RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1192
(108 letters)
>gnl|CDD|99862 cd06109, BsCS-I_like, Bacillus subtilis (Bs) citrate synthase
CS-I_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). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and coenzyme A (CoA) during
propionate metabolism. 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. This group contains proteins
similar to BsCS-I, one of two CS isozymes in the
gram-positive B. subtilis. The majority of CS activity
in B. subtilis is provided by the other isozyme, BsCS-II
(not included in this group). BsCS-I has a lower
catalytic activity than BsCS-II, and has a Glu in place
of a key catalytic Asp residue. This change is conserved
in other members of this group. For E. coli CS (not
included in this group), site directed mutagenesis of
the key Asp residue to a Glu converts the enzyme into
citryl-CoA lyase which cleaves citryl-CoA to AcCoA and
OAA. A null mutation in the gene encoding BsCS-I (citA)
had little effect on B. subtilis CS activity or on
sporulation. However, disruption of the citA gene in a
strain null for the gene encoding BsCS-II resulted in a
sporulation deficiency, a characteristic of strains
defective in the Krebs cycle. This group contains
proteins which functions exclusively as either a CS or a
2MCS, as well as those with relaxed specificity which
have dual functions as both a CS and a 2MCS. Many of the
gram-negative species represented in this group have a
second CS isozyme which is in another group.
Length = 349
Score = 29.2 bits (66), Expect = 0.30
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 34 EYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKSRSGMAGVAS--TSAVLTLKG 91
E PSE + L+ +L + +H N S F T R + + A + S A+ LKG
Sbjct: 149 EPPSEAHVRALDAYLVTVADHGMNASTF------TARVIASTE-ADLTSAVLGAIGALKG 201
Query: 92 P 92
P
Sbjct: 202 P 202
>gnl|CDD|236611 PRK09672, PRK09672, phage exclusion protein Lit; Provisional.
Length = 305
Score = 28.6 bits (64), Expect = 0.57
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 6 IQIIFLSHNFPGKLLHKDLDDRALDALKEYP 36
+Q + L + GK H D D R L +
Sbjct: 228 LQELELENKSCGKGTHPDADQRIFANLSKLE 258
>gnl|CDD|239867 cd04402, RhoGAP_ARHGAP20, RhoGAP_ARHGAP20: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391
and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain,
and ANXL repeats. ArhGAP20 is activated by Rap1 and
induces inactivation of Rho, which in turn leads to
neurite outgrowth. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 192
Score = 27.6 bits (62), Expect = 1.1
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 10 FLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLE 49
FL N PG LL DL + + AL + E IA L + L+
Sbjct: 76 FL-RNIPGSLLSSDLYEEWMSALDQENEEEKIAELQRLLD 114
>gnl|CDD|99863 cd06110, BSuCS-II_like, Bacillus subtilis (Bs) citrate synthase
(CS)-II_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). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and CoA during propionate
metabolism. The overall CS reaction is thought to
proceed through three partial reactions: 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.
This group contains proteins similar to BsCS-II, the
major CS of the gram-positive bacterium Bacillus
subtilis. A mutation in the gene which encodes BsCS-II
(citZ gene) has been described which resulted in a
significant loss of CS activity, partial glutamate
auxotrophy, and a sporulation deficiency, all of which
are characteristic of strains defective in the Krebs
cycle. Streptococcus mutans CS, found in this group, may
participate in a pathway for the anaerobic biosynthesis
of glutamate. This group also contains functionally
uncharacterized CSs of various gram-negative bacteria.
Some of the gram-negative species represented in this
group have a second CS isozyme found in another group.
This group contains proteins which functions exclusively
as either a CS or a 2MCS, as well as those with relaxed
specificity which have dual functions as both a CS and a
2MCS.
Length = 356
Score = 26.9 bits (60), Expect = 2.2
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 11/62 (17%)
Query: 34 EYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQ--KSRSGM-AGVASTSAVLTLK 90
E PSE A + L + +H N S F R + S M + V T+A+ LK
Sbjct: 160 EKPSEEAARAFDVALILHADHELNASTFAA------RVVASTLSDMYSAV--TAAIGALK 211
Query: 91 GP 92
GP
Sbjct: 212 GP 213
>gnl|CDD|223841 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 451
Score = 26.9 bits (60), Expect = 2.6
Identities = 11/22 (50%), Positives = 11/22 (50%)
Query: 28 ALDALKEYPSEGAIAVLNQFLE 49
ALD L P IAVL LE
Sbjct: 345 ALDLLAALPGRKGIAVLGDMLE 366
>gnl|CDD|181044 PRK07577, PRK07577, short chain dehydrogenase; Provisional.
Length = 234
Score = 26.6 bits (59), Expect = 2.9
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 12 SHNFPGKLLHKDLDDRAL--DALKEYPSEGAI-AVLN 45
+FPG+L DL D L + + A++N
Sbjct: 38 IDDFPGELFACDLADIEQTAATLAQINEIHPVDAIVN 74
>gnl|CDD|220769 pfam10463, Peptidase_U49, Peptidase U49. This family contains Lit
peptidase from Escherichia coli. Lit protease functions
in bacterial cell death in response to infection by
bacteriophage T4. Following binding of Gol peptide to
domains II and III of elongation factor Tu, the Lit
peptidase cleaves domain I of the elongation factor.
This prevents binding of guanine nucleotides, shuts down
translation and leads to cell death.
Length = 203
Score = 26.3 bits (58), Expect = 3.1
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 6 IQIIFLSHNFPGKLLHKDLDDRALDALKE-YPSEG 39
+ +FL +N G+ H L DR + + E
Sbjct: 161 VSSLFLRNNLGGRTTHPALQDRIANNISSLQLEED 195
>gnl|CDD|235757 PRK06260, PRK06260, threonine synthase; Validated.
Length = 397
Score = 26.0 bits (58), Expect = 4.5
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 26 DRALDALKEYPSEGAIAVLNQF 47
D ALD + E EG I +LN
Sbjct: 173 DDALDMVVELAKEGKIYLLNSI 194
>gnl|CDD|172668 PRK14180, PRK14180, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 25.8 bits (56), Expect = 4.7
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 17 GKLLHKDLDDRALDALKEYPSEGAI 41
GK L KDL +R ++EY AI
Sbjct: 6 GKSLSKDLKERLATQVQEYKHHTAI 30
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 26.0 bits (58), Expect = 4.8
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 74 RSGMAGVASTSAVLTLKGPD 93
RSG AGVA+T AV+ G +
Sbjct: 261 RSG-AGVAATYAVMKYLGRE 279
>gnl|CDD|149865 pfam08930, DUF1912, Domain of unknown function (DUF1912). This
domain has no known function. It is found in various
Streptococcal proteins.
Length = 84
Score = 25.2 bits (55), Expect = 5.2
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 6 IQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLN--QFLESNLEHVSNKSAF 61
IQI ++ K+ +D D+RA DA Y S+ L+ +FL+ E+ N F
Sbjct: 19 IQINQMAMAASQKVAEEDGDERAKDAYIRYESK-----LDAYEFLQGKFENYKNGKGF 71
>gnl|CDD|202558 pfam03159, XRN_N, XRN 5'-3' exonuclease N-terminus. This family
aligns residues towards the N-terminus of several
proteins with multiple functions. The members of this
family all appear to possess 5'-3' exonuclease activity
EC:3.1.11.-. Thus, the aligned region may be necessary
for 5' to 3' exonuclease function. The family also
contains several Xrn1 and Xrn2 proteins. The 5'-3'
exoribonucleases Xrn1p and Xrn2p/Rat1p function in the
degradation and processing of several classes of RNA in
Saccharomyces cerevisiae. Xrn1p is the main enzyme
catalyzing cytoplasmic mRNA degradation in multiple
decay pathways, whereas Xrn2p/Rat1p functions in the
processing of rRNAs and small nucleolar RNAs (snoRNAs)
in the nucleus.
Length = 237
Score = 25.8 bits (57), Expect = 5.3
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 4 ENIQIIFLSHNFPGKLLHKDLD 25
+N+ +I PG+ HK +D
Sbjct: 171 QNLTVILSDAEVPGEGEHKIMD 192
>gnl|CDD|148700 pfam07245, Phlebovirus_G2, Phlebovirus glycoprotein G2. This
family consists of several Phlebovirus glycoprotein G2
sequences. Members of the Bunyaviridae family acquire
an envelope by budding through the lipid bilayer of the
Golgi complex. The budding compartment is thought to be
determined by the accumulation of the two heterodimeric
membrane glycoproteins G1 and G2 in the Golgi.
Length = 504
Score = 26.0 bits (57), Expect = 5.5
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 78 AGVASTSAVLTLKGPDEEKIKF 99
AG + + L LKGP E + KF
Sbjct: 33 AGPIGSESCLILKGPKENQKKF 54
>gnl|CDD|212595 cd11721, FANCD2, Fanconi anemia D2 protein. The Fanconi anemia ID
complex consists of two subunits, Fanconi anemia I and
Fanconi anemia D2 (FANCI-FANCD2) and plays a central
role in the repair of DNA interstrand cross-links
(ICLs). The complex is activated via DNA damage-induced
phosphorylation by ATR (ataxia telangiectasia and
Rad3-related) and monoubiquitination by the FA core
complex ubiquitin ligase, and it binds to DNA at the ICL
site, recognizing branched DNA structures. Defects in
the complex cause Fanconi anemia, a cancer
predisposition syndrome. The phosphorylation of FANCD2
is required for DNA damage-induced intra-S phase
checkpoint and for cellular resistance to DNA
crosslinking agents.
Length = 1161
Score = 25.7 bits (57), Expect = 6.0
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 40 AIAVLNQFLESNLEHVSNKSAFLCGIM 66
A+ VL + E N + + + F+ GI+
Sbjct: 391 ALDVLRELAEKNPDELLPYATFIKGIL 417
>gnl|CDD|153299 cd07615, BAR_Endophilin_A3, The Bin/Amphiphysin/Rvs (BAR) domain of
Endophilin-A3. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Endophilins
are accessory proteins localized at synapses that
interacts with the endocytic proteins, dynamin and
synaptojanin. They are essential for synaptic vesicle
formation from the plasma membrane. They interact with
voltage-gated calcium channels, thus linking vesicle
endocytosis to calcium regulation. They also play roles
in virus budding, mitochondrial morphology maintenance,
receptor-mediated endocytosis inhibition, and endosomal
sorting. Endophilins contain an N-terminal N-BAR domain
(BAR domain with an additional N-terminal amphipathic
helix), followed by a variable region containing proline
clusters, and a C-terminal SH3 domain. They are
classified into two types, A and B. Endophilin-A
proteins are enriched in the brain and play multiple
roles in receptor-mediated endocytosis. Endophilin-A3
(or endophilin-3) is also referred to as SH3P13 (SH3
domain containing protein 13) or SH3GL3 (SH3 domain
containing Grb2-like protein 3). It regulates
Arp2/3-dependent actin filament assembly during
endocytosis. It binds N-WASP through its SH3 domain and
enhances the ability of N-WASP to activate the Arp2/3
complex. Endophilin-A3 co-localizes with the vesicular
glutamate transporter 1 (VGLUT1), and may play an
important role in the synaptic release of glutamate.
Length = 223
Score = 25.4 bits (55), Expect = 6.4
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 2 HLENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIA--VLNQFLESNLEHVSNKS 59
HL+ ++ L ++ K K D+ A++++ +A + FLE+++E VS S
Sbjct: 133 HLKKLEGRRLDFDYKKKRQGKIPDEEIRQAVEKFEESKELAERSMFNFLENDVEQVSQLS 192
Query: 60 AFLCGIMKTYRQKS 73
+ + +RQ +
Sbjct: 193 VLIEAALDYHRQST 206
>gnl|CDD|227382 COG5049, XRN1, 5'-3' exonuclease [DNA replication, recombination,
and repair / Cell division and chromosome partitioning /
Translation].
Length = 953
Score = 25.3 bits (55), Expect = 7.9
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 5 NIQIIFLSHNFPGKLLHKDLD-DRALDALKEY 35
N++IIF H PG+ HK ++ R+ A Y
Sbjct: 176 NLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSY 207
>gnl|CDD|233989 TIGR02739, TraF, type-F conjugative transfer system pilin assembly
protein TraF. This protein is part of a large group of
proteins involved in conjugative transfer of plasmid
DNA, specifically the F-type system. This protein has
been predicted to contain a thioredoxin fold and has
been shown to be localized to the periplasm. Unlike the
related protein TrbB (TIGR02738), TraF does not contain
a conserved pair of cysteines and has been shown not to
function as a thiol disulfide isomerase by
complementation of an Ecoli DsbA defect. The protein is
believed to be involved in pilin assembly. Even more
closely related than TrbB is a clade of genes
(TIGR02740) which do contain the CXXC motif, but it is
unclear whether these genes are involved in type-F
conjugation systems per se.
Length = 256
Score = 25.1 bits (55), Expect = 7.9
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 19 LLHKDLDDRALDALKEYPSE-GAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKS 73
L H +LD +P+ A V Q + E + + G+ YR KS
Sbjct: 112 LAHPELDYT-----LTHPTSNAARQVYLQLEKEQKEKAIQQLSQSYGLFFFYRGKS 162
>gnl|CDD|188247 TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF. Members of
this protein family are the product of one of seven
genes regularly clustered in operons to encode the
proteins of the tol-pal system, which is critical for
maintaining the integrity of the bacterial outer
membrane. The gene for this periplasmic protein has
been designated orf2 and ybgF. All members of the seed
alignment were from unique tol-pal gene regions from
completed bacterial genomes. The architecture of this
protein is a signal sequence, a low-complexity region
usually rich in Asn and Gln, a well-conserved region
with tandem repeats that resemble the tetratricopeptide
(TPR) repeat, involved in protein-protein interaction.
Length = 117
Score = 24.5 bits (54), Expect = 8.7
Identities = 9/34 (26%), Positives = 12/34 (35%)
Query: 22 KDLDDRALDALKEYPSEGAIAVLNQFLESNLEHV 55
+ D AL LK AI FL+ +
Sbjct: 1 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKST 34
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 25.0 bits (55), Expect = 9.0
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 3 LENIQIIFLSHNFPGKLLHKDLDDRALDALK 33
+I + S N PG+ + D ++ AL+ LK
Sbjct: 317 SLDIPYVMTSANLPGEPMAIDNEE-ALEKLK 346
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
0.317 0.135 0.380
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: 5,424,294
Number of extensions: 446097
Number of successful extensions: 431
Number of sequences better than 10.0: 1
Number of HSP's gapped: 431
Number of HSP's successfully gapped: 21
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)