RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3659
(78 letters)
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 43.2 bits (101), Expect = 8e-07
Identities = 16/28 (57%), Positives = 20/28 (71%)
Query: 8 SAKRIQKELAEITLDPPPNCSAGPKGDN 35
+ KRIQKE ++ DPP NCSAGP +N
Sbjct: 2 ATKRIQKEHKDLLKDPPSNCSAGPSDEN 29
>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 = 37.6 bits (88), Expect = 1e-04
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 10 KRIQKELAEITLDPPPNCSAGPKGDN 35
KR+QKEL ++ DPP SA P +N
Sbjct: 2 KRLQKELKDLKKDPPSGISAEPVEEN 27
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 37.6 bits (88), Expect = 1e-04
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 6 STSAKRIQKELAEITLDPPPNCSAGPKGDN 35
++ KR+ KEL ++ DPPP SAGP D+
Sbjct: 4 PSALKRLLKELKKLQKDPPPGISAGPVDDD 33
>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 = 36.4 bits (85), Expect = 2e-04
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 11 RIQKELAEITLDPPPNCSAGPKGDN 35
R+QKEL E+ DPPP SA P DN
Sbjct: 1 RLQKELKELLKDPPPGISAFPVDDN 25
>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 = 31.1 bits (71), Expect = 0.028
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 11 RIQKELAEITLDPPPNCSAGPKGDN 35
R+ KEL E+ DPPP +A P D
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDE 25
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 28.6 bits (64), Expect = 0.19
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 10 KRIQKELAEITLDPPPNCSAGPKGDN 35
KRI+KE + DPPP A P N
Sbjct: 5 KRIEKETQNLANDPPPGIKAEPDPGN 30
>gnl|CDD|117565 pfam08999, SP_C-Propep, Surfactant protein C, N terminal
propeptide. The N-terminal propeptide of surfactant
protein C adopts an alpha-helical structure, with turn
and extended regions. It's main function is the
stabilisation of metastable surfactant protein C
(SP-C), since the latter can irreversibly transform
from its native alpha-helical structure to beta-sheet
aggregates and form amyloid-like fibrils. The correct
intracellular trafficking of proSP-C has also been
reported to depend on the propeptide.
Length = 93
Score = 27.7 bits (61), Expect = 0.35
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 18 EITLDPPPNCSAGPKGDNPGIPCTTTRARYALDIFTV 54
E+ ++ PP+ SAGP+G IPC + L + V
Sbjct: 7 EVLMESPPDYSAGPRG-RFRIPCCPVHLKRLLIVVVV 42
>gnl|CDD|128335 smart00019, SF_P, Pulmonary surfactant proteins. Pulmonary
surfactant associated proteins promote alveolar
stability by lowering the surface tension at the
air-liquid interface in the peripheral air spaces.
SP-C, a component of surfactant, is a highly
hydrophobic peptide of 35 amino acid residues which is
processed from a larger precursor protein. SP-C is
post-translationally modified by the covalent
attachment of two palmitoyl groups on two adjacent
cysteines.
Length = 191
Score = 27.6 bits (61), Expect = 0.52
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 18 EITLDPPPNCSAGPKGDNPGIPCTTTRARYALDIFTV 54
E+ ++ PP+ SA P+G GIPC + L + V
Sbjct: 7 EVLMESPPDYSAAPRG-RFGIPCCPVHLKRLLIVVVV 42
>gnl|CDD|169691 PRK09173, PRK09173, F0F1 ATP synthase subunit B; Validated.
Length = 159
Score = 27.4 bits (61), Expect = 0.59
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 1 MSKALSTSAKRIQKELAE 18
++++L A RI+ ELAE
Sbjct: 27 IARSLDARADRIKNELAE 44
>gnl|CDD|153172 cd04900, ACT_UUR-like_1, ACT domain family, ACT_UUR-like_1,
includes the first of two C-terminal ACT domains of the
bacterial signal-transducing uridylyltransferase
/uridylyl-removing (UUR) enzyme, GlnD and related
domains. This ACT domain family, ACT_UUR-like_1,
includes the first of two C-terminal ACT domains of the
bacterial signal-transducing uridylyltransferase
/uridylyl-removing (UUR) enzyme, GlnD; including those
enzymes similar to the GlnD found in enteric
Escherichia coli and those found in photosynthetic,
nitrogen-fixing bacterium Rhodospirillum rubrum. Also
included in this CD is the N-terminal ACT domain of a
yet characterized Arabidopsis/Oryza predicted tyrosine
kinase. Members of this CD belong to the superfamily of
ACT regulatory domains.
Length = 73
Score = 25.5 bits (57), Expect = 1.5
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 42 TTRARYALDIFTV 54
TTR YALD F V
Sbjct: 36 TTRDGYALDTFVV 48
>gnl|CDD|129810 TIGR00727, ISP4_OPT, small oligopeptide transporter, OPT family.
This model represents a family of transporters of small
oligopeptides, demonstrated experimentally in three
different species of yeast. A set of related proteins
from the plant Arabidopsis thaliana forms an outgroup
to the yeast set by neighbor joining analysis but is
remarkably well conserved and is predicted here to have
equivalent function [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 681
Score = 26.0 bits (57), Expect = 2.5
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 28 SAGPKGDNPGIPCTTTRARY-ALDIFTVKQGLRYHFCLR 65
+A P D+P IP T RA + L TV G F R
Sbjct: 11 AAVPPTDDPTIPVNTIRAWFIGLIWSTVGSGFNMFFSHR 49
>gnl|CDD|215172 PLN02303, PLN02303, urease.
Length = 837
Score = 25.5 bits (56), Expect = 3.4
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 23 PPPNCSAGPKGDNPGIPCTTTRARYA 48
+ S G G++P T +R +YA
Sbjct: 252 EEDDASEGVIGEDPDFTTTISREKYA 277
>gnl|CDD|131261 TIGR02206, intg_mem_TP0381, conserved hypothetical integral
membrane protein TIGR02206. This model represents a
family of hydrophobic proteins with seven predicted
transmembrane alpha helices. Members are found in
Bacillus subtilis (ywaF), TP0381 from Treponema
pallidum (TP0381), Streptococcus pyogenes, Rhodococcus
erythropolis, etc.
Length = 222
Score = 25.0 bits (55), Expect = 4.7
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 46 RYALDIFTVKQGLRYHFC 63
L FT+ + L H C
Sbjct: 56 YVLLGGFTLDESLPLHLC 73
>gnl|CDD|203486 pfam06616, BsuBI_PstI_RE, BsuBI/PstI restriction endonuclease
C-terminus. This family represents the C-terminus of
bacterial enzymes similar to type II restriction
endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes
of the BsuBI restriction/modification (R/M) system
recognise the target sequence 5'CTGCAG and are
functionally identical with those of the PstI R/M
system.
Length = 306
Score = 24.9 bits (55), Expect = 5.3
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 34 DNPGIPCTTTRARYALD 50
D PG P + + RYAL
Sbjct: 88 DRPGRPTNSPKPRYALS 104
>gnl|CDD|181401 PRK08360, PRK08360, 4-aminobutyrate aminotransferase; Provisional.
Length = 443
Score = 24.7 bits (54), Expect = 5.9
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 4 ALSTSAKRIQKELAEITLDPPPNCSAGPKGDNPG 37
L + + EL+++ P P+C P G PG
Sbjct: 149 GLDFPVRALVGELSDVHYIPYPDCYRCPFGKEPG 182
>gnl|CDD|241384 cd13230, PH1_SSRP1-like, Structure Specific Recognition protein 1
(SSRP1) Pleckstrin homology (PH) domain, repeat 1.
SSRP1 is a component of FACT (facilitator of chromatin
transcription), an essential chromatin reorganizing
factor. In yeast FACT (yFACT) is composed of three
proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the
Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in
human and mouse, respectively. The middle domain of the
Pob3 subunit (Pob3-M) has an unusual double pleckstrin
homology (PH) architecture. yFACT interacts in a
physiologically important way with the central
single-strand DNA binding factor RPA to promote a step
in DNA Replication. Coordinated function by yFACT and
RPA is important during nucleosome deposition. These
results support the model that the FACT family has an
essential role in constructing nucleosomes during DNA
replication, and suggest that RPA contributes to this
process. Members of this cd are composed of the first
PH-like repeat. PH domains have diverse functions, but
in general are involved in targeting proteins to the
appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 137
Score = 24.0 bits (53), Expect = 7.1
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 38 IPCTTTRARYALDIF 52
+ C T R RY +D++
Sbjct: 12 VLCLTPRGRYDIDMY 26
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 0.135 0.427
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: 3,888,216
Number of extensions: 286404
Number of successful extensions: 223
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 16
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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: 53 (24.2 bits)