RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16981
(302 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 = 163 bits (415), Expect = 1e-50
Identities = 57/135 (42%), Positives = 82/135 (60%), Gaps = 3/135 (2%)
Query: 156 DLNEL-NLPKTCTTEFPNPDDLLSFK-LIISPDEGFYRSGKFVFSFKVGPNYPHEPPKVK 213
+L EL P + FP D+L ++ II P+ Y G F + +YP +PPKVK
Sbjct: 5 ELKELLKDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVK 64
Query: 214 CETPVYHPNIDLEGNVCLNILR-EDWKPVLTINSIVYGLQYLFLEPNPEDPLNKEAAEVL 272
T +YHPN+D G +CL+IL+ E+W P LTI ++ +Q L EPNPEDPLN EAA++
Sbjct: 65 FTTKIYHPNVDPSGEICLDILKDENWSPALTIEQVLLSIQSLLSEPNPEDPLNAEAAKLY 124
Query: 273 QNNRRLFEQNVQKAM 287
+ NR FE+ V++ +
Sbjct: 125 RKNREEFEKKVREYV 139
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 148 bits (377), Expect = 9e-45
Identities = 46/133 (34%), Positives = 79/133 (59%), Gaps = 1/133 (0%)
Query: 159 ELNLPKTCTTEFPNPDDLLSFK-LIISPDEGFYRSGKFVFSFKVGPNYPHEPPKVKCETP 217
+ + P + + D+L ++ I P + Y G F + + +YP +PPKV+ T
Sbjct: 18 QKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKPPKVRFTTK 77
Query: 218 VYHPNIDLEGNVCLNILREDWKPVLTINSIVYGLQYLFLEPNPEDPLNKEAAEVLQNNRR 277
++HPN+D GNVCL+IL++ W PV T+ +I+ LQ L L PNP+ PLN EAA + + ++
Sbjct: 78 IFHPNVDPSGNVCLDILKDRWSPVYTLETILLSLQSLLLSPNPDSPLNTEAATLYREDKE 137
Query: 278 LFEQNVQKAMRGG 290
+E+ V++ ++
Sbjct: 138 EYEKKVREWVKKY 150
>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 (321), Expect = 1e-36
Identities = 50/134 (37%), Positives = 77/134 (57%), Gaps = 4/134 (2%)
Query: 154 LSDLNELNLPKTCTTEFPNPDDLLSFK-LIISPDEGFYRSGKFVFSFKVGPNYPHEPPKV 212
L DL + + P + E P ++LL + I P + Y G F + +YP +PPKV
Sbjct: 8 LKDLKK-DPPSGISAE-PVEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKV 65
Query: 213 KCETPVYHPNIDLEGNVCLNILRED-WKPVLTINSIVYGLQYLFLEPNPEDPLNKEAAEV 271
+ T +YHPN+D G +CL+IL+ W P T+ +++ LQ L EPNP DPLN EAA++
Sbjct: 66 RFVTKIYHPNVDENGKICLSILKTHGWSPAYTLRTVLLSLQSLLNEPNPSDPLNAEAAKL 125
Query: 272 LQNNRRLFEQNVQK 285
+ NR F++ ++
Sbjct: 126 YKENREEFKKKARE 139
>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 = 126 bits (319), Expect = 3e-36
Identities = 46/113 (40%), Positives = 70/113 (61%), Gaps = 2/113 (1%)
Query: 174 DDLLSFK-LIISPDEGFYRSGKFVFSFKVGPNYPHEPPKVKCETPVYHPNIDLEGNVCLN 232
++LL + I+ P Y G F + + +YP +PPKVK T +YHPN+D G +CL+
Sbjct: 25 ENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVDSSGEICLD 84
Query: 233 ILR-EDWKPVLTINSIVYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQ 284
IL+ E W P LT+ +++ LQ L EPNP+ PLN +AAE+ + NR F++ +
Sbjct: 85 ILKQEKWSPALTLETVLLSLQSLLSEPNPDSPLNADAAELYKKNREEFKKKAR 137
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 99.1 bits (246), Expect = 2e-25
Identities = 47/124 (37%), Positives = 73/124 (58%), Gaps = 2/124 (1%)
Query: 163 PKTCTTEFPNPDDLLSFKL-IISPDEGFYRSGKFVFSFKVGPNYPHEPPKVKCETPVYHP 221
P C+ P+ ++L + II P + Y G F S P+YP +PPKV+ T +YHP
Sbjct: 18 PSNCSAG-PSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHP 76
Query: 222 NIDLEGNVCLNILREDWKPVLTINSIVYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQ 281
NI+ G++CL+ILR+ W P LT++ ++ + L +PNP+DPL E A V + NR +E
Sbjct: 77 NINSNGSICLDILRDQWSPALTVSKVLLSISSLLTDPNPDDPLVPEIARVFKENRSRYEA 136
Query: 282 NVQK 285
++
Sbjct: 137 TARE 140
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 90.6 bits (225), Expect = 2e-22
Identities = 42/107 (39%), Positives = 63/107 (58%), Gaps = 1/107 (0%)
Query: 171 PNPDDLLSFKLIIS-PDEGFYRSGKFVFSFKVGPNYPHEPPKVKCETPVYHPNIDLEGNV 229
P+P + FK+++ PD Y G + + YP EPPKV+ T +YHPNID G +
Sbjct: 26 PDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNIDKLGRI 85
Query: 230 CLNILREDWKPVLTINSIVYGLQYLFLEPNPEDPLNKEAAEVLQNNR 276
CL+IL++ W P L I +++ +Q L P P+DPL+ A+ +NNR
Sbjct: 86 CLDILKDKWSPALQIRTVLLSIQALLSAPEPDDPLDTSVADHFKNNR 132
>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 = 31.9 bits (73), Expect = 0.11
Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 2/63 (3%)
Query: 177 LSFKLIISPDEGFYRSGKFVFSFKVGPNYPHEPPKVKCETPVYHPNIDLEGNVCLNILRE 236
++ KL S DEG + K+ NYP E P + + L L L E
Sbjct: 25 ITIKLSPSSDEGEDQYVSLTLQVKLPENYPDEAPPISLLNSEGLSDEQLA--ELLKKLEE 82
Query: 237 DWK 239
+
Sbjct: 83 IAE 85
>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 = 31.1 bits (71), Expect = 0.23
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 5/65 (7%)
Query: 178 SFKLIISPDEGFYRSGK---FVFSFKVGPNYPHEPPKVKCETPVYHPNIDLEGNVCLNIL 234
+F + + S V +F + +YP EPPK+ +P D + L L
Sbjct: 32 TFTIKLKLLTSEAESSPLVSLVLTFTLPEDYPDEPPKISLSSP--WLLRDQDKLQLLKEL 89
Query: 235 REDWK 239
E +
Sbjct: 90 EELAE 94
>gnl|CDD|182623 PRK10657, PRK10657, isoaspartyl dipeptidase; Provisional.
Length = 388
Score = 28.2 bits (64), Expect = 5.4
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 275 NRRLFEQNVQKAMRGGYI 292
N LFEQ ++ A +GG I
Sbjct: 229 NEPLFEQALEFAKKGGVI 246
>gnl|CDD|233326 TIGR01239, galT_2, galactose-1-phosphate uridylyltransferase,
family 2. This enzyme is involved in glucose and
galactose interconversion. This model describes one of
two extremely distantly related branches of the model
pfam01087 from PFAM [Energy metabolism, Sugars].
Length = 489
Score = 28.3 bits (63), Expect = 6.1
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 253 YLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQKAMRGGYIGSVYFERCLK 302
YL + N ++KE A+ L+ R + ++NV ++ +G V F R L+
Sbjct: 420 YLLGQDNQLTAIHKEWADRLKEKRNITKENVDLVIKQE-VGHV-FARVLE 467
>gnl|CDD|236435 PRK09261, PRK09261, phospho-2-dehydro-3-deoxyheptonate aldolase;
Validated.
Length = 349
Score = 27.4 bits (62), Expect = 8.7
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 153 FLSDLNELNLPKTCTTEFPNP------DDLLS 178
L D+NEL LP TEF +P DL+S
Sbjct: 129 LLLDINELGLP--AATEFLDPITPQYIADLIS 158
>gnl|CDD|239157 cd02756, MopB_Arsenite-Ox, Arsenite oxidase (Arsenite-Ox) oxidizes
arsenite to the less toxic arsenate; it transfers the
electrons obtained from the oxidation of arsenite
towards the soluble periplasmic electron carriers
cytochrome c and/or amicyanin. Arsenite oxidase is a
heterodimeric enzyme containing a large and a small
subunit. The large catalytic subunit harbors the
molybdopterin cofactor and the [3Fe-4S] cluster; and the
small subunit belongs to the structural class of the
Rieske proteins. The small subunit is not included in
this alignment. Members of MopB_Arsenite-Ox CD belong to
the molybdopterin_binding (MopB) superfamily of
proteins.
Length = 676
Score = 27.8 bits (62), Expect = 9.1
Identities = 20/111 (18%), Positives = 32/111 (28%), Gaps = 4/111 (3%)
Query: 28 CQIKNMI--KLFSLKQQKKDGENPARPGTQQK-KASAAQLRITKAELELPTYSGSVLLHQ 84
I MI +++ L Q++ G + K E
Sbjct: 554 WWIAAMIANRIYELYQEEGKGGSAQYQFFGFIWKTEEDNFMDGSQEFADGGEFSEDYYVL 613
Query: 85 GVLLYKGPTYLFGQESGFNQTNTNLISWSVLLHQGVLLYKGPTYLFGQESG 135
G Y+G TY + G N + + +V V +F E G
Sbjct: 614 GQERYEGVTYNRLKAVGVNGIQLPVTTDTV-TKILVTNVLRTEGVFDTEDG 663
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 0.138 0.422
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: 15,337,001
Number of extensions: 1431985
Number of successful extensions: 981
Number of sequences better than 10.0: 1
Number of HSP's gapped: 977
Number of HSP's successfully gapped: 16
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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: 59 (26.6 bits)