RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15977
(152 letters)
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 173 bits (442), Expect = 1e-56
Identities = 65/150 (43%), Positives = 93/150 (62%), Gaps = 19/150 (12%)
Query: 1 LNKNPVEGFSAGLVDDSDIYKWEVLIIGPPDTMYEGGFFKAHLHFPKEYPLRPPKMKFVT 60
L K+P G SAG VDD +++ WE I GPPDT YEGG FK L FP++YP +PPK++F T
Sbjct: 17 LQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPFKPPKVRFTT 76
Query: 61 EIWHPNIEKNGDVCISILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPNDESP 120
+I+HPN++ +G+VC+ IL +RW PV+T+ETIL+S+ S+L PN +SP
Sbjct: 77 KIFHPNVDPSGNVCLDILK-------------DRWSPVYTLETILLSLQSLLLSPNPDSP 123
Query: 121 ANVDAAV------SQYSSENYHWVRRKKIF 144
N +AA +Y + WV++
Sbjct: 124 LNTEAATLYREDKEEYEKKVREWVKKYAEK 153
>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 = 169 bits (431), Expect = 3e-55
Identities = 57/127 (44%), Positives = 84/127 (66%), Gaps = 13/127 (10%)
Query: 1 LNKNPVEGFSAGLVDDSDIYKWEVLIIGPPDTMYEGGFFKAHLHFPKEYPLRPPKMKFVT 60
L K+P G SA VDD ++++WEV IIGP T YEGG FK + FP++YP +PPK+KF T
Sbjct: 9 LLKDPPPGISAFPVDD-NLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKPPKVKFTT 67
Query: 61 EIWHPNIEKNGDVCISILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPNDESP 120
+I+HPN++ +G++C+ IL + E W P T+E +L+S+ S+L++PN E P
Sbjct: 68 KIYHPNVDPSGEICLDILKD------------ENWSPALTIEQVLLSIQSLLSEPNPEDP 115
Query: 121 ANVDAAV 127
N +AA
Sbjct: 116 LNAEAAK 122
>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 = 166 bits (422), Expect = 6e-54
Identities = 55/145 (37%), Positives = 87/145 (60%), Gaps = 14/145 (9%)
Query: 1 LNKNPVEGFSAGLVDDSDIYKWEVLIIGPPDTMYEGGFFKAHLHFPKEYPLRPPKMKFVT 60
L K+P G SA V++ ++ +W I GPPDT YEGG FK + FP++YP +PPK++FVT
Sbjct: 11 LKKDPPSGISAEPVEE-NLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKPPKVRFVT 69
Query: 61 EIWHPNIEKNGDVCISILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPNDESP 120
+I+HPN+++NG +C+SIL W P +T+ T+L+S+ S+L +PN P
Sbjct: 70 KIYHPNVDENGKICLSILK------------THGWSPAYTLRTVLLSLQSLLNEPNPSDP 117
Query: 121 ANVDAAVSQYSSENYHWVRRKKIFI 145
N +AA Y + ++ + +
Sbjct: 118 LNAEAA-KLYKENREEFKKKAREWT 141
>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 = 156 bits (396), Expect = 7e-50
Identities = 59/146 (40%), Positives = 94/146 (64%), Gaps = 13/146 (8%)
Query: 1 LNKNPVEGFSAGLVDDSDIYKWEVLIIGPPDTMYEGGFFKAHLHFPKEYPLRPPKMKFVT 60
L K+P GF+A VDD ++ +W I+GPP T YEGG FK + FP++YP +PPK+KF+T
Sbjct: 9 LRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKPPKVKFIT 68
Query: 61 EIWHPNIEKNGDVCISILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPNDESP 120
+I+HPN++ +G++C+ IL + E+W P T+ET+L+S+ S+L++PN +SP
Sbjct: 69 KIYHPNVDSSGEICLDILKQ------------EKWSPALTLETVLLSLQSLLSEPNPDSP 116
Query: 121 ANVDAAVSQYSSENYHWVRRKKIFIK 146
N DAA Y + ++ + + K
Sbjct: 117 LNADAAE-LYKKNREEFKKKAREWTK 141
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 101 bits (252), Expect = 4e-28
Identities = 53/146 (36%), Positives = 80/146 (54%), Gaps = 20/146 (13%)
Query: 1 LNKNPVEGFSAGLVDDSDIYKWEVLIIGPPDTMYEGGFFKAHLHFPKEYPLRPPKMKFVT 60
L K+P SAG D+ ++++W IIGP D+ Y GG F + FP +YP +PPK++F T
Sbjct: 13 LLKDPPSNCSAGPSDE-NLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFKPPKVQFTT 71
Query: 61 EIWHPNIEKNGDVCISILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPNDESP 120
+I+HPNI NG +C+ IL ++W P TV +L+S+ S+L DPN + P
Sbjct: 72 KIYHPNINSNGSICLDILR-------------DQWSPALTVSKVLLSISSLLTDPNPDDP 118
Query: 121 ANVDAA------VSQYSSENYHWVRR 140
+ A S+Y + W +R
Sbjct: 119 LVPEIARVFKENRSRYEATAREWTQR 144
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 84.1 bits (208), Expect = 2e-21
Identities = 43/134 (32%), Positives = 77/134 (57%), Gaps = 16/134 (11%)
Query: 1 LNKNPVEGFSAGLVDDSDIYKWEVLIIGPPDTMYEGGFFKAHLHFPKEYPLRPPKMKFVT 60
L +P G A + + +++L+ GP T YEGG++K L P++YP+ PPK++F+T
Sbjct: 14 LANDPPPGIKAEPDPGNYRH-FKILMEGPDGTPYEGGYYKLELFLPEQYPMEPPKVRFLT 72
Query: 61 EIWHPNIEKNGDVCISILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPNDESP 120
+I+HPNI+K G +C+ IL ++W P + T+L+S+ ++L+ P + P
Sbjct: 73 KIYHPNIDKLGRICLDILK-------------DKWSPALQIRTVLLSIQALLSAPEPDDP 119
Query: 121 ANVDAAVSQYSSEN 134
+D +V+ + N
Sbjct: 120 --LDTSVADHFKNN 131
>gnl|CDD|222765 pfam14461, Prok-E2_B, Prokaryotic E2 family B. A member of the
E2/UBC superfamily of proteins found in several
bacteria. The active site residues are similar to the
eukaryotic E2 proteins but lack the conserved
asparagine. Members of this family are usually fused to
an E1 domain at the C-terminus. The protein is usually
in the gene neighborhood of a gene encoding a member of
the pol-beta nucleotidyltransferase superfamily. Many
of the operons in this family are in ICE-like mobile
elements and plasmids.
Length = 131
Score = 28.1 bits (63), Expect = 1.2
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 36 GGFFKAHLHFPKEYPLRPPKMKFV--TEIWHPNIEKNGDVCISILHEPGDDKYGYERAYE 93
GG L P ++PL PK+ E P++E +G +C +L P + A E
Sbjct: 35 GGVPPIRLVIPDDFPLVLPKVFLADREERLLPHVESDGTLC--LLDRPSANWDFNGSAAE 92
Query: 94 R 94
Sbjct: 93 S 93
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated.
Length = 238
Score = 27.5 bits (62), Expect = 2.3
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 14/54 (25%)
Query: 52 RPPKMKFVTEIWHPNIEKNGDV---CISILHEPGDDKYGYERAYERWLPVHTVE 102
R P ++ + +P ++K+G + + ILH+PG R PV V+
Sbjct: 18 RSPSHRYKGPVKYPPLDKDGTLRGKVVDILHDPG-----------RNAPVAKVK 60
>gnl|CDD|236778 PRK10859, PRK10859, membrane-bound lytic transglycosylase F;
Provisional.
Length = 482
Score = 27.1 bits (61), Expect = 4.5
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 3/20 (15%)
Query: 85 KYGYERAYERWLPVHTVETI 104
+YGY R +E VH VE I
Sbjct: 427 RYGYARGHE---AVHYVENI 443
>gnl|CDD|165231 PHA02917, PHA02917, ankyrin-like protein; Provisional.
Length = 661
Score = 26.9 bits (59), Expect = 4.7
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 76 SILHEPGDDKYGYERAYERWLPVHTVETILISVISMLADPND 117
S+L+E DD+YGY AY+ + P + + + +IS L +D
Sbjct: 163 SVLYEDEDDEYGY--AYDDYQPRNCGTVLHLYIISHLYSESD 202
>gnl|CDD|224766 COG1853, COG1853, Conserved protein/domain typically associated
with flavoprotein oxygenases, DIM6/NTAB family [General
function prediction only].
Length = 176
Score = 26.5 bits (59), Expect = 5.8
Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 28/89 (31%)
Query: 64 HPNIEKNGDVCISILHE--------------PGDDKYGYERAYERWLPVHTVETILISVI 109
PNIE+ G+ +++L E PG+DK + A V V ++
Sbjct: 60 WPNIEETGEFVVNVLSEDLQEAVAKTFAGSGPGEDK--FAGA--GLTLVEKVGAPIL--- 112
Query: 110 SMLADPNDESPANVDAAVSQYSSENYHWV 138
E+ A ++ V Q H +
Sbjct: 113 -------AEALAWLECRVVQVIEAGDHDI 134
>gnl|CDD|214735 smart00591, RWD, domain in RING finger and WD repeat containing
proteins and DEXDc-like helicases subfamily related to
the UBCc domain.
Length = 107
Score = 25.4 bits (56), Expect = 9.3
Identities = 4/32 (12%), Positives = 10/32 (31%)
Query: 39 FKAHLHFPKEYPLRPPKMKFVTEIWHPNIEKN 70
+ P+ YP P + + + +
Sbjct: 43 LTLQVKLPENYPDEAPPISLLNSEGLSDEQLA 74
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 0.138 0.438
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,126,593
Number of extensions: 735241
Number of successful extensions: 476
Number of sequences better than 10.0: 1
Number of HSP's gapped: 468
Number of HSP's successfully gapped: 16
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.0 bits)