RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11956
(126 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 = 85.3 bits (212), Expect = 2e-22
Identities = 27/51 (52%), Positives = 36/51 (70%)
Query: 31 LKEFCVKFFGPRDTPYEGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNIDE 81
L E+ GP DTPYEGG++K+ + PE YPFK P + F+ K+YHPN+DE
Sbjct: 28 LLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVDE 78
Score = 68.4 bits (168), Expect = 7e-16
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 64 KSPSIGFMNKMYHPNIDEVSAVF-------YYGGVWKVRVHLPEHYPFKSPSIGFMNKMY 116
K P G + N+ E Y GG++K+ + PE YPFK P + F+ K+Y
Sbjct: 13 KDPPSGISAEPVEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIY 72
Query: 117 HPNIDE 122
HPN+DE
Sbjct: 73 HPNVDE 78
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 85.8 bits (213), Expect = 2e-22
Identities = 33/86 (38%), Positives = 48/86 (55%), Gaps = 6/86 (6%)
Query: 1 MSSASAGNRRMNIDVIKLIESKHEGTTLK-----GLKEFCVKFFGPRDTPYEGGVWKVRV 55
MSS SA +R+ ++ KL + G + L + GP DTPYEGG++K+ +
Sbjct: 1 MSSPSA-LKRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTL 59
Query: 56 HLPEHYPFKSPSIGFMNKMYHPNIDE 81
PE YPFK P + F K++HPN+D
Sbjct: 60 EFPEDYPFKPPKVRFTTKIFHPNVDP 85
>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 = 83.4 bits (207), Expect = 1e-21
Identities = 27/51 (52%), Positives = 34/51 (66%)
Query: 31 LKEFCVKFFGPRDTPYEGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNIDE 81
L E+ V GP TPYEGGV+K+ + PE YPFK P + F K+YHPN+D
Sbjct: 26 LFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNVDP 76
Score = 66.1 bits (162), Expect = 6e-15
Identities = 27/70 (38%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 64 KSPSIGFMNKMYHPNIDEVSAVF-------YYGGVWKVRVHLPEHYPFKSPSIGFMNKMY 116
K P G N+ E Y GGV+K+ + PE YPFK P + F K+Y
Sbjct: 11 KDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIY 70
Query: 117 HPNIDEVSGE 126
HPN+D SGE
Sbjct: 71 HPNVDP-SGE 79
>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 = 81.2 bits (201), Expect = 7e-21
Identities = 26/60 (43%), Positives = 35/60 (58%)
Query: 22 KHEGTTLKGLKEFCVKFFGPRDTPYEGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNIDE 81
+ L E+ GP TPYEGGV+K+ + PE YPFK P + F+ K+YHPN+D
Sbjct: 18 TAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVDS 77
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 65.6 bits (160), Expect = 1e-14
Identities = 24/54 (44%), Positives = 35/54 (64%)
Query: 29 KGLKEFCVKFFGPRDTPYEGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNIDEV 82
+ F + GP TPYEGG +K+ + LPE YP + P + F+ K+YHPNID++
Sbjct: 29 GNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKL 82
Score = 52.1 bits (125), Expect = 2e-09
Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 87 YYGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNIDEV 123
Y GG +K+ + LPE YP + P + F+ K+YHPNID++
Sbjct: 46 YEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKL 82
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 54.0 bits (129), Expect = 3e-10
Identities = 22/50 (44%), Positives = 30/50 (60%)
Query: 31 LKEFCVKFFGPRDTPYEGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNID 80
L + GP D+PY GGV+ + + P YPFK P + F K+YHPNI+
Sbjct: 30 LFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNIN 79
Score = 43.2 bits (101), Expect = 4e-06
Identities = 17/35 (48%), Positives = 23/35 (65%)
Query: 87 YYGGVWKVRVHLPEHYPFKSPSIGFMNKMYHPNID 121
Y GGV+ + + P YPFK P + F K+YHPNI+
Sbjct: 45 YAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNIN 79
>gnl|CDD|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional.
Length = 264
Score = 30.3 bits (68), Expect = 0.21
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 1/60 (1%)
Query: 13 IDVIKLIESKHEGTTLKG-LKEFCVKFFGPRDTPYEGGVWKVRVHLPEHYPFKSPSIGFM 71
ID L + G+ KG KEF V FG +G + LP P+ SPS G
Sbjct: 156 IDAQSLGRVRWYGSGDKGQTKEFPVPTFGAHGLEIDGKLVDPVGGLPLLSPYTSPSHGEH 215
>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 = 27.7 bits (62), Expect = 0.99
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 3/40 (7%)
Query: 32 KEFCVKF-FGPRDTPYEGGVWKVR--VHLPEHYPFKSPSI 68
+ + P E + V LPE+YP ++P I
Sbjct: 21 RIPEITIKLSPSSDEGEDQYVSLTLQVKLPENYPDEAPPI 60
Score = 26.6 bits (59), Expect = 2.3
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 93 KVRVHLPEHYPFKSPSI 109
++V LPE+YP ++P I
Sbjct: 44 TLQVKLPENYPDEAPPI 60
>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 27.4 bits (62), Expect = 1.9
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 12/42 (28%)
Query: 28 LKG-LKEFCVKFFGPRDTPYEGGVWKVRVHL-PEHYPFKSPS 67
LKG L++F FFG V++ P ++PF PS
Sbjct: 225 LKGTLEDFLKAFFGE----------DVKIRFRPSYFPFTEPS 256
>gnl|CDD|227209 COG4872, COG4872, Predicted membrane protein [Function unknown].
Length = 394
Score = 27.1 bits (60), Expect = 2.5
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 67 SIGFMNKMYHPNIDEVSAVFYYG-GVWKVRVHLPEHYPFKSPSIGFM 112
S+ + ++Y+ + D S +G GV Y +S S+ M
Sbjct: 120 SLALIAQIYNISGDTPSLFLAWGLGV------SFMAYSLRSNSLAIM 160
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 27.2 bits (60), Expect = 2.8
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 25 GTTLKGLKEFCVKFFGPRDTPY 46
G + + +C + F P+ PY
Sbjct: 1055 GIKGETIGPYCKELFNPQGLPY 1076
>gnl|CDD|182663 PRK10707, PRK10707, putative NUDIX hydrolase; Provisional.
Length = 190
Score = 26.5 bits (59), Expect = 3.3
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 14/46 (30%)
Query: 52 KVRV--HLPEHYPFKS-------PSIGFM--NKMYHPNIDEVSAVF 86
V V LP P S P +G + + Y N DEV+AVF
Sbjct: 94 AVEVIGVLP---PVDSSTGYQVTPVVGIIPPDLPYRANEDEVAAVF 136
>gnl|CDD|99899 cd05838, WHSC1_related, The PWWP domain was first identified in
the WHSC1 (Wolf-Hirschhorn syndrome candidate 1)
protein, a protein implicated in Wolf-Hirschhorn
syndrome (WHS). When translocated, WHSC1 plays a role
in lymphoid multiple myeloma (MM) disease, also known
as plasmacytoma. WHCS1 proteins typically contain two
copies of the PWWP domain. The PWWP domain, named for
a conserved Pro-Trp-Trp-Pro motif, is a small domain
consisting of 100-150 amino acids. The PWWP domain is
found in numerous proteins that are involved in cell
division, growth and differentiation. Most PWWP-domain
proteins seem to be nuclear, often DNA-binding,
proteins that function as transcription factors
regulating a variety of developmental processes.
Length = 95
Score = 25.7 bits (57), Expect = 3.4
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 33 EFCVKFFGPRD 43
EFCV FFG D
Sbjct: 40 EFCVMFFGTHD 50
>gnl|CDD|236263 PRK08425, flgE, flagellar hook protein FlgE; Validated.
Length = 731
Score = 26.6 bits (59), Expect = 4.3
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 14/59 (23%)
Query: 1 MSSASAGNRRMNIDVIKLIESKHEGTTLKGLKEFCVKFFGPRDTPYEGGVWKVRVHLPE 59
++ +A ID+ + SKH TL+ ++F+ T G W + + +PE
Sbjct: 487 HATHAAS-----IDIYDSLGSKH---TLR------IEFYKSSTTQDGGAEWNMIIIVPE 531
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 25.8 bits (57), Expect = 8.9
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 27 TLKGLKEFCVKFFGPRDTPYEGGVWKVRVHL 57
TL ++E+ V GP TP GG+ + V L
Sbjct: 81 TLDLIREYRVAIKGPLTTPVGGGIRSLNVAL 111
>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 = 25.0 bits (55), Expect = 8.9
Identities = 10/60 (16%), Positives = 21/60 (35%), Gaps = 4/60 (6%)
Query: 13 IDVIKLI--ESKHEGTTLKGLKEFCVKFFGPRDTPYEGGVWKVRVH--LPEHYPFKSPSI 68
++ ++ I + + F +K + + + LPE YP + P I
Sbjct: 10 LEALESIYPDEFEDEVKESSPPTFTIKLKLLTSEAESSPLVSLVLTFTLPEDYPDEPPKI 69
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
0.320 0.139 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: 6,634,895
Number of extensions: 577107
Number of successful extensions: 421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 420
Number of HSP's successfully gapped: 34
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (21.8 bits)
S2: 53 (24.2 bits)