RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15098
(92 letters)
>gnl|CDD|239359 cd03061, GST_N_CLIC, GST_N family, Chloride Intracellular Channel
(CLIC) subfamily; composed of CLIC1-5, p64, parchorin
and similar proteins. They are auto-inserting,
self-assembling intracellular anion channels involved
in a wide variety of functions including regulated
secretion, cell division and apoptosis. They can exist
in both water-soluble and membrane-bound states, and
are found in various vesicles and membranes.
Biochemical studies of the C. elegans homolog, EXC-4,
show that the membrane localization domain is present
in the N-terminal part of the protein. The structure of
soluble human CLIC1 reveals that it is monomeric and it
adopts a fold similar to GSTs, containing an N-terminal
domain with a TRX fold and a C-terminal alpha helical
domain. Upon oxidation, the N-terminal domain of CLIC1
undergoes a structural change to form a non-covalent
dimer stabilized by the formation of an intramolecular
disulfide bond between two cysteines that are far apart
in the reduced form. The CLIC1 dimer bears no
similarity to GST dimers. The redox-controlled
structural rearrangement exposes a large hydrophobic
surface, which is masked by dimerization in vitro. In
vivo, this surface may represent the docking interface
of CLIC1 in its membrane-bound state. The two cysteines
in CLIC1 that form the disulfide bond in oxidizing
conditions are essential for dimerization and chloride
channel activity, however, in other subfamily members,
the second cysteine is not conserved.
Length = 91
Score = 61.6 bits (150), Expect = 3e-14
Identities = 20/44 (45%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 35 DGRRKGACLFCQEYFMDL------LKVTTVDMQKPPPDFRDLYL 72
DG G C FCQ FM L VTTVDM++ P D +DL
Sbjct: 15 DGESIGNCPFCQRLFMVLWLKGVVFNVTTVDMKRKPEDLKDLAP 58
>gnl|CDD|129941 TIGR00862, O-ClC, intracellular chloride channel protein. The
Organellar Chloride Channel (O-ClC) Family (TC 1.A.12)
Proteins of the O-ClC family are voltage-sensitive
chloride channels found in intracellular membranes but
not the plasma membranes of animal cells. They are
found in human nuclear membranes, and the bovine
protein targets to the microsomes, but not the plasma
membrane, when expressed in Xenopus laevis oocytes.
These proteins are thought to function in the
regulation of the membrane potential and in
transepithelial ion absorption and secretion in the
kidney [Transport and binding proteins, Anions].
Length = 236
Score = 37.5 bits (87), Expect = 3e-04
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 34 IDGRRKGACLFCQEYFMDL------LKVTTVDMQKPPPDFRDL 70
DG G C F Q FM L VTTVD+++ P D ++L
Sbjct: 11 SDGESIGNCPFSQRLFMILWLKGVVFNVTTVDLKRKPEDLQNL 53
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 29.2 bits (66), Expect = 0.24
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 49 FMDLLKVTTVDMQKPPPDFRDLYLLK 74
D L+ V ++ PPD R ++ K
Sbjct: 637 LRDSLQAEPVTLEDLPPDLRRRWVAK 662
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 27.3 bits (61), Expect = 1.1
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 19 DYLPTNKLKERLASTIDG------RRKGACLFCQ---EYFMDLLKVTTVDMQKPPPDFRD 69
DY ++KLKERL +G G F Q E++ K+ M+ P RD
Sbjct: 248 DYGLSDKLKERLEERAEGILIAGAPGAGKSTFAQALAEFYASQGKIVKT-MESP----RD 302
Query: 70 LYL 72
L +
Sbjct: 303 LQV 305
>gnl|CDD|237221 PRK12835, PRK12835, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 584
Score = 26.3 bits (58), Expect = 2.2
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 9 LECYWDIKYLDYLPTNKLKERLASTI-----DGRRKGACLFCQEYFMDLLKVTTVDMQKP 63
LE W Y DY P L STI D R+ G +++ + L + +
Sbjct: 115 LEFVWKPGYADYYPELPGGSPLGSTINVPPIDLRKLGE---DEQHLLPPLALAPKGIWFT 171
Query: 64 PPDFRDLYLLKKTFW 78
P D R Y++++T W
Sbjct: 172 PKDLRLFYMVRQT-W 185
>gnl|CDD|237997 cd00032, CASc, Caspase, interleukin-1 beta converting enzyme
(ICE) homologues; Cysteine-dependent aspartate-directed
proteases that mediate programmed cell death
(apoptosis). Caspases are synthesized as inactive
zymogens and activated by proteolysis of the peptide
backbone adjacent to an aspartate. The resulting two
subunits associate to form an (alpha)2(beta)2-tetramer
which is the active enzyme. Activation of caspases can
be mediated by other caspase homologs.
Length = 243
Score = 25.6 bits (57), Expect = 3.4
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 14/56 (25%)
Query: 37 RRKGACL-FCQEYFMDLLKV---TTVDMQKPPPDFRDLYLLKKTFWQLNFNVTGHR 88
+R+G L E F LK T VD + L K F L + V
Sbjct: 7 KRRGLALIINNENFDKGLKDRDGTDVDAEN----------LTKLFESLGYEVEVKN 52
>gnl|CDD|223228 COG0150, PurM, Phosphoribosylaminoimidazole (AIR) synthetase
[Nucleotide transport and metabolism].
Length = 345
Score = 25.2 bits (56), Expect = 5.6
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 18 LDYLPTNKLK-ERLASTIDGRRKGA 41
LDYL T KL E A + G +G
Sbjct: 103 LDYLATGKLDPEVAAQIVKGIAEGC 127
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 24.8 bits (54), Expect = 7.6
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 63 PPPDFRDLYLLKKTFWQLNFNVTG 86
PP + +Y LKK F L + G
Sbjct: 179 PPLRYERVYQLKKDFPHLTIEING 202
>gnl|CDD|221064 pfam11294, DUF3095, Protein of unknown function (DUF3095). Some
members in this bacterial family of proteins are
annotated as adenylyl cyclase however this cannot be
confirmed. Currently no function is known.
Length = 373
Score = 24.5 bits (54), Expect = 8.7
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 6 LTGLECYWD 14
LTGL C WD
Sbjct: 172 LTGLSCRWD 180
>gnl|CDD|237525 PRK13830, PRK13830, conjugal transfer protein TrbE; Provisional.
Length = 818
Score = 24.8 bits (54), Expect = 9.4
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 17 YLDYLPTNKLKERLASTIDGR 37
YLD+L T +L+ L ++ R
Sbjct: 223 YLDWLVTAELQHGLTPKVENR 243
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 0.141 0.455
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,710,659
Number of extensions: 373131
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 12
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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: 41 (22.0 bits)
S2: 53 (24.1 bits)