RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17588
(62 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 = 56.1 bits (136), Expect = 4e-12
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 1 MSLMKEPPPGMEVDSDKAEQNLNLWTIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSPECT 60
L+K+PPPG+ + NL W + + G EGT Y+G F+L +F YPF P+
Sbjct: 7 KELLKDPPPGISAFPV--DDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVK 64
>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 = 48.7 bits (117), Expect = 3e-09
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 1 MSLMKEPPPGMEVDSDKAEQNLNLWTIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSP 57
L K+PP G+ + E+NL W ++G T Y+G F+L +F YPF P
Sbjct: 9 KDLKKDPPSGISAEPV--EENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPP 63
>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 = 48.1 bits (115), Expect = 6e-09
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 1 MSLMKEPPPGMEVDSDKAEQNLNLWTIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSPECT 60
L K+PPPG ++NL WT + G GT Y+G F+L +F YPF P+
Sbjct: 7 KELRKDPPPG-FTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVK 65
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 38.2 bits (89), Expect = 4e-05
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 1 MSLMKEPPPGMEVDSDKAEQNLNLWTIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSPE 58
+L +PPPG++ + D N + I M+G +GT Y+G ++L+ +YP + P+
Sbjct: 12 QNLANDPPPGIKAEPD--PGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPK 67
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 32.6 bits (75), Expect = 0.003
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 1 MSLMKEPPPGM---EVDSDKAEQNLNLWTIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSP 57
L K+PPPG+ VD D NL W + G T Y+G F+L +F YPF P
Sbjct: 15 KKLQKDPPPGISAGPVDDD----NLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKPP 70
Query: 58 ECT 60
+
Sbjct: 71 KVR 73
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 28.9 bits (64), Expect = 0.082
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 3 LMKEPPPGMEVDSDKAEQNLNLWTIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSPE 58
L+K+PP + +++NL WT + G + Y G F L F P YPF P+
Sbjct: 13 LLKDPPS--NCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPK 66
>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 = 25.4 bits (56), Expect = 1.8
Identities = 6/33 (18%), Positives = 11/33 (33%)
Query: 26 TIHMKGAEGTLYDGEEFQLQFKFGPKYPFDSPE 58
+ + +E L F YP + P+
Sbjct: 36 KLKLLTSEAESSPLVSLVLTFTLPEDYPDEPPK 68
>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 = 23.1 bits (50), Expect = 9.7
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 41 EFQLQFKFGPKYPFDSPE 58
LQ K YP ++P
Sbjct: 42 SLTLQVKLPENYPDEAPP 59
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
0.313 0.135 0.417
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: 3,044,609
Number of extensions: 195822
Number of successful extensions: 94
Number of sequences better than 10.0: 1
Number of HSP's gapped: 94
Number of HSP's successfully gapped: 8
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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: 53 (24.2 bits)