RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4279
(129 letters)
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 143 bits (363), Expect = 4e-45
Identities = 59/124 (47%), Positives = 77/124 (62%), Gaps = 28/124 (22%)
Query: 6 QKELQDLGRDPPAQCSAGPVGD-DLFHWQATIMGPPDSPYQGGVFFLTIHFPTDYPFKPP 64
KEL+ L +DPP SAGPV D +LFHW+ATI GPPD+PY+GG+F LT+ FP DYPFKP
Sbjct: 11 LKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKP- 69
Query: 65 KPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSICLDILRSQWSPALT 124
PKV FTT+I+HPN++ +G++CLDIL+ +WSP T
Sbjct: 70 --------------------------PKVRFTTKIFHPNVDPSGNVCLDILKDRWSPVYT 103
Query: 125 ISKA 128
+
Sbjct: 104 LETI 107
>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 = 140 bits (354), Expect = 7e-44
Identities = 61/123 (49%), Positives = 76/123 (61%), Gaps = 28/123 (22%)
Query: 6 QKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPDSPYQGGVFFLTIHFPTDYPFKPPK 65
QKEL++L +DPP SA PV D+LF W+ TI+GP +PY+GGVF L I FP DYPFKP
Sbjct: 3 QKELKELLKDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKP-- 60
Query: 66 PPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSICLDILRSQ-WSPALT 124
PKV FTT+IYHPN++ +G ICLDIL+ + WSPALT
Sbjct: 61 -------------------------PKVKFTTKIYHPNVDPSGEICLDILKDENWSPALT 95
Query: 125 ISK 127
I +
Sbjct: 96 IEQ 98
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 139 bits (352), Expect = 1e-43
Identities = 73/125 (58%), Positives = 83/125 (66%), Gaps = 27/125 (21%)
Query: 3 KNKQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPDSPYQGGVFFLTIHFPTDYPFK 62
K QKE +DL +DPP+ CSAGP ++LF W A+I+GP DSPY GGVFFL+I FP DYPFK
Sbjct: 4 KRIQKEHKDLLKDPPSNCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFK 63
Query: 63 PPKPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSICLDILRSQWSPA 122
P PKV FTT+IYHPNINSNGSICLDILR QWSPA
Sbjct: 64 P---------------------------PKVQFTTKIYHPNINSNGSICLDILRDQWSPA 96
Query: 123 LTISK 127
LT+SK
Sbjct: 97 LTVSK 101
>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 = 137 bits (348), Expect = 5e-43
Identities = 59/127 (46%), Positives = 73/127 (57%), Gaps = 28/127 (22%)
Query: 3 KNKQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPDSPYQGGVFFLTIHFPTDYPFK 62
K QKEL+DL +DPP+ SA PV ++L W TI GPPD+PY+GG+F L I FP DYPFK
Sbjct: 2 KRLQKELKDLKKDPPSGISAEPVEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFK 61
Query: 63 PPKPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSICLDILRSQ-WSP 121
P PKV F T+IYHPN++ NG ICL IL++ WSP
Sbjct: 62 P---------------------------PKVRFVTKIYHPNVDENGKICLSILKTHGWSP 94
Query: 122 ALTISKA 128
A T+
Sbjct: 95 AYTLRTV 101
>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 = 121 bits (305), Expect = 2e-36
Identities = 58/124 (46%), Positives = 74/124 (59%), Gaps = 29/124 (23%)
Query: 6 QKELQDLGRDPPAQCSAGPV-GDDLFHWQATIMGPPDSPYQGGVFFLTIHFPTDYPFKPP 64
KEL++L +DPP +A PV ++L W TI+GPP +PY+GGVF LTI FP DYPFKP
Sbjct: 3 LKELKELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKP- 61
Query: 65 KPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSICLDILRSQ-WSPAL 123
PKV F T+IYHPN++S+G ICLDIL+ + WSPAL
Sbjct: 62 --------------------------PKVKFITKIYHPNVDSSGEICLDILKQEKWSPAL 95
Query: 124 TISK 127
T+
Sbjct: 96 TLET 99
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 86.8 bits (215), Expect = 9e-23
Identities = 46/123 (37%), Positives = 61/123 (49%), Gaps = 27/123 (21%)
Query: 3 KNKQKELQDLGRDPPAQCSAGPVGDDLFHWQATIMGPPDSPYQGGVFFLTIHFPTDYPFK 62
K +KE Q+L DPP A P + H++ + GP +PY+GG + L + P YP +
Sbjct: 5 KRIEKETQNLANDPPPGIKAEPDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPME 64
Query: 63 PPKPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSICLDILRSQWSPA 122
PPK V F T+IYHPNI+ G ICLDIL+ +WSPA
Sbjct: 65 PPK---------------------------VRFLTKIYHPNIDKLGRICLDILKDKWSPA 97
Query: 123 LTI 125
L I
Sbjct: 98 LQI 100
>gnl|CDD|218742 pfam05773, RWD, RWD domain. This domain was identified in WD40
repeat proteins and Ring finger domain proteins. The
function of this domain is unknown. GCN2 is the
alpha-subunit of the only translation initiation factor
(eIF2 alpha) kinase that appears in all eukaryotes. Its
function requires an interaction with GCN1 via the
domain at its N-terminus, which is termed the RWD
domain after three major RWD-containing proteins: RING
finger-containing proteins, WD-repeat-containing
proteins, and yeast DEAD (DEXD)-like helicases. The
structure forms an alpha + beta sandwich fold
consisting of two layers: a four-stranded antiparallel
beta-sheet, and three side-by-side alpha-helices.
Length = 113
Score = 28.1 bits (63), Expect = 0.66
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 49 FFLTIHFPTDYPFKPPK 65
LT P DYP +PPK
Sbjct: 52 LVLTFTLPEDYPDEPPK 68
>gnl|CDD|149126 pfam07884, VKOR, Vitamin K epoxide reductase family. Vitamin K
epoxide reductase (VKOR) recycles reduced vitamin K,
which is used subsequently as a co-factor in the
gamma-carboxylation of glutamic acid residues in blood
coagulation enzymes. VKORC1 is a member of a large
family of predicted enzymes that are present in
vertebrates, Drosophila, plants, bacteria and archaea.
Four cysteine residues and one residue, which is either
serine or threonine, are identified as likely
active-site residues. In some plant and bacterial
homologues the VKORC1 homologous domain is fused with
domains of the thioredoxin family of oxidoreductases.
Length = 138
Score = 26.9 bits (60), Expect = 2.3
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 12 LGRDPP-AQCSAGPV---GDDLFHWQATIMGPPDSPYQGGVFFLTI 53
L DP A C PV L ATI G P+S G + +L +
Sbjct: 26 LLEDPYRASCDINPVVSCSKVLNSPWATIFGIPNSLL-GILAYLVV 70
>gnl|CDD|99918 cd05535, POLBc_epsilon, DNA polymerase type-B epsilon subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase (Pol) epsilon has been proposed to play a
role in elongation of the leading strand during DNA
replication. Pol epsilon might also have a role in DNA
repair. The structure of pol epsilon is characteristic
of this family with the exception that it contains a
large c-terminal domain with an unclear function.
Phylogenetic analyses indicate that Pol epsilon is the
ortholog to the archaeal Pol B3 rather than to Pol
alpha, delta, or zeta. This might be because pol epsilon
is ancestral to both archaea and eukaryotes DNA
polymerases type B.
Length = 621
Score = 27.3 bits (61), Expect = 2.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 54 HFPTDYPFKPPKPPKVSIEYP 74
FP ++ FK KV+I YP
Sbjct: 341 SFPENFTFKTKNGKKVTISYP 361
>gnl|CDD|130861 TIGR01802, CM_pl-yst, monofunctional chorismate mutase, eukaryotic
type. This model represents the plant and yeast
(plastidic) chorismate mutase. These CM's are distinct
from other forms by the presence of an extended
regulatory domain [Amino acid biosynthesis, Aromatic
amino acid family].
Length = 246
Score = 27.0 bits (60), Expect = 2.9
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 17/55 (30%)
Query: 56 PTDYPFKPPKPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSI 110
P ++PF P K PK P+ P KYP L Y P++N N I
Sbjct: 70 PDEHPFFPDKLPK-----PILPPL-----KYPKILH-------PYAPSVNVNSKI 107
>gnl|CDD|214735 smart00591, RWD, domain in RING finger and WD repeat containing
proteins and DEXDc-like helicases subfamily related to
the UBCc domain.
Length = 107
Score = 26.2 bits (58), Expect = 3.0
Identities = 5/17 (29%), Positives = 8/17 (47%)
Query: 49 FFLTIHFPTDYPFKPPK 65
L + P +YP + P
Sbjct: 43 LTLQVKLPENYPDEAPP 59
>gnl|CDD|226384 COG3866, PelB, Pectate lyase [Carbohydrate transport and
metabolism].
Length = 345
Score = 26.7 bits (59), Expect = 4.2
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 31 HWQATIMGPPDSP-YQGGVFFLTIH 54
H +++++G DS Y G + +TIH
Sbjct: 198 HDKSSLLGSSDSSNYDDGKYKVTIH 222
>gnl|CDD|221290 pfam11885, DUF3405, Protein of unknown function (DUF3405). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 636 to 810
amino acids in length.
Length = 483
Score = 26.2 bits (58), Expect = 5.5
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 55 FPTDYPFKPPKPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYH 101
FP P +P +P + P ++S + K P+ A R +H
Sbjct: 55 FPPLGPPRPTRPQGLPTGKPAATDGPRISPRNTKKEPRTAVVIRAWH 101
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 26.1 bits (58), Expect = 6.9
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 5/18 (27%)
Query: 4 NK----QKEL-QDLGRDP 16
NK ++EL Q+LGR+P
Sbjct: 358 NKLGRIERELLQELGREP 375
>gnl|CDD|152255 pfam11819, DUF3338, Domain of unknown function (DUF3338). This
family of proteins are functionally uncharacterized.
This family is found in eukaryotes. This presumed
domain is about 130 amino acids in length.
Length = 138
Score = 25.1 bits (55), Expect = 8.8
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 51 LTIHFPTDYPFKP-PKPPKV 69
LT P +YP +P KPP+V
Sbjct: 65 LTGKLPKEYPLEPGEKPPQV 84
>gnl|CDD|233552 TIGR01736, FGAM_synth_II, phosphoribosylformylglycinamidine
synthase II. Phosphoribosylformylglycinamidine synthase
is a single, long polypeptide in most Proteobacteria and
eukarotes. Three proteins are required in Bacillus
subtilis and many other species. This is the longest of
the three and is designated PurL,
phosphoribosylformylglycinamidine synthase II, or FGAM
synthase II [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 715
Score = 25.7 bits (57), Expect = 9.7
Identities = 8/46 (17%), Positives = 14/46 (30%)
Query: 65 KPPKVSIEYPLKQPKVKVSRKYPLKLPKVAFTTRIYHPNINSNGSI 110
P+ + + P + AF + PNI S +
Sbjct: 355 DAPEYERPSEPPKYPEEEKEPEPPADLEDAFLKVLSSPNIASKEWV 400
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
0.318 0.137 0.438
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,625,521
Number of extensions: 565485
Number of successful extensions: 452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 434
Number of HSP's successfully gapped: 21
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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: 41 (21.7 bits)
S2: 53 (24.2 bits)