RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy648
(72 letters)
>gnl|CDD|220603 pfam10152, DUF2360, Predicted coiled-coil domain-containing
protein (DUF2360). This is the conserved 140 amino
acid region of a family of proteins conserved from
nematodes to humans. One C. elegans member is annotated
as a Daf-16-dependent longevity protein 1 but this
could not be confirmed. The function is unknown.
Length = 147
Score = 35.5 bits (82), Expect = 6e-04
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 34 TDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67
FLN F C S+L L LE + LEA
Sbjct: 9 VQFLNRFSAVCESKLVEAERSLQQLETTLSLLEA 42
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 28.8 bits (65), Expect = 0.17
Identities = 10/34 (29%), Positives = 22/34 (64%)
Query: 3 AVHREAIQKQIQQDWANREYIEIITGSIKKITDF 36
A+ E +K+ ++ W + E +++ G +K++TDF
Sbjct: 458 AILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDF 491
>gnl|CDD|115307 pfam06637, PV-1, PV-1 protein (PLVAP). This family consists of
several PV-1 (PLVAP) proteins which seem to be specific
to mammals. PV-1 is a novel protein component of the
endothelial fenestral and stomatal diaphragms. The
function of this family is unknown.
Length = 442
Score = 26.9 bits (59), Expect = 0.87
Identities = 16/44 (36%), Positives = 21/44 (47%)
Query: 19 NREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRI 62
N +I I S K+ D + SC + L L EK+ TLE I
Sbjct: 129 NNRFIAAIILSEKQCQDQFKDMNKSCDALLFKLGEKVKTLEMEI 172
>gnl|CDD|218324 pfam04912, Dynamitin, Dynamitin. Dynamitin is a subunit of the
microtubule-dependent motor complex and in implicated in
cell adhesion by binding to macrophage-enriched
myristoylated alanine-rice C kinase substrate
(MacMARCKS).
Length = 376
Score = 26.7 bits (59), Expect = 0.93
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 3 AVHREAIQKQIQQDWANREYI-EIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERR 61
++H +A Q A+ E + I S+ + L S + L + + +T LE R
Sbjct: 314 SLHEQASH--FSQSLAHLETTQQTIESSLASNKNLLEEVQESFKQNLETIKDNVTKLEAR 371
Query: 62 IEYL 65
+ L
Sbjct: 372 VAKL 375
>gnl|CDD|219327 pfam07195, FliD_C, Flagellar hook-associated protein 2 C-terminus.
The flagellar hook-associated protein 2 (HAP2 or FliD)
forms the distal end of the flagella, and plays a role
in mucin specific adhesion of the bacteria. This
alignment covers the C-terminal region of this family of
proteins.
Length = 230
Score = 26.5 bits (59), Expect = 0.96
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 21 EYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68
Y G + D LN ++ LN+++ L+RR++ LEAR
Sbjct: 173 PYTGSGNGILASREDSLNK-------QIKRLNKQIEDLDRRLDTLEAR 213
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 26.1 bits (57), Expect = 1.6
Identities = 12/52 (23%), Positives = 25/52 (48%)
Query: 16 DWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67
D A +E + I G +++D ++ ++ + + E+L + E LEA
Sbjct: 676 DEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEA 727
>gnl|CDD|185713 cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA
Ligase IV. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriophages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligase in eukaryotic cells (I, III and IV). DNA ligase
IV is required for DNA non-homologous end joining
pathways, including recombination of the V(D)J
immunoglobulin gene segments in cells of the mammalian
immune system. DNA ligase IV is stabilized by forming a
complex with XRCC4, a nuclear phosphoprotein, which is
phosphorylated by DNA-dependent protein kinase. DNA
ligases have a highly modular architecture consisting of
a unique arrangement of two or more discrete domains.
The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
all members of the ATP-dependent DNA ligase family. The
adenylation domain binds ATP and contains many of the
active-site residues. The common catalytic unit
comprises six conserved sequence motifs (I, III, IIIa,
IV, V and VI) that define this family of related
nucleotidyltransferases.
Length = 225
Score = 26.0 bits (58), Expect = 1.8
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 41 DMSCRSRLAVLNEKLTTLERRIEYLEARK 69
++ R +L + +T + R+E ++ +
Sbjct: 148 NLPLHERKKLLEKIITPIPGRLEVVKRTE 176
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 25.9 bits (58), Expect = 1.8
Identities = 8/34 (23%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 3 AVHREAIQKQIQQDWANREYIEIITGSIKKITDF 36
A RE + + +++ +++ G +K ITD+
Sbjct: 189 AEEREELLENLEEG-------QVVEGVVKNITDY 215
Score = 24.0 bits (53), Expect = 8.6
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 11 KQIQQD-WAN--REYIE--IITGSIKKITDF 36
KQ +++ W +Y ++ G +K ITDF
Sbjct: 357 KQCKENPWEEFAEKYPVGDVVEGKVKNITDF 387
>gnl|CDD|133378 cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of
MerR-like transcription regulators. Helix-turn-helix
(HTH) MerR-like transcription regulator, N-terminal
domain. The MerR family transcription regulators have
been shown to mediate responses to stress including
exposure to heavy metals, drugs, or oxygen radicals in
eubacterial and some archaeal species. They regulate
transcription of multidrug/metal ion transporter genes
and oxidative stress regulons by reconfiguring the
spacer between the -35 and -10 promoter elements. A
typical MerR regulator is comprised of two distinct
domains that harbor the regulatory (effector-binding)
site and the active (DNA-binding) site. Their N-terminal
domains are homologous and contain a DNA-binding winged
HTH motif, while the C-terminal domains are often
dissimilar and bind specific coactivator molecules such
as metal ions, drugs, and organic substrates.
Length = 100
Score = 25.3 bits (56), Expect = 1.9
Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 29 SIKKITDFLN--SFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69
S+K+I + L+ ++S + LA+L+EKL LE +I LEA
Sbjct: 58 SLKEIRELLDARDEELSLAALLALLDEKLAELEEKIARLEALL 100
>gnl|CDD|179393 PRK02250, PRK02250, hypothetical protein; Provisional.
Length = 166
Score = 25.2 bits (55), Expect = 2.8
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 2 AAVHREAIQKQIQQDWANREYIEIITGS 29
A RE I + I DW E I+ GS
Sbjct: 58 AEEQREGIAESIHSDWLKLEVIKTEAGS 85
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 25.4 bits (56), Expect = 2.8
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 43 SCRSRLAVLNEKLTTLERRIEYLE 66
R +A LN KL L+ RIE LE
Sbjct: 569 EAREEVAELNSKLAELKERIESLE 592
>gnl|CDD|234875 PRK00957, PRK00957, methionine synthase; Provisional.
Length = 305
Score = 24.6 bits (54), Expect = 5.3
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 20/56 (35%)
Query: 20 REYIEIIT------------GSIKKITDFLNSFDM--------SCRSRLAVLNEKL 55
++ I+IIT G + I D L F++ S + L +L EK
Sbjct: 179 KKAIDIITKGLNVPVAMHVCGDVSNIIDDLLKFNVDILDHEFASNKKNLEILEEKD 234
>gnl|CDD|219090 pfam06574, FAD_syn, FAD synthetase. This family corresponds to
the N terminal domain of the bifunctional enzyme
riboflavin kinase / FAD synthetase. These enzymes have
both ATP:riboflavin 5'-phospho transferase and
ATP:FMN-adenylyltransferase activity. They catalyze the
5'-phosphorylation of riboflavin to FMN and the
adenylylation of FMN to FAD. This domain is thought to
have the flavin mononucleotide (FMN)
adenylyltransferase activity.
Length = 158
Score = 24.1 bits (53), Expect = 6.4
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 53 EKLTTLERRIEYLEA 67
+LTTL +IE L
Sbjct: 60 FRLTTLREKIELLAE 74
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR
transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic substances
and antibiotics. BmrR is comprised of two distinct
domains that harbor a regulatory (effector-binding) site
and an active (DNA-binding) site. The conserved
N-terminal domain contains a winged HTH motif that
mediates DNA binding, while the C-terminal domain binds
coactivating, toxic compounds. BmrR shares the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements.
Length = 108
Score = 23.6 bits (52), Expect = 8.7
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 29 SIKKITDFLNSFDMS-----CRSRLAVLNEKLTTLERRIEYLEARKSH 71
+++I + L++ + R +LA L ++ L+R + LE R
Sbjct: 60 PLEEIKEILDADNDDELRKLLREKLAELEAEIEELQRILRLLEDRLKQ 107
>gnl|CDD|218051 pfam04380, BMFP, Membrane fusogenic activity. BMFP consists of
two structural domains, a coiled-coil C-terminal domain
via which the protein self-associates as a trimer, and
an N-terminal domain disordered at neutral pH but
adopting an amphipathic alpha-helical structure in the
presence of phospholipid vesicles, high ionic strength,
acidic pH or SDS. BMFP interacts with phospholipid
vesicles though the predicted amphipathic alpha-helix
induced in the N-terminal half of the protein and
promotes aggregation and fusion of vesicles in vitro.
Length = 79
Score = 23.2 bits (51), Expect = 8.9
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 48 LAVLNEKLTTLERRIEYLEAR 68
LA EKL LE R+ LEA+
Sbjct: 59 LARTREKLEALEARVAALEAK 79
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil
motif at the N terminus region. Yeast cells with mutant
Atg14 are defective not only in autophagy but also in
sorting of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically
required for the function of Apg6/Vps30p through the
autophagic pathway. There are 17 auto-phagosomal
component proteins which are categorized into six
functional units, one of which is the AS-PI3K complex
(Vps30/Atg6 and Atg14). The AS-PI3K complex and the
Atg2-Atg18 complex are essential for nucleation, and
the specific function of the AS-PI3K apparently is to
produce phosphatidylinositol 3-phosphate (PtdIns(3)P)
at the pre-autophagosomal structure (PAS). The
localisation of this complex at the PAS is controlled
by Atg14. Autophagy mediates the cellular response to
nutrient deprivation, protein aggregation, and pathogen
invasion in humans, and malfunction of autophagy has
been implicated in multiple human diseases including
cancer. This effect seems to be mediated through direct
interaction of the human Atg14 with Beclin 1 in the
human phosphatidylinositol 3-kinase class III complex.
Length = 307
Score = 23.9 bits (52), Expect = 9.1
Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 6 REAIQKQIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIE 63
E +++++++ K D L + RL + +++ L+ IE
Sbjct: 36 NEELKQKVEE-----ALEGATNEDGKLAADLLKLEVARKKERLNQIRARISQLKEEIE 88
>gnl|CDD|233602 TIGR01856, hisJ_fam, histidinol phosphate phosphatase, HisJ family.
This model represents the histidinol phosphate
phosphatase HisJ of Bacillus subtilis, and related
proteins from a number of species within a larger family
of phosphatases in the PHP hydrolase family. HisJ
catalyzes the penultimate step of histidine biosynthesis
but shows no homology to the functionally equivalent
sequence in E. coli, a domain of the bifunctional HisB
protein. Note, however, that many species have two
members and that Clostridium perfringens, predicted not
to make histidine, has five members of this family; this
family is designated subfamily rather than equivalog to
indicate that members may not all act as HisJ.
Length = 253
Score = 23.9 bits (52), Expect = 9.2
Identities = 7/36 (19%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 12 QIQQDWANREYI------EIITGSIKKITDFLNSFD 41
++++++A++ I + I G DFL+ +
Sbjct: 67 RLKKEYADKLKILIGLEVDYIPGFEDFTKDFLDEYG 102
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 23.8 bits (51), Expect = 9.3
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 4 VHREAIQKQIQQDWANREYIE------IITGSIKKITDFLNSFDMSCRSRLAVLN 52
V E +QK AN E I+ G + +D L D CRSR+ + N
Sbjct: 5 VDEEVLQKAKALQVANEEEIKMKKLKPQSEGLLSPKSDLLQVTDRGCRSRIRICN 59
>gnl|CDD|225508 COG2960, COG2960, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 103
Score = 23.6 bits (51), Expect = 9.5
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 53 EKLTTLERRIEYLEAR 68
EKL LE RIE LEAR
Sbjct: 73 EKLAALEARIEELEAR 88
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 0.132 0.367
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,698,768
Number of extensions: 282466
Number of successful extensions: 498
Number of sequences better than 10.0: 1
Number of HSP's gapped: 494
Number of HSP's successfully gapped: 59
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
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 (21.9 bits)
S2: 53 (24.2 bits)