RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12163
(88 letters)
>gnl|CDD|217378 pfam03124, EXS, EXS family. We have named this region the EXS
family after (ERD1, XPR1, and SYG1). This family
includes C-terminus portions from the SYG1 G-protein
associated signal transduction protein from
Saccharomyces cerevisiae, and sequences that are thought
to be murine leukaemia virus (MLV) receptors (XPR1).
N-terminus portions from these proteins are aligned in
the SPX pfam03105 family. The previously noted
similarity between SYG1 and MLV receptors over their
whole sequences is thus borne out in pfam03105 and this
family. While the N-termini aligned in pfam03105 are
thought to be involved in signal transduction, the role
of the C-terminus sequences aligned in this family is
not known. This region of similarity contains several
predicted transmembrane helices. This family also
includes the ERD1 (ERD: ER retention defective) yeast
proteins. ERD1 proteins are involved in the localisation
of endogenous endoplasmic reticulum (ER) proteins. erd1
null mutants secrete such proteins even though they
possess the C-terminal HDEL ER lumen localisation label
sequence. In addition, null mutants also exhibit defects
in the Golgi-dependent processing of several
glycoproteins, which led to the suggestion that the
sorting of luminal ER proteins actually occurs in the
Golgi, with subsequent return of these proteins to the
ER via `salvage' vesicles.
Length = 337
Score = 61.9 bits (151), Expect = 6e-13
Identities = 23/50 (46%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 2 DNPFFYPWLAASVISSIYSYIWDIKMDWGLFDKNAPPDNPFLREETVYSS 51
+ + W+ S+I+SIYS+ WD+KMDWGLF KN+ N FLR++ +Y
Sbjct: 228 SDAYRILWIVFSIINSIYSFYWDVKMDWGLFQKNSSK-NRFLRDKLLYPR 276
>gnl|CDD|227696 COG5409, COG5409, EXS domain-containing protein [Signal
transduction mechanisms].
Length = 384
Score = 34.8 bits (80), Expect = 0.002
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 6 FYPWLAASVISSIYSYIWDIKMDWGLFDKNAPPDNPFLREETVYSSTTSTLIGYVL 61
F+ + ++++SIY+ WD+ MDW D + R T+ + +I ++L
Sbjct: 266 FHLQIWFALLNSIYTSFWDVFMDWS-LDSLTSLRSWSKRAVTLLKYHIAMIINFLL 320
>gnl|CDD|132766 cd07305, Porin3_Tom40, Translocase of outer mitochondrial membrane
40 (Tom40). Tom40 forms a channel in the mitochondrial
outer membrane with a pore about 1.5 to 2.5 nanometers
wide. It functions as a transport channel for unfolded
protein chains and forms a complex with Tom5, Tom6,
Tom7, and Tom22. The primary receptors Tom20 and Tom70
recruit the unfolded precursor protein from the
mitochondrial-import stimulating factor (MSF) or
cytosolic Hsc70. The precursor passes through the Tom40
channel and through another channel in the inner
membrane, formed by Tim23, to be finally translocated
into the mitochondrial matrix. The process depends on a
proton motive force across the inner membrane and
requires a contact site where the outer and inner
membranes come close. Tom40 is also involved in
inserting outer membrane proteins into the membrane,
most likely not via a lateral opening in the pore, but
by transfering precursor proteins to an outer membrane
sorting and assembly machinery.
Length = 279
Score = 29.5 bits (67), Expect = 0.16
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 51 STTSTLIGYVLFNPTGILMIQFLQSIT---CLGG 81
+ + L + N TGI + +LQS+T LGG
Sbjct: 120 TASLKLANPDILNETGIYVASYLQSVTPKLALGG 153
>gnl|CDD|215746 pfam00144, Beta-lactamase, Beta-lactamase. This family appears to
be distantly related to pfam00905 and PF00768
D-alanyl-D-alanine carboxypeptidase.
Length = 326
Score = 29.0 bits (65), Expect = 0.27
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 34 KNAPPDNPFLREETVYSSTTSTLIGYVLFNPTGILMIQFLQ 74
PP P YS+T L+G +L TG + L
Sbjct: 129 AALPPVWPP-GTRWGYSNTAYGLLGELLERVTGQSYEELLG 168
>gnl|CDD|240374 PTZ00346, PTZ00346, histone deacetylase; Provisional.
Length = 429
Score = 26.5 bits (58), Expect = 2.1
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 9 WLAASVISSIYSYIWDIKMDWGLFDKNAPPDNPFLREETVYSSTTSTLIGYVLFN 63
+LA + S S++W+ + F + PP + E ++ + TL+G VL N
Sbjct: 87 YLANLGLHSCRSWLWNAETSKVFFSGDCPPVEGLM--EHSIATASGTLMGAVLLN 139
>gnl|CDD|176890 cd08881, RHO_alpha_C_NDO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of naphthalene 1,2-dioxygenase
(NDO) and related aromatic ring hydroxylating
dioxygenases. C-terminal catalytic domain of the
oxygenase alpha subunit of naphthalene 1,2-dioxygenase
(NDO) and related Rieske-type non-heme iron aromatic
ring-hydroxylating oxygenases (RHOs, also known as
aromatic ring hydroxylating dioxygenases). This domain
binds non-heme Fe(II). RHOs utilize non-heme Fe(II) to
catalyze the addition of hydroxyl groups to the aromatic
ring, an initial step in the oxidative degradation of
aromatic compounds. RHOs are composed of either two or
three protein components, and are comprised of an
electron transport chain (ETC) and an oxygenase. The ETC
transfers reducing equivalents form the electron donor
to the oxygenase component, which in turn transfers
electrons to the oxygen molecules. The oxygenase
components are oligomers, either (alpha)n or
(alpha)n(beta)n. The alpha subunits are the catalytic
components and have an N-terminal domain, which binds a
Rieske-like 2Fe-2S cluster, and a C-terminal domain
which binds the non-heme Fe(II). The Fe(II) is
co-ordinated by conserved His and Asp residues. Proteins
belonging to this subgroup include the terminal
oxygenase alpha subunits of biphenyl dioxygenase, cumene
dioxygenase from Pseudomonas fluorescens IP01,
ethylbenzene dioxygenase, naphthalene 1,2-dioxygenase,
nitrobenzene dioxygenase from Comamonas sp. strain
JS765, toluene 2,3-dioxygenase from Pseudomonas putida
F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1,
and the polycyclic aromatic hydrocarbons (PAHs)degrading
ring-hydroxylating dioxygenase from Sphingomonas CHY-1.
This subfamily belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 206
Score = 25.7 bits (57), Expect = 3.6
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 29 WGLFDKNAPPDNPFLREETVYSSTTSTLIGYVLFNPTGIL 68
W L DK+AP + +++ V T T F P G
Sbjct: 110 WTLVDKDAPEE---VKDR-VRRQYTRT------FGPAGTF 139
>gnl|CDD|151780 pfam11339, DUF3141, Protein of unknown function (DUF3141). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 581
Score = 25.7 bits (57), Expect = 4.1
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 34 KNAPPDNPFLREETVYSS 51
+ DNPFL+ + S
Sbjct: 495 QPVSEDNPFLQLQEQVSD 512
>gnl|CDD|219443 pfam07515, DUF1528, Protein of unknown function (DUF1528).
Length = 106
Score = 24.9 bits (55), Expect = 4.5
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 31 LFDKNAPPDNPFL 43
LF + PPDNP+L
Sbjct: 92 LFGEGVPPDNPYL 104
>gnl|CDD|188452 TIGR03937, PgaC_IcaA, poly-beta-1,6 N-acetyl-D-glucosamine
synthase. Members of this protein family are
biofilm-forming enzymes that polymerize
N-acetyl-D-glucosamine residues in beta(1,6) linkage.
One named members is IcaA (intercellular adhesin protein
A), an enzyme that acts (with aid of subunit IcaD) in
Polysaccharide Intercellular Adhesin (PIA) biosynthesis
in Staphylococcus epidermis). The homologous member in
E. coli is designated PgaC. Members are often encoded
next to a polysaccharide deacetylase and involved in
biofilm formation. Note that chitin, although also made
from N-acetylglucosamine, is formed with beta-1,4
linkages.
Length = 407
Score = 24.9 bits (55), Expect = 7.1
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 18/79 (22%)
Query: 3 NPFFYPWLAASVISSIYSYIWDIKMDWGLFDKNAPPDNPFLREETVYSSTTSTLIGYVLF 62
N +P L ++S I++Y + + L N P P VYS LF
Sbjct: 286 NRRLWPLLFEYIVSVIWAYSVLLLLILWLIQVNILPYTP-----LVYSI--------SLF 332
Query: 63 NPTGILM-----IQFLQSI 76
+G+L+ +QF S+
Sbjct: 333 QWSGLLLTFICLLQFTVSL 351
>gnl|CDD|180009 PRK05313, PRK05313, hypothetical protein; Provisional.
Length = 452
Score = 24.7 bits (55), Expect = 7.2
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 35 NAPPDNPF 42
NAP DNPF
Sbjct: 192 NAPEDNPF 199
>gnl|CDD|183716 PRK12744, PRK12744, short chain dehydrogenase; Provisional.
Length = 257
Score = 24.7 bits (54), Expect = 7.2
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 1 MDNPFFYP 8
MD PFFYP
Sbjct: 192 MDTPFFYP 199
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
0.324 0.140 0.462
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: 4,509,540
Number of extensions: 356243
Number of successful extensions: 406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 405
Number of HSP's successfully gapped: 18
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
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 (21.5 bits)
S2: 53 (24.1 bits)