RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15855
(118 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 = 180 bits (458), Expect = 6e-60
Identities = 60/113 (53%), Positives = 77/113 (68%), Gaps = 1/113 (0%)
Query: 1 MIWNAVIFGPHDTPFEDGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLDIL- 59
W I GP TP+E G FKL +EF E+YP KPP V+F +K++HPNV G ICLDIL
Sbjct: 27 FEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNVDPSGEICLDILK 86
Query: 60 QNRWSPTYDVSAILTSIQSLLSDPNPNSPANSMAAQLYKENRREYEKRVKACV 112
WSP + +L SIQSLLS+PNP P N+ AA+LY++NR E+EK+V+ V
Sbjct: 87 DENWSPALTIEQVLLSIQSLLSEPNPEDPLNAEAAKLYRKNREEFEKKVREYV 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 = 178 bits (455), Expect = 2e-59
Identities = 59/113 (52%), Positives = 81/113 (71%), Gaps = 1/113 (0%)
Query: 1 MIWNAVIFGPHDTPFEDGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLDIL- 59
+ W+ I GP DTP+E G FKL +EF E+YP KPP VRF +K++HPNV +G ICL IL
Sbjct: 29 LEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVDENGKICLSILK 88
Query: 60 QNRWSPTYDVSAILTSIQSLLSDPNPNSPANSMAAQLYKENRREYEKRVKACV 112
+ WSP Y + +L S+QSLL++PNP+ P N+ AA+LYKENR E++K+ +
Sbjct: 89 THGWSPAYTLRTVLLSLQSLLNEPNPSDPLNAEAAKLYKENREEFKKKAREWT 141
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 177 bits (451), Expect = 9e-59
Identities = 66/115 (57%), Positives = 85/115 (73%)
Query: 1 MIWNAVIFGPHDTPFEDGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLDILQ 60
W A I GP DTP+E G FKLT+EF E+YP KPP VRF +K+FHPNV G +CLDIL+
Sbjct: 36 FHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKPPKVRFTTKIFHPNVDPSGNVCLDILK 95
Query: 61 NRWSPTYDVSAILTSIQSLLSDPNPNSPANSMAAQLYKENRREYEKRVKACVEQS 115
+RWSP Y + IL S+QSLL PNP+SP N+ AA LY+E++ EYEK+V+ V++
Sbjct: 96 DRWSPVYTLETILLSLQSLLLSPNPDSPLNTEAATLYREDKEEYEKKVREWVKKY 150
>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 = 169 bits (431), Expect = 9e-56
Identities = 60/118 (50%), Positives = 84/118 (71%), Gaps = 1/118 (0%)
Query: 1 MIWNAVIFGPHDTPFEDGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLDIL- 59
+ W I GP TP+E G FKLT+EF E+YP KPP V+F +K++HPNV + G ICLDIL
Sbjct: 28 LEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVDSSGEICLDILK 87
Query: 60 QNRWSPTYDVSAILTSIQSLLSDPNPNSPANSMAAQLYKENRREYEKRVKACVEQSFI 117
Q +WSP + +L S+QSLLS+PNP+SP N+ AA+LYK+NR E++K+ + ++
Sbjct: 88 QEKWSPALTLETVLLSLQSLLSEPNPDSPLNADAAELYKKNREEFKKKAREWTKKYAE 145
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 113 bits (283), Expect = 2e-33
Identities = 52/103 (50%), Positives = 73/103 (70%)
Query: 3 WNAVIFGPHDTPFEDGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLDILQNR 62
W A I GP D+P+ G F L++ F +YP KPP V+F +K++HPN+ ++G ICLDIL+++
Sbjct: 33 WTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNINSNGSICLDILRDQ 92
Query: 63 WSPTYDVSAILTSIQSLLSDPNPNSPANSMAAQLYKENRREYE 105
WSP VS +L SI SLL+DPNP+ P A+++KENR YE
Sbjct: 93 WSPALTVSKVLLSISSLLTDPNPDDPLVPEIARVFKENRSRYE 135
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 107 bits (269), Expect = 4e-31
Identities = 46/100 (46%), Positives = 67/100 (67%)
Query: 7 IFGPHDTPFEDGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLDILQNRWSPT 66
+ GP TP+E G +KL + E+YP +PP VRF +K++HPN+ G ICLDIL+++WSP
Sbjct: 38 MEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDILKDKWSPA 97
Query: 67 YDVSAILTSIQSLLSDPNPNSPANSMAAQLYKENRREYEK 106
+ +L SIQ+LLS P P+ P ++ A +K NR + EK
Sbjct: 98 LQIRTVLLSIQALLSAPEPDDPLDTSVADHFKNNRADAEK 137
>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 = 30.4 bits (69), Expect = 0.11
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 20 FKLTVEFTEEYPNKPPTVRFASK 42
LT E+YP++PP + +S
Sbjct: 52 LVLTFTLPEDYPDEPPKISLSSP 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 = 30.0 bits (68), Expect = 0.12
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 10 PHDTPFEDG--TFKLTVEFTEEYPNKPPTVRF 39
P ED + L V+ E YP++ P +
Sbjct: 31 PSSDEGEDQYVSLTLQVKLPENYPDEAPPISL 62
>gnl|CDD|151298 pfam10849, DUF2654, Protein of unknown function (DUF2654). Some
members in this family of proteins are annotated as
a-gt.4 however currently no function is known.
Length = 70
Score = 28.1 bits (63), Expect = 0.40
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 89 ANSMAAQLYKENRREYEKRVKACVEQSFID 118
A AA+ K+NRRE KR+K E++ ID
Sbjct: 1 AEKKAAKHLKKNRREI-KRLKKHAEEALID 29
>gnl|CDD|233001 TIGR00509, bisC_fam, molybdopterin guanine dinucleotide-containing
S/N-oxide reductases. This enzyme family shares
sequence similarity and a requirement for a molydenum
cofactor as the only prosthetic group. The form of the
cofactor is a single molybdenum atom coordinated by two
molybdopterin guanine dinucleotide molecules. Members of
the family include biotin sulfoxide reductase,
dimethylsulfoxide reductase, and trimethylamine-N-oxide
reductase, although a single member may show all those
activities and related activities; it may not be
possible to resolve the primary function for members of
this family by sequence comparison alone. A number of
similar molybdoproteins in which the N-terminal region
contains a CXXXC motif and may bind an iron-sulfur
cluster are excluded from this set, including formate
dehydrogenases and nitrate reductases. Also excluded is
the A chain of a heteromeric, anaerobic DMSO reductase,
which also contains the CXXXC motif.
Length = 770
Score = 27.4 bits (61), Expect = 1.7
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 73 LTSIQSLLSDPNPNSPANSMAAQLYKENRREYEKRVKACVEQSFID 118
+ ++ SDPNP + Q+Y E+R +Y V + F++
Sbjct: 16 IVAVTPFESDPNPTPMLEGVPDQVYSESRIKY-----PMVRKGFLE 56
>gnl|CDD|237335 PRK13286, amiE, acylamide amidohydrolase; Provisional.
Length = 345
Score = 27.4 bits (61), Expect = 1.7
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 18 GTFKLTVEFTEEYPNKPP 35
G F LT E EE+P K P
Sbjct: 98 GVFSLTGERHEEHPRKAP 115
>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 = 26.8 bits (60), Expect = 1.7
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 28 EEYPNKPPT--VRFASKMF---HPNVYADGGICLDILQNRWSPTYDVSAIL 73
+ YP PP V+ M + +V A G + L L N P+ ++ ++
Sbjct: 58 DTYPFSPPICFVKPTPDMVIKVNHHVDAQGRVYLPYLHNWNHPSSNLVDLV 108
>gnl|CDD|238288 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling
factor dissociates the posttermination complex, composed
of the ribosome, deacylated tRNA, and mRNA, after
termination of translation. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis. RRF is believed to bind the ribosome at the
A-site in a manner that mimics tRNA, but the specific
mechanisms remain unclear. RRF is essential for
bacterial growth. It is not necessary for cell growth
in archaea or eukaryotes, but is found in mitochondria
or chloroplasts of some eukaryotic species.
Length = 179
Score = 26.1 bits (58), Expect = 3.7
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 9/54 (16%)
Query: 68 DVSAILTSIQSLLSDPNPNSPANSMAA------QLYKENRREYEKRVKACVEQS 115
+ AI +I + SD N P N A L +E R+E K K E++
Sbjct: 70 AIKAIEKAILN--SDLGLN-PNNDGAVIRVNLPPLTEERRKELVKDAKKIAEEA 120
>gnl|CDD|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 26.3 bits (59), Expect = 3.9
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 13/41 (31%)
Query: 17 DGTFKLTVEFTEEYPNKPPTVRFASKMFHPNVYADGGICLD 57
DG FKL VEF+ P + + +KM DG I L
Sbjct: 47 DGGFKLDVEFS---PTR---LYELAKM-------DGAIVLS 74
>gnl|CDD|236119 PRK07865, PRK07865, N-succinyldiaminopimelate aminotransferase;
Reviewed.
Length = 364
Score = 25.6 bits (57), Expect = 6.4
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 12/38 (31%)
Query: 65 PTYDVSAILTSIQSLLSD-------PNP-----NSPAN 90
PTY+V A L + +D P NSP+N
Sbjct: 122 PTYEVGARLAGATVVRADSLTELGPQRPALIWLNSPSN 159
>gnl|CDD|218661 pfam05622, HOOK, HOOK protein. This family consists of several
HOOK1, 2 and 3 proteins from different eukaryotic
organisms. The different members of the human gene
family are HOOK1, HOOK2 and HOOK3. Different domains
have been identified in the three human HOOK proteins,
and it was demonstrated that the highly conserved
NH2-domain mediates attachment to microtubules, whereas
the central coiled-coil motif mediates homodimerisation
and the more divergent C-terminal domains are involved
in binding to specific organelles (organelle-binding
domains). It has been demonstrated that endogenous HOOK3
binds to Golgi membranes, whereas both HOOK1 and HOOK2
are localised to discrete but unidentified cellular
structures. In mice the Hook1 gene is predominantly
expressed in the testis. Hook1 function is necessary for
the correct positioning of microtubular structures
within the haploid germ cell. Disruption of Hook1
function in mice causes abnormal sperm head shape and
fragile attachment of the flagellum to the sperm head.
Length = 713
Score = 25.5 bits (56), Expect = 7.7
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 71 AILTSIQSLLSDPNPNSPANSMAAQLYKENRREYE 105
++T+IQ L+S +SP+ A L ++ ++ E
Sbjct: 145 VVMTAIQELMSKEQGSSPSRESAGNLDQQLKKALE 179
>gnl|CDD|225425 COG2870, RfaE, ADP-heptose synthase, bifunctional sugar
kinase/adenylyltransferase [Cell envelope biogenesis,
outer membrane].
Length = 467
Score = 25.3 bits (56), Expect = 8.9
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 11/58 (18%)
Query: 72 ILTSIQSL-----------LSDPNPNSPANSMAAQLYKENRREYEKRVKACVEQSFID 118
+LT++Q + L DP A L N +E+E+ V C + ++
Sbjct: 156 VLTNVQKMIDLAREAGIPVLVDPKGKDFEKYRGATLITPNLKEFEEAVGKCKSEEELE 213
>gnl|CDD|185727 cd08986, GH43_7, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes enzymes with
beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC
3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-),
alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase
(EC 3.2.1.99), xylanase (EC 3.2.1.8),
endo-alpha-L-arabinanase and galactan
1,3-beta-galactosidase (EC 3.2.1.145) activities. These
are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
enzymes in this family display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 269
Score = 25.1 bits (55), Expect = 9.7
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 3 WNAVIFGPHDTPFED--GTFKLTVEFTEEYPNKPPTVR 38
+ A F H+TPF+D G + T F N PP R
Sbjct: 230 YFAGRFLGHNTPFQDLDGRWWCTA-FFNPAANVPPLCR 266
>gnl|CDD|237674 PRK14326, PRK14326, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 502
Score = 25.4 bits (56), Expect = 9.8
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 83 PNPNSPANSMAAQLYKENRREYEKRVKACVEQ 114
P +PA M QL K +E +R+ A E+
Sbjct: 348 KRPGTPAAEMEGQLPKAVVQERYERLVALQER 379
>gnl|CDD|218281 pfam04826, Arm_2, Armadillo-like. This domain contains
armadillo-like repeats. Proteins containing this domain
interact with numerous other proteins, through these
interactions they are involved in a wide variety of
processes including carcinogenesis, control of cellular
ageing and survival, regulation of circadian rhythm and
lysosomal sorting of G protein-coupled receptors.
Length = 254
Score = 25.0 bits (55), Expect = 9.9
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 72 ILTSIQSLLSDPNPN-SPANSMAAQLYKENRREYEKRVKACVEQ 114
+ I +LLS+PNP A N K++K V Q
Sbjct: 55 GIPIIANLLSNPNPEIKEKALNALNNLSVNVENQ-KKIKVYVNQ 97
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
0.318 0.134 0.413
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: 5,993,152
Number of extensions: 491261
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 32
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)