RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13759
(114 letters)
>gnl|CDD|202500 pfam02985, HEAT, HEAT repeat. The HEAT repeat family is related
to armadillo/beta-catenin-like repeats (see pfam00514).
Length = 31
Score = 28.6 bits (65), Expect = 0.095
Identities = 12/24 (50%), Positives = 12/24 (50%)
Query: 56 LLPLFLSQLKDECPEVRLNIISNL 79
LLPL L L D PEVR L
Sbjct: 1 LLPLLLELLNDPDPEVREAAAEAL 24
>gnl|CDD|192556 pfam10363, DUF2435, Protein of unknown function (DUF2435). This
is a conserved region of approximately 400 residues
which is found only in eukaryotes. It is associated
with HEAT domains pfam02985 in all members. The
function is not known.
Length = 93
Score = 29.1 bits (66), Expect = 0.23
Identities = 15/28 (53%), Positives = 17/28 (60%)
Query: 52 TVDHLLPLFLSQLKDECPEVRLNIISNL 79
+ +L LFLSQLKDE V LN I L
Sbjct: 41 DLPKVLTLFLSQLKDEDSFVYLNAIKGL 68
>gnl|CDD|221731 pfam12717, Cnd1, non-SMC mitotic condensation complex subunit 1.
The three non-SMC (structural maintenance of
chromosomes) subunits of the mitotic condensation
complex are Cnd1-3. The whole complex is essential for
viability and the condensing of chromosomes in mitosis.
Length = 171
Score = 27.9 bits (63), Expect = 0.89
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 51 NTVDHLLPLFLSQLKDECPEVR---LNIISNL 79
N V+ P + L+DE P VR L ++++L
Sbjct: 21 NLVEPYTPNLYACLRDEDPYVRKTALLVLTHL 52
>gnl|CDD|176103 cd08411, PBP2_OxyR, The C-terminal substrate-binding domain of
the LysR-type transcriptional regulator OxyR, a member
of the type 2 periplasmic binding fold protein
superfamily. OxyR senses hydrogen peroxide and is
activated through the formation of an intramolecular
disulfide bond. The OxyR activation induces the
transcription of genes necessary for the bacterial
defense against oxidative stress. The OxyR of LysR-type
transcriptional regulator family is composed of two
functional domains joined by a linker helix involved in
oligomerization: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal substrate-binding domain,
which is structurally homologous to the type 2
periplasmic binding proteins. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcriptional repressor undergoes a
conformational change upon substrate binding which in
turn changes the DNA binding affinity of the repressor.
The C-terminal domain also contains the redox-active
cysteines that mediate the redox-dependent
conformational switch. Thus, the interaction between
the OxyR-tetramer and DNA is notably different between
the oxidized and reduced forms. The structural topology
of this substrate-binding domain is most similar to
that of 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 = 200
Score = 27.5 bits (62), Expect = 1.2
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 56 LLPLFLSQLKDECPEVRLNI 75
LLP L L+ P++RL +
Sbjct: 15 LLPRLLPALRQAYPKLRLYL 34
>gnl|CDD|222285 pfam13646, HEAT_2, HEAT repeats. This family includes multiple
HEAT repeats.
Length = 88
Score = 26.1 bits (58), Expect = 2.2
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 22 QDLVADPNQHVKSALASVIMGLSPILGKHNTVDHLLPLFLSQLKDECPEVRLNIISNL 79
+ L++DP+ V++A A LG+ LP L LKD PEVR L
Sbjct: 6 EALLSDPDPEVRAAAAR-------ALGELGD-PEALPALLELLKDPDPEVRRAAAEAL 55
>gnl|CDD|236925 PRK11544, hycI, hydrogenase 3 maturation protease; Provisional.
Length = 156
Score = 25.7 bits (57), Expect = 4.9
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 15/43 (34%)
Query: 55 HLLPL--FLSQLKDECPEVRLNIISNLDCVNEVIGIQQD-VSF 94
H +PL + QLK++ PEV +GIQ D V F
Sbjct: 90 HNMPLNYLIDQLKEDVPEVIF------------LGIQPDIVGF 120
>gnl|CDD|205691 pfam13513, HEAT_EZ, HEAT-like repeat. The HEAT repeat family is
related to armadillo/beta-catenin-like repeats (see
pfam00514). These EZ repeats are found in subunits of
cyanobacterial phycocyanin lyase and other proteins and
probably carry out a scaffolding role.
Length = 55
Score = 24.7 bits (54), Expect = 5.0
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 35 ALASVIMGLSPILGKHNTVDHLLPLFLSQLKDECPEVRLNII 76
AL ++ G +L V LLP L LKD+ EVR
Sbjct: 10 ALGALAGGGPELLRPA--VPELLPALLPLLKDDDDEVREAAA 49
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 25.7 bits (56), Expect = 8.6
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 22 QDLVADPNQHVKSALASVIMGLS---PILGKHNTVDHLLPLFLSQLKDECPEVRLNIISN 78
+D + D + + +VI L P G + HLL L + + P V +
Sbjct: 847 EDALTDRDPVHRQTAMNVIRHLVLNCPGTGDEDAAIHLLNLLWPNILEPSPHVIQSFDEG 906
Query: 79 LDCVNEVIGIQ 89
++ V+G
Sbjct: 907 MESFATVLGSG 917
>gnl|CDD|236687 PRK10417, nikC, nickel transporter permease NikC; Provisional.
Length = 272
Score = 25.4 bits (56), Expect = 8.6
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 36 LASVIMGLSPILGKHNTVDHLLPLFLSQL 64
LA+ + G + +DHLLP + QL
Sbjct: 162 LAARLSGAGHV---RVFIDHLLPAVIPQL 187
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
0.320 0.136 0.378
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,413,716
Number of extensions: 454061
Number of successful extensions: 374
Number of sequences better than 10.0: 1
Number of HSP's gapped: 374
Number of HSP's successfully gapped: 24
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)