RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15654
(189 letters)
>gnl|CDD|238117 cd00195, UBCc, Ubiquitin-conjugating enzyme E2, catalytic (UBCc)
domain. This is part of the ubiquitin-mediated protein
degradation pathway in which a thiol-ester linkage forms
between a conserved cysteine and the C-terminus of
ubiquitin and complexes with ubiquitin protein ligase
enzymes, E3. This pathway regulates many fundamental
cellular processes. There are also other E2s which form
thiol-ester linkages without the use of E3s as well as
several UBC homologs (TSG101, Mms2, Croc-1 and similar
proteins) which lack the active site cysteine essential
for ubiquitination and appear to function in DNA repair
pathways which were omitted from the scope of this CD.
Length = 141
Score = 151 bits (383), Expect = 3e-47
Identities = 59/142 (41%), Positives = 89/142 (62%), Gaps = 2/142 (1%)
Query: 15 IRRVSKELQDLTKTPPEGIHVCINEEDITDVQAIIDGPAGTPYSNGYFKVKLLLSKNFPS 74
+R+ KEL+DL K PP GI EE++ + I GP TPY G FK+ + +++P
Sbjct: 1 SKRLQKELKDLKKDPPSGISAEPVEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPF 60
Query: 75 VPPKAFFLTKIFHPNVDTKNGEICVNTLKKD-WNPDLGIKHILLTIKCLLIVPNPESALN 133
PPK F+TKI+HPNVD +NG+IC++ LK W+P ++ +LL+++ LL PNP LN
Sbjct: 61 KPPKVRFVTKIYHPNVD-ENGKICLSILKTHGWSPAYTLRTVLLSLQSLLNEPNPSDPLN 119
Query: 134 EEAGKLLLEHYDDYSRRATMMT 155
EA KL E+ +++ ++A T
Sbjct: 120 AEAAKLYKENREEFKKKAREWT 141
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 145 bits (367), Expect = 9e-45
Identities = 59/142 (41%), Positives = 90/142 (63%), Gaps = 2/142 (1%)
Query: 11 SPQIIRRVSKELQDLTKTPPEGIHV-CINEEDITDVQAIIDGPAGTPYSNGYFKVKLLLS 69
SP ++R+ KEL+ L K PP GI ++++++ +A I GP TPY G FK+ L
Sbjct: 3 SPSALKRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFP 62
Query: 70 KNFPSVPPKAFFLTKIFHPNVDTKNGEICVNTLKKDWNPDLGIKHILLTIKCLLIVPNPE 129
+++P PPK F TKIFHPNVD +G +C++ LK W+P ++ ILL+++ LL+ PNP+
Sbjct: 63 EDYPFKPPKVRFTTKIFHPNVD-PSGNVCLDILKDRWSPVYTLETILLSLQSLLLSPNPD 121
Query: 130 SALNEEAGKLLLEHYDDYSRRA 151
S LN EA L E ++Y ++
Sbjct: 122 SPLNTEAATLYREDKEEYEKKV 143
>gnl|CDD|215772 pfam00179, UQ_con, Ubiquitin-conjugating enzyme. Proteins destined
for proteasome-mediated degradation may be
ubiquitinated. Ubiquitination follows conjugation of
ubiquitin to a conserved cysteine residue of UBC
homologues. TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 139
Score = 143 bits (364), Expect = 1e-44
Identities = 58/136 (42%), Positives = 90/136 (66%), Gaps = 2/136 (1%)
Query: 17 RVSKELQDLTKTPPEGIHVCINEEDITDVQAIIDGPAGTPYSNGYFKVKLLLSKNFPSVP 76
R+ KEL++L K PP GI ++++ + + I GP GTPY G FK+ + +++P P
Sbjct: 1 RLQKELKELLKDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKP 60
Query: 77 PKAFFLTKIFHPNVDTKNGEICVNTLK-KDWNPDLGIKHILLTIKCLLIVPNPESALNEE 135
PK F TKI+HPNVD +GEIC++ LK ++W+P L I+ +LL+I+ LL PNPE LN E
Sbjct: 61 PKVKFTTKIYHPNVD-PSGEICLDILKDENWSPALTIEQVLLSIQSLLSEPNPEDPLNAE 119
Query: 136 AGKLLLEHYDDYSRRA 151
A KL ++ +++ ++
Sbjct: 120 AAKLYRKNREEFEKKV 135
>gnl|CDD|214562 smart00212, UBCc, Ubiquitin-conjugating enzyme E2, catalytic domain
homologues. Proteins destined for proteasome-mediated
degradation may be ubiquitinated. Ubiquitination follows
conjugation of ubiquitin to a conserved cysteine residue
of UBC homologues. This pathway functions in regulating
many fundamental processes required for cell
viability.TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 145
Score = 127 bits (320), Expect = 8e-38
Identities = 55/137 (40%), Positives = 94/137 (68%), Gaps = 3/137 (2%)
Query: 17 RVSKELQDLTKTPPEGIH-VCINEEDITDVQAIIDGPAGTPYSNGYFKVKLLLSKNFPSV 75
R+ KEL++L K PP G +++E++ + I GP GTPY G FK+ + +++P
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFK 60
Query: 76 PPKAFFLTKIFHPNVDTKNGEICVNTLKKD-WNPDLGIKHILLTIKCLLIVPNPESALNE 134
PPK F+TKI+HPNVD+ +GEIC++ LK++ W+P L ++ +LL+++ LL PNP+S LN
Sbjct: 61 PPKVKFITKIYHPNVDS-SGEICLDILKQEKWSPALTLETVLLSLQSLLSEPNPDSPLNA 119
Query: 135 EAGKLLLEHYDDYSRRA 151
+A +L ++ +++ ++A
Sbjct: 120 DAAELYKKNREEFKKKA 136
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 111 bits (278), Expect = 2e-31
Identities = 52/120 (43%), Positives = 77/120 (64%), Gaps = 1/120 (0%)
Query: 14 IIRRVSKELQDLTKTPPEGIHVCINEEDITDVQAIIDGPAGTPYSNGYFKVKLLLSKNFP 73
I +R+ KE Q+L PP GI + + + +++GP GTPY GY+K++L L + +P
Sbjct: 3 ISKRIEKETQNLANDPPPGIKAEPDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYP 62
Query: 74 SVPPKAFFLTKIFHPNVDTKNGEICVNTLKKDWNPDLGIKHILLTIKCLLIVPNPESALN 133
PPK FLTKI+HPN+D K G IC++ LK W+P L I+ +LL+I+ LL P P+ L+
Sbjct: 63 MEPPKVRFLTKIYHPNID-KLGRICLDILKDKWSPALQIRTVLLSIQALLSAPEPDDPLD 121
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 100 bits (250), Expect = 2e-27
Identities = 52/144 (36%), Positives = 83/144 (57%), Gaps = 1/144 (0%)
Query: 16 RRVSKELQDLTKTPPEGIHVCINEEDITDVQAIIDGPAGTPYSNGYFKVKLLLSKNFPSV 75
+R+ KE +DL K PP ++E++ A I GP+ +PY+ G F + +L ++P
Sbjct: 4 KRIQKEHKDLLKDPPSNCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFK 63
Query: 76 PPKAFFLTKIFHPNVDTKNGEICVNTLKKDWNPDLGIKHILLTIKCLLIVPNPESALNEE 135
PPK F TKI+HPN+++ NG IC++ L+ W+P L + +LL+I LL PNP+ L E
Sbjct: 64 PPKVQFTTKIYHPNINS-NGSICLDILRDQWSPALTVSKVLLSISSLLTDPNPDDPLVPE 122
Query: 136 AGKLLLEHYDDYSRRATMMTEIHA 159
++ E+ Y A T+ +A
Sbjct: 123 IARVFKENRSRYEATAREWTQRYA 146
>gnl|CDD|179406 PRK02289, PRK02289, 4-oxalocrotonate tautomerase; Provisional.
Length = 60
Score = 29.9 bits (67), Expect = 0.15
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 11/53 (20%)
Query: 13 QIIRRVSKELQDLTKTPPEGIHVCINEEDITDVQAIIDGPAGTPYSNGYFKVK 65
+ R V++ + + K P E IHV IN D P GT Y G K K
Sbjct: 19 ALAREVTEVVSRIAKAPKEAIHVFIN-----------DMPEGTYYPQGEMKTK 60
>gnl|CDD|143402 cd07083, ALDH_P5CDH, ALDH subfamily NAD+-dependent
delta(1)-pyrroline-5-carboxylate dehydrogenase-like.
ALDH subfamily of the NAD+-dependent,
delta(1)-pyrroline-5-carboxylate dehydrogenases (P5CDH,
EC=1.5.1.12). The proline catabolic enzymes, proline
dehydrogenase and P5CDH catalyze the two-step oxidation
of proline to glutamate. P5CDH catalyzes the oxidation
of glutamate semialdehyde, utilizing NAD+ as the
electron acceptor. In some bacteria, the two enzymes are
fused into the bifunctional flavoenzyme, proline
utilization A (PutA). These enzymes play important roles
in cellular redox control, superoxide generation, and
apoptosis. In certain prokaryotes such as Escherichia
coli, PutA is also a transcriptional repressor of the
proline utilization genes. Monofunctional enzyme
sequences such as those seen in the Bacillus RocA P5CDH
are also present in this subfamily as well as the human
ALDH4A1 P5CDH and the Drosophila Aldh17 P5CDH.
Length = 500
Score = 30.2 bits (68), Expect = 0.58
Identities = 23/103 (22%), Positives = 34/103 (33%), Gaps = 34/103 (33%)
Query: 8 ENLSPQIIRRVSKELQDLTKTPPEGIHVCINEEDITDVQAIIDGPA-------------- 53
+ ++ R+ K + L+ PP EE+ TD+ +ID
Sbjct: 313 QGAYEPVLERLLKRAERLSVGPP--------EENGTDLGPVIDAEQEAKVLSYIEHGKNE 364
Query: 54 GT-------PYSNGYFKVKLLLSKNFPSVPPKAFFLTK-IFHP 88
G GYF + VPPKA + IF P
Sbjct: 365 GQLVLGGKRLEGEGYFVAPTV----VEEVPPKARIAQEEIFGP 403
>gnl|CDD|131378 TIGR02325, C_P_lyase_phnF, phosphonates metabolism transcriptional
regulator PhnF. All members of the seed alignment for
this family are predicted helix-turn-helix
transcriptional regulatory proteins of the broader gntR
and are found associated with genes for the import and
degradation of phosphonates and/or related compounds
(e.g. phosphonites) with a direct C-P bond [Transport
and binding proteins, Anions, Regulatory functions, DNA
interactions].
Length = 238
Score = 29.8 bits (67), Expect = 0.74
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 146 DYSRRATMMTEIHAQASKCSKLG 168
DY R +T ++ HA A C++L
Sbjct: 176 DYRRSSTRISARHADAKDCARLE 198
>gnl|CDD|220071 pfam08921, DUF1904, Domain of unknown function (DUF1904). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 107
Score = 28.4 bits (64), Expect = 1.1
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 11/52 (21%)
Query: 7 VENLSPQIIRRVSKELQDLTKTPPEGIHV-CINEEDITDVQAIIDGPAGTPY 57
V+ LS +I +EL D+ K PPE + IN DG Y
Sbjct: 13 VKELSKTLI----EELADICKCPPEAFTLEWINS------VFFRDGKIDDAY 54
>gnl|CDD|225141 COG2232, COG2232, Predicted ATP-dependent carboligase related to
biotin carboxylase [General function prediction only].
Length = 389
Score = 28.7 bits (64), Expect = 2.1
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 2 NSMSNVENLSPQIIRRVSKELQDLTKTPP 30
N+ S E+++ ++ RV L+ ++ TPP
Sbjct: 356 NTRSGAESMAERLAERVKNFLERVSSTPP 384
>gnl|CDD|241249 cd01213, PTB_tensin, Tensin Phosphotyrosine-binding (PTB) domain.
Tensin is a a focal adhesion protein, which contains a
C-terminal SH2 domain followed by a PTB domain. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif
with differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 136
Score = 27.6 bits (62), Expect = 2.2
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 1 MNSMSNVENLS-PQIIRR-VSKELQDLTKTPPEGIHVCINEEDIT--DVQ 46
+ S+ + E+L+ PQ +R+ VS+ L+ P +H ++E+ IT D Q
Sbjct: 9 LGSV-DTESLTGPQAVRKAVSETLERDPLPTPTVVHFKVSEQGITLTDNQ 57
>gnl|CDD|224853 COG1942, COG1942, Uncharacterized protein, 4-oxalocrotonate
tautomerase homolog [General function prediction only].
Length = 69
Score = 26.5 bits (59), Expect = 2.3
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 13 QIIRRVSKELQDLTKTPPEGIHVCINE 39
++ V++ + P IHV I E
Sbjct: 20 ELAAEVTEVTVETLGKDPSAIHVIIEE 46
>gnl|CDD|216890 pfam02129, Peptidase_S15, X-Pro dipeptidyl-peptidase (S15
family).
Length = 265
Score = 28.1 bits (63), Expect = 2.6
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 31 EGIHVCINEEDITDVQAIIDGPAGTPYSNG 60
EG+ +++ D + +ID AG P+ NG
Sbjct: 66 EGVFTVGGPQEVADGKDVIDWLAGQPWCNG 95
>gnl|CDD|238274 cd00491, 4Oxalocrotonate_Tautomerase, 4-Oxalocrotonate
Tautomerase: Catalyzes the isomerization of
unsaturated ketones. The structure is a homohexamer
that is arranged as a trimer of dimers. The hexamer
contains six active sites, each formed by residues from
three monomers, two from one dimer and the third from a
neighboring monomer. Each monomer is a beta-alpha-beta
fold with two small beta strands at the C-terminus that
fold back on themselves. A pair of monomers form a
dimer with two-fold symmetry, consisting of a
4-stranded beta sheet with two helices on one side and
two additional small beta strands at each end. The
dimers are assembled around a 3-fold axis of rotation
to form a hexamer, with the short beta strands from
each dimer contacting the neighboring dimers.
Length = 58
Score = 25.8 bits (57), Expect = 3.2
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 13 QIIRRVSKELQDLTKTPPEGIHVCINE 39
++I RV++ + ++ P I V I+E
Sbjct: 18 ELIERVTEAVSEILGAPEATIVVIIDE 44
>gnl|CDD|233141 TIGR00820, zip, ZIP zinc/iron transport family. The Zinc
(Zn2+)-Iron (Fe2+) Permease (ZIP) Family (TC
2.A.5)Members of the ZIP family consist of proteins
with eight putative transmembrane spanners. They are
derived from animals, plants and yeast. Theycomprise a
diverse family, with several paralogues in any one
organism (e.g., at least five in Caenorabditis elegans,
at least five in Arabidopsis thaliana and two
inSaccharomyces cervisiae. The two S. cerevisiae
proteins, Zrt1 and Zrt2, both probably transport Zn2+
with high specificity, but Zrt1 transports Zn2+ with
ten-fold higher affinitythan Zrt2. Some members of the
ZIP family have been shown to transport Zn2+ while
others transport Fe2+, and at least one transports a
range of metal ions. The energy source fortransport has
not been characterized, but these systems probably
function as secondary carriers [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 324
Score = 27.4 bits (61), Expect = 5.0
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 67 LLSKNFPSVPP--KAFFLTKIF 86
L+ KN PS+ P FF+ K F
Sbjct: 38 LIGKNVPSLRPEGNFFFVAKAF 59
>gnl|CDD|150014 pfam09181, ProRS-C_2, Prolyl-tRNA synthetase, C-terminal. Members
of this family are predominantly found in prokaryotic
prolyl-tRNA synthetase. They contain a zinc binding
site, and adopt a structure consisting of alpha helices
and antiparallel beta sheets arranged in 2 layers, in a
beta-alpha-beta-alpha-beta motif.
Length = 62
Score = 25.5 bits (56), Expect = 5.0
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 101 TLKKDWNPDLGIKHILLTIKCLLIVPNPESALNEE 135
T+ ++ NPD IK+ L K +++VP ES NEE
Sbjct: 2 TILENINPD-KIKNALSEKKGVILVPFDESIYNEE 35
>gnl|CDD|212524 cd10000, HDAC8, Histone deacetylase 8 (HDAC8). HDAC8 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. HDAC8 is found in human cytoskeleton-bound
protein fraction and insoluble cell pellets. It plays a
crucial role in intramembraneous bone formation;
germline deletion of HDAC8 is detrimental to skull bone
formation. HDAC8 is possibly associated with the smooth
muscle actin cytockeleton and may regulate the
contractive capacity of smooth muscle cells. HDAC8 is
also involved in the metabolic control of the estrogen
receptor related receptor (ERR)-alpha/peroxisome
proliferator activated receptor (PPAR) gamma coactivator
1 alpha (PGC1-alpha) transcriptional complex as well as
in the development of neuroblastoma and T-cell lymphoma.
HDAC8-selective small-molecule inhibitors could be a
therapeutic drug option for these diseases.
Length = 364
Score = 26.9 bits (60), Expect = 7.5
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 9/57 (15%)
Query: 66 LLLSKNFPS-VPPKAFFLTKIFHPNVDTKNGEICVNT-LKKDWNPDLGIKHILLTIK 120
L+L + S +P FF + + P+ E+ ++ L+ D N D I+ IL TIK
Sbjct: 308 LILGEPLSSDIPDHEFFTS--YGPDY-----ELEISPSLRPDLNEDQYIEKILETIK 357
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
0.314 0.132 0.384
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,390,144
Number of extensions: 866210
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 562
Number of HSP's successfully gapped: 22
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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: 42 (22.0 bits)
S2: 56 (25.3 bits)