RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13894
(191 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 = 71.1 bits (175), Expect = 5e-16
Identities = 38/148 (25%), Positives = 63/148 (42%), Gaps = 18/148 (12%)
Query: 18 VDSPDQFYRLWTSLFLHAGVIHLVISVIVQFILMRDLEKLTGSFRIAIIYFGSGIGGNLA 77
+ Q +RL TS+FLHAG +HL+ +++ LE++ GS R ++Y SG+ G+L
Sbjct: 1 LLQRGQLWRLITSMFLHAGWLHLLFNMLALLFFGIPLERILGSVRFLLLYLLSGLAGSLL 60
Query: 78 SAIFVPYRADV---SCLDNVCGMIPFYNVDSPDQFYRLWTSLFLHAGARPFFTYWITTVQ 134
S +F P + S + G++ V P F + +
Sbjct: 61 SYLFSPASSPSVGASGA--IFGLLGALLVLLPRNR-------------ILLFNFPGALLL 105
Query: 135 IIILCLSIFAYGLGPFGFNLAHNSGLVV 162
++ + L G P N AH GL+
Sbjct: 106 LLGIILLNLLLGFLPGISNFAHLGGLIA 133
>gnl|CDD|223777 COG0705, COG0705, Membrane associated serine protease [Amino acid
transport and metabolism].
Length = 228
Score = 51.3 bits (123), Expect = 3e-08
Identities = 23/63 (36%), Positives = 39/63 (61%)
Query: 22 DQFYRLWTSLFLHAGVIHLVISVIVQFILMRDLEKLTGSFRIAIIYFGSGIGGNLASAIF 81
DQ +RL T++FLHAG +HL+ +++ ++ +LE+ G+ R + Y SG+ LA +F
Sbjct: 66 DQLWRLITAIFLHAGFLHLLFNMLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVLF 125
Query: 82 VPY 84
P
Sbjct: 126 GPK 128
>gnl|CDD|185445 PTZ00101, PTZ00101, rhomboid-1 protease; Provisional.
Length = 278
Score = 44.5 bits (105), Expect = 8e-06
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 23 QFYRLWTSLFLHAGVIHLVISVIVQFILMRDLEKLTGSFRIAIIYFGSGIGGNL--ASAI 80
+ +RL +FLHA + H +V Q + LEK G +I I+YF +GI GN+ +S
Sbjct: 101 EIHRLILPIFLHANIFHTFFNVFFQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSSVT 160
Query: 81 FVPYRADVS 89
+ P + S
Sbjct: 161 YCPIKVGAS 169
>gnl|CDD|234518 TIGR04239, rhombo_GlpG, rhomboid family protease GlpG. GlpG in E.
coli is a rhomboid family intramembrane serine protease
that has been extensively characterized as a proxy for
rhomboid family proteases in animals. It efficiently
cleaves eukaryote-derived model substrates. This
multiple membrane-spanning protein excludes
inappropriate substrates from access to its cleavage
site, and shows activity against truncated versions, but
not full-length versions, of the E. coli multidrug
transporter MdfA. This finding suggests a housekeeping
function in removing faulty proteins. In contrast,
several eukaryotic rhomboid family proteases release
peptide hormones for signaling functions, and the
Shewanella and Vibrio protein rhombosortase appears to
be part of a protein-sorting system, cleaving a
C-terminal anchoring helix domain.
Length = 271
Score = 29.5 bits (67), Expect = 0.82
Identities = 14/60 (23%), Positives = 32/60 (53%)
Query: 23 QFYRLWTSLFLHAGVIHLVISVIVQFILMRDLEKLTGSFRIAIIYFGSGIGGNLASAIFV 82
Q +R +T LH ++H++ +++ + L +EK GS ++ +++ S + N A +
Sbjct: 134 QLWRWFTPALLHFSLLHIIFNLLWWWYLGGQIEKRLGSGKLLVLFLVSALLSNWAQYLVS 193
>gnl|CDD|176138 cd08447, PBP2_LTTR_aromatics_like_1, The C-terminal substrate
binding domain of an uncharacterized LysR-type
transcriptional regulator similar to regulators involved
in the catabolism of aromatic compounds, contains type 2
periplasmic binding fold. This CD represents the
substrate binding domain of an uncharacterized LysR-type
regulator similar to CbnR which is involved in the
regulation of chlorocatechol breakdown. The
transcription of the genes encoding enzymes involved in
such degradation is regulated and expression of these
enzymes is enhanced by inducers, which are either an
intermediate in the metabolic pathway or compounds to be
degraded. This substrate-binding domain shows
significant homology to the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 198
Score = 27.2 bits (61), Expect = 4.9
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 109 FYRLWTSLFLHAGARPFFTYWITTVQIIILCLSIFAYGLG 148
F+ L LF AG +P + +++ + + L++ GLG
Sbjct: 111 FHDLVVRLFASAGVQPRYVQYLSQIHTM---LALVRAGLG 147
>gnl|CDD|240138 cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a
member of the SIS (Sugar ISomerase domain) superfamily.
In the ribulose monophosphate pathway of formaldehyde
fixation, hexulose-6-phosphate synthase catalyzes the
condensation of ribulose-5-phosphate with formadelhyde
to become hexulose-6-phosphate, which is then isomerized
to fructose-6-phosphate by PHI.
Length = 179
Score = 26.8 bits (60), Expect = 6.8
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 154 LAHNSGLVVQLEAGTTKARDDGNRTKQDMGS 184
LA + +VV + A T +++ Q +G+
Sbjct: 116 LAKLADVVVVIPAATKDDHGGEHKSIQPLGT 146
>gnl|CDD|234515 TIGR04234, seadorna_RNAP, seadornavirus RNA-directed RNA
polymerase. Members of this protein family are the
seadornavirus VP1 protein, the RNA-directed RNA
polymerase.
Length = 1144
Score = 27.1 bits (60), Expect = 7.2
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 95 CGMIPF--YNVDSPDQFYRLWTSLFLHAGARPFFTY 128
C +IP+ N+D D +R W S F+ FF +
Sbjct: 143 CRIIPYAVTNIDKDDPMWREWLSYFIG--GEDFFKF 176
>gnl|CDD|193493 cd02690, M28, M28 Zn-peptidases include aminopeptidases and
carboxypeptidases. Peptidase M28 family (also called
aminopeptidase Y family) contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions. The
aminopeptidases in this family are also called bacterial
leucyl aminopeptidases, but are able to release a
variety of N-terminal amino acids. IAP aminopeptidase
and aminopeptidase Y preferentially release basic amino
acids while glutamate carboxypeptidase II preferentially
releases C-terminal glutamates. Plasma glutamate
carboxypeptidase (PGCP) and glutamate carboxypeptidase
II (NAALADase) hydrolyze dipeptides. Several members of
the M28 peptidase family have PA domain inserts which
may participate in substrate binding and/or in promoting
conformational changes, which influence the stability
and accessibility of the site to substrate. These
include prostate-specific membrane antigen (PSMA), yeast
aminopeptidase S (SGAP), human transferrin receptors
(TfR1 and TfR2), plasma glutamate carboxypeptidase
(PGCP) and several predicted aminopeptidases where
relatively little is known about them. Also included in
the M28 family are the glutaminyl cyclases (QC) which
are involved in N-terminal glutamine cyclization of many
endocrine peptides. Nicastrin and nicalin belong to this
family but lack the amino-acid conservation required for
catalytically active aminopeptidases.
Length = 252
Score = 26.6 bits (59), Expect = 7.9
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 50 LMRDLEKLTGSFRIAIIYFGSGIGGNLASAIFVPYRADVSCLDNVCGMIPFYNVDS 105
L R L KL I ++FG+ G L S + L+N+ +I N+D
Sbjct: 101 LARVLSKLPLDRTIRFVFFGAEEVGLLGSKYYA-EDLSSYELENIVAVI---NLDM 152
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
0.328 0.145 0.464
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,040,317
Number of extensions: 959910
Number of successful extensions: 1355
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1352
Number of HSP's successfully gapped: 50
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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: 56 (25.4 bits)