RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10014
(72 letters)
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 56.1 bits (136), Expect = 9e-12
Identities = 23/43 (53%), Positives = 30/43 (69%)
Query: 24 ELTINPPEGIIAGPVNEENFFEWEALITGPEGTCFEGGVFPAK 66
+L +PP GI AGPV+++N F WEA ITGP T +EGG+F
Sbjct: 16 KLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLT 58
>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 = 54.9 bits (133), Expect = 1e-11
Identities = 25/43 (58%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 24 ELTINPPEGIIAGPVNEENFFEWEALITGPEGTCFEGGVFPAK 66
EL +PP GI A PV ++N FEWE I GPEGT +EGGVF
Sbjct: 8 ELLKDPPPGISAFPV-DDNLFEWEVTIIGPEGTPYEGGVFKLD 49
>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 = 52.2 bits (126), Expect = 2e-10
Identities = 21/43 (48%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 24 ELTINPPEGIIAGPVNEENFFEWEALITGPEGTCFEGGVFPAK 66
+L +PP GI A PV EEN EW I GP T +EGG+F
Sbjct: 10 DLKKDPPSGISAEPV-EENLLEWHGTIRGPPDTPYEGGIFKLD 51
>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 = 51.9 bits (125), Expect = 3e-10
Identities = 22/43 (51%), Positives = 26/43 (60%)
Query: 24 ELTINPPEGIIAGPVNEENFFEWEALITGPEGTCFEGGVFPAK 66
EL +PP G A PV++EN EW I GP GT +EGGVF
Sbjct: 8 ELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLT 50
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 35.9 bits (82), Expect = 4e-04
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 24 ELTINPPEGIIAGPVNEENFFEWEALITGPEGTCFEGGVF 63
+L +PP AGP +E N F W A I GP + + GGVF
Sbjct: 12 DLLKDPPSNCSAGPSDE-NLFRWTASIIGPSDSPYAGGVF 50
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 35.2 bits (81), Expect = 8e-04
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 10 PSRIELSPEIINCVELTINPPEGIIAGPVNEENFFEWEALITGPEGTCFEGGVF 63
RIE + L +PP GI A P + N+ ++ L+ GP+GT +EGG +
Sbjct: 4 SKRIEKETQ-----NLANDPPPGIKAEP-DPGNYRHFKILMEGPDGTPYEGGYY 51
>gnl|CDD|199906 cd10318, RGL11, Rhamnogalacturonan lyase of the polysaccharide
lyase family 11. The rhamnogalacturonan lyase of the
polysaccharide lyase family 11 (RGL11) cleaves
glycoside bonds in polygalacturonan as well as RG
(rhamnogalacturonan) type-I through a beta-elimination
reaction. Functionally characterized members of this
family, YesW and YesX from Bacillus subtilis, cleave
glycoside bonds between rhamnose and galacturonic acid
residues in the RG-I region of plant cell wall pectin.
YesW and YesX work synergistically, with YesW cleaving
the glycoside bond of the RG chain endolytically, and
YesX converting the resultant oligosaccharides through
an exotype reaction. This domain is sometimes found in
architectures with non-catalytic carbohydrate-binding
modules (CBMs). There are two types of RG lyases, which
both cleave the alpha-1,4 bonds of the RG-I main chain
through a beta-elimination reaction, but belong to two
structurally unrelated polysaccharide lyase (PL)
families, 4 and 11.
Length = 564
Score = 27.6 bits (62), Expect = 0.46
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 32 GIIAGPVNEENFFEWEALITGPEGTCF 58
G++A F W L T P+G F
Sbjct: 7 GLVAVKTGNGVFVSWRLLGTDPDGIGF 33
>gnl|CDD|112668 pfam03865, ShlB, Haemolysin secretion/activation protein
ShlB/FhaC/HecB. This family represents a group of
sequences that are related to ShlB from Serratia
marcescens. ShlB is an outer membrane protein pore
involved in the Type Vb or Two-partner secretion system
where it is functions to secrete and activate the
haemolysin ShlA. The activation of ShlA occurs during
secretion when ShlB imposes a conformational change in
the inactive haemolysin to form the active protein.
Length = 404
Score = 26.9 bits (59), Expect = 0.87
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 2 KRIKFYTGPSRIELSPEIINCVELTINP----PEGIIAGPVNEENFFEW 46
KRI Y R++LS + EL N P G+ + ++ E W
Sbjct: 185 KRIDNYFEQIRLDLSSPKLTLAELGANHLQIIPNGVFSANLSVEKAMGW 233
>gnl|CDD|224944 COG2033, COG2033, Desulfoferrodoxin [Energy production and
conversion].
Length = 126
Score = 25.1 bits (55), Expect = 2.7
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 32 GIIAGPVNEENFFEWEALITGPE 54
G I P+ E+ W L GP+
Sbjct: 58 GEIPHPMTPEHHIAWIELYFGPD 80
>gnl|CDD|185040 PRK15082, PRK15082, glutathione ABC transporter permease GsiD;
Provisional.
Length = 301
Score = 25.1 bits (55), Expect = 3.9
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 37 PVNEENFFEWEALITGP 53
P + EN+F+++AL GP
Sbjct: 60 PYDAENYFDYDALNAGP 76
>gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide
reductase, iron-sulfur ATP-binding protein. The BchL
peptide (ChlL in chloroplast and cyanobacteria) is an
ATP-binding iron-sulfur protein of the dark form
protochlorophyllide reductase, an enzyme similar to
nitrogenase. This subunit resembles the nitrogenase NifH
subunit [Biosynthesis of cofactors, prosthetic groups,
and carriers, Chlorophyll and bacteriochlorphyll].
Length = 268
Score = 24.0 bits (52), Expect = 7.3
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 8 TGPSRIELSPEIINCVELTINPPEGIIAGPVNEENFFE 45
+GP ++ E + E + PEG++ P+ + FE
Sbjct: 225 SGPELAAVTQEYLRMAEYLLAGPEGVVPTPLIDREIFE 262
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
0.318 0.143 0.441
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: 3,872,673
Number of extensions: 301716
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 12
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
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 (21.6 bits)
S2: 53 (24.2 bits)