RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2846
(392 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 = 110 bits (277), Expect = 2e-29
Identities = 42/80 (52%), Positives = 52/80 (65%)
Query: 214 RLRKEYNDIKLDPPDGIQAQPLDNKRCHWMATIAGPVASPYEGGVFYLYIRIPFSYPMHP 273
RL+KE ++ DPP GI A P+D+ W TI GP +PYEGGVF L I P YP P
Sbjct: 1 RLQKELKELLKDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKP 60
Query: 274 PKVKFITRIFHPNVSRHGDL 293
PKVKF T+I+HPNV G++
Sbjct: 61 PKVKFTTKIYHPNVDPSGEI 80
>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 = 1e-26
Identities = 41/80 (51%), Positives = 54/80 (67%)
Query: 214 RLRKEYNDIKLDPPDGIQAQPLDNKRCHWMATIAGPVASPYEGGVFYLYIRIPFSYPMHP 273
RL+KE D+K DPP GI A+P++ W TI GP +PYEGG+F L I P YP P
Sbjct: 3 RLQKELKDLKKDPPSGISAEPVEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKP 62
Query: 274 PKVKFITRIFHPNVSRHGDL 293
PKV+F+T+I+HPNV +G +
Sbjct: 63 PKVRFVTKIYHPNVDENGKI 82
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 101 bits (254), Expect = 7e-26
Identities = 42/82 (51%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 211 RHFRLRKEYNDIKLDPPDGIQAQPLDNKRC-HWMATIAGPVASPYEGGVFYLYIRIPFSY 269
RL KE ++ DPP GI A P+D+ HW ATI GP +PYEGG+F L + P Y
Sbjct: 6 ALKRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDY 65
Query: 270 PMHPPKVKFITRIFHPNVSRHG 291
P PPKV+F T+IFHPNV G
Sbjct: 66 PFKPPKVRFTTKIFHPNVDPSG 87
>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 = 93.9 bits (234), Expect = 4e-23
Identities = 42/81 (51%), Positives = 53/81 (65%), Gaps = 1/81 (1%)
Query: 214 RLRKEYNDIKLDPPDGIQAQPLDNKR-CHWMATIAGPVASPYEGGVFYLYIRIPFSYPMH 272
RL KE +++ DPP G A P+D++ W TI GP +PYEGGVF L I P YP
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFK 60
Query: 273 PPKVKFITRIFHPNVSRHGDL 293
PPKVKFIT+I+HPNV G++
Sbjct: 61 PPKVKFITKIYHPNVDSSGEI 81
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 88.7 bits (219), Expect = 4e-21
Identities = 38/80 (47%), Positives = 51/80 (63%)
Query: 214 RLRKEYNDIKLDPPDGIQAQPLDNKRCHWMATIAGPVASPYEGGVFYLYIRIPFSYPMHP 273
R++KE+ D+ DPP A P D W A+I GP SPY GGVF+L I P YP P
Sbjct: 5 RIQKEHKDLLKDPPSNCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKP 64
Query: 274 PKVKFITRIFHPNVSRHGDL 293
PKV+F T+I+HPN++ +G +
Sbjct: 65 PKVQFTTKIYHPNINSNGSI 84
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 84.9 bits (210), Expect = 1e-19
Identities = 34/78 (43%), Positives = 51/78 (65%)
Query: 214 RLRKEYNDIKLDPPDGIQAQPLDNKRCHWMATIAGPVASPYEGGVFYLYIRIPFSYPMHP 273
R+ KE ++ DPP GI+A+P H+ + GP +PYEGG + L + +P YPM P
Sbjct: 6 RIEKETQNLANDPPPGIKAEPDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPMEP 65
Query: 274 PKVKFITRIFHPNVSRHG 291
PKV+F+T+I+HPN+ + G
Sbjct: 66 PKVRFLTKIYHPNIDKLG 83
>gnl|CDD|221867 pfam12937, F-box-like, F-box-like. This is an F-box-like family.
Length = 47
Score = 51.0 bits (123), Expect = 7e-09
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 113 IHSLPPEVLITVFSYLDDLSLCSVSRACTRWFTIIAD 149
+ LP E+L+ +FSYLD L ++ C RW + +D
Sbjct: 1 LSDLPDEILLQIFSYLDPRDLLRLALVCRRWRELASD 37
Score = 27.5 bits (62), Expect = 1.3
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 344 LDDLSLCSVSRACTRWFTIIAD 365
LD L ++ C RW + +D
Sbjct: 16 LDPRDLLRLALVCRRWRELASD 37
>gnl|CDD|201368 pfam00646, F-box, F-box domain. This domain is approximately 50
amino acids long, and is usually found in the N-terminal
half of a variety of proteins. Two motifs that are
commonly found associated with the F-box domain are the
leucine rich repeats (LRRs; pfam00560 and pfam07723) and
the WD repeat (pfam00400). The F-box domain has a role
in mediating protein-protein interactions in a variety
of contexts, such as polyubiquitination, transcription
elongation, centromere binding and translational
repression.
Length = 48
Score = 40.6 bits (96), Expect = 3e-05
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 111 SSIHSLPPEVLITVFSYLDDLSLCSVSRACTRWFTIIADL 150
S+ LP ++L+ + S LD L +S RW +++ L
Sbjct: 1 FSLLDLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSL 40
>gnl|CDD|197608 smart00256, FBOX, A Receptor for Ubiquitination Targets.
Length = 41
Score = 39.3 bits (93), Expect = 8e-05
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 116 LPPEVLITVFSYLDDLSLCSVSRACTRWFTIIAD 149
LP E+L + S LD L + + +W ++I
Sbjct: 1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDS 34
>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage [Cellular processes, DNA transformation].
Length = 410
Score = 31.2 bits (71), Expect = 0.95
Identities = 20/107 (18%), Positives = 32/107 (29%), Gaps = 12/107 (11%)
Query: 3 ETETHSWNFDFSLTSDEELPVVPARHYVFNAGAAGGGGYHQQDDNHPVPPVRENNLLYDE 62
E ET +N D DE + + Y A Q+D R L D
Sbjct: 36 EEETKGFNADIPQPKDEGIIGDKMKAYEQEALEQ-----KQKDKK------RTLQDLADS 84
Query: 63 VDNELEEGDDLPAPQNNPDEPELQRRIEELSAYNKNNRAVLTSQNTG 109
+ +E D + + DE E E + + ++
Sbjct: 85 FEKSDKESQDYSSSDSGFDE-EPDEPAETAGSLRPIRSSAAAYRDIN 130
>gnl|CDD|180561 PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/
hydroxy-phosphomethylpyrimidine kinase; Reviewed.
Length = 266
Score = 30.9 bits (71), Expect = 1.0
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 103 LTSQNT-GGSSIHSLPPEVL 121
LT+QNT G +H +PPE +
Sbjct: 42 LTAQNTLGVQRVHPIPPEFV 61
>gnl|CDD|219282 pfam07061, Swi5, Swi5. Swi5 is involved in meiotic DNA repair
synthesis and meiotic joint molecule formation. It is
known to interact with Swi2, Rhp51 and Swi6.
Length = 81
Score = 28.8 bits (65), Expect = 1.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 211 RHFRLRKEYNDIK 223
RH RL EYN+IK
Sbjct: 38 RHIRLLHEYNEIK 50
>gnl|CDD|234769 PRK00451, PRK00451, glycine dehydrogenase subunit 1; Validated.
Length = 447
Score = 30.1 bits (69), Expect = 2.0
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 59 LYDEVDNEL--EEGDDLPAPQNNPDEPELQRRIEELSAYNKN 98
L+ ++ EL + DLP E EL R + EL+A NK
Sbjct: 27 LFADIPEELRLKRPLDLPPGL---SEMELLRHLRELAAKNKT 65
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain.
Length = 192
Score = 29.5 bits (67), Expect = 2.3
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 13/51 (25%)
Query: 54 RENNLLYDEVDNELEEGDDLPAPQNNPDEPEL----QRRIEELSAYNKNNR 100
L DE+D EL+E + D+ L ++R+ E+ A + ++
Sbjct: 39 ALEKKLLDELDEELDEEE---------DDRFLEEYRRKRLAEMKALAEKSK 80
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 29.5 bits (67), Expect = 3.4
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 121 LITVFSYLDDLSL 133
LITVFSYLD ++L
Sbjct: 806 LITVFSYLDSITL 818
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 28.7 bits (65), Expect = 4.0
Identities = 13/43 (30%), Positives = 19/43 (44%)
Query: 61 DEVDNELEEGDDLPAPQNNPDEPELQRRIEELSAYNKNNRAVL 103
D+ D+E E+ DD PD E + R EL + R +
Sbjct: 56 DDDDDEDEDEDDEEEADLGPDPEEARERFAELREQYEKTRKAI 98
>gnl|CDD|185678 cd02039, cytidylyltransferase_like, Cytidylyltransferase-like
domain. Cytidylyltransferase-like domain. Many of these
proteins are known to use CTP or ATP and release
pyrophosphate. Protein families that contain at least
one copy of this domain include citrate lyase ligase,
pantoate-beta-alanine ligase, glycerol-3-phosphate
cytidyltransferase, ADP-heptose synthase, phosphocholine
cytidylyltransferase, lipopolysaccharide core
biosynthesis protein KdtB, the bifunctional protein
NadR, and a number whose function is unknown.
Length = 143
Score = 28.2 bits (63), Expect = 4.8
Identities = 11/62 (17%), Positives = 18/62 (29%), Gaps = 6/62 (9%)
Query: 70 GDDLPAPQNNPDEPELQRRIEELSAYNKNNRAVLT------SQNTGGSSIHSLPPEVLIT 123
+ P + N D L R+E L K+ V+ I + +V
Sbjct: 35 VSNPPKKKRNKDPFSLHERVEMLKEILKDRLKVVPVDFPEVKILLAVVFILKILLKVGPD 94
Query: 124 VF 125
Sbjct: 95 KV 96
>gnl|CDD|187836 cd09705, Csf1_U, CRISPR/Cas system-associated protein Csf1. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Zn-finger domain containing
protein; also known as Csf1 family.
Length = 202
Score = 27.9 bits (62), Expect = 7.9
Identities = 12/30 (40%), Positives = 13/30 (43%)
Query: 293 LSHAPAQGEIYHSNISSECAETWGRRHRLY 322
L+ APA E Y S ETW R L
Sbjct: 173 LAEAPAYPEAYQLLQSLTVGETWALRFLLS 202
>gnl|CDD|234111 TIGR03114, cas_csf1, CRISPR type AFERR-associated protein Csf1.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic of
a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster found.
The gene is designated csf1 (CRISPR/cas Subtype as in A.
ferrooxidans protein 1), as it lies closest to the
repeats [Mobile and extrachromosomal element functions,
Other].
Length = 202
Score = 27.9 bits (62), Expect = 7.9
Identities = 12/30 (40%), Positives = 13/30 (43%)
Query: 293 LSHAPAQGEIYHSNISSECAETWGRRHRLY 322
L+ APA E Y S ETW R L
Sbjct: 173 LAEAPAYPEAYQLLQSLTVGETWALRFLLS 202
>gnl|CDD|139538 PRK13390, PRK13390, acyl-CoA synthetase; Provisional.
Length = 501
Score = 28.1 bits (62), Expect = 8.8
Identities = 15/48 (31%), Positives = 20/48 (41%)
Query: 256 GGVFYLYIRIPFSYPMHPPKVKFITRIFHPNVSRHGDLSHAPAQGEIY 303
G V++ R+PF Y P K HP + GDL G +Y
Sbjct: 349 GTVYFERDRLPFRYLNDPEKTAAAQHPAHPFWTTVGDLGSVDEDGYLY 396
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 28.1 bits (63), Expect = 9.4
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 15/71 (21%)
Query: 318 RHRLYSILFSNSIRDHIQRRPRVRFP-LDDLSLCSVSR--ACTRWFTIIADLISSDQ--- 371
R+ L +LFS R F L+ ++ R A W+ I D+ SD
Sbjct: 184 RNTLALLLFS-------SGRRDEGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVA 236
Query: 372 -WRYFVLTRFP 381
+ + L F
Sbjct: 237 ALQKY-LQVFS 246
>gnl|CDD|184902 PRK14938, PRK14938, Ser-tRNA(Thr) hydrolase; Provisional.
Length = 387
Score = 27.9 bits (62), Expect = 10.0
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 53 VRENN----LLYDEVDNELEEGDDLPAPQNNPDEPELQRR 88
+R NN + +E+ E++ D+L N P L +
Sbjct: 345 IRANNEQKSMTVEELVKEIKRADELKERSNLPLYYSLYKH 384
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
0.321 0.136 0.438
Gapped
Lambda K H
0.267 0.0873 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,775,612
Number of extensions: 2010601
Number of successful extensions: 1683
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1681
Number of HSP's successfully gapped: 32
Length of query: 392
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 293
Effective length of database: 6,546,556
Effective search space: 1918140908
Effective search space used: 1918140908
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: 60 (26.6 bits)