RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16998
(98 letters)
>gnl|CDD|176359 cd01763, Sumo, Small ubiquitin-related modifier (SUMO). Small
ubiquitin-related modifier (SUMO) proteins are
conjugated to numerous intracellular targets and serve
to modulate protein interaction, localization, activity
or stability. SUMO (also known as "Smt3" and "sentrin"
in other organisms) is linked to several different
pathways, including nucleocytoplasmic transport.
Attachment of SUMO to targets proteins is stimulated by
PIAS (Protein inhibitor of activated STATs) proteins
which serve as E3-like ligases.
Length = 87
Score = 59.6 bits (145), Expect = 2e-13
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 19 SSADGGDNVEYIKLKVLSSDSNEIHFRVKMTTPMGKLKKSYSERVENKPM 68
+ G+ E+I LKV D NE+ F++K +TP+ KL ++Y +R M
Sbjct: 1 EKSGKGEISEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQ-GLSM 49
>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like. The
small ubiquitin-related modifier SUMO-1 is a Ub/Ubl
family member, and although SUMO-1 shares structural
similarity to Ub, SUMO's cellular functions remain
distinct insomuch as SUMO modification alters protein
function through changes in activity, cellular
localisation, or by protecting substrates from
ubiquitination. Rad60 family members contain
functionally enigmatic, integral SUMO-like domains
(SLDs). Despite their divergence from SUMO, each Rad60
SLD interacts with a subset of SUMO pathway enzymes:
SLD2 specifically binds the SUMO E2 conjugating enzyme
(Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also
called Uba2) activating and E3 (Pli1, also called Siz1
and Siz2) specificity enzymes. Structural analysis of
PDB:2uyz reveals a mechanistic basis for the
near-synonymous roles of Rad60 and SUMO in survival of
genotoxic stress and suggest unprecedented
DNA-damage-response functions for SLDs in regulating
SUMOylation. The Rad60 branch of this family is also
known as RENi (Rad60-Esc2-Nip45), and biologically it
should be two distinct families SUMO and RENi
(Rad60-Esc2-Nip45).
Length = 72
Score = 38.3 bits (90), Expect = 3e-05
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 30 IKLKVLSSDSNEIHFRVKMTTPMGKLKKSYSERV 63
I++K+ D E+ +VK TT + KL +Y ++
Sbjct: 1 IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKR 34
>gnl|CDD|227552 COG5227, SMT3, Ubiquitin-like protein (sentrin)
[Posttranslational modification, protein turnover,
chaperones].
Length = 103
Score = 38.4 bits (89), Expect = 6e-05
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 5 SSVSYQTSKPPMKSSSADGGDNVEYIKLKVLSSDSNEIHFRVKMTTPMGKLKKSYSERV 63
SS S K ++I LKV+ D E+ F++K TT KL ++S R
Sbjct: 3 SSDSGSEFKTNENP---LVKPITKHINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQ 58
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 33.0 bits (76), Expect = 0.004
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 30 IKLKVLSSDSNEIHFRVKMTTPMGKLKKSYSERVENKPMYK 70
I+L V + D I VK + + +LK+ + P +
Sbjct: 1 IELTVKTLDGKTITLEVKPSDTVSELKEKI-AELTGIPPEQ 40
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 27.1 bits (60), Expect = 0.67
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 33 KVLSSDSNEIHFRVKMTTPMGKLKKSYSER 62
KV +D + V T + LK+ +++
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKK 30
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.9 bits (63), Expect = 0.76
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 24 GDNVEYIKLK----VLS-SDSNEIHFRV---KMTTPMGKLKKSYSERVENKPM 68
GD V+Y+ L VLS D E + KM P+ L+K + + K
Sbjct: 640 GDEVKYLSLGQKGEVLSIPDDKEAIVQAGIMKMKVPLSDLEKIQKPKKKKKKK 692
>gnl|CDD|176869 cd08860, TcmN_ARO-CYC_like, N-terminal aromatase/cyclase domain
of the multifunctional protein tetracenomycin (TcmN)
and related domains. This family includes the
N-terminal aromatase/cyclase (ARO/CYC) domain of
Streptomyces glaucescens TcmN, and related domains. It
belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. ARO/CYC domains participate in the
diversification of aromatic polyketides by promoting
polyketide cyclization. They occur in two architectural
forms, monodomain and didomain. Monodomain
aromatase/cyclases have a single ARO/CYC domain. For
some, such as TcmN, this single domain is linked to a
second domain of unrelated function. TcmN is a
multifunctional cyclase-dehydratase-O-methyl
transferase. Its N-terminal ARO/CYC domain participates
in polyketide binding and catalysis; it promotes C9-C14
first-ring (and C7-C16 second-ring) cyclizations. Its
C-terminal domain has O-methyltransferase activity.
Didomain aromatase/cyclases contain two ARO/CYC
domains, and they biosynthesize C7-C12 first ring
cyclized polyketides. These latter domains belong to a
different subfamily in the SRPBCC superfamily.
Length = 146
Score = 26.7 bits (59), Expect = 1.8
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 28 EYIKLKVLSSDSNEIHFRVKM 48
EY + +VL D + + FR+ M
Sbjct: 32 EYAEAEVLEEDGDTVRFRLTM 52
>gnl|CDD|227101 COG4759, COG4759, Uncharacterized protein conserved in bacteria
containing thioredoxin-like domain [Posttranslational
modification, protein turnover, chaperones].
Length = 316
Score = 26.6 bits (59), Expect = 2.1
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 32 LKVLSSDSNE--IHFRVKMTTPMGKLKKSYSERVE--NKPMYK 70
+VL D +E + T+P G + Y RVE M
Sbjct: 252 GQVLEQDEDENWAEVEIDFTSPDGDIWGYYLARVEVEGSVMTV 294
>gnl|CDD|226904 COG4521, TauA, ABC-type taurine transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 334
Score = 26.4 bits (58), Expect = 2.4
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 2 ADNSSVSYQTSKPPMKSSSADG 23
A + +V YQTS P K + ADG
Sbjct: 28 AVDVTVGYQTSAEPAKVAQADG 49
>gnl|CDD|183158 PRK11480, tauA, taurine transporter substrate binding subunit;
Provisional.
Length = 320
Score = 26.5 bits (58), Expect = 2.5
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 2 ADNSSVSYQTSKPPMKSSSADG------GDNVEYIKLKVLSS 37
A N +V+YQTS P K + AD G V++ K +S
Sbjct: 22 AVNVTVAYQTSAEPAKVAQADNTFAKESGATVDWRKFDSGAS 63
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 26.1 bits (58), Expect = 3.3
Identities = 12/48 (25%), Positives = 16/48 (33%), Gaps = 16/48 (33%)
Query: 9 YQTSKPPMKSS--------SADGGDNVEYIKLKVLSSDSNEIHFRVKM 48
YQ PPM S+ + L L D N + RV+
Sbjct: 107 YQI--PPMFSAVKREVERR------KITIYDLLELDFDRNLVTLRVEC 146
>gnl|CDD|180533 PRK06334, PRK06334, long chain fatty acid--[acyl-carrier-protein]
ligase; Validated.
Length = 539
Score = 25.9 bits (57), Expect = 3.4
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 24 GDNVEYIKLKVLSSDSNEIHFRVKMTTPMGKLKKSYSERVENKPMYKAMPMGTGLP 79
G+ V + +E++ +K + LK SY +VE+ PM +GTG P
Sbjct: 474 GEKVRLCLFTTFPTSISEVNDILKNSKTSSILKISYHHQVESIPM-----LGTGKP 524
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 25.4 bits (55), Expect = 7.5
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 16 MKSSSADGGDNVEYIKLKVLSSDSNEI 42
S S+ G +E I +LSSD
Sbjct: 605 FHSCSSIGPLGIEDILKALLSSDDGVF 631
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
0.308 0.125 0.353
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,427,071
Number of extensions: 332937
Number of successful extensions: 174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 174
Number of HSP's successfully gapped: 18
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.1 bits)