RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15482
(302 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 = 175 bits (445), Expect = 3e-55
Identities = 61/86 (70%), Positives = 72/86 (83%)
Query: 192 KNNIEANMEAAMEYNPETFGTVVMLYINCKVNGYPVKAFIDSGAQTTIMSLACAERVNIM 251
+ N++ N+E AME+ PE FG V MLYINC+VNG PVKAF+DSGAQT+IMS CAER IM
Sbjct: 1 QENVDENLEHAMEHTPEAFGRVTMLYINCEVNGVPVKAFVDSGAQTSIMSPRCAERCGIM 60
Query: 252 RLLDTRWAGIAKGVGVQKILGRIHMA 277
RLLDTR+AGIA+GVG KILGR+HMA
Sbjct: 61 RLLDTRFAGIARGVGTAKILGRVHMA 86
>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 = 156 bits (397), Expect = 4e-48
Identities = 54/78 (69%), Positives = 66/78 (84%)
Query: 200 EAAMEYNPETFGTVVMLYINCKVNGYPVKAFIDSGAQTTIMSLACAERVNIMRLLDTRWA 259
+ AME++PE+FG V MLYIN ++NG PVKAF+DSGAQ TIMS ACAE+ +MRL+D R+
Sbjct: 1 QNAMEHHPESFGKVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQ 60
Query: 260 GIAKGVGVQKILGRIHMA 277
GIAKGVG QKILGRIH+A
Sbjct: 61 GIAKGVGTQKILGRIHLA 78
>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 = 82.8 bits (205), Expect = 2e-20
Identities = 35/70 (50%), Positives = 47/70 (67%)
Query: 3 VTVSTQHTNECFLLDVSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKTHG 62
+TV T + F LDV DLELENFKA CE +SG PA + + + G L DNK+ L +G
Sbjct: 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYG 60
Query: 63 IQDGDLVLLK 72
++DGDLV+L+
Sbjct: 61 VKDGDLVVLR 70
>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 = 49.2 bits (118), Expect = 3e-08
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 4 TVSTQHTNECFLLDVSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKTHGI 63
TV T L +VS D + KA + G P + + + G +L+D+ KTL +GI
Sbjct: 1 TVKTLTGKTFEL-EVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDD-KTLSDYGI 58
Query: 64 QDGDLVLL 71
QDG + L
Sbjct: 59 QDGSTLHL 66
>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 = 46.2 bits (110), Expect = 7e-07
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 218 INCKVNGYPVKAFIDSGAQTTIMSLACAERVNIMRLLDTR 257
+ K+NG PV+A +DSGA +S + A+++ + L
Sbjct: 1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPT 40
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 10 TNECFLLDVSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKTHGIQDGDLV 69
+ L+V + K E + G P + + F G +L+D+ TL +GIQDG +
Sbjct: 4 DGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDD-TTLSEYGIQDGSTL 62
Query: 70 LL 71
L
Sbjct: 63 HL 64
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 218 INCKVNGYPVKAFIDSGAQTTIMSLACAERVNI 250
+ +NG PV+ +D+GA T++S + AER+ +
Sbjct: 1 VPVTINGKPVRFLLDTGASGTLLSRSLAERLGL 33
>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 = 36.9 bits (86), Expect = 8e-04
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 1 MKVTVSTQHTNECFLLDVSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKT 60
+++TV T L+V + K +G P + + ++G +L+D++ TL
Sbjct: 1 IELTVKTLDGKT-ITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDR-TLAD 58
Query: 61 HGIQDGDLVLL 71
+GIQDG + L
Sbjct: 59 YGIQDGSTIHL 69
>gnl|CDD|215289 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
Length = 416
Score = 37.8 bits (88), Expect = 0.005
Identities = 38/119 (31%), Positives = 52/119 (43%), Gaps = 20/119 (16%)
Query: 12 ECFLLD--VSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKTHGIQDGDLV 69
EC LL V E ++E F+ CEVQS EI ++G + Q N GD+V
Sbjct: 12 ECELLRWFVKEGDQVEEFQPLCEVQSDKATIEITSRYKGKVAQINFSP--------GDIV 63
Query: 70 -----LLK--HLGSYHATPAAVIPNFDFSGIVVPSASSSSSNGQSSNSLSDDPATVRQL 121
LLK S H +++ D S IV S + S G + + + PA VR L
Sbjct: 64 KVGETLLKIMVEDSQHLRSDSLLLPTDSSNIV--SLAESDERGSNLSGVLSTPA-VRHL 119
>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 = 34.2 bits (79), Expect = 0.010
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 216 LYINCKVNGYPVKAFIDSGAQTTIMSLACAERVNI 250
+ + + G VKA +D+GA + +S + A R+ +
Sbjct: 9 VTVEVSIGGVEVKALVDTGATHSFISESLAARLGL 43
>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 = 34.1 bits (78), Expect = 0.019
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 218 INCKVNGYPVKAFIDSGAQTTIMSLACAERVNI 250
++C+ G ++A +D+G Q ++S AC +R+ +
Sbjct: 1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGL 33
>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 = 33.8 bits (78), Expect = 0.020
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 215 MLYINCKVNGYPVKAFIDSGAQTTIMSLACAERVNI-MRLLDTRWAGIAKG------VGV 267
+ +NG PV+ +D+GA TT++S AER+ + + L A G V +
Sbjct: 2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRL 61
Query: 268 QKI-LGRIHM 276
+ +G I +
Sbjct: 62 DSLQIGGITL 71
>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2.
hPLIC-1 and hPLIC-2 (human homologs of the yeast
ubiquitin-like Dsk2 protein) are type2 UBL's
(ubiquitin-like) proteins that are thought to serve as
adaptors that link the ubiquitination machinery to the
proteasome. The hPLIC's have an N-terminal UBL domain
that binds the S5a subunit of the proteasome and a
C-terminal UBA (ubiquitin-associated) domain that binds
a ubiquitylated protein.
Length = 71
Score = 31.7 bits (72), Expect = 0.059
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 7/73 (9%)
Query: 1 MKVTVSTQHTNECFLLDVSEDLELENFKAFCEVQSGYPAH--EIAIEFQGVLLQDNKKTL 58
+KVTV T E +++ED +++FK V + A+ ++ + F G +L+D TL
Sbjct: 1 IKVTVKTPKDKEEI--EIAEDASVKDFKE--AVSKKFKANQEQLVLIFAGKILKDTD-TL 55
Query: 59 KTHGIQDGDLVLL 71
H I+DG V L
Sbjct: 56 TQHNIKDGLTVHL 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 = 31.4 bits (72), Expect = 0.13
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 217 YINCKVNGYPVKAFIDSGAQTTIMS 241
I KV G P+KA +D+GA T++
Sbjct: 7 RITVKVGGQPIKALLDTGADDTVIP 31
>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 = 30.7 bits (70), Expect = 0.13
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 2 KVTVSTQHTNECFLLDVSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKTH 61
K S HT V E++ + + K + G P + + + G +L+D+ +TL +
Sbjct: 6 KTLDSQTHT-----FTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDD-ETLSEY 59
Query: 62 GIQDG 66
++DG
Sbjct: 60 KVEDG 64
>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 = 29.8 bits (68), Expect = 0.26
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 1 MKVTVSTQHTNECFLLDVSEDLELENFK-AFCEVQSGYPAHE-IAIEFQGVLLQDNKKTL 58
+++ + + + + V L A+ + + G PA + + + F G L N T+
Sbjct: 1 IRIKLKGK-DGKEVFIKVKPTTTLSKLINAYRKKR-GIPADQQVRLIFDGERLDPND-TV 57
Query: 59 KTHGIQDGDLV 69
+ I+DGD +
Sbjct: 58 ADYDIEDGDTI 68
>gnl|CDD|226106 COG3577, COG3577, Predicted aspartyl protease [General function
prediction only].
Length = 215
Score = 32.0 bits (73), Expect = 0.27
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 217 YINCKVNGYPVKAFIDSGAQTTIMSLACAERVNI 250
N +VNG V +D+GA + ++ A R+ I
Sbjct: 107 EANGRVNGKKVDFLVDTGATSVALNEEDARRLGI 140
>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 = 29.9 bits (68), Expect = 0.31
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 221 KVNGYPVKAFIDSGAQTTIMSL 242
+NG + +D+GA +I++
Sbjct: 4 YINGKLFEGLLDTGADVSIIAE 25
>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 = 30.7 bits (70), Expect = 0.34
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 217 YINCKVNGYPVKAFIDSGAQTTIMSLACAERVNI 250
Y +VNG V+ +D+GA + ++ A+R+ +
Sbjct: 13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGL 46
>gnl|CDD|220030 pfam08817, YukD, WXG100 protein secretion system (Wss), protein
YukD. The YukD protein family members participate in
the formation of a translocon required for the
secretion of WXG100 proteins (pfam06013) in monoderm
bacteria, with the WXG100 protein secretion system
(Wss). Like the cytoplasmic protein EsaC in
Staphylococcus aureus, YukD was hypothesized to play a
role of a chaperone. YukD adopts a ubiquitin-like fold.
Usually, ubiquitin covalently binds to protein and
flags them for protein degradation, however conjugation
assays have indicated that the classical YukD lacks the
capacity for covalent bond formation with other
proteins. In contrast to the situation in firmicutes,
YukD-like proteins in actinobacteria are often fused to
a transporter involved in the ESAT-6/ESX/Wss secretion
pathway. Members of the YukD family are also associated
in gene neighborhoods with other enzymatic members of
the ubiquitin signaling and degradation pathway such as
the E1, E2 and E3 trienzyme complex that catalyze
ubiquitin transfer to substrates, and the JAB family
metallopeptidases that are involved in its release.
This suggests that a subset of the YukD family in
bacteria are conjugated and released from proteins as
in the eukaryotic ubiquitin-mediated signaling and
degradation pathway.
Length = 77
Score = 29.1 bits (66), Expect = 0.54
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 48 GVLLQDNKKTLKTHGIQDGD-LVLL 71
G+ L D+ TL G+ DGD LVLL
Sbjct: 54 GIPLSDDD-TLADAGVTDGDILVLL 77
>gnl|CDD|223732 COG0659, SUL1, Sulfate permease and related transporters (MFS
superfamily) [Inorganic ion transport and metabolism].
Length = 554
Score = 31.1 bits (71), Expect = 0.71
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 138 RLADALLNGSPEDFERILRQQYEEREKREQLRLRMLNAHPFDT---EAQKLIAEEIKKNN 194
RL+ L G+ + ER L EER E++ L + + D EA + + +E+++
Sbjct: 449 RLSGPLFFGNADRLERALLGLIEER--PERVILDLKSVPYIDASAAEALEDLIKELERRG 506
Query: 195 IEANM 199
I+ +
Sbjct: 507 IQLLI 511
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 30.4 bits (69), Expect = 0.82
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 5/78 (6%)
Query: 114 DPATVRQLLLDNPKEIALLQQNN-PRLADALLNGSPEDFERILRQQYEEREKREQLRLRM 172
P VR L+D PK L + P L + PED LR E E+R L ++
Sbjct: 67 SPEEVRLYLID-PKGGELAALEDLPHLLSPV-ATDPEDALSALRALVAEMERRYALLKQL 124
Query: 173 LNAH--PFDTEAQKLIAE 188
++ E + I
Sbjct: 125 GVRSIEEYNGEIAEDILG 142
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryote. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAF orthologs
and paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 30.4 bits (69), Expect = 0.85
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 151 FERILRQQYEEREKREQLRLRMLNAHPFDT--------EAQKLIAEEIKKNNIEANMEAA 202
E++ R++ E+R++ E+ RL + E QK EE++ AN A
Sbjct: 119 LEQLEREEEEKRDEEERERLLRAAKSRSEQSRLKQKAKEMQKEEDEEMRHR--AANATAL 176
Query: 203 M 203
Sbjct: 177 A 177
>gnl|CDD|184841 PRK14831, PRK14831, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 249
Score = 30.7 bits (70), Expect = 0.87
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 151 FERILRQQYEEREKREQLRLRML-NAHPFDTEAQKLI--AEEIKKNN 194
FER+LR++ EE + E +R+R + + P Q+ I + E+ KNN
Sbjct: 92 FERVLRRELEELME-ENVRIRFVGDLDPLPKSLQEEISRSTELTKNN 137
>gnl|CDD|129323 TIGR00219, mreC, rod shape-determining protein MreC. MreC (murein
formation C) is involved in the rod shape determination
in E. coli, and more generally in cell shape
determination of bacteria whether or not they are
rod-shaped. Cells defective in MreC are round. Species
with MreC include many of the Proteobacteria,
Gram-positives, and spirochetes [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 283
Score = 30.2 bits (68), Expect = 1.2
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 111 LSDDPATVRQLLLDNPKEIALLQQNNPRLADALLNGSPEDFERILRQQYEEREKREQLRL 170
+ + P V + +N K++ L+ N +L LL + E IL Q ++ E +RL
Sbjct: 50 IQNRPREVFDGISENLKDVNNLEYENYKLRQELL-KKNQQLE-ILTQNLKQ----ENVRL 103
Query: 171 RMLNAHPFDTEAQKLIAEEIKKNN 194
R L P ++ K+ AE I N
Sbjct: 104 RELLNSPLSSDEYKISAEVIYLNY 127
>gnl|CDD|204831 pfam12137, RapA_C, RNA polymerase recycling family C-terminal.
This domain is found in bacteria. This domain is about
360 amino acids in length. This domain is found
associated with pfam00271, pfam00176. The function of
this domain is not known, but structurally it forms an
alpha-beta fold in nature with a central beta-sheet
flanked by helices and loops, the beta-sheet being
mainly antiparallel and flanked by four alpha helices,
among which the two longer helices exhibit a coiled-coil
arrangement.
Length = 362
Score = 30.2 bits (69), Expect = 1.3
Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 130 ALLQQNNPRLADALLNGSPEDFERIL---RQQYEEREKR-EQLRLRMLNAHPFDTEAQKL 185
A+ ++ L L + E ++ RQ +E + EQ R R+L + E +
Sbjct: 38 AVYEEFGEDLESLLAAPDDDALEELIADTRQLHEALKAELEQGRDRLLELNSCGPERAQA 97
Query: 186 IAEEIKKNNIEANMEAAME 204
+ E I++ + + + ME
Sbjct: 98 LIEAIEEEDNDTELPNFME 116
>gnl|CDD|217711 pfam03748, FliL, Flagellar basal body-associated protein FliL.
This FliL protein controls the rotational direction of
the flagella during chemotaxis. FliL is a cytoplasmic
membrane protein associated with the basal body.
Length = 99
Score = 28.7 bits (65), Expect = 1.3
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 12/60 (20%)
Query: 120 QLLLDNPKEIALLQQNNPRLADALLNGSPEDFERILRQQ-YEE---REKREQLRLRMLNA 175
L +D+PK L++ P + DA+L +L + E+ E +E+L+ +L
Sbjct: 27 ALEVDDPKAAEELEEKMPLIRDAILL--------LLSSKTAEDLSTPEGKEKLKEELLER 78
>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 = 29.6 bits (67), Expect = 1.8
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 152 ERILRQQYEEREKREQLRLRMLNAHPFDTEAQKLIAEEIKKNNIEANMEAAMEYNPETFG 211
+I ++ +REK E+ + P D A+KL ++++ E+++ A + FG
Sbjct: 64 AKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRLRKLQE---ESDLNNAA----DLFG 116
Query: 212 TVVM 215
Sbjct: 117 GPAP 120
>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 = 28.0 bits (63), Expect = 2.0
Identities = 23/70 (32%), Positives = 29/70 (41%), Gaps = 23/70 (32%)
Query: 137 PRLADALLNGSPEDFERILR--QQYE-EREKREQLRLRMLNAHPFDTEAQKLIAEEIKKN 193
PR A GS E +E R YE E+++REQL + +KL
Sbjct: 37 PRFAPP---GSFE-YEFGQRWKALYELEKQQREQLEKEL------KEAREKL-------- 78
Query: 194 NIEANMEAAM 203
EA MEAA
Sbjct: 79 --EAEMEAAR 86
>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1. BAG1_N
N-terminal ubiquitin-like (Ubl) domain of the BAG1
protein. This domain occurs together with the BAG
domain and is closely related to the Ubl domain of a
family of deubiquitinases that includes Rpn11, UBP6
(USP14), USP7 (HAUSP).
Length = 71
Score = 27.3 bits (61), Expect = 2.0
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 1 MKVTVSTQHTNECFLLDVSEDLELENFKAFCEVQSGYPAHEIAIEFQGVLLQDNKKTLKT 60
++V V H E L +S + K +G + + F+G D+ +TL
Sbjct: 1 IRVRVK--HGGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKER-DDAETLDM 57
Query: 61 HGIQDGDLVLL 71
G++DG V+L
Sbjct: 58 SGVKDGSKVML 68
>gnl|CDD|221167 pfam11690, DUF3287, Protein of unknown function (DUF3287). This
eukaryotic family of proteins has no known function.
Length = 112
Score = 28.3 bits (63), Expect = 2.1
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 6/30 (20%)
Query: 156 RQQYEEREKREQLR----LRMLNAHPFDTE 181
R++ +KR+ LR +RML +HP D E
Sbjct: 60 RRRL--GKKRQDLRIERKMRMLESHPGDWE 87
>gnl|CDD|238399 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II
core domain. Assignment to class II aminoacyl-tRNA
synthetases (aaRS) based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This family includes AsnRS as well as a
subgroup of AspRS. AsnRS and AspRS are homodimers,
which attach either asparagine or aspartate to the 3'OH
group of ribose of the appropriate tRNA. While archaea
lack asnRS, they possess a non-discriminating aspRS,
which can mischarge Asp-tRNA with Asn. Subsequently, a
tRNA-dependent aspartate amidotransferase converts the
bound aspartate to asparagine. The catalytic core domain
is primarily responsible for the ATP-dependent formation
of the enzyme bound aminoacyl-adenylate.
Length = 322
Score = 29.5 bits (67), Expect = 2.2
Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 25/87 (28%)
Query: 116 ATVRQLLLDNPKEIALLQQNNPRLADALLNGSPEDFERILRQQYEEREKREQLRLRMLNA 175
+++L KE+ L+ Q N L E F RI Y+E + +L
Sbjct: 139 YIFKRVLERCAKELELVNQLNR-----ELLKPLEPFPRI---TYDEA-------IELLRE 183
Query: 176 H----------PFDTEAQKLIAEEIKK 192
TE ++L+ E +K
Sbjct: 184 KGVEEEVKWGEDLSTEHERLLGEIVKG 210
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 29.2 bits (66), Expect = 2.3
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 120 QLLLDNPKEIALLQ-QNNPRLADALLNGSPEDFERILRQQYEEREKREQLRLRMLNAHPF 178
L LD P E+AL + + L D E E++ R+ Y E + R+ +++A
Sbjct: 131 TLYLDVPPEVALERIRKRGELRDRFEKEDDEFLEKV-REGYLELAAKFPERIIVIDA--- 186
Query: 179 DTEAQKLIAEEIKK 192
+ + + EEI K
Sbjct: 187 -SRPLEEVHEEILK 199
>gnl|CDD|239136 cd02671, Peptidase_C19O, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 332
Score = 29.5 bits (66), Expect = 2.4
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 89 DFSGIVVPSASSSSSNGQSSNSLSDDPATVRQLLLDNPKEIA 130
DF I VP S S + S+ +S DP T + L + A
Sbjct: 149 DFQDISVPVQESELSKSEESSEISPDPKTEMKTLKWAISQFA 190
>gnl|CDD|176384 cd01789, Alp11_N, Ubiquitin-like domain of Alp11 tubulin-folding
cofactor B. Alp11, also known as tubulin-folding
cofactor B, is one of at least three proteins required
for the proper folding of tubulins prior to their
incorporation into microtubules. These cofactors are
necessary for the biogenesis of microtubules and for
cell viability. Alp11 has three domains including an
N-terminal ubiquitin-like domain (represented by this
CD) which executes the essential function, a central
coiled-coil domain necessary for maintenance of
cellular alpha-tubulin levels, and a C-terminal
CLIP-170 domain is required for efficient binding to
alpha-tubulin.
Length = 84
Score = 27.7 bits (62), Expect = 2.4
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 3 VTVSTQHTNECFLLDV--SEDLELENFKAFCEVQSGYPAHEIAIEFQGV------LLQDN 54
VTV+ + + F + S L + K E+ G PA + ++ L D+
Sbjct: 2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDD 61
Query: 55 KKTLKTHGIQDG 66
L ++ + DG
Sbjct: 62 DALLGSYPVDDG 73
>gnl|CDD|182695 PRK10747, PRK10747, putative protoheme IX biogenesis protein;
Provisional.
Length = 398
Score = 29.3 bits (66), Expect = 2.5
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 113 DDPATVRQLLLDNPKEIALLQQNNPRLA---DALLNGSPEDFERILRQQ 158
DD T +Q++LD K +Q + RL L +PE E++LRQQ
Sbjct: 277 DDHDTAQQIILDGLK-----RQYDERLVLLIPRLKTNNPEQLEKVLRQQ 320
>gnl|CDD|178174 PLN02560, PLN02560, enoyl-CoA reductase.
Length = 308
Score = 29.3 bits (66), Expect = 2.5
Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 21/110 (19%)
Query: 1 MKVTVSTQHTNECFL--LDVSEDLELENFKA--FCEVQSGYPAHE-IAIEFQ-----GVL 50
MKVTV ++ E L+V + + + K + YP+ + + + +
Sbjct: 1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTV 60
Query: 51 LQDNKKTLKTHGIQDGDLVLLKHLG---SY-------HATPAAVIPNFDF 90
L D+ K+LK +G+ DG V+ K LG SY + P + P F F
Sbjct: 61 L-DDSKSLKDYGLGDGGTVVFKDLGPQVSYRTLFFFEYLGPLLIYPLFYF 109
>gnl|CDD|178524 PLN02936, PLN02936, epsilon-ring hydroxylase.
Length = 489
Score = 29.4 bits (66), Expect = 2.8
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 121 LLLDNPKEIALLQQNNPRLADALLNGSPEDFERILRQQYEEREKREQLRL 170
LL NP+ + Q+ D +L G P +E I +Y R E +RL
Sbjct: 304 LLSKNPEALRKAQEE----LDRVLQGRPPTYEDIKELKYLTRCINESMRL 349
>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 = 29.2 bits (66), Expect = 3.0
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 25/86 (29%)
Query: 107 SSNSLSDDPATVRQLLLDNPKEIALLQQNNPRLADALLNGSPEDFERILRQQYEER--EK 164
+ DP +R++ N K+ A +N L L RQQ +E EK
Sbjct: 385 GHGGIGGDPDILREVYSSNTKKSARGY-DNEELNALL------------RQQLQEMDPEK 431
Query: 165 REQLRLRMLNAHPFDTEAQKLIAEEI 190
R++L + Q+L AEE+
Sbjct: 432 RKELVFEI----------QELYAEEL 447
>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 = 28.9 bits (65), Expect = 3.3
Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 11/54 (20%)
Query: 158 QYEEREKREQLRLRMLNAHPFDT--------EAQKLIAEEIKKNNIEANMEAAM 203
Q EE E+R + R R L + E QK +EE + AN A
Sbjct: 122 QKEEEERRVE-RRRELGLEDPEQLRLKQKAKEEQKAESEETRHR--AANATALA 172
>gnl|CDD|182871 PRK10966, PRK10966, exonuclease subunit SbcD; Provisional.
Length = 407
Score = 28.8 bits (65), Expect = 3.9
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 9/68 (13%)
Query: 111 LSDDPATVRQLLLDNPKEIALL----QQNNPRLADA----LLNGSPED-FERILRQQYEE 161
L D ++ L P E+ L+ +Q LA L S E+ FER L + +
Sbjct: 323 LHDIQRRIQALTESLPVEVLLVRRSREQRERSLASEQRETLSELSVEEVFERRLALEELD 382
Query: 162 REKREQLR 169
++++L
Sbjct: 383 EPQQQRLT 390
>gnl|CDD|133381 cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the
transcription regulators TipAL, Mta, and SkgA.
Helix-turn-helix (HTH) TipAL, Mta, and SkgA
transcription regulators, and related proteins,
N-terminal domain. TipAL regulates resistance to and
activation by numerous cyclic thiopeptide antibiotics,
such as thiostrepton. Mta is a global transcriptional
regulator; the N-terminal DNA-binding domain of Mta
interacts directly with the promoters of mta, bmr, blt,
and ydfK, and induces transcription of these
multidrug-efflux transport genes. SkgA has been shown to
control stationary-phase expression of
catalase-peroxidase in Caulobacter crescentus. These
proteins are comprised of distinct domains that harbor
an N-terminal active (DNA-binding) site and a
regulatory (effector-binding) site. The conserved
N-terminal domain of these transcription regulators
contains winged HTH motifs that mediate DNA binding.
These proteins share the N-terminal DNA binding domain
with other transcription regulators of the MerR
superfamily that promote transcription by reconfiguring
the spacer between the -35 and -10 promoter elements.
Unique to this family, is a TipAL-like, lineage specific
Bacilli subgroup, which has five conserved cysteines in
the C-terminus of the protein.
Length = 103
Score = 27.1 bits (61), Expect = 4.1
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 142 ALLNGSPEDFERILRQQYEE-REKREQLRLRMLNA 175
LL ED LR+Q E EK+E+L +++
Sbjct: 65 ELLKDPSEDLLEALREQKELLEEKKERL-DKLIKT 98
>gnl|CDD|235367 PRK05222, PRK05222,
5-methyltetrahydropteroyltriglutamate--homocysteine
S-methyltransferase; Provisional.
Length = 758
Score = 28.9 bits (66), Expect = 4.2
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 111 LSDDPATVRQLLLDNPKEIALLQQ----NNPRLADALLNGSPEDFERILRQQYEEREKRE 166
L+ V + L N IA + +NP + L + DF+R + Y ER +
Sbjct: 362 LNGGRGAVAEALAANRAAIAARRTSPRVHNPAVRARLAALTEADFQR--QSPYAERAAAQ 419
Query: 167 QLRLR 171
+ RL
Sbjct: 420 RARLN 424
>gnl|CDD|140293 PTZ00267, PTZ00267, NIMA-related protein kinase; Provisional.
Length = 478
Score = 28.4 bits (63), Expect = 4.5
Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 96 PSASSSSSNGQSSNSLSDDPA---TVRQLL-LDNPKEIALLQQNNPRLADALLNGSPEDF 151
P SS LS +PA T +QLL + K +A L Q+ R ++ + SP D
Sbjct: 292 PCPVSSGMKALLDPLLSKNPALRPTTQQLLHTEFLKYVANLFQDIVRHSETI---SPHDR 348
Query: 152 ERILRQQYEEREK 164
E ILRQ E E+
Sbjct: 349 EEILRQLQESGER 361
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 28.3 bits (64), Expect = 4.6
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 151 FERILRQQYEEREKR---EQLRLRMLNAHPFDTEAQKLIAEEIKKNNIEANMEAAME 204
R+ QQ E ++R ++LR + E QK E K+ + ++ A E
Sbjct: 184 VARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRARE 240
>gnl|CDD|222346 pfam13728, TraF, F plasmid transfer operon protein. TraF protein
undergoes proteolytic processing associated with export.
The 19 amino acids at the amino terminus of the
polypeptides appear to constitute a typical membrane
leader peptide - not included in this family, while the
remainder of the molecule is predicted to be primarily
hydrophilic in character. F plasmid TraF and TraH are
required for F pilus assembly and F plasmid transfer,
and they are both localised to the outer membrane in the
presence of the complete F transfer region, especially
TraV, the putative anchor.
Length = 215
Score = 27.9 bits (63), Expect = 4.9
Identities = 10/39 (25%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 123 LDNPKEIALLQQNNPR-LADALLNGSPEDFERILR-QQY 159
+++A L++ LA A+LN + E+ +R Q++
Sbjct: 27 PSATEQMAWLREYLEEALAKAILNPTEENVAAYMRLQRF 65
>gnl|CDD|202159 pfam02212, GED, Dynamin GTPase effector domain.
Length = 90
Score = 26.7 bits (60), Expect = 5.3
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 118 VRQLLLDN-PKEI--ALLQQNNPRLADALLN--GSPEDFERILRQQYEEREKREQLRLRM 172
VR+ + D PK I L+ ++ L LL ED + +L++ E +KR++L+ +
Sbjct: 18 VRKRIADQIPKAIMYFLVNESKESLQKELLQLLYKKEDLDELLKEDPEIAQKRKELK-KR 76
Query: 173 LNAHPFDTEAQKLIAE 188
L +A++++AE
Sbjct: 77 LERL---KKAREILAE 89
>gnl|CDD|222719 pfam14377, DUF4414, Domain of unknown function (DUF4414). This
family is frequently found on DNA binding proteins of
the URE-B1 type and on ligases.
Length = 105
Score = 26.9 bits (60), Expect = 5.4
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 128 EIALLQQNNPRLADALLNGSPEDFER-ILRQQYEEREKREQLRLRMLNAHPFDTEAQKLI 186
+ + + L P + +L+Q+ +ER++R + A P + + +
Sbjct: 29 STSASGEEPTEINPEFLAALPPEIREEVLQQERQERQRRAREIAAAGAATPQEMDPASFL 88
Query: 187 A 187
A
Sbjct: 89 A 89
>gnl|CDD|215152 PLN02269, PLN02269, Pyruvate dehydrogenase E1 component subunit
alpha.
Length = 362
Score = 28.1 bits (63), Expect = 6.3
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 160 EEREKREQLRLRMLNAHPFDTEAQ-KLIAEEIKKNNIEANMEAAMEYNPETFGTVVMLYI 218
+ER+ E++R ++L AH TEA+ K I +EI+K +A +A P+ L+
Sbjct: 284 QERDPIERVR-KLLLAHELATEAELKDIEKEIRKEVDDAVAKAKESPMPDP----SELFT 338
Query: 219 NCKVNGYPVKAF 230
N V G V+++
Sbjct: 339 NVYVKGLGVESY 350
>gnl|CDD|184624 PRK14327, PRK14327, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 509
Score = 28.1 bits (63), Expect = 6.8
Identities = 23/67 (34%), Positives = 29/67 (43%), Gaps = 11/67 (16%)
Query: 116 ATVRQLLLDNPKEIALLQQNNPRLADALLNGSPEDFERI---LRQQYEEREKREQLRLRM 172
VR L KEI LL QN +N +DFE I L +E K + R+R
Sbjct: 248 QEVRHLARQGYKEITLLGQN--------VNAYGKDFEDIEYGLGDLMDEIRKIDIPRVRF 299
Query: 173 LNAHPFD 179
+HP D
Sbjct: 300 TTSHPRD 306
>gnl|CDD|219927 pfam08601, PAP1, Transcription factor PAP1. The transcription
factor Pap1 regulates antioxidant-gene transcription in
response to H2O2. This region is cysteine rich.
Alkylation of cysteine residues following treatment with
a cysteine alkylating agent can mask the accessibility
of the nuclear exporter Crm1, triggering nuclear
accumulation and Pap1 dependent transcriptional
expression.
Length = 344
Score = 28.0 bits (62), Expect = 6.9
Identities = 10/59 (16%), Positives = 17/59 (28%), Gaps = 2/59 (3%)
Query: 94 VVPSASSSSSNGQSSNSLSDDPATVRQLLLDNPKEI--ALLQQNNPRLADALLNGSPED 150
PS+ S Q +SL P + A ++ N ++ S
Sbjct: 128 DSPSSGSDGFTNQLLSSLGTSPEPSTESPPQLASVNNFAAIRNNAESNSNVPSAASSTP 186
>gnl|CDD|233718 TIGR02089, TTC, tartrate dehydrogenase. Tartrate dehydrogenase
catalyzes the oxidation of both meso- and (+)-tartrate
as well as a D-malate. These enzymes are closely related
to the 3-isopropylmalate and isohomocitrate
dehydrogenases found in TIGR00169 and TIGR02088,
respectively [Energy metabolism, Other].
Length = 352
Score = 27.9 bits (62), Expect = 7.0
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 12/74 (16%)
Query: 152 ERILRQQYEEREKREQLRLRMLNAH------PF-DTEAQKLIAE----EIKKNNIEANME 200
ERI+R +E +KR + ++ PF D ++ AE E +I+A +
Sbjct: 167 ERIMRFAFELAQKRRKHLTSATKSNGIRHSMPFWDEVFAEVAAEYPDVEWDSYHIDA-LA 225
Query: 201 AAMEYNPETFGTVV 214
A PETF +V
Sbjct: 226 ARFVLKPETFDVIV 239
>gnl|CDD|219624 pfam07894, DUF1669, Protein of unknown function (DUF1669). This
family is composed of sequences derived from
hypothetical eukaryotic proteins of unknown function.
Some members of this family are annotated as being
potential phospholipases but no literature was found to
support this.
Length = 284
Score = 27.6 bits (62), Expect = 7.1
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 138 RLA-DALLNGSPEDFERILRQQYEERE 163
RLA +ALL G PE + L+ EE E
Sbjct: 24 RLALEALLEGGPEAYLEFLK---EEGE 47
>gnl|CDD|236060 PRK07581, PRK07581, hypothetical protein; Validated.
Length = 339
Score = 28.0 bits (63), Expect = 7.3
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 278 IAELTNFNGDKKKALAALLAKSLI 301
I+ + GD AL ++ AK+ +
Sbjct: 257 ISRNPAYGGDLAAALGSITAKTFV 280
>gnl|CDD|234397 TIGR03920, T7SS_EccD, type VII secretion integral membrane protein
EccD. Members of this family are EccD, a component of
actinobacterial type VII secretion systems (T7SS) with
ten to eleven predicted transmembrane helix regions
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 431
Score = 27.7 bits (62), Expect = 7.9
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 53 DNKKTLKTHGIQDGDLVLLKHLGSYHATPAAVIPNFDFSGIVVPSASSSSSNGQSSNSLS 112
D +L G+ DGDL+ L T A P + + + SSS S + +
Sbjct: 59 DLDLSLDEAGVVDGDLL---VLRPVSDTEPA--PVIEDVADALAALSSSRSRPWRARTTR 113
Query: 113 DDPA 116
+ A
Sbjct: 114 ELGA 117
>gnl|CDD|173903 cd00806, TrpRS_core, catalytic core domain of tryptophanyl-tRNA
synthetase. Tryptophanyl-tRNA synthetase (TrpRS)
catalytic core domain. TrpRS is a homodimer which
attaches Tyr to the appropriate tRNA. TrpRS is a class I
tRNA synthetases, so it aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains class I characteristic
HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 280
Score = 27.5 bits (62), Expect = 8.1
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 81 PAAVIPNFDF-SGIVVPSASSSSSNGQSSNSLSDDPATVRQ 120
PAA++ F G+ PS S S+ ++ L+D P +++
Sbjct: 172 PAALLSKGAFLPGLQGPSKKMSKSDPNNAIFLTDSPKEIKK 212
>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 = 27.6 bits (62), Expect = 8.5
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 161 EREKREQLRLRMLNAHPFDTEAQKLIAEE-IKKNNIEANMEAAMEYNPETFGTVVMLY 217
RE + L M + A + E + + + AA E NPE F +++L
Sbjct: 220 VREVQRALA--MFSGRHLIMPAHHEVRELDVDLRRLWKVLRAAYERNPEDFEELLLLK 275
>gnl|CDD|197278 cd09181, PLDc_FAM83A_N, N-terminal phospholipase D-like domain of
the uncharacterized protein, Family with sequence
similarity 83A. N-terminal phospholipase D (PLD)-like
domain of the uncharacterized protein, Family with
sequence similarity 83A (FAM83A), also known as tumor
antigen BJ-TSA-9. FAM83A or BJ-TSA-9 is a novel
tumor-specific gene highly expressed in human lung
adenocarcinoma. Due to this specific expression pattern,
it may serve as a biomarker for lung cancer, especially
in the early detection of micrometastasis for lung
adenocarcinoma patients. Since the N-terminal PLD-like
domain of FAM83 proteins shows only trace similarity to
the PLD catalytic domain and lacks the functionally
important histidine residue, FAM83 proteins may share a
similar three-dimensional fold with PLD enzymes, but are
most unlikely to carry PLD activity.
Length = 276
Score = 27.5 bits (61), Expect = 8.7
Identities = 11/24 (45%), Positives = 19/24 (79%), Gaps = 1/24 (4%)
Query: 138 RLA-DALLNGSPEDFERILRQQYE 160
RLA DALL+G +++ ++LR++ E
Sbjct: 13 RLATDALLDGGLDEYHQVLRKEGE 36
>gnl|CDD|218342 pfam04948, Pox_A51, Poxvirus A51 protein.
Length = 334
Score = 27.8 bits (62), Expect = 8.8
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 61 HGIQDGDLVLLKHLGSYHATPAAVIPNFDFSGIVVPSA 98
I+ G +++K +G + A+ PNFD+ I + SA
Sbjct: 271 ESIRGGLHIIIKDVGKFGASYVGKYPNFDYIKIALSSA 308
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
0.317 0.132 0.371
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,533,324
Number of extensions: 1538856
Number of successful extensions: 2149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2135
Number of HSP's successfully gapped: 108
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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: 59 (26.5 bits)