RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13072
(257 letters)
>gnl|CDD|197718 smart00427, H2B, Histone H2B.
Length = 97
Score = 154 bits (392), Expect = 2e-48
Identities = 81/97 (83%), Positives = 93/97 (95%)
Query: 28 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 87
KK+ +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60
Query: 88 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61 STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97
Score = 154 bits (392), Expect = 2e-48
Identities = 81/97 (83%), Positives = 93/97 (95%)
Query: 159 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 218
KK+ +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60
Query: 219 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 255
ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61 STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97
>gnl|CDD|215081 PLN00158, PLN00158, histone H2B; Provisional.
Length = 116
Score = 135 bits (342), Expect = 9e-41
Identities = 82/112 (73%), Positives = 95/112 (84%), Gaps = 1/112 (0%)
Query: 14 AGKAQKNIAKSDKKKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFER 73
+ K K AK KKK K + E+Y IYIYKVLKQVHPDTG+SSKAMSIMNSF+NDIFE+
Sbjct: 6 SKKPAKKAAKGAKKKGSK-SKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEK 64
Query: 74 IAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 125
IA E+ +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 65 IATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Score = 135 bits (342), Expect = 1e-40
Identities = 78/107 (72%), Positives = 92/107 (85%)
Query: 150 AQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAES 209
A+K + KK + E+Y IYIYKVLKQVHPDTG+SSKAMSIMNSF+NDIFE+IA E+
Sbjct: 10 AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEA 69
Query: 210 SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 256
+LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 70 GKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
>gnl|CDD|185642 PTZ00463, PTZ00463, histone H2B; Provisional.
Length = 117
Score = 124 bits (312), Expect = 3e-36
Identities = 76/113 (67%), Positives = 93/113 (82%)
Query: 12 KKAGKAQKNIAKSDKKKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 71
KK KA+K D KKK+K R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63
Query: 72 ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
E+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 64 EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Score = 118 bits (296), Expect = 7e-34
Identities = 75/113 (66%), Positives = 92/113 (81%), Gaps = 2/113 (1%)
Query: 145 KKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 202
KK KA+K D KK+K R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63
Query: 203 ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 255
E+IA E+SRL Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 64 EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 84.1 bits (209), Expect = 3e-21
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 32 HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 87
R + +V++++ +SSKA + + D+ E I ++ LA + KR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 88 STITSREIQTAVRLL 102
TIT R+IQ AVRL
Sbjct: 61 KTITPRDIQLAVRLD 75
Score = 84.1 bits (209), Expect = 3e-21
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 163 HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 218
R + +V++++ +SSKA + + D+ E I ++ LA + KR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 219 STITSREIQTAVRLL 233
TIT R+IQ AVRL
Sbjct: 61 KTITPRDIQLAVRLD 75
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 31.5 bits (72), Expect = 0.45
Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 7/86 (8%)
Query: 9 KAVKKAGKAQKNIAKSDKKKKKKHRRKESYAIY----IYKVLKQVHPDTGVSSKAMSIM- 63
KA A +A + + + + +E + + L + D S K ++
Sbjct: 100 KATSVAAEATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNLKD 159
Query: 64 --NSFVNDIFERIAAESSRLAHYNKR 87
S + E + S +LA
Sbjct: 160 DLESLIASAKEELDQLSKKLAELKAE 185
Score = 28.8 bits (65), Expect = 3.5
Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 138 KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIY----IYKVLKQVHPDTGVSSKAMSI 193
++ +V K+I + + + +E + + L + D S K ++
Sbjct: 98 EAKATSVAAEATTPKSIQELVEALEELLEELLKETASDPVVQELVSIFNDLIDSIKEDNL 157
Query: 194 M---NSFVNDIFERIAAESSRLAHYNKR 218
S + E + S +LA
Sbjct: 158 KDDLESLIASAKEELDQLSKKLAELKAE 185
>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 = 27.6 bits (62), Expect = 1.2
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 42 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 99
+ +++K +S A ++ V + E IA+E++ + KR TI + I+ AV
Sbjct: 8 VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
Score = 27.6 bits (62), Expect = 1.2
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 173 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 230
+ +++K +S A ++ V + E IA+E++ + KR TI + I+ AV
Sbjct: 8 VKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 28.4 bits (64), Expect = 1.2
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 55 VSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 105
VSS A+ + + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 37 VSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
Score = 28.4 bits (64), Expect = 1.2
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 186 VSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG 236
VSS A+ + + + E IA ++ LA + KR T+ + +I+ A++ L
Sbjct: 37 VSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>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 = 26.8 bits (60), Expect = 3.0
Identities = 10/51 (19%), Positives = 25/51 (49%)
Query: 46 LKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 96
LK++ P + ++ +D + + ++ RLA + K T+ +++Q
Sbjct: 11 LKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQ 61
Score = 26.8 bits (60), Expect = 3.0
Identities = 10/51 (19%), Positives = 25/51 (49%)
Query: 177 LKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 227
LK++ P + ++ +D + + ++ RLA + K T+ +++Q
Sbjct: 11 LKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQ 61
>gnl|CDD|223223 COG0145, HyuA, N-methylhydantoinase A/acetone carboxylase, beta
subunit [Amino acid transport and metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 674
Score = 28.1 bits (63), Expect = 5.0
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 52 DTGVSSKAMSIMNSFVNDIFERIAAESSR 80
GV + A+S + S+ N E AE R
Sbjct: 150 AAGVEAIAVSSLFSYRNPEHELRVAEIIR 178
Score = 28.1 bits (63), Expect = 5.0
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 183 DTGVSSKAMSIMNSFVNDIFERIAAESSR 211
GV + A+S + S+ N E AE R
Sbjct: 150 AAGVEAIAVSSLFSYRNPEHELRVAEIIR 178
>gnl|CDD|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID
subunit A.
Length = 67
Score = 25.8 bits (57), Expect = 5.5
Identities = 10/55 (18%), Positives = 26/55 (47%)
Query: 42 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 96
+ +++Q+ +T + ++ +D E + + +LA + K + R+IQ
Sbjct: 5 LQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQ 59
Score = 25.8 bits (57), Expect = 5.5
Identities = 10/55 (18%), Positives = 26/55 (47%)
Query: 173 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 227
+ +++Q+ +T + ++ +D E + + +LA + K + R+IQ
Sbjct: 5 LQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQ 59
>gnl|CDD|218571 pfam05378, Hydant_A_N, Hydantoinase/oxoprolinase N-terminal region.
This family is found at the N-terminus of the pfam01968
family.
Length = 175
Score = 27.2 bits (61), Expect = 6.0
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 52 DTGVSSKAMSIMNSFVNDIFERIAAESSR 80
D GV + A+S+++S+ N E E R
Sbjct: 144 DAGVEAVAVSLLHSYRNPEHELRVKEIIR 172
Score = 27.2 bits (61), Expect = 6.0
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 183 DTGVSSKAMSIMNSFVNDIFERIAAESSR 211
D GV + A+S+++S+ N E E R
Sbjct: 144 DAGVEAVAVSLLHSYRNPEHELRVKEIIR 172
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 27.5 bits (62), Expect = 7.5
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 1 MAAGKSSGKAVKKAGKAQKNIAKSDKKKKKKHRRKESYAI 40
+ A K +K KAQK K + K K + + +
Sbjct: 56 LKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSKPRLFVL 95
>gnl|CDD|212547 cd11581, GINS_A, Alpha-helical domain of GINS complex proteins;
Sld5, Psf1, Psf2 and Psf3. The GINS complex is involved
in both initiation and elongation stages of eukaryotic
chromosome replication, with GINS being the component
that most likely serves as the replicative helicase that
unwinds duplex DNA ahead of the moving replication fork.
In eukaryotes, GINS is a tetrameric arrangement of four
subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has
been found in eukaryotes and archaea, but not in
bacteria. The four subunits of the complex are
homologous and consist of two domains each, termed the
alpha-helical (A) and beta-strand (B) domains. The A and
B domains of Sld5/Psf1 are permuted with respect to
Psf1/Psf3.
Length = 103
Score = 25.9 bits (57), Expect = 9.0
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 5/79 (6%)
Query: 11 VKKAGKAQKNIAKSDKKKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDI 70
VK+ +S+ ++ +HR K YI +LK ++S+ I + +
Sbjct: 28 VKELLHRLSKRQRSETQEILEHRLKILELSYIRDLLKTY-----LNSRLDKIRDLSPEFL 82
Query: 71 FERIAAESSRLAHYNKRST 89
+ E +
Sbjct: 83 PSNLTEEEIGYFQTYWKEV 101
>gnl|CDD|225682 COG3140, COG3140, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 60
Score = 25.2 bits (55), Expect = 9.8
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 130 LQFIMAAGKSSGKAVKKAGKAQKNIAKSDKKKKHR 164
+Q +MA G SSG+A+ + + K + + R
Sbjct: 20 IQELMAEGMSSGEAIALVAQELRENHKGENRIVAR 54
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
0.310 0.122 0.317
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,984,382
Number of extensions: 1081536
Number of successful extensions: 1592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1542
Number of HSP's successfully gapped: 78
Length of query: 257
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 162
Effective length of database: 6,723,972
Effective search space: 1089283464
Effective search space used: 1089283464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.3 bits)