RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5105
(100 letters)
>gnl|CDD|218833 pfam05971, Methyltransf_10, Protein of unknown function (DUF890).
This family consists of several conserved hypothetical
proteins from both eukaryotes and prokaryotes. The
function of this family is unknown.
Length = 299
Score = 94.5 bits (235), Expect = 5e-25
Identities = 32/93 (34%), Positives = 54/93 (58%), Gaps = 1/93 (1%)
Query: 1 MSFNKFMHPRNKYRVPPDFKQLAIEYPEFRKHLHQELSGKLKFNFQNPDALRIFTTTVLR 60
M+ +HPRN+++ DF L YPE ++H+ +G+ NF +P+A++ +LR
Sbjct: 1 MALKSGLHPRNRHKGRYDFAYLISVYPELKQHVQLNPNGRQSINFADPEAVKALNKALLR 60
Query: 61 KDFGL-NVEIPPMRLVPTLPLRLNYILWIEDLL 92
+ +G+ +IP L P +P R +YI W+ DLL
Sbjct: 61 EFYGVSIWDIPDGFLCPPVPGRADYIHWVADLL 93
>gnl|CDD|236964 PRK11727, PRK11727, 23S rRNA mA1618 methyltransferase; Provisional.
Length = 321
Score = 53.7 bits (130), Expect = 6e-10
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 7 MHPRNKYRVPPDFKQLAIEYPEFRKHLHQELSGKLKFNFQNPDALRIFTTTVLRKDFGL- 65
+HPRN++R DF L +PE + + G+ +F NP A++ +L +G+
Sbjct: 16 LHPRNRHRGRYDFAALIQSHPELKPFVILNPYGEQSIDFANPLAVKALNKALLAHFYGVA 75
Query: 66 NVEIPPMRLVPTLPLRLNYILWIEDLL 92
+ +IP L P +P R +YI + DLL
Sbjct: 76 HWDIPAGYLCPPIPGRADYIHHLADLL 102
>gnl|CDD|225671 COG3129, COG3129, Predicted SAM-dependent methyltransferase
[General function prediction only].
Length = 292
Score = 50.9 bits (122), Expect = 5e-09
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 27 PEFRKHLHQELSGKLKFNFQNPDALRIFTTTVLRKDFGL-NVEIPPMRLVPTLPLRLNYI 85
PE L +G+ +F NP A++ +L + + +IP L P +P R +YI
Sbjct: 2 PELILFLRLTPAGRQSIDFANPLAVKALNKALLAHFYAVRYWDIPEGFLCPPVPGRADYI 61
Query: 86 LWIEDLL 92
+ DLL
Sbjct: 62 HHLADLL 68
>gnl|CDD|227807 COG5520, COG5520, O-Glycosyl hydrolase [Cell envelope biogenesis,
outer membrane].
Length = 433
Score = 28.3 bits (63), Expect = 0.66
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 43 FNFQNPDA---LRIFTTTVLRKDFGLNVEIPPMRLVPTLPLR 81
FNFQNPD ++ L N+ R +LP +
Sbjct: 380 FNFQNPDGSNVSSWVNSSTLNMAKTSNILAAGGRFNASLPAQ 421
>gnl|CDD|182810 PRK10885, cca, multifunctional tRNA nucleotidyl
transferase/2'3'-cyclic
phosphodiesterase/2'nucleotidase/phosphatase; Reviewed.
Length = 409
Score = 26.7 bits (60), Expect = 1.9
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 14 RVPPDFKQLAIEYPEFRKHLHQ--ELSGK--LKFNFQNPDALR 52
RVP + + LA+ E ++H+ EL K +K DA R
Sbjct: 289 RVPNECRDLALLVAEEHDNIHRAPELRPKTLVKL-LDRIDAWR 330
>gnl|CDD|221000 pfam11145, DUF2921, Protein of unknown function (DUF2921). This
eukaryotic family of proteins has no known function.
Length = 871
Score = 26.7 bits (59), Expect = 2.4
Identities = 22/98 (22%), Positives = 35/98 (35%), Gaps = 5/98 (5%)
Query: 7 MHPRNKYRV----PPDFKQLAIEYPEFRKHLHQ-ELSGKLKFNFQNPDALRIFTTTVLRK 61
N + P K + K L + + SGK K P L +++ + L
Sbjct: 398 SDMFNSFNRSLSNPRVVKYEYTKVERAGKLLRRNKPSGKKKSLVSYPGNLGMYSLSDLAF 457
Query: 62 DFGLNVEIPPMRLVPTLPLRLNYILWIEDLLEANQISS 99
D + P R PL + +L+ D L N S+
Sbjct: 458 DLSVKFSAGPNRTGRASPLFVGPLLYRFDPLSRNSGST 495
>gnl|CDD|238874 cd01836, FeeA_FeeB_like, SGNH_hydrolase subfamily, FeeA, FeeB and
similar esterases/lipases. FeeA and FeeB are part of a
biosynthetic gene cluster and may participate in the
biosynthesis of long-chain N-acyltyrosines by providing
saturated and unsaturated fatty acids, which it turn are
loaded onto the acyl carrier protein FeeL. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 191
Score = 26.5 bits (59), Expect = 2.4
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 69 IPPMRLVPTLPLRLNYILWI 88
+PP+ P LP L ++L
Sbjct: 114 VPPLGRFPALPQPLRWLLGR 133
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 26.1 bits (57), Expect = 3.1
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 13 YRVPPDFKQLAIEYPEFRKHLHQELSGKLKFNFQNPDALRI--FTTTVLRKDF 63
YRVPPD + L Y ++ +H + +S +N N L + +L+ F
Sbjct: 280 YRVPPDLRDL--NYGKYVEHGDRRISEVEDYNSHNTQRLDVEGMKELLLKLPF 330
>gnl|CDD|225228 COG2353, COG2353, Uncharacterized conserved protein [Function
unknown].
Length = 192
Score = 26.1 bits (58), Expect = 3.2
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 54 FTTTVLRKDFGLNVEIPPM 72
T + R DFG+ V P +
Sbjct: 157 ATGKINRSDFGIKVGRPLI 175
>gnl|CDD|233707 TIGR02071, PBP_1b, penicillin-binding protein 1B. Bacterial that
synthesize a cell wall of peptidoglycan (murein)
generally have several transglycosylases and
transpeptidases for the task. This family consists of a
particular bifunctional transglycosylase/transpeptidase
in E. coli and other Proteobacteria, designated
penicillin-binding protein 1B [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 730
Score = 26.2 bits (58), Expect = 3.5
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 21 QLAIEYPEFRKHLHQELSGKLKFNFQNPDALRIFTT 56
+ P F + + +EL KL ++ LRIFTT
Sbjct: 340 GIISRQPAFLQLVRRELRQKLGDKVKDLSGLRIFTT 375
>gnl|CDD|225527 COG2980, RlpB, Rare lipoprotein B [Cell envelope biogenesis,
outer membrane].
Length = 178
Score = 25.4 bits (56), Expect = 4.5
Identities = 9/34 (26%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 8 HPRNKYRVPPDFKQLAIE----YPEFRKHLHQEL 37
H R ++PP+ K L++E Y + + ++L
Sbjct: 22 HLRGTTQIPPELKTLSLESSDPYGPLTRAVRRQL 55
>gnl|CDD|202693 pfam03583, LIP, Secretory lipase. These lipases are expressed and
secreted during the infection cycle of these pathogens.
In particular, C. albicans has a large number of
different lipases, possibly reflecting broad lipolytic
activity, which may contribute to the persistence and
virulence of C. albicans in human tissue.
Length = 291
Score = 25.8 bits (57), Expect = 4.9
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 22 LAIEYPEFRKHLHQELSGKLKFNFQ 46
LA EYP+F+K L++EL+ + +
Sbjct: 138 LANEYPDFKKILYEELNDAGREALK 162
>gnl|CDD|224232 COG1313, PflX, Uncharacterized Fe-S protein PflX, homolog of
pyruvate formate lyase activating proteins [General
function prediction only].
Length = 335
Score = 25.4 bits (56), Expect = 6.0
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 11 NKYRVPPDFKQLAIEYPEFRKHLHQE 36
+YR P++K A EYPE + L +E
Sbjct: 294 FQYR--PEYK--AEEYPEINRRLTRE 315
>gnl|CDD|225536 COG2989, COG2989, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 561
Score = 25.5 bits (56), Expect = 6.4
Identities = 7/12 (58%), Positives = 7/12 (58%)
Query: 39 GKLKFNFQNPDA 50
G KFNF N A
Sbjct: 440 GSYKFNFPNSHA 451
>gnl|CDD|193507 cd03886, M20_Acy1, M20 Peptidase Aminoacylase 1 family.
Peptidase M20 family, Aminoacylase 1 (ACY1;
hippuricase; acylase I; amido acid deacylase; IAA-amino
acid hydrolase; dehydropeptidase II;
N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14)
subfamily. ACY1 is the most abundant of the
aminoacylases, a class of zinc binding homodimeric
enzymes involved in the hydrolysis of N-acetylated
proteins. It is encoded by the aminoacylase 1 gene
(Acy1) on chromosome 3p21 that comprises 15 exons.
N-terminal acetylation of proteins is a widespread and
highly conserved process that is involved in the
protection and stability of proteins. Several types of
aminoacylases can be distinguished on the basis of
substrate specificity; substrates include indoleacetic
acid (IAA) N-conjugates of amino acids,
N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1
breaks down cytosolic aliphatic N-acyl-alpha-amino
acids (except L-aspartate), especially
N-acetyl-methionine and acetyl-glutamate into L-amino
acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine). ACY1
appears to physically interact with Sphingosine kinase
type 1 (SphK1) and may influence its physiological
functions; SphK1 and its product
sphingosine-1-phosphate have been shown to promote cell
growth and inhibit apoptosis of tumor cells. Strong
expression of the human gene and its mouse ortholog
Acy1 in brain, liver, and kidney, suggest a role of the
enzyme in amino acid metabolism of these organs.
Defects in ACY1 are the cause of aminoacylase-1
deficiency (ACY1D), resulting in a metabolic disorder
manifesting encephalopathy and psychomotor delay.
Length = 372
Score = 25.1 bits (56), Expect = 6.5
Identities = 8/17 (47%), Positives = 10/17 (58%), Gaps = 2/17 (11%)
Query: 28 EFRKHLHQ--ELSGKLK 42
E R+ LHQ ELS +
Sbjct: 3 EIRRDLHQHPELSFEEP 19
>gnl|CDD|213701 TIGR02336, TIGR02336, 1,3-beta-galactosyl-N-acetylhexosamine
phosphorylase. Members of this family are found in
phylogenetically diverse bacteria, including Clostridium
perfringens (in the Firmicutes), Bifidobacterium longum
and Propionibacterium acnes (in the Actinobacteria), and
Vibrio vulnificus (in the Proteobacteria), most of which
occur as mammalian pathogens or commensals. The nominal
activity, 1,3-beta-galactosyl-N-acetylhexosamine
phosphorylase (EC 2.4.1.211), varies somewhat from
instance to instance in relative rates for closely
related substrates [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 719
Score = 25.2 bits (55), Expect = 6.6
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 8 HPRNKYRVPPDFKQLAIEYPEFRKHLHQELSGKLKFNFQNPDALRIFTT 56
H N + I +P RKH+ LK + D +R FTT
Sbjct: 166 HLTNDWGDKEHEIPFDIYHPATRKHVFDTFEQWLKDS-PQTDVVR-FTT 212
>gnl|CDD|176134 cd08443, PBP2_CysB, The C-terminal substrate domain of LysR-type
transcriptional regulator CysB contains type 2
periplasmic binding fold. CysB is a transcriptional
activator of genes involved in sulfate and thiosulfate
transport, sulfate reduction, and cysteine synthesis.
In Escherichia coli, the regulation of transcription in
response to sulfur source is attributed to two
transcriptional regulators, CysB and Cbl. CysB, in
association with Cbl, downregulates the expression of
ssuEADCB operon which is required for the utilization
of sulfur from aliphatic sulfonates, in the presence of
cysteine. Also, Cbl and CysB together directly function
as transcriptional activators of tauABCD genes, which
are required for utilization of taurine as sulfur
source for growth. Like many other members of the LTTR
family, CysB 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 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 = 198
Score = 25.2 bits (55), Expect = 7.0
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 8 HPRNKYRVPPDFKQLAIEYPEFRKHLHQ 35
H + +Y +PP K YP +HQ
Sbjct: 8 HTQARYVLPPVIKGFIERYPRVSLQMHQ 35
>gnl|CDD|166642 PLN03001, PLN03001, oxidoreductase, 2OG-Fe(II) oxygenase family
protein.
Length = 262
Score = 25.0 bits (54), Expect = 7.5
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 16 PPDFKQLAIEYPEFRKHLHQELSG 39
PPD++++ EY + K L Q+L
Sbjct: 71 PPDYREVVGEYGDCMKALAQKLLA 94
>gnl|CDD|183676 PRK12679, cbl, transcriptional regulator Cbl; Reviewed.
Length = 316
Score = 25.2 bits (55), Expect = 7.8
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 8 HPRNKYRVPPDFKQLAIEYPEFRKHLHQ 35
H + +Y +P K +PE R L Q
Sbjct: 101 HTQARYSLPEVIKAFRELFPEVRLELIQ 128
>gnl|CDD|237835 PRK14850, PRK14850, penicillin-binding protein 1b; Provisional.
Length = 764
Score = 25.2 bits (55), Expect = 8.8
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 26 YPEFRKHLHQELSGKLKFNFQNPDALRIFTT 56
+P F + + +E K+ + F+N +IFTT
Sbjct: 355 HPAFIQLVCEEFHKKIHYPFKNFSGTKIFTT 385
>gnl|CDD|217996 pfam04264, YceI, YceI-like domain. E. coli YceI is a base-induced
periplasmic protein. The recent structure of a member of
this family shows that it binds to polyisoprenoid. The
structure consists of an extended, eight-stranded,
antiparallel beta-barrel that resembles the lipocalin
fold.
Length = 161
Score = 24.6 bits (54), Expect = 9.6
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 40 KLKFNFQNPDALRI-FTTTVLRKDFGLNVEIPPMRLV-PTLPLRLN 83
+ L T T+ R DFG+ P + + + + N
Sbjct: 112 PVTLTGLGDTPLVFSATGTIDRSDFGIGYGSPLLGKIGDEVEVTFN 157
>gnl|CDD|235481 PRK05464, PRK05464, Na(+)-translocating NADH-quinone reductase
subunit F; Provisional.
Length = 409
Score = 24.8 bits (55), Expect = 9.7
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 18 DFKQLAIEYPEFRKHL 33
DF QLA E P F+ H+
Sbjct: 323 DFDQLAAENPNFKWHV 338
>gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of
LysR-type transcriptional regulators CysB-like contains
type 2 periplasmic binding fold. CysB is a
transcriptional activator of genes involved in sulfate
and thiosulfate transport, sulfate reduction, and
cysteine synthesis. In Escherichia coli, the regulation
of transcription in response to sulfur source is
attributed to two transcriptional regulators, CysB and
Cbl. CysB, in association with Cbl, downregulates the
expression of ssuEADCB operon which is required for the
utilization of sulfur from aliphatic sulfonates, in the
presence of cysteine. Also, Cbl and CysB together
directly function as transcriptional activators of
tauABCD genes, which are required for utilization of
taurine as sulfur source for growth. Like many other
members of the LTTR family, CysB 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 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. Besides transport
proteins, the PBP2 superfamily includes the
substrate-binding domains from ionotropic glutamate
receptors, LysR-like transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 198
Score = 24.5 bits (54), Expect = 9.7
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 8 HPRNKYRVPPDFKQLAIEYPEFRKHLHQ 35
H + +Y +PP YP+ + LHQ
Sbjct: 8 HTQARYVLPPVIAAFRKRYPKVKLSLHQ 35
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
0.325 0.142 0.436
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,447,836
Number of extensions: 469464
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 594
Number of HSP's successfully gapped: 35
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.1 bits)