RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14900
(245 letters)
>gnl|CDD|202377 pfam02755, RPEL, RPEL repeat. The RPEL repeat is named after four
conserved amino acids it contains. The function of the
RPEL repeat is unknown however it might be a DNA binding
repeat based on the observation that the Drosophila
myocardin-related transcription factor contains a
pfam02037 domain that is also implicated in DNA binding.
Length = 26
Score = 35.7 bits (84), Expect = 6e-04
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 116 DQLNDQLAHRPGPLELIKKNILHTEE 141
D L +L+ RP EL+++NIL +E
Sbjct: 1 DSLERKLSQRPTREELVERNILKEDE 26
Score = 32.6 bits (76), Expect = 0.008
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 68 DLLKAKIQARPARTELVRQHIL 89
D L+ K+ RP R ELV ++IL
Sbjct: 1 DSLERKLSQRPTREELVERNIL 22
>gnl|CDD|128947 smart00707, RPEL, Repeat in Drosophila CG10860, human KIAA0680 and
C. elegans F26H9.2.
Length = 26
Score = 34.0 bits (79), Expect = 0.003
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 116 DQLNDQLAHRPGPLELIKKNILHTEE 141
D LN +L+ RP EL ++NIL
Sbjct: 1 DVLNRKLSQRPTREELEERNILKELS 26
Score = 30.5 bits (70), Expect = 0.045
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 68 DLLKAKIQARPARTELVRQHIL 89
D+L K+ RP R EL ++IL
Sbjct: 1 DVLNRKLSQRPTREELEERNIL 22
>gnl|CDD|233693 TIGR02032, GG-red-SF, geranylgeranyl reductase family. This model
represents a subfamily which includes geranylgeranyl
reductases involved in chlorophyll and
bacteriochlorophyll biosynthesis as well as other
related enzymes which may also act on geranylgeranyl
groups or related substrates [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 295
Score = 31.1 bits (71), Expect = 0.41
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 53 AFHAQRRQLERAKTGDLLKAKIQARPARTELVRQHILL-GDEGVGFVDPSLAE 104
F A+R +L+ A+T ++ A I +LVR ++LL GD G V+P E
Sbjct: 228 DFLARRPELKDAETVEVCGALIPIGRPDEKLVRGNVLLVGDAA-GHVNPLTGE 279
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 30.0 bits (68), Expect = 1.2
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 128 PLELIKKNILHTEEPIERAVKEGV--IAFRATCE---GQSSRPEPPDHYMTLDDDSRSSE 182
PL ++ N+ T +E A + +T E P DH + + RS
Sbjct: 88 PLSYVETNVFGTLNVLEAACVLYRKRVVHTSTSEVYGTAQDVPIDEDHPLLYINKPRSPY 147
Query: 183 ATS 185
+ S
Sbjct: 148 SAS 150
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 30.0 bits (67), Expect = 1.3
Identities = 25/108 (23%), Positives = 41/108 (37%), Gaps = 13/108 (12%)
Query: 145 RAVKEGVIAFRATCEGQSSRPEPPDHYMTLDDDSRSSEATSPPSLSGEAGGVRASSPPSL 204
A K+G R ++ E D ++ + +EA P G G ASS
Sbjct: 91 DASKKGHGKSRVRSASAAAILEEDDSKDDMEFKANPNEAGKPGKPKGNQGEGLASSSDGK 150
Query: 205 SEERERGGRRASSP---TSLSEE----------RERGIVGSDMLETAA 239
S+ + G +++S ++ S+E GIVG+D A
Sbjct: 151 SKASAKSGSKSASKHGESNSSDESATDSGKASASVAGIVGADEEAPPA 198
>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
factor. Replicative DNA polymerases are capable of
polymerising tens of thousands of nucleotides without
dissociating from their DNA templates. The high
processivity of these polymerases is dependent upon
accessory proteins that bind to the catalytic subunit of
the polymerase or to the substrate. The Epstein-Barr
virus (EBV) BMRF1 protein is an essential component of
the viral DNA polymerase and is absolutely required for
lytic virus replication. BMRF1 is also a transactivator.
This family is predicted to have a UL42 like structure.
Length = 381
Score = 28.5 bits (64), Expect = 3.3
Identities = 21/96 (21%), Positives = 28/96 (29%), Gaps = 25/96 (26%)
Query: 115 ADQLNDQLAHRPGPLELIKKNILHTEEPIERAVKEGVIAFRATCEGQSSRPEPPDHYMTL 174
AD + P P + H S P PPD
Sbjct: 289 ADSSVEANGVEPEPTGSVSDRPRHLSSD--------------------SSPSPPD----- 323
Query: 175 DDDSRSSEATSPPSLSGEAGGVRASSPPSLSEERER 210
DS S T PP+ + P +LS +R+R
Sbjct: 324 TSDSDPSTETPPPASLSHSPPAAFERPLALSPKRKR 359
>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 = 27.2 bits (60), Expect = 7.6
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 128 PLELIKKNILHTEEPIERAVKEGV 151
P+E +K N+L TE +E A+ GV
Sbjct: 93 PMEAVKTNVLGTENVLEAAIANGV 116
>gnl|CDD|182472 PRK10454, PRK10454, PTS system N,N'-diacetylchitobiose-specific
transporter subunit IIA; Provisional.
Length = 115
Score = 26.4 bits (58), Expect = 7.9
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 61 LERAKTGDLLKAKI---QARPARTE--LVRQHILLGDEGVGFVDPS--LAEKQRRLSKCR 113
L++AK GD AK Q+R A E LV+ ++ GD+G G + S L Q L
Sbjct: 39 LKQAKQGDFAAAKAMMDQSRMALNEAHLVQTKLIEGDQGEGKMKVSLVLVHAQDHLMTSM 98
Query: 114 LADQLNDQL 122
LA +L +L
Sbjct: 99 LARELITEL 107
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 27.2 bits (61), Expect = 9.2
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 128 PLELIKKNILHTEEPIERAVKEGVIAF 154
P E IK N+L TE E A+K GV F
Sbjct: 345 PEEAIKTNVLGTENVAEAAIKNGVKKF 371
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
0.312 0.129 0.358
Gapped
Lambda K H
0.267 0.0849 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,576,886
Number of extensions: 1196111
Number of successful extensions: 923
Number of sequences better than 10.0: 1
Number of HSP's gapped: 917
Number of HSP's successfully gapped: 35
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (25.9 bits)