RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6012
(168 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 = 118 bits (297), Expect = 9e-35
Identities = 42/115 (36%), Positives = 63/115 (54%), Gaps = 13/115 (11%)
Query: 24 EVTILGAV--FYYGGVWKVRVHLPEHYSSKSPSIGFKNKMYHPNIDGGTLNRIFYISGTV 81
EVTI+G Y GGV+K+ + PE Y K P + F K+YHPN+ SG +
Sbjct: 30 EVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTTKIYHPNV---------DPSGEI 80
Query: 82 CLDVIN-QAWTALYDLSNIFECFLPQLLTYPNPIDPLNGDAAAMYLHKPDEYKKK 135
CLD++ + W+ + + + LL+ PNP DPLN +AA +Y +E++KK
Sbjct: 81 CLDILKDENWSPALTIEQVLL-SIQSLLSEPNPEDPLNAEAAKLYRKNREEFEKK 134
>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 = 109 bits (276), Expect = 1e-31
Identities = 37/104 (35%), Positives = 54/104 (51%), Gaps = 11/104 (10%)
Query: 33 YYGGVWKVRVHLPEHYSSKSPSIGFKNKMYHPNIDGGTLNRIFYISGTVCLDVINQ-AWT 91
Y GG++K+ + PE Y K P + F K+YHPN+ +G +CL ++ W+
Sbjct: 43 YEGGIFKLDIEFPEDYPFKPPKVRFVTKIYHPNV---------DENGKICLSILKTHGWS 93
Query: 92 ALYDLSNIFECFLPQLLTYPNPIDPLNGDAAAMYLHKPDEYKKK 135
Y L + LL PNP DPLN +AA +Y +E+KKK
Sbjct: 94 PAYTLRTVLLSLQS-LLNEPNPSDPLNAEAAKLYKENREEFKKK 136
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 105 bits (263), Expect = 2e-29
Identities = 54/154 (35%), Positives = 75/154 (48%), Gaps = 29/154 (18%)
Query: 1 MSSPSAGKRRMDTDVIKLIESKH----------------EVTILGA--VFYYGGVWKVRV 42
MSSPSA KR + ++ KL + E TI G Y GG++K+ +
Sbjct: 1 MSSPSALKRLL-KELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTL 59
Query: 43 HLPEHYSSKSPSIGFKNKMYHPNIDGGTLNRIFYISGTVCLDVINQAWTALYDLSNIFEC 102
PE Y K P + F K++HPN+D SG VCLD++ W+ +Y L I
Sbjct: 60 EFPEDYPFKPPKVRFTTKIFHPNVDP---------SGNVCLDILKDRWSPVYTLETILLS 110
Query: 103 FLPQLLTYPNPIDPLNGDAAAMYLHKPDEYKKKC 136
LL+ PNP PLN +AA +Y +EY+KK
Sbjct: 111 LQSLLLS-PNPDSPLNTEAATLYREDKEEYEKKV 143
>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 = 99.7 bits (249), Expect = 2e-27
Identities = 45/115 (39%), Positives = 61/115 (53%), Gaps = 13/115 (11%)
Query: 24 EVTILGA--VFYYGGVWKVRVHLPEHYSSKSPSIGFKNKMYHPNIDGGTLNRIFYISGTV 81
TI+G Y GGV+K+ + PE Y K P + F K+YHPN+D SG +
Sbjct: 31 TGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFITKIYHPNVDS---------SGEI 81
Query: 82 CLDVINQA-WTALYDLSNIFECFLPQLLTYPNPIDPLNGDAAAMYLHKPDEYKKK 135
CLD++ Q W+ L + L LL+ PNP PLN DAA +Y +E+KKK
Sbjct: 82 CLDILKQEKWSPALTLETVLLS-LQSLLSEPNPDSPLNADAAELYKKNREEFKKK 135
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 58.7 bits (142), Expect = 2e-11
Identities = 32/99 (32%), Positives = 49/99 (49%), Gaps = 10/99 (10%)
Query: 33 YYGGVWKVRVHLPEHYSSKSPSIGFKNKMYHPNIDGGTLNRIFYISGTVCLDVINQAWTA 92
Y GG +K+ + LPE Y + P + F K+YHPNID L RI CLD++ W+
Sbjct: 46 YEGGYYKLELFLPEQYPMEPPKVRFLTKIYHPNID--KLGRI-------CLDILKDKWSP 96
Query: 93 LYDLSNIFECFLPQLLTYPNPIDPLNGDAAAMYLHKPDE 131
+ + + LL+ P P DPL+ A + + +
Sbjct: 97 ALQIRTVL-LSIQALLSAPEPDDPLDTSVADHFKNNRAD 134
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 56.3 bits (135), Expect = 1e-10
Identities = 32/101 (31%), Positives = 51/101 (50%), Gaps = 10/101 (9%)
Query: 33 YYGGVWKVRVHLPEHYSSKSPSIGFKNKMYHPNIDGGTLNRIFYISGTVCLDVINQAWTA 92
Y GGV+ + + P Y K P + F K+YHPNI+ +G++CLD++ W+
Sbjct: 45 YAGGVFFLSILFPPDYPFKPPKVQFTTKIYHPNINS---------NGSICLDILRDQWSP 95
Query: 93 LYDLSNIFECFLPQLLTYPNPIDPLNGDAAAMYLHKPDEYK 133
+S + + LLT PNP DPL + A ++ Y+
Sbjct: 96 ALTVSKVL-LSISSLLTDPNPDDPLVPEIARVFKENRSRYE 135
>gnl|CDD|177538 PHA03136, PHA03136, thymidine kinase; Provisional.
Length = 378
Score = 29.3 bits (65), Expect = 0.93
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 5/73 (6%)
Query: 90 WTALYDLSNIFECFLPQLLTY----PNPIDPLNGDAAAMYLHKPDEYKKKCLPTMLAPES 145
L L NI+ CF+ +TY P D D A+ D+ KK+CL +PE
Sbjct: 221 VRFLCALHNIYICFM-NTITYAKQAPIMWDADKKDKDALSSAIFDDDKKECLEAADSPEI 279
Query: 146 NPGLPRARRVTTM 158
G T+
Sbjct: 280 VGGKKNPSIDQTL 292
>gnl|CDD|149291 pfam08153, NGP1NT, NGP1NT (NUC091) domain. This N terminal domain
is found in a subfamily of hypothetical nucleolar
GTP-binding proteins similar to human NGP1.
Length = 130
Score = 27.2 bits (61), Expect = 2.9
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 133 KKKCLPTMLAPESNPGLPRARRVTTMPWEQTY 164
K+ LP L +S + + + T P+E T+
Sbjct: 69 KRSKLPMSLLKDSTKKQKKVKILETEPFEDTF 100
>gnl|CDD|163660 cd07417, MPP_PP5_C, PP5, C-terminal metallophosphatase domain.
Serine/threonine protein phosphatase-5 (PP5) is a member
of the PPP gene family of protein phosphatases that is
highly conserved among eukaryotes and widely expressed
in mammalian tissues. PP5 has a C-terminal phosphatase
domain and an extended N-terminal TPR (tetratricopeptide
repeat) domain containing three TPR motifs. The PPP
(phosphoprotein phosphatase) family, to which PP5
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4
hydrolase. The PPP catalytic domain is defined by three
conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The
PPP enzyme family is ancient with members found in all
eukaryotes, and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 316
Score = 27.2 bits (61), Expect = 4.5
Identities = 18/43 (41%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 80 TVCLDVINQAWTALYDLSNIFECFLPQLLTYPNPIDPL--NGD 120
TVC D Q YDL NIFE L P+ +P NGD
Sbjct: 63 TVCGDTHGQ----FYDLLNIFE-----LNGLPSETNPYLFNGD 96
>gnl|CDD|234005 TIGR02774, rexB_recomb, ATP-dependent nuclease subunit B. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RecAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
The partner may be designated AddB, as in Bacillus and
in alphaproteobacteria, or RexB as in Streptococcus and
Lactococcus. Note, however, that RexB proteins lack an
N-terminal GxxGxGK[ST] ATP-binding motif found in
Bacillus subtilis and related species, and this
difference may be important; this model represents
specifically RexB proteins as found in Streptococcus and
Lactococcus [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1076
Score = 27.1 bits (60), Expect = 5.5
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 13/72 (18%)
Query: 69 GTLNRIFYISGTVCLDVINQAWTAL-YDLSNIFECFLPQLLTYPNPIDPLNGDA------ 121
G ++RI +S L V++ +A +D+ + + PQL TY + L A
Sbjct: 881 GIIDRIDRLSDGGSLGVVDYKSSATQFDIPHFYNGLSPQLPTY---LAALKRIAPHEGEQ 937
Query: 122 ---AAMYLHKPD 130
AMYLH +
Sbjct: 938 PIFGAMYLHMQE 949
>gnl|CDD|220265 pfam09491, RE_AlwI, AlwI restriction endonuclease. This family
includes the AlwI (recognises GGATC), Bsp6I (recognises
GC^NGC), BstNBI (recognises GASTC), PleI(recognises
GAGTC) and MlyI (recognises GAGTC) restriction
endonucleases.
Length = 429
Score = 27.0 bits (60), Expect = 5.6
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 94 YDLSNIFECFLPQLLTY--PNPIDP 116
+L E FL QLL Y P+P
Sbjct: 27 TNLKRDQEVFLKQLLKYQIPSPYSK 51
>gnl|CDD|225772 COG3232, HpaF, 5-carboxymethyl-2-hydroxymuconate isomerase [Amino
acid transport and metabolism].
Length = 127
Score = 26.2 bits (58), Expect = 5.6
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 10 RMDTDVIKLIESKHEVTILGAVFYYGGVWKVRVHLPEHY 48
R + D+ L+E + I +F GG+ + R + Y
Sbjct: 13 REEADLPGLLEKVNAALIASGLFPLGGI-RSRALRLDAY 50
>gnl|CDD|233354 TIGR01312, XylB, D-xylulose kinase. This model describes
D-xylulose kinases, a subfamily of the FGGY family of
carbohydrate kinases. The member from Klebsiella
pneumoniae, designated DalK (see PMID:9324246), was
annotated erroneously in GenBank as D-arabinitol kinase
but is authentic D-xylulose kinase. D-xylulose kinase
(XylB) generally is found with xylose isomerase (XylA)
and acts in xylose utilization [Energy metabolism,
Sugars].
Length = 481
Score = 26.9 bits (60), Expect = 6.9
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 78 SGTVCLDVINQAW-TALYDLSNIFECFLPQLL 108
SGT DV +AW L D ++ E LP+L+
Sbjct: 174 SGTGWFDVAKRAWSKELLDALDLPESQLPELI 205
>gnl|CDD|200131 TIGR01804, BADH, glycine betaine aldehyde dehydrogenase. Under
osmotic stress, betaine aldehyde dehydrogenase oxidizes
glycine betaine aldehyde into the osmoprotectant glycine
betaine, via the second of two oxidation steps from
exogenously supplied choline or betaine aldehyde. This
choline-glycine betaine synthesis pathway can be found
in gram-positive and gram-negative bacteria. In
Escherichia coli, betaine aldehyde dehydrogenase (betB)
is osmotically co-induced with choline dehydrogenase
(betA) in the presence of choline. These dehydrogenases
are located in a betaine gene cluster with the upstream
choline transporter (betT) and transcriptional regulator
(betI). Similar to E.coli, betaine synthesis in
Staphylococcus xylosus is also influenced by osmotic
stress and the presence of choline with genes localized
in a functionally equivalent gene cluster. Organization
of the betaine gene cluster in Sinorhizobium meliloti
and Bacillus subtilis differs from that of E.coli by the
absence of upstream choline transporter and
transcriptional regulator homologues. Additionally,
B.subtilis co-expresses a type II alcohol dehydrogenase
with betaine aldehyde dehydrogenase instead of choline
dehydrogenase as in E.coli, St.xylosus, and Si.meliloti.
Betaine aldehyde dehydrogenase is a member of the
aldehyde dehydrogenase family (pfam00171) [Cellular
processes, Adaptations to atypical conditions].
Length = 467
Score = 26.7 bits (59), Expect = 7.0
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 51 KSPSIGFKNKMYHPNIDGGTLNRIFYISGTVCLDVINQAWTALYDLSNIFECFLPQLL 108
KSP I F + +DG + F+ +G VC T ++ I E FL +L+
Sbjct: 246 KSPLIVFDDADLESAVDGA-MLGNFFSAGQVC-----SNGTRVFVHKKIKERFLARLV 297
>gnl|CDD|163685 cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase
and related proteins, catalytic TIM barrel domain.
Homocitrate synthase (HCS) catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate,
the first step in the lysine biosynthesis pathway. This
family includes the Yarrowia lipolytica LYS1 protein as
well as the Saccharomyces cerevisiae LYS20 and LYS21
proteins. This family belongs to the DRE-TIM
metallolyase superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 262
Score = 26.1 bits (58), Expect = 9.2
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 112 NPIDPLNGDAAAMYLHKPDE----YKKKCLP 138
N I PL G A MY P+ YK + LP
Sbjct: 224 NGITPLGGLIARMYTADPEYVVSKYKLELLP 254
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
0.320 0.137 0.434
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: 8,906,490
Number of extensions: 807682
Number of successful extensions: 476
Number of sequences better than 10.0: 1
Number of HSP's gapped: 462
Number of HSP's successfully gapped: 20
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
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 (21.8 bits)
S2: 55 (24.9 bits)