RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8018
(280 letters)
>gnl|CDD|118200 pfam09668, Asp_protease, Aspartyl protease. This family of
eukaryotic aspartyl proteases have a fold similar to
retroviral proteases which implies they function
proteolytically during regulated protein turnover.
Length = 124
Score = 217 bits (556), Expect = 2e-72
Identities = 76/123 (61%), Positives = 94/123 (76%)
Query: 126 KSNIQANMEAAMEYNPETFGSVIMLYINCRVNGHPVKAFIDSGAQTTIMSAACAARVNIT 185
+ N+ N+E AME+ PE FG V MLYINC VNG PVKAF+DSGAQT+IMS CA R I
Sbjct: 1 QENVDENLEHAMEHTPEAFGRVTMLYINCEVNGVPVKAFVDSGAQTSIMSPRCAERCGIM 60
Query: 186 RLIDTRWAGIAKGVGVQRIIGRIHMVQIAIENDFLTTSFSVLEDQPMDMLLGLDMLKRHQ 245
RL+DTR+AGIA+GVG +I+GR+HM + + + FL SF+V+EDQ MD+L GLDMLKRHQ
Sbjct: 61 RLLDTRFAGIARGVGTAKILGRVHMADLKLGDLFLPCSFTVIEDQDMDLLFGLDMLKRHQ 120
Query: 246 VQI 248
I
Sbjct: 121 CCI 123
>gnl|CDD|133146 cd05479, RP_DDI, RP_DDI; retropepsin-like domain of DNA damage
inducible protein. The family represents the
retropepsin-like domain of DNA damage inducible protein.
DNA damage inducible protein has a retropepsin-like
domain and an amino-terminal ubiquitin-like domain
and/or a UBA (ubiquitin-associated) domain. This CD
represents the retropepsin-like domain of DDI.
Length = 124
Score = 207 bits (530), Expect = 2e-68
Identities = 74/123 (60%), Positives = 93/123 (75%)
Query: 134 EAAMEYNPETFGSVIMLYINCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDTRWA 193
+ AME++PE+FG V MLYIN +NG PVKAF+DSGAQ TIMS ACA + + RLID R+
Sbjct: 1 QNAMEHHPESFGKVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQ 60
Query: 194 GIAKGVGVQRIIGRIHMVQIAIENDFLTTSFSVLEDQPMDMLLGLDMLKRHQVQIAIEND 253
GIAKGVG Q+I+GRIH+ Q+ I N FL SF+VLED +D L+GLDMLKRHQ I ++ +
Sbjct: 61 GIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVIDLKEN 120
Query: 254 FLT 256
L
Sbjct: 121 VLR 123
>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like
domain. DDI1_N DDI1 (DNA damage inducible protein 1)
has an amino-terminal ubiquitin-like domain, an
retroviral protease-like (RVP-like) domain, and a UBA
(ubiquitin-associated) domain. This CD represents the
amino-terminal ubiquitin-like domain of DDI1.
Length = 71
Score = 76.3 bits (188), Expect = 4e-18
Identities = 36/71 (50%), Positives = 48/71 (67%), Gaps = 1/71 (1%)
Query: 3 VTV-TSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDYN 61
+TV T+ F LDV DLELENFKA CE +SGI A + + + G LVDNK+ L Y
Sbjct: 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYG 60
Query: 62 IQDGDLVLLKR 72
++DGDLV+L++
Sbjct: 61 VKDGDLVVLRQ 71
>gnl|CDD|133136 cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate
proteases. The family includes pepsin-like aspartate
proteases from retroviruses, retrotransposons and
retroelements, as well as eukaryotic
dna-damage-inducible proteins (DDIs), and bacterial
aspartate peptidases. While fungal and mammalian pepsins
are bilobal proteins with structurally related N and
C-terminals, retropepsins are half as long as their
fungal and mammalian counterparts. The monomers are
structurally related to one lobe of the pepsin molecule
and retropepsins function as homodimers. The active site
aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it
does in pepsin. Retroviral aspartyl protease is
synthesized as part of the POL polyprotein that contains
an aspartyl protease, a reverse transcriptase, RNase H,
and an integrase. The POL polyprotein undergoes specific
enzymatic cleavage to yield the mature proteins. In
aspartate peptidases, Asp residues are ligands of an
activated water molecule in all examples where catalytic
residues have been identified. This group of aspartate
peptidases is classified by MEROPS as the peptidase
family A2 (retropepsin family, clan AA), subfamily A2A.
Length = 92
Score = 68.1 bits (167), Expect = 7e-15
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 1/92 (1%)
Query: 152 INCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDTRWAGIAKGVG-VQRIIGRIHM 210
+ ++NG PV+A +DSGA +S + A ++ + + + G + +G I
Sbjct: 1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60
Query: 211 VQIAIENDFLTTSFSVLEDQPMDMLLGLDMLK 242
V I I T F VL+ D++LG L+
Sbjct: 61 VTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92
>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL. UBLs function by
remodeling the surface of their target proteins,
changing their target's half-life, enzymatic activity,
protein-protein interactions, subcellular localization
or other properties. At least 10 different
ubiquitin-like modifications exist in mammals, and
attachment of different ubls to a target leads to
different biological consequences. Ubl-conjugation
cascades are initiated by activating enzymes, which
also coordinate the ubls with their downstream
pathways.
Length = 69
Score = 48.8 bits (117), Expect = 5e-08
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 4 TVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDYNIQ 63
TV +L + F L+VS D + KA + G+ ++ + + G L D+ KTL DY IQ
Sbjct: 1 TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDD-KTLSDYGIQ 59
Query: 64 DGD-LVLLKR 72
DG L L+ R
Sbjct: 60 DGSTLHLVLR 69
>gnl|CDD|222288 pfam13650, Asp_protease_2, Aspartyl protease. This family consists
of predicted aspartic proteases, typically from 180 to
230 amino acids in length, in MEROPS clan AA. This model
describes the well-conserved 121-residue C-terminal
region. The poorly conserved, variable length N-terminal
region usually contains a predicted transmembrane helix.
Length = 89
Score = 48.1 bits (115), Expect = 1e-07
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 152 INCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDTRWAGIAKGVGVQRIIGRIHMV 211
+ +NG PV+ +D+GA T++S + A R+ + G + +
Sbjct: 1 VPVTINGKPVRFLLDTGASGTLLSRSLAERLGLK--PTKLTIGRVSTANGTVRAALVRLD 58
Query: 212 QIAIENDFLT-TSFSVLEDQPM-DMLLGLD 239
+ I L VL+ + D LLG+D
Sbjct: 59 SLKIGGITLRNVPAVVLDLGDLIDGLLGMD 88
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 44.5 bits (106), Expect = 2e-06
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 8 LDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDYNIQDGDL 67
LD + L+V + K E + GI + + F G L D+ TL +Y IQDG
Sbjct: 3 LDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDD-TTLSEYGIQDGST 61
Query: 68 VLL 70
+ L
Sbjct: 62 LHL 64
>gnl|CDD|133147 cd05480, NRIP_C, NRIP_C; putative nuclear receptor interacting
protein. Proteins in this family have been described as
probable nuclear receptor interacting proteins. The
C-terminal domain of this family is homologous to the
retroviral aspartyl protease domain. The domain is
structurally related to one lobe of the pepsin molecule.
The conserved active site aspartate occurs within a
motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp
residues are ligands of an activated water molecule in
all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 103
Score = 42.9 bits (101), Expect = 1e-05
Identities = 26/102 (25%), Positives = 53/102 (51%), Gaps = 2/102 (1%)
Query: 152 INCRVNGHPVKAFIDSGAQTTIMSAACAARVNI-TRLIDTRWAGIAKGVGVQ-RIIGRIH 209
++C+ G ++A +D+G Q ++SAAC R+ + R++ + A + ++IG+I
Sbjct: 1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIE 60
Query: 210 MVQIAIENDFLTTSFSVLEDQPMDMLLGLDMLKRHQVQIAIE 251
+ + + + S V++D + LGL LK + I +E
Sbjct: 61 RLVLQLGQLTVECSAQVVDDNEKNFSLGLQTLKSLKCVINLE 102
>gnl|CDD|133150 cd05483, retropepsin_like_bacteria, Bacterial aspartate proteases,
retropepsin-like protease family. This family of
bacteria aspartate proteases is a subfamily of
retropepsin-like protease family, which includes enzymes
from retrovirus and retrotransposons. While fungal and
mammalian pepsin-like aspartate proteases are bilobal
proteins with structurally related N- and C-termini,
this family of bacteria aspartate proteases is half as
long as their fungal and mammalian counterparts. The
monomers are structurally related to one lobe of the
pepsin molecule and function as homodimers. The active
site aspartate occurs within a motif (Asp-Thr/Ser-Gly),
as it does in pepsin. In aspartate peptidases, Asp
residues are ligands of an activated water molecule in
all examples where catalytic residues have been
identified. This group of aspartate proteases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 96
Score = 42.2 bits (100), Expect = 2e-05
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 19/104 (18%)
Query: 149 MLYINCRVNGHPVKAFIDSGAQTTIMSAACAARVNIT-RLIDTRWAGIAKG------VGV 201
+ +NG PV+ +D+GA TT++S A R+ + L A G V +
Sbjct: 2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRL 61
Query: 202 QRI-IGRIHMVQIAIENDFLTTSFSVLEDQPM--DMLLGLDMLK 242
+ IG I + + VL + D LLG+D L+
Sbjct: 62 DSLQIGGITLRNVPA---------VVLPGDALGVDGLLGMDFLR 96
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDY 60
+++TV +LD + L+V + K +GI ++ + ++G L D++ TL DY
Sbjct: 1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDR-TLADY 59
Query: 61 NIQDGDLVLL 70
IQDG + L
Sbjct: 60 GIQDGSTIHL 69
>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 = 37.9 bits (89), Expect = 4e-04
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFK-AFCEVQSGISA-QEIAIEFQGNALVDNKKTLK 58
+++ + D + + V L A+ + + GI A Q++ + F G L N T+
Sbjct: 1 IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKR-GIPADQQVRLIFDGERLDPND-TVA 58
Query: 59 DYNIQDGDLV 68
DY+I+DGD +
Sbjct: 59 DYDIEDGDTI 68
>gnl|CDD|215697 pfam00077, RVP, Retroviral aspartyl protease. Single domain
aspartyl proteases from retroviruses, retrotransposons,
and badnaviruses (plant dsDNA viruses). These proteases
are generally part of a larger polyprotein; usually pol,
more rarely gag. Retroviral proteases appear to be
homologous to a single domain of the two-domain
eukaryotic aspartyl proteases such as pepsins,
cathepsins, and renins (pfam00026).
Length = 99
Score = 38.0 bits (89), Expect = 7e-04
Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 16/103 (15%)
Query: 151 YINCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDTRWAGIAKGVGVQRIIGRIH- 209
I +V G P+KA +D+GA T++ + W + I G+I
Sbjct: 7 RITVKVGGQPIKALLDTGADDTVIP---------ENDLPGSW-PPWGPTTIGGIGGQIRV 56
Query: 210 ----MVQIAIENDFLTTSFSVLEDQPMDMLLGLDMLKRHQVQI 248
+ + I +F VL P++ +LG D+L + ++
Sbjct: 57 KQSIQILVEIGGKKFRGTFLVLPSTPVN-ILGRDLLTQLGAKL 98
>gnl|CDD|206145 pfam13975, gag-asp_proteas, gag-polyprotein putative aspartyl
protease. This family of putative aspartyl proteases is
found pre-dominantly in retroviral proteins.
Length = 72
Score = 36.9 bits (86), Expect = 8e-04
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 150 LYINCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDT 190
+ + + G VKA +D+GA + +S + AAR+ + D
Sbjct: 9 VTVEVSIGGVEVKALVDTGATHSFISESLAARLGLPLEADQ 49
>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein.
Scythe protein (also known as Bat3) is an apoptotic
regulator that is highly conserved in eukaryotes and
contains a ubiquitin-like domain near its N-terminus.
Scythe binds reaper, a potent apoptotic inducer, and
Scythe/Reaper are thought to signal apoptosis, in part
through regulating the folding and activity of
apoptotic signaling molecules.
Length = 72
Score = 36.4 bits (85), Expect = 0.001
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDY 60
+++ V +LD++ V E++ + + K + GI ++ + + G L D+ +TL +Y
Sbjct: 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDD-ETLSEY 59
Query: 61 NIQDGDLV-LLKR 72
++DG + L+KR
Sbjct: 60 KVEDGHTIHLVKR 72
>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 = 34.4 bits (79), Expect = 0.007
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 4 TVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDYNIQ 63
V D + L V + + K + G+ ++ + G L D+ TL+DY +Q
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSL-TLEDYGLQ 59
Query: 64 DGDLVLL 70
DGD ++L
Sbjct: 60 DGDELVL 66
>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin. Ubiquitin (includes Ubq/RPL40e
and Ubq/RPS27a fusions as well as homopolymeric
multiubiquitin protein chains).
Length = 76
Score = 34.1 bits (78), Expect = 0.008
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDY 60
M++ V +L + L+V +EN KA + + GI + + F G L D +TL DY
Sbjct: 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLSDY 59
Query: 61 NIQ 63
NIQ
Sbjct: 60 NIQ 62
>gnl|CDD|116868 pfam08284, RVP_2, Retroviral aspartyl protease. Single domain
aspartyl proteases from retroviruses, retrotransposons,
and badnaviruses (plant dsDNA viruses). These proteases
are generally part of a larger polyprotein; usually pol,
more rarely gag. Retroviral proteases appear to be
homologous to a single domain of the two-domain
eukaryotic aspartyl proteases.
Length = 135
Score = 35.5 bits (82), Expect = 0.008
Identities = 23/93 (24%), Positives = 38/93 (40%)
Query: 156 VNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDTRWAGIAKGVGVQRIIGRIHMVQIAI 215
VN P DSGA + +S A R + + G R V I I
Sbjct: 28 VNSIPATVLFDSGASHSFISQAFVGRHGLPLEALRTPMLVHSPGGDMTATHRCPSVNIEI 87
Query: 216 ENDFLTTSFSVLEDQPMDMLLGLDMLKRHQVQI 248
+ + +L+ + +D++LG+D L +H+ I
Sbjct: 88 QGVDFPANLILLDSKDLDVILGMDWLAQHKGVI 120
>gnl|CDD|131334 TIGR02281, clan_AA_DTGA, clan AA aspartic protease, TIGR02281
family. This family consists of predicted aspartic
proteases, typically from 180 to 230 amino acids in
length, in MEROPS clan AA. This model describes the
well-conserved 121-residue C-terminal region. The poorly
conserved, variable length N-terminal region usually
contains a predicted transmembrane helix. Sequences in
the seed alignment and those scoring above the trusted
cutoff are Proteobacterial; homologs scroing between
trusted and noise are found in Pyrobaculum aerophilum
str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and
Nostoc sp. PCC 7120 (Cyanobacteria) [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 121
Score = 33.8 bits (78), Expect = 0.029
Identities = 27/97 (27%), Positives = 43/97 (44%), Gaps = 7/97 (7%)
Query: 151 YINCRVNGHPVKAFIDSGAQTTIMSAACAARV--NITRLIDTRWAGIAKGVGVQRIIGRI 208
Y RVNG V+ +D+GA + ++ A R+ ++ RL T A G Q R+
Sbjct: 13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANG---QIKAARV 69
Query: 209 HMVQIAIENDFLT-TSFSVLEDQPMD-MLLGLDMLKR 243
+ ++AI + V E + LLG+ L R
Sbjct: 70 TLDRVAIGGIVVNDVDAMVAEGGALSESLLGMSFLNR 106
>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23. RAD23 belongs
to a family of adaptor molecules having affinity for
both the proteasome and ubiquitinylated proteins and
thought to shuttle these ubiquitinylated proteins to
the proteasome for destruction. RAD23 interacts with
ubiquitin through its C-terminal ubiquitin-associated
domains (UBA) and with the proteasome through its
N-terminal ubiquitin-like domain (UBL).
Length = 77
Score = 31.1 bits (71), Expect = 0.11
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSG--ISAQEIAIEFQGNALVDNKKTLK 58
MK+T +L + F ++V D + K E + G ++ + + G L D TL+
Sbjct: 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKD-DTTLE 59
Query: 59 DYNIQDGDLV 68
+Y I + D V
Sbjct: 60 EYKIDEKDFV 69
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC
protein. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 378
Score = 32.9 bits (75), Expect = 0.16
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIA---IEFQGNALVDNKKTL 57
M +T +L + F +D+ D ++ K E + G A +A + + G L D+K T+
Sbjct: 1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDK-TV 59
Query: 58 KDYNIQDGDLVL 69
K+Y I++ D V+
Sbjct: 60 KEYKIKEKDFVV 71
>gnl|CDD|226106 COG3577, COG3577, Predicted aspartyl protease [General function
prediction only].
Length = 215
Score = 32.3 bits (74), Expect = 0.16
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 151 YINCRVNGHPVKAFIDSGAQTTIMSAACAARVNI 184
N RVNG V +D+GA + ++ A R+ I
Sbjct: 107 EANGRVNGKKVDFLVDTGATSVALNEEDARRLGI 140
>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein. Nedd8 (also known
as Rub1) has a single conserved ubiquitin-like domain
that is part of a protein modification pathway similar
to that of ubiquitin. Nedd8 modifies a family of
molecular scaffold proteins called cullins that are
responsible for assembling the ROC1/Rbx1 RING-based E3
ubiquitin ligases, of which several play a direct role
in tumorigenesis.
Length = 76
Score = 30.5 bits (69), Expect = 0.19
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDY 60
M + V +L + +D+ ++E K E + GI Q+ + + G + D KT DY
Sbjct: 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMND-DKTAADY 59
Query: 61 NIQDGD---LVLLKR 72
++ G LVL R
Sbjct: 60 KLEGGSVLHLVLALR 74
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 30.8 bits (70), Expect = 0.62
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 86 ARILRQQYEEREKREQLRQRMLTADPFDTEAQKLIAEEIKKSNIQANMEAAMEYNPETFG 145
A+I ++ +REK E+ + + P D A+KL ++++ ++++ A + FG
Sbjct: 64 AKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRLRKLQE---ESDLNNAA----DLFG 116
>gnl|CDD|205688 pfam13510, Fer2_4, 2Fe-2S iron-sulfur cluster binding domain. The
2Fe-2S ferredoxin family have a general core structure
consisting of beta(2)-alpha-beta(2) which a beta-grasp
type fold. The domain is around one hundred amino acids
with four conserved cysteine residues to which the
2Fe-2S cluster is ligated. This cluster appears within
sarcosine oxidase proteins.
Length = 82
Score = 29.0 bits (66), Expect = 0.63
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 4/36 (11%)
Query: 152 INCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRL 187
+ +G PV A T+ SA A + + R
Sbjct: 4 VTFTFDGRPVTAP----EGDTVASALLANGIRVPRS 35
>gnl|CDD|218517 pfam05236, TAF4, Transcription initiation factor TFIID component
TAF4 family. This region of similarity is found in
Transcription initiation factor TFIID component TAF4.
Length = 255
Score = 30.4 bits (69), Expect = 0.81
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 9/69 (13%)
Query: 76 ARTSNPSDDFARILRQQYEEREKREQLRQRMLTADP-------FDTEAQKLIAEEIKKSN 128
S+ + ++Q EE E+R + R+ + DP E QK +EE +
Sbjct: 106 EIRSDVRRQLRFLAQKQKEEEERRVERRRELGLEDPEQLRLKQKAKEEQKAESEETRHR- 164
Query: 129 IQANMEAAM 137
AN A
Sbjct: 165 -AANATALA 172
>gnl|CDD|200101 TIGR01435, glu_cys_lig_rel, glutamate--cysteine
ligase/gamma-glutamylcysteine synthetase, Streptococcus
agalactiae type. This model represents a bifunctional
protein family for the biosynthesis of glutathione, and
perhaps a range of related gamma-glutamyltripeptides of
the form gamma-Glu-Cys-X(aa). The N-terminal region is
similar to proteobacterial glutamate-cysteine ligase.
The C-terminal region is homologous to cyanophycin
synthetase of cyanobacteria and, more distantly, to
D-alanine-D-alanine ligases. Members of This model
family are found in Listeria and Enterococcus,
Gram-positive lineages in which glutathione is produced
(see PUBMED:8606174), and in Pasteurella multocida, a
Proteobacterium. In Clostridium acetobutylicum, adjacent
genes include separate proteins rather than a fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Glutathione and analogs].
Length = 737
Score = 31.0 bits (70), Expect = 0.84
Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 14/107 (13%)
Query: 39 QEIAIEFQGNALVDNKKTLKDY-NIQDGDLVLLKRVQVARTSNPSDDFARILRQQYEERE 97
Q++ + NA V + L+ +G+LVLL+ + + + F + ++
Sbjct: 313 QQVELGKARNAEVALEHPLEKTAYAVEGELVLLELLSMLEQLAEPELFEIV-------KK 365
Query: 98 KREQLRQRMLTADPFDTEAQKLIAEEIKKSNIQANMEAAMEYNPETF 144
K QL DP T A +L+ E + S+ + + A +Y + F
Sbjct: 366 KLTQLT------DPSKTVAGRLVRIEQEGSDQELGAQLAQQYKAQAF 406
>gnl|CDD|218638 pfam05559, DUF763, Protein of unknown function (DUF763). This
family consists of several uncharacterized bacterial and
archaeal proteins of unknown function.
Length = 319
Score = 29.5 bits (67), Expect = 1.8
Identities = 27/131 (20%), Positives = 43/131 (32%), Gaps = 29/131 (22%)
Query: 22 ELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDYNIQDGDLVLLKRVQVARTSNP 81
+E+F E SGIS + QG L N+ D + ++ V
Sbjct: 173 SVESF--VEEPHSGISGRR-----QGEVL----------NLVDKESEEARKAIVDLVREG 215
Query: 82 SDDFARILRQQYEEREKREQLRQRMLTADPFDTEAQKLIAEE-IKKSNIQANMEAAMEYN 140
RE + L M + A + E + + + AA E N
Sbjct: 216 PSRI---------VREVQRALA--MFSGRHLIMPAHHEVRELDVDLRRLWKVLRAAYERN 264
Query: 141 PETFGSVIMLY 151
PE F +++L
Sbjct: 265 PEDFEELLLLK 275
>gnl|CDD|215289 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
Length = 416
Score = 29.3 bits (66), Expect = 2.2
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 11 ECFLLD--VSEDLELENFKAFCEVQSGISAQEIAIEFQG 47
EC LL V E ++E F+ CEVQS + EI ++G
Sbjct: 12 ECELLRWFVKEGDQVEEFQPLCEVQSDKATIEITSRYKG 50
>gnl|CDD|147642 pfam05585, DUF1758, Putative peptidase (DUF1758). This is a family
of nematode proteins of unknown function. However, it
seems likely that these proteins act as aspartic
peptidases.
Length = 164
Score = 28.7 bits (64), Expect = 2.5
Identities = 26/116 (22%), Positives = 43/116 (37%), Gaps = 13/116 (11%)
Query: 164 FIDSGAQTTIMSAACAARVNITRLIDTRWAGIAKGVGVQRIIG--RIHMVQIAIENDFLT 221
DSG++ + +S C R+ + R G + G R + + N L
Sbjct: 16 LFDSGSELSYISERCINRLGLARTPSRILVIGISGDKAPQTRGSNRTV-ISSRLSNGTLA 74
Query: 222 TSFSVLEDQPMDMLLGLDMLKRHQVQIAIE---NDFLTTSFSVLEDQPMDMLLGLD 274
VL+ L+RH + +I ND + + P+D+LLG D
Sbjct: 75 VRAHVLKKITSS-------LERHVIDDSILAVFNDLKPADLNFRKIAPIDILLGSD 123
>gnl|CDD|133149 cd05482, HIV_retropepsin_like, Retropepsins, pepsin-like aspartate
proteases. This is a subfamily of retropepsins. The
family includes pepsin-like aspartate proteases from
retroviruses, retrotransposons and retroelements. While
fungal and mammalian pepsins are bilobal proteins with
structurally related N- and C-termini, retropepsins are
half as long as their fungal and mammalian counterparts.
The monomers are structurally related to one lobe of the
pepsin molecule and retropepsins function as homodimers.
The active site aspartate occurs within a motif
(Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral
aspartyl protease is synthesized as part of the POL
polyprotein that contains an aspartyl protease, a
reverse transcriptase, RNase H, and an integrase. The
POL polyprotein undergoes specific enzymatic cleavage to
yield the mature proteins. In aspartate peptidases, Asp
residues are ligands of an activated water molecule in
all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 87
Score = 27.6 bits (62), Expect = 2.5
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 155 RVNGHPVKAFIDSGAQTTIMSA 176
+NG + +D+GA +I++
Sbjct: 4 YINGKLFEGLLDTGADVSIIAE 25
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.5 bits (64), Expect = 2.6
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 68 VLLKRVQVARTSNPSDDFARILRQQYEEREKREQLRQRMLTADPFDTEAQKLIAE 122
VL R+ AR + SD ILR Q E E + T + +L
Sbjct: 116 VLRGRLA-ARKGDASDATFDILRVQLAEDEPWTEWE-TADTDTARTRDVSQLARI 168
>gnl|CDD|176402 cd01807, GDX_N, ubiquitin-like domain of GDX. GDX contains an
N-terminal ubiquitin-like domain as well as an
uncharacterized c-terminal domain. The function of GDX
is unknown.
Length = 74
Score = 27.2 bits (60), Expect = 2.6
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQEIAIEFQGNALVDNKKTLKDY 60
M +TV L L VSE + K + ++ + F+G AL D+K+ L DY
Sbjct: 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKR-LSDY 59
Query: 61 NI 62
+I
Sbjct: 60 SI 61
>gnl|CDD|236751 PRK10755, PRK10755, sensor protein BasS/PmrB; Provisional.
Length = 356
Score = 28.8 bits (65), Expect = 2.9
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 7/85 (8%)
Query: 134 EAAMEYNPETFGSVIMLYINCRVNGHPVKAFIDSGAQTTIMSAACAARVNITRLIDTRWA 193
E A Y+PE GS I + ++ +G V A D G I + C +D+R+
Sbjct: 257 ENAHRYSPE--GSTITIKLSQE-DGGAVLAVEDEGP--GIDESKCGELSKAFVRMDSRYG 311
Query: 194 GIAKGVG-VQRIIGRIHMVQIAIEN 217
GI G+ V RI ++H Q ++N
Sbjct: 312 GIGLGLSIVSRIT-QLHHGQFFLQN 335
>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance. This is a
metal-binding protein which is involved in resistance to
heavy-metal ions. The protein forms a four-helix hooked
hairpin, consisting of two long alpha helices each
flanked by a shorter alpha helix. It binds a metal ion
in a type-2 like centre. It contains two copies of an
LTXXQ motif.
Length = 125
Score = 27.6 bits (62), Expect = 3.3
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 85 FARILRQQYEE-REKREQLRQRM------LTADPFDTEAQKLIAEEIKK--SNIQANMEA 135
LR E R R LR L A+PFD A + ++ + +QA ++
Sbjct: 50 LRAALRAHRREVRPLRRALRAARRELLALLRAEPFDPAALRAALARQREARAALQARVQE 109
Query: 136 AM 137
A+
Sbjct: 110 AL 111
>gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase IV
is a DNA-binding module that is part of the catalytic
core unit. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriohages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
IV is required for DNA non-homologous end joining
pathways, including recombination of the V(D)J
immunoglobulin gene segments in cells of the mammalian
immune system. DNA ligase IV is stabilized by forming a
complex with XRCC4, a nuclear phosphoprotein, which is
phosphorylated by DNA-dependent protein kinase. DNA
ligases have a highly modular architecture consisting
of a unique arrangement of two or more discrete
domains. The adenylation and C-terminal
oligouncleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common
to most members of the ATP-dependent DNA ligase family.
The catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is
required for the ATP-dependent DNA ligase
nucleotidylation step. The RxDK motif (motif VI), which
is essential for ATP hydrolysis, is located in the
OB-fold domain.
Length = 140
Score = 27.9 bits (63), Expect = 3.3
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 5/33 (15%)
Query: 13 FLLDVSEDLELEN-----FKAFCEVQSGISAQE 40
FL V+ED + E+ F +FC+V SG S +E
Sbjct: 25 FLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEE 57
>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator. This protein is
found in a wide range of eukaryotes. It is a nuclear
protein and is suggested to be DNA binding. In plants,
this family is essential for correct circadian clock
functioning by acting as a light-quality regulator
coordinating the activities of blue and red light
signalling pathways during plant growth - inhibiting
growth in red light but promoting growth in blue light.
Length = 233
Score = 28.5 bits (64), Expect = 3.8
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 10/83 (12%)
Query: 44 EFQGNALVDNKKTLKDYNIQDGDLVLLKRVQVARTSNPSDDFARILRQQYEERE--KREQ 101
E + D KK K+ + D V + ++ + NPS D + + + EE+E RE+
Sbjct: 19 EEDEDEGEDEKKVPKESSEPDEANVNPNKKKIGK--NPSVDTSFLPDKAREEKEAELREE 76
Query: 102 LRQRMLTADPFDTEAQKLIAEEI 124
LR+ L EA K EEI
Sbjct: 77 LREEFLK----KQEAVK--EEEI 93
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 28.4 bits (64), Expect = 4.5
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 12/44 (27%)
Query: 83 DDFARILRQQYEER--EKREQLRQRMLTADPFDTEAQKLIAEEI 124
++ +LRQQ +E EKR++L + Q+L AEE+
Sbjct: 414 EELNALLRQQLQEMDPEKRKELVFEI----------QELYAEEL 447
>gnl|CDD|214986 smart01035, BOP1NT, BOP1NT (NUC169) domain. This N terminal
domain is found in BOP1-like WD40 proteins.
Length = 264
Score = 28.1 bits (63), Expect = 4.6
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 51 VDNKKTLKDYNIQDGDLVLLKRVQVARTSNPSDD 84
V +K+T KD N+ D +L L+KR+Q + + D
Sbjct: 41 VYDKQTGKDVNLTDEELELIKRIQRGEIPDENYD 74
>gnl|CDD|181674 PRK09148, PRK09148, aminotransferase; Validated.
Length = 405
Score = 28.5 bits (64), Expect = 4.7
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 161 VKAFIDSGAQTTIMSAACAA 180
VK+++D GA T I AA AA
Sbjct: 263 VKSYLDYGAFTPIQVAATAA 282
>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1. AN1 (also known as
ANUBL1 and RSD-7) is ubiquitin-like protein with a
testis-specific expression in rats that has an
N-terminal ubiquitin-like domain and a C-terminal
zinc-binding domain. Unlike ubiquitin polyproteins and
most ubiquitin fusion proteins, the N-terminal
ubiquitin-like domain of An1 does not undergo
proteolytic processing. The function of AN1 is unknown.
Length = 103
Score = 26.8 bits (59), Expect = 5.2
Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 14/80 (17%)
Query: 1 MKVTVTSLDNECFLLDVSEDLELENFKAFCEVQSGISAQE-IAIEFQ----GNALVDNKK 55
M++ + +L CF L VS F+ V++ I E I + Q N ++++
Sbjct: 28 MELFIETLTGTCFELRVSP------FETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEY 81
Query: 56 TLKDYNIQDG---DLVLLKR 72
L DYNI +G LVL R
Sbjct: 82 CLNDYNISEGCTLKLVLAMR 101
>gnl|CDD|224684 COG1770, PtrB, Protease II [Amino acid transport and metabolism].
Length = 682
Score = 28.4 bits (64), Expect = 5.2
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 56 TLKDYNIQDGDLVLLKRVQVARTSNPSDDFARIL 89
TL DY++ G+ LLK+ +V +P D +R +
Sbjct: 389 TLFDYDMATGERTLLKQQEVPGGFDPEDYVSRRI 422
>gnl|CDD|238817 cd01639, IMPase, IMPase, inositol monophosphatase and related
domains. A family of Mg++ dependent phosphatases,
inhibited by lithium, many of which may act on inositol
monophosphate substrate. They dephosphorylate inositol
phosphate to generate inositol, which may be recycled
into inositol lipids; in eukaryotes IMPase plays a vital
role in intracellular signaling. IMPase is one of the
proposed targets of Li+ therapy in manic-depressive
illness. This family contains some bacterial members of
the inositol monophosphatase family classified as
SuhB-like. E. coli SuhB has been suggested to
participate in posstranscriptional control of gene
expression, and its inositol monophosphatase activity
doesn't appear to be sufficient for its cellular
function. It has been proposed, that SuhB plays a role
in the biosynthesis of phosphatidylinositol in
mycobacteria.
Length = 244
Score = 27.9 bits (63), Expect = 5.8
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 86 ARILRQQYEEREKREQLRQRMLTADP---FDTEAQKLIAEEIKKS 127
IL + YE+ + ++ D D +KLI E +KK+
Sbjct: 13 GEILLEAYEKLGL--NVEEKGSPVDLVTEVDKAVEKLIIEILKKA 55
>gnl|CDD|219836 pfam08429, PLU-1, PLU-1-like protein. Sequences in this family
bear similarity to the central region of PLU-1. This is
a nuclear protein that may have a role in DNA-binding
and transcription, and is closely associated with the
malignant phenotype of breast cancer. This region is
found in various other Jumonji/ARID domain-containing
proteins (see pfam02373, pfam01388).
Length = 335
Score = 28.0 bits (63), Expect = 5.9
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 100 EQLRQRMLTADPFDTEAQKLIAEEIKKSNIQ 130
+QLR+ + + F AQ ++ +IQ
Sbjct: 106 DQLRELLEAIEEFRERAQSALSTPEDSLSIQ 136
>gnl|CDD|239205 cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl
diphosphate isomerase type 2 (IDI-2) FMN-binding domain.
Two types of IDIs have been characterized at present.
The long known IDI-1 is only dependent on divalent
metals for activity, whereas IDI-2 requires a metal, FMN
and NADPH. IDI-2 catalyzes the interconversion of
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP) in the mevalonate pathway.
Length = 326
Score = 27.5 bits (62), Expect = 7.3
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 16/66 (24%)
Query: 193 AGIAKGVGVQRIIGRIHMVQIAIENDFLTTSFSVLEDQPMDMLL----GLDMLKRH---Q 245
GIA GVG QR A+E+ L SF+V+ + P + L G L + +
Sbjct: 81 LGIAMGVGSQR---------AALEDPELAESFTVVREAPPNGPLIANLGAVQLNGYGVEE 131
Query: 246 VQIAIE 251
+ A+E
Sbjct: 132 ARRAVE 137
>gnl|CDD|172358 PRK13831, PRK13831, conjugal transfer protein TrbI; Provisional.
Length = 432
Score = 27.8 bits (62), Expect = 7.5
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 86 ARILRQQYEEREKREQLRQRM 106
AR+ R+Q EE+ RE+ RQRM
Sbjct: 130 ARLKREQ-EEQYLRERQRQRM 149
>gnl|CDD|181958 PRK09564, PRK09564, coenzyme A disulfide reductase; Reviewed.
Length = 444
Score = 27.7 bits (62), Expect = 8.2
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 101 QLRQRMLTADPFDTEAQKLIAEEIKKSNI 129
QL R+L D FD E ++ EE++++ +
Sbjct: 179 QLEDRILP-DSFDKEITDVMEEELRENGV 206
>gnl|CDD|240579 cd12931, eNOPS_SF, NOPS domain, including C-terminal helical
extension region, in the p54nrb/PSF/PSP1 family. All
members in this family contain a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRM1 and RRM2),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1) domain
with a long helical C-terminal extension. The NOPS
domain specifically binds to RRM2 domain of the partner
DBHS protein via a substantial interaction surface. Its
highly conserved C-terminal residues are critical for
functional DBHS dimerization while the highly conserved
C-terminal helical extension, forming a right-handed
antiparallel heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies. PSF
has an additional large N-terminal domain that
differentiates it from other family members. The
p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein 1 (PSP1), which are
ubiquitously expressed and are well conserved in
vertebrates. p54nrb, also termed NONO or NMT55, is a
multi-functional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. PSF, also termed POMp100, is also a
multi-functional protein that binds RNA, single-stranded
DNA (ssDNA), double-stranded DNA (dsDNA) and many
factors, and mediates diverse activities in the cell.
PSP1, also termed PSPC1, is a novel nucleolar factor
that accumulates within a new nucleoplasmic compartment,
termed paraspeckles, and diffusely distributes in the
nucleoplasm. The cellular function of PSP1 remains
unknown currently. The family also includes some
p54nrb/PSF/PSP1 homologs from invertebrate species. For
instance, the Drosophila melanogaster gene
no-ontransient A (nonA) encoding puff-specific protein
Bj6 (also termed NONA) and Chironomus tentans hrp65 gene
encoding protein Hrp65. D. melanogaster NONA is involved
in eye development and behavior and may play a role in
circadian rhythm maintenance, similar to vertebrate
p54nrb. C. tentans Hrp65 is a component of nuclear
fibers associated with ribonucleoprotein particles in
transit from the gene to the nuclear pore.
Length = 90
Score = 26.1 bits (58), Expect = 8.6
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 17/55 (30%)
Query: 84 DFARILRQQYE-EREKREQLRQRMLTADPFDTEAQKLIAEEIKKSNIQANMEAAM 137
+F + + YE E+++REQL + + +KL AE MEAA
Sbjct: 48 EFGQRWKALYELEKQQREQLEKEL------KEAREKLEAE----------MEAAR 86
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 0.134 0.373
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,317,165
Number of extensions: 1401957
Number of successful extensions: 1733
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1705
Number of HSP's successfully gapped: 84
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
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 (21.9 bits)
S2: 58 (26.1 bits)