RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11961
(109 letters)
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 110 bits (277), Expect = 2e-32
Identities = 45/120 (37%), Positives = 64/120 (53%), Gaps = 20/120 (16%)
Query: 1 MSSPSAGTRRMNIDVIKLIESKHELF------------------GPRDTPYEGGVWKVRV 42
MSSPSA +R+ ++ KL + GP DTPYEGG++K+ +
Sbjct: 1 MSSPSA-LKRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTL 59
Query: 43 HLPENYPFKSPSIGFMNKIYHPNICEGSGTVCLNVINQAWTPLYDLSNIFECFLPQLLTP 102
PE+YPFK P + F KI+HPN+ SG VCL+++ W+P+Y L I LL+P
Sbjct: 60 EFPEDYPFKPPKVRFTTKIFHPNVDP-SGNVCLDILKDRWSPVYTLETILLSLQSLLLSP 118
>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 = 107 bits (269), Expect = 3e-31
Identities = 34/79 (43%), Positives = 50/79 (63%), Gaps = 2/79 (2%)
Query: 25 LFGPRDTPYEGGVWKVRVHLPENYPFKSPSIGFMNKIYHPNICEGSGTVCLNVINQ-AWT 83
+ GP DTPYEGG++K+ + PE+YPFK P + F+ KIYHPN+ E +G +CL+++ W+
Sbjct: 35 IRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVDE-NGKICLSILKTHGWS 93
Query: 84 PLYDLSNIFECFLPQLLTP 102
P Y L + L P
Sbjct: 94 PAYTLRTVLLSLQSLLNEP 112
>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 = 102 bits (257), Expect = 1e-29
Identities = 32/78 (41%), Positives = 49/78 (62%), Gaps = 3/78 (3%)
Query: 25 LFGPRDTPYEGGVWKVRVHLPENYPFKSPSIGFMNKIYHPNICEGSGTVCLNVIN-QAWT 83
+ GP TPYEGGV+K+ + PE+YPFK P + F KIYHPN+ SG +CL+++ + W+
Sbjct: 33 IIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNVDP-SGEICLDILKDENWS 91
Query: 84 PLYDLSNIFECFLPQLLT 101
P + + + LL+
Sbjct: 92 PALTIEQVLL-SIQSLLS 108
>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 = 92.7 bits (231), Expect = 2e-25
Identities = 32/70 (45%), Positives = 47/70 (67%), Gaps = 2/70 (2%)
Query: 25 LFGPRDTPYEGGVWKVRVHLPENYPFKSPSIGFMNKIYHPNICEGSGTVCLNVINQA-WT 83
+ GP TPYEGGV+K+ + PE+YPFK P + F+ KIYHPN+ + SG +CL+++ Q W+
Sbjct: 34 IVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNV-DSSGEICLDILKQEKWS 92
Query: 84 PLYDLSNIFE 93
P L +
Sbjct: 93 PALTLETVLL 102
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 71.0 bits (174), Expect = 5e-17
Identities = 28/61 (45%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 24 ELFGPRDTPYEGGVWKVRVHLPENYPFKSPSIGFMNKIYHPNICEGSGTVCLNVINQAWT 83
+ GP TPYEGG +K+ + LPE YP + P + F+ KIYHPNI + G +CL+++ W+
Sbjct: 37 LMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNI-DKLGRICLDILKDKWS 95
Query: 84 P 84
P
Sbjct: 96 P 96
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 67.5 bits (164), Expect = 1e-15
Identities = 28/68 (41%), Positives = 44/68 (64%), Gaps = 1/68 (1%)
Query: 25 LFGPRDTPYEGGVWKVRVHLPENYPFKSPSIGFMNKIYHPNICEGSGTVCLNVINQAWTP 84
+ GP D+PY GGV+ + + P +YPFK P + F KIYHPNI +G++CL+++ W+P
Sbjct: 37 IIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNI-NSNGSICLDILRDQWSP 95
Query: 85 LYDLSNIF 92
+S +
Sbjct: 96 ALTVSKVL 103
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 28.8 bits (64), Expect = 0.51
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 4/37 (10%)
Query: 1 MSSPSAGTRRMNIDVIKLIESKH----ELFGPRDTPY 33
+S+P+ G E+ ELF P+ PY
Sbjct: 1040 LSNPTYGISPTYNTSGIKGETIGPYCKELFNPQGLPY 1076
>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 = 27.3 bits (61), Expect = 0.92
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 28 PRDTPYEGGVWKVR--VHLPENYPFKSPSI 55
P E + V LPENYP ++P I
Sbjct: 31 PSSDEGEDQYVSLTLQVKLPENYPDEAPPI 60
>gnl|CDD|178098 PLN02480, PLN02480, Probable pectinesterase.
Length = 343
Score = 27.9 bits (62), Expect = 0.96
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 36 GVWKVRVHLPENYPF 50
GV++ +VH+PEN PF
Sbjct: 85 GVYREKVHIPENKPF 99
>gnl|CDD|178165 PLN02550, PLN02550, threonine dehydratase.
Length = 591
Score = 26.4 bits (58), Expect = 3.4
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 63 HPNICEGSGTVCLNVINQAWTPLY 86
HP++ G GTV + ++ Q PL+
Sbjct: 237 HPDVIAGQGTVGMEIVRQHQGPLH 260
>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 = 25.4 bits (56), Expect = 5.7
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 39 KVRVHLPENYPFKSPSI 55
+ LPE+YP + P I
Sbjct: 53 VLTFTLPEDYPDEPPKI 69
>gnl|CDD|132036 TIGR02991, ectoine_eutB, ectoine utilization protein EutB. Members
of this protein family are EutB, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti, Silicibacter pomeroyi,
Agrobacterium tumefaciens, and Pseudomonas putida.
Members of this family resemble threonine dehydratases.
Length = 317
Score = 25.6 bits (56), Expect = 5.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 63 HPNICEGSGTVCLNVINQA 81
HP+I G GT+ L V+ Q
Sbjct: 147 HPDIVAGQGTLGLEVVEQM 165
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 25.9 bits (56), Expect = 6.0
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 34 EGGVWKVRVHLPENYPFK 51
EG +W+++ H PE + K
Sbjct: 2397 EGALWEIQFHTPETFALK 2414
>gnl|CDD|184689 PRK14459, PRK14459, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 373
Score = 25.3 bits (56), Expect = 8.1
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 93 ECFLPQLLTPIRT 105
E P LLTP+RT
Sbjct: 77 EALFPTLLTPVRT 89
>gnl|CDD|181427 PRK08445, PRK08445, hypothetical protein; Provisional.
Length = 348
Score = 25.1 bits (55), Expect = 9.9
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 5 SAGTR-RMNID-VIKLIESKHELFGPRDTPYE 34
+AG RMN +I+LI+ E+ R+T YE
Sbjct: 312 AAGASFRMNQAEMIELIKDIGEIPAKRNTAYE 343
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
0.322 0.141 0.455
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: 5,693,336
Number of extensions: 467494
Number of successful extensions: 319
Number of sequences better than 10.0: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 20
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
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 (21.9 bits)
S2: 53 (24.2 bits)