RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12515
(174 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 = 142 bits (360), Expect = 4e-44
Identities = 48/103 (46%), Positives = 70/103 (67%)
Query: 62 DNPPYNKGAFKIEINFPAEYPFKPPKINFKTKIYHPNIDEKGQVCLPIISAENWKPATKT 121
+ PY G FK++I FP +YPFKPPK+ F TKIYHPN+D G++CL I+ ENW PA
Sbjct: 37 EGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNVDPSGEICLDILKDENWSPALTI 96
Query: 122 DQVIQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYT 164
+QV+ ++ +L+++P PE PL A+ A + K R++F K +Y
Sbjct: 97 EQVLLSIQSLLSEPNPEDPLNAEAAKLYRKNREEFEKKVREYV 139
>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 = 140 bits (355), Expect = 2e-43
Identities = 51/108 (47%), Positives = 74/108 (68%)
Query: 62 DNPPYNKGAFKIEINFPAEYPFKPPKINFKTKIYHPNIDEKGQVCLPIISAENWKPATKT 121
PY G FK+ I FP +YPFKPPK+ F TKIYHPN+D G++CL I+ E W PA
Sbjct: 38 PGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVDSSGEICLDILKQEKWSPALTL 97
Query: 122 DQVIQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYTKKHSE 169
+ V+ +L +L+++P P+ PL AD A+ + K R++F K A ++TKK++E
Sbjct: 98 ETVLLSLQSLLSEPNPDSPLNADAAELYKKNREEFKKKAREWTKKYAE 145
>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 = 140 bits (354), Expect = 3e-43
Identities = 48/117 (41%), Positives = 70/117 (59%), Gaps = 3/117 (2%)
Query: 48 LSYFQYYFFPLEFQDNPPYNKGAFKIEINFPAEYPFKPPKINFKTKIYHPNIDEKGQVCL 107
L + + PY G FK++I FP +YPFKPPK+ F TKIYHPN+DE G++CL
Sbjct: 28 LLEWHGTIRGPP---DTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVDENGKICL 84
Query: 108 PIISAENWKPATKTDQVIQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYT 164
I+ W PA V+ +L +L+N+P P PL A+ A + + R++F K A ++T
Sbjct: 85 SILKTHGWSPAYTLRTVLLSLQSLLNEPNPSDPLNAEAAKLYKENREEFKKKAREWT 141
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 112 bits (282), Expect = 3e-32
Identities = 41/106 (38%), Positives = 68/106 (64%), Gaps = 1/106 (0%)
Query: 65 PYNKGAFKIEINFPAEYPFKPPKINFKTKIYHPNIDEKGQVCLPIISAENWKPATKTDQV 124
PY G FK+ + FP +YPFKPPK+ F TKI+HPN+D G VCL I+ + W P + +
Sbjct: 49 PYEGGIFKLTLEFPEDYPFKPPKVRFTTKIFHPNVDPSGNVCLDILK-DRWSPVYTLETI 107
Query: 125 IQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYTKKHSEK 170
+ +L +L+ P P+ PL + A + ++++++ K ++ KK++EK
Sbjct: 108 LLSLQSLLLSPNPDSPLNTEAATLYREDKEEYEKKVREWVKKYAEK 153
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 94.0 bits (233), Expect = 5e-25
Identities = 42/106 (39%), Positives = 68/106 (64%), Gaps = 1/106 (0%)
Query: 63 NPPYNKGAFKIEINFPAEYPFKPPKINFKTKIYHPNIDEKGQVCLPIISAENWKPATKTD 122
+ PY G F + I FP +YPFKPPK+ F TKIYHPNI+ G +CL I+ + W PA
Sbjct: 42 DSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNINSNGSICLDILR-DQWSPALTVS 100
Query: 123 QVIQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYTKKHS 168
+V+ ++ +L+ DP P+ PL ++A F + R ++ A ++T++++
Sbjct: 101 KVLLSISSLLTDPNPDDPLVPEIARVFKENRSRYEATAREWTQRYA 146
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 91.0 bits (226), Expect = 8e-24
Identities = 45/118 (38%), Positives = 74/118 (62%), Gaps = 1/118 (0%)
Query: 51 FQYYFFPLEFQDNPPYNKGAFKIEINFPAEYPFKPPKINFKTKIYHPNIDEKGQVCLPII 110
++++ +E D PY G +K+E+ P +YP +PPK+ F TKIYHPNID+ G++CL I+
Sbjct: 31 YRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDIL 90
Query: 111 SAENWKPATKTDQVIQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYTKKHS 168
+ W PA + V+ ++ AL++ PEP+ PL +AD F R K A ++ +K++
Sbjct: 91 K-DKWSPALQIRTVLLSIQALLSAPEPDDPLDTSVADHFKNNRADAEKVAREWNQKYA 147
>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 = 33.8 bits (78), Expect = 0.012
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 12/84 (14%)
Query: 57 PLEFQDNPPYNKGAFKIEINFPAEYPFKPPKI-----NFKTKIYHPNIDEKGQVCLPIIS 111
P+ ++ N YN I I P YPF PP + ++D +G+V LP +
Sbjct: 40 PVTYRGNT-YN---IPILIWLPDTYPFSPPICFVKPTPDMVIKVNHHVDAQGRVYLPYLH 95
Query: 112 AENWKPATKT-DQVIQALIALVND 134
NW + ++Q L + +
Sbjct: 96 --NWNHPSSNLVDLVQELAQVFGE 117
>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 = 31.5 bits (72), Expect = 0.066
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 5/60 (8%)
Query: 38 IFSLKFKPWVLSY----FQYYFFPLEFQDNPPYNKGAFKIEINFPAEYPFKPPKINFKTK 93
I+ +F+ V F L + + + P +YP +PPKI+ +
Sbjct: 16 IYPDEFEDEVKESSPPTFTIKLKLLTSEAESSPLV-SLVLTFTLPEDYPDEPPKISLSSP 74
>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 = 29.6 bits (67), Expect = 0.29
Identities = 7/42 (16%), Positives = 13/42 (30%), Gaps = 2/42 (4%)
Query: 50 YFQYYFFPLEFQDNPPYNKGAFKIEINFPAEYPFKPPKINFK 91
P D + +++ P YP + P I+
Sbjct: 24 EITIKLSPSS--DEGEDQYVSLTLQVKLPENYPDEAPPISLL 63
>gnl|CDD|227635 COG5325, COG5325, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 283
Score = 28.7 bits (64), Expect = 1.4
Identities = 9/49 (18%), Positives = 12/49 (24%), Gaps = 1/49 (2%)
Query: 126 QALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYTKKHSEKRPSD 174
Q A + E R+ KH+E SD
Sbjct: 24 QHRKEDDALTPTFILSAASVDQELTAVRRSI-SRLGKVYAKHTEPSFSD 71
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 28.4 bits (64), Expect = 2.3
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 8/59 (13%)
Query: 99 IDEKGQVCLPIISAENWKPATKTDQVIQALIALVN--------DPEPEHPLRADLADEF 149
I + V P ++ PA ++V AL L +P+ LA
Sbjct: 547 IADLALVLGPTLNPGEADPAPSAEEVAAALRRLAARLRAAAAKSQDPDAAAAGRLAASL 605
>gnl|CDD|99799 cd06202, Nitric_oxide_synthase, The ferredoxin-reductase (FNR) like
C-terminal domain of the nitric oxide synthase (NOS)
fuses with a heme-containing N-terminal oxidase domain.
The reductase portion is similar in structure to NADPH
dependent cytochrome-450 reductase (CYPOR), having an
inserted connecting sub-domain within the FAD binding
portion of FNR. NOS differs from CYPOR in a requirement
for the cofactor tetrahydrobiopterin and unlike most
CYPOR is dimeric. Nitric oxide synthase produces nitric
oxide in the conversion of L-arginine to L-citruline.
NOS has been implicated in a variety of processes
including cytotoxicity, anti-inflamation,
neurotransmission, and vascular smooth muscle
relaxation.
Length = 406
Score = 27.3 bits (61), Expect = 5.0
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 117 PATKTDQVIQALIA-LVNDPEPEHPLRADLADEFLKERK 154
PA + + V AL+ L + P P+ ++ E L+ER
Sbjct: 42 PANRPELV-DALLDRLHDAPPPDQVIKL----EVLEERS 75
>gnl|CDD|221303 pfam11902, DUF3422, Protein of unknown function (DUF3422). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 426 to 444 amino acids in length.
Length = 419
Score = 27.1 bits (61), Expect = 5.2
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 137 PEHPLRADLADE 148
P+HPLR L +E
Sbjct: 2 PDHPLRRALLNE 13
>gnl|CDD|183726 PRK12756, PRK12756, phospho-2-dehydro-3-deoxyheptonate aldolase;
Provisional.
Length = 348
Score = 26.8 bits (60), Expect = 5.6
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 120 KTDQVIQALIALVNDPEP---EHPLRADLADEFLKERKKFMK--NAED 162
KTD++ A I + P E+P+ D+AD R++ K N ED
Sbjct: 3 KTDELRTARIESLITPAELASEYPITPDVADHVTDSRRRIEKILNGED 50
>gnl|CDD|234583 PRK00029, PRK00029, hypothetical protein; Validated.
Length = 487
Score = 27.0 bits (61), Expect = 5.7
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 115 WKPATKTD-QVIQALIALVNDPEPEHPLRADLA 146
+ A + D ++ L+ ++ P E P A
Sbjct: 439 IEAAEEGDWSELERLLEVLRRPYDEQPEFEAYA 471
>gnl|CDD|224309 COG1391, GlnE, Glutamine synthetase adenylyltransferase
[Posttranslational modification, protein turnover,
chaperones / Signal transduction mechanisms].
Length = 963
Score = 26.9 bits (60), Expect = 7.3
Identities = 12/58 (20%), Positives = 18/58 (31%)
Query: 115 WKPATKTDQVIQALIALVNDPEPEHPLRADLADEFLKERKKFMKNAEDYTKKHSEKRP 172
+ D L + PE A L +E L+ R + D+ H P
Sbjct: 10 SSLSQAADADAALLPLKRLEEAPEAIAAALLGEESLRGRLFAVLALSDFLADHLVAHP 67
>gnl|CDD|215646 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family).
This family contains, amongst other G-protein-coupled
receptors (GCPRs), members of the opsin family, which
have been considered to be typical members of the
rhodopsin superfamily. They share several motifs,
mainly the seven transmembrane helices, GCPRs of the
rhodopsin superfamily. All opsins bind a chromophore,
such as 11-cis-retinal. The function of most opsins
other than the photoisomerases is split into two steps:
light absorption and G-protein activation.
Photoisomerases, on the other hand, are not coupled to
G-proteins - they are thought to generate and supply
the chromophore that is used by visual opsins.
Length = 251
Score = 26.1 bits (58), Expect = 9.3
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 33 CVTDLIFSLKFKPWVLSYFQYYFFPL 58
V DL+F L PW L Y +P
Sbjct: 21 AVADLLFLLTLPPWALYYLVGGDWPF 46
>gnl|CDD|130217 TIGR01147, V_ATP_synt_G, vacuolar ATP synthase, subunit G. This
model describes the vacuolar ATP synthase G subunit in
eukaryotes and includes members from diverse groups
e.g., fungi, plants, parasites etc. V-ATPases are
multi-subunit enzymes composed of two functional
domains: A transmembrane Vo domain and a peripheral
catalytic domain V1. The G subunit is one of the
subunits of the catalytic domain. V-ATPases are
responsible for the acidification of endosomes and
lysosomes, which are part of the central vacuolar system
[Energy metabolism, ATP-proton motive force
interconversion].
Length = 113
Score = 25.6 bits (56), Expect = 9.5
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 118 ATKTDQVIQALIALVNDPEPE 138
D VI+ L+ LV D PE
Sbjct: 89 QKNKDAVIKDLLHLVCDISPE 109
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 0.135 0.424
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: 8,945,367
Number of extensions: 813295
Number of successful extensions: 855
Number of sequences better than 10.0: 1
Number of HSP's gapped: 852
Number of HSP's successfully gapped: 27
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
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: 56 (25.4 bits)