RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3459
(296 letters)
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
(CBF/NF-Y) and archaeal histone. This family includes
archaebacterial histones and histone like transcription
factors from eukaryotes.
Length = 65
Score = 92.3 bits (230), Expect = 5e-24
Identities = 36/66 (54%), Positives = 47/66 (71%), Gaps = 1/66 (1%)
Query: 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGE 67
LPIA V +IMK P++G+I++DA+E + ECV EFI FI SEA++ C EKRKTIN E
Sbjct: 1 AELPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAE 59
Query: 68 DILFAM 73
I A+
Sbjct: 60 HIKLAV 65
Score = 69.2 bits (170), Expect = 2e-15
Identities = 26/48 (54%), Positives = 33/48 (68%)
Query: 130 NETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177
I++DA+E + ECV EFI FI SEA++ C EKRKTIN E I A+
Sbjct: 18 AGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
Score = 45.7 bits (109), Expect = 5e-07
Identities = 19/32 (59%), Positives = 23/32 (71%)
Query: 203 EKFISFITSEASDRCHLEKRKTINGEDILFAM 234
E+FI FI SEA++ C EKRKTIN E I A+
Sbjct: 34 EEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 81.6 bits (202), Expect = 8e-20
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 2 PLREQDRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKR 61
R D LP A V +I++KA E +++ A E +QE + E++ I +A + KR
Sbjct: 12 YQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKR 69
Query: 62 KTINGEDILFAMSALGFDSYVE 83
KT+ EDI A+ LG Y E
Sbjct: 70 KTVKAEDIKLALKRLGRRIYGE 91
Score = 58.9 bits (143), Expect = 2e-11
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 131 ETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE 187
E ++ A E +QE + E++ I +A + KRKT+ EDI A+ LG Y E
Sbjct: 35 ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYGE 91
Score = 41.9 bits (99), Expect = 2e-05
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 203 EKFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE 244
E+++ I +A + KRKT+ EDI A+ LG Y E
Sbjct: 50 EEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYGE 91
>gnl|CDD|227479 COG5150, COG5150, Class 2 transcription repressor NC2, beta subunit
(Dr1) [Transcription].
Length = 148
Score = 64.6 bits (157), Expect = 7e-13
Identities = 39/130 (30%), Positives = 64/130 (49%), Gaps = 10/130 (7%)
Query: 10 LPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDI 69
LP A V K++ +P+ K+ARE EFI+ ++SEA++ C E +KTI E +
Sbjct: 12 LPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHV 71
Query: 70 LFAMSALGFDSYVEPLKIYLQKYREATKGEKSVNCEVYQEISVEDVFQSSGTILEQQNGQ 129
+ A+ L F+ Y+E + Y+ K Q+ S F+ SG +E+ Q
Sbjct: 72 IKALENLEFEEYIESCMEEHENYKSYQK----------QKESKISKFKDSGLSMEELLRQ 121
Query: 130 NETIAKDARE 139
E + ++AR
Sbjct: 122 QEELFQNARL 131
Score = 55.0 bits (132), Expect = 2e-09
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 129 QNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP 188
++ K+ARE EFI+ ++SEA++ C E +KTI E ++ A+ L F+ Y+E
Sbjct: 27 KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86
Query: 189 LKIYLQKYREATK 201
+ Y+ K
Sbjct: 87 CMEEHENYKSYQK 99
Score = 39.9 bits (93), Expect = 3e-04
Identities = 19/58 (32%), Positives = 34/58 (58%)
Query: 205 FISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYREATKGEKS 262
FI+ ++SEA++ C E +KTI E ++ A+ L F+ Y+E + Y+ K ++S
Sbjct: 46 FINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEHENYKSYQKQKES 103
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 34.5 bits (80), Expect = 0.006
Identities = 18/64 (28%), Positives = 30/64 (46%)
Query: 10 LPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDI 69
LP + V + +K+ +I+ A +QE + + + I +A KRKTI DI
Sbjct: 9 LPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDI 68
Query: 70 LFAM 73
A+
Sbjct: 69 QLAV 72
Score = 26.0 bits (58), Expect = 7.1
Identities = 14/45 (31%), Positives = 21/45 (46%)
Query: 133 IAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177
I+ A +QE + + + I +A KRKTI DI A+
Sbjct: 28 ISSKAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDIQLAV 72
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) 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 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of seven General Transcription
Factors (GTFs) (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 assembly of the pre-initiation complex. TFIID
complex is composed of the TBP and at least 13 TAFs.
TAFs are named after their electrophoretic mobility in
polyacrylamide gels in different species. A new, unified
nomenclature has been suggested for the pol II TAFs 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. These TAFs, with the help of
specific activators, are required only for expression of
a subset of genes and are 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; the 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. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 34.6 bits (80), Expect = 0.047
Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 13/83 (15%)
Query: 110 ISVEDVFQSSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTIN 169
S++ + +S G ++++ + + + E V + I EA+ KR+ +
Sbjct: 3 ESIKLIAESLG---------IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLT 53
Query: 170 GEDILFAMSALGFDSYVEPLKIY 192
D+ A+ VEPL +
Sbjct: 54 TSDVNHALRLRN----VEPLYGF 72
Score = 34.2 bits (79), Expect = 0.072
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 21 KAIPES---GKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 77
K I ES ++ + + + E V + I EA+ KR+ + D+ A+
Sbjct: 6 KLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRN 65
Query: 78 FDSYVEPLKIY 88
VEPL +
Sbjct: 66 ----VEPLYGF 72
>gnl|CDD|148624 pfam07124, Phytoreo_P8, Phytoreovirus outer capsid protein P8.
This family consists of several Phytoreovirus outer
capsid protein P8 sequences.
Length = 426
Score = 31.4 bits (71), Expect = 0.63
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 32 DARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP 84
D R +Q +EF+ FI++ +DRC RKT D+ A++ +Y++P
Sbjct: 56 DPRTPLQTMSNEFVDFIST--TDRCGYMLRKTWFDSDVKPAVTDNFITTYIKP 106
Score = 31.4 bits (71), Expect = 0.63
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 136 DARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP 188
D R +Q +EF+ FI++ +DRC RKT D+ A++ +Y++P
Sbjct: 56 DPRTPLQTMSNEFVDFIST--TDRCGYMLRKTWFDSDVKPAVTDNFITTYIKP 106
>gnl|CDD|173962 cd07978, TAF13, The TATA Binding Protein (TBP) Associated Factor 13
(TAF13) 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 13 (TAF13) 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 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 TAFs
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 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; the 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 are
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF13 interacts with TAF11 and makes a
histone-like heterodimer similar to H3/H4-like proteins.
The dimer may be structurally and functionally similar
to the spt3 protein within the SAGA histone
acetyltransferase complex.
Length = 92
Score = 29.4 bits (67), Expect = 0.66
Identities = 12/52 (23%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 126 QNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177
QN ET+ + +++ V E+I + +A++ + K + ED++F +
Sbjct: 19 QNPLPETV-----DLLEDIVVEYIIELCHKAAEVAQRRRGK-VKVEDLIFLL 64
Score = 27.1 bits (61), Expect = 3.5
Identities = 8/39 (20%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 35 ECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73
+ +++ V E+I + +A++ + K + ED++F +
Sbjct: 27 DLLEDIVVEYIIELCHKAAEVAQRRRGK-VKVEDLIFLL 64
>gnl|CDD|227456 COG5127, COG5127, Vacuolar H+-ATPase V1 sector, subunit C [Energy
production and conversion].
Length = 383
Score = 29.5 bits (66), Expect = 2.1
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 39 ECVSEFISFITSEASDRCHLEKRKTINGED-ILFAMSALGFDSYVEPLKIYLQKY 92
+ ++ I+ + S+R EK N E ILFA + L D EP +++ Y
Sbjct: 329 KVKAQLIAIAKNLPSNRIVYEKEGDNNDEGEILFAFAELSTDGEYEPFVLFVFNY 383
Score = 29.5 bits (66), Expect = 2.1
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 143 ECVSEFISFITSEASDRCHLEKRKTINGED-ILFAMSALGFDSYVEPLKIYLQKY 196
+ ++ I+ + S+R EK N E ILFA + L D EP +++ Y
Sbjct: 329 KVKAQLIAIAKNLPSNRIVYEKEGDNNDEGEILFAFAELSTDGEYEPFVLFVFNY 383
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) 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 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(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 assembly of
the pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF orthologs and paralogs. Several hypotheses
are proposed for TAFs function such as serving as
activator-binding sites, core-promoter recognition or a
role in essential catalytic activity. These TAFs, with
the help of specific activators, are required only for
expression of a subset of genes and are 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; the 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. TAF12 domain interacts with
TAF4 and makes a novel histone-like heterodimer that
binds DNA and has a core promoter function of a subset
of genes.
Length = 72
Score = 27.2 bits (61), Expect = 2.4
Identities = 9/49 (18%), Positives = 19/49 (38%)
Query: 129 QNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177
E + D E + E +F+ + +A K T+ +D+ +
Sbjct: 16 PREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHL 64
Score = 26.8 bits (60), Expect = 3.5
Identities = 10/53 (18%), Positives = 21/53 (39%)
Query: 21 KAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73
K I ++ D E + E +F+ + +A K T+ +D+ +
Sbjct: 12 KEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHL 64
>gnl|CDD|227128 COG4790, EscR, Type III secretory pathway, component EscR
[Intracellular trafficking and secretion].
Length = 214
Score = 27.7 bits (62), Expect = 5.7
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 14/88 (15%)
Query: 155 EASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYREATKGEKFISFITSEAS 214
+ DR E+ ++ +I + D + P + +L+K E E+ +SF A
Sbjct: 70 QIYDRLQNEE---LSYTNIASVVKFD--DKGLSPYRDFLKKNTE----EEEVSFFERSAQ 120
Query: 215 DRCHLEKRKTINGEDIL-----FAMSAL 237
+ E + + + + F +S L
Sbjct: 121 KKWPEEYAEKLKPDSLFILLPAFTLSEL 148
>gnl|CDD|190265 pfam02269, TFIID-18kDa, Transcription initiation factor IID, 18kD
subunit. This family includes the Spt3 yeast
transcription factors and the 18kD subunit from human
transcription initiation factor IID (TFIID-18).
Determination of the crystal structure reveals an
atypical histone fold.
Length = 93
Score = 26.2 bits (58), Expect = 9.1
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 35 ECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73
+ +++ V + + +A L + I EDI F +
Sbjct: 26 QLLEDLVRGQLIELLQQAMKTAQLRGSRKITLEDIKFLI 64
Score = 26.2 bits (58), Expect = 9.1
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 139 ECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177
+ +++ V + + +A L + I EDI F +
Sbjct: 26 QLLEDLVRGQLIELLQQAMKTAQLRGSRKITLEDIKFLI 64
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
0.316 0.132 0.367
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,394,701
Number of extensions: 1324653
Number of successful extensions: 1152
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1149
Number of HSP's successfully gapped: 30
Length of query: 296
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 200
Effective length of database: 6,679,618
Effective search space: 1335923600
Effective search space used: 1335923600
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 (21.6 bits)
S2: 59 (26.8 bits)