RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4804
(332 letters)
>gnl|CDD|201070 pfam00191, Annexin, Annexin. This family of annexins also includes
giardin that has been shown to function as an annexin.
Length = 66
Score = 102 bits (257), Expect = 1e-27
Identities = 40/66 (60%), Positives = 49/66 (74%)
Query: 53 RDAEILRKAMKGFGTDEKAIISVLAARTNAQRQEIATRFKTLYGKDLIKDLKSELSGKFE 112
DAE+LR AMKG GTDE +I +LA R+NAQ Q I +K LYGKDL KD+KSE SG FE
Sbjct: 1 YDAELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFE 60
Query: 113 DLIIAM 118
L++A+
Sbjct: 61 KLLLAL 66
Score = 90.6 bits (226), Expect = 3e-23
Identities = 32/64 (50%), Positives = 47/64 (73%)
Query: 127 ARELHHAMDGIGTNEETLVEILCTASNADIHAIRHAYEREYNSSLERDLAGETSGNFKRL 186
A L AM G+GT+E+TL+ IL T SNA + AIR AY++ Y LE+D+ ETSG+F++L
Sbjct: 3 AELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFEKL 62
Query: 187 LVSI 190
L+++
Sbjct: 63 LLAL 66
Score = 57.8 bits (141), Expect = 4e-11
Identities = 18/52 (34%), Positives = 33/52 (63%)
Query: 274 YFAQQLRGSVEGMGTHDRALIRIVTWRSEIDMLDIKKVYGEMFHTSVEADIE 325
Y A+ LR +++G+GT + LIRI+ RS + I++ Y +++ +E DI+
Sbjct: 1 YDAELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIK 52
Score = 48.2 bits (116), Expect = 9e-08
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 225 RSYPQLAEVFSQYYTLTGHELDEAIGREFSGDIKEGLIAI 264
RS QL + Y L G +L++ I E SGD ++ L+A+
Sbjct: 27 RSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFEKLLLAL 66
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 85.2 bits (212), Expect = 2e-21
Identities = 30/53 (56%), Positives = 39/53 (73%)
Query: 66 GTDEKAIISVLAARTNAQRQEIATRFKTLYGKDLIKDLKSELSGKFEDLIIAM 118
GTDEK +I +LA+R+NAQ Q I +K YGKDL D+KSE SG FE L++A+
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
Score = 79.0 bits (196), Expect = 5e-19
Identities = 26/53 (49%), Positives = 41/53 (77%)
Query: 138 GTNEETLVEILCTASNADIHAIRHAYEREYNSSLERDLAGETSGNFKRLLVSI 190
GT+E+TL+EIL + SNA + AI+ AY++ Y LE D+ ETSG+F++LL+++
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
Score = 45.5 bits (109), Expect = 5e-07
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 287 GTHDRALIRIVTWRSEIDMLDIKKVYGEMFHTSVEADIE 325
GT ++ LI I+ RS + IK+ Y + + +E DI+
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIK 39
Score = 43.9 bits (105), Expect = 2e-06
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 225 RSYPQLAEVFSQYYTLTGHELDEAIGREFSGDIKEGLIAI 264
RS QL + Y G +L++ I E SGD ++ L+A+
Sbjct: 14 RSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
>gnl|CDD|173861 cd08496, PBP2_NikA_DppA_OppA_like_9, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA can bind peptides of a wide range of lengths (2-35
amino-acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains 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. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 454
Score = 30.4 bits (69), Expect = 1.5
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 29 FPPGPDFPYPG-RPSVVPAHPFDPERDAEILRKA 61
FPPG PS+ +P+DPE+ E+L +A
Sbjct: 281 FPPG----SWAYDPSLENTYPYDPEKAKELLAEA 310
>gnl|CDD|143354 cd07849, STKc_ERK1_2_like, Catalytic domain of Extracellular
signal-Regulated Kinase 1 and 2-like Serine/Threonine
Kinases. Serine/Threonine Kinases (STKs), Extracellular
signal-regulated kinases 1 and 2 (ERK1/2) and Fus3
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. This
ERK1/2-like subfamily is part of a larger superfamily
that includes the catalytic domains of other protein
STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. This subfamily is composed of
the mitogen-activated protein kinases (MAPKs) ERK1,
ERK2, baker's yeast Fus3, and similar proteins. MAPK
pathways are important mediators of cellular responses
to extracellular signals. ERK1/2 activation is
preferentially by mitogenic factors, differentiation
stimuli, and cytokines, through a kinase cascade
involving the MAPK kinases MEK1/2 and a MAPK kinase
kinase from the Raf family. ERK1/2 have numerous
substrates, many of which are nuclear and participate in
transcriptional regulation of many cellular processes.
They regulate cell growth, cell proliferation, and cell
cycle progression from G1 to S phase. Although the
distinct roles of ERK1 and ERK2 have not been fully
determined, it is known that ERK2 can maintain most
functions in the absence of ERK1, and that the deletion
of ERK2 is embryonically lethal. The MAPK, Fus3,
regulates yeast mating processes including
mating-specific gene expression, G1 arrest, mating
projection, and cell fusion.
Length = 336
Score = 29.6 bits (67), Expect = 2.1
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 115 IIA-MMTPTPLFLARELHHAMDGIGTNEETLVEILCTASNADIHAIRHAYEREYNSSL 171
I+A M++ PLF ++ H ++ I + +L T S D++ I R Y SL
Sbjct: 199 ILAEMLSNRPLFPGKDYLHQLNLI-------LGVLGTPSQEDLNCIISLRARNYIKSL 249
>gnl|CDD|222922 PHA02697, PHA02697, hypothetical protein; Provisional.
Length = 255
Score = 29.5 bits (66), Expect = 2.1
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 38 PGRPSVVPAHPFDPERDAEILRKAMKGFGTDEKAIISVLAA--RTNAQRQEIATRFKTL 94
GR VPA + R A + R + G+ D + LA R +R+ R L
Sbjct: 184 EGRHPQVPAARLEASRGASVRRAILHGYA-DTEMYNQALAEARRAGVRRRRRRARDDVL 241
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 28.1 bits (64), Expect = 2.8
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 152 SNADIHAIRHAYEREYNSSLERDLAGETSGNFKRL 186
++ ++ IR ++ Y +E DL E S N KRL
Sbjct: 49 TDEELDKIREEIDKNY--KVEGDLRREVSMNIKRL 81
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 28.4 bits (64), Expect = 2.9
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 75 VLAARTNAQRQEIATRFKTLYGKDLIKDLKSELSGKFEDLIIAMMTPTPLFLARELHHAM 134
+A RT + +E+A F + +L+ EL + + +I A PTP+ + A+
Sbjct: 40 TIANRTLEKAKELAEEFPVGGEALPLDELE-ELLAEADIVISATSAPTPIITKEMVEEAL 98
>gnl|CDD|215949 pfam00496, SBP_bac_5, Bacterial extracellular solute-binding
proteins, family 5 Middle. The borders of this family
are based on the PDBSum definitions of the domain edges
for Salmonella typhimurium oppA.
Length = 362
Score = 29.4 bits (66), Expect = 3.0
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 30 PPGPDFPYPGRPSVVPAHPFDPERDAEILRKAMKGF-GTDEKAIISVLAARTNAQRQEIA 88
P FP P P+DPE+ ++L +A G+ D + +L N + IA
Sbjct: 242 LLPPSFPGYDPSYTDPPPPYDPEKAKKLLAEA--GYKDGDGDGRLLLLLTNDNPPAKAIA 299
Query: 89 T 89
Sbjct: 300 E 300
>gnl|CDD|234398 TIGR03921, T7SS_mycosin, type VII secretion-associated serine
protease mycosin. Members of this family are
subtilisin-related serine proteases, found strictly in
the Actinobacteria and associated with type VII
secretion operons. The designation mycosin is used for
members from Mycobacterium [Protein fate, Protein and
peptide secretion and trafficking, Protein fate, Protein
modification and repair].
Length = 350
Score = 29.2 bits (66), Expect = 3.1
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 30 PPGPDFPYPGRPSVVPAHPFDPERDAEILRKAMKGFGTDEKAIISVLAARTNAQR 84
P P P RP PA P P D R A+ G G A++ LAA +R
Sbjct: 292 RPLRPAPAPARPVAAPAPP-PPPDDTPRGRVALWGAGLAALAVVVGLAAAAVRRR 345
>gnl|CDD|185623 PTZ00444, PTZ00444, hypothetical protein; Provisional.
Length = 184
Score = 27.9 bits (62), Expect = 5.6
Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 21/78 (26%)
Query: 98 DLIKDLKSELSGKFEDLIIAMMTPTPLFLARELHH----AMDGIGT---NEETLVEILCT 150
LIKD+ EL E L PTP ++ ++H + + EE
Sbjct: 37 GLIKDIAKELKLASETL------PTPEQVSAKIHRIDKEVIKKLDKDIIKEENE------ 84
Query: 151 ASNADIHAIRH-AYEREY 167
H+ +YER+Y
Sbjct: 85 -DKKKHHSCGEPSYERDY 101
>gnl|CDD|173878 cd08513, PBP2_thermophilic_Hb8_like, The substrate-binding
component of ABC-type thermophilic oligopeptide-binding
protein Hb8-like import systems, contains the type 2
periplasmic binding fold. This family includes the
substrate-binding domain of an ABC-type
oligopeptide-binding protein Hb8 from Thermus
thermophilius and its closest homologs from other
bacteria. The structural topology of this
substrate-binding domain is similar to those of DppA
from Escherichia coli and OppA from Salmonella
typhimurium, and thus belongs to the type 2 periplasmic
binding fold protein (PBP2) superfamily. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
The type 2 periplasmic binding proteins are soluble
ligand-binding components of ABC or tripartite
ATP-independent transporters and chemotaxis systems.
Members of the PBP2 superfamily function in uptake of a
variety of metabolites in bacteria such as amino acids,
carbohydrate, ions, and polyamines. Ligands are then
transported across the cytoplasmic membrane energized by
ATP hydrolysis or electrochemical ion gradient. Besides
transport proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 28.4 bits (64), Expect = 6.6
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 29 FPPGPDFPYPGRPSVVPAHPFDPERDAEILRKA----MKGFGTDEKA----IISVLAART 80
P P +VPA+ +DPE+ ++L +A G EK ++L
Sbjct: 289 TPVPPGSWAD--DPLVPAYEYDPEKAKQLLDEAGWKLGPDGGIREKDGTPLSFTLLTTSG 346
Query: 81 NAQRQEIATRFK 92
NA R+ +A +
Sbjct: 347 NAVRERVAELIQ 358
>gnl|CDD|225335 COG2710, NifD, Nitrogenase molybdenum-iron protein, alpha and beta
chains [Energy production and conversion].
Length = 456
Score = 28.1 bits (63), Expect = 6.8
Identities = 15/59 (25%), Positives = 19/59 (32%)
Query: 39 GRPSVVPAHPFDPERDAEILRKAMKGFGTDEKAIISVLAARTNAQRQEIATRFKTLYGK 97
G P + P E LR K G E+ V+ R E+ L GK
Sbjct: 256 GIPWIEVPSPLGIENTDRFLRNLAKLLGKIEEIPEEVIEERGALIDAELDRYRPRLSGK 314
>gnl|CDD|181072 PRK07661, PRK07661, acetyl-CoA acetyltransferase; Provisional.
Length = 391
Score = 28.2 bits (63), Expect = 7.7
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 214 MVPILHRVIKPRSYPQLAEVFSQYYTLTGHELDE 247
+VP++ V++P P+L E +YY GH ++
Sbjct: 122 LVPMMGHVVRPN--PRLVEAAPEYYMGMGHTAEQ 153
>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance. This is a
metal-binding protein which is involved in resistance
to heavy-metal ions. The protein forms a four-helix
hooked hairpin, consisting of two long alpha helices
each flanked by a shorter alpha helix. It binds a metal
ion in a type-2 like centre. It contains two copies of
an LTXXQ motif.
Length = 125
Score = 26.8 bits (60), Expect = 7.7
Identities = 17/81 (20%), Positives = 27/81 (33%), Gaps = 15/81 (18%)
Query: 16 FIACLVIARSRIRFPPGPDFPYPGRPSVVP--AHPFDPERDAEILRKAMKGFGTDEKAII 73
F+A +V + +R P GP P R + A PE LR A++
Sbjct: 8 FLAGVVAGAA-LRGPGGPGPGGPRRRPGLGPAALALPPE-QRRALRAALRAH-------- 57
Query: 74 SVLAARTNAQRQEIATRFKTL 94
R+ + + L
Sbjct: 58 ---RREVRPLRRALRAARREL 75
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 27.7 bits (62), Expect = 9.5
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 51 PERDAEILRKAMKGFGTD------EKAIISVLAARTNAQRQEIATR 90
E A IL+K +K +A+I+V A +AQRQ AT+
Sbjct: 108 QEISAMILQK-LKKDAEAYLGEKVTEAVITVPAYFNDAQRQ--ATK 150
>gnl|CDD|132655 TIGR03616, RutG, pyrimidine utilization transport protein G. This
protein is observed in operons extremely similar to that
characterized in E. coli K-12 responsible for the import
and catabolism of pyrimidines, primarily uracil. This
protein is a member of the uracil-xanthine permease
family defined by TIGR00801. As well as the The
Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40).
Length = 429
Score = 27.5 bits (61), Expect = 9.8
Identities = 23/73 (31%), Positives = 30/73 (41%), Gaps = 25/73 (34%)
Query: 240 LTGHELDEAIGREFSGDIKEGLIAIFKVVLNKPGYFAQQLRGSVEGMGTHDRALIRIVTW 299
+TG LD +GR F GD GL A L GSV G G + T+
Sbjct: 273 MTGRNLDPYMGRAFVGD---GL--------------ATMLSGSVGGTG--------VTTY 307
Query: 300 RSEIDMLDIKKVY 312
I ++ + KVY
Sbjct: 308 AENIGVMAVTKVY 320
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
0.321 0.138 0.403
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,631,132
Number of extensions: 1767030
Number of successful extensions: 1783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1783
Number of HSP's successfully gapped: 40
Length of query: 332
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 235
Effective length of database: 6,635,264
Effective search space: 1559287040
Effective search space used: 1559287040
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: 59 (26.4 bits)