RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3655
(194 letters)
>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 = 150 bits (382), Expect = 3e-47
Identities = 68/140 (48%), Positives = 79/140 (56%), Gaps = 34/140 (24%)
Query: 19 YSSLTFISPPSI-----GDNLYEWVSTILGPPGSVYEGGVFFLDIHFSPEYPFKPPKVTF 73
L PP I DNL+EW TI+GP G+ YEGGVF LDI F +YPFKPPKV F
Sbjct: 6 LKELLKDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKF 65
Query: 74 RTRIYHCNINSQGVICLDILKDNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTI 133
T+IYH N++ G ICLDILKD +NWSPALTI
Sbjct: 66 TTKIYHPNVDPSGEICLDILKD-----------------------------ENWSPALTI 96
Query: 134 SKVLLSICSLLTDCNPADPL 153
+VLLSI SLL++ NP DPL
Sbjct: 97 EQVLLSIQSLLSEPNPEDPL 116
>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 = 145 bits (368), Expect = 6e-45
Identities = 62/135 (45%), Positives = 76/135 (56%), Gaps = 29/135 (21%)
Query: 23 TFISPPSIGDNLYEWVSTILGPPGSVYEGGVFFLDIHFSPEYPFKPPKVTFRTRIYHCNI 82
F + P +NL EW TI+GPPG+ YEGGVF L I F +YPFKPPKV F T+IYH N+
Sbjct: 16 GFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNV 75
Query: 83 NSQGVICLDILKDNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTISKVLLSICS 142
+S G ICLDILK ++ WSPALT+ VLLS+ S
Sbjct: 76 DSSGEICLDILK-----------------------------QEKWSPALTLETVLLSLQS 106
Query: 143 LLTDCNPADPLVAKH 157
LL++ NP PL A
Sbjct: 107 LLSEPNPDSPLNADA 121
>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 = 144 bits (365), Expect = 1e-44
Identities = 57/126 (45%), Positives = 69/126 (54%), Gaps = 29/126 (23%)
Query: 30 IGDNLYEWVSTILGPPGSVYEGGVFFLDIHFSPEYPFKPPKVTFRTRIYHCNINSQGVIC 89
+ +NL EW TI GPP + YEGG+F LDI F +YPFKPPKV F T+IYH N++ G IC
Sbjct: 24 VEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVDENGKIC 83
Query: 90 LDILKDNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTISKVLLSICSLLTDCNP 149
L ILK WSPA T+ VLLS+ SLL + NP
Sbjct: 84 LSILKT-----------------------------HGWSPAYTLRTVLLSLQSLLNEPNP 114
Query: 150 ADPLVA 155
+DPL A
Sbjct: 115 SDPLNA 120
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 141 bits (358), Expect = 3e-43
Identities = 52/128 (40%), Positives = 66/128 (51%), Gaps = 30/128 (23%)
Query: 28 PSIGDNLYEWVSTILGPPGSVYEGGVFFLDIHFSPEYPFKPPKVTFRTRIYHCNINSQGV 87
P DNL+ W +TI GPP + YEGG+F L + F +YPFKPPKV F T+I+H N++
Sbjct: 29 PVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKPPKVRFTTKIFHPNVDP--- 85
Query: 88 ICLDILKDNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTISKVLLSICSLLTDC 147
G +CLDILKD WSP T+ +LLS+ SLL
Sbjct: 86 ---------------------------SGNVCLDILKDRWSPVYTLETILLSLQSLLLSP 118
Query: 148 NPADPLVA 155
NP PL
Sbjct: 119 NPDSPLNT 126
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 129 bits (325), Expect = 1e-38
Identities = 71/157 (45%), Positives = 85/157 (54%), Gaps = 36/157 (22%)
Query: 27 PPS------IGDNLYEWVSTILGPPGSVYEGGVFFLDIHFSPEYPFKPPKVTFRTRIYHC 80
PPS +NL+ W ++I+GP S Y GGVFFL I F P+YPFKPPKV F T+IYH
Sbjct: 17 PPSNCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHP 76
Query: 81 NINSQGVICLDILKDNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTISKVLLSI 140
NINS G ICLDIL+ D WSPALT+SKVLLSI
Sbjct: 77 NINSNGSICLDILR------------------------------DQWSPALTVSKVLLSI 106
Query: 141 CSLLTDCNPADPLVAKHSDTVSTKQGRTRSDVQTMDQ 177
SLLTD NP DPLV + + + R + + Q
Sbjct: 107 SSLLTDPNPDDPLVPEIARVFKENRSRYEATAREWTQ 143
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 96.0 bits (239), Expect = 1e-25
Identities = 56/140 (40%), Positives = 67/140 (47%), Gaps = 38/140 (27%)
Query: 26 SPPSIG-----DNLYEWVSTILGPPGSVYEGGVFFLDIHFSPEYPFKPPKVTFRTRIYHC 80
PP I N + + GP G+ YEGG + L++ +YP +PPKV F T+IYH
Sbjct: 18 PPPGIKAEPDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHP 77
Query: 81 NINSQGVICLDILKDNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTISKVLLSI 140
NI D L G ICLDILKD WSPAL I VLLSI
Sbjct: 78 NI--------DKL----------------------GRICLDILKDKWSPALQIRTVLLSI 107
Query: 141 CSLLTDCNPADPL---VAKH 157
+LL+ P DPL VA H
Sbjct: 108 QALLSAPEPDDPLDTSVADH 127
>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 = 28.8 bits (65), Expect = 0.71
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 54 FFLDIHFSPEYPFKPPKVTFRT 75
L +YP +PPK++ +
Sbjct: 52 LVLTFTLPEDYPDEPPKISLSS 73
>gnl|CDD|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
Length = 289
Score = 28.5 bits (64), Expect = 1.9
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 161 VSTKQGRTRSDVQTMDQTLCHAE-SLNA 187
++T G + SDV+ MD L + SLNA
Sbjct: 154 IATALGVSLSDVEMMDARLSGPDASLNA 181
>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 = 26.9 bits (60), Expect = 3.4
Identities = 4/21 (19%), Positives = 8/21 (38%)
Query: 54 FFLDIHFSPEYPFKPPKVTFR 74
L + YP + P ++
Sbjct: 43 LTLQVKLPENYPDEAPPISLL 63
>gnl|CDD|237789 PRK14690, PRK14690, molybdopterin biosynthesis protein MoeA;
Provisional.
Length = 419
Score = 27.6 bits (61), Expect = 4.5
Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 99 PALTPFYCSILCLDLNQGV------ICLDILKDNWSPALTISKVLLS 139
P LTP C L GV LD+L+ P I ++ LS
Sbjct: 2 PPLTPPPLKNDCFALPPGVDWTPVDTALDLLRARLGPVTDIKELDLS 48
>gnl|CDD|198449 cd10481, EphR_LBD_A3, Ligand Binding Domain of Ephrin type-A
Receptor 3. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphA3 has been implicated in leukemia, lung and
other cancers. EphRs contain a ligand binding domain and
two fibronectin repeats extracellularly, a transmembrane
segment, and a cytoplasmic tyrosine kinase domain.
Binding of the ephrin ligand to EphR requires cell-cell
contact since both are anchored to the plasma membrane.
The resulting downstream signals occur bidirectionally
in both EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling). Ephrin/EphR
interaction mainly results in cell-cell repulsion or
adhesion.
Length = 173
Score = 26.6 bits (58), Expect = 7.0
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 95 DNWSPALTPFYCSILCLDLNQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLV 154
++++P T C+++ D +Q + L+ NW P + K+ + + L DCN + PLV
Sbjct: 32 EHYTPIRTYQVCNVM--DHSQN----NWLRTNWIPRNSAQKIYVELKFTLRDCN-SIPLV 84
>gnl|CDD|203324 pfam05743, UEV, UEV domain. This family includes the eukaryotic
tumour susceptibility gene 101 protein (TSG101). Altered
transcripts of this gene have been detected in sporadic
breast cancers and many other human malignancies.
However, the involvement of this gene in neoplastic
transformation and tumorigenesis is still elusive.
TSG101 is required for normal cell function of embryonic
and adult tissues but that this gene is not a tumour
suppressor for sporadic forms of breast cancer. This
family is related to the ubiquitin conjugating enzymes.
Length = 119
Score = 26.1 bits (58), Expect = 8.6
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 6/43 (13%)
Query: 63 EYPFKPPKV-----TFRTRIYHCNINSQGVICLDILKDNWSPA 100
YPF PP + ++++QG + L L NW+
Sbjct: 59 TYPFSPPICFVKPTPDMVIKVNHHVDAQGRVYLPYL-HNWNHP 100
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
0.322 0.138 0.444
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: 9,586,568
Number of extensions: 859032
Number of successful extensions: 543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 536
Number of HSP's successfully gapped: 18
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.4 bits)