RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17486
(172 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 = 111 bits (281), Expect = 4e-32
Identities = 38/79 (48%), Positives = 54/79 (68%), Gaps = 2/79 (2%)
Query: 19 SVKFLTKIWHPNISSVTGAICLDILKDQ-WAAAMTLRTVLLSLQALMAAAEPDDPQDAVV 77
VKF TKI+HPN+ +G ICLDILKD+ W+ A+T+ VLLS+Q+L++ P+DP +A
Sbjct: 62 KVKFTTKIYHPNVDP-SGEICLDILKDENWSPALTIEQVLLSIQSLLSEPNPEDPLNAEA 120
Query: 78 AKQYKENPEMFTLTARHWT 96
AK Y++N E F R +
Sbjct: 121 AKLYRKNREEFEKKVREYV 139
>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 = 111 bits (281), Expect = 4e-32
Identities = 44/79 (55%), Positives = 52/79 (65%), Gaps = 2/79 (2%)
Query: 19 SVKFLTKIWHPNISSVTGAICLDILKDQ-WAAAMTLRTVLLSLQALMAAAEPDDPQDAVV 77
V+F+TKI+HPN+ G ICL ILK W+ A TLRTVLLSLQ+L+ P DP +A
Sbjct: 64 KVRFVTKIYHPNVDE-NGKICLSILKTHGWSPAYTLRTVLLSLQSLLNEPNPSDPLNAEA 122
Query: 78 AKQYKENPEMFTLTARHWT 96
AK YKEN E F AR WT
Sbjct: 123 AKLYKENREEFKKKAREWT 141
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 111 bits (280), Expect = 6e-32
Identities = 46/82 (56%), Positives = 57/82 (69%), Gaps = 1/82 (1%)
Query: 20 VKFLTKIWHPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALMAAAEPDDPQDAVVAK 79
V+FLTKI+HPNI + G ICLDILKD+W+ A+ +RTVLLS+QAL++A EPDDP D VA
Sbjct: 68 VRFLTKIYHPNIDKL-GRICLDILKDKWSPALQIRTVLLSIQALLSAPEPDDPLDTSVAD 126
Query: 80 QYKENPEMFTLTARHWTNVYAG 101
+K N AR W YA
Sbjct: 127 HFKNNRADAEKVAREWNQKYAK 148
>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 = 106 bits (267), Expect = 5e-30
Identities = 46/84 (54%), Positives = 60/84 (71%), Gaps = 2/84 (2%)
Query: 19 SVKFLTKIWHPNISSVTGAICLDILK-DQWAAAMTLRTVLLSLQALMAAAEPDDPQDAVV 77
VKF+TKI+HPN+ S +G ICLDILK ++W+ A+TL TVLLSLQ+L++ PD P +A
Sbjct: 63 KVKFITKIYHPNVDS-SGEICLDILKQEKWSPALTLETVLLSLQSLLSEPNPDSPLNADA 121
Query: 78 AKQYKENPEMFTLTARHWTNVYAG 101
A+ YK+N E F AR WT YA
Sbjct: 122 AELYKKNREEFKKKAREWTKKYAE 145
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 103 bits (259), Expect = 8e-29
Identities = 37/82 (45%), Positives = 52/82 (63%), Gaps = 1/82 (1%)
Query: 19 SVKFLTKIWHPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALMAAAEPDDPQDAVVA 78
V+F TKI+HPN+ +G +CLDILKD+W+ TL T+LLSLQ+L+ + PD P + A
Sbjct: 71 KVRFTTKIFHPNVDP-SGNVCLDILKDRWSPVYTLETILLSLQSLLLSPNPDSPLNTEAA 129
Query: 79 KQYKENPEMFTLTARHWTNVYA 100
Y+E+ E + R W YA
Sbjct: 130 TLYREDKEEYEKKVREWVKKYA 151
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 86.0 bits (212), Expect = 6e-22
Identities = 42/81 (51%), Positives = 57/81 (70%), Gaps = 1/81 (1%)
Query: 20 VKFLTKIWHPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALMAAAEPDDPQDAVVAK 79
V+F TKI+HPNI+S G+ICLDIL+DQW+ A+T+ VLLS+ +L+ PDDP +A+
Sbjct: 67 VQFTTKIYHPNINS-NGSICLDILRDQWSPALTVSKVLLSISSLLTDPNPDDPLVPEIAR 125
Query: 80 QYKENPEMFTLTARHWTNVYA 100
+KEN + TAR WT YA
Sbjct: 126 VFKENRSRYEATAREWTQRYA 146
>gnl|CDD|238116 cd00194, UBA, Ubiquitin Associated domain. The UBA domain is a
commonly occurring sequence motif in some members of the
ubiquitination pathway, UV excision repair proteins, and
certain protein kinases. Although its specific role is
so far unknown, it has been suggested that UBA domains
are involved in conferring protein target specificity.
The domain, a compact three helix bundle, has a
conserved GFP-loop and the proline is thought to be
critical for binding. The UBA domain is distinct from
the conserved three helical domain seen in the
N-terminus of EF-TS and eukaryotic NAC proteins.
Length = 38
Score = 36.3 bits (85), Expect = 3e-04
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 136 DSKIQRLTDMGVMSHDARVALSTYNWELERATEAIF 171
+ K+++L +MG +AR AL N +ERA E +
Sbjct: 2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLL 37
>gnl|CDD|197551 smart00165, UBA, Ubiquitin associated domain. Present in Rad23,
SNF1-like kinases. The newly-found UBA in p62 is known
to bind ubiquitin.
Length = 37
Score = 35.2 bits (82), Expect = 7e-04
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 136 DSKIQRLTDMGVMSHDARVALSTYNWELERATEAIF 171
+ KI +L +MG +A AL N +ERA E +
Sbjct: 2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37
>gnl|CDD|201355 pfam00627, UBA, UBA/TS-N domain. This small domain is composed of
three alpha helices. This family includes the previously
defined UBA and TS-N domains. The UBA-domain (ubiquitin
associated domain) is a novel sequence motif found in
several proteins having connections to ubiquitin and the
ubiquitination pathway. The structure of the UBA domain
consists of a compact three helix bundle. This domain is
found at the N terminus of EF-TS hence the name TS-N.
The structure of EF-TS is known and this domain is
implicated in its interaction with EF-TU. The domain has
been found in non EF-TS proteins such as alpha-NAC and
MJ0280.
Length = 37
Score = 32.0 bits (74), Expect = 0.012
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 136 DSKIQRLTDMGVMSHDARVALSTYNWELERATE 168
+ I++L +MG +A+ AL N +ERA E
Sbjct: 3 EELIKQLREMGFSREEAKKALRATNGNVERAVE 35
>gnl|CDD|201127 pfam00273, Serum_albumin, Serum albumin family.
Length = 178
Score = 28.1 bits (63), Expect = 1.7
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 68 EPDDPQDAVVAKQYKENPEMFT------LTARHWTNVYAGV---VAKQYKE 109
+ D P+ V + YKE+P+ F + RH ++Y +AK+Y+E
Sbjct: 114 KTDFPEPEEVCQAYKEDPDKFLGRFLYEYSRRH-PDLYVPELLRLAKEYEE 163
>gnl|CDD|214517 smart00103, ALBUMIN, serum albumin.
Length = 187
Score = 28.0 bits (63), Expect = 1.7
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 18/64 (28%)
Query: 64 MAAAEPDD----------PQDAVVAKQYKENPEMFTLT-----ARHWTNVYAGV---VAK 105
A + D+ P+D V + Y+E+ ++F +R + VAK
Sbjct: 107 FLALKNDEVPPELPPDKFPEDKDVCQAYEEDKDVFLGKFLYELSRRHPELSEPQLLRVAK 166
Query: 106 QYKE 109
+Y+
Sbjct: 167 EYEA 170
>gnl|CDD|221051 pfam11265, Med25_VWA, Mediator complex subunit 25 von Willebrand
factor type A. The overall function of the full-length
Med25 is efficiently to coordinate the transcriptional
activation of RAR/RXR (retinoic acid receptor/retinoic X
receptor) in higher eukaryotic cells. Human Med25
consists of several domains with different binding
properties, the N-terminal, VWA domain which is this
one, an SD2 domain from residues 229-381, a PTOV(B) or
ACID domain from 395-545, an SD2 domain from residues
564-645 and a C-terminal NR box-containing domain
(646-650) from 646-747. This VWA or von Willebrand
factor type A domain when bound to RAR and the histone
acetyltransferase CBP is responsible for recruiting Med1
to the rest of the Mediator complex.
Length = 226
Score = 27.9 bits (62), Expect = 2.2
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 45 DQWAAAMTLRTVLLS---------LQALMAAAEPDDPQDAVVAKQYKENP 85
DQ AA + R + LS L+ L A+PD + Y +NP
Sbjct: 167 DQLAAIIYERGIHLSIIAPRKLPALRLLFEKAKPDQQLPMKSSIDYAKNP 216
>gnl|CDD|151921 pfam11483, DUF3209, Protein of unknown function (DUF3209). This
family of proteins has no known function.
Length = 122
Score = 27.1 bits (60), Expect = 2.9
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 28 HPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALMAAAEPDDPQ 73
P I ++ A L L+ L L+ L+ +AA EP+DP+
Sbjct: 36 EPPIEALAEAKTLAALERH------LDAALVDLEEEIAATEPEDPE 75
>gnl|CDD|131423 TIGR02370, pyl_corrinoid, methyltransferase cognate corrinoid
proteins, Methanosarcina family. This model describes a
subfamily of the B12 binding domain (pfam02607,
pfam02310) proteins. Members of the seed alignment
include corrinoid proteins specific to four different,
mutally non-homologous enzymes of the genus
Methanosarcina. Three of the four cognate enzymes
(trimethylamine, dimethylamine, and monomethylamine
methyltransferases) all have the unusual, ribosomally
incorporated amino acid pyrrolysine at the active site.
All act in systems in which a methyl group is
transferred to the corrinoid protein to create
methylcobalamin, from which the methyl group is later
transferred elsewhere.
Length = 197
Score = 27.5 bits (61), Expect = 3.0
Identities = 22/71 (30%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 70 DDPQDAVVAKQYKENPEMFTLTARHWTNVYAGV-VAKQYKENPEMFTLTARHWTNVYAGG 128
D P D VV K KE P M T +A T +Y + + KE R GG
Sbjct: 121 DVPIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDKLKEE------GYRDSVKFMVGG 174
Query: 129 PSKNPDFDSKI 139
D+ KI
Sbjct: 175 APVTQDWADKI 185
>gnl|CDD|202976 pfam04340, DUF484, Protein of unknown function, DUF484. This
family consists of several proteins of uncharacterized
function.
Length = 219
Score = 27.0 bits (60), Expect = 4.5
Identities = 9/41 (21%), Positives = 17/41 (41%)
Query: 130 SKNPDFDSKIQRLTDMGVMSHDARVALSTYNWELERATEAI 170
++P+F + L + + H +S +L R E I
Sbjct: 16 RQHPEFFVQHPELLEELRLPHQPANTVSLVERQLARLRERI 56
>gnl|CDD|181927 PRK09522, PRK09522, bifunctional glutamine
amidotransferase/anthranilate phosphoribosyltransferase;
Provisional.
Length = 531
Score = 27.3 bits (60), Expect = 4.6
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 105 KQYKENPEMFTLTARHWTNVYAGGPSKNPDFDSKIQRLTDMGVMSHDARVA 155
K Y+ E F LT H + G P +N D +++ L G +H+A VA
Sbjct: 441 KSYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRL--LQGKGDAAHEAAVA 489
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
0.319 0.129 0.397
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: 8,743,088
Number of extensions: 785197
Number of successful extensions: 723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 28
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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: 55 (24.9 bits)