAI-IYFSLKS 355
>gnl|CDD|217911 pfam04123, DUF373, Domain of unknown function (DUF373). Archaeal
domain of unknown function. Predicted to be an integral
membrane protein with six transmembrane regions.
Length = 344
Score = 29.1 bits (66), Expect = 1.9
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 10/45 (22%)
Query: 17 WWLALTIAFTIGGRFGLLRGSDLILIYDLFVNNFHIWRPITALFY 61
WLAL G+ LI + F +WR I A F+
Sbjct: 268 PWLALAALIAFLGK----------LIDEYLNGRFRLWRYINAPFF 302
>gnl|CDD|236029 PRK07487, PRK07487, amidase; Provisional.
Length = 469
Score = 28.8 bits (65), Expect = 2.9
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 17/59 (28%)
Query: 202 TPAFMYKWFPNERTTVHGFGQVPRRPAEPTSAGGRSWG-------------RGNVLGGS 247
TPAF Y+WF + +HG P P+ + GG S G G +GGS
Sbjct: 126 TPAFSYRWFTDNP--LHGRTLNPWDPS--LTPGGSSGGAAAAVAAGIGAIAHGTDIGGS 180
>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 = 27.6 bits (62), Expect = 3.6
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 47 VNNFHIWRPITALFYYPLSPANGFHFLMNCYFLYSYSGLLEK 88
+ +WR IT++F + A H L N L + LE+
Sbjct: 2 LQRGQLWRLITSMFLH----AGWLHLLFNMLALLFFGIPLER 39
>gnl|CDD|129862 TIGR00780, ccoN, cytochrome c oxidase, cbb3-type, subunit I. This
model represents the largest subunit, I, of the
ccb3-type cytochrome c oxidase, with two protohemes and
copper. It shows strong homology to subunits of other
types of cytochrome oxidases. Species with this type,
all from the Proteobacteria so far, include Neisseria
meningitidis, Helicobacter pylori, Campylobacter jejuni,
Rhodobacter sphaeroides, Rhizobium leguminosarum, and
others. Gene symbols ccoN and fixN are synonymous
[Energy metabolism, Electron transport].
Length = 474
Score = 27.9 bits (62), Expect = 5.9
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 11/74 (14%)
Query: 132 VWCQLNKDANVTFMFRTQFKAMYLPWVLFACNLILFGGGVMELIGILIGHLYFFLTFKYP 191
+W +++ N+T+ F K VL +I GG++ LIG +I F+T
Sbjct: 408 MWRDVDQYGNLTYQFIDTVK------VLIPYYVIRGVGGLLYLIGFIIMAYNIFMTI--- 458
Query: 192 QEMGGPALLSTPAF 205
G L P
Sbjct: 459 --TAGKKLEREPNA 470
>gnl|CDD|220583 pfam10118, Metal_hydrol, Predicted metal-dependent hydrolase.
Members of this family of proteins comprise various
bacterial transition metal-dependent hydrolases.
Length = 251
Score = 27.2 bits (61), Expect = 7.4
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 6 DWFNSQPFFTRWWLALTIAFTIGGRF 31
W PF T ++ AL++ F G RF
Sbjct: 17 HWLPGDPFATHFFNALSLLFPAGERF 42
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
0.331 0.147 0.506
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,375,606
Number of extensions: 1325014
Number of successful extensions: 1658
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1647
Number of HSP's successfully gapped: 63
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 58 (26.0 bits)