RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy90
(125 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 = 146 bits (371), Expect = 1e-46
Identities = 59/129 (45%), Positives = 76/129 (58%), Gaps = 16/129 (12%)
Query: 8 RLSEERKGWRKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTPWESGSYKLRMIFKDD 67
RL +E K KD P G A P + NL WE +I G +GTP+E G +KL + F +D
Sbjct: 1 RLQKELKELLKDPPPGISAFPVDD-----NLFEWEVTIIGPEGTPYEGGVFKLDIEFPED 55
Query: 68 YPSTPPKCKFEPPLFHPNVYPS-----------DWKPAITIKQILLGIQDLLNEPNIKDP 116
YP PPK KF ++HPNV PS +W PA+TI+Q+LL IQ LL+EPN +DP
Sbjct: 56 YPFKPPKVKFTTKIYHPNVDPSGEICLDILKDENWSPALTIEQVLLSIQSLLSEPNPEDP 115
Query: 117 AQAEAYTIY 125
AEA +Y
Sbjct: 116 LNAEAAKLY 124
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 139 bits (353), Expect = 1e-43
Identities = 55/135 (40%), Positives = 71/135 (52%), Gaps = 14/135 (10%)
Query: 1 MSGIAIGRLSEERKGWRKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTPWESGSYKL 60
S A+ RL +E K +KD P G A P + NL +WE +I G TP+E G +KL
Sbjct: 2 SSPSALKRLLKELKKLQKDPPPGISAGPVDDD----NLFHWEATITGPPDTPYEGGIFKL 57
Query: 61 RMIFKDDYPSTPPKCKFEPPLFHPNVYPS----------DWKPAITIKQILLGIQDLLNE 110
+ F +DYP PPK +F +FHPNV PS W P T++ ILL +Q LL
Sbjct: 58 TLEFPEDYPFKPPKVRFTTKIFHPNVDPSGNVCLDILKDRWSPVYTLETILLSLQSLLLS 117
Query: 111 PNIKDPAQAEAYTIY 125
PN P EA T+Y
Sbjct: 118 PNPDSPLNTEAATLY 132
>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 = 137 bits (346), Expect = 9e-43
Identities = 54/129 (41%), Positives = 72/129 (55%), Gaps = 15/129 (11%)
Query: 8 RLSEERKGWRKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTPWESGSYKLRMIFKDD 67
RL +E K RKD P GF A P + NL+ W +I G GTP+E G +KL + F +D
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDE----NLLEWTGTIVGPPGTPYEGGVFKLTIEFPED 56
Query: 68 YPSTPPKCKFEPPLFHPNVYPS-----------DWKPAITIKQILLGIQDLLNEPNIKDP 116
YP PPK KF ++HPNV S W PA+T++ +LL +Q LL+EPN P
Sbjct: 57 YPFKPPKVKFITKIYHPNVDSSGEICLDILKQEKWSPALTLETVLLSLQSLLSEPNPDSP 116
Query: 117 AQAEAYTIY 125
A+A +Y
Sbjct: 117 LNADAAELY 125
>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 = 127 bits (322), Expect = 5e-39
Identities = 52/129 (40%), Positives = 71/129 (55%), Gaps = 16/129 (12%)
Query: 8 RLSEERKGWRKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTPWESGSYKLRMIFKDD 67
RL +E K +KD P G A+P + NL+ W +I G TP+E G +KL + F +D
Sbjct: 3 RLQKELKDLKKDPPSGISAEPVEE-----NLLEWHGTIRGPPDTPYEGGIFKLDIEFPED 57
Query: 68 YPSTPPKCKFEPPLFHPNVYPS-----------DWKPAITIKQILLGIQDLLNEPNIKDP 116
YP PPK +F ++HPNV + W PA T++ +LL +Q LLNEPN DP
Sbjct: 58 YPFKPPKVRFVTKIYHPNVDENGKICLSILKTHGWSPAYTLRTVLLSLQSLLNEPNPSDP 117
Query: 117 AQAEAYTIY 125
AEA +Y
Sbjct: 118 LNAEAAKLY 126
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 69.4 bits (169), Expect = 4e-16
Identities = 43/132 (32%), Positives = 64/132 (48%), Gaps = 15/132 (11%)
Query: 4 IAIGRLSEERKGWRKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTPWESGSYKLRMI 63
+A R+ +E K KD P A P+ NL W SI G +P+ G + L ++
Sbjct: 1 MATKRIQKEHKDLLKDPPSNCSAGPSDE-----NLFRWTASIIGPSDSPYAGGVFFLSIL 55
Query: 64 FKDDYPSTPPKCKFEPPLFHPNVYPS----------DWKPAITIKQILLGIQDLLNEPNI 113
F DYP PPK +F ++HPN+ + W PA+T+ ++LL I LL +PN
Sbjct: 56 FPPDYPFKPPKVQFTTKIYHPNINSNGSICLDILRDQWSPALTVSKVLLSISSLLTDPNP 115
Query: 114 KDPAQAEAYTIY 125
DP E ++
Sbjct: 116 DDPLVPEIARVF 127
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 68.7 bits (168), Expect = 8e-16
Identities = 40/119 (33%), Positives = 60/119 (50%), Gaps = 15/119 (12%)
Query: 8 RLSEERKGWRKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTPWESGSYKLRMIFKDD 67
R+ +E + D P G A+P +P N +++ + G GTP+E G YKL + +
Sbjct: 6 RIEKETQNLANDPPPGIKAEP--DPG---NYRHFKILMEGPDGTPYEGGYYKLELFLPEQ 60
Query: 68 YPSTPPKCKFEPPLFHPN----------VYPSDWKPAITIKQILLGIQDLLNEPNIKDP 116
YP PPK +F ++HPN + W PA+ I+ +LL IQ LL+ P DP
Sbjct: 61 YPMEPPKVRFLTKIYHPNIDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPEPDDP 119
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 29.4 bits (66), Expect = 0.44
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 16/55 (29%)
Query: 61 RMIFKDDYPSTPPKCKFE------------PPLFHPNVYPSDWKPAITIKQILLG 103
R I+KD Y ST P ++ P LF P WK A+TI ++LLG
Sbjct: 1292 RGIYKDSYGSTKPWTDYQLRPNFAIAMTVAPELFVPE---KAWK-ALTIAEVLLG 1342
>gnl|CDD|199884 cd02854, E_set_GBE_euk_N, N-terminal Early set domain associated
with the catalytic domain of eukaryotic glycogen
branching enzyme (also called 1,4 alpha glucan
branching enzyme). This subfamily is composed of
predominantly eukaryotic 1,4 alpha glucan branching
enzymes, also called glycogen branching enzymes or
starch binding enzymes in plants. E or "early" set
domains are associated with the catalytic domain of the
1,4 alpha glucan branching enzymes at the N-terminal
end. These enzymes catalyze the formation of alpha-1,6
branch points in either glycogen or starch by cleavage
of the alpha-1,4 glucosidic linkage, yielding a
non-reducing end oligosaccharide chain, as well as the
subsequent attachment of short glucosyl chains to the
alpha-1,6 position. Starch is composed of two types of
glucan polymer: amylose and amylopectin. Amylose is
mainly composed of linear chains of alpha-1,4 linked
glucose residues and amylopectin consists of shorter
alpha-1,4 linked chains connected by alpha-1,6
linkages. Amylopectin is synthesized from linear chains
by starch branching enzyme. The N-terminal domains of
the branching enzyme proteins may be related to the
immunoglobulin and/or fibronectin type III
superfamilies. These domains are associated with
different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions.
Members of this family include members of the alpha
amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase,
and chitinase, among others.
Length = 95
Score = 26.7 bits (60), Expect = 1.9
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 15 GW-RKDHPFGFVAKPAKNPDGSLNLMNWECSIPGKKGTP-WESGS-YKLRMIFKD 66
W R+ HP ++ G WE +P K+G+P GS KL + D
Sbjct: 24 NWNRESHPL------KRDEFG-----KWELFLPPKEGSPAIPHGSKVKLHVETWD 67
>gnl|CDD|236871 PRK11175, PRK11175, universal stress protein UspE; Provisional.
Length = 305
Score = 26.8 bits (60), Expect = 2.8
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 68 YPSTPPKCKFEPPLFHPNVY 87
YP TP E P F P+VY
Sbjct: 197 YPVTPINIAIELPEFDPSVY 216
>gnl|CDD|236322 PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 368
Score = 26.3 bits (59), Expect = 5.0
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 28 PAKNPDGSLNLM 39
P+ PDG+ NL+
Sbjct: 331 PSHLPDGTHNLV 342
>gnl|CDD|217882 pfam04084, ORC2, Origin recognition complex subunit 2. All DNA
replication initiation is driven by a single conserved
eukaryotic initiator complex termed he origin
recognition complex (ORC). The ORC is a six protein
complex. The function of ORC is reviewed in.
Length = 318
Score = 25.7 bits (57), Expect = 8.2
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 77 FEPPLFHPNVYPSDWKPAITIKQILLGIQDLLNEPNIKDPAQ 118
+ P+ N + P++ IK IL I +LL E K P
Sbjct: 79 DKGPVVVVNGF----FPSLNIKDILNEITELLLEATDKKPNS 116
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
0.317 0.138 0.452
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: 6,682,199
Number of extensions: 572757
Number of successful extensions: 404
Number of sequences better than 10.0: 1
Number of HSP's gapped: 394
Number of HSP's successfully gapped: 19
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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 (21.6 bits)
S2: 53 (24.2 bits)