RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6439
(114 letters)
>gnl|CDD|130171 TIGR01101, V_ATP_synt_F, vacuolar ATP synthase F subunit. This
model describes the vacuolar ATP synthase F subunit (14
kDa subunit) in eukaryotes. In some archaeal species
this protein subunit is referred as G subunit [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 115
Score = 200 bits (509), Expect = 3e-68
Identities = 87/110 (79%), Positives = 101/110 (91%)
Query: 5 SAVKGKLLAVIGDEDTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDD 64
SA KGKL+AVIGDEDT VGFLLGGIGEINK+R PNFLVVDKNT+VS+IE+ F +F+KRDD
Sbjct: 1 SAEKGKLIAVIGDEDTVVGFLLGGIGEINKNRHPNFLVVDKNTTVSEIEDCFNRFLKRDD 60
Query: 65 VDIILINQNVAELIRHCIDDHTQPIPAVLEIPSKDHPYDASKDSILRRAK 114
+ IILINQ++AE+IRH +D HT+ IPAVLEIPSKDHPYDASKDSILRRA+
Sbjct: 61 IAIILINQHIAEMIRHAVDAHTRSIPAVLEIPSKDHPYDASKDSILRRAR 110
>gnl|CDD|216832 pfam01990, ATP-synt_F, ATP synthase (F/14-kDa) subunit. This
family includes 14-kDa subunit from vATPases, which is
in the peripheral catalytic part of the complex. The
family also includes archaebacterial ATP synthase
subunit F.
Length = 92
Score = 107 bits (270), Expect = 5e-32
Identities = 45/103 (43%), Positives = 61/103 (59%), Gaps = 12/103 (11%)
Query: 12 LAVIGDEDTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDIILIN 71
+AVIGDEDT GF L GIG + S + EEAF + ++R+D+ IILI
Sbjct: 1 IAVIGDEDTVTGFRLAGIGVVYVV------------SPEEAEEAFEELLEREDIGIILIT 48
Query: 72 QNVAELIRHCIDDHTQPIPAVLEIPSKDHPYDASKDSILRRAK 114
+++AE IR ID + +PA+LEIPSKD PY KDS+ +
Sbjct: 49 EDIAEEIRETIDRYESVLPAILEIPSKDGPYGPGKDSVRELVR 91
>gnl|CDD|224353 COG1436, NtpG, Archaeal/vacuolar-type H+-ATPase subunit F [Energy
production and conversion].
Length = 104
Score = 63.9 bits (156), Expect = 1e-14
Identities = 35/108 (32%), Positives = 50/108 (46%), Gaps = 14/108 (12%)
Query: 8 KGKLLAVIGDEDTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDI 67
+AVIGD DT GF L G+ + V D D A + + DDV I
Sbjct: 1 MMMKIAVIGDRDTVTGFRLAGVRVVY--------VAD---DEEDELRAALRVLAEDDVGI 49
Query: 68 ILINQNVAELIRHCID--DHTQPIPAVLEIPSK-DHPYDASKDSILRR 112
ILI +++AE IR I + +PA++EIPS + ++ I R
Sbjct: 50 ILITEDLAEKIREEIRRIIRSSVLPAIVEIPSPGKEEEEPLRELIRRA 97
>gnl|CDD|179685 PRK03957, PRK03957, V-type ATP synthase subunit F; Provisional.
Length = 100
Score = 49.6 bits (119), Expect = 4e-09
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 23/108 (21%)
Query: 12 LAVIGDEDTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEA---FRKFIKRDDVDII 68
+AV+GD DT GF L G+ E+ V + EEA ++ ++ D++ II
Sbjct: 3 IAVVGDRDTVTGFRLAGLTEV--------------YEVKNPEEAKNAIKELVENDEIGII 48
Query: 69 LINQNVAELIRHCIDDHTQPIPAVLEIPSKDHPYDASKD---SILRRA 113
+I + +AE IR I +P ++EIP K + D ++RRA
Sbjct: 49 IITERIAEEIRDLISVA---LPIIVEIPDKSGSIERENDPVKELVRRA 93
>gnl|CDD|179293 PRK01395, PRK01395, V-type ATP synthase subunit F; Provisional.
Length = 104
Score = 33.8 bits (78), Expect = 0.004
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 20/89 (22%)
Query: 13 AVIGDEDTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKR---DDVDIIL 69
V+GD+D+ + F GI F V+D+ +EA +++ +D II
Sbjct: 7 GVVGDKDSILPFKALGID--------VFPVIDE-------QEA-INTLRKLAMEDYGIIY 50
Query: 70 INQNVAELIRHCIDDH-TQPIPAVLEIPS 97
I + +A I I+ + Q +PA++ IPS
Sbjct: 51 ITEQIAADIPETIERYDNQVLPAIILIPS 79
>gnl|CDD|179387 PRK02228, PRK02228, V-type ATP synthase subunit F; Provisional.
Length = 100
Score = 33.0 bits (76), Expect = 0.009
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 12 LAVIGDEDTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDIILIN 71
+AVIG + GF L GI + V + ++EA + ++ DDV I++++
Sbjct: 3 IAVIGSPEFTTGFRLAGIRK-----------VYEVPDDEKLDEAVEEVLEDDDVGILVMH 51
Query: 72 QN 73
+
Sbjct: 52 DD 53
>gnl|CDD|148668 pfam07199, DUF1411, Protein of unknown function (DUF1411). This
family represents a conserved region approximately 150
residues long that is sometimes repeated within some
Babesia bovis proteins of unknown function.
Length = 188
Score = 29.1 bits (65), Expect = 0.34
Identities = 22/104 (21%), Positives = 45/104 (43%), Gaps = 19/104 (18%)
Query: 5 SAVKGKLLAVIGD------EDTCVGFLLGGIGEINKHRQPNFLVVDKN-----TSVSDI- 52
SA G + A + E G + + + N + K TS+SDI
Sbjct: 28 SAFSGNVWADEAEVPQEPVEKKKEGGCFSWSVKEDYQKLQNLPDITKTDNTEKTSLSDIS 87
Query: 53 ------EEAFRKFIKRDDVDIILINQNVAELIRHCIDDHTQPIP 90
+++ ++K+ DVD+ L+N+ ++ L++H + ++ P
Sbjct: 88 VKLGPAKKSMNLWVKKVDVDMSLLNKRISVLLQH-VTNYGPDSP 130
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 29.0 bits (66), Expect = 0.42
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 36 RQPNFLVVDKNTS------VSDIEEAFRKFIKRDDVDIILINQNVA 75
+P L++D+ + V +I EA ++ K + I+L+ QN
Sbjct: 153 SRPKLLLLDEPSEGLAPKIVEEIFEAIKELRKEGGMTILLVEQNAR 198
>gnl|CDD|107355 cd06360, PBP1_alkylbenzenes_like, Type I periplasmic binding
component of active transport systems that are
predicted be involved in anaerobic biodegradation of
alkylbenzenes such as toluene and ethylbenzene. This
group includes the type I periplasmic binding component
of active transport systems that are predicted be
involved in anaerobic biodegradation of alkylbenzenes
such as toluene and ethylbenzene; their substrate
specificity is not well characterized, however.
Length = 336
Score = 28.4 bits (64), Expect = 0.66
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 23 GFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDIIL 69
G LGG R+ F+V D E RK I++D VD+++
Sbjct: 31 GGKLGG-------REVEFVVEDDEAKPDVAVEKARKLIEQDKVDVVV 70
>gnl|CDD|234199 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
protein UrtE. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 230
Score = 28.3 bits (64), Expect = 0.82
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 37 QPNFLVVDKNTS------VSDIEEAFRKFIKRDDVDIILINQNV 74
+P L++D+ T + DI R+ + I+L+ Q +
Sbjct: 149 RPKLLLLDEPTEGIQPSIIKDIGRVIRRLRAEGGMAILLVEQYL 192
>gnl|CDD|148209 pfam06466, PCAF_N, PCAF (P300/CBP-associated factor) N-terminal
domain. This region is spliced out of human histone
acetyltranfersase KAT2A isoform 2. It is predicted to be
of a mixed alpha/beta fold - though predominantly
helical.
Length = 252
Score = 28.0 bits (62), Expect = 0.94
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 49 VSDIEEAFRKFIKRDDVDIILINQNVAELIRHCIDDHTQPIPAVLEIPSKDHPYD 103
V D+E F K +D D + + +L+R CI QP V+E D P++
Sbjct: 91 VIDVENLFMSVHKEEDEDTKQVYFYLFKLLRKCILQRQQP---VVEGSLGDPPFE 142
>gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain
of active transport proteins. Periplasmic
solute-binding domain of active transport proteins
found in bacteria and Archaea that is predicted to be
involved in the efflux of toxic compounds. Members of
this subgroup include proteins from Herminiimonas
arsenicoxydans, which is resistant to arsenic and
various heavy metals such as cadmium and zinc.
Moreover, they show significant sequence similarity to
the cluster of AmiC and active transport systems for
short-chain amides and urea (FmdDEF), and thus are
likely to exhibit a ligand-binding mode similar to that
of the amide sensor protein AmiC from Pseudomonas
aeruginosa.
Length = 346
Score = 28.0 bits (63), Expect = 1.0
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 27 GGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDII--LINQNVAE 76
GGIG R+ +V D+ + R+ ++ + VD++ LI+ VA
Sbjct: 34 GGIGG----RKIELVVRDEAGKPDEAIREARELVENEGVDMLIGLISSGVAL 81
>gnl|CDD|233234 TIGR01016, sucCoAbeta, succinyl-CoA synthetase, beta subunit. This
model is designated subfamily because it does not
discriminate the ADP-forming enzyme ((EC 6.2.1.5) from
the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half
is described by the CoA-ligases model (pfam00549). The
C-terminal half is described by the ATP-grasp model
(pfam02222). This family contains a split seen both in a
maximum parsimony tree (which ignores gaps) and in the
gap pattern near position 85 of the seed alignment.
Eukaryotic and most bacterial sequences are longer and
contain a region similar to TXQTXXXG. Sequences from
Deinococcus radiodurans, Mycobacterium tuberculosis,
Streptomyces coelicolor, and the Archaea are 6 amino
acids shorter in that region and contain a motif
resembling [KR]G [Energy metabolism, TCA cycle].
Length = 386
Score = 27.7 bits (62), Expect = 1.3
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 39 NFLVVDKNTSVSDIEEAFRKFIKRDDVDIILIN--------QNVAELIRHCIDDHTQPIP 90
NFL V S + EA + + V ++ IN VA+ + + + +P
Sbjct: 285 NFLDVGGGASAERVREALKLVLSDKSVKVVFINIFGGITRCDLVAKGLVEALKEVGVNVP 344
Query: 91 AV 92
V
Sbjct: 345 VV 346
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 26.4 bits (59), Expect = 1.7
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 48 SVSDIEEAFRKFIKRDDVDII 68
+ SD+EE F +F DV+II
Sbjct: 12 TESDLEERFSRFGTVSDVEII 32
>gnl|CDD|163316 TIGR03542, DAPAT_plant, LL-diaminopimelate aminotransferase.
This clade of the pfam00155 superfamily of
aminotransferases includes several which are adjacent
to elements of the lysine biosynthesis via
diaminopimelate pathway (GenProp0125). This clade
includes characterized species in plants and Chlamydia.
Every member of this clade is from a genome which
possesses most of the lysine biosynthesis pathway but
lacks any of the known succinylases, desuccinylases,
acetylases or deacetylases typical of the acylated
versions of this pathway nor do they have the direct,
NADPH-dependent enzyme (ddh).
Length = 402
Score = 27.4 bits (61), Expect = 1.8
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 36 RQPNFLVVDKNTSVSDIEEAFRKF-IKRDDVDIILINQNVAELIRHCIDDHTQPIPA 91
R P+FL + + S+I + +F K DII R I D TQP+PA
Sbjct: 3 RNPHFLKLKSSYLFSEINKRVAEFRKKNPSADII----------RLGIGDTTQPLPA 49
>gnl|CDD|188140 TIGR01422, phosphonatase, phosphonoacetaldehyde hydrolase. This
enzyme catalyzes the cleavage of the carbon phosphorous
bond of a phosphonate. The mechanism depends on the
substrate having a carbonyl one carbon away from the
cleavage position. This enzyme is a member of the
Haloacid Dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases (pfam00702), and
contains a modified version of the conserved catalytic
motifs of that superfamily: the first motif is usually
DxDx(T/V), here it is DxAxT, and in the third motif the
normal conserved lysine is instead an arginine.
Additionally, the enzyme contains a unique conserved
catalytic lysine (B. cereus pos. 53) which is involved
in the binding and activation of the substrate through
the formation of a Schiff base. The substrate of this
enzyme is the product of 2-aminoethylphosphonate (AEP)
transaminase, phosphonoacetaldehyde. This degradation
pathway for AEP may be related to its toxic properties
which are utilized by microorganisms as a chemical
warfare agent [Central intermediary metabolism, Other].
Length = 253
Score = 26.9 bits (60), Expect = 2.0
Identities = 7/46 (15%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 52 IEEAFRKFIKR--DDVDIILINQNVAELIRHCIDDHTQPIPAVLEI 95
+ E ++ R + D+ + + + + ++ PIP +E+
Sbjct: 62 VAERWQAKFGRLPTEADVQALYEAFEPMQLAKLAEYASPIPGAIEV 107
>gnl|CDD|238152 cd00248, Mth938-like, Mth938-like domain. The members of this
family include: Mth938, 2P1, Xcr35, Rpa2829, and
several uncharacterized sequences. Mth938 is a
hypothetical protein encoded by the Methanobacterium
thermoautotrophicum (Mth) genome. This protein
crystallizes as a dimer, although it is monomeric in
solution, with one disulfide bond in each monomer. 2P1
is a partially characterized nuclear protein which is
homologous to E3-3 from rat and known to be alternately
spliced. Xcr35 and Rpa2829 are hypothetical proteins of
unknown function from the Xanthomonas campestris and
Rhodopseudomonas palustris genomes, respectively, for
which the crystal structures have been determined.
Length = 109
Score = 26.4 bits (59), Expect = 2.1
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 23 GFLLGGIGEINKHRQPNFLVVDK-----NTSVSDI-EEAFRKFIKRDDVDIILI 70
GF + G +R P ++ D TS+SD+ EA + D DI+LI
Sbjct: 9 GFRIAGQ----VYRGPLLVLPDGVVPWDGTSLSDLDPEALLPLLAEDRPDILLI 58
>gnl|CDD|172778 PRK14290, PRK14290, chaperone protein DnaJ; Provisional.
Length = 365
Score = 27.2 bits (60), Expect = 2.1
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 41 LVVDKNTSVSDIEEAFRKFIKRDDVDIILINQNVAELIRHCIDDHTQPIPAVLEIPSKDH 100
L VD+N S DI++AFR+ K+ D+ N+ AE I + + VL P K
Sbjct: 9 LGVDRNASQEDIKKAFRELAKKWHPDLHPGNKAEAEEKFKEISEAYE----VLSDPQKRR 64
Query: 101 PYD 103
YD
Sbjct: 65 QYD 67
>gnl|CDD|179391 PRK02240, PRK02240, GTP cyclohydrolase III; Provisional.
Length = 254
Score = 26.9 bits (60), Expect = 2.3
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 40 FLVVDKNTSVSDIEEAFRKFIKRDDVDIILINQNVAELIRHCIDDH 85
F + D + +DIE AF F++ I Q L+R H
Sbjct: 140 FDINDITGTYTDIENAFDTFLE--------IEQAYLALMRELRKAH 177
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 25.8 bits (57), Expect = 3.1
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 40 FLVVDKNTSVSDIEEAFRKF 59
F+V K+ + D+ EAF F
Sbjct: 7 FIVCGKSVTEDDLREAFAPF 26
>gnl|CDD|238484 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
helicase DnaB unwinds the DNA duplex at the chromosome
replication fork. Although the mechanism by which DnaB
both couples ATP hydrolysis to translocation along DNA
and denatures the duplex is unknown, a change in the
quaternary structure of the protein involving
dimerization of the N-terminal domain has been observed
and may occur during the enzymatic cycle. This
C-terminal domain contains an ATP-binding site and is
therefore probably the site of ATP hydrolysis.
Length = 242
Score = 26.3 bits (59), Expect = 3.3
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 32 INKHRQPNFLVVDK-NTSVSDIEEAFRKFIKRDDVDIILI 70
I + ++ + D + +VSDI R+ K + +I+I
Sbjct: 90 IGELKELPIYIDDSSSLTVSDIRSRARRLKKEHGLGLIVI 129
>gnl|CDD|216986 pfam02350, Epimerase_2, UDP-N-acetylglucosamine 2-epimerase. This
family consists of UDP-N-acetylglucosamine 2-epimerases
EC:5.1.3.14 this enzyme catalyzes the production of
UDP-ManNAc from UDP-GlcNAc. Note that some of the
enzymes is this family are bifunctional, and in those
instances Pfam matches only the N-terminal half of the
protein suggesting that the additional C-terminal part
(when compared to mono-functional members of this
family) is responsible for the UPD-N-acetylmannosamine
kinase activity of these enzymes. This hypothesis is
further supported by the assumption that the C-terminal
part of rat UDP-GlcNAc-2-epimerase is the kinase domain.
Length = 346
Score = 26.3 bits (59), Expect = 3.9
Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 10/64 (15%)
Query: 32 INKHRQPNFLV-------VDKNTSVSDIEEAFRKFIKRDDVDIILI---NQNVAELIRHC 81
+ + LV D + I EA + +R DV ++ N + I
Sbjct: 175 LADLGKRYILVTFHRRENEDDPERLEQILEALKALAERPDVPVVFPVHNNPRTRKRINEL 234
Query: 82 IDDH 85
+++
Sbjct: 235 LEEL 238
>gnl|CDD|107327 cd06332, PBP1_aromatic_compounds_like, Type I periplasmic binding
proteins of active transport systems that are predicted
to be involved in transport of aromatic compounds such
as 2-nitrobenzoic acid and alkylbenzenes. This group
includes the type I periplasmic binding proteins of
active transport systems that are predicted to be
involved in transport of aromatic compounds such as
2-nitrobenzoic acid and alkylbenzenes; their substrate
specificities are not well characterized, however.
Members also exhibit close similarity to active
transport systems for short chain amides and/or urea
found in bacteria and archaea.
Length = 333
Score = 26.4 bits (59), Expect = 4.1
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 40 FLVVDKNTSVSDIEEAFRKFIKRDDVDII 68
+V D +A RK I++D VD++
Sbjct: 41 VVVEDDELKPDVAVQAARKLIEQDKVDVV 69
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 26.2 bits (58), Expect = 4.2
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 41 LVVDKNTSVSDIEEAFRKFIKRDDVDI 67
L V K+ S +I++A+RK K+ DI
Sbjct: 10 LGVSKDASQDEIKKAYRKLSKKYHPDI 36
>gnl|CDD|164848 PHA01078, PHA01078, putative upper collar protein.
Length = 249
Score = 26.2 bits (57), Expect = 4.6
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 29 IGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDIIL 69
I E++ + N L VDK + VSD E + + +I L
Sbjct: 164 ISELSNYLGINSLAVDKESGVSDEEAKSNRGFTTSNSNIYL 204
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 25.1 bits (55), Expect = 4.8
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 43 VDKNTSVSDIEEAFRKFIKRDDVDIILINQN 73
++K T+ SD+ EAF +F + D+DI N
Sbjct: 10 LEKTTTYSDLREAFERFGEIIDIDIKKQGGN 40
>gnl|CDD|234804 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 791
Score = 26.3 bits (59), Expect = 5.0
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 41 LVVDKNTSVSDIEEAFRKF 59
LVVD++ +DI +A +K
Sbjct: 708 LVVDEDVPAADILKAIKKA 726
>gnl|CDD|202554 pfam03147, FDX-ACB, Ferredoxin-fold anticodon binding domain.
This is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold.
Length = 94
Score = 25.1 bits (56), Expect = 5.2
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 41 LVVDKNTSVSDIEEAFRKFIKRDDVDIILI 70
VVD++ +DI + RK D+ L
Sbjct: 12 FVVDEDVPAADILDVIRKAGGELLEDVELF 41
>gnl|CDD|238451 cd00886, MogA_MoaB, MogA_MoaB family. Members of this family are
involved in biosynthesis of the molybdenum cofactor
(MoCF) an essential cofactor of a diverse group of
redox enzymes. MoCF biosynthesis is an evolutionarily
conserved pathway present in eubacteria, archaea, and
eukaryotes. MoCF contains a tricyclic pyranopterin,
termed molybdopterin (MPT). MogA, together with MoeA,
is responsible for the metal incorporation into MPT,
the third step in MoCF biosynthesis. The plant homolog
Cnx1 is a MoeA-MogA fusion protein. The mammalian
homolog gephyrin is a MogA-MoeA fusion protein, that
plays a critical role in postsynaptic anchoring of
inhibitory glycine receptors and major GABAa receptor
subtypes. In contrast, MoaB shows high similarity to
MogA, but little is known about its physiological role.
All well studied members of this family form highly
stable trimers.
Length = 152
Score = 25.5 bits (57), Expect = 5.3
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 49 VSDIEEAFRKFIKRDDVDIILIN 71
+I EA ++ D VD+IL
Sbjct: 46 KDEIREALIEWADEDGVDLILTT 68
>gnl|CDD|184075 PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional.
Length = 267
Score = 25.6 bits (57), Expect = 5.9
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 53 EEAFRKFIKRDDVDIILINQNVAELIRHCIDDHTQPIPAVLE 94
+ F + DVD + L + D+ PIP VLE
Sbjct: 69 QAVFGRLPTEADVD--ALYAAFEPLQIAKLADYATPIPGVLE 108
>gnl|CDD|144538 pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).
This protein is also known as NSP1. NS53 is encoded by
gene 5. It is made in low levels in the infected cells
and is a component of early replication. The protein is
known to accumulate on the cytoskeleton of the infected
cell. NS53 is an RNA binding protein that contains a
characteristic cysteine rich region.
Length = 488
Score = 25.8 bits (57), Expect = 6.0
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 11/71 (15%)
Query: 19 DTCVGFLLGGIGEINKHRQPNFLVVDKNTSVSD--------IEEAFRKFIKRDDVDIILI 70
D C+GF + E++K +PN++ + S+ I +F+ + +D I I
Sbjct: 285 DRCLGFTKYKLFELSKLIKPNYIASNHWQPASEVHNCKWCSINNSFKVW---NDFRIRKI 341
Query: 71 NQNVAELIRHC 81
N+ IR
Sbjct: 342 YNNLMSFIRAL 352
>gnl|CDD|237659 PRK14287, PRK14287, chaperone protein DnaJ; Provisional.
Length = 371
Score = 25.7 bits (56), Expect = 6.2
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 41 LVVDKNTSVSDIEEAFRKFIKRDDVDI 67
L VD+N SV ++++A+RK ++ D+
Sbjct: 10 LGVDRNASVDEVKKAYRKLARKYHPDV 36
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules.
Length = 222
Score = 25.5 bits (57), Expect = 6.7
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 36 RQPNFLVVDKNTS------VSDIEEAFRKFIKRDDVDIILINQNVA 75
+P L++D+ + V +I EA R+ ++ + V I+L+ QN
Sbjct: 149 SRPKLLLLDEPSEGLAPKIVEEIFEAIRE-LRDEGVTILLVEQNAR 193
>gnl|CDD|234438 TIGR03999, thiol_BshA, N-acetyl-alpha-D-glucosaminyl L-malate
synthase BshA. Members of this protein family are BshA,
a glycosyltransferase required for bacillithiol
biosynthesis. This enzyme combines UDP-GlcNAc and
L-malate to form N-acetyl-alpha-D-glucosaminyl L-malate
synthase. Bacillithiol is a low-molecular-weight thiol,
an analog of glutathione and mycothiol, and is found
largely in the Firmicutes [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 374
Score = 25.6 bits (57), Expect = 7.2
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 5/41 (12%)
Query: 21 CVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIK 61
+ GGI E+ +H FL V D+E I
Sbjct: 299 VIASNAGGIPEVVEHGVTGFLC-----DVGDVETMAEYAIS 334
>gnl|CDD|153141 cd04869, ACT_GcvR_2, ACT domains that comprise the Glycine
Cleavage System Transcriptional Repressor (GcvR)
protein, and other related domains. This CD includes
the second of the two ACT domains that comprise the
Glycine Cleavage System Transcriptional Repressor
(GcvR) protein, and other related domains. The glycine
cleavage enzyme system in Escherichia coli provides
one-carbon units for cellular methylation reactions.
This enzyme system, encoded by the gcvTHP operon and
lpd gene, catalyzes the cleavage of glycine into CO2 +
NH3 and transfers a one-carbon unit to
tetrahydrofolate, producing
5,10-methylenetetrahydrofolate. The gcvTHP operon is
activated by the GcvA protein in response to glycine
and repressed by a GcvA/GcvR interaction in the absence
of glycine. It has been proposed that the co-activator
glycine acts through a mechanism of de-repression by
binding to GcvR and preventing GcvR from interacting
with GcvA to block GcvA's activator function. Evidence
also suggests that GcvR interacts directly with GcvA
rather than binding to DNA to cause repression. Members
of this CD belong to the superfamily of ACT regulatory
domains.
Length = 81
Score = 24.5 bits (54), Expect = 7.4
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 41 LVVDKNTSVSDIEEAFRKFIKRDDVDIILI 70
L + T + + E + +VDI L
Sbjct: 51 LALPAGTDLDALREELEELCDDLNVDISLE 80
>gnl|CDD|177736 PLN00124, PLN00124, succinyl-CoA ligase [GDP-forming] subunit beta;
Provisional.
Length = 422
Score = 25.5 bits (56), Expect = 7.9
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 39 NFLVVDKNTSVSDIEEAFRKFIKRDDVDIILIN 71
NFL V N S + EAF+ D V IL+N
Sbjct: 320 NFLDVGGNASEQQVVEAFKILTSDDKVKAILVN 352
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 25.3 bits (56), Expect = 7.9
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 43 VDKNTSVSDIEEAFRKFIK 61
V K+ S +I++A+RK K
Sbjct: 12 VSKDASEEEIKKAYRKLAK 30
>gnl|CDD|233161 TIGR00870, trp, transient-receptor-potential calcium channel
protein. The Transient Receptor Potential Ca2+ Channel
(TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also
been called the store-operated calcium channel (SOC)
family. The prototypical members include the Drosophila
retinal proteinsTRP and TRPL (Montell and Rubin, 1989;
Hardie and Minke, 1993). SOC members of the family
mediate the entry of extracellular Ca2+ into cells in
responseto depletion of intracellular Ca2+ stores
(Clapham, 1996) and agonist stimulated production of
inositol-1,4,5 trisphosphate (IP3). One member of the
TRP-CCfamily, mammalian Htrp3, has been shown to form a
tight complex with the IP3 receptor (TC #1.A.3.2.1).
This interaction is apparently required for IP3
tostimulate Ca2+ release via Htrp3. The vanilloid
receptor subtype 1 (VR1), which is the receptor for
capsaicin (the ?hot? ingredient in chili peppers) and
servesas a heat-activated ion channel in the pain
pathway (Caterina et al., 1997), is also a member of
this family. The stretch-inhibitable non-selective
cation channel(SIC) is identical to the vanilloid
receptor throughout all of its first 700 residues, but
it exhibits a different sequence in its last 100
residues. VR1 and SICtransport monovalent cations as
well as Ca2+. VR1 is about 10x more permeable to Ca2+
than to monovalent ions. Ca2+ overload probably causes
cell deathafter chronic exposure to capsaicin.
(McCleskey and Gold, 1999) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 743
Score = 25.4 bits (56), Expect = 8.2
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 36 RQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDII--------LINQNVAELIR 79
R P +V + + +SD E+AF +R D+ + +N N + +
Sbjct: 1 RGPLDIVPAEESPLSDEEKAFLPAAERGDLASVYRDLEEPKKLNINCPDRLG 52
>gnl|CDD|239971 cd04598, CBS_pair_GGDEF_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in association with the GGDEF
(DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain
has been suggested to be homologous to the adenylyl
cyclase catalytic domain and is thought to be involved
in regulating cell surface adhesiveness in bacteria.
CBS is a small domain originally identified in
cystathionine beta-synthase and subsequently found in a
wide range of different proteins. CBS domains usually
come in tandem repeats, which associate to form a
so-called Bateman domain or a CBS pair which is
reflected in this model. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains. It has been proposed that the
CBS domain may play a regulatory role, although its
exact function is unknown.
Length = 119
Score = 24.8 bits (55), Expect = 8.3
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 38 PNFLVVDKNTSVSDIEEAFRKFIKRDDVDI 67
P+ L+V+ +T +EE R RD ++
Sbjct: 69 PDPLIVEADTP---LEEVSRLATGRDSQNL 95
>gnl|CDD|107332 cd06337, PBP1_ABC_ligand_binding_like_4, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that
are predicted to be involved in transport of amino
acids, peptides, or inorganic ions. This subgroup
includes the type I periplasmic ligand-binding domain
of uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been
determined experimentally.
Length = 357
Score = 25.4 bits (56), Expect = 8.9
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 25 LLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIKRDDVDIILIN 71
L G+ + +V D ++ + ++ I D VD++L
Sbjct: 30 LADGLVVGGSTYEVEIIVRDSQSNPNRAGLVAQELILTDKVDLLLAG 76
>gnl|CDD|100002 cd04962, GT1_like_5, This family is most closely related to the GT1
family of glycosyltransferases. Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. This group of glycosyltransferases
is most closely related to the previously defined
glycosyltransferase family 1 (GT1). The members of this
family may transfer UDP, ADP, GDP, or CMP linked sugars.
The diverse enzymatic activities among members of this
family reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in bacteria, while some of them are also found in
Archaea and eukaryotes.
Length = 371
Score = 25.3 bits (56), Expect = 9.2
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 7/46 (15%)
Query: 21 CVGFLLGGIGEINKHRQPNFLVVDKNTSVSDIEEAFRKFIK--RDD 64
V GGI E+ KH + FLV V D+E + DD
Sbjct: 297 VVASNAGGIPEVVKHGETGFLV-----DVGDVEAMAEYALSLLEDD 337
>gnl|CDD|214893 smart00896, FDX-ACB, Ferredoxin-fold anticodon binding domain.
This is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold, consisting of an alpha+beta sandwich
with anti-parallel beta-sheets (beta-alpha-beta x2).
Length = 93
Score = 24.3 bits (54), Expect = 9.8
Identities = 5/21 (23%), Positives = 12/21 (57%)
Query: 41 LVVDKNTSVSDIEEAFRKFIK 61
VVD++ +++ +A R+
Sbjct: 12 FVVDEDVPAAELLDAIREAGG 32
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 0.140 0.404
Gapped
Lambda K H
0.267 0.0879 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,947,000
Number of extensions: 530821
Number of successful extensions: 852
Number of sequences better than 10.0: 1
Number of HSP's gapped: 845
Number of HSP's successfully gapped: 79
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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: 53 (23.9 bits)