RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3466
(103 letters)
>gnl|CDD|131283 TIGR02228, sigpep_I_arch, signal peptidase I, archaeal type.
This model represents signal peptidase I from most
archaea, a subunit of the eukaryotic endoplasmic
reticulum signal peptidase I complex, and an apparent
signal peptidase I from a small number of bacteria. It
is related to but does not overlap in hits with
TIGR02227, the bacterial and mitochondrial signal
peptidase I.
Length = 158
Score = 69.8 bits (171), Expect = 1e-16
Identities = 29/79 (36%), Positives = 50/79 (63%)
Query: 21 VLSFGMIVSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGE 80
V+ F +I+ +++ GL+ P+VVVLSGSMEP F+ GDL+ +T ++VG+
Sbjct: 6 VIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFNTGDLILVTGADPNDIQVGD 65
Query: 81 IVVFKVEGRDIPIVHRVLK 99
++ +K G + P+ HRV++
Sbjct: 66 VITYKSPGFNTPVTHRVIE 84
>gnl|CDD|119398 cd06530, S26_SPase_I, The S26 Type I signal peptidase (SPase;
LepB; leader peptidase B; leader peptidase I; EC
3.4.21.89) family members are essential membrane-bound
serine proteases that function to cleave the
amino-terminal signal peptide extension from proteins
that are translocated across biological membranes. The
bacterial signal peptidase I, which is the most
intensively studied, has two N-terminal transmembrane
segments inserted in the plasma membrane and a
hydrophilic, C-terminal catalytic region that is
located in the periplasmic space. Although the
bacterial signal peptidase I is monomeric, signal
peptidases of eukaryotic cells commonly function as
oligomeric complexes containing two divergent copies of
the catalytic monomer. These are the IMP1 and IMP2
signal peptidases of the mitochondrial inner membrane
that remove leader peptides from nuclear- and
mitochondrial-encoded proteins. Also, two components of
the endoplasmic reticulum signal peptidase in mammals
(18-kDa and 21-kDa) belong to this family and they
process many proteins that enter the ER for retention
or for export to the Golgi apparatus, secretory
vesicles, plasma membranes or vacuole. An atypical
member of the S26 SPase type I family is the TraF
peptidase which has the remarkable activity of
producing a cyclic protein of the Pseudomonas pilin
system. The type I signal peptidases are unique serine
proteases that utilize a serine/lysine catalytic dyad
mechanism in place of the classical
serine/histidine/aspartic acid catalytic triad
mechanism.
Length = 85
Score = 60.7 bits (148), Expect = 9e-14
Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 47 PIVVVLSGSMEPAFHRGDLLFLTN--YQEEPVRVGEIVVFKVEGR-DIPIVHRV 97
VVV GSMEP GDL+ + Y + G++VVFK G PI+ RV
Sbjct: 1 EPVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRV 54
>gnl|CDD|119396 cd06462, Peptidase_S24_S26, The S24, S26 LexA/signal peptidase
superfamily contains LexA-related and type I signal
peptidase families. The S24 LexA protein domains
include: the lambda repressor CI/C2 family and related
bacterial prophage repressor proteins; LexA (EC
3.4.21.88), the repressor of genes in the cellular SOS
response to DNA damage; MucA and the related UmuD
proteins, which are lesion-bypass DNA polymerases,
induced in response to mitogenic DNA damage; RulA, a
component of the rulAB locus that confers resistance to
UV, and RuvA, which is a component of the RuvABC
resolvasome that catalyzes the resolution of Holliday
junctions that arise during genetic recombination and
DNA repair. The S26 type I signal peptidase (SPase)
family also includes mitochondrial inner membrane
protease (IMP)-like members. SPases are essential
membrane-bound proteases which function to cleave away
the amino-terminal signal peptide from the translocated
pre-protein, thus playing a crucial role in the
transport of proteins across membranes in all living
organisms. All members in this superfamily are unique
serine proteases that carry out catalysis using a
serine/lysine dyad instead of the prototypical
serine/histidine/aspartic acid triad found in most
serine proteases.
Length = 84
Score = 54.6 bits (132), Expect = 2e-11
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 47 PIVVVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLHEK 103
+ V SMEP GDL+ + + + G+IVVF++ G V RV+ L +
Sbjct: 1 FALRVEGDSMEPTIPDGDLVLV-DKSSYEPKRGDIVVFRLPG-GELTVKRVIGLPGE 55
>gnl|CDD|216079 pfam00717, Peptidase_S24, Peptidase S24-like.
Length = 69
Score = 45.7 bits (109), Expect = 5e-08
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 50 VVLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRDIPIVHRVLKLHEK 103
V SMEP GDLL + + + G+IVV +++G + V R++ L
Sbjct: 1 RVKGDSMEPTIPDGDLLLV--DKTSEPKRGDIVVARLDG-EEATVKRLIGLPGD 51
>gnl|CDD|223753 COG0681, LepB, Signal peptidase I [Intracellular trafficking and
secretion].
Length = 166
Score = 38.4 bits (89), Expect = 1e-04
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 30 SALMIWKGLMVLTGSES---PIVVVLSGSMEPAFHRGDLLFLTNY 71
S+L+I L ++ G + VVV SGSMEP + GD + + +
Sbjct: 12 SSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKF 56
>gnl|CDD|233790 TIGR02227, sigpep_I_bact, signal peptidase I, bacterial type.
This model represents signal peptidase I from most
bacteria. Eukaryotic sequences are likely organellar.
Several bacteria have multiple paralogs, but these
represent isozymes of signal peptidase I. Virtually all
known bacteria may be presumed to A related model finds
a simlar protein in many archaea and a few bacteria, as
well as a microsomal (endoplasmic reticulum) protein in
eukaryotes [Protein fate, Protein and peptide secretion
and trafficking].
Length = 163
Score = 36.8 bits (86), Expect = 4e-04
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 48 IVVVLSGSMEPAFHRGDLLFLT--NYQEEPVRVGEIVVFKVEG 88
V GSMEP GD + + Y + G+IVVFK
Sbjct: 22 PYKVPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPD 64
>gnl|CDD|119397 cd06529, S24_LexA-like, Peptidase S24 LexA-like proteins are
involved in the SOS response leading to the repair of
single-stranded DNA within the bacterial cell. This
family includes: the lambda repressor CI/C2 family and
related bacterial prophage repressor proteins; LexA (EC
3.4.21.88), the repressor of genes in the cellular SOS
response to DNA damage; MucA and the related UmuD
proteins, which are lesion-bypass DNA polymerases,
induced in response to mitogenic DNA damage; RulA, a
component of the rulAB locus that confers resistance to
UV, and RuvA, which is a component of the RuvABC
resolvasome that catalyzes the resolution of Holliday
junctions that arise during genetic recombination and
DNA repair. The LexA-like proteins contain two-domains:
an N-terminal DNA binding domain and a C-terminal
domain (CTD) that provides LexA dimerization as well as
cleavage activity. They undergo autolysis, cleaving at
an Ala-Gly or a Cys-Gly bond, separating the
DNA-binding domain from the rest of the protein. In the
presence of single-stranded DNA, the LexA, UmuD and
MucA proteins interact with RecA, activating self
cleavage, thus either derepressing transcription in the
case of LexA or activating the lesion-bypass polymerase
in the case of UmuD and MucA. The LexA proteins are
serine proteases that carry out catalysis using a
serine/lysine dyad instead of the prototypical
serine/histidine/aspartic acid triad found in most
serine proteases. LexA sequence homologs are found in
almost all of the bacterial genomes sequenced to date,
covering a large number of phyla, suggesting both, an
ancient origin and a widespread distribution of lexA
and the SOS response.
Length = 81
Score = 33.3 bits (77), Expect = 0.003
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 55 SMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGR 89
SMEP GDL+ + + R G+IVV +++G
Sbjct: 9 SMEPTIPDGDLVLV--DPSDTPRDGDIVVARLDGE 41
>gnl|CDD|225484 COG2932, COG2932, Predicted transcriptional regulator
[Transcription].
Length = 214
Score = 28.2 bits (63), Expect = 0.70
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 51 VLSGSMEPAFHRGDLLFLTNYQEEPVRVGEIVVFKVEGRD--IPIVHRV 97
V SMEP + GD L + R G+ V + +G + + + R
Sbjct: 128 VTGDSMEPTYEDGDTLLVD--PGVNTRRGDRVYVETDGGELYVKKLQRE 174
>gnl|CDD|219528 pfam07703, A2M_N_2, Alpha-2-macroglobulin family N-terminal
region. This family includes a region of the
alpha-2-macroglobulin family.
Length = 136
Score = 26.0 bits (58), Expect = 2.7
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 10/72 (13%)
Query: 16 QFLYQVLSFGMIVSSALMIWKGLMVLTGSESPIVVVLSGSMEPAFHRGDLLFLTNYQEEP 75
LY V S G I+SS G++ + G + I + ++ M P + + +
Sbjct: 28 TALYTVESRGKILSS------GVVDVKGGSTTIELPVTADMAPNAY----VSAYYIRPGG 77
Query: 76 VRVGEIVVFKVE 87
RV V VE
Sbjct: 78 ERVAGSVWLDVE 89
>gnl|CDD|224885 COG1974, LexA, SOS-response transcriptional repressors
(RecA-mediated autopeptidases) [Transcription / Signal
transduction mechanisms].
Length = 201
Score = 25.3 bits (56), Expect = 5.8
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 48 IVVVLSGSMEPAF-HRGDLLFLTNYQEEPVRVGEIVVFKVEG 88
+ V SM A GDL+ + E G+IVV ++G
Sbjct: 114 FLRVSGDSMIDAGILDGDLVVVD--PTEDAENGDIVVALIDG 153
>gnl|CDD|169269 PRK08192, PRK08192, aspartate carbamoyltransferase; Provisional.
Length = 338
Score = 25.5 bits (56), Expect = 7.0
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 50 VVLSGSMEPAFHRGDLLFLTNYQEE 74
+ ++ +E + D+L+LT QEE
Sbjct: 214 ITITDQLEGNLDKADILYLTRIQEE 238
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 25.4 bits (56), Expect = 7.3
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 59 AFHRGDLLFLTNY 71
F RGDL+F+ N+
Sbjct: 648 VFERGDLVFVFNF 660
>gnl|CDD|240065 cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homology domain, as
present in mammalian BAHCC1 and similar proteins. BAHCC1
stands for BAH domain and coiled-coil containing 1. BAH
domains are found in a variety of proteins playing roles
in transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 121
Score = 24.7 bits (54), Expect = 8.0
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 73 EEPVRVGEIVVFKVEGR-DIPIVHRVLKLHE 102
+E +RVG+ V+FK GR +P V R+ L E
Sbjct: 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWE 31
>gnl|CDD|234323 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha
subunit. This family of proteins contains a C-terminal
thiamine diphosphate (TPP) binding domain typical of
flavodoxin/ferredoxin oxidoreductases (pfam01855) as
well as an N-terminal domain similar to the gamma
subunit of the same group of oxidoreductases
(pfam01558). The genes represented by this model are
always found in association with a neighboring gene for
a beta subunit (TIGR02177) which also occurs in a
4-subunit (alpha/beta/gamma/ferredoxin) version of the
system. This alpha/gamma plus beta structure was used to
define the set of sequences to include in this model.
This pair of genes is not consistantly observed in
proximity to any electron acceptor genes, but is found
next to putative ferredoxins or ferredoxin-domain
proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum
USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM
15236, Rhodopseudomonas palustris BisB5, Os,
Sphingomonas wittichii RW1 and Streptomyces
clavuligerus. Other potential acceptors are also
sporadically observed in close proximity including
ferritin-like proteins, reberythrin, peroxiredoxin and a
variety of other flavin and iron-sulfur
cluster-containing proteins. The phylogenetic
distribution of this family encompasses archaea, a
number of deeply-branching bacterial clades and only a
small number of firmicutes and proteobacteria. The
enzyme from Sulfolobus has been characterized with
respect to its substrate specificity which is described
as wide, encompassing various 2-oxoacids such as
2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme
from Hydrogenobacter thermophilus has been shown to have
a high specificity towards 2-oxoglutarate and is one of
the key enzymes in the reverse TCA cycle in this
organism. Furthermore, considering its binding of
coenzyme A, it can be reasonably inferred that the
product of the reaction is succinyl-CoA. The genes for
this enzyme in Prevotella intermedia 17, Persephonella
marina EX-H1 and Picrophilus torridus DSM 9790 are in
close proximity to a variety of TCA cycle genes.
Persephonella marina and P. torridus are believed to
encode complete TCA cycles, and none of these contains
the lipoate-based 2-oxoglutarate dehydrogenase
(E1/E2/E3) system. That system is presumed to be
replaced by this one. In fact, the lipoate system is
absent in most organisms possessing a member of this
family, providing additional circumstantial evidence
that many of these enzymes are capable of acting as
2-oxoglutarate dehydrogenases and.
Length = 562
Score = 25.2 bits (56), Expect = 8.3
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 38 LMVLTGS--ESPIVVVLSGSMEPAFH 61
L L G E P +V+ GS E F+
Sbjct: 313 LFALYGGHGEFPRIVLAPGSPEECFY 338
>gnl|CDD|236889 PRK11273, glpT, sn-glycerol-3-phosphate transporter; Provisional.
Length = 452
Score = 25.1 bits (55), Expect = 9.1
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 11 RLNKRQFLYQVLSFGMIVSSALMIWKGLMVLTGSESPIVVVL 52
R N R FL G+I+++A+M++ G + S ++ VL
Sbjct: 89 RSNPRVFL----PAGLILAAAVMLFMGFVPWATSSIAVMFVL 126
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
0.325 0.142 0.406
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,277,770
Number of extensions: 449361
Number of successful extensions: 696
Number of sequences better than 10.0: 1
Number of HSP's gapped: 688
Number of HSP's successfully gapped: 38
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)