RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy89
(119 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 = 135 bits (342), Expect = 2e-42
Identities = 48/95 (50%), Positives = 64/95 (67%), Gaps = 1/95 (1%)
Query: 24 CGFKNPTNTPWESGSYKLRMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEKD 83
P TP+E G +KL + F +DYP PPK KF ++HPNV PSG +CL +L +E +
Sbjct: 31 VTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNVDPSGEICLDILKDE-N 89
Query: 84 WKPAITIKQILLGIQDLLNEPNIKDPAQAEAYTIY 118
W PA+TI+Q+LL IQ LL+EPN +DP AEA +Y
Sbjct: 90 WSPALTIEQVLLSIQSLLSEPNPEDPLNAEAAKLY 124
>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 = 127 bits (321), Expect = 5e-39
Identities = 43/96 (44%), Positives = 60/96 (62%), Gaps = 1/96 (1%)
Query: 23 RCGFKNPTNTPWESGSYKLRMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEK 82
P TP+E G +KL + F +DYP PPK KF ++HPNV SG +CL +L +EK
Sbjct: 31 TGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVDSSGEICLDILKQEK 90
Query: 83 DWKPAITIKQILLGIQDLLNEPNIKDPAQAEAYTIY 118
W PA+T++ +LL +Q LL+EPN P A+A +Y
Sbjct: 91 -WSPALTLETVLLSLQSLLSEPNPDSPLNADAAELY 125
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 125 bits (316), Expect = 3e-38
Identities = 43/95 (45%), Positives = 56/95 (58%), Gaps = 2/95 (2%)
Query: 24 CGFKNPTNTPWESGSYKLRMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEKD 83
P +TP+E G +KL + F +DYP PPK +F +FHPNV PSG VCL +L +
Sbjct: 40 ATITGPPDTPYEGGIFKLTLEFPEDYPFKPPKVRFTTKIFHPNVDPSGNVCLDILKD--R 97
Query: 84 WKPAITIKQILLGIQDLLNEPNIKDPAQAEAYTIY 118
W P T++ ILL +Q LL PN P EA T+Y
Sbjct: 98 WSPVYTLETILLSLQSLLLSPNPDSPLNTEAATLY 132
>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 = 124 bits (314), Expect = 5e-38
Identities = 43/96 (44%), Positives = 60/96 (62%), Gaps = 1/96 (1%)
Query: 23 RCGFKNPTNTPWESGSYKLRMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEK 82
+ P +TP+E G +KL + F +DYP PPK +F ++HPNV +G +CLS+L
Sbjct: 32 HGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVDENGKICLSILKTHG 91
Query: 83 DWKPAITIKQILLGIQDLLNEPNIKDPAQAEAYTIY 118
W PA T++ +LL +Q LLNEPN DP AEA +Y
Sbjct: 92 -WSPAYTLRTVLLSLQSLLNEPNPSDPLNAEAAKLY 126
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 74.5 bits (183), Expect = 3e-18
Identities = 34/81 (41%), Positives = 49/81 (60%), Gaps = 2/81 (2%)
Query: 29 PTNTPWESGSYKLRMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEKDWKPAI 88
P TP+E G YKL + + YP PPK +F ++HPN+ G +CL +L ++ W PA+
Sbjct: 41 PDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRICLDILKDK--WSPAL 98
Query: 89 TIKQILLGIQDLLNEPNIKDP 109
I+ +LL IQ LL+ P DP
Sbjct: 99 QIRTVLLSIQALLSAPEPDDP 119
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 72.5 bits (177), Expect = 2e-17
Identities = 33/90 (36%), Positives = 57/90 (63%), Gaps = 2/90 (2%)
Query: 29 PTNTPWESGSYKLRMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEKDWKPAI 88
P+++P+ G + L ++F DYP PPK +F ++HPN+ +G++CL +L ++ W PA+
Sbjct: 40 PSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNINSNGSICLDILRDQ--WSPAL 97
Query: 89 TIKQILLGIQDLLNEPNIKDPAQAEAYTIY 118
T+ ++LL I LL +PN DP E ++
Sbjct: 98 TVSKVLLSISSLLTDPNPDDPLVPEIARVF 127
>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 = 37.9 bits (88), Expect = 5e-04
Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 42 RMIFKDDYPSTPPKCKFEPPLFHPNVYPSGTVCLSLLDEEKDWKPAITIKQILLG 96
R I+KD Y ST P ++ PN + TV L EK WK A+TI ++LLG
Sbjct: 1292 RGIYKDSYGSTKPWTDYQ---LRPNFAIAMTVAPELFVPEKAWK-ALTIAEVLLG 1342
>gnl|CDD|222765 pfam14461, Prok-E2_B, Prokaryotic E2 family B. A member of the
E2/UBC superfamily of proteins found in several
bacteria. The active site residues are similar to the
eukaryotic E2 proteins but lack the conserved
asparagine. Members of this family are usually fused to
an E1 domain at the C-terminus. The protein is usually
in the gene neighborhood of a gene encoding a member of
the pol-beta nucleotidyltransferase superfamily. Many of
the operons in this family are in ICE-like mobile
elements and plasmids.
Length = 131
Score = 30.5 bits (69), Expect = 0.10
Identities = 22/82 (26%), Positives = 32/82 (39%), Gaps = 8/82 (9%)
Query: 37 GSYKLRMIFKDDYPSTPPKCKFEPP----LFHPNVYPSGTVCLSLLDEEKDWKP-AITIK 91
G +R++ DD+P P K P+V GT+CL L +W +
Sbjct: 36 GVPPIRLVIPDDFPLVLP--KVFLADREERLLPHVESDGTLCL-LDRPSANWDFNGSAAE 92
Query: 92 QILLGIQDLLNEPNIKDPAQAE 113
+ IQ LL + D Q E
Sbjct: 93 SLDRQIQLLLKGSSDGDENQEE 114
>gnl|CDD|236871 PRK11175, PRK11175, universal stress protein UspE; Provisional.
Length = 305
Score = 26.8 bits (60), Expect = 2.7
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 49 YPSTPPKCKFEPPLFHPNVY 68
YP TP E P F P+VY
Sbjct: 197 YPVTPINIAIELPEFDPSVY 216
>gnl|CDD|143500 cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Proteobacterial Alanine
Racemases. This subfamily is composed mainly of
proteobacterial alanine racemases (EC 5.1.1.1), fold
type III PLP-dependent enzymes that catalyze the
interconversion between L- and D-alanine, which is an
essential component of the peptidoglycan layer of
bacterial cell walls. hese proteins are similar to other
bacterial ARs and are fold type III PLP-dependent
enzymes containing contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
They exist as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Homodimer formation and the presence of the PLP
cofactor are required for catalytic activity.
Length = 354
Score = 26.7 bits (60), Expect = 3.6
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 4/20 (20%)
Query: 14 IGYGHGYPQRCGFKNPTNTP 33
IGYG GYP+ P+ TP
Sbjct: 268 IGYGDGYPRHA----PSGTP 283
>gnl|CDD|179950 PRK05166, PRK05166, histidinol-phosphate aminotransferase;
Provisional.
Length = 371
Score = 26.3 bits (58), Expect = 4.5
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 11 GLRIGYG-HGYPQRCGFKNPTNTPWESGSYKLRM 43
GLR+GYG P+ G + TP+
Sbjct: 237 GLRVGYGLVSDPELVGLLDRVRTPFNVNGAAQAA 270
>gnl|CDD|217958 pfam04197, Birna_RdRp, Birnavirus RNA dependent RNA polymerase
(VP1). Birnaviruses are dsRNA viruses. This family
corresponds to the RNA dependent RNA polymerase. This
protein is also known as VP1. All of the birnavirus VP1
proteins contain conserved RdRp motifs that reside in
the catalytic "palm" domain of all classes of
polymerases. However, the birnavirus RdRps lack the
highly conserved Gly-Asp-Asp (GDD) sequence, a component
of the proposed catalytic site of this enzyme family
that exists in the conserved motif VI of the palm domain
of other RdRps.
Length = 855
Score = 26.4 bits (58), Expect = 4.9
Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 9/70 (12%)
Query: 27 KNPTNTPWESGSYKLRMIFK--DDY-PSTPPKC--KFEPPLFHPNVYPSGTVCLSLLDEE 81
+NP +P E G Y + + D P PP + P L S V E
Sbjct: 184 RNPNKSPKEMG-YTNEEVAELLDQTLPIGPPGEDDEPWPDL---TWTLSWLVYTGDPAEG 239
Query: 82 KDWKPAITIK 91
+D+ P IT K
Sbjct: 240 EDYLPHITQK 249
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 26.1 bits (58), Expect = 4.9
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 11 GLRIGYGHGY 20
G R+GYG GY
Sbjct: 132 GYRLGYGGGY 141
>gnl|CDD|233985 TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.
This enzyme, 5,10-methenyltetrahydrofolate synthetase,
is also called 5-formyltetrahydrofolate cycloligase.
Function of bacterial proteins in this family was
inferred originally from the known activity of
eukaryotic homologs. Recently, activity was shown
explicitly for the member from Mycoplasma pneumonia.
Members of this family from alpha- and
gamma-proteobacteria, designated ygfA, are often found
in an operon with 6S structural RNA, and show a similar
pattern of high expression during stationary phase. The
function may be to deplete folate to slow 1-carbon
biosynthetic metabolism [Central intermediary
metabolism, One-carbon metabolism].
Length = 179
Score = 25.7 bits (57), Expect = 6.7
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 9 HLGLRIGYGHGY 20
G R+GYG GY
Sbjct: 128 RRGYRLGYGGGY 139
>gnl|CDD|216145 pfam00842, Ala_racemase_C, Alanine racemase, C-terminal domain.
Length = 125
Score = 25.1 bits (56), Expect = 6.9
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 14 IGYGHGYPQRCGFKNP 29
IGY GYP+ +
Sbjct: 39 IGYADGYPRALSNRGY 54
>gnl|CDD|241368 cd13214, PH-GRAM_WBP2, WW binding protein 2 (WB2) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. WBP2
plays a number of roles including: acting as a tyrosine
kinase substrate, activation of estrogen receptor alpha
(ERalpha)/progesterone receptor (PR) transcription, and
playing a role in breast cancer. WBP2 contain a
N-terminal PH-GRAM domain and a C-terminal WWbp domain.
The GRAM domain, found in myotubularins,
glucosyltransferases, and other putative
membrane-associated proteins, is part of a larger motif
with a pleckstrin homology (PH) domain fold. The WWbp
domain is characterized by several short PY and PT-like
motifs of the PPPPY form and binds to WW domains. WW
domains contain two highly conserved tryptophans that
are spaced 20-23 residues apart. They bind proline-rich
peptide motifs [AP]-P-P-[AP]-Y, and/or phosphoserine-
phosphothreonine-containing motifs.
Length = 106
Score = 25.2 bits (56), Expect = 7.1
Identities = 9/18 (50%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 56 CKFEPPLFHPNVYPSGTV 73
KFE P+F N GTV
Sbjct: 51 TKFEQPVFGANYI-KGTV 67
>gnl|CDD|178164 PLN02549, PLN02549, asparagine synthase (glutamine-hydrolyzing).
Length = 578
Score = 25.5 bits (56), Expect = 8.1
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 29 PTNTPWESGSYKLRMIFKDDYP 50
P NTP +Y RMIF+ +P
Sbjct: 486 PHNTPTTKEAYYYRMIFEKHFP 507
>gnl|CDD|217059 pfam02480, Herpes_gE, Alphaherpesvirus glycoprotein E.
Glycoprotein E (gE) of Alphaherpesvirus forms a complex
with glycoprotein I (gI) (pfam01688), functioning as an
immunoglobulin G (IgG) Fc binding protein. gE is
involved in virus spread but is not essential for
propagation.
Length = 437
Score = 25.5 bits (56), Expect = 8.7
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 8/29 (27%)
Query: 52 TPPKCK----FEPPLFHPNVYPSGTVCLS 76
P+C +EP ++HP+ P CLS
Sbjct: 192 YDPECAEMRIYEPCIYHPHA-PE---CLS 216
>gnl|CDD|151791 pfam11350, DUF3152, Protein of unknown function (DUF3152). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently there is no known function.
Length = 189
Score = 25.0 bits (55), Expect = 9.7
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 7 NHHLGLRIGYGH 18
NH +G IGYGH
Sbjct: 143 NHEVGHAIGYGH 154
>gnl|CDD|216717 pfam01812, 5-FTHF_cyc-lig, 5-formyltetrahydrofolate cyclo-ligase
family. 5-formyltetrahydrofolate cyclo-ligase or
methenyl-THF synthetase EC:6.3.3.2 catalyzes the
interchange of 5-formyltetrahydrofolate (5-FTHF) to
5-10-methenyltetrahydrofolate, this requires ATP and
Mg2+. 5-FTHF is used in chemotherapy where it is
clinically known as Leucovorin.
Length = 182
Score = 25.0 bits (55), Expect = 9.8
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 11 GLRIGYGHGY 20
G R+G G GY
Sbjct: 130 GYRLGRGGGY 139
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 0.140 0.465
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: 6,272,641
Number of extensions: 537165
Number of successful extensions: 419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 413
Number of HSP's successfully gapped: 26
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
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 (21.7 bits)
S2: 53 (24.2 bits)