RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15140
(227 letters)
>gnl|CDD|217381 pfam03134, TB2_DP1_HVA22, TB2/DP1, HVA22 family. This family
includes members from a wide variety of eukaryotes. It
includes the TB2/DP1 (deleted in polyposis) protein,
which in humans is deleted in severe forms of familial
adenomatous polyposis, an autosomal dominant oncological
inherited disease. The family also includes the plant
protein of known similarity to TB2/DP1, the HVA22
abscisic acid-induced protein, which is thought to be a
regulatory protein.
Length = 94
Score = 128 bits (324), Expect = 1e-38
Identities = 45/93 (48%), Positives = 68/93 (73%), Gaps = 1/93 (1%)
Query: 98 FGYAAQVICNCIGFLYPAYKSMKAIESENKQDDTKWLTYWVVFALFSIVEYPAEFILSIF 157
FG A+++ N IGFLYPAY S KA+ES++K+DDT+WLTYWVV++ ++ E ++ ILS
Sbjct: 1 FGIGARLLSNLIGFLYPAYASYKALESKDKEDDTQWLTYWVVYSFLTLFESFSDIILSWI 60
Query: 158 PFYWLIKCIFFIWCFAPMENNGSIFIYNRIIRP 190
PFY+ +K +F +W P + G+ +IY++ IRP
Sbjct: 61 PFYYELKLLFLVWLVLP-KTQGASYIYDKFIRP 92
>gnl|CDD|227385 COG5052, YOP1, Protein involved in membrane traffic [Intracellular
trafficking and secretion].
Length = 186
Score = 88.3 bits (219), Expect = 7e-22
Identities = 47/164 (28%), Positives = 68/164 (41%), Gaps = 7/164 (4%)
Query: 67 APFLTLAEQKTGVKRIYIVLGLIGFLALYLV--FGYAAQVICNCIGFLYPAYKSMKAIES 124
P L E + Y + G L L ++ N GF PA S+ A +
Sbjct: 22 FPILREIENLYNRYKKYFMAGASFLYLLNLFSTVLGFGLILTNVAGFSLPAQLSLVAFYT 81
Query: 125 ENKQDDTKWLTYWVVFALFSIVEYPAEFILSIFPFYWLIKCIFFIWCFAPMENNGSIFIY 184
N DDT+ LTYW+VF S +E + ILS PFYW +K +F +W G+ IY
Sbjct: 82 LNFMDDTQLLTYWMVFGFLSAIEKYSGAILSKVPFYWTLKNVFLLW-LLLPRTEGARIIY 140
Query: 185 NRIIRPKFLEHE-SFINSAFTKATDSAVKFATAKILEAEKPKKN 227
+ II P +H I T ++ A+ +K +
Sbjct: 141 DDIIAPDVSDHGFRTIEKTVKNGTKASAAVAS---SLEKKTAAD 181
>gnl|CDD|224825 COG1913, COG1913, Predicted Zn-dependent proteases [General
function prediction only].
Length = 181
Score = 27.7 bits (62), Expect = 3.8
Identities = 14/54 (25%), Positives = 20/54 (37%)
Query: 67 APFLTLAEQKTGVKRIYIVLGLIGFLALYLVFGYAAQVICNCIGFLYPAYKSMK 120
+L+L E+ VK + + I L VFG A + Y Y S
Sbjct: 59 LLYLSLVEKDNDVKILGVTDVDIYAPGLNFVFGLAYLGGKVAVVSTYRLYPSFY 112
>gnl|CDD|238839 cd01681, aeEF2_snRNP_like_IV, This family represents domain IV of
archaeal and eukaryotic elongation factor 2 (aeEF-2) and
of an evolutionarily conserved U5 snRNP-specific
protein. U5 snRNP is a GTP-binding factor closely
related to the ribosomal translocase EF-2. In complex
with GTP, EF-2 promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site of the small subunit
of ribosome and the mRNA is shifted one codon relative
to the ribosome. It has been shown that EF-2_IV domain
mimics the shape of anticodon arm of the tRNA in the
structurally homologous ternary complex of Phe-tRNA,
EF-1 (another transcriptional elongation factor) and GTP
analog. The tip portion of this domain is found in a
position that overlaps the anticodon arm of the A-site
tRNA, implying that EF-2 displaces the A-site tRNA to
the P-site by physical interaction with the anticodon
arm.
Length = 177
Score = 27.1 bits (61), Expect = 5.6
Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 169 IWCFAPMENNGSIFI----YNRIIRPKFLEHESFINSAFTKATDS 209
IW F P +I + + + E + I + F AT
Sbjct: 76 IWAFGPDRTGPNILVDDTKGVQYDKSLLNEIKDSIVAGFQWATKE 120
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 26.9 bits (60), Expect = 7.7
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 12/65 (18%)
Query: 3 ISEIRENLNQALNDESKPWAPFLTLAEQKTGVKRIYIVLDSGTMTISEIRENLN-QALND 61
+ +E L + L E A L LA K +K G MT +EI E+L ++ D
Sbjct: 98 LPLTKEELYKMLAHEDLRKAVLLVLA-NKQDLK--------GAMTPAEISESLGLTSIRD 148
Query: 62 ESKPW 66
W
Sbjct: 149 --HTW 151
>gnl|CDD|221416 pfam12090, Spt20, Spt20 family. This presumed domain is found in
the Spt20 proteins from both human and yeast. The Spt20
protein is part of the SAGA complex which is a large
cmplex mediating histone deacetylation. Yeast Spt20 has
been shown to play a role in structural integrity of the
SAGA complex as as no intact SAGA could be purified in
spt20 deletion strains.
Length = 191
Score = 27.0 bits (60), Expect = 7.7
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 10/48 (20%)
Query: 148 YPAEFILSIFPFYWLIKCIFFIWCFAPMENNGSIFIYNRIIRPKFLEH 195
YP I+ ++P ++ F+ + IF YN ++ FLEH
Sbjct: 12 YPPSLIIHLYPTHFR---------FSLNNSQDIIFPYNSPMKE-FLEH 49
>gnl|CDD|236284 PRK08541, PRK08541, flagellin; Validated.
Length = 211
Score = 26.7 bits (60), Expect = 7.9
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 88 LIGFLALYLVFGYAAQVICNCIGFL 112
LI F+A+ LV AA V+ N G+L
Sbjct: 11 LIVFIAMVLVAAVAAAVLINTSGYL 35
>gnl|CDD|216866 pfam02076, STE3, Pheromone A receptor.
Length = 284
Score = 27.2 bits (61), Expect = 8.2
Identities = 8/40 (20%), Positives = 12/40 (30%), Gaps = 13/40 (32%)
Query: 139 VFALFSIVEYPAEFILSIFPFYWLIK------CIFFIWCF 172
V A + F+L + P W + W F
Sbjct: 2 VLAFLA-------FVLVLPPLPWHWRARNIPTLSLIFWLF 34
>gnl|CDD|227085 COG4742, COG4742, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 26.8 bits (60), Expect = 8.4
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 24 FLTLAEQKTGVKRIYIVLDSGTMTISEIRENLN 56
L L+E++ K + ++L G TI EI+ LN
Sbjct: 8 LLFLSEKR---KDLLLLLKEGPKTIEEIKNELN 37
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. 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 = 303
Score = 26.9 bits (60), Expect = 9.8
Identities = 5/35 (14%), Positives = 14/35 (40%)
Query: 25 LTLAEQKTGVKRIYIVLDSGTMTISEIRENLNQAL 59
++V D ++ +E+ + + +AL
Sbjct: 209 YLCISLPKAANGTFLVSDGPPVSTAELVDEIRRAL 243
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
0.324 0.138 0.424
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,559,219
Number of extensions: 1091934
Number of successful extensions: 1898
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1888
Number of HSP's successfully gapped: 59
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
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: 57 (25.7 bits)