RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10837
(316 letters)
>gnl|CDD|111626 pfam02750, Synapsin_C, Synapsin, ATP binding domain. Ca dependent
ATP binding in this ATP grasp fold. Function unknown.
Length = 203
Score = 167 bits (425), Expect = 3e-51
Identities = 71/122 (58%), Positives = 86/122 (70%), Gaps = 19/122 (15%)
Query: 204 NTLQGVYNFQVPKLVLDKPWVFAHLLQLQRKLGKENFPLIDITYYPNFKEMVSKMTAPKY 263
N+L +YNF DKPWVFA L+Q+Q+KLG E FPLI+ TYYPN KEM +T P +
Sbjct: 1 NSLHSIYNFC------DKPWVFAQLIQIQKKLGAEKFPLIEQTYYPNHKEM---LTTPTF 51
Query: 264 PVVFKIGHAHSGFGK----------DMAGVVAVANTYCTTEPYIDSKFDVHVQKIGSNYK 313
PVV KIGHAHSG GK D+A VVA+ TY TTEP+IDSK+D+ VQKIG+NYK
Sbjct: 52 PVVVKIGHAHSGMGKVKVDNHHDFQDIASVVALTKTYATTEPFIDSKYDIRVQKIGNNYK 111
Query: 314 AF 315
A+
Sbjct: 112 AY 113
>gnl|CDD|111020 pfam02078, Synapsin, Synapsin, N-terminal domain.
Length = 105
Score = 147 bits (372), Expect = 1e-44
Identities = 60/104 (57%), Positives = 75/104 (72%), Gaps = 2/104 (1%)
Query: 101 NKDRCFSLLVIDDQNTDWSKYFRGRRLHGDYDVRVEQAEFKELSLTANGDLGCVVSMAVF 160
RC LLVIDD +TDWSKYFRG+++ GD D+RVEQAEF EL+L A D G +V M V
Sbjct: 2 AARRCKVLLVIDDPHTDWSKYFRGKKIFGDIDIRVEQAEFSELNLAAYADGGTMVDMQVL 61
Query: 161 RGGTKVVRSFKPDMILIRQNLRDAG--EDHKNLLLGFNIGGIPS 202
R GTKVVRSFKPD +L+RQ+ ED+++L++G GGIPS
Sbjct: 62 RNGTKVVRSFKPDFVLVRQHAFSMALNEDYRSLIIGLQYGGIPS 105
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 30.6 bits (69), Expect = 1.1
Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 7/85 (8%)
Query: 23 STAPPLPARTAGGPPSSGDLSLNLSKQSSRTTSAPTSPAKTRESLLQRVQS--LTGQARD 80
+ P PA P+S + S T +AP SP+ + S S + G R+
Sbjct: 99 PSPPASPASGMSAAPASAVEE-KSPSEESATATAPESPSTSVPSSGSDAASTLVVGSERE 157
Query: 81 QGASIIGAM----TQTASAARASYN 101
I M + A RA++N
Sbjct: 158 TTIEEIMEMGYEREEVERALRAAFN 182
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.1 bits (70), Expect = 1.1
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 12 RDKFQDQSSFVSTAPPLPARTAGGPPSS-----GDLSLNLSKQSSRTTSAPTSPAKTRES 66
RD ++ +F L + PP+ + L S+ T AP +P E
Sbjct: 633 RDVIRETDAFHGELAELERQLRATPPAEVYARLSEWLLERSRAGPDTLFAPATPTHP-EP 691
Query: 67 LLQRVQSLTGQAR 79
LLQRVQ+L G AR
Sbjct: 692 LLQRVQALAGFAR 704
>gnl|CDD|143593 cd07569, DCase, N-carbamyl-D-amino acid amidohydrolase (DCase,
class 6 nitrilases). DCase hydrolyses
N-carbamyl-D-amino acids to produce D-amino acids. It
is an important biocatalyst in the pharmaceutical
industry, producing useful D-amino acids for example in
the preparation of beta-lactam antibiotics. This
subgroup belongs to a larger nitrilase superfamily
comprised of nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified
in the literature based on global and structure based
sequence analysis into thirteen different enzyme
classes (referred to as 1-13), this subgroup
corresponds to class 6. Members of this superfamily
generally form homomeric complexes, the basic building
block of which is a homodimer. Agrobacterium
radiobacter DCase forms a tetramer (dimer of dimers).
Some DCases may form trimers.
Length = 302
Score = 30.4 bits (69), Expect = 1.2
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 57 PTSPAKTRESLLQRVQSLTGQARDQGASII 86
P + A+TRES++ R+ +L +A +GA ++
Sbjct: 13 PIARAETRESVVARLIALLEEAASRGAQLV 42
>gnl|CDD|218305 pfam04877, Hairpins, HrpZ. HrpZ from the plant pathogen
Pseudomonas syringae binds to lipid bilayers and forms
a cation-conducting pore in vivo. This pore-forming
activity may allow nutrient release or delivery of
virulence factors during bacterial colonisation of host
plants. The family of hairpinN proteins, Harpin, has
been merged into this family. HrpN is a virulence
determinant which elicits lesion formation in
Arabidopsis and tobacco and triggers systemic
resistance in Arabidopsis.
Length = 277
Score = 30.2 bits (68), Expect = 1.4
Identities = 18/62 (29%), Positives = 31/62 (50%)
Query: 35 GPPSSGDLSLNLSKQSSRTTSAPTSPAKTRESLLQRVQSLTGQARDQGASIIGAMTQTAS 94
G + + L + S+ T+ A TS + ++ + Q Q+LTG + +S +G M A
Sbjct: 9 GLLGTPLSAFVLGRPSAATSGASTSSKELQDVIDQLAQALTGNGQGDSSSPLGKMLAKAL 68
Query: 95 AA 96
AA
Sbjct: 69 AA 70
>gnl|CDD|221452 pfam12168, DNA_pol3_tau_4, DNA polymerase III subunits tau domain
IV DnaB-binding. This domain family is found in
bacteria, and is approximately 80 amino acids in
length. The family is found in association with
pfam00004. Domains I-III are shared between the tau and
the gamma subunits, while most of the DnaB-binding
Domain IV and all of the alpha-interacting Domain V are
unique to tau.
Length = 80
Score = 27.8 bits (62), Expect = 2.1
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 43 SLNLSKQSSRTT--SAPTSPAKTRESLLQRVQSLTGQA 78
+Q + + S P S K S L+R+ S+T +
Sbjct: 2 QQLSRRQGNTGSKKSEPASAKKAATSALERLASVTERV 39
>gnl|CDD|182167 PRK09956, PRK09956, hypothetical protein; Provisional.
Length = 308
Score = 28.9 bits (64), Expect = 3.3
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 230 QLQRKLGKENFPLIDITYYPNFKEMVSKMTA 260
QL R+L E FPL+DIT P+ + M + A
Sbjct: 144 QLARQLYTEAFPLVDITIVPDDEIMQHRRIA 174
>gnl|CDD|177641 PHA03413, PHA03413, putative internal core protein; Provisional.
Length = 1304
Score = 29.3 bits (65), Expect = 3.4
Identities = 30/110 (27%), Positives = 46/110 (41%), Gaps = 21/110 (19%)
Query: 39 SGDLSLNLSKQSSRTTSAPTSPAKTRESLLQRVQSLTGQARDQGASIIGAMTQTASAARA 98
+GDL LN +++++ A T A ES A G SII A + ASA
Sbjct: 40 AGDLGLNAAERAALLAQAETPAATGLESF----------AAGMGNSIIAAAIRKASA--P 87
Query: 99 SYNKDRCFSL---LVIDDQ------NTDWSKYFRGRRLHGDYDVRVEQAE 139
++++D F L D + N + ++ R DY+ R E E
Sbjct: 88 AFDEDPNFDAGQTLSADTRAKLLAPNEEEIEFIGDSRSLDDYNYRKEAME 137
>gnl|CDD|180801 PRK07033, PRK07033, hypothetical protein; Provisional.
Length = 427
Score = 29.2 bits (66), Expect = 3.4
Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 25 APPLPARTAGGPP--SSGDLSLNLSKQSSRTTSAPTSPAKTRESLLQRVQSLTGQARDQG 82
P +G P ++ + LNL Q T P PA RE LL ++ +A+ G
Sbjct: 36 PRPGRGAASGLNPLVAAANPLLNLIPQIRSTVHHP-DPASLREQLLDEIRQFEERAQQAG 94
Query: 83 AS---IIGA 88
IIGA
Sbjct: 95 VPYEVIIGA 103
>gnl|CDD|217837 pfam04003, Utp12, Dip2/Utp12 Family. This domain is found at the
C-terminus of proteins containing WD40 repeats. These
proteins are part of the U3 ribonucleoprotein the yeast
protein is called Utp12 or DIP2.
Length = 109
Score = 27.6 bits (62), Expect = 3.9
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 165 KVVRSFKPDMILIRQNLRDAGEDHKNLLLGFNIGGI 200
+ P + +++ LR +D ++ LLG N GG+
Sbjct: 68 VSNPNLLPQLRSLQKVLRRRVKDLRD-LLGLNKGGL 102
>gnl|CDD|218985 pfam06315, AceK, Isocitrate dehydrogenase kinase/phosphatase
(AceK). This family consists of several bacterial
isocitrate dehydrogenase kinase/phosphatase (AceK)
proteins (EC:2.7.1.116).
Length = 562
Score = 28.7 bits (65), Expect = 4.8
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 249 PNFKEMVSKMTA---PKYPVVFKIGHAHSGFGKDM 280
P K MV M P YP VFK+ K++
Sbjct: 310 PGIKGMV--MLVFTLPSYPYVFKVIKDRFAPPKEV 342
>gnl|CDD|193531 cd05654, M20_ArgE_RocB, M20 Peptidase Arginine utilization protein,
RocB. Peptidase M20 family, ArgE RocB (Arginine
utilization protein, RocB; arginine degradation protein,
RocB) subfamily. This group of proteins is possibly
related to acetylornithine deacetylase (ArgE) and may be
involved in the arginine and/or ornithine degradation
pathway. In Bacillus subtilis, RocB is one of the three
genes found in the rocABC operon, which is sigma L
dependent and induced by arginine. The function of
members of this family is as yet unknown, although they
are predicted as deacetylases.
Length = 535
Score = 28.7 bits (65), Expect = 5.0
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 9/43 (20%)
Query: 237 KENFPLIDITYYPNFKEMVSKMTAPKYPVVFKIGHAHSGFGKD 279
K+N P Y+ +E+ K+ P V IG +GKD
Sbjct: 473 KDNMPGWGKLYHLPLEEI-KKLNIP----VVNIG----PWGKD 506
>gnl|CDD|187752 cd09271, RNase_H2-C, Ribonuclease H2-C is a subunit of the
eukaryotic RNase H complex which cleaves RNA-DNA
hybrids. Ribonuclease H2C is one of the three protein
of eukaryotic RNase H2 complex that is required for
nucleic acid binding and hydrolysis. RNase H is
classified into two families, type I (prokaryotic RNase
HI, eukaryotic RNase H1 and viral RNase H) and type II
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). RNase H endonucleolytically hydrolyzes an RNA
strand when it is annealed to a complementary DNA strand
in the presence of divalent cations, in DNA replication
and repair. The enzyme can be found in bacteria,
archaea, and eukaryotes. Most prokaryotic and eukaryotic
genomes contain multiple RNase H genes. Despite a lack
of evidence for homology from sequence comparisons, type
I and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. Eukaryotic RNase HII is active during
replication and is believed to play a role in removal of
Okazaki fragment primers and single ribonucleotides in
DNA-DNA duplexes. Eukaryotic RNase HII is functional
when it forms a complex with RNase H2B and RNase H2C
proteins. It is speculated that the two accessory
subunits are required for correct folding of the
catalytic subunit of RNase HII. Mutations in the three
subunits of human RNase HII cause neurological disorder.
Length = 93
Score = 26.9 bits (60), Expect = 5.4
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 121 YFRGRRLHG 129
YFRGR+L G
Sbjct: 35 YFRGRKLVG 43
>gnl|CDD|99869 cd06116, CaCS_like, Chloroflexus aurantiacus (Ca) citrate synthase
(CS)_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). This group is similar to
gram-negative Escherichia coli (Ec) CS (type II, gltA)
and Arabidopsis thaliana (Ath) peroxisomal (Per) CS.
However EcCS and AthPerCS are not found in this group.
The overall CS reaction is thought to proceed through
three partial reactions and involves both closed and
open conformational forms of the enzyme: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. C. aurantiacus is a
gram-negative thermophilic green gliding bacterium, its
CS belonging to this group may be a type I CS; it is not
inhibited by NADH or 2-oxoglutarate and is inhibited by
ATP. Both gram-positive and gram-negative bacteria are
found in this group.
Length = 384
Score = 27.9 bits (62), Expect = 8.1
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 239 NFPLIDITYYPNFKEMVSKMTAPKYPVVFKIGHA 272
P D++Y NF M+ KMT PKY + A
Sbjct: 148 VLPDNDLSYTGNFLSMLFKMTEPKYEPNPVLAKA 181
>gnl|CDD|220096 pfam09052, SipA, Salmonella invasion protein A. Salmonella
invasion protein A is an actin-binding protein that
contributes to host cytoskeletal rearrangements by
stimulating actin polymerisation and counteracting
F-actin destabilising proteins. Members of this family
possess an all-helical fold consisting of eight
alpha-helices arranged so that six long, amphipathic
helices form a compact fold that surrounds a final,
predominantly hydrophobic helix in the middle of the
molecule.
Length = 674
Score = 27.7 bits (61), Expect = 9.3
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 11/91 (12%)
Query: 8 FIGRRDKFQDQSSFV--STAPPLPARTAGGPPSSGDLSLNLSKQSSRTTSAPTSPAKTRE 65
F R D + + ++ A P S + +LS+ + S P SPA +
Sbjct: 318 FDNRGDTYLGGARRHYDNSYHENSENDAQSPTSQTN---DLSRNGNSLLSPPASPAAGQH 374
Query: 66 SLLQRVQSLTGQARDQGASIIGAMTQTASAA 96
+L+Q+V S+ SI G + A+ +
Sbjct: 375 ALVQKVTSVLPH------SISGTVDTFANNS 399
>gnl|CDD|173937 cd08178, AAD_C, C-terminal alcohol dehydrogenase domain of the
acetaldehyde dehydrogenase-alcohol dehydrogenase
bifunctional two-domain protein (AAD). Alcohol
dehydrogenase domain located on the C-terminal of a
bifunctional two-domain protein. The N-terminal of the
protein contains an acetaldehyde-CoA dehydrogenase
domain. This protein is involved in pyruvate metabolism.
Pyruvate is converted to acetyl-CoA and formate by
pyruvate formate-lysase (PFL). Under anaerobic
condition, acetyl-CoA is reduced to acetaldehyde and
ethanol by this two-domain protein. Acetyl-CoA is first
converted into an enzyme-bound thiohemiacetal by the
N-terminal acetaldehyde dehydrogenase domain. The
enzyme-bound thiohemiacetal is subsequently reduced by
the C-terminal NAD+-dependent alcohol dehydrogenase
domain. In E. coli, this protein is called AdhE and was
shown pyruvate formate-lysase (PFL) deactivase activity,
which is involved in the inactivation of PFL, a key
enzyme in anaerobic metabolism. In Escherichia coli and
Entamoeba histolytica, this enzyme forms homopolymeric
peptides composed of more than 20 protomers associated
in a helical rod-like structure.
Length = 398
Score = 27.6 bits (62), Expect = 9.8
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 156 SMAVFRGGTKVVRSFKPDMI 175
S+ R G +++ SFKPD I
Sbjct: 63 SLETVRKGLELMNSFKPDTI 82
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
0.319 0.134 0.392
Gapped
Lambda K H
0.267 0.0651 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,704,592
Number of extensions: 1473128
Number of successful extensions: 1373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1369
Number of HSP's successfully gapped: 26
Length of query: 316
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 219
Effective length of database: 6,635,264
Effective search space: 1453122816
Effective search space used: 1453122816
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 (21.7 bits)
S2: 59 (26.7 bits)