RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy621
(289 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 = 106 bits (267), Expect = 1e-28
Identities = 33/61 (54%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 224 FRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPNVY 283
V DDNLFEWEV I GP T Y+GG FK ++FP DYP+ PP ++F TK++HPNV
Sbjct: 17 ISAFPV-DDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNVD 75
Query: 284 E 284
Sbjct: 76 P 76
Score = 68.0 bits (167), Expect = 3e-14
Identities = 27/51 (52%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 13 LSMEYKSLQEEPVEGFRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAIIE 63
L E K L ++P G V DDNLFEWEV I GP T Y+GG FK IE
Sbjct: 2 LQKELKELLKDPPPGISAFPV-DDNLFEWEVTIIGPEGTPYEGGVFKLDIE 51
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 106 bits (266), Expect = 2e-28
Identities = 34/61 (55%), Positives = 42/61 (68%)
Query: 224 FRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPNVY 283
V+DDNLF WE I GPPDT Y+GG FK ++FP DYP+ PP +RF TK++HPNV
Sbjct: 25 ISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKPPKVRFTTKIFHPNVD 84
Query: 284 E 284
Sbjct: 85 P 85
Score = 71.1 bits (175), Expect = 3e-15
Identities = 30/59 (50%), Positives = 37/59 (62%)
Query: 5 PTSSALRALSMEYKSLQEEPVEGFRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAIIE 63
+ SAL+ L E K LQ++P G V+DDNLF WE I GPPDT Y+GG FK +E
Sbjct: 2 SSPSALKRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLE 60
>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 = 103 bits (259), Expect = 2e-27
Identities = 32/64 (50%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 224 FRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPNVY 283
+ V ++NL EW I GPPDT Y+GG FK ++FP DYP+ PP +RF+TK++HPNV
Sbjct: 19 ISAEPV-EENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNVD 77
Query: 284 EGTA 287
E
Sbjct: 78 ENGK 81
Score = 66.8 bits (164), Expect = 8e-14
Identities = 24/53 (45%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 11 RALSMEYKSLQEEPVEGFRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAIIE 63
+ L E K L+++P G + V ++NL EW I GPPDT Y+GG FK IE
Sbjct: 2 KRLQKELKDLKKDPPSGISAEPV-EENLLEWHGTIRGPPDTPYEGGIFKLDIE 53
>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 = 99.3 bits (248), Expect = 7e-26
Identities = 31/61 (50%), Positives = 42/61 (68%)
Query: 224 FRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPNVY 283
F V+D+NL EW I GPP T Y+GG FK ++FP DYP+ PP ++F+TK++HPNV
Sbjct: 17 FTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVD 76
Query: 284 E 284
Sbjct: 77 S 77
Score = 61.9 bits (151), Expect = 5e-12
Identities = 25/51 (49%), Positives = 31/51 (60%)
Query: 13 LSMEYKSLQEEPVEGFRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFKAIIE 63
L E K L+++P GF V+D+NL EW I GPP T Y+GG FK IE
Sbjct: 2 LLKELKELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIE 52
>gnl|CDD|217050 pfam02460, Patched, Patched family. The transmembrane protein
Patched is a receptor for the morphogene Sonic Hedgehog.
This protein associates with the smoothened protein to
transduce hedgehog signals.
Length = 801
Score = 81.6 bits (202), Expect = 3e-17
Identities = 36/157 (22%), Positives = 71/157 (45%), Gaps = 10/157 (6%)
Query: 75 NQIENLTKTFEASSFISAPLYTESWLRSFVSYVRRNQDFLNVTIDTREGFLKTLNDLWLF 134
+++ + FE++ + P T WLR + ++ + N L D + + +L
Sbjct: 512 DRLNEMVDEFESTPYSMGPNSTSFWLREYENFYKTNGSELE---DEEKSWSYDELKWFLK 568
Query: 135 KP--NPFSLDIKFN----DDGTKIIASRFMIQAVNITDGNMEKEMVKELRRIAHE-SSLN 187
P +P+ D+ ++ D+ T++ RF +++ +++E R +A E N
Sbjct: 569 WPGNSPWQGDLVWDNKSDDNTTEVTKFRFTTAGKDLSTWTDRTRLLQEWRGVADEYPEFN 628
Query: 188 VSVFHPYFVFFDQFELVRPTTIQSMLGGSVTMMFIRF 224
V+VF F DQ + P TIQS++ + M + F
Sbjct: 629 VTVFDEDSPFLDQILTILPDTIQSIIWTLICMAIVCF 665
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 68.6 bits (167), Expect = 2e-14
Identities = 25/51 (49%), Positives = 35/51 (68%)
Query: 232 DNLFEWEVAIFGPPDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPNV 282
+NLF W +I GP D+ Y GG F + FP DYP+ PP ++F TK++HPN+
Sbjct: 28 ENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNI 78
Score = 35.5 bits (81), Expect = 0.011
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 9 ALRALSMEYKSLQEEPVEGFRVKLVNDDNLFEWEVAIFGPPDTLYQGGYF 58
A + + E+K L ++P ++ NLF W +I GP D+ Y GG F
Sbjct: 2 ATKRIQKEHKDLLKDPPSNCSAGPSDE-NLFRWTASIIGPSDSPYAGGVF 50
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 57.9 bits (140), Expect = 2e-10
Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 230 NDDNLFEWEVAIFGPPDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPNV 282
+ N +++ + GP T Y+GGY+K + P YP PP +RFLTK++HPN+
Sbjct: 27 DPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNI 79
Score = 27.1 bits (60), Expect = 7.4
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 8 SALRALSMEYKSLQEEPVEGFRVKLVNDDNLFEWEVAIFGPPDTLYQGGYFK 59
S + + E ++L +P G + + + N +++ + GP T Y+GGY+K
Sbjct: 2 SISKRIEKETQNLANDPPPGIKAEP-DPGNYRHFKILMEGPDGTPYEGGYYK 52
>gnl|CDD|234000 TIGR02760, TraI_TIGR, conjugative transfer relaxase protein TraI.
This protein is a component of the relaxosome complex.
In the process of conjugative plasmid transfer the
realaxosome binds to the plasmid at the oriT (origin of
transfer) site. The relaxase protein TraI mediates the
single-strand nicking and ATP-dependent unwinding
(relaxation, helicase activity) of the plasmid molecule.
These two activities reside in separate domains of the
protein.
Length = 1960
Score = 38.0 bits (88), Expect = 0.006
Identities = 17/105 (16%), Positives = 36/105 (34%), Gaps = 9/105 (8%)
Query: 89 FISAPLYTESWLRSFVSYVRRNQDFLNVTIDTREGFLKTLNDLWLFKPNPFSLDIKFNDD 148
F L+T + + ++ + T +G L+ + K + F+L D
Sbjct: 387 FTQKGLFTTQTM------LTNEKELIARTEG-GKGALRVIVSKQ--KLSEFALSPSNKDA 437
Query: 149 GTKIIASRFMIQAVNITDGNMEKEMVKELRRIAHESSLNVSVFHP 193
+ + S +N G E+ + L +A E + +
Sbjct: 438 VSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASEQGYEIQIITA 482
>gnl|CDD|212105 cd10793, GH57N_TLGT_like, N-terminal catalytic domain of
4-alpha-glucanotransferase; glycoside hydrolase family
57 (GH57). 4-alpha-glucanotransferase (TLGT, EC
2.4.1.25) plays a key role in the maltose metabolism. It
catalyzes the disproportionation of amylose and the
formation of large cyclic alpha-1,4-glucan
(cycloamylose) from linear amylose. TLGT functions as a
homodimer. Each monomer is composed of two domains, an
N-terminal catalytic domain with a (beta/alpha)7 barrel
fold and a C-terminal domain with a twisted
beta-sandwich fold. Some family members have been
designated as alpha-amylases, such as the heat-stable
eubacterial amylase from Dictyoglomus thermophilum
(DtAmyA) and the extremely thermostable archaeal amylase
from Pyrococcus furiosus(PfAmyA). However, both of these
proteins are 4-alpha-glucanotransferases. DtAmyA was
shown to have transglycosylating activity and PfAmyA
exhibits 4-alpha-glucanotransferase activity.
Length = 279
Score = 29.9 bits (68), Expect = 1.2
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 95 YTESWLRSFVSYVRRNQDFLNVT 117
Y WL F+ + N D++ T
Sbjct: 226 YERGWLERFLELLLENSDWIETT 248
>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model
describes Niemann-Pick C type protein in eukaryotes. The
defective protein has been associated with Niemann-Pick
disease which is described in humans as autosomal
recessive lipidosis. It is characterized by the lysosomal
accumulation of unestrified cholesterol. It is an
integral membrane protein, which indicates that this
protein is most likely involved in cholesterol transport
or acts as some component of cholesterol homeostasis
[Transport and binding proteins, Other].
Length = 1204
Score = 29.8 bits (67), Expect = 1.8
Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 15/93 (16%)
Query: 146 NDDGTKIIASRFMIQAVNITDGNMEKEMVKELR-------RIAHESSLNVSVFHPYFVFF 198
T I AS FM T N + + + LR + + V + ++VFF
Sbjct: 984 GHANTIIQASYFMTYH---TPLNTQADFINALRAAREISANVTRSLKMEVFPYSVFYVFF 1040
Query: 199 DQFELVRPTTIQSM---LGG--SVTMMFIRFRV 226
+Q+ + + ++ LG VT++ +
Sbjct: 1041 EQYLTIWSDALINLGISLGAIFIVTLVLLGLNA 1073
>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 = 28.1 bits (63), Expect = 2.1
Identities = 8/37 (21%), Positives = 12/37 (32%)
Query: 245 PDTLYQGGYFKAHMKFPIDYPYSPPTIRFLTKVWHPN 281
+ Q +K P +YP P I L +
Sbjct: 34 DEGEDQYVSLTLQVKLPENYPDEAPPISLLNSEGLSD 70
>gnl|CDD|173541 PTZ00348, PTZ00348, tyrosyl-tRNA synthetase; Provisional.
Length = 682
Score = 29.1 bits (65), Expect = 2.8
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 15/75 (20%)
Query: 63 EGE----LPHWDVNVQNQIENLTKTFEASSFISAPLYTESWLRSFVSYVRRNQDFLNVTI 118
+G LP W ++I K A+ ++ L L S V VR N+ L
Sbjct: 407 DGTVTLVLPDWSAVASDEITGEEKDISAALEVNCALLKAYGLPSEVKIVRENEVILG--- 463
Query: 119 DTREGFLKTLNDLWL 133
ND W+
Sbjct: 464 --------NPNDFWV 470
>gnl|CDD|107197 PHA02515, PHA02515, hypothetical protein; Provisional.
Length = 508
Score = 28.6 bits (63), Expect = 4.4
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 49 PDTLY-QGGYFKAIIEGELPHWDVNVQNQIENLTKTFEA 86
P+TL QGG++ +IE L + +Q + L++T +A
Sbjct: 93 PETLTNQGGFYPKVIEHALDRLVIQIQQLADKLSRTVQA 131
>gnl|CDD|236422 PRK09234, fbiC, FO synthase; Reviewed.
Length = 843
Score = 28.0 bits (63), Expect = 6.2
Identities = 23/79 (29%), Positives = 31/79 (39%), Gaps = 18/79 (22%)
Query: 9 ALRALSMEYKSLQEEPVEGFRVKL------VNDDNLFE--WEVA----IFGP------PD 50
A+R L EY +QE V+ FR K V D L E +A + GP P
Sbjct: 255 AIRKLHREYGHIQEVIVQNFRAKPDTAMAGVPDAGLEELLATIAVARLVLGPKMRIQAPP 314
Query: 51 TLYQGGYFKAIIEGELPHW 69
L G A++ + W
Sbjct: 315 NLVSGDECAALLGAGIDDW 333
>gnl|CDD|214798 smart00743, Agenet, Tudor-like domain present in plant sequences.
Domain in plant sequences with possible
chromatin-associated functions.
Length = 59
Score = 25.4 bits (56), Expect = 7.6
Identities = 7/41 (17%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 50 DTLYQGGYFKAIIEGELPHWDVNV--QNQIENLTKTFEASS 88
+ + +++A++ L V + + E L T + S
Sbjct: 10 EVFSEDSWWEAVVTKVLGDGKYLVEYKGESEPLELTVDWSD 50
>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 = 26.5 bits (59), Expect = 9.1
Identities = 7/23 (30%), Positives = 8/23 (34%)
Query: 254 FKAHMKFPIDYPYSPPTIRFLTK 276
P DYP PP I +
Sbjct: 52 LVLTFTLPEDYPDEPPKISLSSP 74
>gnl|CDD|223506 COG0429, COG0429, Predicted hydrolase of the alpha/beta-hydrolase
fold [General function prediction only].
Length = 345
Score = 27.3 bits (61), Expect = 10.0
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 90 ISAPLYTESWLRSFVSYVRRNQDFLNVTI-DTREGFLKTLNDLWLF 134
S LY+ LR+ R L ++ T +K + F
Sbjct: 198 FSLRLYSRYLLRNLKRNAARKLKELEPSLPGTVLAAIKRCRTIREF 243
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 0.139 0.424
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,186,533
Number of extensions: 1461753
Number of successful extensions: 1301
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1297
Number of HSP's successfully gapped: 32
Length of query: 289
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 193
Effective length of database: 6,679,618
Effective search space: 1289166274
Effective search space used: 1289166274
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: 58 (26.1 bits)