RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15032
(226 letters)
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 85.0 bits (211), Expect = 6e-21
Identities = 31/85 (36%), Positives = 47/85 (55%), Gaps = 3/85 (3%)
Query: 77 PRNFRLLEELEHGQRGVGDGTISWGLENDDDMTLTHWTGMIIGPPRTPYENRMYSLKIEC 136
RLL+EL+ Q+ G IS G +DD++ HW I GPP TPYE ++ L +E
Sbjct: 5 SALKRLLKELKKLQKDPPPG-ISAGPVDDDNLF--HWEATITGPPDTPYEGGIFKLTLEF 61
Query: 137 GPRYPDEPPQCRFVSRINMTCINNT 161
YP +PP+ RF ++I ++ +
Sbjct: 62 PEDYPFKPPKVRFTTKIFHPNVDPS 86
>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 = 84.3 bits (209), Expect = 9e-21
Identities = 27/81 (33%), Positives = 51/81 (62%), Gaps = 3/81 (3%)
Query: 81 RLLEELEHGQRGVGDGTISWGLENDDDMTLTHWTGMIIGPPRTPYENRMYSLKIECGPRY 140
RLL+EL+ ++ G ++ +++++ L WTG I+GPP TPYE ++ L IE Y
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDEN---LLEWTGTIVGPPGTPYEGGVFKLTIEFPEDY 57
Query: 141 PDEPPQCRFVSRINMTCINNT 161
P +PP+ +F+++I ++++
Sbjct: 58 PFKPPKVKFITKIYHPNVDSS 78
>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 = 63.0 bits (154), Expect = 9e-13
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 81 RLLEELEHGQRGVGDGTISWGLENDDDMTLTHWTGMIIGPPRTPYENRMYSLKIECGPRY 140
RL +EL+ + G IS +D+ L W IIGP TPYE ++ L IE Y
Sbjct: 1 RLQKELKELLKDPPPG-ISAFPVDDN---LFEWEVTIIGPEGTPYEGGVFKLDIEFPEDY 56
Query: 141 PDEPPQCRFVSRI 153
P +PP+ +F ++I
Sbjct: 57 PFKPPKVKFTTKI 69
>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 = 59.5 bits (145), Expect = 2e-11
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 97 TISWGLENDDDMTLTHWTGMIIGPPRTPYENRMYSLKIECGPRYPDEPPQCRFVSRI 153
IS ++ L W G I GPP TPYE ++ L IE YP +PP+ RFV++I
Sbjct: 18 GISAEPVEEN---LLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKI 71
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 44.7 bits (105), Expect = 5e-06
Identities = 22/60 (36%), Positives = 33/60 (55%)
Query: 110 LTHWTGMIIGPPRTPYENRMYSLKIECGPRYPDEPPQCRFVSRINMTCINNTSGIVVVIM 169
L WT IIGP +PY ++ L I P YP +PP+ +F ++I IN+ I + I+
Sbjct: 30 LFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNINSNGSICLDIL 89
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 41.7 bits (98), Expect = 6e-05
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 112 HWTGMIIGPPRTPYENRMYSLKIECGPRYPDEPPQCRFVSRI 153
H+ ++ GP TPYE Y L++ +YP EPP+ RF+++I
Sbjct: 33 HFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKI 74
>gnl|CDD|216215 pfam00961, LAGLIDADG_1, LAGLIDADG endonuclease.
Length = 99
Score = 29.5 bits (67), Expect = 0.48
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 17 YLLYQIQMK-GIKKITLKHSINICALRIFHQESSTILVCFHKENYPFCTNFH 67
LLY+I+ GI I + N R+ +++ ++ + YP T +
Sbjct: 40 KLLYKIKNYLGIGSIKKRKKDNTVRYRVSNKKLLEKII-PYFNKYPLLTKKY 90
>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 = 29.2 bits (66), Expect = 0.60
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 6/36 (16%)
Query: 131 SLKIECGPRYPDEPPQCRFVSRINMTCINNTSGIVV 166
L YPDEPP+ I+++
Sbjct: 53 VLTFTLPEDYPDEPPK------ISLSSPWLLRDQDK 82
>gnl|CDD|239501 cd03407, Band_7_4, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and are known to interact
with a variety of proteins. Stomatin interacts with and
regulates members of the degenerin/epithelia Na+ channel
family in mechanosensory cells of Caenorhabditis elegans
and vertebrate neurons and participates in trafficking
of Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome.
Length = 262
Score = 30.0 bits (68), Expect = 0.80
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 163 GIVVVIMFWVMIEAKAT----HYPVDLKTGTPDQVYLIVCVLIRYQV 205
G VI + + + V ++T T D V++ V I+Y+V
Sbjct: 20 GCHFVIPLVETVAGRLSLRVQQLDVRVETKTKDNVFVTVVGQIQYRV 66
>gnl|CDD|213565 TIGR00842, bcct, choline/carnitine/betaine transport. The
Betaine/Carnitine/Choline Transporter (BCCT) Family (TC
2.A.15) Proteins of the BCCT family share the common
functional feature of transporting molecules with a
quaternary ammonium group [R-N+(CH3)3]. The BCCT family
includes transporters for carnitine, choline and glycine
betaine. BCCT transporters have 12 putative TMS, and are
energized by pmf-driven proton symport. Some of these
permeases exhibit osmosensory and osmoregulatory
properties inherent to their polypeptide chains
[Transport and binding proteins, Other].
Length = 452
Score = 28.5 bits (64), Expect = 2.8
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 133 KIECGPRYPDEPPQCRFVSRINMTCINNTSGIVVVIMFWVMIEAKATHY 181
KI G DE P+ +S + M +G+ +MFW + E T+Y
Sbjct: 25 KIRLGR--DDEKPEFSTLSWLAMLF---AAGMGAGLMFWGVAEP-LTYY 67
>gnl|CDD|216852 pfam02028, BCCT, BCCT family transporter.
Length = 484
Score = 28.2 bits (64), Expect = 3.6
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 9/64 (14%)
Query: 133 KIECGPRYPDEPPQCRFVSRINMTCINNTSGIVVVIMFWVMIEAKATHY---PVDLKTGT 189
I G DE P+ S M +G+ + ++FW + E H+ P + G+
Sbjct: 63 NIRLGG--DDEKPEFSTFSWFAMLF---AAGMGIGLLFWGVAEP-LYHFQSPPPGGEPGS 116
Query: 190 PDQV 193
P+
Sbjct: 117 PEAA 120
>gnl|CDD|224211 COG1292, BetT, Choline-glycine betaine transporter [Cell envelope
biogenesis, outer membrane].
Length = 537
Score = 28.0 bits (63), Expect = 5.2
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 6/58 (10%)
Query: 133 KIECGPRYPDEPPQCRFVSRINMTCINNTSGIVVVIMFWVMIEAKATHYPVDLKTGTP 190
I G DE P+ +S + M +G+ + ++FW + E +Y P
Sbjct: 76 NIRLGK--DDEKPEFSTLSWLAMLF---AAGMGIGLLFWGVAEP-VYYYATPPPGAEP 127
>gnl|CDD|236974 PRK11768, PRK11768, serine/threonine protein kinase; Provisional.
Length = 325
Score = 26.7 bits (60), Expect = 9.6
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 125 YENRMYSLKIECGPRY 140
YENR+Y E G R
Sbjct: 37 YENRVYQFGDEDGRRV 52
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
0.326 0.141 0.461
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: 11,786,757
Number of extensions: 1086123
Number of successful extensions: 971
Number of sequences better than 10.0: 1
Number of HSP's gapped: 968
Number of HSP's successfully gapped: 16
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.7 bits)