RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3604
(496 letters)
>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase,
Saccharomyces cerevisiae Pus3 like. This group consists
of eukaryotic pseudouridine synthases similar to S.
cerevisiae Pus3p, mouse Pus3p and, human PUS2.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse
Pus3p has been shown to makes psi38 and, possibly also
psi 39, in tRNAs. Psi38 and psi39 are highly conserved
in tRNAs from eubacteria, archea and eukarya.
Length = 256
Score = 187 bits (478), Expect = 3e-56
Identities = 73/182 (40%), Positives = 97/182 (53%), Gaps = 32/182 (17%)
Query: 196 VVTLKIRSKLTSPGEES---------DDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSAR 246
V++L +RS L D+ ELPY K+LN LP DI+++AW+PVP +SAR
Sbjct: 61 VISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSAR 120
Query: 247 FDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVT 306
F C+ R Y+Y+FP+ LDI+ M KAA+ L+G HDFRN CKM+V N V N+ R V A V
Sbjct: 121 FSCVSRTYRYFFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVE 180
Query: 307 ------SAWQNVQFN------------DIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKY 348
F + V+ F GQG E P +I QL+D+EK
Sbjct: 181 PVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVL-----FLIGQGLEPPSVISQLLDVEKN 235
Query: 349 PR 350
PR
Sbjct: 236 PR 237
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 91.2 bits (227), Expect = 1e-20
Identities = 31/92 (33%), Positives = 45/92 (48%), Gaps = 16/92 (17%)
Query: 211 ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAG-------- 262
+D ++ LN LP DI+V+ + VP+ + ARF R Y+Y A
Sbjct: 67 PADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAPLRPPFLAN 126
Query: 263 --------LDIDAMHKAAQYLVGTHDFRNLCK 286
LD+DAM +AA+ L+GTHDF + K
Sbjct: 127 YVWHVPYPLDLDAMREAAKLLLGTHDFTSFRK 158
>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase. Members
of this family are the tRNA modification enzyme TruA,
tRNA pseudouridine(38-40) synthase. In a few species
(e.g. Bacillus anthracis), TruA is represented by two
paralogs [Protein synthesis, tRNA and rRNA base
modification].
Length = 227
Score = 88.9 bits (221), Expect = 4e-20
Identities = 42/183 (22%), Positives = 70/183 (38%), Gaps = 47/183 (25%)
Query: 196 VVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255
V++ ++ DN+L LN LP DI+V A +PV + + ARF R+Y+
Sbjct: 60 VISFDTPKEIP-------DNKLNA--KLNALLPPDIRVKALAPVNDNFHARFSASKRHYR 110
Query: 256 YWFP-----QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQ 310
Y + LD++ M AA+ L+G HDF N K + S +
Sbjct: 111 YILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKAK--------------SKSRSPIR 156
Query: 311 NVQFNDIKE-----VVDSEPS--------------FKKGQGNEKPEIIQQLVDIEKYPRI 351
+ + E + D + G+G PE + +L+D +K
Sbjct: 157 TISDIKVSESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLA 216
Query: 352 KSA 354
+
Sbjct: 217 PTT 219
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 84.4 bits (210), Expect = 2e-18
Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 18/93 (19%)
Query: 211 ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKY-------------- 256
+ + + LN LP DI V+ VP+ + ARF R Y+Y
Sbjct: 67 PAPRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRPARPPFLRG 126
Query: 257 ---WFPQAGLDIDAMHKAAQYLVGTHDFRNLCK 286
+P LD+DAM++AAQYL+G HDF +
Sbjct: 127 YVWHYPYP-LDVDAMNEAAQYLLGEHDFTSFRA 158
>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruA, Saccharomyces cerevisiae Pus1p,
S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and
human PUS1. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. S. cerevisiae PUS1 catalyzes the formation of
psi34 and psi36 in the intron containing tRNAIle, psi35
in the intron containing tRNATyr, psi27 and/or psi28 in
several yeast cytoplasmic tRNAs and, psi44 in U2 small
nuclear RNA (U2 snRNA). The presence of the intron is
required for the formation of psi 34, 35 and 36. In
addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C.
elegans Pus1p does not modify psi44 in U2 snRNA. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44
in U2 snRNA and, psi38 and psi39 in tRNAs are highly
phylogenetically conserved. Psi 26,27,28,34,35,36,65
and 67 in tRNAs are less highly conserved. Mouse Pus1p
regulates nuclear receptor activity through
pseudouridylation of Steroid Receptor RNA Activator.
Missense mutation in human PUS1 causes mitochondrial
myopathy and sideroblastic anemia (MLASA).
Length = 215
Score = 81.7 bits (202), Expect = 8e-18
Identities = 36/137 (26%), Positives = 52/137 (37%), Gaps = 15/137 (10%)
Query: 222 MLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDF 281
LN LP DI+V A VP + A C R Y+Y+ P LD + + AA +GTHDF
Sbjct: 67 ALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPSFPLDDERLKSAASRFLGTHDF 126
Query: 282 RNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQF---------NDIKEVVDSEPSFKKGQG 332
N K N R + V + ++ +V G+G
Sbjct: 127 TNFSK----KDTRNTVRTIISIECKDLNPFVVVEFKAKSFLWHQVRRMVGF--LMLVGEG 180
Query: 333 NEKPEIIQQLVDIEKYP 349
P + +L+ P
Sbjct: 181 LHSPSSVSRLLAGPAPP 197
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 79.1 bits (195), Expect = 2e-16
Identities = 27/65 (41%), Positives = 38/65 (58%)
Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFR 282
LN LP DI W+ VPE + R+D + R Y+Y+F + DI+AM AA +GTHDF
Sbjct: 79 LNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFSRPPSDINAMRDAAGEFIGTHDFS 138
Query: 283 NLCKM 287
++
Sbjct: 139 CFARV 143
>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial
pseudouridine synthases similar to E. coli TruA. This
group consists of eukaryotic and bacterial pseudouridine
synthases similar to E. coli TruA, Pseudomonas
aeruginosa truA and human pseudouridine synthase-like 1
(PUSL1). Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruA makes psi38/39 and/or 40 in tRNA.
psi38 and psi39 in tRNAs are highly phylogenetically
conserved. P. aeruginosa truA is required for induction
of type III secretory genes and may act through
modifying tRNAs critical for the expression of type III
genes or their regulators.
Length = 239
Score = 78.3 bits (194), Expect = 2e-16
Identities = 31/98 (31%), Positives = 46/98 (46%), Gaps = 20/98 (20%)
Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDC-----------------LFRNYKYWFPQAGLDI 265
LN+ LP DI+V++ VP+ + ARF R Y + P+ LDI
Sbjct: 74 LNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRP-LDI 132
Query: 266 DAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHA 303
+AM +AA+ L+GTHDF + G + R + A
Sbjct: 133 EAMQEAAKLLLGTHDFSSFRA--AGCQSKSTVRTIYRA 168
>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine
synthases. This group consists of archeal pseudouridine
synthases.Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. This group of proteins make Psedouridine in
tRNAs.
Length = 219
Score = 71.3 bits (175), Expect = 4e-14
Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 218 PYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVG 277
P M+N LP+DI V+A + VPE + R + Y+Y D++AM +AA+ L+G
Sbjct: 67 PIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYRYNLGS-DYDVEAMKEAAKKLIG 125
Query: 278 THDFRNLCKMN 288
THDF N K +
Sbjct: 126 THDFSNFSKRD 136
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 61.3 bits (149), Expect = 1e-10
Identities = 31/77 (40%), Positives = 39/77 (50%), Gaps = 18/77 (23%)
Query: 223 LNNNLPRDIKVVAWSPVPEKYSARFDC----------------LF-RNYKYWFPQAGLDI 265
+N NLP DI V VP+ + RFD +F R Y +WFP LD+
Sbjct: 80 MNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYE-LDL 138
Query: 266 DAMHKAAQYLVGTHDFR 282
+AM KAA+YL G HDF
Sbjct: 139 EAMRKAAKYLEGEHDFT 155
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 58.4 bits (142), Expect = 1e-09
Identities = 31/96 (32%), Positives = 50/96 (52%), Gaps = 7/96 (7%)
Query: 189 HAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFD 248
HA R VV+LK+ + E E ++ LN++LP DI+V + V + ++AR
Sbjct: 61 HA-ARN-VVSLKV---IIDDPEGLGILED-LVEKLNSHLPSDIRVFGITRVTKSFNARKA 114
Query: 249 CLFRNYKYWFPQAGLD-IDAMHKAAQYLVGTHDFRN 283
C R Y+Y P L+ + ++ + VGTH+F N
Sbjct: 115 CDSRTYEYLLPTFALETLQRFNEILKEYVGTHNFHN 150
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 54.0 bits (130), Expect = 3e-08
Identities = 27/79 (34%), Positives = 36/79 (45%), Gaps = 18/79 (22%)
Query: 220 LKMLNNNLPRDIKVVAWSPVPEKYSARF-----------------DCLFRNYKYWFPQAG 262
K LN LP DI V V E++ AR+ + R Y +
Sbjct: 77 KKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEK- 135
Query: 263 LDIDAMHKAAQYLVGTHDF 281
LD+ AM +AA+YLVG+HDF
Sbjct: 136 LDVKAMKEAAKYLVGSHDF 154
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 54.1 bits (130), Expect = 4e-08
Identities = 32/86 (37%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 202 RSKLTSPGEESDDN------ELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255
R T PG + N +LP L +N+ LPR + A + VPE ++ R R Y
Sbjct: 38 RGSRTDPGVSAVGNVVMTSQKLP-LGYVNSKLPRGVWAWAVAEVPEGFNPR-RAKRRRYL 95
Query: 256 YWFPQAGLDIDAMHKAAQYLVGTHDF 281
Y P G D++AM +AA+ L GTHD+
Sbjct: 96 YVAPHWGEDVEAMREAAELLAGTHDY 121
>gnl|CDD|176263 cd08049, TAF8, TATA Binding Protein (TBP) Associated Factor 8. The
TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is
one of several TAFs that bind TBP, and is 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 eukaryotes. TFIID
plays an important role in the recognition of promoter
DNA and the assembly of the preinitiation complex. The
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,
involvement in the core-promoter recognition, or a role
in the essential catalytic activity of the complex. The
mouse ortholog of TAF8 is called taube nuss protein
(TBN), and is required for early embryonic development.
TBN mutant mice exhibit disturbances in the balance
between cell death and cell survival in the early
embryo. TAF8 plays a role in the differentiation of
preadipocyte fibroblasts to adipocytes; it is also
required for the integration of TAF10 into the TAF
complex. In yeast and human cells, TAFs have been found
as components of other complexes besides TFIID. TAF8 is
also a component of a small TAF complex (SMAT), which
contains TAF8, TAF10 and SUPT7L. Several TAFs interact
via histone-fold motifs. The histone fold (HFD) is the
interaction motif involved in heterodimerization of the
core histones and their assembly into nucleosome
octamer. TAF8 contains an H4 related histone fold motif,
and interacts with several subunits of TFIID, including
TBP and the histone-fold protein TAF10. Currently, five
HF-containing TAF pairs have been described or suggested
to exist in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13,
TAF8-TAF10 and TAF3-TAF10.
Length = 54
Score = 45.7 bits (109), Expect = 6e-07
Identities = 14/21 (66%), Positives = 15/21 (71%)
Query: 176 PHIPPYLPLFPDPHAYIRTPV 196
HIP +LP FPDPH Y RTP
Sbjct: 1 AHIPSWLPPFPDPHTYKRTPT 21
>gnl|CDD|192573 pfam10406, TAF8_C, Transcription factor TFIID complex subunit 8
C-term. This is the C-terminal, Delta, part of the TAF8
protein. The N-terminal is generally the histone fold
domain, Bromo_TP (pfam07524). TAF8 is one of the key
subunits of the transcription factor for pol II, TFIID.
TAF8 is one of the several general cofactors which are
typically involved in gene activation to bring about the
communication between gene-specific transcription
factors and components of the general transcription
machinery.
Length = 51
Score = 44.5 bits (106), Expect = 2e-06
Identities = 23/54 (42%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 176 PHIPPYLPLFPDPHAYIRTPVVTL------KIRSKLTSPGEESDDNELPYLKML 223
+IP +LP FP H Y +TPV T KIR KL EES E K+L
Sbjct: 1 SYIPSWLPDFPPDHTYKKTPVYTEPVTDPRKIREKLV---EESRLAEKALRKLL 51
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 48.0 bits (114), Expect = 5e-06
Identities = 26/77 (33%), Positives = 34/77 (44%), Gaps = 16/77 (20%)
Query: 221 KMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAG----------------LD 264
+ LN +LP DI V P + ARF + R Y+Y A LD
Sbjct: 77 RGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLD 136
Query: 265 IDAMHKAAQYLVGTHDF 281
+ AM A + L+GTHDF
Sbjct: 137 VAAMDAALKLLIGTHDF 153
>gnl|CDD|128846 smart00576, BTP, Bromodomain transcription factors and PHD domain
containing proteins. subdomain of archael histone-like
transcription factors.
Length = 77
Score = 42.7 bits (101), Expect = 2e-05
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134
I+E+G +H + ELA R +P L DV+LAL LGI
Sbjct: 40 IQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73
Score = 34.6 bits (80), Expect = 0.012
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 9 RSLLKSSVVALLAEVGFDAADNAALETLVEICQ 41
+LL+ +V +L GFD+ +ALETL +I Q
Sbjct: 5 FALLRIAVAQILESAGFDSFQESALETLTDILQ 37
>gnl|CDD|219450 pfam07524, Bromo_TP, Bromodomain associated. This domain is
predicted to bind DNA and is often found associated with
pfam00439 and in transcription factors. It has a
histone-like fold.
Length = 77
Score = 39.2 bits (92), Expect = 2e-04
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134
I+E+G + F E A R +P L DV+L L E+GI
Sbjct: 40 IQELGRQAKRFAEHAGRSEPTLFDVVLTLKEMGI 73
Score = 38.1 bits (89), Expect = 7e-04
Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 9 RSLLKSSVVALLAEVGFDAADNAALETLVEICQACKY-TCLTVTAKVLSSHKER 61
LLK V +L GFD+A+ +ALETL +I Q Y L AK + H R
Sbjct: 5 HDLLKVVVAQILETAGFDSAEESALETLTDIAQ--SYIQELGRQAKRFAEHAGR 56
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 37.6 bits (87), Expect = 0.013
Identities = 17/81 (20%), Positives = 35/81 (43%)
Query: 211 ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHK 270
+ D + + K +N++LP +I+V + P + R +C R Y Y P + I +
Sbjct: 155 KDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFS 214
Query: 271 AAQYLVGTHDFRNLCKMNVGN 291
+ + +F ++ G
Sbjct: 215 SEEIDEHISEFNSILNGFEGE 235
>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase. Involved
in the formation of pseudouridine at the anticodon stem
and loop of transfer-RNAs Pseudouridine is an isomer of
uridine (5-(beta-D-ribofuranosyl) uracil, and id the
most abundant modified nucleoside found in all cellular
RNAs. The TruA-like proteins also exhibit a conserved
sequence with a strictly conserved aspartic acid, likely
involved in catalysis.
Length = 103
Score = 32.8 bits (75), Expect = 0.096
Identities = 8/23 (34%), Positives = 9/23 (39%)
Query: 271 AAQYLVGTHDFRNLCKMNVGNGV 293
AA+ GTHDF K
Sbjct: 1 AAKLYDGTHDFSGFQKQRTVQKS 23
>gnl|CDD|200147 TIGR01972, NDH_I_M, proton-translocating NADH-quinone
oxidoreductase, chain M. This model describes the 13th
(based on E. coli) structural gene, M, of bacterial NADH
dehydrogenase I, as well as chain 4 of the corresponding
mitochondrial complex I and of the chloroplast NAD(P)H
dehydrogenase complex [Energy metabolism, Electron
transport].
Length = 481
Score = 34.1 bits (79), Expect = 0.17
Identities = 32/121 (26%), Positives = 44/121 (36%), Gaps = 32/121 (26%)
Query: 95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLAL-IELGIPIHGLDTYAKRPMRTVFP- 152
+++GL GG + D EL N P L L + + K P+ FP
Sbjct: 175 AILGLYFL--GGGTFDLLELLNLPLPFGVQTWLFLAFFIAFAV-------KVPL---FPL 222
Query: 153 ----PVAPSTQPKPLSILQAGV--KQPHPPHIPPY------LPLFPDPHAYIRTPVVTLK 200
P A P S++ AGV K + Y LPLFPD Y + L
Sbjct: 223 HTWLPDAHVEAPTAGSVILAGVLLK------MGTYGFLRFNLPLFPDASLYFAPVLAALG 276
Query: 201 I 201
+
Sbjct: 277 V 277
>gnl|CDD|219805 pfam08347, CTNNB1_binding, N-terminal CTNNB1 binding. This region
tends to appear at the N-terminus of proteins also
containing DNA-binding HMG (high mobility group) boxes
(pfam00505) and appears to bind the armadillo repeat of
CTNNB1 (beta-catenin), forming a stable complex.
Signaling by Wnt through TCF/LCF is involved in
developmental patterning, induction of neural tissues,
cell fate decisions and stem cell differentiation.
Isoforms of HMG T-cell factors lacking the N-terminal
CTNNB1-binding domain cannot fulfill their role as
transcriptional activators in T-cell differentiation.
Length = 200
Score = 31.8 bits (72), Expect = 0.56
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 5/63 (7%)
Query: 135 PIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGV-KQPHPPHIPPYLPLFPDPHAYIR 193
P+ L TY+ F P P + G+ + PHPP I P+ PL P I
Sbjct: 140 PLTPLITYSNEH----FSPGTPPPHLPYDVDPKTGIPRPPHPPDISPFYPLSPGGVGQIP 195
Query: 194 TPV 196
P+
Sbjct: 196 HPL 198
>gnl|CDD|222871 PHA02553, 6, baseplate wedge subunit; Provisional.
Length = 611
Score = 30.0 bits (68), Expect = 3.8
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 13/68 (19%)
Query: 290 GNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVVDSEPSFKKGQGNEKPEIIQQLVDIEKY- 348
NG NF ++A N+Q I E +P + G PE I+++ +
Sbjct: 255 ANGARNF----SYADTL---TNIQGVSIDENPTDDPDYVGADGGGDPESIERI----REL 303
Query: 349 -PRIKSAQ 355
PR++ AQ
Sbjct: 304 APRMREAQ 311
>gnl|CDD|224447 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal
structure and biogenesis].
Length = 487
Score = 29.6 bits (67), Expect = 4.5
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 33 LETLVEICQACKYTCLTVTAKVLSSHKER--EKEDRIGESEGTCAEVTSVEDCYQRNWYK 90
LE L E C CK T + + H R E+E I ++ EV Y N +
Sbjct: 391 LEVLSERCPGCKGTGHVRSTESELLHILRYIEEEADINKTPEVGVEVPPAVAKYLLNEER 450
Query: 91 RAVTSV 96
A+ +
Sbjct: 451 GAIAEL 456
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 28.7 bits (64), Expect = 7.6
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 145 RPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPPYLPLFPDPH 189
P P++ P P ++ PP +PP P+ P H
Sbjct: 226 PGPSPAQPSAPPASIPAPPI--PPVIQYVAPPPVPPPQPIIPIQH 268
>gnl|CDD|223940 COG1008, NuoM, NADH:ubiquinone oxidoreductase subunit 4 (chain M)
[Energy production and conversion].
Length = 497
Score = 28.7 bits (65), Expect = 9.1
Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 22/71 (30%)
Query: 144 KRPMRTVFP-----PVAPSTQPKPLSILQAGV--KQPHPPHIPPY------LPLFPDPHA 190
K P+ FP P A P S++ AG+ K + Y LPLFPD A
Sbjct: 221 KMPL---FPLHTWLPDAHVEAPTAGSVILAGILLK------MGGYGLLRFSLPLFPDASA 271
Query: 191 YIRTPVVTLKI 201
Y +V L +
Sbjct: 272 YFAPLLVALGV 282
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 0.135 0.411
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,096,217
Number of extensions: 2439894
Number of successful extensions: 2194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2181
Number of HSP's successfully gapped: 30
Length of query: 496
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 395
Effective length of database: 6,457,848
Effective search space: 2550849960
Effective search space used: 2550849960
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: 61 (27.5 bits)