RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4609
(242 letters)
>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 = 132 bits (334), Expect = 3e-39
Identities = 54/144 (37%), Positives = 88/144 (61%), Gaps = 8/144 (5%)
Query: 91 KLLIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVISPDEG-YWRGGKFLFSVSVPEEYNM 149
K L KE+++++++ P+ + N L E+ I + GG F + PE+Y
Sbjct: 2 KRLQKELKDLKKDPPSGISAEPVEEN-LLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPF 60
Query: 150 APPKVKCLTKLWHPNINENGDICLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNF 209
PPKV+ +TK++HPN++ENG ICLS+L+ + GW+P L+ V+ L SL + N
Sbjct: 61 KPPKVRFVTKIYHPNVDENGKICLSILKTH-----GWSPAYTLRTVLLSLQSLLNE-PNP 114
Query: 210 DDPLNIEAAEMYQKNKELFRERAR 233
DPLN EAA++Y++N+E F+++AR
Sbjct: 115 SDPLNAEAAKLYKENREEFKKKAR 138
>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 = 131 bits (332), Expect = 7e-39
Identities = 54/142 (38%), Positives = 88/142 (61%), Gaps = 7/142 (4%)
Query: 93 LIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVIS-PDEGYWRGGKFLFSVSVPEEYNMAP 151
L+KE++E+ ++ P + +L E+T I P + GG F ++ PE+Y P
Sbjct: 2 LLKELKELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFKP 61
Query: 152 PKVKCLTKLWHPNINENGDICLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNFDD 211
PKVK +TK++HPN++ +G+ICL +L+Q W+P L+ V+ L SL ++ N D
Sbjct: 62 PKVKFITKIYHPNVDSSGEICLDILKQE-----KWSPALTLETVLLSLQSLLSE-PNPDS 115
Query: 212 PLNIEAAEMYQKNKELFRERAR 233
PLN +AAE+Y+KN+E F+++AR
Sbjct: 116 PLNADAAELYKKNREEFKKKAR 137
>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 = 130 bits (330), Expect = 1e-38
Identities = 50/143 (34%), Positives = 85/143 (59%), Gaps = 8/143 (5%)
Query: 93 LIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVIS-PDEGYWRGGKFLFSVSVPEEYNMAP 151
L KE++E+ ++ P + N L E+ + I P+ + GG F + PE+Y P
Sbjct: 2 LQKELKELLKDPPPGISAFPVDDN-LFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKP 60
Query: 152 PKVKCLTKLWHPNINENGDICLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNFDD 211
PKVK TK++HPN++ +G+ICL +L+ + W+P ++ V+ + SL ++ N +D
Sbjct: 61 PKVKFTTKIYHPNVDPSGEICLDILKDEN-----WSPALTIEQVLLSIQSLLSE-PNPED 114
Query: 212 PLNIEAAEMYQKNKELFRERARC 234
PLN EAA++Y+KN+E F ++ R
Sbjct: 115 PLNAEAAKLYRKNREEFEKKVRE 137
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 129 bits (326), Expect = 6e-38
Identities = 45/145 (31%), Positives = 84/145 (57%), Gaps = 8/145 (5%)
Query: 91 KLLIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVIS-PDEGYWRGGKFLFSVSVPEEYNM 149
K L+KE+++++++ P + ++L + I+ P + + GG F ++ PE+Y
Sbjct: 8 KRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLTLEFPEDYPF 67
Query: 150 APPKVKCLTKLWHPNINENGDICLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNF 209
PPKV+ TK++HPN++ +G++CL +L+ W+P L+ ++ L SL N
Sbjct: 68 KPPKVRFTTKIFHPNVDPSGNVCLDILKD------RWSPVYTLETILLSLQSLLLS-PNP 120
Query: 210 DDPLNIEAAEMYQKNKELFRERARC 234
D PLN EAA +Y+++KE + ++ R
Sbjct: 121 DSPLNTEAATLYREDKEEYEKKVRE 145
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 92.1 bits (228), Expect = 2e-23
Identities = 49/143 (34%), Positives = 78/143 (54%), Gaps = 7/143 (4%)
Query: 91 KLLIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVISPDEGYWRGGKFLFSVSVPEEYNMA 150
K + KE +++ ++ P+ C ++ N +I P + + GG F S+ P +Y
Sbjct: 4 KRIQKEHKDLLKDPPSNCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYPFK 63
Query: 151 PPKVKCLTKLWHPNINENGDICLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNFD 210
PPKV+ TK++HPNIN NG ICL +LR W+P + V+ ++SL TD N D
Sbjct: 64 PPKVQFTTKIYHPNINSNGSICLDILRDQ------WSPALTVSKVLLSISSLLTD-PNPD 116
Query: 211 DPLNIEAAEMYQKNKELFRERAR 233
DPL E A ++++N+ + AR
Sbjct: 117 DPLVPEIARVFKENRSRYEATAR 139
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 73.3 bits (180), Expect = 2e-16
Identities = 43/136 (31%), Positives = 76/136 (55%), Gaps = 9/136 (6%)
Query: 91 KLLIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVIS-PDEGYWRGGKFLFSVSVPEEYNM 149
K + KE Q + + P K + +P + F I++ PD + GG + + +PE+Y M
Sbjct: 5 KRIEKETQNLANDPPPGIKAE-PDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYPM 63
Query: 150 APPKVKCLTKLWHPNINENGDICLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNF 209
PPKV+ LTK++HPNI++ G ICL +L+ W+P +++ V+ + +L +
Sbjct: 64 EPPKVRFLTKIYHPNIDKLGRICLDILKDK------WSPALQIRTVLLSIQALLSA-PEP 116
Query: 210 DDPLNIEAAEMYQKNK 225
DDPL+ A+ ++ N+
Sbjct: 117 DDPLDTSVADHFKNNR 132
>gnl|CDD|218000 pfam04269, DUF440, Protein of unknown function, DUF440. This
family consists of uncharacterized bacterial proteins.
Length = 102
Score = 32.8 bits (75), Expect = 0.039
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 3 WVGSEEDEEEQNLLFSPALMSRRANHPNIHTLVH 36
WVG + +E + +F+ L+SR + H L
Sbjct: 68 WVGLVNENDEIDDVFARFLISRDKDEKFCHILWK 101
>gnl|CDD|171609 PRK12613, PRK12613, galactose-6-phosphate isomerase subunit LacA;
Provisional.
Length = 141
Score = 29.9 bits (67), Expect = 0.65
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 70 MQNEGCDIVDKSSNKRIFIRDKLLI-KEVQEMEQNL 104
+Q EG DI+D + FI + L + K V E E L
Sbjct: 22 LQEEGYDIIDVTDINSDFIDNTLAVAKAVNEAEGRL 57
>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 = 28.5 bits (64), Expect = 1.4
Identities = 8/33 (24%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 143 VPEEYNMAPPKV--KCLTKLWHPNINENGDICL 173
+P+++ + PKV + P++ +G +CL
Sbjct: 44 IPDDFPLVLPKVFLADREERLLPHVESDGTLCL 76
>gnl|CDD|143234 cd05757, Ig2_IL1R_like, Second immunoglobulin (Ig)-like domain of
interleukin-1 receptor (IL1R) and similar proteins.
Ig2_IL1R_like: domain similar to the second
immunoglobulin (Ig)-like domain of interleukin-1
receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines
which participate in the regulation of inflammation,
immune responses, and hematopoiesis. These cytokines
bind to the IL-1 receptor type 1 (IL1R1), which is
activated on additional association with an accessory
protein, IL1RAP. IL-1 also binds a second receptor
designated type II (IL1R2). Mature IL1R1 consists of
three IG-like domains, a transmembrane domain, and a
large cytoplasmic domain. Mature IL1R2 is organized
similarly except that it has a short cytoplasmic domain.
The latter does not initiate signal transduction. A
naturally occurring cytokine IL-1RA (IL-1 receptor
antagonist) is widely expressed and binds to IL-1
receptors, inhibiting the binding of IL-1 alpha and IL-1
beta. This group also contains ILIR-like 1 (IL1R1L)
which maps to the same chromosomal location as IL1R1 and
IL1R2.
Length = 92
Score = 28.1 bits (63), Expect = 1.5
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 82 SNKRIFIRDKLLIKEVQEMEQNLPNTCKTKFTNPNHLHEFTIVIS 126
KR KLLI+ V E + TCK FT+ + T IS
Sbjct: 44 DRKRFVKGSKLLIQNVTEEDAGN-YTCKLTFTHNGKQYNVTRTIS 87
>gnl|CDD|200513 cd11252, Sema_3D, The Sema domain, a protein interacting module, of
semaphorin 3D (Sema3D). Sema3D is a secreted semaphorin
expressed during the development of the nervous system.
In zebrafish, Sema3D is expressed in the ventral tectum.
It guides retinal axons along the dorsoventral axis of
the tectum and guides the laterality of retinal ganglion
cell (RGC) projections. Both Sema3D knockdown or its
ubiquitous overexpression induced aberrant ipsilateral
projections. Proper balance of Sema3D is needed at the
midline for the progression of RGC axons from the chiasm
midline into the contralateral optic tract. Sema3D is a
member of the class 3 semaphorin family of proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 474
Score = 29.5 bits (66), Expect = 1.6
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 106 NTCKTKFTNPNHLHEFTIVISPDEGYW-RGGKFLFSVSVPEEYN 148
+T T+ P H + I E YW G KF+ + +P+ YN
Sbjct: 152 DTTFTRSLGPTPDHHY-IRTDISEHYWLNGAKFIGTFPIPDTYN 194
>gnl|CDD|179934 PRK05094, PRK05094, dsDNA-mimic protein; Reviewed.
Length = 107
Score = 27.6 bits (62), Expect = 2.9
Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 3 WVG-SEEDEEEQNLLFSPALMSRRANHPNIHTL 34
W+G + +++E + +F+ L+SR +H H L
Sbjct: 72 WIGLANSEDDEIDDVFARFLISREKDHKLCHIL 104
>gnl|CDD|132147 TIGR03103, trio_acet_GNAT, GNAT-family acetyltransferase TIGR03103.
Members of this protein family belong to the GNAT
family of acetyltransferases. Each is part of a
conserved three-gene cassette sparsely distributed
across at least twenty different species known so far,
including alpha, beta, and gamma Proteobacteria,
Mycobacterium, and Prosthecochloris, which is a member
of the Chlorobi. The other two members of the cassette
are a probable protease and an asparagine synthetase
family protein.
Length = 547
Score = 27.4 bits (61), Expect = 8.7
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 172 CLSLLRQNSIDGLGWAPTRKLKDVIWGLNSLFTDLLNFDDPLNIEAAEMYQK 223
CL++ Q + G+G A R L + + DL D N +A +Y+K
Sbjct: 160 CLAVDPQAAHPGVGEALVRALAEHFQSRGCAYMDLSVMHD--NEQAIALYEK 209
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
0.321 0.138 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: 12,687,709
Number of extensions: 1185982
Number of successful extensions: 895
Number of sequences better than 10.0: 1
Number of HSP's gapped: 884
Number of HSP's successfully gapped: 16
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
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: 58 (26.1 bits)